Massey Documents by Type
Permanent URI for this communityhttps://mro.massey.ac.nz/handle/10179/294
Browse
8 results
Search Results
Item Prevalence and genetic diversity of Theileria equi from horses in Xinjiang Uygur Autonomous region, China.(Elsevier B.V., 2023-07-01) Zhang Y; Shi Q; Laven R; Li C; He W; Zheng H; Liu S; Lu M; Yang DA; Guo Q; Chahan BTheileria equi is a tick-borne intracellular apicomplexan protozoan parasite that causes equine theileriosis (ET). ET is an economically important disease with a worldwide distribution that significantly impacts international horse movement. Horses are an essential part of the economy in Xinjiang which is home to ∼10% of all the horses in China. However, there is very limited information on the prevalence and genetic complexity of T. equi in this region. Blood samples from 302 horses were collected from May to September 2021 in Ili, Xinjiang, and subjected to PCR examination for the presence of T. equi. In addition, a Bayesian latent class model was employed to estimate the true prevalence of T. equi, and a phylogenetic analysis was carried out based on the 18S rRNA gene of T. equi isolates. Seventy-two horses (23.8%) were PCR positive. After accounting for the imperfect PCR test using a Bayesian latent class model, the estimated true prevalence differed considerably between age groups, being 10.8% (95%CrI: 5.8% - 17.9%) in ≤ 3-year-old horses and 35.7% (95%CrI: 28.1% - 44.5%) in horses that were > 3 year-old. All T. equi isolates had their 18S rRNA gene (430bp) sequenced and analyzed in order to identify whether there were multiple genotypes of T. equi in the Xinjiang horse population. All of the 18S rRNA genes clustered into one phylogenetic group, clade E, which is thus probably the dominant genotype of T. equi in Xinjiang, China. To summarize, we monitored the prevalence of T. equi in horses of Xinjiang, China, with a focus on the association between age and the occurrence of T. equi by Bayesian modelling, accompanied by the genotyping of T. equi isolates. Obtaining the information on genotypes and age structure is significant in monitoring the spread of T. equi and studying the factors responsible for the distribution.Item Molecular epidemiology of Salmonella in the broiler industry of Sri Lanka : thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand(Massey University, 2021) Liyanagunawardena, NilukshiThe increasing occurrence of non-typhoidal Salmonella in poultry is an emerging threat for public health in Sri Lanka, and salmonellosis has incurred massive economic loss for the poultry industry in the country. Thus, the thesis presented encompasses a comprehensive study to understand prevalence and possible risk factors for Salmonella carriage in broiler farms as well as whole-genome sequence-based population structure, phylogenetic relationships and antimicrobial resistance in Salmonella in Sri Lankan poultry. The studies described in this thesis include a cross-sectional survey (i.e., sampling and questionnaire-based study) conducted from July to December 2017 in broiler farms (115) from poultry-dense areas and associated hatcheries (15) as well as an outbreak study (from 2010 to 2018), based on isolates and metadata from poultry salmonellosis outbreaks. After initial identification and PCR confirmation of a total of 164 Salmonella isolates, whole-genome sequencing was performed and antimicrobial resistance profiles of the isolates were determined. Results revealed a Salmonella prevalence of 32.2%, CI 95% [23.6-40.7] in broiler farms and 66.7%, CI 95% [42.8-90.5] in the associated hatcheries. Litter management, rest period between flocks, feed storage, district and farmers’ knowledge of sick birds were identified as risk factors for Salmonella carriage in the broiler farms, through multivariate logistic regression modelling. Eighteen different multi-locus sequence types of Salmonella were identified, including nine which were reported for the first time in Sri Lankan poultry. The most common serovars were S. Kentucky ST314 (26.8%, CI 95% [20.0-33.6]) and S. Enteritidis ST11 (19.5%, CI 95% [13.4-25.6]). A high percentage of quinolone resistance manifesting as resistance to nalidixic acid (41.5%, CI 95% [33.9-49.1]) and intermediate resistance to ciprofloxacin (45.1%, CI 95% [37.5-52.7]) and enrofloxacin (35.4%, CI 95% [28.0-42.7]) was found. The findings of this thesis, especially in the absence of previous comprehensive studies, will enable the design of control strategies to strengthen the national Salmonella control programme in Sri Lanka.Item Molecular epidemiological studies of Campylobacter isolated from different sources in New Zealand between 2005 and 2015 : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Massey University, Manawatu, New Zealand(Massey University, 2017) Nohra, AntoineCampylobacteriosis is one of the most important food-borne diseases worldwide, and a significant health burden in New Zealand. C. jejuni is the predominant species worldwide, accounting for approximately 90% of human cases, followed by C. coli. The first study evaluated whether the time elapsing from sampling to culture has an impact on the recovery rate of Campylobacter, and explored whether some sequence types are more likely than others to be missed due to delayed culture. The study revealed that, whereas delayed culture may affect the recovery rate of Campylobacter, there was no evidence of a bias due to specific sequence types