Next Article in Journal
Bacillus subtilis Inoculation Improves Nutrient Uptake and Physiological Activity in Sugarcane under Drought Stress
Next Article in Special Issue
The Presence of Mycobacterium leprae in Wild Rodents
Previous Article in Journal
Spread of West Nile Virus and Usutu Virus in the German Bird Population, 2019–2020
Previous Article in Special Issue
Viral and Bacterial Zoonotic Agents in Dromedary Camels from Southern Tunisia: A Seroprevalence Study
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Microorganisms
Volume 10
Issue 4
10.3390/microorganisms10040808
microorganisms-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

High Genetic Diversity and Antimicrobial Resistance in Escherichia coli Highlight Arapaima gigas (Pisces: Arapaimidae) as a Reservoir of Quinolone-Resistant Strains in Brazilian Amazon Rivers

by
Luciana Sampaio Lima
1,*,
Aldo Aparecido Proietti-Junior
1,†,
Yan Corrêa Rodrigues
2,†,
Marcelo Cleyton da Silva Vieira
2,
Luana Nepomuceno Gondim Costa Lima
2,
Cintya de Oliveira Souza
2,
Verônica Dias Gonçalves
3,
Marcelo de Oliveira Lima
4,
Dália dos Prazeres Rodrigues
3 and
Karla Valéria Batista Lima
3,*
1
Faculty of Pharmaceutical Sciences, Federal University of Amapá (UNIFAP), Macapá 68903-419, AP, Brazil
2
Bacteriology and Mycology Section, Evandro Chagas Institute (SABMI/IEC), Health Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil
3
Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Pavilhão Rocha Lima, Enterobacteria Laboratory, Rio de Janeiro 21040-900, RJ, Brazil
4
Environment Section, Evandro Chagas Institute (SAMAM/IEC), Health Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, PA, Brazil
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Microorganisms 2022, 10(4), 808; https://doi.org/10.3390/microorganisms10040808
Submission received: 23 February 2022 / Revised: 3 March 2022 / Accepted: 6 March 2022 / Published: 13 April 2022
(This article belongs to the Special Issue Farm Animal and Wildlife Zoonotic Microorganisms)
Browse Figures
Versions Notes

Abstract

:
The increasing prevalence of multi-drug resistant (MDR) Escherichia coli in distinct ecological niches, comprising water sources and food-producing animals, such as fish species, has been widely reported. In the present study, quinolone-resistant E. coli isolates from Arapirama gigas, a major fish species in the Brazilian Amazon rivers and fish farms, were characterized regarding their antimicrobial susceptibility, virulence, and genetic diversity. A total of forty (40) specimens of A. gigas, including 20 farmed and 20 wild fish, were included. Thirty-four quinolone-resistant E. coli isolates were phenotypically tested by broth microdilution, while resistance and virulence genes were detected by PCR. Molecular epidemiology and genetic relatedness were analyzed by MLST and PFGE typing. The majority of isolates were classified as MDR and detected harboring blaCTX-M, qnrA and qnrB genes. Enterotoxigenic E. coli pathotype (ETEC) isolates were presented in low prevalence among farmed animals. MLST and PFGE genotyping revealed a wide genetic background, including the detection of internationally spread clones. The obtained data point out A. gigas as a reservoir in Brazilian Amazon aquatic ecosystems and warns of the interference of AMR strains in wildlife and environmental matrices.

1. Introduction

Antimicrobial-resistant (AMR) bacteria are constantly reported in water systems as this type of environment receives most of the hospital, domestic and industrial waste without proper treatment, leading to the existence of different and complex AMR determinants pools, encompassing both terrestrial and aquatic ecosystems [1,2,3]. Furthermore, the increasing detection of several multidrug-resistant (MDR) bacterial species in fish and other food-producing animals has been widely reported and has raised concern among authorities regarding the transmission to humans through food chains, as well as survival and mortality aspects in animal farming [3,4,5,6,7,8].
Although typically part of the normal microbiota of warm-blooded animals, Escherichia coli is also abundant in water systems and considered a resistance-indicator species of major epidemiological relevance due to its ability to transfer genes to other pathogenic bacteria, playing a significant role in the dissemination of AMR genetic determinants [7,9,10]. In addition, E. coli isolates can be classified as commensal or pathogenic, where pathogenic isolates related to intestinal diseases in animals, and can be subdivided based on the detection of genes: enterotoxigenic—ETEC (lt or st), enterohemorrhagic—EHEC/STEC (eaeA and at least one sxt), enteropathogenic—EPEC (aeaA), possibly diffusely adherent—DAEC (fimbrial adhesins afa and dr), entero-invasive—EIEC (ial), entero-aggregating—EAEC (eagg), adherent-invasive—AIEC (fimH) and enteroaggregative hemorrhagic E. coli—EAHEC (stx2) [11,12].
Among the several antimicrobial classes, quinolones and beta-lactams are often used in the human and veterinary fields. Previously reported data demonstrated resistance against those antimicrobials in water and fish E. coli isolates along with the plasmid-mediated quinolone-resistance determinants (PMQR) and extended spectrum β-lactamases (ESBLs), demonstrating the importance of such bacterial species as reservoirs and in the spread of AMR determinants to humans [2,7,13,14,15,16,17,18,19,20].
In the Brazilian Amazon region, the Arapaima gigas species, also known as “pirarucu or the giant of the Amazon” is a fish of major ecological, economic, and cultural importance, occupying a prominent place in Brazilian aquaculture [5,21]. The production of this species is concentrated in the Amazon region and reaches 11,763 tons annually, the seventh-largest species in the volume of production in Brazil [22]. Considering that fish species may pose as resistance reservoirs and the importance of A. gigas farming in the Amazon region, the present study reports the resistance and virulence features, as well as the genetic diversity of E. coli isolated from the intestinal content of wild and farmed A. gigas in the far north of the Brazilian Amazon.

2. Materials and Methods

2.1. Study Setting and Sample Collection

The collection of A. gigas specimens was performed in five fish farms and five rivers in the state of Amapá, in the far north of the Brazilian Amazon (Figure 1). The five fish farms (F1—0°11′41.7″ N 51°01′29.6″ W, F2—0°04′23.8″ N 51°02′28″ W, F3—0°00′26.4″ N 51°06′46″ W, F4—0°02′34.9″ S 51°07′50.0″ W, and F5—0°00′24.2″ S 51°06′15.6″ W) were selected based on information provided by the Amapá State Fisheries Agency (PESCAP). Wild A. gigas were recovered in the municipalities of Mazagão (MZG—0°06′56.8″ S 51°38′21.9″ W), Cutias (CUT—1°07′35.6″ N 50°19′13″ W), Ferreira Gomes (FG—0°56′53.4″ N 51°10′39.2″ W), Oiapoque (OPQ—3°34′19.3″ N 51°23′15.3″ W) and Tartarugalzinho (TT—1°29′58.7″ N 50°41′07.4″ W). A total of forty (40) specimens of A. gigas were collected between November (2017) and June (2019), including 20 farmed and 20 wild fish.

2.2. Bacterial Isolates and Antimicrobial Susceptibility Testing

The A. gigas specimens were individually transported to the laboratory in sterile plastic bags within a water tank in an isothermal box and submitted to cryoanesthesia, followed by euthanasia by the spinal cord section. Samples of four grams of A. gigas intestinal content were incubated overnight at 37 °C in 36 mL of MacConkey (BD) broth supplemented with ciprofloxacin (CIP, 10 µg/mL), for selection of quinolone-resistant E. coli isolates. One hundred µL (100 µL) aliquots of this culture were inoculated on MacConkey agar plates and incubated under the same conditions. Isolated colonies were phenotypically identified on the automated VITEK 2® system equipment (bioMérieux, Marcy I’Etoile, France).
The antimicrobial susceptibility testing (AST) determined the minimum inhibitory concentration (MIC) by broth microdilution using the AST 239 card on the automated VITEK 2® system equipment (bioMérieux, Marcy I’Etoile, France) for the following antimicrobials: ampicillin (AMP), ampicillin/sulbactam (SAM), piperacillin/tazobactam (TZP), cefuroxime (CXM), cefuroxime axetil (CXM), cefoxitin (FOX), ceftazidime (CAZ), ceftriaxone (CRO), cefepime (FEP), ertapenem (ETP), imipenem (IMP), meropenem (MEM), amikacin (AMK), gentamicin (GEN), ciprofloxacin (CIP), tigecycline (TGC), and colistin (COL). Results were interpreted according to the guidelines and breakpoints of the Clinical and Laboratory Standards Institute [23]. The reference strain E. coli ATCC 25922 was used as a quality control. In addition, E. coli isolates were phenotypically categorized as MDR if resistant to ≥1 drug in ≥3 antimicrobial categories, according to criteria proposed by [24].The Multi-Antibiotic Resistance Index (MAR) was determined by means of the following formula: x/y, where ‘x’ indicates the number antibiotics for which the isolate was resistant, and ‘y’ indicates the number of antibiotics tested against the isolate. Results higher than 0.2 indicate that the microorganism is a potential reservoir of resistance determinants [25].

