Low prevalence of zoonotic multidrug‐resistant bacteria in veterinarians in a country with prudent use of antimicrobials in animals

The occurrence of multidrug‐resistant zoonotic bacteria in animals has been increasing worldwide. Working in close contact with livestock increases the risk of carriage of these bacteria. We investigated the occurrence of extended‐spectrum beta‐lactamase (ESBL) and plasmidic AmpC beta‐lactamase producing Enterobacteriaceae (ESBL/pAmpC‐PE) and livestock‐associated methicillin‐resistant Staphylococcus aureus (LA‐MRSA) in Finnish veterinarians (n = 320). In addition to microbiological samples, background information was collected. Bacterial whole genome sequencing was performed to deduce sequence types (STs), spa types and resistance genes of the isolates. In total, 3.0% (9/297) of the veterinarians carried ESBL producing Escherichia coli, with one ESBL producing E. coli isolate producing also AmpC. Seven different STs, sequences of several different plasmid groups as well as several different bla_ESBL/pAmpC genes existed in different combinations. No carbapenemase or colistin resistance genes were detected. MRSA was detected in 0.3% (1/320) of the samples. The strain belonged to LA‐MRSA clonal complex (CC) 398 (ST398, spa type 011, lacking Panton‐Valentine leukocidin genes). In conclusion, this study shows low carriage of multidrug‐resistant zoonotic bacteria in Finnish veterinarians. However, finding LA‐MRSA for the first time in a sample from a veterinarian in a country with prudent use of animal antimicrobials and regarding the recent rise of LA‐MRSA on Finnish pig farms, a strong recommendation to protect people working in close contact with animals carrying LA‐MRSA CC398 is given. Further studies are needed to explain why the prevalence of LA‐MRSA in veterinarians is lower in Finland than in other European countries.     

Low Occurrence of Extended‐Spectrum β‐lactamase‐Producing Escherichia coli in Finnish Food‐Producing Animals

ESBL/AmpC‐producing Escherichia coli is increasingly isolated from humans and animals worldwide. The occurrence of ESBL/AmpC‐producing E. coli was studied in food‐producing animals in Finland, a country with a low and controlled use of antimicrobials in meat production chain. A total of 648 cattle, 531 pig, 495 broiler and 35 turkey faecal samples were collected from four Finnish slaughterhouses to determine the presence of extended‐spectrum β‐lactamase (ESBL/AmpC)‐producing E. coli. In addition, 260 broiler and 15 turkey samples were screened for carbapenemase‐producing E. coli. Susceptibility to different class of cephalosporins and meropenem was determined with disc diffusion tests according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Determination of ESBL/AmpC production was performed with a combination disc diffusion test according to the recommendations of the European Food Safety Authority (EFSA). Plasmidic bla_ESBL/AmpC genes were characterized by polymerase chain reaction and sequencing. A collection of isolates producing AmpC enzyme but not carrying plasmidic bla_AmpC was analysed by PCR and sequencing for possible chromosomal ampC promoter area mutations. Altogether ESBL/AmpC‐producing E. coli was recovered from five cattle (0.8%), eight pig (1.5%) and 40 broiler samples (8.1%). No ESBL/AmpC‐producing E. coli was found in turkey samples. Carbapenem resistance was not detected. Altogether ESBL/AmpC‐producing E. coli was found on 4 (2.0%), 3 (4.5%) and 14 (25%) cattle, pig and broiler farms, respectively. From cattle samples 3 (27%) bla_CTX‐M‐1 and from broiler samples 13 (33%) bla_CTX‐M‐1 and 22 (55%) bla_CMY‐2 gene‐carrying isolates were detected. In pigs, no plasmidic bla_ESBL/AmpC gene‐carrying isolates were found. In all analysed isolates, the same mutations in the promoter region of chromosomal ampC were detected. The results showed low occurrence of ESBL/AmpC‐producing E. coli in Finnish food‐producing animals. In pigs, plasmidic bla_ESBL/AmpC‐carrying E. coli was not detected at all.     

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.     

