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Non Tuberculous Mycobacteria Genomics

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https://read.qxmd.com/read/30863380/whole-genome-sequencing-of-mycobacterium-tuberculosis-clinical-isolates-from-india-reveals-genetic-heterogeneity-and-region-specific-variations-that-might-affect-drug-susceptibility
#1
Jayshree Advani, Renu Verma, Oishi Chatterjee, Praveen Kumar Pachouri, Prashant Upadhyay, Rajesh Singh, Jitendra Yadav, Farah Naaz, Raju Ravikumar, Shashidhar Buggi, Mrutyunjay Suar, Umesh D Gupta, Akhilesh Pandey, Devendra S Chauhan, Srikanth Prasad Tripathy, Harsha Gowda, T S Keshava Prasad
Whole genome sequencing (WGS) of Mycobacterium tuberculosis has been constructive in understanding its evolution, genetic diversity and the mechanisms involved in drug resistance. A large number of sequencing efforts from across the globe have revealed genetic diversity among clinical isolates and the genetic determinants for their resistance to anti-tubercular drugs. Considering the high TB burden in India, the availability of WGS studies is limited. Here we present, WGS results of 200 clinical isolates of M...
2019: Frontiers in Microbiology
https://read.qxmd.com/read/30740107/a-syrian-refugee-in-iraq-diagnosed-as-a-case-of-il12rb1-deficiency-in-japan-using-dried-blood-spots
#2
Lika'a Fasih Y Al-Kzayer, Ahmed K Yassin, Khalid Hama Salih, Tomonari Shigemura, Kenji Sano, Ruwaid Behnam Y Al-Simaani, Miyuki Tanaka, Yozo Nakazawa, Yusuke Okuno
Mendelian susceptibility to mycobacterial diseases (MSMD) is a rare condition of primary immunodeficiency disorder. Interleukin-12 receptor β1 (IL12RB1) deficiency, is the most common genetic etiology of MSMD, which is characterized by the selective predisposition to clinical disease caused by weakly-virulent mycobacteria, such as Bacillus Calmette-Guérin (BCG) vaccines, and environmental non-tuberculous mycobacteria (NTM). To the best of our knowledge, this is the first case of IL12RB1 deficiency to be reported from Iraq...
2019: Frontiers in Immunology
https://read.qxmd.com/read/30397677/isolation-of-mycobacterium-tuberculosis-from-livestock-workers-and-implications-for-zooanthroponotic-transmission-in-ibadan-south-western-nigeria
#3
S Cadmus, V Akinseye, A Adegbulu, N Ovwighose, M Ayoola, J Ogugua, H Adesokan, E Cadmus
Introduction: Tuberculosis (TB) remains a public health problem in sub-Saharan Africa coupled with dearth of information about the disease among livestock workers at risk of infection. We determined the prevalence of pulmonary TB infection and factors associated with its occurrence among livestock workers in south-western Nigeria. Methods: A cross-sectional study was conducted using active case-finding among livestock workers with sub-clinical pulmonary TB between August 2014 and March 2015...
September 2018: Journal of Preventive Medicine and Hygiene
https://read.qxmd.com/read/30367075/pulmonary-isolation-of-multidrug-resistant-mycobacterium-simulans-and-mycobacterium-tuberculosis-from-a-patient-in-the-horn-of-africa
#4
Fériel Bouzid, Djaltou Aboubaker Osman, Emeline Baptiste, Jeremy Delerce, Mohamed Osman Hassan, Warsama Ibrahim Arreh, Anthony Levasseur, Eric Garnotel, Michel Drancourt
In low-income countries of the Horn of Africa, pulmonary infections are usually considered as tuberculosis, which diagnosis relies on clinical data and positive microscopic observation. This strategy allows non-tuberculous mycobacteria to escape detection, facilitating their emergence in populations. A non-tuberculous mycobacterium strain FB-527 was unexpectedly cultured from the sputum of a Djiboutian patient otherwise diagnosed with multi-drug resistant (MDR) tuberculosis. The sequencing of the rpoB and 16S rRNA genes showed that the isolate was identical to strain FI-09026 previously named "Mycobacterium simulans" and reported only once from a Somali patient...
October 26, 2018: Scientific Reports
https://read.qxmd.com/read/30026735/fluoromycobacteriophages-can-detect-viable-mycobacterium-tuberculosis-and-determine-phenotypic-rifampicin-resistance-in-3-5-days-from-sputum-collection
#5
Liliana Rondón, Estefanía Urdániz, Cecilia Latini, Florencia Payaslian, Mario Matteo, Ezequiel J Sosa, Darío F Do Porto, Adrian G Turjanski, Sergio Nemirovsky, Graham F Hatfull, Susana Poggi, Mariana Piuri
The World Health Organization (WHO) estimates that 40% of tuberculosis (TB) cases are not diagnosed and treated correctly. Even though there are several diagnostic tests available in the market, rapid, easy, inexpensive detection, and drug susceptibility testing (DST) of Mycobacterium tuberculosis is still of critical importance specially in low and middle-income countries with high incidence of the disease. In this work, we have developed a microscopy-based methodology using the reporter mycobacteriophage mCherrybomb ϕ for detection of Mycobacterium spp...
