Next Article in Journal
Thermogenic Fat: Development, Physiological Function, and Therapeutic Potential
Next Article in Special Issue
Colistin Resistance in Aeromonas spp.
Previous Article in Journal
NKL Homeobox Gene VENTX Is Part of a Regulatory Network in Human Conventional Dendritic Cells
Previous Article in Special Issue
Ribosome Protection Proteins—“New” Players in the Global Arms Race with Antibiotic-Resistant Pathogens
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
IJMS
Volume 22
Issue 11
10.3390/ijms22115905
ijms-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals

by
Olivia M. Grünzweil
1,
Lauren Palmer
2,
Adriana Cabal
3,
Michael P. Szostak
1,
Werner Ruppitsch
3,
Christian Kornschober
4,
Maciej Korus
5,
Dusan Misic
5,
Tanja Bernreiter-Hofer
1,6,
Anna D. J. Korath
1,
Andrea T. Feßler
7,
Franz Allerberger
3,
Stefan Schwarz
7,
Joachim Spergser
1,
Elke Müller
8,9,
Sascha D. Braun
8,9,
Stefan Monecke
8,9,10,
Ralf Ehricht
8,9,11,
Chris Walzer
12,13,
Hrvoje Smodlaka
14 and
Igor Loncaric
1,*add Show full author list remove Hide full author list
1
Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria
2
Marine Mammal Care Center, Los Angeles, CA 90731, USA
3
Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, 1090 Vienna, Austria
4
Austrian Agency for Health and Food Safety (AGES), National Reference Centre for Salmonella, 8010 Graz, Austria
5
Department of Functional Food Products Development, Faculty of Biotechnology and Food Science, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland
6
Department for Farm Animals and Veterinary Public Health, University Clinic for Swine, University of Veterinary Medicine, 1210 Vienna, Austria
7
Centre for Infection Medicine, Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany
8
Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany
9
InfectoGnostics Research Campus, 07743 Jena, Germany
10
Institute for Medical Microbiology and Hygiene, Technical University of Dresden, 01307 Dresden, Germany
11
Institute of Physical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
12
Research Institute of Wildlife Ecology, University of Veterinary Medicine, 1160 Vienna, Austria
13
Health Program, Wildlife Conservation Society, Bronx, New York City, NY 10460, USA
14
College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766-1854, USA
 
add Show full affiliation list
 
remove Hide full affiliation list
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2021, 22(11), 5905; https://doi.org/10.3390/ijms22115905
Submission received: 30 April 2021 / Revised: 27 May 2021 / Accepted: 28 May 2021 / Published: 31 May 2021
(This article belongs to the Special Issue Antibiotic Resistance: Appearance, Evolution, and Spread)
Browse Figure
Versions Notes

Abstract

:
Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant β-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.

1. Introduction

Antimicrobial resistance (AMR) in bacteria is an emerging public health concern worldwide. Particularly, AMR among Enterobacterales is globally widespread and constitutes a public health threat due to a high prevalence of multidrug-resistant (MDR) strains [1,2]. MDR Gram-negative bacteria may complicate antimicrobial therapy. In addition to resistance classification of bacteria (multidrug resistance (MDR), extensive drug resistance (XDR), and pandrug resistance (PDR)) in the last decade, several novel classification criteria that correlate well with clinical outcomes were introduced (e.g., difficult-to-treat resistance (DTR)). This additional classification criterion will lead to significant benefits in assessing the significance of bacterial resistance in therapeutics [3,4].
Extended-spectrum beta (β)-lactamases (ESBL) and AmpC β-lactamases (AmpC) are the most common enzymes imparting broad-spectrum cephalosporin resistance in Enterobacterales [5,6]. Many enterobacterial species, e.g., Citrobacter spp. and Enterobacter spp., harbor inducible chromosomally-encoded AmpC β-lactamases, whose production can be triggered by exposure to β-lactam antibiotics, especially strong inducers (benzylpenicillin, ampicillin, amoxicillin, and cephalosporins (cefazolin and cephalothin)) [6,7,8]. In contrast, β-lactamase (bla) genes of Escherichia (E.) coli, Klebsiella spp., and Salmonella spp. are mainly carried on mobile genetic elements, such as plasmids, which are considered to be primarily responsible for the rapid spread of β-lactam resistances among these Enterobacterales [6,8,9].
Despite the intensively studied occurrence of AMR in bacteria from humans and domestic animals, there is a lack of knowledge about the distribution of AMR among bacteria from marine mammals. The Northeastern Pacific Ocean is a rich habitat that sustains a massive amount of phytoplankton, zooplankton, krill, and fish, all of which support a diverse and abundant community of more than 30 species of marine mammals [10]. Previous observations indicate that the marine environment may act as a reservoir of antimicrobial resistance genes [11,12,13,14]. Different mechanisms can lead to the presence of antimicrobial-resistant bacteria in the oceans: first, anthropogenic antimicrobial-containing runoff, challenging native bacteria to become resistant; second, coastal runoff of already resistant bacteria from terrestrial sources; and third—although less important in this context—antimicrobial production by marine microorganisms [11,15].
Wildlife sampled in habitats impacted by livestock production, solid waste disposal, wastewater treatment, and other anthropogenic influences have been found to result in a higher prevalence of antimicrobial-resistant bacteria compared to less influenced habitats [16]. The global use of antimicrobial agents reaching the oceans via municipal sewage, commercial fish farms, and hospitals [17,18] is likely to increase AMR in bacteria from marine mammals and marine microbial communities [19]. It has been reported that wildlife, in general, might act as an indicator of the burden of resistance within a local environment and could help to identify sources of anthropogenic contamination with antimicrobial resistance determinants [16,20,21,22]. For these reasons, marine mammals, such as pinnipeds and dolphins residing in coastal waters, have been described as sentinels of the health of coastal marine ecosystems and, consequently, also the health of humans living in or visiting these areas [23,24,25]. Nevertheless, information on AMR in bacteria from marine mammals remains scarce [19,26,27,28,29,30].
The present study aimed to determine the occurrence and to characterize ESBL- and AmpC β-lactamase-producing Enterobacterales, including non-resistant Salmonella spp., in stranded marine mammals temporarily housed in the Marine Mammal Care Center Los Angeles (MMCCLA), California. Included in this study were California sea lions (Zalophus californianus), northern fur seals (Callorhinus ursinus) and one Guadalupe fur seal (Arctocephalus townsendi) representing Otariid seals, northern elephant seals (Mirounga angustirostris) and harbor seals (Phoca vitulina) representing Phocid seals, and a long-beaked common dolphin (Delphinus capensis) and a pygmy sperm whale (Kogia breviceps) representing Cetaceans.

2. Results

2.1. β-Lactamase Producing Isolates, Species Identification and Phenotypic Resistance

Out of a total of 283 samples, 62 β-lactamase-producing Enterobacterales were obtained and identified as E. coli (n = 27), Klebsiella (K.) pneumoniae (n = 12), Citrobacter (C.) freundii complex and C. koseri (each n = 9), Enterobacter (En.) cloacae complex and En. cancerogenus (each n = 1), Lelliottia (L.) amnigena (n = 2), and Proteus (P.) mirabilis (n = 1). Most of them (n = 51) displayed an AmpC phenotype, whereas all Citrobacter and Enterobacter isolates were identified as stably de-repressed AmpC-producers. Five E. coli isolates (IDs 41, 68, 183, 209, and 234) displayed an ESBL phenotype, and two E. coli (IDs 21, 90) and the two L. amnigena isolates (IDs 130 and 132) displayed both AmpC and ESBL phenotypes (Table 1 and Table 2).
In addition to β-lactam resistance, resistance to trimethoprim-sulfamethoxazole (n = 47; 75.81%), tetracycline (n = 42; 67.74%), chloramphenicol (n = 32; 51.61%), gentamicin (n = 30; 48.39%), tobramycin (n = 25; 40.32%), ciprofloxacin (n = 12; 19.35%), and fosfomycin (n = 9; 14.52%) were expressed by the enterobacterial isolates. Forty-four isolates exhibited a multidrug-resistant phenotype [31]. All of the isolates were susceptible to carbapenems.
Seventeen of the 18 Salmonella isolates obtained in this study were susceptible to all tested antimicrobial agents. One Salmonella isolate (ID 42 S.) displayed an AmpC phenotype, but no further resistance to non-β-lactam antibiotics was observed.
Biocide susceptibility testing revealed elevated minimal inhibitory concentration (MIC) values for chlorhexidine in 45 out of the 62 enterobacterial isolates (79%) and in all Salmonella isolates (18/18). MIC values for isopropanol were elevated in 23 Enterobacterales (31%) and two Salmonella isolates. One Salmonella isolate (ID 245 S.) exhibited an elevated MIC value for glutardialdehyde. For all but one isolate (ID 230b; MIC 0.000125%), the MICs of benzalkonium chloride ranged between 0.001% and 0.002% (Supplementary Table S1).

2.2. Characterization of Genotypic Resistance

Within the group of β-lactamase genes, blaCMY (n = 51) was the most prevalent and was detected solely (n = 13) or together with blaCTX-M, blaOXA, blaSHV, and/or blaTEM. All sequenced blaCMY genes were identified as blaCMY-2, except one E. coli isolate (ID 171) harboring blaCMY-4. Sequencing of blaCMY was not carried out in intrinsically AmpC-producing Enterobacterales, such as Citrobacter spp. and Enterobacter spp. The gene blaTEM was detected in 38 isolates—solely (n = 1) or together with blaCMY, blaCTX-M, blaOXA, and/or blaSHV. All blaTEM genes were identified as blaTEM-1. blaSHV genes were detected in 13 different isolates. The broad-spectrum β-lactamase genes blaSHV-11 (n = 3) and blaSHV-33 (n = 8) were detected in 11 of the 12 K. pneumoniae isolates, together with blaTEM and blaCMY (n = 8) or together with blaTEM, blaCMY, and blaOXA (n = 3). The ESBL gene blaSHV-12 (n = 2) was harbored by the two L. amnigena isolates (IDs 130, 132), which also carried the gene blaDHA-1. The genes blaCTX-M-15 and blaOXA-1 were observed in seven isolates, respectively (Table 1 and Table 2).
The gene blaCMY-2 was detected in the Salmonella isolate 42 S.
In two of the E. coli isolates (IDs 3 and 202) displaying an AmpC phenotype, no β-lactamase gene was detected, but mutations in the promoter and attenuator region of the chromosomal ampC gene were found at positions –18 (G→A), –1 (C→T) and +58 (C→T) in E. coli isolate 3 and at position –32 (T→A) in E. coli isolate 202. Further, mutations were found at position –18 (G→A), –1 (C→T), and +58 (C→T) of the ampC gene of E. coli isolates 8/2 and 21, at positions –18 (G→A) and –1 (C→T) in E. coli 192/2, at position +58 (C→T) in E. coli 17, and at position –28 (G→A) of the ampC gene of E. coli isolates 197/1 and 224a.
The most prevalent non-β-lactamase genes detected were sul2 (n = 38), strA (n = 34), strB (n = 34), tet(A) (n = 34), and sul1 (n = 33).
The analysis of the quinolone resistance-determining regions (QRDR) of gyrA and parC revealed mutations that resulted in amino acid exchanges at positions 83 (Ser→Leu) and 87 (Asp→Asn) in GyrA of five ciprofloxacin-resistant isolates and at position 80 (Ser→Ile) in ParC of six ciprofloxacin-resistant isolates.
Even though phenotypic resistance to tetracycline was present, none of the tested tet genes were detected in C. freundii complex isolate 224b.
Antimicrobial resistance phenotypes and genes are summarized in Table 1 and Table 2.

2.3. Molecular Typing Methods

The most common E. coli phylogenetic group was A (n = 8). Four E. coli isolates each were assigned to the groups B1, B2, D, and F, while three isolates represented phylogroup E (Table 1 and Table 3).
The fumC and fimH (CH) typing divided the E. coli isolates into 19 distinct CH clonotypes and revealed clonal relatedness of E. coli isolates 147a and 149a (CH7-0); 3 and 8/2 (CH65-26); 117 and 202 (CH103-9); 53/1, 92 and 158 (CH148-25); and 68, 156, 183, and 230b (CH11-0) (Figure 1).
Multilocus sequence typing (MLST) of Klebsiella pneumoniae identified two different types among the tested isolates: ST466 (n = 9) and ST406 (n = 3).

2.4. Characterization of E. coli Virulence Genes

The most common E. coli virulence genes determined via microarray were fimH (15/15), iucD and papC (each 5/15), astA (4/15), and cnf1 (3/15) (Table 1). The gene hlyA was detected in one isolate (ID 17) accompanied by cnf1. The genes iucD and papC were detected simultaneously in five E. coli isolates. Those five E. coli isolates (IDs 21, 53/1, 92, 156, and 158) were assigned to extraintestinal pathogenic E. coli (ExPEC)/uropathogenic E. coli (UPEC) pathotype due to the presence of the virulence genes fimH, iucD, and papC [32].

2.5. Whole-Genome Sequencing (WGS) of Selected E. coli Isolates

Of the 12 whole-genome sequenced E. coli isolates, eleven originated from California sea lions and one from a northern elephant seal. Three isolates (IDs 68, 183, and 230b) belonged to the sequence type (ST)167 and clustered together by core genome multilocus sequence-based typing (cgMLST), which suggested clonal relatedness between them. Other sequence types obtained were ST38, ST349, ST372, ST484, ST648, ST963, ST1431, ST4957, and ST5748. E. coli predicted serotype (somatic O and flagellar H antigens) was clearly determined in one isolate (ID 192/2) as O9:H10 (Table 3).
The multidrug transporter gene mdfA, which confers resistance to a diverse group of biocides and antimicrobial agents [33], was detected in all 12 isolates analyzed by WGS.
The genes associated with biocide resistance emrK (n = 12), mdtE (n = 12), mdtF (n = 12), tolC (n = 12), acrF (n = 12), acrE (n = 9), and emrE (n = 5), which impart decreased susceptibility to benzalkonium chloride, were identified. Furthermore, the genes cpxA (n = 10) and qacEΔ1 (n = 5), conferring decreased susceptibility to benzalkonium chloride and chlorhexidine, were detected. Biocide susceptibility phenotypes and genes associated with elevated biocide MICs are summarized in Supplementary Table S1.
WGS revealed that different virulence genes were present in the E. coli isolates with the tellurite resistance gene terC (n = 12), the increased serum survival gene iss, the serum-resistance associated gene traT, the yersiniabactin encoding gene irp2, the yersiniabactin receptor encoding gene fyuA, and the iron and manganese transport gene sitA (each n = 8) being predominant (Table 3).
The determination of plasmids via the PlasmidFinder software revealed that the predominant plasmid was IncFIB (n = 7). In the E. coli isolate 209, the blaTEM-1B gene was carried by an IncI1-Iα plasmid (Supplementary Tables S2 and S3).
The mlplasmids analyses predicted that the majority of the antimicrobial resistance genes might be plasmid-encoded, whereas most virulence genes appeared to be chromosomally-encoded (Supplementary Tables S3 and S4). The blaCTX-M-15 gene might be located in the chromosomal DNA of two isolates (IDs 209 and 234). In E. coli 68 and 183, a prediction for the location of the blaCTX-M-15 gene could not be made. A chromosomally-encoded blaCMY-2 gene might have been obtained in E. coli 206 and 230a, and a chromosomally-encoded blaCMY-4 in E. coli 171.

