Predictive Modeling of Phenotypic Antimicrobial Susceptibility of Selected Beta-Lactam Antimicrobials from Beta-Lactamase Resistance Genes.

The outcome of bacterial infection management relies on prompt diagnosis and effective treatment, but conventional antimicrobial susceptibility testing can be slow and labor-intensive. Therefore, this study aims to predict phenotypic antimicrobial susceptibility of selected beta-lactam antimicrobials in the bacteria of the family Enterobacteriaceae from different beta-lactamase resistance genotypes. Using human datasets extracted from the Antimicrobial Testing Leadership and Surveillance (ATLAS) program conducted by Pfizer and retail meat datasets from the National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS), we used a robust or weighted least square multivariable linear regression modeling framework to explore the relationship between antimicrobial susceptibility data of beta-lactam antimicrobials and different types of beta-lactamase resistance genes. In humans, in the presence of the blaCTX-M-1, blaCTX-M-2, blaCTX-M-8/25, and blaCTX-M-9 groups, MICs of cephalosporins significantly increased by values between 0.34-3.07 µg/mL, however, the MICs of carbapenem significantly decreased by values between 0.81-0.87 µg/mL. In the presence of carbapenemase genes (blaKPC, blaNDM, blaIMP, and blaVIM), the MICs of cephalosporin antimicrobials significantly increased by values between 1.06-5.77 µg/mL, while the MICs of carbapenem antimicrobials significantly increased by values between 5.39-67.38 µg/mL. In retail meat, MIC of ceftriaxone increased significantly in the presence of blaCMY-2, blaCTX-M-1, blaCTX-M-55, blaCTX-M-65, and blaSHV-2 by 55.16 µg/mL, 222.70 µg/mL, 250.81 µg/mL, 204.89 µg/mL, and 31.51 µg/mL respectively. MIC of cefoxitin increased significantly in the presence of blaCTX-M-65 and blaTEM-1 by 1.57 µg/mL and 1.04 µg/mL respectively. In the presence of blaCMY-2, MIC of cefoxitin increased by an average of 8.66 µg/mL over 17 years. Compared to E. coli isolates, MIC of cefoxitin in Salmonella enterica isolates decreased significantly by 0.67 µg/mL. On the other hand, MIC of ceftiofur increased in the presence of blaCTX-M-1, blaCTX-M-65, blaSHV-2, and blaTEM-1 by 8.82 µg/mL, 9.11 µg/mL, 8.18 µg/mL, and 1.04 µg/mL respectively. In the presence of blaCMY-2, MIC of ceftiofur increased by an average of 10.20 µg/mL over 14 years. The ability to predict antimicrobial susceptibility of beta-lactam antimicrobials directly from beta-lactamase resistance genes may help reduce the reliance on routine phenotypic testing with higher turnaround times in diagnostic, therapeutic, and surveillance of antimicrobial-resistant bacteria of the family Enterobacteriaceae.

Understanding Communication Barriers: Demographic Variables and Language Needs in the Interaction between English-Speaking Animal Professionals and Spanish-Speaking Animal Caretakers.

This study focused on assessing the language needs of English-speaking animal professionals in their interactions with Hispanic/Spanish-speaking animal caretakers. A survey was administered to a target audience of non-Spanish speaking and bilingual animal professionals to identify communication gaps while interacting with Hispanic/Spanish-speaking animal caretakers. The data was analyzed with descriptive and inferential statistics, including ordinal regression analyses to examine the impact of demographic variables on respondents' answer choices. The results showed that English-speaking professionals struggled with written and oral communication, which differed compared to bilingual professionals (p < 0.05). Additionally, responses of female professionals varied regarding the aspects of Spanish necessary for interacting with Hispanic/Spanish-speaking animal caretakers, as well as the topics likely to be addressed when agriculture professionals communicate with animal caretakers (p < 0.05). Communication difficulties in the oral medium for both oral receptive skills (listening) and oral productive skills (speaking) were reported as the major barriers that animal professionals need to overcome in their attempt to communicate with the Hispanic/Spanish-speaking workforce in farm settings. This emphasizes the need to address oral communication barriers, and to a lesser degree, the development of reading and writing skills. The topics: typical clinical signs of illness, euthanasia, treatment-drugs, and identification of sick or injured animals were identified as the most likely to be addressed during on-farm interactions. These findings indicate that there are gaps in communication that need to be overcome to improve communication with on-farm Hispanic/Spanish-speaking animal caretakers and consequently contribute to enhancing animal health, welfare, and production.