2.3. Molecular Detection of Antimicrobial Resistance and Virulence Markers

Bacterial DNA was extracted using the PureLink® commercial kit (Invitrogen), according to the manufacturer’s guidelines. The molecular detection of quinolone and beta-lactam-resistance genes was performed by PCR on Veriti thermocycler (Applied Biosystems, Foster City, CA, USA), using previously describer primers [26,27,28,29,30,31,32]. Each PCR reaction was prepared with a total volume of 20 µL, including 2.5 µL of 10× PCR buffer (New England BioLabs, Ipswich, MA, USA), 5 pmol of each primer (MWG- Biotech AG, Ebersberg, Germany), deoxynucleoside triphosphates at a concentration of 200 µM (Promega, Madison, WI, USA), 1U Taq DNA polymerase (New England BioLabs), and 50 ng of genomic DNA.
The virulence genes were detected by multiplex PCR, applying a slightly modified protocol by Omar et al. [33]. Each reaction was prepared with a total volume of 20 µL, 2.5 µL of 10× PCR buffer (New England BioLabs, Ipswich, MA, USA), 5 pmol of each primer (MWG-Biotech AG, Ebersberg, Germany), deoxynucleoside triphosphates at a concentration of 200 µM (Promega), 1U Taq DNA polymerase (New England BioLabs) and 50 ng of genomic DNA. Amplifications were performed on Veriti thermocycler (Applied Biosystems, Foster City, CA, USA) under the following conditions: 95 °C for 15 min; followed by 30 cycles at 94 °C for 45 s, 55 °C for 45 s, 68 °C for 2 min and final extension at 72 °C for 5 min. PCR products were subjected to electrophoresis on 2% agarose gel (Sigma) stained with ethidium bromide and amplicons were visualized in the Image Quant transilluminator.

2.4. Molecular Typing by Multilocus Sequence Typing (MLST)

MLST genotyping was performed according to the protocol of [34]. The seven housekeeping genes—adk (adenylate kinase), fumC (fumarate hydratase), gyrB (DNA gyrase), icd (isopropylmalate dehydrogenase), mdh (malate dehydrogenase), purA (adenylosuccinate dehydrogenase), and recA (ATP/GTP binding motif) —were amplified for each sample by PCR on the Veriti thermocycler (Applied Biosystems, Foster City, CA, USA). Reaction products were sequenced in both strands with previously published primers on the ABI Prism 3130 Genetic Analyzer Platform (Applied Biosystems, Foster City, CA, USA). The results obtained were analyzed according to the PubMLST database (https://pubmlst.org/escherichia/, accessed on 21 February 2022) for determination of sequence types (STs).

2.5. Molecular Typing by Pulsifield Gel Eletroforese (PFGE)

The genetic relationship of E. coli isolates was analyzed by Pulsed Field Gel Electrophoresis (PFGE) with XbaI (Roche) DNA digestion, according to the PulseNet protocol [35]. The preparation of the inoculum was initially obtained by sowing the microorganism by depletion in Nutrient Agar and subsequent incubation (24 h/35 °C) to obtain isolated colonies, from which suspensions were prepared in 4 mL of buffer for cell suspension with the aid of a sterile swab until turbidity between 8 and 10% absorbance was obtained in the 610 nm wavelength spectrophotometer (corresponding 3 × 108 CFU/mL).
Agarose plugs were produced from 200 μL aliquots of each bacterial suspension and transferred to sterile polypropylene R tubes, to which 10 μL of Proteinase K (20 mg/mL), were added to 200 μL of Seakem Gold agarose 1% in TE buffer. Under constant homogenization and dispensing in 46 molds at 50 °C, small blocks of agarose gel containing genomic DNA (2 blocks per sample) were obtained. After proper assembly of the digested blocks in the comb, the agarose was introduced in the horizontal gel holder, where it remained for 30 min at room temperature for solidification. The enzyme used to digest the bacterial DNA was XbaI, which generated fragments of 50–300 kpb, with a 5 “-30”/23 h. The fragments generated by the enzymatic restriction were visualized in UV light in a photo-documentation device for further analysis. Finally, the agarose-soaked bacterial DNA was digested with restriction enzyme XbaI at 37 °C for 4 h. In addition, electrophoresis was performed on 1% agarose gel with 0.5× Tris-borate-EDTA buffer.
PFGE standards and computer-assisted cluster analysis were visually analyzed using BioNumerics® software, version 7.6 (Applied Maths, SintMartens-Lantem, Bélgica). The similarity between the pairs was obtained by analysis based on a dendrogram, calculated with the data coefficient and the unweighted arithmetic mean pairs (UPGMA) method. Salmonella enterica serotype Braenderup, strain H9812 (ATCC BAA 664) was used as the molecular size standard.

2.6. Statistical Analysis

Statistical analyses to compare isolates’ resistance profiles from wild and captive groups were performed using the binomial proportion test. Values of p ≤ 0.05 were considered statistically significant. All analyzes were performed using the statistical software BioEstat® 5.3 [36].

2.7. Ethical Considerations

This study was evaluated by the Animal Research Ethics Committee of the Federal University of Acre (CEUA/UFAC), process Nº. 23107.009564/2014-29 (approval date: 10 July 2014), in compliance with the Brazilian regulation Law Nº 11,794 of 2008, which deals with animal experimentation in Brazil.

3. Results

3.1. Antimicrobial Resistance and Virulence Features

A total of 34 quinolone-resistant E. coli were recovered from 16 farmed and 18 wild fish. AST revealed that the majority of E. coli isolates were MDR (21, 61.7%), presenting non-susceptible to AMP (n = 27, 79.4%), followed by CXM (n = 24, 70.6%), and SAM (n = 22, 64.7%). Oppositely, all tested isolates were susceptible to ETP, IMP, MEM, AMK, GEN, TGC, and COL. The MAR index differed among isolates group, with a MAR index of 0.28 and 0.2 observed on E. coli from wild and farmed fish, respectively. The E. coli isolates recovered from wild fish demonstrated a significantly higher frequency of nonsusceptibility phenotypes (p = 0.005) (Table 1). The molecular detection of AMR markers revealed 15 (44.1%) isolates harboring the blaCTX-M gene, including 10 (55.5%) from wild and five (31.2%) from farmed fish. In addition, PMQR genes were mostly detected among farmed fish, including qnrA (4–25.0%) and qnrB (2–12.5%), while one isolated from wild fish at CUT was detected harboring the qnrB gene (Table 2).
Concerning the presence of genes related to virulence investigated by PCR, only three strains (8.82%) revealed the presence of the st gene responsible for the enterotoxigenic E. coli pathotype (ETEC), all from farmed animals at F3.

3.2. Molecular Typing by MLST and PFGE

Thirty-two (32) and 30 isolates were genotyped by MLST and PFGE, respectively, revealing a wide genetic background. MLST analysis demonstrated the presence of eleven distinct types, including: ST155 (3, 9.4%), ST224 (4, 12.5%), ST226 (1, 3.0%), ST448 (4, 12.5%), ST949 (1, 3.0%), ST1196 (1, 3.0%), ST1249 (3, 9.4%), ST1431 (2, 6.25%), ST4380 (1, 3.0%), ST4482 (1, 3.0%) and ST7973 (8, 25.0%). The blaCTX-M gene associated with several E. coli genotypes: ST448, ST155, ST4482, ST226, ST1431 and ST7973; while qnrA gene with ST448, ST1249 and ST155, and qnrB with ST448. Worryingly, the ST448 was detected at F1 among isolates harboring the blaCTX-M and qnr genes (Table 2). At F3, enterotoxigenic E. coli isolates were suggested to be genetically related by MLST and PFGE (ST155 and subcluster B1) (Table 2 and Figure 2).
Through the PFGE technique, 16 pulsotypes were identified, divided into four distinct clusters and seven subclusters (Figure 2 and Table 2). Interestingly, E. coli isolates presenting similar genetic signatures by PFGE were detected in distinct locations: strains of subcluster A2, including ST1249 and ST949, were associated with wild and farmed fish in F2 and MZG; strains of subcluster A3, including ST1431 and ST4380, were associated with wild and farmed fish in F4 and MZG; strains of subcluster B1, including ST155 and ST1196, were associated with wild and farmed fish in F3, F4, CUT and MZG; strains of subcluster B2, including S224 and ST7973, were associated with farmed fish in F2 and F4; strains belonging to subcluster C2, which also included ST7973 and ST226, were associated with wild and farmed fish in TT, FG and F4 locations; ST224, ST226, ST1196 and ST1431 were associated with farmed fish at F4 location; ST949, ST4380 and ST4482 were associated with wild fish at MZG location (Table 2 and Figure 2). On the other hand, genetic related strains were also found among isolates from the same location: strains belonging to subcluster A1, including ST448, were associated with farmed fish in F1, while strains from subcluster C1, including ST224, were associated with wild fish in OPQ (Figure 2 and Table 2).