2.6. Characterization of Salmonella Isolates

The most common serotypes among the 18 analyzed Salmonella isolates were Salmonella (S.) Havana (antigenic formula: 1,13,23 : f,g : -) (n = 8) and S. Reading (antigenic formula: 1,4,5,12 : e,h : 1,5) (n = 3). Furthermore, S. Albany (n = 2), S. Newport (n = 2), S. Saintpaul (n = 2), and S. Braenderup (n = 1) were identified. (Table 4).
In all Salmonella isolates (n = 18) the transcriptional regulator gene hilA and Salmonella enterotoxin gene stn were detected. The virulence gene tviA was not found.

3. Discussion

In this study, we investigated the phenotypic and genotypic characteristics of ESBL- and AmpC-producing Enterobacterales, as well as the presence of Salmonella isolates in stranded marine mammals prior to their rehabilitation. The majority of the investigated β-lactamase-producing Enterobacterales exhibited an AmpC phenotype, an ESBL phenotype was observed in five E. coli isolates, and both AmpC and ESBL phenotypes were present in two E. coli and two L. amnigena isolates. In the scope of this study, three types of AmpC resistance mechanisms have been identified: plasmid-mediated AmpC (pAmpC) genes, overexpression of chromosomal AmpC in E. coli, and de-repressed AmpC in Citrobacter spp. and Enterobacter spp. AmpC-producers have been reported as particularly common in North America, whereas in Europe, β-lactamases are primarily represented by ESBLs [34]. Among the bla genes investigated in this study, the pAmpC gene blaCMY was detected most frequently. It was in all K. pneumoniae and P. mirabilis isolates, in one Salmonella isolate, and in 18 E. coli isolates identified as blaCMY-2, which encodes the most prevalent pAmpC enzyme in humans, livestock, and companion animals worldwide [7,9]. Moreover, blaCMY-2 has been detected in different wildlife species [35,36,37,38]. In two E. coli isolates (IDs 206 and 230a), blaCMY-2 is predicted to be encoded chromosomally, which was described in 2015 for the first time in E. coli [39]. In addition, we obtained a high number of isolates exhibiting blaTEM-1 (n = 38) and, less frequently, blaOXA-1 (n = 7). Both bla genes were recently detected in E. coli isolates from harbor seals and grey seals (Halichoerus grypus) in Ireland [40], in which, in contrast to the findings of the present study, blaOXA-1 was more frequently represented than blaTEM-1. All but one (ID 160) K. pneumoniae isolates carried a blaSHV gene. The broad-spectrum β-lactamase genes blaSHV-11 and blaSHV-33 were detected exclusively in ST466 K. pneumoniae and ST405 K. pneumoniae, respectively. Chaves et al. were the first to detect the novel SHV-type variant SHV-33 in K. pneumoniae, and they hypothesized that the ancestor of SHV-1 β-lactamase originated from the K. pneumoniae chromosomal DNA [41]. Furthermore, the pAmpC gene blaDHA-1, which was detected in the two L. amnigena isolates (IDs 130 and 132), was previously also obtained in a K. pneumoniae isolate originating from a free-living mouflon in Austria [42].
Besides resistance to β-lactam antibiotics, resistance to other antibiotic classes was common among the investigated Enterobacterales. In total, 71% of the isolates exhibited a MDR phenotype and genotype. The study on E. coli in seals in Ireland determined a high proportion of MDR bacteria (66.6%) in the animals tested [40]. Already in the 1990s, AMR in Enterobacterales appeared widespread among Californian pinnipeds [26]. Wallace et al. [19] observed an increase of AMR in bacteria of stranded pinnipeds of the Northwest Atlantic over a period of 6 years (2004–2010). E. coli especially displayed a considerable increase in resistance to β-lactams, sulfonamides, and aminoglycosides, while Klebsiella spp. exhibited an increase in resistance to aminoglycosides and fluoroquinolones [19].
Biocide susceptibility testing revealed a high proportion of elevated MIC values for chlorhexidine (79%) and isopropanol (31%). Information regarding biocide susceptibility of Enterobacterales isolated from wildlife is scarce. A recent study on K. pneumoniae from Californian pinnipeds investigated environmental persistence, as well as disinfectant susceptibility, of these bacteria [43]. Commonly recommended concentrations of chlorine and hydrogen peroxide turned out to be ineffective in eradication of the biofilm formed by hypermucoviscous K. pneumoniae, whereas ethanol and chloramine-T effectively eradicated K. pneumoniae, irrespective of whether formed in biofilm or not [43].
Furthermore, sublethal concentrations of biocidal agents, in particular, benzalkonium chloride, chlorhexidine, and triclosan, may enhance antimicrobial tolerance and resistance in Gram-negative bacteria [44,45].
Among the E. coli isolates, six different phylogenetic groups were determined, with the most common being phylogroup A (n = 8), described as being widespread among human commensal E. coli strains [46]. Contrary to our findings, investigations in Australia revealed the human-associated phylogroups B2 and D as the predominating E. coli phylotypes in pinnipeds [47,48,49].
cgMLST revealed that three E. coli clones (IDs 68, 183, and 230b) belonged to A-ONT:H9-ST167-CH11-0. These isolates were obtained from different individuals over a time-span of several months and exhibited in part highly diverse resistance pheno- and genotypes. This could indicate that these clones were already circulating for an extended period of time within the tested population of marine mammals and in their environment. Therefore, several resistance gene exchanges with other bacteria could have taken place. Related investigations have been reported regarding interspecies transmission of an E. coli ST410 clone between wildlife, humans, companion animals and the environment within several years in Berlin, Germany [50].
E. coli ST167 is considered a pandemic clone of significant public health concern due to its ESBL-producing strains [9]. Rising numbers of ST167 strains carrying the blaNDM carbapenemase gene were being reported and highlighted the threat emanating from this clone [51,52,53]. Guenther et al. were the first to report occurrence of ST167 ESBL-E. coli in wildlife [54]. Moreover, E. coli ST167 was detected in cloacal samples of silver gulls in Australia [55].
The MDR AmpC-producing E. coli isolate 197/1 belonged to ST648, a pandemic high risk clone combining MDR and high-level virulence [56], which has already been isolated from wild birds in Germany [50,57] and zoo animals in Israel [58].
E. coli isolate 209 was identified as ST38, a prevalent human clinical pathogen that has also been reported in wild birds of prey in Mongolia [59], rats in Africa [60], and silver gulls in Australia [61]. Furthermore, ST38 has had an entry in the Enterobase Escherichia/Shigella Database, whose corresponding isolate originated from a sea lion in Ecuador, South America (https://enterobase.warwick.ac.uk/species/index/ecoli, accessed on 21 March 2021) [62]. Both E. coli ST38 and ST648 are known as emerging ExPEC worldwide [63,64].
E. coli ST349, ST963, and ST1431 have also been detected in samples from wild birds [65], and an ST372 E. coli, isolated from a straw-coloured fruit bat in the Republic of Congo, has previously been detected and classified as ExPEC [66]. Additionally, E. coli ST372 has had an entry in the aforementioned database and the respective originated from a common bottlenose dolphin (Tursiops truncatus) in Mexico. There are no reports describing the isolation of E. coli ST484, ST4957, and ST5748 from wildlife to the authors knowledge.
An alarmingly high prevalence of different E. coli virulence genes was found in the isolates investigated. Most of these virulence genes could be put into context with ExPEC and/or UPEC, e.g., cnf1, fimH, fyuA, iroN, iss, iucD, iutA, kpsMII, papA, papC, sitA, and traT [67,68]. E. coli virulence genes associated with ExPEC were also detected in seals in Ireland [40] and in marine sediments from coasts of the Adriatic Sea [69].
K. pneumoniae is a nosocomial pathogen with increasing MDR rates and global dissemination of high risk clones [70]. Although several studies have previously focused on K. pneumoniae in farm and companion animals [71,72,73,74], information about this pathogen in wildlife is still scarce [42,55,75,76,77,78]. Nevertheless, there are some reports about the isolation of K. pneumoniae from marine mammals along the U.S. Pacific Coast [19,79,80,81]. Among the K. pneumoniae isolates in the present study, two distinct sequence types were obtained: ST405 (n = 3) and ST466 (n = 9). The three K. pneumoniae isolates (IDs 161, 173, and 175) belonging to ST405 displayed indistinguishable resistance pheno- and genotypes and exhibited 17 different resistance genes each. This might indicate the importance of this clone in the investigated environment. K. pneumoniae ST405 strains isolated from humans have been reported worldwide to harbor ESBL and carbapenemase genes [82,83,84,85]. However, reports about K. pneumoniae ST466 are scarce. One study revealed a context of K. pneumoniae ST466 harboring blaCTX-M-15 with causing neonatal sepsis [86].
Salmonella spp. have been previously isolated from marine mammals in California [87,88,89,90]. Within the scope of the present study, 18 Salmonella isolates belonging to six different serotypes (S. Havana, S. Reading, S. Albany, S. Newport, S. Saintpaul, S. Braenderup) were obtained, and one isolate exhibited AMR. Our findings regarding Salmonella are in general accordance with those of Stoddard et al. [82]. They investigated the prevalence and antimicrobial susceptibility of Salmonella spp. in northern elephant seals on the Californian coast. They further determined a higher prevalence and higher antimicrobial resistance rates of Salmonella in stranded seals than in young pinnipeds that had never entered the seawater on their natal beaches, presumably because stranded animals are more susceptible to infection by pathogens in the marine environment from terrestrial sources [87]. Furthermore, another study on Salmonella in Californian seals revealed that the amount of precipitation within the immediate pre-sampling period correlates positively with the presence of fecal Salmonella spp. [90].
As previously reported, marine mammals living in coastal habitats as predatory species with long lifespans can serve as sentinels of the health of the ocean and its inhabitants [24,91]. The high burden of AMR bacteria among marine mammals reported in this study might be the result of increasing anthropogenic pollution of the marine environment with antimicrobial agents, biocides, and already resistant bacteria. To get more detailed insights into the broad field of possible environmental risk factors and to identify notable sources of contamination, further comparative studies are needed.

4. Materials and Methods

4.1. Bacterial Isolates

Samples were collected from April 2019 to December 2020 upon admission of the stranded marine mammals to the Marine Mammal Care Center Los Angeles (MMCCLA) as part of diagnostic health evaluation. In all but four cases, samples were collected prior to any antimicrobial treatment. Overall, 145 rectal swabs, 130 oral swabs, four wound swabs, two swabs of a blow hole, and two swabs of the nictitating membrane were sampled from 148 individual animals, including 122 California sea lions (Zalophus californianus), 15 northern elephant seals (Mirounga angustirostris), six harbor seals (Phoca vitulina), two northern fur seals (Callorhinus ursinus), one Guadalupe fur seal (Arctocephalus townsendi), one long-beaked common dolphin (Delphinus capensis), and one pygmy sperm whale (Kogia breviceps).
Each sample was preincubated at 37 °C overnight in buffered peptone water (BPW) (Merck, Germany). For selective isolation of β-lactamase-producing Enterobacterales, 200 µL of the incubated sample were cultured at 37 °C overnight in BPW supplemented with cefotaxime (1 mg/L) (BPWCTX) and then cultivated at 37 °C overnight on MacConkey agar (Oxoid, Basingstoke, United Kingdom) supplemented with cefotaxime (1 mg/L) (MacCTX). In parallel, another 200 µL of the preincubated sample were cultured at 42 °C overnight in Rappaport–Vassiliadis-broth (RV) (Oxoid, Basingstoke, UK) and in Selenit-broth (Merck, Darmstadt, Germany) and then cultivated at 37 °C on BD™ XLD Agar (Xylose-Lysine-Desoxycholate Agar) (BD, Heidelberg, Germany) for selective isolation of Salmonella sp. After incubation on MacCTX, one colony representing a distinct colony morphotype was regrown on BD MacConkey II Agar (MC) at 37 °C overnight. After incubation on XLD, the respective colonies of Salmonella isolates showed the typical colony appearance of Salmonella and were selected for further characterization. Colonies selected from MacCTX and XLD were identified to the species level by matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry (Bruker Daltonik, Heidelberg, Germany). Isolates, which grew on MacCTX and were confirmed as belonging to Enterobacterales, were examined for ESBL production by combination disk tests using cefotaxime and ceftazidime with and without clavulanic acid (Becton Dickinson, Heidelberg, Germany) according to the Clinical and Laboratory Standards Institute (CLSI) standards [92]. Furthermore, cefoxitin (30 μg) (BD, Heidelberg, Germany) was added to this test to detect AmpC phenotypes.