Cross-sectional study of antimicrobial-resistant bacteria in horses. Part 1: Prevalence of antimicrobial-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus

Reasons for performing study: The increasing prevalence of antimicrobial‐resistant bacteria such as methicillin‐resistant Staphylococcus aureus (MRSA) and antimicrobial‐resistant Escherichia coli represents a significant problem. However, the carriage of such bacteria by horses in the UK has not been well characterised. Objectives: To estimate the prevalence of nasal carriage of MRSA and faecal carriage of antimicrobial‐resistant E. coli amongst horses in the general equine community of the mainland UK. Methods: A cross‐sectional study of horses recruited by 65 randomly selected equine veterinary practices was conducted, with nasal swabs and faecal samples collected. Faecal samples were cultured for antimicrobial‐resistant E. coli. Nasal swabs were cultured for staphylococcal species; methicillin‐resistant isolates identified as S. aureus were characterised by SCCmec and spa gene typing. Multilevel logistic regression models were used to calculate prevalence estimates with adjustment for clustering at practice and premises levels. Spatial variation in risk of antimicrobial resistance was also examined. Results: In total, 650 faecal samples and 678 nasal swabs were collected from 692 horses located on 525 premises. The prevalence of faecal carriage of E. coli with resistance to any antimicrobial was 69.5% (95% CI 65.9–73.1%) and the prevalence of extended‐spectrum β‐lactamase (ESBL)‐producing E. coli was 6.3% (95% CI 4.1–9.6%). The prevalence of nasal carriage of MRSA was 0.6% (95% CI 0.2–1.5%). Spatial analysis indicated variation across the UK for risk of carriage of resistant and multidrug‐resistant (resistant to more than 3 antimicrobial classes) E. coli. Conclusions and potential relevance: Carriage of MRSA by horses in the community appears rare, but the prevalence of antimicrobial‐resistant E. coli (including ESBL‐producing E. coli) is higher. A high prevalence of antimicrobial‐resistant bacteria could have significant health implications for the horse population of the UK.     

Extended‐spectrum beta‐lactamase‐producing Escherichia coli in common vampire bats Desmodus rotundus and livestock in Peru

Antibiotic resistance mediated by bacterial production of extended‐spectrum beta‐lactamase (ESBL) is a global threat to public health. ESBL resistance is most commonly hospital‐acquired; however, infections acquired outside of hospital settings have raised concerns over the role of livestock and wildlife in the zoonotic spread of ESBL‐producing bacteria. Only limited data are available on the circulation of ESBL‐producing bacteria in animals. Here, we report ESBL‐producing Escherichia coli in wild common vampire bats Desmodus rotundus and livestock near Lima, Peru. Molecular analyses revealed that most of this resistance resulted from the expression of bla_CTX‐M‐15 genes carried by plasmids, which are disseminating worldwide in hospital settings and have also been observed in healthy children of Peru. Multilocus sequence typing showed a diverse pool of E. coli strains carrying this resistance that were not always host species‐specific, suggesting sharing of strains between species or infection from a common source. This study shows widespread ESBL resistance in wild and domestic animals, supporting animal communities as a potential source of resistance. Future work is needed to elucidate the role of bats in the dissemination of antibiotic‐resistant strains of public health importance and to understand the origin of the observed resistance.     

Meta‐analysis of the prevalence of thermotolerant Campylobacter in food‐producing animals worldwide

