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.

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.

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.

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.

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 blaCMY−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.

Whole genome sequencing reveals great diversity of Vibrio spp in prawns at retail

Consumption of prawns as a protein source has been on the rise worldwide with seafood identified as the predominant attributable source of human vibriosis. However, surveillance of non-cholera Vibrio is limited both in public health and in food. Using a population- and market share-weighted study design, 211 prawn samples were collected and cultured for Vibrio spp. Contamination was detected in 46 % of samples, and multiple diverse Vibrio isolates were obtained from 34 % of positive samples. Whole genome sequencing (WGS) and phylogenetic analysis illustrated a comprehensive view of Vibrio species diversity in prawns available at retail, with no known pathogenicity markers identified in Vibrio parahaemolyticus and V. cholerae. Antimicrobial resistance genes were found in 77 % of isolates, and 12 % carried genes conferring resistance to three or more drug classes. Resistance genes were found predominantly in V. parahaemolyticus, though multiple resistance genes were also identified in V. cholerae and V. vulnificus. This study highlights the large diversity in Vibrio derived from prawns at retail, even within a single sample. Although there was little evidence in this study that prawns are a major source of vibriosis in the UK, surveillance of non-cholera Vibrio is very limited. This study illustrates the value of expanding WGS surveillance efforts of non-cholera Vibrios in the food chain to identify critical control points for food safety through the production system and to determine the full extent of the public health impact.

Evaluation of selective media in antimicrobial surveillance programs capturing broad-spectrum β-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.

Molecular characterization of plasmid-mediated AmpC beta-lactamase- and extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae among corvids (Corvus brachyrhynchos and Corvus corax) roosting in Canada

This study evaluated the carriage of AmpC and extended-spectrum beta-lactamase (ESBL) genes and associated plasmids in faecal bacteria of Canadian corvids. Faecal samples from 449 birds in five roosting sites across Canada were analyzed using selective media, screening for AmpC and ESBL genes by PCR, and sequencing. Genomic relatedness was determined by PFGE and MLST. Plasmid mobility was studied by conjugation and transformation experiments, followed by plasmid typing. In total, 96 (21%, n = 449) cefotaxime-resistant Escherichia coli and three (0.7%) Klebsiella pneumoniae isolates were identified. ESBL genes blaCTX-M-1 (n = 3), blaCTX-M-14 (n = 2), blaCTX-M-32 (n = 2) and blaCTX-M-124 (n = 1) were detected in eight E. coli isolates, whereas blaSHV-2 (2) was found in two K. pneumoniae. E. coli isolates contained blaCMY-2 (n = 83) and blaCMY-42 (n = 1). The high genetic diversity of the isolates and presence of clinically important E. coli ST69 (n = 1), ST117 (n = 7) and ST131 (n = 1) was revealed. AmpC genes were predominantly carried by plasmids of incompatibility groups I1 (45 plasmids), A/C (10) and K (7). The plasmid IncI1/ST12 was most common and found in diverse E. coli STs in all sites. Highly diverse E. coli isolates containing AmpC and ESBL genes, including clinically important clones and emerging plasmids, are in circulation throughout Canadian wildlife.

Salmonella, Campylobacter, Clostridium difficile, and anti-microbial resistant Escherichia coli in the faeces of sympatric meso-mammals in southern Ontario, Canada

The role of free-ranging wildlife in the epidemiology of enteropathogens causing clinical illness in humans and domestic animals is unclear. Salmonella enterica and anti-microbial resistant bacteria have been detected in the faeces of raccoons (Procyon lotor), but little is known about the carriage of these bacteria in other sympatric meso-mammals. Our objectives were to: (a) report the prevalence of Salmonella and associated anti-microbial resistance, Campylobacter spp, Clostridium difficile, and anti-microbial resistant Escherichia coli in the faeces of striped skunks (Mephitis mephitis) and Virginia opossums (Didelphis virginiana) in southern Ontario; and (b) compare the prevalence of these bacteria in the faeces of these meso-mammal hosts with raccoons from a previously reported study. Faecal swabs were collected from striped skunks and Virginia opossums on five swine farms and five conservation areas from 2011 to 2013. Salmonella was detected in 41% (9/22) and 5% (5/95) of faecal swabs from Virginia opossums and striped skunks, respectively. None of the Salmonella serovars carried resistance to anti-microbials. The prevalence of Campylobacter spp., C. difficile, and anti-microbial resistant E. coli ranged from 6% to 22% in striped skunk and Virginia opossums. Using exact logistic regression, Salmonella was significantly more likely to be detected in faecal swabs of Virginia opossums than skunks and significantly less likely in faecal swabs from skunks than raccoons from a previously reported study. In addition, Campylobacter spp. was significantly more likely to be detected in raccoons than opossums. Salmonella Give was detected in 8/9 (89%) of Salmonella-positive Virginia opossum faecal swabs. Our results suggest that striped skunks and Virginia opossums have the potential to carry pathogenic enteric bacteria in their faeces. The high prevalence of Salmonella Give in Virginia opossum faecal swabs in this study as well as its common occurrence in other Virginia opossum studies throughout North America suggests Virginia opossums may be reservoirs of this serovar.