4.2. Antimicrobial and Biocide Susceptibility Testing

Antimicrobial susceptibility testing of β-lactamase-producing Enterobacterales and Salmonella isolates was carried out by agar disk-diffusion according to the CLSI standards [92]. Escherichia coli ATCC® 25922 served as the quality control strain. Disks containing the following antimicrobial agents were used: amoxicillin-clavulanate (20/10 µg), piperacillin (10 µg), cefotaxime (30 µg), ceftazidime (30 µg), cefoxitin (30 µg), aztreonam (30 µg), imipenem (10 µg), meropenem (10 µg), gentamicin (10 µg), tobramycin (10 µg), amikacin (30 µg), ciprofloxacin (5 µg), trimethoprim-sulfamethoxazole (1.25/23.75 µg), tetracycline (30 µg), doxycycline (30 µg), chloramphenicol (30 µg), and fosfomycin (200 µg) (Becton Dickinson, Heidelberg, Germany). AmpC-hyperproducing isolates (stably de-repressed) of Enterobacter sp. and Citrobacter sp. were defined as those with a cefotaxime and ceftazidime MIC of ≥32 mg/L without ESBL production, and the boronic acid inhibition test was performed by the standard disk diffusion method, using cefotaxime disks alone and in combination with 300 μg of 3-aminophenylboronic acid [93].
Biocide susceptibility testing was performed according to the previously established protocol of Schug et al. [94]. Benzalkonium chloride (Acros Organics, Geel, Belgium, 21541), representing the quaternary ammonium compounds, was tested at concentration ranges 0.000015%–0.016%, chlorhexidine (Sigma-Aldrich, Schnelldorf, Germany, 55-56-1), representing cationic compounds, was tested at concentration ranges 0.000015%–0.002%, glutardialdehyde (Chempur, Piekary Slaskie, Poland, 424610240), representing aldehydes, was tested at concentration ranges 0.0075%–1%, and isopropanol (99.9%, PHPU Eurochem BGD, Tarnow, Poland), representing alcohols, was tested at concentration ranges 1–14%. The method was performed in 96-wells U-bottom polystyrene microtiter plates (Sarstedt, Numbrecht, Germany, 82.1582.001). The bacterial inoculum was prepared according to the CLSI standards [92] using Trypticasein soy broth (Biomaximna, Lublin, Poland, PS 23–500). The final concentration of bacteria inoculated into the wells was 2.5–5 × 105 CFU/mL.

4.3. Characterization of Genotypic Resistance

Resistance genes were analyzed by CarbDetect-AS-2 Kit microarray (Alere, Jena, Germany) [95]. Since CarbDetect-AS-2 Kit was not available to analyze all isolates, the following resistance genes were screened via PCRs: blaCMY, blaCTX-M, blaOXA-1, blaOXA-2, blaSHV, blaTEM, sul1, sul2, sul3, dfrA1, dfrA12, dfrA14, dfrA17, dfrA19, strA, strB, aadA1, aadA2, aadA4, aadB, qepA, qnrA, qnrB, qnrC, qnrD, qnrS, and aac(6´)-Ib [96,97,98,99,100,101,102,103,104,105,106,107], depending on their resistance phenotype and those genes that responded positively in the array. If resistance genes were not included in the array kit (i.e., catA, cfr, cmlA, floR, aadA5, tet(A), tet(B), tet(C), tet(D), tet(E), tet(G)), they were analyzed by PCRs as described elsewhere [104,108]. A list of all primers and PCR conditions used in this study is provided in Supplementary Table S5. Multiplex PCR for detection of AmpC genes was performed in L. amnigena and Enterobacter spp. isolates [109,110]. In addition, the genes blaCMY, blaCTX-M, blaSHV, and blaTEM were sequenced after PCR amplification. All amplicons in the present study were sequenced at LGC Genomics, Berlin, Germany. Sequences were aligned with BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi, accessed on 30 April 2021) and compared with reference sequences available in GenBank and the National Center for Biotechnology Information (NCBI) database (http://www.ncbi.nlm.nih.gov/pathogens/beta-lactamase-data-resources/, accessed on 30 April 2021). The quinolone resistance-determining regions (QRDR) of gyrA and parC in ciprofloxacin-resistant isolates were amplified by PCR and sequenced [111]. E. coli isolates displaying an AmpC phenotype were also analyzed for mutations in the chromosomal ampC promoter/attenuator region as described previously [112].

4.4. Molecular Typing Methods

The phylogroup of the E. coli isolates was determined by the revisited Clermont method [113]. Clonal relatedness of E. coli isolates was assessed by two-locus sequence typing of combined data of fumC and fimH sequences, as described by Weissman et al. [114], using CHTyper hosted at Center for Genomic Epidemiology (https://cge.cbs.dtu.dk/services/chtyper/, accessed on 30 April 2021) [115]. Allele and CH clonotype numbers were used for goeBURST analysis using PHYLOViZ [116]. Clonal relatedness of Klebsiella pneumoniae isolates was characterized by MLST database available at Institute Pasteur MLST (https://bigsdb.pasteur.fr/klebsiella/klebsiella.html, accessed on 30 April 2021) [117,118].

4.5. Virulence Genes

Detection and analysis of virulence genes was performed using primer and probe sets derived from microarray-based methods, as described previously [119,120], and used in custom made microarrays from INTER-ARRAY (INTER-ARRAY by fzmb GmbH, Bad Langensalza, Germany) according to manufacturers instructions. The list of virulence-associated genes is available at INTER-ARRAY website (https://www.inter-array.com/#microarrays, accessed on 30 April 2021) upon request.

4.6. Whole-Genome Sequencing (WGS)

Selected E. coli isolates were analyzed by WGS, which was performed by isolating bacterial DNA using the MagAttract HMW DNA Kit (Qiagen, Hilden, Germany). Ready-to-sequence libraries were prepared using Nextera XT DNA Library Preparation Kit (Illumina, San Diego, United States). Isolates were paired-end-sequenced using the Illumina MiSeq platform with a read length of 2 × 300 bp [121]. De novo assembly of raw reads was performed using SPAdes v.3.9.0 [122], and WGS data analysis was performed with SeqSphere+ software (Ridom, Münster, Germany). To assess the genetic relatedness between the E. coli isolates, MLST and cgMLST were performed as previously described [123]. E. coli phylotypes were extracted from WGS by Clermontyping (http://clermontyping.iame-research.center/, accessed on 30 April 2021) [124,125]. To identify acquired resistance genes and/or chromosomal mutations, Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca/home, accessed on 30 April 2021) [126], as well as ResFinder 4.1 (https://cge.cbs.dtu.dk/services/ResFinder/, accessed on 30 April 2021) [127,128], were used. Genes associated with biocide resistance were compared with BacMet database (Antibacterial Biocide and Metal Resistance Genes Database, http://bacmet.biomedicine.gu.se/, accessed on 30 April 2021) [129]. Virulence genes were identified using VirulenceFinder 2.0 (https://cge.cbs.dtu.dk/services/VirulenceFinder/, accessed on 30 April 2021) [130,131], CH types were characterized as mentioned above, and serogenotypes were analyzed by SerotypeFinder (https://cge.cbs.dtu.dk/services/SerotypeFinder/, accessed on 30 April 2021) [132]. The presence of plasmids was determined using PlasmidFinder 2.1 (https://cge.cbs.dtu.dk/services/PlasmidFinder/, accessed on 30 April 2021) [133]. Probability prediction of the location of a given antimicrobial resistance gene or virulence gene was achieved by applying mlplasmids trained on E. coli [134]. Posterior probability scores >0.7 and a minimum contig length of 1000 bp indicate that a given contig is plasmid-derived. For resistance and virulence genes with ppp scores below 0.7 but above 0.5, BLAST searches for the respective contig sequence were performed. If the BLAST search listed only plasmids for the first 30 entries with 100% coverage and identities, a plasmid location was assumed. The genomes of WGS isolates were deposited under PRJNA725684 in the NCBI BioProject database.

4.7. Characterization of Salmonella Isolates

The antigenic formula of all Salmonella isolates was determined by the National Reference Centre for Salmonella Austria using standard agglutination methods (ISO/TR 6579-3, 2014), and the serotype name was assigned according to the White–Kauffmann–Le Minor scheme [135].
The following virulence genes associated with Salmonella spp. were analyzed by PCRs: hilA, stn, and tviA [136,137].

5. Conclusions

In conclusion, the present study contributes to the growing evidence that β-lactamase-producing and multidrug-resistant Enterobacterales, as well as Salmonella, are currently part of the microbiome of wild animals. The presence of pandemic clones in samples originating from marine mammals demonstrates the complexity in the dissemination of antimicrobial drug resistance and highlights the public health threats. Furthermore, the resistance and virulence genes frequently encoded on mobile genetic elements can easily be transferred horizontally and also between different species in such a habitat and ecosystem, emphasizing the need of a One Health approach to tackling the global AMR crisis.

Supplementary Materials

The following are available online at https://www.mdpi.com/article/10.3390/ijms22115905/s1.

Author Contributions

Conceptualization, L.P., C.W., H.S., and I.L.; methodology, O.M.G., L.P., A.C., M.P.S., W.R., C.K., D.M., A.T.F., S.S., J.S., E.M., S.D.B., S.M., R.E., H.S., and I.L.; validation, O.M.G., L.P., A.C., M.P.S., W.R., C.K., S.S., S.D.B., S.M., R.E., C.W., and I.L.; formal analysis, O.M.G., L.P., A.C., M.P.S., W.R., C.K., M.K., D.M., T.B.-H., A.D.J.K., E.M., and I.L.; investigation, O.M.G., L.P., A.C., M.P.S., W.R, C.K., M.K., D.M., T.B.-H., A.D.J.K., E.M., H.S., and I.L.; resources, L.P., D.M., F.A., S.S., J.S., R.E., C.W., and H.S.; data curation, O.M.G., L.P., A.C., M.P.S., W.R., C.K., M.K., D.M., T.B.-H., A.D.J.K., A.T.F., S.S., E.M., S.D.B., H.S., and I.L.; writing—original draft preparation, O.M.G., L.P., D.M., C.W., H.S., and I.L.; writing—review and editing, O.M.G., L.P., A.C., M.P.S., W.R., C.K., D.M., A.T.F., F.A., S.S., S.D.B., S.M., R.E., C.W., H.S., and I.L.; visualization, O.M.G. and I.L.; supervision, L.P., C.W., H.S., and I.L.; project administration, L.P. and I.L.; funding acquisition, L.P., F.A., R.E., C.W., and I.L. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Institutional Review Board Statement

Ethical review and approval were waived for this study, because all clinical samples were obtained within the scope of routine diagnostic health assessments and only subsequently evaluated within the scope of this study and, therefore, not subject to reporting obligations of the Ethics and Animal Welfare Commission of the University of Veterinary Medicine in Vienna.

Informed Consent Statement

Not applicable.

Data Availability Statement

All data is contained within the article or supplementary material.