Beta-lactamase genes in bacteria from food animals, retail meat, and human surveillance programs in the United States from 2002 to 2021.

The spread of beta-lactamase-producing bacteria is a global public-health concern. This study aimed to explore the distribution of beta-lactamases reported in three sampling sources (cecal, retail meat, and human) collected as part of integrated surveillance in the United States. We retrieved and analyzed data from the United States National Antimicrobial Resistance Monitoring Systems (NARMS) from 2002 to 2021. A total of 115 beta-lactamase genes were detected in E. coli, Salmonella enterica, Campylobacter, Shigella and Vibrio: including 35 genes from cecal isolates, 32 genes from the retail meat isolates, and 104 genes from the human isolates. Three genes in E. coli (blaCMY-2,blaTEM-1A, and blaTEM-1B), 6 genes in Salmonella enterica (blaCARB-2, blaCMY-2, blaCTXM-65, blaTEM-1A, blaTEM-1B, and blaHERA-3), and 2 genes in Campylobacter spp. (blaOXA-61 and blaOXA-449) have been detected across food animals (cattle, chicken, swine, and turkey) and humans over the study period. blaCTXM-55 has been detected in E. coli isolates from the four food animal sources while blaCTXM-15 and blaCTXM-27 were found only in cattle and swine. In Salmonella enterica, blaCTXM-2, blaCTXM-9, blaCTXM-14, blaCTXM-15, blaCTXM-27, blaCTXM-55, and blaNDM-1 were only detected among human isolates. blaOXAs and blaCARB were bacteria-specific and the only beta-lactamase genes detected in Campylobacter spp. and Vibrio spp respectively. The proportions of beta-lactamase genes detected varies from bacteria to bacteria. This study provided insights on the beta-lactamase genes detected in bacteria in food animals and humans in the United States. This is necessary for better understanding the molecular epidemiology of clinically important beta-lactamases in one health interface.

Global antimicrobial resistance and use surveillance system (GLASS 2022): Investigating the relationship between antimicrobial resistance and antimicrobial consumption data across the participating countries.

For the first time since 2015, the World Health Organization's (WHO) global Antimicrobial Resistance and Use Surveillance (GLASS) featured both global reports for antimicrobial resistance (AMR) and antimicrobial consumption (AMC) data in its annual reports. In this study we investigated the relationship of AMR with AMC within participating countries reported in the GLASS 2022 report. Our analysis found a statistically significant correlation between beta-lactam/cephalosporin and fluoroquinolones consumption and AMR to these antimicrobials associated with bloodstream E. coli and Klebsiella pneumoniae among the participating countries (P<0.05). We observed that for every 1 unit increase in defined daily dose DDD of beta-lactam/cephalosporins and quinolone consumptions among the countries, increased the recoveries of bloodstream-associated beta-lactam/cephalosporins-resistant E. coli/Klebsiella spp. by 11-22% and quinolone-resistant E. coli/Klebsiella spp. by 31-40%. When we compared the antimicrobial consumptions between the antimicrobial ATC (Alphanumeric codes developed by WHO) groups and countries, we observed a statistically significant higher daily consumption of beta-lactam-penicillins (J01C, DDD difference range: 5.23-8.13) and cephalosporins (J01D, DDD difference range: 2.57-5.13) compared to other antimicrobial groups among the countries (adjusted for multiple comparisons using Tukey's method). Between the participating countries, we observed a statistically significant higher daily consumption of antimicrobial groups in Iran (DDD difference range: 3.63-4.84) and Uganda (DDD difference range: 3.79-5.01) compared to other participating countries (adjusted for multiple comparisons using Tukey's method). Understanding AMC and how it relates to AMR at the global scale is critical in the global AMR policy development and implementation of global antimicrobial stewardship.

Change in Urinary Inflammatory Biomarkers and Psychological Health with Gut Microbiome Modulation after Six Months of a Lifestyle Modification Program in Children.

