A one health genomic investigation of gentamicin resistance in Salmonella from human and chicken sources in Canada, 2014-2017

2021 ◽  
Author(s):  
Graham W. Cox ◽  
E. Jane Parmley ◽  
Brent P. Avery ◽  
Rebecca J. Irwin ◽  
Richard J. Reid-Smith ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Broiler Chickens ◽  
Phylogenomic Analysis ◽  
Spectinomycin Resistance ◽  
Retail Meat ◽  
Gentamicin Resistance ◽  
N 93 ◽  
Human Infections ◽  
On Farm ◽  
Integrated Program

Objectives: We investigated whether the increased prevalence of gentamicin resistance in Salmonella from human infections was related to a similar increased prevalence in isolates from broiler chickens and whether this increase may have been due to co-selection from use of lincomycin-spectinomycin in chickens on farms. Methods: Whole genome sequencing was performed on gentamicin-resistant (gen-R) Salmonella isolates from human and chicken sources collected from 2014-2017 by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). We determined the genomic relatedness of strains and characterized resistance genes and plasmids. Results: From 2014-2017, 247 isolates of gen-R Salmonella were identified by CIPARS: 188 were from humans and 59 from chicken sources (26 from live animals on farm and 33 from retail meat). The five most common gen-R serovars were Heidelberg (n=93, 31.5%), 4,[5],12:i:- (n=42, 14.2%), Kentucky (n=37, 12.5%), Infantis (n=33, 11.2%), and Typhimurium (n=23, 7.8%). Phylogenomic analysis revealed that for S. Heidelberg and S. Infantis, there were closely related isolates from human and chicken sources. In both sources, resistance to gentamicin and spectinomycin was most frequently conferred by aac(3)-VIa and ant(3’’)-Ia , respectively. Plasmid closure confirmed linkages of gentamicin and spectinomycin resistance genes and revealed instances of similar plasmids from both sources. Conclusions: Gentamicin and spectinomycin resistance genes were linked on the same plasmids, and some plasmids and isolates from humans and chickens were genetically similar, suggesting that the use of lincomycin-spectinomycin in chickens may be selecting for gentamicin-resistant Salmonella in broiler chickens and that these resistant strains may be acquired by humans.

scholarly journals Genomic Investigation of the Emergence of Invasive Multidrug-Resistant Salmonella enterica Serovar Dublin in Humans and Animals in Canada

2019 ◽  
Vol 63 (6) ◽  
Author(s):  
Chand S. Mangat ◽  
Sadjia Bekal ◽  
Brent P. Avery ◽  
Geneviève Côté ◽  
Danielle Daignault ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Bloodstream Infections ◽  
The United States ◽  
Multidrug Resistant ◽  
Phylogenomic Analysis ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Content Type ◽  
Human Infections ◽  
Integrated Program

ABSTRACT Salmonella enterica subsp. enterica serovar Dublin is a zoonotic pathogen that often leads to invasive bloodstream infections in humans that are multidrug resistant. Described here are the results of Canadian national surveillance of S. Dublin from 2003 to 2015 in humans and bovines, principally collected through the Canadian Integrated Program for Antibiotic Resistance Surveillance (CIPARS). An increase in human infections due to multidrug-resistant (MDR) S. Dublin was observed in 2010, many of which were bloodstream infections. Phylogenomic analysis of human and bovine isolates revealed a closely related network that differed by only 0 to 17 single nucleotide variants (SNVs), suggesting some potential transmission between humans and bovines. Phylogenomic comparison of global publicly available sequences of S. Dublin showed that Canadian isolates clustered closely with those from the United States. A high correlation between phenotypic and genotypic antimicrobial susceptibility was observed in Canadian isolates. IS26 replication was widespread among U.S. and Canadian isolates and caused the truncation and inactivation of the resistance genes strA and blaTEM-1B. A hybrid virulence and MDR plasmid (pN13-01125) isolated from a Canadian S. Dublin isolate was searched against NCBI SRA data of bacteria. The pN13-01125 coding sequences were found in 13 Salmonella serovars, but S. Dublin appears to be a specific reservoir. In summary, we have observed the rise of invasive MDR S. Dublin in humans in Canada and found that they are closely related to bovine isolates and to American isolates in their mobile and chromosomal contents.

scholarly journals The Interplay between Campylobacter and the Caecal Microbial Community of Commercial Broiler Chickens over Time

