Prevalence, Detection of Resistance Genes and Antimicrobial Resistance of Campylobacter jejuni in Broilers in North Macedonia

AbstractCampylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals.Although antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern. Considering the significant contribution of ruminants as reservoirs of resistant Campylobacter, Illumina whole-genome sequencing was used to characterise the mechanisms of AMR in Campylobacter jejuni and Campylobacter coli recovered from beef cattle, dairy cattle, and sheep in northern Spain. Genome analysis showed extensive genetic diversity that clearly separated both species. Resistance genotypes were identified by screening assembled sequences with BLASTn and ABRicate, and additional sequence alignments were performed to search for frameshift mutations and gene modifications. A high correlation was observed between phenotypic resistance to a given antimicrobial and the presence of the corresponding known resistance genes. Detailed sequence analysis allowed us to detect the recently described mosaic tet(O/M/O) gene in one C. coli, describe possible new alleles of blaOXA-61-like genes, and decipher the genetic context of aminoglycoside resistance genes, as well as the plasmid/chromosomal location of the different AMR genes and their implication for resistance spread. Updated resistance gene databases and detailed analysis of the matched open reading frames are needed to avoid errors when using WGS-based analysis pipelines for AMR detection in the absence of phenotypic data.

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Whole-Genome Sequences of Two Campylobacter coli Isolates from the Antimicrobial Resistance Monitoring Program in Colombia: TABLE 1

Genome Announcements ◽

10.1128/genomea.00131-16 ◽

2016 ◽

Vol 4 (2) ◽

Author(s):

Johan F. Bernal ◽

Pilar Donado-Godoy ◽

María Fernanda Valencia ◽

Maribel León ◽

Yolanda Gómez ◽

...

Keyword(s):

Multidrug Resistance ◽

Antimicrobial Resistance ◽

Campylobacter Jejuni ◽

Resistance Genes ◽

Monitoring Program ◽

Campylobacter Coli ◽

Whole Genome ◽

Genome Sequences ◽

Resistance Monitoring ◽

Antimicrobial Resistance Genes

Campylobacter coli , along with Campylobacter jejuni , is a major agent of gastroenteritis and acute enterocolitis in humans. We report the whole-genome sequences of two multidrug-resistance C. coli strains, isolated from the Colombian poultry chain. The isolates contain a variety of antimicrobial resistance genes for aminoglycosides, lincosamides, fluoroquinolones, and tetracycline.

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Isolation and antimicrobial resistance of Campylobacter jejuni and Campylobacter coli found in chilled chicken carcasses in the Federal District Region and surrounding areas

Semina Ciências Agrárias ◽

10.5433/1679-0359.2019v40n5supl1p2247 ◽

2019 ◽

Vol 40 (5Supl1) ◽

pp. 2247

Author(s):

Patricia Renault Silva ◽

Joana Marchesini Palma ◽

Nara Rubia Souza ◽

Helenira Melo de Moura ◽

Simone Perecmanis ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Nalidixic Acid ◽

Campylobacter Jejuni ◽

Resistance Genes ◽

Federal District ◽

Occurrence Rate ◽

Campylobacter Coli ◽

Antimicrobial Resistance Genes ◽

Polymerase Chain ◽

Surrounding Areas

This study aimed to isolate Campylobacter jejuni and Campylobacter coli from chilled chicken carcasses marketed in the Federal District Region and surrounding areas, as well as to detect the occurrence of antimicrobial resistance and genes responsible for the same. A total of 105 chilled chicken carcasses were collected, of which 7 (6.67%) were positive for C. jejuni and 4 (3.81%) were positive for C. coli. These results were obtained using both the conventional microbiological isolation method and polymerase chain reaction assays. All of the positive strains were subjected to antimicrobial susceptibility testing for seven antimicrobials. The resistance incidences found in the C. jejuni strains were as follows: 71.43% for tetracycline and nalidixic acid, 42.86% for streptomycin and gentamicin, 57.14% for ciprofloxacin and erythromycin, and 28.57% for chloramphenicol. Among the C. coli strains, 100% were resistant to tetracycline and streptomycin, 75% were resistant to erythromycin, 50% were resistant to ciprofloxacin, gentamicin, and nalidixic acid, and no strains were resistant to chloramphenicol. While analyzing the presence of antimicrobial resistance genes in the isolated C. jejuni strains, the aph3-1 (resistance to aminoglycosides), aadE (resistance to streptomycin), and tet(O) (resistance to tetracycline) genes were identified, with occurrence rates of 57.14%, 28.57%, and 42.86%, respectively, whereas in the C. coli strains, there was a 25% occurrence rate for both the aph3-1 and tet(O) genes. The aadE gene was not found in the C. coli isolates. The results of this study demonstrated the presence of C. jejuni and C. coli in chilled chicken carcasses marketed in the Federal District Region and surrounding areas, as well as the antimicrobial resistance and the presence of resistance genes in these bacteria, which may pose threats to public health.