Background: Obesity is a metabolic disorder that negatively impacts the quality of life. Long-term methods such as exercise and low-fat diets can help regulate this health issue, but 93.3 million Americans continue to struggle. Our research investigates if lifestyle changes can affect urinary inflammation markers and psychological aspects through the modification of gut microbiome composition. Methods: Our study included 16 healthy controls with normal BMI as a comparison group and 22 overweight/obese (OW/OB) adolescents. We collected demographic, clinical, psychological, stool, and urine sample data at enrollment and six months after implementing lifestyle modifications. Bacterial genomic data and inflammatory markers in these samples were analyzed. Results: The lifestyle interventions were associated with decreased inflammation and enhanced mental health among overweight teens. We observed differences in bacterial community compositions between healthy participants and those who underwent treatment, including exercise and dietary habit adjustments, although there was no significant change in bacterial species richness. Mental health correlated with gut microbiota compositions without any demographic influences. The research also uncovered connections between inflammatory markers, psychological factors, and gut microbiota phyla through carbohydrate metabolism alterations. Conclusion: Our findings demonstrate that lifestyle modifications are associated with improved mental health and a reduction in inflammation in overweight adolescents by adjusting the gut microbiota composition.

Effect of Tryptic Digestion on Sensitivity and Specificity in MALDI-TOF-Based Molecular Diagnostics through Machine Learning.

The digestion of protein into peptide fragments reduces the size and complexity of protein molecules. Peptide fragments can be analyzed with higher sensitivity (often > 102 fold) and resolution using MALDI-TOF mass spectrometers, leading to improved pattern recognition by common machine learning algorithms. In turn, enhanced sensitivity and specificity for bacterial sorting and/or disease diagnosis may be obtained. To test this hypothesis, four exemplar case studies have been pursued in which samples are sorted into dichotomous groups by machine learning (ML) software based on MALDI-TOF spectra. Samples were analyzed in 'intact' mode in which the proteins present in the sample were not digested with protease prior to MALDI-TOF analysis and separately after the standard overnight tryptic digestion of the same samples. For each case, sensitivity (sens), specificity (spc), and the Youdin index (J) were used to assess the ML model performance. The proteolytic digestion of samples prior to MALDI-TOF analysis substantially enhanced the sensitivity and specificity of dichotomous sorting. Two exceptions were when substantial differences in chemical composition between the samples were present and, in such cases, both 'intact' and 'digested' protocols performed similarly. The results suggest proteolytic digestion prior to analysis can improve sorting in MALDI/ML-based workflows and may enable improved biomarker discovery. However, when samples are easily distinguishable protein digestion is not necessary to obtain useful diagnostic results.

Comparing individual antimicrobial resistant and multi-drug resistant Salmonella enterica across serotypes, sampling sources, sampling periods, and food animal types in the United States (2014-2018).

This study aimed to compare the antimicrobial-resistant Salmonella enterica profiles from three sampling sources cecal contents, HACCP (during processing), and retail meat using phenotypic antibiotic susceptibility and serotype data gathered from 2014 and 2018. Antimicrobial resistance data for 29 major Salmonella serotypes from three sampling sources and associated food animal types (cattle, swine, chicken, and turkey) were obtained from the database of the United States National Antimicrobial Resistance Monitoring System. Using multivariable logistic regression models, we compared individual and multi-drug resistance (MDR) in Salmonella enterica between the three sampling sources, food animal types, sampling period, and Salmonella serotypes. Across the three sources and throughout the sampling period, the recovery of antimicrobial-resistant Salmonella enterica - including MDR, MDR-AmpC, and ACSSuT - among food animal types were dependent on the sampling period and, in some cases, sampling sources and period for the selected antimicrobials. The predicted probability of antimicrobial resistance was greater in Salmonella serotypes from turkey compared to other food animal types, conditional on sampling sources. Ceftriaxone-resistant (OR=0.83, 95% CI: 0.69-0.99), and Sulfisoxazole-resistant (OR=0.84, 95% CI: 0.72-0.98) Salmonella serotypes were less likely to be recovered from the Hazard Analysis and Critical Control Point (HACCP) sources than with the cecal sources. Except for Salmonella serotypes Dublin and Newport, most of the Salmonella serotypes were less likely to be resistant to the selected antimicrobials, or found as MDR, compared to serotype Typhimurium. This study offers an integrated view on the predicted probability of MDR Salmonella serotypes, as well as insights into which serotypes are persistent, emerging or declining across sampling sources and food animal types in the United States.

Genomic Characterization of Fecal Escherichia coli Isolates with Reduced Susceptibility to Beta-Lactam Antimicrobials from Wild Hogs and Coyotes.

