Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand

Abstract Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.

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Whole Genome Sequencing for Determining the Source of Mycobacterium bovis Infections in Livestock Herds and Wildlife in New Zealand

Frontiers in Veterinary Science ◽

10.3389/fvets.2018.00272 ◽

2018 ◽

Vol 5 ◽

Cited By ~ 13

Author(s):

Marian Price-Carter ◽

Rudiger Brauning ◽

Geoffrey W. de Lisle ◽

Paul Livingstone ◽

Mark Neill ◽

...

Keyword(s):

New Zealand ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Mycobacterium Bovis ◽

Whole Genome

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Whole-Genome Sequencing ofSalmonellaMississippi and Typhimurium Definitive Type 160, Australia and New Zealand

Emerging Infectious Diseases ◽

10.3201/eid2509.181811 ◽

2019 ◽

Vol 25 (9) ◽

pp. 1690-1697

Author(s):

Laura Ford ◽

Danielle Ingle ◽

Kathryn Glass ◽

Mark Veitch ◽

Deborah A. Williamson ◽

...

Keyword(s):

New Zealand ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome

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Mycobacterium bovisPersistence in Two Different Captive Wild Animal Populations in Germany: a Longitudinal Molecular Epidemiological Study Revealing Pathogen Transmission by Whole-Genome Sequencing

Journal of Clinical Microbiology ◽

10.1128/jcm.00302-18 ◽

2018 ◽

Vol 56 (9) ◽

Cited By ~ 6

Author(s):

Thomas A. Kohl ◽

Christian Utpatel ◽

Stefan Niemann ◽

Irmgard Moser

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Bovine Tuberculosis ◽

Animal Health ◽

Variable Number Tandem Repeat ◽

Pathogen Transmission ◽

Whole Genome ◽

The European Union ◽

Content Type ◽

Animal Populations

ABSTRACTBovine tuberculosis (bTB) caused byMycobacterium bovisis a transmissible disease notifiable to the World Organization for Animal Health and to the European Union, with ongoing efforts of surveillance and eradication in every EU member state. In Germany, a country which has been declared officially free from bovine tuberculosis since 1997 by the EU,M. bovisinfections still occur sporadically in cattle and other mammals, including humans. Here, the transmission routes of a bTB outbreak in a wildlife park in Germany affecting different cervid species, bison, lynx, and pot-bellied pigs were followed by employing whole-genome sequencing (WGS) combined with spoligotyping and mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) typing. One singleM. bovisstrain persisted from 2002 to 2015, and transmission between the park and a distantly located captive cervid farm was verified. The spoligotyping patterns remained identical, while MIRU-VNTR typing of 24 loci of the standardized panel and locus 2163a as an additional locus revealed one change at locus 2165 in a strain from a fallow deer and one at locus 2461 in isolates from red deer over the whole time period. WGS analysis confirmed the close relatedness of the isolates, with a maximum of 12 single nucleotide polymorphisms (SNPs) detected between any two sequenced isolates. In conclusion, our data confirm a longitudinal outbreak ofM. bovisin a German wildlife park and provide the first insights into the dynamics of different genotyping markers inM. bovis.

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An outbreak of multiple genotypes of Listeria monocytogenes in New Zealand linked to contaminated ready‐to‐eat meats—a retrospective analysis using whole‐genome sequencing

Letters in Applied Microbiology ◽

10.1111/lam.13227 ◽

2019 ◽

Vol 69 (6) ◽

pp. 392-398 ◽

Cited By ~ 1

Author(s):

L. Rivas ◽

P.‐Y. Dupont ◽

M. Wilson ◽

M. Rohleder ◽

B. Gilpin

Keyword(s):

New Zealand ◽

Listeria Monocytogenes ◽

Whole Genome Sequencing ◽

Retrospective Analysis ◽

Genome Sequencing ◽

Whole Genome

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Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis

Epidemics ◽

10.1016/j.epidem.2015.08.003 ◽

2016 ◽

Vol 14 ◽

pp. 26-35 ◽

Cited By ~ 35

Author(s):

Hannah Trewby ◽

David Wright ◽

Eleanor L. Breadon ◽

Samantha J. Lycett ◽

Tom R. Mallon ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Bovine Tuberculosis ◽

Whole Genome

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Whole-genome sequencing and ad hoc shared genome analysis of Staphylococcus aureus isolates from a New Zealand primary school

Scientific Reports ◽

10.1038/s41598-021-99080-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Pippa Scott ◽

Ji Zhang ◽

Trevor Anderson ◽

Patricia C. Priest ◽

Stephen Chambers ◽

...

