Journal Articles

Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915

Browse

Filters

2017 - 201912020 - 202521

Settings

Author: search.filters.author.Marshall JCHas files: Yes

Search Results

Now showing 1 - 10 of 23
  • Thumbnail Image
    Item
    Spatial risk of pathogen transmission from cattle to vulnerable and endangered wild bovids in Thailand
    (Wiley Periodicals LLC on behalf of Society for Conservation Biology, 2025-08-12) Horpiencharoen W; Marshall JC; Muylaert RL; John RS; Hayman DTS
    The interaction between livestock and wildlife causes challenges for wildlife conservation and public health. Mapping interface areas is essential for prioritizing disease surveillance, implementing mitigation measures, and developing targeted control programs to protect threatened wildlife. We used spatial overlays of habitat suitability to predict interface areas with high risk of pathogen transmission for three Thai wild bovids (gaur [Bos gaurus], banteng [Bos javanicus] and wild water buffalo [Bubalus arnee]) and domestic cattle. We assumed that domestic cattle are the reservoir of important bovine infectious diseases and that high cattle density is a proxy for a higher transmission risk. We calculated the interface inside and outside Thai protected areas and classified these by land use types. Then, we counted the number of bovine infectious disease occurrences reported in high-risk areas. Our study indicated that the highest risk areas for these species are at the forest edges where high habitat suitability and cattle densities overlap. Suitable habitats for wild water buffalo had the largest proportion of high-risk areas (9%), while gaur and banteng had similar risk areas (4%). Kuiburi National Park had the largest risk area (274 km2) for gaur and banteng, whereas the largest risk area for wild water buffalo overlapped with Huai Thabthan-Had Samran by 126 km2. Cropland and unclassified forests had the highest percentage of interface areas, indicating a higher risk of pathogen transmission. Our results highlight how habitat suitability analyses could help infectious disease prevention and control strategies and may also support wild bovid conservation initiatives.
  • Thumbnail Image
    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 AJ
    Background: 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.
  • Thumbnail Image
    Item
    Investigating animals and environments in contact with leptospirosis patients in Aotearoa New Zealand reveals complex exposure pathways.
    (Taylor and Francis Group, 2025-02-12) Benschop J; Collins-Emerson JM; Vallee E; Prinsen G; Yeung P; Wright J; Littlejohn S; Douwes J; Fayaz A; Marshall JC; Baker MG; Quin T; Nisa S
    CASE HISTORY: Three human leptospirosis cases from a case-control study were recruited for in-contact animal and environment sampling and Leptospira testing between October 2020 and December 2021. These cases were selected because of regular exposure to livestock, pets, and/or wildlife, and sampling was carried out on their farms or lifestyle blocks (sites A-C), with veterinarians overseeing the process for livestock, and cases collecting environmental and wildlife samples. LABORATORY FINDINGS: Across the three sites, a total of 137 cattle, > 40 sheep, 28 possums, six dogs, six rats, three pigs and three rabbits were tested. Herd serology results on Site A, a dairy farm, showed infection with Tarassovi and Pomona; urinary shedding showed Leptospira borgpetersenii str. Pacifica. Animals were vaccinated against Hardjo, Pomona and Copenhageni. The farmer was diagnosed with Ballum. On Site B, a beef and sheep farm, serology showed infection with Pomona; animals were not vaccinated, and the farmer was diagnosed with Hardjo. On Site C, cattle were shedding L. borgpetersenii; animals were not vaccinated, and the case's serovar was indeterminate. Six wild animals associated with Sites A and C and one environmental sample from Site A were positive for pathogenic Leptospira by PCR. CONCLUSION: These findings highlight the complexity of potential exposures and the difficulty in identifying infection sources for human cases. This reinforces the need for multiple preventive measures such as animal vaccination, the use of personal protective equipment, pest control, and general awareness of leptospirosis to reduce infection risk in agricultural settings. CLINICAL RELEVANCE: Farms with unvaccinated livestock had Leptospira infections, highlighting the importance of animal vaccination. Infections amongst stock that were vaccinated emphasise the importance of best practice vaccination recommendations and pest control. Abbreviations: MAT: Microscopic agglutination test; PIC: Person in charge; PPE: Personalprotective equipment
