Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae

AbstractDiphtheria is a respiratory disease caused by the bacterium Corynebacterium diphtheriae. Although the development of a toxin-based vaccine in the 1930s has allowed a high level of control over the disease, cases have increased in recent years. Here, we describe the genomic variation of 502 C. diphtheriae isolates across 16 countries and territories over 122 years. We generate a core gene phylogeny and determine the presence of antimicrobial resistance genes and variation within the tox gene of 291 tox+ isolates. Numerous, highly diverse clusters of C. diphtheriae are observed across the phylogeny, each containing isolates from multiple countries, regions and time of isolation. The number of antimicrobial resistance genes, as well as the breadth of antibiotic resistance, is substantially greater in the last decade than ever before. We identified and analysed 18 tox gene variants, with mutations estimated to be of medium to high structural impact.

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Multiple-Antibiotic Resistance of Enterococcus faecalis and Enterococcus faecium from Cecal Contents in Broiler Chicken and Turkey Flocks Slaughtered in Canada and Plasmid Colocalization of tetO and ermB Genes

Journal of Food Protection ◽

10.4315/0362-028x.jfp-10-451 ◽

2011 ◽

Vol 74 (10) ◽

pp. 1639-1648 ◽

Cited By ~ 33

Author(s):

CINDY-LOVE TREMBLAY ◽

ANN LETELLIER ◽

SYLVAIN QUESSY ◽

MARTINE BOULIANNE ◽

DANIELLE DAIGNAULT ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Enterococcus Faecalis ◽

Resistance Genes ◽

Enterococcus Faecium ◽

Broiler Chicken ◽

Multidrug Resistant ◽

Poultry Meat ◽

Antimicrobial Resistance Genes ◽

High Level ◽

Level Resistance

This study was conducted to characterize the antimicrobial resistance determinants and investigate plasmid colocalization of tetracycline and macrolide genes in Enterococcus faecalis and Enterococcus faecium from broiler chicken and turkey flocks in Canada. A total of 387 E. faecalis and E. faecium isolates were recovered from poultry cecal contents from five processing plants. The percentages of resistant E. faecalis and E. faecium isolates, respectively, were 88.1 and 94% to bacitracin, 0 and 0.9% to chloramphenicol, 0.7 and 14.5% to ciprofloxacin, 72.6 and 80.3% to erythromycin, 3.7 and 41% to flavomycin, 9.6 and 4.3% (high-level resistance) to gentamicin, 25.2 and 17.1% (high-level resistance) to kanamycin, 100 and 94% to lincomycin, 0 and 0% to linezolid, 2.6 and 20.5% to nitrofurantoin, 3 and 27.4% to penicillin, 98.5 and 89.7% to quinupristin-dalfopristin, 7 and 12.8% to salinomycin, 46.7 and 38.5% (high-level resistance) to streptomycin, 95.6 and 89.7% to tetracycline, 73 and 75.2% to tylosin, and 0 and 0% to vancomycin. One predominant multidrug-resistant phenotypic pattern was identified in both E. faecalis and E. faecium (bacitracin, erythromycin, lincomycin, quinupristin-dalfopristin, tetracycline, and tylosin). These isolates were further examined by PCR and sequencing for the genes encoding their antimicrobial resistance. Various combinations of vatD, vatE, bcrR, bcrA, bcrB, bcrD, ermB, msrC, linB, tetM, and tetO genes were detected, and ermB, tetM, and bcrB were the most common antimicrobial resistance genes identified. For the first time, plasmid extraction and hybridization revealed colocalization of tetO and ermB genes on a ca. 11-kb plasmid in E. faecalis isolates, and filter mating experiments demonstrated its transferability. Results indicate that the intestinal enterococci of healthy poultry, which can contaminate poultry meat at slaughter, could be a reservoir for quinupristin-dalfopristin, bacitracin, tetracycline, and macrolide resistance genes.

