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

Machine learning to attribute the source of Campylobacter infections in the United States: A retrospective analysis of national surveillance data

OBJECTIVES

Integrating pathogen genomic surveillance with bioinformatics can enhance public health responses by identifying risk and guiding interventions. This study focusses on the two predominant Campylobacter species, which are commonly found in the gut of birds and mammals and often infect humans via contaminated food. Rising incidence and antimicrobial resistance (AMR) are a global concern, and there is an urgent need to quantify the main routes to human infection.

METHODS

During routine US national surveillance (2009-2019), 8856 Campylobacter genomes from human infections and 16,703 from possible sources were sequenced. Using machine learning and probabilistic models, we target genetic variation associated with host adaptation to attribute the source of human infections and estimate the importance of different disease reservoirs.

RESULTS

Poultry was identified as the primary source of human infections, responsible for an estimated 68% of cases, followed by cattle (28%), and only a small contribution from wild birds (3%) and pork sources (1%). There was also evidence of an increase in multidrug resistance, particularly among isolates attributed to chickens.

CONCLUSIONS

National surveillance and source attribution can guide policy, and our study suggests that interventions targeting poultry will yield the greatest reductions in campylobacteriosis and spread of AMR in the US.

DATA AVAILABILITY

All sequence reads were uploaded and shared on NCBI's Sequence Read Archive (SRA) associated with BioProjects; PRJNA239251 (CDC / PulseNet surveillance), PRJNA287430 (FSIS surveillance), PRJNA292668 & PRJNA292664 (NARMS) and PRJNA258022 (FDA surveillance). Publicly available genomes, including reference genomes and isolates sampled worldwide from wild birds are associated with BioProject accessions: PRJNA176480, PRJNA177352, PRJNA342755, PRJNA345429, PRJNA312235, PRJNA415188, PRJNA524300, PRJNA528879, PRJNA529798, PRJNA575343, PRJNA524315 and PRJNA689604. Contiguous assemblies of all genome sequences compared are available at Mendeley data (assembled C. coli genomes doi: 10.17632/gxswjvxyh3.1; assembled C. jejuni genomes doi: 10.17632/6ngsz3dtbd.1) and individual project and accession numbers can be found in Supplementary tables S1 and S2, which also includes pubMLST identifiers for assembled genomes. Figshare (10.6084/m9.figshare.20279928). Interactive phylogenies are hosted on microreact separately for C. jejuni (https://microreact.org/project/pascoe-us-cjejuni) and C. coli (https://microreact.org/project/pascoe-us-ccoli).

Prediction of edapho-climatic parameters in the incidence of Campylobacter spp. in northwestern Mexico

Campylobacter spp. is one of the main causes of enteric zoonotic infections worldwide. In Mexico, although a commonly detected pathogen in both children and adults, there is limited surveillance and few studies. The northern part of Mexico stands out for an unnoticed outbreak of Campylobacter jejuni due to contaminated drinking water, which caused an abrupt increase in Guillain-Barré syndrome in the local population. Although it is suggested that its distribution in nature is related to edaphic and climatic factors, this relationship is scarcely known. To understand abiotic factors driving the occurrence and prevalence of Campylobacter spp. in three municipalities from three states in northwestern Mexico (Chihuahua, Sonora, and Baja California), we used the kriging interpolation method of unsampled areas and the correspondence analysis of 23 environmental variables. Of the three municipalities evaluated, Janos in Chihuahua (CHIH), has the highest number of geographic areas classified as high and medium incidence, followed by Santa Cruz, Sonora (SON) and Mexicali, Baja California (BC). Mexicali (BC) edaphic variables limit the potential incidence of the bacterium, mainly due to the lack of soil moisture and its difficulty of surviving on dry surfaces, related to electrical conductivity and salinity. Janos (CHIH) presents limitations in terms of soil water availability, although its presence is more heterogeneous (2 to 8 months). Santa Cruz (SON) has the highest soil water availability (4 to 5 months), and presents pH, texture and low percentage of salinity conditions for the potential incidence of Campylobacter spp. Mexicali (BC) reports a temperature in the warmest month of up to 43°C, which could influence the presence of thermophilic species. The annual precipitation is another limiting factor for the potential incidence of Campylobacter spp. since it does not exceed 509.5 mm, contributing to Janos (CHIH) as the municipality with the highest potential incidence of this bacterium.

A mathematical, classical stratification modeling approach to disentangling the impact of weather on infectious diseases: A case study using spatio-temporally disaggregated Campylobacter surveillance data for England and Wales

Disentangling the impact of the weather on transmission of infectious diseases is crucial for health protection, preparedness and prevention. Because weather factors are co-incidental and partly correlated, we have used geography to separate out the impact of individual weather parameters on other seasonal variables using campylobacteriosis as a case study. Campylobacter infections are found worldwide and are the most common bacterial food-borne disease in developed countries, where they exhibit consistent but country specific seasonality. We developed a novel conditional incidence method, based on classical stratification, exploiting the long term, high-resolution, linkage of approximately one-million campylobacteriosis cases over 20 years in England and Wales with local meteorological datasets from diagnostic laboratory locations. The predicted incidence of campylobacteriosis increased by 1 case per million people for every 5° (Celsius) increase in temperature within the range of 8°-15°. Limited association was observed outside that range. There were strong associations with day-length. Cases tended to increase with relative humidity in the region of 75-80%, while the associations with rainfall and wind-speed were weaker. The approach is able to examine multiple factors and model how complex trends arise, e.g. the consistent steep increase in campylobacteriosis in England and Wales in May-June and its spatial variability. This transparent and straightforward approach leads to accurate predictions without relying on regression models and/or postulating specific parameterisations. A key output of the analysis is a thoroughly phenomenological description of the incidence of the disease conditional on specific local weather factors. The study can be crucially important to infer the elusive mechanism of transmission of campylobacteriosis; for instance, by simulating the conditional incidence for a postulated mechanism and compare it with the phenomenological patterns as benchmark. The findings challenge the assumption, commonly made in statistical models, that the transformed mean rate of infection for diseases like campylobacteriosis is a mere additive and combination of the environmental variables.

Evidence of potential Campylobacter jejuni zooanthroponosis in captive macaque populations

Non-human primates share recent common ancestry with humans and exhibit comparable disease symptoms. Here, we explored the transmission potential of enteric bacterial pathogens in monkeys exhibiting symptoms of recurrent diarrhoea in a biomedical research facility in China. The common zoonotic bacterium Campylobacter jejuni was isolated from macaques (Macaca mulatta and Macaca fascicularis) and compared to isolates from humans and agricultural animals in Asia. Among the monkeys sampled, 5 % (44/973) tested positive for C. jejuni, 11 % (5/44) of which displayed diarrhoeal symptoms. Genomic analysis of monkey isolates, and 1254 genomes from various sources in Asia, were used to identify the most likely source of human infection. Monkey and human isolates shared high average nucleotide identity, common MLST clonal complexes and clustered together on a phylogeny. Furthermore, the profiles of putative antimicrobial resistance genes were similar between monkeys and humans. Taken together these findings suggest that housed macaques became infected with C. jejuni either directly from humans or via a common contamination source.

Campylobacter spp. Prevalence in Santiago, Chile: A Study Based on Molecular Detection in Clinical Stool Samples from 2014 to 2019

Campylobacter spp. is an emerging cause of infectious diarrhea worldwide. In South American countries such as Chile, its prevalence is underestimated due to inadequate detection methods. Gastrointestinal multiplex PCR panels (GMP) permit rapid and sensitive detection of bacterial pathogens and provide important epidemiological information. This study aimed to analyze Campylobacter epidemiology using the results of molecular methods and to compare molecular detection results to those of culture methods. We performed a retrospective, descriptive analysis of Campylobacter spp. detected in clinical stool samples between 2014-2019 by GMP and culture. Within 16,582 specimens examined by GMP, Campylobacter was the most prevalent enteropathogenic bacteria (8.5%), followed by Salmonella spp. (3.9%), Shigella spp./enteroinvasive Escherichia coli (EIEC) (1.9%), and Yersinia enterocolitica (0.8%). The highest Campylobacter prevalence occurred in 2014/2015. Campylobacteriosis affected more males (57.2%) and adults from 19-65 years (47.9%) and showed a bimodal seasonality with summer and winter peaks. In 11,251 routine stool cultures, Campylobacter spp. was detected in 4.6%, mostly C. jejuni (89.6%). Among 4533 samples tested by GMP and culture in parallel, GMP showed a superior sensitivity (99.1% versus 50%, respectively). The study suggests that Campylobacter spp. is the most frequent bacterial enteropathogen in Chile.

Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance

Campylobacter is the most common cause of bacterial gastroenteritis worldwide, and diarrhoeal disease is a major cause of child morbidity, growth faltering and mortality in low- and middle-income countries. Despite evidence of high incidence and differences in disease epidemiology, there is limited genomic data from studies in developing countries. In this study, we aimed to quantify the extent of gene sharing in local and global populations. We characterized the genetic diversity and accessory-genome content of a collection of Campylobacter isolates from the Cairo metropolitan area, Egypt. In total, 112 Campylobacter isolates were collected from broiler carcasses (n=31), milk and dairy products (n=24), and patients suffering from gastroenteritis (n=57). Among the most common sequence types (STs), we identified the globally disseminated host generalist ST-21 clonal complex (CC21) and the poultry specialists CC206, CC464 and CC48. Notably, CC45 and the cattle-specialist CC42 were under-represented, with a total absence of CC61. Core- and accessory-genome sharing was compared among isolates from Egypt and a comparable collection from the UK (Oxford). Lineage-specific accessory-genome sharing was significantly higher among isolates from the same country, particularly CC21, which demonstrated greater local geographical clustering. In contrast, no geographical clustering was noted in either the core or accessory genome of CC828, suggesting a highly admixed population. A greater proportion of Campylobacter coli isolates were multidrug resistant compared to Campylobacter jejuni. Our results suggest that there is more horizontal transfer of accessory genes between strains in Egypt. This has strong implications for controlling the spread of antimicrobial resistance among this important pathogen.

Dairy Cattle Density and Temporal Patterns of Human Campylobacteriosis and Cryptosporidiosis in New Zealand

Public health risks associated with the intensification of dairy farming are an emerging concern. Dairy cattle are a reservoir for a number of pathogens that can cause human illness. This study examined the spatial distribution of dairy cattle density and explored temporal patterns of human campylobacteriosis and cryptosporidiosis notifications in New Zealand from 1997 to 2015. Maps of dairy cattle density were produced, and temporal patterns of disease rates were assessed for urban versus rural areas and for areas with different dairy cattle densities using descriptive temporal analyses. Campylobacteriosis and cryptosporidiosis rates displayed strong seasonal patterns, with highest rates in spring in rural areas and, for campylobacteriosis, summer in urban areas. Increases in rural cases often preceded increases in urban cases. Furthermore, disease rates in areas with higher dairy cattle densities tended to peak before areas with low densities or no dairy cattle. Infected dairy calves may be a direct or indirect source of campylobacteriosis or cryptosporidiosis infection in humans through environmental or occupational exposure routes, including contact with animals or feces, recreational contact with contaminated waterways, and consumption of untreated drinking water. These results have public health implications for populations living, working, or recreating in proximity to dairy farms.

Genomic Screening of Antimicrobial Resistance Markers in UK and US Campylobacter Isolates Highlights Stability of Resistance over an 18-Year Period

Campylobacter jejuni and Campylobacter coli are important bacterial causes of human foodborne illness. Despite several years of reduced antibiotics usage in livestock production in the United Kingdom (UK) and United States (US), a high prevalence of antimicrobial resistance (AMR) persists in Campylobacter. Both countries have instigated genome sequencing-based surveillance programs for Campylobacter, and in this study, we have identified AMR genes in 32,256 C. jejuni and 8,776 C. coli publicly available genome sequences to compare the prevalence and trends of AMR in Campylobacter isolated in the UK and US between 2001 and 2018. AMR markers were detected in 68% of C. coli and 53% of C. jejuni isolates, with 15% of C. coli isolates being multidrug resistant (MDR), compared to only 2% of C. jejuni isolates. The prevalence of aminoglycoside, macrolide, quinolone, and tetracycline resistance remained fairly stable from 2001 to 2018 in both C. jejuni and C. coli, but statistically significant differences were observed between the UK and US. There was a statistically significant higher prevalence of aminoglycoside and tetracycline resistance for US C. coli and C. jejuni isolates and macrolide resistance for US C. coli isolates. In contrast, UK C. coli and C. jejuni isolates showed a significantly higher prevalence of quinolone resistance. Specific multilocus sequence type (MLST) clonal complexes (e.g., ST-353/464) showed >95% quinolone resistance. This large-scale comparison of AMR prevalence has shown that the prevalence of AMR remains stable for Campylobacter in the UK and the US. This suggests that antimicrobial stewardship and restricted antibiotic usage may help contain further expansion of AMR prevalence in Campylobacter but are unlikely to reduce it in the short term.

Impact of the COVID-19 pandemic on gastrointestinal infection trends in England, February-July 2020

OBJECTIVE

To establish the impact of the first 6 months of the COVID-19 outbreak response on gastrointestinal (GI) infection trends in England.

DESIGN

Retrospective ecological study using routinely collected national and regional surveillance data from seven UK Health Security Agency coordinated laboratory, outbreak and syndromic surveillance systems using key dates of UK governmental policy change to assign phases for comparison between 2020 and historic data.

RESULTS

Decreases in GI illness activity were observed across all surveillance indicators as COVID-19 cases began to peak. Compared with the 5-year average (2015-2019), during the first 6 months of the COVID-19 response, there was a 52% decrease in GI outbreaks reported (1544 vs 3208 (95% CI 2938 to 3478)) and a 34% decrease in laboratory confirmed cases (27 859 vs 42 495 (95% CI 40 068 to 44 922)). GI indicators began to rise during the first lockdown and lockdown easing, although all remained substantially lower than historic figures. Reductions in laboratory confirmed cases were observed across all age groups and both sexes, with geographical heterogeneity observed in diagnosis trends. Health seeking behaviour changed substantially, with attendances decreasing prior to lockdown across all indicators.

CONCLUSIONS

There has been a marked change in trends of GI infections in the context of the COVID-19 pandemic. The drivers of this change are likely to be multifactorial; while changes in health seeking behaviour, pressure on diagnostic services and surveillance system ascertainment have undoubtably played a role, there has likely been a true decrease in the incidence for some pathogens resulting from the control measures and restrictions implemented. This suggests that if some of these changes in behaviour such as improved hand hygiene were maintained, then we could potentially see sustained reductions in the burden of GI illness.

Livestock microbial landscape patterns: Retail poultry microbiomes significantly vary by region and season

Microbes play key roles in animal welfare and food safety but there is little understanding of whether microbiomes associated with livestock vary in space and time. Here we analysed the bacteria associated with the carcasses of the same breed of 28 poultry broiler flocks at different stages of processing across two climatically similar UK regions over two seasons with 16S metabarcode DNA sequencing. Numbers of taxa types did not differ by region, but did by season (P = 1.2 × 10-19), and numbers increased with factory processing, especially in summer. There was also a significant (P < 1 × 10-4) difference in the presences and abundances of taxa types by season, region and factory processing stage, and the signal for seasonal and regional differences remained highly significant on final retail products. This study therefore revealed that both season and region influence the types and abundances of taxa on retail poultry products. That poultry microbiomes differ in space and time should be considered when testing the efficacy of microbial management interventions designed to increase animal welfare and food safety: these may have differential effects on livestock depending on location and timing.

Linking pathogens, people and places: Using geo-ethnography to understand place-based, socio-economic inequalities in gastrointestinal infections in the UK

This ethnographic study in two socio-economically contrasting areas employed geo-ethnography, underpinned by a relational approach, to understand inequalities in gastrointestinal infections in families with young children. In our 'relatively disadvantaged' area, gastrointestinal infections spread to multiple households within a small radius, whereas in our 'relatively advantaged' area, illness was confined to one household or dispersed long distances. These differences were shaped by historical, social and economic contrasts in: housing; social networks and childcare arrangements; employment and household income. Our findings show how linking places, pathogens and people helps us understand inequalities in gastrointestinal infections and may be pertinent to other infectious diseases such as COVID-19.

Capsular Genotype and Lipooligosaccharide Class Associated Genomic Characterizations of Campylobacter jejuni Isolates From Food Animals in China

Campylobacter jejuni (C. jejuni) is the leading causative agent of gastroenteritis and Guillain–Barré syndrome (GBS). Capsular polysaccharide (CPS) and lipooligosaccharide (LOS) contribute to the susceptibility of campylobacteriosis, which have been concern the major evaluation indicators of C. jejuni isolates from clinical patients. As a foodborne disease, food animal plays a primary role in the infection of campylobacteriosis. To assess the pathogenic characterizations of C. jejuni isolates from various ecological origins, 1609 isolates sampled from 2005 to 2019 in China were analyzed using capsular genotyping. Strains from cattle and poultry were further characterized by LOS classification and multilocus sequence typing (MLST), compared with the isolates from human patients worldwide with enteritis and GBS. Results showed that the disease associated capsular genotypes and LOS classes over-represented in human isolates were also dominant in animal isolates, especially cattle isolates. Based on the same disease associated capsular genotype, more LOS class types were represented by food animal isolates than human disease isolates. Importantly, high-risk lineages CC-22, CC-464, and CC-21 were found dominated in human isolates with GBS worldwide, which were also represented in the food animal isolates with disease associated capsular types, suggesting a possibility of clonal spread of isolates across different regions and hosts. This is the first study providing genetic evidence for food animal isolates of particular capsular genotypes harbor similar pathogenic characteristics to human clinical isolates. Collective efforts for campylobacteriosis hazard control need to be focused on the zoonotic pathogenicity of animal isolates, along the food chain “from farm to table.”

