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Gu G, Pei H, Zhou A, Fan B, Zhou H, Choi A, Huang Z. A Comprehensive Study of Historical Detection Data for Pathogen Isolates from U.S. Cattle. Antibiotics (Basel) 2023; 12:1509. [PMID: 37887210 PMCID: PMC10604524 DOI: 10.3390/antibiotics12101509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Foodborne pathogens pose substantial health hazards and result in considerable economic losses in the U.S. Fortunately, the National Center for Biotechnology Information Pathogen Detection Isolates Browser (NPDIB) provides valuable access to antimicrobial resistance (AMR) genes and antimicrobial assay data. This study aimed to conduct the first comprehensive investigation of AMR genes in pathogens isolated from U.S. cattle over the past decade, driven by the urgent need to address the dangers of AMR specifically originating in pathogens isolated from U.S. cattle. In this study, around 28,000 pathogen isolate samples were extracted from the NPDIB and then analyzed using multivariate statistical methods, mainly principal component analysis (PCA) and hierarchical clustering (H-clustering). These approaches were necessary due to the high dimensions of the raw data. Specifically, PCA was utilized to reduce the dimensions of the data, converting it to a two-dimensional space, and H-clustering was used to better identify the differences among data points. The findings from this work highlighted Salmonella enterica and Escherichia coli as the predominant pathogens among the isolates, with E. coli being the more concerning pathogen due to its increasing prevalence in recent years. Moreover, tetracycline was observed as the most commonly resistant antimicrobial, with the resistance genes mdsA, mdsB, mdtM, blaEC, and acrF being the most prevalent in pathogen isolates from U.S. cattle. The occurrence of mdtM, blaEC, acrF, and glpT_E448k showed an increase in pathogens isolated from U.S. cattle in recent years. Furthermore, based on the data collected for the locations of AMR cases, Texas, California, and Nebraska were the major areas carrying major AMR genes or antimicrobials with detected resistance. The results from this study provide potential directions for targeted interventions to mitigate pathogens' antimicrobial resistance in U.S. cattle.
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Affiliation(s)
| | | | | | | | | | | | - Zuyi Huang
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA 19085, USA; (G.G.); (H.P.); (A.Z.); (B.F.); (H.Z.); (A.C.)
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Kamala K, Sivaperumal P. Predominance of multi-drug resistant extended spectrum β lactamase producing bacteria from marine fishes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121314. [PMID: 36813100 DOI: 10.1016/j.envpol.2023.121314] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
The present study aimed to determine the extended spectrum beta lactamase (ESBL) genes in the bacteria from fresh exportable fish samples collected along South east coast of India, Chennai. ESBL genes are the base for the antibiotic resistance in pathogens and it transmitted from one to other species. Totally 2670 isolates were isolated from 293 fish samples which belong to 31 species dominated by Aeromonas, Klebsiella, Serratia, Leclerica, Proteus, Enterobacter, Acinetobacter, Haemophilus, Escherichia, Shigella sp. Out of 2670 isolates, 1958 isolates have multi drug resistant capacity with ESBL genes of blaCTX, blaSHV, blaTEM and blaAmpC and 712 isolates are not detected ESBL genes. The present study revealed that, the contamination of fresh fish sample with pathogenic bacteria resistant to multiple antibiotics can incriminate seafood as a potential carrier and accentuate an immediate need to prevent environmental infectivity and distribution. Further, hygienic facilitated markets should be developed with ensured quality of seafood.
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Affiliation(s)
- Kannan Kamala
- Department of Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, 600077, India
| | - Pitchiah Sivaperumal
- Marine Biomedical Research Lab & Environmental Toxicology Unit, Cellular and Molecular Research Centre, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, 600077, India.