This study was carried out to determine the antimicrobial resistance (AMR) genes and mobile genetic elements of 16 Escherichia coli isolates-with reduced susceptibility to ceftazidime and imipenem-that were recovered from the fecal samples of coyotes and wild hogs from West Texas, USA. Whole-genome sequencing data analyses revealed distinct isolates with a unique sequence type and serotype designation. Among 16 isolates, 4 isolates were multidrug resistant, and 5 isolates harbored at least 1 beta-lactamase gene (blaCMY-2, blaCTX-M-55, or blaCTX-M-27) that confers resistance to beta-lactam antimicrobials. Several isolates carried genes conferring resistance to tetracyclines (tet(A), tet(B), and tet(C)), aminoglycosides (aac(3)-IId, ant(3″)-Ia, aph(3')-Ia, aph(3″)-lb, aadA5, and aph(6)-ld), sulfonamides (sul1, sul2, and sul3), amphenicol (floR), trimethoprim (dfrA1 and dfrA17), and macrolide, lincosamide, and streptogramin B (MLSB) agents (Inu(F), erm(B), and mph(A)). Nine isolates showed chromosomal mutations in the promoter region G of ampC beta-lactamase gene, while three isolates showed mutations in gyrA, parC, and parE quinolone resistance-determining regions, which confer resistance to quinolones. We also detected seven incompatibility plasmid groups, with incF being the most common. Different types of virulence genes were detected, including those that enhance bacterial fitness and pathogenicity. One blaCMY-2 positive isolate (O8:H28) from a wild hog was also a Shiga toxin-producing E. coli and was a carrier of the stx2A virulence toxin subtype. We report the detection of blaCMY-2, blaCTX-M-55, and blaCTX-M-27 beta-lactamase genes in E. coli from coyotes for the first time. This study demonstrates the importance of wildlife as reservoirs of important multi-drug-resistant bacteria and provides information for future comparative genomic analysis with the limited literature on antimicrobial resistance dynamics in wildlife such as coyotes.

Fecal Microbial Diversity of Coyotes and Wild Hogs in Texas Panhandle, USA.

The ecology of infectious diseases involves wildlife, yet the wildlife interface is often neglected and understudied. Pathogens related to infectious diseases are often maintained within wildlife populations and can spread to livestock and humans. In this study, we explored the fecal microbiome of coyotes and wild hogs in the Texas panhandle using polymerase chain reactions and 16S sequencing methods. The fecal microbiota of coyotes was dominated by members of the phyla Bacteroidetes, Firmicutes, and Proteobacteria. At the genus taxonomic level, Odoribacter, Allobaculum, Coprobacillus, and Alloprevotella were the dominant genera of the core fecal microbiota of coyotes. While for wild hogs, the fecal microbiota was dominated by bacterial members of the phyla Bacteroidetes, Spirochaetes, Firmicutes, and Proteobacteria. Five genera, Treponema, Prevotella, Alloprevotella, Vampirovibrio, and Sphaerochaeta, constitute the most abundant genera of the core microbiota of wild hogs in this study. Functional profile of the microbiota of coyotes and wild hogs identified 13 and 17 human-related diseases that were statistically associated with the fecal microbiota, respectively (p < 0.05). Our study is a unique investigation of the microbiota using free-living wildlife in the Texas Panhandle and contributes to awareness of the role played by gastrointestinal microbiota of wild canids and hogs in infectious disease reservoir and transmission risk. This report will contribute to the lacking information on coyote and wild hog microbial communities by providing insights into their composition and ecology which may likely be different from those of captive species or domesticated animals. This study will contribute to baseline knowledge for future studies on wildlife gut microbiomes.

Management and environmental factors influence the prevalence and abundance of food-borne pathogens and commensal bacteria in peanut hull-based broiler litter.

In this study, we conducted a longitudinal sampling of peanut hull-based litter from a farm under a "no antibiotics ever" program. Our objective was to determine broiler management practices and environmental factors that are associated with the occurrence of food-borne pathogens (Salmonella and Campylobacter) and the abundance of commensal bacteria (Escherichia coli, Enterococcus spp., and Staphylococcus spp.). Litter (n = 288) was collected from 4 broiler houses over three consecutive flocks, starting with a complete house cleanout and fresh peanut hull. Litter was sampled at the beginning of each grow-out cycle and at the end of the cycle. Logistic and linear regression models were used to model the relationships between pathogen prevalence, commensal abundance and management practices, and environmental factors. The number of flocks raised on litter, grow-out period, broiler house, litter pH, litter moisture, and house temperature were associated with the prevalence of pathogens and the abundance of commensal bacteria in litter. The final logistic model for pathogens showed that a higher probability of detecting Salmonella in litter was associated with the number of flocks raised on litter and the grow-out period. A higher probability of detecting Campylobacter in litter was associated with the number of flocks raised on litter, broiler house and the sections of the house, and the pH of litter. Our results suggest that management practices and environmental factors affect Salmonella and Campylobacter differently and suggest that each pathogen will require its own tailored intervention to stop their persistence in broiler litter.