Prevalence and molecular characterization of Toxoplasma gondii DNA in retail fresh meats in Canada

Toxoplasma gondii is a protozoan parasite which infects a wide variety of mammals and birds worldwide, including humans. Human toxoplasmosis is primarily transmitted through the ingestion of tissue cysts in raw or poorly cooked meat and organs of infected animals, or through the ingestion of oocysts in food, water or soil contaminated with cat faeces. There is a distinct paucity of information on the prevalence and molecular characteristics of T. gondii in retail meats in Canada. This study reports the presence of T. gondii DNA in 4.3% (12 of 281) of packages of fresh ground beef, chicken breasts and ground pork purchased at retail in three Canadian provinces. T. gondii prevalence was very similar among all three meat types tested, and among the provinces sampled. Genotyping of positive samples by means of PCR-RFLP and DNA sequencing demonstrated the presence of both T. gondii type II (66.7%) and type III (33.3%). These findings provide baseline data on the prevalence of T. gondii DNA in fresh meats purchased at retail in Canada and will allow for more accurate and meaningful health risk assessments for the purposes of developing food safety guidelines and policies.

A repeated cross-sectional study of the epidemiology of Campylobacter and antimicrobial resistant Enterobacteriaceae in free-living Canada geese in Guelph, Ontario, Canada

From May through October 2016, we conducted a repeated cross-sectional study examining the effects of temporal, spatial, flock and demographic factors (i.e. juvenile vs. adult) on the prevalence of Campylobacter and antimicrobial resistant Enterobacteriaceae among 344 fresh faecal samples collected from Canada geese (Branta canadensis) from four locations where birds nested in Guelph, Ontario, Canada. The overall prevalence of Campylobacter among all fresh faecal samples was 9.3% and was greatest in the fall when these birds became more mobile following the nesting season. Based on 40 gene comparative genomic fingerprinting (CGF40), the increase in prevalence noted in the fall was matched by an increase in the number of unique CGF40 subtypes identified. Resistance to colistin was detected most commonly, in 6% of Escherichia coli isolates, and was highest in the late summer months. All colistin-resistant isolates were negative for the mcr-1 to mcr-5 genes; a chromosomal resistance mechanism (PmrB) was identified in all of these isolates. The prevalence of samples with E. coli exhibiting multi-class resistance or extended spectrum beta-lactamase was low (i.e. <2% of samples). The intra-class correlation coefficients, estimated from the variance components of multilevel logistic regression models, indicated that the shedding of Campylobacter and antimicrobial resistant E. coli among geese within a flock (i.e. birds collected from the same site on the same day) was moderately correlated. Spatial, temporal, and spatiotemporal clusters identified using the spatial scan statistic, largely supported the findings from our multi-level models. Salmonella was not isolated from any of the fresh faecal samples collected suggesting that its prevalence in this population of birds was very low.

Epidemiology of Campylobacter, Salmonella and antimicrobial resistant Escherichia coli in free-living Canada geese (Branta canadensis) from three sources in southern Ontario

Antimicrobial resistant bacteria and zoonotic pathogens have previously been isolated from Canada geese. We examined the prevalence of three enteric bacteria (i.e. Campylobacter, Salmonella, Escherichia coli) among Canada geese from three sampling sources in southern Ontario from 2013 through 2015. Samples were obtained by convenience from hunting groups, diagnostic birds submitted for post-mortem, and fresh faeces from live birds in parks. Escherichia coli isolates were isolated and tested for susceptibility to 15 antimicrobials using the Canadian Integrated Program for Antimicrobial Resistance Surveillance test panel. The prevalences of Salmonella, Campylobacter and E. coli were 0%, 11.2% and 72.6%, respectively. Among E. coli isolates, 7.9% were resistant to ≥1 class of antimicrobials and 5.6% were resistant to ≥2 classes of antimicrobials, with some including resistance to antimicrobials of highest importance in human medicine. A significant association between season and E. coli resistance among samples from live birds was noted; summer samples had no resistant E. coli isolates, whereas spring samples demonstrated the highest prevalence of E. coli resistant to ≥1 class of antimicrobials (20.0%) among all sources. In addition, Campylobacter coli were only isolated from the spring faecal samples. Flock-level clustering was an important statistical consideration, as flock was a significant random effect in all but two of our models. Detection of Campylobacter and antimicrobial resistant E. coli from Canada geese suggests that these birds may play a role in disseminating these organisms within the environment.

