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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: closed (29 February 2020) | Viewed by 45716

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Special Issue Editor

Dr. Kim Stanford

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Department of Biological Sciences, University of Lethbridge, 4401 University Dr., Lethbridge, AB T1K 3M4, Canada
Interests: food and feed-borne pathogens; Escherichia coli; ergot alkaloids
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Background: Antimicrobial resistance (AMR) in livestock can lead to increased morbidity and mortality of livestock, as well as potentially transferring AMR to humans. As a result, antimicrobial use in livestock production is becoming increasingly regulated and livestock raised without antibiotics are being marketed as a result of consumer concerns.

Goal: Research which explores AMR in livestock is needed to separate marketing campaigns from demonstrated impacts and mechanisms of AMR. Research studies describing the changing patterns of AMR in livestock, mechanisms for transfer of AMR, the potential for transfer of AMR from livestock to humans or vice versa, and impacts of restricting antimicrobial use in livestock on AMR are urgently needed to inform policy decisions.

Scope: The scope of this Special issue is to present the results of research trials and reviews, considering antimicrobial resistance in livestock from a One Health Perspective.

Details for Authors: Original clinical studies in humans and/or livestock and experimental research articles on AMR. Reviews on controlling AMR and treatment options for humans and livestock in light of AMR are welcomed.

Dr. Kim Stanford
Guest Editor

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Keywords

antimicrobial resistance
antimicrobial resistance transfer
antimicrobial use
livestock
animal health
human health

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Published Papers (11 papers)

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Editorial

Jump to: Research, Other

2 pages, 163 KiB

Open AccessEditorial

Special Issue: Antimicrobial Resistance in Livestock

by Kim Stanford

Microorganisms 2020, 8(5), 645; https://doi.org/10.3390/microorganisms8050645 - 28 Apr 2020

Viewed by 1658

Abstract

Antimicrobial resistance threatens the health of both humans and livestock as antimicrobials become continually less effective for controlling infectious disease [...] Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Livestock)

Research

Jump to: Editorial, Other

28 pages, 3630 KiB

Open AccessArticle

Whole Genome Sequencing Differentiates Presumptive Extended Spectrum Beta-Lactamase Producing Escherichia coli along Segments of the One Health Continuum

by Emelia H. Adator, Matthew Walker, Claudia Narvaez-Bravo, Rahat Zaheer, Noriko Goji, Shaun R. Cook, Lisa Tymensen, Sherry J. Hannon, Deirdre Church, Calvin W. Booker, Kingsley Amoako, Celine A. Nadon, Ron Read and Tim A. McAllister

Microorganisms 2020, 8(3), 448; https://doi.org/10.3390/microorganisms8030448 - 22 Mar 2020

Cited by 19 | Viewed by 5447

Abstract

Antimicrobial resistance (AMR) has important implications for the continued use of antibiotics to control infectious diseases in both beef cattle and humans. AMR along the One Health continuum of the beef production system is largely unknown. Here, whole genomes of presumptive extended-spectrum β-lactamase E. coli (ESBL-EC) from cattle feces (n = 40), feedlot catch basins (n = 42), surrounding streams (n = 21), a beef processing plant (n = 4), municipal sewage (n = 30), and clinical patients (n = 25) are described. ESBL-EC were isolated from ceftriaxone selective plates and subcultured on ampicillin selective plates. Agreement of genotype-phenotype prediction of AMR ranged from 93.2% for ampicillin to 100% for neomycin, trimethoprim/sulfamethoxazole, and enrofloxacin resistance. Overall, β-lactam (100%; bla_EC, bla_TEM-1, bla_SHV, bla_OXA, bla_CTX-M-), tetracycline (90.1%; tet(A), tet(B)) and folate synthesis (sul2) antimicrobial resistance genes (ARGs) were most prevalent. The ARGs tet(C), tet(M), tet(32), bla_CTX-M-1, bla_CTX-M-14, bla_OXA-1, dfrA18, dfrA19, catB3, and catB4 were exclusive to human sources, while bla_TEM-150, bla_SHV-11–12_, dfrA12, cmlA1, and cmlA5 were exclusive to beef cattle sources. Frequently encountered virulence factors across all sources included adhesion and type II and III secretion systems, while IncFIB(AP001918) and IncFII plasmids were also common. Specificity and prevalence of ARGs between cattle-sourced and human-sourced presumptive ESBL-EC likely reflect differences in antimicrobial use in cattle and humans. Comparative genomics revealed phylogenetically distinct clusters for isolates from human vs. cattle sources, implying that human infections caused by ESBL-EC in this region might not originate from beef production sources. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Livestock)