A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

Microbial genomes are highly adaptable, with mobile genetic elements (MGEs) such as integrative conjugative elements (ICEs) mediating the dissemination of new genetic information throughout bacterial populations. This is countered by defence mechanisms such as CRISPR-Cas systems, which limit invading MGEs by sequence-specific targeting. Here we report the distribution of the pVir, pTet and PCC42 plasmids and a new 70–129 kb ICE (CampyICE1) in the foodborne bacterial pathogens Campylobacter jejuni and Campylobacter coli. CampyICE1 contains a degenerated Type II-C CRISPR system consisting of a sole Cas9 protein, which is distinct from the previously described Cas9 proteins from C. jejuni and C. coli. CampyICE1 is conserved in structure and gene order, containing blocks of genes predicted to be involved in recombination, regulation and conjugation. CampyICE1 was detected in 134/5829 (2.3 %) C. jejuni genomes and 92/1347 (6.8 %) C. coli genomes. Similar ICEs were detected in a number of non-jejuni/coli Campylobacter species, although these lacked a CRISPR-Cas system. CampyICE1 carries three separate short CRISPR spacer arrays containing a combination of 108 unique spacers and 16 spacer-variant families. A total of 69 spacers and 10 spacer-variant families (63.7 %) were predicted to target Campylobacter plasmids. The presence of a functional CampyICE1 Cas9 protein and matching anti-plasmid spacers was associated with the absence of the pVir, pTet and pCC42 plasmids (188/214 genomes, 87.9 %), suggesting that the CampyICE1-encoded CRISPR-Cas has contributed to the exclusion of competing plasmids. In conclusion, the characteristics of the CRISPR-Cas9 system on CampyICE1 suggests a history of plasmid warfare in Campylobacter.

Machine learning to predict the source of campylobacteriosis using whole genome data

Campylobacteriosis is among the world's most common foodborne illnesses, caused predominantly by the bacterium Campylobacter jejuni. Effective interventions require determination of the infection source which is challenging as transmission occurs via multiple sources such as contaminated meat, poultry, and drinking water. Strain variation has allowed source tracking based upon allelic variation in multi-locus sequence typing (MLST) genes allowing isolates from infected individuals to be attributed to specific animal or environmental reservoirs. However, the accuracy of probabilistic attribution models has been limited by the ability to differentiate isolates based upon just 7 MLST genes. Here, we broaden the input data spectrum to include core genome MLST (cgMLST) and whole genome sequences (WGS), and implement multiple machine learning algorithms, allowing more accurate source attribution. We increase attribution accuracy from 64% using the standard iSource population genetic approach to 71% for MLST, 85% for cgMLST and 78% for kmerized WGS data using the classifier we named aiSource. To gain insight beyond the source model prediction, we use Bayesian inference to analyse the relative affinity of C. jejuni strains to infect humans and identified potential differences, in source-human transmission ability among clonally related isolates in the most common disease causing lineage (ST-21 clonal complex). Providing generalizable computationally efficient methods, based upon machine learning and population genetics, we provide a scalable approach to global disease surveillance that can continuously incorporate novel samples for source attribution and identify fine-scale variation in transmission potential.

Campylobacter jejuni genotypes are associated with post-infection irritable bowel syndrome in humans

Campylobacter enterocolitis may lead to post-infection irritable bowel syndrome (PI-IBS) and while some C. jejuni strains are more likely than others to cause human disease, genomic and virulence characteristics promoting PI-IBS development remain uncharacterized. We combined pangenome-wide association studies and phenotypic assays to compare C. jejuni isolates from patients who developed PI-IBS with those who did not. We show that variation in bacterial stress response (Cj0145_phoX), adhesion protein (Cj0628_CapA), and core biosynthetic pathway genes (biotin: Cj0308_bioD; purine: Cj0514_purQ; isoprenoid: Cj0894c_ispH) were associated with PI-IBS development. In vitro assays demonstrated greater adhesion, invasion, IL-8 and TNFα secretion on colonocytes with PI-IBS compared to PI-no-IBS strains. A risk-score for PI-IBS development was generated using 22 genomic markers, four of which were from Cj1631c, a putative heme oxidase gene linked to virulence. Our finding that specific Campylobacter genotypes confer greater in vitro virulence and increased risk of PI-IBS has potential to improve understanding of the complex host-pathogen interactions underlying this condition.

Stephanie Peters, Ben Pascoe, et al. use whole-genome sequencing and phenotypic analysis of clinical strains from patients to identify potential genetic factors involved in irritable bowel syndrome resulting from Campylobacter jejuni infection. Their data suggest that genes involved in the bacterial stress response and biosynthetic pathways may contribute toward irritable bowel syndrome, providing further insight into links between Campylobacter genotypes and risk of disease.

Sexual Contact as Risk Factor for Campylobacter Infection, Denmark

Campylobacteriosis is a disease of worldwide importance, but aspects of its transmission dynamics, particularly risk factors, are still poorly understood. We used data from a matched case-control study of 4,269 men who have sex with men (MSM) and 26,215 controls, combined with national surveillance data on Campylobacter spp., Salmonella spp., and Shigella spp., to calculate matched odds ratios (mORs) for infection among MSM and controls. MSM had higher odds of Campylobacter (mOR 14, 95% CI 10–21) and Shigella (mOR 74, 95% CI 27–203) infections, but not Salmonella (mOR 0.2, 95% CI 0–13), and were less likely than controls to have acquired Campylobacter infection abroad (χ² = 21; p<0.001). Our results confirm that sexual contact is a risk factor for campylobacteriosis and also suggest explanations for unique features of Campylobacter epidemiology. These findings provide a baseline for updating infection risk guidelines to the general population.

Prevalence and Antibiotic Resistance of Campylobacter spp. in Urban and Rural Black-Headed Gulls Chroicocephalus ridibundus

We investigate the role of black-headed gulls (Chroicocephalus ridibundus), an omnivorous species that is among the most likely wild bird candidates for transmission of zoonotic agents, as a potential reservoir of Campylobacter spp. Colonies with different anthropogenic pressures were studied to examine differences in exposure to sources of Campylobacter between rural and urban birds. We recorded Campylobacter spp. in 4.87% of adult black-headed gulls and 2.22% of their chicks after analysing 1036 cloacal swabs collected over two breeding seasons in three colonies in northern Poland. Campylobacter jejuni was found most frequently (85.72%), and Campylobacter lari and Campylobacter coli were much scarcer. Prevalence of Campylobacter did not differ significantly between black-headed gulls breeding in urban (4.27%) and rural (3.80%) habitats. Almost all isolates from chicks and adults were susceptible to azithromycin (97.62%) and erythromycin (95.24%), but fewer to tetracycline (50.00%) and ciprofloxacin (47.62%). Campylobacter prevalence was unrelated to the date of sampling. Our study indicates that black-headed gulls are carriers of resistant to antibiotics Campylobacter and they can contaminate natural waterbodies with their faeces, which poses a threat to human and farm animal health.

Inactivation of the core cheVAWY chemotaxis genes disrupts chemotactic motility and organised biofilm formation in Campylobacter jejuni

Flagellar motility plays a central role in the bacterial foodborne pathogen Campylobacter jejuni, as flagellar motility is required for reaching the intestinal epithelium and subsequent colonisation or disease. Flagellar proteins also contribute strongly to biofilm formation during transmission. Chemotaxis is the process directing flagellar motility in response to attractant and repellent stimuli, but its role in biofilm formation of C. jejuni is not well understood. Here we show that inactivation of the core chemotaxis genes cheVAWY in C. jejuni strain NCTC 11168 affects both chemotactic motility and biofilm formation. Inactivation of any of the core chemotaxis genes (cheA, cheY, cheV or cheW) impaired chemotactic motility but did not affect flagellar assembly or growth. The ∆cheY mutant swam in clockwise loops, while complementation restored normal motility. Inactivation of the core chemotaxis genes interfered with the ability to form a discrete biofilm at the air-media interface, and the ∆cheY mutant displayed reduced dispersal/shedding of bacteria into the planktonic fraction. This suggests that while the chemotaxis system is not required for biofilm formation per se, it is necessary for organized biofilm formation. Hence interference with the Campylobacter chemotaxis system at any level disrupts optimal chemotactic motility and transmission modes such as biofilm formation.

