Accordingly, four M. bovis CCs have been described (African 1 and 2, European 1 and 2), and these are determined based on specific deletions ranging from 806 to 14,094 bp (base pairs), SNPs and spoligotypes (Mller et al., 2009; Berg et al., 2011; Smith et al., 2011; Rodriguez-Campos et al., 2012). We cannot assume for certain that the disease bovine TB originated only during this period. Resistance to hydrogen peroxide of M. bovis, BCG-Russia and -Japan was higher than that of other BCG substrains (Fig. VH S 2000 Jan;38(1):152-7. doi: 10.1128/JCM.38.1.152-157.2000. Mycobacterium bovis is the main causative agent of zoonotic tuberculosis in humans and frequently devastates livestock and wildlife worldwide. In addition, bovine TB results in severe economic losses for livestock producers worldwide, respecting no borders and repeatedly affecting animal conservation efforts due to the establishment of wildlife reservoirs or spillover events from cattle to associated animal populations (Ayele et al., 2004; De Kantor and Ritacco, 2006; Godfray et al., 2013; Miller and Sweeney, 2013; Palmer, 2013; Nugent et al., 2015a, b). M L We also selected 30 additional M. bovis genomes that were sequenced or identified after September 2018 by Brites et al. Nineteen SNPs were found to be unique to the group comprising the four genomes of M. bovis classified as CC Af2 and the 30 closely related M. bovis genomes without CC classification (i.e. In another phylogenetic tree that we generated, using fewer genomes and with M. tuberculosis H37Rv as an outgroup, these genomes clustered with Lb1 (data not shown). dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering. 2015 Mar 3;15:112. doi: 10.1186/s12879-015-0846-7. Baltimore: Williams & Wilkins Co.; 1986. p. 143557. Mycobacterium tuberculosis, along with M. bovis, M. africanum, M. microti and others, make up the Mycobacterium tuberculosis complex, a group of bacteria that cause clinical tuberculosis (TB) in humans. We next investigated the susceptibility of BCG substrains to nitrosative stress by exposing them to sodium nitrite for 3 days (Fig. BCG-Japan (Tokyo 172) was purchased from Japan BCG Laboratory (Kiyose, Tokyo, Japan). Koboldt D. C., Zhang Q., Larson D. E., Shen D., McLellan M. D., Lin L., et al. Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity. Few studies that have compared transboundary M. bovis strains analyzed bacterial isolates obtained from a reduced number of countries (n < 9) and included small sample sizes (Dippenaar et al., 2017; Patan et al., 2017; Zimpel et al., 2017a; Ghebremariam et al., 2018; Lasserre et al., 2018). Zarza E., Hara R. B. O., Klussmann-kolb A. The CC Eu2 is not a stable marker for Lb3 as a whole; instead, the five unique SNPs may be used as identification markers for Lb3 (Supplementary Table S3). Before Bohrssen Furthermore, evolutionary rates obtained herein are also in agreement with a study based on careful examination of Pre-Columbian Peruvian mummies infected with M. pinnipedii that were analyzed against modern MTBC genomes (Bos et al., 2014), even though our rate priors allowed values one order of magnitude higher, and lower. We have screened over 2,600 publicly available M. bovis genomes and newly sequenced four wildlife M. bovis strains, gathering 1,969 genomes from 23 countries and at least 24 host species, including humans, to complete a phylogenomic analyses. Main research funding was made available through Morris Animal Foundation (grant number D17ZO-307). Learn what mycobacterium bovis is, what it causes, and more - WebMD Iroki: automatic customization and visualization of phylogenetic trees. Mycobacterium bovis isolates with M. tuberculosis specific characteristics Epidemiology of Human Mycobacterium bovis Disease, California, USA This resistance relates well to survival in host cells, THP-1 and BMMs (Fig. Intriguingly, optimal pH levels were found to be different among the BCG substrains (Table 2). (2012). Feline tuberculosis: a literature review and discussion of 19 cases caused by an unusual mycobacterial variant. 1.1 Characteristics of Mycobacterium tuberculosis bacillus Phylogenetic tree was generated using IQ-Tree with 1,000 bootstrap replicas and annotated using Iroki (Moore et al., 2019) and Adobe Illustrator. The growth curve assay showed that the isolates cultured in PPLO medium were in lag phase for 24 h, entered stable period in 42 h, and entered decline phase after 78 h. The isolates were found resistant to macrolides, aminoglycosides and lincomycin at various degrees, but they were sensitive or moderately sensitive to doxycycline and kanamycin under antimicrobial susceptibility analysis. PA Clipboard, Search History, and several other advanced features are temporarily unavailable. Vertical bars indicate the number of unique SNPs in each