Repeated cross-sectional study identifies differing risk factors associated with microbial contamination in common food products in the United Kingdom.

All foods carry microbes, many of which are harmless, but foods can also carry pathogens and/or microbial indicators of contamination. Limited information exists on the co-occurrence of microbes of food safety concern and the factors associated with their presence. Here, a population-based repeated cross-sectional design was used to determine the prevalence and co-occurrence of Escherichia coli, Klebsiella spp., Salmonella spp. and Vibrio spp. in key food commodities - chicken, pork, prawns, salmon and leafy greens. Prevalence in 1,369 food samples for these four target bacterial genera/species varied, while 25.6% of all samples had at least two of the target bacteria and eight different combinations of bacteria were observed as co-occurrence profiles in raw prawns. Imported frozen chicken was 6.4 times more likely to contain Salmonella than domestic chicken, and imported salmon was 5.5 times more likely to be contaminated with E. coli. Seasonality was significantly associated with E. coli and Klebsiella spp. contamination in leafy greens, with higher detection in summer and autumn. Moreover, the odds of Klebsiella spp. contamination were higher in summer in chicken and pork samples. These results provide insight on the bacterial species present on foods at retail, and identify factors associated with the presence of individual bacteria, which are highly relevant for food safety risk assessments and the design of surveillance programmes.

Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics.

Food products carry bacteria unless specifically sterilised. These bacteria can be pathogenic, commensal or associated with food spoilage, and may also be resistant to antimicrobials. Current methods for detecting bacteria on food rely on culturing for specific bacteria, a time-consuming process, or 16S rRNA metabarcoding that can identify different taxa but not their genetic content. Directly sequencing metagenomes of food is inefficient as its own DNA vastly outnumbers the bacterial DNA present. We optimised host DNA depletion enabling efficient sequencing of food microbiota, thereby increasing the proportion of non-host DNA sequenced 13-fold (mean; range: 1.3-40-fold) compared to untreated samples. The method performed best on chicken, pork and leafy green samples which had high mean prokaryotic read proportions post-depletion (0.64, 0.74 and 0.74, respectively), with lower mean prokaryotic read proportions in salmon (0.50) and prawn samples (0.19). We show that bacterial compositions and concentrations of antimicrobial resistance (AMR) genes differed by food type, and that salmon metagenomes were influenced by the production/harvesting method. The approach described in this study is an efficient and effective method of identifying and quantifying the predominant bacteria and AMR genes on food.

Integrated surveillance of extended-spectrum beta-lactamase (ESBL)-producing Salmonella and Escherichia coli from humans and animal species raised for human consumption in Canada from 2012 to 2017.

Resistance to beta-lactam antimicrobials caused by extended-spectrum beta-lactamase (ESBL)-producing organisms is a global health concern. The objectives of this study were to (1) summarise the prevalence of potential ESBL-producing Escherichia coli (ESBL-EC) and Salmonella spp. (ESBL-SA) isolates from agrifood and human sources in Canada from 2012 to 2017, and (2) describe the distribution of ESBL genotypes among these isolates. All data were obtained from the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). CIPARS analysed samples for the presence of ESBLs through phenotypic classification and identified beta-lactamase genes (blaTEM, blaSHV, blaCTX, blaOXA, blaCMY-2) using polymerase chain reaction (PCR) and whole genome sequencing (WGS). The prevalence of PCR-confirmed ESBL-EC in agrifood samples ranged from 0.5% to 3% across the surveillance years, and was detected most frequently in samples from broiler chicken farms. The overall prevalence of PCR-confirmed ESBL-SA varied between 1% and 4% between 2012 and 2017, and was most frequently detected in clinical isolates from domestic cattle. The TEM-CMY2 gene combination was the most frequently detected genotype for both ESBL-EC and ESBL-SA. The data suggest that the prevalence of ESBL-EC and ESBL-SA in Canada was low (i.e. <5%), but ongoing surveillance is needed to detect emerging or changing trends.

A Clostridioides difficile surveillance study of Canadian retail meat samples from 2016-2018.

