New information following the change in COVID-19 alert levels.

Publications - Food safety 

Recent mEpiLab publications: peer reviewed journal articles 2009/2014

Duncan, J. S., Leatherbarrow, A. J., French, N. P. & Grove-White, D. H. Temporal and farm-management-associated variation in faecal-pat prevalence of Campylobacter fetus in sheep and cattle. Epidemiol Infect  1-9, 2014

Grange, Z., van Andel, M., French, N. & Gartrell, B. Social networking of an endangered flightless bird and its use in targeting disease surveillance. Conservation Biology  28, 518-528, 2014

Grove-White, D. H., Leatherbarrow, A. J., Cripps, P. J., Diggle, P. & French, N. Temporal and farm-management-associated variation in faecal pat prevalence of Arcobacter spp. in ruminants. Epidemiology and Infection  142, 861-870, 2014

Mughini-Gras, L., Smid, J. H., Wagenaar, J., De Boer, A., Havelaar, A. H., Friesema, I. H. M., French, N., Graziani, C., Busani, L. & van Pelt, W. 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 Epidemiol Infect  accepted, 2014

Prangle, D., Fearnhead, P., Cox, M. P., Biggs, P. J. & French, N. P. Semi-automatic selection of summary statistics for ABC model choice. Stat Appl Genet Mol Biol 13, 67-82, 2014

Almawly, J., Prattley, D., French, N., Lopez-Villalobos, N., Hedgespeth, B. & Grinberg, A. Utility of halofuginone lactate for the prevention of natural cryptosporidiosis of calves, in the presence of co-infection with rotavirus and< i> Salmonella</i> Typhimurium. Veterinary Parasitology  197, 59-67, 2013

Banda, M. E., Howe, L., Gartrell, B. D., McInnes, K., Hunter, S. & French, N. P. A cluster of avian malaria cases in a kiwi management programme. N Z Vet J  61, 121-126, 2013
Bolwell, C. F., Rogers, C. W., French, N. P. & Firth, E. C. The effect of interruptions during training on the time to the first trial and race start in Thoroughbred racehorses. Prev Vet Med  108, 188-198, 2013

Davis, M., Moore, D., Baker, K., French, N., Patnode, M., Hensley, J., MacDonald, K. & Besser, T. Risk factors for campylobacteriosis in two Washington State counties with high numbers of dairy farms. Journal of Clinical Microbiology  51, 3921-3927, 2013

Gartrell, B. D., French, N. P., Howe, L., Nelson, N. J., Houston, M., Burrows, E. A., Russell, J. C. & Anderson, S. H. First detection of Chlamydia psittaci from a wild native passerine bird in New Zealand. N Z Vet J  61, 174-176, 2013

Gilpin, B. J., Walsh, G., On, S. L., Smith, D., Marshall, J. C. & French, N. P. Application of molecular epidemiology to understanding campylobacteriosis in the Canterbury region of New Zealand. Epidemiol Infect  141, 1253-1266, 2013

Irshad, H., Cookson, A. & French, N. 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. Epidemiol Infectaccepted, 2014

Jaros, P., Cookson, A. L., Campbell, D. M., Besser, T. E., Shringi, S., Mackereth, G. F., Lim, E., Lopez, L., Dufour, M., Marshall, J. C., Baker, M. G., Hathaway, S., Prattley, D. J. & French, N. P. A prospective case-control and molecular epidemiological study of human cases of Shiga toxin-producing Escherichia coli in New Zealand. BMC Infect Dis 13, 450, 2013

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

Lal, A., Ikeda, T., French, N., Baker, M. & Hales, S. Climate Variability, Weather and Enteric Disease Incidence in New Zealand: Time Series Analysis. PlosOne 8, e83484, 2013
Mohan, V., Stevenson, M., Marshall, J., Fearnhead, P., Holland, B. R., Hotter, G. & French, N. P. Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand. Microbiologyopen 2, 659-673, 2013

Muellner, P., Pleydell, E., Pirie, R., Baker, M., Campbell, D., Carter, P. & French, N. 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, 2013

Mughini-Gras, L., Smid, J., Wagenaar, J., de Boer, A., Havelaar, A., Friesema, I., French, N., Graziani, C., Busani, L. & van Pelt, W. 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 2526-2535, 2013

On, S., Brandt, S., Cornelius, A., Fusco, V., Quero, G., Maćkiw, E., Houf, K., Bilbao, A., Díaz, A. & Benejat, L. 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, 2013

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. Progressive genome-wide introgression in agricultural Campylobacter coli. Mol Ecol  22, 1051-1064, 2013

Smid, J. H., Mughini Gras, L., de Boer, A. G., French, N. P., Havelaar, A. H., Wagenaar, J. A. & van Pelt, W. 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, e55029, 2013

Wagenaar, J. A. & French, N. P. Preventing Campylobacter at the source - why is it so difficult? Clinical Infectious Diseases  57, 1600-1606, 2013


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)


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


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.


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.

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

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

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.

Clough, H.E., Clancy, D., and French, N.P., Quantifying exposure to Vero-cytotoxigenic Escherichia coli O157 in milk sold as pasteurized: a model-based approach International Journal of Food Microbiology, 2009. 131(2-3):95-105. 

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.

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.

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.

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.

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

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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