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Item Source attribution of campylobacteriosis in Australia, 2017-2019.(John Wiley and Sons, Inc., 2023-12-01) McLure A; Smith JJ; Firestone SM; Kirk MD; French N; Fearnley E; Wallace R; Valcanis M; Bulach D; Moffatt CRM; Selvey LA; Jennison A; Cribb DM; Glass KCampylobacter jejuni and Campylobacter coli infections are the leading cause of foodborne gastroenteritis in high-income countries. Campylobacter colonizes a variety of warm-blooded hosts that are reservoirs for human campylobacteriosis. The proportions of Australian cases attributable to different animal reservoirs are unknown but can be estimated by comparing the frequency of different sequence types in cases and reservoirs. Campylobacter isolates were obtained from notified human cases and raw meat and offal from the major livestock in Australia between 2017 and 2019. Isolates were typed using multi-locus sequence genotyping. We used Bayesian source attribution models including the asymmetric island model, the modified Hald model, and their generalizations. Some models included an "unsampled" source to estimate the proportion of cases attributable to wild, feral, or domestic animal reservoirs not sampled in our study. Model fits were compared using the Watanabe-Akaike information criterion. We included 612 food and 710 human case isolates. The best fitting models attributed >80% of Campylobacter cases to chickens, with a greater proportion of C. coli (>84%) than C. jejuni (>77%). The best fitting model that included an unsampled source attributed 14% (95% credible interval [CrI]: 0.3%-32%) to the unsampled source and only 2% to ruminants (95% CrI: 0.3%-12%) and 2% to pigs (95% CrI: 0.2%-11%) The best fitting model that did not include an unsampled source attributed 12% to ruminants (95% CrI: 1.3%-33%) and 6% to pigs (95% CrI: 1.1%-19%). Chickens were the leading source of human Campylobacter infections in Australia in 2017-2019 and should remain the focus of interventions to reduce burden.Item Genomic and clinical characteristics of campylobacteriosis in Australia.(Microbiology Society, 2024-01) Cribb DM; Moffatt CRM; Wallace RL; McLure AT; Bulach D; Jennison AV; French N; Valcanis M; Glass K; Kirk MDCampylobacter spp. are a common cause of bacterial gastroenteritis in Australia, primarily acquired from contaminated meat. We investigated the relationship between genomic virulence characteristics and the severity of campylobacteriosis, hospitalisation, and other host factors.We recruited 571 campylobacteriosis cases from three Australian states and territories (2018-2019). We collected demographic, health status, risk factors, and self-reported disease data. We whole genome sequenced 422 C. jejuni and 84 C. coli case isolates along with 616 retail meat isolates. We classified case illness severity using a modified Vesikari scoring system, performed phylogenomic analysis, and explored risk factors for hospitalisation and illness severity.On average, cases experienced a 7.5 day diarrhoeal illness with additional symptoms including stomach cramps (87.1 %), fever (75.6 %), and nausea (72.0 %). Cases aged ≥75 years had milder symptoms, lower Vesikari scores, and higher odds of hospitalisation compared to younger cases. Chronic gastrointestinal illnesses also increased odds of hospitalisation. We observed significant diversity among isolates, with 65 C. jejuni and 21 C. coli sequence types. Antimicrobial resistance genes were detected in 20.4 % of isolates, but multidrug resistance was rare (0.04 %). Key virulence genes such as cdtABC (C. jejuni) and cadF were prevalent (>90 % presence) but did not correlate with disease severity or hospitalisation. However, certain genes (e.g. fliK, Cj1136, and Cj1138) appeared to distinguish human C. jejuni cases from food source isolates.Campylobacteriosis generally presents similarly across cases, though some are more severe. Genotypic virulence factors identified in the literature to-date do not predict disease severity but may differentiate human C. jejuni cases from food source isolates. Host factors like age and comorbidities have a greater influence on health outcomes than virulence factors.Item 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.(Public Library of Science (PLoS), 2024-01-18) Lo Iacono G; Cook AJC; Derks G; Fleming LE; French N; Gillingham EL; Gonzalez Villeta LC; Heaviside C; La Ragione RM; Leonardi G; Sarran CE; Vardoulakis S; Senyah F; van Vliet AHM; Nichols G; Vega NDisentangling 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.Item Dientamoeba fragilis associated with microbiome diversity changes in acute gastroenteritis patients.