Centre For Infectious Disease - Research Highlights from the Infectious Disease Research Centre http://www.idrec.ac.nz/research-highlights-new.html en-uk 2022-12-09T19:01:20+01:00 Covid-19 control measures alter transmission patterns of <i>Cryptosporidium hominis</i> in New Zealand http://www.idrec.ac.nz/research-highlights-new,listing,,,231,covid-19-control-measures-alter-transmission-patterns-of-icryptosporidium-hominisi-in-new-zealand.html Covid-19 nonpharmaceutical interventions have been effective control measures for a range of respiratory illnesses throughout the world. These measures, which include isolation, strict border controls, social distancing and improved hygiene also have effects on other human pathogens, including parasitic diseases of the gut such as cryptosporidiosis. Cryptosporidium infections in humans are mostly caused by two species: C. hominis, which is primarily transmitted from human-to-human, and C. parvum, which is mainly derived from animals, particularly livestock. New Zealand&#39;s initial Covid-19 control measures began in March 2020, with a nationwide lockdown period of more than 7 weeks. By monitoring Cryptosporidium species and subtype families in human cases of cryptosporidiosis before and after the introduction of Covid-19 control measures, IDReC researchers have found C. hominis infections were completely absent after the first months of 2020 and remained so until the beginning of 2021. Meanwhile, C. parvum followed its typical transmission pattern and continued to be widely reported. These results suggest that isolation during the initial lockdown period interrupted human-to-human transmission of cryptosporidiosis caused by C. hominis, leaving only the primarily zoonotic transmission pathway used by C. parvum. We are looking forward to reporting our ongoing monitoring of Cryptosporidium species and subtypes, particularly as border restrictions ease. &#160; Access to the full article, recently published in Parasitology can be found here https://pubmed.ncbi.nlm.nih.gov/34120663/ &#160; http://www.idrec.ac.nz/research-highlights-new,listing,,,231,covid-19-control-measures-alter-transmission-patterns-of-icryptosporidium-hominisi-in-new-zealand.html Source attributed case-control study of campylobacteriosis in New Zealand http://www.idrec.ac.nz/research-highlights-new,listing,,,229,source-attributed-case-control-study-of-campylobacteriosis-in-new-zealand.html Scanning electron microscope image of Campylobacter cells. Photo credit: Manawatu Microscopy and Imaging Centre The implementation of poultry food chain-focused interventions during 2006-2008 reduced human campylobacteriosis by ~50%, but further decline since then has been relatively small. To the assess current relative contributions of different Campylobacter sources (poultry, cattle, sheep) IDReC researchers Jackie Benschop, Jonathan Marshall, Anne Midwinter, David Wilkinson and Nigel French collaborated with colleagues to conduct a year-long source-attributed case-control study of human campylobacteriosis in New Zealand. Most cases (84%) were infected with strains attributed to a poultry source, while 14% were attributed to a cattle source. The overall findings indicate that poultry meat remains a dominant pathway for exposure and infection with Campylobacter in New Zealand. Access to the full article, recently published in International Journal of Infectious Diseases can be found here &#160; http://www.idrec.ac.nz/research-highlights-new,listing,,,229,source-attributed-case-control-study-of-campylobacteriosis-in-new-zealand.html Improved Methods for Purifying <i>Giardia</i> http://www.idrec.ac.nz/research-highlights-new,listing,,,226,improved-methods-for-purifying-igiardiai.html Giardia is a protozoan parasite that causes gastroenteritis in all classes of vertebrates and affects approximately 280 million people worldwide annually. Giardia is difficult to manipulate in in vitro environments, which hampers the development of effective disease management strategies. To redress this, IDReC researchers have developed an improved method for the purification of viable Giardia cysts from faecal samples. This protocol produces a 10&#8208;fold increase in yield over current methods. By combining sucrose flotation with gated filtration, the protocol significantly reduces the amount of debris in the purified cysts suspension. The ability to purify larger quantities of Giardia from faecal samples could advance the development of effective treatments to target this worldwide prevalent parasite. IDReC researchers Paul Ogbuigwe, Anthony Pita,Matthew Knox, Niluka Velathanthiri and David Hayman published these findings in the most recent issue of Current Protocols in Microbiology. &#160;Access to the full article can be found here https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpmc.117 http://www.idrec.ac.nz/research-highlights-new,listing,,,226,improved-methods-for-purifying-igiardiai.html Investigating the meat pathway as a source of human <i>Salmonella</i> infections and diarrhea in East Africa http://www.idrec.ac.nz/research-highlights-new,listing,,,225,investigating-the-meat-pathway-as-a-source-of-human-isalmonellai-infections-and-diarrhea-in-east-africa.html Salmonella Enteritidis and Salmonella Typhimurium are major causes of bloodstream infection and diarrheal disease in East Africa. However, the sources of human infections, including the role of the meat pathway, are poorly understood. To investigate this, the authors (including several IDReC researchers) of a recent paper in Clinical Infectious Diseases collected cattle, goat, and poultry meat pathway samples in Tanzania and isolated Salmonella. Isolates were characterized for antimicrobial resistance, virulence genes, and diversity and compared with nontyphoidal Salmonella isolated from humans with bloodstream infection and diarrheal disease in nearby Kenya. The findings suggest that the meat pathway may be an important source of human infection by some Salmonella Enteritidis ST11 in East Africa, but not of human Salmonella Typhimurium ST313 infection. Access to the full article can be found here http://www.idrec.ac.nz/research-highlights-new,listing,,,225,investigating-the-meat-pathway-as-a-source-of-human-isalmonellai-infections-and-diarrhea-in-east-africa.html Contrasting evolutionary histories of <i>Escherichia coli </i>serogroup O145 revealed with genomic epidemiology and carbon metabolism characteristics. http://www.idrec.ac.nz/research-highlights-new,listing,,,224,contrasting-evolutionary-histories-of-iescherichia-coli-iserogroup-o145-revealed-with-genomic-epidemiology-and-carbon-metabolism-characteristics-.html Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens residing harmlessly in the gut of bovine reservoirs, but capable of causing human disease. To manage food-related risk, seven serogroups have been declared adulterants of ground beef in the United States of America impacting food safety regulations and international trade. In a cross-sectional study investigating the prevalence of STEC in young calves (2-21 days of age) throughout New Zealand IDReC researchers previously identified STEC O145 as the most prevalent serogroup (43%) at the dairy farm level compared with the other serogroups. However, STEC serogroup O145 are difficult to isolate as routine diagnostic methods are unable to distinguish them due to their heterogeneous metabolic characteristics. In this study, published in PLOS ONE, Rose Collis and co-authors use genomic epidemiology and metabolic characteristics to investigate improved methods for diagnostic-based culture of STEC O145. The study highlights the phenotypic and genotypic heterogeneity within E. coli serogroup O145, suggesting that the development of a differential media targeting this serogroup will be challenging. &#160; Access to the full article can be found here&#160; http://www.idrec.ac.nz/research-highlights-new,listing,,,224,contrasting-evolutionary-histories-of-iescherichia-coli-iserogroup-o145-revealed-with-genomic-epidemiology-and-carbon-metabolism-characteristics-.html Species and genotypes causing human cryptosporidiosis in New Zealand http://www.idrec.ac.nz/research-highlights-new,listing,,,223,species-and-genotypes-causing-human-cryptosporidiosis-in-new-zealand.html In a recent IDReC publication in Parasitology Research Juan C. Garcia-R and others present their research into the biodiversity of Cryptosporidium infections in New Zealand. The authors use Cryptosporidium DNA sequence data from over 2500 human faecal samples collected during an 11-year period (2009&#8211;2019) to better understand the impact of different species and subtypes on public health and to gain insights into the variation of human cryptosporidiosis in New Zealand. The key findings show that Cryptosporidium hominis cases appear to peak during autumn (March&#8211;May) whereas most cases of human cryptosporidiosis caused by C. parvum occur during the calving and lambing season in spring (September&#8211;November). The study also reports certain Cryptosporidium subtypes at higher than expected frequencies compared with overseas, and a low prevalence of hypertransmissible and virulent subtypes which are more common elsewhere. This study provides insight into the variability of cryptosporidiosis in New Zealand essential for disease management and surveillance to prevent the introduction or spread of new species and subtypes in the country. Several other IDReC researchers were involved in this work including Anthony Pita, Niluka Velathanthiri, Nigel French and David Hayman. Access to the full article can be found here https://link.springer.com/article/10.1007%2Fs00436-020-06729-w More information and examples of the work of the Protozoa Research Unit can be found here http://protozoa.org/ &#160; Image : Immunofluorescence image of C. parvum