Source attributed case-control study of campylobacteriosis in New Zealand

Lake, Robin; Campbell, Dan H.; Hathaway, S.C.; Ashmore, Ellen; Cressey, Peter; Horn, Beverley; Pirikahu, Sarah; Sherwood, Jill; Baker, Michael G; Shoemack, Phil; Benschop, Jackie; Marshall, Jonathan; Midwinter, Anne C.; Wilkinson, David; French, Nigel P.

doi:10.1016/j.ijid.2020.11.167

Cited by 30 publications

(24 citation statements)

References 21 publications

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“…C. jejuni ST45 is one of the most frequently isolated strains of Campylobacter collected from humans, domestic animals and the environment [32][33][34]. It is regarded as a 'generalist' strain, as it has been isolated from multiple host species and environments [35,36], and has demonstrated frequent host switching [37].…”

Section: Discussionmentioning

confidence: 99%

Genomic adaptations of Campylobacter jejuni to long-term human colonization

et al. 2021

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Background Campylobacter is a genus of bacteria that has been isolated from the gastrointestinal tract of humans and animals, and the environments they inhabit around the world. Campylobacter adapt to new environments by changes in their gene content and expression, but little is known about how they adapt to long-term human colonization. In this study, the genomes of 31 isolates from a New Zealand patient and 22 isolates from a United Kingdom patient belonging to Campylobacter jejuni sequence type 45 (ST45) were compared with 209 ST45 genomes from other sources to identify the mechanisms by which Campylobacter adapts to long-term human colonization. In addition, the New Zealand patient had their microbiota investigated using 16S rRNA metabarcoding, and their level of inflammation and immunosuppression analyzed using biochemical tests, to determine how Campylobacter adapts to a changing gastrointestinal tract. Results There was some evidence that long-term colonization led to genome degradation, but more evidence that Campylobacter adapted through the accumulation of non-synonymous single nucleotide polymorphisms (SNPs) and frameshifts in genes involved in cell motility, signal transduction and the major outer membrane protein (MOMP). The New Zealand patient also displayed considerable variation in their microbiome, inflammation and immunosuppression over five months, and the Campylobacter collected from this patient could be divided into two subpopulations, the proportion of which correlated with the amount of gastrointestinal inflammation. Conclusions This study demonstrates how genomics, phylogenetics, 16S rRNA metabarcoding and biochemical markers can provide insight into how Campylobacter adapts to changing environments within human hosts. This study also demonstrates that long-term human colonization selects for changes in Campylobacter genes involved in cell motility, signal transduction and the MOMP; and that genetically distinct subpopulations of Campylobacter evolve to adapt to the changing gastrointestinal environment.

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Section: Discussionmentioning

confidence: 99%

Genomic adaptations of Campylobacter jejuni to long-term human colonization

et al. 2021

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“…Overall, considering Campylobacter spp. as a whole, most studies suggest that poultry or poultry followed by ruminants are the most prevalent sources [15][16][17][18][19][20][21]. Additionally, Liao et al found a positive correlation between rurality and ruminant-sourced campylobacteriosis [22].…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania

et al. 2021

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Campylobacteriosis is the most common bacterial foodborne illness in the United States and is frequently associated with foods of animal origin. The goals of this study were to compare clinical and non-clinical Campylobacter populations from Tennessee (TN) and Pennsylvania (PA), use phylogenetic relatedness to assess source attribution patterns, and identify potential outbreak clusters. Campylobacter isolates studied (n = 3080) included TN clinical isolates collected and sequenced for routine surveillance, PA clinical isolates collected from patients at the University of Pennsylvania Health System facilities, and non-clinical isolates from both states for which sequencing reads were available on NCBI. Phylogenetic analyses were conducted to categorize isolates into species groups and determine the population structure of each species. Most isolates were C. jejuni (n = 2132, 69.2%) and C. coli (n = 921, 29.9%), while the remaining were C. lari (0.4%), C. upsaliensis (0.3%), and C. fetus (0.1%). The C. jejuni group consisted of three clades; most non-clinical isolates were of poultry (62.7%) or cattle (35.8%) origin, and 59.7 and 16.5% of clinical isolates were in subclades associated with poultry or cattle, respectively. The C. coli isolates grouped into two clades; most non-clinical isolates were from poultry (61.2%) or swine (29.0%) sources, and 74.5, 9.2, and 6.1% of clinical isolates were in subclades associated with poultry, cattle, or swine, respectively. Based on genomic similarity, we identified 42 C. jejuni and one C. coli potential outbreak clusters. The C. jejuni clusters contained 188 clinical isolates, 19.6% of the total C. jejuni clinical isolates, suggesting that a larger proportion of campylobacteriosis may be associated with outbreaks than previously determined.

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“…The proportion of cases attributed to pork increased from approximately 20% in 2009-2016 to approximately 40% in 2017-2019, coinciding with a rise in cases due to Salmonella enterica ser 4,5,12:i:-, which has been found to be a persistent coloniser of pigs in Australia [33]. The proportion of cases attributed to layers was lower amongst rural-dwelling than urban-dwelling populations, similar to the rural-urban gradient found in a source attribution analysis of Campylobacter infections in New Zealand [20,34].…”

Section: Discussionmentioning

confidence: 63%

Source Attribution of Salmonellosis by Time and Geography in New South Wales, Australia

McLure

Shadbolt

Desmarchelier³

et al. 2021

Preprint

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BackgroundSalmonella is major cause of zoonotic illness around the world, arising from direct or indirect contact with a range of animal reservoirs. In the Australian state of New South Wales (NSW), salmonellosis is believed to be primarily foodborne, but the relative contribution of animal reservoirs is unknown.MethodsThe analysis included 4,543 serotyped isolates from animal reservoirs and 30,073 serotyped isolates from domestically acquired human cases in NSW between January 2008 and August 2019. We used a Bayesian source attribution methodology to estimate the proportion of foodborne Salmonella infections attributable to broiler chickens, layer chickens, ruminants, pigs, and an unknown or unsampled source. Additional analyses included covariates for four time periods and five levels of rurality.ResultsA single serotype, S. Typhimurium, accounted for 65-75% of included cases during 2008-2014 but <50% during 2017-2019. Attribution to layer chickens was highest during 2008-2010 (48.7%, 95%CrI: 24.2-70.3%) but halved by 2017-2019 (23.1%, 95%CrI: 5.7-38.9%) and was lower in the rural and remote populations than in the majority urban population. The proportion of cases attributed to the unsampled source was 11.3% (95%CrI: 1.2%–22.1%) overall, but higher in rural and remote populations. The proportion of cases attributed to pork increased from approximately 20% in 2009-2016 to approximately 40% in 2017-2019 coinciding with a rise in cases due to S. ser 4,5,12:i:-.Conclusion Layer chickens were likely the primary reservoir of domestically acquired Salmonella infections in NSW circa 2010, but attribution to the source declined contemporaneously with increased vaccination of layer flocks and tighter food safety regulations for the handling of eggs.

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Source attributed case-control study of campylobacteriosis in New Zealand

Cited by 30 publications

References 21 publications

Genomic adaptations of Campylobacter jejuni to long-term human colonization

Genomic adaptations of Campylobacter jejuni to long-term human colonization

Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania

Source Attribution of Salmonellosis by Time and Geography in New South Wales, Australia

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