The programme on food safety and zoonoses applies an array of molecular and modelling tools to advance our understanding of the biology and transmission of bacterial pathogens. This has lead to the development of new surveillance and disease control tools, and informed national policy for the control of some of the most important infectious diseases related to food and food production in New Zealand. Specific projects include :

Escherichia coli

The control of Escherichia coli O157 and other STECs in the food chain. The laboratory provides a key component of the FRST and Industry funded Improved Pathogen Control Technologies (IMPACT) programme. The programme is a collaboration between ESR, AgResearch and Massey and is developing new tools for the control of these pathogens, including phage control and quorum sensing.

Researchers in the Hopkirk team are also conducting epidemiological studies at a number of meat processing plants in both the North and South Islands to further our understanding of the transmission and propagation of these pathogens along the food chain.

Recent Publications


Hamid Irshad (2013) Molecular epidemiology of shiga toxin-producing Escherichia coli O157 and non-O157 STEC in calves in the North Island of New Zealand.

Journal articles

Franz, E., Rotariu, O., Lopes, B.S., MacRae, M., Bono, J.L., Laing, C., Gannon, V., Soderlund, R., van Hoek, A.H.A.M, Friesema, I., French, N.P., George, T., Biggs, P.J., Jaros, P., Rivas, M., Chinen, I., Campos, J., Jernberg, C., Gobius, K., Mellor, G.E., Chandry, P.S., Perez-Reche, F., Forbes, K.J., Strachan, N.J.C. [2018] Phylogeographic analysis reveals multiple international transmission events have driven the global emergence of Escherichia coli O157:H7. Clinical Infectious Diseases. doi

Jaros, P., Cookson, A.L., Reynolds, A., Withers, H., Clemens, R., Brightwell, G., Mills, J., Marshall, J., Prattley, D.J., Campbell, D.M., Hathaway, S., French, N.P. [2018] The effect of transportation and lairage on faecal shedding and carcass contamination with Escherichia coli O157 and O26 in very young calves in New Zealand. Epidemiology & Infection 146:1089-1100. doi 

Browne, A.S., Midwinter,A.C., Withers, H., Cookson, A.L., Biggs, P.J., Marshall, J.C. Benschop, J.,Hathaway, S., Haack, N.A., Akhter, R.N., French, N.P. [2018] Molecular Epidemiology of Shiga Toxin-Producing Escherichia Coli (Stec) on New Zealand Dairy Farms: Application of a Culture-Independent Assay and Whole Genome Sequencing. Appl Environ Microbiol. doi

Browne, A.S., Biggs, P.J., Elliott, A., Jaros, P., French, N.P., Midwinter, A.C. [2018] Draft Whole-Genome Sequences of Three Diarrheagenic Escherichia coli Strains Isolated from Farmed Deer in New Zealand. Genome Announc 6[16]. doi:10.1128/genomeA.00300-18 

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

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

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

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

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. 

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:

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).

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 

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:

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

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..

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 Microbiology78(9), 3361-3368.

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.

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.

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.

Clough, H.E., Fenton, S.E., French, N.P., Miller, A.J., and Cook, A.J., Evidence from the UK Zoonoses Action Plan in favour of localised anomalies of Salmonella infection on United Kingdom pig farms. Prev Vet Med, 2009. 89(1-2):67-74

Robinson, S.E., Brown, P.E., Wright, E.J., Hart, C.A., and French, N.P., Quantifying within- and between-animal variation and uncertainty associated with counts of Escherichia coli O157 occurring in naturally infected cattle faeces. J R Soc Interface, 2009. 6(31): p. 169-77.


Molecular typing, pathogen survival and source attribution for Campylobacter. This programme, funded by the NZFSA, Industry, HRC and the Royal Society Marsden fund, has advanced our understanding of the epidemiology, evolution and emergence of this pathogen and has contributed to the dramatic decline in human cases observed in recent years.

This work involved setting up the Manawatu Sentinel surveillance site in 2005, and the subsequent culture, enumeration and sequencing of Campylobacter from human cases, food sources, farmed and wild animals and recreational water. New risk modelling tools were developed to address the simple question “where are humans getting infected from?"

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

Petra Mullner (2009) Estimating the contribution of different sources to the burden of human campylobacteriosis and salmonellosis (View PDF)

Vathsala Mohan (2011) Molecular epidemiology of campylobacteriosis and evolution of Campylobacter jejuni ST-474 in New Zealand

Recent Publications

Vallee, E., Heuer, C., Collins-Emerson, J.M., Benschop, J., Ridler, A.L., Wilson, P.R. [2018] Effects of natural infection by L. borgpetersenii serovar Hardjo type Hardjo-bovis, L. interrogans serovar Pomona, and leptospiral vaccination, on sheep growth. Prev Vet Med 159:196-202. doi