2018: Frontiers in Microbiology
https://read.qxmd.com/read/29712660/novel-mutations-associated-with-clofazimine-resistance-in-mycobacterium-abscessus
#6
Yuanyuan Chen, Jiazhen Chen, Shuo Zhang, Wanliang Shi, Wenhong Zhang, Min Zhu, Ying Zhang
Mycobacterium abscessus is a major nontuberculous mycobacterial (NTM) pathogen and is responsible for about 80% of all pulmonary infections caused by rapidly growing mycobacteria. Clofazimine is an effective drug active against M. abscessus , but the mechanism of resistance to clofazimine in M. abscessus is unknown. To investigate the molecular basis of clofazimine resistance in M. abscessus , we isolated 29 M. abscessus mutants resistant to clofazimine and subjected them to whole-genome sequencing to identify possible mutations associated with clofazimine resistance...
July 2018: Antimicrobial Agents and Chemotherapy
https://read.qxmd.com/read/29702266/genome-sequence-of-mycobacterium-yongonense-rt-955-2015-isolate-from-a-patient-misdiagnosed-with-multidrug-resistant-tuberculosis-first-clinical-detection-in-tanzania
#7
Nicholaus Peter Mnyambwa, Dong-Jin Kim, Esther Ngadaya, Jongsik Chun, Sung-Min Ha, Pammla Petrucka, Kennedy Kwasi Addo, Rudovick R Kazwala, Sayoki G Mfinanga
BACKGROUND: Mycobacterium yongonense is a recently described novel species belonging to Mycobacterium avium complex, which is the most prevalent aetiology of non-tuberculous mycobacteria associated with pulmonary infections, and poses tuberculosis diagnostic challenges in high-burden, resource-constrained settings. METHODS: Whole genome shotgun sequencing and comparative microbial genomic analyses were used to characterize the isolate from a patient diagnosed with multidrug-resistant tuberculosis (MDR-TB) after relapse...
June 2018: International Journal of Infectious Diseases: IJID
https://read.qxmd.com/read/29555701/esx-paralogs-are-functionally-equivalent-to-esx-1-proteins-but-are-dispensable-for-virulence-in-mycobacterium-marinum
#8
Rachel E Bosserman, Cristal Reyna Thompson, Kathleen R Nicholson, Patricia A Champion
Mycobacterium marinum is a nontuberculous pathogen of poikilothermic fish and an opportunistic human pathogen. Like tuberculous mycobacteria, the M. marinum M strain requires the ESX-1 (ESAT-6 system 1) secretion system for virulence in host cells. EsxB and EsxA, two major virulence factors exported by the ESX-1 system, are encoded by the esxBA genes within the ESX-1 locus. Deletion of the esxBA genes abrogates ESX-1 export and attenuates M. marinum in ex vivo and in vivo models of infection. Interestingly, there are several duplications of the esxB and esxA genes ( esxB_1 , esxB_2 , esxA_1 , esxA_2 , and esxA_3 ) in the M...
June 1, 2018: Journal of Bacteriology
https://read.qxmd.com/read/29543151/mycobacterium-komaniense-sp-nov-a-rapidly-growing-non-tuberculous-mycobacterium-species-detected-in-south-africa
#9
Nomakorinte Gcebe, Victor P M G Rutten, Nicolaas Gey van Pittius, Brendon Naicker, Anita L Michel
Some species of non-tuberculous mycobacteria (NTM) have been reported to be opportunistic pathogens of animals and humans. Recently there has been an upsurge in the number of cases of NTM infections, such that some NTM species are now recognized as pathogens of humans and animals. From a veterinary point of view, the major significance of NTM is the cross-reactive immune response they elicit against Mycobacterium bovis antigens, leading to misdiagnosis of bovine tuberculosis. Four NTM isolates were detected from a bovine nasal swab, soil and water, during an NTM survey in South Africa...
