An epidemiological framework for improving the accuracy of whole-genome sequence-based antimicrobial resistance surveillance in .

Whole-genome sequence-based surveillance of bacteria for determinants of antimicrobial resistance (AMR) promises many advantages over traditional, wet-lab approaches. However, adjustments to parameters used to identify genetic determinants from sequencing data can affect results and interpretation of the important determinants in circulation. Using a dataset of whole-genome sequences from 1633 isolates of Heidelberg and Kentucky collected from surveillance of Canadian poultry production, we queried the genomic data using an in silico AMR detection tool, StarAMR, applying a range of parameter values required for the detection pipeline to test for differences in detection accuracy.

Insights on the genomic diversity, virulence and resistance profile of a Campylobacter jejuni strain isolated from a hospitalized patient in Brazil.

Campylobacteriosis is currently recognized as one of the major causes of foodborne bacterial diseases worldwide. In Brazil, there is insufficient data to estimate the impact of Campylobacter in public health. The aim of this present study was to characterize a C.

Commensal Strains of Bovine Origin Competitively Mitigated O157:H7 in a Gnotobiotic Murine Intestinal Colonization Model with or without Physiological Stress.

Cattle are a primary reservoir of enterohemorrhagic (EHEC) O157:H7. Currently, there are no effective methods of eliminating this important zoonotic pathogen from cattle, and colonization resistance in relation to EHEC O157:H7 in cattle is poorly understood. We developed a gnotobiotic EHEC O157:H7 murine model to examine aspects of the cattle pathogen-microbiota interaction, and to investigate competitive suppression of EHEC O157:H7 by 18 phylogenetically distinct commensal strains of bovine origin.

Antimicrobial resistance genotypes and phenotypes of Campylobacter coli isolated from different sources over a 16-year period in Brazil.

Objectives: This study aimed to identify antimicrobial resistance genotypes in 63 Campylobacter coli strains isolated from humans (12), animals (21), the environment (20), and food (10) in Brazil using whole genome sequencing (WGS) tools, comparing them with results obtained by antimicrobial susceptibility testing (AST) against some important antimicrobials in clinical use.

Methods: Phenotypic resistance profiles were determined by minimal inhibitory concentrations and the disk diffusion technique. The prediction of the resistance genes was performed using ABRicate v.

Combining analytical epidemiology and genomic surveillance to identify risk factors associated with the spread of antimicrobial resistance in subsp. serovar Heidelberg.

Antimicrobial resistance (AMR) has become a critical threat to public health worldwide. The use of antimicrobials in food and livestock agriculture, including the production of poultry, is thought to contribute to the dissemination of antibiotic resistant bacteria (ARB) and the genes and plasmids that confer the resistant phenotype (ARG). However, the relative contribution of each of these processes to the emergence of resistant pathogens in poultry production and their potential role in the transmission of resistant pathogens in human infections, requires a deeper understanding of the dynamics of ARB and ARG in food production and the factors involved in the increased risk of transmission.

Molecular Epidemiological Evidence Implicates Cattle as a Primary Reservoir of Infecting People via Contaminated Chickens.

The study aimed to determine the relative contribution of cattle to the burden of illness in a model agroecosystem with high rates of human campylobacteriosis (≥ 115 cases/100 K), and high densities of cattle, including large numbers of cattle housed in confined feeding operations (i.e., in southwestern Alberta, Canada).

Systematic Evaluation of Whole-Genome Sequencing Based Prediction of Antimicrobial Resistance in and .

The increasing prevalence of antimicrobial resistance (AMR) in spp. is a global concern. This study evaluated the use of whole-genome sequencing (WGS) to predict AMR in er and .

Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel.

Hierarchical genotyping approaches can provide insights into the source, geography and temporal distribution of bacterial pathogens. Multiple hierarchical SNP genotyping schemes have previously been developed so that new isolates can rapidly be placed within pre-computed population structures, without the need to rebuild phylogenetic trees for the entire dataset. This classification approach has, however, seen limited uptake in routine public health settings due to analytical complexity and the lack of standardized tools that provide clear and easy ways to interpret results.

Campylobacter coli isolated in Brazil typed by core genome Multilocus Sequence Typing shows high genomic diversity in a global context.

Unlabelled: Campylobacter has been one of the most common causative agent of bacterial food-borne gastroenteritis in humans worldwide. However, in Brazil the campylobacteriosis has been a neglected disease and there is insufficient data to estimate the incidence of this pathogen in the country.

Aims: The current study aimed to determine the phylogenetic relationships among Campylobacter coli strains isolated in Brazil and to compare them with international Campylobacter isolates available in some public databases.

Epidemiology of Campylobacter jejuni in raccoons (Procyon lotor) on swine farms and in conservation areas in southern Ontario.

Campylobacter is a leading cause of foodborne illness in humans worldwide. Sources of infection are often difficult to identify, and are, generally, poorly understood. Recent work suggests that wildlife may represent a source of Campylobacter for human infections.

Analysis of Campylobacter jejuni Subtype Distribution in the Chicken Broiler Production Continuum: a Longitudinal Examination To Identify Primary Contamination Points.

Significant knowledge gaps exist in our understanding of contamination of the poultry production continuum. Microbiological surveillance and genotypic characterization were undertaken on isolates longitudinally recovered from three poultry farms (weekly samples), the abattoir at which birds were processed, and at retail over a 542-day period in southwestern Alberta, Canada, as a model location. Subtypes were compared to concurrent isolates from diarrheic humans living in the study region.