Acknowledgments

We thank the CHTyper curators Louise Roer and Henrik Hasman of the Statens Serum Institut for curating the data and making them publicly available at https://cge.cbs.dtu.dk/services/chtyper/, accessed on 30 April 2021. We would also like to express our thanks to Michael Steinbrecher, Barbara Tischler, and Anna Stöger for technical assistance. Open Access Funding by the University of Veterinary Medicine Vienna.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Bassetti, M.; Pecori, D.; Sibani, M.; Corcione, S.; Rosa, F.G.d. Epidemiology and Treatment of MDR Enterobacteriaceae. Curr. Treat. Options Infect. Dis. 2015, 7, 291–316. [Google Scholar] [CrossRef]
  2. Wilson, H.; Török, M.E. Extended-Spectrum Β-Lactamase-Producing and Carbapenemase-Producing Enterobacteriaceae. Microb. Genom. 2018, 4, e000197. [Google Scholar] [CrossRef]
  3. Gajdács, M.; Bátori, Z.; Ábrók, M.; Lázár, A.; Burián, K. Characterization of Resistance in Gram-Negative Urinary Isolates Using Existing and Novel Indicators of Clinical Relevance: A 10-Year Data Analysis. Life 2020, 10, 16. [Google Scholar] [CrossRef] [Green Version]
  4. Kadri, S.S.; Adjemian, J.; Lai, Y.L.; Spaulding, A.B.; Ricotta, E.; Prevots, D.R.; Palmore, T.N.; Rhee, C.; Klompas, M.; Dekker, J.P.; et al. Difficult-to-Treat Resistance in Gram-Negative Bacteremia at 173 US Hospitals: Retrospective Cohort Analysis of Prevalence, Predictors, and Outcome of Resistance to All First-line Agents. Clin. Infect. Dis. 2018, 67, 1803–1814. [Google Scholar] [CrossRef] [Green Version]
  5. Jacoby, G.A.; Munoz-Price, L.S. The New Beta-Lactamases. N. Engl. J. Med. 2005, 352, 380–391. [Google Scholar] [CrossRef] [PubMed]
  6. Bush, K. Past and Present Perspectives on β-Lactamases. Antimicrob. Agents Chemother. 2018, 62, e01076-18. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  7. Jacoby, G.A. AmpC Beta-Lactamases. Clin. Microbiol. Rev. 2009, 22, 161–182. [Google Scholar] [CrossRef] [Green Version]
  8. Tamma, P.D.; Doi, Y.; Bonomo, R.A.; Johnson, J.K.; Simner, P.J. A Primer on AmpC β-Lactamases: Necessary Knowledge for an Increasingly Multidrug-Resistant World. Clin. Infect. Dis. 2019, 69, 1446–1455. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  9. Ewers, C.; Bethe, A.; Semmler, T.; Guenther, S.; Wieler, L.H. Extended-Spectrum β-Lactamase-Producing and AmpC-Producing Escherichia coli from Livestock and Companion Animals, and Their Putative Impact on Public Health: A Global Perspective. Clin. Microbiol. Infect. 2012, 18, 646–655. [Google Scholar] [CrossRef] [Green Version]
  10. Karl, H.A.; Chin, J.L.; Ueber, E.; Stauffer, P.H.; Hendley, J.W., II (Eds.) Beyond the Golden Gate—Oceanography, Geology, Biology, and Environmental Issues in the Gulf of the Farallones; U.S. Geological Survey: Reston, VA, USA; USGS Information Services: Denver, CO, USA, 2001.
  11. Hatosy, S.M.; Martiny, A.C. The Ocean as a Global Reservoir of Antibiotic Resistance Genes. Appl. Environ. Microbiol. 2015, 81, 7593–7599. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  12. Yang, Y.; Liu, G.; Song, W.; Ye, C.; Lin, H.; Li, Z.; Liu, W. Plastics in the Marine Environment Are Reservoirs for Antibiotic and Metal Resistance Genes. Environ. Int. 2019, 123, 79–86. [Google Scholar] [CrossRef] [PubMed]
  13. Cohen, R.; Paikin, S.; Rokney, A.; Rubin-Blum, M.; Astrahan, P. Multidrug-Resistant Enterobacteriaceae in Coastal Water: An Emerging Threat. Antimicrob. Resist. Infect. Control 2020, 9, 169. [Google Scholar] [CrossRef]
  14. Nappier, S.P.; Liguori, K.; Ichida, A.M.; Stewart, J.R.; Jones, K.R. Antibiotic Resistance in Recreational Waters: State of the Science. Int. J. Environ. Res. Public Health 2020, 17, 8034. [Google Scholar] [CrossRef]
  15. Shallcross, L.J.; Howard, S.J.; Fowler, T.; Davies, S.C. Tackling the Threat of Antimicrobial Resistance: From Policy to Sustainable action. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2015, 370, 20140082. [Google Scholar] [CrossRef]
  16. Ramey, A.M.; Ahlstrom, C.A. Antibiotic Resistant Bacteria in Wildlife: Perspectives on Trends, Acquisition and Dissemination, Data Gaps, and Future Directions. J. Wildl. Dis. 2020, 56, 1–15. [Google Scholar] [CrossRef]
  17. Hocquet, D.; Muller, A.; Bertrand, X. What Happens IN Hospitals Does Not Stay in Hospitals: Antibiotic-Resistant Bacteria in Hospital Wastewater Systems. J. Hosp. Infect. 2016, 93, 395–402. [Google Scholar] [CrossRef]
  18. Muziasari, W.I.; Pitkänen, L.K.; Sørum, H.; Stedtfeld, R.D.; Tiedje, J.M.; Virta, M. The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms. Front. Microbiol. 2017, 7, 2137. [Google Scholar] [CrossRef]
  19. Wallace, C.C.; Yund, P.O.; Ford, T.E.; Matassa, K.A.; Bass, A.L. Increase in antimicrobial resistance in bacteria isolated from stranded marine mammals of the Northwest Atlantic. EcoHealth 2013, 10, 201–210. [Google Scholar] [CrossRef] [PubMed]
  20. Carroll, D.; Wang, J.; Fanning, S.; McMahon, B.J. Antimicrobial Resistance in Wildlife: Implications for Public Health. Zoonoses Public Health 2015, 62, 534–542. [Google Scholar] [CrossRef] [Green Version]
  21. Furness, L.E.; Campbell, A.; Zhang, L.; Gaze, W.H.; McDonald, R.A. Wild Small Mammals as Sentinels for the Environmental Transmission of Antimicrobial Resistance. Environ. Res. 2017, 154, 28–34. [Google Scholar] [CrossRef] [PubMed]
  22. Plaza-Rodríguez, C.; Alt, K.; Grobbel, M.; Hammerl, J.A.; Irrgang, A.; Szabo, I.; Stingl, K.; Schuh, E.; Wiehle, L.; Pfefferkorn, B.; et al. Wildlife as Sentinels of Antimicrobial Resistance in Germany? Front. Vet. Sci. 2021, 7, 627821. [Google Scholar] [CrossRef] [PubMed]
  23. Wells, R.; Rhinehart, H.; Hansen, L.; Sweeney, J.; Townsend, F.; Stone, R.; Casper, D.R.; Scott, M.; Hohn, A.; Rowles, T. Bottlenose Dolphins as Marine Ecosystem Sentinels: Developing a Health Monitoring System. EcoHealth 2004, 1, 246–254. [Google Scholar] [CrossRef]
  24. Bossart, G.D. Marine Mammals as Sentinel Species for Oceans and Human Health. Vet. Pathol. 2011, 48, 676–690. [Google Scholar] [CrossRef] [Green Version]
  25. Reif, J.S. Animal Sentinels for Environmental and Public Health. Public Heal. Rep. 2011, 126, 50–57. [Google Scholar] [CrossRef] [Green Version]
  26. Johnson, S.P.; Nolan, S.; Gulland, F.M. Antimicrobial Susceptibility of Bacteria Isolated from Pinnipeds Stranded in Central and Northern California. J. Zoo Wildl. Med. 1998, 29, 288–294. [Google Scholar]
  27. Thornton, S.M.; Nolan, S.; Gulland, F.M. Bacterial Isolates from California Sea Lions (Zalophus californianus), Harbor Seals (Phoca vitulina), and Northern Elephant Seals (Mirounga angustirostris) Admitted to a Rehabilitation Center Along the Central California Coast, 1994–1995. J. Zoo Wildl. Med. 1998, 29, 171–176. [Google Scholar]
  28. Stoddard, R.A.; Atwill, E.R.; Conrad, P.A.; Byrne, B.A.; Jang, S.; Lawrence, J.; McCowan, B.; Gulland, F.M.D. The Effect of Rehabilitation of Northern Elephant Seals (Mirounga angustirostris) on Antimicrobial Resistance of Commensal Escherichia coli. Vet. Microbiol. 2009, 133, 264–271. [Google Scholar] [CrossRef]
  29. Lockwood, S.K.; Chovan, J.L.; Gaydos, J.K. Aerobic Bacterial Isolations from Harbor Seals (Phoca vitulina) Stranded in Washington: 1992–2003. J. Zoo Wildl. Med. 2006, 37, 281–291. [Google Scholar] [CrossRef]
  30. Santestevan, N.A.; Angelis Zvoboda, D.d.; Prichula, J.; Pereira, R.I.; Wachholz, G.R.; Cardoso, L.A.; Moura, T.M.d.; Medeiros, A.W.; Amorin, D.B.d.; Tavares, M.; et al. Antimicrobial Resistance and Virulence Factor Gene Profiles of Enterococcus spp. Isolates from wild Arctocephalus australis (South American Fur Seal) and Arctocephalus tropicalis (Subantarctic Fur Seal). World J. Microbiol. Biotechnol. 2015, 31, 1935–1946. [Google Scholar] [CrossRef] [PubMed]
  31. Sweeney, M.T.; Lubbers, B.V.; Schwarz, S.; Watts, J.L. Applying Definitions for Multidrug Resistance, Extensive Drug Resistance and Pandrug Resistance to Clinically Significant Livestock and Companion Animal Bacterial Pathogens. J. Antimicrob. Chemother. 2018, 73, 1460–1463. [Google Scholar] [CrossRef]
  32. Sarowska, J.; Futoma-Koloch, B.; Jama-Kmiecik, A.; Frej-Madrzak, M.; Ksiazczyk, M.; Bugla-Ploskonska, G.; Choroszy-Krol, I. Virulence Factors, Prevalence and Potential Transmission of Extraintestinal Pathogenic Escherichia coli Isolated from Different Sources: Recent Reports. Gut Pathog. 2019, 11, 10. [Google Scholar] [CrossRef] [Green Version]
  33. Edgar, R.; Bibi, E. MdfA, an Escherichia coli Multidrug Resistance Protein with an Extraordinarily Broad Spectrum of Drug Recognition. J. Bacteriol. 1997, 179, 2274–2280. [Google Scholar] [CrossRef] [Green Version]
  34. Liebana, E.; Carattoli, A.; Coque, T.M.; Hasman, H.; Magiorakos, A.-P.; Mevius, D.; Peixe, L.; Poirel, L.; Schuepbach-Regula, G.; Torneke, K.; et al. Public Health Risks of Enterobacterial Isolates Producing Extended-Spectrum Β-Lactamases or AmpC β-Lactamases in Food and Food-Producing Animals: An EU Perspective of Epidemiology, Analytical Methods, Risk Factors, and Control Options. Clin. Infect. Dis. 2013, 56, 1030–1037. [Google Scholar] [CrossRef] [Green Version]
  35. Darwich, L.; Vidal, A.; Seminati, C.; Albamonte, A.; Casado, A.; López, F.; Molina-López, R.A.; Migura-Garcia, L. High Prevalence and Diversity of Extended-Spectrum β-Lactamase and Emergence of OXA-48 Producing Enterobacterales in Wildlife in Catalonia. PLoS ONE 2019, 14, e0210686. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  36. Athanasakopoulou, Z.; Tsilipounidaki, K.; Sofia, M.; Chatzopoulos, D.C.; Giannakopoulos, A.; Karakousis, I.; Giannakis, V.; Spyrou, V.; Touloudi, A.; Satra, M.; et al. Poultry and Wild Birds as a Reservoir of CMY-2 Producing Escherichia coli: The First Large-Scale Study in Greece. Antibiotics 2021, 10, 235. [Google Scholar] [CrossRef]
  37. Poirel, L.; Potron, A.; La Cuesta, C.d.; Cleary, T.; Nordmann, P.; Munoz-Price, L.S. Wild Coastline Birds as Reservoirs of Broad-Spectrum-β-Lactamase-Producing Enterobacteriaceae in Miami Beach, Florida. Antimicrob. Agents Chemother. 2012, 56, 2756–2758. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  38. Skarżyńska, M.; Zając, M.M.; Bomba, A.; Bocian, Ł.; Kozdruń, W.; Polak, M.; Wiącek, J.; Wasyl, D. Antimicrobial Resistance Glides in the Sky—Free-Living Birds as a Reservoir of Resistant Escherichia coli With Zoonotic Potential. Front. Microbiol. 2021, 12, 656223. [Google Scholar] [CrossRef]
  39. Fang, L.-X.; Sun, J.; Li, L.; Deng, H.; Huang, T.; Yang, Q.-E.; Li, X.; Chen, M.-Y.; Liao, X.-P.; Liu, Y.-H. Dissemination of the Chromosomally Encoded Cmy-2 Cephalosporinase Gene in Escherichia coli Isolated from Animals. Int. J. Antimicrob. Agents 2015, 46, 209–213. [Google Scholar] [CrossRef]
  40. Vale, A.P.; Shubin, L.; Cummins, J.; Leonard, F.C.; Barry, G. Detection of blaOXA-1, blaTEM-1, and Virulence Factors in E. coli Isolated From Seals. Front. Vet. Sci. 2021, 8, 583759. [Google Scholar] [CrossRef]
  41. Chaves, J.; Ladona, M.G.; Segura, C.; Coira, A.; Reig, R.; Ampurdanés, C. SHV-1 Beta-Lactamase Is Mainly a Chromosomally Encoded Species-Specific Enzyme in Klebsiella pneumoniae. Antimicrob. Agents Chemother. 2001, 45, 2856–2861. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  42. Loncaric, I.; Beiglböck, C.; Feßler, A.T.; Posautz, A.; Rosengarten, R.; Walzer, C.; Ehricht, R.; Monecke, S.; Schwarz, S.; Spergser, J.; et al. Characterization of ESBL- and AmpC-Producing and Fluoroquinolone-Resistant Enterobacteriaceae Isolated from Mouflons (Ovis orientalis musimon) in Austria and Germany. PLoS ONE 2016, 11, e0155786. [Google Scholar] [CrossRef]
  43. Soto, E.; Abdelrazek, S.M.R.; Basbas, C.; Duignan, P.J.; Rios, C.; Byrne, B.A. Environmental Persistence and Disinfectant Susceptibility of Klebsiella pneumoniae Recovered from Pinnipeds Stranded on the California Coast. Vet. Microbiol. 2020, 241, 108554. [Google Scholar] [CrossRef]
  44. Kampf, G. Biocidal Agents Used for Disinfection Can Enhance Antibiotic Resistance in Gram-Negative Species. Antibiotics 2018, 7, 110. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  45. Behzadi, P.; Baráth, Z.; Gajdács, M. It’s Not Easy Being Green: A Narrative Review on the Microbiology, Virulence and Therapeutic Prospects of Multidrug-Resistant Pseudomonas aeruginosa. Antibiotics 2021, 10, 42. [Google Scholar] [CrossRef]
  46. Escobar-Páramo, P.; Le Menac’h, A.; Le Gall, T.; Amorin, C.; Gouriou, S.; Picard, B.; Skurnik, D.; Denamur, E. Identification of Forces Shaping the Commensal Escherichia coli Genetic Structure by Comparing Animal and Human Isolates. Environ. Microbiol. 2006, 8, 1975–1984. [Google Scholar] [CrossRef]
  47. Delport, T.C.; Harcourt, R.G.; Beaumont, L.J.; Webster, K.N.; Power, M.L. Molecular Detection of Antibiotic-Resistance Determinants in Escherichia coli Isolated from the Endangered Australian Sea Lion (Neophoca cinerea). J. Wildl. Dis. 2015, 51, 555–563. [Google Scholar] [CrossRef] [PubMed]
  48. Fulham, M.; Power, M.; Gray, R. Comparative ecology of Escherichia coli in Endangered Australian Sea Lion (Neophoca cinerea) Pups. Infect. Genet. Evol. 2018, 62, 262–269. [Google Scholar] [CrossRef]
  49. Fulham, M.; Power, M.; Gray, R. Diversity and Distribution of Escherichia coli in Three Species of Free-Ranging Australian Pinniped Pups. Front. Mar. Sci. 2020, 7, 571171. [Google Scholar] [CrossRef]