The objective of this meta‐analysis was to summarize available information on the prevalence of thermotolerant Campylobacter (TC) in different food‐producing animals worldwide. Databases (i.e., PubMed, ScienceDirect, Scopus) were searched from 1980 to 2017 unrestricted by language. The inclusion criteria were as follows: prevalence or incidence studies, published in peer‐reviewed journals, and they must have reported the total number of animal samples studied and the number of samples that were positive for the presence of TC. When the identification of Campylobacter species was available, this information was included in the analysis. Multilevel random‐effect meta‐analysis models were fitted to estimate mean occurrence rate of TC and to compare them among different factors potentially associated with the outcome. The mean occurrence rate of TC in food‐producing animals was 0.424 (95% CI: 0.394–0.455), and the mean occurrence rate of Campylobacter jejuni and Campylobacter coli were 0.214 and 0.133, respectively. Pigs and poultry showed the highest prevalence of TC; however, there were differences in the prevalence of each Campylobacter species. Campylobacter jejuni was observed in broilers (0.322; 95% CI: 0.273–0.377) and hens (0.395; 95% CI: 0.265–0.542), while C. coli was restricted essentially in pigs (0.553; 95% CI: 0.541–0.650). The prevalence of C. jejuni in intensively bred cattle was higher (0.302; 95% CI: 0.227–0.389) than the prevalence in extensively bred cattle (0.172; 95% CI: 0.119–0.242) while the prevalence of C. coli was similar (0.051; 95% CI: 0.028–0.091 vs. 0.050; 95% CI: 0.027–0.091) in both production systems. Agar with or without blood used for the isolation of TC did not affect the prevalence observed. The method of species identification did not seem to generate differences in the prevalence of Campylobacter species. The prevalence of Campylobacter in primary food production has a strong impact on the entire agri‐food chain. National authorities must monitor the situation with the aim to establish the appropriate risk management measures.     

Characterisation of extended-spectrum β-lactamase and AmpC β-lactamase-producing Enterobacteriaceae isolated from companion animals in New Zealand

Abstract

AIMS: To assess the occurrence of, and characterise, extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase (AmpC)-producing Enterobacteriaceae isolated by veterinary diagnostic laboratories from infection sites in companion animals in New Zealand.

METHODS: Selected Enterobacteriaceae isolates were submitted by seven New Zealand veterinary diagnostic laboratories. They were isolated from infection sites in companion animals between June 2012 and June 2013, and were resistant to amoxicillin-clavulanic acid, fluoroquinolones, or any combination of two or more antimicrobials. Based on disk diffusion test results, the isolates were phenotypically categorised according to production of ESBL and AmpC. Genes for ESBL and AmpC production were amplified by PCR and sequenced. Escherichia coli isolates were also typed by multilocus sequence typing.

RESULTS: A total of 115 isolates matching the inclusion criteria were obtained from the participating laboratories, of which 74 (64%) originated from dogs and 29 (25%) from cats. Seven bacterial species were identified, of which E. coli was the most common (87/115, 76%). Of the 115 isolates, 10 (9%) expressed the ESBL phenotype, 43 (37%) the AmpC phenotype, and seven (6%) both ESBL and AmpC phenotypes. Of the 60 ESBL and AmpC-producing isolates, 36 (60%) were E. coli. Amongst these isolates, 27/60 (45%) were classified as multidrug resistant, compared with 15/55 (27%) non-ESBL or AmpC-producing isolates (p<0.01). Ninety five isolates were resistant to amoxicillin-clavulanic acid and 58 (61%) of these were ESBL or AmpC-producing. The predominant ESBL genes were bla_CTX-M-14 and bla_CTX-M-15, and the dominant plasmid-encoded AmpC gene was bla_CMY-2. Thirty-eight E. coli multilocus sequence types (ST) were identified, and the most prevalent were ST12 (12/89, 13%), ST131 (6/89, 7%) and ST648 (6/89, 7%). ESBL and AmpC-producing isolates accounted for 35/1,082 (3.2%) of the Enterobacteriaceae isolated by one laboratory network over the study period.

CONCLUSIONS AND CLINICAL RELEVANCE: ESBL and AmpC-producing Enterobacteriaceae were associated with clinical infections in companion animals in New Zealand, and were often multidrug resistant. In this study, these organisms accounted for <5% of all Enterobacteriaceae isolated from infection sites by one laboratory network, but their prevalence among isolates resistant to amoxicillin-clavulanic acid was 61%. Therefore routine secondary testing for ESBL and AmpC production by Enterobacteriaceae that are resistant to amoxicillin-clavulanic acid in primary testing could improve the accuracy of definitive antimicrobial therapy in companion animals in New Zealand.     