Resistance to extended-spectrum cephalosporins in Escherichia coli and Salmonella enterica isolated from food-producing animals: Ecological study from selected national surveillance programs.

Extended-spectrum cephalosporins (ESC) are categorized by World Health Organization as critically important antimicrobials with limited therapeutic alternatives for the treatment of severe bacterial infections in humans. Preserving the effectiveness of ESC requires continuous monitoring of resistance and comparison of associated data across national surveillance programs in the face of globalization. In this ecological study, we compared ESC resistance in Escherichia coli and Salmonella enterica isolated from food-producing animals from 2003 to 2019 between nine countries (Canada, Denmark, Finland, Japan, Netherlands, Norway, Sweden, United Kingdom, and the United States). Using the beta-regression model, compared to Canada, non-selective ESC-R Salmonella enterica was less likely isolated from food producing animals in other eight countries (Odds ratio range: 0.07-0.76). We observed an interaction between the country and the year with a significantly decreased proportion (P < 0.05) of non-selective ESC-R Escherichia coli from the Netherlands, the United Kingdom, and the United States compared to Canada over the years. There was a linear correlation between non-selective ESC-R Escherichia coli and ESC use from Netherlands (Spearman's ρ = 0.91, P < 0.0001). For the six European countries, the interaction between the country and year showed a significant decrease in the proportion of selective ESC-R Escherichia coli over the years for the Netherlands compared to Denmark (P = 0.002). While there were variations in the proportion of beta-lactamase genes reported over the years, blaCTX-M and blaCMY-2 genes were commonly detected among the selective ESC-R Escherichia coli. This study reveals variability in the recovery of ESC-resistant bacteria among the countries that seems likely influenced by the individual country policy on the use of critically important antimicrobials and resistance surveillance programs. However, there is a need for harmonization and consistency in food animal sources of bacterial isolates used in surveillance programs within and between the countries for easy comparability.

Beta-lactamase resistance genes in Enterobacteriaceae from Nigeria.

Background: Beta-lactamase genes are one of the most important groups of antimicrobial resistance genes in human and animal health. Therefore, continuous surveillance of this group of resistance genes is needed for a better understanding of the local epidemiology within a country and global dissemination. Aim: This review was carried out to identify different beta-lactamase resistance genes reported in published literature from Nigeria. Methods: Systematic review and meta-analysis was carried out on eligible Nigerian articles retrieved from electronic literature searches of PubMed®, African Journals Online, and Google Scholar published between January 1990 and December 2019. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses method was adopted to facilitate clarity and transparency in reporting review findings. Results: Fifty-seven articles were included. All beta-lactamases reported were detected from Gram-negative bacteria, particularly from Enterobacteriaceae. Thirty-six different beta-lactamase genes were reported in Nigeria. These genes belong to the narrow-spectrum, AmpC, extended-spectrum and carbapenemase beta-lactamase resistance genes. The pooled proportion estimate of extended-spectrum beta-lactamase genes in Nigeria was 31% (95% confidence interval [CI]: 26% - 36%, p < 0.0001), while the estimate of the bla CTX-M-15 gene in Nigeria was 46% (95% CI: 36% - 57%, p < 0.0001). The proportion estimate of AmpC genes was 32% (95% CI: 11% - 52%, p < 0.001), while the estimate for carbapenemases was 8% (95% CI: 5% - 12%, p < 0.001). Conclusion: This study provides information on beta-lactamase distribution in Nigeria. This is necessary for a better understanding of molecular epidemiology of clinically important beta-lactamases, especially the extended-spectrum beta-lactamases and carbapenemases in Nigeria.

Occurrence of extended-spectrum ß-lactamase and AmpC-producing Escherichia coli in retail meat products from the Maritime Provinces, Canada.