4. Discussion

A. gigas is a native fish that occupies the top of the aquatic food chain in the Brazilian Amazon, reaching weights close to 125 kg, highlighting its elevated economic value; therefore, it can be considered a critical epidemiological indicator of environmental resistance, and may also act as a possible source of dispersion of AMR bacteria to humans and other wild and farmed animals. Gram-negative bacteria in the water are usually related to fecal contamination, showing how vital are the tracking process and characterization of E. coli isolates in the environment. E. coli is one of the major bacterial species capable of transferring/exchanging genetic information with other bacterial groups, contributing to the dissemination of AMR to distinct environments [37]. Different fish species have been found carrying E. coli resistance genes related to essential antimicrobials, such as quinolones and beta-lactams [7,38,39,40]. In the present study, this bacterial species was found among farmed and wild A. gigas, highlighting the geographical aspects of the presence of resistant isolates in fish in the Amazon region, and suggests an impact of human and antimicrobials interference in different ecological niches.
Data from the Netherlands evaluating ESBL-producing E. coli from water samples demonstrated that approximately 84% of this bacterial species exhibits resistance in up to three drug classes, including beta-lactams, tetracyclines, and aminoglycosides [38]. In addition, E. coli was the only species isolated in different fishes (Oncorhynchus mykiss, Squalius cephalus and Cyprinus carpio) from the farms and local markets in Turkey, including quinolone-resistant and MDR isolates [39]. ESBL-producing enterobacteria represent a significant role in health infections, increasing hospitalization time, morbidity, and mortality rates. Several bacterial species harboring blaCTX-M gene have become a major burden in clinical settings [41,42,43,44,45]. Other studies with ESBL-producing E. coli conducted in North America, Europe, South America, and Africa have shown similar high frequency results of CTX-M group strains showing simultaneous resistance to cephalosporins and quinolones [2,15,38,42,46]. Information regarding E. coli strains and circulation of resistance genes is produced by the present study, and this data is epidemiologically crucial to establish measures aiming to reduce the resistance burden.
In recent years, many studies have shown a worldwide exponential increase in quinolone and beta-lactam drug resistance in animal E. coli isolates, including fish, primarily associated with the presence of PMQR and ESBLs, demonstrating the importance of these reservoirs in the spread of antimicrobial resistance determinants to humans [9,14,15,16,39,40]. PMQR contribute with the selection of highly resistance pathogens, posing a threat to treatment, and act as a latent reservoir for disseminating these attributes to other aquatic organisms [47,48]. Among the surveyed PMQR, the qnrA (14.7%) gene was the most frequent in samples from farmed and wild fish, while the qnrB was detected in only 5.8%. Such determinants were previously reported among Brazilian clinical E. coli isolates, while the qnrS and aac(6-)-Ib-cr genes, frequently detected in Brazil and other Latin American countries, were not observed in this study [49,50,51].
MLST is a globally applied and reliable tool for investigating the population structure of bacteria such as E. coli, providing data on lineages, resistance and virulence features that are often involved in human and animal diseases, in addition to those isolates which are not typable by the standard PFGE method due to DNA methylation [52,53,54]. MLST genotyping revealed wide genetic diversity also supported by the PFGE analysis, with the presence of 11 different STs recognized for harboring distinct AMR markers at several locations, in addition to rarely detected clones. Data regarding MLST genotypes of E. coli from the Brazilian Amazon is scarce; therefore, results from the present report are also valuable for epidemiological surveillance of international clones of clinical and veterinary importance.
ST7973 was the most frequently detected clone (23.4%) and was associated with the carriage of the blaCTX-M among genetically related E. coli isolates from wild fish at TT and FG (subcluster C2). This is the first report of this clone in Brazil. Concerningly, this ST has been previously associated with mcr-1 gene in an abscess isolate in Venezuela and raw turkey meat in Poland, underscoring this genotype role in the threat to last-resort antibiotics [55,56,57].
Several studies demonstrated the typical relation of ST448 with ESBL-producing and quinolone-resistant E. coli, among which were those conducted with a veterinary approach in Spain and the Netherlands which describe several isolates harboring the blaCTX-M gene [58,59]. In clinical settings, this genotype has been reported in Brazil among CMY-producing isolates, and in other locations, such as: among ESBL-producing E. coli in Dutch patients with gastrointestinal complaints; in a wound sample in Nigeria; in a urinary infection isolate exhibiting co-resistance to aminoglycosides and oxyiminocephalosporins in the USA, and recently, with an IncX3 NDM-5-producing plasmid isolate in Mali [60,61,62,63,64]. n the present report, E. coli strains belonging to ST448 were associated with different AMR markers, including blaCTX-M, qnrA and qnrB genes, highlighting its transference capability of genetic traits and high-risk clone potential of causing outbreaks and dissemination in both clinical and veterinary settings.
E. coli ST155 is a major reported lineage among poultry from Africa, Europe, and South America, and water sources in India and Japan, and demonstrated as being critically responsible for the spreading of highly drug resistant strains from animal and food-producing sources to humans [65,66,67,68,69,70,71,72]. Molecular typing data obtained suggest the dissemination, among wild and farmed fish (F3 and CUT), of genetically related enterotoxigenic, commensal and MDR E. coli ST 155 carrying distinct AMR markers, which may be related to previous evidence of efficient transference of resistance features to pathogenic E. coli strains via conjugation, favoring epidemiological success of resistant isolates [16,73].
The E. coli ST224 is an international high-risk clone, which presents a high genetic plasticity, enabling its pandemic dissemination and adaptation to several ecosystems. Indeed, clinical, animal, and environmental ST224 strains have been commonly associated with MDR isolates harboring a wide range of resistance mechanisms, including blaNDM, blaCTX-M, blaKPC, mcr-1, and fosA genes in China, Pakistan, Brazil, Spain, India, Egypt, and Thailand [2,71,74,75,76,77,78,79,80]. Interestingly, most of E. coli ST224 were recovered from wild fish, found to be genetically related (PFGE—subcluster C1) and susceptible to the tested antibiotics, suggesting a low/limited anthropogenic and selective pressure at OPQ, a location with difficult access in the region and more remote compared to other A. gigas capture and farming sites.
The international high-risk clone ST1196 plays a critical role in the expansion of multiple AMR markers among E. coli isolates from distinct settings, leading to the emergence of heterogenous antibiotic resistance phenotypes, including a strong association with colistin, third generation cephalosporins, and aminoglycoside-resistant isolates. Among animal-related samples, this ST has been highly associated with E. coli in poultry samples from Germany, Czech Republic, Thailand, and Egypt, along with the carriage of AMR genes variants, such as blaTEM, blaCTX-m, blaCYM, blaNDM and mcr [56,79,81,82]. In Spain, it was detected in high prevalence in waste-water treatment plants among genetically related strains co-harboring rmtB, blaCTX-m-55 and mcr-1 genes [2]. In clinical settings, it has been responsible for the dissemination of KPC-2- and NDM-1-producing isolates in Pakistan hospitals [45]. Diverging from previous reports, ST1196 was related only with a highly susceptible isolate from F4, suggesting initial spread of this clone and/or selective pressure against it due to the presence of resistant strains.
The E. coli ST226, which was related with a CTX-M-producing MDR isolate at F4, has been previously linked with blaCTX-M variants among different animal hosts, including humans. In Egypt and Portugal, this genotype was detected in human, beef and bovine isolates presenting blaCTX-M-1, blaCTX-M-32 and blaCTX-M-2 genes, respectively, and in China where blaoxa-1 was harbored among farmed minks [78,82,83,84]. In addition, human fecal carriage in Portugal and Cambodia, and a patient with MCR-1-producing isolates causing acute diarrhea in Thailand, were also reported [85,86,87].
There are few reports of E. coli ST1249, which has been described as ESBL- and MCR-producing E. coli among food items in the Netherlands, diseased chicken in the Czech Republic, and companion animals (dogs and cats) in Europe [88,89,90,91]. This clone was restricted to F2 among genetically related isolates (subcluster A2) harboring the qnrA gene, also being the first report in Brazil of this clone among animal samples.
There are limited data regarding the prevalence E. coli ST949, which is known for its pathogenic potential due to a wide range of virulence capabilities [12]. Recent evidence indicates it is an emerging clone with pathogenic potential that could mainly spread through water sources, even though it has been reported as causing infection in animals and humans [92,93,94,95]. This ST was curiously related to a commensal E. coli isolate from wild fish at MZG, contrary to the evidence of virulence potential, but also pointing to its emergence as it was first reported in Brazil and has the potential of dissemination as genetically revealed by PFGE (subcluster A2).
The few reports of ST1431 are from different sources, and mostly related with ESBL- and MCR-producing isolates from different sources, including E. coli isolates harboring blaCTX-M detected in gulls in Canada and Chile, and wastewater in Algeria, along with MCR-producing isolates in raw meat and farmed rabbits in Portugal [96,97,98]. Curiously, this ST was related with a highly resistant CTX-M-producing and susceptible isolate at F4, suggesting a possible acquisition and transmission potential of genetic elements containing blaCTX-M variants.
Rarely reported clones, such as ST4380 and ST4482, were found firstly in Brazil. ST4380 was previously related to ESBL-producing isolates from animal samples (European starlings in USA and monkeys in France), while ST4482 was related to uropathogenic E. coli (UPEC) strains in Pakistan and quinolone-resistant strains from poultry in the Philippines [99,100,101,102]. Both STs were detected in MZG, however only ST4482 was associated with a highly resistant CTX-M-producing isolate.
The PFGE typing allowed deeper insights into the remarkable genetic diversity of E. coli isolates, demonstrating genetic relatedness among strains from distinct sources (wild and farmed fish) as observed in subclusters A2, A3, B1, B2 and C2, which might be explained by the fact that many fish farmers capture A. gigas matrices in the natural environment to start breeding and production. Yet, genetically similar isolated (subclusters A1 and C1) in the same locations were verified, suggesting selection and clonal expansion of strains within a localized site. Moreover, differences on the phenotypical and molecular resistance features of isolates belonging to the same cluster (clone) suggest the impact and dissemination of mobile genetic elements containing blaCTX-M, qnrA and qnrB genes in this region. Previous reports of extensive genetic diversity among E. coli isolates in seafood from Brazil and the United States, as well as data on the present study, corroborate the need for molecular typing and genetic relatedness investigations on the surveillance of E. coli strains from different natural hosts, sources, and locations, as their critical role in transmission of AMR characteristics [103].

5. Conclusions

The present study demonstrated a high genetic background among quinolone-resistant E. coli isolates in A. gigas, revealing that this fish species could act as bioindicators of clinically significant AMR genes in aquatic niches and food-producing animals, even in poorly explored environments with low antimicrobial drugs exposure, in the Brazilian Amazon region. International high-risk clones and genetically related strains were associated with ESBL and PMQR genes (blaCTX-M, qnrA and qnrB), suggesting a multiclonal spread of E. coli strains harboring AMR genes in distinct genetic contexts, and highlight the importance of molecular typing studies for surveillance of potential threatening strains. Finally, this study underscores the emergence, spread and interference of AMR bacteria in wildlife and environmental matrices in the vicinity of anthropogenic environments.