Changes in antimicrobial resistance levels among Escherichia coli, Salmonella, and Campylobacter in Ontario broiler chickens between 2003 and 2015

Poultry has been identified as a reservoir of foodborne enteric pathogens and antimicrobial resistant bacteria. The objective of this study was to describe and compare antimicrobial resistant isolates from an Ontario broiler chicken farm-level baseline project (2003 to 2004) to the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) Ontario abattoir and retail surveillance data from 2003, and to the most recent (2015) CIPARS Ontario chicken surveillance data in order to assess the impact of an industry-wide policy change in antimicrobial use. Ceftiofur resistance (TIO-R) prevalence in Salmonella decreased by 7% on farm between 2003 and 2004 and 2015. During the same timeframe, TIO-R E. coli prevalence decreased significantly by 16%, 11%, and 8% in farm, abattoir, and retail samples, respectively. Gentamicin resistant (GEN-R) E. coli, however, increased by 10% in farm and 15% in retail-derived isolates, and trimethoprim-sulfamethoxazole resistant (TMSm-R) E. coli increased significantly by 20%, 18%, and 5% in farm, abattoir, and retail isolates, respectively. Similarly, ciprofloxacin-resistant (CIP-R) Campylobacter spp. significantly increased in retail isolates by 11% and increased in farm (33%) and abattoir isolates (7%). The decrease in TIO-R Salmonella/E. coli in recent years is consistent with the timing of an industry-led intervention eliminating the preventive use of ceftiofur, a third generation cephalosporin and class of antimicrobials deemed critically important to human medicine. The rise in GEN-R and TMSm-R prevalence is indicative of recent shifts in antimicrobial use. Our study highlights the importance of integrated surveillance in detecting emerging trends and determining the efficacy of interventions to improve food safety.

Occurrence of plasmid-mediated quinolone resistance genes in Escherichia coli and Klebsiella spp. recovered from Corvus brachyrhynchos and Corvus corax roosting in Canada

The spread of antimicrobial resistance from human activity derived sources to natural habitats implicates wildlife as potential vectors of antimicrobial resistance transfer. Wild birds, including corvid species can disseminate mobile genetic resistance determinants through faeces. This study aimed to determine the occurrence of plasmid-mediated quinolone resistance (PMQR) genes in Escherichia coli and Klebsiella spp. isolates obtained from winter roosting sites of American crows (Corvus brachyrhynchos) and common ravens (Corvus corax) in Canada. Faecal swabs were collected at five roosting sites across Canada. Selective media isolation and multiplex PCR screening was utilized to identify PMQR genes followed by gene sequencing, pulse-field gel electrophoresis and multilocus sequence typing to characterize isolates. Despite the low prevalence of E. coli containing PMQR (1·3%, 6/449), qnrS1, qnrB19, qnrC, oqxAB and aac(6')-Ib-cr genes were found in five sequence types (ST), including E. coli ST 131. Conversely, one isolate of Klebsiella pneumoniae contained the plasmid-mediated resistance gene qnrB19. Five different K. pneumoniae STs were identified, including two novel types. The occurrence of PMQR genes and STs of public health significance in E. coli and Klebsiella pneumoniae recovered from corvids gives further evidence of the anthropogenic derived dissemination of antimicrobial resistance determinants at the human activity-wildlife-environment interface.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study examined large corvids as possible vector species for the dissemination of antimicrobial resistance in indicator and pathogenic bacteria as a means to assess the anthropogenic dissemination of plasmid-mediated quinolone resistance (PMQR) genes. Although rare, PMQR genes were found among corvid populations across Canada. The clinically important Escherichia coli strain ST131 containing aac(6')-Ib-cr gene along with a four-class phenotypic antimicrobial resistance (AMR) pattern as well as one Klebsiella pneumoniae strain containing a qnrB19 gene were identified in one geographical location. Corvids are a viable vector for the circulation of PMQR genes and clinically important clones in wide-ranging environments.

