Publications

Recent mEpiLab publications: peer reviewed journal articles

2017

Benschop, J., Booker, C., Shadbolt, T., Weston, J. [2017] A Retrospective Cohort Study of an Outbreak of Cryptosporidiosis among Veterinary Students. Veterinary Sciences 4, no. 2:29. doi:10.3390/vetsci4020029

Bloomfield, S.J., Benschop, J., Biggs, P.J., Marshall, J.C., Hayman, D.T.S, Carter, P. E., Midwinter, A.C., Mather, A. E., French, N.P. [2017]. Genomic Analysis of Salmonella enterica Serovar Typhimurium DT160 Associated with a 14-Year Outbreak, New Zealand, 1998-2012. Emerging Infectious Diseases, 23(6), 906-913. doi:10.3201/eid2306.161934

Burgess, S.A., Flint, S.H., Lindsay, D, Cox, M.P., Biggs, P.J. [2017] Insights into the Geobacillus Stearothermophilus Species Based on Phylogenomic Principles. BMC Microbiol 17, no. 1 (Jun 26 2017): 140. doi:10.1186/s12866-017-1047-x 

Cookson, A.L., Biggs, P.J., Marshall, J.C., Reynolds, A., Collis, R.M., French, N.P., Brightwell, G.[2017] Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure. Sci Rep, 7(1): 814. doi: 10.1038/s41598-017-00890-6

Da Silva, A.G., Baines, S., Carter, G., Heffernan, H., French, N.P., Ren, U.,Stinear, T., Howden, B., Williamson, D. [2017] A phylogenomic framework for assessing the global emergence and evolution of clonal complex 398 methicillin-resistant Staphylococcus aureus. Microbial Genomics 3, no. 1.doi:10.1099/mgen.0.000105

Dixon, M, Flint, S, Palmer, J, Love, R, Biggs,P.J, Beuger, A. [2017] Analysis of Culturable and Non-Culturable Bacteria and Their Potential to Form Biofilms in a Primary Treated Dairy Wastewater System. Environ Technol (Jul 18 2017): 1-8. doi: 10.1080/09593330.2017.1352034

French, N.P. [2017] Impacts of non-native species on livestock. Impact of biological invasions on ecosystem services pp 139–154.

Garcia, J.C., Hayman, D.T.S.[2017] Evolutionary Processes in Populations of Cryptosporidium Inferred from Gp60 Sequence Data. Parasitol Res . doi:10.1007/s00436-017-5459-1

Grange, Z.L., Biggs, P J., Rose, S.P., Gartrell, B.D., Nelson, N.J., French, N.P. [2017]  Genomic Epidemiology and Management of Salmonella in Island Ecosystems Used for Takahe Conservation. Microb Ecol (2017). doi:10.1007/s00248-017-0959-1

Hayman, D.T.S., Marshall, J.C, French, N.P., Carpenter, T.E., Roberts, M.G., Kiedrzynski, T.[2017] Global Importation and Population Risk Factors for Measles in New Zealand: A Case Study for Highly Immunized Populations. Epidemiol Infect 145, no. 9 (Jul 2017): 1875-85. doi:10.1017/S0950268817000723

Heuer, C., Yuplana, Y., Collins-Emerson, J., Benschop, J., Weston, J., Wilkinson, D., Vallee, E., Wilson, P.[2017] Leptospira shedding in dairy herds: New findings. VetScript 45-46.

Irshad, H., Cookson, A.L., Prattley, D.J., Marshall, J., French, N.P. [2017] Epidemiology of Escherichia coli serogroups O26, O103, O111 and O145 in very young ('bobby') calves in the North Island, New Zealand.Epidemiol Infect. 2017 Mar 7:1-11. doi: 10.1017/S0950268817000401

Karkaba, A., Benschop, J., Hill, K. E., Grinberg, A. [2017]  Characterisation of methicillin-resistant Staphylococcus aureus clinical isolates from animals in New Zealand, 2012–2013, and subclinical colonisation in dogs and cats in Auckland. N Z Vet J 65, no.2:78-83 . doi: 10.1080/00480169.2016.1222919

McMeekin, C. H., Hill, K. E., Gibson, I. R., Bridges, J. P., Benschop, J. [2017] Antimicrobial Resistance Patterns of Bacteria Isolated from Canine Urinary Samples Submitted to a New Zealand Veterinary Diagnostic Laboratory between 2005-2012. N Z Vet J 65, no. 2: 99-104. doi:10.1080/00480169.2016.1259594 

Miller, P., Marshall, J.C., French, N.P., Jewell, C. [2017] sourceR: Classification and Source Attribution of Infectious Agents among Heterogeneous Populations. arXiv preprint arXiv:1702.07422

Mohan, V, Stevenson, M.A., Marshall, J.C,  French, N.P [2017] Characterisation by multilocus sequence and porA and flaA typing of Campylobacter jejuni isolated from samples of dog faeces collected in one city in New Zealand. NZVJ  65(4)L:209-213. doi:10.1080/00480169.2017.1311810

Peel, A.J., Wood, J.L.N., Baker, K.S., Breed, A.C., Carvalho, A.D., Fernández-Loras, A., Gabrieli, H.S., Gembu, G.C., Kakengi, V.A., Kaliba, P.M., Kityo, R.M., Lembo, T., Mba, F.E., Ramos, D., Rodriguez-Prieto, I., Suu-Ire, R., Cunningham, A.A., Hayman, D.T.S. [2017] How Does Africa's Most Hunted Bat Vary across the Continent? Population Traits of the Straw-Coloured Fruit Bat (Eidolon Helvum) and Its Interactions with Humans. Acta Chiropterologica 19, no. 1:77-92. doi:10.3161/15081109acc2017.19.1.006 

Pittavino, M., Dreyfus, A., Heuer, C., Benschop, J., Wilson, P.R., Collins-Emerson, J.M., Torgerson, P.R, Furrer. R. [2017] Comparison between Generalized Linear Modelling and Additive Bayesian Network; Identification of Factors Associated with the Incidence of Antibodies against Leptospira Interrogans sv Pomona in Meat Workers in New Zealand. Acta Trop . doi:10.1016/j.actatropica.2017.04.034 

Pittavino, M., Dreyfus, A., Heuer, C., Benschop, J., Wilson, P.R., Collins-Emerson, J.M., Torgerson, P.R., Furrer, R. [2017] Data on Leptospira Interrogans sv Pomona Infection in Meat Workers in New Zealand. Data in Brief . doi:10.1016/j.dib.2017.05.053

Priest, P., Toombs-Ruane, L., Benschop, J., Burgess, S., French, N., Murdoch, D., [2017]. A One Health future to meet the AMR challenge? N Z Vet J 65, 60-61.doi:10.1080/00480169.2016.1270651

Purcell, R., Visnovska, M., Biggs, P.J, Schmeier, S., Frizelle, F. [2017] Consensus Molecular Classification of Colorectal Cancer and Association with the Colonic Microbiome. Diseases of the Colon & Rectum, v60-i60: e90-e91.  

Rulli, M.C., Santini, M., Hayman, D.T.S., D'Odorico, P. [2017] The Nexus between Forest Fragmentation in Africa and Ebola Virus Disease Outbreaks. Sci Rep 7:41613. doi:10.1038/srep41613 

Slow, S., Anderson, T., Miller, J., Singh, S., Murdoch, D., Biggs, P.J. [2017] Complete Genome Sequence of a Legionella Longbeachae Serogroup 1 Strain Isolated from a Patient with Legionnaires' Disease. Genome Announc 5, no. 24. doi: 10.1128/genomeA.00564-17 

Toombs-Ruane, L.J., Benschop, J., Burgess, S., Priest, P., Murdoch, D.R., French, N.P., [2017]. Multidrug resistant Enterobacteriaceae in New Zealand: a current perspective. N Z Vet J 65, 62-70.doi:10.1080/00480169.2016.1269621

Vallee, E., Ridler, A.L., Heuer, C., Collins-Emerson, J.M., Benschop, J., Wilson, P.R. [2017] Effectiveness of a commercial leptospiral vaccine on urinary shedding in naturally exposed sheep in New Zealand. Vaccine 35, no. 9:1362-68. doi:10.1016/j.vaccine.2016.04.037 

Vaughan, T.G., Welch, D., Drummond, A.J., Biggs, P.J., George, T., French, N.P., 2017. Inferring Ancestral Recombination Graphs from Bacterial Genomic Data. Genetics 205, 857-870.

