Occurrence and antimicrobial resistance of Campylobacter isolates from broiler chicken and slaughter house environment in India

2021 ◽  
pp. 1-9
Author(s):  
M. Suman Kumar ◽  
T. P. Ramees ◽  
H. Dhanze ◽  
S. Gupta ◽  
Z. B. Dubal ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Broiler Chicken ◽  
Slaughter House

scholarly journals Identification of Primary Antimicrobial Resistance Drivers in Agricultural Nontyphoidal Salmonella enterica Serovars by Using Machine Learning

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Finlay Maguire ◽  
Muhammad Attiq Rehman ◽  
Catherine Carrillo ◽  
Moussa S. Diarra ◽  
Robert G. Beiko
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Antimicrobial Resistance ◽  
Broiler Chicken ◽  
Genomic Data ◽  
Set Covering ◽  
Learning Models ◽  
Commercial Chicken ◽  
The Impact ◽  
Machine Learning Models

ABSTRACT Nontyphoidal Salmonella (NTS) is a leading global cause of bacterial foodborne morbidity and mortality. Our ability to treat severe NTS infections has been impaired by increasing antimicrobial resistance (AMR). To understand and mitigate the global health crisis AMR represents, we need to link the observed resistance phenotypes with their underlying genomic mechanisms. Broiler chickens represent a key reservoir and vector for NTS infections, but isolates from this setting have been characterized in only very low numbers relative to clinical isolates. In this study, we sequenced and assembled 97 genomes encompassing 7 serotypes isolated from broiler chicken in farms in British Columbia between 2005 and 2008. Through application of machine learning (ML) models to predict the observed AMR phenotype from this genomic data, we were able to generate highly (0.92 to 0.99) precise logistic regression models using known AMR gene annotations as features for 7 antibiotics (amoxicillin-clavulanic acid, ampicillin, cefoxitin, ceftiofur, ceftriaxone, streptomycin, and tetracycline). Similarly, we also trained “reference-free” k-mer-based set-covering machine phenotypic prediction models (0.91 to 1.0 precision) for these antibiotics. By combining the inferred k-mers and logistic regression weights, we identified the primary drivers of AMR for the 7 studied antibiotics in these isolates. With our research representing one of the largest studies of a diverse set of NTS isolates from broiler chicken, we can thus confirm that the AmpC-like CMY-2 β-lactamase is a primary driver of β-lactam resistance and that the phosphotransferases APH(6)-Id and APH(3″-Ib) are the principal drivers of streptomycin resistance in this important ecosystem. IMPORTANCE Antimicrobial resistance (AMR) represents an existential threat to the function of modern medicine. Genomics and machine learning methods are being increasingly used to analyze and predict AMR. This type of surveillance is very important to try to reduce the impact of AMR. Machine learning models are typically trained using genomic data, but the aspects of the genomes that they use to make predictions are rarely analyzed. In this work, we showed how, by using different types of machine learning models and performing this analysis, it is possible to identify the key genes underlying AMR in nontyphoidal Salmonella (NTS). NTS is among the leading cause of foodborne illness globally; however, AMR in NTS has not been heavily studied within the food chain itself. Therefore, in this work we performed a broad-scale analysis of the AMR in NTS isolates from commercial chicken farms and identified some priority AMR genes for surveillance.

Prevalence and antimicrobial resistance of non-typhoidal Salmonella serotypes isolated from laying hens and broiler chicken farms in N’Djamena, Chad

2013 ◽  
Vol 166 (1-2) ◽  
pp. 293-298 ◽  
Author(s):  
Djim-adjim Tabo ◽  
Colette D. Diguimbaye ◽  
Sophie A. Granier ◽  
Frédérique Moury ◽  
Anne Brisabois ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Broiler Chicken ◽  
Laying Hens ◽  
Salmonella Serotypes

Multiple-Antibiotic Resistance of Enterococcus faecalis and Enterococcus faecium from Cecal Contents in Broiler Chicken and Turkey Flocks Slaughtered in Canada and Plasmid Colocalization of tetO and ermB Genes

2011 ◽  
Vol 74 (10) ◽  
pp. 1639-1648 ◽  
Author(s):  
CINDY-LOVE TREMBLAY ◽  
ANN LETELLIER ◽  
SYLVAIN QUESSY ◽  
MARTINE BOULIANNE ◽  
DANIELLE DAIGNAULT ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Enterococcus Faecalis ◽  
Resistance Genes ◽  
Enterococcus Faecium ◽  
Broiler Chicken ◽  
Multidrug Resistant ◽  
Poultry Meat ◽  
Antimicrobial Resistance Genes ◽  
High Level ◽  
Level Resistance