Prevalence, Risk Factors, and Molecular Detection of Campylobacter in Farmed Cattle of Selected Districts in Bangladesh

A cross-sectional survey was conducted in selected districts of Bangladesh to estimate prevalence, risk factors, and molecular detection of Campylobacter isolates from 540 farmed cattle of 90 herds. As an individual sample, 540 feces, and as a pooled sample, 180 milk samples, 90 feed samples, 90 water samples, 90 manure samples, and 90 animal attendants' hand-rinse water were collected and tested via culture, biochemical, and molecular assays. A pretested semi-structured questionnaire was used to collect herd-level data on risk factors with the herd owners. The herd-level data on risk factors were analyzed through univariate and multivariate analyses, and a p-value <0.05 was considered statistically significant for all analyses. Overall, farm-level prevalence of bovine Campylobacter was enumerated to be 53.3% (95% confidence interval [CI]: 42.5-63.9%). The feces sample was found to be a high level of contamination of 30.9% (95% CI: 27-35%) followed by the manure swab (pooled) at 15.6% (95% CI: 8.8-24.7%). Campylobacter jejuni was documented as an abundant species (12.6%), followed by Campylobacter coli (5.1%), and Campylobacter fetus (0.3%). Older farms (>5 years of age), no/minimum cleaning and disinfection practices, along with animal roaming outside of the farm, were documented as significant risk factors for farm-level Campylobacter occurrence. Evidence-based control measures need to be taken through stringent biosecurity and hygienic measurement to lessen the load of the Campylobacter pathogen in the farm environment and prevent further transmission to animals and humans.

Seasonality of Common Pediatric Infectious Diseases

BACKGROUND/OBJECTIVE

Traditional sources cite seasonal patterns for common infectious diseases, often based on microbiologic data, but little is known about cyclical trends in clinically diagnosed infectious conditions in the emergency department (ED). We leveraged the publicly available Nationwide Emergency Department Sample database to measure the seasonality of the most common pediatric infectious diseases diagnosed in US EDs.

METHODS

We searched the Nationwide Emergency Department Sample database to identify infectious diagnoses comprising at least 1% of all diagnosis codes ascribed to patients 21 years and younger in US EDs from 2009 to 2013. We used Fourier regression to examine seasonal trends in disease and calculated the peak-to-nadir ratio for each infectious condition.

RESULTS

Over 20% of pediatric visits during the study period were for infectious conditions. Upper respiratory infection, otitis media, gastroenteritis, urinary tract infection/pyelonephritis, cellulitis/abscess, and pneumonia showed a seasonal pattern that matched trends found in prior regional or microbiologic-based studies. The strongest seasonal trend as measured by goodness of model fit was found in pneumonia (peak-to-nadir incidence ratio of 2.7), followed by otitis media (2.0), cellulitis/abscess (2.0), gastroenteritis (1.6), upper respiratory infection (3.2), and urinary tract infection/pyelonephritis (1.4). Pharyngitis did not show a strong seasonal trend.

CONCLUSIONS

Many of the most common pediatric infectious diseases diagnosed in US EDs exhibited seasonal patterns. Large administrative databases can be used to track seasonal disease patterns, with the advantage that they reflect clinician diagnosis beyond microbiologic confirmation. This methodology could aid in resource planning, infection control, and public health educational initiatives.

Epidemiological trends of foodborne Campylobacter outbreaks in the United States of America, 1998-2016

Campylobacter is a major cause of foodborne diarrheal infections in the United States of America (USA). This study aimed to elucidate the patterns of Campylobacter foodborne outbreaks temporally and spatially concerning food vehicles. We collected the data of foodborne outbreaks from 1998 to 2016 reported to the Centers for Disease Control and Prevention. The incidence rate of outbreaks for each food source was calculated and analyzed for each variable including season, food location, and census region. Overall, 465 single-state outbreaks and 8003 cases were reported during 1998-2016. Outbreaks were frequently attributed to dairy products (32%), chicken (17%) and vegetables (6%). Binomial regression analysis showed that compared to chicken items, the highest rate ratio of outbreaks was associated with dairy products (1.86) followed by vegetables (1.35) and meat products (0.76). More outbreaks were reported in the summer (35%) followed by the spring (26%) and fall (22%) season. We found that the highest number of outbreaks occurred in the West 159 (34%) and Midwest 137 (29%) census regions. The study highlights the role of dairy, chicken, and vegetables as food vehicles in Campylobacter outbreaks. Findings from this study can help in devising strategies to mitigate the increasing occurrence of Campylobacter foodborne outbreaks.

Campylobacter-associated hospitalisations in an Australian provincial setting

BACKGROUND

Campylobacter spp. infections are a globally important cause of enterocolitis, causing substantial morbidity. Capturing accurate information on hospitalisations is challenging and limited population-level data exist to describe the clinico-epidemiological characteristics of hospitalised cases.

METHODS

Hospital administrative and laboratory datasets were linked to identify Campylobacter-associated hospitalisations between 2004 and 2013. Accuracy of morbidity coding was assessed using laboratory diagnosis as a gold standard, with health department surveillance data used to calculate population-based rates. Additional patient-level data were collected via review of medical records. Descriptive statistics were used to assess changes in rates and proportions and to assess relationships between key variables including age, length of stay, comorbidity and complications.

RESULTS

In total 685 Campylobacter-associated hospital admissions were identified, with the sensitivity of morbidity coding 52.8% (95% CI 48.9-56.7%). The mean annual rate of hospitalisation was 13.6%. Hospitalisation rates were higher for females across most age-groups, while for both genders marked increases were observed for those aged ≥60 years. Median admission age was 39.5 years, with an average length of stay of 3.5 days. Comorbidities were present in 34.5% (237/685) of admissions, with these patients more likely to develop electrolyte disturbances, hypotension, renal impairment or acute confusion (all p < 0.001). Bacteraemia and acute kidney injury were observed in 4.1% (28/685) and 3.6% (23/685) of admissions, respectively. Inpatient mortality was low (0.15%).

CONCLUSION

Under reporting of Campylobacter-associated hospitalisations is substantial but can be improved through data linkage. We observed demographic differences among those hospitalised but further work is needed to determine risk factors and predictors for hospitalisation.

Systematic analysis of infectious disease outcomes by age shows lowest severity in school-age children

The COVID-19 pandemic has ignited interest in age-specific manifestations of infection but surprisingly little is known about relative severity of infectious disease between the extremes of age. In a systematic analysis we identified 142 datasets with information on severity of disease by age for 32 different infectious diseases, 19 viral and 13 bacterial. For almost all infections, school-age children have the least severe disease, and severity starts to rise long before old age. Indeed, for many infections even young adults have more severe disease than children, and dengue was the only infection that was most severe in school-age children. Together with data on vaccine response in children and young adults, the findings suggest peak immune function is reached around 5-14 years of age. Relative immune senescence may begin much earlier than assumed, before accelerating in older age groups. This has major implications for understanding resilience to infection, optimal vaccine scheduling, and appropriate health protection policies across the life course.

Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon

Campylobacter is the leading bacterial cause of gastroenteritis worldwide and its incidence is especially high in low- and middle-income countries (LMIC). Disease epidemiology in LMICs is different compared to high income countries like the USA or in Europe. Children in LMICs commonly have repeated and chronic infections even in the absence of symptoms, which can lead to deficits in early childhood development. In this study, we sequenced and characterized C. jejuni (n = 62) from a longitudinal cohort study of children under the age of 5 with and without diarrheal symptoms, and contextualized them within a global C. jejuni genome collection. Epidemiological differences in disease presentation were reflected in the genomes, specifically by the absence of some of the most common global disease-causing lineages. As in many other countries, poultry-associated strains were likely a major source of human infection but almost half of local disease cases (15 of 31) were attributable to genotypes that are rare outside of Peru. Asymptomatic infection was not limited to a single (or few) human adapted lineages but resulted from phylogenetically divergent strains suggesting an important role for host factors in the cryptic epidemiology of campylobacteriosis in LMICs.

Influence of socio-economic status on Shiga toxin-producing Escherichia coli (STEC) infection incidence, risk factors and clinical features

Shiga toxin-producing Escherichia coli (STEC) infection can cause serious illness including haemolytic uraemic syndrome. The role of socio-economic status (SES) in differential clinical presentation and exposure to potential risk factors amongst STEC cases has not previously been reported in England. We conducted an observational study using a dataset of all STEC cases identified in England, 2010–2015. Odds ratios for clinical characteristics of cases and foodborne, waterborne and environmental risk factors were estimated using logistic regression, stratified by SES, adjusting for baseline demographic factors. Incidence was higher in the highest SES group compared to the lowest (RR 1.54, 95% CI 1.19–2.00). Odds of Accident and Emergency attendance (OR 1.35, 95% CI 1.10–1.75) and hospitalisation (OR 1.71, 95% CI 1.36–2.15) because of illness were higher in the most disadvantaged compared to the least, suggesting potential lower ascertainment of milder cases or delayed care-seeking behaviour in disadvantaged groups. Advantaged individuals were significantly more likely to report salad/fruit/vegetable/herb consumption (OR 1.59, 95% CI 1.16–2.17), non-UK or UK travel (OR 1.76, 95% CI 1.40–2.27; OR 1.85, 95% CI 1.35–2.56) and environmental exposures (walking in a paddock, OR 1.82, 95% CI 1.22–2.70; soil contact, OR 1.52, 95% CI 2.13–1.09) suggesting other unmeasured risks, such as person-to-person transmission, could be more important in the most disadvantaged group.

