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    Campylobacter jejuni microevolution and phenotype:genotype relationships : a thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand
    (Massey University, 2014) Friedrich, Anja
    Campylobacter spp. are a major cause of human gastroenteritis. Their wide host range, environmental distribution and high genetic diversity contribute to the complex molecular epidemiology of campylobacteriosis. The aim of this multidisciplinary thesis is to investigate the phenotype:genotype relationships of C. jejuni and how they in uence the micro-evolution of these bacteria in New Zealand. The first study used a time series of genotyped human campylobacteriosis cases from a region of New Zealand to investigate if the clonal complexes (CCs) identified in human cases showed a seasonal pattern. The analysis revealed a prevalent clonal complex (CC-45) which showed a consistent summer peak. The second study applied phylogenetic and population genetic tools to describe the population structure and host associated genotypes within the C. jejuni population in wild and agricultural animals. The findings showed that the C. jejuni isolates from non-agricultural animals exhibit a higher number of mosaic alleles and fewer shared sequence types (STs) between the host groups, whereas the C. jeuni in agricultural animals show a higher number of shared STs and fewer occurrences of admixture. The third study tested the ability of a variety of C. jejuni isolates to utilise 95 substrates as carbon sources and tested their tolerance to different osmotic conditions using phenotypic microarray (PM) technology. These phenotypic expressions were correlated with their genomes and a genome wide association study was used to identify genes associated with the observed phenotype. The last study made use of data from a dual isolate chicken challenge. The study showed the out-competition of one challenge strain and genetic variations of 15 core single nucleotide polymorphisms (SNPs), 14 of which were non-synonymous point mutations. These SNPs were confined to nine genes all of which were associated with cell shape, chemotaxis or motility of the bacteria. This thesis has furthered our understanding of the seasonality of human campylobacteriosis in New Zealand, the existing population structure of C. jejuni, its biochemical requirements and tolerance to osmolytes and novel insights into short-term evolutionary dynamics in vivo. Based on these findings and the recommendations for future directions, this could lead to a greater understanding of host-association and new intervention strategies.
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    The effect of climate variation on infectious diseases in humans in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Masters in Veterinary Studies in Epidemiology at Massey University, Palmerston North, New Zealand
    (Massey University, 2011) Brock, Aleisha
    The emergence and spread of infectious disease are a major issue associated with environmental change. Contributing to this is the effect climate variability and change may play in altering disease risk. The aims of this study were to investigate the association between climate and infectious diseases in humans throughout New Zealand from 1997 - 2007, then use the identified associations to project the burden of disease in 2015, 2040 and 2090 with respect to future climate change scenarios. The four infectious diseases selected and investigated were campylobacteriosis, cryptosporidiosis, influenza hospitalisations and meningococcal disease. The association of weather variables and other confounders with the incidence risk (IR) of disease were explored using a quasi-Poisson generalized linear model, indicating that weather variables were significantly associated with disease risk. These results, along with expert opinion on epidemiological plausibility, were used to select confounders for the past association models. Climate variation was associated with the IR of campylobacteriosis and cryptosporidiosis in New Zealand from 1997 - 2007. Campylobacteriosis notifications were found to be positively associated with the weekly absolute humidity. Additionally, campylobacteriosis notification risk factors were increasing beef and dairy density, intermediate and poor drinking water quality, being over 65 years of age and identifying with Pacific Island or Asian ethnicity. Protective factors were being less than 4 years of age and identifying with Maori ethnicity. Cryptosporidiosis notifications were found to be positively associated with the weekly average temperature and negatively associated with the weekly average rainfall. Risk factors for cryptosporidiosis notifications were poor drinking water quality, being less than 4 years of age and living in rural areas. Protective factors were identifying with Maori ethnicity and unknown drinking water quality. Influenza hospitalisations and meningococcal disease notifications were not significantly associated with past climate variation. Identifying with Maori ethnicity was found to be a risk factor for influenza hospitalisations, with no protective factors identified. Risk factors for meningococcal disease notifications were an increasing social deprivation index (SDI) score, being less than 4 years of age and identifying with Maori ethnicity. Identifying with Asian ethnicity was a protective factor for meningococcal disease. The projection calculations of the change in disease incidence from the study period to 2015, 2040 and 2090 were carried out under a combination 3 Intergovernmental Panel of Climate Change (IPCC) climate scenarios (A2, B1 and A1B) and 12 downscaled global climate models. The projected change in campylobacteriosis and cryptosporidiosis suggested increases in the rate of notifications, and a small to no decrease in influenza hospitalisation and meningococcal disease notifications.