Wilkinson, D.A., Hayman, D.T.S. [2017] Bat and virus ecology in a dynamic world. Microbiology Australia v38(1):33-35.   

Williamson, D.A., Baines, S.L., Carter, G.,Gonçalves da Silva, A.,Ren, X., Sherwood, J., Dufour, M., Schultz, M.B., French, N.P.,Seemann, T., Stinear, Timothy P.,Howden, B.P.[2017] Genomic Insights into a Sustained National Outbreak of Yersinia pseudotuberculosis. Genome Biol Evol (2016) 8 (12): 3806-3814. doi:10.1093/gbe/evw285

2016

Azarpeykan, S., Dittmer, K.E., Gee, E.K., Marshall, J.C., Elder, P., Acke, E., Thompson, K.G. [2016] Circadian rhythm of calciotropic hormones, serum calcium, phosphorus and magnesium during the shortest and longest days of the year in horses in New Zealand. Journal of Animal Physiology and Animal Nutrition. doi:10.1111/jpn.12477

Azarpeykan, S., Dittmer, K.E., Gee, E.K., Marshall, J.C., Wallace, J., Elder, P., Acke, E., Thompson, K.G. [2016] Influence of blanketing and season on vitamin D and parathyroid hormone, calcium, phosphorus, and magnesium concentrations in horses in New Zealand. Domestic Animal Endocrinology 56:75–84. doi:10.1016/j.domaniend.2016.03.003 

Barrett, L.A., Beausoleil, N.G., Benschop, J., Stafford, K.J. Pain-related behavior was not observed in dairy cattle in the days after liver biopsy, regardless of whether NSAIDs were administered. Research in Veterinary Science 104 (2016) 195–199. doi:10.1016/j.rvsc.2015.12.020

Bogers, S.H.,Rogers, C.W.,Bolwell, C.,Roe, W.,Gee, E.,McIlwraith, C.W.(2016) Quantitative comparison of bone mineral density characteristics of the distal epiphysis of third metacarpal bones from Thoroughbred racehorses with or without condylar fracture. Am J Vet Res v77-1 p32-38. doi:10.2460/ajvr.77.1.32 

Bojanic, K., Midwinter, A. C., Marshall, J. C., Rogers, L. E., Biggs, P. J., Acke, E. (2016) Variation in the limit-of-detection of the ProSpecT Campylobactermicroplate enzyme immunoassay in stools spiked with emerging Campylobacter species. J Microbiol Methods doi:10.1016/j.mimet.2016.06.016

Bolwell C.F., Rogers C.W., Gee E.K., Rosanowski S.M. (2016) Descriptive statistics and the pattern of horse racing in New Zealand. 1. Thoroughbred racing. Animal Production Science 56, 77–81. doi:10.1071/AN13442

Garcia, R.Jc., Hayman, D.T.S. [2016] Origin of a major infectious disease in vertebrates: The timing of Cryptosporidium evolution and its hosts. Parasitology. doi:10.1017/S0031182016001323

Han, B.A., Schmidt, J.P., Alexander, L.W., Bowden, S.E., Hayman, D.T.S, Drake, J.M. [2016] Undiscovered Bat Hosts of Filoviruses. PLoS Negl Trop Dis 10(7): e0004815. doi:10.1371/journal.pntd.0004815 

Hayman, D.T.S. (2016) Conservation as vaccination: Integrated approaches to public health and environmental protection could prevent future disease outbreaks. EMBO reports(2016). doi:10.15252/embr.201541675

Hayman, D.T.S. (2016) Bats as Viral Reservoirs. Annual Review of Virology. Vol. 3. doi:10.1146/annurev-virology-110615-042203

Hayman, D.T.S., Peel, A.J. (2016) Can survival analyses detect hunting pressure in a highly connected species? Lessons from straw-coloured fruit bats. Biological Conservation v200:131-139. doi:10.1016/j.biocon.2016.06.003

Hayman, D.T.S., Pulliam, J.R.C., Marshall, J.C., Cryan, P.M., Webb, C.T. (2016) Environment, host, and fungal traits predict continental-scale white-nose syndrome in bats. Science Advances v2-1. doi:10.1126/sciadv.1500831

Jaros, P., Cookson, A.L., Reynolds, A., Prattley, D.J., Campbell, D.M., Hathaway, S., French, N.P. (2016) Nationwide prevalence and risk factors for faecal carriage of Escherichia coli O157 and O26 in very young calves and adult cattle at slaughter in New Zealand. Epidemiology and Infection. doi:10.1017/S0950268815003209

Karkaba, A., Grinberg, A., Benschop, J., Pleydell, E. (2016). Characterisation of extended spectrum β-lactamase and AmpC β-lactamase-producing Enterobacteriaceae isolated from companion animals in New Zealand. New Zealand Veterinary Journal 65:2, 105-112, doi:10.1080/00480169.2016.1271730

Lal, A., Dobbins, T., Bagheri, N., Baker, M.G., French, N.P., Hales, S., 2016. Cryptosporidiosis Risk in New Zealand Children Under 5 Years Old is Greatest in Areas with High Dairy Cattle Densities. EcoHealth.

Marshall, J.C., Soboleva, T.K., Jamieson, P., French, N.P. [2016] Estimating Bacterial Pathogen Levels in New Zealand Bulk Tank Milk. Journal of Food Protection 79(5). doi:10.4315/0362-028X.JFP-15-230 

McKee, C.D., Hayman, D.T.S., Kosoy, M.Y., Webb, C.T. [2016] Phylogenetic and geographic patterns of bartonella host shifts among bat species. Infection, Genetics and Evolution 44:382–394. doi:10.1016/j.meegid.2016.07.033

Morgan-Richards, M., Hills, S.F.K, Biggs, P.J., Trewick, S.A. [2016] Sticky Genomes: Using NGS Evidence to Test Hybrid Speciation Hypotheses. PLoS ONE 11(5): e0154911. doi:10.1371/journal.pone.0154911 

Nohra, A., Grinberg, A., Midwinter, A. C., Marshall, J. C., Collins-Emerson, J. M., French, N. P. [2016] Molecular Epidemiology of Campylobacter coli Strains Isolated from Different Sources in New Zealand between 2005 and 2014. Applied and Environmental Microbiology 82(14):4363-4370 01  doi:10.1128/AEM.00934-16

O'Shea, T.J., Cryan, P.M., Hayman, D.T.S., Plowright, R.K., Streicker, D.G. (2016) Multiple mortality events in bats: a global review. Mammal Review. doi:10.1111/mam.12064

Peel, A. J., Baker, K. S., Hayman, D. T. S., Suu-Ire, R., Breed, A. C., Gembu, G., Lembo, T., Fernández-Loras, A., Sargan, D. R.,Fooks, A. R., Cunningham, A.A., Wood, J. L. N. (2016). Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats, Eidolon helvum. Scientific Data. doi:10.17863/CAM.325

Peel, A. J., Field, H. E., Reid, P. A., Plowright, R. K., Broder, C. C., Skerratt, L. F., Hayman, D. T. S., Restif, O., Taylor, M., Martin, G., Crameri, G., Smith, I., Baker, M., Marsh, G. A., Barr, J., Breed, A. C., Wood, J. L., Dhand, N., Toribio, J. A., Cunningham, A. A., Fulton, I., Bryden, W. L., Secombe, C., Wang, L. F.(2016) The equine Hendra virus vaccine remains a highly effective preventative measure against infection in horses and humans: 'The imperative to develop a human vaccine for the Hendra virus in Australia'. Infection Ecology and Epidemiology 2016, 6: 31658 - doi:10.3402/iee.v6.31658

Rouco, C., Richardson, K.S., Buddle, B.M., French, N.P., Tompkins, D.M. [2016] Sex difference in the survival rate of wild brushtail possums (Trichosurus vulpecula) experimentally challenged with bovine tuberculosis. Research in Veterinary Science v107:p102-105. doi:10.1016/j.rvsc.2016.05.008

Van Andel, M., McInnes, K., Tana, T., French, N.P., 2016. Network analysis of wildlife translocations in New Zealand. N Z Vet J 64, 169-173.