Epidemiology and antimicrobial resistance of Campylobacter spp. in animals in Sub-Saharan Africa: A systematic review

INTRODUCTION

Low sanitary conditions characterize the rural and urban households in Sub-Saharan African region. Those environmental conditions propitiate the transmission of bacterial infections between animals and humans. Campylobacter spp. is a zoonotic bacterium and cause of human gastroenteritis worldwide, whose main symptom is diarrhea. It is normally found in the digestive tract of many farm animals as a commensal but some species cause diseases in animals. It is important to understand the occurrence of these bacteria in animals, as they may also play a role in transmission to humans. The main objective of this review was to describe the prevalence of Campylobacter in animals in Sub-Saharan Africa. We also report findings on antibiotic resistance.

METHODS

We followed PRISMA guidelines to find studies about occurrence of Campylobacter spp. in animals in all countries from Sub-Saharan Africa. PubMed, Cochrane Library, CINAHL, African Index Medicus, African Journals Online, Google Scholar and Science Direct were searched for studies published between 2000 and 2019.

RESULTS

We found 70 studies that described occurrence of Campylobacter spp. in animals in 18 out of 53 countries of Sub-Saharan Africa. Campylobacter jejuni and C. coli were the predominant species isolated. The majority of studies were found in Western Africa. Middle Africa had the lowest amount of data. Most records presented data from Nigeria (n = 25), South Africa (n = 14) and Tanzania (n = 11). Cattle and chickens appear to be important hosts and may be playing an important role in transmitting to humans. Most Campylobacter isolates were resistant to erythromycin (44%), ampicillin (39%), tetracycline (33%), nalidixic acid (31%) and ciprofloxacin (30%).

CONCLUSION

Several studies about Campylobacter spp. in animals have been published in the last 19 years but information on the epidemiology of campylobacteriosis is scarce in most Sub-Saharan African countries. Antibiotic resistance is an increasing concern in many countries. Measures should be taken to prevent infection by this pathogen in the region and to control antibiotic resistance.

Characteristics of Campylobacter Gastroenteritis Outbreaks in Australia, 2001 to 2016

Campylobacter spp. are a globally important cause of bacterial gastroenteritis, with Australia experiencing higher rates of illness than many comparable high-income countries. Despite the high disease incidence, outbreaks of campylobacteriosis in Australia are infrequently detected and reported. We examined the epidemiology of Campylobacter outbreaks in Australia, with particular emphasis on assessing transmission routes and evidence as reported during public health investigations. A national register of enteric and foodborne disease outbreaks was used to summarize data on all Campylobacter outbreaks reported in Australia between 2001 and 2016. Outbreak data were reviewed and analyzed for trends over time. Additional information was sought from state and territory epidemiologists, to validate transmission routes. A total of 84 Campylobacter outbreaks were reported, with 51 (61%) being classified as foodborne. Specific food vehicles were identified for 33 (65%) outbreaks, with 28 (85%) implicating chicken or chicken-containing dishes. Although no increase in the proportion of foodborne Campylobacter outbreaks was observed, examination of specific food vehicles demonstrated a significant increase in outbreaks because of poultry-liver containing foods (p = 0.04). One quarter of all 1042 outbreak-associated cases occurred in aged-care facilities (ACFs), including 17 associated hospitalizations and three deaths. After review of evidence data, 23 outbreaks (27%) were determined to have an unknown route of transmission, including 10 (43%) outbreaks occurring in ACFs. Campylobacter spp. remain a less commonly reported cause of gastroenteritis outbreaks in Australia. Although many reported outbreaks can be linked to foodborne transmission, over a quarter were unable to identify either a food vehicle or transmission source, particularly for outbreaks occurring in aged care. Increased efforts to improve evidence collection and understanding of transmission dynamics for outbreaks of campylobacteriosis, particularly in aged care, are required.

Spatio-temporal analysis of differences in campylobacteriosis incidence between urban and rural areas in the Southern District Health Board, New Zealand

The objective of this paper is to investigate differences in campylobacteriosis incidence between urban and rural areas in the Southern District Health Board of New Zealand between 2000 and 2015. The data were analysed using a Bayesian change-point model to evaluate how campylobacteriosis incidence changed over time and to see whether the dynamics differed between rural and urban areas. A conditional auto regressive error term was introduced to account for any spatial effects. The results of our analysis showed that campylobacteriosis incidence increased between 2000 and 2005, decreased between 2006 and 2008 then stabilised from 2009 onward. In addition we found that the changes in incidence were greater in urban areas than in rural ones.

Molecular detection of Campylobacter jejuni in patients with Crohn's disease in Iran

Background: Crohn's disease is one of the most significant intestinal disorders and is known as inflammatory bowel disease; Campylobacter spp. are one of the leading causes of bacterial gastroenteritis in humans. Methods: In this study, 60 tissue samples, including 30 cases with Crohn's disease and 30 cases with no inflammatory bowel disease, were collected. Patients were referred to Taleghani hospital and Behboud clinic between March 2015 and May 2016. Biopsies were used for DNA extraction and assessment of Campylobacter jejuni in patients with Crohn's disease and controls using polymerase chain reaction and quantitative real-time polymerase chain reaction. All positive amplified fragments were sequenced. The gene encoding 16S rRNA, specific to Campylobacter genus, was amplified. Results: The results were positive for Campylobacter genus in patients with Crohn's disease compared to healthy individuals. The quantitative real-time PCR showed a significantly higher prevalence of Campylobacter jejuni, particularly in hippurate hydrolase in tissue specimens of patients with Crohn's disease compared to control group. The correlation between Campylobacter jejuni and diarrhea symptoms in patients with Crohn's disease and controls was investigated. One positive case of Campylobacter jejuni found in patients without diarrhea was compared with 13 patients with diarrhea. Conclusion: The present study demonstrated the alarmingly high rate of Campylobacter jejuni prevalence in Crohn's disease patients with diarrhea symptoms. However, further investigation is needed to determine the possible causing factors of this disease.

Quinolone and Macrolide-Resistant Campylobacter jejuni in Pediatric Gastroenteritis Patients from Central Iran

Aims: To determine the prevalence and the antibiotic resistance patterns of Campylobacter jejuni isolated from pediatric diarrhea patients in central Iran. Materials and Methods: Stool specimens (n = 230) were investigated using a modified Gram stain, two specific culture media, and C. jejuni-specific PCR. Antibiotic resistance profiles and relevant resistance genes were determined. Genetic relationships among a selection of the isolates were studied by Fla typing. Results: Out of the 230 diarrhea samples, 48 (20.8%) cases of C. jejuni were identified using modified Gram stain, 45 (19.5%) using the culture media, and 76 (33%) cases were identified using PCR. The highest antibiotic resistance rates were observed in 37 (82.2%) strains against tetracycline, in 32 (71.1%) against ciprofloxacin, and in 31 (68.8%) against erythromycin. Twenty (44.4%) isolates were resistant to ciprofloxacin and erythromycin simultaneously. Genotypic investigations found 36 (97.3%) strains carrying the tet (o) gene, 31 (96.8%) harboring the cmeB gene, 22 (68.7%) strains with the gyrA6 gene, 20 (64.5%) strains containing a 23S rRNA mutation, and 21 (65.6%) strains with the qnrS gene. Fla typing of a random subset of 14 strains revealed 11 different types showing the genomic diversity of the isolates. Strains sharing the same Fla type could be easily distinguished by their resistance gene profile. Conclusions: This is the first study to demonstrate that genetically diverse quinolone-macrolide-resistant C. jejuni is an important cause of gastroenteritis in children from central Iran. Pediatricians should consider these resistance features once the antibiotic prescription is necessary for prevention of possible complications, especially in those under 5 years of age. Of note, most cases of Campylobacter diarrhea are self-limiting and antibiotics should only be prescribed in those cases where severe complications evolve.

Exploring Campylobacter seasonality across Europe using The European Surveillance System (TESSy), 2008 to 2016

BackgroundCampylobacteriosis is the most commonly reported food-borne infection in the European Union, with an annual number of cases estimated at around 9 million. In many countries, campylobacteriosis has a striking seasonal peak during early/mid-summer. In the early 2000s, several publications reported on campylobacteriosis seasonality across Europe and associations with temperature and precipitation. Subsequently, many European countries have introduced new measures against this food-borne disease.AimTo examine how the seasonality of campylobacteriosis varied across Europe from 2008-16, to explore associations with temperature and precipitation, and to compare these results with previous studies. We also sought to assess the utility of the European Surveillance System TESSy for cross-European seasonal analysis of campylobacteriosis.MethodsWard's Minimum Variance Clustering was used to group countries with similar seasonal patterns of campylobacteriosis. A two-stage multivariate meta-analysis methodology was used to explore associations with temperature and precipitation.ResultsNordic countries had a pronounced seasonal campylobacteriosis peak in mid- to late summer (weeks 29-32), while most other European countries had a less pronounced peak earlier in the year. The United Kingdom, Ireland, Hungary and Slovakia had a slightly earlier peak (week 24). Campylobacteriosis cases were positively associated with temperature and, to a lesser degree, precipitation.ConclusionAcross Europe, the strength and timing of campylobacteriosis peaks have remained similar to those observed previously. In addition, TESSy is a useful resource for cross-European seasonal analysis of infectious diseases such as campylobacteriosis, but its utility depends upon each country's reporting infrastructure.