Author Contributions

Conceptualization, L.S.L., A.A.P.-J., D.d.P.R. and K.V.B.L.; validation, L.S.L., A.A.P.-J., D.d.P.R., Y.C.R. and K.V.B.L.; formal analysis, L.S.L.; investigation, L.S.L., Y.C.R. and V.D.G.; resources, L.S.L., K.V.B.L., D.d.P.R., A.A.P.-J., L.N.G.C.L., C.d.O.S. and M.d.O.L.; writing—original draft preparation, L.S.L., Y.C.R., A.A.P.-J., D.d.P.R. and K.V.B.L.; writing—review and editing, L.S.L., Y.C.R., M.C.d.S.V., M.d.O.L. and K.V.B.L.; supervision, L.S.L., A.A.P.-J., D.d.P.R., C.d.O.S. and K.V.B.L.; project administration, L.S.L., A.A.P.-J., D.d.P.R. and K.V.B.L.; funding acquisition, L.S.L., A.A.P.-J., D.d.P.R., C.d.O.S., L.N.G.C.L. and K.V.B.L. All authors have read and agreed to the published version of the manuscript.

Funding

This study received financial support from the Federal University of Amapá through the educational incentive grant to Luciana Sampaio Lima (No. 01/2019-PSPIE/PROGEP/UNIFAP) and through the DECENTRALIZED Term of Reference of Municipal Plans of 6 Municipalities in the State of Amapá (TEDPLAN)—UNIFAP/FUNASA—Process UNIFAP No. 23125.012850/2018-87. 51 p. 2018. The APC was funded by Evandro Chagas Institute (IEC/Pa/Brazil). Yan Corrêa Rodrigues scholarship is funded by Fundação para o Desenvolvimento Científico e Tecnológico em Saúde (FIOTEC).

Institutional Review Board Statement

The study was conducted according to the guidelines of the Declaration of Helsinki, and approved by the Animal Research Ethics Committee of the Federal University of Acre (CEUA/UFAC), process No. 23107.009564/2014-29 (approval date: 10 July 2014), in compliance with the Brazilian regulation Law No. 11,794 of 2008, which deals with animal experimentation in Brazil.

Informed Consent Statement

Not applicable.

Data Availability Statement

All relevant data are presented within the manuscript.