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Characterization of Escherichia coli and Other Enterobacterales Resistant to Extended-Spectrum Cephalosporins Isolated from Dairy Manure in Ontario, Canada. Appl Environ Microbiol 2023; 89:e0186922. [PMID: 36695602 PMCID: PMC9972979 DOI: 10.1128/aem.01869-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Extended-spectrum cephalosporins (ESCs) resistance genes, such as blaCTX-M, blaCMY, and blaSHV, have been found regularly in bacteria from livestock. However, information on their distribution in dairy cattle in Canada and on the associated genome sequences of ESC-resistant Enterobacterales is sparse. In this study, the diversity and distribution of ESC-resistant Escherichia coli throughout manure treatments in six farms in Southern Ontario were assessed over a one-year period, and their ESC-resistance plasmids were characterized. The manure samples were enriched using selective media. The resulting isolates were screened via polymerase chain reaction for blaCTX-M, blaCMY, and blaSHV. No E. coli carrying blaSHV were detected. Escherichia coli (n = 248) carrying blaCTX-M or blaCMY underwent whole-genome sequencing using an Illumina MiSeq/NextSeq. These isolates were typed using multilocus sequence typing (MLST) and their resistance gene profiles. A subset of E. coli (n = 28) were sequenced using Oxford Nanopore Technologies. Plasmids were assembled using Unicycler and characterized via the resistance genes pattern, replicon type, plasmid MLST, phylogenetic analysis, and Mauve alignments. The recovery of ESC-resistant Enterobacterales (18 species, 8 genera) was drastically reduced in manure outputs. However, multiple treatment stages were needed to attain a significant reduction. 62 sequence types were identified, with ST10, ST46, ST58, ST155, ST190, ST398, ST685, and ST8761 being detected throughout the treatment pipeline. These STs overlapped with those found on multiple farms. The ESC-resistance determinants included CTX-M-1, -14, -15, -17, -24, -32, -55, and CMY-2. The plasmids carrying blaCTX-M were more diverse than were the plasmids carrying blaCMY. Known "epidemic plasmids" were detected for both blaCTX-M and blaCMY. IMPORTANCE The increase in antimicrobial resistance is of concern for human and animal health, especially when resistance is conferred to extended-spectrum cephalosporins, which are used to treat serious infections in both human and veterinary medicine. Bacteria carrying extended-spectrum cephalosporin resistance genes, including blaCTX-M and blaCMY, are frequently found in dairy manure. Manure treatment influences the loads and diversity of bacteria, including those carrying antimicrobial resistance genes, such as Enterobacterales and Escherichia coli. Any bacteria that survive the treatment process are subsequently applied to the environment. Enterobacterales carrying blaCTX-M or blaCMY can contaminate soil and crops consumed by humans and animals, thereby increasing the potential for antimicrobial resistance genes to integrate into the human gut microflora through horizontal gene transfer. This furthers the dissemination of resistance. Therefore, it is imperative to understand the effects manure treatments have on ESC-resistance in environmentally applied manure.
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Whole-Genome Characterisation of ESBL-Producing E. coli Isolated from Drinking Water and Dog Faeces from Rural Andean Households in Peru. Antibiotics (Basel) 2022; 11:antibiotics11050692. [DOI: 10.3390/antibiotics11050692] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 02/04/2023] Open
Abstract
E. coli that produce extended-spectrum β-lactamases (ESBLs) are major multidrug-resistant bacteria. In Peru, only a few reports have characterised the whole genome of ESBL enterobacteria. We aimed to confirm the identity and antimicrobial resistance (AMR) profile of two ESBL isolates from dog faeces and drinking water of rural Andean households and determine serotype, phylogroup, sequence type (ST)/clonal complex (CC), pathogenicity, virulence genes, ESBL genes, and their plasmids. To confirm the identity and AMR profiles, we used the VITEK®2 system. Whole-genome sequencing (WGS) and bioinformatics analysis were performed subsequently. Both isolates were identified as E. coli, with serotypes -:H46 and O9:H10, phylogroups E and A, and ST/CC 5259/- and 227/10, respectively. The isolates were ESBL-producing, carbapenem-resistant, and not harbouring carbapenemase-encoding genes. Isolate 1143 ST5259 harboured the astA gene, encoding the EAST1 heat-stable toxin. Both genomes carried ESBL genes (blaEC-15, blaCTX-M-8, and blaCTX-M-55). Nine plasmids were detected, namely IncR, IncFIC(FII), IncI, IncFIB(AP001918), Col(pHAD28), IncFII, IncFII(pHN7A8), IncI1, and IncFIB(AP001918). Finding these potentially pathogenic bacteria is worrisome given their sources and highlights the importance of One-Health research efforts in remote Andean communities.
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Neffe L, Abendroth L, Bautsch W, Häussler S, Tomasch J. High plasmidome diversity of extended-spectrum beta-lactam-resistant Escherichia coli isolates collected during one year in one community hospital. Genomics 2022; 114:110368. [PMID: 35447310 DOI: 10.1016/j.ygeno.2022.110368] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/04/2022] [Accepted: 04/09/2022] [Indexed: 01/14/2023]
Abstract
Plasmid-encoded antibiotic resistance encompasses many classes of currently used antibiotics. In globally distributed Escherichia coli lineages plasmids, which spread via horizontal gene transfer, are responsible for the dissemination of genes encoding extended-spectrum β-lactamases (ESBL). In this study, we combined 2nd and 3rd generation sequencing techniques to reconstruct the plasmidome of overall 97 clinical ESBL-E. coli isolates. Our results highlight the enormous plasmid diversity in respect to size, replicon-type and genetic content. Furthermore, we emphasize the diverse plasmid distribution patterns among the clinical isolates and the high intra- and extracellular mobility potential of resistance conferring genes. While the majority of resistance conferring genes were located on large plasmids of known replicon type, small cryptic plasmids seem to be underestimated resistance gene vectors. Our results contribute to a better understanding of the dissemination of resistance-conferring genes through horizontal gene transfer as well as clonal spread.
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Affiliation(s)
- Lisa Neffe
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lisa Abendroth
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany; Institute for Molecular Bacteriology, Twincore, Centre for Clinical and Experimental Infection Research, Hannover, Germany; Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, 2100 Copenhagen, Denmark; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30265 Hannover, Germany.
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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Vogt NA, Hetman BM, Vogt AA, Pearl DL, Reid-Smith RJ, Parmley EJ, Kadykalo S, Ziebell K, Bharat A, Mulvey MR, Janecko N, Ricker N, Allen SE, Bondo KJ, Jardine CM. Using whole-genome sequence data to examine the epidemiology of antimicrobial resistance in Escherichia coli from wild meso-mammals and environmental sources on swine farms, conservation areas, and the Grand River watershed in southern Ontario, Canada. PLoS One 2022; 17:e0266829. [PMID: 35395054 PMCID: PMC8993012 DOI: 10.1371/journal.pone.0266829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/28/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) threatens the health of humans and animals and has repeatedly been detected in wild animal species across the world. This cross-sectional study integrates whole-genome sequence data from Escherichia coli isolates with demonstrated phenotypic resistance that originated from a previous longitudinal wildlife study in southern Ontario, as well as phenotypically resistant E. coli water isolates previously collected as part of a public health surveillance program. The objective of this work was to assess for evidence of possible transmission of antimicrobial resistance determinants between wild meso-mammals, swine manure pits, and environmental sources on a broad scale in the Grand River watershed, and at a local scale—for the subset of samples collected on both swine farms and conservation areas in the previous wildlife study. Logistic regression models were used to assess potential associations between sampling source, location type (swine farm vs. conservation area), and the occurrence of select resistance genes and predicted plasmids. In total, 200 isolates from the following sources were included: water (n = 20), wildlife (n = 73), swine manure pit (n = 31), soil (n = 73), and dumpsters (n = 3). Several genes and plasmid incompatibility types were significantly more likely to be identified on swine farms compared to conservation areas. Conversely, internationally distributed sequence types (e.g., ST131), extended-spectrum beta-lactamase- and AmpC-producing E. coli were isolated in lower prevalences (<10%) and were almost exclusively identified in water sources, or in raccoon and soil isolates obtained from conservation areas. Differences in the odds of detecting resistance genes and predicted plasmids among various sources and location types suggest different primary sources for individual AMR determinants, but, broadly, our findings suggest that raccoons, skunks and opossums in this region may be exposed to AMR pollution via water and agricultural sources, as well as anthropogenic sources in conservation areas.
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Affiliation(s)
- Nadine A. Vogt
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Benjamin M. Hetman
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Adam A. Vogt
- Independent Researcher, Mississauga, Ontario, Canada
| | - David L. Pearl
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Richard J. Reid-Smith
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - E. Jane Parmley
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Stefanie Kadykalo
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nicol Janecko
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Nicole Ricker
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Samantha E. Allen
- Wyoming Game and Fish Department, Laramie, Wyoming, United States of America
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, United States of America
| | - Kristin J. Bondo
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Claire M. Jardine
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, Guelph, Ontario, Canada
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Chau KK, Barker L, Budgell EP, Vihta KD, Sims N, Kasprzyk-Hordern B, Harriss E, Crook DW, Read DS, Walker AS, Stoesser N. Systematic review of wastewater surveillance of antimicrobial resistance in human populations. ENVIRONMENT INTERNATIONAL 2022; 162:107171. [PMID: 35290866 PMCID: PMC8960996 DOI: 10.1016/j.envint.2022.107171] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 01/23/2022] [Accepted: 02/28/2022] [Indexed: 05/05/2023]
Abstract
OBJECTIVES We systematically reviewed studies using wastewater for AMR surveillance in human populations, to determine: (i) evidence of concordance between wastewater-human AMR prevalence estimates, and (ii) methodological approaches which optimised identifying such an association, and which could be recommended as standard. We used Lin's concordance correlation coefficient (CCC) to quantify concordance between AMR prevalence estimates in wastewater and human compartments (where CCC = 1 reflects perfect concordance), and logistic regression to identify study features (e.g. sampling methods) associated with high agreement studies (defined as >70% of within-study wastewater-human AMR prevalence comparisons within ±10%). RESULTS Of 8,867 records and 441 full-text methods reviewed, 33 studies were included. AMR prevalence data was extractable from 24 studies conducting phenotypic-only (n = 7), genotypic-only (n = 1) or combined (n = 16) AMR detection. Overall concordance of wastewater-human AMR prevalence estimates was reasonably high for both phenotypic (CCC = 0.85 [95% CI 0.8-0.89]) and genotypic approaches (CCC = 0.88 (95% CI 0.84-0.9)) despite diverse study designs, bacterial species investigated and phenotypic/genotypic targets. No significant relationships between methodological approaches and high agreement studies were identified using logistic regression; however, this was limited by inconsistent reporting of study features, significant heterogeneity in approaches and limited sample size. Based on a secondary, descriptive synthesis, studies conducting composite sampling of wastewater influent, longitudinal sampling >12 months, and time-/location-matched sampling of wastewater and human compartments generally had higher agreement. CONCLUSION Wastewater-based surveillance of AMR appears promising, with high overall concordance between wastewater and human AMR prevalence estimates in studies irrespective of heterogenous approaches. However, our review suggests future work would benefit from: time-/location-matched sampling of wastewater and human populations, composite sampling of influent, and sampling >12 months for longitudinal studies. Further research and clear and consistent reporting of study methods is required to identify optimal practice.
