Journal Articles
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Item Transmission pathways of Campylobacter jejuni between humans and livestock in rural Ethiopia are highly complex and interdependent(BioMed Central Limited, London, United Kingdom, 2025-12-01) Singh N; Thystrup CAN; Hassen BM; Bhandari M; Rajashekara G; Hald TM; Manary MJ; McKune SL; Hassen JY; Smith HL; Marshall JC; French NP; Havelaar AH; Mekuria ZH; Weldesenbet YD; Yang Y; Li X; Gebreyes W; Shaikh N; Bhrane M; Dawid MM; Usmail MM; Deblais L; Mechlowitz K; Umer KA; Roba KT; Hassen KA; Amin JK; Usmane IA; Ahmed IA; Yimer G; Yusuf EA; Chen D; Saleem C; Ahmedo BU; Ojeda AE; Ibrahim AM; Seran AJBackground: Campylobacter jejuni and C. coli are the most common causes of bacterial enteritis worldwide whereas symptomatic and asymptomatic infections are associated with stunting in children in low- and middle-income countries. Little is known about their sources and transmission pathways in low- and middle-income countries, and particularly for infants and young children. We assessed the genomic diversity of C. jejuni in Eastern Ethiopia to determine the attribution of infections in infants under 1 year of age to livestock (chickens, cattle, goats and sheep) and other humans (siblings, mothers). Results: Among 287 C. jejuni isolates, 48 seven-gene sequence types (STs), including 11 previously unreported STs were identified. Within an ST, the core genome STs of multiple isolates differed in fewer than five alleles. Many of these isolates do not belong to the most common STs reported in high-resource settings, and of the six most common global STs, only ST50 was found in our study area. Isolates from the same infant sample were closely related, while those from consecutive infant samples often displayed different STs, suggesting rapid clearance and new infection. Four different attribution models using different genomic profiling methods, assumptions and estimation methods predicted that chickens are the primary reservoir for infant infections. Infections from chickens are transmitted with or without other humans (mothers, siblings) as intermediate sources. Model predictions differed in terms of the relative importance of cattle versus small ruminants as additional sources. Conclusions: The transmission pathways of C. jejuni in our study area are highly complex and interdependent. While chickens are the most important reservoir of C. jejuni, ruminant reservoirs also contribute to the infections. The currently nonculturable species Candidatus C. infans is also highly prevalent in infants and is likely anthroponotic. Efforts to reduce the colonization of infants with Campylobacter and ultimately stunting in low-resource settings are best aimed at protecting proximate sources such as caretakers’ hands, food and indoor soil through tight integration of the currently siloed domains of nutrition, food safety and water, sanitation and hygiene.Item Genomic diversity of Campylobacter jejuni and Campylobacter coli isolates recovered from human and poultry in Australia and New Zealand, 2017 to 2019.(Microbiology Society, 2024-11-05) Cribb DM; Biggs PJ; McLure AT; Wallace RL; French NP; Glass K; Kirk MDWe used genomic and epidemiological data to assess and compare the population structure and origins of Campylobacter, a major foodborne pathogen, in two neighbouring countries with strong trade and cultural links, similar poultry production systems and frequent movement of people and food products. The most common sequence types (STs) differed between Australia and New Zealand, with many unique to each country. Over half of all STs were represented by a single isolate. Multidrug-resistant (MDR) genotypes were detected in 0.8% of all samples, with no MDR isolates detected in poultry. Quinolone and tetracycline resistant ST6964 was prevalent in New Zealand (10.6% of C. jejuni). Closely related isolates suggested some similar food sources or contacts. We have shown that there is little genetic overlap in human and poultry STs of Campylobacter between the countries, which highlights that this common foodborne pathogen has domestic origins in Australia and New Zealand.Item Population Structure and Antimicrobial Resistance in Campylobacter jejuni and C. coli Isolated from Humans with Diarrhea and from Poultry, East Africa.(Centers for Disease Control and Prevention, 2024-10) French NP; Thomas KM; Amani NB; Benschop J; Bigogo GM; Cleaveland S; Fayaz A; Hugho EA; Karimuribo ED; Kasagama E; Maganga R; Melubo ML; Midwinter AC; Mmbaga BT; Mosha VV; Mshana FI; Munyua P; Ochieng JB; Rogers L; Sindiyo E; Swai ES; Verani JR; Widdowson M-A; Wilkinson DA; Kazwala RR; Crump JA; Zadoks RNCampylobacteriosis and antimicrobial resistance (AMR) are global public health concerns. Africa is estimated to have the world's highest incidence of campylobacteriosis and a relatively high prevalence of AMR in Campylobacter spp. from humans and animals. Few studies have compared Campylobacter spp. isolated from humans and poultry in Africa using whole-genome sequencing and antimicrobial susceptibility testing. We