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21 pages, 1260 KiB

Open AccessArticle

Antimicrobial Resistance in Members of the Bacterial Bovine Respiratory Disease Complex Isolated from Lung Tissue of Cattle Mortalities Managed with or without the Use of Antimicrobials

by Kim Stanford, Rahat Zaheer, Cassidy Klima, Tim McAllister, Delores Peters, Yan D. Niu and Brenda Ralston

Microorganisms 2020, 8(2), 288; https://doi.org/10.3390/microorganisms8020288 - 20 Feb 2020

Cited by 36 | Viewed by 4627

Abstract

Over a two-year period, Mannheimia haemolytica (MH; n = 113), Pasteurella multocida (PM; n = 47), Histophilus somni (HS; n = 41) and Mycoplasma bovis (MB; n = 227) were isolated from bovine lung tissue at necropsy from cattle raised conventionally (CON, n = 29 feedlots) or without antimicrobials [natural (NAT), n = 2 feedlots]. Excluding MB, isolates were assayed by PCR to detect the presence of 13 antimicrobial resistance (AMR) genes and five core genes associated with integrative and conjugative elements (ICEs). Antimicrobial susceptibility phenotypes and minimum inhibitory concentrations (MICs, µg/mL) were determined for a subset of isolates (MH, n = 104; PM, n = 45; HS, n = 23; and MB, n = 61) using Sensititre analyses. A subset of isolates (n = 21) was also evaluated by whole-genome sequencing (WGS) based on variation in AMR phenotype. All five ICE core genes were detected in PM and HS by PCR, but only 3/5 were present in MH. Presence of mco and tnpA ICE core genes in MH was associated with higher MICs (p < 0.05) for all tetracyclines, and 2/3 of all macrolides, aminoglycosides and fluoroquinolones evaluated. In contrast, association of ICE core genes with MICs was largely restricted to macrolides for PM and to individual tetracyclines and macrolides for HS. For MH, the average number of AMR genes markedly increased (p < 0.05) in year 2 of the study due to the emergence of a strain that was PCR positive for all 13 PCR-tested AMR genes as well as two additional AMR genes (aadA31 and bla_ROB-1) detected by WGS. Conventional management of cattle increased (p < 0.05) MICs of tilmicosin and tulathromycin for MH; neomycin and spectinomycin for PM; and gamithromycin and tulathromycin for MB. The average number of PCR-detected AMR genes in PM was also increased (p < 0.05) in CON mortalities. This study demonstrates increased AMR especially to macrolides by bovine respiratory disease organisms in CON as compared to NAT feedlots and a rapid increase in AMR following dissemination of strain(s) carrying ICE-associated multidrug resistance. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Livestock)

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23 pages, 980 KiB

Open AccessArticle

Antimicrobial Sensitivity Testing of Mycoplasma bovis Isolates Derived from Western Canadian Feedlot Cattle

by Murray Jelinski, Andrea Kinnear, Karen Gesy, Sara Andrés-Lasheras, Rahat Zaheer, Scott Weese and Tim A. McAllister

Microorganisms 2020, 8(1), 124; https://doi.org/10.3390/microorganisms8010124 - 16 Jan 2020

Cited by 25 | Viewed by 4969

Abstract

Mycoplasma bovis is particularly adept at evading the immune system, resulting in chronic infections of the lungs and joints of feedlot cattle. The chronicity of the lesions results in prolonged antimicrobial therapy, possibly exacerbating antimicrobial resistance. This cross-sectional study generated in vitro antimicrobial susceptibility testing (AST) data on 211 M. bovis isolates recovered from 159 healthy, diseased, and dead cattle, spanning the period of 2006–2018. Nine antimicrobials commonly administered to western Canadian feedlot cattle were assessed. The data were analyzed with non-parametric statistical tests with a level of significance of p < 0.05 (two-tailed). Minimum inhibitory concentration (MIC) values tended to increase between the isolates from healthy versus dead cattle and over time (2006–2018). Isolates from dead versus healthy cattle were more likely to be resistant to tulathromycin, gamithromycin, tylosin and enrofloxacin. There was no difference in the distributions of the MICs generated from the isolates recovered from the lungs and joints (p ≥ 0.124) and the lungs and deep nasal passages (p ≥ 0.157) of the same animals. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Livestock)