being under detected. The second study aimed to analyse the differences in the Campylobacter viable counts and in population genetic structure between chicken drumsticks and whole carcass meat for retail sale. The results indicate that the Campylobacter population genetic structure did not differ between the two types of retail chicken meat. However, the difference in Campylobacter viable counts suggest that consumption of different chicken meat products may pose different risks of campylobacteriosis associated with an exposure to different infection doses. In the third study, we genotyped C. coli isolates collected from different sources between 2005 and 2014, to study their population structure and estimate the contribution of each source to the burden of human C. coli disease. Modelling indicated ruminants and poultry as the main sources of C. coli infection. The fourth study aimed to genotype C. jejuni isolates collected between 2005 and 2015 from different sources, to assess changes in the molecular epidemiology of C. jejuni following the food safety interventions implemented by the New Zealand poultry industry in 2007/2008. Modelling indicated that chicken meat from ‘Supplier A’ was the main source of C. jejuni human infection before the interventions; but after the interventions, ruminants became the main source of infection, followed by chicken meat from Supplier A. This thesis has made us aware of the aetiology of C. coli infections and the change in the attribution of C. jejuni infections. These findings should be used in developing further strategies to reduce the total burden of human campylobacteriosis.Item Molecular epidemiology of waterborne zoonoses in the North Island of New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science (Epidemiology and Public Health) at Institute of Veterinary, Animal and Biomedical Sciences (IVABS), Massey University, Palmerston North, New Zealand(Massey University, 2016) Shrestha, Rima DeviCampylobacter, Cryptosporidium and Giardia species are three important waterborne zoonotic pathogens of global public health concern. This PhD opens with an interpretive overview of the literature on Campylobacter, Cryptosporidium and Giardia spp. in ruminants and their presence in surface water (Chapter 1), followed by five epidemiological studies of Campylobacter, Cryptosporidium and Giardia spp. in cattle, sheep and aquatic environment in New Zealand (Chapters 2-6). The second chapter investigated four years of retrospective data on Campylobacter spp. (n=507) to infer the source, population structure and zoonotic potential of Campylobacter jejuni from six high-use recreational rivers in the Wanganui-Manawatu region of New Zealand through the generalised additive model, generalised linear/logistic regression model, and minimum spanning trees. This study highlights the ubiquitous presence of Campylobacter spp. in both low and high river flows, and during winter months. It also shows the presence of C. jejuni in 21% of samples containing highly diverse strains, the majority of which were associated with wild birds only. These wild birds-associated C. jejuni have not been detected in human, suggesting they may not be infectious to human. However, the presence of some poultry and ruminant-associated strains that are potentially zoonotic suggested the possibility of waterborne transmission of C. jejuni to the public. Good biosecurity measures and water treatment plants may be helpful in reducing the risk of waterborne Campylobacter transmission. In the third study, a repeated cross-sectional study was conducted every month for four months to investigate the source of drinking source-water contamination. A total of 99 ruminant faecal samples and 24 river/stream water samples were collected from two rural town water catchments (Dannevirke and Shannon) in the Manawatu-Wanganui region of New Zealand, and molecular analysis of those samples was performed to determine the occurrence of Campylobacter, Cryptosporidium, and Giardia spp. and their zoonotic potential. The major pathogens found in faecal samples were Campylobacter (n=225 from 7/8 farms), followed by Giardia (n=151 from 8/8 farms), whereas Giardia cysts were found in many water samples (n=18), followed by Campylobacter (n=4). On the contrary, Cryptosporidium oocysts were only detected in a few faecal (n=18) and water (n=3) samples. Cryptosporidium and Giardia spp. were detected in a higher number of faecal samples from young animals (≤ 3 months) than juvenile and adult animals, whereas Campylobacter spp. were highly isolated in the faecal samples from juvenile and adult ruminants. RCRsequencing of the detected pathogens indicated the presence of potentially zoonotic C. jejuni and C. coli, Cryptosporidium parvum (gp60 allelic types IIA18G3R1 and IIA19G4R1) and Giardia duodenalis (assemblages AII, BII, BIII, and BIV) in cattle and sheep. In addition, potentially zoonotic C. jejuni and Giardia duodenalis assemblages AII, BI, BII, and BIV were also determined in water samples. These findings indicate that these three pathogens of public health significance are present in ruminant faecal samples of farms and in water, and may represent a possible source of human infection in New Zealand. In the fourth study, PCR-sequencing of Cryptosporidium spp. isolates obtained from the faeces of 6-week- old dairy calves (n=15) in the third study were investigated at multiple loci (18S SSU rDNA, HSP70, Actin and