Acknowledgments

We all need to thank and acknowledge the contributions of specific colleagues, institutions, and agencies that aided the authors’ efforts.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Haberecht, H.B.; Nealon, N.J.; Gilliland, J.R.; Holder, A.V.; Runyan, C.; Oppel, R.C.; Ibrahim, H.M.; Mueller, L.; Schrupp, F.; Vilchez, S.; et al. Antimicrobial-Resistant Escherichia coli from Environmental Waters in Northern Colorado. J. Environ. Public Health 2019, 2019, 3862949. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  2. Delgado-Blas, J.F.; Ovejero, C.M.; David, S.; Montero, N.; Calero-Caceres, W.; Garcillan-Barcia, M.P.; de la Cruz, F.; Muniesa, M.; Aanensen, D.M.; Gonzalez-Zorn, B. Population genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments. Commun. Biol. 2021, 4, 457. [Google Scholar] [CrossRef] [PubMed]
  3. Berendonk, T.U.; Manaia, C.M.; Merlin, C.; Fatta-Kassinos, D.; Cytryn, E.; Walsh, F.; Bürgmann, H.; Sørum, H.; Norström, M.; Pons, M.-N.; et al. Tackling antibiotic resistance: The environmental framework. Nat. Rev. Microbiol. 2015, 13, 310–317. [Google Scholar] [CrossRef] [PubMed]
  4. Ma, F.; Xu, S.; Tang, Z.; Li, Z.; Zhang, L. Use of antimicrobials in food animals and impact of transmission of antimicrobial resistance on humans. Biosaf. Health 2021, 3, 32–38. [Google Scholar] [CrossRef]
  5. Proietti-Junior, A.A.; Lima, L.S.; Roges, E.M.; Rodrigues, Y.C.; Lima, K.V.B.; Rodrigues, D.P.; Tavares-Dias, M. Experimental co-infection by Aeromonas hydrophila and Aeromonas jandaei in pirarucu Arapaima gigas (Pisces: Arapaimidae). Aquac. Res. 2021, 52, 1688–1696. [Google Scholar] [CrossRef]
  6. Gillings, M.R.; Stokes, H.W. Are humans increasing bacterial evolvability? Trends Ecol. Evol. 2012, 27, 346–352. [Google Scholar] [CrossRef]
  7. Saharan, V.V.; Verma, P.; Singh, A.P. High prevalence of antimicrobial resistance in Escherichia coli, Salmonella spp. and Staphylococcus aureus isolated from fish samples in India. Aquac. Res. 2020, 51, 1200–1210. [Google Scholar] [CrossRef]
  8. The European Union One Health 2018 Zoonoses Report. EFSA J. 2019, 17, 5926. [CrossRef] [Green Version]
  9. Dib, A.L.; Agabou, A.; Chahed, A.; Kurekci, C.; Moreno, E.; Espigares, M.; Espigares, E. Isolation, molecular characterization and antimicrobial resistance of enterobacteriaceae isolated from fish and seafood. Food Control 2018, 88, 54–60. [Google Scholar] [CrossRef]
  10. Jang, J.; Hur, H.-G.; Sadowsky, M.J.; Byappanahalli, M.N.; Yan, T.; Ishii, S. Environmental Escherichia coli: Ecology and public health implications-a review. J. Appl. Microbiol. 2017, 123, 570–581. [Google Scholar] [CrossRef] [Green Version]
  11. Farfán-García, A.E.; Ariza-Rojas, S.C.; Vargas-Cárdenas, F.A.; Vargas-Remolina, L.V. Mecanismos de virulencia de Escherichia coli enteropatógena. Rev. Chil. Infectol. 2016, 33, 438–450. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  12. Oh, K.-H.; Kim, D.W.; Jung, S.-M.; Cho, S.-H. Molecular Characterization of Enterotoxigenic Escherichia coli Strains Isolated from Diarrheal Patients in Korea during 2003–2011. PLoS ONE 2014, 9, e96896. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  13. Aedo, S.; Ivanova, L.; Tomova, A.; Cabello, F.C. Plasmid-Related Quinolone Resistance Determinants in Epidemic Vibrio parahaemolyticus, Uropathogenic Escherichia coli, and Marine Bacteria from an Aquaculture Area in Chile. Microb. Ecol. 2014, 68, 324–328. [Google Scholar] [CrossRef] [PubMed]
  14. Tomova, A.; Ivanova, L.; Buschmann, A.H.; Godfrey, H.P.; Cabello, F.C. Plasmid-Mediated Quinolone Resistance (PMQR) Genes and Class 1 Integrons in Quinolone-Resistant Marine Bacteria and Clinical Isolates of Escherichia coli from an Aquacultural Area. Microb. Ecol. 2018, 75, 104–112. [Google Scholar] [CrossRef] [PubMed]
  15. Plantamura, J.; Bousquet, A.; Védy, S.; Larréché, S.; Bigaillon, C.; Delacour, H.; Mérens, A. Molecular epidemiological of extended-spectrum β-lactamase producing Escherichia coli isolated in Djibouti. J. Infect. Dev. Ctries 2019, 13, 753–758. [Google Scholar] [CrossRef]
  16. Raimondi, S.; Righini, L.; Candeliere, F.; Musmeci, E.; Bonvicini, F.; Gentilomi, G.; Erjavec, M.S.; Amaretti, A.; Rossi, M. Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of E. coli Isolated from the Feces of Healthy Subjects. Microorganisms 2019, 7, 251. [Google Scholar] [CrossRef] [Green Version]
  17. von Wintersdorff, C.J.H.; Penders, J.; van Niekerk, J.M.; Mills, N.D.; Majumder, S.; van Alphen, L.B.; Savelkoul, P.H.M.; Wolffs, P.F.G. Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer. Front. Microbiol. 2016, 7, 173. [Google Scholar] [CrossRef] [Green Version]
  18. Zhang, Y.-J.; Hu, H.-W.; Chen, Q.-L.; Singh, B.K.; Yan, H.; Chen, D.; He, J.-Z. Transfer of antibiotic resistance from manure-amended soils to vegetable microbiomes. Environ. Int. 2019, 130, 104912. [Google Scholar] [CrossRef]
  19. Kimera, Z.I.; Mgaya, F.X.; Mshana, S.E.; Karimuribo, E.D.; Matee, M.I.N. Occurrence of Extended Spectrum Beta Lactamase (ESBL) Producers, Quinolone and Carbapenem Resistant Enterobacteriaceae Isolated from Environmental Samples along Msimbazi River Basin Ecosystem in Tanzania. Int. J. Environ. Res. Public. Health 2021, 18, 8264. [Google Scholar] [CrossRef]
  20. Miller, R.A.; Harbottle, H. Antimicrobial Drug Resistance in Fish Pathogens. Microbiol. Spectr. 2018, 6. [Google Scholar] [CrossRef]
  21. Dias, M.K.R.; Sampaio, L.S.; Proietti-Junior, A.A.; Yoshioka, E.T.O.; Rodrigues, D.P.; Rodriguez, A.F.R.; Ribeiro, R.A.; Faria, F.S.E.D.V.; Ozório, R.O.A.; Tavares-Dias, M. Lethal dose and clinical signs of Aeromonas hydrophila in Arapaima gigas (Arapaimidae), the giant fish from Amazon. Vet. Microbiol. 2016, 188, 12–15. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  22. Proietti-Junior, A.A.; Lima, L.S.; Cardoso, F.M.N.; Rodrigues, D.d.P.; Dias, M.T. Bacterioses Em Alevinos de Pirarucu de Cultivo, Com Ênfase Em Edwardsielose e Aeromonose, 1st ed.; Belém, Ed.; Centro de Pesquisa Agroflorestal do Amapá—EMBRAPA: Macapá, Brazil, 2017. [Google Scholar]
  23. Weinstein, M.P.; Clinical and Laboratory Standards Institute. Performance Standards for Antimicrobial Susceptibility Testing: Supplement M100; Clinical and Laboratory Standards Institute: Wayne, PA, USA, 2010; ISBN 978-1-68440-066-9. [Google Scholar]
  24. Magiorakos, A.-P.; Srinivasan, A.; Carey, R.B.; Carmeli, Y.; Falagas, M.E.; Giske, C.G.; Harbarth, S.; Hindler, J.F.; Kahlmeter, G.; Olsson-Liljequist, B.; et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: An international expert proposal for interim standard definitions for acquired resistance. Clin. Microbiol. Infect. 2012, 18, 268–281. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  25. Krumperman, P.H. Multiple antibiotic resistance indexing of Escherichia coli to identify high-risk sources of fecal contamination of foods. Appl. Environ. Microbiol. 1983, 46, 165–170. [Google Scholar] [CrossRef] [Green Version]
  26. Jacoby, G.A.; Gacharna, N.; Black, T.A.; Miller, G.H.; Hooper, D.C. Temporal Appearance of Plasmid-Mediated Quinolone Resistance Genes. Antimicrob. Agents Chemother. 2009, 53, 1665–1666. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  27. Kim, H.B.; Park, C.H.; Kim, C.J.; Kim, E.-C.; Jacoby, G.A.; Hooper, D.C. Prevalence of plasmid-mediated quinolone resistance determinants over a 9-year period. Antimicrob. Agents Chemother. 2009, 53, 639–645. [Google Scholar] [CrossRef] [Green Version]
  28. 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]
  29. 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]
  30. Naas, T.; Oxacelay, C.; Nordmann, P. Identification of CTX-M-Type Extended-Spectrum-β-Lactamase Genes Using Real-Time PCR and Pyrosequencing. Antimicrob. Agents Chemother. 2007, 51, 223–230. [Google Scholar] [CrossRef] [Green Version]
  31. Eaves, D.J.; Liebana, E.; Woodward, M.J.; Piddock, L.J.V. Detection of gyrA Mutations in Quinolone-Resistant Salmonella enterica by Denaturing High-Performance Liquid Chromatography. J. Clin. Microbiol. 2002, 40, 4121–4125. [Google Scholar] [CrossRef] [Green Version]
  32. Poirel, L.; Walsh, T.R.; Cuvillier, V.; Nordmann, P. Multiplex PCR for detection of acquired carbapenemase genes. Diagn. Microbiol. Infect. Dis. 2011, 70, 119–123. [Google Scholar] [CrossRef]
  33. Omar, K.B.; Barnard, T.G. Detection of diarrhoeagenic Escherichia coli in clinical and environmental water sources in South Africa using single-step 11-gene m-PCR. World J. Microbiol. Biotechnol. 2014, 30, 2663–2671. [Google Scholar] [CrossRef] [Green Version]
  34. 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] [Green Version]
  35. Ribot, E.M.; Fair, M.A.; Gautom, R.; Cameron, D.N.; Hunter, S.B.; Swaminathan, B.; Barrett, T.J. Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. Foodborne Pathog. Dis. 2006, 3, 59–67. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  36. Ayres, M. BioEstat 5.0: Aplicações Estatísticas nas Áreas de Ciências Biomédicas, 4th ed.; Sociedade Civil Mamirauá; MCT-CNPq: Manaus, Brazil, 2007; ISBN 85-85924-10-1. [Google Scholar]
  37. Alexander, T.W.; Inglis, G.D.; Yanke, L.J.; Topp, E.; Read, R.R.; Reuter, T.; McAllister, T.A. Farm-to-fork characterization of Escherichia coli associated with feedlot cattle with a known history of antimicrobial use. Int. J. Food Microbiol. 2010, 137, 40–48. [Google Scholar] [CrossRef] [PubMed]
  38. Franz, E.; Veenman, C.; van Hoek, A.H.A.M.; Husman, A.d.R.; Blaak, H. Pathogenic Escherichia coli producing Extended-Spectrum β-Lactamases isolated from surface water and wastewater. Sci. Rep. 2015, 5, 14372. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  39. Onmaz, N.E.; Yildirim, Y.; Karadal, F.; Hizlisoy, H.; Al, S.; Gungor, C.; Disli, H.B.; Barel, M.; Dishan, A.; Akai Tegin, R.A.; et al. Escherichia coli O157 in fish: Prevalence, antimicrobial resistance, biofilm formation capacity, and molecular characterization. LWT 2020, 133, 109940. [Google Scholar] [CrossRef]
  40. de Almeida, M.V.A.; Cangussú, Í.M.; de Carvalho, A.L.S.; Brito, I.L.P.; Costa, R.A. Drug resistance, AmpC-β-lactamase and extended-spectrum β-lactamase-producing Enterobacteriaceae isolated from fish and shrimp. Rev. Inst. Med. Trop. São Paulo 2017, 59, e70. [Google Scholar] [CrossRef]
  41. Pavez, M.; Troncoso, C.; Osses, I.; Salazar, R.; Illesca, V.; Reydet, P.; Rodríguez, C.; Chahin, C.; Concha, C.; Barrientos, L. High prevalence of CTX-M-1 group in ESBL-producing enterobacteriaceae infection in intensive care units in southern Chile. Braz. J. Infect. Dis. 2019, 23, 102–110. [Google Scholar] [CrossRef]
  42. Pitout, J.D.; Laupland, K.B. Extended-spectrum β-lactamase-producing Enterobacteriaceae: An emerging public-health concern. Lancet Infect. Dis. 2008, 8, 159–166. [Google Scholar] [CrossRef]
  43. Rodrigues, Y.C.; Furlaneto, I.P.; Maciel, A.H.P.; Quaresma, A.J.P.G.; de Matos, E.C.O.; Conceição, M.L.; Vieira, M.C.d.S.; Brabo, G.L.d.C.; Sarges, E.d.S.N.F.; Lima, L.N.G.C.; et al. High prevalence of atypical virulotype and genetically diverse background among Pseudomonas aeruginosa isolates from a referral hospital in the Brazilian Amazon. PLoS ONE 2020, 15, e0238741. [Google Scholar] [CrossRef]