This study was conducted to determine the occurrence of antimicrobial resistance to the extended-spectrum cephalosporins (ESC) in Escherichia coli isolates. The isolates were collected from retail meat products collected in the Maritime Provinces of Canada. Our analyses involved the use of both selective and traditional culture methods; we also conducted genotype analyses using multiplex polymerase chain reactions. ESC-resistant (ESC-R) E. coli were detected in 33 of 559 samples (5.9%) using the traditional culture method, compared with 151 of 557 samples (27.1%) using the selective culture method. We recovered more isolates of ESC-R E. coli from poultry compared with beef and pork (P < 0.001). Multidrug resistance, extended-spectrum ß-lactamase (ESBL), and AmpC phenotypes were more common in chicken-derived isolates than other retail meat products (P < 0.001). From the 98 isolates examined, 76 isolates (77.6%) were positive for either ESBL and AmpC ß-lactamases or both. Among the 76 isolates, blaCMY-2 (78.9%), blaCTXM (46.1%), blaTEM (21.1%), and blaSHV (1.3%) genes were detected. Among the blaCTXM-producing isolates, blaCTXM-1, blaCTXM-2, and blaCTXM-9 phylogenetic groups were detected. ß-lactamase genes were more commonly detected in chicken-derived isolates compared with other meat types (P < 0.01). This study demonstrates the occurrence of ESBL- and AmpC-resistance genes in retail meat products in the Maritime Provinces of Canada. We found that selective culture significantly improved the recovery of ESC-R E. coli isolates from retail meat samples.

Review of infectious agent occurrence in wild salmonids in British Columbia, Canada.

Wild Pacific salmonids (WPS) are economically and culturally important to the Pacific North region. Most recently, some populations of WPS have been in decline. Of hypothesized factors contributing to the decline, infectious agents have been postulated to increase the risk of mortality in Pacific salmon. We present a literature review of both published journal and unpublished data to describe the distribution of infectious agents reported in wild Pacific salmonid populations in British Columbia (BC), Canada. We targeted 10 infectious agents, considered to potentially cause severe economic losses in Atlantic salmon or be of conservation concern for wild salmon in BC. The findings indicated a low frequency of infectious hematopoietic necrosis virus, piscine orthoreovirus, viral haemorrhagic septicaemia virus, Aeromonas salmonicida, Renibacterium salmoninarum, Piscirickettsia salmonis and other Rickettsia-like organisms, Yersinia ruckeri, Tenacibaculum maritimum and Moritella viscosa. No positive results were reported for infestations with Paramoeba perurans in peer-reviewed papers and the DFO Fish Pathology Program database. This review synthesizes existing information, as well as gaps therein, that can support the design and implementation of a long-term surveillance programme of infectious agents in wild salmonids in BC.

Short communication: Whole-genome sequence analysis of 4 fecal blaCMY-2-producing Escherichia coli isolates from Holstein dairy calves.

This study was carried out to determine the antimicrobial resistance (AMR) genes and mobile genetic elements of 4 fecal blaCMY-2-producing Escherichia coli isolated from Holstein dairy calves on the same farm using whole-genome sequencing. Genomic analysis revealed that 3 of the 4 isolates shared similar genetic features, including sequence type (ST), serotype, plasmid characteristics, insertion ST, and virulence genes. In addition to genes encoding for complex multidrug resistance efflux systems, all 4 isolates were carriers of genes conferring resistance to ß-lactams (blaCMY-2, blaTEM-1B), tetracyclines (tetA, tetB, tetD), aminoglycosides [aadA1, aph(3")-lb, aph(6)-ld], sulfonamides (sul2), and trimethoprim (dfrA1). We also detected 4 incompatibility plasmid groups: Inc.F, Inc.N, Inc.I, and Inc.Q. A novel ST showing a new purA and mdh allelic combination was found. The 4 isolates were likely enterotoxigenic pathotypes of E. coli, based on serotype and presence of the plasmid Inc.FII(pCoo). This study provides information for comparative genomic analysis of AMR genes and mobile genetic elements. This analysis could give some explanation to the multidrug resistance characteristics of bacteria colonizing the intestinal tract of dairy calves in the first few weeks of life.

Antimicrobial resistance in mastitis, respiratory and enteric bacteria isolated from ruminant animals from the Atlantic Provinces of Canada from 1994-2013.

Diagnostic laboratory antimicrobial susceptibility data for bacteria isolated from clinical samples of cattle, sheep, and goats from 1994 to 2013 were evaluated retrospectively. Among bacteria from bovine mastitis, Staphylococcus aureus and Streptococcus uberis were the most commonly isolated organisms. Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni were commonly isolated from the respiratory tract, while Escherichia coli isolates were frequently recovered from the intestinal tract. Isolates from mastitis were generally highly susceptible to the antimicrobials tested, except neomycin and oxytetracycline. Respiratory tract isolates were highly susceptible to trimethoprim-sulfamethoxazole, penicillin, florfenicol, and ceftiofur, while enteric bacteria were frequently susceptible to ceftiofur. Antimicrobial resistance trends over the study period were generally stable for small ruminant and cattle isolates. Multi-drug resistance was more common among respiratory isolates from small ruminants compared to those from cattle but more common in enteric bacteria from cattle compared to those from small ruminants. This information may guide clinicians when they are choosing empirical therapies for the treatment of ruminant animals in Atlantic Canada.