Prevalence and antimicrobial resistance among Escherichia coli and Salmonella in Ontario smallholder chicken flocks

Surveillance is an important component of an overall strategy to address antimicrobial resistant bacteria in food animals and the food chain. The poultry market has many points of entry into the Canadian food chain, and some production practices are underrepresented in terms of surveillance. For example, pathogen carriage and antimicrobial resistance surveillance data are limited in smallholder chicken flocks raised for slaughter at provincially inspected abattoirs. In Canada, antimicrobial resistance in Escherichia coli and Salmonella isolated from commercial broiler chicken flocks, slaughtered at federally inspected abattoirs, is monitored by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). The objective of this study was to establish baseline information of antimicrobial resistance presence in E. coli and Salmonella isolated from smallholder flocks in Ontario, utilizing CIPARS collection and isolation methodologies, and to compare findings with CIPARS federally inspected abattoir data from Ontario, Canada. Five chickens per flock were sampled from 205 smallholder flocks. Of 1,025 samples, the E. coli prevalence was 99% (1,022/1,025), and 47% (483/1,022) of positive E. coli isolates were resistant to one or more of the 14 antimicrobials. Furthermore, as compared to results reported for the CIPARS commercial flocks, E. coli isolates from smallholder flocks had significantly lower resistance prevalence to six of 14 individual antimicrobials. Recovery of E. coli did not differ between federally inspected and provincially inspected flocks. Salmonella prevalence at the bird level in smallholder flocks was 0.3% (3/1,025), significantly lower (p ≪ 0.0001, 95% CI 0.080%-0.86%) than federally inspected commercial flocks. The overall differences found between the commercial and smallholder flocks may be explained by differences in poultry husbandry practices and hatchery sources.

Implications of fluoroquinolone contamination for the aquatic environment-A review

Until recently, the behaviors of antibiotics and their ecotoxicological impact have been overlooked in the environment. The topic is broad and encompasses a wide range of organisms including microorganisms, algae, invertebrates, and vertebrates inhabiting various aquatic ecosystems. Changing the equilibrium of any 1 component in such systems disrupts the balance of the whole system. The manufacturing and frequent use of fluoroquinolones in human and animal medicine raises great concern over the increase of antibiotic resistance prevalence in microorganisms; however, in addition, the fate of antibiotic parent and metabolite compounds entering environmental ecosystems through various pathways raises environmental impact concerns. Research has focused on the concentration of antibiotics present in environmental samples and the acute toxicity to organisms by way of animal assessment models; however, it remains unclear what role low-level chronic exposure plays in ecotoxicological effects on lifeforms in aquatic environments. The aim of the present review was to assess the levels of fluorquinolone use in animal and human medicine, to determine the pathways of dissemination, and to highlight the ecotoxicological implications in freshwater environments. Environ Toxicol Chem 2016;35:2647-2656. © 2016 SETAC.

Impact of Season, Demographic and Environmental Factors on Salmonella Occurrence in Raccoons (Procyon lotor) from Swine Farms and Conservation Areas in Southern Ontario

Salmonella has been detected in the feces of many wildlife species, including raccoons (Procyon lotor), but little is known about the epidemiology of Salmonella in wildlife living in different habitat types. Our objective was to investigate demographic, temporal, and climatic factors associated with the carriage of Salmonella in raccoons and their environment on swine farms and conservation areas. Using a repeated cross-sectional study design, we collected fecal samples from raccoons and environmental samples (soil, manure pits, dumpsters) on 5 swine farms and 5 conservation areas in Ontario, Canada once every five weeks from May to November, 2011-2013. Salmonella was detected in 26% (279/1093; 95% CI 22.9-28.2) of raccoon fecal samples, 6% (88/1609; 95% CI 4.5-6.8) of soil samples, 30% (21/69; 95% CI 20.0-42.7) of manure pit samples, and 23% (7/31; 95% CI 9.6-41.0) of dumpster samples. Of samples testing positive for Salmonella, antimicrobial resistance was detected in 5% (14/279; 95% CI 2.8-8.3) of raccoon fecal, 8% (7/89; 95% CI 3.2-15.5) of soil, 10% (2/21; 95% CI 1.2-30.4) of manure pit, and 0/7 dumpster samples. Using multi-level multivariable logistic regression analyses, we found location type (swine farm or conservation area) was not a significant explanatory variable for Salmonella occurrence in raccoon feces or soil (p > 0.05). However, detection of Salmonella in raccoon feces was associated with rainfall, season, and sex with various interaction effects among these variables. We detected a variety of Salmonella serovars that infect humans and livestock in the feces of raccoons indicating that raccoons living near humans, regardless of location type, may play a role in the epidemiology of salmonellosis in livestock and humans in southwestern Ontario.