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Affiliation(s)
- K K Chau
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - L Barker
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - E P Budgell
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - K D Vihta
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - N Sims
- Department of Chemistry, Faculty of Science, University of Bath, Bath BA2 7AY, United Kingdom.
| | - B Kasprzyk-Hordern
- Department of Chemistry, Faculty of Science, University of Bath, Bath BA2 7AY, United Kingdom.
| | - E Harriss
- Bodleian Healthcare Libraries, University of Oxford, Oxford OX3 9DU, United Kingdom.
| | - D W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - D S Read
- UK Centre for Ecology & Hydrology, Wallingford OX10 8BB, United Kingdom.
| | - A S Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford OX4 2PG, United Kingdom.
| | - N Stoesser
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
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de Lagarde M, Fairbrother JM, Archambault M, Dufour S, Francoz D, Massé J, Lardé H, Aenishaenslin C, Paradis MÈ, Roy JP. Impact of a Regulation Restricting Critical Antimicrobial Usage on Prevalence of Antimicrobial Resistance in Escherichia coli Isolates From Fecal and Manure Pit Samples on Dairy Farms in Québec, Canada. Front Vet Sci 2022; 9:838498. [PMID: 35252426 PMCID: PMC8893019 DOI: 10.3389/fvets.2022.838498] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
To tackle antimicrobial resistance (AMR), one of the major health threats of this century, the World Health Organization (WHO) endorsed a global action plan in 2015. This plan calls countries to develop national actions to address AMR. The province of Québec, Canada, adopted a new regulation on the 25th of February 2019, to limit the use in food animals of antimicrobials of very high importance in human medicine. We aimed to establish the impact of this regulation by comparing the AMR situation in dairy cattle in Québec ~2 years before and 2 years after its introduction. We sampled calves, cows, and the manure pit in 87 farms. Generic and putative ESBL/AmpC E. coli were tested for susceptibility to 20 antimicrobials. Logistic regression was used to investigate whether the probability of antimicrobial resistance differed between isolates obtained from the pre and post regulation periods by sample type (calves, cows, manure pit) and in general. To identify AMR genes dissemination mechanisms, we sequenced the whole genome of 15 generic isolates. In the generic collection, at the herd level, the proportion of multidrug resistant (MDR) isolates, decreased significantly from 83 to 71% (p = 0.05). Folate inhibitor and aminoglycoside resistances demonstrated a significant decrease. However, when analyzed by sample type (calves, cows, manure pit), we did not observe a significant AMR decrease in any of these categories. In the ESBL/AmpC collection, we did not detect any significant difference between the two periods. Also, the general resistance gene profile was similar pre and post regulation. We identified both clonal and plasmidic dissemination of resistance genes. In conclusion, as early as 2 years post regulation implementation, we observed a significant decrease in MDR in the dairy industry in Quebec in the generic E. coli collection with folate inhibitor and aminoglycoside resistances showing the most significant decrease. No other significant decreases were yet observed.
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Affiliation(s)
- Maud de Lagarde
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Regroupement FRQNT Op+lait, Saint-Hyacinthe, QC, Canada
| | - John M. Fairbrother
- OIE Reference Laboratory for Escherichia coli, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Swine and Poultry Infectious Research Center (CRIPA-FQRNT), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Marie Archambault
- Regroupement FRQNT Op+lait, Saint-Hyacinthe, QC, Canada
- Swine and Poultry Infectious Research Center (CRIPA-FQRNT), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Simon Dufour
- Regroupement FRQNT Op+lait, Saint-Hyacinthe, QC, Canada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - David Francoz
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Regroupement FRQNT Op+lait, Saint-Hyacinthe, QC, Canada
| | - Jonathan Massé
- Regroupement FRQNT Op+lait, Saint-Hyacinthe, QC, Canada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Hélène Lardé
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Regroupement FRQNT Op+lait, Saint-Hyacinthe, QC, Canada
- Department of Clinical Sciences, Ross University School of Veterinary Medicine, Basseterre, Federation of Saint Christopher and Nevis
| | - Cécile Aenishaenslin
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Marie-Ève Paradis
- Association des Médecins Vétérinaires Praticiens du Québec, Saint-Hyacinthe, QC, Canada
| | - Jean-Philippe Roy
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Regroupement FRQNT Op+lait, Saint-Hyacinthe, QC, Canada
- *Correspondence: Jean-Philippe Roy
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Insights and genetic features of extended-spectrum beta-lactamase producing Escherichia coli isolates from two hospitals in Ghana. Sci Rep 2022; 12:1843. [PMID: 35115628 PMCID: PMC8813988 DOI: 10.1038/s41598-022-05869-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 01/17/2022] [Indexed: 12/18/2022] Open
Abstract
Recently, the emergence and rapid dissemination of extended-spectrum beta-lactamase (ESBL)-producing bacteria, particularly of the family Enterobacteriaceae, has posed serious healthcare challenges. Here, we determined the antimicrobial susceptibility and genetic characteristics of 164 Escherichia coli strains isolated from infected patients in two hospitals in Ghana. In total, 102 cefotaxime-resistant isolates (62.2%) were identified as ESBL-producers. Multilocus sequence typing of the ESBL-producers identified 20 different sequence types (STs) with ST131 (n = 25, 24.5%) as the dominant group. Other detected STs included ST410 (n = 21, 20.6%) and ST617 (n = 19, 18.6%). All identified ESBL-producers harbored blaCTX-M-14, blaCTX-M-15, or blaCTX-M-27, with blaCTX-M-15 (n = 96, 94.1%) being the most predominant ESBL allele. Further analysis showed that the immediate genetic environment around blaCTX-M-15 is conserved within blaCTX-M-15 containing strains. Five of the 25 ST131 isolates were clustered with clade A, one with sub-clade C1, and 19 with the dominant sub-clade C2. The results show that fluoroquinolone-resistant, blaCTX-M-14- and blaCTX- M-15-producing ESBL E. coli ST131 strains belonging to clade A and sub-clades C1 and C2 are disseminating in Ghanaian hospitals. To the best of our knowledge, this is the first report of the ST131 phylogeny in Ghana.
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Yoon S, Lee YJ. Molecular characteristics of ESBL-producing Escherichia coli isolated from chickens with colibacillosis. J Vet Sci 2022; 23:e37. [PMID: 35332711 PMCID: PMC9149503 DOI: 10.4142/jvs.21105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 12/31/2021] [Accepted: 02/03/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Sunghyun Yoon
- College of Veterinary Medicine & Zoonoses Research Institute, Kyungpook National University, Daegu 41566, Korea
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Young Ju Lee
- College of Veterinary Medicine & Zoonoses Research Institute, Kyungpook National University, Daegu 41566, Korea
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Montso PK, Bezuidenhout CC, Mienie C, Somorin YM, Odeyemi OA, Mlambo V, Ateba CN. Genetic diversity and whole genome sequence analysis data of multidrug resistant atypical enteropathogenic Escherichia coli O177 strains: An assessment of food safety and public health implications. Int J Food Microbiol 2022; 365:109555. [DOI: 10.1016/j.ijfoodmicro.2022.109555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/12/2022] [Accepted: 01/21/2022] [Indexed: 11/28/2022]
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Richter L, du Plessis EM, Duvenage S, Allam M, Ismail A, Korsten L. Whole Genome Sequencing of Extended-Spectrum- and AmpC- β-Lactamase-Positive Enterobacterales Isolated From Spinach Production in Gauteng Province, South Africa. Front Microbiol 2021; 12:734649. [PMID: 34659162 PMCID: PMC8517129 DOI: 10.3389/fmicb.2021.734649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
The increasing occurrence of multidrug-resistant (MDR) extended-spectrum β-lactamase- (ESBL) and/or AmpC β-lactamase- (AmpC) producing Enterobacterales in irrigation water and associated irrigated fresh produce represents risks related to the environment, food safety, and public health. In South Africa, information about the presence of ESBL/AmpC-producing Enterobacterales from non-clinical sources is limited, particularly in the water-plant-food interface. This study aimed to characterize 19 selected MDR ESBL/AmpC-producing Escherichia coli (n=3), Klebsiella pneumoniae (n=5), Serratia fonticola (n=10), and Salmonella enterica (n=1) isolates from spinach and associated irrigation water samples from two commercial spinach production systems within South Africa, using whole genome sequencing (WGS). Antibiotic resistance genes potentially encoding resistance to eight different classes were present, with bla CTX-M-15 being the dominant ESBL encoding gene and bla ACT-types being the dominant AmpC encoding gene detected. A greater number of resistance genes across more antibiotic classes were seen in all the K. pneumoniae strains, compared to the other genera tested. From one farm, bla CTX-M-15-positive K. pneumoniae strains of the same sequence type 985 (ST 985) were present in spinach at harvest and retail samples after processing, suggesting successful persistence of these MDR strains. In addition, ESBL-producing K. pneumoniae ST15, an emerging high-risk clone causing nosocomical outbreaks worldwide, was isolated from irrigation water. Known resistance plasmid replicon types of Enterobacterales including IncFIB, IncFIA, IncFII, IncB/O, and IncHI1B were observed in all strains following analysis with PlasmidFinder. However, bla CTX-M-15 was the only β-lactamase resistance gene associated with plasmids (IncFII and IncFIB) in K. pneumoniae (n=4) strains. In one E. coli and five K. pneumoniae strains, integron In191 was observed. Relevant similarities to human pathogens were predicted with PathogenFinder for all 19 strains, with a confidence of 0.635-0.721 in S. fonticola, 0.852-0.931 in E. coli, 0.796-0.899 in K. pneumoniae, and 0.939 in the S. enterica strain. The presence of MDR ESBL/AmpC-producing E. coli, K. pneumoniae, S. fonticola, and S. enterica with similarities to human pathogens in the agricultural production systems reflects environmental and food contamination mediated by anthropogenic activities, contributing to the spread of antibiotic resistance genes.
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Affiliation(s)
- Loandi Richter
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Erika M. du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
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Athanasakopoulou Z, Reinicke M, Diezel C, Sofia M, Chatzopoulos DC, Braun SD, Reissig A, Spyrou V, Monecke S, Ehricht R, Tsilipounidaki K, Giannakopoulos A, Petinaki E, Billinis C. Antimicrobial Resistance Genes in ESBL-Producing Escherichia coli Isolates from Animals in Greece. Antibiotics (Basel) 2021; 10:389. [PMID: 33916633 PMCID: PMC8067336 DOI: 10.3390/antibiotics10040389] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/13/2022] Open
Abstract
The prevalence of multidrug resistant, extended spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is increasing worldwide. The present study aimed to provide an overview of the multidrug resistance phenotype and genotype of ESBL-producing Escherichia coli (E. coli) isolates of livestock and wild bird origin in Greece. Nineteen phenotypically confirmed ESBL-producing E. coli strains isolated from fecal samples of cattle (n = 7), pigs (n = 11) and a Eurasian magpie that presented resistance to at least one class of non β-lactam antibiotics, were selected and genotypically characterized. A DNA-microarray based assay was used, which allows the detection of various genes associated with antimicrobial resistance. All isolates harbored blaCTX-M-1/15, while blaTEM was co-detected in 13 of them. The AmpC gene blaMIR was additionally detected in one strain. Resistance genes were also reported for aminoglycosides in all 19 isolates, for quinolones in 6, for sulfonamides in 17, for trimethoprim in 14, and for macrolides in 8. The intI1 and/or tnpISEcp1 genes, associated with mobile genetic elements, were identified in all but two isolates. This report describes the first detection of multidrug resistance genes among ESBL-producing E. coli strains retrieved from feces of cattle, pigs, and a wild bird in Greece, underlining their dissemination in diverse ecosystems and emphasizing the need for a One-Health approach when addressing the issue of antimicrobial resistance.
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Affiliation(s)
- Zoi Athanasakopoulou
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
| | - Martin Reinicke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Celia Diezel
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Marina Sofia
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
| | - Dimitris C. Chatzopoulos
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
| | - Sascha D. Braun
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Annett Reissig
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Vassiliki Spyrou
- Faculty of Animal Science, University of Thessaly, 41110 Larissa, Greece;
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institut fuer Medizinische Mikrobiologie und Hygiene, Medizinische Fakultaet “Carl Gustav Carus”, TU Dresden, 01307 Dresden, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, 07737 Jena, Germany
| | | | - Alexios Giannakopoulos
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
| | - Efthymia Petinaki
- Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (K.T.); (E.P.)