gp60) to determine the presence of mixed Cryptosporidium spp. infections. Cryptosporidium parvum (15/15), C. bovis (3/15) and C. andersoni (1/15), and two new genetic variants were determined along with molecular evidence of mixed infections in five specimens. Three main Cryptosporidium species of cattle, C. parvum, C. bovis and C. andersoni, were detected together in one specimen. Genetic evidence of the presence of C. Anderson and two new Cryptosporidium genetic variants are provided here for the first time in New Zealand. These findings provided additional evidence that describes Cryptosporidium parasites as genetically heterogeneous populations and highlighted the need for iterative genotyping at multiple loci to explore the genetic makeup of the isolates. The C. jejuni and C. coli isolates (n=96) obtained from cattle, sheep and water in the third study were subtyped to determine their genetic diversity and zoonotic potential using a modified, novel multi-locus sequence typing method (“massMLST”; Chapter 5). Primers were developed and optimised, PCR-based target-MLST alleles’ amplification were performed, followed by next generation sequencing on an Illumina MiSeq machine. A bioinformatics pipeline of the sequencing data was developed to define C. jejuni and C. coli multi-locus sequence types. This study demonstrated the utility and potential of this novel typing method, massMLST, as a strain typing method. In addition to identifying the possible C. jejuni/coli clonal complexes or sequence types of 68/96 isolates from ruminant faeces and water samples, this study reported three new C. jejuni strains in cattle in New Zealand, along with many strains, such as CC-61, CC-828 and CC-21, that have also been found in humans, indicating the public health significance of these isolates circulating on the farms in the two water catchment areas. Automation of the massMLST method and may allow a cost-effective high-resolution typing method in the near future for multilocus sequence typing of large collections of Campylobacter strains. In the final study (Chapter 6), a pilot metagenomic study was carried out to obtain a snapshot of the microbial ecology of surface water used in the two rural towns of New Zealand for drinking purposes, and to identify the zoonotic pathogens related to waterborne diseases. Fresh samples collected in 2011 and 2012, samples from the same time that were frozen, and samples that were kept in the preservative RNAlater were sequenced using whole-genome shotgun sequencing on an Illumina MiSeq machine. Proteobacteria was detected in all the samples characterised, although there were differences in the genus and species between the samples. The microbial diversity reported varied between the grab and stomacher methods, between samples collected in the year 2011 and 2012, and among the fresh, frozen and RNAlater preserved samples. This study also determined the presence of DNA of potentially zoonotic pathogens such as Cryptosporidium, Campylobacter and Mycobacterium spp. in water. Use of metagenomics could potentially be used to monitor the ecology of drinking water sources so that effective water treatment plans can be formulated, and for reducing the risk of waterborne zoonosis. As a whole, this PhD project provides new data on G. duodenalis assemblages in cattle, sheep and surface water, new information on mixed Cryptosporidium infections in calves, a novel “massMLST” method to subtype Campylobacter species, and shows the utility of shotgun metagenomic sequencing for drinking water monitoring. Results indicate that ruminants (cattle and sheep) in New Zealand shed potentially zoonotic pathogens in the environment and may contribute to the contamination of surface water. A better understanding of waterborne zoonotic transmission would help in devising appropriate control strategies, which could reduce the shedding of Campylobacter, Cryptosporidium, and Giardia spp. in the environment and thereby reduce waterborne transmission.Item Canine parvovirus in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Masters of Veterinary Studies in Virology at Massey University, Turitea, Palmerston North, New Zealand(Massey University, 2013) Ohneiser, Sylvia AnnaSince the initial global emergence of canine parvovirus type 2 (CPV-2) in the early 1980s the virus has continued to evolve in its new host. As a result, the original CVP-2 was replaced by newly emerged subtypes designated CPV-2a and CPV-2b. Recently, a third antigenic subtype CPV-2c has emerged in several countries. In New Zealand the evolution of CVP-2 has not been monitored since its emergence in the early 1980s, largely because of the high efficacy of the vaccines available on the market. This lack of monitoring of CPV-2 has left a dearth of knowledge regarding the epidemiological features of CPV-2 in New Zealand. Hence, the aim of this study was to determine what subtypes of CPV-2 circulate in New Zealand and to investigate the phylogenetic relationships between CPV-2 from New Zealand and from other parts of the world. As part of this project, a virological survey was conducted across New Zealand. A total of 79 faecal samples were collected from dogs suspected to be infected with CPV-2, as judged by submitting veterinarians. Of those, 70 tested positive for CPV-2 DNA. All but one of the CPV-2 sequences were subtyped as CPV-2a. The remaining sequence was subtyped as CPV- 2, and most likely represented a vaccine strain of