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

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.

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Prevalence, Persistence, and Antimicrobial Resistance ofCampylobacterspp. from Eggs and Laying Hens Housed in Five Commercial Housing Systems

Foodborne Pathogens and Disease ◽

10.1089/fpd.2017.2404 ◽

2018 ◽

Vol 15 (8) ◽

pp. 506-516 ◽

Cited By ~ 3

Author(s):

Estefanía Novoa Rama ◽

Matthew Bailey ◽

Deana R. Jones ◽

Richard K. Gast ◽

Ken Anderson ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Laying Hens ◽

Housing Systems ◽

Commercial Housing

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Surveillance and Antimicrobial Resistance of Salmonella Strains Isolated from Slaughtered Pigs in Spain

Journal of Food Protection ◽

10.4315/0362-028x-70.6.1502 ◽

2007 ◽

Vol 70 (6) ◽

pp. 1502-1506 ◽

Cited By ~ 23

Author(s):

RAFAEL JESÚS ASTORGA MÁRQUEZ ◽

AURORA ECHEITA SALABERRIA ◽

ALFONSO MALDONADO GARCÍA ◽

SILVIA VALDEZATE JIMENEZ ◽

ALFONSO CARBONERO MARTINEZ ◽

...

Keyword(s):

Antibiotic Resistance ◽

Multidrug Resistance ◽

Antimicrobial Resistance ◽

Antimicrobial Agents ◽

Phage Type ◽

Multidrug Resistant ◽

Gold Coast ◽

Resistance Patterns ◽

Salmonella Serotypes ◽

Slaughtered Pigs

The prevalence of and the antibiotic resistance shown by Salmonella isolated from pigs in Andalusia (southern Spain) is reported. Salmonella enterica was recovered from 40 (33%) of 121 sampled herds, and a total of 65 isolates were serotyped. The most common Salmonella serotypes were Typhimurium and Rissen (30.7% each); others included Derby (9.2%), Brandenburg (9.2%), Newport (7.7%), Bredeney (4.6%), Anatum (3.0%), Hadar (1.5%), and Goldcoast (1.5%). One strain (1.5%) belonging to the monophasic variant of the Typhimurium serotype (Salmonella 4,5,12:i:−) was also detected. Definitive phage type (DT) 104b was the most common Typhimurium phage type isolated. These Salmonella strains were resistant to various antimicrobial agents, including tetracycline (84.6%), streptomycin (69.2%), neomycin (63.0%), sulfonamides (61.5%), ampicillin (53.8%), and amoxicillin (53.8%). All isolates were fully susceptible to ceftriaxone, ciprofloxacin, and colistin. Thirty-nine strains (64%) resistant to four or more antimicrobial agents were defined as multidrug resistant. Multidrug resistance profiles were observed in Salmonella serotypes Typhimurium, Rissen, Brandenburg, Bredeney, a monophasic variant, Gold-coast, Hadar, and Anatum, with serotypes Typhimurium and Brandenburg showing the most complicated resistance patterns (resistant to ≥11 drugs).

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Changing trends in antimicrobial resistance among salmonella serotypes in Southern India

International Journal of Infectious Diseases ◽

10.1016/j.ijid.2010.02.1562 ◽

2010 ◽

Vol 14 ◽

pp. e34

Author(s):

S. rao ◽

B. Kabir

Keyword(s):

Antimicrobial Resistance ◽

Southern India ◽

Changing Trends ◽

Salmonella Serotypes

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Zoonotic bacteria in the food chain: antimicrobial resistance and associated factors in Portugal

European Journal of Public Health ◽

10.1093/eurpub/ckaa166.237 ◽

2020 ◽

Vol 30 (Supplement_5) ◽

Author(s):

M Costa ◽

A Cara d'Anjo ◽

M Cardo ◽

A Leite

Keyword(s):

Antimicrobial Resistance ◽

Associated Factors ◽

Laying Hens ◽

Control Measures ◽

Processing Plant ◽

Sample Type ◽

Bacterial Isolates ◽

Final Model ◽

E Coli ◽

Animal Populations

Abstract Antimicrobial resistance (AMR) poses a threat to public health and animal food-production plays a crucial role in AMR spread. We thus aimed to characterize AMR profiles and associated factors in zoonotic bacterial isolates in Portugal. Data from the Portuguese AMR surveillance program on animal populations and derived food, 2014-2018, was used. AMR frequency was described in E coli, Campylobacter and Salmonella isolates from poultry and pigs, according to antibiotic and samples tested. For Salmonella, AMR associated factors were studied: animal populations (broilers, laying hens, pigs) and derived meat, sampling stage (farm, slaughterhouse, processing plant), sample type (environmental, carcase, food), sampler (HACCP, industry, official, official and industry), sample context (control and eradication programmes, monitoring), year (2014-2018) and season. Logistic regression was applied to estimate crude (OR) and adjusted odds ratio (aOR) with 95% confidence intervals (95%CI). The final model was obtained using a backward stepwise method. We assessed 2157 E Coli, 561 Campylobacter and 826 Salmonella isolates. AMR rates were higher to cefepime (91-98%) in E coli in all sample types; cefotaxime (100%) in E coli in broiler's meat; nalidixic acid (79-96%) in E coli and Campylobacter in poultry and derived meat; ciprofloxacin (50-98%) in all bacteria isolates from poultry and derived meat. For Salmonella, AMR was more likely in pig's meat (OR 3.66; 95%CI:1.19-2.82), slaughterhouses (OR 10.18; 95%CI:4.69-26.70), carcases (OR 5.90;95%CI:3.74-9.69). The final model indicated a lesser chance of AMR in laying hens (aOR .21; 95%CI:.11-.37), industry sampling (aOR .25; 95%CI:.07-.73), 2018 (aOR .24; 95%CI:.13-.42), and a higher chance in summer (aOR 2.39; 95%CI:1.34-4.28). The findings support the need for control measures on the use of key antibiotics in veterinary medicine. AMR occurrence in Portugal seems to be related to summer, although less in laying hens and in 2018. Key messages AMR in bacterial isolates suggests the need for integrated actions to mitigate and control the use of 3rd and 4rd generation cephalosporins, fluoroquinolones and quinolones in animal production. AMR occurrence in Portugal seems to be further related to summer conditions, while comparing to other seasons.

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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

Journal of Food Protection ◽

10.4315/0362-028x.jfp-10-451 ◽

2011 ◽

Vol 74 (10) ◽

pp. 1639-1648 ◽

Cited By ~ 33

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.

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