oocysts. http://www.idrec.ac.nz/research-highlights-new,listing,,,223,species-and-genotypes-causing-human-cryptosporidiosis-in-new-zealand.html Genotyping of <i>Campylobacter</i> reveals likely source of Havelock North Campylobacteriosis outbreak http://www.idrec.ac.nz/research-highlights-new,listing,,,222,genotyping-of-icampylobacteri-reveals-likely-source-of-havelock-north-campylobacteriosis-outbreak.html The 2016 outbreak of Campylobacteriosis in Havelock North made over 5000 people violently ill and has been linked to four deaths. In a recent issue of the Journal of Infection, IDReC researchers David Hayman, Nigel French, Ji Zhang, David Wilkinson, Anne Midwinter and Patrick Biggs describe their investigation of this outbreak, linked to contamination of an untreated drinking water supply. Genotyping of Campylobacter isolates from cases, groundwater samples and sheep fecal specimens helped define the source of the outbreak. Of the 12 Campylobacter genotypes observed in cases, four were also observed in water, three were also observed in sheep and one was also observed in both water and sheep. The authors conclude that contamination of the water supply occurred following a very heavy rainfall event which caused drainage of sheep feces into a shallow aquifer. &#160; Access to the full article can be found here https://www.sciencedirect.com/science/article/pii/S016344532030445X?via%3Dihub &#160; &#160; Sheep Picture - Public Domain, commons.wikimedia.org/w/index.php?curid=16818 &#160; http://www.idrec.ac.nz/research-highlights-new,listing,,,222,genotyping-of-icampylobacteri-reveals-likely-source-of-havelock-north-campylobacteriosis-outbreak.html Predicting Ebola virus disease risk and the role of African bat birthing http://www.idrec.ac.nz/research-highlights-new,listing,,,215,predicting-ebola-virus-disease-risk-and-the-role-of-african-bat-birthing.html Ebola virus disease (EVD) presents a threat to public health throughout equatorial Africa. The maintenance reservoirs of EVD in wild animal populations and the mechanism of spillover into humans (and apes) are poorly understood. Fruit bats may play a role in both, yet data on this remain sparse. IDReC researchers Reed Hranac, Jonathan Marshall and David Hayman, along with Eswatini colleague Ara Monadjem, developed niche models to examine how birthing cycles of African bats inform the spatio-temporal occurrence of EVD spillover. The model results improve spatio-temporal models of EVD spillover across mainland Africa and will be useful in predicting outbreaks in future. &#160; Read the full paper here http://www.idrec.ac.nz/research-highlights-new,listing,,,215,predicting-ebola-virus-disease-risk-and-the-role-of-african-bat-birthing.html Genomic analysis of an antimicrobial drug-resistant Campylobacter isolated from New Zealand poultry http://www.idrec.ac.nz/research-highlights-new,listing,,,214,genomic-analysis-of-an-antimicrobial-drug-resistant-campylobacter-isolated-from-new-zealand-poultry.html In 2014, antimicrobial drug&#8211;resistant Campylobacter jejuni sequence type 6964 emerged in poultry from 3 supply companies in the North Island of New Zealand and as a major cause of campylobacteriosis in humans in New Zealand. This lineage, not previously identified in New Zealand, was resistant to tetracycline and fluoroquinolones. To determine which factors contributed to the spread of this clone in New Zealand, IDReC researchers led by Nigel French undertook a detailed genomic analysis of ST6964 isolates from humans and poultry collected during 2014&#8211;2016 and this work was recently published in Emerging Infectious Diseases. Genomic analysis revealed divergence into 2 major clades, each restricted to specific poultry supply companies and associated with human infection. Accessory genome evolution was associated with a plasmid, phage insertions, and natural transformation. The emergence and rapid spread of a resistant clone of C. jejuni in New Zealand demonstrates the need for ongoing Campylobacter surveillance among poultry and humans. &#160; Read the full paper here http://www.idrec.ac.nz/research-highlights-new,listing,,,214,genomic-analysis-of-an-antimicrobial-drug-resistant-campylobacter-isolated-from-new-zealand-poultry.html Why do bats tolerate the viral infections they transmit to other species? http://www.idrec.ac.nz/research-highlights-new,listing,,,210,why-do-bats-tolerate-the-viral-infections-they-transmit-to-other-species.html Bats are unusual among mammals in a number of ways and are notable for their tendency to host a wide range of viruses, some of which cause severe disease in humans and other mammals. By comparing the immune responses of bats with other mammalian hosts, it is possible to see why bats seem to tolerate these viral infections which are highly pathogenic in other hosts. In a recent paper, IDReC researcher Dave Hayman summarises differences in traits related to longevity and infection between bats and other mammals. The results reveal that by mitigating the effects inflammatory molecules brought on by infection, bats better tolerate viral infections and may have inadvertently increased bat lifespan by reducing DNA damage to telomeres. &#160; Access the full text here http://www.idrec.ac.nz/research-highlights-new,listing,,,210,why-do-bats-tolerate-the-viral-infections-they-transmit-to-other-species.html Epidemiological investigation of <i>Leptospira </i>spp. after three human leptospirosis cases http://www.idrec.ac.nz/research-highlights-new,listing,,,208,epidemiological-investigation-of-ileptospira-ispp-after-three-human-leptospirosis-cases.html IDReC researchers have published the results of a study into leptospirosis epidemiology following the diagnosis of three cases among dairy farm workers early in 2015. The lead author, Yuni Yupiana of IDReC has recently defended her PhD thesis, which included this work. This case study was published in Zoonoses and Public Health and demonstrated the high risk of Leptospira infection in farm workers exposed to unvaccinated dairy cattle and the importance of Leptospira vaccination to protect workers. Currently, ~ 95% of New Zealand dairy herds use vaccination, however this only protects against two or three of the six known serovars in New Zealand. In an outbreak situation, the combination of whole herd vaccination and antibiotic treatment in adult cows appeared to be effective in decreasing Leptospira shedding rate of vaccine serovars. However, the study identified the continued presence of non&#8208;vaccine susceptible Leptospira serovars in vaccinated animals which pose an ongoing risk to workers. &#160; Access the full text here http://www.idrec.ac.nz/research-highlights-new,listing,,,208,epidemiological-investigation-of-ileptospira-ispp-after-three-human-leptospirosis-cases.html Street-level diplomacy improves meat safety in Northern Tanzania http://www.idrec.ac.nz/research-highlights-new,listing,,,206,street-level-diplomacy-improves-meat-safety-in-northern-tanzania.html IDReC researcher Jackie Benschop and co-authors have published the results of a study into relationships among authorities responsible for ensuring meat safety and the people involved in meat supply chains in Northern Tanzania. The research was based on interviews with government employees and sought to delve into the contrasting effectiveness of strict regulation vs &#8216;street-level diplomacy&#8217; in developing countries. The paper reports that regulators&#8217; hesitancy to act punitively helped to develop trust and positive relations, making those engaged in animal-based livelihoods more open to learning from and cooperating with extension officers and inspectors. This may result in higher levels of meat safety than might be the case if regulations were more stringently enforced. &#160; Access to the full text is available here https://bmcpublichealth.biomedcentral.com/articles/10.1186/s12889-019-7067-8 &#160; This work is part of a broader project investigating Hazards Associated with Zoonotic enteric pathogens in Emerging Livestock meat pathways (HAZEL). http://livestocklivelihoodsandhealth.org/research/meat-risks/ &#160; &#160; http://www.idrec.ac.nz/research-highlights-new,listing,,,206,street-level-diplomacy-improves-meat-safety-in-northern-tanzania.html Drug resistance in <i>Staphylococcus pseudintermedius</i> from New Zealand dogs http://www.idrec.ac.nz/research-highlights-new,listing,,,204,drug-resistance-in-istaphylococcus-pseudintermediusi-from-new-zealand-dogs.html Staphylococcus pseudintermedius is an opportunistic zoonotic pathogen that primarily colonises the skin of dogs. Drug resistance within S. pseudintermedius is increasingly reported across the globe, including methicillin resistance (MRSP) or multidrug resistance (MDR). MRSP isolation remains rare in clinics in New Zealand, but is a growing threat. In a new paper published in Scientific Reports, IDReC researchers Shahista Nisa, Anne Midwinter, Nigel French Jackie Benschop and David Wilkinson, demonstrate new, sensitive methods for detecting S. pseudintermedius, MRSP and MDR-MRSP from New Zealand dogs using a combination of methodologies, which can be used to identify common subtype variants and improve surveillance. In addition, the authors utilise comparative genomics to compare isolates from New Zealand to a global S. pseudintermedius dataset. Their findings show that MRSP moves frequently across the globe, and is likely to have been imported to New Zealand on multiple occasions, but that horizontal gene transfer events resulting in the acquisition additional resistance classes are less frequent than previously estimated. This suggests that biosecurity and surveillance in addition to antibiotic stewardship should play important roles in mitigating the risk of MRSP, especially in countries such as New Zealand where MRSP is still rare. The full article is available here