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Detection and prevalence of antimicrobial resistance genes in Campylobacter spp. isolated from chickens and humans

Onderstepoort Journal of Veterinary Research ◽

10.4102/ojvr.v84i1.1411 ◽

2017 ◽

Vol 84 (1) ◽

Cited By ~ 13

Author(s):

Samantha Reddy ◽

Oliver T. Zishiri

Keyword(s):

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Pathogenic Bacteria ◽

Antibiotic Resistance Genes ◽

Quinolone Resistance ◽

Campylobacter Coli ◽

Antimicrobial Resistance Genes ◽

Campylobacter Spp ◽

Clinical Cases

Campylobacter spp. are common pathogenic bacteria in both veterinary and human medicine. Infections caused by Campylobacter spp. are usually treated using antibiotics. However, the injudicious use of antibiotics has been proven to spearhead the emergence of antibiotic resistance. The purpose of this study was to detect the prevalence of antibiotic resistance genes in Campylobacter spp. isolated from chickens and human clinical cases in South Africa. One hundred and sixty one isolates of Campylobacter jejuni and Campylobacter coli were collected from chickens and human clinical cases and then screened for the presence of antimicrobial resistance genes. We observed a wide distribution of the tetO gene, which confers resistance to tetracycline. The gyrA genes that are responsible quinolone resistance were also detected. Finally, our study also detected the presence of the blaOXA-61, which is associated with ampicillin resistance. There was a higher (p < 0.05) prevalence of the studied antimicrobial resistance genes in chicken faeces compared with human clinical isolates. The tetO gene was the most prevalent gene detected, which was isolated at 64% and 68% from human and chicken isolates, respectively. The presence of gyrA genes was significantly (p < 0.05) associated with quinolone resistance. In conclusion, this study demonstrated the presence of gyrA (235 bp), gyrA (270 bp), blaOXA-61 and tetO antimicrobial resistance genes in C. jejuni and C. coli isolated from chickens and human clinical cases. This indicates that Campylobacter spp. have the potential of resistance to a number of antibiotic classes.

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Unravelling native plant resistomes – The Sphagnum microbiome harbours versatile and novel antimicrobial resistance genes

10.1101/695973 ◽

2019 ◽

Cited By ~ 1

Author(s):

Melanie-Maria Obermeier ◽

Julian Taffner ◽

Alessandro Bergna ◽

Anja Poehlein ◽

Tomislav Cernava ◽

...

Keyword(s):

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Resistance Mechanisms ◽

Culture Collection ◽

Metagenomic Data ◽

Native Plant ◽

Resistance Determinants ◽

Target Spectrum ◽

Antimicrobial Resistance Genes

The expanding antibiotic resistance crisis calls for a more in depth understanding of the importance of antimicrobial resistance genes (ARGs) in pristine environments. We, therefore, studied the microbiota associated with Sphagnum forming the main vegetation in undomesticated, evolutionary old bog ecosystems. In our complementary analysis of a culture collection, metagenomic data and a fosmid library, we identified a low abundant but highly diverse pool of resistance determinants, which targets an unexpected broad range of antibiotics including natural and synthetic compounds. This derives both, from the extraordinarily high abundance of efflux pumps (80%), and the unexpectedly versatile set of ARGs underlying all major resistance mechanisms. The overall target spectrum of detected resistance determinants spans 21 antibiotic classes, whereby β-lactamases and vancomycin resistance appeared as the predominant resistances in all screenings. Multi-resistance was frequently observed among bacterial isolates, e.g. in Serratia, Pandorea, Paraburkhotderia and Rouxiella. In a search for novel ARGs we identified the new class A β-lactamase Mm3. The native Sphagnum resistome comprising a highly diversified and partially novel set of ARGs contributes to the bog ecosystem’s plasticity. Our results shed light onto the antibiotic resistance background of non-agricultural plants and highlight the ecological link between natural and clinically relevant resistomes.

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First Report of Coexistence of blaSFO–1 and blaNDM–1 β-Lactamase Genes as Well as Colistin Resistance Gene mcr-9 in a Transferrable Plasmid of a Clinical Isolate of Enterobacter hormaechei

Frontiers in Microbiology ◽

10.3389/fmicb.2021.676113 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wenxiu Ai ◽

Ying Zhou ◽

Bingjie Wang ◽

Qing Zhan ◽

Longhua Hu ◽

...