Seasonality and the effects of weather on Campylobacter infections

Background

Campylobacteriosis is a major public health concern. The weather factors that influence spatial and seasonal distributions are not fully understood.

Methods

To investigate the impacts of temperature and rainfall on Campylobacter infections in England and Wales, cases of Campylobacter were linked to local temperature and rainfall at laboratory postcodes in the 30 days before the specimen date. Methods for investigation included a comparative conditional incidence, wavelet, clustering, and time series analyses.

Results

The increase of Campylobacter infections in the late spring was significantly linked to temperature two weeks before, with an increase in conditional incidence of 0.175 cases per 100,000 per week for weeks 17 to 24; the relationship to temperature was not linear. Generalized structural time series model revealed that changes in temperature accounted for 33.3% of the expected cases of Campylobacteriosis, with an indication of the direction and relevant temperature range. Wavelet analysis showed a strong annual cycle with additional harmonics at four and six months. Cluster analysis showed three clusters of seasonality with geographic similarities representing metropolitan, rural, and other areas.

Conclusions

The association of Campylobacteriosis with temperature is likely to be indirect. High-resolution spatial temporal linkage of weather parameters and cases is important in improving weather associations with infectious diseases. The primary driver of Campylobacter incidence remains to be determined; other avenues, such as insect contamination of chicken flocks through poor biosecurity should be explored.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-3840-7) contains supplementary material, which is available to authorized users.

Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni

Campylobacter jejuni is the most common cause of bacterial diarrheal disease in the world. Clinical outcomes of infection can range from asymptomatic infection to life-threatening extraintestinal infections. This variability in outcomes for infected patients has raised questions as to whether genetic differences between C. jejuni isolates contribute to their likelihood of causing severe disease. In this study, we compare the genomes of ten C. jejuni isolates that were implicated in extraintestinal infections with reference gastrointestinal isolates, in order to identify unusual patterns of sequence variation associated with infection outcome. We identified a collection of genes that display a higher burden of uncommon mutations in invasive isolates compared with gastrointestinal close relatives, including some that have been previously linked to virulence and invasiveness in C. jejuni. Among the top genes identified were mreB and pgp1, which are both involved in determining cell shape. Electron microscopy confirmed morphological differences in isolates carrying unusual sequence variants of these genes, indicating a possible relationship between extraintestinal infection and changes in cell morphology.

Vaccine development for enteric bacterial pathogens: Where do we stand?

Gut infections triggered by pathogenic bacteria lead to most frequently occurring diarrhea in humans accounting for million deaths annually. Currently, only a few licensed vaccines are available against these pathogens for mostly travelers moving to diarrheal endemic areas. Besides commercialized vaccines, there are many formulations that are either under clinical or pre-clinical stages of development and despite several efforts to improve safety, immunogenicity and efficacy, none of them can confer long-term protective immunity, for which repeated booster doses are always recommended. Further in many countries, financial, social and political constraints have jeopardized vaccine development program against these pathogens that enforce us to gather knowledge on safety, tolerability, immunogenicity and protective efficacy regarding the same. In this review, we analyze safety and efficacy issues of vaccines against five major gut bacteria causing enteric infections. The article also simultaneously describes several barriers for vaccine development and further discusses possible strategies to enhance immunogenicity and efficacy.

Climate, human behaviour or environment: individual-based modelling of Campylobacter seasonality and strategies to reduce disease burden

Background

With over 800 million cases globally, campylobacteriosis is a major cause of food borne disease. In temperate climates incidence is highly seasonal but the underlying mechanisms are poorly understood, making human disease control difficult. We hypothesised that observed disease patterns reflect complex interactions between weather, patterns of human risk behaviour, immune status and level of food contamination. Only by understanding these can we find effective interventions.

Methods

We analysed trends in human Campylobacter cases in NE England from 2004 to 2009, investigating the associations between different risk factors and disease using time-series models. We then developed an individual-based (IB) model of risk behaviour, human immunological responses to infection and environmental contamination driven by weather and land use. We parameterised the IB model for NE England and compared outputs to observed numbers of reported cases each month in the population in 2004–2009. Finally, we used it to investigate different community level disease reduction strategies.

Results

Risk behaviours like countryside visits (t = 3.665, P < 0.001 and t = − 2.187, P = 0.029 for temperature and rainfall respectively), and consumption of barbecued food were strongly associated with weather, (t = 3.219, P = 0.002 and t = 2.015, P = 0.045 for weekly average temperature and average maximum temperature respectively) and also rain (t = 2.254, P = 0.02527). This suggests that the effect of weather was indirect, acting through changes in risk behaviour. The seasonal pattern of cases predicted by the IB model was significantly related to observed patterns (r = 0.72, P < 0.001) indicating that simulating risk behaviour could produce the observed seasonal patterns of cases. A vaccination strategy providing short-term immunity was more effective than educational interventions to modify human risk behaviour. Extending immunity to 1 year from 20 days reduced disease burden by an order of magnitude (from 2412–2414 to 203–309 cases per 50,000 person-years).

Conclusions

This is the first interdisciplinary study to integrate environment, risk behaviour, socio-demographics and immunology to model Campylobacter infection, including pathways to mitigation. We conclude that vaccination is likely to be the best route for intervening against campylobacteriosis despite the technical problems associated with understanding both the underlying human immunology and genetic variation in the pathogen, and the likely cost of vaccine development.

Pathogen seasonality and links with weather in England and Wales: a big data time series analysis

Background

Many infectious diseases of public health importance display annual seasonal patterns in their incidence. We aimed to systematically document the seasonality of several human infectious disease pathogens in England and Wales, highlighting those organisms that appear weather-sensitive and therefore may be influenced by climate change in the future.

Methods

Data on infections in England and Wales from 1989 to 2014 were extracted from the Public Health England (PHE) SGSS surveillance database. We conducted a weekly, monthly and quarterly time series analysis of 277 pathogen serotypes. Each organism’s time series was forecasted using the TBATS package in R, with seasonality detected using model fit statistics. Meteorological data hosted on the MEDMI Platform were extracted at a monthly resolution for 2001–2011. The organisms were then clustered by K-means into two groups based on cross correlation coefficients with the weather variables.

Results

Examination of 12.9 million infection episodes found seasonal components in 91/277 (33%) organism serotypes. Salmonella showed seasonal and non-seasonal serotypes. These results were visualised in an online Rshiny application. Seasonal organisms were then clustered into two groups based on their correlations with weather. Group 1 had positive correlations with temperature (max, mean and min), sunshine and vapour pressure and inverse correlations with mean wind speed, relative humidity, ground frost and air frost. Group 2 had the opposite but also slight positive correlations with rainfall (mm, > 1 mm, > 10 mm).

Conclusions

The detection of seasonality in pathogen time series data and the identification of relevant weather predictors can improve forecasting and public health planning. Big data analytics and online visualisation allow the relationship between pathogen incidence and weather patterns to be clarified.

Electronic supplementary material

The online version of this article (10.1186/s12889-018-5931-6) contains supplementary material, which is available to authorized users.

Beyond Climate Change and Health: Integrating Broader Environmental Change and Natural Environments for Public Health Protection and Promotion in the UK

Increasingly, the potential short and long-term impacts of climate change on human health and wellbeing are being demonstrated. However, other environmental change factors, particularly relating to the natural environment, need to be taken into account to understand the totality of these interactions and impacts. This paper provides an overview of ongoing research in the Health Protection Research Unit (HPRU) on Environmental Change and Health, particularly around the positive and negative effects of the natural environment on human health and well-being and primarily within a UK context. In addition to exploring the potential increasing risks to human health from water-borne and vector-borne diseases and from exposure to aeroallergens such as pollen, this paper also demonstrates the potential opportunities and co-benefits to human physical and mental health from interacting with the natural environment. The involvement of a Health and Environment Public Engagement (HEPE) group as a public forum of “critical friends” has proven useful for prioritising and exploring some of this research; such public involvement is essential to minimise public health risks and maximise the benefits which are identified from this research into environmental change and human health. Research gaps are identified and recommendations made for future research into the risks, benefits and potential opportunities of climate and other environmental change on human and planetary health.