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Prediction of antimicrobial resistance in clinical Campylobacter jejuni isolates from whole-genome sequencing data

European Journal of Clinical Microbiology & Infectious Diseases ◽

10.1007/s10096-020-04043-y ◽

2020 ◽

Author(s):

Louise Gade Dahl ◽

Katrine Grimstrup Joensen ◽

Mark Thomas Østerlund ◽

Kristoffer Kiil ◽

Eva Møller Nielsen

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Campylobacter Jejuni ◽

Genome Sequencing ◽

Resistance Genes ◽

Point Mutations ◽

23S Rrna ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data

Abstract Campylobacter jejuni is recognised as the leading cause of bacterial gastroenteritis in industrialised countries. Although the majority of Campylobacter infections are self-limiting, antimicrobial treatment is necessary in severe cases. Therefore, the development of antimicrobial resistance (AMR) in Campylobacter is a growing public health challenge and surveillance of AMR is important for bacterial disease control. The aim of this study was to predict antimicrobial resistance in C. jejuni from whole-genome sequencing data. A total of 516 clinical C. jejuni isolates collected between 2014 and 2017 were subjected to WGS. Resistance phenotypes were determined by standard broth dilution, categorising isolates as either susceptible or resistant based on epidemiological cutoffs for six antimicrobials: ciprofloxacin, nalidixic acid, erythromycin, gentamicin, streptomycin, and tetracycline. Resistance genotypes were identified using an in-house database containing reference genes with known point mutations and the presence of resistance genes was determined using the ResFinder database and four bioinformatical methods (modified KMA, ABRicate, ARIBA, and ResFinder Batch Upload). We identified seven resistance genes including tet(O), tet(O/32/O), ant(6)-Ia, aph(2″)-If, blaOXA, aph(3′)-III, and cat as well as mutations in three genes: gyrA, 23S rRNA, and rpsL. There was a high correlation between phenotypic resistance and the presence of known resistance genes and/or point mutations. A correlation above 98% was seen for all antimicrobials except streptomycin with a correlation of 92%. In conclusion, we found that WGS can predict antimicrobial resistance with a high degree of accuracy and have the potential to be a powerful tool for AMR surveillance.

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Antibiotic susceptibility and prevalence of foodborne pathogens in poultry meat in Romania

The Journal of Infection in Developing Countries ◽

10.3855/jidc.4958 ◽

2015 ◽

Vol 9 (01) ◽

pp. 035-041 ◽

Cited By ~ 23

Author(s):

Sorin Daniel Dan ◽

Alexandra Tabaran ◽

Liora Mihaiu ◽

Marian Mihaiu

Keyword(s):

Antimicrobial Resistance ◽

Campylobacter Jejuni ◽

Resistance Genes ◽

Foodborne Pathogens ◽

Pathogenic Bacteria ◽

Multidrug Resistant ◽

Poultry Meat ◽

Continuous Increase ◽

E Coli ◽

Microbiological Methods

Introduction: The occurrence of pathogenic strains in poultry meat is of growing concern in Romania. Another problem found on a global level is the continuous increase of antimicrobial resistance in bacteria isolated from food. This study aimed to evaluate the prevalence of pathogenic bacteria in poultry carcasses obtained in Romania in 2012–2013 and to reveal the most prevalent patterns of antimicrobial resistance in the isolated strains. Methodology: A total of 144 broiler chicken carcasses were evaluated according to classical microbiological methods. The DNA was extracted from the bacterial colonies and the resistance genes were identified by PCR. Results: In 2012, 47.2% of the samples revealed at least one of the following bacteria: Campylobacter jejuni (9.72%; n = 7), Salmonella enterica serotype Enteritidis (4.17%; n = 3), Listeria monocytogenes (15.28%; n = 11), and Escherichia coli (16.67%; n = 12). In 2013, the number of positive samples of pathogenic bacteria decreased, although Campylobacter jejuni was isolated in a higher percentage (20.8% vs. 9.72%). The percentage of multidrug-resistant (MDR) bacteria was high (23%); the most prevalent pattern included resistance to tetracycline, sulfonamides, and quinolones/fluoroquinolones. All the resistant Salmonella and E. coli strains were tested for the presence of characteristic resistance genes (Kn, blaTEM, tetA, tetB, tetG, DfrIa, aadA1a, Sul) and revealed that these isolates represent an important reservoir in the spread of this phenomenon. Conclusions: Our findings suggest that Romania urgently needs an integrated surveillance system within the entire chain, for drug-resistant pathogens isolated from poultry meat.