http://www.idrec.ac.nz/research-highlights-new,listing,,,204,drug-resistance-in-istaphylococcus-pseudintermediusi-from-new-zealand-dogs.html Exploring the Challenges of Analysing Highly Diverse Picobirnavirus Sequences http://www.idrec.ac.nz/research-highlights-new,listing,,,202,exploring-the-challenges-of-analysing-highly-diverse-picobirnavirus-sequences-.html The sequencing of nucleic acids directly from the environment using metagenomics has provided researchers with a snapshot of the enormous diversity of the viral world. There are an estimated 1031 viruses on Earth, but less than 1% of their diversity has been explored. Metagenomic studies provide access to previously unsequenceable genetic information, but rely on existing taxonomic framework to characterise the sequence information that they generate. This presents challenges for the analysis of sequence data from uncommon, highly divergent, or newly discovered virus types. To investigate some of these challenges, IDReC researchers Matt Knox, Kristene Gedye and David Hayman have recently published a paper in the journal Viruses using picobirnaviruses as a model. Picobirnaviruses are double stranded RNA (dsRNA) viruses, associated with acute watery diarrhoea and gastroenteritis in humans and animals as well in as asymptomatic individuals. They are distributed widely, in terms of both geography and host, and are increasingly common in viral metagenomic studies. In order to gain a better understanding of the diversity and taxonomy of picobirnaviruses, the authors analysed sequence data using phylogenetic and comparative protein structure approaches and found that sequence diversity within picobirnavirus exceeds that seen between many other dsRNA genera. Further, they also found that commonly used practices employed to classify and group picobirnavirus, such as analysis of short fragments and trimming of sequences, can influence phylogenetic conclusions. The full article can be accessed here http://www.idrec.ac.nz/research-highlights-new,listing,,,202,exploring-the-challenges-of-analysing-highly-diverse-picobirnavirus-sequences-.html Modelling the risk of novel infectious disease emergence from biodiversity hotspots http://www.idrec.ac.nz/research-highlights-new,listing,,,201,modelling-the-risk-of-novel-infectious-disease-emergence-from-biodiversity-hotspots.html As human activities continue to expand globally, we increase the rate of habitat fragmentation and biodiversity loss and further the encroachment of human populations in previously wild areas. Since the diversity of parasitic organisms likely correlates with the diversity and abundance of hosts they live in, these actions may increase the exposure of people to novel infectious agents from wildlife. In a new paper published in the Journal of the Royal Society Interface, IDReC researchers David Wilkinson, Jonathan Marshall, Nigel French and David Hayman present a theoretical framework based on the species-area relationship to link the exposure of people to novel infections with habitat biodiversity. The authors model changes in human exposure to microbes through defined classes of habitat and apply the model to African tropical forests as an example. Their results suggest that it is possible to identify high-risk areas for the mitigation and surveillance of novel disease emergence and that mitigation measures may reduce this risk, while conserving biodiversity. The full article is available here http://www.idrec.ac.nz/research-highlights-new,listing,,,201,modelling-the-risk-of-novel-infectious-disease-emergence-from-biodiversity-hotspots.html IDReC researchers Publish Review of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in New Zealand Dairy Farm Environments http://www.idrec.ac.nz/research-highlights-new,listing,,,199,idrec-researchers-publish-review-of-extended-spectrum-beta-lactamase-producing-enterobacteriaceae-in-new-zealand-dairy-farm-environments-.html Rose Collis and co-authors present a review of extended-spectrum beta-lactamase-producing Enterobacteriaceae in dairy farm environments with a New Zealand perspective. This review is published in a special edition of the journal Foodborne Pathogens and Disease that focuses on antimicrobial resistance (AMR) of foodborne pathogens on dairy farms. AMR is a global issue for both human and animal health, and inappropriate antimicrobial use is thought to be the main driver of increased incidence of antibiotic resistant bacteria. Increasing levels of antimicrobial use in food production animals and the subsequent development and spread of AMR, especially in poultry and swine production, has been identified as a food safety risk, but the risks associated with dairy production systems are unknown. Several AMR transmission pathways between dairy cattle, the environment and humans have been proposed such as contact with faeces-contaminated environments or via direct contact (for example, farmers are at high risk during close contact with animals during milking or calving). However, the actual contribution of each pathway is undetermined. Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) are of particular concern to human health. ESBL enzymes can break down commonly used antibiotics such as penicillin and cephalosporins, which may result in persistent infections. ESBL-E have also been associated with dairy cattle and the wider farm environment as well as animal-derived food products. This review addresses the current understanding of dairy farming in the prevalence and transmission of AMR, highlighting research gaps using ESBL-E as an exemplar; and secondly, a New Zealand dairy farm systems perspective is used to examine how farm management practices and on-farm antimicrobial use may contribute to increased levels of AMR in dairy cattle. The full publication can be found at https://www.ncbi.nlm.nih.gov/pubmed/30418042 http://www.idrec.ac.nz/research-highlights-new,listing,,,199,idrec-researchers-publish-review-of-extended-spectrum-beta-lactamase-producing-enterobacteriaceae-in-new-zealand-dairy-farm-environments-.html Prevalence of Toxic <i>Escherichia coli</i> on New Zealand Dairy Farms http://www.idrec.ac.nz/research-highlights-new,listing,,,195,prevalence-of-toxic-iescherichia-colii-on-new-zealand-dairy-farms.html Shiga toxin-producing Escherichia coli (STEC) is a type of E. coli baceteria that produces a potent toxin which can cause bloody diarrhoea and kidney failure in people, particularly young children. Cattle are natural (asymptomatic) carriers of STEC and previous IDReC research found that people living around cattle and who had direct contact with cattle faeces were at higher risk for the disease.&#160; &#160; Springer Browne, who recently completed his PhD, drove over 12,000km in 9 weeks to visit over 100 dairy farms during the 2014 calving season to provide the first national estimate of STEC prevalence.&#160; His work focused on young dairy calves, a cattle population previously identified to have a higher prevalence of STEC.&#160; &#160; The recent IDReC publication in Applied and Environmental Microbiology used an advanced molecular laboratory method to identify STEC in 20% of calves on 75% of the farms studied, indicating widespread prevalence across New Zealand. The study provides information that will be useful for designing on-farm interventions to reduce human STEC exposure and inform future risk analysis decisions. &#160; Springer noted &quot;Driving from Northland to Southland and seeing the beautiful New Zealand countryside was a highlight, but by far the best experience was working with all the New Zealand dairy farmers, who graciously participated in the study.&#160; &#160; Several other IDReC researchers were involved in this work including Anne Midwinter, Adrian Cookson, Patrick Biggs, Jonathan Marshall, Jackie Benschop, Neville Haack, Rukhshana Akhter and Nigel French. Access to the full article can be found at http://aem.asm.org/content/84/14/e00481-18 http://www.idrec.ac.nz/research-highlights-new,listing,,,195,prevalence-of-toxic-iescherichia-colii-on-new-zealand-dairy-farms.html New approaches for assessing genealogical relationships between bacteria http://www.idrec.ac.nz/research-highlights-new,listing,,,191,new-approaches-for-assessing-genealogical-relationships-between-bacteria.html IDReC researchers led by Ji Zhang have recently published a paper entitled &#8220;Genome-by-genome approach for fast bacterial genealogical relationship evaluation&#8221; in the journal Bioinformatics. Recent advances in DNA sequencing technology have led to an increase in the amount of data available and the need for improved analysis tools. The paper presents a new algorithm (Fast-GeP), which infers high-resolution genealogical relationships between bacterial isolates using whole-genome sequencing data. Fast-GeP has several advantages compared to conventional gene-by-gene approaches and will allow researchers to better understand the biological information in DNA sequence data. Access to the full article is found at https://www.ncbi.nlm.nih.gov/pubmed/29608746 http://www.idrec.ac.nz/research-highlights-new,listing,,,191,new-approaches-for-assessing-genealogical-relationships-between-bacteria.html <i>Toxoplasma gondii</i> and <i>Giardia duodenalis</i> detected in commercial green-lipped mussels http://www.idrec.ac.nz/research-highlights-new,listing,,,189,itoxoplasma-gondiii-and-igiardia-duodenalisi-detected-in-commercial-green-lipped-mussels.html A recently published study undertaken by Alicia Coupe, in collaboration with IDReC, has detected the protozoan parasites Toxoplasma gondii and Giardia duodenalis in green-lipped mussels.&#160; Molecular prevalence of T. gondii was estimated to be 16.4%, while G. duodenalis was discovered in 1% of mussels.&#160; In addition, the study was the first to use molecular techniques to demonstrate that sporulated oocysts of T. gondii were present in positive samples.