2021 ◽  
Vol 9 (2) ◽  
pp. 221
Author(s):  
Ilaria Patuzzi ◽  
Massimiliano Orsini ◽  
Veronica Cibin ◽  
Sara Petrin ◽  
Eleonora Mastrorilli ◽  
...  
Keyword(s):  
Campylobacter Jejuni ◽  
Broiler Chickens ◽  
Control Strategies ◽  
Chicken Meat ◽  
Control Measures ◽  
Microbial Network ◽  
Gut Colonization ◽  
Commercial Broiler ◽  
Zoonotic Bacteria ◽  
Human Infections

Campylobacter is the most frequent foodborne zoonotic bacteria worldwide, with chicken meat being overwhelmingly the most important reservoir for human infections. Control measures implemented at the farm level (i.e., biosecurity or vaccination), which have been successfully applied to limit other pathogens, such as Salmonella, have not been effective in reducing Campylobacter occurrence. Thus, new approaches are needed to fully understand the ecological interactions of Campylobacter with host animals to effectively comprehend its epidemiology. The objective of this study was to analyse longitudinally the gut microbiota composition of Campylobacter-infected and non-infected farms to identify any difference that could potentially be indicative of gut colonization by Campylobacter spp. Differences in the colonization rate and timing were observed at the farms that became positive for Campylobacter jejuni over the investigated time points, even though in positive tests, the occurrence of Campylobacter jejuni gut colonization was not observed before the second week of the life of the birds. Significant differences were observed in the abundances of specific bacterial taxa between the microbiota of individuals belonging to farms that became Campylobacter positive during the study and those who remained negative with particular reference to Bacteroidales and Clostridiales, respectively. Moreover, Campylobacter colonization dramatically influenced the microbiota richness, although to a different extent depending on the infection timing. Finally, a key role of Faecalibacterium and Lactobacillus genera on the Campylobacter microbial network was observed. Understanding the ecology of the Campylobacter interaction with host microbiota during infection could support novel approaches for broiler microbial barrier restoration. Therefore, evidence obtained through this study can be used to identify options to reduce the incidence of infection at a primary production level based on the targeted influence of the intestinal microbiota, thus helping develop new control strategies in order to mitigate the risk of human exposure to Campylobacter by chicken meat consumption.

scholarly journals Impact of On-Farm Interventions against CTX-Resistant Escherichia coli on the Contamination of Carcasses before and during an Experimental Slaughter

Antibiotics ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 228
Author(s):  
Michaela Projahn ◽  
Jana Sachsenroeder ◽  
Guido Correia-Carreira ◽  
Evelyne Becker ◽  
Annett Martin ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Broiler Chickens ◽  
Stocking Density ◽  
Resistant Bacteria ◽  
Control Group ◽  
Cross Contamination ◽  
High Prevalence ◽  
On Farm ◽  
The Impact ◽  
Slow Growing

Cefotaxime (CTX)-resistant Enterobacteriaceae are still an ongoing challenge in human and veterinary health. High prevalence of these resistant bacteria is detected in broiler chickens and the prevention of their dissemination along the production pyramid is of major concern. The impact of certain on-farm interventions on the external bacterial contamination of broiler chickens, as well as their influence on single processing steps and (cross-) contamination, have not yet been evaluated. Therefore, we investigated breast skin swab samples of broiler chickens before and during slaughter at an experimental slaughter facility. Broiler chickens were previously challenged with CTX-resistant Escherichia coli strains in a seeder-bird model and subjected to none (control group (CG)) or four different on-farm interventions: drinking water supplementation based on organic acids (DW), slow growing breed Rowan × Ranger (RR), reduced stocking density (25 kg/sqm) and competitive exclusion with Enterobacteriales strain IHIT36098(CE). Chickens of RR, 25 kg/sqm, and CE showed significant reductions of the external contamination compared to CG. The evaluation of a visual scoring system indicated that wet and dirty broiler chickens are more likely a vehicle for the dissemination of CTX-resistant and total Enterobacteriaceae into the slaughterhouses and contribute to higher rates of (cross-) contamination during processing.