Risk factors for carriage of antimicrobial-resistant Salmonella spp and Escherichia coli in pet dogs from volunteer households in Ontario, Canada, in 2005 and 2006

OBJECTIVE To determine pet-related management factors associated with the carriage of antimicrobial-resistant Salmonella spp and Escherichia coli in a population of pet dogs. SAMPLE 138 dogs from 84 households in Ontario, Canada. PROCEDURES From October 2005 through May 2006, dogs and households in Ontario, Canada, were recruited to participate in a cross-sectional study. Fecal samples were submitted for culture of Salmonella spp and E coli, which provided 515 bacterial isolates for antimicrobial susceptibility testing. Multilevel logistic regression models with random effects for household and dog were created to identify pet-related management factors associated with antimicrobial resistance. RESULTS Bacterial species, feeding a homemade diet or adding homemade food to the diet, feeding a raw diet or adding anything raw to the diet, feeding a homemade raw food diet, and feeding raw chicken in the past week were significant risk factors for antimicrobial resistance in this population of dogs. CONCLUSIONS AND CLINICAL RELEVANCE In this study, several potentially important pet-related risk factors for the carriage of antimicrobial-resistant Salmonella spp and E coli in pet dogs were identified. Further evaluation of risk factors for antimicrobial resistance in dogs may lead to development of evidence-based guidelines for safe and responsible dog ownership and management to protect the public, especially pet owners who are immunocompromised.

Salmonella bacteriuria in a cat fed a Salmonella-contaminated diet

CASE DESCRIPTION

A 9-year-old castrated male domestic shorthair cat was evaluated because of hematuria and weight loss after an 8-year history of intermittent signs of feline lower urinary tract disease (FLUTD). A complete diet history revealed that the cat was eating a commercial diet that does not undergo the same processing procedures as most pet foods and so might be at increased risk for bacterial contamination owing to a nonstandard industry cooking procedure.

CLINICAL FINDINGS

The cat had a history consistent with FLUTD, but bacteriologic culture of the urine revealed Salmonella organisms. Additional analysis revealed Salmonella enterica serotype I:ROUGH-O:g,m,s:- in samples of urine and feces as well as Salmonella enterica serotype Johannesburg and Salmonella enterica serotype Senftenberg in the diet.

TREATMENT AND OUTCOME

The cat responded positively to antimicrobial treatment for the Salmonella bacteriuria as well as to dietary and environmental management for the clinical signs associated with FLUTD.

CLINICAL RELEVANCE

Findings in this case highlighted an additional health consequence associated with ingestion of Salmonella-contaminated food. Such contamination is of particular concern with raw meat-based diets or diets that have not undergone standard industry cooking practices. Veterinarians should obtain a diet history for every companion animal during every evaluation to help with diagnosis and optimal treatment.

Epidemiology of Salmonella on the Paws and in the Faeces of Free-Ranging Raccoons (Procyon Lotor) in Southern Ontario, Canada

Raccoons are common in urban and rural environments and can carry a wide range of bacteria, including Salmonella, that can negatively affect human and livestock health. Although previous studies have reported that raccoons shed a variety of Salmonella serovars in their faeces, it is unknown whether Salmonella is carried on raccoon paws. Our objective was to compare the prevalence of Salmonella on the paws and in the faeces of raccoons in south-western Ontario. Raccoons were sampled in a repeat cross-sectional study on five swine farms and five conservation areas from May to October 2012. A total of 416 paired faecal and paw samples were collected from 285 individual raccoons. Salmonella was detected in 18% (75/416; 95% CI, 14-22%) and 27% (111/416; 95% CI, 22-31%) of paw and faecal samples, respectively. Salmonella was detected only on paws in 8% (35/416; 95% CI, 5.9-11.5%), only in faeces in 17% (71/416; 95% CI, 13.6-21.0%) and on both paws and in faeces in 10% (40/416; 95% CI, 7.0-12.9%) of raccoon captures. Multilevel logistic regression models were used to examine associations between the presence of Salmonella and age (adult, juvenile), sex (male, female), location type (swine farm, conservation area), sample type (faeces, paw) and season (May-July and August-October). Random intercepts were included to account for clustering by individual animal and location. Significant differences, that varied by sample type and season, were noted in the prevalence of Salmonella carriage between sexes. Raccoons can carry Salmonella serovars known to infect humans and livestock on their paws and/or in their faeces and therefore have the potential to mechanically and biologically disseminate Salmonella among livestock facilities and human recreational areas.

Prevalence, characterization and antibiotic resistance of Salmonella isolates in large corvid species of europe and north America between 2010 and 2013

It is well understood that Salmonella is carried by animals and in majority of cases as asymptomatic hosts. Surveillance efforts have focused on the role of agriculture and contamination points along the food chain as the main source of human infection; however, very little attention has been paid to the contribution of wildlife in the dissemination of Salmonella and what effect anthropogenic sources have on the circulation of antibiotic resistant Salmonella serovars in wildlife species. A purposive survey was taken of large corvids roosting yearly between November and March in Europe and North America. Two thousand and seven hundred and seventy-eight corvid faecal specimens from 11 countries were submitted for Salmonella spp. culture testing. Presumptive positive isolates were further serotyped, susceptibility tested and analysed for antibiotic resistance genes. Overall, 1.40% (39/2778) (CI = 1.01, 1.90) of samples were positive for Salmonella spp. Salmonella Enteritidis was the most prevalent serovar followed by S. Infantis, S. Montevideo and S. Typhimurium. No significant difference (P > 0.05) was found in the proportion of Salmonella recovered in Europe versus North America. The most variability of serovars within a site was in Kansas, USA with five different serovars recovered. European sites were significantly more likely to yield Salmonella resistant to more than one antibiotic (OR 71.5, P < 0.001, CI = 3.77, 1358) than North American sites, where no resistance was found. Resistance to nalidixic acid, a quinolone, was recovered in nine isolates from four serovars in four different sites across Europe. Large corvids contribute to the transmission and dissemination of Salmonella and resistance genes between human and animal populations and across great distances. This information adds to the knowledge base of zoonotic pathogen prevalence and antibiotic resistance ecology in wild birds.