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21 pages, 5004 KiB

Open AccessArticle

Tetracycline Resistant Campylobacter jejuni Subtypes Emanating from Beef Cattle Administered Non-Therapeutic Chlortetracycline are Longitudinally Transmitted within the Production Continuum but are Not Detected in Ground Beef

by G. Douglas Inglis, Jenny F. Gusse, Kathaleen E. House, Tara G. Shelton and Eduardo N. Taboada

Microorganisms 2020, 8(1), 23; https://doi.org/10.3390/microorganisms8010023 - 21 Dec 2019

Cited by 10 | Viewed by 2783

Abstract

The impacts of the antimicrobial growth promoter (AGP), chlortetracycline with sulfamethazine (AS700), on the development of antimicrobial resistance and longitudinal transmission of Campylobacter jejuni within the beef production continuum were empirically determined. Carriage of tetracycline resistance determinants in the enteric bacterial community increased at a greater rate for AS700-treatment cattle. The majority of the bacteria from animals administered AS700 carried tetW. Densities of C. jejuni shed in feces increased over the confined feeding period, and the administration of AS700 did not conspicuously reduce C. jejuni densities in feces or within the intestine. The majority of C. jejuni isolates recovered were resistant to tetracycline, but the resistance rates to other antibiotics was low (≤20.1%). The richness of C. jejuni subtypes recovered from AS700-treated animals that were either resistant or susceptible to tetracycline was reduced, indicating selection pressure due to AGP administration. Moreover, a degree of subtype-specific resistance to tetracycline was observed. tetO was the primary tetracycline resistance determinant conferring resistance in C. jejuni isolates recovered from cattle and people. Clinically-relevant C. jejuni subtypes (subtypes that represent a risk to human health) that were resistant to tetracycline were isolated from cattle feces, digesta, hides, the abattoir environment, and carcasses, but not from ground beef. Thus, study findings indicate that clinically-relevant C. jejuni subtypes associated with beef cattle, including those resistant to antibiotics, do not represent a significant foodborne risk. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Livestock)

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11 pages, 819 KiB

Open AccessArticle

Listeria monocytogenes in Export-approved Beef from Mato Grosso, Brazil: Prevalence, Molecular Characterization and Resistance to Antibiotics and Disinfectants

by Larrayane A.C. Teixeira, Fernanda T. Carvalho, Deyse C. Vallim, Rodrigo C.L. Pereira, Adelino Cunha Neto, Bruno S. Vieira, Ricardo C.T. Carvalho and Eduardo E.S. Figueiredo

Microorganisms 2020, 8(1), 18; https://doi.org/10.3390/microorganisms8010018 - 20 Dec 2019

Cited by 19 | Viewed by 4699

Abstract

The Brazilian state of Mato Grosso is the largest producer and exporter of beef in the country, but few studies of relevance have been conducted to evaluate the microbiological safety of its products. This study aimed to estimate the prevalence of Listeria monocytogenes (LM) in export-approved beef from Mato Grosso and to characterize the isolates in terms of molecular properties and antimicrobial resistance. From a total of 50 samples analyzed, Listeria sp. was isolated in 18 (36% prevalence). Listeria monocytogenes was confirmed in 6 (12% prevalence). Among the serotype groups assessed by multiplex PCR, serotype 4 (4b, 4d or 4e) was the most prevalent. Although antibiotic resistance was not an issue, two strains isolated from different plants showed high resistance to sodium hypochlorite. Overall, this scenario causes concern because it puts at risk not only the Brazilian customer, but also the population of countries that import beef from Mato Grosso. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Livestock)

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19 pages, 280 KiB

Open AccessArticle

Identification, Genotyping and Antimicrobial Susceptibility Testing of Brucella spp. Isolated from Livestock in Egypt

by Aman Ullah Khan, Waleed S. Shell, Falk Melzer, Ashraf E. Sayour, Eman Shawkat Ramadan, Mandy C. Elschner, Amira A. Moawad, Uwe Roesler, Heinrich Neubauer and Hosny El-Adawy

Microorganisms 2019, 7(12), 603; https://doi.org/10.3390/microorganisms7120603 - 22 Nov 2019

