Trends in fluoroquinolone resistance in Campylobacter

Members of the genus Campylobacter remain a leading cause of bacterial gastroenteritis worldwide. Infection is usually self-limiting but in severe cases may require antibiotic treatment. In a recent statement by the World Health Organization (WHO) Campylobacter was named as one of the 12 bacteria that pose the greatest threat to human health because they are resistant to antibiotics. In this mini review we describe recent trends in fluoroquinolone (FQ) (particularly ciprofloxacin) resistance in strains of members of the genus Campylobacter isolated from livestock and clinical samples from several countries. Using evidence from phenotyping surveys and putative resistance prediction from DNA sequence data, we discuss the acquisition and spread of FQ resistance and the role of horizontal gene transfer and describe trends in FQ-resistance in samples from livestock and clinical cases. This review emphasises that FQ resistance remains common among isolates of members of the genus Campylobacter from various sources

Partial Failure of Milk Pasteurization as a Risk for the Transmission of Campylobacter From Cattle to Humans

Background. Cattle are the second most common source of human campylobacteriosis. However, routes to account for this scale of transmission have not been identified. In contrast to chicken, red meat is not heavily contaminated at point of sale. Although effective pasteurization prevents milk-borne infection, apparently sporadic infections may include undetected outbreaks from raw or perhaps incompletely pasteurized milk.Methods. A rise in Campylobacter gastroenteritis in an isolated population was investigated using whole-genome sequencing (WGS), an epidemiological study, and environmental investigations.Results. A single strain was identified in 20 cases, clearly distinguishable from other local strains and a reference population by WGS. A case-case analysis showed association of infection with the outbreak strain and milk from a single dairy (odds ratio, 8; Fisher exact test P value = .023). Despite temperature records indicating effective pasteurization, mechanical faults likely to lead to incomplete pasteurization of part of the milk were identified by further testing and examination of internal components of dairy equipment.Conclusions. Here, milk distribution concentrated on a small area, including school-aged children with low background incidence of campylobacteriosis, facilitated outbreak identification. Low-level contamination of widely distributed milk would not produce as detectable an outbreak signal. Such hidden outbreaks may contribute to the substantial burden of apparently sporadic Campylobacter from cattle where transmission routes are not certain. The effective discrimination of outbreak isolates from a reference population using WGS shows that integrating these data and approaches into surveillance could support the detection as well as investigation of such outbreaks

Wild bird-associated Campylobacter jejuni isolates are a consistent source of human disease, in Oxfordshire, United Kingdom

The contribution of wild birds as a source of human campylobacteriosis was investigated in Oxfordshire, United Kingdom (UK) over a 10 year period. The probable origin of human Campylobacter jejuni genotypes, as described by multilocus sequence typing, was estimated by comparison with reference populations of isolates from farm animals and five wild bird families, using the STRUCTURE algorithm. Wild bird-attributed isolates accounted for between 476 (2.1%) and 543 (3.5%) cases annually. This proportion did not vary significantly by study year (P = 0.934) but varied seasonally, with wild bird-attributed genotypes comprising a greater proportion of isolates during warmer compared with cooler months (P = 0.003). The highest proportion of wild bird-attributed illness occurred in August (P < 0.001), with a significantly lower proportion in November (P = 0.018). Among genotypes attributed to specific groups of wild birds, seasonality was most apparent for Turdidae-attributed isolates, which were absent during cooler, winter months. This study is consistent with some wild bird species representing a persistent source of campylobacteriosis, and contributing a distinctive seasonal pattern to disease burden. If Oxfordshire is representative of the UK as a whole in this respect, these data suggest that the national burden of wild bird-attributed isolates could be in the order of 10,000 annually

Genome-wide association of functional traits linked with<i> Campylobacter jejuni </i>survival from farm to fork

Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, primarily associated with the consumption of contaminated poultry. C. jejuni lineages vary in host range and prevalence in human infection, suggesting differences in survival throughout the poultry processing chain. From 7,343 MLST-characterised isolates, we sequenced 600 C. jejuni and C. coli isolates from various stages of poultry processing and clinical cases. A genome-wide association study (GWAS) in C. jejuni ST-21 and ST-45 complexes identified genetic elements over-represented in clinical isolates that increased in frequency throughout the poultry processing chain. Disease-associated SNPs were distinct in these complexes, sometimes organised in haplotype blocks. The function of genes containing associated elements was investigated, demonstrating roles for cj1377c in formate metabolism, nuoK in aerobic survival and oxidative respiration, and cj1368-70 in nucleotide salvage. This work demonstrates the utility of GWAS for investigating transmission in natural zoonotic pathogen populations and provides evidence that major C. jejuni lineages have distinct genotypes associated with survival, within the host specific niche, from farm to fork. </p

