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Campylobacter jejuni is the leading cause of bacterial gastroenteritis globally, and infections are often transmitted through consumption of raw or undercooked poultry. Campylobacter jejuni ST50 is among the top ten sequence types (STs) reported in the collected isolates listed at PubMLST records from poultry, food and clinical sources for Asia, Europe, North America, Oceania and South America. This study was designed to determine the most commonly reported C. jejuni STs globally using the PubMLST database and assess similarities between genomes of C. jejuni ST50 isolates from geographically distinct locations. To gain a better understanding of C. jejuni diversity, we compared draft genome sequences of 182 ST50 isolates recovered from retail or caecal poultry samples in Oceania, Europe and North America that were collected over a period of 9 years (2010 to 2018). Overall, phylogenetic analysis revealed that isolates from geographically distinct locations tended to cluster based on the continent where the sample was collected. Among ST50 isolates from Europe and North America, we identified resistance determinants associated with phenotypic resistance to beta-lactams (EU: 55%; GB: 43.1%), tetracyclines (CA: 77.3%; EU: 37.5%; GB: 9.8%; US: 43.5%) and fluoroquinolones (EU: 60.0%; GB: 15.7%); no resistance determinants were identified in isolates from Australia. In general, the majority of the virulence genes, with rare exceptions such as wlaN, cj1138, hddA and rfbC, were evenly distributed throughout the genomes of all ST50 isolates in this study. Genomic-based characterization of C. jejuni ST50 isolates from poultry on three continents highlighted that geographically distinct isolates have evolved independently but only represent a glimpse into the diversity of C. jejuni.

Salmonella enterica subspecies enterica serovar Typhimurium and its monophasic variant are among the most common Salmonella serovars associated with human salmonellosis each year. Related infections are often due to consumption of contaminated meat of pig, cattle, and poultry origin. In order to evaluate novel microbial subtyping methods for source attribution, an approach based on weighted networks was applied on 141 human and 210 food and animal isolates of pigs, broilers, layers, ducks, and cattle collected in Denmark from 2013 to 2014. A whole-genome SNP calling was performed along with cgMLST and wgMLST. Based on these genomic input data, pairwise distance matrices were built and used as input for construction of a weighted network where nodes represent genomes and links to distances. Analyzing food and animal Typhimurium genomes, the coherence of source clustering ranged from 89 to 90% for animal source, from 84 to 85% for country, and from 63 to 65% for year of isolation and was equal to 82% for serotype, suggesting animal source as the first driver of clustering formation. Adding human isolate genomes to the network, a percentage between 93.6 and 97.2% clustered with the existing component and only a percentage between 2.8 and 6.4% appeared as not attributed to any animal sources. The majority of human genomes were attributed to pigs with probabilities ranging from 83.9 to 84.5%, followed by broilers, ducks, cattle, and layers in descending order. In conclusion, a weighted network approach based on pairwise SNPs, cgMLST, and wgMLST matrices showed promising results for source attribution studies.

adults Abstract Fulltext Metrics Get Permission Authors Gaardbo Kuhn K, Nielsen EM, Mølbak K, Ethelberg S Received 13 June 2018 Accepted for publication 14 September 2018 Published 21 November 2018 Volume 2018:10 Pages 1695—1707 DOI https://doi.org/10.2147/CLEP.S177141 Checked for plagiarism Yes Review by Single-blind Peer reviewers approved by Dr Amy Norman Peer reviewer comments 3 Editor who approved publication: Professor Vera Ehrenstein Article has an altmetric score of 9 Katrin Gaardbo Kuhn,1 Eva Møller Nielsen,2 Kåre Mølbak,1,3 Steen Ethelberg1 1Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark; 2Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark; 3Institute of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark Background: Each year more than 4,000 cases of campylobacteriosis are reported in Denmark, making it the most common bacterial gastrointestinal infection. Here we describe a case-control study to identify sources of infection with a focus on environmental factors. Methods: From January to December 2016, we conducted a prospective case-control study among Danish persons aged 1–30 years. Participants were invited by letter to complete an online questionnaire. Crude and adjusted ORs were calculated and final parsimonious multivariate models developed using logistic regression. Results: The study recruited 1366 cases and 4,418 controls, of whom 65% and 66%, respectively, completed the questionnaire. A multivariate model for domestically acquired cases showed, among others, increased risk of infection with bathing in fresh water (OR=5.1), contact to beach sand (OR=1.8), owning a pet dog with diarrhea (OR=4.6), and eating minced beef (OR=2.6) or chicken (OR=2.5). The model for children highlighted similar risk factors but also included bathing in a paddling pool (OR=13.6) and eating fresh strawberries (OR=5.3). A separate analysis for persons reporting foreign tra

Whole-genome sequencing is rapidly replacing current molecular typing methods for surveillance purposes. Our study evaluates core-genome single-nucleotide polymorphism analysis for outbreak detection and linking of sources of Salmonella enterica serovar Typhimurium and its monophasic variants during a 7-month surveillance period in Denmark. We reanalyzed and defined 8 previously characterized outbreaks from the phylogenetic relatedness of the isolates, epidemiologic data, and food traceback investigations. All outbreaks were identified, and we were able to exclude unrelated and include additional related human cases. We were furthermore able to link possible food and veterinary sources to the outbreaks. Isolates clustered according to sequence types (STs) 19, 34, and 36. Our study shows that core-genome single-nucleotide polymorphism analysis is suitable for surveillance and outbreak investigation for Salmonella Typhimurium (ST19 and ST36), but whole genome–wide analysis may be required for the tight genetic clone of monophasic variants (ST34).

The development of diagnostic metagenomics is driven by the need for universal, culture-independent methods for detection and characterization of pathogens to substitute the time-consuming, organism-specific, and often culture-based laboratory procedures for epidemiological source-tracing. Some of the challenges in diagnostic metagenomics are, that it requires a great next-generation sequencing depth and unautomated data analysis. DNA from human fecal samples spiked with 7.75 × 101-7.75 × 107 colony forming unit (CFU)/ml Campylobacter jejuni and chicken fecal samples spiked with 1 × 102-1 × 106 CFU/g Campylobacter jejuni was sequenced and data analysis was done by the metagenomic tools Kraken and CLARK. More hits were obtained at higher spiking levels, however with no significant linear correlations (human samples p = 0.12, chicken samples p = 0.10). Therefore, no definite detection limit could be determined, but the lowest spiking levels found positive were 7.75 × 104 CFU/ml in human feces and 103 CFU/g in chicken feces. Eight human clinical fecal samples with estimated Campylobacter infection loads from 9.2 × 104-1.0 × 109 CFU/ml were analyzed using the same methods. It was possible to detect Campylobacter in all the clinical samples. Sensitivity in diagnostic metagenomics is improving and has reached a clinically relevant level. There are still challenges to overcome before real-time diagnostic metagenomics can replace quantitative polymerase chain reaction (qPCR) or culture-based surveillance and diagnostics, but it is a promising new technology.