Keyword(s):

Staphylococcus Aureus ◽

New Zealand ◽

Primary School ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Ad Hoc ◽

Epidemiological Studies ◽

Whole Genome ◽

Typing Method ◽

Allelic Differences

AbstractEpidemiological studies of communicable diseases increasingly use large whole-genome sequencing (WGS) datasets to explore the transmission of pathogens. It is important to obtain an initial overview of datasets and identify closely related isolates, but this can be challenging with large numbers of isolates and imperfect sequencing. We used an ad hoc whole-genome multi locus sequence typing method to summarise data from a longitudinal study of Staphylococcus aureus in a primary school in New Zealand. Each pair of isolates was compared and the number of genes where alleles differed between isolates was tallied to produce a matrix of “allelic differences”. We plotted histograms of the number of allelic differences between isolates for: all isolate pairs; pairs of isolates from different individuals; and pairs of isolates from the same individual. 340 sequenced isolates were included, and the ad hoc shared genome contained 445 genes. There were between 0 and 420 allelic differences between isolate pairs and the majority of pairs had more than 260 allelic differences. We found many genetically closely related S. aureus isolates from single individuals and a smaller number of closely-related isolates from separate individuals. Multiple S. aureus isolates from the same individual were usually very closely related or identical over the ad hoc shared genome. Siblings carried genetically similar, but not identical isolates. An ad hoc shared genome approach to WGS analysis can accommodate imperfect sequencing of the included isolates, and can provide insights into relationships between isolates in epidemiological studies with large WGS datasets containing diverse isolates.

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Evaluating transmission dynamics of Shiga toxin-producing E. coli (STEC) in New Zealand cattle from farm to slaughter using PCR/MALDI-TOF and genome sequencing

Applied and Environmental Microbiology ◽

10.1128/aem.02907-20 ◽

2021 ◽

Author(s):

A. Springer Browne ◽

Anne C. Midwinter ◽

Helen Withers ◽

Adrian L. Cookson ◽

Patrick J. Biggs ◽

...

Keyword(s):

New Zealand ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Shiga Toxin ◽

Whole Genome ◽

Meat Processing ◽

Serious Illness ◽

E Coli ◽

Maldi Tof ◽

Processing Plants

Cattle are asymptomatic carriers of Shiga toxin-producing E. coli (STEC) that can cause serious illness or death in humans. In New Zealand, contact with cattle feces and living near cattle populations are known risk factors for human STEC infection. Contamination of fresh meat with STECs also has the potential for rejection of consignments by importing countries. We used a combination of PCR/MALDI-TOF and whole genome sequencing to evaluate the presence and transmission of STEC on farms and in processing plants to better understand the potential pathways for human exposure and thus mitigate risk. Animal and environmental samples (n=2,580) were collected from six farms and three meat processing plants in New Zealand during multiple sampling sessions in spring of 2015 and 2016. PCR/MALDI-TOF analysis revealed 6.2% were positive for ‘Top 7’ STEC. ‘Top 7’ STEC were identified in all sample sources (n=17) tested. A marked increase in ‘Top 7’ STEC prevalence was observed between calf hides on-farm (6.3% prevalence), and calf hides at processing plants (25.1% prevalence). Whole genome sequencing was performed on ‘Top 7’ STEC bacterial isolates (n=40). Analysis of STEC O26 (n=25 isolates) revealed relatively low genetic diversity on individual farms, consistent with the presence of a resident strain disseminated within the farm environment. Public health efforts should focus on minimizing human contact with fecal material on farms and during handling, transport and slaughter of calves. Meat processing plants should focus on minimizing cross-contamination between the hides of calves in a cohort during transport, lairage and slaughter. Importance Cattle are asymptomatic carriers of Shiga toxin-producing E. coli (STEC), which can cause serious illness or death in humans. Contact with cattle feces and living near cattle are known risk factors for human STEC infection. This study evaluated STEC carriage in young calves and the farm environment with an in-depth evaluation of six farms and three meat processing plants over two years. An advanced molecular detection method and whole genome sequencing were used to provide a detailed evaluation of the transmission of STEC both within and between farms. The study revealed widespread STEC contamination within the farm environment, but no evidence of recent spread between farms. Contamination of young dairy calf hides increased following transport and holding at meat processing plants. The elimination of STEC in farm environments may be very difficult given the multiple transmission routes; interventions should be targeted at decreasing fecal contamination of calf hides during transport, lairage, and processing.