Circulation of emerging NDM‐5‐producing Escherichia coli among humans and dogs in Egypt

The emergence of NDM‐producing Escherichia coli has considerably threatened human and animal health worldwide. This study describes for the first time in Egypt, the draft genome sequences of emerging NDM‐5‐producing E. coli from humans and dogs, and investigates genetic relatedness between isolates from both sources. Two E. coli from human urine and seven from environmental clinical samples of dogs exhibited resistance to carbapenems and harbouring bla_NDM were subjected to Illumina Miseq whole‐genome sequencing (WGS). Assembly and analysis of the reads were performed to identify resistance genes, multilocus sequence types (MLST), plasmid replicon types (Inc) and insertion sequences (IS) of the bla_NDM region; core genome MLST (cgMLST) analysis was also performed. Two different NDM alleles were identified; bla_NDM‐5 in E. coli HR119 from the urine of a healthy person and environmental samples of dogs, and bla_NDM‐1 in E. coli HR135 from a human patient's urine. Multiple mobilizable resistance genes to different antimicrobial classes were identified except the colistin resistance gene, mcr. E. coli isolates from humans and dogs were assigned to different sequence types (STs). Using cgMLST, dog isolates clustered together with only 1–2 allellic differences; however, human E. coli showed 1,978 different allelles compared with dog isolates. Plasmidfinder results indicated the presence of an IncX3 replicon in bla_NDM‐5‐producing E. coli; however, bla_NDM‐1 was linked to IncCoIKP3. Notably, the NDM region (3 Kb) in all isolates from humans and dogs was highly similar with variable flanking sequences that represented different IS elements. This study reports the first emergence of NDM‐5‐producing E. coli from dogs in Egypt that shared some genetic features with human isolates and could be considered potential public health threats.     

The occurrence of Salmonella,extended‐spectrum β‐lactamase producing Escherichia coli and carbapenem resistant non‐fermenting Gram‐negative bacteria in a backyard poultry flock environment

Increase in the number of small‐scale backyard poultry flocks in the USA has substantially increased human‐to‐live poultry contact, leading to increased public health risks of the transmission of multi‐drug resistant (MDR) zoonotic and food‐borne bacteria. The objective of this study was to detect the occurrence of Salmonella and MDR Gram‐negative bacteria (GNB) in the backyard poultry flock environment. A total of 34 backyard poultry flocks in Washington State (WA) were sampled. From each flock, one composite coop sample and three drag swabs from nest floor, waterer‐feeder, and a random site with visible faecal smearing, respectively, were collected. The samples were processed for isolation of Salmonella and other fermenting and non‐fermenting GNB under ceftiofur selection. Each isolate was identified to species level using MALDI‐TOFF and tested for resistance against 16 antibiotics belonging to eight antibiotic classes. Salmonella serovar 1,4,[5],12:i:‐ was isolated from one (3%) out of 34 flocks. Additionally, a total of 133 ceftiofur resistant (Cef^R) GNB including Escherichia coli (53), Acinetobacter spp. (45), Pseudomonas spp. (22), Achromobacter spp. (8), Bordetella trematum (1), Hafnia alvei (1), Ochrobactrum intermedium (1), Raoultella ornithinolytica (1), and Stenotrophomonas maltophilia (1) were isolated. Of these, 110 (82%) isolates displayed MDR. Each flock was found positive for the presence of one or more Cef^R GNB. Several MDR E. coli (n = 15) were identified as extended‐spectrum β‐lactamase (ESBL) positive. Carbapenem resistance was detected in non‐fermenting GNB including Acinetobacter spp. (n = 20), Pseudomonas spp. (n = 11) and Stenotrophomonas maltophila (n = 1). ESBL positive E. coli and carbapenem resistant non‐fermenting GNB are widespread in the backyard poultry flock environment in WA State. These GNB are known to cause opportunistic infections, especially in immunocompromised hosts. Better understanding of the ecology and epidemiology of these GNB in the backyard poultry flock settings is needed to identify potential risks of transmission to people in proximity.     