explored the population structure and AMR of 178 Campylobacter isolates from East Africa, 81 from patients with diarrhea in Kenya and 97 from 56 poultry samples in Tanzania, collected during 2006-2017. Sequence type diversity was high in both poultry and human isolates, with some sequence types in common. The estimated prevalence of multidrug resistance, defined as resistance to >3 antimicrobial classes, was higher in poultry isolates (40.9%, 95% credible interval 23.6%-59.4%) than in human isolates (2.5%, 95% credible interval 0.3%-6.8%), underlining the importance of antimicrobial stewardship in livestock systems.Item Risk factors for campylobacteriosis in Australia: outcomes of a 2018-2019 case-control study(BioMed Central Ltd, 2022-12) Cribb DM; Varrone L; Wallace RL; McLure AT; Smith JJ; Stafford RJ; Bulach DM; Selvey LA; Firestone SM; French NP; Valcanis M; Fearnley EJ; Sloan-Gardner TS; Graham T; Glass K; Kirk MDBACKGROUND: We aimed to identify risk factors for sporadic campylobacteriosis in Australia, and to compare these for Campylobacter jejuni and Campylobacter coli infections. METHODS: In a multi-jurisdictional case-control study, we recruited culture-confirmed cases of campylobacteriosis reported to state and territory health departments from February 2018 through October 2019. We recruited controls from notified influenza cases in the previous 12 months that were frequency matched to cases by age group, sex, and location. Campylobacter isolates were confirmed to species level by public health laboratories using molecular methods. We conducted backward stepwise multivariable logistic regression to identify significant risk factors. RESULTS: We recruited 571 cases of campylobacteriosis (422 C. jejuni and 84 C. coli) and 586 controls. Important risk factors for campylobacteriosis included eating undercooked chicken (adjusted odds ratio [aOR] 70, 95% CI 13-1296) or cooked chicken (aOR 1.7, 95% CI 1.1-2.8), owning a pet dog aged < 6 months (aOR 6.4, 95% CI 3.4-12), and the regular use of proton-pump inhibitors in the 4 weeks prior to illness (aOR 2.8, 95% CI 1.9-4.3). Risk factors remained similar when analysed specifically for C. jejuni infection. Unique risks for C. coli infection included eating chicken pâté (aOR 6.1, 95% CI 1.5-25) and delicatessen meats (aOR 1.8, 95% CI 1.0-3.3). Eating any chicken carried a high population attributable fraction for campylobacteriosis of 42% (95% CI 13-68), while the attributable fraction for proton-pump inhibitors was 13% (95% CI 8.3-18) and owning a pet dog aged < 6 months was 9.6% (95% CI 6.5-13). The population attributable fractions for these variables were similar when analysed by campylobacter species. Eating delicatessen meats was attributed to 31% (95% CI 0.0-54) of cases for C. coli and eating chicken pâté was attributed to 6.0% (95% CI 0.0-11). CONCLUSIONS: The main risk factor for campylobacteriosis in Australia is consumption of chicken meat. However, contact with young pet dogs may also be an important source of infection. Proton-pump inhibitors are likely to increase vulnerability to infection.Item Transmission dynamics of an antimicrobial resistant Campylobacter jejuni lineage in New Zealand’s commercial poultry network(Elsevier B.V, 2021-12) Greening SS; Zhang J; Midwinter AC; Wilkinson DA; Fayaz A; Williamson DA; Anderson MJ; Gates MC; French NPUnderstanding the relative contribution of different between-farm transmission pathways is essential in guiding recommendations for mitigating disease spread. This study investigated the association between contact pathways linking poultry farms in New Zealand and the genetic relatedness of antimicrobial resistant Campylobacter jejuni Sequence Type 6964 (ST-6964), with the aim of identifying the most likely contact pathways that contributed to its rapid spread across the industry. Whole-genome sequencing was performed on 167C. jejuni ST-6964 isolates sampled from across 30 New Zealand commercial poultry enterprises. The genetic relatedness between isolates was determined using whole genome multilocus sequence typing (wgMLST). Permutational multivariate analysis of variance and distance-based linear models were used to explore the strength of the relationship between pairwise genetic associations among the C. jejuni isolates and each of several pairwise distance matrices, indicating either the geographical distance between farms or the network distance of transportation vehicles. Overall, a significant association was found between the pairwise genetic relatedness of the C. jejuni isolates and the parent company, the road distance and the network distance of transporting feed vehicles. This result suggests that the transportation of feed within the commercial poultry industry as well as other local contacts between flocks, such as the movements of personnel, may have played a significant role in the spread of C. jejuni. However, further information on the historical contact patterns between farms is needed to fully characterise the risk of these pathways and to understand how they could be targeted to reduce the spread of C. jejuni.