&#160; Only sporulated oocysts can be infectious, so the research further establishes shellfish consumption as a health concern.&#160; The study was funded by the Massey University Research Foundation, the Lewis Fitch Foundation, the Marian Cunningham Memorial Fund, and the New Zealand Ministry of Health. &#160; The full publication can be accessed at https://www.ncbi.nlm.nih.gov/pubmed/29550995 http://www.idrec.ac.nz/research-highlights-new,listing,,,189,itoxoplasma-gondiii-and-igiardia-duodenalisi-detected-in-commercial-green-lipped-mussels.html Updating the genomic taxonomy and epidemiology of <i>Campylobacter hyointestinalis</i> http://www.idrec.ac.nz/research-highlights-new,listing,,,185,updating-the-genomic-taxonomy-and-epidemiology-of-icampylobacter-hyointestinalisi.html In their recent paper published in Scientific Reports, David Wilkinson and colleagues demonstrated the presence of the enteric bacterium Campylobacter hyointestinalis in sheep, cattle and deer from the Manawatu region. Campylobacter spp. are one of the most common causative agents of global human gastric disease, and many emerging Campylobacter species are also associated with other severe forms of disease. In their article, they provided a comprehensive literature review for C. hyointestinalis, a member of the emerging Campylobacter spp. and used whole genome sequencing to explore the evolutionary characteristics and taxonomic classification of the species. Genomic data generated in this study allowed them to investigate a number of important, previously unexplored characteristics of the organism including virulence, defence and metabolism-associated genetic elements. They demonstrated that the C. hyointestinalis genome is extremely mobile, with horizontal gene-transfer commonly playing a role in its genetic diversification. This genomic flexibility has important consequences for the way in which we understand the taxonomic classification of this, and other, prokaryotic organisms.&#8221; Photo :&#160;IDReC researchers and study authors Lynn Rogers, Anne Midwinter, David Wilkinson and Ahmed Fayaz in Hopkirk Lab. Photo by Matt Knox. http://www.idrec.ac.nz/research-highlights-new,listing,,,185,updating-the-genomic-taxonomy-and-epidemiology-of-icampylobacter-hyointestinalisi.html Genomic Analysis of long-term <i>Campylobacter</i> colonisation http://www.idrec.ac.nz/research-highlights-new,listing,,,181,genomic-analysis-of-long-term-icampylobacteri-colonisation.html Campylobacteriosis is inflammation of the gastrointestinal tract as a result of Campylobacter infection. Most campylobacteriosis cases are acute and self-limiting, with Campylobacter excretion ceasing a few weeks after symptoms cease. Longer periods of excretion can arise from chronic, asymptomatic and subsequent infections.&#160; Multiple studies have investigated long-term Campylobacter excretion in animals, but few have investigated it in humans. In a new paper published in&#160;the Journal of Infectious Diseases (https://academic.oup.com/jid/article/217/1/103/4584509), the authors used genomic and phenotypic testing to investigate a patient that had been continuously excreting Campylobacter for 10 years. Phylogenetics revealed that isolates collected from the patient were closely related, sharing a date of common ancestor around the same time the patient began suffering from daily episodes of diarrhoea. Phenotypic testing revealed that the patient that the Campylobacter had become resistant to antibiotics during periods of time that the patient was prescribed them and that there was selection for changes in motility genes. The authors concluded that the patient had been continuously colonised with Campylobacter for at least 10 years, and that the Campylobacter had adapted to colonisation by becoming resistant to the antibiotics prescribed and altering their motility. The first author on this work is IDREC&#39;s Dr Samuel Bloomfield, who recently completed his PhD entitled &quot;Transmission and evolution of bacteria during the course of enteritis outbreaks&quot; under the supervision of Jackie Benschop, Patrick Biggs, Anne Midwinter, David Hayman, Jonathan Marshall, Phil Carter and Nigel French. The full paper citation is &quot;Bloomfield SJ, Midwinter AC, Biggs BJ, French NP, Marshall HC, Hayman DTS, Carter PE, Thornley C, Yap R, and Benschop J (2017). Long-term colonization by Campylobacter jejuni within a human host: evolution, antimicrobial resistance and adaptation. Journal of Infectious Diseases, 217, 103-111&quot; http://www.idrec.ac.nz/research-highlights-new,listing,,,181,genomic-analysis-of-long-term-icampylobacteri-colonisation.html Genomic Analysis of a <i>Salmonella enterica</i> outbreak http://www.idrec.ac.nz/research-highlights-new,listing,,,175,genomic-analysis-of-a-isalmonella-entericai-outbreak.html Salmonellosis, caused by nontyphoidal serovars of Salmonella enterica subsp. enterica is the second largest cause of bacterial enteritis in New Zealand and a significant burden on public health. For example, during 1998-2012, an extended outbreak of S. enterica serovar Typhimurium definitive type 160 (DT160) affected &#62;3,000 humans and killed wild birds in New Zealand. In a new paper published in&#160;Emerging Infectious Diseases (DOI: https://dx.doi.org/10.3201/eid2306.161934), the authors used genomic epidemiologic approaches to characterize the origin, evolution, and transmission of this outbreak. Since DT160 was a previously unreported subtype in New Zealand and a probable point source introduction, it was possible to track the evolution of this pathogen as it spread across multiple host species. Whole genome sequence analysis of Salmonella Typhimurium DT160 isolates from human, wild bird, poultry and bovine hosts suggest that DT160 was introduced on a single occasion from 1996 through 1998, before spreading throughout the country and becoming more genetically diverse over time. Isolates collected from different hosts were highly similar, indicating frequent cross-species transmissions. The first author on this work is IDREC&#39;s Dr Samuel Bloomfield, who recently completed his PhD entitled &quot;Transmission and evolution of bacteria during the course of enteritis outbreaks&quot; under the supervision of Nigel French, Jackie Benschop, David Hayman, Anne Midwinter, Patrick Biggs and Johnathan Marshall.&#160; The full paper citation is &quot;Bloomfield SJ, Benschop J, Biggs PJ, Marshall JC, Hayman D, Carter PE, et al. Genomic Analysis of Salmonella enterica Serovar Typhimurium DT160 Associated with a 14-Year Outbreak, New Zealand, 1998-2012. Emerg Infect Dis. 2017;23(6):906-913.&quot; http://www.idrec.ac.nz/research-highlights-new,listing,,,175,genomic-analysis-of-a-isalmonella-entericai-outbreak.html PhD student Samuel Bloomfield presents genomic analysis of Salmonella outbreak at ASM Microbe conference http://www.idrec.ac.nz/research-highlights-new,listing,,,173,phd-student-samuel-bloomfield-presents-genomic-analysis-of-salmonella-outbreak-at-asm-microbe-conference-.html From the 1st to the 5th of June, 2017 IDRECs Samuel Bloomfield attended the ASM Microbe conference in New Orleans, Louisiana, USA. During the conference Samuel attended a workshop on new bacterial genomics software (PATRIC), networked with a large number of experts performing similar work, and presented some of his work on Salmonella. The presentation was entitled: Genomic analysis of a decade-long outbreak of Salmonella enterica serovar Typhimurium DT160 in New Zealand. Travel,registration and accommodation for this conference were funded by the IVABS travel fund. http://www.idrec.ac.nz/research-highlights-new,listing,,,173,phd-student-samuel-bloomfield-presents-genomic-analysis-of-salmonella-outbreak-at-asm-microbe-conference-.html Soil bacteria and their invertebrate consumer respond differently to warming and freeze-thaw cycles, in the Antarctic Dry Valleys http://www.idrec.ac.nz/research-highlights-new,listing,,,172,soil-bacteria-and-their-invertebrate-consumer-respond-differently-to-warming-and-freeze-thaw-cycles-in-the-antarctic-dry-valleys.html Recently published research by IDREC researcher Matt Knox and co-authors show decoupled responses of soil bacteria and their invertebrate consumer to warming, but not freeze-thaw cycles (FTCs), in the Antarctic Dry Valleys. Using a laboratory microcosm experiment the authors investigate how temperature variability affects soil bacterial cell numbers, as well as the abundance and traits of soil microfauna (the microbivorous nematode&#160;Scottnema lindsayae). The findings suggest that higher occurrence of FTCs in cold ecosystems will select for large body size within soil microinvertebrates while reducing their abundance overall. In contrast, warm temperatures without FTCs could lead to divergent responses in soil bacteria and their microinvertebrate consumers, potentially affecting energy and nutrient transfer rates in soil food webs of cold ecosystems. &#160; Read the full publication at http://onlinelibrary.wiley.com/doi/10.1111/ele.12819/full (Photo : Matt Knox ,The shores of Lake Bonney in Taylor Valley, Antarctica.) http://www.idrec.ac.nz/research-highlights-new,listing,,,172,soil-bacteria-and-their-invertebrate-consumer-respond-differently-to-warming-and-freeze-thaw-cycles-in-the-antarctic-dry-valleys.html Population risk factors for measles in New Zealand http://www.idrec.ac.nz/research-highlights-new,listing,,,167,population-risk-factors-for-measles-in-new-zealand.html Despite eliminating endemic measles in New Zealand, small outbreaks continue to occur, with recorded cases in Auckland , Palmerston North&#160; and Waikato&#160; within the last 12 months alone. Since measles outbreaks over the last decade in New Zealand occur as introductions from abroad, IDReC researchers David Hayman, Jonathan