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    Enhanced surveillance of potentially foodborne enteric disease within a New Zealand public health service : thesis presented in partial fulfilment of the requirements for the degree of Master of Veterinary Studies in Public Health at Massey University, Palmerston North, New Zealand
    (Massey University, 2009) Shadbolt, Tui Louise
    An enhanced notified enteric disease surveillance trial began on 1 July 2007 and continued until 30 June 2008. The aim of the trial was to measure the quality, timeliness and completeness of data collected and submitted by a regional Public Health Service (PHS) to the Institute of Environmental Science and Research Limited (ESR), via the national disease database (EpiSurv) for notified cases of enteric diseases. The trial evaluated two different methods of data collection: postal questionnaires and telephone interviews. Telephone interview techniques were used to improve the contact rate, timeliness and completeness of data gathered from all notified cases of campylobacteriosis in the Manawatu, Horowhenua and Tararua regions. The target set for the project was to achieve a 95% contact rate with 90% full completion of all EpiSurv data fields. For all notified cases of campylobacteriosis a 97% contact rate was achieved in a time frame of between zero to 20 days (three day median) and completeness of all the EpiSurv case report fields ranged between 96 – 100% in the final data. Prior to the commencement of the study, between 1 July 2004 to 30 June 2005, MidCentral PHS (MCPHS) made contact with around 58% of all notified cases of campylobacteriosis and 77% of all other notified enteric disease cases1 . A short pre-screen mail questionnaire, with reply-paid envelope, was sent to all notified cases of cryptosporidiosis, giardiasis, salmonellosis and yersiniosis in the MCPHS regions. EpiSurv case report fields were completed using information supplied in the returned questionnaires. Return rate, timeliness, and completeness were compared with the telephone interview group. Fifty three percent of cases we attempted to contact via mail questionnaire responded within two to 63 days (six day median) and completeness of all the EpiSurv case report fields ranged between 81 – 100%. In addition, we monitored the newly introduced ESR Early Aberration Reporting System (EARS) flags for increased levels of disease compared to historical disease rates, and assessed its usefulness as a tool to identify potential outbreaks in the region. While no outbreaks that had not already been identified by PHS staff were found by monitoring the EARS system, EARS has become an important tool in the MCPHS for comparing our rates of disease with bordering PHSs. EARS also provided a good quick reference tool for media enquiries and the graphs produced in EARS have been well utilised as visual aids for training and seminars presented during the trial period. The results of the surveillance trial initiatives were compared to the rest of New Zealand (NZ) over the same time frame and with a comparable, medium-sized, PHS. While the results of the telephone interviews from the MCPHS trial were close to the comparable PHS, they were significantly higher than for the rest of NZ. The postal questionnaires achieved a lower contact rate than the comparable PHS but similar to the rest of NZ. However, the quality of data gathered in the returned MCPHS postal questionnaire was significantly higher in most fields. Additional analysis was undertaken which indicated that those cases living in higher deprivation and rural areas were less likely to respond to a postal questionnaire. An over-representation of common enteric disease notifications from rural areas in the MCPHS was also highlighted by our research. This trial has shown the effectiveness of utilising telephone interviews and telemarketing techniques for gathering timely and complete data for human enteric disease surveillance within the MCPHS. It has also demonstrated that a short pre-screen questionnaire can be effective in collecting good quality data needed to complete the standard EpiSurv case report form.