The molecular epidemiology and ecology of Campylobacter in the UK

Campylobacter is a major Public Health problem in the UK, responsible for more than 50,000 recorded cases of gastroenteritis annually. This thesis examines the molecular epidemiology of clinical campylobacteriosis in Oxfordshire over a one-year period, considering the distribution of Campylobacter jejuni and Campylobacter coli clonal complexes, the relationship between clonal complex and ciprofloxacin resistance and the relationship between travel-associated campylobacteriosis and Campylobacter genotype. The clinical picture is related back to the molecular epidemiology of Campylobacter isolated from retail poultry and the prevalence of resistance to antimicrobial substances. A widespread but non-random distribution of antibiotic resistance phenotypes among Campylobacter Sequence Types is indicative of the importance of horizontal transfer of resistant genes as well as clonal expansions of resistant genotypes. Continuing backwards along the food production chain the molecular epidemiology of Campylobacter amongst livestock and farmyard commensals is considered. A study of Campylobacter in rats reveals considerable genetic diversity, and three distinct clades of 'rat-associated' Campylobacter. The use of whole genome sequence data here allows a higher resolution study of the population structure of Campylobacter, identifying a major split in the ST-45 clonal complex. The potential to use next generation sequence data to improve the attribution of clinical campylobacteriosis cases to animal host source is investigated. Whole genome sequencing reveals that there is insufficient differentiation between populations of Campylobacter isolated from farm animals. Throughout this thesis data from conventional MLST and from next generation sequencing of whole genomes are compared and the relative benefits considered.</p

The molecular epidemiology and ecology of Campylobacter in the UK

Campylobacter is a major Public Health problem in the UK, responsible for more than 50,000 recorded cases of gastroenteritis annually. This thesis examines the molecular epidemiology of clinical campylobacteriosis in Oxfordshire over a one-year period, considering the distribution of Campylobacter jejuni and Campylobacter coli clonal complexes, the relationship between clonal complex and ciprofloxacin resistance and the relationship between travel-associated campylobacteriosis and Campylobacter genotype. The clinical picture is related back to the molecular epidemiology of Campylobacter isolated from retail poultry and the prevalence of resistance to antimicrobial substances. A widespread but non-random distribution of antibiotic resistance phenotypes among Campylobacter Sequence Types is indicative of the importance of horizontal transfer of resistant genes as well as clonal expansions of resistant genotypes. Continuing backwards along the food production chain the molecular epidemiology of Campylobacter amongst livestock and farmyard commensals is considered. A study of Campylobacter in rats reveals considerable genetic diversity, and three distinct clades of 'rat-associated' Campylobacter. The use of whole genome sequence data here allows a higher resolution study of the population structure of Campylobacter, identifying a major split in the ST-45 clonal complex. The potential to use next generation sequence data to improve the attribution of clinical campylobacteriosis cases to animal host source is investigated. Whole genome sequencing reveals that there is insufficient differentiation between populations of Campylobacter isolated from farm animals. Throughout this thesis data from conventional MLST and from next generation sequencing of whole genomes are compared and the relative benefits considered.</p

Widespread acquisition of antimicrobial resistance among Campylobacter isolates from UK retail poultry and evidence for clonal expansion of resistant lineages

BACKGROUND: Antimicrobial resistance is increasing among clinical Campylobacter cases and is common among isolates from other sources, specifically retail poultry - a major source of human infection. In this study the antimicrobial susceptibility of isolates from a UK-wide survey of Campylobacter in retail poultry in 2001 and 2004–5 was investigated. The occurrence of phenotypes resistant to tetracycline, quinolones (ciprofloxacin and naladixic acid), erythromycin, chloramphenicol and aminoglycosides was quantified. This was compared with a phylogeny for these isolates based upon Multi Locus Sequence Typing (MLST) to investigate the pattern of antimicrobial resistance acquisition. RESULTS: Antimicrobial resistance was present in all lineage clusters, but statistical testing showed a non-random distribution. Erythromycin resistance was associated with Campylobacter coli. For all antimicrobials tested, resistant isolates were distributed among relatively distant lineages indicative of widespread acquisition. There was also evidence of clustering of resistance phenotypes within lineages; indicative of local expansion of resistant strains. CONCLUSIONS: These results are consistent with the widespread acquisition of antimicrobial resistance among chicken associated Campylobacter isolates, either through mutation or horizontal gene transfer, and the expansion of these lineages as a proportion of the population. As Campylobacter are not known to multiply outside of the host and long-term carriage in humans is extremely infrequent in industrialized countries, the most likely location for the proliferation of resistant lineages is in farmed chickens

Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain

No single genealogical reconstruction or typing method currently encompasses all levels of bacterial diversity, from domain to strain. We propose ribosomal multilocus sequence typing (rMLST), an approach which indexes variation of the 53 genes encoding the bacterial ribosome protein subunits (rps genes), as a means of integrating microbial genealogy and typing. As with multilocus sequence typing (MLST), rMLST employs curated reference sequences to identify gene variants efficiently and rapidly. The rps loci are ideal targets for a universal characterization scheme as they are: (i) present in all bacteria; (ii) distributed around the chromosome; and (iii) encode proteins which are under stabilizing selection for functional conservation. Collectively, the rps loci exhibit variation that resolves bacteria into groups at all taxonomic and most typing levels, providing significantly more resolution than 16S small subunit rRNA gene phylogenies. A web-accessible expandable database, comprising whole-genome data from more than 1900 bacterial isolates, including 28 draft genomes assembled de novo from the European Bioinformatics Institute (EBI) sequence read archive, has been assembled. The rps gene variation catalogued in this database permits rapid and computationally non-intensive identification of the phylogenetic position of any bacterial sequence at the domain, phylum, class, order, family, genus, species and strain levels. The groupings generated with rMLST data are consistent with current nomenclature schemes and independent of the clustering algorithm used. This approach is applicable to the other domains of life, potentially providing a rational and universal approach to the classification of life that is based on one of its fundamental features, the translation mechanism