Marshall, Nigel French, Tim Carpenter and Mick Roberts assess the current risk factors in a recent paper in Epidemiology and Infection. Using a generalized linear model the authors analyse risk factors for 1137 measles cases from 2007 to June 2014, provide estimates of national immunity levels, and model measles importation risk. The results suggest that overseas visitors and/or returning NZ travellers are seeding measles outbreaks and that this risk is highest at peak visitation time during December. They also caution that current immunization levels in New Zealand are insufficient to prevent future outbreaks because of heterogeneous immunity in the population, leaving particular age groups at risk. Read the full publication here http://www.idrec.ac.nz/research-highlights-new,listing,,,167,population-risk-factors-for-measles-in-new-zealand.html Bat and Virus Ecology in a Dynamic World http://www.idrec.ac.nz/research-highlights-new,listing,,,166,bat-and-virus-ecology-in-a-dynamic-world.html The March 2017 issue of Microbiology Australia features an &quot;Under the Microscope&quot; article by IDReC researchers David Wilkinson and David Hayman. Understanding of ecological relationships leading up to viral spillover can potentially help reduce the threat of emerging virus both in Australia and elsewhere. In the article, they present a review of the potential impacts of anthropogenic changes such as land-use change, habitat loss and introduced species and how these factors impact bat-viral ecology in Australia. Read the publication &#160; http://www.idrec.ac.nz/research-highlights-new,listing,,,166,bat-and-virus-ecology-in-a-dynamic-world.html Antimicrobial Resistance Challenges in New Zealand http://www.idrec.ac.nz/research-highlights-new,listing,,,152,antimicrobial-resistance-challenges-in-new-zealand.html The March 2017 issue of the New Zealand Veterinary Journal focuses on antimicrobial resistance (AMR) and features papers authored by several researchers in IDReC. Leah Toombs-Ruane and co-authors present a review of multidrug resistant Enterobacteriaceae in New Zealand. Enterobacteriaceae include familiar pathogens such as Escherichia coli, Klebsiella pneumoniae and Salmonella enterica. One AMR mechanism commonly employed by these bacteria is the production of the beta-lactamase enzyme, specifically extended-spectrum beta-lactamase (ESBL) enzymes. These have the ability to break down commonly used antibiotics, such as penicillin and cephalosporin, and render them ineffective for treatment, thus increasing the severity and duration of infections. In addition to ESBL-production, these strains are often associated with other mechanisms of resistance, causing them to be multidrug resistant. The review describes the mechanisms and potential transmission pathways of MDR in Enterobacteriaceae which include interactions among humans, animals and the environment. Accordingly, the authors advocate a One Health approach for controlling AMR that includes increased surveillance of resistant bacteria, monitoring antimicrobial use and antimicrobial stewardship. &#160;In the same issue of the NZVJ is an accompanying commentary by the authors of the above review. The commentary expands upon the message of utilising a One Health framework when tacking the challenges presented by antimicrobial resistance. http://www.idrec.ac.nz/research-highlights-new,listing,,,152,antimicrobial-resistance-challenges-in-new-zealand.html Molecular epidemiology of New Zealand <i>Campylobacter coli </i> strains http://www.idrec.ac.nz/research-highlights-new,listing,,,150,molecular-epidemiology-of-new-zealand-icampylobacter-coli-i-strains-.html Campylobacteriosis is one of the most common foodborne diseases worldwide and a significant health burden in New Zealand. Campylobacter jejuni is the predominant Campylobacter species worldwide, accounting for approximately 90% of human cases, followed by Campylobacter coli. Since most studies in New Zealand have focused on C. jejuni, the impact of C. coli strains on human health is not well understood. In a new paper published in&#160;Applied and Environmental Microbiology (doi:10.1128/AEM.00934-16), we analysed C. coli genotypes collected in the Manawatu region of New Zealand from clinical cases, fresh poultry meat, ruminant feces and environmental water sources, between 2005 and 2014, to study their population structure and estimate the contribution of each source to the burden of human disease. Our findings show that New Zealand C. coli strains are genetically similar to those found in the United Kingdom. Further analysis identified ruminants and poultry as the main infection sources for human cases in New Zealand, as well as a smaller contribution from surface water sources. We also showed that in contrast to C. jejuni, ruminant sources might have a greater relative contribution to infection burden than poultry in C. coli. These results highlight the need to consider each Campylobacter species separately when designing public health interventions. http://www.idrec.ac.nz/research-highlights-new,listing,,,150,molecular-epidemiology-of-new-zealand-icampylobacter-coli-i-strains-.html The origin of <i>Cryptosporidium</i> - a major infectious disease in vertebrates. http://www.idrec.ac.nz/research-highlights-new,listing,,,146,the-origin-of-icryptosporidiumi---a-major-infectious-disease-in-vertebrates.html Cryptosporidium species are parasites that have been found in all vertebrate groups although most of their diversity is associated with mammal and bird species. They are increasingly known as major contributors to diarrhoea morbidity and mortality in humans, mainly in children and AIDS patients, and economic losses in agriculture and medical care. There is a lack of information about the time of origin for this group of parasites and the reciprocally effect with their hosts. Current tools in biology for investigation of evolutionary history using molecular sequences can help to infer the similarity or not of the dates of divergences and interactions between Cryptosporidium and their hosts. In a new paper published in Parasitology , (doi: 10.1017/S0031182016001323) we estimated that the origin of Cryptosporidium is concordant with the rise of vertebrates about 600 Mya. Furthermore, the formation of several species in Cryptosporidium occurred after the bolide impact of an asteroid resulted in the extinction of numerous animal groups (Dinosaurs among the most known), which left major ecological opportunities for terrestrial mammals and birds to flourish (the Cretaceous-Paleogene extinction event). Despite the evidence that some species are shifting to infect new hosts there is also evidence of coevolution with vertebrate species. All of this together will help in our understanding of the evolution of Cryptosporidium and open new avenues of research in the ecology, dynamics and epidemiology of cryptosporidiosis disease in humans and other animals. &#160; Detail Picture&#160; Cryptosporidium.png (0.28MB) &#160; http://www.idrec.ac.nz/research-highlights-new,listing,,,146,the-origin-of-icryptosporidiumi---a-major-infectious-disease-in-vertebrates.html David Hayman and Reed Hranac present at the International Bat Research Conference http://www.idrec.ac.nz/research-highlights-new,listing,,,143,david-hayman-and-reed-hranac-present-at-the-international-bat-research-conference.html Dr David Hayman and PhD student Reed Hranac recently presented at the International Bat Research Conference in Umhlanga, Durban. With warm weather and beautiful scenery (as depicted in some of the photos) it was clearly an ideal location for a conference. The conference brings together researchers from around the world to present their research on a range of topics including disease ecology, bats and pollution, reproduction, bat hunting, and the biology of sensory adaptations. Dr Hayman gave two presentations: &quot;Can survival analyses detect hunting pressure in a highly connected species? Lessons from Straw-coloured fruit bats&quot; [in the hunting session], &quot;Maternal antibody and the persistence of Lagos bat virus in populations of the African Straw-coloured fruit bat&quot; [in the disease ecology session]. In addition, Dr Hayman presented to the South African Centre for Epidemiological Modelling &#38; Analysis (SACEMA) on predicting undiscovered filovirus reservoirs and patterns of disease emergence. Reed Hranac presented some of the work from his PhD. His talk was titled &quot;:Modeling the Impact of White-Nose Syndrome on Two Western Myotis Bats&quot; [in the disease ecology session]. Reed&#39;s PhD is focused on modelling infectious diseases of wildlife, specifically bats and is broken into two parts. The first involves spatial-temporal modelling of Filoviruses in central and western Africa to investigate potential sylvatic viral maintenance within the Chiropteran community. The other half of his project concerns the White-nose Syndrome outbreak among bats in North America and uses models to evaluate the metabolic consequences of fungal infection during hibernation. &#160; &#160; &#160; Photo 1: Lighthouse in Umhlanga, Durban Photo 2: South African Centre for Epidemiological Modelling &#38; Analysis (SACEMA), Stellenbosch University Photo 3: Botanical gardens in Durban Photo 4: Beach in Durban http://www.idrec.ac.nz/research-highlights-new,listing,,,143,david-hayman-and-reed-hranac-present-at-the-international-bat-research-conference.html IDReC and University of Glasgow researchers establish an African Leptospirosis Network http://www.idrec.ac.nz/research-highlights-new,listing,,,141,idrec-and-university-of-glasgow-researchers-establish-an-african-leptospirosis-network.html There is growing evidence of a substantial burden of human leptospirosis in Africa but it is rarely considered as a differential diagnosis for acute febrile illness, and