First record of vancomycin-resistant Enterococcus faecium in Canadian wildlife

In this study, we focused on spreading of vancomycin-resistant enterococci (VRE) to the environment. We studied that weather crows in Canada may be carriers and potentially reservoirs of VRE with vanA gene. We have found one multi-resistant isolate of Enterococcus faecium sequence type (ST) 448 with vanA gene on Prince Edward Island. This study is the first report of VRE in Canadian wildlife.

Survey of Canadian retail pork chops and pork livers for detection of hepatitis E virus, norovirus, and rotavirus using real time RT-PCR

Over the past 15 years, hepatitis E virus (HEV), norovirus (NoV), and rotavirus (RV) have been hypothesized to be potentially zoonotic; swine and pork have been suggested as possible human infection sources for all 3 viruses. Our objective was to estimate HEV, NoV, and RV prevalence and load on Canadian retail pork chops and livers. Using the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) sampling platform, pork livers (n=283) and chops (n=599) were collected, processed, and assayed for the 3 viruses by four collaborating federal laboratories using validated real time reverse transcriptase polymerase chain reactions (qRT-PCR). Follow-up qRT-PCR estimating viral load in genomic copies/g was followed by nested classical RT-PCR and isolate sequencing of a partial segment of the ORF2 gene. Local alignments were performed using MUSCLE (Multiple Sequence Comparison by Log-Expectation); a phylogenetic tree was created. Twenty-five livers and 6 chops were classified 'positive' (thresholds for viral RNA detected in both replicates of the assay) or 'suspect' (thresholds detected in one of two replicates) for HEV. Follow-up qRT-PCR detected HEV on 16 livers, 0 chops, and nested classical RT-PCR, on 14 livers and 0 chops. Initial qRT-PCR classified 12 chops 'suspect' for NoV. Follow-up qRT-PCR detected viral RNA on only one sample with thresholds greater than 40 in both replicates. No amplicon was yielded, and therefore no isolate was sequenced from this sample. Partial ORF2 genes from 14 HEV isolates were sequenced, and compared via sequence identity and phylogenetic analysis with selected human case isolates listed in NCBI-GenBank. Overall, HEV prevalence on retail pork was comparable with other published reports.

A cross-sectional study examining the prevalence and risk factors for anti-microbial-resistant generic Escherichia coli in domestic dogs that frequent dog parks in three cities in south-western Ontario, Canada

Anti-microbial resistance can threaten health by limiting treatment options and increasing the risk of hospitalization and severity of infection. Companion animals can shed anti-microbial-resistant bacteria that may result in the exposure of other dogs and humans to anti-microbial-resistant genes. The prevalence of anti-microbial-resistant generic Escherichia coli in the faeces of dogs that visited dog parks in south-western Ontario was examined and risk factors for shedding anti-microbial-resistant generic E. coli identified. From May to August 2009, canine faecal samples were collected at ten dog parks in three cities in south-western Ontario, Canada. Owners completed a questionnaire related to pet characteristics and management factors including recent treatment with antibiotics. Faecal samples were collected from 251 dogs, and 189 surveys were completed. Generic E. coli was isolated from 237 of the faecal samples, and up to three isolates per sample were tested for anti-microbial susceptibility. Eighty-nine percent of isolates were pan-susceptible; 82.3% of dogs shed isolates that were pan-susceptible. Multiclass resistance was detected in 7.2% of the isolates from 10.1% of the dogs. Based on multilevel multivariable logistic regression, a risk factor for the shedding of generic E. coli resistant to ampicillin was attending dog day care. Risk factors for the shedding of E. coli resistant to at least one anti-microbial included attending dog day care and being a large mixed breed dog, whereas consumption of commercial dry and home cooked diets was protective factor. In a multilevel multivariable model for the shedding of multiclass-resistant E. coli, exposure to compost and being a large mixed breed dog were risk factors, while consumption of a commercial dry diet was a sparing factor. Pet dogs are a potential reservoir of anti-microbial-resistant generic E. coli; some dog characteristics and management factors are associated with the prevalence of anti-microbial-resistant generic E. coli in dogs.