May 2018: International Journal of Systematic and Evolutionary Microbiology
https://read.qxmd.com/read/29174730/how-to-identify-non-tuberculous-mycobacterium-species-using-maldi-tof-mass-spectrometry
#10
REVIEW
F Alcaide, J Amlerová, G Bou, P J Ceyssens, P Coll, D Corcoran, M-S Fangous, I González-Álvarez, R Gorton, G Greub, G Hery-Arnaud, J Hrábak, A Ingebretsen, B Lucey, I Marekoviċ, C Mediavilla-Gradolph, M R Monté, J O'Connor, J O'Mahony, O Opota, B O'Reilly, D Orth-Höller, M Oviaño, J J Palacios, B Palop, A B Pranada, L Quiroga, D Rodríguez-Temporal, M J Ruiz-Serrano, G Tudó, A Van den Bossche, J van Ingen, B Rodriguez-Sanchez
BACKGROUND: The implementation of MALDI-TOF MS for microorganism identification has changed the routine of the microbiology laboratories as we knew it. Most microorganisms can now be reliably identified within minutes using this inexpensive, user-friendly methodology. However, its application in the identification of mycobacteria isolates has been hampered by the structure of their cell wall. Improvements in the sample processing method and in the available database have proved key factors for the rapid and reliable identification of non-tuberculous mycobacteria isolates using MALDI-TOF MS...
June 2018: Clinical Microbiology and Infection
https://read.qxmd.com/read/29030167/turnaround-time-of-whole-genome-sequencing-for-mycobacterial-identification-and-drug-susceptibility-testing-in-routine-practice
#11
I D Olaru, H Patel, K Kranzer, N Perera
OBJECTIVES: Until recently whole genome sequencing (WGS) for mycobacteria has been restricted mostly to the research setting. However, in 2017 Public Health England has implemented WGS for routine mycobacterial identification and susceptibility testing for Mycobacterium tuberculosis. Our objective was to evaluate the impact of this change on the laboratory turnaround times and availability of results. METHODS: Over the years 2016 and 2017, the period 1 January to 30 April was selected to represent before and after implementation of WGS...
June 2018: Clinical Microbiology and Infection
https://read.qxmd.com/read/28771786/case-of-mycobacterium-haemophilum-misdiagnosed-as-mycobacterium-intracellulare-due-to-one-base-insertion-in-the-bacterial-genome
#12
Rika Nishikawa, Yozo Yamada, Haruhisa Kanki, Hiroshi Matsuoka, Tatsuya Nakamura, Takumi Jikimoto, Mari Kusuki, Norihisa Ishii, Kenichiro Ohnuma, Kazue Nakanaga, Chikako Nishigori
Mycobacterium haemophilum is a slow-growing, non-tuberculous mycobacteria that causes cutaneous infection. We describe a case of cutaneous infection in a 68-year-old Japanese man with polymyositis. This was caused by M. haemophilum harboring one base insertion in gene sequence. At first, the causal microorganism was misidentified as M. intracellulare by COBAS® TaqMan® MAI test. However, poor growth on Ogawa media and growth enhancement on 7H11C agar around a hemin-containing disk prompted us to reinvestigate the causal microorganisms, which were revealed to be M...
January 2018: Journal of Dermatology
https://read.qxmd.com/read/28629484/outbreak-of-non-tuberculous-mycobacteria-skin-or-soft-tissue-infections-associated-with-handling-fish-new-york-city-2013-2014
#13
K Yacisin, J L Hsieh, D Weiss, J Ackelsberg, E Lee, L Jones, Y L Leung, L Li, J Yung, S Slavinski, H Hanson, A Ridpath, J Kornblum, Y Lin, S Robbe-Austerman, J Rakeman, U Siemetzki-Kapoor, T Stuber, S K Greene
Mycobacterium marinum, a bacterium found in freshwater and saltwater, can infect persons with direct exposure to fish or aquariums. During December 2013, the New York City Department of Health and Mental Hygiene learned of four suspected or confirmed M. marinum skin or soft tissue infections (SSTIs) among persons who purchased whole fish from Chinese markets. Ninety-eight case-patients with non-tuberculous mycobacteria (NTM) SSTIs were identified with onset June 2013-March 2014. Of these, 77 (79%) were female...
August 2017: Epidemiology and Infection
https://read.qxmd.com/read/28340510/the-diverse-family-of-mmpl-transporters-in-mycobacteria-from-regulation-to-antimicrobial-developments
#14
REVIEW
Albertus Viljoen, Violaine Dubois, Fabienne Girard-Misguich, Mickaël Blaise, Jean-Louis Herrmann, Laurent Kremer
Mycobacterial genomes contain large sets of loci encoding membrane proteins that belong to a family of multidrug resistance pumps designated Resistance-Nodulation-Cell Division (RND) permeases. Mycobacterial membrane protein Large (MmpL) transporters represent a subclass of RND transporters known to participate in the export of lipid components across the cell envelope. These surface-exposed lipids with unusual structures play key roles in the physiology of mycobacteria and/or can act as virulence factors and immunomodulators...