cluster. Evaluation of pathogenesis caused in cattle and guinea pig by a. Menardo F., Duchene S., Brites D., Gagneux S. (2019). Clonal complexes (circled tips): European 1 (Eu1) in orange, and European 2 (Eu2) in purple, African 1 (Af1) in green, African 2 (Af2) in brown, Unknown CC in black. The following positions, based on M. tuberculosis H37Rv reference genome, were used: RD1 (4,354,000 4,358,331) and RD4 (1,703,743 1,705,033). Its cells are shaped like an elongated rod, which can be straight or slightly curved. A customized script in Python language version 3 (snp_matrix.py; available in github see below) was developed to build a matrix of the polymorphic positions identified in all M. bovis genomes. ( Mycobacterium family). 2005 Jul;43(7):3530-2. doi: 10.1128/JCM.43.7.3530-3532.2005. The first aurochs genome reveals the breeding history of British and European cattle. Moore R. M., Harrison A. O., Mcallister S. M., Shawn W., Wommack K. E. (2019). VS Non-European countries imported specialized breed cattle from single sources and then exported to other countries, while others imported animals from multiple locations. Accessibility No mutation in the coding region of the ahpC gene among was observed among the substrains (data not shown). J AMG designed and coordinated the study, analyzed the data and wrote the manuscript. JL FC Retrieved from: oie.int, Mycobacterium bovis. Before (2013). SNP annotation was based on M. bovis AF2122/97 ({"type":"entrez-nucleotide","attrs":{"text":"NC_002945.4","term_id":"1185580147","term_text":"NC_002945.4"}}NC_002945.4). Dating estimates reported herein correspond to the origin of M. bovis, and not necessarily to the origin of the disease or similar clinical presentations known as bovine TB. The presence of both African CCs in European countries, infecting a wild boar in (France), humans (Germany) and unknown hosts (Switzerland), is interesting and warrants further investigation into the actual origin of these isolates. As recommended by the United States Centers for Disease Control and Prevention, treatment of disease due to M. bovis usually consists of rifampicin, isoniazid and ethambutol [ 6 ]. (2016). Predicted proteins associated with SNP markers of M. bovis lineages and unknown clusters were then classified with EggNOG (Huerta-Cepas et al., 2016) into Clusters of Orthologous Groups (COG) using a graph-based unsupervised clustering algorithm extending the COG methodology (Tatusov et al., 1997). Lasserre M., Fresia P., Greif G., Iraola G., Castro-Ramos M., Juambeltz A., et al. This is consistent with the introduction of Lb3 (CC Eu2) and Lb4 (CC Eu1) into United States and Mexico, common lineages in the Iberian Peninsula and the United Kingdom, respectively. W As MTBC is believed to have originated in East or West Africa (Brites and Gagneux, 2017; ONeill et al., 2019), it is possible that this was also the case for M. bovis. Paul Genomic position and annotation of SNPs are reported in Supplementary Table S3, while COG and STRING analyses of affected genes are reported in Supplementary Figures S8S13. Archeological data from cattle specimens found in the UK (United Kingdom) indicates that these animals had a shared ancestry with wild British aurochs, being unrelated to the modern European taurine (Orlando, 2015). Likewise, their cells do not have a protective capsule nor do they produce spores. Epub 2018 May 16. And ten strains of Mycoplasma bovis (M. bovis) were found from collected samples. Our dating estimates are consistent with bovine TB introduction into these countries during the New World colonization period, with Lb3 dating from 347 to 1,665 years BP by the Const_Pop model (3351623 and 352765 years BP by Birth-Death and Exp_Pop models, respectively), and Lb4 estimated with similar ranges (353 755, 365 954, and 360 939 years BP by the respective models). bTB is still one of the largely neglected zoonotic diseases, particularly in developing countries, as the control and surveillance programs for this . VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Isolation, identification and biological characteristics of Mycoplasma Despite the small sample size, they are not present in the most ancient lineages, Lb1 and Lb2. sharing sensitive information, make sure youre on a federal Claro-Almea FE, Delgado-Noguera LA, Motaban A, Espaa M, de Waard JH. 2016 Feb;78(2):293-6. doi: 10.1292/jvms.15-0304. Viability of BCG strains in THP-1 and mouse BMMs. FASTQ files of all 2,202 initially selected M. bovis genomes were downloaded from SRA, NCBI and trimmed using Trimmomatic (Sliding window: 5:20) (Bolger et al., 2014). Other symptoms might occur depending on the part of the body affected by the disease. BS the contents by NLM or the National Institutes of Health. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Therefore, it is possible that a systematic error of long branch attraction and/or number of genomes may interfere with the correct placement of these genomes. Mycobacterium bovisis a slow-growing (16-20 h generation time), aerobic bacterium, Gram positive and acid-fast, and the causative agent of tuberculosis (TB) in cattle (known as bovine TB) (ICD-10 A16), although it can produce infection in other animals (in addition to cattle, important maintenance hosts of the pathogen include goats, bison, deer. Phylogenetic reconstruction of the reduced dataset of Mycobacterium bovis genomes (n = 1,201). We employed the function princomp in R software 3.5.0 (Mardia et al., 1979; Venables and Ripley, 2002) to generate 2- and 3-dimensions PCA graphs from the SNP matrices, and dots corresponding to individual M. bovis genomes were colored based on pre-established lineages or clusters. It may take 16-20 hours as the build time. The human monocytic cell line THP-1 (ATCC TIB202) was purchased from ATCC and maintained in RPMI 1640 medium containing 100 U mL1 penicillin G and 5% heat-inactivated fetal bovine serum (FBS). First Isolation and Characteristics of Bovine Parainfluenza Virus Type 3 from Yaks. As disease prevalence in cattle decreases these efforts are sometimes impeded by passage of M. bovis from wildlife to cattle. Kaplan (, Darwin (2014). 8600 Rockville Pike It is expected that the sequencing of additional genomes from the same geographic region and the search for specific genetic markers (SNPs and deletions) in the future will provide a better opportunity to robustly characterize this lineage. In the urease test, urease-deficient recombinant BCG (Mukai et al., 2008) was used as a negative control. 2b). Mycobacterium - an overview | ScienceDirect Topics Further genomes should be sequenced to better characterize this group. Use of whole-genome sequencing and evaluation of the apparent sensitivity and specificity of antemortem tuberculosis tests in the investigation of an unusual outbreak of. Cells were washed three times with culture medium and used for the assays. The ladder-like tips observed in Lb4 are consistent with recent population expansion across subpopulations of Lb4, which may be directly influenced by the persistence of M. bovis in different wildlife populations, variations in the efficiency of bovine TB control programs and geographic isolation. 2017 Jun;61(6):215-224. doi: 10.1111/1348-0421.12490. M clonal complexes), and the evolution and ecology of this pathogen has been only marginally explored at the global level. FC No significant regression (or correlation) of isolation dates to root-to-tip distances was observed (corr. The 9 types of psychological therapies (and their characteristics). Lineage Lb1 is composed of 34 M. bovis isolates, encompassing the four representatives of CC Af2 and the 30 closely related genomes without CC classification (Figure 3 - in purple). In (b), statistically significant differences were found between BCG group Japan, Danish, Glaxo and Pasteur and BCG group Russia, Sweden, Birkhaug, Connaught and Phipps (Student's t-test, P <0.05). sharing sensitive information, make sure youre on a federal (2011). Explaining the long divergent branch, a total of 573 SNPs were found to be unique in M. bovis genomes from Malawi (Figure 3 cluster 2, in red). Four decades of transmission of a multidrug-resistant. Most human tuberculosis (TB). Each human-adapted MTBC lineage is associated with specific global geographical locations, and lineage-associated variations in virulence, transmission capacity and in the propensity to acquire drug resistance have been reported (de Jong et al., 2010; Portevin et al., 2011, 2014; Gagneux, 2012; Sarkar et al., 2012; Coscolla and Gagneux, 2014). M. tuberculosis and M. bovis belong to Mycobacteriaceae, a family integrated into the order Actinomycetales, class Actinobacteria, phylum Actinobacteria, and Bacteria domain [].The genus Mycobacterium contains species typically grouped into complexes, such as the MTBC. X All procedures involving live tuberculous mycobacteria were performed in a Biosafety Level 3+ Laboratory (BSL-3+ Prof. Dr. Klaus Eberhard Stewien) located at the Department of Microbiology, Institute of Biomedical Sciences, University of So Paulo, Brazil. J Clin Microbiol. Mycobacterium tuberculosis stricto sensu is the main responsible for the TB numbers and is adapted to human hosts (Brites and Gagneux, 2015; Malone and Gordon, 2017). Recent analyses point toward the evolutionary rate defined by Bos et al. Vasil B The Mycobacterium bovisIn order to replicate, develop and grow, it must be inside a host. Many M. bovis genomes originating from each of these countries formed clusters of highly similar genomes, representing redundancy in the dataset (possibly from densely sampled TB outbreaks).
