Statistical comparison of Campylobacter jejuni subtypes from human cases and environmental sources

Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics

Avian pathogenic Escherichia coli (APEC) causes colibacillosis, the disease with the highest economic loss for the broiler industry. However, studies focusing on the prevalence and population structure of APEC in the broiler production pyramid are scarce. Here, we used genotyping and serotyping data to elucidate the APEC population structure and its changes in different broiler production stages along with whole-genome sequencing (WGS) in a subset of APEC isolates to determine transmission patterns amongst dominant APEC sequence types (STs) and characterize them in detail. Comparison of genotypes encountered in both APEC and avian fecal E. coli (AFEC) provided further insights. Overall, APEC-related mortality, as the proportion of the total sampled mortality in the broiler production, was high (35%), while phylogroup C and serogroup O78 were predominant amongst APEC isolates. We found a low (34.0%) and high (53.3%) incidence of colibacillosis in chicks and end-cycle broilers, respectively, which may be related to a shift in APEC genotypes, suggesting a trend from commensalism to pathogenicity across different broiler production stages. Despite considerable APEC genotypic diversity, there was substantial genotype overlap (40.9%, overall) over the production stages and convergence of STs to the four clusters. Within these clusters, WGS data provided evidence of clonal transmission events and revealed an enriched virulence and resistance APEC repertoire. More specifically, sequenced APEC were assigned to defined pathotypes based on their virulence gene content while the majority (86%) was genotypically multi-drug resistant. Interestingly, WGS-based phylogeny showed that a subset of APEC, which are cephalosporin-resistant, may originate directly from cephalosporin-resistant AFEC. Finally, exploration of the APEC plasmidome indicated that the small fraction of the APEC virulome carried by IncF plasmids is pivotal for the manifestation of the APEC pathotype; thus, plasmid exchange can promote pathogenicity in strains that are at the edge of the commensal and pathogenic states.

Shifts in the Molecular Epidemiology of Campylobacter jejuni Infections in a Sentinel Region of New Zealand following Implementation of Food Safety Interventions by the Poultry Industry

In 2006, New Zealand had the highest notification rate of campylobacteriosis in the world, and poultry was considered the leading source of campylobacteriosis. Implementation of food safety interventions by the poultry industry led to a decrease in the campylobacteriosis notification rate. The aim is to examine the impact of targeted food safety interventions implemented by the New Zealand poultry industry on the source attribution of Campylobacter jejuni infections in a sentinel region. Campylobacter jejuni isolates collected from the Manawatu region of New Zealand between 2005 and 2007 ("before intervention") and 2008 and 2015 ("after intervention") from human clinical cases, chicken meat, ruminant feces, environmental water, and wild bird sources were subtyped by multilocus sequence typing. Viable counts of Campylobacter spp. from carcasses were analyzed using a zero-inflated Poisson regression model. In the period before intervention, sequence type 474 (ST-474) was the most common sequence type (ST) recovered from human cases, accounting for 28.2% of the isolates. After intervention, the proportion of human cases positive for ST-474 reduced to 9.3%. Modeling indicated that chicken meat, primarily from one supplier, was the main source of C. jejuni infection in the Manawatu region before intervention. However, after intervention poultry collectively had a similar attribution to ruminants, but more human cases were attributed to ruminants than any single chicken supplier. Viable counts on carcasses were lower in all poultry suppliers after intervention. This study provides evidence of changes in the source attribution of campylobacteriosis following targeted food safety interventions in one sector of the food supply chain.IMPORTANCE This study provides a unique insight into the effects of food safety interventions implemented in one sector of the food industry on the transmission routes of a major foodborne agent. Following the implementation of food safety interventions by the poultry industry, shifts in the molecular epidemiology of Campylobacter jejuni infections in a sentinel region of New Zealand were observed. Targeted interventions to reduce disease incidence are effective but require continued surveillance and analysis to indicate where further interventions may be beneficial.

MLST-based genetic relatedness of Campylobacter jejuni isolated from chickens and humans in Poland

Campylobacter jejuni infection is one of the most frequently reported foodborne bacterial diseases worldwide. The main transmission route of these microorganisms to humans is consumption of contaminated food, especially of chicken origin. The aim of this study was to analyze the genetic relatedness of C. jejuni from chicken sources (feces, carcasses, and meat) and from humans with diarrhea as well as to subtype the isolates to gain better insight into their population structure present in Poland. C. jejuni were genotyped using multilocus sequence typing (MLST) and sequence types (STs) were assigned in the MLST database. Among 602 isolates tested, a total of 121 different STs, including 70 (57.9%) unique to the isolates' origin, and 32 STs that were not present in the MLST database were identified. The most prevalent STs were ST464 and ST257, with 58 (9.6%) and 52 (8.6%) C. jejuni isolates, respectively. Isolates with some STs (464, 6411, 257, 50) were shown to be common in chickens, whereas others (e.g. ST21 and ST572) were more often identified among human C. jejuni. It was shown that of 47 human sequence types, 26 STs (106 isolates), 23 STs (102 isolates), and 29 STs (100 isolates) were also identified in chicken feces, meat, and carcasses, respectively. These results, together with the high and similar proportional similarity indexes (PSI) calculated for C. jejuni isolated from patients and chickens, may suggest that human campylobacteriosis was associated with contaminated chicken meat or meat products or other kinds of food cross-contaminated with campylobacters of chicken origin. The frequency of various sequence types identified in the present study generally reflects of the prevalence of STs in other countries which may suggest that C. jejuni with some STs have a global distribution, while other genotypes may be more restricted to certain countries.