In this study, we isolated and molecularly characterized 10 (1.6%) C. difficile isolates from 644 commercially available raw meat samples. Molecular typing by PFGE and ribotyping revealed NAP and ribotypes commonly associated with human clinical cases, suggesting retail meat could be a possible source of transmission warranting further investigation.

Evaluation of selective media in antimicrobial surveillance programs capturing broad-spectrum ß-lactamase producing Escherichia coli from chickens at slaughter.

Antimicrobial resistance surveillance targeting agricultural animals is practiced in many countries but does not often include media selective for cephalosporin resistance. Here, we compared the frequency of recovery of resistant Escherichia coli using selective and non-selective media from the cecal contents of 116 chickens collected by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). Third generation cephalosporin resistance was detected in 24 samples including 12, 10, and 2 on selective, non-selective, and both media, respectively. Isolates producing the CTX-M-1 ESBL were grown from 11 samples, 10 on selective medium only. Our results suggest that current surveillance approaches underestimate the true prevalence of resistance to critically important antimicrobials.

Évaluation de milieux sélectifs dans des programmes de surveillance antimicrobienne isolant Escherichia coli produisant des ß-lactamases à large spectre provenant de poulets à l'abattage. La surveillance de la résistance aux antimicrobiens ciblant les animaux d'élevage est pratiquée dans de nombreux pays mais n'inclut pas souvent les milieux sélectifs pour la résistance aux céphalosporines. Ici, nous avons comparé la fréquence d'isolement d'Escherichia coli résistants à l'aide de milieux sélectifs et non sélectifs à partir du contenu caecal de 116 poulets collectés dans le cadre du Programme intégré canadien de surveillance de la résistance aux antimicrobiens (PICRA). Une résistance aux céphalosporines de troisième génération a été détectée dans 24 échantillons dont 12, 10 et 2 sur des milieux sélectifs, non sélectifs et les deux, respectivement. Les isolats produisant les BLSE CTX-M-1 ont été cultivés à partir de 11 échantillons, 10 sur un milieu sélectif uniquement. Nos résultats suggèrent que les approches de surveillance actuelles sous-estiment la prévalence réelle de la résistance aux antimicrobiens d'importance critique.(Traduit par Dr Serge Messier).

Characterization of VCC-1, a Novel Ambler Class A Carbapenemase from Vibrio cholerae Isolated from Imported Retail Shrimp Sold in Canada.

One of the core goals of the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) is to monitor major meat commodities for antimicrobial resistance. Targeted studies with methodologies based on core surveillance protocols are used to examine other foods, e.g., seafood, for antimicrobial resistance to detect resistances of concern to public health. Here we report the discovery of a novel Ambler class A carbapenemase that was identified in a nontoxigenic strain of Vibrio cholerae (N14-02106) isolated from shrimp that was sold for human consumption in Canada. V. cholerae N14-02106 was resistant to penicillins, carbapenems, and monobactam antibiotics; however, PCR did not detect common ß-lactamases. Bioinformatic analysis of the whole-genome sequence of V. cholerae N14-02106 revealed on the large chromosome a novel carbapenemase (referred to here as VCC-1, for Vibrio cholerae carbapenemase 1) with sequence similarity to class A enzymes. Two copies of blaVCC-1 separated and flanked by ISVch9 (i.e., 3 copies of ISVch9) were found in an acquired 8.5-kb region inserted into a VrgG family protein gene. Cloned blaVCC-1 conferred a ß-lactam resistance profile similar to that in V. cholerae N14-02106 when it was transformed into a susceptible laboratory strain of Escherichia coli. Purified VCC-1 was found to hydrolyze penicillins, 1st-generation cephalosporins, aztreonam, and carbapenems, whereas 2nd- and 3rd-generation cephalosporins were poor substrates. Using nitrocefin as a reporter substrate, VCC-1 was moderately inhibited by clavulanic acid and tazobactam but not EDTA. In this report, we present the discovery of a novel class A carbapenemase from the food supply.

Surveillance of antimicrobial resistance in Escherichia coli, Salmonella, and Campylobacter recovered from laying hens, their environment and products in Canada indicated a stable level of resistance to critically important antimicrobials, in varying time periods between 2007 and 2021.