Genetic background of CTX‐M‐15‐producing Enterobacter hormaechei ST114 and Citrobacter freundii ST265 co‐infecting a free‐living green turtle (Chelonia mydas)

CTX‐M‐type extended‐spectrum β‐lactamase (ESBL)‐producing Enterobacteriaceae have become identified in marine ecosystem constituting a serious ecological issue. In this respect, although contamination of coastal waters and seafood, and even colonization of seabirds and fishes have been increasingly reported, molecular data are lacking to elucidate the clinical impact of ESBL producers in infected marine animals. In this study, using a genomic approach, we have analysed the genetic background of CTX‐M‐15‐producing Enterobacter hormaechei (belonging to the international human clone ST114) and Citrobacter freundii (ST265) co‐infecting a free‐living green turtle (Chelonia mydas) suffering from septic arthritis, which progressed to generalized coelomitis and death. Wide resistome of these pathogens contributed to treatment failure and death of the animal.     

The Use of Direct‐Fed Microbials to Reduce Shedding of Escherichia coli O157 in Beef Cattle: A Systematic Review and Meta‐analysis

Human illness due to infections with Escherichia coli O157 is a serious health concern. Infection occurs through direct contact with infected animals or their faeces, through contaminated food or water and/or through person‐to‐person transmission. A reduction in faecal E. coli O157 shedding in cattle might reduce the burden of human infections. We used systematic review and meta‐analysis to assess the efficacy of direct‐fed microbials (DFM), compared with placebo or no treatment, fed during the pre‐harvest stage of production in reducing faecal E. coli O157 shedding in beef cattle during field trials. Four electronic databases, Nebraska Beef Reports and review article reference lists were searched. A total of 16 publications assessing faecal shedding at the end of the trial and/or throughout the trial period were included. The majority of publicly disseminated trials evaluated the prevalence of E. coli O157 faecal shedding; only two evaluated the concentration of organisms in faeces. The prevalence of faecal E. coli O157 shedding in cattle is significantly reduced by DFM treatments (summary effect size for all DFM – OR = 0.46; CI = 0.36–0.60). The DFM combination Lactobacillus acidophilus (NP51) and Propionibacterium freudenreichii (NP24) was more efficacious in reducing the prevalence of faecal E. coli O157 shedding at the time of harvest and throughout the trial period compared with the group of other DFM, although this difference was not statistically significant. Furthermore, we found that the combination [NP51 and NP24] treatment was more efficacious in reducing the prevalence of faecal E. coli O157 shedding at the time of harvest and throughout the trial period when fed at the dose of 10⁹ CFU/animal/day than any lesser amount, although this difference was not statistically significant. Feeding beef cattle DFM during the pre‐harvest stage of production reduces the prevalence of E. coli O157 faecal shedding and might effectively reduce human infections.     

In vitro assessment of chloramphenicol and florfenicol as second‐line antimicrobial agents in dogs

The aim of this study was to evaluate the potential of chloramphenicol and florfenicol as second‐line antimicrobial agents for treatment of infections caused by methicillin‐resistant Staphyococcus pseudintermedius (MRSP) and extended‐spectrum β‐lactamase (ESBL)‐producing Escherichia coli in dogs, through a systematic in vitro assessment of the pharmacodynamic properties of the two drugs. Minimum inhibitory concentrations (MIC) and phenicol resistance genes were determined for 169 S. pseudintermedius and 167 E. coli isolates. Minimum bactericidal concentrations (MBC), time‐killing kinetics, and postantibiotic effect (PAE) of both agents against wild‐type isolates of each species were assessed. For S. pseudintermedius, the chloramphenicol MIC₉₀ was 32 μg/mL. No florfenicol resistance was detected in this species (MIC_90 = 4 μg/mL). The MIC₉₀ of both agents against E. coli was 8 μg/mL. Resistance genes found were cat_pC221 in S. pseudintermedius and catA1 and/or floR in E. coli. The phenicols displayed a time‐dependent, mainly, bacteriostatic effect on both species. Prolonged PAEs were observed for S. pseudintermedius, and no PAEs were detected for E. coli. More research into determination of PK/PD targets of efficacy is needed to further assess the clinical use of chloramphenicol and florfenicol as second‐line agents in dogs, optimize dosage regimens, and set up species‐specific clinical break points.     