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.

Longitudinal study of Clostridium difficile and antimicrobial susceptibility of Escherichia coli in healthy horses in a community setting

Point prevalence studies have reported carriage rates of enteric pathogens in healthy horses, but longitudinal data are lacking. Commensal E. coli is an indicator organism to evaluate antimicrobial resistance of enteric bacteria, yet there are limited data for horses. The objectives of this study were to investigate and molecularly characterize isolates of Clostridium difficile, Clostridium perfringens and Salmonella, collected sequentially over a one year period, and to determine the antibiotic susceptibility profile for E. coli. Fecal samples were collected monthly from 25 adult horses for one year. Selective cultures were performed for all above bacteria. C. difficile isolates were characterized via PCR toxin gene profiling and ribotyping. Broth microdilution was performed to assess antimicrobial susceptibility profiles of E. coli. Toxigenic Clostridium difficile was isolated from 15/275 (5.45%) samples from 10/25 (40%) horses. Four horses were positive at multiple sampling times but different ribotypes were found in three. Ribotypes included 078 (n=6), 001 (n=6) and C (n=3). C. perfringens was not isolated, nor was Salmonella. E. coli was isolated from 232/300 (77%) fecal samples. Resistance to ≥ 1 and ≥ 3 antimicrobials was present in 31/232 (13.4%) and 6/232 (2.6%) respectively. Only two horses shed the same strain of toxigenic C. difficile for more than one month, indicating that shedding is transient. The high number of ribotype 078 is consistent with recent emergence of this strain in the local horse population. The low prevalence of antibiotic resistance in commensal E. coli suggests that healthy horses are not likely a major reservoir of resistance for enteric bacteria.

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 β-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.

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.

Evaluation of pet-related management factors and the risk of Salmonella spp. carriage in pet dogs from volunteer households in Ontario (2005-2006)

The purpose of this study was to determine pet-related management factors that may be associated with the presence of Salmonella spp. in feces of pet dogs from volunteer households. From October 2005 until May 2006, 138 dogs from 84 households in Ontario were recruited to participate in a cross-sectional study. Five consecutive daily fecal samples were collected from each dog and enrichment culture for Salmonella spp. was performed. A higher than expected number of the dogs (23.2%; 32/138) had at least one fecal sample positive for Salmonella, and 25% (21/84) of the households had at least one dog shedding Salmonella. Twelve serotypes of Salmonella enterica subsp. enterica were identified, with the predominant serotypes being Typhimurium (33.3%; 13/39), Kentucky (15.4%; 6/39), Brandenburg (15.4%; 6/39) and Heidelberg (12.8%; 5/39). Univariable logistic regression models were created with a random effect for household to account for clustering. Statistically significant risk factors for a dog testing positive included having contact with livestock, receiving a probiotic in the previous 30 days, feeding a commercial or homemade raw food diet, feeding raw meat and eggs, feeding a homemade cooked diet, and having more than one dog in the household. In two-variable models that controlled for feeding raw food, the non-dietary variables were no longer statistically significant. These results highlight the potential public health risk of including raw animal products in canine diets.

Clostridium difficile in seafood and fish

The objective of this study was to determine the prevalence of Clostridium difficile contamination in retail seafood and fish from Canadian grocery stores. C. difficile was found in 4.8% (5/119) of the samples. This study, combined with studies of other food sources, suggests that widespread contamination of food is common.

Escherichia coli and selected veterinary and zoonotic pathogens isolated from environmental sites in companion animal veterinary hospitals in southern Ontario

Hospital-based infection control in veterinary medicine is emerging and the role of the environment in hospital-acquired infections (HAI) in veterinary hospitals is largely unknown. This study was initiated to determine the recovery of Escherichia coli and selected veterinary and zoonotic pathogens from the environments of 101 community veterinary hospitals. The proportion of hospitals with positive environmental swabs were: E. coli--92%, Clostridium difficile--58%, methicillin-resistant Staphylococcus aureus (MRSA)--9%, CMY-2 producing E. coli--9%, methicillin-resistant Staphylococcus pseudintermedius--7%, and Salmonella--2%. Vancomycin-resistant Enterococcus spp., canine parvovirus, and feline calicivirus were not isolated. Prevalence of antimicrobial resistance in E. coli isolates was low. Important potential veterinary and human pathogens were recovered including Canadian epidemic strains MRSA-2 and MRSA-5, and C. difficile ribotype 027. There is an environmental reservoir of pathogens in veterinary hospitals; therefore, additional studies are required to characterize risk factors associated with HAI in companion animals, including the role of the environment.