  50. Schaufler, K.; Semmler, T.; Wieler, L.H.; Wöhrmann, M.; Baddam, R.; Ahmed, N.; Müller, K.; Kola, A.; Fruth, A.; Ewers, C.; et al. Clonal Spread and Interspecies Transmission of Clinically Relevant ESBL-Producing Escherichia coli of ST410—Another Successful Pandemic Clone? FEMS Microbiol. Ecol. 2016, 92, fiv155. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  51. Giufrè, M.; Errico, G.; Accogli, M.; Monaco, M.; Villa, L.; Distasi, M.A.; Del Gaudio, T.; Pantosti, A.; Carattoli, A.; Cerquetti, M. Emergence of NDM-5-Producing Escherichia coli Sequence Type 167 Clone in Italy. Int. J. Antimicrob. Agents 2018, 52, 76–81. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  52. Huang, Y.; Yu, X.; Xie, M.; Wang, X.; Liao, K.; Xue, W.; Chan, E.W.-C.; Zhang, R.; Chen, S. Widespread Dissemination of Carbapenem-Resistant Escherichia coli Sequence Type 167 Strains Harboring blaNDM-5 in Clinical Settings in China. Antimicrob. Agents Chemother. 2016, 60, 4364–4368. [Google Scholar] [CrossRef] [Green Version]
  53. Dadashi, M.; Yaslianifard, S.; Hajikhani, B.; Kabir, K.; Owlia, P.; Goudarzi, M.; Hakemivala, M.; Darban-Sarokhalil, D. Frequency Distribution, Genotypes and Prevalent Sequence Types of New Delhi Metallo-β-Lactamase-Producing Escherichia coli among Clinical Isolates around the World: A Review. J. Glob. Antimicrob. Resist. 2019, 19, 284–293. [Google Scholar] [CrossRef]
  54. Guenther, S.; Aschenbrenner, K.; Stamm, I.; Bethe, A.; Semmler, T.; Stubbe, A.; Stubbe, M.; Batsajkhan, N.; Glupczynski, Y.; Wieler, L.H.; et al. Comparable High Rates of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli in Birds of Prey from Germany and Mongolia. PLoS ONE 2012, 7, e53039. [Google Scholar] [CrossRef] [Green Version]
  55. Dolejska, M.; Masarikova, M.; Dobiasova, H.; Jamborova, I.; Karpiskova, R.; Havlicek, M.; Carlile, N.; Priddel, D.; Cizek, A.; Literak, I. High Prevalence of Salmonella and IMP-4-Producing Enterobacteriaceae in the Silver Gull on Five Islands, Australia. J. Antimicrob. Chemother. 2016, 71, 63–70. [Google Scholar] [CrossRef] [Green Version]
  56. Schaufler, K.; Semmler, T.; Wieler, L.H.; Trott, D.J.; Pitout, J.; Peirano, G.; Bonnedahl, J.; Dolejska, M.; Literak, I.; Fuchs, S.; et al. Genomic and Functional Analysis of Emerging Virulent and Multidrug-Resistant Escherichia coli Lineage Sequence Type 648. Antimicrob. Agents Chemother. 2019, 63, e00243-19. [Google Scholar] [CrossRef] [Green Version]
  57. Guenther, S.; Grobbel, M.; Beutlich, J.; Bethe, A.; Friedrich, N.D.; Goedecke, A.; Lübke-Becker, A.; Guerra, B.; Wieler, L.H.; Ewers, C. CTX-M-15-Type Extended-Spectrum Beta-Lactamases-Producing Escherichia coli from Wild Birds in Germany. Environ. Microbiol. Rep. 2010, 2, 641–645. [Google Scholar] [CrossRef] [PubMed]
  58. Shnaiderman-Torban, A.; Steinman, A.; Meidan, G.; Paitan, Y.; Abu Ahmad, W.; Navon-Venezia, S. Petting Zoo Animals as an Emerging Reservoir of Extended-Spectrum β-Lactamase and AmpC-Producing Enterobacteriaceae. Front. Microbiol. 2019, 10, 2488. [Google Scholar] [CrossRef] [Green Version]
  59. Guenther, S.; Semmler, T.; Stubbe, A.; Stubbe, M.; Wieler, L.H.; Schaufler, K. Chromosomally Encoded Esbl Genes in Escherichia coli of ST38 from Mongolian Wild Birds. J. Antimicrob. Chemother. 2017, 72, 1310–1313. [Google Scholar] [CrossRef]
  60. Schaufler, K.; Nowak, K.; Düx, A.; Semmler, T.; Villa, L.; Kourouma, L.; Bangoura, K.; Wieler, L.H.; Leendertz, F.H.; Guenther, S. Clinically Relevant ESBL-Producing K. pneumoniae ST307 and E. coli ST38 in an Urban West African Rat Population. Front. Microbiol. 2018, 9, 150. [Google Scholar] [CrossRef] [PubMed]
  61. Mukerji, S.; Stegger, M.; Truswell, A.V.; Laird, T.; Jordan, D.; Abraham, R.J.; Harb, A.; Barton, M.; O’Dea, M.; Abraham, S. Resistance to critically important antimicrobials in Australian silver gulls (Chroicocephalus novaehollandiae) and evidence of anthropogenic origins. J. Antimicrob. Chemother. 2019, 74, 2566–2574. [Google Scholar] [CrossRef]
  62. Zhou, Z.; Alikhan, N.F.; Mohamed, K.; Achtman, M.; the Agama Study Group. The EnteroBase User’s Guide, with Case Studies on Salmonella Transmissions, Yersinia pestis Phylogeny and Escherichia core Genomic Diversity. Genome Res. 2020, 30, 138–152. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  63. Pitout, J.D.D. Extraintestinal Pathogenic Escherichia coli: A Combination of Virulence with Antibiotic Resistance. Front. Microbiol. 2012, 3, 9. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  64. Chattaway, M.A.; Jenkins, C.; Ciesielczuk, H.; Day, M.; DoNascimento, V.; Day, M.; Rodríguez, I.; van Essen-Zandbergen, A.; Schink, A.-K.; Wu, G.; et al. Evidence of Evolving Extraintestinal Enteroaggregative Escherichia coli ST38 Clone. Emerg. Infect. Dis. 2014, 20, 1935–1937. [Google Scholar] [CrossRef]
  65. Wang, J.; Ma, Z.-B.; Zeng, Z.-L.; Yang, X.-W.; Huang, Y.; Liu, J.-H. The Role of Wildlife (Wild Birds) in the Global Transmission of Antimicrobial Resistance Genes. Zool. Res. 2017, 38, 55–80. [Google Scholar] [CrossRef] [Green Version]
  66. Nowak, K.; Fahr, J.; Weber, N.; Lübke-Becker, A.; Semmler, T.; Weiss, S.; Mombouli, J.-V.; Wieler, L.H.; Guenther, S.; Leendertz, F.H.; et al. Highly Diverse and Antimicrobial Susceptible Escherichia coli Display a Naïve Bacterial Population in Fruit Bats from the Republic of Congo. PLoS ONE 2017, 12, e0178146. [Google Scholar] [CrossRef] [Green Version]
  67. Johnson, T.J.; Wannemuehler, Y.; Johnson, S.J.; Stell, A.L.; Doetkott, C.; Johnson, J.R.; Kim, K.S.; Spanjaard, L.; Nolan, L.K. Comparison of Extraintestinal Pathogenic Escherichia coli Strains from Human and Avian Sources Reveals a Mixed Subset Representing Potential Zoonotic Pathogens. Appl. Environ. Microbiol. 2008, 74, 7043–7050. [Google Scholar] [CrossRef] [Green Version]
  68. Singer, R.S. Urinary Tract Infections Attributed to Diverse ExPEC Strains in Food Animals: Evidence and Data Gaps. Front. Microbiol. 2015, 6, 28. [Google Scholar] [CrossRef] [Green Version]
  69. Luna, G.M.; Vignaroli, C.; Rinaldi, C.; Pusceddu, A.; Nicoletti, L.; Gabellini, M.; Danovaro, R.; Biavasco, F. Extraintestinal Escherichia coli Carrying Virulence Genes in Coastal Marine Sediments. Appl. Environ. Microbiol. 2010, 76, 5659–5668. [Google Scholar] [CrossRef] [Green Version]
  70. Navon-Venezia, S.; Kondratyeva, K.; Carattoli, A. Klebsiella Pneumoniae: A Major Worldwide Source and Shuttle for Antibiotic Resistance. FEMS Microbiol. Rev. 2017, 41, 252–275. [Google Scholar] [CrossRef] [PubMed]
  71. Loncaric, I.; Cabal Rosel, A.; Szostak, M.P.; Licka, T.; Allerberger, F.; Ruppitsch, W.; Spergser, J. Broad-Spectrum Cephalosporin-Resistant Klebsiella spp. Isolated from Diseased Horses in Austria. Animals 2020, 10, 332. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  72. Marques, C.; Belas, A.; Aboim, C.; Cavaco-Silva, P.; Trigueiro, G.; Gama, L.T.; Pomba, C. Evidence of Sharing of Klebsiella pneumoniae Strains between Healthy Companion Animals and Cohabiting Humans. J. Clin. Microbiol. 2019, 57, e01537-18. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  73. Cheng, F.; Li, Z.; Lan, S.; Liu, W.; Li, X.; Zhou, Z.; Song, Z.; Wu, J.; Zhang, M.; Shan, W. Characterization of Klebsiella pneumoniae Associated with Cattle Infections in Southwest China Using Multi-Locus Sequence Typing (MLST), Antibiotic Resistance and Virulence-Associated Gene Profile Analysis. Braz. J. Microbiol. 2018, 49, 93–100. [Google Scholar] [CrossRef]
  74. Yang, F.; Deng, B.; Liao, W.; Wang, P.; Chen, P.; Wei, J. High Rate of Multiresistant Klebsiella pneumoniae from Human and Animal Origin. Infect. Drug Resist. 2019, 12, 2729–2737. [Google Scholar] [CrossRef] [Green Version]
  75. Bonnedahl, J.; Hernandez, J.; Stedt, J.; Waldenström, J.; Olsen, B.; Drobni, M. Extended-Spectrum β-Lactamases in Escherichia coli and Klebsiella pneumoniae in Gulls, Alaska, USA. Emerg. Infect. Dis. 2014, 20, 897–899. [Google Scholar] [CrossRef]
  76. Janatova, M.; Albrechtova, K.; Petrzelkova, K.J.; Dolejska, M.; Papousek, I.; Masarikova, M.; Cizek, A.; Todd, A.; Shutt, K.; Kalousova, B.; et al. Antimicrobial-Resistant Enterobacteriaceae from Humans and Wildlife in Dzanga-Sangha Protected Area, Central African Republic. Vet. Microbiol. 2014, 171, 422–431. [Google Scholar] [CrossRef] [PubMed]
  77. Du, Y.; Luo, J.; Wang, C.; Wen, Q.; Duan, M.; Zhang, H.; He, H. Detection of Drug-Resistant Klebsiella pneumoniae in Chinese Hares (Lepus sinensis). J. Wildl. Dis. 2014, 50, 109–112. [Google Scholar] [CrossRef]
  78. Bachiri, T.; Bakour, S.; Lalaoui, R.; Belkebla, N.; Allouache, M.; Rolain, J.M.; Touati, A. Occurrence of Carbapenemase-Producing Enterobacteriaceae Isolates in the Wildlife: First Report of OXA-48 in Wild Boars in Algeria. Microb. Drug Resist. 2018, 24, 337–345. [Google Scholar] [CrossRef]
  79. Seguel, M.; Gottdenker, N.L.; Colegrove, K.; Johnson, S.; Struve, C.; Howerth, E.W. Hypervirulent Klebsiella pneumoniae in California Sea Lions (Zalophus californianus): Pathologic Findings in Natural Infections. Vet. Pathol. 2017, 54, 846–850. [Google Scholar] [CrossRef] [Green Version]
  80. Whitaker, D.M.; Reichley, S.R.; Griffin, M.J.; Prager, K.; Richey, C.A.; Kenelty, K.V.; Stevens, B.N.; Lloyd-Smith, J.O.; Johnson, C.K.; Duignan, P.; et al. Hypermucoviscous Klebsiella pneumoniae Isolates from Stranded and Wild-Caught Marine Mammals of the US Pacific Coast: Prevalence, Phenotype, and Genotype. J. Wildl. Dis. 2018, 54, 659–670. [Google Scholar] [CrossRef]
  81. Jang, S.; Wheeler, L.; Carey, R.B.; Jensen, B.; Crandall, C.M.; Schrader, K.N.; Jessup, D.; Colegrove, K.; Gulland, F.M.D. Pleuritis and Suppurative Pneumonia Associated with a Hypermucoviscosity Phenotype of Klebsiella pneumoniae in California Sea Lions (Zalophus californianus). Vet. Microbiol. 2010, 141, 174–177. [Google Scholar] [CrossRef] [PubMed]
  82. Lepuschitz, S.; Schill, S.; Stoeger, A.; Pekard-Amenitsch, S.; Huhulescu, S.; Inreiter, N.; Hartl, R.; Kerschner, H.; Sorschag, S.; Springer, B.; et al. Whole Genome Sequencing Reveals Resemblance between ESBL-Producing and Carbapenem Resistant Klebsiella pneumoniae Isolates from Austrian Rivers and Clinical Isolates from Hospitals. Sci. Total Environ. 2019, 662, 227–235. [Google Scholar] [CrossRef]
  83. Liapis, E.; Pantel, A.; Robert, J.; Nicolas-Chanoine, M.-H.; Cavalié, L.; van der Mee-Marquet, N.; Champs, C.d.; Aissa, N.; Eloy, C.; Blanc, V.; et al. Molecular Epidemiology of OXA-48-Producing Klebsiella pneumoniae in France. Clin. Microbiol. Infect. 2014, 20, O1121–O1123. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  84. Gharout-Sait, A.; Alsharapy, S.-A.; Brasme, L.; Touati, A.; Kermas, R.; Bakour, S.; Guillard, T.; de Champs, C. Enterobacteriaceae Isolates Carrying the New Delhi Metallo-β-Lactamase Gene in Yemen. J. Med. Microbiol. 2014, 63, 1316–1323. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  85. López-Camacho, E.; Paño-Pardo, J.R.; Ruiz-Carrascoso, G.; Wesselink, J.-J.; Lusa-Bernal, S.; Ramos-Ruiz, R.; Ovalle, S.; Gómez-Gil, R.; Pérez-Blanco, V.; Pérez-Vázquez, M.; et al. Population Structure of OXA-48-Producing Klebsiella pneumoniae ST405 Isolates During a Hospital Outbreak Characterised by Genomic Typing. J. Glob. Antimicrob. Resist. 2018, 15, 48–54. [Google Scholar] [CrossRef]
  86. Ballén, V.; Sáez, E.; Benmessaoud, R.; Houssain, T.; Alami, H.; Barkat, A.; Kabiri, M.; Moraleda, C.; Bezad, R.; Vila, J.; et al. First Report of a Klebsiella pneumoniae ST466 Strain Causing Neonatal Sepsis Harbouring the blaCTX-M-15 Gene in Rabat, Morocco. FEMS Microbiol. Lett. 2015, 362, 1–4. [Google Scholar] [CrossRef] [Green Version]
  87. Stoddard, R.A.; Gulland, M.D.F.; Atwill, E.R.; Lawrence, J.; Jang, S.; Conrad, P.A. Salmonella and Campylobacter spp. in Northern Elephant Seals, California. Emerg. Infect. Dis. 2005, 11, 1967–1969. [Google Scholar] [CrossRef]
  88. Stoddard, R.A.; DeLong, R.L.; Byrne, B.A.; Jang, S.; Gulland, F.M.D. Prevalence and Characterization of Salmonella spp. among Marine Animals in the Channel Islands, California. Dis. Aquat. Organ. 2008, 81, 5–11. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  89. Berardi, T.; Shapiro, K.; Byrne, B.A.; Miller, W. Prevalence and Characterization of Salmonella Shed by Captive and Free-Range California Sea Lions (Zalophus californianus) from a Rehabilitation Center and Three State Reserves along the California Coast. J. Zoo Wildl. Med. 2014, 45, 527–533. [Google Scholar] [CrossRef]
  90. Stoddard, R.A.; Atwill, E.R.; Gulland, F.M.D.; Miller, M.A.; Dabritz, H.A.; Paradies, D.M.; Worcester, K.R.; Jang, S.; Lawrence, J.; Byrne, B.A.; et al. Risk Factors for Infection with Pathogenic and Antimicrobial-Resistant Fecal Bacteria in Northern Elephant Seals in California. Public Heal. Rep. 2008, 123, 360–370. [Google Scholar] [CrossRef] [Green Version]
  91. Aguirre, A.A.; Tabor, G. Introduction: Marine Vertebrates as Sentinels of Marine Ecosystem Health. EcoHealth 2004, 1, 236–238. [Google Scholar] [CrossRef]
  92. CLSI. Performance Standards for Antimicrobial Susceptibility Testing, CLSI Supplement M100, 30th ed.; Clinical and Laboratory Standards Institute: Wayne, PA, USA, 2020. [Google Scholar]
  93. Kohlmann, R.; Bähr, T.; Gatermann, S.G. Species-Specific Mutation Rates for AmpC Derepression in Enterobacterales with Chromosomally Encoded Inducible AmpC β-Lactamase. J. Antimicrob. Chemother. 2018, 73, 1530–1536. [Google Scholar] [CrossRef] [Green Version]
  94. Schug, A.R.; Bartel, A.; Scholtzek, A.D.; Meurer, M.; Brombach, J.; Hensel, V.; Fanning, S.; Schwarz, S.; Feßler, A.T. Biocide Susceptibility Testing of Bacteria: Development of a Broth Microdilution Method. Vet. Microbiol. 2020, 248, 108791. [Google Scholar] [CrossRef] [PubMed]
  95. Braun, S.D.; Jamil, B.; Syed, M.A.; Abbasi, S.A.; Weiß, D.; Slickers, P.; Monecke, S.; Engelmann, I.; Ehricht, R. Prevalence of Carbapenemase-Producing Organisms at the Kidney Center of Rawalpindi (Pakistan) and Evaluation of an Advanced Molecular Microarray-Based Carbapenemase Assay. Future Microbiol. 2018, 13, 1225–1246. [Google Scholar] [CrossRef] [PubMed]
