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Item Zoonotic transmission of asymptomatic carriage Staphylococcus aureus on dairy farms in Canterbury, New Zealand.(Microbiology Society, 2024-12-04) Straub C; Taylor W; French NP; Murdoch DR; Priest P; Anderson T; Scott PZoonotic pathogen transmission is of growing concern globally, with agricultural intensification facilitating interactions between humans, livestock and wild animals. Staphylococcus aureus is a major human pathogen, but it also causes mastitis in dairy cattle, leading to an economic burden on the dairy industry. Here, we investigated transmission within and between cattle and humans, including potential zoonotic transmission of S. aureus isolated from cattle and humans from three dairy farms and an associated primary school in New Zealand. Nasal swabs (N=170) were taken from healthy humans. Inguinal and combined nasal/inguinal swabs were taken from healthy cattle (N=1163). Whole-genome sequencing was performed for 96 S. aureus isolates (44 human and 52 cattle). Multilocus sequence typing and assessments of antimicrobial resistance and virulence were carried out. Potential within- and across-species transmission events were determined based on single nucleotide polymorphisms (SNPs). Thirteen potential transmission clusters were detected, with 12 clusters restricted to within-species and one potential zoonotic transmission cluster (ST5). Potential transmission among cattle was mostly limited to single age groups, likely because different age groups are managed separately on farms. While the prevalence of antimicrobial resistance (AMR) was low among both bovine and human isolates, the discovery of an extended-spectrum beta-lactamase gene (bla TEM-116) in a bovine isolate was concerning. This study provides evidence around frequency and patterns of potential transmission of S. aureus on dairy farms and highlights the AMR and virulence profile of asymptomatic carriage S. aureus isolates.Item Campylobacter colonization and undernutrition in infants in rural eastern Ethiopia - a longitudinal community-based birth cohort study.(Frontiers Media S.A., 2025-01-07) Chen D; McKune SL; Yang Y; Usmane IA; Ahmed IA; Amin JK; Ibrahim AM; Seran AJ; Shaik N; Ojeda A; Hassen BM; Deblais L; Ahmedo BU; Hassen KA; Bhrane M; Li X; Singh N; Roba KT; French NP; Rajashekara G; Manary MJ; Hassen JY; Havelaar AH; CAGED Research TeamBackground: Campylobacter is associated with environmental enteric dysfunction (EED) and malnutrition in children. Campylobacter infection could be a linchpin between livestock fecal exposure and health outcomes in low-resource smallholder settings. Methods: We followed a birth cohort of 106 infants in rural smallholder households in eastern Ethiopia up to 13 months of age. We measured anthropometry, surveyed sociodemographic determinants, and collected stool and urine samples. A short survey was conducted during monthly visits, infant stool samples were collected, and Campylobacter spp. was quantified using genus-specific qPCR. In month 13, we collected stool and urine samples to assay for EED biomarkers. We employed regression analyses to assess the associations of household determinants with Campylobacter colonization, EED, and growth faltering. Results: The Campylobacter load in infant stools increased with age. The mean length-for-age Z-score (LAZ) decreased from −0.45 at 3–4 months of age to −2.06 at 13 months, while the prevalence of stunting increased from 3 to 51%. The prevalence of EED at 13 months of age was 56%. A higher Campylobacter load was associated with more frequent diarrhea. Prelacteal feeding significantly increased Campylobacter load in the first month of life. Over the whole follow-up period, Campylobacter load was increased by keeping chickens unconfined at home and unsanitary disposal of infant stools while decreased by mothers’ handwashing with soap. Longitudinally, Campylobacter load was positively associated with food insecurity, introduction of complementary foods, and raw milk consumption. There were no significant associations between Campylobacter load, EED, and LAZ. Conclusion: This study found that most determinants associated with increased Campylobacter infection were related to suboptimal feeding practices and hygiene. The findings related to livestock-associated risks were inconclusive. Although stunting, EED, and Campylobacter prevalence rates all increased to high levels by the end of the first year of life, no significant association between them was identified. While additional research is needed to investigate whether findings from this study are replicable in other populations, community efforts to improve infant and young child feeding practices and food hygiene, and water, sanitation, and hygiene (WaSH) at the household level, could reduce (cross-)contamination at the point of exposure.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.Item Spread of Nontyphoidal Salmonella in the Beef Supply Chain in Northern Tanzania: Sensitivity in a Probabilistic Model Integrating Microbiological Data and Data from Stakeholder Interviews(Wiley Periodicals LLC on behalf of Society for Risk Analysis, 2022-05) Zadoks RN; Barker GC; Benschop J; Allan KJ; Chaters G; Cleaveland S; Crump JA; Davis MA; Mmbaga BT; Prinsen G; Thomas KM; Waldman L; French NPEast Africa is a hotspot for foodborne diseases, including infection by nontyphoidal Salmonella (NTS), a zoonotic pathogen that may originate from livestock. Urbanization and increased demand for animal protein drive intensification of livestock production and food processing, creating risks and opportunities for food safety. We built a probabilistic mathematical model, informed by prior beliefs and dedicated stakeholder interviews and microbiological research, to describe sources and prevalence of NTS along the beef supply chain in Moshi, Tanzania. The supply chain was conceptualized using a bow tie model, with terminal livestock markets as pinch point, and a forked pathway postmarket to compare traditional and emerging supply chains. NTS was detected in 36 (7.7%) of 467 samples throughout the supply chain. After combining prior belief and observational data, marginal estimates of true NTS prevalence were 4% in feces of cattle entering the beef supply and 20% in raw meat at butcheries. Based on our model and sensitivity analyses, true NTS prevalence was not significantly different between supply chains. Environmental contamination, associated with butchers and vendors, was estimated to be the most likely source of NTS in meat for human consumption. The model provides a framework for assessing the origin and propagation of NTS along meat supply chains. It can be used to inform decision making when economic factors cause changes in beef production and consumption, such as where to target interventions to reduce risks to consumers. Through sensitivity and value of information analyses, the model also helps to prioritize investment in additional research.Item Extended-spectrum β-lactamase- and AmpC β-lactamase-producing Enterobacterales associated with urinary tract infections in the New Zealand community: a case-control study(Elsevier Ltd on behalf of International Society for Infectious Diseases, 2023-03) Toombs-Ruane LJ; Marshall JC; Benschop J; Drinković D; Midwinter AC; Biggs PJ; Grange Z; Baker MG; Douwes J; Roberts MG; French NP; Burgess SAOBJECTIVES: To assess whether having a pet in the home is a risk factor for community-acquired urinary tract infections associated with extended-spectrum β-lactamase (ESBL)- or AmpC β-lactamase (ACBL)- producing Enterobacterales. METHODS: An unmatched case-control study was conducted between August 2015 and September 2017. Cases (n = 141) were people with community-acquired urinary tract infection (UTI) caused by ESBL- or ACBL-producing Enterobacterales. Controls (n = 525) were recruited from the community. A telephone questionnaire on pet ownership and other factors was administered, and associations were assessed using logistic regression. RESULTS: Pet ownership was not associated with ESBL- or ACBL-producing Enterobacterales-related human UTIs. A positive association was observed for recent antimicrobial treatment, travel to Asia in the previous year, and a doctor's visit in the last 6 months. Among isolates with an ESBL-/ACBL-producing phenotype, 126/134 (94%) were Escherichia coli, with sequence type 131 being the most common (47/126). CONCLUSIONS: Companion animals in the home were not found to be associated with ESBL- or ACBL-producing Enterobacterales-related community-acquired UTIs in New Zealand. Risk factors included overseas travel, recent antibiotic use, and doctor visits.