Vaughan, T.G.,Welch, D.,Drummond, A.J.,Biggs, P.J.,George, T., French, N.P. [2016] Bayesian inference of ancestral recombination graphs for bacterial populations. bioRxiv, 059105. doi:10.1101/059105(submitted) 

Williamson, D., Baker, M., French, N.P., Thomas, M. [2016] Missing in action: an antimicrobial resistance strategy for New Zealand. New Zealand Medical Journal 128(128):65-67.    

2015

Acke, E., Midwinter, A.C., Lawrence, K., Gordon, S.J.G., Moore, S., Rasiah, I., Steward, K., French, N.P., & Waller, A. 2015. Prevalence of Streptococcus dysgalactiae subsp. equisimilis and S. equi subsp. zooepidemicus in a sample of healthy dogs, cats and horses., New Zealand Veterinary Journal, doi: 10.1080/00480169.2015.1016133

Al Mawly, J., Grinberg, A., Prattley, D., Moffat, J., Marshall, J., & French, N. (2015) Risk factors for neonatal calf diarrhoea and enteropathogen shedding in New Zealand dairy farms. The Veterinary Journal. doi: 10.1016/j.tvjl.2015.01.010

Al Mawly, J., Grinberg, A., Prattley, D., Moffat, J., and French, N. (2015) Prevalence of endemic enteropathogens of calves in New Zealand dairy farms. New Zealand Veterinary Journal, 1-18. doi: 10.1080/00480169.2014.966168 

Al Mawly, J., Grinberg, A., Velathanthiri, N., & French, N. (2015). Cross sectional study of prevalence, genetic diversity and zoonotic potential of Cryptosporidium parvum cycling in New Zealand dairy farms. Parasites & Vectors, 8, 240. doi:10.1186/s13071-015-0855-9

Bai, Y., Hayman, D. T.S., McKee, C. D., Kosoy, M. Y., & Walker, D. H. 2015. Classification of Bartonella Strains Associated with Straw-Colored Fruit Bats (Eidolon helvum) across Africa Using a Multi-locus Sequence Typing Platform. PLOS Neglected Tropical Diseases, 9(1). 

Bolwell, C. F., Gilpin, B. J., Campbell, D., & French, N. P. 2015. Evaluation of the representativeness of a sentinel surveillance site for campylobacteriosis. Epidemiology and Infection / Volume 143 / Issue 09 . doi :  10.1017/S09502688140031

Bolwell C. F., Rogers C. W., Gee E. K., Rosanowski S. M. (2015) Descriptive statistics and the pattern of horse racing in New Zealand. 2. Harness racing. Animal Production Science 56, 82–86.doi:10.1071/AN13443

Bolwell, C. F.,Rogers, C. W.,Rosanowski, S. M., Weston, J. F., Gee, E. K., Gordon, S. J. G. 2015. Cross-sectional survey of the management and training practices of endurance horses in New Zealand: a pilot study. Journal of Equine Veterinary Science. doi: 10.1016/j.jevs.2015.07.019

Bolwell, C. F., Rosanowski, S. M., Scott, I., Sells, P. D., Rogers, C. W. 2015. Questionnaire study on parasite control practices on Thoroughbred and Standardbred breeding farms in New Zealand.Veterinary parasitology. doi : 10.1016/j.vetpar.2015.02.011

Burgess, S.A., Cox, M.P., Flint, S.H., Lindsay, D., Biggs, P.J. [2015] Draft genome sequences of three strains of Geobacillus stearothermophilus isolated from a milk powder manufacturing plant. Genome Announc 3(5):e00939-15. doi:10.1128/genomeA.00939-15

Dreyfus, A, Wilson, P, Collins-Emerson, J, Benschop, J, Moore, S, & Heuer, C. (2015)  Risk factors for new infection with Leptospira in meat workers in New Zealand. Occupational and Environmental Medicine. doi: 10.1136/oemed-2014-102457

Fang, F., Collins-Emerson, J.M., Cullum, A., Heuer, C., Wilson, P.R., & Benschop. J. 2015. 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

Fearnhead, P., Yu, S., Biggs, P., Holland, B.,  French, N. 2015. Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods. Annals of Applied Statistics arXiv preprint arXiv:1411.1200.

Friedrich, A., Marshall, J. C., Biggs, P. J., Midwinter, A. C. ,French, N. P. (2015) Seasonality of Campylobacter jejuni isolates associated with human campylobacteriosis in the Manawatu region, New Zealand. Epidemiology and Infection, available on CJO2015. doi:10.1017/S0950268815002009.

Gordon S. J. G., Bolwell C., Rogers C., Musuka G., Kelly P.,  Labuschagne K.,Guthrie A. J.,Denison E., Mellor P. S.,Hamblin C. 2015. The occurrence of Culicoides species, the vectors of arboviruses, at selected trap sites in Zimbabwe. Onderstepoort J Vet Res; Vol 82, No 1. doi: 10.4102/ojvr.v82i1.900 

Grange, Z., Gartrell, B. D., Biggs, P. J.,Nelson, N. J., Marshall,  J. C. Howe, L., Balm, M. G., French, N. P. 2015. Using a common commensal bacterium in endangered Takahe as a model to explore pathogen dynamics in isolated wildlife populations. Conserv Biol. doi : 10.1111/cobi.12521

Grange, Z.L., Gartrell, B.D.,Biggs, P.J.,Nelson, N.J., Anderson, M., French, N.P. (2015) Microbial Genomics of a Host-Associated Commensal Bacterium in Fragmented Populations of Endangered Takahe. Microbe Interactions. doi:10.1007/s00248-015-0721-5

Gregory S. J.,  Anderson C. W. N., Camps-Arbestain M., Biggs P. J., Ganley A. R. D., O'Sullivan J. M., McManus M. T. (2015) Biochar in Co-Contaminated Soil Manipulates Arsenic Solubility and Microbiological Community Structure, and Promotes Organochlorine Degradation. PLoS ONE 10(4): e0125393. doi: 10.1371/journal.pone.0125393 

Hayman D. T. S. 2015 Biannual birth pulses allow filoviruses to persist in bat populations. Proc. R. Soc. B 282: 20142591. http://dx.doi.org/10.1098/rspb.2014.2591

Heuer, C., Yupiana, Y., Wilson, P., Benschop, J., Collins-Emerson, J., Vallée, E., Weston, J. (2015) Are vaccinated dairy cows shedding leptospires? VetScript XXXVIII 7-34. (In Press)

Hill, K. E., Chambers, J. P., Jones, B. R., Bolwell, C. F., Aberdein, D,. Mills, P. C. 2015. Regional variations in percutaneous absorption of methimazole: an in vitro study on cat skin. doi: 10.1111/jvp.12220

Hill, K. E., Chambers, J. P., Jones, B. R., Bolwell, C. F., Aberdein, D,. Mills, P. C. 2015. Trans-pinnal movement of methimazole: an in vitro study showing that methimazole can cross from the inner to outer pinna of cats. Journal of feline medicine and surgery. doi: 10.1177/1098612X14567548

Hill, K. E., Mills, P. C, Jones, B. R, Bolwell, C. F., Aberdein, D. Chambers, J. P. 2015. Percutaneous absorption of methimazole: an in vitro study of the absorption pharmacokinetics for two different vehicles. Journal of veterinary pharmacology and therapeutics. doi: 10.1111/jvp.12213

Irshad, H., Cookson, A. L., Ross, C. M., Jaros, P., Prattley, D. J., Donnison, A., Mc, Bride G., Marshall, J., French, N. P. (2015) Diversity and relatedness of Shiga toxin-producing Escherichia coli and Campylobacter jejuni between farms in a dairy catchment. Epidemiology and Infection. 2015 Nov 23:1-12.doi:10.1017/S0950268815002782.

Jaros, P. Dufour, M. Gilpin, B. Freeman, M. M. Ribot, E. M. 2015. PFGE for Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) and non-O157 STEC. Pulse Field Gel Electrophoresis: Methods and Protocols, Methods in Molecular Biology, vol. 1301, doi:10.1007/978-1-4939-2599-5_15. 