Quantitative real‐time PCR monitoring of Escherichia coli and Clostridium perfringens with oral administration of Lactobacillus plantarum strain Lq80 to weaning piglets

Levels of fecal or intestinal lactobacilli, Escherichia coli and Clostridium perfringens, and the prevalence of clostridial alpha toxin gene and heat‐stable toxin (ST) gene of enterotoxigenic E. coli (ETEC) were monitored in weaned piglets before (day 0) and during (days 7, 14, and 21) the administration of Lactobacillus plantarum strain Lq80. Lactobacilli were enumerated in a culture‐dependent method. The remainders were determined by quantitative real‐time PCR. In this quantitative real‐time PCR method, the detection limit was proved to be as low as 10³ cells/g feces or intestinal contents. Number of lactobacilli increased from day 0 to day 7 (P < 0.05), to day 14 (P < 0.05), and to day 21 (P = 0.07) in the Lq80‐administered group. L. plantarum contributed to as low as 10% of the lactobacillal population in the Lq80‐administered group. The number of E. coli and C. perfringens, and the prevalence of alpha toxin gene in feces or intestinal contents of the Lq80‐administered group decreased, at least in the first week of the postweaning period. Oral administration of L. plantarum strain Lq80 can stimulate the growth of indigenous lactobacilli and decrease ST‐producing ETEC and C. perfringens in the intestine of postweaning piglets.     

Prevalence and Genetic Relatedness of Antimicrobial‐Resistant Escherichia coli Isolated From Animals,Foods and Humans in Iceland

The prevalence of resistant bacteria in food products in Iceland is unknown, and little is known of the prevalence in production animals. The aim of this study was to investigate the prevalence and genetic relatedness of antimicrobial‐resistant Escherichia coli from healthy pigs and broiler chicken, pork, broiler meat, slaughterhouse personnel and outpatients in Iceland. A total of 419 E. coli isolates were tested for antimicrobial susceptibility using a microbroth dilution method (VetMIC), and resistant strains were compared using pulsed‐field gel electrophoresis (PFGE). All samples were screened for enrofloxacin‐resistant strains with selective agar plates. The resistance rates among E. coli isolates were moderate to high from caecal and meat samples of pigs (54.1% and 28%), broilers (33.6% and 52%) and slaughterhouse personnel (39.1%), whereas isolates from outpatients showed moderate resistance rates (23.1%). Of notice was resistance to quinolones (minimum inhibitory concentrations: nalidixic acid ≥ 32, ciprofloxacin ≥ 0.12 and enrofloxacin ≥ 0.5), particularly among broiler and broiler meat isolates (18.2% and 36%), as there is no known antimicrobial selection pressure in the broiler production in Iceland. The majority (78.6%) of the resistant E. coli isolates was genotypically different, based on PFGE fingerprint analyses and clustering was limited. However, the same resistance pattern and pulsotype were found among isolates from broiler meat and a slaughterhouse worker, indicating spread of antimicrobial‐resistant E. coli from animals to humans. Diverse resistance patterns and pulsotypes suggest the presence of a large population of resistant E. coli in production animals in Iceland. This study gives baseline information on the prevalence of antimicrobial‐resistant E. coli from production animals, and their food products in Iceland and the moderate to high resistance rates emphasize the need for continuing surveillance. Further studies on the origin of the resistant strains and the genetic relatedness of strains of different origin are needed.     

