Analysis of bovine tuberculosis transmission in Jalisco, Mexico through whole-genome sequencing

AbstractIntroductionBovine tuberculosis, caused by M. bovis, is endemic in Mexico and has had a big impact on public health. Jalisco is considered to be an important dairy region in the country, accounting for approximately 19% of the total milk production. Within Jalisco, the region of Altos Sur holds the largest proportion of the cattle inventory of the state.Material and MethodsTo determine the frequency of bovine tuberculosis in Altos Sur, Jalisco, as well as M. bovis genetic diversity, sampling of tissue (lymph nodes, lungs, and liver) from Holstein cattle was performed in four abattoirs belonging to three municipalities of this region (Tepatitlán de Morelos, San Miguel el Alto, and Arandas). Spoligotyping and whole-genome sequencing were carried out to assess the genetic relationships of M. bovis strains circulating in this area, as well as a comparison to isolates from other places in Mexico.ResultsPrevalence was 15.06%, and distribution similar among the three municipalities. The most frequent spoligotypes were SB0673, SB121, and SB0145. Whole-genome sequencing revealed three main clades (I, II, III), but isolates did not show clustering by region.ConclusionPhylogenetic analysis suggested ongoing transmission between herds of the different regions, and no unique source of infection was determined. This hinders efforts under the national program for the control and eradication of the disease, so serious attention must be paid to rural regions such as Altos Sur in order to improve its success.

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

BMC Genomics ◽

10.1186/s12864-017-3569-x ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 31

Author(s):

Joseph Crispell ◽

Ruth N. Zadoks ◽

Simon R. Harris ◽

Brent Paterson ◽

Desmond M. Collins ◽

...

Keyword(s):

New Zealand ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Bovine Tuberculosis ◽

Whole Genome ◽

Host System

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Whole genome sequencing provides an unambiguous link between Salmonella Dublin outbreak strain and a historical isolate

Epidemiology and Infection ◽

10.1017/s0950268815001636 ◽

2015 ◽

Vol 144 (3) ◽

pp. 576-581 ◽

Cited By ~ 16

Author(s):

M. MOHAMMED ◽

N. DELAPPE ◽

J. O'CONNOR ◽

P. McKEOWN ◽

P. GARVEY ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Gel Electrophoresis ◽

Invasive Disease ◽

Pulsed Field Gel Electrophoresis ◽

Whole Genome ◽

Outbreak Strain ◽

Salmonella Dublin ◽

Source Of Infection ◽

Human Salmonellosis

SUMMARYSalmonella enterica subsp. enterica serovar Dublin is an uncommon cause of human salmonellosis; however, a relatively high proportion of cases are associated with invasive disease. The serotype is associated with cattle. A geographically diffuse outbreak of S. Dublin involving nine patients occurred in Ireland in 2013. The source of infection was not identified. Typing of outbreak associated isolates by pulsed-field gel electrophoresis (PFGE) was of limited value because PFGE has limited discriminatory power for S. Dublin. Whole genome sequencing (WGS) showed conclusively that the isolates were closely related to each other, to an apparently unrelated isolate from 2011 and distinct from other isolates that were not readily distinguishable by PFGE.

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Genotyping and Whole-Genome Sequencing to Identify Tuberculosis Transmission to Pediatric Patients in British Columbia, Canada, 2005–2014

The Journal of Infectious Diseases ◽

10.1093/infdis/jiy278 ◽

2018 ◽

Vol 218 (7) ◽

pp. 1155-1163 ◽

Cited By ~ 8

Author(s):

Jennifer L Guthrie ◽

Andy Delli Pizzi ◽

David Roth ◽

Clare Kong ◽

Danielle Jorgensen ◽

...

Keyword(s):

British Columbia ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Pediatric Patients ◽

Whole Genome ◽

Tuberculosis Transmission

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Role and value of whole genome sequencing in studying tuberculosis transmission

Clinical Microbiology and Infection ◽

10.1016/j.cmi.2019.03.022 ◽

2019 ◽

Vol 25 (11) ◽

pp. 1377-1382 ◽

Cited By ~ 13

Author(s):

V. Nikolayevskyy ◽

S. Niemann ◽

R. Anthony ◽

D. van Soolingen ◽

E. Tagliani ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Tuberculosis Transmission

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Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of Olea europaea L.

Plants ◽

10.3390/plants10112514 ◽

2021 ◽

Vol 10 (11) ◽

pp. 2514

Author(s):

James Friel ◽

Aureliano Bombarely ◽

Carmen Dorca Fornell ◽

Francisco Luque ◽

Ana Maria Fernández-Ocaña

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Olea Europaea ◽

Genetic Relationships ◽

Germplasm Collection ◽

Whole Genome ◽

Population Genetic Analysis ◽

Olea Europaea L ◽

The World ◽

Olea Europaéa

Olive, Olea europaea L., is a tree of great economic and cultural importance in the Mediterranean basin. Thousands of cultivars have been described, of which around 1200 are conserved in the different olive germplasm banks. The genetic characterisation of these cultivars can be performed in different ways. Whole-genome sequencing (WGS) provides more information than the reduced representation methods such as genotype by sequencing (GBS), but at a much higher cost. This may change as the cost of sequencing continues to drop, but, currently, genotyping hundreds of cultivars using WGS is not a realistic goal for most research groups. Our aim is to systematically compare both methodologies applied to olive genotyping and summarise any possible recommendations for the geneticists and molecular breeders of the olive scientific community. In this work, we used a selection of 24 cultivars from an olive core collection from the World Olive Germplasm Collection of the Andalusian Institute of Agricultural and Fisheries Research and Training (WOGBC), which represent the most of the cultivars present in cultivated fields over the world. Our results show that both methodologies deliver similar results in the context of phylogenetic analysis and popular population genetic analysis methods such as clustering. Furthermore, WGS and GBS datasets from different experiments can be merged in a single dataset to perform these analytical methodologies with proper filtering. We also tested the influence of the different olive reference genomes in this type of analysis, finding that they have almost no effect when estimating genetic relationships. This work represents the first comparative study between both sequencing techniques in olive. Our results demonstrate that the use of GBS is a perfectly viable option for replacing WGS and reducing research costs when the goal of the experiment is to characterise the genetic relationship between different accessions. Besides this, we show that it is possible to combine variants from GBS and WGS datasets, allowing the reuse of publicly available data.

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Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana

Frontiers in Medicine ◽

10.3389/fmed.2020.00161 ◽

2020 ◽

Vol 7 ◽

Author(s):

Prince Asare ◽

Isaac Darko Otchere ◽

Edmund Bedeley ◽

Daniela Brites ◽

Chloé Loiseau ◽

...

Keyword(s):

Spatial Analysis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Tuberculosis Transmission

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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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