This study was conducted to characterize the antimicrobial resistance determinants and investigate plasmid colocalization of tetracycline and macrolide genes in Enterococcus faecalis and Enterococcus faecium from broiler chicken and turkey flocks in Canada. A total of 387 E. faecalis and E. faecium isolates were recovered from poultry cecal contents from five processing plants. The percentages of resistant E. faecalis and E. faecium isolates, respectively, were 88.1 and 94% to bacitracin, 0 and 0.9% to chloramphenicol, 0.7 and 14.5% to ciprofloxacin, 72.6 and 80.3% to erythromycin, 3.7 and 41% to flavomycin, 9.6 and 4.3% (high-level resistance) to gentamicin, 25.2 and 17.1% (high-level resistance) to kanamycin, 100 and 94% to lincomycin, 0 and 0% to linezolid, 2.6 and 20.5% to nitrofurantoin, 3 and 27.4% to penicillin, 98.5 and 89.7% to quinupristin-dalfopristin, 7 and 12.8% to salinomycin, 46.7 and 38.5% (high-level resistance) to streptomycin, 95.6 and 89.7% to tetracycline, 73 and 75.2% to tylosin, and 0 and 0% to vancomycin. One predominant multidrug-resistant phenotypic pattern was identified in both E. faecalis and E. faecium (bacitracin, erythromycin, lincomycin, quinupristin-dalfopristin, tetracycline, and tylosin). These isolates were further examined by PCR and sequencing for the genes encoding their antimicrobial resistance. Various combinations of vatD, vatE, bcrR, bcrA, bcrB, bcrD, ermB, msrC, linB, tetM, and tetO genes were detected, and ermB, tetM, and bcrB were the most common antimicrobial resistance genes identified. For the first time, plasmid extraction and hybridization revealed colocalization of tetO and ermB genes on a ca. 11-kb plasmid in E. faecalis isolates, and filter mating experiments demonstrated its transferability. Results indicate that the intestinal enterococci of healthy poultry, which can contaminate poultry meat at slaughter, could be a reservoir for quinupristin-dalfopristin, bacitracin, tetracycline, and macrolide resistance genes.

scholarly journals Antimicrobial Resistance of Escherichia coli and Salmonella isolated from Raw Retail Broiler Chicken Carcasses in Zambia

2020 ◽  
Author(s):  
Elizabeth Muligisa Muonga ◽  
Geoffrey Mainda ◽  
Mercy Mukuma ◽  
Geoffrey Kwenda ◽  
Bernard Hang'ombe ◽  
...  
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Foodborne Pathogens ◽  
Broiler Chicken ◽  
Target Genes ◽  
Health Concern ◽  
Public Health Concern ◽  
E Coli ◽  
Genes Encoding

Abstract BackgroundAntimicrobial resistance (AMR) of foodborne pathogens is of public health concern, especially in developing countries such as Zambia. This study was undertaken to determine the antimicrobial resistance profiles of Escherichia coli ( E. coli ) and Salmonella isolated from raw retail broiler chicken carcasses purchased from open and supermarkets in Zambia.ResultsA total of 189 E. coli and five Salmonella isolates were isolated. Identification and confirmation of the isolates were done using Analytical Profile Index (API 20E) (Biomerieux ® ) and 16S rRNA sequencing. Antimicrobial susceptibility tests (AST) were performed using the Kirby Bauer disk diffusion technique using a panel of 10 antibiotics. Multiplex PCR was used to determine the presence of three target genes encoding for resistance: tet A, Sul 1 and bla CTX-M . WHONET 2018 software was used to analyse AST results. The E. coli isolates were mostly resistant to tetracycline (79.4%), ampicillin (51.9%), and trimethoprim/sulfamethoxazole (49.7%). Two of the five Salmonella isolates were resistant to at least one antibiotic. Forty- seven (45.2%) of the 104 isolates that were screened for the presence of the resistant genes possessed at least one of the targeted resistance genes.ConclusionThis study has demonstrated the presence of AMR E. coli and Salmonella on raw retail broiler chicken carcasses from open and supermarkets, which is of public health concern.

scholarly journals Antimicrobial Resistance of Campylobacter in Broiler Chicken Along the Food Chain in Canada

2020 ◽  
Vol 17 (8) ◽  
pp. 512-520 ◽  
Author(s):  
Ousmane Dramé ◽  
Daniel Leclair ◽  
E. Jane Parmley ◽  
Anne Deckert ◽  
Blaise Ouattara ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Food Chain ◽  
Broiler Chicken

Prevalence and Antimicrobial Resistance of Salmonella Recovered from Processed Poultry

2007 ◽  
Vol 70 (11) ◽  
pp. 2466-2472 ◽  
Author(s):  
SALINA PARVEEN ◽  
MARYAM TAABODI ◽  
JURGEN G. SCHWARZ ◽  
THOMAS P. OSCAR ◽  
JEANINE HARTER-DENNIS ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Water Samples ◽  
Broiler Chicken ◽  
Traditional Culture ◽  
Processing Plant ◽  
Culture Methods ◽  
Significant Difference ◽  
High Prevalence ◽  
Poultry Processing ◽  
Amoxicillin Clavulanic Acid

This study was conducted to determine the prevalence and antimicrobial resistance of Salmonella isolates recovered from processed poultry. Four hundred eighty pre- and postchill whole broiler chicken carcasses were collected from a poultry processing plant between July 2004 and June 2005. Water samples also were collected at the entrance and exit of the chiller. After preenrichment, carcass and water samples were analyzed for the presence of Salmonella using the automated BAX system followed by traditional culture methods. The proportions of pre- and postchill carcasses that were positive for Salmonella were 88.4 and 84.1%, respectively. Ninety-two percent of water samples collected at the entrance of the chiller were positive for Salmonella, but all exit samples were negative. There was no significant difference in the prevalence of Salmonella between pre- and postchill carcasses (P > 0.05). Salmonella isolates recovered were serotyped and tested for susceptibility to antimicrobials. Thirteen serotypes were identified; the most common were Salmonella Kentucky (59.5%) and Salmonella Typhimurium (17.8%). Three hundred thirty-nine (79.8%) of the isolates were resistant to at least one antimicrobial, and 53.4% were resistant to three or more antimicrobials. Resistance was most often observed to tetracycline (73.4% of isolates), ampicillin (52.9%), amoxicillin–clavulanic acid (52%), ceftiofur (51.7%), streptomycin (35.2%), and sulfisoxazole (21.8%). These results indicate the high prevalence of Salmonella contamination in whole broiler carcasses, and a large number of these Salmonella isolates were resistant to commonly used antimicrobials.

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