the virus. The majority (74.3%) of CPV-2 positive samples originated from dogs six months of age and younger, with 70% of samples collected from dogs considered not fully vaccinated (unvaccinated dogs or those with only single vaccination), a further 17% of samples originated from dogs with an unknown vaccination history. Two separate phylogenetic analyses were performed. Seventy one CPV-2 positive sequences originated from New Zealand (61 survey samples, six historic samples, two vaccine sequences and one parvovirus sequence obtained from a cat) and the reference sequence were trimmed to produce contiguous sequences of equal length. These 72 sequences were used to investigate the genetic structure of CPV-2 within New Zealand. Haplotype network analyses revealed that Cook-straight [i.e. Cook Strait] is not an effective geographical barrier to CVP-2 gene flow with an equal distribution of genotypes in the North and South Islands. Translocation of the virus between the islands is likely occurring by transportation of sub-clinically infected animals and fomites. Additional CPV-2 VP2 sequences (n=95) originating from various countries were obtained from the National Centre for Biotechnology Information (NCBI) database. The selection of 27 samples originating from New Zealand for which a full length contiguous sequence of VP-2 gene was available were aligned with sequences obtained from the NCBI database. The resulting dataset of 123 CPV-2 sequences was used to assess the New Zealand CPV-2 sequences in the context of the worldwide radiation of CPV-2. Phylogenetic analyses of this dataset revealed that New Zealand has a closed monophyletic population of CPV-2 sequences. This suggests that CPV-2 is not being continuously introduced to New Zealand from overseas, but has evolved following a limited number of introductions in the past. Phylogenetic analysis also revealed that CPV-2 subtypes from around the world have emerged independently of one another. This work has contributed to our understanding of molecular epidemiology of CPV-2 in New Zealand. The knowledge of predominant CPV-2 subtypes circulating in this country is important for evidence driven recommendations with regard to CPV-2 vaccination. Understanding of the genetic structure of the current CPV-2 circulating in New Zealand is also crucial for timely recognition, detection and management of any novel antigenic subtypes that may emerge in the future.Item Molecular epidemiology of campylobacteriosis and evolution of Campylobacter jejuni ST-474 in New Zealand : a thesis presented in partial fullfilment [sic] of the requirements for the degree of Doctor of Philosophy at Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand(Massey University, 2011) Mohan, VathsalaPopulation genetics and phylogenetics have the potential to provide enormous insights into the epidemiology and ecology of disease causing pathogens. Molecular datasets are the basis to infer population structure, gene flow (between host populations and between different geographical locations) and to predict the evolutionary dynamics of pathogens. Campylobacter colonisation in food producing animals has been extensively studied and the population structure and host association of C. jejuni, the most commonly reported gastro-enteric pathogen, has also been well defined. In contrast, host-pathogen relationships and the population structure of C. jejuni in urban wild birds and pets have not been well defined on a wide range of spatial and/or temporal scales. A greater understanding of these details should allow disease control authorities to track the transmission of pathogens from one host species to another, identify the origin of pathogens and to better understand environmental factors influencing underlying molecular mechanisms. In the first study in this thesis the presence of C. jejuni in mallard ducks and starlings within five playgrounds in Palmerston North, New Zealand was studied. The prevalence of Campylobacter and C. jejuni in both species showed a bimodal seasonal pattern. The population structure and population differentiation of C. jejuni in these species were examined using multilocus sequence typing (MLST). Rarefaction analyses showed that the C. jejuni populations within mallard ducks were more diverse than starlings, particularly during the winter. Pairwise fixation indices showed that the population of C. jejuni in ducks was significantly different from that of starlings and that it differed over time. Conspicuous host association was evident with clonal complexes of C. jejuni such as ST-1034, ST-692 and ST-1332 specific to ducks and ST-177 and ST-682 specific to starlings. In addition, a larger proportion of C. jejuni genotypes that could not be assigned a clonal complex were found in both ducks and starlings, particularly during the winter. In the second study, C. jejuni from domestic pets (dogs and cats) were characterised using MLST and by typing the cell surface antigens, porA and flaA. The ST-45 complex, a clonal complex predominantly reported in human campylobacteriosis cases, was found to be the predominant clone present in both species. These findings shed some light on the contribution of pets as a putative source of human campylobacteriosis cases in New Zealand. In the third study, the ST-474 C. jejuni genotype, considered to be the endemic strain in New Zealand, was isolated from human cases and poultry carcasses from the Manawatu region from 