Impact of selective and non-selective media on prevalence and genetic makeup of ESBL/pAmpC-producing Escherichia coli in the broiler production pyramid

Presence of extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase (pAmpC)-producing Escherichia coli (ESBL/pAmpC-EC) in humans and animals is alarming due to the associated risks of antibiotic therapy failure. ESBL/pAmpC-EC transmission between the human and animal compartments remains controversial. Using cefotaxime-supplemented (selective) media, we recently showed high sample prevalence of ESBL/pAmpC-EC in an integrated broiler chain [i.e. Parent Stock (PS), offspring broilers and their carcasses]. Here, we used a different approach. In parallel with the selective isolation, samples were processed on non-selective media. E. coli isolates were tested for ESBL/pAmpC-production and those found positive were genotyped. For carcasses, total E. coli were enumerated. This approach enabled us to estimate prevalence at the isolate level, which mirrors ESBL/pAmpC-EC colonisation levels. We showed that although present in many animals, ESBL/pAmpC-EC were overall subdominant to intestinal E. coli, indicating that high sample prevalence is not associated with high levels of resistance in individual hosts. This is a relevant aspect for risk assessments, especially regarding the immediate exposure of farm personnel. An exception was a particularly dominant B2/bla_CMY-2 lineage in the gut of imported PS chicks. This predominance obscured presence of latent genotypes, however bias towards particular ESBL/pAmpC-EC genotypes from the selective method or underestimation by the non-selective approach did not occur. At the slaughterhouse, we showed a link between total E. coli and ESBL/pAmpC-EC on carcasses. Mitigation strategies for reducing consumers' exposure should aim at suppressing ESBL/pAmpC-EC in the broiler gut as well as controlling critical points in the processing line.

flaA-SVR Based Genetic Diversity of Multiresistant Campylobacter jejuni Isolated From Chickens and Humans

Campylobacter jejuni is one of the most common causes of human foodborne bacterial infections worldwide. The objective of this study was to assess the molecular diversity, using flaA sequencing, of 602 C. jejuni isolated from chicken food chain, i.e., chicken feces (n = 151), chicken carcasses (n = 150), chicken meat (n = 150), and from humans (n = 151) and to determine antimicrobial multiresistant profiles of the isolates as well as to analyze the relationship of the isolate genotypes with their antimicrobial resistance profiles and source of isolation. Multidrug resistant patterns were identified in 110 (18.3%) C. jejuni isolates recovered from all sources and most isolates were resistant to ciprofloxacin (CIP), nalidixic acid (NAL), streptomycin (STR), and tetracycline (TET) (92; 15.3%) or ciprofloxacin, streptomycin, and tetracycline (13; 2.2%). Only a few isolates were multiresistant to ciprofloxacin, nalidixic acid, tetracycline, and erythromycin (3; 0.5%) or ciprofloxacin, nalidixic acid, streptomycin, tetracycline, and erythromycin (2; 0.3%). A total of 79 flaA-SVR subtypes were identified, including 40 (50.6%) unique to the isolates' origins, with the most common sequence types 16, 54, 36, 34, and 287 which covered 56 (9.3%), 50 (8.3%), 48 (8.0%), 35 (5.8%), and 32 (5.3%) of C. jejuni isolates, respectively. It was found that 13 isolates had the novel flaA-SVR subtypes which were not present in the pubMLST database. These isolates were recovered from chicken feces (6 isolates), carcasses (2 isolates), meat (one isolate) and from humans (4 isolates). Multiresistant C. jejuni were classified into 26 different sequence subtypes. Among the most numerous multidrug resistant profile CIP+NAL+STR+TET 21 different flaA-SVR subtypes, with total of 92 isolates, were identified. Most of them were classified to 287 (18; 19.6% isolates), 100 (13; 14.1%), 34 (9; 9.8%), 208 (8; 8.7%), and 781 (8; 8.7%) molecular variants. Isolates resistant to CIP, STR and TET (13 isolates) were mainly from chicken feces (12 isolates) and classified into 5 flaA-SVR sequence types, with the most common 36 (8 isolates). The obtained results show a broad molecular diversity of multiresistant C. jejuni isolates and suggest chickens as a possible source of human Campylobacter infections in Poland.

Assessing the occurrence and transfer dynamics of ESBL/pAmpC-producing Escherichia coli across the broiler production pyramid

Extended-spectrum β-lactamase (ESBL)- and plasmid mediated AmpC-type cephalosporinase (pAmpC)-producing Escherichia coli (ESBL/pAmpC E. coli) in food-producing animals is a major public health concern. This study aimed at quantifying ESBL/pAmpC-E. coli occurrence and transfer in Italy’s broiler production pyramid. Three production chains of an integrated broiler company were investigated. Cloacal swabs were taken from parent stock chickens and offspring broiler flocks in four fattening farms per chain. Carcasses from sampled broiler flocks were collected at slaughterhouse. Samples were processed on selective media, and E. coli colonies were screened for ESBL/pAmpC production. ESBL/pAmpC genes and E. coli phylogroups were determined by PCR and sequencing. Average pairwise overlap of ESBL/pAmpC E. coli gene and phylogroup occurrences between subsequent production stages was estimated using the proportional similarity index, modelling uncertainty in a Monte Carlo simulation setting. In total, 820 samples were processed, from which 513 ESBL/pAmpC E. coli isolates were obtained. We found a high prevalence (92.5%, 95%CI 72.1–98.3%) in day-old parent stock chicks, in which bla_CMY-2 predominated; prevalence then dropped to 20% (12.9–29.6%) at laying phase. In fattening broilers, prevalence was 69.2% (53.6–81.3%) at the start of production, 54.2% (38.9–68.6%) at slaughter time, and 61.3% (48.1–72.9%) in carcasses. Significantly decreasing and increasing trends for respectively bla_CMY-2 and bla_CTX-M-1 gene occurrences were found across subsequent production stages. ESBL/pAmpC E. coli genetic background appeared complex and bla-gene/phylogroup associations indicated clonal and horizontal transmission. Modelling revealed that the average transfer of ESBL/pAmpC E. coli genes between subsequent production stages was 47.7% (42.3–53.4%). We concluded that ESBL/pAmpC E. coli in the broiler production pyramid is prevalent, with substantial transfer between subsequent production levels.

Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the environment: a pooled analysis

Background

In recent years, ESBL/AmpC-producing Escherichia coli (ESBL/AmpC-EC) have been isolated with increasing frequency from animals, food, environmental sources and humans. With incomplete and scattered evidence, the contribution to the human carriage burden from these reservoirs remains unclear.

Objectives

To quantify molecular similarities between different reservoirs as a first step towards risk attribution.

Methods

Pooled data on ESBL/AmpC-EC isolates were recovered from 35 studies in the Netherlands comprising >27 000 samples, mostly obtained between 2005 and 2015. Frequency distributions of ESBL/AmpC genes from 5808 isolates and replicons of ESBL/AmpC-carrying plasmids from 812 isolates were compared across 22 reservoirs through proportional similarity indices (PSIs) and principal component analyses (PCAs).

Results

Predominant ESBL/AmpC genes were identified in each reservoir. PCAs and PSIs revealed close human-animal ESBL/AmpC gene similarity between human farming communities and their animals (broilers and pigs) (PSIs from 0.8 to 0.9). Isolates from people in the general population had higher similarities to those from human clinical settings, surface and sewage water and wild birds (0.7-0.8), while similarities to livestock or food reservoirs were lower (0.3-0.6). Based on rarefaction curves, people in the general population had more diversity in ESBL/AmpC genes and plasmid replicon types than those in other reservoirs.

Conclusions

Our 'One Health' approach provides an integrated evaluation of the molecular relatedness of ESBL/AmpC-EC from numerous sources. The analysis showed distinguishable ESBL/AmpC-EC transmission cycles in different hosts and failed to demonstrate a close epidemiological linkage of ESBL/AmpC genes and plasmid replicon types between livestock farms and people in the general population.

Exposure to whole chicken carcasses may present a greater risk of campylobacteriosis compared to exposure to chicken drumsticks

In New Zealand, the major risk factor for campylobacteriosis has been identified as poultry consumption. New Zealanders consume different types of chicken meat which undergo different processing before entering the retail chain. The manipulations and jointing of chicken carcasses into pieces and the subsequent processing and packaging have the potential to cross-contaminate and reshuffle bacterial pathogens among the different products sold. The aim of this study was to analyse: (a) the differences in the viable count and population genetic structure between Campylobacter isolated from chicken drumsticks and whole carcass meat for retail sale over a 1-year period; and (b) the genetic relatedness of human and chicken isolates collected concurrently. Enumeration of Campylobacter was performed using a spiral plater combined with manual spread plating. Campylobacter isolates were identified by polymerase chain reaction and typed by multilocus sequence typing (MLST). C. jejuni was the dominant species among both whole carcasses (63.5%) and drumsticks samples (73.8%), followed by C. coli (27% and 23.1%, respectively). After sample weight adjustment, whole carcasses showed significantly higher Campylobacter counts than drumsticks, with a significant difference in the counts between the commercial suppliers in both types of retail meat. MLST revealed 28 different sequence types among the two types of meat. Using permutational multivariate analysis of variance, statistically significant differences in the population genetic structures were observed between different suppliers but were not observed between the two types of chicken retail meat. In conclusion, we found differences in Campylobacter viable counts, suggesting consumption of whole carcasses may determine an exposure to a higher number of Campylobacter bacteria than consumption of chicken drumsticks. The Campylobacter population genetic structure did not differ between the two types of chicken retail meat. Therefore, source attribution studies based on MLST are unlikely to be biased by the selection of these types of retail meat during sampling.

Serotypes and Antimicrobial Resistance in Salmonella enterica Recovered from Clinical Samples from Cattle and Swine in Minnesota, 2006 to 2015

Salmonellosis remains one of the leading causes of foodborne disease worldwide despite preventive efforts at various stages of the food production chain. The emergence of multi-drug resistant (MDR) non-typhoidal Salmonella enterica represents an additional challenge for public health authorities. Food animals are considered a major reservoir and potential source of foodborne salmonellosis; thus, monitoring of Salmonella strains in livestock may help to detect emergence of new serotypes/MDR phenotypes and to gain a better understanding of Salmonella epidemiology. For this reason, we analyzed trends over a nine-year period in serotypes, and antimicrobial resistance, of Salmonella isolates recovered at the Minnesota Veterinary Diagnostic Laboratory (MVDL) from swine (n = 2,537) and cattle (n = 1,028) samples. Prevalence of predominant serotypes changed over time; in swine, S. Typhimurium and S. Derby decreased and S. Agona and S. 4,5,12:i:- increased throughout the study period. In cattle, S. Dublin, S. Montevideo and S. Cerro increased and S. Muenster became less frequent. Median minimum inhibitory concentration (MIC) values and proportion of antibiotic resistant isolates were higher for those recovered from swine compared with cattle, and were particularly high for certain antibiotic-serotype combinations. The proportion of resistant swine isolates was also higher than observed in the NARMS data, probably due to the different cohort of animals represented in each dataset. Results provide insight into the dynamics of antimicrobial resistant Salmonella in livestock in Minnesota, and can help to monitor emerging trends in antimicrobial resistance.