  44. Naeem, S.; Bilal, H.; Muhammad, H.; Khan, M.A.; Hameed, F.; Bahadur, S.; Rehman, T.U. Detection of blaNDM-1 gene in ESBL producing Escherichia coli and Klebsiella pneumoniae isolated from urine samples. J. Infect. Dev. Ctries 2021, 15, 516–522. [Google Scholar] [CrossRef] [PubMed]
  45. Bilal, H.; Rehman, T.U.; Khan, M.A.; Hameed, F.; Jian, Z.G.; Han, J.; Yang, X. Molecular Epidemiology of mcr-1, blaKPC-2, and blaNDM-1 Harboring Clinically Isolated Escherichia coli from Pakistan. Infect. Drug Resist. 2021, 14, 1467–1479. [Google Scholar] [CrossRef] [PubMed]
  46. Jacoby, G.A.; Strahilevitz, J.; Hooper, D.C. Plasmid-Mediated Quinolone Resistance. Microbiol. Spectr. 2014, 2, 1–24. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  47. Yan, L.; Liu, D.; Wang, X.-H.; Wang, Y.; Zhang, B.; Wang, M.; Xu, H. Bacterial plasmid-mediated quinolone resistance genes in aquatic environments in China. Sci. Rep. 2017, 7, 40610. [Google Scholar] [CrossRef] [PubMed]
  48. Yeh, J.-C.; Lo, D.-Y.; Chang, S.-K.; Chou, C.-C.; Kuo, H.-C. Prevalence of plasmid-mediated quinolone resistance in Escherichia coli isolated from diseased animals in Taiwan. J. Vet. Med. Sci. 2017, 79, 730–735. [Google Scholar] [CrossRef] [Green Version]
  49. Castanheira, M.; Pereira, A.S.; Nicoletti, A.G.; Pignatari, A.C.C.; Barth, A.L.; Gales, A.C. First Report of Plasmid-Mediated qnrA1 in a Ciprofloxacin-Resistant Escherichia coli Strain in Latin America. Antimicrob. Agents Chemother. 2007, 51, 1527–1529. [Google Scholar] [CrossRef] [Green Version]
  50. Viana, A.L.M.; Cayô, R.; Avelino, C.C.; Gales, A.C.; Franco, M.C.; Minarini, L.A.R. Extended-spectrum β-lactamases in Enterobacteriaceae isolated in Brazil carry distinct types of plasmid-mediated quinolone resistance genes. J. Med. Microbiol. 2013, 62, 1326–1331. [Google Scholar] [CrossRef] [Green Version]
  51. Paiva, M.C.; Nascimento, A.M.A.; Camargo, I.L.B.C.; Lima-Bittencourt, C.I.; Nardi, R.M.D. The first report of the qnrB19, qnrS1 and aac(6´)-Ib-cr genes in urinary isolates of ciprofloxacin-resistant Escherichia coli in Brazil. Mem. Inst. Oswaldo Cruz 2012, 107, 687–689. [Google Scholar] [CrossRef] [Green Version]
  52. Bens, C.C.P.M.; Voss, A.; Klaassen, C.H.W. Presence of a Novel DNA Methylation Enzyme in Methicillin-Resistant Staphylococcus aureus Isolates Associated with Pig Farming Leads to Uninterpretable Results in Standard Pulsed-Field Gel Electrophoresis Analysis. J. Clin. Microbiol. 2006, 44, 1875–1876. [Google Scholar] [CrossRef] [Green Version]
  53. Riley, L.W. Pandemic lineages of extraintestinal pathogenic Escherichia coli. Clin. Microbiol. Infect. 2014, 20, 380–390. [Google Scholar] [CrossRef] [Green Version]
  54. Woodford, N.; Turton, J.F.; Livermore, D.M. Multiresistant Gram-negative bacteria: The role of high-risk clones in the dissemination of antibiotic resistance. FEMS Microbiol. Rev. 2011, 35, 736–755. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  55. Zelendova, M.; Papagiannitsis, C.C.; Valcek, A.; Medvecky, M.; Bitar, I.; Hrabak, J.; Gelbicova, T.; Barakova, A.; Kutilova, I.; Karpiskova, R.; et al. Characterization of the Complete Nucleotide Sequences of mcr-1-Encoding Plasmids From Enterobacterales Isolates in Retailed Raw Meat Products From the Czech Republic. Front. Microbiol. 2021, 11, 604067. [Google Scholar] [CrossRef] [PubMed]
  56. Kubelová, M.; Koláčková, I.; Gelbíčová, T.; Florianová, M.; Kalová, A.; Karpíšková, R. Virulence Properties of mcr-1-Positive Escherichia coli Isolated from Retail Poultry Meat. Microorganisms 2021, 9, 308. [Google Scholar] [CrossRef] [PubMed]
  57. Wise, M.G.; Estabrook, M.A.; Sahm, D.F.; Stone, G.G.; Kazmierczak, K.M. Prevalence of mcr-type genes among colistin-resistant Enterobacteriaceae collected in 2014-2016 as part of the INFORM global surveillance program. PLoS ONE 2018, 13, e0195281. [Google Scholar] [CrossRef] [Green Version]
  58. Blaak, H.; Hamidjaja, R.A.; van Hoek, A.H.A.M.; de Heer, L.; de Roda Husman, A.M.; Schets, F.M. Detection of Extended-Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli on Flies at Poultry Farms. Appl. Environ. Microbiol. 2014, 80, 239–246. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  59. Vredenburg, J.; Varela, A.R.; Hasan, B.; Bertilsson, S.; Olsen, B.; Narciso-da-Rocha, C.; Bonnedahl, J.; Stedt, J.; Da Costa, P.M.; Manaia, C.M. Quinolone-resistant Escherichia coli isolated from birds of prey in Portugal are genetically distinct from those isolated from water environments and gulls in Portugal, Spain and Sweden: Molecular epidemiology of quinolone resistant E. coli. Environ. Microbiol. 2014, 16, 995–1004. [Google Scholar] [CrossRef]
  60. Reuland, E.A.; Overdevest, I.T.M.A.; al Naiemi, N.; Kalpoe, J.S.; Rijnsburger, M.C.; Raadsen, S.A.; Ligtenberg-Burgman, I.; van der Zwaluw, K.W.; Heck, M.; Savelkoul, P.H.M.; et al. High prevalence of ESBL-producing Enterobacteriaceae carriage in Dutch community patients with gastrointestinal complaints. Clin. Microbiol. Infect. 2013, 19, 542–549. [Google Scholar] [CrossRef] [Green Version]
  61. Koga, V.L.; Maluta, R.P.; da Silveira, W.D.; Ribeiro, R.A.; Hungria, M.; Vespero, E.C.; Nakazato, G.; Kobayashi, R.K.T. Characterization of CMY-2-type beta-lactamase-producing Escherichia coli isolated from chicken carcasses and human infection in a city of South Brazil. BMC Microbiol. 2019, 19, 174. [Google Scholar] [CrossRef] [Green Version]
  62. Li, B.; Pacey, M.P.; Doi, Y. Chromosomal 16S Ribosomal RNA Methyltransferase RmtE1 in Escherichia coli Sequence Type 448. Emerg. Infect. Dis. 2000, 23, 876–878. [Google Scholar] [CrossRef]
  63. Aibinu, I.; Odugbemi, T.; Koenig, W.; Ghebremedhin, B. Sequence Type ST131 and ST10 Complex (ST617) predominant among CTX-M-15-producing Escherichia coli isolates from Nigeria. Clin. Microbiol. Infect. 2012, 18, E49–E51. [Google Scholar] [CrossRef] [Green Version]
  64. Muggeo, A.; Maiga, A.; Maiga, I.; Brasme, L.; Dicko, O.A.; de Champs, C.; Guillard, T. First description of IncX3 NDM-5-producing plasmid within Escherichia coli ST448 in Mali. J. Med. Microbiol. 2020, 69, 685–688. [Google Scholar] [CrossRef] [PubMed]
  65. Anyanwu, M.U.; Okpala, C.O.R.; Chah, K.F.; Shoyinka, V.S. Prevalence and Traits of Mobile Colistin Resistance Gene Harbouring Isolates from Different Ecosystems in Africa. BioMed Res. Int. 2021, 2021, 6630379. [Google Scholar] [CrossRef] [PubMed]
  66. Foster-Nyarko, E.; Alikhan, N.-F.; Ravi, A.; Thomson, N.M.; Jarju, S.; Kwambana-Adams, B.A.; Secka, A.; O’Grady, J.; Antonio, M.; Pallen, M.J. Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia. Microb. Genomics 2021, 7, mgen000484. [Google Scholar] [CrossRef] [PubMed]
  67. Day, M.J.; Hopkins, K.L.; Wareham, D.W.; Toleman, M.A.; Elviss, N.; Randall, L.; Teale, C.; Cleary, P.; Wiuff, C.; Doumith, M.; et al. Extended-spectrum β-lactamase-producing Escherichia coli in human-derived and foodchain-derived samples from England, Wales, and Scotland: An epidemiological surveillance and typing study. Lancet Infect. Dis. 2019, 19, 1325–1335. [Google Scholar] [CrossRef] [Green Version]
  68. Seenama, C.; Thamlikitkul, V.; Ratthawongjirakul, P. Multilocus sequence typing and blaESBL characterization of extended-spectrum beta-lactamase-producing Escherichia coli isolated from healthy humans and swine in Northern Thailand. Infect. Drug Resist. 2019, 12, 2201–2214. [Google Scholar] [CrossRef] [Green Version]
  69. Overdevest, I. Extended-Spectrum β-Lactamase Genes of Escherichia coli in Chicken Meat and Humans, The Netherlands. Emerg. Infect. Dis. 2011, 17, 1216–1222. [Google Scholar] [CrossRef]
  70. Gomi, R.; Matsuda, T.; Matsumura, Y.; Yamamoto, M.; Tanaka, M.; Ichiyama, S.; Yoneda, M. Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water. Appl. Environ. Microbiol. 2017, 83, e02703-16. [Google Scholar] [CrossRef] [Green Version]
  71. Rayasam, S.D.G.; Ray, I.; Smith, K.R.; Riley, L.W. Extraintestinal Pathogenic Escherichia coli and Antimicrobial Drug Resistance in a Maharashtrian Drinking Water System. Am. J. Trop. Med. Hyg. 2019, 100, 1101–1104. [Google Scholar] [CrossRef] [Green Version]
  72. Salim, A.; Babu, P.; Mohan, K.; Moorthy, M.; Raj, D.; Kallampillil Thirumeni, S.; Suresh, S.; Madhavan, A.; Nair, B.G.; Chattopadhyay, S.; et al. Draft Genome Sequence of an Escherichia coli Sequence Type 155 Strain Isolated from Sewage in Kerala, India. Microbiol. Resour. Announc. 2019, 8, e01707-18. [Google Scholar] [CrossRef] [Green Version]
  73. Skurnik, D.; Clermont, O.; Guillard, T.; Launay, A.; Danilchanka, O.; Pons, S.; Diancourt, L.; Lebreton, F.; Kadlec, K.; Roux, D.; et al. Emergence of Antimicrobial-Resistant Escherichia coli of Animal Origin Spreading in Humans. Mol. Biol. Evol. 2016, 33, 898–914. [Google Scholar] [CrossRef] [Green Version]
  74. Ramadan, H.; Soliman, A.M.; Hiott, L.M.; Elbediwi, M.; Woodley, T.A.; Chattaway, M.A.; Jenkins, C.; Frye, J.G.; Jackson, C.R. Emergence of Multidrug-Resistant Escherichia coli Producing CTX-M, MCR-1, and FosA in Retail Food from Egypt. Front. Cell. Infect. Microbiol. 2021, 11, 681588. [Google Scholar] [CrossRef] [PubMed]
  75. Liao, X.-P.; Xia, J.; Yang, L.; Li, L.; Sun, J.; Liu, Y.-H.; Jiang, H.-X. Characterization of CTX-M-14-producing Escherichia coli from food-producing animals. Front. Microbiol. 2015, 6, 1136. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  76. Liu, Z.; Li, W.; Wang, J.; Pan, J.; Sun, S.; Yu, Y.; Zhao, B.; Ma, Y.; Zhang, T.; Qi, J.; et al. Identification and Characterization of the First Escherichia coli Strain Carrying NDM-1 Gene in China. PLoS ONE 2013, 8, e66666. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  77. Mohsin, M.; Raza, S.; Schaufler, K.; Roschanski, N.; Sarwar, F.; Semmler, T.; Schierack, P.; Guenther, S. High Prevalence of CTX-M-15-Type ESBL-Producing E. coli from Migratory Avian Species in Pakistan. Front. Microbiol. 2017, 8, 2476. [Google Scholar] [CrossRef] [PubMed]
  78. Aizawa, J.; Neuwirt, N.; Barbato, L.; Neves, P.R.; Leigue, L.; Padilha, J.; Pestana de Castro, A.F.; Gregory, L.; Lincopan, N. Identification of fluoroquinolone-resistant extended-spectrum β-lactamase (CTX-M-8)-producing Escherichia coli ST224, ST2179 and ST2308 in buffalo (Bubalus bubalis). J. Antimicrob. Chemother. 2014, 69, 2866–2869. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  79. Nittayasut, N.; Yindee, J.; Boonkham, P.; Yata, T.; Suanpairintr, N.; Chanchaithong, P. Multiple and High-Risk Clones of Extended-Spectrum Cephalosporin-Resistant and blaNDM-5-Harbouring Uropathogenic Escherichia coli from Cats and Dogs in Thailand. Antibiotics 2021, 10, 1374. [Google Scholar] [CrossRef]
  80. Silva, K.C.; Moreno, M.; Cabrera, C.; Spira, B.; Cerdeira, L.; Lincopan, N.; Moreno, A.M. First Characterization of CTX-M-15-Producing Escherichia coli Strains Belonging to Sequence Type (ST) 410, ST224, and ST1284 from Commercial Swine in South America. Antimicrob. Agents Chemother. 2016, 60, 2505–2508. [Google Scholar] [CrossRef] [Green Version]