there is little access to diagnostic services for leptospirosis on the continent. Research efforts have remained fragmented with researchers often working in isolation, and little sustainable investment in disease-specific infrastructure or expertise in many African countries. &#160; Collectively, we have identified a need to bring together researchers and other professionals, interested in leptospirosis in Africa who would benefit from international support and collaboration. In early 2016 a virtual African Leptospirosis Network was founded by Dr Jackie Benschop, co-director mEpiLab, Massey University and Dr Kathryn Allan, Wellcome Trust Veterinary Training Fellow, University of Glasgow. &#160;Dr Allan&#8217;s work in Northern Tanzania has identified that cattle appear to be important sources of human infection. One serovar identified from cattle in this area, Leptospira borgpetersenii serovar Hardjo is an important cause of human leptospirosis in farming communities around the world, including in New Zealand. &#160; Dr Benschop is a steering committee member of the World Health Organisation&#8217;s Global Leptospirosis Environmental Action Network and investigates food safety risks in Northern Tanzanian. The African Leptospirosis Network currently has 41 members from academia, clinical practice, government and non-governmental agencies and others. Founding members were based predominantly in institutions outside the continent but increasingly colleagues based in public health, laboratories, veterinary, and academic institutions within Africa are joining. &#160; Work to date has included identification of new members, preparing a proposal for the WHO to support the network, document sharing, linking colleagues with mentors and a submission of an abstract to a One Health meeting. Future plans are focused on capacity building and include protocol sharing and seeking funding support to identify and address knowledge gaps in our understanding of leptospirosis in Africa. Picture : A cattle market in Northern Tanzania, which Dr Jackie Benschop visited in early 2016. http://www.idrec.ac.nz/research-highlights-new,listing,,,141,idrec-and-university-of-glasgow-researchers-establish-an-african-leptospirosis-network.html IDReC Sam Bloomfield , Research into cause of human salmonellosis cases in New Zealand. http://www.idrec.ac.nz/research-highlights-new,listing,,,139,idrec-sam-bloomfield--research-into-cause-of-human-salmonellosis-cases-in-new-zealand.html In New Zealand, most salmonellosis cases are caused by Salmonella enterica serovar Typhimurium. In 1998, Salmonella Typhimurium DT160 was isolated from a human salmonellosis patient in New Zealand. S. Typhimurium DT160 then became the predominant strain isolated from human salmonellosis cases until 2010. During this time, S. Typhimurium DT160 infected and killed multiple wild birds throughout New Zealand, and was isolated from a large number of other animals (e.g. cows and chickens). Samuel has been using whole genome sequencing to determine how S. Typhimurium evolved over the course of the outbreak, how it was transmitted between the various affected populations, and how it was superseded by other Salmonella strains as the predominant cause of human salmonellosis cases in New Zealand. Current work indicates that S. Typhimurium DT160 radiated out from a point source over time, and that there was a large amount of transmission between the various affected populations. &#160; &#160; Figure 1. NeighbourNet tree of 109 Salmonella Typhimurium DT160 isolates (based on 793 core SNPs) and coloured by year. The red dots represent DT160 isolates collected from 1999 &#8211; 2000, the orange dots represent DT160 isolates isolated from 2001 &#8211; 2003, the green dots represent DT160 isolates collected from 2004 &#8211; 2006, the blue dots represent DT160 isolates collected from 2007 &#8211; 2009, and the purple dots represent DT160 isolated collected from 2010 &#8211; 2012. &#160; http://www.idrec.ac.nz/research-highlights-new,listing,,,139,idrec-sam-bloomfield--research-into-cause-of-human-salmonellosis-cases-in-new-zealand.html IDReC Dr David A Wilkinson, has made the front cover of the latest issue of Environmental Microbiology. http://www.idrec.ac.nz/research-highlights-new,listing,,,131,idrec-dr-david-a-wilkinson-has-made-the-front-cover-of-the-latest-issue-of-environmental-microbiology-.html Research by one of IDReC&#39;s new postdoctoral researchers, Dr David A Wilkinson, has made the front cover of the latest issue of Environmental Microbiology. Together with other researchers from Reunion Island, in the Indian Ocean, he was looking at the dynamics of microbial infection within a bat maternity colony. The front cover depicts two juvenile bats of the species Mormopterus francoismoutoui, a photo which was taken during field trips for this study. &#160; Figure 1: Front cover of this month&#39;s edition of Environmental Microbiology. &quot;Bats are particularly interesting reservoirs of disease. We often cite the emergence of diseases such as Ebola, the henipaviruses or the coronaviruses SARS and MERS due to the tragic impact that these diseases have had on human populations and that, in one way or another, their emergence has been associated with bat reservoirs. The jury is still out as to whether bats are &#8216;worse&#39; sources of disease than other wild animals such as rodents, and a number of hypotheses have been put forward as to why their physiologies, immune systems or behaviours may influence their ability to carry disease-causing microbes. However, there is no denying that these flying mammals are fascinating. Whether it be because of the wide range of ecological niches that they inhabit, the fact that they can live in huge groups or just the &#8216;spook factor&#39; that you get from vampire bats or some of the weirder-looking old world bats. &#160; &#160; Figure 2: Seasonal dynamics of infections in a maternity colony of M. francoismoutoui. The continuous lines represent the proportion of PCR-positive samples for Leptospira (green) and paramyxovirus (purple), and the shaded area the 95% CI. Studying the bats in Reunion was absolutely amazing - M. francoismoutoui is a very small insectivorous bat that weighs approximately 5-6 grams, and is extremely common in La Reunion. During the breeding season, female bats group together in very large numbers (at one point we estimated nearly 150,000 individuals in the cave we were studying). As we did not want to disturb the colony, we collected urine samples under the bats as they would leave their roost to feed in the evenings, and used these samples to look for two different sorts of microbe - one bacterial and one viral. Our study showed that, despite the different nature of these microbes, the dynamics of infection followed nearly identical patterns over the studied period. This helps us to understand potential risk factors that may lead to spill-over and the emergence of disease, which in this instance seem to be directly linked to animal ecology.&quot; David Wilkinson, Postdoctoral Researcher, IDReC http://www.idrec.ac.nz/research-highlights-new,listing,,,131,idrec-dr-david-a-wilkinson-has-made-the-front-cover-of-the-latest-issue-of-environmental-microbiology-.html Biannual birth pulses allow filoviruses to persist in bat populations http://www.idrec.ac.nz/research-highlights-new,listing,,,115,biannual-birth-pulses-allow-filoviruses-to-persist-in-bat-populations.html Pioneers of the application of mathematics to infectious disease biology posed three interrelated questions about infectious disease dynamics: can we predict and explain the size and periodicity of epidemics, how does the flow of susceptible individuals affect endemic persistence and do critical community sizes exist? Those pioneers applied their models to human infectious diseases, however most emerging infectious diseases are zoonoses from wildlife hosts. Thus, today disease ecologists often aim to address the same questions in wildlife systems. Filoviruses Ebolavirus (EBOV) and Marburgvirus (MARV) cause hemorrhagic fevers with high mortality rates, posing significant threats to public health. To understand transmission into human populations, filovirus dynamics within reservoir host populations must be understood. Studies have directly linked filoviruses to bats, but the mechanisms allowing viral persistence within bat populations are poorly understood. Theory suggests seasonal birthing may decrease the probability of pathogen persistence within populations, but data suggest MARV may persist within colonies of seasonally breeding Egyptian fruit bats. This study used stochastic modelling to explore fundamental questions relating to filovirus ecology: 1) can filoviruses persist within isolated bat colonies; 2) do critical community sizes exist; and 3) how do host-pathogen relationships affect spillover transmission potential? Data from serological surveys were used to test if the model findings were supported by field data. The results showed that synchronous annual breeding and shorter incubation periods did not allow filovirus persistence, whereas bi-annual breeding and longer incubation periods, such as reported for Egyptian fruit bats and EBOV in experimental studies, allowed persistence in colony sizes often found in nature. Serological data supported the findings, with bats from species with two annual birth pulses more likely to be seropositive (odds ratio 4.4, 95% confidence interval 2.5-8.7) than those with one, suggesting biannual birthing is necessary for filovirus persistence. &#160; &#160; Figure 1. Number of susceptible and infected juveniles and infected adults over the final years for 500 stochastic simulations of a 25 year simulation model of filovirus-bat infection dynamics. This model has biannual birth pulses, with the synchrony parameter (s) 14.3, a birth rate of 0.98 per female per year, and an incubation period (1/&#963;) of 21 days. (Hayman, 2015) &#160; The results of this study can perhaps explain the periodicity of infection prevalence within the host, and suggest that filovirus peak prevalences may be found in juvenile bats and be seasonally peaked. Given current knowledge we might expect colony sizes of tens of thousands of bat for filovirus persistence, given the periodicity of birth and infection prevalence. The results of this study provide a useful framework for future studies and offer insights into filovirus ecology that can be used to guide fieldwork, experimental studies and emerging infectious disease management. This work has recently been published in Proceedings of the Royal Society B. Hayman DTS. 2015 Biannual birth pulses allow filoviruses to persist in bat populations. Proc. R. Soc. B 20142591 http://dx.doi.org/10.1098/rspb.2014.2591 &#160; http://www.idrec.ac.nz/research-highlights-new,listing,,,115,biannual-birth-pulses-allow-filoviruses-to-persist-in-bat-populations.html Shedding and Seroprevalence of Pathogenic Leptospira spp. in Sheep and Cattle at a New Zealand Abattoir http://www.idrec.ac.nz/research-highlights-new,listing,,,98,shedding-and-seroprevalence-of-pathogenic-leptospira-spp-in-sheep-and-cattle-at-a-new-zealand-abattoir.html Fang Fang PhD Candidate, mEpiLab /IVABS / EpiCentre Leptospirosis is a zoonotic disease of worldwide importance caused by pathogenic spirochaetes belonging to the genus Leptospira. Feral and domestic mammals can be maintenance hosts to various serovars. Leptospires colonize the renal proximal tubules of carrier animals and may persist and be shed in the urine without causing apparent illness. Humans usually serve as an incidental host, and the infection occurs through direct contact with infected animal urine, or indirect contact with contaminated soil or water. In New Zealand, leptospirosis is the most common occupationally acquired zoonotic disease, mainly associated with meat workers and farmers. Cattle and sheep are important animal reservoirs. Previous surveys of farms and abattoirs have shown that 69% (59/85) of beef cattle herds and 44% (42/95) of sheep slaughter lines were seropositive for leptospirosis. We conducted a cross-sectional study on sheep and cattle slaughtered at a New Zealand abattoir from September to November 2010 to investigate the supplier specific shedding rate, renal carriage rate and seroprevalence of leptospires. Urine, kidney and blood samples were collected from carcasses of 399 sheep and 146 cattle. The urine and kidney samples were tested by quantitative real-time PCR (qPCR), while serum samples were tested by microscopic agglutination test (MAT). In total, 27% (73/274) of urine samples tested positive by qPCR. Species-specific shedding rates were 31% for sheep and 21% for cattle. For 545 kidney samples tested, 145 were qPCR positive (27%). The average prevalence of kidney qPCR positivity was 29% for sheep and 21% for cattle. Three hundred and thirty of 542 sampled sheep and cattle had antibodies against Leptospira borgpetersenii serovar Hardjobovis and/or Leptospira interrogans serovar Pomona, based on reciprocal MAT titre &#8805; 1 : 48 (overall seroprevalence of 61%). Seroprevalence was 57% for sheep and 73% for cattle (Figure. 1.). Among the seropositive animals, 41% (70/170) were shedding and 42% (137/330) had renal carriage. Figure. 1. Seroprevalence of serum samples with positive reciprocal microscopic agglutination test (MAT) titre (&#8805; 1 : 48) from sheep and cattle by serovar. The findings from this study demonstrated that urinary shedding and renal carriage rates of leptospires in livestock entering slaughter premises in New Zealand, and the potential risk of acquiring leptospirosis infection for workers in contact with unvaccinated livestock, can be high. Urinary shedding and renal carriage rates found in this study in both sheep and cattle help reinforce the value of vaccination programmes aimed to reduce the prevalence of leptospirosis in these animals, and to protect workers against the disease in New Zealand.&#160;&#160; This work has been published in Zoonoses and Public Health and is available online. Fang, F., Collins-Emerson, J. M., Cullum, A., Heuer, C., Wilson, P. R. and Benschop, J. 2014. Shedding and Seroprevalence of Pathogenic Leptospira spp. in Sheep and Cattle at a New Zealand Abattoir. Zoonoses and Public Health. doi: 10.1111/zph.12146 http://www.idrec.ac.nz/research-highlights-new,listing,,,98,shedding-and-seroprevalence-of-pathogenic-leptospira-spp-in-sheep-and-cattle-at-a-new-zealand-abattoir.html The transmission of Mycobacterium avium subsp. paratuberculosis between farms via livestock movements http://www.idrec.ac.nz/research-highlights-new,listing,,,90,the-transmission-of-mycobacterium-avium-subsp-paratuberculosis-between-farms-via-livestock-movements-.html Nelly Marquetoux PhD candidate, EpiCentre / IVABS Mycobacterium avium subsp. paratuberculosis (MAP) is the causal agent for paratuberculosis (PTB) or Johne&#8217;s disease in livestock. The purchase of infected stock is thought to be an important pathway for introducing MAP onto properties. However, no documented evidence of farm-to-farm transmission of MAP exists so far. This may have important implications for the control of paratuberculosis (PTB) on farms and in areas free of infection. The objective of this work was to analyze molecular data combined with animal movement records to evaluate the transmission of MAP between farms. The study population included 119 farms of Landcorp Farming Limited (LC) scattered throughout New Zealand (dairy, beef, sheep and deer). Livestock movement records between LC properties were available from 2006 to 2010. All farms were screened for evidence of MAP infection in samples of 20 animals per farm and species in 2010. Isolates from pooled fecal samples were typed using VNTR/SSR. We combined social network analysis with molecular data to analyze the probability for 2 in-contact farms to share the same strain type, as a function of their relative position in the contact network. &#160; Figure 1: Network of LC farms (circles) connected via livestock movements (arrows). Farms in grey were not tested; farms in yellow were negative for pooled fecal culture. The colors of other farms represent VNTR/SSR strains of MAP identified on a property. The two apparent clusters represent farms in the South Island (SI) and the North Island (NI) of New Zealand&#160; The probability that two farms harbored the same strain type of MAP tested in 2010 was associated with the path length of annual livestock movements in 3 years (2007 &#8211; 2010) after adjusting for the effect of species, island and geographical distance (p&#60;0.05): the more distant two farms were in the network, the less likely they shared the same strain. This association was not significant in the 2006-2007 season. Our findings suggest that livestock movements contribute to the transmission of PTB between farms. This is likely to impact on the currently high endemic MAP infection prevalence of dry stock and dairy farms (sheep 48%, deer 63%, beef 43%, dairy 74%).&#160; The findings suggest that farm biosecurity may be instrumental for controlling PTB even in herd and flock populations where MAP is endemic. http://www.idrec.ac.nz/research-highlights-new,listing,,,90,the-transmission-of-mycobacterium-avium-subsp-paratuberculosis-between-farms-via-livestock-movements-.html Identification of populations for disease surveillance in a translocated network of endangered Takahe http://www.idrec.ac.nz/research-highlights-new,listing,,,67,identification-of-populations-for-disease-surveillance-in-a-translocated-network-of-endangered-takahe.html Zo&#235; Grange PhD Candidate, Allan Wilson Centre, mEpilab, Wildbase and&#160;Victoria University of Wellington Social network analysis is being increasingly used in epidemiology and disease modelling in humans, domestic animals, and wildlife. We investigated this tool in describing a translocation network (area that allows movement of animals between geographically isolated locations) used for the conservation of an endangered flightless rail endemic to New Zealand, the Takah&#275; (Porphyrio hochstetteri). The takah&#275; was believed to be extinct until it was rediscovered in the Murchison Mountains, Fiordland in 1948. Subsequently, individuals were moved into offshore predator free reserves to ensure their survival. With a current population of approximately 230 individuals, active conservation management involving multiple translocations per year is required to reduce the detrimental effects of inbreeding. The extent of isolation and human mediated mixing of individuals may influence the dynamics of pathogen prevalence and transmission in the population as a whole. As such analysis of the population in terms of subpopulations and their connectivity to each other can provide insight into the epidemiology of pathogen transmission and identify locations for disease surveillance. Five years of takah&#275; translocation records within New Zealand were collated and social network principles were applied to describe the connectivity of the translocation network (Figure 1). Common network descriptors and measures of centrality highlighted key locations for targeting disease surveillance. Identification of sink (wild population) and source (offshore island) locations were important in understanding potential pathogen evolution and disease threats. Additionally, the breeding centre acts as a hub of the network, an intermediary between many takah&#275; subpopulations, thus important in pathogen transmission. The analysis has found that the takah&#275; network is highly variable in terms of subpopulation connectivity, which has implications on understanding the epidemiology of