Molecular Epidemiology of Campylobacter coli Strains Isolated from Different Sources in New Zealand between 2005 and 2014

Campylobacteriosis is one of the most important foodborne diseases worldwide and a significant health burden in New Zealand. Campylobacter jejuni is the predominant species worldwide, accounting for approximately 90% of human cases, followed by Campylobacter coli Most studies in New Zealand have focused on C. jejuni; hence, the impact of C. coli strains on human health is not well understood. The aim of this study was to genotype C. coli isolates collected in the Manawatu region of New Zealand from clinical cases, fresh poultry meat, ruminant feces, and environmental water sources, between 2005 and 2014, to study their population structure and estimate the contribution of each source to the burden of human disease. Campylobacter isolates were identified by PCR and typed by multilocus sequence typing. C. coli accounted for 2.9% (n = 47/1,601) of Campylobacter isolates from human clinical cases, 9.6% (n = 108/1,123) from poultry, 13.4% (n = 49/364) from ruminants, and 6.4% (n = 11/171) from water. Molecular subtyping revealed 27 different sequence types (STs), of which 18 belonged to clonal complex ST-828. ST-1581 was the most prevalent C. coli sequence type isolated from both human cases (n = 12/47) and poultry (n = 44/110). When classified using cladistics, all sequence types belonged to clade 1 except ST-7774, which belonged to clade 2. ST-854, ST-1590, and ST-4009 were isolated only from human cases and fresh poultry, while ST-3232 was isolated only from human cases and ruminant sources. Modeling indicated ruminants and poultry as the main sources of C. coli human infection.

IMPORTANCE

We performed a molecular epidemiological study of Campylobacter coli infection in New Zealand, one of few such studies globally. This study analyzed the population genetic structure of the bacterium and included a probabilistic source attribution model covering different animal and water sources. The results are discussed in a global context.

Diversity and relatedness of Shiga toxin-producing Escherichia coli and Campylobacter jejuni between farms in a dairy catchment

The aim of this study was to examine the population structure, transmission and spatial relationship between genotypes of Shiga toxin-producing Escherichia coli (STEC) and Campylobacter jejuni, on 20 dairy farms in a defined catchment. Pooled faecal samples (n = 72) obtained from 288 calves were analysed by real-time polymerase chain reaction (rtPCR) for E. coli serotypes O26, O103, O111, O145 and O157. The number of samples positive for E. coli O26 (30/72) was high compared to E. coli O103 (7/72), O145 (3/72), O157 (2/72) and O111 (0/72). Eighteen E. coli O26 and 53 C. jejuni isolates were recovered from samples by bacterial culture. E. coli O26 and C. jejuni isolates were genotyped using pulsed-field gel electrophoresis and multilocus sequence typing, respectively. All E. coli O26 isolates could be divided into four clusters and the results indicated that E. coli O26 isolates recovered from calves on the same farm were more similar than isolates recovered from different farms in the catchment. There were 11 different sequence types of C. jejuni isolated from the cattle and 22 from water. An analysis of the population structure of C. jejuni isolated from cattle provided evidence of clustering of genotypes within farms, and among groups of farms separated by road boundaries.

Antimicrobial Resistance and Genotypic Diversity of Campylobacter Isolated from Pigs, Dairy, and Beef Cattle in Tanzania

Foodborne Campylobacter infections pose a serious threat to public health worldwide. However, the occurrence and characteristics of Campylobacter in food animals and products remain largely unknown in Tanzania. The objective of this study was to determine the prevalence, antibiotic resistance, and genetic profiles (sequence types, STs) of Campylobacter isolated from feces of pigs and dairy and beef cattle in Tanzania. Overall, 259 (~30%) of 864 samples were positive for Campylobacter spp, which were detected in 32.5, 35.4, and 19.6% of the pig, dairy, and beef cattle samples, respectively. Multiplex PCR analysis identified 64.5 and 29.3% of the Campylobacter isolates as C. coli and C. jejuni, respectively. The majority (91.9%) of the isolates from pig samples were identified as C. coli, while C. jejuni accounted for 65.5% of the isolates from cattle. Antimicrobial susceptibility testing using the disk diffusion assay and the broth microdilution method revealed resistance to: ampicillin (Amp) (70.3% and 75.7%, respectively), gentamicin (Gen) (1.8% and 12.6%), streptomycin (Str) (65.8 and 74.8%), erythromycin (Ery) (41.4 and 48.7%), tetracycline (Tet) (18.9 and 23.4%), and ciprofloxacin (Cip) (14.4 and 7.2%). Resistance to nalidixic acid (Nal) (39.6%), azithromycin (Azm) (13.5%), and chloramphenicol (Chl) (4.5%) was determined using the disk diffusion assay only, while resistance to tylosin (Tyl) (38.7%) was quantified using the broth microdilution method. Multilocus sequence typing of 111 Campylobacter isolates resulted in the identification of 48 STs (26 C. jejuni and 22 C. coli) of which seven were novel (six C. jejuni and one C. coli). Taken together, this study revealed the high prevalence, genetic diversity and antimicrobial resistance of Campylobacter in important food animals in Tanzania, which highlights the urgent need for the surveillance and control of Campylobacter in this country.

Environmental change and enteric zoonoses in New Zealand: a systematic review of the evidence

OBJECTIVE

To review the available evidence that examines the association between climatic and agricultural land use factors and the risks of enteric zoonoses in humans and consider information needs and possible pathways of intervention.

METHODS

The electronic databases PubMed, Web of Science and Embase and government websites were searched systematically for published literature that investigated the association of climatic and/or agricultural exposures with the incidence of the four most common enteric zoonotic diseases in New Zealand (campylobacteriosis, salmonellosis, cryptosporidiosis and giardiasis). Results The 16 studies in the review demonstrated significant associations between climate, agricultural land use and enteric disease occurrence. The evidence suggests that enteric disease risk from environmental reservoirs is pathogen specific. In some rural regions, environmental pathogen load is considerable, with multiple opportunities for zoonotic transmission.

CONCLUSIONS

Enteric disease occurrence in NZ is associated with climate variability and agricultural land use. However, these relationships interact with demographic factors to influence disease patterns.

IMPLICATIONS

Improved understanding of how environmental and social factors interact can inform effective public health interventions under scenarios of projected environmental change.

Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis isolated from sheep, cattle and deer on New Zealand pastoral farms

The present study aimed to describe the molecular diversity of Mycobacterium avium subsp. paratuberculosis (MAP) isolates obtained from sheep, cattle (beef and dairy) and deer farms in New Zealand. A total of 206 independent MAP isolates (15 beef cattle, 89 dairy cattle, 35 deer, 67 sheep) were sourced from 172 species-mobs (15 beef cattle, 66 dairy cattle, 31 deer, 60 sheep). Seventeen subtypes were identified, using a combination of variable number of tandem repeats (VNTR) and short sequence repeat (SSR) methods. Rarefaction analysis, analysis of molecular variance (AMOVA), Fst pairwise comparisons and proportional similarity index (PSI) were used to describe subtype population richness, genetic structure and potential associations between livestock sectors and New Zealand two main islands (North and South). The rarefaction analysis suggests a significantly higher subtype richness in dairy cattle herds when compared to the other livestock sectors. AMOVA results indicate that the main source of subtype variation is attributable to the livestock sector from which samples were sourced suggesting that subtypes are generally sector-specific. The pairwise Fst results were similar, with low Fst values for island differences within a livestock sector when compared to between sector analyses, representing a low subtype differentiation between islands. However, for a given island, potential associations were seen between dominant subtypes and specific livestock sectors. Three subtypes accounted for 76% of the isolates. The most common of these was isolated from sheep and beef cattle in the North Island, the second most frequent subtype was mainly isolated from dairy cattle (either island), while the third most common subtype was associated with deer farmed in the South Island. The PSI analysis suggests similarities in subtypes sourced from sheep and beef cattle. This contrasted with the isolates sourced from other livestock sectors, which tended to present sector-specific subtypes. Sheep and beef cattle were mainly infected with MAP Type I, while dairy cattle and deer were almost exclusively infected with MAP Type II. However, when beef cattle and deer were both present at farm level, they harboured similar subtypes. This study indicates that cross-species transmission of MAP occurs on New Zealand farms although close contact between species appears to be required, as in the case of sheep and beef cattle which are commonly grazed together in New Zealand.

Prevalence, quantitative load and genetic diversity of Campylobacter spp. in dairy cattle herds in Lithuania

BACKGROUND

Campylobacteriosis is a zoonotic disease, and animals such as poultry, pigs and cattle may act as reservoirs for Campylobacter spp. Cattle shed Campylobacter spp. into the environment and they can act as a reservoir for human infection directly via contact with cattle or their faeces or indirectly by consumption of contaminated food. The aim of this study was to determine the prevalence, the quantitative load and the genetic strain diversity of Campylobacter spp. in dairy cattle of different age groups.

RESULTS

Faecal samples of 200 dairy cattle from three farms in the central part of Lithuania were collected and examined for Campylobacter. Cattle herds of all three farms were Campylobacter spp. positive, with a prevalence ranging from 75% (farm I), 77.5% (farm II) to 83.3% (farm III). Overall, the highest prevalence was detected in calves (86.5%) and heifers (86.2%). In contrast, the lowest Campylobacter prevalence was detectable in dairy cows (60.6%). C. jejuni, C. coli, C. lari and C. fetus subsp. fetus were identified in faecal samples of dairy cattle. C. upsaliensis was not detectable in any sample. The high counts of Campylobacter spp. were observed in faecal material of dairy cattle (average 4.5 log10 cfu/g). The highest numbers of Campylobacter spp. were found in faecal samples from calves (average 5.3 log10 cfu/g), whereas, faecal samples from cows harboured the lowest number of Campylobacter spp. (average 3.7 log10 cfu/g). Genotyping by flaA PCR-RFLP analysis of selected C. jejuni isolates showed that some genotypes were present in all farms and all age groups. However, farm or age specific genotypes were also identified.

CONCLUSIONS

Future studies are needed to investigate risk factors related to the degree of colonisation in cattle. Based on that, possible measures to reduce the colonisation and subsequent shedding of Campylobacter in cattle could be established. It is important to further investigate the epidemiology of Campylobacter in the cattle population in order to assess associated risks to public health.

Source attribution of human Campylobacter isolates by MLST and fla-typing and association of genotypes with quinolone resistance

Campylobacteriosis is the most frequent zoonosis in developed countries and various domestic animals can function as reservoir for the main pathogens Campylobacter jejuni and Campylobacter coli. In the present study we compared population structures of 730 C. jejuni and C. coli from human cases, 610 chicken, 159 dog, 360 pig and 23 cattle isolates collected between 2001 and 2012 in Switzerland. All isolates had been typed with multi locus sequence typing (MLST) and flaB-typing and their genotypic resistance to quinolones was determined. We used complementary approaches by testing for differences between isolates from different hosts with the proportion similarity as well as the fixation index and by attributing the source of the human isolates with Bayesian assignment using the software STRUCTURE. Analyses were done with MLST and flaB data in parallel and both typing methods were tested for associations of genotypes with quinolone resistance. Results obtained with MLST and flaB data corresponded remarkably well, both indicating chickens as the main source for human infection for both Campylobacter species. Based on MLST, 70.9% of the human cases were attributed to chickens, 19.3% to cattle, 8.6% to dogs and 1.2% to pigs. Furthermore we found a host independent association between sequence type (ST) and quinolone resistance. The most notable were ST-45, all isolates of which were susceptible, while for ST-464 all were resistant.

Risk factors for campylobacteriosis in two washington state counties with high numbers of dairy farms

Campylobacteriosis is a frequently reported, food-borne, human bacterial disease that can be associated with ruminant reservoirs, although public health messages primarily focus on poultry. In Washington State, the two counties with the highest concentrations of dairy cattle also report the highest incidences of campylobacteriosis. Conditional logistic regression analysis of case-control data from both counties found living or working on a dairy farm (odds ratio [OR], 6.7 [95% confidence interval [CI], 1.7 to 26.4]) and Hispanic ethnicity (OR, 6.4 [95% CI, 3.1 to 13.1]) to have the strongest significant positive associations with campylobacteriosis. When the analysis was restricted to residents of one county, Hispanic ethnicity (OR, 9.3 [95% CI, 3.9 to 22.2]), contact with cattle (OR, 5.0 [95% CI, 1.3 to 19.5]), and pet ownership (OR, 2.6 [95% CI, 1.1 to 6.3]) were found to be independent risk factors for disease. Campylobacter jejuni isolates from human (n = 65), bovine (n = 28), and retail poultry (n = 27) sources from the same counties were compared using multilocus sequence typing. These results indicated that sequence types commonly found in human isolates were also commonly found in bovine isolates. These findings suggest that, in areas with high concentrations of dairy cattle, exposure to dairy cattle may be more important than food-borne exposure to poultry products as a risk for campylobacteriosis.