Investigating the Association Between the Caecal Microbiomes of Broilers and Campylobacter Burden

One of the major transmission routes for the foodborne bacterial pathogen Campylobacter is undercooked poultry meat, contaminated from intestinal contents during processing. In broilers, Campylobacter can grow to very high densities in the caeca, and is often considered to be a commensal or an opportunistic pathogen in poultry. Reduction of caecal loads of Campylobacter may assist in lowering incidence rates of Campylobacter food poisoning. To achieve this, there needs to be a better understanding of the dynamics of Campylobacter colonization in its natural niche, and the effect of the local microbiome on colonization. Previous studies have shown that the microbiome differed between Campylobacter colonized and non-colonized chicken intestinal samples. To characterize the microbiome of Campylobacter-colonized broilers, caecal samples of 100 randomly selected birds from four farms were analyzed using amplified 16S rRNA gene sequences. Bacterial taxonomic analysis indicated that inter-farm variation was greater than intra-farm variation. The two most common bacterial groups were Bacteroidetes and Firmicutes which were present in all samples and constituted 29.7-63.5 and 30.2-59.8% of the bacteria present, respectively. Campylobacter was cultured from all samples, ranging from 2 to 9 log₁₀ CFU g^-1. There was no clear link between Campylobacter counts and Firmicutes, Bacteroidetes, or Tenericutes levels in the 16S rRNA operational taxonomic unit (OTU)-based analysis of the caecal microbiome, but samples with high Campylobacter counts (>9 log CFU g^-1) contained increased levels of Enterobacteriaceae. A decrease in Lactobacillus abundance in chicken caeca was also associated with high Campylobacter loads. The reported associations with Lactobacillus and Enterobacteriaceae match changes in the intestinal microbiome of chickens and mice previously reported for Campylobacter infection, and raises the question about temporality and causation; as to whether increases in Campylobacter loads create conditions adverse to Lactobacilli and/or beneficial to Enterobacteriaceae, or that changes in Lactobacilli and Enterobacteriaceae levels created conditions beneficial for Campylobacter colonization. If these changes can be controlled, this may open opportunities for modulation of chicken microbiota to reduce Campylobacter levels for improved food safety.

Antibiotic Sensitivity Profiling and Virulence Potential of Campylobacter jejuni Isolates from Estuarine Water in the Eastern Cape Province, South Africa

Campylobacter jejuni (CJ) is a zoonotic microbe and a major causative organism of diarrheal infection in humans that often has its functional characteristics inactivated in stressed conditions. The current study assessed the correlation between recovered CJ and water quality parameters and the drug sensitivity patterns of the pathogen to frontline antibiotics in human and veterinary medicine. Water samples (n = 244) from rivers/estuarines were collected from April⁻September 2016, and physicochemical conditions were recorded on-site. CJ was isolated from the samples using standard microbiological methods and subjected to sensitivity testing to 10 antibiotics. Mean CJ counts were between 1 and 5 logs (CFU/mL). Ninety-five isolates confirmed as CJ by PCR showed varying rates of resistance. Sensitivity testing showed resistance to tetracycline (100%), azithromycin (92%), clindamycin (84.2%), clarithromycin and doxycycline (80%), ciprofloxacin (77.8%), vancomycin (70.5%), erythromycin (70%), metronidazole (36.8%) and nalidixic acid (30.5%). Virulence encoding genes were detected in the majority 80/95, 84.2%) of the confirmed isolates from cdtB; 60/95 (63.2%) from cstII; 49/95 (51.6%) from cadF; 45/95 (47.4%) from clpP; 30/95 (31.6%) from htrB, and 0/95 (0%) from csrA. A multiple resistance cmeABC active efflux pump system was present in 69/95 (72.6) isolates. The presence of CJ was positively correlated with temperature (r = 0.17), pH (r = 0.02), dissolved oxygen (r = 0.31), and turbidity (r = 0.23) but negatively correlated with salinity (r = −0.39) and conductivity (r = −0.28). The detection of multidrug resistant CJ strains from estuarine water and the differential gene expressions they possess indicates a potential hazard to humans. Moreover, the negative correlation between the presence of the pathogen and physicochemical parameters such as salinity indicates possible complementary expression of stress tolerance response mechanisms by wild-type CJ strains.

A comparison of weather variables linked to infectious disease patterns using laboratory addresses and patient residence addresses

BACKGROUND

To understand the impact of weather on infectious diseases, information on weather parameters at patient locations is needed, but this is not always accessible due to confidentiality or data availability. Weather parameters at nearby locations are often used as a proxy, but the accuracy of this practice is not known.

METHODS

Daily Campylobacter and Cryptosporidium cases across England and Wales were linked to local temperature and rainfall at the residence postcodes of the patients and at the corresponding postcodes of the laboratory where the patient's specimen was tested. The paired values of daily rainfall and temperature for the laboratory versus residence postcodes were interpolated from weather station data, and the results were analysed for agreement using linear regression. We also assessed potential dependency of the findings on the relative geographic distance between the patient's residence and the laboratory.

RESULTS

There was significant and strong agreement between the daily values of rainfall and temperature at diagnostic laboratories with the values at the patient residence postcodes for samples containing the pathogens Campylobacter or Cryptosporidium. For rainfall, the R-squared was 0.96 for the former and 0.97 for the latter, and for maximum daily temperature, the R-squared was 0.99 for both. The overall mean distance between the patient residence and the laboratory was 11.9 km; however, the distribution of these distances exhibited a heavy tail, with some rare situations where the distance between the patient residence and the laboratory was larger than 500 km. These large distances impact the distributions of the weather variable discrepancies (i.e. the differences between weather parameters estimated at patient residence postcodes and those at laboratory postcodes), with discrepancies up to ±10 °C for the minimum and maximum temperature and 20 mm for rainfall. Nevertheless, the distributions of discrepancies (estimated separately for minimum and maximum temperature and rainfall), based on the cases where the distance between the patient residence and the laboratory was within 20 km, still exhibited tails somewhat longer than the corresponding exponential fits suggesting modest small scale variations in temperature and rainfall.

CONCLUSION

The findings confirm that, for the purposes of studying the relationships between meteorological variables and infectious diseases using data based on laboratory postcodes, the weather results are sufficiently similar to justify the use of laboratory postcode as a surrogate for domestic postcode. Exclusion of the small percentage of cases where there is a large distance between the residence and the laboratory could increase the precision of estimates, but there are generally strong associations between daily weather parameters at residence and laboratory.

Cytokine responses in campylobacteriosis: Linking pathogenesis to immunity

Campylobacter jejuni is an important enteric pathogen that causes diarrheas of different degrees of severity and several extra-intestinal manifestations, including Guillain-Barre syndrome. The variability of disease outcomes is thought to be linked to the immune response induced by C. jejuni. The virulence factors of C. jejuni induce a pro-inflammatory response, that is initiated by the intestinal epithelial cells, propagated by innate immune cells and modulated by the cells of the adaptive immune response. This review focuses on cytokines, that are reported to orchestrate the induction and propagation of pro-inflammatory immune response, and also those that are involved in control and resolution of inflammation. We describe the functional roles of a number of cytokines in modulating anti-Campylobacter immune responses: 1. cytokines of innate immunity (TNF-α, IL-6, and IL-8) as initiators of inflammatory response, 2. cytokines of antigen-presenting cells (IL-1β, IL-12, and IL-23) as promoters of pro-inflammatory response, 3. cytokines produced by T cells (IFN-γ, IL-17, IL-22) as activators of T cells, and 4. anti-inflammatory cytokines (IL-4 and IL-10) as inhibitors of pro-inflammatory responses. We highlight the roles of cytokines as potential therapeutic agents that are under investigation. In the end, we pose several questions that remain unanswered in our quest to understand Campylobacter immunity.

Campylobacter and Ethnicity-A Case-Case Analysis to Determine Differences in Disease Presentation and Risk Factors

BACKGROUND

Rates of Campylobacter infection in Arizona have historically been higher than the national average, with the highest rates in Hispanic populations. The purpose of this retrospective case-case analysis was to determine how risk factors and disease presentation differ by ethnicity (Hispanic vs. Non-Hispanic) in cases of campylobacteriosis from 2012 to 2015 in Maricopa County, Arizona.

METHODS

Basic demographics and seasonality, including standardized morbidity ratios (SMRs), were analyzed to determine differences by ethnicity. To determine differences in risk factors, adjusted univariate and multivariable logistic regression was conducted.

RESULTS

There were significant differences by ethnicity by age (1-14 years and >60 years), location of residence (urban vs. suburban), and testing methodology. Most months in the seasonality analysis showed higher than expected values of Hispanic cases based on population distributions (SMR Range: 0.91-1.78, annual mean: 1.23). Differences in disease presentation showed that Hispanics (adjusted for age and location of residence) were more likely to experience vomiting (OR = 1.41) and fever (OR = 1.08), as well as seek care through an urgent care or emergency department (OR = 1.50), than non-Hispanic cases. Hispanics had a higher odds of reporting consumption of tomatoes (OR = 1.45), salsa (OR = 2.35), cilantro (OR = 2.21), queso fresco (OR = 8.53), and sprouts (OR = 1.94) than non-Hispanic cases. Multivariable analyses found queso fresco (aOR = 6.58), cilantro (aOR = 3.93), and animal products (aOR = 0.38) all to be significant by ethnicity.