Occurrence of antimicrobial resistant bacteria in healthy dogs and cats presented to private veterinary hospitals in southern Ontario: A preliminary study

The prevalence and patterns of antimicrobial susceptibility of fecal Escherichia coli, Salmonella spp., extended beta-lactamase producing E. coli (ESBL-E. coli), methicillin-resistant Staphylococcus aureus (MRSA), and methicillin-resistant Staphylococcus pseudintermedius (MRSP) were determined for healthy dogs (n = 188) and cats (n = 39) from veterinary hospitals in southern Ontario that had not had recent exposure to antimicrobials. The prevalence of antimicrobial resistance in E. coli was as follows: streptomycin (dogs - 17%, cats - 2%), ampicillin (dogs - 13%, cats - 4%), cephalothin (dogs - 13%, cats - < 1%), and tetracycline (dogs - 11%, cats - 2%). Eleven percent of dogs and 15% of cats had isolates that were resistant to at least 2 antimicrobials. Cephamycinase (CMY)-2 producing E. coli was cultured from 2 dogs. No Salmonella spp., ESBL-E. coli, MRSA, or MRSP isolates were recovered. The observed prevalence of resistance in commensal E. coli from this population was lower than that previously reported in companion animals, but a small percentage of dogs may be a reservoir for CMY-2 E. coli.

Possible seasonality of Clostridium difficile in retail meat, Canada

We previously reported Clostridium difficile in 20% of retail meat in Canada, which raised concerns about potential foodborne transmissibility. Here, we studied the genetic diversity of C. difficile in retail meats, using a broad Canadian sampling infrastructure and 3 culture methods. We found 6.1% prevalence and indications of possible seasonality (highest prevalence in winter).

Chloramphenicol and kanamycin resistance among porcine Escherichia coli in Ontario

OBJECTIVES

The purpose of this study was to compare the distribution of chloramphenicol and kanamycin resistance genes across three populations of porcine Escherichia coli.

METHODS

PCR was used to assess the distribution of the major chloramphenicol and kanamycin resistance genes catA1, cmlA and floR, and aphA1, aphA2 and aadB in enterotoxigenic E. coli (ETEC), non-ETEC isolates from cases of diarrhoea and commensal E. coli from healthy pigs. Associations between these genes and resistance genes for other antimicrobials or virulence genes were assessed.

RESULTS

The chloramphenicol and kanamycin resistance genes were distributed differently among the three E. coli populations. While aphA1, aphA2 and aadB were evenly distributed among resistant ETEC, non-ETEC and commensals, the catA1 gene was significantly more frequent in ETEC than in non-ETEC and commensals. Transformation experiments confirmed statistical associations by demonstrating that elt, estB, astA, aadA and sul1 were located with catA1 on a large ETEC plasmid. Plasmids carrying cmlA also carried sul3 and aadA. Other plasmids carrying floR and aadB also carried tet(A), sul2, strA/strB, bla(CMY-2) and occasionally aac(3)IV.

CONCLUSIONS

The clustering of genes observed is a likely cause for chloramphenicol resistance persistence. Similar to tetracycline, chloramphenicol resistance genes are physically linked to virulence genes. This is not the case for kanamycin resistance determinants, which were linked to other resistance genes only.

Antimicrobial resistance and virulence genes of Escherichia coli isolates from swine in Ontario

A total of 318 Escherichia coli isolates obtained from diarrheic and healthy pigs in Ontario from 2001 to 2003 were examined for their susceptibility to 19 antimicrobial agents. They were tested by PCR for the presence of resistance genes for tetracycline, streptomycin, sulfonamides, and apramycin and of 12 common virulence genes of porcine E. coli. Antimicrobial resistance frequency among E. coli isolates from swine in Ontario was moderate in comparison with other countries and was higher in isolates from pigs with diarrhea than in isolates from healthy finisher pigs. Resistance profiles suggest that cephamycinases may be produced by > or = 8% of enterotoxigenic E. coli (ETEC). Resistance to quinolones was detected only in enterotoxigenic E. coli (< or = 3%). The presence of sul3 was demonstrated for the first time in Canada in porcine E. coli isolates. Associations were observed among tetA, sul1, aadA, and aac(3)IV and among tetB, sul2, and strA/strB, with a strong negative association between tetA and tetB. The paa and sepA genes were detected in 92% of porcine ETEC, and strong statistical associations due to colocation on a large plasmid were observed between tetA, estA, paa, and sepA. Due at least in part to gene linkages, the distribution of resistance genes was very different between ETEC isolates and other porcine E. coli isolates. This demonstrates that antimicrobial resistance epidemiology differs significantly between pathogenic and commensal E. coli isolates. These results may have important implications with regards to the spread and persistence of resistance and virulence genes in bacterial populations and to the prudent use of antimicrobial agents.