Résistance antimicrobienne des bactéries respiratoires et entériques et de la mammite isolées des ruminants dans les provinces de l'Atlantique de 1994 à 2013. Les données de susceptibilité antimicrobienne des laboratoires diagnostiques, de 1994 à 2013, pour les bactéries isolées d'échantillons cliniques de bovins, de moutons et de chèvres, ont été évaluées rétrospectivement. Parmi les bactéries trouvées en lien avec la mammite bovine, Staphylococcus aureus et Streptococcus uberis ont été les organismes les plus communément isolés. Pasteurella multocida, Mannheimia haemolytica et Histophilus somni ont été communément isolés de l'appareil respiratoire, tandis que des isolats d'Escherichia coli étaient fréquemment récupérés du tractus intestinal. Les isolats de la mammite étaient généralement hautement susceptibles aux antimicrobiens testés, sauf pour la néomycine et l'oxytétracycline. Les isolats de l'appareil respiratoire étaient hautement susceptibles au triméthoprime-sulfaméthoxazole, à la pénicilline, au florfénicol et au ceftiofur, tandis que les bactéries entériques étaient fréquemment susceptibles au ceftiofur. Les tendances d'antibiorésistance pendant la période de l'étude étaient généralement stables pour les isolats des petits ruminants et des bovins. La multirésistance aux médicaments était plus commune pour les isolats respiratoires provenant des petits ruminants comparativement à ceux des bovins et plus commune dans les bactéries entériques des bovins par rapport à celles des petits ruminants. Ces données pourront guider les cliniciens qui choisissent des thérapies empiriques pour le traitement des ruminants dans les provinces de l'Atlantique.(Traduit par Isabelle Vallières).

Antimicrobial resistance in bacteria isolated from horses from the Atlantic Provinces, Canada (1994 to 2013).

This study determined the antimicrobial susceptibility patterns and trends for selected bacteria isolated from horses using diagnostic data from the Atlantic Veterinary College Diagnostic Services Bacteriology Laboratory, Charlottetown, Prince Edward Island over a 20-year period. Streptococcus equi subsp. zooepidemicus and Escherichia coli were the most commonly isolated bacteria over the study period. Clinical samples were most frequently submitted from respiratory and reproductive systems. Most bacterial isolates were susceptible to ceftiofur. Resistance was most common in Gram-negative enteric bacteria, while streptococci were frequently susceptible to most of the antimicrobials tested including penicillin and trimethoprim-sulfamethoxazole. The antimicrobial resistance trends over the study period were relatively stable. Multi-drug resistance was observed in 9% of the bacterial isolates. Information provided in this study could be used to help guide rational, empirical antimicrobial treatment selection in equine practices in Atlantic Canada.

Résistance aux antimicrobiens dans les bactéries isolées des chevaux dans les provinces de l'Atlantique, au Canada, de 1994 à 2013. Cette étude a déterminé les modèles et les tendances de susceptibilité antimicrobienne pour certaines bactéries isolées des chevaux en s'appuyant sur des données diagnostiques du Laboratoire de bactériologie des services diagnostiques de l'Atlantic Veterinary College à Charlottetown, à l'Île-du-Prince-Édouard, pendant une période de 20 ans. Streptococcus equi ssp. zooepidemicus et Escherichia coli ont été les bactéries les plus communément isolées pendant la période à l'étude. Des échantillons cliniques des systèmes respiratoires et reproducteurs étaient les plus fréquemment soumis. La plupart des isolats bactériens étaient susceptibles au ceftiofur. La résistance était la plus courante chez les bactéries entériques à Gram négatif, tandis que les streptocoques étaient fréquemment susceptibles à la plupart des antimicrobiens testés incluant la pénicilline et le triméthoprime-sulfaméthoxazole. Les tendances de résistance aux antimicrobiens pendant la période à l'étude étaient relativement stables. Une multirésistance aux médicaments a été observée dans 9 % des isolats bactériens. Les renseignements fournis dans cette étude pourraient servir à guider un choix rationnel et empirique pour les traitements antimicrobiens dans les pratiques équines des provinces de l'Atlantique.(Traduit par Isabelle Vallières).