Lal, A, Lill, A, Mcintyre, M, Baker, M, Hales, S, and French, N. 2015. Environmental change and enteric zoonoses in New Zealand: A systematic review of the evidence. Australian and New Zealand Journal of Public Health. doi:  10.1111/1753-6405.12274

Lal, A., Hales, S., Kirk, M., Baker, M. G. and French, N. P. 2015, Spatial and temporal variation in the association between temperature and salmonellosis in NZ. Australian and New Zealand Journal of Public Health. doi: 10.1111/1753-6405.12413

Lucas-Roxburgh, R., Benschop, J., Dunowska, M., Perrott, M. 2015. Prevalence of Human Papilloma Viruses in the mouths of New Zealand women. Accepted New Zealand Medical Journal

Luis, A. D., O'Shea, T. J., Hayman, D. T. S., Wood, J. L. N., Cunningham, A. A., Gilbert, A. T., Mills, J. N., Webb, C. T. (2015),  Network analysis of host-virus communities in bats and rodents reveals determinants of cross-species transmission. Ecology Letters. doi: 10.1111/ele.12491

Mather, A. E., Vaughan, T. G., French, N. P. [2015] Molecular Approaches to Understanding Transmission and Source Attribution in Nontyphoidal Salmonella and Their Application in Africa. Clin Infect Dis.(2015)61(suppl 4): S259-S265. doi:10.1093/cid/civ727 

Pepin K.M., Leach C. B., Marques-ToledoC., LaassK. H., Paixao K. S., LuisA. D., Hayman D. T. S., Johnson N. G., Buhnerkempe M. G., Carver S., Grear D. A., Tsao K., Eiras A. E. and Webb C. T. 2015. Utility of mosquito surveillance data for spatial prioritization of vector control against dengue viruses in three Brazilian cities. Pepin et al. Parasites & Vectors (2015) 8:98 DOI 10.1186/s13071-015-0659-y

Rosanowski, S.M., Scott, I., Sells, P.D., Rogers, C.W. and Bolwell, C.F. (2015), Cross-sectional survey of parasite control practices on Thoroughbred and Standardbred training yards in New Zealand. Equine Veterinary Journal. doi: 10.1111/evj.12558   doi:10.1111/evj.12558 

Sanhueza J.M., Heuer C., Wilson P.R., Benschop J., Collins-Emerson J.M. 2015.  Prevalence and risk factors for Leptospira exposure in New Zealand veterinarians.. Epidemiology and infection doi: dx.doi.org/10.1017/S0950268815000515

Spencer, S. E., Besser, T. E., Cobbold, R. N., French, N. P. 2015.'Super' or just 'above average'? Supershedders and the transmission of Escherichia coli O157:H7 among feedlot cattle.J R Soc Interfac: 12-110. doi:10.1098/rsif.2015.0446

Strachan, N. J., Rotariu, O., Lopes, B., MacRae, M., Fairley, S., Laing, C., Gannon, V., Allison, L. J., Hanson, M. F., Dallman, T., Ashton, P., Franz, E., van Hoek, A. H., French, N. P., George, T., Biggs, P. J., Forbes, K. J. (2015) Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli  O157 Genotypes Dominates Host Association. Sci Rep. 2015 Oct 7;5:14145. doi: 10.1038/srep14145

Theoret, C. L., Bolwell, C. F., Riley, C. B. (2015) A cross-sectional survey on wounds in horses in New Zealand. N Z Vet J 1-16 doi: 10.1080/00480169.2015.1091396

Toombs-Ruane, L.J., Riley, C.B., Kendall, A.T., Bolwell, C.F., Benschop, J. and Rosanowski, S.M. (2015), Antimicrobial Susceptibilities of Aerobic Isolates from Respiratory Samples of Young New Zealand Horses. Journal of Veterinary Internal Medicine. doi: 10.1111/jvim.13600 

Toombs-Ruane, L. J., Riley, C. B., Kendall, A. T., Hill, K. E., Benschop, J., Rosanowski, S. M. (2015) Antimicrobial susceptibility of bacteria isolated from neonatal foal samples submitted to a New Zealand veterinary pathology laboratory (2004 to 2013). N Z Vet J. 2015 Nov 23:1-5. doi:10.1080/00480169.2015.1109006

Toombs-Ruane, L.J., Riley, C.B., Rosanowski, S.M., Kendall, A.T. , Benschop, J. (2015), Antimicrobial Resistance of Aerobic Respiratory Isolates From Young New Zealand Horses. Equine Veterinary Journal, 47: 20. doi: 10.1111/evj.12486_45 

Toombs-Ruane, L., Rosanowski, S., Riley, C., Kendall, A., Bolwell, C., Benschop, J. (2015) Antimicrobial sensitivities of aerobic isolates from respiratory samples of young New Zealand horses submitted to a commercial laboratory. Accepted Journal of Veterinary Internal Medicine  

Vallée E., Heuer C., Collins-Emerson J.M., Benschop J., Wilson P.R. (2015) Serological patterns, antibody half-life and shedding in urine of Leptospira spp. in naturally exposed sheep. New Zealand Veterinary Journal: 1-32. doi: 10.1080/00480169.2015.1049668

van Andel, M., Jackson, B., Midwinter, A., Alley, M., Ewen, J., McInnes, K., Jakob Hoff, R., Reynolds, A., and French, N. 2015. Investigation of mortalities associated with Salmonella spp. infection in wildlife on Tiritiri Matangi Island in the Hauraki Gulf of New Zealand. New Zealand Veterinary Journal, 1-12. doi: 10.1080/00480169.2014.990065

van Andel, M., McInnes, K., Tana, T. & French, N.P. (2015) Network analysis of wildlife translocations in New Zealand, New Zealand Veterinary Journal, doi:10.1080/00480169.2015.1110065 

 

2014

Al Mawly, J., Grinberg, A., Prattley, D., Moffat, J., & French, N. 2014. Prevalence of endemic enteropathogens of calves in New Zealand dairy farms. New Zealand Veterinary Journal, 1-18. doi: 10.1080/00480169.2014.966168  

Baker, K.S., Suu-Ire, R., Barr, J., Hayman, D.T.S., Broder, C.C., Horton, D.L., Durrant, C., Murcia, P.R., Cunningham, A.A., & Wood, J.L.N. 2014. Viral antibody dynamics in a chiropteran host. Journal of Animal Ecology. 83(2), 415–428. doi: 10.1111/1365-2656.12153

Binney, B.M., Biggs, P.J., Carter P.E., Holland, B.R. & French, N.P. 2014. Quantification of historical livestock importation into New Zealand. New Zealand Veterinary Journal,  doi: 10.1080/00480169.2014.914861

Bolwell, C. F., Rogers, C. W. , Gee, E. K., Rosanowski, S. M. 2014. Descriptive statistics and the pattern of horse racing in New Zealand: Part One Thoroughbred racing. Animal Production Science. doi : dx.doi.org/10.1071/AN13442

Bolwell, C. F., Rogers, C. W. , Gee, E. K., Rosanowski, S. M. 2014. Descriptive statistics and the pattern of horse racing in New Zealand: Part Two Harness racing. Animal Production Science. doi : dx.doi.org/10.1071/AN13443

Dreyfus, A, Heuer, C., Wilson, P., Collins-Emerson, J., Baker, M., & Benschop, J. 2014. Risk of infection and associated flu-like disease among abattoir workers due to two Leptospira species. Epidemiology and Infection. doi:10.1017/S0950268814002477

Dreyfus, A, Benschop, J., Collins-Emerson, J., Wilson, P., Baker, M. & Heuer, C. 2014. Sero-prevalence and Risk Factors for Leptospirosis in Abattoir Workers in New Zealand. International Journal of Environmental Research and Public Health. 11(2), 1756-1775. doi:10.3390/ijerph110201756

Duncan, J. S., Leatherbarrow, A. J., French, N.P., & Grove-White, D. H. 2014. Temporal and farm-management-associated variation in faecal-pat prevalence of Campylobacter fetus in sheep and cattle. Epidemiology and Infection. 142(6), 1196-1204. doi:http://dx.doi.org/10.1017/S0950268813002379

Fang, F., Benschop, J., Wilson, P., Collins-Emerson, J., Heuer, C., & Prattley, D. 2014. Sero-prevalence and exposure to risk factors for leptospirosis among veterinary students at Massey University. New  Zealand  Veterinary Journal 62(3), 130-135. doi: 10.1080/00480169.2013.862161.  