  96. Sandvang, D.; Aarestrup, F.M. Characterization of Aminoglycoside Resistance Genes and Class 1 Integrons in Porcine and Bovine Gentamicin-Resistant Escherichia coli. Microb. Drug Resist. 2000, 6, 19–27. [Google Scholar] [CrossRef] [PubMed]
  97. Boerlin, P.; Travis, R.; Gyles, C.L.; Reid-Smith, R.; Janecko, N.; Lim, H.; Nicholson, V.; McEwen, S.A.; Friendship, R.; Archambault, M. Antimicrobial Resistance and Virulence Genes of Escherichia coli Isolates from Swine in Ontario. Appl. Environ. Microbiol. 2005, 71, 6753–6761. [Google Scholar] [CrossRef] [Green Version]
  98. Gay, K.; Robicsek, A.; Strahilevitz, J.; Park, C.H.; Jacoby, G.; Barrett, T.J.; Medalla, F.; Chiller, T.M.; Hooper, D.C. Plasmid-Mediated Quinolone Resistance in Non-Typhi Serotypes of Salmonella enterica. Clin. Infect. Dis. 2006, 43, 297–304. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  99. Park, C.H.; Robicsek, A.; Jacoby, G.A.; Sahm, D.; Hooper, D.C. Prevalence in the United States of Aac(6’)-Ib-cr Encoding a Ciprofloxacin-Modifying Enzyme. Antimicrob. Agents Chemother. 2006, 50, 3953–3955. [Google Scholar] [CrossRef] [Green Version]
  100. Yamane, K.; Wachino, J.; Suzuki, S.; Arakawa, Y. Plasmid-Mediated qepA Gene among Escherichia coli Clinical Isolates from Japan. Antimicrob. Agents Chemother. 2008, 52, 1564–1566. [Google Scholar] [CrossRef] [Green Version]
  101. Cavaco, L.M.; Hasman, H.; Xia, S.; Aarestrup, F.M. qnrD, a Novel Gene Conferring Transferable Quinolone Resistance in Salmonella enterica Serovar Kentucky and Bovismorbificans Strains of Human Origin. Antimicrob. Agents Chemother. 2009, 53, 603–608. [Google Scholar] [CrossRef] [Green Version]
  102. Szczepanowski, R.; Linke, B.; Krahn, I.; Gartemann, K.-H.; Gützkow, T.; Eichler, W.; Pühler, A.; Schlüter, A. Detection of 140 Clinically Relevant Antibiotic-Resistance Genes in the Plasmid Metagenome of Wastewater Treatment Plant Bacteria Showing Reduced Susceptibility to Selected Antibiotics. Microbiology 2009, 155, 2306–2319. [Google Scholar] [CrossRef] [Green Version]
  103. Šeputienė, V.; Povilonis, J.; Ružauskas, M.; Pavilonis, A.; Sužiedėlienė, E. Prevalence of Trimethoprim Resistance Genes in Escherichia coli Isolates of Human and Animal Origin in Lithuania. J. Med. Microbiol. 2010, 59, 315–322. [Google Scholar] [CrossRef] [PubMed]
  104. Dolejska, M.; Frolkova, P.; Florek, M.; Jamborova, I.; Purgertova, M.; Kutilova, I.; Cizek, A.; Guenther, S.; Literak, I. CTX-M-15-Producing Escherichia coli Clone B2-O25b-ST131 and Klebsiella spp. Isolates in Municipal Wastewater Treatment Plant Effluents. J. Antimicrob. Chemother. 2011, 66, 2784–2790. [Google Scholar] [CrossRef]
  105. Miranda, A.; Ávila, B.; Díaz, P.; Rivas, L.; Bravo, K.; Astudillo, J.; Bueno, C.; Ulloa, M.T.; Hermosilla, G.; Del Canto, F.; et al. Emergence of Plasmid-Borne dfrA14 Trimethoprim Resistance Gene in Shigella sonnei. Front. Cell. Infect. Microbiol. 2016, 6, 77. [Google Scholar] [CrossRef] [Green Version]
  106. Wang, M.; Guo, Q.; Xu, X.; Wang, X.; Ye, X.; Wu, S.; Hooper, D.C.; Wang, M. New Plasmid-Mediated Quinolone Resistance Gene, qnrC, Found in a Clinical Isolate of Proteus mirabilis. Antimicrob. Agents Chemother. 2009, 53, 1892–1897. [Google Scholar] [CrossRef] [Green Version]
  107. Dierikx, C.M.; van Duijkeren, E.; Schoormans, A.H.W.; van Essen-Zandbergen, A.; Veldman, K.; Kant, A.; Huijsdens, X.W.; van der Zwaluw, K.; Wagenaar, J.A.; Mevius, D.J. Occurrence and Characteristics of Extended-Spectrum-β-Lactamase- and AmpC-Producing Clinical Isolates Derived from Companion Animals and Horses. J. Antimicrob. Chemother. 2012, 67, 1368–1374. [Google Scholar] [CrossRef] [PubMed]
  108. Kehrenberg, C.; Schwarz, S. Distribution of Florfenicol Resistance Genes fexA and cfr among Chloramphenicol-Resistant Staphylococcus isolates. Antimicrob. Agents Chemother. 2006, 50, 1156–1163. [Google Scholar] [CrossRef] [Green Version]
  109. Dallenne, C.; Da Costa, A.; Decré, D.; Favier, C.; Arlet, G. Development of a Set of Multiplex PCR Assays for the Detection of Genes Encoding Important Beta-Lactamases in Enterobacteriaceae. J. Antimicrob. Chemother. 2010, 65, 490–495. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  110. Pérez-Pérez, F.J.; Hanson, N.D. Detection of Plasmid-Mediated AmpC Beta-Lactamase Genes in Clinical Isolates by Using Multiplex PCR. J. Clin. Microbiol. 2002, 40, 2153–2162. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  111. Everett, M.J.; Jin, Y.F.; Ricci, V.; Piddock, L.J. Contributions of Individual Mechanisms to Fluoroquinolone Resistance in 36 Escherichia coli Strains Isolated from Humans and Animals. Antimicrob. Agents Chemother. 1996, 40, 2380–2386. [Google Scholar] [CrossRef] [Green Version]
  112. Caroff, N.; Espaze, E.; Bérard, I.; Richet, H.; Reynaud, A. Mutations in the AmpC Promoter of Escherichia coli Isolates Resistant to Oxyiminocephalosporins without Extended Spectrum Beta-Lactamase Production. FEMS Microbiol. Lett. 1999, 173, 459–465. [Google Scholar] [CrossRef] [Green Version]
  113. Clermont, O.; Christenson, J.K.; Denamur, E.; Gordon, D.M. The Clermont Escherichia coli Phylo-Typing Method Revisited: Improvement of Specificity and Detection of New Phylo-Groups. Environ. Microbiol. Rep. 2013, 5, 58–65. [Google Scholar] [CrossRef] [PubMed]
  114. Weissman, S.J.; Johnson, J.R.; Tchesnokova, V.; Billig, M.; Dykhuizen, D.; Riddell, K.; Rogers, P.; Qin, X.; Butler-Wu, S.; Cookson, B.T.; et al. High-Resolution Two-Locus Clonal Typing of Extraintestinal Pathogenic Escherichia coli. Appl. Environ. Microbiol. 2012, 78, 1353–1360. [Google Scholar] [CrossRef] [Green Version]
  115. Roer, L.; Johannesen, T.B.; Hansen, F.; Stegger, M.; Tchesnokova, V.; Sokurenko, E.; Garibay, N.; Allesøe, R.; Thomsen, M.C.F.; Lund, O.; et al. CHTyper, a Web Tool for Subtyping of Extraintestinal Pathogenic Escherichia coli Based on the fumC and fimH Alleles. J. Clin. Microbiol. 2018, 56, e00063-18. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  116. Francisco, A.P.; Vaz, C.; Monteiro, P.T.; Melo-Cristino, J.; Ramirez, M.; Carriço, J.A. PHYLOViZ: Phylogenetic Inference and Data Visualization for Sequence Based Typing Methods. BMC Bioinform. 2012, 13, 1–10. [Google Scholar] [CrossRef] [Green Version]
  117. Brisse, S.; Fevre, C.; Passet, V.; Issenhuth-Jeanjean, S.; Tournebize, R.; Diancourt, L.; Grimont, P. Virulent Clones of Klebsiella pneumoniae: Identification and Evolutionary Scenario Based on Genomic and Phenotypic Characterization. PLoS ONE 2009, 4, e4982. [Google Scholar] [CrossRef] [Green Version]
  118. Diancourt, L.; Passet, V.; Verhoef, J.; Grimont, P.A.D.; Brisse, S. Multilocus Sequence Typing of Klebsiella pneumoniae Nosocomial Isolates. J. Clin. Microbiol. 2005, 43, 4178–4182. [Google Scholar] [CrossRef] [Green Version]
  119. Braun, S.D.; Ziegler, A.; Methner, U.; Slickers, P.; Keiling, S.; Monecke, S.; Ehricht, R. Fast DNA Serotyping and Antimicrobial Resistance Gene Determination of Salmonella enterica with an Oligonucleotide Microarray-Based Assay. PLoS ONE 2012, 7, e46489. [Google Scholar] [CrossRef]
  120. Geue, L.; Schares, S.; Mintel, B.; Conraths, F.J.; Müller, E.; Ehricht, R. Rapid Microarray-Based Genotyping of Enterohemorrhagic Escherichia coli Serotype O156:H25/H-/Hnt Isolates from Cattle and Clonal Relationship Analysis. Appl. Environ. Microbiol. 2010, 76, 5510–5519. [Google Scholar] [CrossRef] [Green Version]
  121. Lepuschitz, S.; Huhulescu, S.; Hyden, P.; Springer, B.; Rattei, T.; Allerberger, F.; Mach, R.L.; Ruppitsch, W. Characterization of a Community-Acquired-MRSA USA300 Isolate from a River Sample in Austria and Whole Genome Sequence Based Comparison to a Diverse Collection of USA300 Isolates. Sci. Rep. 2018, 8, 1–9. [Google Scholar] [CrossRef]
  122. Bankevich, A.; Nurk, S.; Antipov, D.; Gurevich, A.A.; Dvorkin, M.; Kulikov, A.S.; Lesin, V.M.; Nikolenko, S.I.; Pham, S.; Prjibelski, A.D.; et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J. Comput. Biol. 2012, 19, 455–477. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  123. Wirth, T.; Falush, D.; Lan, R.; Colles, F.; Mensa, P.; Wieler, L.H.; Karch, H.; Reeves, P.R.; Maiden, M.C.J.; Ochman, H.; et al. Sex and Virulence in Escherichia coli: An Evolutionary Perspective. Mol. Microbiol. 2006, 60, 1136–1151. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  124. Beghain, J.; Bridier-Nahmias, A.; Le Nagard, H.; Denamur, E.; Clermont, O. ClermonTyping: An Easy-to-Use and Accurate in Silico Method for Escherichia Genus Strain Phylotyping. Microb. Genom. 2018, 4, e000192. [Google Scholar] [CrossRef]
  125. Clermont, O.; Dixit, O.V.A.; Vangchhia, B.; Condamine, B.; Dion, S.; Bridier-Nahmias, A.; Denamur, E.; Gordon, D. Characterization and Rapid Identification of Phylogroup G in Escherichia coli, a Lineage with High Virulence and Antibiotic Resistance Potential. Environ. Microbiol. 2019, 21, 3107–3117. [Google Scholar] [CrossRef]
  126. Alcock, B.P.; Raphenya, A.R.; Lau, T.T.Y.; Tsang, K.K.; Bouchard, M.; Edalatmand, A.; Huynh, W.; Nguyen, A.-L.V.; Cheng, A.A.; Liu, S.; et al. CARD 2020: Antibiotic Resistome Surveillance with the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 2020, 48, D517–D525. [Google Scholar] [CrossRef] [PubMed]
  127. Bortolaia, V.; Kaas, R.S.; Ruppe, E.; Roberts, M.C.; Schwarz, S.; Cattoir, V.; Philippon, A.; Allesoe, R.L.; Rebelo, A.R.; Florensa, A.F.; et al. ResFinder 4.0 for Predictions of Phenotypes from Genotypes. J. Antimicrob. Chemother. 2020, 75, 3491–3500. [Google Scholar] [CrossRef]
  128. Zankari, E.; Allesøe, R.; Joensen, K.G.; Cavaco, L.M.; Lund, O.; Aarestrup, F.M. PointFinder: A Novel Web Tool for WGS-Based Detection of Antimicrobial Resistance Associated with Chromosomal Point Mutations in Bacterial Pathogens. J. Antimicrob. Chemother. 2017, 72, 2764–2768. [Google Scholar] [CrossRef] [Green Version]
  129. Pal, C.; Bengtsson-Palme, J.; Rensing, C.; Kristiansson, E.; Larsson, D.G.J. BacMet: Antibacterial Biocide and Metal Resistance Genes Database. Nucleic Acids Res. 2014, 42, D737–D743. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  130. Joensen, K.G.; Scheutz, F.; Lund, O.; Hasman, H.; Kaas, R.S.; Nielsen, E.M.; Aarestrup, F.M. Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli. J. Clin. Microbiol. 2014, 52, 1501–1510. [Google Scholar] [CrossRef] [Green Version]
  131. Tetzschner, A.M.M.; Johnson, J.R.; Johnston, B.D.; Lund, O.; Scheutz, F. In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data. J. Clin. Microbiol. 2020, 58, e01269-20. [Google Scholar] [CrossRef]
  132. Joensen, K.G.; Tetzschner, A.M.M.; Iguchi, A.; Aarestrup, F.M.; Scheutz, F. Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data. J. Clin. Microbiol. 2015, 53, 2410–2426. [Google Scholar] [CrossRef] [Green Version]
  133. Carattoli, A.; Zankari, E.; García-Fernández, A.; Voldby Larsen, M.; Lund, O.; Villa, L.; Møller Aarestrup, F.; Hasman, H. In Silico Detection and Typing of Plasmids Using PlasmidFinder and Plasmid Multilocus Sequence Typing. Antimicrob. Agents Chemother. 2014, 58, 3895–3903. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  134. Arredondo-Alonso, S.; Rogers, M.R.C.; Braat, J.C.; Verschuuren, T.D.; Top, J.; Corander, J.; Willems, R.J.L.; Schürch, A.C. Mlplasmids: A User-Friendly Tool to Predict Plasmid- and Chromosome-Derived Sequences for Single Species. Microb. Genom. 2018, 4, e000224. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  135. Grimont, P.; Weill, F.X. Antigenic Formulae of the Salmonella Serovars; WHO: Paris, France, 1997. [Google Scholar]
  136. Ziemer, C.J.; Steadham, S.R. Evaluation of the Specificity of Salmonella PCR Primers Using Various Intestinal Bacterial Species. Lett. Appl. Microbiol. 2003, 37, 463–469. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  137. Hashimoto, Y.; Itho, Y.; Fujinaga, Y.; Khan, A.Q.; Sultana, F.; Miyake, M.; Hirose, K.; Yamamoto, H.; Ezaki, T. Development of Nested PCR Based on the ViaB Sequence to Detect Salmonella typhi. J. Clin. Microbiol. 1995, 33, 775–777. [Google Scholar] [CrossRef] [Green Version]
Ijms 22 05905 g001 550
Figure 1. Clonal phylogeny characterized by goeBURST diagram of the CH clonotyping data set of E. coli isolates. An eBURST diagram was calculated using PHYLOViZ with the goeBURST algorithm. E. coli isolates were grouped according to their CH profiles.
Figure 1. Clonal phylogeny characterized by goeBURST diagram of the CH clonotyping data set of E. coli isolates. An eBURST diagram was calculated using PHYLOViZ with the goeBURST algorithm. E. coli isolates were grouped according to their CH profiles.
Ijms 22 05905 g001
Table
Table 1. Characterization of ESBL-/AmpC-producing Escherichia (E.) coli isolated from marine mammals.
Table 1. Characterization of ESBL-/AmpC-producing Escherichia (E.) coli isolated from marine mammals.
IsolateAnimal 1SpeciesPhylo-
Group		CH-
Clonotype		ESBL/
AmpC		Phenotype 2GenotypeVirulence
Genes		ampC-Promoter 3QRDR
GyrA 4		QRDR
ParC 4
3ZcE. coliB1CH65-26AmpCAMP, AMC, PIP, CFZ fimH39n.d.n.d.
8/2ZcE. coliACH65-26AmpCAMP, AMC, PIP, CFZ, CTX, CAZblaCMY-2fimH39n.d.n.d.
11/1MaE. coliFCH88-145AmpCAMP, AMC, PIP, CFZblaTEM-1, blaCMY-2, sul2, dfrA1, aadA1, strA, strBfimH, astAw.t.n.d.n.d.
17PvE. coliB2CH103-212AmpCAMP, AMC, PIP, CFZ, FOFblaCMY-2, dfrA14, dfrA19fimH, cnf1, hylA58n.d.n.d.
21ZcE. coliB1CH65-38AmpC and ESBLAMC, PIP, CFZ, CTX, CAZ, ATM, SXT, TET, CHL, GEN, TOB, CIPblaCTX-M-15, blaOXA-1, sul1, dfrA17, tet(B), cmlA, aadA4, aadA5, aac(6’)-IbfimH, iucD, papC39Ser83Leu, Asp87AsnSer80Ile
41ZcE. coliB1CH29-31ESBLAMC, PIP, CFZ, CTX, CAZ, SXTblaCTX-M-15, dfrA17, aadA4fimH, astAn.a.n.d.n.d.