CONCLUSIONS

Hispanics had a higher likelihood of consuming high risk foods, while non-Hispanics were more likely to have environmental exposures linked to Campylobacter infection. Focused questionnaires can reveal differences and contribute to improving public health action/education for specific populations.

Relationship between socioeconomic status and gastrointestinal infections in developed countries: A systematic review and meta-analysis

BACKGROUND

The association between socioeconomic status (SES) and health is well-documented; however limited evidence on the relationship between SES and gastrointestinal (GI) infections exists, with published studies producing conflicting results. This systematic review aimed to assess the association between SES and GI infection risk, and explore possible sources of heterogeneity in effect estimates reported in the literature.

METHODS

MEDLINE, Scopus, Web of Science and grey literature were searched from 1980 to October 2015 for studies reporting an association between GI infections and SES in a representative population sample from a member-country of the Organisation for Economic Co-operation and Development. Harvest plots and meta-regression were used to investigate potential sources of heterogeneity such as age; level of SES variable; GI infection measurement; and predominant mode of transmission. The protocol was registered on PROSPERO: CRD42015027231.

RESULTS

In total, 6021 studies were identified; 102 met the inclusion criteria. Age was identified as the only statistically significant potential effect modifier of the association between SES and GI infection risk. For children, GI infection risk was higher for those of lower SES versus high (RR 1.51, 95% CI;1.26-1.83), but there was no association for adults (RR 0.79, 95% CI;0.58-1.06). In univariate analysis, the increased risk comparing low and high SES groups was significantly higher for pathogens spread by person-to-person transmission, but lower for environmental pathogens, as compared to foodborne pathogens.

CONCLUSIONS

Disadvantaged children, but not adults, have greater risk of GI infection compared to their more advantaged counterparts. There was high heterogeneity and many studies were of low quality. More high quality studies are needed to investigate the association between SES and GI infection risk, and future research should stratify analyses by age and pathogen type. Gaining further insight into this relationship will help inform policies to reduce inequalities in GI illness in children.

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.

Health impacts of climate change and health and social inequalities in the UK

This article examines how social and health inequalities shape the health impacts of climate change in the UK, and what the implications are for climate change adaptation and health care provision. The evidence generated by the other articles of the special issue were interpreted using social justice reasoning in light of additional literature, to draw out the key implications of health and social inequalities for health outcomes of climate change. Exposure to heat and cold, air pollution, pollen, food safety risks, disruptions to access to and functioning of health services and facilities, emerging infections and flooding are examined as the key impacts of climate change influencing health outcomes. Age, pre-existing medical conditions and social deprivation are found to be the key (but not only) factors that make people vulnerable and to experience more adverse health outcomes related to climate change impacts. In the future, climate change, aging population and decreasing public spending on health and social care may aggravate inequality of health outcomes related to climate change. Health education and public preparedness measures that take into account differential exposure, sensitivity and adaptive capacity of different groups help address health and social inequalities to do with climate change. Adaptation strategies based on individual preparedness, action and behaviour change may aggravate health and social inequalities due to their selective uptake, unless they are coupled with broad public information campaigns and financial support for undertaking adaptive measures.

Food-borne disease and climate change in the United Kingdom

This review examined the likely impact of climate change upon food-borne disease in the UK using Campylobacter and Salmonella as example organisms. Campylobacter is an important food-borne disease and an increasing public health threat. There is a reasonable evidence base that the environment and weather play a role in its transmission to humans. However, uncertainty as to the precise mechanisms through which weather affects disease, make it difficult to assess the likely impact of climate change. There are strong positive associations between Salmonella cases and ambient temperature, and a clear understanding of the mechanisms behind this. However, because the incidence of Salmonella disease is declining in the UK, any climate change increases are likely to be small. For both Salmonella and Campylobacter the disease incidence is greatest in older adults and young children. There are many pathways through which climate change may affect food but only a few of these have been rigorously examined. This provides a high degree of uncertainty as to what the impacts of climate change will be. Food is highly controlled at the National and EU level. This provides the UK with resilience to climate change as well as potential to adapt to its consequences but it is unknown whether these are sufficient in the context of a changing climate.

Novel Sampling Method for Assessing Human-Pathogen Interactions in the Natural Environment Using Boot Socks and Citizen Scientists, with Application to Campylobacter Seasonality

This paper introduces a novel method for sampling pathogens in natural environments. It uses fabric boot socks worn over walkers' shoes to allow the collection of composite samples over large areas. Wide-area sampling is better suited to studies focusing on human exposure to pathogens (e.g., recreational walking). This sampling method is implemented using a citizen science approach: groups of three walkers wearing boot socks undertook one of six routes, 40 times over 16 months in the North West (NW) and East Anglian (EA) regions of England. To validate this methodology, we report the successful implementation of this citizen science approach, the observation that Campylobacter bacteria were detected on 47% of boot socks, and the observation that multiple boot socks from individual walks produced consistent results. The findings indicate higher Campylobacter levels in the livestock-dominated NW than in EA (55.8% versus 38.6%). Seasonal differences in the presence of Campylobacter bacteria were found between the regions, with indications of winter peaks in both regions but a spring peak in the NW. The presence of Campylobacter bacteria on boot socks was negatively associated with ambient temperature (P = 0.011) and positively associated with precipitation (P < 0.001), results consistent with our understanding of Campylobacter survival and the probability of material adhering to boot socks. Campylobacter jejuni was the predominant species found; Campylobacter coli was largely restricted to the livestock-dominated NW. Source attribution analysis indicated that the potential source of C. jejuni was predominantly sheep in the NW and wild birds in EA but did not differ between peak and nonpeak periods of human incidence.IMPORTANCE There is debate in the literature on the pathways through which pathogens are transferred from the environment to humans. We report on the success of a novel method for sampling human-pathogen interactions using boot socks and citizen science techniques, which enable us to sample human-pathogen interactions that may occur through visits to natural environments. This contrasts with traditional environmental sampling, which is based on spot sampling techniques and does not sample human-pathogen interactions. Our methods are of practical value to scientists trying to understand the transmission of pathogens from the environment to people. Our findings provide insight into the risk of Campylobacter exposure from recreational visits and an understanding of seasonal differences in risk and the factors behind these patterns. We highlight the Campylobacter species predominantly encountered and the potential sources of C. jejuni.

The recurrent campylobacteriosis epidemic over Christmas and New Year in European countries, 2006-2014

OBJECTIVE

Campylobacteriosis is the most frequently reported foodborne disease in Europe with a notification rate of 71 per 100,000 population in the European Union in 2014. Surveillance data show a clear seasonality whereby case numbers peak during summer months in entire Europe and at the turn of the year, especially in Germany and Switzerland. A detailed description of European surveillance data by country at the turn of the year was missing so far. The objectives of the presented work were to describe national surveillance data of The European Surveillance System for 14 countries during winter times and to generate hypotheses for the observed seasonality of campylobacteriosis cases.

RESULTS

The analysis included 317,986 cases notified between calendar weeks 45 and 8 of winter seasons 2006/2007-2013/2014. Winter peaks in weekly case notifications and notification rates were observed for Austria, Belgium, Finland, Germany, Luxembourg, The Netherlands, Switzerland and Sweden while for Denmark, France, Ireland, Italy, Norway and the United Kingdom no unusual increase was observed. Generally, weekly notification rates peaked in calendar week 1 or 2 after a strong decline in the last week of December and reached values of a multiple of the observed notification rates in the weeks before or after the peak e.g. up to 6.5 notifications per 100,000 population per week in Luxembourg. Disease onset of cases notified during winter peaks occurred predominantly in calendar weeks 52 and 1 and point towards risk exposures around Christmas and New Year. The consumption of meat fondue or table top grilling poses such a risk and is popular in many countries with an observed winter peak. Additionally, increased travel activities over the festive season could foster campylobacteriosis transmission. Surveillance artefacts (e.g. reporting delays due to public holidays) should be excluded as causes for country-specific winter peaks before investigating risk exposures.

A systematic review and meta-analysis on the incubation period of Campylobacteriosis

Accurate knowledge of pathogen incubation period is essential to inform public health policies and implement interventions that contribute to the reduction of burden of disease. The incubation period distribution of campylobacteriosis is currently unknown with several sources reporting different times. Variation in the distribution could be expected due to host, transmission vehicle, and organism characteristics, however, the extent of this variation and influencing factors are unclear. The authors have undertaken a systematic review of published literature of outbreak studies with well-defined point source exposures and human experimental studies to estimate the distribution of incubation period and also identify and explain the variation in the distribution between studies. We tested for heterogeneity using I 2 and Kolmogorov-Smirnov tests, regressed incubation period against possible explanatory factors, and used hierarchical clustering analysis to define subgroups of studies without evidence of heterogeneity. The mean incubation period of subgroups ranged from 2·5 to 4·3 days. We observed variation in the distribution of incubation period between studies that was not due to chance. A significant association between the mean incubation period and age distribution was observed with outbreaks involving only children reporting an incubation of 1·29 days longer when compared with outbreaks involving other age groups.