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Molecular Epidemiology of Shiga Toxin-ProducingEscherichia coli(STEC) on New Zealand Dairy Farms: Application of a Culture-Independent Assay and Whole-Genome Sequencing

Applied and Environmental Microbiology ◽

10.1128/aem.00481-18 ◽

2018 ◽

Vol 84 (14) ◽

Cited By ~ 13

Author(s):

A. Springer Browne ◽

Anne C. Midwinter ◽

Helen Withers ◽

Adrian L. Cookson ◽

Patrick J. Biggs ◽

...

Keyword(s):

Risk Factors ◽

New Zealand ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Shiga Toxin ◽

Dairy Farms ◽

Whole Genome ◽

Content Type ◽

E Coli ◽

Culture Independent

ABSTRACTNew Zealand has a relatively high incidence of human cases of Shiga toxin-producingEscherichia coli(STEC), with 8.9 STEC cases per 100,000 people reported in 2016. Previous research showed living near cattle and contact with cattle feces as significant risk factors for STEC infections in humans in New Zealand, but infection was not linked to food-associated factors. During the 2014 spring calving season, a random, stratified, cross-sectional study of dairy farms (n= 102) in six regions across New Zealand assessed the prevalence of the “Top 7” STEC bacteria (serogroups O157, O26, O45, O103, O111, O121, and O145) in young calves (n= 1,508), using a culture-independent diagnostic test (PCR/MALDI-TOF). Twenty percent (306/1,508) of calves on 75% (76/102) of dairy farms were positive for at least one of the “Top 7” STEC bacteria. STEC carriage by calves was associated with environmental factors, increased calf age, region, and increased number of calves in a shared calf pen. The intraclass correlation coefficient (ρ) indicated strong clustering of “Top 7” STEC-positive calves for O157, O26, and O45 serogroups within the same pens and farms, indicating that if one calf was positive, others in the same environment were likely to be positive as well. This finding was further evaluated with whole-genome sequencing, which indicated that a singleE. coliO26 clonal strain could be found in calves in the same pen or farm, but different strains existed on different farms. This study provides evidence that would be useful for designing on-farm interventions to reduce direct and indirect human exposure to STEC bacteria.IMPORTANCECattle are asymptomatic carriers of Shiga toxin-producingE. coli(STEC) bacteria that can cause bloody diarrhea and kidney failure in humans if ingested. New Zealand has relatively high numbers of STEC cases, and contact with cattle feces and living near cattle are risk factors for human infection. This study assessed the national prevalence of STEC in young dairy cattle by randomly selecting 102 farms throughout New Zealand. The study used a molecular laboratory method that has relatively high sensitivity and specificity compared to traditional methods. “Top 7” STEC was found in 20% of calves on 75% of the farms studied, indicating widespread prevalence across the country. By examining the risk factors associated with calf carriage, potential interventions that could decrease the prevalence of “Top 7” STEC bacteria at the farm level were identified, which could benefit both public health and food safety.

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Whole-Genome Sequencing of Clostridium sp. Strain FP2, Isolated from Spoiled Venison

Microbiology Resource Announcements ◽

10.1128/mra.00334-20 ◽

2020 ◽

Vol 9 (18) ◽

Author(s):

Nikola Palevich ◽

Faith P. Palevich ◽

Paul H. Maclean ◽

Ruy Jauregui ◽

Eric Altermann ◽

...

Keyword(s):

New Zealand ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Draft Genome ◽

Draft Genome Sequence ◽

Functional Genomic ◽

Whole Genome ◽

Genomic Studies ◽

Red Meats

Clostridium sp. strain FP2 was isolated from vacuum-packaged refrigerated spoiled venison in New Zealand. This report describes the generation and annotation of the 5.6-Mb draft genome sequence of Clostridium sp. FP2, which will facilitate future functional genomic studies to improve our understanding of premature spoilage of red meats.

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