53/1ZcE. coliECH148-25AmpCAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHLblaTEM-1, blaCMY-2, dfrA17, tet(B), catA, strA, strBfimH, iucD, papC, bfpA, cdtA, tcdAp2n.a.n.d.n.d.
90ZcE. coliFCH4-153AmpC and ESBLAMC, PIP, CFZ, CTX, CAZ, ATM, SXTblaCTX-M-15, blaCMY-2, sul2, dfrA14, strA, strB, qnrSfimHn.a.n.d.n.d.
92ZcE. coliECH148-25AmpCAMC, PIP, CFZ, CTX, CAZ, SXT, TETblaTEM-1, blaCMY-2, sul2, dfrA17, tet(B), aadA4, strA, strBfimH, iucD, papCw.t.n.d.n.d.
117ZcE. coliB2CH103-9AmpCAMC, PIP, CFZ, CTX, CAZblaCMY-2fimH, cnf1n.a.n.d.n.d.
147aZcE. coliACH7-0AmpCAMC, PIP, CFZ, CTX, CAZ, ATM, TETblaTEM-1, blaCMY-2, dfrA5, tet(A)fimHw.t.n.d.n.d.
147bZcE. coliB2CH40-21AmpCAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOBblaTEM-1, blaCMY-2, sul1, sul2, dfrA1, tet(A), catA, cmlA, floR, aadB, strA, strBfimH, astA, cnf1w.t.n.d.n.d.
149aMaE. coliACH7-0AmpCAMC, PIP, CFZ, CTX, CAZ, ATM, TETblaTEM-1, blaCMY-2, tet(A)fimHn.a.n.d.n.d.
156ZcE. coliACH11-0AmpCAMC, CFZ, CTX, CAZ, SXT, TET, CIPblaCMY-2, sul1, dfrA17, tet(B), aadA4fimH, astA, iucD, papCw.t.Ser83Leu, Asp87AsnSer80Ile
158ZcE. coliECH148-25AmpCAMC, PIP, CFZ, CTX, CAZ, ATM, SXT, TET, CHLblaTEM-1, blaCMY-2, sul2, dfrA17, tet(B), catA, aadA4, strA, strBfimH, iucD, papCw.t.n.d.n.d.
1 Abbreviations: Ma, Mirounga angustirostris; Pv, Phoca vitulina; Zc, Zalophus californianus. 2 Abbreviations: AMC, amoxicillin/clavulanate; ATM, aztreonam; CAZ, ceftazidime; CHL, chloramphenicol; CIP, ciprofloxacin; CFZ, cefazolin; CTX, cefotaxime; FOF, fosfomycin; FOX, cefoxitin; GEN, gentamicin; PIP, piperacillin; SXT, trimethoprim/sulfamethoxazole; TET, tetracycline; TOB, tobramycin. 3 n.a., not amplifiable; w.t., wild type. 4 QRDR, quinolone resistance-determining region; n.d., not done.
Table
Table 2. Characterization of ESBL-/AmpC-producing Enterobacterales, other than E. coli, isolated from marine mammals.
Table 2. Characterization of ESBL-/AmpC-producing Enterobacterales, other than E. coli, isolated from marine mammals.
IsolateAnimal 1Species 2ST
(Klebsiella) 3		ESBL/AmpCPhenotype 4GenotypeQRDR
GyrA 5		QRDR
ParC 5
8/1ZcK. pneumoniae466AmpCAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOB,blaSHV-33, blaTEM-1, blaCMY-2, sul1, sul2, dfrA1, tet(A), catA, cmlA, floR, aadB, strA, strBn.d.n.d.
10ZcK. pneumoniae466AmpCAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOB, FOF, NITblaSHV-33, blaTEM-1, blaCMY-2, sul1, sul2, dfrA1, tet(A), catA, cmlA, floR, aadB, strA, strBn.d.n.d.
11/2MaK. pneumoniae466AmpCAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOB, FOF, NITblaSHV-33, blaTEM-1, blaCMY-2, sul1, sul2, dfrA1, tet(A), catA, cmlA, floR aadB, strA, strBn.d.n.d.
14PvK. pneumoniae466AmpCAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOB, FOF, NITblaSHV-33, blaTEM-1, blaCMY-2, sul1, sul2, dfrA1, tet(A), catA, cmlA, floR, aadB, strA, strBn.d.n.d.
16PvK. pneumoniae466AmpCAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOB, FOF, NITblaSHV-33, blaTEM-1, blaCMY-2, sul1, dfrA1, tet(A), catA, cmlA, floR, aadB, strA, strBn.d.n.d.
19PvK. pneumoniae466AmpCAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOB, FOF, NITblaSHV-33, blaTEM-1, blaCMY-2, sul1, sul2, dfrA1, tet(A), catA, cmlA, floR, aadB, strA, strBn.d.n.d.
154aZcK. pneumoniae466AmpCAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOBblaSHV-33, blaTEM-1, blaCMY-2, sul1, sul2, dfrA1, tet(A), catA, cmlA, floR, aadB, strA, strBn.d.n.d.
160ZcK. pneumoniae466AmpCAMC, PIP, CTX, CAZ, SXT, TET, CHL, GEN, TOBblaTEM-1, blaCMY-2, sul1, sul2, dfrA1, tet(A), catA, cmlA, floR, aadB, strA, strBn.d.n.d.
161PvK. pneumoniae405AmpCAMC, PIP, SXT, TET, CHL, GEN, TOB, CIPblaSHV-11, blaTEM-1, blaOXA-1, blaCMY-2, sul1, sul2, dfrA1, dfrA14, tet(A), catA, cmlA, floR, aac(6´)-Ib, aadB, strA, strB, qnrBw.t.w.t.
164ZcK. pneumoniae466AmpCAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOBblaSHV-33, blaTEM-1, blaCMY-2, sul2, dfrA1, tet(A), catA, cmlA, floR, aadB, strA, strBn.d.n.d.
173MaK. pneumoniae405AmpCAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOB, CIPblaSHV-11, blaTEM-1, blaOXA-1, blaCMY-2, sul1, sul2, dfrA1, dfrA14, tet(A), catA, cmlA, floR, aac(6′)-Ib, aadB, strA, strB, qnrBw.t.n.a.
175ZcK. pneumoniae405AmpCAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOB, CIPblaSHV-11, blaTEM-1, blaOXA-1, blaCMY-2, sul1, sul2, dfrA1, dfrA14, tet(A), catA, cmlA, floR, aac(6′)-Ib, aadB, strA, strB, qnrBw.t.n.a.
9ZcC. koserin.a.AmpC de-repressionintrinsic + CTX, CAZ, TET, CHLblaCMY, sul2, tet(A), cmlA, floR, strA, strBn.d.n.d.
28ZcC. koserin.a.AmpC de-repressionintrinsic + CTX, CAZ, SXT, TET, CHL, GEN, TOB, FOF, CIPblaTEM-1, blaOXA-1, blaCMY, sul1, sul2, dfrA1, dfrA14, tet(A), cmlA, aadB, aac(6′)-Ib, strA, strB, qnrBw.t.w.t.
30ZcC. koserin.a.AmpC de-repressionintrinsic + CTX, CAZ, SXTblaCMY, sul2w.t.n.a.
35ZcC. koserin.a.AmpC de-repressionintrinsic + CTX, CAZ, SXT, TET, CHL, GEN, TOB, FOF, CIPblaTEM-1, blaOXA-1, blaCMY, sul1, sul2, dfrA1, dfrA14, tet(A), cmlA, aadB, aac(6´)-Ib, strA, strB, qnrBw.t.w.t.
53/2ZcC. koserin.a.AmpC de-repressionintrinsic + CTX, CAZ, SXT, TET, CHLblaTEM-1, blaCMY, sul2, dfrA14, tet(A), tet(B), catA, cmlA, floR, strA, strB, qnrBn.d.n.d.
149bMaC. freundii complexn.a.AmpC de-repressionAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOBblaTEM-1, blaCMY, sul1, dfrA12, dfrA19, tet(A), aadA2, aac(6´)-IIc, strA, strBn.d.n.d.
151ZcC. freundii complexn.a.AmpC de-repressionAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GENblaTEM-1, blaCMY, sul1, dfrA12, dfrA19, tet(A), aadA2, aac(6´)-IIc, strA, strBn.d.n.d.
154bZcC. freundii complexn.a.AmpC de-repressionAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GENblaTEM-1, blaCMY, sul1, sul2, dfrA12, dfrA19, tet(A), aadA2, aac(6´)-IIc, strA, strBn.d.n.d.
163ZcC. freundii complexn.a.AmpC de-repressionAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOB, CIPblaTEM-1, blaCMY, sul1, sul2, dfrA12, dfrA19, tet(A), aadA2, strA, strB, qnrBn.a.n.a.
165ZcC. freundii complexn.a.AmpC de-repressionAMC, PIP, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOBblaTEM-1, blaCMY, sul1, sul2, dfrA12, dfrA19, tet(A), aadA2, strA, strBn.d.n.d.
169ZcC. koserin.a.AmpC de-repressionAMC, PIP, CFZ, CTX, CAZ, SXT, TET, GENblaTEM-1, blaCMY, sul2, dfrA14, tet(A), strA, strBn.d.n.d.
179ZcC. koserin.a.AmpC de-repressionAMC, PIP, CFZ, CTX, CAZ, SXT, TET, GENblaTEM-1, blaCMY, sul2, dfrA14, tet(A), strA, strBn.d.n.d.
192/1ZcC. freundii complexn.a.AmpC de-repressionAMC, PIP, FOX, CFZ, CAZ, CTX, SXT, TETblaTEM-1, blaCMY, sul1, sul2, dfrA12, tet(A)n.d.n.d.
213KbC. freundii complexn.a.AmpC de-repressionAMC, PIP, FOX, CFZ, CTX, CAZ, SXT, TETblaCMY, sul1, dfrA12, tet(A)n.d.n.d.
215KbC. freundii complexn.a.AmpC de-repressionAMC, PIP, FOX, CFZ, CTX, CAZ, SXTblaCMY, sul1, dfrA12n.d.n.d.
224bMaC. freundii complexn.a.AmpC de-repressionAMC, PIP, FOX, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOBblaTEM-1, blaCMY, sul1, sul2, dfrA1, cmlA, floR, aadB, strA, strBn.d.n.d.
226ZcC. koserin.a.AmpC de-repressionAMC, PIP, FOX, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOBblaCMY, sul2, tet(A), tet(D), floR, strA, strBn.d.n.d.
230cZcC. koserin.a.AmpC de-repressionAMC, PIP, FOX, CFZ, CTX, CAZ, SXT, TET, GENblaTEM-1, blaCMY, sul2, dfrA14, tet(D), strA, strBn.d.n.d.
43ZcEn. cloacae complexn.a.AmpC de-repressionintrinsic + CTX, CAZ, TET, SXTblaTEM-1, sul2, dfrA14, tet(D), strA, strBn.d.n.d.
66ZcEn. cancerogenusn.a.AmpC de-repressionintrinsic + CTX, CAZ n.d.n.d.
130MaL. amnigenan.a.AmpC and ESBLAMC, PIP, CFZ, CTX, CAZ, SXT, CHLblaDHA-1, blaSHV-12, sul1, sul2, dfrA14, cmlA, floR, aac(6´)-Ib, qnrBn.d.n.d.
132MaL. amnigenan.a.AmpC and ESBLAMC, PIP, CFZ, CTX, CAZ, SXT, CHLblaDHA-1, blaSHV-12, sul1, sul2, dfrA14, cmlA, floR, aac(6´)-Ib, qnrBn.d.n.d.
197/2ZcP. mirabilisn.a.AmpCAMC, PIP, CAZ, CTX, SXT, CHL, GENblaTEM-1, blaCMY-2, sul1, sul2, dfrA1, catA, cmlA, floR, aadB, strA, strBn.d.n.d.
1 Abbreviations: Kb, Kogia breviceps; Ma, Mirounga angustirostris; Pv, Phoca vitulina; Zc, Zalophus californianus. 2 Abbreviations: C., Citrobacter; En., Enterobacter; K., Klebsiella; L., Lelliottia; P., Proteus. 3 n.a., not applicable. 4 Abbreviations: AMC, amoxicillin/clavulanate; ATM, aztreonam; CAZ, ceftazidime; CHL, chloramphenicol; CIP, ciprofloxacin; CFZ, cefazolin; CTX, cefotaxime; FOF, fosfomycin; FOX, cefoxitin; GEN, gentamicin; PIP, piperacillin; SXT, trimethoprim/sulfamethoxazole; TET, tetracycline; TOB, tobramycin. 5 QRDR: quinolone resistance-determining region; n.a., not amplifiable; n.d., not done; w.t., wild type.
Table
Table 3. Characterization of ESBL/AmpC-producing E. coli isolated from marine mammals via whole-genome sequencing.
Table 3. Characterization of ESBL/AmpC-producing E. coli isolated from marine mammals via whole-genome sequencing.
IsolateAnimal 1Phylo-GroupCH-Clono-TypingSEROGENOTYPE 2STESBL/AmpCPhenotype 3GenotypeVirulence GenesampC Promoter 4QRDR 5 GyrA 4QRDR ParC 4ParE 4
68ZcACH11-0ONT:H9167ESBLAMC, PIP, CFZ, CTX, CAZ, ATM, SXT, TET, GEN, TOB, CIPblaCTX-M-15, blaOXA-1, sul1, dfrA17, tet(A), tet(B), catB3, aadA4, aadA5, aac(3)-IIa, aac(6′)-Ib-cr, mdfAastA, capU, fyuA, irp2, iss, iucC, iutA, sitA, terCw.t.Ser83Leu, Asp87AsnSer80IleS458A
171PvDCH50-299ONT:H15748AmpCAMC, PIP, CFZ, CTX, CAZblaCMY-4, mdfAair, chuA, cia, eilA, lpfA, terC, traTw.t.w.t.w.t.w.t.
183ZcACH11-0ONT:H9167ESBLAMC, PIP, CFZ, CTX, CAZ, ATM, SXT, TET, TOB, CIPblaCTX-M-15, sul1, sul2, dfrA17, tet(A), tet(B), catB3, aadA5, aph(3″)-Ib, aph(6)-Id, aac(6′)-Ib-cr, mdfAastA, capU, fyuA, irp2, iss, iucC, iutA, sitA, terC, traTw.t.Ser83Leu, Asp87AsnSer80IleS458A
192/2ZcB1CH65-32O9:H101431AmpCAMC, PIP, FOX, CFZ, CAZ, CTX, SXT, CIPblaTEM-1B, blaCMY-2, sul2, dfrA5, aph(3″)-Ib, aph(6)-Id, mdfAcapU, cba, cia, cma, cvaC, etsC, fyuA, hlyF, iroN, irp2, iss, iucC, iutA, lpfA, mchF, ompT, sitA, terC, traT-19Ser83Leu, Asp87AsnSer80IleS458A
197/1ZcFCH4-58ONT:H42648AmpCAMC, PIP, FOX, CFZ, CAZ, CTX, ATM, SXT, TET, CHL, GEN, TOBblaTEM-1B, blaCMY-2, sul1, sul2, dfrA1, tet(A), cmlA1, floR, aph(3″)-Ib, aph(6)-Id, ant(2″)-Ia, mdfAair, cea, celb, chuA, focCsfaE, focG, fyuA, iroN, irp2, kpsE, kpsMII, lpfA, mchB, mchC, mchF, mcmA, sfaD, sitA, terC, yfcV-28w.t.w.t.w.t.
202ZcB2CH103-9ONT:H31372AmpCAMC, PIP, FOX, CFZmdfAcea, chuA, cnf1, focCsfaE, focG, focI, fyuA, hra, ibeA, iroN, irp2, iss, mchB, mchC, mchF, mcmA, ompT, papA, papC, sitA, terC, usp, vat, yfcV-32w.t.w.t.w.t.
206ZcDCH26-26ONT:H18963AmpCAMC, PIP, FOX, CFZ, CTX, CAZblaCMY-2, mdfAair, astA, chuA, eilA, fyuA, irp2, kpsE, senB, sitA, terC, traTw.t.w.t.w.t.w.t.
209ZcDCH26-0ONT:H1538ESBLAMC, PIP, FOX, CFZ, CTX, CAZblaCTX-M-15, blaTEM-1B, qnrS1, mdfAair, chuA, eilA, iss, kpsE, kpsMII, terCw.t.w.t.w.t.w.t.
224aMaFCH37-1572 *ONT:H284957AmpCAMC, PIP, FOX, CFZ, CTX, CAZ, SXT, TET, CHL, GEN, TOBblaTEM-1B, blaCMY-2, sul1, sul2, dfrA1, tet(A), cmlA1, floR, aph(3″)-Ib, aph(6)-Id, ant(2″)-Ia, mdfAair, chuA, cia, cvaC, etsC, hlyF, iroN, iss, lpfA, mchF, ompT, sitA, terC, traT, usp, yfcV-28w.t.w.t.w.t.
230aZcDCH36-93ONT:H15349AmpCAMC, FOX, CFZ, CAZblaCMY-2, mdfAcba, chuA, cia, cma, eilA, fyuA, hra, irp2, kpsE, terC, traTw.t.w.t.w.t.S458A
230bZcACH11-0ONT:H9167AmpCAMC, FOX, CFZ, CTX, CAZ, SXT, TET, FOF, CIPblaCMY-2, sul1, dfrA17, tet(A), tet(B), aadA5, mdfAastA, capU, cba, cia, cma, fyuA, irp2, iss, iucC, iutA, sitA, terC, traTw.t.w.t.Ser80Ilew.t.
234ZcACH11-54ONT:H4484ESBLAMP, CFZ, CTXblaCTX-M-15, qnrS1, mdfAaap, astA, iss, kpsE, kpsMII, ompT, terC, traTw.t.w.t.w.t.I355T
1 Abbreviations: Ma, Mirounga angustirostris; Pv, Phoca vitulina; Zc, Zalophus californianus. 2 NT, not typeable. 3 Abbreviations: AMC, amoxicillin/clavulanate; ATM, aztreonam; CAZ, ceftazidime; CHL, chloramphenicol; CIP, ciprofloxacin; CFZ, cefazolin; CTX, cefotaxime; FOF, fosfomycin; FOX, cefoxitin; GEN, gentamicin; PIP, piperacillin; SXT, trimethoprim/sulfamethoxazole; TET, tetracycline; TOB, tobramycin. 4 w.t., wild type. 5 QRDR: quinolone resistance-determining region. * new allele.
Table
Table 4. Characterization of Salmonella isolated from marine mammals.
Table 4. Characterization of Salmonella isolated from marine mammals.
IsolateAnimal 1Serotype 2Phenotype 3GenotypeVirulence Genes
8. S.ZcS. Saintpaul (antigenic formula: 1,4,5,12 : e,h : 1,2)n.r. hilA, stn
27 S.ZcS. Newport (antigenic formula 6,8 : e,h : 1,2)n.r. hilA, stn
42 S.ZcAmpC S. Saintpaul (antigenic formula 1,4,5,12 : e,h : 1,2)AMC, PIP, CFZ, CTX, CAZblaCMY-2hilA, stn
56 S.ZcS. Havana (antigenic formula 1,13,23 : f,g : -)n.r. hilA, stn
62 S.ZcS. Havana (antigenic formula 1,13,23 : f,g : -)n.r. hilA, stn
91 S.ZcS. Havana (antigenic formula 1,13,23 : f,g : -)n.r. hilA, stn
113 S.ZcS. Havana (antigenic formula 1,13,23 : f,g : -)n.r. hilA, stn
115 S.MaS. Havana (antigenic formula 1,13,23 : f,g : -)n.r. hilA, stn
125 S.MaS. Newport (antigenic formula 6,8 : e,h : 1,2)n.r. hilA, stn
127 S.MaS. Havana (antigenic formula 1,13,23 : f,g : -)n.r. hilA, stn
135 S.MaS. Reading (antigenic formula 1,4,5,12 : e,h : 1,5)n.r. hilA, stn
226 S.ZcS. Braenderup (antigenic formula 6,7 : e,h : e,n,z15)n.r. hilA, stn
245 S.ZcS. Reading (antigenic formula 1,4,5,12 : e,h : 1,5)n.r. hilA, stn
255 S.ZcS. Reading (antigenic formula 1,4,5,12 : e,h . 1,5)n.r. hilA, stn
273 S.ZcS. Albany (antigenic formula 8,20 : z4,z24 : -)n.r. hilA, stn
277 S.MaS. Albany (antigenic formula 8,20 : z4,z24 : -)n.r. hilA, stn
279 S.MaS. Havana (antigenic formula 1,13,23 : f,g : -)n.r. hilA, stn
281 S.ZcS. Havana (antigenic formula 1,13,23 : f,g : -)n.r. hilA, stn
1 Abbreviations: Ma, Mirounga angustirostris; Zc, Zalophus californianus. 2 S., Salmonella. 3 Abbreviations: n.r., non-resistant; AMC, amoxicillin/clavulanate; CAZ, ceftazidime; CFZ, cefazolin; CTX, cefotaxime; PIP, piperacillin.
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Share and Cite