Effect of on-farm interventions in the aftermath of an outbreak of hypervirulent verocytotoxin-producing Escherichia coli O157:H7 in Sweden

2018 ◽  
Vol 182 (18) ◽  
pp. 516-516 ◽  
Author(s):  
Lena-Mari Tamminen ◽  
Helena Fransson ◽  
Madeleine Tråvén ◽  
Anna Aspán ◽  
Stefan Alenius ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Control Measures ◽  
Processing Plant ◽  
Escherichia Coli O157 ◽  
Meat Processing ◽  
Cattle Farm ◽  
Human Infections ◽  
On Farm

In 2007, human infections with a hypervirulent strain of verocytotoxin-producing Escherichia coli O157:H7 increased in Sweden and especially in the Halland County. A connection between the cases and a local beef cattle farm with an on-farm abattoir and meat processing plant was established. In this observational study the control measures implemented on the infected farm and the dynamics of infection in the herd are described. In May 2008, when measures were initiated and animals put to pasture, the prevalence of positive individuals was 40 per cent and 18 carcasses out of 24 slaughtered animals were contaminated. During summer the monthly prevalence of positive carcasses varied between 8 and 41 per cent and at turning-in 22 out of 258 individually sampled animals were shedding the pathogen. After January 2009 no positive carcasses were found at slaughter and follow-up samplings of environment and individuals remained negative until the study period ended in May 2010. The results indicate that on-farm measures have potential to reduce the prevalence of the pathogen in a long-term perspective. However, as self-clearance cannot be excluded the effectiveness of the suggested measures needs to be confirmed.

Virulence and antimicrobial resistance genes associated with the in-vivo pathogenicity of avian pathogenic E. coli isolates

2021 ◽  
Vol 1 (1) ◽  
pp. 17-20
Author(s):  
Ahmed Abd El-Mawgoud ◽  
Azza El-Sawah ◽  
Soad Nasef ◽  
Al-Hussien Dahshan ◽  
Ahmed Ali
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Broiler Chickens ◽  
Virulence Genes ◽  
Virulence Gene ◽  
Health Concern ◽  
Pathogenicity Test ◽  
E Coli ◽  
Antimicrobial Resistance Genes

In the current study, ten avian pathogenic E. coli (APEC) isolates of the most predominant APEC serogroups isolated from broiler chickens in Egypt were screened for their virulence and antimicrobial resistance genes pattern using PCR. Five selected virulence gene patterns were further investigated for their in-vivo pathogenicity test. Results showed a 100% prevalence of the β-lactams and tetracyclines resistance genes. However, aminoglycoside and quinolone resistance genes were not detected. Also, 80% of the tested isolates harbored mcr-1 gene, colistin resistance gene. In-vivo pathogenic strains consistently harbored the virulence gene pattern of fimH, fimA, papC, iutA, and tsh. Additionally, the tsh gene was consistently detected with lethal APEC isolates in day-old chicks. These results highlighted the high prevalence of antimicrobial and virulence genes in APEC that potentially represent a public health concern. In this study, the virulence genes fimH, fimA, papC, iutA, and tsh were the most common virulence gene patterns associated with pathogenicity in day-old chicks.

scholarly journals A review on combined effects of moniliformin and co-occurring Fusarium toxins in farm animals

2019 ◽  
Vol 12 (3) ◽  
pp. 281-291 ◽  
Author(s):  
J.-M. Fremy ◽  
I. Alassane-Kpembi ◽  
I.P. Oswald ◽  
B. Cottrill ◽  
H.P. Van Egmond
Keyword(s):  
Weight Gain ◽  
Broiler Chickens ◽  
Body Weight Gain ◽  
Farm Animals ◽  
Feed Consumption ◽  
Oral Exposure ◽  
Combined Effects ◽  
Combined Toxicity ◽  
Food And Feed ◽  
On Farm

Co-occurrence of mycotoxins in food and feed represents the rule rather than the exception. Information about combinatory toxic effects of co-occurring mycotoxins is scarce, in particular the effects that mixtures of mycotoxins in feed may have on farm animals. This review focusses on studies on the combined effects of moniliformin and co-occurring mycotoxins in feed on farm animals. Moniliformin is a mycotoxin of emerging scientific interest, which may co-occur with many other mycotoxins, especially Fusarium mycotoxins. Oral exposure to moniliformin reduces feed consumption and body weight gain in poultry, in pigs and catfish, and induces cardiotoxic effects and/or alterations in serum biochemical and haematological parameters. In this review only experiments comparing effects as a result of the exposure to a combination of mycotoxins with effects due to the exposure to single mycotoxins were considered. Identified published studies on combined toxicity have been limited to combinations of moniliformin with either fumonisin B1 or deoxynivalenol, and were performed with poultry, pigs, and catfish. Most of the moniliformin/fumonisin B1 investigations involved poultry and focussed on adverse effects on feed intake, weight gain and immune response, as well as organ lesions. These studies mainly reported an interactive toxicity of moniliformin and fumonisin B1 but did not allow identification of the type of interaction. Likewise, no indication could be given for the interaction detected for both mycotoxins on weight gains of catfish. For the moniliformin/deoxynivalenol combination, only one study with broiler chickens was found relevant. This study concluded additive or less than additive toxicity, using kidney lesions and renal tubular epithelial degeneration as endpoints. While possible interactions between moniliformin and fumonisin B1 or deoxynivalenol were identified, the conclusions are based on limited studies and experimental designs. Further studies on the combined toxicity of moniliformin with other mycotoxins and other animal species would be needed.