past, present and future disease threats. The visual representation of movements of animals in a population that this technique provides can aid decision makers when they evaluate translocation proposals, conduct pathogen surveillance or attempt to control a disease outbreak. This work has been published in Conservation Biology and is available online. Grange, Z., van Andel, M., French, N.P., &#38; Gartrell, B. 2014. Social networking of an endangered flightless bird and its use in targeting disease surveillance. Conservation Biology, doi: 10.1111/cobi.12178 &#160; &#160;a)&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; b) Figure 1: Node (circles) and tie (lines) networks of cumulative Takah&#275; translocations from 2007 to 2011: (a) tie weight between locations (the thicker the line, the more translocations between 2 directly connected locations) and (b) weighted betweenness for individual locations (i.e., measure of centrality determining the likelihood of a node connecting 2 random nodes via the shortest path while accounting for node strength [sum of node weights] of an individual node). Nodes are isolated geographic locations used for Takah&#275; conservation. Lines with either uni- or bidirectional arrows show the direction of human-mediated Takah&#275; translocations between locations. Size of the circle illustrates extent of centrality; the larger the node, the more central the location in the network (A, Burwood Bush breeding center; B, Kapiti Island; C, Mana Island; D, Maud Island; E, Maungatautari reserve; F, Pukaha Mt Bruce; G, Wildbase Hospital; H, Private island; I, Te Anau wildlife reserve; J, Tiritiri Matangi Island; K, Motutapu Island; L, Peacock Springs wildlife park; M, Secretary Island; N, Wellington Zoo; O, Willowbank reserve; P, Zealandia / Karori Sanctuary; Q, Murchison Mountains). http://www.idrec.ac.nz/research-highlights-new,listing,,,67,identification-of-populations-for-disease-surveillance-in-a-translocated-network-of-endangered-takahe.html Risk factors for Shiga toxin-producing Escherichia coli infections in humans in New Zealand http://www.idrec.ac.nz/research-highlights-new,listing,,,58,risk-factors-for-shiga-toxin-producing-escherichia-coli-infections-in-humans-in-new-zealand.html Patricia Jaros &#160; PhD Candidate, mEpiLab &#160; Shiga toxin-producing Escherichia coli (STEC) such as E. coli O157:H7 and related non-O157 STEC strains are pathogens of public health concern worldwide.&#160; They can cause gastrointestinal diseases ranging from diarrhoea to life-threatening kidney failures. Ruminants, in particular cattle, are considered as a reservoir of STEC and have been shown to be a source of infection for both foodborne and environmental outbreaks in humans. Since 1993, when New Zealand&#8217;s first case of STEC infection in humans was reported, the annual number of reported STEC cases has increased steadily.&#160; Outbreaks of STEC infections are rare in New Zealand and most of the reported STEC cases appear as sporadic infections. To investigate the risk factors associated with sporadic STEC infections in humans in New Zealand, we conducted a national case-control and molecular epidemiology study. &#160;From July 2011 to July 2012, any confirmed case of STEC infection reported to any regional public health unit in New Zealand was interviewed for risk factor evaluation.&#160; A total of 113 eligible STEC cases and a random selection of 506 controls, representative of the national demography, were interviewed.&#160; E. coli O157:H7 caused 88.5% (100/113) of clinical STEC infections in this study. During the study period the number of cases showed a peak in summer/autumn (January until April), with no cases reported in July 2011 (Figure 1). Animal and environmental risk factors for human STEC infections were identified, notably &#8216;cattle livestock being present in meshblock&#8217; (the smallest geographical unit), &#8216;contact with animal manure&#8217;, and &#8216;contact with recreational waters&#8217;.&#160; No food-associated risk factors were identified as sources of STEC infection. Figure 1:Temporal distribution of sporadic STEC cases from July 2011 to July 2012 (Jaros et. al. 2013). Our findings implicate environmental and animal contact, but not food, as significant exposure pathways for sporadic STEC infections in humans in New Zealand. &#160;Risk factors associated with beef and dairy cattle suggest that ruminants are the most important sources of STEC infection in New Zealand. This work has been published in BMC Infectious Diseases and is available online Jaros, P., Cookson, A., Campbell, D., Besser,T., Shiringi, S., Mackereth, G. F., Lim.E., Lopez.L., Dufour,M., Marshall, J.,Baker,M., Hathaway,S., &#160;French, N.P.&#160;2013. A prospective case-control and molecular epidemiological study of human cases of Shiga toxin-producing Escherichia coli in New Zealand. BMC Infectious Diseases 13, 450. doi:10.1186/1471-2334-13-450&#160; &#160; http://www.idrec.ac.nz/research-highlights-new,listing,,,58,risk-factors-for-shiga-toxin-producing-escherichia-coli-infections-in-humans-in-new-zealand.html Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. Actinidiae http://www.idrec.ac.nz/research-highlights-new,listing,,,53,genomic-analysis-of-the-kiwifruit-pathogen-pseudomonas-syringae-pv-actinidiae.html Photo credit: Rami El-Shareif&#160; HONOUR McCANN Postdoctoral Researcher, Rainey Lab / IDReC / NZIAS, Massey University I work on the plant pathogen Pseudomonas syringae, which numbers among the most destructive bacterial pathogens of food crops. The P. syringae species complex comprises dozens of strains with highly specific interactions with diverse host species and cultivars. Kiwifruit infection by P. syringae pv. actinidiae (Psa) produces symptoms ranging from necrotic leaf spot to oozing stem cankers. An aggressive new lineage referred to as Psa-V emerged in 2008 and was soon detected in most of the world&#8217;s kiwifruit growing regions, including New Zealand. Psa-V has had a devastating impact on kiwifruit cultivation, as it is both highly transmissible and the severity of infection frequently results in the complete destruction of orchards. Linking plant domestication and pathogen emergence Modern agriculture remains vulnerable to significant losses caused by microbial pathogens, particularly where it relies on crops with limited genetic heterogeneity. The commercial cultivation of kiwifruit is largely reliant on the vegetative or clonal propagation of gold &#8216;Hort16A&#8217; (A. chinensis) and green &#8216;Hayward&#8217; (A. deliciosa) cultivars. Unlike most other crops, whose domestication began millennia ago, kiwifruit was domesticated less than a century ago. This presents us with the unusual opportunity to study the initial stages in the emergence of an agricultural pathogen. Our recent genomic and population analysis of more than 30 Psa strains has provided some insight into the origin and evolution this destructive infectious disease. Untangling the origin and evolution of Psa Kiwifruit outbreaks over the last three decades have been caused by distinct lineages of Psa. Each lineage of Psa exhibits little within-clade diversity, and patterns of polymorphism among Psa-V strains isolated during the recent global epidemic are consistent with the expansion and diversification of a single clone within the last decade (Figure 1).Evidence of between-clade recombination suggests the ancestors of each clade coexisted in a potentially non-agricultural source population. Outbreaks likely occurred as a result of transmission events from the source population, followed by selection in agricultural environments for host specialization. An isolate of Psa-V exhibits more rapid spread in &#8216;Hort16A&#8217; compared to earlier Psa isolates, and an apparent tradeoff in systemic spread in &#8216;Hayward&#8217; is suggestive of Psa-V specialization on &#8216;Hort16A&#8217;. The expansion in commercial cultivation of susceptible gold kiwifruit genotypes during the last decade may have exacerbated the severity of the latest outbreak. All lineages of Psa harbour unique repertoires of predicted virulence factors and toxins. Despite these differences, strains from the earlier outbreaks can grow to high levels in both cultivars. Figure 1: Phylogeny of Psa and recombination between canker-causing Psa clades. RAxML Maximum likelihood phylogenetic analysis of 32 draft and complete genome sequences based on 15,329 SNPs and 463,396 invariant sites (A). Each phylogenetic group is assigned its own color. With the exception of a single Italian strain (*) isolated in 1992 grouping with the Japanese clade, the canker-causing Japanese, Korean and low-virulent foliar NZ isolates form monophyletic clades reflecting their geographic origin, while global isolates from the 2008&#8211;2010 outbreakform a single clade.&#160; A Splitstree analysis of recombination predicts recombination between canker-causing clades of Psa (B). doi:10.1371/journal.ppat.1003503.g002 Implications for breeding resistant kiwifruit The source population may be a reservoir of novel pathogen variants. Defining the population structure and host range of Psa isolated in wild and agricultural environments will clarify the evolutionary potential of this pathogen in response to disease control, and assist plant breeders in developing cultivars of kiwifruit with broad resistance to the pathogen population rather than a single strain. This work has recently been published in PLOS Pathogens and is available online: McCann HC, Rikkerink EHA, Bertels F, Fiers M, Lu A, et al. (2013) Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease. PLoS Pathog 9(7): e1003503. doi:10.1371/journal.ppat.1003503 http://www.idrec.ac.nz/research-highlights-new,listing,,,53,genomic-analysis-of-the-kiwifruit-pathogen-pseudomonas-syringae-pv-actinidiae.html