The study objective was to determine the occurrence and antimicrobial resistance (AMR) attributes of select foodborne bacteria recovered from egg-producing (layer) chickens between 2007 and 2021 using different sample matrices (Study 1: liquid whole eggs, Study 2: spent hen cecal samples, Study 3: environmental sponge swabs and fecal samples from layer chicken barns, and Study 4: fecal samples from layer chicken barns). Samples from each study were submitted for the culture of Escherichia coli and Salmonella. In addition, samples from layer chicken barns were submitted for the culture of Campylobacter. Isolates were tested by microbroth dilution and interpreted using both clinical breakpoints and epidemiological cut-offs (ECOFFs). The ECOFFs were applied to detect non-wild type (NWT) strains. The proportion of resistant, NWT, and distribution of minimum inhibitory concentrations (MIC) were assessed. Ceftriaxone resistance was detected at a low-level in E. coli (< 2 %, all studies) and Salmonella (4.3 %, Study 2). Very low-level ciprofloxacin resistance was detected in E. coli (<1 %, Study 1) but a slightly elevated ciprofloxacin NWT E. coli (1 % to 6 %) observed. Only the farm fecal samples in Studies 2 and 3 were tested for Campylobacter as part of its study design, and moderate level ciprofloxacin resistance (<15 %) was observed. The MIC distribution patterns were similar across the organisms tested/studies and no substantial shifts in the distributions were detected. This analysis demonstrated that resistance to very important antimicrobials in bacteria from layers in Canada remains low, however, the detection of ciprofloxacin-resistant Campylobacter and the implications of this observation to the safety of egg products, and the role of laying flocks (i.e., as reservoir for resistant organisms) needs to be investigated.

Nutritional and microbial analysis of bully sticks and survey of opinions about pet treats.

The objectives of this study were to measure the caloric density of bully sticks, to analyze the bully sticks for bacterial contamination, and to assess owner opinions about these and other pet treat products. Mean caloric density was 15 kcal/inch (38 kcal/cm) [range: 9 to 22 kcal/inch (23 to 56 kcal/cm), 2.96 to 3.07 kcal/g]. Of 26 bully sticks that were tested for bacterial contamination 1 (4%) was contaminated with Clostridium difficile, 1 was contaminated with methicillin-resistant Staphylococcus aureus (MRSA), and 1 with a tetracycline resistant Escherichia coli.

Analyse nutritionnelle et microbienne des bâtonnets en peau de buffle et sondage d'opinion à propos des gâteries pour animaux de compagnie. Les objectifs de cette étude consistaient à mesurer la densité calorique des bâtonnets en peau de bovin, à analyser les bâtonnets en peau de bovin pour une contamination bactérienne et à évaluer les opinions des propriétaires à propos de ces gâteries et d'autres gâteries pour animaux de compagnie. La densité calorique moyenne était de 15 kcal/pouce (38 kcal/cm) [écart : de 9 à 22 kcal/pouce (de 23 à 56 kcal/cm), de 2,96 à 3,07 kcal/g]. Parmi les 26 bâtonnets en peau de bovin qui ont été testés pour une contamination bactérienne, 1 (4 %) était contaminé par Clostridium difficile, 1 était contaminé par Staphylococcus aureus résistant à la méthicilline (SARM) et 1 par Escherichia coli résistant à la tétracycline.(Traduit par Isabelle Vallières).

Foodborne protozoan parasites in fresh mussels and oysters purchased at retail in Canada.

Studies worldwide have reported the presence of protozoan parasites in a variety of commercial bivalve shellfish. The uptake of these parasites by shellfish occurs during filter feeding in faecally-contaminated waters. The objective of the present study was to determine the prevalence of Giardia, Cryptosporidium and Toxoplasma in fresh, live shellfish purchased in three Canadian provinces as part of the retail surveillance activities led by FoodNet Canada (Public Health Agency of Canada). Packages containing mussels (n = 253) or oysters (n = 130) were purchased at grocery stores in FoodNet Canada sentinel sites on a biweekly basis throughout 2018 and 2019, and shipped in coolers to Health Canada for testing. A small number of packages were not tested due to insufficient quantity or poor quality. Following DNA extraction from homogenized, pooled tissues, nested PCR and DNA sequencing were used to detect parasite-specific sequences. Epifluorescence microscopy was used to confirm the presence of intact cysts and oocysts in sequence-confirmed PCR-positive samples. Giardia duodenalis DNA was present in 2.4 % of 247 packages of mussels and 4.0 % of 125 packages of oysters, while Cryptosporidium parvum DNA was present in 5.3 % of 247 packages of mussels and 7.2 % of 125 packages of oysters. Toxoplasma gondii DNA was only found in mussels in 2018 (1.6 % of 249 packages). Parasite DNA was detected in shellfish purchased in all three Canadian provinces sampled, and there was no apparent seasonal variation in prevalence. While the present study did not test for viability, parasites are known to survive for long periods in the marine environment, and these findings suggest that there is a risk of infection, especially when shellfish are consumed raw.

Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk, UK.

Non-typhoidal Salmonella (NTS) is a major cause of bacterial gastroenteritis. Although many countries have implemented whole genome sequencing (WGS) of NTS, there is limited knowledge on NTS diversity on food and its contribution to human disease. In this study, the aim was to characterise the NTS genomes from retail foods in a particular region of the UK and assess the contribution to human NTS infections. Raw food samples were collected at retail in a repeated cross-sectional design in Norfolk, UK, including chicken (n=311), leafy green (n=311), pork (n=311), prawn (n=279) and salmon (n=157) samples. Up to eight presumptive NTS isolates per positive sample underwent WGS and were compared to publicly available NTS genomes from UK human cases. NTS was isolated from chicken (9.6 %), prawn (2.9 %) and pork (1.3 %) samples and included 14 serovars, of which Salmonella Infantis and Salmonella Enteritidis were the most common. The S. Enteritidis isolates were only isolated from imported chicken. No antimicrobial resistance determinants were found in prawn isolates, whilst 5.1 % of chicken and 0.64 % of pork samples contained multi-drug resistant NTS. The maximum number of pairwise core non-recombinant single nucleotide polymorphisms (SNPs) amongst isolates from the same sample was used to measure diversity and most samples had a median of two SNPs (range: 0-251). NTS isolates that were within five SNPs to clinical UK isolates belonged to specific serovars: S. Enteritidis and S. Infantis (chicken), and S. I 4,[5],12:i- (pork and chicken). Most NTS isolates that were closely related to human-derived isolates were obtained from imported chicken, but further epidemiological data are required to assess definitively the probable source of the human cases. Continued WGS surveillance of Salmonella on retail food involving multiple isolates from each sample is necessary to capture the diversity of Salmonella and determine the relative importance of different sources of human disease.

Comparison of antimicrobial resistance patterns of Salmonella spp. and Escherichia coli recovered from pet dogs from volunteer households in Ontario (2005-06).

OBJECTIVES: To compare the antimicrobial resistance (AMR) patterns of Salmonella spp. and Escherichia coli in the faeces of pet dogs from volunteer households in Southwestern Ontario, Canada. METHODS: From October 2005 to May 2006, 138 dogs from 84 Ontario households were recruited to participate in a cross-sectional study. Five consecutive daily faecal samples were collected from each dog and cultured for Salmonella spp. and E. coli. A panel of 15 antimicrobials from seven antimicrobial classes was used for susceptibility testing. RESULTS: E. coli and Salmonella spp. were recovered from 96.4% and 23.2% of dogs, respectively. In total, 515 bacterial isolates from 136 dogs from 83 households were sent for antimicrobial susceptibility testing with 80.4% of isolates being pan-susceptible. The most common resistance pattern was to amoxicillin/clavulanic acid, ampicillin, cefoxitin, ceftiofur and ceftriaxone, present in 13.3% of Salmonella isolates and 1.3% of E. coli isolates. Fifty-eight of the isolates were resistant to two or more drug classes, with 70.7% and 29.3% being E. coli and Salmonella, respectively. Based on multilevel logistic regression, the odds of resistance were greater in E. coli than Salmonella [odds ratio = 3.2; 95% confidence interval (CI) = 1.22-8.43]. Agreement in resistance between E. coli and Salmonella isolates from the same dog was low [prevalence-adjusted, bias-adjusted kappa (PABAK) = 0.38; 95% CI = 0.30-0.46]. CONCLUSIONS: Pet dogs are a potential household source of antimicrobial-resistant Salmonella spp. and E. coli. However, extrapolating the epidemiology of antimicrobial resistance in pathogens, like Salmonella, from E. coli should be done with caution.

Antimicrobial resistance in Escherichia coli isolates from raccoons (Procyon lotor) in Southern Ontario, Canada.

We conducted a cross-sectional study to determine the prevalence of antimicrobial resistance (AMR) in fecal Escherichia coli isolates from raccoons (Procyon lotor) living in Ontario, Canada. From June to October 2007, we trapped raccoons in three areas: one primarily urban site around Niagara, one primarily rural site north of Guelph, and one at the Toronto Zoo. In addition, we conducted a longitudinal study at the Toronto Zoo site to investigate the temporal dynamics of fecal E. coli and AMR in raccoons. Reduced susceptibility to ≥1 antimicrobial agent was detected in E. coli isolates from 19% of 16 raccoons at the urban site, 17% of 29 raccoons from the rural site, and 42% of 130 samples collected from 59 raccoons at the zoo site. Raccoons from the zoo site were significantly more likely to shed E. coli with reduced susceptibility to ≥1 antimicrobial agent than animals from the rural site (odds ratio [OR], 3.41; 95% confidence interval [CI], 1.17 to 12.09; P = 0.02). Resistance to expanded-spectrum cephalosporins (and the associated bla(CMY-2) gene) was detected in two animals from the zoo site and one animal from the rural site. Serotyping and pulsed-field gel electrophoresis analysis show that raccoons on the zoo grounds harbor a diverse assemblage of E. coli, with rapid bacterial turnover within individuals over time. Our study indicates that raccoons may shed resistant bacteria of public health significance and that raccoons have the potential to disseminate these bacteria throughout their environment.

Out-patient antimicrobial drug use in dogs and cats for new disease events from community companion animal practices in Ontario.

This study investigated oral and parenteral antimicrobial use in dogs and cats, and evaluated antimicrobial use in feline upper respiratory tract disease (FURTD), feline lower urinary tract disease (FLUTD), and canine infectious tracheobronchitis. Study journals (n = 1807) were submitted by 84 veterinarians. Sixty-five percent of the antimicrobials prescribed in dogs and 67% in cats were ß-lactams. Most frequently prescribed in dogs were cephalexin (33%) and amoxicillin-clavulanic acid (16%), and in cats, amoxicillin-clavulanic acid (40%) and cefovecin (17%); 7% of the prescriptions in dogs and 12% in cats were for fluoroquinolones. Sixty-seven percent of the disease events associated with canine infectious tracheobronchitis, and 70% and 74% associated with FURTD and FLUTD, respectively, were treated with antimicrobials. These results suggest that cefovecin and fluoroquinolones may be over-used and antimicrobial use for the treatment of FURTD, FLUTD, and canine infectious tracheobronchitis could probably be reduced to lessen resistance selection pressure without compromising patient health.

Comparative genomics of Campylobacter jejuni from clinical campylobacteriosis stool specimens.

BACKGROUND: Campylobacter jejuni is a pervasive pathogen of major public health concern with a complex ecology requiring accurate and informative approaches to define pathogen diversity during outbreak investigations. Source attribution analysis may be confounded if the genetic diversity of a C. jejuni population is not adequately captured in a single specimen. The aim of this study was to determine the genomic diversity of C. jejuni within individual stool specimens from four campylobacteriosis patients. Direct plating and pre-culture filtration of one stool specimen per patient was used to culture multiple isolates per stool specimen. Whole genome sequencing and pangenome level analysis were used to investigate genomic diversity of C. jejuni within a patient. RESULTS: A total 92 C. jejuni isolates were recovered from four patients presenting with gastroenteritis. The number of isolates ranged from 13 to 30 per patient stool. Three patients yielded a single C. jejuni multilocus sequence type: ST-21 (n = 26, patient 4), ST-61 (n = 30, patient 1) and ST-2066 (n = 23, patient 2). Patient 3 was infected with two different sequence types [ST-51 (n = 12) and ST-354 (n = 1)]. Isolates belonging to the same sequence type from the same patient specimen shared 12-43 core non-recombinant SNPs and 0-20 frameshifts with each other, and the pangenomes of each sequence type consisted of 1406-1491 core genes and 231-264 accessory genes. However, neither the mutation nor the accessory genes were connected to a specific functional gene category. CONCLUSIONS: Our findings show that the C. jejuni population recovered from an individual patient's stool are genetically diverse even within the same ST and may have shared common ancestors before specimens were obtained. The population is unlikely to have evolved from a single isolate at the time point of initial patient infection, leading us to conclude that patients were likely infected with a heterogeneous C. jejuni population. The diversity of the C. jejuni population found within individual stool specimens can inform future methodological approaches to attribution and outbreak investigations.