An investigation of shedding and super‐shedding of Shiga toxigenic Escherichia coli O157 and E. coli O26 in cattle presented for slaughter in the Republic of Ireland

Shiga toxigenic Escherichia coli (STEC) are an important group of pathogens and can be transmitted to humans from direct or indirect contact with cattle faeces. This study investigated the shedding of E. coli O157 and O26 in cattle at the time of slaughter and factors associated with super‐shedding (SS) animals. Rectoanal mucosal swab (RAMS) samples were collected from cattle (n = 1,317) at three large Irish commercial beef abattoirs over an 18 month period, and metadata were collected at the time of sampling regarding farm of origin, animal age, breed and gender. RAMS swabs were examined for the presence and numbers of E. coli O157 and O26 using a previously developed quantitative real‐time PCR protocol. Samples positive by PCR were culturally examined and isolates analysed for the presence of stx subtypes, eae and phylogroup. Any samples with counts >10⁴ CFU/swab of STEC O157 or O26 were deemed to be super‐shedders. Overall, 4.18% (55/1,317) of RAMS samples were positive for STEC O157, and 2.13% (28/1,317) were classified as STEC O157 SS. For STEC O26, 0.76% (10/1,317) of cattle were positive for STEC O26, and 0.23% (3/1,317) were classified as super‐shedders. Fewer STEC shedders and SS were noted among older animals (>37 months). There was a seasonal trend observed for STEC O157, with the highest prevalence of shedding and SS events in the autumn (August to October). The majority of E. coli O157 (50/55) isolates had stx2 and were eae positive, with no significant difference between SS and low shedders (LS). Interestingly, all STEC O26 (n = 10) were eae negative and had varied stx profiles. This study demonstrates that, while the overall shedding rates are relatively low in cattle at slaughter, among positive animals there is a high level of SS, which may pose a higher risk of cross‐contamination during slaughter.     

Extended‐Spectrum β‐lactam Resistance in the Enteric Flora of Patients at a Tertiary Care Medical Centre

The dissemination of Enterobacteriaceae expressing resistance to extended‐spectrum cephalosporins, which are therapeutically used in both human and veterinary medicine, is of critical concern. The normal commensal flora of food animals may serve as an important reservoir for the zoonotic food‐borne transmission of Enterobacteriaceae harbouring β‐lactam resistance. We hypothesized that the predominant AmpC and ESBL genes reported in US livestock and fresh retail meat products, bla_CMY‐2 and bla_CTX‐M, would also be predominant in human enteric flora. We recovered enteric flora from a convenience sample of patients included in a large tertiary medical centre's Clostridium difficile surveillance programme to screen for and estimate the frequency of carriage of AmpC and ESBL resistance genes. In‐ and outpatient diarrhoeic submissions (n = 692) received for C. difficile testing at the medical centre's clinical diagnostic laboratory from July to December, 2013, were included. Aliquoted to a transport swab, each submission was inoculated to MacConkey broth with cefotaxime, incubated at 37°C and then inoculated to MacConkey agars supplemented with cefoxitin and cefepime to select for the AmpC and ESBL phenotypes, with bla_CMY and bla_CTX‐M genotypes confirmed by PCR and sequencing. From the 692 diarrhoeic submissions, our selective culture yielded 184 isolates (26.6%) with reduced susceptibility to cefotaxime. Of these, 46 (6.7%) samples harboured commensal isolates carrying the AmpC bla_CMY. Another 21 (3.0%) samples produced isolates harbouring the ESBL bla_CTX‐M: 19 carrying CTX‐M‐15 and 2 with CTX‐M‐27. Our results indicate that β‐lactam resistance genes likely acquired through zoonotic food‐borne transmission are present in the enteric flora of this hospital‐associated population at lower levels than reported in livestock and fresh food products.     

Antibiotic resistant Escherichia coli in southeastern Australian pig herds and implications for surveillance