Cited by 28 | Viewed by 4669

Abstract

Brucellosis is a highly contagious zoonosis worldwide with economic and public health impacts. The aim of the present study was to identify Brucella (B.) spp. isolated from animal populations located in different districts of Egypt and to determine their antimicrobial resistance. In total, 34-suspected Brucella isolates were recovered from lymph nodes, milk, and fetal abomasal contents of infected cattle, buffaloes, sheep, and goats from nine districts in Egypt. The isolates were identified by microbiological methods and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Differentiation and genotyping were confirmed using multiplex PCR for B. abortus, Brucella melitensis, Brucella ovis, and Brucella suis (AMOS) and Bruce-ladder PCR. Antimicrobial susceptibility testing against clinically used antimicrobial agents (chloramphenicol, ciprofloxacin, erythromycin, gentamicin, imipenem, rifampicin, streptomycin, and tetracycline) was performed using E-Test. The antimicrobial resistance-associated genes and mutations in Brucella isolates were confirmed using molecular tools. In total, 29 Brucella isolates (eight B. abortus biovar 1 and 21 B. melitensis biovar 3) were identified and typed. The resistance of B. melitensis to ciprofloxacin, erythromycin, imipenem, rifampicin, and streptomycin were 76.2%, 19.0%, 76.2%, 66.7%, and 4.8%, respectively. Whereas, 25.0%, 87.5%, 25.0%, and 37.5% of B. abortus were resistant to ciprofloxacin, erythromycin, imipenem, and rifampicin, respectively. Mutations in the rpoB gene associated with rifampicin resistance were identified in all phenotypically resistant isolates. Mutations in gyrA and gyrB genes associated with ciprofloxacin resistance were identified in four phenotypically resistant isolates of B. melitensis. This is the first study highlighting the antimicrobial resistance in Brucella isolated from different animal species in Egypt. Mutations detected in genes associated with antimicrobial resistance unravel the molecular mechanisms of resistance in Brucella isolates from Egypt. The mutations in the rpoB gene in phenotypically resistant B. abortus isolates in this study were reported for the first time in Egypt. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Livestock)

13 pages, 1857 KiB

Open AccessArticle

Characteristics of a Colistin-Resistant Escherichia coli ST695 Harboring the Chromosomally-Encoded mcr-1 Gene

by Zhong Peng, Zizhe Hu, Zugang Li, Xiaosong Li, Chaoying Jia, Xiaoxue Zhang, Bin Wu, Huanchun Chen and Xiangru Wang

Microorganisms 2019, 7(11), 558; https://doi.org/10.3390/microorganisms7110558 - 12 Nov 2019

Cited by 14 | Viewed by 4486

Abstract

Enterobacteriaceae having chromosomally-encoded mcr-1 is rarely reported. In this study, we recovered a chromosomal mcr-1 carrying Escherichia coli, designated HeN100, from the feces of a diarrheal pig in China. Antimicrobial susceptibility testing showed that HeN100 was resistant to three aminoglycosides, twelve β-lactams including three carbapenems, one phenicol, two tetracyclines, two fluoroquinolones, nitrofurantoin, and colistin tested. Oxford Nanopore MinION sequencing revealed that the complete genomes of the multidrug resistant (MDR) HeN100 consisted of a single circular chromosome and five circular plasmids. Bioinformatical analysis determined HeN100 as ST695 and it contained many acquired resistance genes responsible for its MDR phenotypes, including colistin resistance mcr-1 and the carbapenem resistance bla_NDM-1, and most of these genes were located on plasmids. However, the mcr-1 was found on the chromosome, and it was located between an IS30-like element ISApl1 and a PAP2-like encoding gene. These three genes consisted of an “ISApl1-mcr-1-orf” segment and inserted in high AT-rich regions. Finally, we found the bla_NDM-1 was carried on an IncFII type conjugative plasmid. The conjugation frequency of this plasmid was 7.61 ± 2.11 × 10⁻⁵ per recipient, and its conjugation conferred resistance to carbapenems and other β-lactams, as well as aminoglycosides. The spread of this mcr-1/bla_NDM-1-carrying E. coli ST695 represents a great concern of public health. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Livestock)