scholarly journals A Biocontrol Option to Control a Foodborne Pathogen; Using Campylobacter Bacteriophages to Control Campylobacter in Poultry

Proceedings ◽  
2020 ◽  
Vol 36 (1) ◽  
pp. 162
Author(s):  
Nalini Chinivasagam ◽  
Wiyada Estella ◽  
Samuel Cockerill ◽  
Lance Maddock ◽  
David Mayer ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Environmental Science ◽  
Management Strategies ◽  
Collaborative Study ◽  
Scale Up ◽  
Foodborne Pathogen ◽  
Small Sample ◽  
High Performing ◽  
The Uk ◽  
On Farm

Campylobacter is a leading cause of foodborne illnesses both in Australia and internationally, and is frequently found in poultry. There is a need for sustainable options to support current farm management strategies that address food-safety. The use of bacteriophages provides a safe biocontrol option. A collaborative study by the Department of Agriculture and Fisheries (QLD), the University of Nottingham (UK) and the Institute of Environmental Science and Research (NZ) is focused on the control of Campylobacter in broiler chickens. Campylobacter bacteriophages were sourced from Queensland poultry farms and following extensive screening, suitable candidates to be used in cocktails were identified. This followed an on-farm proof of concept study on a small sample of chickens, using selected cocktail candidates, to provide an understanding of the hurdles for practical application. The trial demonstrated a 2-log CFU/g reduction of Campylobacter in the caeca of treated birds compared to non-treated (p < 0.05). Another important finding of this study was the absence of bacteriophage resistance, a concern with phage therapy. Work at ESR has addressed approaches to select and adapt bacteriophage cocktails to particular hosts, which included screening against NZ and Australian hosts. This approach enabled the formulation of high performing bacteriophage cocktails for Australian and international markets. Work in the UK is exploring the understanding of the host-bacteriophage relationships to ensure safety to meet regulatory requirements and support potential scale-up options. In summary, the work in progress via international collaborations is aimed at delivering a safe biocontrol option that can meet both commercial and regulatory needs aiming at controlling on-farm Campylobacter.

scholarly journals Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella

2016 ◽  
Vol 60 (9) ◽  
pp. 5515-5520 ◽  
Author(s):  
Patrick F. McDermott ◽  
Gregory H. Tyson ◽  
Claudine Kabera ◽  
Yuansha Chen ◽  
Cong Li ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
The United States ◽  
Whole Genome ◽  
Content Type ◽  
Structural Resistance ◽  
Retail Meat

ABSTRACTLaboratory-basedin vitroantimicrobial susceptibility testing is the foundation for guiding anti-infective therapy and monitoring antimicrobial resistance trends. We used whole-genome sequencing (WGS) technology to identify known antimicrobial resistance determinants among strains of nontyphoidalSalmonellaand correlated these with susceptibility phenotypes to evaluate the utility of WGS for antimicrobial resistance surveillance. Six hundred fortySalmonellaof 43 different serotypes were selected from among retail meat and human clinical isolates that were tested for susceptibility to 14 antimicrobials using broth microdilution. The MIC for each drug was used to categorize isolates as susceptible or resistant based on Clinical and Laboratory Standards Institute clinical breakpoints or National Antimicrobial Resistance Monitoring System (NARMS) consensus interpretive criteria. Each isolate was subjected to whole-genome shotgun sequencing, and resistance genes were identified from assembled sequences. A total of 65 unique resistance genes, plus mutations in two structural resistance loci, were identified. There were more unique resistance genes (n =59) in the 104 human isolates than in the 536 retail meat isolates (n =36). Overall, resistance genotypes and phenotypes correlated in 99.0% of cases. Correlations approached 100% for most classes of antibiotics but were lower for aminoglycosides and beta-lactams. We report the first finding of extended-spectrum β-lactamases (ESBLs) (blaCTX-M1andblaSHV2a) in retail meat isolates ofSalmonellain the United States. Whole-genome sequencing is an effective tool for predicting antibiotic resistance in nontyphoidalSalmonella, although the use of more appropriate surveillance breakpoints and increased knowledge of new resistance alleles will further improve correlations.

Sign in / Sign up

Export Citation Format

Share Document