Keyword(s):

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Clinical Isolate ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Mobile Elements ◽

Conjugative Plasmid ◽

S1 Nuclease ◽

Antimicrobial Resistance Genes ◽

Enterobacter Hormaechei

Many antimicrobial resistance genes usually located on transferable plasmids are responsible for multiple antimicrobial resistance among multidrug-resistant (MDR) Gram-negative bacteria. The aim of this study is to characterize a carbapenemase-producing Enterobacter hormaechei 1575 isolate from the blood sample in a tertiary hospital in Wuhan, Hubei Province, China. Antimicrobial susceptibility test showed that 1575 was an MDR isolate. The whole genome sequencing (WGS) and comparative genomics were used to deeply analyze the molecular information of the 1575 and to explore the location and structure of antibiotic resistance genes. The three key resistance genes (blaSFO–1, blaNDM–1, and mcr-9) were verified by PCR, and the amplicons were subsequently sequenced. Moreover, the conjugation assay was also performed to determine the transferability of those resistance genes. Plasmid files were determined by the S1 nuclease pulsed-field gel electrophoresis (S1-PFGE). WGS revealed that p1575-1 plasmid was a conjugative plasmid that possessed the rare coexistence of blaSFO–1, blaNDM–1, and mcr-9 genes and complete conjugative systems. And p1575-1 belonged to the plasmid incompatibility group IncHI2 and multilocus sequence typing ST102. Meanwhile, the pMLST type of p1575-1 was IncHI2-ST1. Conjugation assay proved that the MDR p1575-1 plasmid could be transferred to other recipients. S1-PFGE confirmed the location of plasmid with molecular weight of 342,447 bp. All these three resistant genes were flanked by various mobile elements, indicating that the blaSFO–1, blaNDM–1, and mcr-9 could be transferred not only by the p1575-1 plasmid but also by these mobile elements. Taken together, we report for the first time the coexistence of blaSFO–1, blaNDM–1, and mcr-9 on a transferable plasmid in a MDR clinical isolate E. hormaechei, which indicates the possibility of horizontal transfer of antibiotic resistance genes.

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Mobilization of tet (X4) by IS 1 family elements in porcine Esc herichia coli isolates

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01597-21 ◽

2021 ◽

Author(s):

Runhao Yu ◽

Zheng Chen ◽

Stefan Schwarz ◽

Hong Yao ◽

Xiang-Dang Du

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Suicide Plasmid ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

High Level

The dissemination mechanism of the high-level tigecycline resistance gene tet (X4) in porcine Escherichia coli was investigated . tet (X4) and other antimicrobial resistance genes were located on the plasmids p1919D3-1 and p1919D62-1 and flanked by two or three copies of IS 1 family elements, which can form one to three translocatable units (TUs). Using a reduced transposition model, IS 1A was experimentally demonstrated to mediate the transposition of tet (X4) from a suicide plasmid into the E. coli chromosome.

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Antimicrobial Resistance Genes in Enterotoxigenic Escherichia coli O149:K91 Isolates Obtained over a 23-Year Period from Pigs

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.47.10.3214-3221.2003 ◽

2003 ◽

Vol 47 (10) ◽

pp. 3214-3221 ◽

Cited By ~ 161

Author(s):

Christine Maynard ◽

John M. Fairbrother ◽

Sadjia Bekal ◽

François Sanschagrin ◽

Roger C. Levesque ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Antimicrobial Agents ◽

Enterotoxigenic Escherichia Coli ◽

Genotypic Resistance ◽

Class 1 Integron ◽

Phenotypic Resistance ◽

Antimicrobial Resistance Genes

ABSTRACT A total of 112 Escherichia coli O149:K91 strains isolated from pigs with diarrhea in Quebec, Canada, between 1978 and 2000 were characterized for their genotypic antimicrobial resistance profiles. Tests for resistance to 10 antimicrobial agents were conducted. Resistance to tetracycline and sulfonamides was found to be the most frequent, but resistance to cefotaxime and ceftiofur was absent. An increase in the number of isolates resistant to at least three antimicrobials was observed over time. The distribution of 28 resistance genes covering six antimicrobial families (beta-lactams, aminoglycosides, phenicols, tetracycline, trimethoprim, and sulfonamides) was assessed by colony hybridization. Significant differences in the distributions of tetracycline [tet(A), tet(B), tet(C)], trimethoprim (dhfrI, dhfrV, dhfrXIII), and sulfonamide (sulI, sulII) resistance genes were observed during the study period (1978 to 2000). Sixty percent of the isolates possessed a class 1 integron, illustrating the importance of integrons in the epidemiology of antibiotic resistance in E. coli strains from pigs. Amplification of the integron's variable region resulted in four distinct fragments of 1, 1.3, 1.6, and 1.8 kb, with the 1.6- and 1.8-kb fragments appearing only during the last half of the study period. Examination of linkages among the different resistance genes showed a variety of positive and negative associations. Association analysis of isolates divided into two groups, those isolated between 1978 and 1989 and those isolated between 1990 and 2000, revealed the appearance of new positive resistance gene associations. Our genotypic resistance analyses of ETEC isolates from pigs indicate that many of the antibiotic resistance genes behind phenotypic resistance are not static but, rather, are in a state of flux driven by various selection forces such as the use of specific antimicrobials.