Practicalities of using non-local or non-recent multilocus sequence typing data for source attribution in space and time of human campylobacteriosis

In this study, 1208 Campylobacter jejuni and C. coli isolates from humans and 400 isolates from chicken, collected in two separate periods over 12 years in The Netherlands, were typed using multilocus sequence typing (MLST). Statistical evidence was found for a shift of ST frequencies in human isolates over time. The human MLST data were also compared to published data from other countries to determine geographical variation. Because only MLST typed data from chicken, taken from the same time point and spatial location, were available in addition to the human data, MLST datasets for other Campylobacter reservoirs from selected countries were used. The selection was based on the degree of similarity of the human isolates between countries. The main aim of this study was to better understand the consequences of using non-local or non-recent MLST data for attributing domestically acquired human Campylobacter infections to specific sources of origin when applying the asymmetric island model for source attribution. In addition, a power-analysis was done to find the minimum number of source isolates needed to perform source attribution using an asymmetric island model. This study showed that using source data from other countries can have a significant biasing effect on the attribution results so it is important to carefully select data if the available local data lack in quality and/or quantity. Methods aimed at reducing this bias were proposed.

Respiratory proteins contribute differentially to Campylobacter jejuni's survival and in vitro interaction with hosts' intestinal cells

Background

The genetic features that facilitate Campylobacter jejuni’s adaptation to a wide range of environments are not completely defined. However, whole genome expression studies showed that respiratory proteins (RPs) were differentially expressed under varying conditions and stresses, suggesting further unidentified roles for RPs in C. jejuni’s adaptation. Therefore, our objectives were to characterize the contributions of selected RPs to C. jejuni’s i- key survival phenotypes under different temperature (37°C vs. 42°C) and oxygen (microaerobic, ambient, and oxygen-limited/anaerobic) conditions and ii- its interactions with intestinal epithelial cells from disparate hosts (human vs. chickens).

Results

C. jejuni mutant strains with individual deletions that targeted five RPs; nitrate reductase (ΔnapA), nitrite reductase (ΔnrfA), formate dehydrogenase (ΔfdhA), hydrogenase (ΔhydB), and methylmenaquinol:fumarate reductase (ΔmfrA) were used in this study. We show that only the ΔfdhA exhibited a decrease in motility; however, incubation at 42°C significantly reduced the deficiency in the ΔfdhA’s motility as compared to 37°C. Under all tested conditions, the ΔmfrA showed a decreased susceptibility to hydrogen peroxide (H₂O₂), while the ΔnapA and the ΔfdhA showed significantly increased susceptibility to the oxidant as compared to the wildtype. Further, the susceptibility of the ΔnapA to H₂O₂ was significantly more pronounced at 37°C. The biofilm formation capability of individual RP mutants varied as compared to the wildtype. However, the impact of the deletion of certain RPs affected biofilm formation in a manner that was dependent on temperature and/or oxygen concentration. For example, the ΔmfrA displayed significantly deficient and increased biofilm formation under microaerobic conditions at 37°C and 42°C, respectively. However, under anaerobic conditions, the ΔmfrA was only significantly impaired in biofilm formation at 42°C. Additionally, the RPs mutants showed differential ability for infecting and surviving in human intestinal cell lines (INT-407) and primary chicken intestinal epithelial cells, respectively. Notably, the ΔfdhA and the ΔhydB were deficient in interacting with both cell types, while the ΔmfrA displayed impairments only in adherence to and invasion of INT-407. Scanning electron microscopy showed that the ΔhydB and the ΔfdhA exhibited filamentous and bulging (almost spherical) cell shapes, respectively, which might be indicative of defects in cell division.

Conclusions

We conclude that the RPs contribute to C. jejuni’s motility, H₂O₂ resistance, biofilm formation, and in vitro interactions with hosts’ intestinal cells. Further, the impact of certain RPs varied in response to incubation temperature and/or oxygen concentration. Therefore, RPs may facilitate the prevalence of C. jejuni in a variety of niches, contributing to the pathogen’s remarkable potential for adaptation.

Poultry culling and Campylobacteriosis reduction among humans, the Netherlands

In the Netherlands in 2003, an outbreak of avian influenza in poultry resulted in extensive culling, especially of layer hens. Concurrently, human campylobacteriosis cases decreased, particularly in the culling area. These observations raise the hypothesis that Campylobacter spp. dissemination from poultry farms or slaughterhouses might contribute to human campylobacteriosis.

Campylobacter epidemiology: a descriptive study reviewing 1 million cases in England and Wales between 1989 and 2011

OBJECTIVES

To review Campylobacter cases in England and Wales over 2 decades and examine the main factors/mechanisms driving the changing epidemiology.

DESIGN

A descriptive study of Campylobacter patients between 1989 and 2011. Cases over 3 years were linked anonymously to postcode, population density, deprivation indices and census data. Cases over 5 years were anonymously linked to local weather exposure estimates.

SETTING

Patients were from general practice, hospital and environmental health investigations through primary diagnostic laboratories across England and Wales.

PARTICIPANTS

There were 1 109 406 cases.

OUTCOME MEASURES

Description of changes in Campylobacter epidemiology over 23 years and how the main drivers may influence these.