Nohra, A., Grinberg, A., Midwinter, A.C., Marshall, J.C., Collins-Emerson, J.M., French, N.P. [2018] Exposure to Whole Chicken Carcasses May Present a Greater Risk of Campylobacteriosis Compared to Exposure to Chicken Drumsticks. Zoonoses Public Health (Jul 11 2018). doi   

Iraola, G., Forster, S.C., Kumar, N., Lehours, P., Bekal, S., Garcia-Pena, F.J., Paolicchi, F., Morsella, C., Hotzel, H., Hsueh, P.R., Vidal, A., Levesque, S., Yamazaki, W., Balzan, C., Vargas, A., Piccirillo, A., Chaban, B., Hill, J.E., Betancor, L., Collado, L., Truyers, I., Midwinter, A.C., Dagi, H.T., Megraud, F., Calleros, L., Perez, R., Naya, H., Lawley, T.D. [2017] Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota. Nat Commun 8(1):1367. doi:10.1038/s41467-017-01449-9 

Cornelius, A.J., Miller, W.G.,Lastovica, A.J., On, S.L.W., French, N.P., Vandenberg, O., Biggs, P.J. [2017] Complete Genome Sequence of Campylobacter concisus ATCC 33237(T) and Draft Genome Sequences for an Additional Eight Well-Characterized C.concisus Strains. Genome Announc v5:29. doi:10.1128/genomeA.00711-17

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

Bojanić, K., Midwinter, A. C., Marshall, J. C., Rogers, L. E., Biggs, P. J., Acke, E. [2016] Isolation of Campylobacter spp. from Client-Owned Dogs and Cats, and Retail Raw Meat Pet Food in the Manawatu, New Zealand. Zoonoses Public Health. doi:10.1111/zph.12323

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

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 

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

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.

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.

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

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.

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, In press. 10.1111/1753-6405.12274

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:

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

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

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:

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

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 press.

Muellner, P., Pleydell, E., Pirie, R., Baker, M., Campbell, D., Carter, P., French, N., 2013. The contribution of molecular-based surveillance to successful prevention and control of campylobacteriosis in New Zealand - from source attribution to genomic epidemiology. Eurosurveillance 18, Article 7.

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 in press.

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. Mol Ecol 22, 1051-1064.

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 One8, e55029.

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

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.

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 andCampylobacter coli. Journal of Molecular Evolution74(5-6), 273-280.

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.

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.

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.

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.

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.

Mullner P, Spencer, SEF, Daniel J. Wilson, Geoff Jones, Alasdair D. Noble, Anne C. Midwinter, Julie M. Collins-Emerson, Philip Carter, Steve Hathaway, Nigel P. Frencha .  Assigning the source of human campylobacteriosis in New Zealand: A comparative genetic and epidemiological approach.  2009 Infection, Genetics and Evolution 9: 1311-9

Carter PE, McTavish SM, Brooks HJ, Campbell D, Collins-Emerson JM, Midwinter AC, French NP.  Novel clonal complexes with unknown animal reservoir dominate Campylobacter jejuni isolated from river water in New Zealand. Applied and Environmental Microbiology. 2009 75: 6038-46

McTavish SM, Pope CE, Nicol C, Campbell, D, French N and Carter PE Multilocus Sequence Typing of Campylobacter jejuni, and the Correlation between Clonal Complex and Pulsed-field Gel Electrophoresis Macrorestriction Profile.  2009 FEMS Microbiology Letters 298(2):149-56

French, N.P., Midwinter, A., Holland, B., Collins-Emerson, J., Pattison, R., Colles, F.M., and Carter, P., Molecular epidemiology of Campylobacter jejuni isolated from wild bird faecal material in children’s playgrounds. Applied and Environmental Microbiology, 2009. 75(3): p. 779-83.

Mullner, P., Jones, G., Noble, A., Spencer, S., Hathaway, S., and French, N.P., Source Attribution of Food Borne Zoonosis in New Zealand: A Modified Hald Model. Risk Anal, 2009. 29(7):970-84.


Controlling Leptospira infections in meat workers and livestock. The laboratory has unique expertise in the culture and genotyping of these fastidious organisms, and has conducted a number of epidemiological studies that have informed the prevention and control of infection in abattoir workers, and evaluated the use of vaccine-based control measures in animal populations.


Fang Fang was awarded "Best Full JVDI Manuscript Award"

Fang completed her PhD 2014. Her paper "Interlaboratory and between-specimen comparisons of diagnostic tests for leptospirosis in sheep and cattle" was awarded the best Full Journal of Veterinary Diagnostic Investigation Manuscript award for 2015 by the American Association of Veterinary Laboratory Diagnosticians.

Recent Publications

Dreyfus, A., Wilson, P., Benschop, J., Collins-Emerson, J., Verdugo, C., Heuer, C. [2018] Seroprevalence and Herd-Level Risk Factors for Seroprevalence of Leptospira Spp. In Sheep, Beef Cattle and Deer in New Zealand. N Z Vet J (Aug 19 2018): 1-27. doi 

Shrestha, R., McKenzie, J.S., Gautam, M., Adhikary, R., Pandey, K., Koirala, P., Bc, G.B., Miller, L.C., Collins-Emerson, J., Craig, S.B., Shrestha, S., Heuer, C. [2018]. Determinants of clinical leptospirosis in Nepal.. Zoonoses Public Health. doi 

Guernier, V., Goarant, C., Benschop, J.Lau, C.L. [2018] A systematic review of human and animal leptospirosis in the Pacific Islands reveals pathogen and reservoir diversity. PLoS Negl Trop Dis 12[5].doi 10.1371/journal.pntd.0006503 

Benschop, J., Collins-Emerson, J., Maskill, A., O'Connor, P., Tunbridge, M., Yupiana, Y., Weston, J. [2017] Leptospirosis in three workers on a dairy farm with unvaccinated cattle. N Z Med J v130(1462). 

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 

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

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.

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)

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

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

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: 10.1017/S0950268815000515

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

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

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., Cullum, A., Heuer, C., Wilson, P.R., & 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

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

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.

Mansell, C., & Benschop, J. 2014. Leptospirosis is an important multi-species zoonotic disease in New Zealand. Invited editorial. New Zealand Medical Journal, 127 (1388).

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:

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

Supatsak Subharat, 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

S. Subharat, 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

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

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

Benschop, J., Heuer, C., Jaros, P., Collins-Emerson, J. M., Midwinter, A. C., Wilson, P. R. (2009). Sero-prevalence of leptospirosis in workers at a New Zealand slaughterhouse. New Zealand Medical Journal, 122(1307), 39-47.

Dorjee S, Heuer C, Jackson R, West DM, Collins-Emerson JM, Midwinter AC, Ridler AL. Are white-spot lesions in kidneys in sheep associated with leptospirosis? 2009 New Zealand Vet J. 57(1):28-33


The development and optimisation of surveillance systems for Salmonella in both humans and animals using advanced molecular and spatial modelling tools. The team has also developed modular process risk models that capture the propagation of these pathogenic bacteria along the food chain, and during the slaughtering process.

Jackie Benschop (2009) Epidemiological investigations of surveillance strategies for zoonotic Salmonella (View PDF)
Simone Titus (2007) A novel model developed for Quantitative Microbial Risk Assessment in the pork food chain. (View PDF)

Recent Publications

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 entericaSerovar Typhimurium DT160 Associated with a 14-Year Outbreak, New Zealand, 1998-2012. Emerging Infectious Diseases, 23(6), 906-913. doi:10.3201/eid2306.161934

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

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

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 

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

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

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.

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.

Benschop, J., Stevenson, M.A., Dahl, J., Morris, R.S., and French, N., Informing surveillance programmes by investigating spatial dependency of subclinical Salmonella infection. 2009 Epidemiol Infect, 137(9):1348-59

Clough, H.E., Fenton, S.E., French, N.P., Miller, A.J., and Cook, A.J., Evidence from the UK Zoonoses Action Plan in favour of localised anomalies of Salmonella infection on United Kingdom pig farms. Prev Vet Med, 2009. 89(1-2):67-74

Fenton, S.E., Clough, H.E., Diggle, P.J., Evans, S.J., Davison, H.C., Vink, W.D., and French, N.P., Spatial and spatio-temporal analysis of Salmonella infection in dairy herds in England and Wales. Epidemiol Infect, 2009: 137(6):847-57.

Cryptosporidium and Giardia

Molecular genotyping and infectivity assays for protozoal pathogens such as Cryptosporidium and Giardia(MoH funded). This work includes screening of isolates from surface and ground water, including waste water from meat processing plants, and the assessment of catchments used for the supply of drinking and recreational water.

Recent Publications

Garcia, R.J.C., French, N.P., Pita, A., Velathanthiri, N., Shrestha, R., Hayman, D.T.S. [2017] Local and global genetic diversity of protozoan parasites: Spatial distribution of Cryptosporidium and Giardia genotypes. PLoS Negl Trop Dis 11(7): e0005736. doi:10.1371/journal.pntd.0005736

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  

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

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

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

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., & 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  

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 .

Lal, A., Baker, M.G., Hales, S., French, N.P., 2013. Potential effects of global environmental changes on cryptosporidiosis and giardiasis transmission. Trends Parasitol 29, 83-90.

Brook, E.J., Anthony Hart, C., French, N.P., and Christley, R.M., Molecular epidemiology of Cryptosporidium subtypes in cattle in England. 2009 Vet J, 2009. 179(3): p. 378-82.

Snel, S., Baker, M., Kamalesh, V., French, N., and Learmonth, J., A tale of two parasites: The comparative epidemiology of cryptosporidiosis and giardiasis in New Zealand, 1997-2006. Epidemiol Infect, 2009. 137(11):1641-50.