Genomic diversity, virulence and source of Campylobacter jejuni contamination in Irish poultry slaughterhouses by whole genome sequencing

Prendergast, Deirdre M.; Lynch, Helen; Whyte, Paul; Golden, Olwen; Murphy, Declan; Gutiérrez, Montserrat; Cummins, Juliana; Johnston, Dayle; Bolton, Declan; Coffey, Aidan; Lucey, Brigid; O’Connor, Lisa; Byrne, William R.

doi:10.1111/jam.15753

Cited by 12 publications

(10 citation statements)

References 53 publications

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“…Poultry meat has been the predominant source attributable to human campylobacteriosis cases [ 16 , 17 ]. Further back from the direct exposure to consumers, genetic diversity of C. jejuni isolated from chicken carcasses at a slaughter plant included multiple genotypes that are associated with strains found in human infections [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics of Campylobacter jejuni from clinical campylobacteriosis stool specimens

et al. 2022

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Background Campylobacter jejuni is a pervasive pathogen of major public health concern with a complex ecology requiring accurate and informative approaches to define pathogen diversity during outbreak investigations. Source attribution analysis may be confounded if the genetic diversity of a C. jejuni population is not adequately captured in a single specimen. The aim of this study was to determine the genomic diversity of C. jejuni within individual stool specimens from four campylobacteriosis patients. Direct plating and pre-culture filtration of one stool specimen per patient was used to culture multiple isolates per stool specimen. Whole genome sequencing and pangenome level analysis were used to investigate genomic diversity of C. jejuni within a patient. Results A total 92 C. jejuni isolates were recovered from four patients presenting with gastroenteritis. The number of isolates ranged from 13 to 30 per patient stool. Three patients yielded a single C. jejuni multilocus sequence type: ST-21 (n = 26, patient 4), ST-61 (n = 30, patient 1) and ST-2066 (n = 23, patient 2). Patient 3 was infected with two different sequence types [ST-51 (n = 12) and ST-354 (n = 1)]. Isolates belonging to the same sequence type from the same patient specimen shared 12–43 core non-recombinant SNPs and 0–20 frameshifts with each other, and the pangenomes of each sequence type consisted of 1406–1491 core genes and 231–264 accessory genes. However, neither the mutation nor the accessory genes were connected to a specific functional gene category. Conclusions Our findings show that the C. jejuni population recovered from an individual patient’s stool are genetically diverse even within the same ST and may have shared common ancestors before specimens were obtained. The population is unlikely to have evolved from a single isolate at the time point of initial patient infection, leading us to conclude that patients were likely infected with a heterogeneous C. jejuni population. The diversity of the C. jejuni population found within individual stool specimens can inform future methodological approaches to attribution and outbreak investigations.

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Section: Introductionmentioning

confidence: 99%

Comparative genomics of Campylobacter jejuni from clinical campylobacteriosis stool specimens

et al. 2022

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“…Isolates were recovered on Columbia Agar supplemented with horse blood (E & O Laboratories LTD, Scotland, United Kingdom) and incubated at 37°C for 18–24 h. Using a 1 μL inoculation loop, a loopful of pure culture was taken from the plate and re-suspended in 100 μL nuclease free water and DNA was extracted and quality checked as previously described using the MagNA Pure 96 system (Roche Diagnostics, Rotkreuz, Switzerland) ( Prendergast et al, 2022b ).…”

Section: Methodsmentioning

confidence: 99%

“…Sample libraries for all isolates were prepared using the Illumina DNA Prep kit (Illumina, Eindhoven, Netherlands) The library was amplified by 5 PCR cycles and normalization, denaturing and sequencing of libraries was as previously described ( Prendergast et al, 2022b ). The isolates included in this study were distributed over eight sequencing runs on a MiSeq (Illumina).…”

Section: Methodsmentioning

confidence: 99%

“…The generated raw sequence reads (FASTQ files) were imported directly from Illumina BaseSpace to BioNumerics (Version 8.1; Applied Maths NV, a BioMérieux company, Sint-Martens-Letem, Belgium). FASTQ files were assembled using the SPAdes assembler within the BioNumerics software via its integrated calculation engine as previously described ( Prendergast et al, 2022b ). The FASTQ files were submitted to the BioNumerics wgMLST scheme for assembly-free calling and assembled genomes were submitted to the scheme for assembly-based allele calling.…”

Section: Methodsmentioning

confidence: 99%

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Characterization of cephalosporin and fluoroquinolone resistant Enterobacterales from Irish farm waste by whole genome sequencing

Prendergast¹,

Slowey²,

Burgess

et al. 2023

Front. Microbiol.