| | - Charalambos Billinis
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
- Faculty of Public and Integrated Health, University of Thessaly, 43100 Karditsa, Greece
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Cao C, Niu Q, Chen J, Xu X, Sheng H, Cui S, Liu B, Yang B. Epidemiology and Characterization of CTX-M-55-Type Extended-Spectrum β-Lactamase-Producing Salmonella enterica Serovar Enteritidis Isolated from Patients in Shanghai, China. Microorganisms 2021; 9:microorganisms9020260. [PMID: 33513880 PMCID: PMC7912593 DOI: 10.3390/microorganisms9020260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 11/16/2022] Open
Abstract
The emergence of extended-spectrum β-lactamase-producing Salmonella enterica serovar Enteritidis (ESBL-SE) in humans and foods has gained global attention. In particular, CTX-M-type ESBL-SE are increasingly being detected from various sample types. The aim of this study was to comprehensively analyze the epidemiology and characteristics of blaCTX-M-55-carrying ESBL-SE isolates of clinical origin in Shanghai, China. A total of 292 S. Enteritidis isolates were recovered from the feces and blood of outpatients and inpatients between 2006 and 2014. Overall, there was a high frequency of cefotaxime-resistant isolates (97.3%), which was significantly higher (p < 0.01) than that of isolates resistant to the other tested antibiotics. All S. Enteritidis isolates exhibited resistance to ≥1 antibiotic, and 98.0% were multidrug resistant. A total of 233 isolates were identified as ESBL-SE, 166 of which were CTX-M type. Six subtypes of CTX-M-encoding genes were detected, among which blaCTX-M-55 (91.6%, 152/166) was the most prevalent genotype. There was high genetic similarity among blaCTX-M-55-positive ESBL-SE. The blaCTX-M-55 gene in the ESBL-SE donor strains could be easily transferred into Enterobacteriaceae recipient strains. This study highlights that CTX-M-55 should be considered an important surveillance target in Shanghai, China. Cephalosporins, especially cefotaxime, must be used with caution in empirical treatment for Salmonella infections.
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Affiliation(s)
- Chenyang Cao
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China; (C.C.); (Q.N.); (H.S.); (B.L.)
| | - Qinya Niu
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China; (C.C.); (Q.N.); (H.S.); (B.L.)
| | - Jia Chen
- College of Chemical Technology, Shijiazhuang University, Shijiazhuang 050035, China;
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control & Prevention, Shanghai 200336, China;
| | - Huanjing Sheng
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China; (C.C.); (Q.N.); (H.S.); (B.L.)
| | - Shenghui Cui
- National Institutes for Food and Drug Control, Beijing 100050, China;
| | - Bin Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China; (C.C.); (Q.N.); (H.S.); (B.L.)
| | - Baowei Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China; (C.C.); (Q.N.); (H.S.); (B.L.)
- Correspondence: ; Tel./Fax: +86-29-87092486
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Alawneh JI, Vezina B, Ramay HR, Al-Harbi H, James AS, Soust M, Moore RJ, Olchowy TWJ. Survey and Sequence Characterization of Bovine Mastitis-Associated Escherichia coli in Dairy Herds. Front Vet Sci 2020; 7:582297. [PMID: 33365333 PMCID: PMC7750360 DOI: 10.3389/fvets.2020.582297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/05/2020] [Indexed: 01/29/2023] Open
Abstract
Escherichia coli is frequently associated with mastitis in cattle. “Pathogenic” and “commensal” isolates appear to be genetically similar. With a few exceptions, no notable genotypic differences have been found between commensal and mastitis-associated E. coli. In this study, 24 E. coli strains were isolated from dairy cows with clinical mastitis in three geographic regions of Australia (North Queensland, South Queensland, and Victoria), sequenced, then genomically surveyed. There was no observed relationship between sequence type (ST) and region (p = 0.51). The most common Multi Locus Sequence Type was ST10 (38%), then ST4429 (13%). Pangenomic analysis revealed a soft-core genome of 3,463 genes, including genes associated with antibiotic resistance, chemotaxis, motility, adhesion, biofilm formation, and pili. A total of 36 different plasmids were identified and generally found to have local distributions (p = 0.02). Only 2 plasmids contained antibiotic resistance genes, a p1303_5-like plasmid encoding multidrug-resistance (trimethoprim, quaternary ammonium, beta-lactam, streptomycin, sulfonamide, and kanamycin) from two North Queensland isolates on the same farm, while three Victorian isolates from the same farm contained a pCFSAN004177P_01-like plasmid encoding tetracycline-resistance. This pattern is consistent with a local spread of antibiotic resistance through plasmids of bovine mastitis cases. Notably, co-occurrence of plasmids containing virulence factors/antibiotic resistance with putative mobilization was rare, though the multidrug resistant p1303_5-like plasmid was predicted to be conjugative and is of some concern. This survey has provided greater understanding of antibiotic resistance within E. coli-associated bovine mastitis which will allow greater prediction and improved decision making in disease management.