RESULTS

There was an increase in Campylobacter cases over the past 23 years, with the largest increase in people over 50 years. Changes in the underlying population have contributed to this, including the impacts of population increases after World War I, World War II and the 'baby boom' of the 1960s. A recent increase in risk or ascertainment within this population has caused an increase in cases in all age groups from 2004 to 2011. The seasonal increase in cases between weeks 18 (Early May) and 22 (Early June) was consistent across ages, years and regions and was most marked in children and in more rural regions. Campylobacter prevalence by week in each region correlated with temperature 2 weeks before. There were higher prevalences in areas with a low population density, low deprivation and lower percentage of people of ethnic origin. Data from sero-phage and multilocus sequence typing show a few common types and many uncommon types.

CONCLUSIONS

The drivers/mechanisms influencing seasonality, age distribution, population density, socioeconomic and long-term differences are diverse and their relative contributions remain to be established. Surveillance and typing provide insights into Campylobacter epidemiology and sources of infection, providing a sound basis for targeted interventions.

Survival of Escherichia coli, Enterococci, and Campylobacter spp. in sheep feces on pastures

The survival of enteric bacteria in 10 freshly collected sheep fecal samples on pastures was measured in each of four seasons. Ten freshly collected feces were placed on pasture, and concentrations of Escherichia coli, enterococci, and Campylobacter spp. were monitored until exhaustion of the fecal samples. In all four seasons, there was an increase in enterococcal concentrations by up to 3 orders of magnitude, with peak concentrations recorded between 11 and 28 days after deposition. E. coli concentrations increased in three out of four seasons by up to 1.5 orders of magnitude, with peak concentrations recorded between 8 and 14 days after deposition. The apparent growth of E. coli and enterococci was strongly influenced by the initial water content of the feces and the moisture gained during periods of rehydration following rainfalls. Conversely, the results suggested that dehydration promoted inactivation. Campylobacter spp. did not grow and were rapidly inactivated at a rate that tended to be faster at higher temperatures. Pulsed-field gel electrophoresis (PFGE) of a selection of Campylobacter spp. suggested that these survival data are applicable to a range of Campylobacter spp., including the most frequently isolated PFGE genotype from sheep in New Zealand, and to genotypes previously observed to cause disease in humans. The results of this study are currently being incorporated into a fecal microbe reservoir model that is designed to assist water managers' abilities to estimate microbial loads on pastures grazed by sheep, including the influence of factors such as rainfall and temperature.

Molecular epidemiology of Campylobacter jejuni in a geographically isolated country with a uniquely structured poultry industry

In New Zealand the number of campylobacteriosis notifications increased markedly between 2000 and 2007. Notably, this country's poultry supply is different than that of many developed countries as the fresh and frozen poultry available at retail are exclusively of domestic origin. To examine the possible link between human cases and poultry, a sentinel surveillance site was established to study the molecular epidemiology of Campylobacter jejuni over a 3-year period from 2005 to 2008 using multilocus sequence typing. Studies showed that 60.1 to 81.4% of retail poultry carcasses from the major suppliers were contaminated with C. jejuni. Differences were detected in the probability and level of contamination and the relative frequency of genotypes for individual poultry suppliers and humans. Some carcasses were contaminated with isolates belonging to more than one sequence type (ST), and there was evidence of both ubiquitous and supplier-associated strains, an epidemiological pattern not recognized yet in other countries. The common poultry STs were also common in human clinical cases, providing evidence that poultry is a major contributor to human infection. Both internationally rare genotypes, such as ST-3069 and ST-474, and common genotypes, such as ST-45 and ST-48, were identified in this study. The dominant human sequence type in New Zealand, ST-474, was found almost exclusively in isolates from one poultry supplier, which provided evidence that C. jejuni has a distinctive molecular epidemiology in this country. These results may be due in part to New Zealand's geographical isolation and its uniquely structured poultry industry.

Temporal and farm-management-associated variation in the faecal-pat prevalence ofCampylobacter jejuniin ruminants

In a 2-year longitudinal study of adult animals on 15 dairy farms and four sheep farms in Lancashire, UK.C. jejuniwas isolated from all farms, although not on every occasion. Faecal samples were collected and cultured using standard techniques for isolation ofCampylobacter. Assignment to species was via PCR assays. Peak prevalence ofC. jejuniin both cattle and sheep was observed during the summer and in cattle this apparent seasonality was associated with grazing pasture [odds ratio (OR) 2·14], while in sheep it was independent of grazing. Increased prevalence was associated with increased milk yield (OR 1·05) and herd size (OR 1·01) in dairy cattle, and with increased stocking density (OR 1·29) and pasture quality (OR 2·16) in sheep. There was considerable variation in prevalence between farms but no evidence of large-scale spatial variation. The association betweenC. jejuniprevalence and diet in dairy cattle deserves further investigation.

Assigning the source of human campylobacteriosis in New Zealand: a comparative genetic and epidemiological approach

Integrated surveillance of infectious multi-source diseases using a combination of epidemiology, ecology, genetics and evolution can provide a valuable risk-based approach for the control of important human pathogens. This includes a better understanding of transmission routes and the impact of human activities on the emergence of zoonoses. Until recently New Zealand had extraordinarily high and increasing rates of notified human campylobacteriosis, and our limited understanding of the source of these infections was hindering efforts to control this disease. Genetic and epidemiological modeling of a 3-year dataset comprising multilocus sequence typed isolates from human clinical cases, coupled with concurrent data on food and environmental sources, enabled us to estimate the relative importance of different sources of human disease. Our studies provided evidence that poultry was the leading cause of human campylobacteriosis in New Zealand, causing an estimated 58-76% of cases with widely varying contributions by individual poultry suppliers. These findings influenced national policy and, after the implementation of poultry industry-specific interventions, a dramatic decline in human notified cases was observed in 2008. The comparative-modeling and molecular sentinel surveillance approach proposed in this study provides new opportunities for the management of zoonotic diseases.