  81. RESET Study Group; Pietsch, M.; Irrgang, A.; Roschanski, N.; Brenner Michael, G.; Hamprecht, A.; Rieber, H.; Käsbohrer, A.; Schwarz, S.; Rösler, U.; et al. Whole genome analyses of CMY-2-producing Escherichia coli isolates from humans, animals and food in Germany. BMC Genom. 2018, 19, 601. [Google Scholar] [CrossRef]
  82. Ramadan, H.; Jackson, C.R.; Frye, J.G.; Hiott, L.M.; Samir, M.; Awad, A.; Woodley, T.A. Antimicrobial Resistance, Genetic Diversity and Multilocus Sequence Typing of Escherichia coli from Humans, Retail Chicken and Ground Beef in Egypt. Pathogens 2020, 9, 357. [Google Scholar] [CrossRef]
  83. Leão, C.; Clemente, L.; Moura, L.; Seyfarth, A.M.; Hansen, I.M.; Hendriksen, R.S.; Amaro, A. Emergence and Clonal Spread of CTX-M-65-Producing Escherichia coli From Retail Meat in Portugal. Front. Microbiol. 2021, 12, 653595. [Google Scholar] [CrossRef]
  84. Qiu, J.; Jiang, Z.; Ju, Z.; Zhao, X.; Yang, J.; Guo, H.; Sun, S. Molecular and Phenotypic Characteristics of Escherichia coli Isolates from Farmed Minks in Zhucheng, China. BioMed Res. Int. 2019, 2019, 3917841. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  85. Kamjumphol, W.; Wongboot, W.; Suebwongsa, N.; Kluabwang, P.; Chantaroj, S.; Okada, K. Draft genome sequence of a colistin-resistant Escherichia coli ST226: A clinical strain harbouring an mcr-1 variant. J. Glob. Antimicrob. Resist. 2019, 16, 168–169. [Google Scholar] [CrossRef] [PubMed]
  86. Stoesser, N.; Sheppard, A.E.; Moore, C.E.; Golubchik, T.; Parry, C.M.; Nget, P.; Saroeun, M.; Day, N.P.J.; Giess, A.; Johnson, J.R.; et al. Extensive Within-Host Diversity in Fecally Carried Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli Isolates: Implications for Transmission Analyses. J. Clin. Microbiol. 2015, 53, 2122–2131. [Google Scholar] [CrossRef] [Green Version]
  87. Rodrigues, C.; Machado, E.; Fernandes, S.; Peixe, L.; Novais, Â. An update on faecal carriage of ESBL-producing Enterobacteriaceae by Portuguese healthy humans: Detection of the H 30 subclone of B2-ST131 Escherichia coli producing CTX-M-27: Table 1. J. Antimicrob. Chemother. 2016, 71, 1120–1122. [Google Scholar] [CrossRef] [Green Version]
  88. Papouskova, A.; Masarikova, M.; Valcek, A.; Senk, D.; Cejkova, D.; Jahodarova, E.; Cizek, A. Genomic analysis of Escherichia coli strains isolated from diseased chicken in the Czech Republic. BMC Vet. Res. 2020, 16, 189. [Google Scholar] [CrossRef] [PubMed]
  89. Dadashi, M.; Sameni, F.; Bostanshirin, N.; Yaslianifard, S.; Khosravi-Dehaghi, N.; Nasiri, M.J.; Goudarzi, M.; Hashemi, A.; Hajikhani, B. Global prevalence and molecular epidemiology of mcr-mediated colistin resistance in Escherichia coli clinical isolates: A systematic review. J. Glob. Antimicrob. Resist. 2021, S2213716521002447. [Google Scholar] [CrossRef] [PubMed]
  90. Martak, D.; Guther, J.; Verschuuren, T.D.; Valot, B.; Conzelmann, N.; Bunk, S.; Riccio, M.E.; Salamanca, E.; Meunier, A.; Henriot, C.P.; et al. Populations of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae are different in human-polluted environment and food items: A multicentre European study. Clin. Microbiol. Infect. 2021, S1198743X21004146. [Google Scholar] [CrossRef]
  91. Salgado-Caxito, M.; Benavides, J.A.; Adell, A.D.; Paes, A.C.; Moreno-Switt, A.I. Global prevalence and molecular characterization of extended-spectrum β-lactamase producing-Escherichia coli in dogs and cats—A scoping review and meta-analysis. One Health 2021, 12, 100236. [Google Scholar] [CrossRef]
  92. Falgenhauer, L.; zur Nieden, A.; Harpel, S.; Falgenhauer, J.; Domann, E. Clonal CTX-M-15-Producing Escherichia coli ST-949 Are Present in German Surface Water. Front. Microbiol. 2021, 12, 617349. [Google Scholar] [CrossRef]
  93. Fagerström, A.; Mölling, P.; Khan, F.A.; Sundqvist, M.; Jass, J.; Söderquist, B. Comparative distribution of extended-spectrum beta-lactamase–producing Escherichia coli from urine infections and environmental waters. PLoS ONE 2019, 14, e0224861. [Google Scholar] [CrossRef] [Green Version]
  94. Potel, C.; Ortega, A.; Martínez-Lamas, L.; Bautista, V.; Regueiro, B.; Oteo, J. Interspecies Transmission of the bla OXA-48 Gene from a Klebsiella pneumoniae High-Risk Clone of Sequence Type 147 to Different Escherichia coli Clones in the Gut Microbiota. Antimicrob. Agents Chemother. 2018, 62, e01699-17. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  95. Tahar, S.; Nabil, M.M.; Safia, T.; Ngaiganam, E.P.; Omar, A.; Hafidha, C.; Hanane, Z.; Rolain, J.-M.; Diene, S.M. Molecular Characterization of Multidrug-Resistant Escherichia coli Isolated from Milk of Dairy Cows with Clinical Mastitis in Algeria. J. Food Prot. 2020, 83, 2173–2178. [Google Scholar] [CrossRef] [PubMed]
  96. Bonnedahl, J.; Stedt, J.; Waldenström, J.; Svensson, L.; Drobni, M.; Olsen, B. Comparison of Extended-Spectrum β-Lactamase (ESBL) CTX-M Genotypes in Franklin Gulls from Canada and Chile. PLoS ONE 2015, 10, e0141315. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  97. Alouache, S.; Estepa, V.; Messai, Y.; Ruiz, E.; Torres, C.; Bakour, R. Characterization of ESBLs and Associated Quinolone Resistance in Escherichia coli and Klebsiella pneumoniae Isolates from an Urban Wastewater Treatment Plant in Algeria. Microb. Drug Resist. 2014, 20, 30–38. [Google Scholar] [CrossRef] [PubMed]
  98. Freitas-Silva, J.; Inácio, Â.S.; Mourão, J.; Antunes, P.; Mendes, Â.; de Carvalho, A.P.; Vasconcelos, V.; Peixe, L.; da Costa, P.M. Occurrence of mcr-1 in Escherichia coli from rabbits of intensive farming. Vet. Microbiol. 2018, 227, 78–81. [Google Scholar] [CrossRef] [Green Version]
  99. Chandler, J.C.; Anders, J.E.; Blouin, N.A.; Carlson, J.C.; LeJeune, J.T.; Goodridge, L.D.; Wang, B.; Day, L.A.; Mangan, A.M.; Reid, D.A.; et al. The Role of European Starlings (Sturnus vulgaris) in the Dissemination of Multidrug-Resistant Escherichia coli among Concentrated Animal Feeding Operations. Sci. Rep. 2020, 10, 8093. [Google Scholar] [CrossRef]
  100. Lupo, A.; Saras, E.; Madec, J.-Y.; Haenni, M. Emergence of blaCTX-M-55 associated with fosA, rmtB and mcr gene variants in Escherichia coli from various animal species in France. J. Antimicrob. Chemother. 2018, 73, 867–872. [Google Scholar] [CrossRef]
  101. Belotindos, L.; Villanueva, M.; Miguel, J.; Bwalya, P.; Harada, T.; Kawahara, R.; Nakajima, C.; Mingala, C.; Suzuki, Y. Prevalence and Characterization of Quinolone-Resistance Determinants in Escherichia coli Isolated from Food-Producing Animals and Animal-Derived Food in the Philippines. Antibiotics 2021, 10, 413. [Google Scholar] [CrossRef]
  102. Ali, I.; Rafaque, Z.; Ahmed, I.; Tariq, F.; Graham, S.E.; Salzman, E.; Foxman, B.; Dasti, J.I. Phylogeny, sequence-typing and virulence profile of uropathogenic Escherichia coli (UPEC) strains from Pakistan. BMC Infect. Dis. 2019, 19, 620. [Google Scholar] [CrossRef] [Green Version]
  103. Miotto, M.; Ossai, S.A.; Meredith, J.E.; Barretta, C.; Kist, A.; Prudencio, E.S.; Vieira, C.R.W.; Parveen, S. Genotypic and phenotypic characterization of Escherichia coli isolated from mollusks in Brazil and the United States. Microbiol. Open 2019, 8, e00738. [Google Scholar] [CrossRef] [Green Version]
Microorganisms 10 00808 g001 550
Figure 1. Collection points of farmed and wild Arapaima gigas specimens, State of Macapá, Brazilian Amazon. W: wild, F: Fish farm.
Figure 1. Collection points of farmed and wild Arapaima gigas specimens, State of Macapá, Brazilian Amazon. W: wild, F: Fish farm.
Microorganisms 10 00808 g001
Microorganisms 10 00808 g002 550
Figure 2. PFGE dendogram of demonstrating the genetic relatedness of E. coli isolated from A. gigas in the Brazilian Amazon. F: Fish farm, CUT: Cutias; FG: Ferreira Gomes, MZG: Mazagão; OPQ: Oiapoque; TT: Tartarugalzinho; (A–D): clusters; (A1–C2): subclusters.
Figure 2. PFGE dendogram of demonstrating the genetic relatedness of E. coli isolated from A. gigas in the Brazilian Amazon. F: Fish farm, CUT: Cutias; FG: Ferreira Gomes, MZG: Mazagão; OPQ: Oiapoque; TT: Tartarugalzinho; (A–D): clusters; (A1–C2): subclusters.
Microorganisms 10 00808 g002
Table
Table 1. Antimicrobial susceptibility characteristics of E. coli isolates from farmed and wild A. gigas in the Brazilian Amazon.
Table 1. Antimicrobial susceptibility characteristics of E. coli isolates from farmed and wild A. gigas in the Brazilian Amazon.
AntimicrobialFarmed (n = 16)Wild * (n = 18)
S (%)NS (%)S (%)NS * (%)
AMP 4 (25)12 (75.0)3 (16.6)15 (83.4)
SAM 5 (31.25)11 (68.75)7 (38.9)11 (61.1)
TZP 14 (87.25)2 (12.75)18 (100)0
CXM 4 (25)12 (75.0)6 (33.3)12 (66.7)
FOX 11 (68.75)5 (31.25)7 (38.9)11 (61.1)
CAZ 13 (81.25)3 (18.75)8 (44.4)10 (55.6)
CRO 12 (75)4 (25.0)6 (33.3)12 (66.7)
FEP 15 (93.75)1 (6.25)7 (38.9)11 (61.1)
CIP 016 (100.0)018 (100.0)
S: susceptive; NS: non-susceptive (intermediate and resistant isolates). * Higher frequency of NS isolates (p = 0.005).
Table
Table 2. Phenotypical and molecular resistance features of E. coli strains isolated from Arapaima gigas in the Brazilian Amazon.
Table 2. Phenotypical and molecular resistance features of E. coli strains isolated from Arapaima gigas in the Brazilian Amazon.
SampleSourceResistance ProfileMDRMolecular ProfileVirulenceSTPFGE
01F1AMP, CIP−qnrACommensal448D
02F1AMP, SAM, CRX, CFO, CIP+blaCTX-MCommensal448A1
04F1AMP, CIP−qnrBCommensal448A1
06F1AMP, CIP−qnrBCommensal448A1
07F2AMP, SAM, CIP+qnrACommensal1249A2
08F2AMP, SAM, CIP+qnrACommensal1249A2
09F2AMP, SAM, CIP+ Commensal7973B2
10F2AMP, CIP− Commensal1249NT
12OPQAMP, CIP− Commensal224C1
14OPQAMP, CIP− Commensal224C1
16OPQCIP− Commensal224C1
17OPQCIP− Commensal224C1
18CUTCIP−qnrACommensal155B1
19F3AMP, SAM, CRX, CFO, CRO, CIP+blaCTX-METECNTB1
20F3AMP, SAM, CRX, CFO, CRO, CIP+blaCTX-METEC155NT
21F3CIP−qnrAETEC155B1
27MZGAMP, SAM, CIP+ Commensal4380A3
28MZGAMP, SAM, CIP+ Commensal949A2
30MZGAMP, CRX, CFO, CRO, CIP+ CommensalNTNT
31MZGAMP, CRX, CFO, CAZ, CRO, CPM, CIP+blaCTX-MCommensal4482B
33MZGAMP, CRX, CFO, CAZ, CRO, CPM, CIP+blaCTX-MCommensalNTB1
45F4AMP, SAM, PPT, CRX, CFO, CAZ, CRO, CPM, CIP+blaCTX-MCommensal226C2
46F4AMP, SAM, PPT, CRX, CFO, CAZ, CRO, CIP+blaCTX-MCommensal1431A3
47F4CIP− Commensal224B2
48F4CIP− Commensal1196B1
49F4CIP− Commensal1431A3
50TTAMP, CRX, CFO, CAZ, CRO, CPM, CIP+blaCTX-MCommensal7973C2
51TTAMP, CRX, CFO, CAZ, CRO, CPM, CIP+blaCTX-MCommensal7973C2
52TTAMP, CRX, CFO, CAZ, CRO, CPM, CIP+blaCTX-MCommensal7973C2
53TTAMP, CRX, CFO, CAZ, CRO, CPM, CIP+blaCTX-MCommensal7973C2
54TTAMP, CRX, CFO, CAZ, CRO, CPM, CIP+blaCTX-MCommensal7973C2
56TTAMP, CRX, CFO, CAZ, CRO, CPM, CIP+blaCTX-MCommensal7973C2
66FGAMP, SAM, CRX, CFO, CAZ, CRO, CPM, CIP+blaCTX-MCommensal7973C2
67FGAMP, SAM, CRX, CFO, CAZ, CRO, CPM, CIP+blaCTX-MCommensalNTNT
AMP: Ampicillin, SAM: Ampicillin/Sulbactan, PPT: Piperacillin/Tazobactan, CRX: Cefuroxime, CFO: Cefoxitin, CAZ: Ceftazidime, CRO: Ceftriaxone, CPM: Cefepime, CIP: Ciprofloxacin, OPQ: Oiapoque, CUT: Cutias, MZG: Mazagão, TT: Tartarugalzinho, FG: Ferreira Gomes, ST: sequence type.
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Share and Cite