2005 to 2009. Seven samples of ST-474 were sequenced and a subset of 50 full length genes were studied. These analyses demonstrated molecular differences between full length genes that were identical in the region used for MLST. Further, alleles characteristic of the ST-474 genome within the investigated metabolic housekeeping genes (n = 25) were identified. Our findings were that ST-474 genome is genetically distinct from other C. jejuni reference genomes with respect to certain alleles. In addition, MLST alleles were found to be robust predictors of the most recent common ancestors of a genome. The fourth study investigated the genetic stability and vulnerability of the informational genes to various evolutionary forces within the seven ST- 474 genomes. Twenty five genes comprised of nucleotide metabolism, repair and ribosomal functions were investigated showing a high level of genetic diversity in the DNA repair as well as nucleotide metabolic genes such as gidA, ogt, recJ, ssb, uvrA, uvrB and xseA. In contrast, the ribosomal genes were stable and identical across the seven genomes. The insertion of selenocysteine in three of the 25 genes indicates the presence of horizontal gene transfer within the ST-474 genomes. It is hypothesised that the genetic uniqueness of ST-474 may have arisen due to the geographic isolation of New Zealand, its poultry industry and an absence of exchange of sequence types which might typically occur through international trade of fresh poultry meat. Collectively, the studies presented in this thesis provide a better understanding of the dynamism of C. jejuni as a species and ST-474’s adaptational capacity and evolutionary potential (within the investigated set of genes) in response to changing intracellular and extracellular environments. This thesis has introduced the idea of using individual full length gene analysis, demonstrating the molecular differences between genes that contained identical alleles at the MLST loci. The research approaches implemented in this thesis can be readily applied to any pathogenic bacteria, particularly foodborne and emerging pathogens such as E. coli and Salmonella. This, in turn should provide new opportunities for bacterial drug targets and vaccine candidates.Item Post-vaccination surveillance and molecular epidemiology of highly pathogenic H5N1 avian influenza in Vietnam : a thesis presented in partial fullfilment [sic] of the requirements for the degree of Master of Veterinary Studies at Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand(Massey University, 2011) Nguyen, Thi DiepAbstract not availableItem Estimating the contribution of different sources to the burden of human campylobacteriosis and salmonellosis : a thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Massey University, Palmerston North, New Zealand(Massey University, 2009) Mullner, PetraThis thesis is concerned with the molecular epidemiology of Campylobacter jejuni and Salmonella in New Zealand and the development of source attribution tools for these pathogens. Although campylobacteriosis is the leading enteric zoonosis worldwide, the pathogen's complex epidemiology and di culties with existing typing schemes, have posed challenges for the control of this disease. The rst study of this thesis gives an overview of existing approaches to microbial risk assessment and source attribution, with particular respect to campylobacteriosis, and describes their advantages and shortcomings. Further, the chapter discusses phenoand genotyping techniques for Campylobacter spp. and the value of including microbial typing data in risk assessments. In the second study, data from a sentinel surveillance site in the Manawatu region was used to investigate the molecular epidemiology of human campylobacteriosis cases. This analysis revealed the presence of a dominant C. jejuni clone, namely sequence type (ST) 474, which accounted for 30.7 % of human cases in the study and identi ed risk factors for infection with ruminant and poultry associated STs. The third study investigated the link between C. jejuni in human cases and samples taken from poultry. By applying epidemiological and population genetic techniques this part of the thesis provided further evidence that poultry is a major contributor to human infection. In the fourth study an existing Bayesian source attribution model was modi ed and consecutively applied to New Zealand's major foodborne zoonoses: campylobacteriosis and salmonellosis. The majority (80 %) of human campylobacteriosis cases attributable to C. jejuni were estimated to have been acquired from poultry sources, whereas wildlife source were estimated to contribute only a minor proportion of cases. In the fth study the Salmonella dataset was descriptively analysed and a large proportion of human cases was found to be caused by `exotic' Salmonella types. In the nal study of this thesis four di erent genetic and epidemiological source attribution methodologies were applied to the same dataset in a comparative modelling framework. iv The studies in this thesis show that epidemiological studies combined with molecular tools and modeling can provide valuable risk-based tools to inform the surveillance and control of zoonotic pathogens. Methods from these studies may be readily applied to the control of other (food borne) zoonoses and provide new opportunities for epidemiological investigations and source attribution modelling of major pathogens.