  • Thumbnail Image
    Item
    Impact of Infectious Diseases on Wild Bovidae Populations in Thailand: Insights from Population Modelling and Disease Dynamics
    (2023-08-31) Horpiencharoen W; Marshall JC; Muylaert RL; John RS; Hayman DTS
  • Thumbnail Image
    Item
    Mapping threatened Thai bovids provides opportunities for improved conservation outcomes in Asia
    (2023-08-27) Horpiencharoen W; Muylaert RL; Marshall JC; John RS; Lynam AJ; Riggio A; Godfrey A; Ngoprasert D; Gale GA; Ash E; Bisi F; Cremonesi G; Clements GR; Yindee M; Shwe NM; Pin C; Gray TNE; Aung SS; Nakbun S; Manka SG; Steinmetz R; Phoonjampa R; Seuaturien N; Phumanee W; Hayman DTS
  • Thumbnail Image
    Item
    New Campylobacter Lineages in New Zealand Freshwater: Pathogenesis and Public Health Implications
    (John Wiley and Sons, 2024-12) Cookson AL; Burgess S; Midwinter AC; Marshall JC; Moinet M; Rogers L; Fayaz A; Biggs PJ; Brightwell G
    This study investigated the diversity of thermophilic Campylobacter species isolated from three New Zealand freshwater catchments affected by pastoral and urban activities. Utilising matrix-assisted laser desorption ionisation-time of flight and whole genome sequence analysis, the study identified Campylobacter jejuni (n = 46, 46.0%), C. coli (n = 39, 39%), C. lari (n = 4, 4.0%), and two novel Campylobacter species lineages (n = 11, 11%). Core genome sequence analysis provided evidence of prolonged persistence or continuous faecal shedding of closely related strains. The C. jejuni isolates displayed distinct sequence types (STs) associated with human, ruminant, and environmental sources, whereas the C. coli STs included waterborne ST3302 and ST7774. Recombination events affecting loci implicated in human pathogenesis and environmental persistence were observed, particularly in the cdtABC operon (encoding the cytolethal distending toxin) of non-human C. jejuni STs. A low diversity of antimicrobial resistance genes (aadE-Cc in C. coli), with genotype/phenotype concordance for tetracycline resistance (tetO) in three ST177 isolates, was noted. The data suggest the existence of two types of naturalised waterborne Campylobacter: environmentally persistent strains originating from waterbirds and new environmental species not linked to human campylobacteriosis. Identifying and understanding naturalised Campylobacter species is crucial for accurate waterborne public health risk assessments and the effective allocation of resources for water quality management.
  • Thumbnail Image
    Item
    Out of (the) bag—encoding categorical predictors impacts out-of-bag samples
    (PeerJ Inc., 2024-01-01) Smith HL; Biggs PJ; French NP; Smith ANH; Marshall JC; Aleem M
    Performance of random forest classification models is often assessed and interpreted using out-of-bag (OOB) samples. Observations which are OOB when a tree is trained may serve as a test set for that tree and predictions from the OOB observations used to calculate OOB error and variable importance measures (VIM). OOB errors are popular because they are fast to compute and, for large samples, are a good estimate of the true prediction error. In this study, we investigate how target-based vs. target-agnostic encoding of categorical predictor variables for random forest can bias performance measures based on OOB samples. We show that, when categorical variables are encoded using a target-based encoding method, and when the encoding takes place prior to bagging, the OOB sample can underestimate the true misclassification rate, and overestimate variable importance. We recommend using a separate test data set when evaluating variable importance and/or predictive performance of tree based methods that utilise a target-based encoding method.
  • Thumbnail Image
    Item
    Mapping threatened Thai bovids provides opportunities for improved conservation outcomes in Asia.
    (The Royal Society, 2024-09-25) Horpiencharoen W; Muylaert RL; Marshall JC; John RS; Lynam AJ; Riggio A; Godfrey A; Ngoprasert D; Gale GA; Ash E; Bisi F; Cremonesi G; Clements GR; Yindee M; Shwe NM; Pin C; Gray TNE; Aung SS; Nakbun S; Manka SG; Steinmetz R; Phoonjampa R; Seuaturien N; Phumanee W; Hayman DTS