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Affiliation(s)
- John I Alawneh
- Good Clinical Practice Research Group, School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia.,School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - Ben Vezina
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
| | - Hena R Ramay
- International Microbiome Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Hulayyil Al-Harbi
- Good Clinical Practice Research Group, School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia.,School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - Ameh S James
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - Martin Soust
- Terragen Biotech Pty Ltd., Coolum Beach, QLD, Australia
| | - Robert J Moore
- School of Science, RMIT University, Melbourne, VIC, Australia
| | - Timothy W J Olchowy
- Good Clinical Practice Research Group, School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia.,Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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16
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Adator EH, Narvaez-Bravo C, Zaheer R, Cook SR, Tymensen L, Hannon SJ, Booker CW, Church D, Read RR, McAllister TA. A One Health Comparative Assessment of Antimicrobial Resistance in Generic and Extended-Spectrum Cephalosporin-Resistant Escherichia coli from Beef Production, Sewage and Clinical Settings. Microorganisms 2020; 8:microorganisms8060885. [PMID: 32545206 PMCID: PMC7355928 DOI: 10.3390/microorganisms8060885] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/27/2020] [Accepted: 06/08/2020] [Indexed: 12/18/2022] Open
Abstract
This study aimed to compare antimicrobial resistance (AMR) in extended-spectrum cephalosporin-resistant and generic Escherichia coli from a One Health continuum of the beef production system in Alberta, Canada. A total of 705 extended-spectrum cephalosporin-resistant E. coli (ESCr) were obtained from: cattle feces (CFeces, n = 382), catch basins (CBasins, n = 137), surrounding streams (SStreams, n = 59), beef processing plants (BProcessing, n = 4), municipal sewage (MSewage; n = 98) and human clinical specimens (CHumans, n = 25). Generic isolates (663) included: CFeces (n = 142), CBasins (n = 185), SStreams (n = 81), BProcessing (n = 159) and MSewage (n = 96). All isolates were screened for antimicrobial susceptibility to 9 antimicrobials and two clavulanic acid combinations. In ESCr, oxytetracycline (87.7%), ampicillin (84.4%) and streptomycin (73.8%) resistance phenotypes were the most common, with source influencing AMR prevalence (p < 0.001). In generic E. coli, oxytetracycline (51.1%), streptomycin (22.6%), ampicillin (22.5%) and sulfisoxazole (14.3%) resistance were most common. Overall, 88.8% of ESCr, and 26.7% of generic isolates exhibited multi-drug resistance (MDR). MDR in ESCr was high from all sources: CFeces (97.1%), MSewage (96.9%), CHumans (96%), BProcessing (100%), CBasins (70.5%) and SStreams (61.4%). MDR in generic E. coli was lower with CFeces (45.1%), CBasins (34.6%), SStreams (23.5%), MSewage (13.6%) and BProcessing (10.7%). ESBL phenotypes were confirmed in 24.7% (n = 174) ESCr and 0.6% of generic E. coli. Prevalence of bla genes in ESCr were blaCTXM (30.1%), blaCTXM-1 (21.6%), blaTEM (20%), blaCTXM-9 (7.9%), blaOXA (3.0%), blaCTXM-2 (6.4%), blaSHV (1.4%) and AmpC β-lactamase blaCMY (81.3%). The lower AMR in ESCr from SStreams and BProcessing and higher AMR in CHumans and CFeces likely reflects antimicrobial use in these environments. Although MDR levels were higher in ESCr as compared to generic E. coli, AMR to the same antimicrobials ranked high in both ESCr and generic E. coli sub-populations. This suggests that both sub-populations reflect similar AMR trends and are equally useful for AMR surveillance. Considering that MDR ESCr MSewage isolates were obtained without enrichment, while those from CFeces were obtained with enrichment, MSewage may serve as a hot spot for MDR emergence and dissemination.
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Affiliation(s)
- Emelia H. Adator
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.H.A.); (C.N.-B.)
| | - Claudia Narvaez-Bravo
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.H.A.); (C.N.-B.)
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada;
| | - Shaun R. Cook
- Irrigation and Farm Water Branch, Alberta Agriculture and Forestry, Lethbridge, AB T1J 4V6, Canada; (S.R.C.); (L.T.)
| | - Lisa Tymensen
- Irrigation and Farm Water Branch, Alberta Agriculture and Forestry, Lethbridge, AB T1J 4V6, Canada; (S.R.C.); (L.T.)
| | - Sherry J. Hannon
- Health Management Services Ltd, Okotoks, AB T1S 2A2, Canada; (S.J.H.); (C.W.B.)
| | - Calvin W. Booker
- Health Management Services Ltd, Okotoks, AB T1S 2A2, Canada; (S.J.H.); (C.W.B.)
| | - Deirdre Church
- Department of Pathology & Laboratory Medicine and Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (D.C.); (R.R.R.)
| | - Ron R. Read
- Department of Pathology & Laboratory Medicine and Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (D.C.); (R.R.R.)
| | - Tim A. McAllister
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (E.H.A.); (C.N.-B.)
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada;
- Correspondence:
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Special Issue: Antimicrobial Resistance in Livestock. Microorganisms 2020; 8:microorganisms8050645. [PMID: 32354177 PMCID: PMC7285062 DOI: 10.3390/microorganisms8050645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 11/17/2022] Open
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