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14 pages, 1718 KiB

Open AccessArticle

Characteristics of Carbapenem-Resistant and Colistin-Resistant Escherichia coli Co-Producing NDM-1 and MCR-1 from Pig Farms in China

by Zhong Peng, Xiaosong Li, Zizhe Hu, Zugang Li, Yujin Lv, Minggang Lei, Bin Wu, Huanchun Chen and Xiangru Wang

Microorganisms 2019, 7(11), 482; https://doi.org/10.3390/microorganisms7110482 - 23 Oct 2019

Cited by 34 | Viewed by 4858

Abstract

The emergence of carbapenem-resistant and colistin-resistant Enterobacteriaceae represents a great risk for public health. In this study, the phenotypical and genetic characteristics of eight carbapenem-resistant and colistin-resistant isolates from pig farms in China were determined by the broth microdilution method and whole genome sequencing. Antimicrobial susceptibility testing showed that the eight carbapenem-resistant and colistin-resistant strains were resistant to three aminoglycosides, twelve β-lactams, one of the phenicols, one of the tetracyclines, and one of the fluoroquinolones tested, simultaneously. The prediction of acquired resistant genes using the whole genome sequences revealed the co-existence of bla_NDM-1 and mcr-1 as well as the other genes that were responsible for the multidrug-resistant phenotypes. Bioinformatics analysis also showed that the carbapenem-resistant gene bla_NDM-1 was located on a putative IncFII-type plasmid, which also carried the other acquired resistant genes identified, including fosA3, blaTEM-1B and rmtB, while the colistin-resistant gene mcr-1 was carried by a putative IncX4-type plasmid. Finally, we found that these resistant genes/plasmids were conjugative, and they could be co-conjugated, conferring resistance to multiple types of antibiotics, including the carbapenems and colistin, to the recipient Escherichia coli strains. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Livestock)

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19 pages, 1473 KiB

Open AccessArticle

Characterization of Non-O157 Escherichia coli from Cattle Faecal Samples in the North-West Province of South Africa

by Emmanuel W. Bumunang, Tim A. McAllister, Rahat Zaheer, Rodrigo Ortega Polo, Kim Stanford, Robin King, Yan D. Niu and Collins N. Ateba

Microorganisms 2019, 7(8), 272; https://doi.org/10.3390/microorganisms7080272 - 20 Aug 2019

Cited by 40 | Viewed by 4987

Abstract

Escherichia coli are commensal bacteria in the gastrointestinal tract of mammals, but some strains have acquired Shiga-toxins and can cause enterohemorrhagic diarrhoea and kidney failure in humans. Shiga-toxigenic E. coli (STEC) strains such as E. coli O157:H7 and some non-O157 strains also contain other virulence traits, some of which contribute to their ability to form biofilms. This study characterized non-O157 E. coli from South African cattle faecal samples for their virulence potential, antimicrobial resistance (AMR), biofilm-forming ability, and genetic relatedness using culture-based methods, pulsed-field gel electrophoresis (PFGE), and whole genome sequencing (WGS). Of 80 isolates screened, 77.5% (62/80) possessed Shiga-toxins genes. Of 18 antimicrobials tested, phenotypic resistance was detected against seven antimicrobials. Resistance ranged from 1.3% (1/80) for ampicillin-sulbactam to 20% (16/80) for tetracycline. Antimicrobial resistance genes were infrequently detected except for tetA, which was found in 31.3% (25/80) and tetB detected in 11.3% (9/80) of isolates. Eight biofilm-forming associated genes were detected in STEC isolates (n = 62) and two non-STEC strains. Prevalence of biofilm genes ranged from 31.3% (20/64) for ehaA^β passenger to 100% for curli structural subunit (csgA) and curli regulators (csgA and crl). Of the 64 STEC and multi-drug resistant isolates, 70.3% (45/64) and 37.5% (24/64) formed strong biofilms on polystyrene at 22 and 37 °C, respectively. Of 59 isolates screened by PFGE, 37 showed unique patterns and the remaining isolates were grouped into five clusters with a ≥90% relatedness. In silico serotyping following WGS on a subset of 24 non-O157 STEC isolates predicted 20 serotypes comprising three novel serotypes, indicating their diversity as potential pathogens. These findings show that North West South African cattle harbour genetically diverse, virulent, antimicrobial-resistant and biofilm-forming non-O157 E. coli. Biofilm-forming ability may increase the likelihood of persistence of these pathogens in the environment and facilitate their dissemination, increasing the risk of cross contamination or establishment of infections in hosts. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Livestock)

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