    Wild bovids provide important ecosystem functions as seed dispersers and vegetation modifiers. Five wild bovids remain in Thailand: gaur (Bos gaurus), banteng (Bos javanicus), wild water buffalo (Bubalus arnee), mainland serow (Capricornis sumatraensis) and Chinese goral (Naemorhedus griseus). Their populations and habitats have declined substantially and become fragmented by land-use change. We use ecological niche models to quantify how much potential suitable habitat for these species remains within protected areas in Asia and then specifically Thailand. We combined species occurrence data from several sources (e.g. mainly camera traps and direct observation) with environmental variables and species-specific and single, large accessible areas in ensemble models to generate suitability maps, using out-of-sample predictions to validate model performance against new independent data. Gaur, banteng and buffalo models showed reasonable model accuracy throughout the entire distribution (greater than or equal to 62%) and in Thailand (greater than or equal to 80%), whereas serow and goral models performed poorly for the entire distribution and in Thailand, though 5 km movement buffers markedly improved the performance for serow. Large suitable areas were identified in Thailand and India for gaur, Cambodia and Thailand for banteng and India for buffalo. Over 50% of suitable habitat is located outside protected areas, highlighting the need for habitat management and conflict mitigation outside protected areas.
  • Thumbnail Image
    Item
    Impact of infectious diseases on wild bovidae populations in Thailand: insights from population modelling and disease dynamics.
    (The Royal Society, 2024-07-03) Horpiencharoen W; Marshall JC; Muylaert RL; John RS; Hayman DTS
    The wildlife and livestock interface is vital for wildlife conservation and habitat management. Infectious diseases maintained by domestic species may impact threatened species such as Asian bovids, as they share natural resources and habitats. To predict the population impact of infectious diseases with different traits, we used stochastic mathematical models to simulate the population dynamics over 100 years for 100 times in a model gaur (Bos gaurus) population with and without disease. We simulated repeated introductions from a reservoir, such as domestic cattle. We selected six bovine infectious diseases; anthrax, bovine tuberculosis, haemorrhagic septicaemia, lumpy skin disease, foot and mouth disease and brucellosis, all of which have caused outbreaks in wildlife populations. From a starting population of 300, the disease-free population increased by an average of 228% over 100 years. Brucellosis with frequency-dependent transmission showed the highest average population declines (-97%), with population extinction occurring 16% of the time. Foot and mouth disease with frequency-dependent transmission showed the lowest impact, with an average population increase of 200%. Overall, acute infections with very high or low fatality had the lowest impact, whereas chronic infections produced the greatest population decline. These results may help disease management and surveillance strategies support wildlife conservation.
  • Thumbnail Image
    Item
    Population structure and pathogen interaction of Escherichia coli in freshwater: Implications of land-use for water quality and public health in Aotearoa New Zealand.
    (John Wiley & Sons, Inc., 2024-08-02) Cookson AL; Devane M; Marshall JC; Moinet M; Gardner A; Collis RM; Rogers L; Biggs PJ; Pita AB; Cornelius AJ; Haysom I; Hayman DTS; Gilpin BJ; Leonard M
    Freshwater samples (n = 199) were obtained from 41 sites with contrasting land-uses (avian, low impact, dairy, urban, sheep and beef, and mixed sheep, beef and dairy) and the E. coli phylotype of 3980 isolates (20 per water sample enrichment) was determined. Eight phylotypes were identified with B1 (48.04%), B2 (14.87%) and A (14.79%) the most abundant. Escherichia marmotae (n = 22), and Escherichia ruysiae (n = 1), were rare (0.68%) suggesting that these environmental strains are unlikely to confound water quality assessments. Phylotypes A and B1 were overrepresented in dairy and urban sites (p < 0.0001), whilst B2 were overrepresented in low impact sites (p < 0.0001). Pathogens ((Salmonella, Campylobacter, Cryptosporidium or Giardia) and the presence of diarrhoeagenic E. coli-associated genes (stx and eae) were detected in 89.9% (179/199) samples, including 80.5% (33/41) of samples with putative non-recent faecal inputs. Quantitative PCR to detect microbial source tracking targets from human, ruminant and avian contamination were concordant with land-use type and E. coli phylotype abundance. This study demonstrated that a potential recreational health risk remains where pathogens occurred in water samples with low E. coli concentration, potential non-recent faecal sources, low impact sites and where human, ruminant and avian faecal sources were absent.