Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
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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 Lost in the Forest: Encoding categorical variables and the absent levels problem(Springer Nature, 2024-04-10) Smith HL; Biggs PJ; French NP; Smith ANH; Marshall JC; Gama JLevels of a predictor variable that are absent when a classification tree is grown can not be subject to an explicit splitting rule. This is an issue if these absent levels are present in a new observation for prediction. To date, there remains no satisfactory solution for absent levels in random forest models. Unlike missing data, absent levels are fully observed and known. Ordinal encoding of predictors allows absent levels to be integrated and used for prediction. Using a case study on source attribution of Campylobacter species using whole genome sequencing (WGS) data as predictors, we examine how target-agnostic versus target-based encoding of predictor variables with absent levels affects the accuracy of random forest models. We show that a target-based encoding approach using class probabilities, with absent levels designated the highest rank, is systematically biased, and that this bias is resolved by encoding absent levels according to the a priori hypothesis of equal class probability. We present a novel method of ordinal encoding predictors via principal coordinates analysis (PCO) which capitalizes on the similarity between pairs of predictor levels. Absent levels are encoded according to their similarity to each of the other levels in the training data. We show that the PCO-encoding method performs at least as well as the target-based approach and is not biased.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 Genomic adaptations of Campylobacter jejuni to long-term human colonization(BioMed Central Ltd, 2021-12-10) Bloomfield SJ; Midwinter AC; Biggs PJ; French NP; Marshall JC; Hayman DTS; Carter PE; Mather AE; Fayaz A; Thornley C; Kelly DJ; Benschop JBACKGROUND: Campylobacter is a genus of bacteria that has been isolated from the gastrointestinal tract of humans and animals, and the environments they inhabit around the world. Campylobacter adapt to new environments by changes in their gene content and expression, but little is known about how they adapt to long-term human colonization. In this study, the genomes of 31 isolates from a New Zealand patient and 22 isolates from a United Kingdom patient belonging to Campylobacter jejuni sequence type 45 (ST45) were compared with 209 ST45 genomes from other sources to identify the mechanisms by which Campylobacter adapts to long-term human colonization. In addition, the New Zealand patient had their microbiota investigated using 16S rRNA metabarcoding, and their level of inflammation and immunosuppression analyzed using biochemical tests, to determine how Campylobacter adapts to a changing gastrointestinal tract. RESULTS: There was some evidence that long-term colonization led to genome degradation, but more evidence that Campylobacter adapted through the accumulation of non-synonymous single nucleotide polymorphisms (SNPs) and frameshifts in genes involved in cell motility, signal transduction and the major outer membrane protein (MOMP). The New Zealand patient also displayed considerable variation in their microbiome, inflammation and immunosuppression over five months, and the Campylobacter collected from this patient could be divided into two subpopulations, the proportion of which correlated with the amount of gastrointestinal inflammation. CONCLUSIONS: This study demonstrates how genomics, phylogenetics, 16S rRNA metabarcoding and biochemical markers can provide insight into how Campylobacter adapts to changing environments within human hosts. This study also demonstrates that long-term human colonization selects for changes in Campylobacter genes involved in cell motility, signal transduction and the MOMP; and that genetically distinct subpopulations of Campylobacter evolve to adapt to the changing gastrointestinal environment.Item Lost in the Forest(Cold Spring Harbor Laboratory, 2022) Smith HL; Biggs PJ; French NP; Smith ANH; Marshall JCTo date, there remains no satisfactory solution for absent levels in random forest models. Absent levels are levels of a predictor variable encountered during prediction for which no explicit rule exists. Imposing an order on nominal predictors allows absent levels to be integrated and used for prediction. The ordering of predictors has traditionally been via class probabilities with absent levels designated the lowest order. Using a combination of simulated data and pathogen source-attribution models using whole-genome sequencing data, we examine how the method of ordering predictors with absent levels can (i) systematically bias a model, and (ii) affect the out-of-bag error rate. We show that the traditional approach is systematically biased and underestimates out-of-bag error rates, and that this bias is resolved by ordering absent levels according to the a priori hypothesis of equal class probability. We present a novel method of ordering predictors via principal coordinates analysis (PCO) which capitalizes on the similarity between pairs of predictor levels. Absent levels are designated an order according to their similarity to each of the other levels in the training data. We show that the PCO method performs at least as well as the traditional approach of ordering and is not biased.