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Extensive antimicrobial resistance mobilization via multicopy plasmid encapsidation mediated by temperate phages

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa311 ◽

2020 ◽

Vol 75 (11) ◽

pp. 3173-3180

Author(s):

Lorena Rodríguez-Rubio ◽

Carlos Serna ◽

Manuel Ares-Arroyo ◽

Bosco R Matamoros ◽

Jose F Delgado-Blas ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

High Efficiency ◽

Marker Gene ◽

Multicopy Plasmid ◽

Aminoglycoside Resistance ◽

Plasmid Copy ◽

Antimicrobial Resistance Genes ◽

Complete Sequences ◽

High Level

Abstract Objectives To investigate the relevance of multicopy plasmids in antimicrobial resistance and assess their mobilization mediated by phage particles Methods Several databases with complete sequences of plasmids and annotated genes were analysed. The 16S methyltransferase gene armA conferring high-level aminoglycoside resistance was used as a marker in eight different plasmids, from different incompatibility groups, and with differing sizes and plasmid copy numbers. All plasmids were transformed into Escherichia coli bearing one of four different lysogenic phages. Upon induction, encapsidation of armA in phage particles was evaluated using qRT–PCR and Southern blotting. Results Multicopy plasmids carry a vast set of emerging clinically important antimicrobial resistance genes. However, 60% of these plasmids do not bear mobility (MOB) genes. When carried on these multicopy plasmids, mobilization of a marker gene armA into phage capsids was up to 10000 times more frequent than when it was encoded by a large plasmid with a low copy number. Conclusions Multicopy plasmids and phages, two major mobile genetic elements (MGE) in bacteria, represent a novel high-efficiency transmission route of antimicrobial resistance genes that deserves further investigation.

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Withdraw of prophylactic antimicrobials does not change resistome in pigs

10.21203/rs.2.18011/v1 ◽

2019 ◽

Author(s):

Maria Fernanda Loayza Villa ◽

Alejandro Torres ◽

Lixin Zhang ◽

Gabriel Trueba

Keyword(s):

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Resistant Bacteria ◽

Productive Performance ◽

Fitness Costs ◽

Antibiotic Resistant ◽

Human Microbiota ◽

Antimicrobial Resistance Genes ◽

The Impact

Abstract Background: The use of antimicrobials in the animal industry has increased the prevalence of antibiotic resistant bacteria and antimicrobial-resistance genes which can be transferred to human microbiota through the food chain or the environment. To reduce the influx of antibiotic-resistance to the human microbiota, restrictions on antimicrobials (in food animals) have been implemented in different countries. We investigated the impact of an antimicrobial restriction on the frequency of antimicrobial-resistant bacteria in pigs (PCI 1050) from an Ecuadorian farm. Results: No differences in antimicrobial resistant coliforms or antimicrobial resistance genes (richness and abundance) were found when we compared animals fed with or without antibiotics. Nevertheless, the absence of antimicrobials in pigs didn’t impact the productive performance of animals. Conclusion: Fitness costs of antimicrobial resistance in bacteria within intestinal microbiota of animals seems to be overestimated. Avoiding antimicrobials as prophylactics in pigs fed is not enough to control maintenance and spread of antimicrobial resistance.