MDPI and ACS Style

Lima, L.S.; Proietti-Junior, A.A.; Rodrigues, Y.C.; da Silva Vieira, M.C.; Lima, L.N.G.C.; de Oliveira Souza, C.; Dias Gonçalves, V.; de Oliveira Lima, M.; dos Prazeres Rodrigues, D.; Lima, K.V.B. High Genetic Diversity and Antimicrobial Resistance in Escherichia coli Highlight Arapaima gigas (Pisces: Arapaimidae) as a Reservoir of Quinolone-Resistant Strains in Brazilian Amazon Rivers. Microorganisms 2022, 10, 808. https://doi.org/10.3390/microorganisms10040808

AMA Style

Lima LS, Proietti-Junior AA, Rodrigues YC, da Silva Vieira MC, Lima LNGC, de Oliveira Souza C, Dias Gonçalves V, de Oliveira Lima M, dos Prazeres Rodrigues D, Lima KVB. High Genetic Diversity and Antimicrobial Resistance in Escherichia coli Highlight Arapaima gigas (Pisces: Arapaimidae) as a Reservoir of Quinolone-Resistant Strains in Brazilian Amazon Rivers. Microorganisms. 2022; 10(4):808. https://doi.org/10.3390/microorganisms10040808

Chicago/Turabian Style

Lima, Luciana Sampaio, Aldo Aparecido Proietti-Junior, Yan Corrêa Rodrigues, Marcelo Cleyton da Silva Vieira, Luana Nepomuceno Gondim Costa Lima, Cintya de Oliveira Souza, Verônica Dias Gonçalves, Marcelo de Oliveira Lima, Dália dos Prazeres Rodrigues, and Karla Valéria Batista Lima. 2022. "High Genetic Diversity and Antimicrobial Resistance in Escherichia coli Highlight Arapaima gigas (Pisces: Arapaimidae) as a Reservoir of Quinolone-Resistant Strains in Brazilian Amazon Rivers" Microorganisms 10, no. 4: 808. https://doi.org/10.3390/microorganisms10040808

APA Style

Lima, L. S., Proietti-Junior, A. A., Rodrigues, Y. C., da Silva Vieira, M. C., Lima, L. N. G. C., de Oliveira Souza, C., Dias Gonçalves, V., de Oliveira Lima, M., dos Prazeres Rodrigues, D., & Lima, K. V. B. (2022). High Genetic Diversity and Antimicrobial Resistance in Escherichia coli Highlight Arapaima gigas (Pisces: Arapaimidae) as a Reservoir of Quinolone-Resistant Strains in Brazilian Amazon Rivers. Microorganisms, 10(4), 808. https://doi.org/10.3390/microorganisms10040808

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