MDPI and ACS Style

Grünzweil, O.M.; Palmer, L.; Cabal, A.; Szostak, M.P.; Ruppitsch, W.; Kornschober, C.; Korus, M.; Misic, D.; Bernreiter-Hofer, T.; Korath, A.D.J.; et al. Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals. Int. J. Mol. Sci. 2021, 22, 5905. https://doi.org/10.3390/ijms22115905

AMA Style

Grünzweil OM, Palmer L, Cabal A, Szostak MP, Ruppitsch W, Kornschober C, Korus M, Misic D, Bernreiter-Hofer T, Korath ADJ, et al. Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals. International Journal of Molecular Sciences. 2021; 22(11):5905. https://doi.org/10.3390/ijms22115905

Chicago/Turabian Style

Grünzweil, Olivia M., Lauren Palmer, Adriana Cabal, Michael P. Szostak, Werner Ruppitsch, Christian Kornschober, Maciej Korus, Dusan Misic, Tanja Bernreiter-Hofer, Anna D. J. Korath, and et al. 2021. "Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals" International Journal of Molecular Sciences 22, no. 11: 5905. https://doi.org/10.3390/ijms22115905

APA Style

Grünzweil, O. M., Palmer, L., Cabal, A., Szostak, M. P., Ruppitsch, W., Kornschober, C., Korus, M., Misic, D., Bernreiter-Hofer, T., Korath, A. D. J., Feßler, A. T., Allerberger, F., Schwarz, S., Spergser, J., Müller, E., Braun, S. D., Monecke, S., Ehricht, R., Walzer, C., ... Loncaric, I. (2021). Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals. International Journal of Molecular Sciences, 22(11), 5905. https://doi.org/10.3390/ijms22115905

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop