Fraser J. Gormley

Campylobacter genotyping to determine the source of human infection.

BACKGROUND Campylobacter species cause a high proportion of bacterial gastroenteritis cases and are a significant burden on health care systems and economies worldwide; however, the relative contributions of the various possible sources of infection in humans are unclear. METHODS National-scale genotyping of Campylobacter species was used to quantify the relative importance of various possible sources of human infection. Multilocus sequence types were determined for 5674 isolates obtained from cases of human campylobacteriosis in Scotland from July 2005 through September 2006 and from 999 Campylobacter species isolates from 3417 contemporaneous samples from potential human infection sources. These data were supplemented with 2420 sequence types from other studies, representing isolates from a variety of sources. The clinical isolates were attributed to possible sources on the basis of their sequence types with use of 2 population genetic models, STRUCTURE and an asymmetric island model. RESULTS The STRUCTURE and the asymmetric island models attributed most clinical isolates to chicken meat (58% and 78% of Campylobacter jejuni and 40% and 56% of Campylobacter coli isolates, respectively), identifying it as the principal source of Campylobacter infection in humans. Both models attributed the majority of the remaining isolates to ruminant sources, with relatively few isolates attributed to wild bird, environment, swine, and turkey sources. CONCLUSIONS National-scale genotyping was a practical and efficient methodology for the quantification of the contributions of different sources to human Campylobacter infection. Combined with the knowledge that retail chicken is routinely contaminated with Campylobacter, these results are consistent with the view that the largest reductions in human campylobacteriosis in industrialized countries will come from interventions that focus on the poultry industry.

Campylobacter genotypes from food animals, environmental sources and clinical disease in Scotland 2005/6

A nationwide multi-locus sequence typing (MLST) survey was implemented to analyze patterns of host association among Campylobacter jejuni and Campylobacter coli isolates from clinical disease in Scotland (July 2005-September 2006), food animals (chickens, cattle, sheep, pigs and turkey), non-food animals (wild birds) and the environment. Sequence types (STs) were determined for 5247 clinical isolates and 999 from potential disease sources (augmented with 2420 published STs). Certain STs were over represented among particular sample sets/host groups. These host-associated STs were identified for all sample groups in both Campylobacter species and host associated clonal complexes (groups of related STs) were characterized for C. jejuni. Some genealogical lineages were present in both human disease and food animal samples. This provided evidence for the relative importance of different infection routes/food animal sources in human disease. These results show robust associations of particular genotypes with potential infection sources supporting the contention that contaminated poultry is a major source of human disease.

Attribution of Campylobacter Infections in Northeast Scotland to Specific Sources by Use of Multilocus Sequence Typing

We show that a higher incidence of campylobacteriosis is found in young children (age, <5 years) living in rural, compared with urban, areas. Association of this difference with particular animal sources was evaluated using multilocus sequence typing. This evaluation was achieved by comparing Campylobacter isolates originating from these children, retail poultry, and a range of animal sources by use of source attribution and phylogenetic analysis methods. The results indicate that chicken is a major source of infection in young urban children, although not in their rural counterparts, for which ruminant and other avian sources are more important.

Has Retail Chicken Played a Role in the Decline of Human Campylobacteriosis

ABSTRACT Between 2001 and 2006, the incidence of human Campylobacter infections decreased by 10 and 27% in Scotland and the Grampian region of Scotland, respectively. Contemporaneous collection and analyses of human and retail-chicken isolates from Grampian were carried out over a 10-week period in 2001 and again in 2006 in order to determine whether the fall in the incidence of human infections was related to the retail-chicken exposure route. Rates of carriage of Campylobacter on chicken carcasses from retail outlets in Grampian in 2001 and 2006 were estimated. Chicken-derived Campylobacter isolates from 2001 (n = 84) and 2006 (n = 105) and human-derived isolates from patients with clinical cases of infection in 2001 (n = 172) and 2006 (n = 119) were typed by multilocus sequence typing. We found no evidence for statistically significant changes in prevalence and counts per carcass. We found by rarefaction that although the degree of diversity in humans tended to be higher than that in chickens, these differences were not significant. The genetic distance between chicken and human isolates from 2001 according to sequence type, clonal complex (CC), or allele composition was not significant, whereas the distances between 2006 isolates at the CC and allele levels were significant. This difference was attributable to a lower proportion of CC-21s being found in retail-chicken isolates from 2006 than in chicken isolates from 2001. We conclude that human exposure to Campylobacter via retail chicken is important and that changes in the population structure of campylobacters in this reservoir need to be taken into account in investigating human infection.