(Elsevier B.V., 2023-12-01) Muhsin-Sharafaldine M-R; Abdel Rahman L; Suwanarusk R; Grant J; Parslow G; French N; Tan KSW; Russell B; Morgan XC; Ussher JEThis study examined the correlation between intestinal protozoans and the bacterial microbiome in faecal samples collected from 463 patients in New Zealand who were diagnosed with gastroenteritis. In comparison to traditional microscopic diagnosis methods, Multiplexed-tandem PCR proved to be more effective in detecting intestinal parasites. Among the identified protozoans, Blastocystis sp. and Dientamoeba fragilis were the most prevalent. Notably, D. fragilis was significantly associated with an increase in the alpha-diversity of host prokaryotic microbes. Although the exact role of Blastocystis sp. and D. fragilis as the primary cause of gastroenteritis remains debatable, our data indicates a substantial correlation between these protozoans and the prokaryote microbiome of their hosts, particularly when compared to other protists or patients with gastroenteritis but no detectable parasitic cause. These findings underscore the significance of comprehending the contributions of intestinal protozoans, specifically D. fragilis, to the development of gastroenteritis and their potential implications for disease management.Item The impact of primary and secondary processing steps on Campylobacter concentrations on chicken carcasses and portions(Elsevier Ltd, 2023-04) Kingsbury JM; Horn B; Armstrong B; Midwinter A; Biggs P; Callander M; Mulqueen K; Brooks M; van der Logt P; Biggs RCampylobacteriosis is the most commonly notified foodborne disease in New Zealand and poultry meat is the major source for human infection. Carcasses and portions were sampled from key points along primary and secondary processing chains of three New Zealand poultry processors to determine the impact of processing steps on Campylobacter concentrations. Primary processing reduced Campylobacter concentrations on carcasses by almost 6-log; the biggest reduction was achieved by the spinchill, followed by the scald step. Significant plant differences in the degree of Campylobacter reduction were also observed at these steps. The spinchill and final acidified sodium chlorite wash resulted in carcasses with low-to-no levels of Campylobacter regardless of concentrations at prior steps. A similar study was conducted at primary processing for one plant in 2013; significant improvements in Campylobacter mitigation since 2013 were noted. Campylobacter concentrations from final product from secondary processing were higher than concentrations at the end of primary processing. Drumsticks had lower Campylobacter concentrations than other portion types. Skin removal from product did not consistently result in product with lower Campylobacter concentrations. Results identify key areas to target for further reduction of Campylobacter on poultry meat, and provide a benchmark to compare the efficacy of future interventions.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 Gastrointestinal infection in a New Zealand community : a one year study : a thesis presented in fulfilment of the requirements for the degree of Master of Science in Microbiology at Massey University(Massey University, 1996) Wright, Jacqueline MargaretDiagnostic medical microbiology laboratories detect and identify pathogens in submitted specimens. The techniques used should maximise the detection of pathogens (sensitivity) while minimising the number of tests for their detection (efficiency). To achieve the best compromise between sensitivity and efficiency, it is necessary to have information on both the relative prevalence and clinical importance of various pathogens within the relevant community, and the relative efficiency of various detection techniques. This investigation had three primary objectives: to establish what pathogens were associated with community-acquired gastrointestinal symptoms in the Eastern Bay of Plenty, and the incidence and relative importance of each; to compare the merits of various methods for detecting these pathogens (in those cases where more than one method was available); and to collect data from patients so as to identify potential sources and/or risk factors for infection. 997 faecal specimens from 716 episodes of illness were tested over a one year period. Patients completed a questionnaire on symptoms, and food and environmental exposures. Using one or more standard techniques, the specimens were tested for bacteria and parasites which may cause gastroenteritis. Specimens from young children were also tested for the presence of rotavirus. The incidence rates of the various pathogens, expressed as a rate per 100 000 persons per year, were as follows: Blastocystis hominis, 358; Campylobacter species, 208; Giardia lamblia, 158; Yersinia species, 87; Cryptosporidium parvum, 67; Salmonella species, 62; Aeromonas species, 62; Dientamoeba fragilis, 29; Plesiomonas shigelloides, 21; Escherichia coli (E coli) O157, 4; Vibrio cholerae non-O1, non-O139, 4; and Shigella species < 4. Faecal specimen macroscopic form, microscopic findings, season, and patient age showed little correlation with the presence of specific pathogens. Consequently the tests