Whole genome sequencing improves the discrimination between Mycobacterium bovis strains on the southern border of Kruger National Park, South Africa

Smith, 2006, Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis, Nat. Rev. Microbiol., 4, 670, 10.1038/nrmicro1472 Musoke, 2015, Spillover of Mycobacterium bovis from wildlife to livestock, South Africa, Emerg. Infect. Dis., 21, 448, 10.3201/eid2103.131690 Garnier, 2003, The complete genome sequence of Mycobacterium bovis, Proc. Natl. Acad. Sci. U. S. A., 100, 7877, 10.1073/pnas.1130426100 Hlavsa, 2008, Human tuberculosis due to Mycobacterium bovis in the United States, 1995–2005, Clin. Infect. Dis., 47, 168, 10.1086/589240 Hlokwe, 2014, Evidence of increasing intra and inter-species transmission of Mycobacterium bovis in South Africa: are we losing the battle?, Prev. Vet. Med., 115, 10, 10.1016/j.prevetmed.2014.03.011 Sichewo, 2020, Tracing cross species transmission of Mycobacterium bovis at the wildlife/livestock interface in South Africa, BMC Microbiol., 20, 49, 10.1186/s12866-020-01736-4 Hlokwe, 2013, Evaluation of the discriminatory power of variable number of tandem repeat typing of Mycobacterium bovis isolates from southern Africa., Transbound, Emerg. Dis., 60, 111, 10.1111/tbed.12096 Stucki, 2016, Standard genotyping overestimates transmission of Mycobacterium tuberculosis among immigrants in a low-incidence country, J. Clin. Microbiol., 54, 1862, 10.1128/JCM.00126-16 Dippenaar, 2017, Progenitor strain introduction of Mycobacterium bovis at the wildlife-livestock interface can lead to clonal expansion of the disease in a single ecosystem, Infect. Genet. Evol., 51, 235, 10.1016/j.meegid.2017.04.012 Crispell, 2017, Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand, BMC Genomics, 18, 180, 10.1186/s12864-017-3569-x Meehan, 2018, The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology, EBioMedicine., 37, 410, 10.1016/j.ebiom.2018.10.013 Joshi, 2012, Single nucleotide polymorphisms in the Mycobacterium bovis genome resolve phylogenetic relationships, J. Clin. Microbiol., 50, 3853, 10.1128/JCM.01499-12 Rausch, 2012, DELLY: structural variant discovery by integrated paired-end and split-read analysis, Bioinformatics., 28, i333, 10.1093/bioinformatics/bts378 Walker, 2013, Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study, Lancet Infect. Dis., 13, 137, 10.1016/S1473-3099(12)70277-3 Dippenaar, 2015, Whole genome sequence analysis of Mycobacterium suricattae, Tuberculosis., 95, 682, 10.1016/j.tube.2015.10.001 Nikolayevskyy, 2019, Role and value of whole genome sequencing in studying tuberculosis transmission, Clin. Microbiol. Infect., 25, 1377, 10.1016/j.cmi.2019.03.022 Zakham, 2019, Whole-genome sequencing for rapid, reliable and routine investigation of Mycobacterium tuberculosis transmission in local communities, New Microbes New Infect., 31, 10.1016/j.nmni.2019.100582 Roos, 2016, Test performance of three serological assays for the detection of Mycobacterium bovis infection in common warthogs (Phacochoerus africanus), Vet. Immunol. Immunopathol., 182, 79, 10.1016/j.vetimm.2016.10.006 Goosen, 2014, Agreement between assays of cell-mediated immunity utilizing Mycobacterium bovis-specific antigens for the diagnosis of tuberculosis in African buffaloes (Syncerus caffer), Vet. Immunol. Immunopathol., 160, 133, 10.1016/j.vetimm.2014.03.015 Leclerc, 2000, Molecular characterization of environmental Mycobacterium strains by PCR-restriction fragment length polymorphism of hsp65 and by sequencing of hsp65, and of 16S and ITS1 rDNA, Res. Microbiol., 151, 629, 10.1016/S0923-2508(00)90129-3 Warren, 2006, Differentiation of Mycobacterium tuberculosis complex by PCR amplification of genomic regions of difference, Int. J. Tuberc. Lung Dis., 10, 818 Warren, 2006, Safe Mycobacterium tuberculosis DNA extraction method that does not compromise integrity, J. Clin. Microbiol., 44, 254, 10.1128/JCM.44.1.254-256.2006 Kamerbeek, 1997, Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology, J. Clin. Microbiol., 35, 907, 10.1128/jcm.35.4.907-914.1997 Smith, 2012, Naming spoligotype patterns for the RD9-deleted lineage of the Mycobacterium tuberculosis complex; www.Mbovis.org, Infect. Genet. Evol., 12, 873, 10.1016/j.meegid.2011.08.002 Black, 2015, Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates, BMC Genomics, 16, 1, 10.1186/s12864-015-2067-2 Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics., 30, 2114, 10.1093/bioinformatics/btu170 Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics., 25, 1754, 10.1093/bioinformatics/btp324 Ponsting, 2010, 1 McKenna, 2010, The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res., 20, 1297, 10.1101/gr.107524.110 Coscolla, 2013, Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee, Emerg. Infect. Dis., 19, 969, 10.3201/eid1906.121012 Minh, 2020, IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era, Mol. Biol. Evol., 37, 1530, 10.1093/molbev/msaa015 Letunic, 2019, Interactive tree of life (iTOL) v4: recent updates and new developments, Nucleic Acids Res., 47, W256, 10.1093/nar/gkz239 Van Tonder, 2021, Inferring Mycobacterium bovis transmission between cattle and badgers using isolates from the randomised badger culling trial, PLoS Pathog., 17, 1, 10.1371/journal.ppat.1010075 Carver, 2005, ACT: the Artemis comparison tool, Bioinformatics., 21, 3422, 10.1093/bioinformatics/bti553 Hauer, 2019, Accurate phylogenetic relationships among Mycobacterium bovis strains circulating in France based on whole genome sequencing and single nucleotide polymorphism analysis, Front. Microbiol., 10, 1, 10.3389/fmicb.2019.00955 Gardy, 2011, Whole-genome sequencing and social-network analysis of a tuberculosis outbreak, N, Engl. J. Med., 364, 730, 10.1056/NEJMoa1003176 Smith, 2012, The global distribution and phylogeography of Mycobacterium bovis clonal complexes, Infect. Genet. Evol., 12, 857, 10.1016/j.meegid.2011.09.007 Guimaraes, 2020, Mycobacterium bovis: from genotyping to genome sequencing, Microorganisms., 8, 667, 10.3390/microorganisms8050667 Nikolayevskyy, 2016, Whole genome sequencing of Mycobacterium tuberculosis for detection of recent transmission and tracing outbreaks: a systematic review, Tuberculosis., 98, 77, 10.1016/j.tube.2016.02.009