Effect of using a stand-off pad on Campylobacter jejuni strain diversity in a herd of dairy cows

AIM

To determine the effect of stand-off pad (SOP) use on the prevalence and strain diversity of Campylobacter jejuni in a small herd of dairy cows.

METHODS AND RESULTS

Faecal samples were collected from 21 cows on four sampling occasions (events), one in each season, over 1 year. The cows usually grazed on pasture but during winter they spent 18 h a day on a SOP. Campylobacter prevalence ranged from 48-52% on pasture but was 62% on the SOP. The diversity of 386 C. jejuni isolates was determined using Enterobacterial Repetitive Intergenic Consensus polymerase chain reaction (ERIC/PCR). There were 11 ERIC types identified for the herd over the course of the study. Of those 11, four to seven (per event) were present when the cows were grazing pasture but only two during SOP use.

CONCLUSIONS

The use of the SOP was associated with an increase in prevalence and a reduction in diversity of C. jejuni.

SIGNIFICANCE AND IMPACT OF THE STUDY

The reduction in ERIC types on the SOP indicated an increase in transfer of only some strains of C. jejuni among the cows. One of these strains persisted throughout the study. The zoonotic potential of this strain warrants further investigation.

Chickens and cattle as sources of sporadic domestically acquired Campylobacter jejuni infections in Finland

A substantial sampling among domestic human campylobacter cases, chicken process lots, and cattle at slaughter was performed during the seasonal peak of human infections. Campylobacter jejuni isolates (n = 419) were subtyped using pulsed-field gel electrophoresis with SmaI, and isolates representing overlapping types (n = 212) were further subtyped using KpnI for restriction. The SmaI/KpnI profiles of 55.4% (97/175) of the human isolates were indistinguishable from those of the chicken or cattle isolates. The overlapping SmaI/KpnI subtypes accounted for 69.8% (30/43) and 15.9% (32/201) of the chicken and cattle isolates, respectively. The occurrence of identical SmaI/KpnI subtypes with human C. jejuni isolates was significantly associated with animal host species (P < 0.001). A temporal association of isolates from chickens and patients was possible in 31.4% (55/175) of the human infections. Besides chickens as sources of C. jejuni in the sporadic infections, the role of cattle appears notable. New approaches to restrict the occurrence of campylobacters in other farm animals may be needed in addition to hygienic measures in chicken production. However, only about half of the human infections were attributable to these sources.

Shedding of Campylobacter spp. in Finnish cattle on dairy farms

AIMS

The aim of this study was to determine variation of prevalence throughout a year, colonization levels and genotypes of Campylobacter jejuni in Finnish dairy cattle herds.

METHODS AND RESULTS

Faecal samples and tank milk samples from three dairy cattle herds were taken five times, and swab samples from drinking troughs once during a 1-year sampling period. The samples were enriched in Bolton broth and subsequently spread on mCCDA. Isolates were then subtyped by pulsed-field gel electrophoresis using SmaI. Campylobacter jejuni was detected in 169 of the 340 faecal samples and in one drinking trough sample. Prevalences between herds and sampling times varied widely. The faecal levels of C. jejuni were mainly low. Between one and four SmaI subtypes were identified from each herd per sampling. Two SmaI subtypes persisted in two of the herds throughout the study.

CONCLUSIONS

Dairy cattle can be a long-term reservoir of C. jejuni subtypes similar to clinical isolates. Differences in the colonization potential among C. jejuni strains as well as in the resistance to campylobacter colonization among animals are possible.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study provides data on contamination dynamics, colonization levels and the persistence of C. jejuni in dairy cattle.

Tracing the source of campylobacteriosis

Campylobacter jejuni is the leading cause of bacterial gastro-enteritis in the developed world. It is thought to infect 2–3 million people a year in the US alone, at a cost to the economy in excess of US $4 billion. C. jejuni is a widespread zoonotic pathogen that is carried by animals farmed for meat and poultry. A connection with contaminated food is recognized, but C. jejuni is also commonly found in wild animals and water sources. Phylogenetic studies have suggested that genotypes pathogenic to humans bear greatest resemblance to non-livestock isolates. Moreover, seasonal variation in campylobacteriosis bears the hallmarks of water-borne disease, and certain outbreaks have been attributed to contamination of drinking water. As a result, the relative importance of these reservoirs to human disease is controversial. We use multilocus sequence typing to genotype 1,231 cases of C. jejuni isolated from patients in Lancashire, England. By modeling the DNA sequence evolution and zoonotic transmission of C. jejuni between host species and the environment, we assign human cases probabilistically to source populations. Our novel population genetics approach reveals that the vast majority (97%) of sporadic disease can be attributed to animals farmed for meat and poultry. Chicken and cattle are the principal sources of C. jejuni pathogenic to humans, whereas wild animal and environmental sources are responsible for just 3% of disease. Our results imply that the primary transmission route is through the food chain, and suggest that incidence could be dramatically reduced by enhanced on-farm biosecurity or preventing food-borne transmission.

C. jejuni is a bacterium commonly found in the guts of birds and mammals. In humans, it is responsible for causing more gastro-enteritis than any other identified bacterial species. Humans may contract campylobacter from a variety of sources. Eating raw or undercooked meat or poultry, and poor food hygiene that leads to cross-contamination of uncooked food, can cause human disease. However, humans may be exposed to the feces of infected wild animals, and campylobacter can survive in water. Contamination of drinking water can lead to outbreaks, and previous genetic studies have suggested that livestock are not the principal source of human infection. We extracted campylobacter DNA from patients and compared it to campylobacter DNA found in livestock, wild animals, and the environment. We developed a new evolutionary model to identify the most probable source populations. In 97% of cases, we identified chicken, cattle, or sheep as the source of infection. Very few cases were attributable to campylobacter found in wild animals or the environment. Our results imply that the primary transmission route is the food chain and also add new impetus to measures that reduce infection in livestock and prevent food-borne transmission.