selected for the detection of pathogens in faeces should not be based on any of the above parameters. Furthermore, the symptoms associated with parasitic and bacterial infections were similar, so it is not possible to select the appropriate tests on this basis. The presence of rotavirus in patients older than five years was not investigated so incidence in the general population can not be calculated. A study of all age groups for the presence of this organism would be appropriate. From the above findings, and an evaluation of the literature, it is recommended that all specimens should be examined for the following organisms and, on the basis of our observations, the most cost-effective method is shown in brackets: Salmonella (selenite enrichment subcultured to xylose lysine desoxycholate agar); Shigella (none were detected, so a cost-effective medium could not be determined), Campylobacter (5% sheep blood agar supplemented with 32 mg/1 cefoperazone); Yersinia (Yersinia selective agar (YSA), plus selenite enrichment subcultured to YSA); Giardia lamblia (detection of antigen); Cryptosporidium parvum (detection of antigen). While routine testing for E coli O157 is not recommended, laboratories should have the capability to test for this pathogen if a patient presents with haemolytic uraemic syndrome, thrombotic thrombocytopenic purpura or unexplained bloody diarrhoea. Likewise, routine culture for Vibrio species is not recommended; however, laboratories should test specimens using thiosulphate citrate bilesalt sucrose agar if the requesting clinician suspects cholera, or the patient has a recent history of shellfish consumption. A trichome stain for Dientamoeba fragilis is recommended for patients with chronic gastrointestinal symptoms who are to be investigated for neoplastic and other non-infectious conditions. Pathogenic parasites other than those noted above were not detected. However, since such organisms are isolated in New Zealand, usually in association with overseas travel or institutionalisation, it is recommended that a trichrome stain and a faecal concentration technique should be performed on specimens from all cases of gastroenteritis who have recently travelled overseas or who are institutionalised. Close liaison between the laboratory and the clinician is essential to ensure appropriate selective testing for these less common pathogens. The presence of Blastocystis hominis and Aeromonads should be reported, but the report should note that their pathogenicity is uncertain. Dientamoeba fragilis and Plesiomonas shigelloides are probably pathogenic, but further work is needed to clarify this point. Correlation of data from the questionnaires and the laboratory findings identified the following risk factors: (the relative risk, 95% confidence interval and p-value are shown in the brackets). Campylobacter species: consumption of unpasteurised milk (4.67,2.39 - 9.11, p = <0.001); Salmonella species: overseas travel (7.20, 1.67 - 20.9, p = 0.040), eating a barbecued meal (4.55, 1.37 - 15.12, p = 0.026), eating shellfish (3.80, 1.18 - 12.21, p = 0.032); Yersinia species: consumption of water from a home supply (3.46, 1.32 - 9.10, p = 0.016), handling cattle (4.88, 1.73 - 13.76, p = 0.008), handling sheep (14.80. 4.93 - 44.46, p = 0.001); Giardia lamblia: consumption of unpasteurised milk (3.93, 1.63 - 9.46, p = 0.011), attendance at a day care centre (2.70, 1.17 - 6.27, p = 0.033), handling cattle (3.39, 1.59 - 7.22, p = 0.005), handling horses (5.27, 1.85 - 14.97, p = 0.002); Cryptosporidium parvum: consumption of water from a home supply (5.08, 1.88 - 13.71, p = 0.002), consumption of unboiled water from a natural waterway (3.97, 1.29 - 12.24, p = 0.031), attendance at a day care centre (3.30, 1.06 - 10.22, p = 0.054), handling cattle (5.41, 1.88 - 15.58, p = 0.006), owning a cat (4.50,1.02 - 19.91, p = 0.029); Plesiomonas shigelloides: eating shellfish (13.67, 1.44 - 130.13, p = 0.020); and Dientamoeba fragilis: consumption of unboiled water from a natural waterway (7.46, 1.71 - 32.48, p = 0.019). The risk factors suggest the value of the following precautions to prevent gastrointestinal infection: maintaining a high standard of both personal hygiene (particularly in the rural environment) and environmental hygiene in areas that food is prepared; avoiding consumption of untreated water or unpasteurised milk; cooking animal-derived food thoroughly - especially barbecued food and shellfish; and washing hands thoroughly after animal contact. Persons with diarrhoeal symptoms should take particular care with personal hygiene. Those travelling overseas should be conscious of the risk associated with the consumption of food and water which is not properly cooked or treated. These findings should assist New Zealand laboratories to optimise their approach to the detection of faecal pathogens and should also assist in formulating policy for prevention of infection by enteric pathogens.