Spatiotemporal Homogeneity of Campylobacter Subtypes from Cattle and Sheep across Northeastern and Southwestern Scotland

ABSTRACT Source attribution using molecular subtypes has implicated cattle and sheep as sources of human Campylobacter infection. Whether the Campylobacter subtypes associated with cattle and sheep vary spatiotemporally remains poorly known, especially at national levels. Here we describe spatiotemporal patterns of prevalence, bacterial enumeration, and subtype composition in Campylobacter isolates from cattle and sheep feces from northeastern (63 farms, 414 samples) and southwestern (71 farms, 449 samples) Scotland during 2005 to 2006. Isolates (201) were categorized as sequence type (ST), as clonal complex (CC), and as Campylobacter jejuni or Campylobacter coli using multilocus sequence typing (MLST). No significant difference in average prevalence (cattle, 22%; sheep, 25%) or average enumeration (cattle, 2.7 × 104 CFU/g; sheep, 2.0 × 105 CFU/g) was found between hosts or regions. The four most common STs (C. jejuni ST-19, ST-42, and ST-61 and C. coli ST-827) occurred in both hosts, whereas STs of the C. coli ST-828 clonal complex were more common in sheep. Neither host yielded evidence for regional differences in ST, CC, or MLST allele composition. Isolates from the two hosts combined, categorized as ST or CC, were more similar within than between farms but showed no further spatiotemporal trends up to 330 km and 50 weeks between farm samples. In contrast, both regions yielded evidence for significant differences in ST, CC, and allele composition between hosts, such that 65% of isolates could be attributed to a known host. These results suggest that cattle and sheep within the spatiotemporal scales analyzed are each capable of contributing homogeneous Campylobacter strains to human infections.

Campylobacter colonization and proliferation in the broiler chicken upon natural field challenge is not affected by the bird growth rate or breed.

ABSTRACT The zoonotic association between Campylobacter bacteria in poultry and humans has been characterized by decades of research which has attempted to elucidate the epidemiology of this complex relationship and to reduce carriage within poultry. While much work has focused on the mechanisms facilitating its success in contaminating chicken flocks (and other animal hosts), it remains difficult to consistently exclude Campylobacter under field conditions. Within the United Kingdom poultry industry, various bird genotypes with widely varying growth rates are available to meet market needs and consumer preferences. However, little is known about whether any differences in Campylobacter carriage exist across this modern broiler range. The aim of this study was to establish if a relationship exists between growth rate or breed and cecal Campylobacter concentration after natural commercial flock Campylobacter challenge. In one investigation, four pure line genotypes of various growth rates were grown together, while in the second, eight different commercial broiler genotypes were grown individually. In both studies, the Campylobacter concentration was measured in the ceca at 42 days of age, revealing no significant difference in cecal load between birds of different genotypes both in mixed- and single-genotype pens. This is important from a public health perspective and suggests that other underlying reasons beyond genotype are likely to control and affect Campylobacter colonization within chickens. Further studies to gain a better understanding of colonization dynamics and subsequent proliferation are needed, as are novel approaches to reduce the burden in poultry.

Recombination-Mediated Host Adaptation by Avian Staphylococcus aureus

Staphylococcus aureus are globally disseminated among farmed chickens causing skeletal muscle infections, dermatitis, and septicaemia. The emergence of poultry-associated lineages has involved zoonotic transmission from humans to chickens but questions remain about the specific adaptations that promote proliferation of chicken pathogens. We characterized genetic variation in a population of genome-sequenced S. aureus isolates of poultry and human origin. Genealogical analysis identified a dominant poultry-associated sequence cluster within the CC5 clonal complex. Poultry and human CC5 isolates were significantly distinct from each other and more recombination events were detected in the poultry isolates. We identified 44 recombination events in 33 genes along the branch extending to the poultry-specific CC5 cluster, and 47 genes were found more often in CC5 poultry isolates compared with those from humans. Many of these gene sequences were common in chicken isolates from other clonal complexes suggesting horizontal gene transfer among poultry associated lineages. Consistent with functional predictions for putative poultry-associated genes, poultry isolates showed enhanced growth at 42 °C and greater erythrocyte lysis on chicken blood agar in comparison with human isolates. By combining phenotype information with evolutionary analyses of staphylococcal genomes, we provide evidence of adaptation, following a human-to-poultry host transition. This has important implications for the emergence and dissemination of new pathogenic clones associated with modern agriculture.

Antimicrobial resistance profiles of Campylobacter from humans, retail chicken meat, and cattle feces

We determined the antimicrobial resistance profiles of Campylobacter isolates from cases of sporadic human infection (n = 119), retail chicken meat (n = 105), and cattle feces (n = 105). Ampicillin and tetracycline resistance was highest in human isolates (32% and 29%, respectively) and retail chicken isolates (25% and 25%, respectively), whereas nalidixic acid resistance was highest in cattle fecal isolates (20%). We found that the antimicrobial resistance profiles were more similar in human and chicken meat isolates than those observed when comparing human and cattle fecal isolates. When we analyzed the distribution of minimum inhibitory concentrations for each antibiotic, in each host, the distribution was similar between human and chicken meat isolates, whereas cattle fecal isolates remained highly distinct from the other two hosts. This study suggests that chicken may be a major source of human Campylobacter infection and that the antimicrobial resistances found in the Campylobacter from this source will therefore also be prevalent in clinical isolates.

CaMPS: The Campylobacter MLST project in Scotland

Cultured micro-organisms form a vital cornerstone of all microbial research. With more than 500 biological resource centres worldwide, it may however become a daunting task to track down an interesting specimen of a given taxon (e.g. Campylobacter jejuni or Helicobacter pylori). Moreover, as biological research is inherently distributed in nature, with many researchers in different research institutes collecting data on the same organisms, knowledge generated on these microorganisms also has a tendency to become spread across the information jungle. As science and technology are moving rapidly, thereby increasingly making use of the scientific merits of previous research results, instant and effortless visibility of this creative and scientific downstream information has become imperative for the realization of successful innovation chains that take full opportunity of the exploitation of biological resources. The StrainInfo.net bioportal (www.StrainInfo.net) was established to stimulate this movement towards using multi-perspective integrated information in a broadened biological and clinical context. It brings together the biological material kept at multiple biological resource centres into a single portal interface, with direct pointers to the relevant information at the collections’ websites, and provides both historical traces and geographic distribution of the organisms they keep in culture. In addition, each organism is automatically linked to related sequences in the public domain and refers to all known scientific publications that deal with the organism. As the bioportal further unfolds itself as a helpful add-on to the microbiologists’ toolbox, we hope to gather around it a growing community of users that might become active contributors to both its content and implementation.

Local Outbreaks of Campylobacteriosis in Scotland Involving More Than One Strain: A CaMPS study

Cultured micro-organisms form a vital cornerstone of all microbial research. With more than 500 biological resource centres worldwide, it may however become a daunting task to track down an interesting specimen of a given taxon (e.g. Campylobacter jejuni or Helicobacter pylori). Moreover, as biological research is inherently distributed in nature, with many researchers in different research institutes collecting data on the same organisms, knowledge generated on these microorganisms also has a tendency to become spread across the information jungle. As science and technology are moving rapidly, thereby increasingly making use of the scientific merits of previous research results, instant and effortless visibility of this creative and scientific downstream information has become imperative for the realization of successful innovation chains that take full opportunity of the exploitation of biological resources. The StrainInfo.net bioportal (www.StrainInfo.net) was established to stimulate this movement towards using multi-perspective integrated information in a broadened biological and clinical context. It brings together the biological material kept at multiple biological resource centres into a single portal interface, with direct pointers to the relevant information at the collections’ websites, and provides both historical traces and geographic distribution of the organisms they keep in culture. In addition, each organism is automatically linked to related sequences in the public domain and refers to all known scientific publications that deal with the organism. As the bioportal further unfolds itself as a helpful add-on to the microbiologists’ toolbox, we hope to gather around it a growing community of users that might become active contributors to both its content and implementation.