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BackgroundThe Enterobacterales are a group of Gram-negative bacteria frequently exhibiting extended antimicrobial resistance (AMR) and involved in the transmission of resistance genes to other bacterial species present in the same environment. Due to their impact on human health and the paucity of new antibiotics, the World Health Organization (WHO) categorized carbapenem resistant and ESBL-producing as critical. Enterobacterales are ubiquitous and the role of the environment in the transmission of AMR organisms or antimicrobial resistance genes (ARGs) must be examined in tackling AMR in both humans and animals under the one health approach. Animal manure is recognized as an important source of AMR bacteria entering the environment, in which resistant genes can accumulate.MethodsTo gain a better understanding of the dissemination of third generation cephalosporin and fluoroquinolone resistance genes between isolates in the environment, we applied whole genome sequencing (WGS) to Enterobacterales (79 E. coli, 1 Enterobacter cloacae, 1 Klebsiella pneumoniae, and 1 Citrobacter gillenii) isolated from farm effluents in Ireland before (n = 72) and after (n = 10) treatment by integrated constructed wetlands (ICWs). DNA was extracted using the MagNA Pure 96 system (Roche Diagnostics, Rotkreuz, Switzerland) followed by WGS on a MiSeq platform (Illumina, Eindhoven, Netherlands) using v3 chemistry as 300-cycle paired-end runs. AMR genes and point mutations were identified and compared to the phenotypic results for better understanding of the mechanisms of resistance and resistance transmission.ResultsA wide variety of cephalosporin and fluoroquinolone resistance genes (mobile genetic elements (MGEs) and chromosomal mutations) were identified among isolates that mostly explained the phenotypic AMR patterns. A total of 31 plasmid replicon types were identified among the 82 isolates, with a subset of them (n = 24), identified in E. coli isolates. Five plasmid replicons were confined to the Enterobacter cloacae isolate and two were confined to the Klebsiella pneumoniae isolate. Virulence genes associated with functions including stress, survival, regulation, iron uptake secretion systems, invasion, adherence and toxin production were identified.ConclusionOur study showed that antimicrobial resistant organisms (AROs) can persist even following wastewater treatment and could transmit AMR of clinical relevance to the environment and ultimately pose a risk to human or animal health.

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“…The used WGS data revealed a high genetic diversity amongst C. jejuni isolated from broilers and definite types and virulence genes are implicated with the development of more severe human illness ( 28 ).…”

Section: Introductionmentioning

confidence: 99%

Genomic insight into Campylobacter jejuni isolated from commercial turkey flocks in Germany using whole-genome sequencing analysis

El-Adawy

Hotzel²,

García-Soto³

et al. 2023

Front. Vet. Sci.

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Campylobacter (C.) jejuni is a zoonotic bacterium of public health significance. The present investigation was designed to assess the epidemiology and genetic heterogeneity of C. jejuni recovered from commercial turkey farms in Germany using whole-genome sequencing. The Illumina MiSeq® technology was used to sequence 66 C. jejuni isolates obtained between 2010 and 2011 from commercial meat turkey flocks located in ten German federal states. Phenotypic antimicrobial resistance was determined. Phylogeny, resistome, plasmidome and virulome profiles were analyzed using whole-genome sequencing data. Genetic resistance markers were identified with bioinformatics tools (AMRFinder, ResFinder, NCBI and ABRicate) and compared with the phenotypic antimicrobial resistance. The isolates were assigned to 28 different sequence types and 11 clonal complexes. The average pairwise single nucleotide-polymorphisms distance of 14,585 SNPs (range: 0–26,540 SNPs) revealed a high genetic distinction between the isolates. Thirteen virulence-associated genes were identified in C. jejuni isolates. Most of the isolates harbored the genes flaA (83.3%) and flaB (78.8%). The wlaN gene associated with the Guillain–Barré syndrome was detected in nine (13.6%) isolates. The genes for resistance to ampicillin (blaOXA), tetracycline [tet(O)], neomycin [aph(3')-IIIa], streptomycin (aadE) and streptothricin (sat4) were detected in isolated C. jejuni using WGS. A gene cluster comprising the genes sat4, aph(3′)-IIIa and aadE was present in six isolates. The single point mutation T86I in the housekeeping gene gyrA conferring resistance to quinolones was retrieved in 93.6% of phenotypically fluoroquinolone-resistant isolates. Five phenotypically erythromycin-susceptible isolates carried the mutation A103V in the gene for the ribosomal protein L22 inferring macrolide resistance. An assortment of 13 β-lactam resistance genes (blaOXA variants) was detected in 58 C. jejuni isolates. Out of 66 sequenced isolates, 28 (42.4%) carried plasmid-borne contigs. Six isolates harbored a pTet-like plasmid-borne contig which carries the tet(O) gene. This study emphasized the potential of whole-genome sequencing to ameliorate the routine surveillance of C. jejuni. Whole-genome sequencing can predict antimicrobial resistance with a high degree of accuracy. However, resistance gene databases need curation and updates to revoke inaccuracy when using WGS-based analysis pipelines for AMR detection.

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Genomic diversity, virulence and source of Campylobacter jejuni contamination in Irish poultry slaughterhouses by whole genome sequencing

Cited by 12 publications

References 53 publications

Comparative genomics of Campylobacter jejuni from clinical campylobacteriosis stool specimens

Comparative genomics of Campylobacter jejuni from clinical campylobacteriosis stool specimens

Characterization of cephalosporin and fluoroquinolone resistant Enterobacterales from Irish farm waste by whole genome sequencing

Genomic insight into Campylobacter jejuni isolated from commercial turkey flocks in Germany using whole-genome sequencing analysis

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