Antimicrobial resistance in bacteria isolated from cats and dogs from the Atlantic Provinces, Canada from 1994-2013.

Antimicrobial susceptibility patterns and trends in bacteria isolated from cats and dogs were determined from diagnostic laboratory data from the Atlantic Veterinary College Diagnostic Services Bacteriology Laboratory over a 20-year period. Clinical samples were most commonly from the urinary tract and the ear. Staphylococcus spp. and Escherichia coli were the bacteria that were most frequently isolated. Increases in percentage resistant were seen with E. coli to cephalexin (57% to 61%), Pasteurella spp. to erythromycin (35% to 53%), and Pseudomonas aeruginosa (31% to 39%), and Streptococcus spp. (46% to 53%) to enrofloxacin. The frequency of resistance did not change significantly over the study period; however, increased enrofloxacin resistance was identified for canine isolates of Staphylococcus spp., Streptococcus spp., Enterococcus spp., E. coli, P. aeruginosa, and Proteus spp. Multidrug resistance was observed in 12% and 9% of the isolates from dogs and cats, respectively. Data from this study could be used to guide empirical antimicrobial selection in companion animal veterinary practices in Atlantic Canada.

Résistance antimicrobienne des bactéries isolées chez des chats et des chiens des provinces de l'Atlantique, Canada, de 1994 à 2013. Les tendances de susceptibilité antimicrobienne des bactéries isolées chez des chats et des chiens ont été déterminées d'après les données des laboratoires de diagnostic du Diagnostic Services Bacteriology Laboratory de l'Atlantic Veterinary College pendant une période de 20 ans. Les échantillons cliniques provenaient le plus communément des voies urinaires et de l'oreille. Staphylococcus spp. et Escherichia coli étaient les bactéries les plus fréquemment isolées. Une hausse du pourcentage de la résistance a été observée pour E. coli à la céphalexine (de 57 % à 61 %), pour Pasteurella spp. à l'érythromycine (de 35 % à 53 %) ainsi que pour Pseudomonas aeruginosa (de 31 % à 39 %) et Streptococcus spp. (de 46 % à 53 %) à l'enrofloxacine. La fréquence de la résistance n'a pas changé significativement pendant la période de l'étude. Cependant, une résistance accrue à l'enrofloxacine a été identifiée pour les isolats canins de Staphylococcus spp., de Streptococcus spp., d'Enterococcus spp., d'E. coli, de P. aeruginosa, et de Proteus spp. La multirésistance aux médicaments a été observée dans 12 % et 9 % des isolats des chiens et des chats, respectivement. Les données de cette étude pourraient être utilisées pour guider le choix empirique des antimicrobiens dans les pratiques vétérinaires pour animaux de compagnie des provinces de l'Atlantique.(Traduit par Isabelle Vallières).

Determination of antimicrobial resistance to extended-spectrum cephalosporin, quinolones, and vancomycin in selected human enteric pathogens from Prince Edward Island, Canada.

The aim of this study was to determine the frequency of fecal carriage of vancomycin-resistant Enterococcus spp. and Escherichia coli with reduced susceptibilities to extended-spectrum cephalosporins (ESCs) and quinolones in humans on Prince Edward Island, Canada. Convenience fecal samples from individuals on Prince Edward Island were screened phenotypically using selective culture and genotypically using multiplex polymerase chain reactions to detect E. coli and Enterococcus spp. resistant to critically important antimicrobials. Twenty-six (5.3%) of 489 individuals had E. coli with reduced susceptibility to ESCs. Twenty-five (96.2%) of the 26 isolates harbored blaTEM, 18 (69.2%) harbored blaCMY-2, 16 (61.5%) harbored blaCTX-M groups, 2 (7.7%) harbored blaSHV genes. None of the ESC-resistant E. coli was positive for carbapenem resistance. Twenty-one (8.3%) of 253 individuals had E. coli isolates with reduced quinolone susceptibility. All 21 isolates were positive for at least 1 qnr gene, with 3 (14.3%) isolates positive for qnrB, 5 (23.8%) positive for qnrS, and 13 (61.9%) positive for both qnrB and qnrS genes. All the enterococci isolates were vancomycin-susceptible. Higher susceptibility to the critically important antimicrobials was found in this study. This study can serve as a baseline for future antimicrobial resistance surveillance within this region.