Rates of fluoroquinolone resistance in domestically acquired are increasing in people living within a model study location in Canada.

Antimicrobial resistance was evaluated in isolated from 1291 diarrheic people over a 15-year period (2004-2018) in southwestern Alberta, a model location in Canada with a high rate of campylobacteriosis. The prevalence of resistance to chloramphenicol, clindamycin, erythromycin, and gentamicin was low during the examination period (≤4.8%).

"These Aren't the Strains You're Looking for": Recovery Bias of Common Subtypes in Mixed Cultures.

Microbiological surveillance of the food chain plays a critical role in improving our understanding of the distribution and circulation of food-borne pathogens along the farm to fork continuum toward the development of interventions to reduce the burden of illness. The application of molecular subtyping to bacterial isolates collected through surveillance has led to the identification of strains posing the greatest risk to public health. Past evidence suggests that enrichment methods for , a leading bacterial foodborne pathogen worldwide, may lead to the differential recovery of subtypes, obscuring our ability to infer the composition of a mixed-strain sample and potentially biasing prevalence estimates in surveillance data.

Strain Dynamics in a Raccoon () Population in Southern Ontario, Canada: High Prevalence and Rapid Subtype Turnover.

Free-ranging wildlife are increasingly recognized as potential reservoirs of disease-causing species such as and . Raccoons (), which live at the interface of rural, urban, and more natural environments, are ideal subjects for exploring the potential role that wildlife play in the epidemiology of campylobacteriosis. We studied the prevalence and genetic diversity of from live-captured raccoons on five swine farms and five conservation areas in southwest Ontario.

Erratum: Inglis, G.D., et al. Tetracycline Resistant Subtypes Emanating from Beef Cattle Administered Non-Therapeutic Chlortetracycline Are Longitudinally Transmitted within the Production Continuum but Are Not Detected in Ground Beef. 2020, , 23.

The authors wish to make the following correction to this paper [...

Generalizability and comparability of prevalence estimates in the wild bird literature: methodological and epidemiological considerations.

Wild birds have been the focus of a great deal of research investigating the epidemiology of zoonotic bacteria and antimicrobial resistance in the environment. While enteric pathogens (e.g.

Tetracycline Resistant Subtypes Emanating from Beef Cattle Administered Non-Therapeutic Chlortetracycline are Longitudinally Transmitted within the Production Continuum but are Not Detected in Ground Beef.

The impacts of the antimicrobial growth promoter (AGP), chlortetracycline with sulfamethazine (AS700), on the development of antimicrobial resistance and longitudinal transmission of within the beef production continuum were empirically determined. Carriage of tetracycline resistance determinants in the enteric bacterial community increased at a greater rate for AS700-treatment cattle. The majority of the bacteria from animals administered AS700 carried .

Clinically Relevant Campylobacter jejuni Subtypes Are Readily Found and Transmitted within the Cattle Production Continuum but Present a Limited Foodborne Risk.

Increasing evidence exists for the role that cattle play in the epidemiology of campylobacteriosis. In this study, the prevalence and distribution of were longitudinally examined at the subspecies level in the beef cattle production continuum. Animals were subdivided into two groups: those that were not administered antibiotics and those that were administered the antimicrobial growth promoter chlortetracycline and sulfamethazine (AS700).

Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges.

Whole-genome sequencing (WGS) will soon replace traditional phenotypic methods for routine testing of foodborne antimicrobial resistance (AMR). WGS is expected to improve AMR surveillance by providing a greater understanding of the transmission of resistant bacteria and AMR genes throughout the food chain, and therefore support risk assessment activities. At this stage, it is unclear how WGS data can be integrated into quantitative microbial risk assessment (QMRA) models and whether their integration will impact final risk estimates or the assessment of risk mitigation measures.

Enhanced microbiological surveillance reveals that temporal case clusters contribute to the high rates of campylobacteriosis in a model agroecosystem.

Infections by pathogenic Campylobacter species were determined in diarrheic (n = 2,217) and non-diarrheic control (n = 104) people in Southwestern Alberta (SWA), Canada over a 1-year period using specialized and conventional isolation, and direct PCR. Overall, 9.9% of diarrheic individuals were positive for C.

Carriage of , , and Antimicrobial-Resistant, Nonspecific by Waterfowl Species Collected from Three Sources in Southern Ontario, Canada.

Wild birds are considered a potential source of zoonotic pathogens. We report on the occurrence of and antimicrobial-resistant, nonspecific in ducks, grebes, and swans obtained by convenience while conducting related research with Canada Geese (). Samples were obtained in southern Ontario, Canada, between 2013 and 2015 from hunter-caught birds, birds submitted for postmortem diagnosis, and fresh feces from live birds in parks.

Genome-wide identification of geographical segregated genetic markers in Salmonella enterica serovar Typhimurium variant 4,[5],12:i:

Salmonella enterica ser. Typhimurium monophasic variant 4,[5],12:i:- has been associated with food-borne epidemics worldwide and swine appeared to be the main reservoir in most of the countries of isolation. However, the monomorphic nature of this serovar has, so far, hindered identification of the source due to expansion of clonal lineages in multiple hosts and food producing systems.

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.

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.