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.

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.

Rural Raccoons (Procyon lotor) Not Likely to Be a Major Driver of Antimicrobial Resistant Human Salmonella Cases in Southern Ontario, Canada: A One Health Epidemiological Assessment Using Whole-Genome Sequence Data.

Non-typhoidal Salmonella infections represent a substantial burden of illness in humans, and the increasing prevalence of antimicrobial resistance among these infections is a growing concern. Using a combination of Salmonella isolate short-read whole-genome sequence data from select human cases, raccoons, livestock and environmental sources, and an epidemiological framework, our objective was to determine if there was evidence for potential transmission of Salmonella and associated antimicrobial resistance determinants between these different sources in the Grand River watershed in Ontario, Canada. Logistic regression models were used to assess the potential associations between source type and the presence of select resistance genes and plasmid incompatibility types. A total of 608 isolates were obtained from the following sources: humans (n = 58), raccoons (n = 92), livestock (n = 329), and environmental samples (n = 129). Resistance genes of public health importance, including bla CMY-2, were identified in humans, livestock, and environmental sources, but not in raccoons. Most resistance genes analyzed were significantly more likely to be identified in livestock and/or human isolates than in raccoon isolates. Based on a 3,002-loci core genome multi-locus sequence typing (cgMLST) scheme, human Salmonella isolates were often more similar to isolates from livestock and environmental sources, than with those from raccoons. Rare instances of serovars S. Heidelberg and S. Enteritidis in raccoons likely represent incidental infections and highlight possible acquisition and dissemination of predominantly poultry-associated Salmonella by raccoons within these ecosystems. Raccoon-predominant serovars were either not identified among human isolates (S. Agona, S. Thompson) or differed by more than 350 cgMLST loci (S. Newport). Collectively, our findings suggest that the rural population of raccoons on swine farms in the Grand River watershed are unlikely to be major contributors to antimicrobial resistant human Salmonella cases in this region.

Antimicrobial resistance in generic Escherichia coli isolates from wild small mammals living in swine farm, residential, landfill, and natural environments in southern Ontario, Canada.

To assess the impacts of different types of human activity on the development of resistant bacteria in the feces of wild small mammals, we compared the prevalences and patterns of antimicrobial resistance and resistance genes in generic Escherichia coli and Salmonella enterica isolates from fecal samples collected from wild small mammals living in four environments: swine farms, residential areas, landfills, and natural habitats. Resistance to antimicrobials was observed in E. coli isolates from animals in all environments: 25/52 (48%) animals trapped at swine farms, 6/69 (9%) animals trapped in residential areas, 3/20 (15%) animals trapped at landfills, and 1/22 (5%) animals trapped in natural habitats. Animals trapped on farms were significantly more likely to carry E. coli isolates with resistance to tetracycline, ampicillin, sulfisoxazole, and streptomycin than animals trapped in residential areas. The resistance genes sul2, aadA, and tet(A) were significantly more likely to be detected in E. coli isolates from animals trapped on farms than from those trapped in residential areas. Three S. enterica serotypes (Give, Typhimurium, and Newport) were recovered from the feces of 4/302 (1%) wild small mammals. All Salmonella isolates were pansusceptible. Our results show that swine farm origin is significantly associated with the presence of resistant bacteria and resistance genes in wild small mammals in southern Ontario, Canada. However, resistant fecal bacteria were found in small mammals living in all environments studied, indicating that environmental exposure to antimicrobials, antimicrobial residues, resistant bacteria, or resistance genes is widespread.