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Long-Read Sequencing Reveals Evolution and Acquisition of Antimicrobial Resistance and Virulence Genes in Salmonella enterica

Frontiers in Microbiology ◽

10.3389/fmicb.2021.777817 ◽

2021 ◽

Vol 12 ◽

Author(s):

Cong Li ◽

Gregory H. Tyson ◽

Chih-Hao Hsu ◽

Lucas Harrison ◽

Errol Strain ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Salmonella Enterica ◽

Heavy Metal Resistance ◽

Multidrug Resistant ◽

Metal Resistance ◽

Virulence Plasmids ◽

Antimicrobial Resistance Genes ◽

Long Read ◽

High Level

Salmonella enterica is a significant and phylogenetically diverse zoonotic pathogen. To understand its genomic heterogeneity and antimicrobial resistance, we performed long-read sequencing on Salmonella isolated from retail meats and food animals. A collection of 134 multidrug-resistant isolates belonging to 33 serotypes were subjected to PacBio sequencing. One major locus of diversity among these isolates was the presence and orientation of Salmonella pathogenic islands (SPI), which varied across different serotypes but were largely conserved within individual serotypes. We also identified insertion of an IncQ resistance plasmid into the chromosome of fourteen strains of serotype I 4,[5],12:i:– and the Salmonella genomic island 1 (SGI-1) in five serotypes. The presence of various SPIs, SGI-1 and integrated plasmids contributed significantly to the genomic variability and resulted in chromosomal resistance in 55.2% (74/134) of the study isolates. A total of 93.3% (125/134) of isolates carried at least one plasmid, with isolates carrying up to seven plasmids. We closed 233 plasmid sequences of thirteen replicon types, along with twelve hybrid plasmids. Some associations between Salmonella isolate source, serotype, and plasmid type were seen. For instance, IncX plasmids were more common in serotype Kentucky from retail chicken. Plasmids IncC and IncHI had on average more than five antimicrobial resistance genes, whereas in IncX, it was less than one per plasmid. Overall, 60% of multidrug resistance (MDR) strains that carried >3 AMR genes also carried >3 heavy metal resistance genes, raising the possibility of co-selection of antimicrobial resistance in the presence of heavy metals. We also found nine isolates representing four serotypes that carried virulence plasmids with the spv operon. Together, these data demonstrate the power of long-read sequencing to reveal genomic arrangements and integrated plasmids with a high level of resolution for tracking and comparing resistant strains from different sources. Additionally, the findings from this study will help expand the reference set of closed Salmonella genomes that can be used to improve genome assembly from short-read data commonly used in One Health antimicrobial resistance surveillance.

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Antibiotic Resistance Genes and Associated Phenotypes in Escherichia coli and Enterococcus from Cattle at Different Production Stages on a Dairy Farm in Central California

Antibiotics ◽

10.3390/antibiotics10091042 ◽

2021 ◽

Vol 10 (9) ◽

pp. 1042

Author(s):

Saharuetai Jeamsripong ◽

Xunde Li ◽

Sharif S. Aly ◽

Zhengchang Su ◽

Richard V. Pereira ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Wide Spectrum ◽

Cross Sectional ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

Enterococcus Spp ◽

Production Stages

The objectives of this study were to characterize overall genomic antibiotic resistance profiles of fecal Escherichia coli and Enterococcus spp. from dairy cattle at different production stages using whole-genome sequencing and to determine the association between antimicrobial resistance (AMR) phenotypes and their corresponding genotypes. The Comprehensive Antibiotic Resistance Database (CARD) and ResFinder, two publicly available databases of antimicrobial resistance genes, were used to annotate isolates. Based on the ResFinder database, 27.5% and 20.0% of tested E. coli isolates (n = 40) harbored single and ≥3 antimicrobial resistance genes, respectively; for Enterococcus spp., we observed 87.8% and 8.2%, respectively. The highest prevalence of AMR genes in E. coli was for resistance to tetracycline (27.5%), followed by sulphonamide (22.5%) and aminoglycoside (20.0%); the predominant antimicrobial resistance genes in Enterococcus spp. targeted macrolide drugs (77.6%). Based on the CARD database, resistance to ≥3 antimicrobial classes was observed in all E. coli and 77.6% in Enterococcus spp. isolates. A high degree of agreement existed between the resistance phenotype and the presence of resistance genes for various antimicrobial classes for E. coli but much less so for isolates of Enterococcus. Consistent with prior work, fecal E. coli and Enterococcus spp. isolates from calves harbored a wide spectrum of resistance genes, compared to those from cattle at other production stages, based on the cross-sectional samples from the studied farm.

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