Fang, F., Collins-Emerson, J.M., Heuer, C., Hill, F.J., Tisdall, D. J., Wilson, P.R., & Benschop, J. 2014. Inter-laboratory and between-specimen comparisons of diagnostic tests for leptospirosis in sheep and cattle. Journal of Veterinary Diagnostic Investigation, doi: 10.1177/1040638714548476

Fearnhead, P., Biggs, P., & French, N. 2014. Learning about recombination in Campylobacter. In: Sheppard, S., & Méric, G. (Eds.), Campylobacter Ecology and Evolution. Horizon Scientific Press, 9-22  http://www.horizonpress.com/campy2

French, N., Yu, S., Biggs, P., Holland, B., Fearnhead, P., Binney, B., Fox, A., Grove-White, D.H., Leigh, J., Miller, W., Muellner, P., & Carter, P. 2014. Evolution of Campylobacter species in New Zealand. In: Sheppard, S., & Méric, G. (Eds.), Campylobacter Ecology and Evolution. Horizon Scientific Press, 221-240 http://www.horizonpress.com/campy2

Franz, E., Delaquis, P., Morabito, S., Beutin, L., Gobius, K., Rasko, D. A., Bono, J., French, N., Osek, J., Lindstedt, B.-A., Muniesa, M., Manning, S., LeJeune, J., Callaway, T., Beatson, S., Eppinger, M., Dallman, T., Forbes, K. J., Aarts, H., Pearl, D. L., Gannon, V. P. J., Laing, C. R., & Strachan, N. J. C. 2014. Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems. International Journal of Food Microbiology, 187(0), 57-72. doi: http://dx.doi.org/10.1016/j.ijfoodmicro.2014.07.002

Grange, Z., van Andel, M., French, N.P., & Gartrell, B. 2014. Social networking of an endangered flightless bird and its use in targeting disease surveillance. Conservation Biology. 28(2), 518-528. doi: 10.1111/cobi.12178

Grove-White, D.H., Leatherbarrow, A.J., Cripps, P.J., & French, N.P. 2014. Temporal and farm-management-associated variation in faecal pat prevalence of Arcobacter spp. in ruminants. Epidemiology and Infection. 142(4), 861-870. http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=8951596&fulltextType=RA&fileId=S095026881300160X

Holden, N. J., Wright, F., Mackenzie, K., Marshall, J., Mitchell, S., Mahajan, A., Wheatley, R., & Daniell, T. J. 2014. Prevalence and diversity of Escherichia coli isolated from a barley trial supplemented with bulky organic soil amendments: Green compost and bovine slurry. Letters in Applied Microbiology, 58(3), 205-212. doi: 10.1111/lam.12180

Holland, K.; Jones, G.; & Benschop, J. 2014. Spatio-temporal modeling of disease incidence with missing covariate values. Epidemiology and Infection. doi: http://dx.doi.org/10.1017/S0950268814002854

Irshad, H., Cookson, A.,  Prattley, D.J., Dufour, M., & French, N.P. 2014. Distribution of Escherichia coli strains harbouring Shiga toxin-producing E. coli (STEC)-associated virulence factors (stx1, stx2, eae, ehxA) from very young calves in the North Island of New Zealand. Epidemiology and Infection. doi: http://dx.doi.org/10.1017/S0950268814000089

Jancloes, M.F., Bertherat, E., Scheider, C., Belmain, S., Munoz-Zanzi, C., Hartskeerl, R., Costa, F., Denis, J., & Benschop, J. 2014. Towards a “One Health” Strategy Against Leptospirosis. Planet@Risk, 2(3), 204-206. http://planet-risk.org/index.php/pr/article/view/94

Jaros, P., Cookson, A., Campbell, D., Duncan, G., Prattley, D., Carter, P., Besser, T., Shiringi, S., Hathaway, S., Marshall, J., & French, N. 2014. Geographic divergence of bovine and human Shiga toxin-producing Escherichia coli O157:H7 genotypes in New Zealand. Emerging Infectious Diseases. 20(12). http://dx.doi.org/10.3201/eid2012.140281

Kvalsvig, A., Baker, M.G., Sears, A. & French, N. 2014 Bacteria: Campylobacter. In: Encyclopedia of Food Safety, Elsevier, Academic Press, 369-380.

Lal, A., Lill, A., Mcintyre, M., Baker, M., Hales, S., & French, N. 2014. Environmental change and enteric zoonoses in New Zealand: A systematic review of the evidence. Australian and New Zealand Journal of Public Health, doi: 10.1111/1753-6405.12274

Lindgreen S, Umu, S U, Lai A S-W, Eldai H, Liu W, McGimpsey S, Wheeler N, Biggs, P.J., Thomson N, Barquist L, Poole A M, Gardner P P. 2014. Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling” PLoS Comp Biol, In Press 

Mansell, C., & Benschop, J. 2014. Leptospirosis is an important multi-species zoonotic disease in New Zealand. Invited editorial. New Zealand Medical Journal, 127 (1388). http://journal.nzma.org.nz/journal/127-1388/5980/

McLean, D., Biggs, P., Leblanc-Maridor, M., Hall, R., French, N., Pearce, N., & Douwes, J. 2014. 0164 Metagenomic detection of bacteria in aerosol samples in animal slaughterhouses to develop exposure profiles for an epidemiological analysis.. Occup Environ Med. , A21. doi: 10.1136/oemed-2014-102362.65

Mughini-Gras, L., Smid, J. H., Wagenaar, J., De Boer, A., Havelaar, A. H., Friesema, I.H.M.,. French, N.P., Graziani, C., Busani, L., & van Pelt, W. 2014. Campylobacteriosis in travellers returning to The Netherlands: multilocus sequence types, risk factors, and evidence for person-to-person transmission of exotic strains in domestically acquired infections. Epidemiology and Infection. 142(6), 1277-1288. doi:  http://dx.doi.org/10.1017/S0950268813002069

Olival, K.J., & Hayman, D.T.S. 2014. Filoviruses in Bats: Current Knowledge and Future Directions. Viruses. 6(4), 1759-1788. doi:10.3390/v6041759

O’Shea, T.J., Cryan, P,M., Cunningham, A.A., Fooks, A.R., Hayman, D.T.S., Luis, A.D., Peel, A.J., Plowright, R.K., & Wood, J.L.N. 2014. Bat flight and zoonotic viruses. Emerging infectious diseases. 20(5), 741-745. doi:10.3201/eid2005.130539

Peel, A.J., Pulliam, J. R. C., Luis, A. D., Plowright, R. K., O'Shea, T. J., Hayman, D. T. S., Wood, J. L. N., Webb, C. T., & Restif, O. 2014. The effect of seasonal birth pulses on pathogen persistence in wild mammal populations. Proceedings of the Royal Society B: Biological Sciences. 281(1786). doi:10.1098/rspb.2013.2962 1471-2954

Prangle, D., Fearnhead, P., Cox, M., Biggs, P., & French, N. 2014. Semi-automatic selection of summary statistics for ABC model choice. Statistical Applications in Genetics and Molecular Biology. 13(1), 67-82. doi: 10.1515/sagmb-2013-0012

Preziuso, S., Pinho, M.D., Attili, A.R., Melo-Cristino, J., Acke, E., Midwinter, A.C., Cuteri, V., Ramirez, M. 2014. PCR based differentiation between Streptococcus dysgalactiae subsp. equisimilis strains isolated from humans and horses. Comparative Immunology, Microbiology and Infectious Diseases. doi: http://dx.doi.org/10.1016/j.cimid.2014.04.001

Roe, W. D., Mayhew, I. G., Jolly, R. D., Marshall, J., & Chilvers, B. L. 2014. Traumatic brain injury, axonal injury and shaking in New Zealand sea lion pups. The Veterinary Journal, 200(1), 96-102. doi: http://dx.doi.org/10.1016/j.tvjl.2014.01.025  

Rosanowski, S.M.,Cogger,N., Rogers,C.W., Bolwell, C.F. 2014.Prevalence and risk factors for respiratory disease on Thorougbred and Standardbred stud farms in New Zealand. Proceedings of the New Zealand Society of Animal Production, Volume 74, Napier, p.5-10. 

Shrestha, R.D., Grinberg, A., Dukkipati, V.S.R., Pleydell, E.J., Prattley, D.J., & French, N.P. 2014. Infections with multiple Cryptosporidium species and new genetic variants in young dairy calves on a farm located within a drinking water catchment area in New Zealand. Veterinary Parasitology . http://dx.doi.org/10.101/j.vetpar.2014.03.034

Souther, S., Tingley, M.W., Popescu, V. D., Hayman, D.T.S., Ryan, M.E., Graves, T.A., Hartl, B., & Terrell, K. 2014. Biotic impacts of energy development from shale: research priorities and knowledge gaps. Frontiers in Ecology and the Environment, 12(6), 330-338. doi: 10.1890/130324

Verhaar, N. , Rogers, C. W., Gee, E. K., Bolwell, C. F., Rosanowski, S. M. 2014. The Feeding Practices and Estimated Workload in a Cohort of New Zealand Competition Horses. Journal of Equine Veterinary Science 34 (2014) 1257-1262. doi:10.1016/j.jevs.2014.08.008 

2013

Ahmed, I., Matthews, P.J., Biggs, P.J., Naeem, M., McLenachan, P.A., & Lockhart, P.J. 2013. Identification of chloroplast genome loci suitable for high-resolution phylogeographic studies of Colocasia esculenta (L.) Schott (Araceae) and closely related taxa. Molecular Ecology Resources. 13(5), 929-937. doi: 10.1111/1755-0998.12128

Almawly, J., Prattley, D., French, N.P., Lopez-Villalobos, N., Hedgespeth, B., & Grinberg, A. 2013. Utility of halofuginone lactate for the prevention of natural cryptosporidiosis of calves, in the presence of co-infection with rotavirus and Salmonella Typhimurium. Veterinary Parasitology  197(1-2), 59-67. http://www.sciencedirect.com/science/article/pii/S0304401713002410

Baker, K.S., Marsh G.A., Todd S., Crameri G., Barr .J, Kamins A.O., Peel A.C., Yu M, Hayman D.T.S., Nagjm B., Mtove G., Amos B., Reyburn H., Nyarko E.O., Suu-Ire R., Murcia P.R., Cunningham A.A., Wood J.L.N., Wang L.F. 2013. Novel potentially-zoonotic paramyxoviruses from the African straw-coloured fruit bat, Eidolon helvum. Journal of Virology, 87:1348-1358. doi: 10.1128/JVI.01202-12.

Banda, M.E., Howe, L.J., & French, N. 2013. A cluster of avian malaria cases in a kiwi management program. New Zealand Veterinary Journal 61(3), 121-126. doi/abs/10.1080/00480169.2012.736130

Bolwell, C. F., Rogers, C. W., French, N. P. & Firth, E. C. 2013. The effect of interruptions during training on the time to the first trial and race start in Thoroughbred racehorses. Preventive Veterinary Medicine.  108, 188-198

Davis, M.A., Moore, D.l., Baker,K.N.K., French,N.P., Patnode.M., Hensley,J., MacDonald,K., & Besser, T.E. 2013. Risk factors for campylobacteriosis in two Washington State counties with high numbers of dairy farms. Journal of Clinical Microbiology. 51(2): 3921 doi: 10.1128/JCM.01433-13   

Gartrell, B., French, N., Howe, L.J., Nelson, N., Houston, M., Burrows, L., Russel, J., Anderson, S.H. 2013. First detection of Chlamydia psittaci from a wild native passerine bird in New Zealand. New Zealand Veterinary Journal 61(3), 174-176. doi/0.1080/00480169.2012.740656

Gilbert A., Fooks A.R., Hayman D.T.S., Horton D.L., Müller T., Plowright R.K., Peel A., Bowen R., Wood J.L.N., Mills J.N., Cunningham A.A., & Rupprecht C.E. 2013. The utility and limitations of serologic testing: implications for the study of wildlife diseases. EcoHealth, In Press.

Gilpin, B., Walsh, G., On, S.L., Smith, D., Marshall, J., French, N.P. 2013. Application of molecular epidemiology to understanding campylobacteriosis in the Canterbury region of New Zealand. Epidemiology and Infection 141(6), 1253-1266.  doi:10.1017/S0950268812001719

Grinberg, A., Biggs, P.J., Dukkipati, V.S.R., & George, T.T. 2013. Extensive intra-host genetic diversity uncovered in Cryptosporidium parvum using Next Generation Sequencing. Infection, Genetics and Evolution. 15, 18-24. http://www.sciencedirect.com/science/article/pii/S1567134812002869

Harland, A.L., Cave, N.J., Jones,  B.R., Benschop, J., Donald, J.J., Midwinter, A.C., Squires, R.A. & Collins-Emerson, J.M. 2013. A serological survey of leptospiral antibodies in dogs in New Zealand. New Zealand Veterinary Journal 61(2), 98-106 doi:10.1080/00480169.2012.719212  

Hayman, D.T.S., Bowen, R.A., Cryan, P.M., McCracken, G.F., O’Shea, T.J., Peel, A.J., Gilbert, A., Webb, C.T. & Wood, J.L.N. 2013. Ecology of Zoonotic Infectious Diseases in Bats: Current Knowledge and Future Directions. Zoonoses and Public Health. 60, 2–21. doi: 10.1111/zph.12000

Hayman, D.T.S., McDonald, K.D., & Kosoy, K.Y. 2013. Evolutionary history of rat-borne Bartonella: the importance of commensal rats in the dissemination of bacterial infections globally, Ecology and Evolution. 3(10), 3195–3203. doi: 10.1002/ece3.702 

Han, J., Collins, L.J., Biggs, P.J., White, W.T. & Penny, D. 2013. Are Signature Proteins the Key to Evaluating Eukaryotic Phylogeny? Rev Bioinform Biometr 2(2), 37-44.

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.,  French, N.P. 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 

Lal, A., Baker, M.G., Hales, S., French, N.P. 2013. Potential effects of global environmental changes on cryptosporidiosis and giardiasis transmission. Trends in Parasitology 29, 83-90. doi/10.1016/j.pt.2012.10.005

Lal, A, Ikeda, T, French, N, Baker, MG, & Hales, S. 2013. Climate Variability, Weather and Enteric Disease Incidence in New Zealand: Time Series Analysis. PlosOne, 8(12):e83484. doi: 10.1371/journal.pone.0083484

Luis A.D., Hayman D.T.S., O’Shea T.J., Cryan P.M., Gilbert A.T., Pulliam J.R.C., Mills J.N., Willis C.K.R., Timonin M.E., Cunningham A.A., Fooks A.R., Rupprecht C.E., Wood J.L.N., & Webb C.T. 2013. A comparison of bats and rodents as reservoirs of zoonotic viruses: Are bats special? Proceedings of the Royal Society B: Biological Sciences, 280(1756): doi: 10.1098/rspb.2012.2753 

Mohan, V., Stevenson, M., Marshall, J., Fearnhead, P., Holland, B., Hotter, G., & French, N.P. 2013. Campylobacter jejuni colonisation and population structure in urban populations of ducks and starlings in New Zealand. MicrobiologyOpen 2(4) 659-673. doi: 10.1002/mbo3.102

Muellner, P., Pleydell, E., Pirie, R., Baker, M., Campbell, D., Carter, P., French, N., 2013. Molecular-based surveillance of campylobacteriosis in New Zealand - from source attribution to genomic epidemiology. Eurosurveillance 18(3), pii=20365 http://www.eurosurveillance.org/images/dynamic/EE/V18N03/art20365.pdf

Mughini-Gras, L., Smid, J., Wagenaar, J., de Boer, A., Havelaar, A., Friesema, I., French, N., Graziani, C., Busani, L., van Pelt, W. 2013. Increased risk for Campylobacter jejuni and C. coli infection of pet origin in dog owners and evidence for genetic association between strains causing infection in humans and their pets. Epidemiology and Infection, 141 (12), 2526-2535. doi:10.1017/S0950268813000356

On, S.L.W., Brandt, S.M., Cornelius, A.J., Fusco, V., Quero, G.M., Maćkiw, E., Houf, K., Bilbao, A., Díaz, A.I., Benejat, L., Megraud, F., Collins-Emerson, J., French, N.P., Gotcheva, V., Angelov, A., Alakomi, H.L., Saarela, M., & Paulin, S.M. 2013. PCR revisited: a case for revalidation of PCR assays for microorganisms using identification of Campylobacter species as an exemplar. Quality Assurance and Safety of Crops & Foods 5, 49-62.

Peel, A.J., McKinley, T.J., Baker, K.S., Barr, J.A., Crameri, G., Hayman, D.T.S., Feng, Y-R., Broder, C.C., Wang, L-F., Cunningham, A.A., & Wood, J.L.N. 2013. Use of cross-reactive serological assays for detecting novel pathogens in wildlife: Assessing an appropriate cutoff for henipavirus assays in African bats. Journal of Virological Methods. 193, 295-303. http://dx.doi.org/10.1016/j.jviromet.2013.06.030

Peel, A.J., Sargan, D.R., Baker, K.S., Hayman, D.T.S., Barr, J.A., Crameri, G., Suu-Ire, R., Broder, C.C., Wang, L.F., Fooks, A.R., Rossiter, S.J., Wood, J.L.N., & Cunningham, A.A. 2013. Continent-wide panmixia of an African fruit bat facilitates transmission of potentially-zoonotic viruses. Nature Communications. 4(2770). doi:10.1038/ncomms3770

Rosanowski, S., Cogger, N., Rogers, C., Bolwell, C., Benschop, J., & Stevenson, M. (2013).  Analysis of horse movements from non-commercial horse properties in New Zealand. New  Zealand  Veterinary Journal, 61(5), 245-253 doi: 10.1080/00480169.2012.750571  

Sheppard, S.K., Didelot, X., Jolley, K.A., Darling, A.E., Pascoe, B., Meric, G., Kelly, D.J., Cody, A., Colles, F.M., Strachan, N.J., Ogden, I.D., Forbes, K., French, N.P., Carter, P., Miller, W.G., McCarthy, N.D., Owen, R., Litrup, E., Egholm, M., Affourtit, J.P., Bentley, S.D., Parkhill, J., Maiden, M.C., Falush, D., 2013. Progressive genome-wide introgression in agricultural Campylobacter coli. Molecular Ecology 22, 1051-1064. doi/10.1111/mec.12162

Smid, J.H., Mughini Gras, L., de Boer, A.G., French, N.P., Havelaar, A.H., Wagenaar, J.A., van Pelt, W., 2013. Practicalities of using non-local or non-recent multilocus sequence typing data for source attribution in space and time of human campylobacteriosis. PLoS One 8(2), e55029. doi: 10.1371/journal.pone.0055029

Thornley, C.N., Hewitt, J., Perumal, L., Van Gessel, S.M., Wong, J., David, S.A., Rapana, J.P., Li, S., Marshall, J.C., & Greening, GE. 2013. Multiple outbreaks of a novel norovirus GII.4 linked to an infected post-symptomatic food handler. Epimiology and Infection. 141(8), 1585-1597 doi: http://dx.doi.org/10.1017/S0950268813000095

Wagenaar, J., French, N.P., & Havelaar, A.H. 2013. Preventing Campylobacter at the source - why is it so difficult? Clinical Infectious Diseases, 57(11), 1600-1606. doi: 10.1093/cid/cit555

Wang, J., McLenachan, P.A., Biggs, P.J., Winder, L.H., Schoenfeld, B.I., Narayan, V.V., Phiri, B.J., & Lockhart, P.J. 2013. Environmental bio-monitoring with high-throughput sequencing.. Brief Bioinform. 14(5), 575-588. doi:10.1093/bib/bbt032

2012

Irshad, H., Cookson, A., Hotter, G., Besser, T., On, S., French, N., 2012. Epidemiology of Shiga toxin-producing Escherichia coli O157 in very young calves in the North Island of New Zealand. N Z Vet J 60, 21-26.

Jones, G., Johnson, W.O., Vink, W.D., French, N., 2012. A Framework for the Joint Modeling of Longitudinal Diagnostic Outcome Data and Latent Infection Status: Application to Investigating the Temporal Relationship between Infection and Disease. Biometrics 68, 371-379.

Lal, A., Baker, M.G., French, N.P., Dufour, M., Hales, S., 2012a. The epidemiology of human salmonellosis in New Zealand, 1997-2008. Epidemiol Infect140(9), 1685-1694.

Lal, A., Hales, S., French, N., Baker, M.G., 2012b. Seasonality in human zoonotic enteric diseases: a systematic review. PLoS One7, e31883.

Lee, K., French, N.P., Jones, G., Hara-Kudo, Y., Iyoda, S., Kobayashi, H., Sugita-Konishi, Y., Tsubone, H., Kumagai, S., 2012. Variation in stress-resistance patterns among stx genotypes and genetic lineages in Shiga toxin-producing Escherichia coli O157. Applied and Environmental Microbiology 78(9), 3361-3368.

Mughini Gras, L., Smid, J.H., Wagenaar, J.A., de Boer, A.G., Havelaar, A.H., Friesema, I.H.M., French, N.P., Busani, L., van Pelt, W., 2012. Risk Factors for Campylobacteriosis of Chicken, Ruminant, and Environmental Origin: A Combined Case-Control and Source Attribution Analysis. PLoS One7(8), e42599.

Phiri, B.J., Benschop, J., Stevenson, M., Swai, E.S., Karimuribo, E.D., French, N.P., 2012. Spatiosurvival analysis of mortality on smallholder dairy farms in Tanga and Iringa regions of Tanzania. Trop Anim Health Prod44(4), 827-834.

Pleydell, E., Souphavanh, K., Hill, K., French, N., Prattley, D., 2012. Descriptive epidemiological study of the use of antimicrobial drugs by companion animal veterinarians in New Zealand. New Zealand Veterinary Journal60(2), 115-122.

Spencer, S.E., Marshall, J., Pirie, R., Campbell, D., Baker, M.G., French, N.P., 2012. The spatial and temporal determinants of campylobacteriosis notifications in New Zealand, 2001-2007. Epidemiol Infect140(9), 663-677.

Yu, S., Fearnhead, P., Holland, B., Biggs, P., Maiden, M., French, N., 2012. Estimating the relative roles of recombination and point mutation to the generation of single locus variants in Campylobacter jejuni and Campylobacter coli. Journal of Molecular Evolution74(5-6), 273-280.

Subharat, S., Wilson, P. R., Heuer, C., & Collins-Emerson, J. M. (2012, January). Growth response and shedding of Leptospira spp. in urine following vaccination for leptospirosis in young farmed deer.. N Z Vet J, 60(1), 14-20. doi:10.1080/00480169.2011.624985

AL Harland, NJ Cave, BR Jones, J Benschop, JJ Donald, AC Midwinter, RA Squires & JM Collins- Emerson (2012): A serological survey of leptospiral antibodies in dogs in New Zealand, New Zealand Veterinary Journal, Eprint, DOI:10.1080/00480169.2012.719212

Collins-Emerson, J. and Abdul-Careem, M.F. (2012) Chapter 4. Microbiology. Section 4.8. "Molecular microbiology as a diagnostic tool." P. 290-305. In "The Veterinary Laboratory and Field Manual." 2nd Edition.Editors: S.C. Cork and R.W. Halliwell. Nottingham University Press, 2012. ISBN 978-1-908062-09-3

S Subharat, PR Wilson, C Heuer, JM Collins-Emerson . Longitudinal serological survey and herd-level risk factors for Leptospira spp. serovars Hardjo-bovis and Pomona on deer farms with sheep and/or beef cattle. in press available on-line (2012)

2011

Biggs, P., P. Fearnhead, G.S. Hotter, V. Mohan, J. Collins-Emerson, E. Kwan, T. Besser, A. Cookson, P. Carter, and N. French, 2011 Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage. PLoS One, 6, e27121.10.1371/journal.pone.0027121.

Grove-White, D.H., Leatherbarrow, A.J., Cripps, P.J., Diggle, P.J., French, N.P., 2011. Molecular epidemiology and genetic diversity of Campylobacter jejuni in ruminants. Epidemiol Infect, 139, 1661-1671. 

Hepworth, P.J., Ashelford, K.E., Hinds, J., Gould, K.A., Witney, A.A., Williams, N.J., Leatherbarrow, H., French, N.P., Birtles, R.J., Mendonca, C., Dorrell, N., Wren, B.W., Wigley, P., Hall, N., Winstanley, C., 2011. Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes. Environ Microbiol 13, 1549-1560.

Lee, K., French, N.P., Hara-Kudo, Y., Iyoda, S., Kobayashi, H., Sugita-Konishi, Y., Tsubone, H., Kumagai, S., 2011. Multivariate analyses revealed distinctive features differentiating human and cattle isolates of Shiga toxin-producing Escherichia coli O157 in Japan. J Clin Microbiol 49, 1495-1500. 

Minh, P., Stevenson, M., Jewell, C., French, N., Schauer, B., 2011. Spatio-temporal analyses of highly pathogenic avian influenza H5N1 outbreaks in the Mekong River Delta, Vietnam, 2009. Spatial and Spatio-temporal Epidemiology  2, 49-57. 

Muellner, P., Marshall, J., Spencer, S., Noble, A.D., Shadbolt, T., Collins-Emerson, J., Midwinter, A.C., Carter, P., Pirie, R., Wilson, D.J., Campbell, D., Stevenson, M.A., French, N., 2011a. Utilising a combination of molecular and spatial tools to assess the effect of a public health intervention. Preventive Veterinary Medicine 02, 242-253. 

Muellner, P., Zadoks, R., Perez, A., Spencer, S., Schukken, Y., French, N., 2011b. The integration of molecular tools into veterinary and spatial epidemiology.   .Spatial and Spatio-temporal Epidemiology 2, 173-183.

Sears, A., Baker, M.G., Wilson, N., Marshall, J., Muellner, P., Campbell, D.M., Lake, R.J., French, N.P., 2011. Marked campylobacteriosis decline after interventions aimed at poultry, New Zealand. Emerg Infect Dis 17, 1007-1015. 

Spencer, S., Marshall, J., Pirie, R., Campbell, D., French, N., 2011. The detection of spatially localised outbreaks in campylobacteriosis notification data. Spatial and Spatio-temporal Epidemiology 2, 159-171.

Williams, N.J., Sherlock, C., Jones, T.R., Clough, H.E., Telfer, S.E., Begon, M., French, N., Hart, C.A., Bennett, M., 2011. The prevalence of antimicrobial-resistant Escherichia coli in sympatric wild rodents varies by season and host. J Appl Microbiol. 110, 962-970.

Subharat, S.,Peter R. Wilson, Cord Heuer, Julie M. Collins-Emerson. Evaluation of a SYTO9 real-time polymerase chain reaction assay to detect and identify pathogenic Leptospira species in kidney tissue and urine of New Zealand farmed deer. JVDI July 2011 vol. 23 no. 4 743-752

Subharat, S., PR Wilson, C. Heuer, JM Collins-Emerson . Vaccination for leptospirosis improved the weaning percentage of 2-year-old farmed red deer hinds in New Zealand. New Zealand Vet Journal 59(4):191-196

Subharat S, Wilson P, Heuer C, Collins-Emerson J, Smythe L, Dohnt M, Craig S, Burns M. Serosurvey of leptospirosis and investigation of a possible novel serovar Arborea in farmed deer in New Zealand. New Zealand Vet Journal 59(3):139-42

2010

Cox MP, Peterson DA, Biggs PJ. 2010 . SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics. 2010 Sep 27;11:485.

Benschop J, Spencer S, Alban L, Stevenson M, French N. 2010. Bayesian zero-inflated predictive modelling of herd-level Salmonella prevalence for risk-based surveillance. Zoonoses and Public Health 2010 Nov 57 Suppl 1:60-70.

Dorjee, S., C. Heuer, R. Jackson, D. M. West, J. M. Collins-Emerson, A. C. Midwinter, and A. L. Ridler. 2010. Assessment of occupational exposure to leptospirosis in a sheep-only abattoir. Epidemiol Infect: in press available on-line

Pleydell EJ, Rogers L, Kwan E and French NP. 2010 Low levels of antibacterial drug resistance expressed by Gram-negative bacteria isolated from poultry carcasses in New Zealand. New Zealand Vet Journal 58, 229-236

Teh, K., Flint, S,. and French, N.P., 2010. Biofilm Formation by Campylobacter jejuni in Controlled Mixed-microbial populations. International Journal of Food Microbiology. 143, 118-124.

Grove-White, D.H., Leatherbarrow, A.J., Cripps, P.J., Diggle, P.J., French, N.P., 2010. Temporal and farm-management-associated variation in the faecal-pat prevalence of Campylobacter jejuni in ruminants. Epidemiol Infect1 38, 549-558.

Ayanegui-Alcerreca MA., Wilson PR., Mackintosh CG., Collins-Emerson JM., Heuer C. Midwinter AC., Castillo-Alcala F, 2010 Regional seroprevalence of leptospirosis on deer farms in New Zealand. New Zealand Veterinary Journal, Volume 58, Issue 4, pp 184-189

Hotter, G.S., Li, I.H., French, N.P., 2010. Binary genomotyping using lipooligosaccharide biosynthesis genes distinguishes between Campylobacter jejuni isolates within poultry-associated multilocus sequence types. Epidemiol Infect. 138, 992-1003.

John, K., Fitzpatrick, J., French, N., Kazwala, R., Kambarage, D., Mfinanga, G.S., MacMillan, A., Cleaveland, S., 2010. Quantifying risk factors for human brucellosis in rural northern Tanzania. PLoS One5, e9968.

Lockhart, C.Y., Stevenson, M.A., Rawdon, T.G., Gerber, N., French, N.P., 2010. Patterns of contact within the New Zealand poultry industry. Prev Vet Med. 95(3-4):258-66

Mullner, P., Collins-Emerson, J.M., Midwinter, A.C., Carter, P., Spencer, S.E., van der Logt, P., Hathaway, S., French, N.P., 2010a. Molecular epidemiology of Campylobacter jejuni in a geographically isolated country with a uniquely structured poultry industry. Appl Environ Microbiol76, 2145-2154.

Mullner, P., Shadbolt, T., Collins-Emerson, J.M., Midwinter, A.C., Spencer, S.E., Marshall, J., Carter, P.E., Campbell, D.M., Wilson, D.J., Hathaway, S., Pirie, R., French, N.P., 2010b. Molecular and spatial epidemiology of human campylobacteriosis: source association and genotype-related risk factors. Epidemiol Infect, 138(10):1372-83.

Phiri, B.J., Benschop, J., French, N.P., 2010. Systematic review of causes and factors associated with morbidity and mortality on smallholder dairy farms in eastern and southern Africa. Prev Vet Med. 94, 1-8.

Pleydell, E., Rogers, L., Kwan, E., French, N., 2010. Evidence for the clustering of antibacterial resistance phenotypes of enterococci within integrated poultry companies. Microb Ecol 59, 678-688.

Whitworth, J., Zhang, Y., Bono, J., Pleydell, E., French, N., Besser, T., 2010. Diverse genetic markers concordantly identify bovine origin Escherichia coli O157 genotypes underrepresented in human disease. Appl Environ Microbiol 76, 361-365.

Client reports for the New Zealand Food Safety Authority are available on the following websites

Recent presentation given to Australian College of Veterinary Science, Gold Coast

Dr Chris Jewell has been working with us on mapping and modelling human cases of zoonotic disease. Below are some examples of Google maps of waterborne disease notifications over a 10-year period overlayed on riverflow levels in surface water catchments (data provided by ESR and NIWA, funded by HRC).

Download Cryptosporidium avi file click on icon below

   crypto and river flow.avi (31,420 KB)

Download Giardia avi file click on icon below

   giardia and river flow.avi (29,768 KB)

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