To investigate public health implications of antibiotics to control post‐weaning scours, we surveyed 22 commercial pig herds in southeastern Australia. Fifty faecal samples per herd were collected from pre‐ and post‐weaned piglets. Presumptive Escherichia coli isolates were confirmed by MALDI‐TOF MS. Isolates (n = 325) were screened for susceptibility to 19 veterinary antibiotics using MIC broth microdilution. All 325 E. coli isolates underwent further testing against 27 antibiotics used in human medicine and were screened for ETEC adhesin and enterotoxin genes (F4 (K88), F5 (K99), F6 (987P), F18, F41, STa, STb, Stx2e and LT) by multiplex PCR. Isolates identified as phenotypically resistant to third‐generation cephalosporin (3GC) and aminoglycoside antibiotics were screened by multiplex PCR/reverse line blot to detect common β‐lactam and aminoglycosides resistance genes, confirmed by sequencing. Twenty (6.1%) of the E. coli isolates were resistant to 3GC antibiotics and 24 (7.4%) to the aminoglycoside antibiotic gentamicin. Genetic analysis revealed six different extended spectrum β‐lactamase (ESBL) genes (blaCTX‐M‐1, ‐14, ‐15, ‐27, blaSHV‐12 and blaCMY‐2‐like genes), four of which have not been previously reported in Australian pigs. Critically, the prevalence of 3GC resistance was higher in non‐pathogenic (non‐ETEC) isolates and those from clinically normal (non‐diarrhoeal) samples. This highlights the importance of non‐ETECE. coli as reservoirs of antimicrobial resistance genes in piglet pens. Antimicrobial resistance surveillance in pig production focused on diagnostic specimens from clinically‐affected animals might be potentially misleading. We recommend that surveillance for emerging antimicrobial resistance such as to 3GC antibiotics should include clinically healthy pigs.     

Molecular characterization of community‐associated methicillin‐resistant Staphylococcus aureus from pet dogs

Community‐associated methicillin‐resistant Staphylococcus aureus (MRSA) is a serious public health concern and in Australia, one that disproportionately affects Aboriginal people. Paralleling MRSA in human medicine, methicillin‐resistant S. pseudintermedius (MRSP) is an increasingly prevalent pathogen in veterinary medicine. We aimed to characterize the carriage of MRSA and MRSP in dogs and cats from predominantly Aboriginal communities in a very remote region of New South Wales (NSW), Australia. Pets (303 dogs and 80 cats) were recruited from six communities in western NSW. Three swabs were collected from each animal (anterior nares, oropharynx and perineum) and from skin lesions or wounds (if present) and cultured on selective media for methicillin‐resistant staphylococci. Human host‐adapted community‐associated MRSA representing four multilocus sequence types (ST1‐IV, ST5‐IV, ST72‐IV, ST93‐IV) were isolated from eight dogs (prevalence 2.6%, 95% confidence interval 1.3%–5.1%). Two ST5‐IV isolates from a single dog were phenotypically trimethoprim‐resistant, harbouring trimethoprim‐resistant gene dfrG within the SCCmec type IVo mobile genetic element. MRSA was not isolated from any cats and MRSP was not isolated from any dogs or cats. This study estimated a high prevalence of human host‐adapted community‐associated MRSA carriage in dogs despite an absence of MRSP. This suggests MRSA carried by dogs in remote NSW originate from human hosts. The cycle of transmission between people, dogs and common environmental sources warrants further investigation. To our knowledge, this is the first report of trimethoprim‐resistant ST5‐IV in eastern Australia and the first report of trimethoprim‐resistant ST5‐IV from a dog.     

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.     

Fecal carriage of multi-drug resistant and extended spectrum β-lactamases producing E. coli in household pigeons,Bangladesh

Antibiotic resistance and ESBL constitute a risk to human and animal health. Birds residing close to humans could mirror the spectrum of human associated antibiotic resistance. Household pigeons were screened in Bangladesh to shed light on human associated, as well as, environmental antibiotic resistance. Escherichia coli from pigeons (n = 150) were tested against 11 antibiotics. 89% E. coli isolates were resistant to one or more critically important human antibiotics like ampicillin, cefadroxil, mecillinam, ciprofloxacin, gentamicin and tigecycline. No carbapenamase-producers were detected and the lower ESBL prevalence (5%) in pigeons. ESBL-producing E. coli isolates had bla_CTX-M-15 genes. Pigeons shared some bacterial clones and had bird associated sequence types like E. coli ST1408. Fecal carriage of bacteria resistance of critically important human antibiotics, together with examples of shared genotypes among pigeons, indicate the human-birds and bird to bird transmissions are important in the epidemiology of antibiotic resistance.