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Distribution of Colonization and Antimicrobial Resistance Genes in Campylobacter jejuni Isolated from Chicken

Foodborne Pathogens and Disease ◽

10.1089/fpd.2012.1271 ◽

2013 ◽

Vol 10 (4) ◽

pp. 382-391 ◽

Cited By ~ 8

Author(s):

Alexandre Thibodeau ◽

Philippe Fravalo ◽

Philippe Garneau ◽

Luke Masson ◽

Sylvette Laurent-Lewandowski ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Campylobacter Jejuni ◽

Resistance Genes ◽

Antimicrobial Resistance Genes

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Antimicrobial Resistance Genes and Plasmids in Campylobacter jejuni from Broiler Production Chain in Southern Brazil

LWT ◽

10.1016/j.lwt.2021.111202 ◽

2021 ◽

pp. 111202

Author(s):

Natalie Rauber Kleinubing ◽

Tassiana Ramires ◽

Simone de Fátima Rauber Würfel ◽

Louise Haubert ◽

Leticia Klein Scheik ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Campylobacter Jejuni ◽

Resistance Genes ◽

Southern Brazil ◽

Production Chain ◽

Broiler Production ◽

Antimicrobial Resistance Genes

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Antimicrobial resistance of Campylobacter jejuni isolated from chicken, some animal products and human in Kalyoubia , Egypt , with special reference to its viability

Benha Veterinary Medical Journal ◽

10.21608/bvmj.2019.103407 ◽

2019 ◽

Vol 36 (1) ◽

pp. 156-163

Author(s):

Lobna Salem ◽

Nashwa Kh ◽

S.A Mona ◽

A.M.A Barakat

Keyword(s):

Antimicrobial Resistance ◽

Special Reference ◽

Campylobacter Jejuni ◽

Animal Products

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Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated Infections

Microorganisms ◽

10.3390/microorganisms9040707 ◽

2021 ◽

Vol 9 (4) ◽

pp. 707

Author(s):

J. Christopher Noone ◽

Fabienne Antunes Ferreira ◽

Hege Vangstein Aamot

Keyword(s):

Staphylococcus Aureus ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Virulence Gene ◽

Orthopaedic Implant ◽

Metagenomic Sequencing ◽

Gene Detection ◽

Shotgun Metagenomic Sequencing ◽

Antimicrobial Resistance Genes ◽

Culture Independent

Our culture-independent nanopore shotgun metagenomic sequencing protocol on biopsies has the potential for same-day diagnostics of orthopaedic implant-associated infections (OIAI). As OIAI are frequently caused by Staphylococcus aureus, we included S. aureus genotyping and virulence gene detection to exploit the protocol to its fullest. The aim was to evaluate S. aureus genotyping, virulence and antimicrobial resistance genes detection using the shotgun metagenomic sequencing protocol. This proof of concept study included six patients with S. aureus-associated OIAI at Akershus University Hospital, Norway. Five tissue biopsies from each patient were divided in two: (1) conventional microbiological diagnostics and genotyping, and whole genome sequencing (WGS) of S. aureus isolates; (2) shotgun metagenomic sequencing of DNA from the biopsies. Consensus sequences were analysed using spaTyper, MLST, VirulenceFinder, and ResFinder from the Center for Genomic Epidemiology (CGE). MLST was also compared using krocus. All spa-types, one CGE and four krocus MLST results matched Sanger sequencing results. Virulence gene detection matched between WGS and shotgun metagenomic sequencing. ResFinder results corresponded to resistance phenotype. S. aureus spa-typing, and identification of virulence and antimicrobial resistance genes are possible using our shotgun metagenomics protocol. MLST requires further optimization. The protocol has potential application to other species and infection types.

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