June 2017: Molecular Microbiology
https://read.qxmd.com/read/27688977/chromosomal-rearrangements-and-protein-globularity-changes-in-mycobacterium-tuberculosis-isolates-from-cerebrospinal-fluid
#15
Seow Hoon Saw, Joon Liang Tan, Xin Yue Chan, Kok Gan Chan, Yun Fong Ngeow
BACKGROUND: Meningitis is a major cause of mortality in tuberculosis (TB). It is not clear what factors promote central nervous system invasion and pathology but it has been reported that certain strains of Mycobacterium tuberculosis (Mtb) might have genetic traits associated with neurotropism. METHODS: In this study, we generated whole genome sequences of eight clinical strains of Mtb that were isolated from the cerebrospinal fluid (CSF) of patients presenting with tuberculous meningitis (TBM) in Malaysia, and compared them to the genomes of H37Rv and other respiratory Mtb genomes either downloaded from public databases or extracted from local sputum isolates...
2016: PeerJ
https://read.qxmd.com/read/27672191/fluorescent-reporter-ds6a-mycobacteriophages-reveal-unique-variations-in-infectibility-and-phage-production-in-mycobacteria
#16
COMPARATIVE STUDY
Oren Mayer, Paras Jain, Torin R Weisbrod, Daniel Biro, Libby Ho, Deborah Jacobs-Sera, Graham F Hatfull, William R Jacobs
Mycobacteriophage DS6A is unique among the more than 8,000 isolated mycobacteriophages due to its ability to form plaques exclusively on mycobacteria belonging to the Mycobacterium tuberculosis complex (MTBC). Speculation surrounding this specificity has led to unsupported assertions in published studies and patents that nontuberculous mycobacteria (NTM) are wholly resistant to DS6A infection. In this study, we identified two independent nonessential regions in the DS6A genome and replaced them with an mVenus-expressing plasmid to generate fluorescent reporter phages Φ2 GFP12 and Φ2 GFP13...
December 1, 2016: Journal of Bacteriology
https://read.qxmd.com/read/27495169/functional-characterization-of-the-mycobacterium-abscessus-genome-coupled-with-condition-specific-transcriptomics-reveals-conserved-molecular-strategies-for-host-adaptation-and-persistence
#17
Aleksandra A Miranda-CasoLuengo, Patrick M Staunton, Adam M Dinan, Amanda J Lohan, Brendan J Loftus
BACKGROUND: Mycobacterium abscessus subsp. abscessus (MAB) is a highly drug resistant mycobacterium and the most common respiratory pathogen among the rapidly growing non-tuberculous mycobacteria. MAB is also one of the most deadly of the emerging cystic fibrosis (CF) pathogens requiring prolonged treatment with multiple antibiotics. In addition to its "mycobacterial" virulence genes, the genome of MAB harbours a large accessory genome, presumably acquired via lateral gene transfer including homologs shared with the CF pathogens Pseudomonas aeruginosa and Burkholderia cepacia...
August 5, 2016: BMC Genomics
https://read.qxmd.com/read/27375559/comparative-genomics-and-proteomic-analysis-of-four-non-tuberculous-mycobacterium-species-and-mycobacterium-tuberculosis-complex-occurrence-of-shared-immunogenic-proteins
#18
Nomakorinte Gcebe, Anita Michel, Nicolaas C Gey van Pittius, Victor Rutten
The Esx and PE/PPE families of proteins are among the most immunodominant mycobacterial antigens and have thus been the focus of research to develop vaccines and immunological tests for diagnosis of bovine and human tuberculosis, mainly caused by Mycobacterium bovis and Mycobacterium tuberculosis, respectively. In non-tuberculous mycobacteria (NTM), multiple copies of genes encoding homologous proteins have mainly been identified in pathogenic Mycobacterium species phylogenically related to Mycobacterium tuberculosis and Mycobacterium bovis...
2016: Frontiers in Microbiology
https://read.qxmd.com/read/27035710/comparative-genomic-analysis-reveals-a-possible-novel-non-tuberculous-mycobacterium-species-with-high-pathogenic-potential
#19
Siew Woh Choo, Avirup Dutta, Guat Jah Wong, Wei Yee Wee, Mia Yang Ang, Cheuk Chuen Siow
Mycobacteria have been reported to cause a wide range of human diseases. We present the first whole-genome study of a Non-Tuberculous Mycobacterium, Mycobacterium sp. UM_CSW (referred to hereafter as UM_CSW), isolated from a patient diagnosed with bronchiectasis. Our data suggest that this clinical isolate is likely a novel mycobacterial species, supported by clear evidence from molecular phylogenetic, comparative genomic, ANI and AAI analyses. UM_CSW is closely related to the Mycobacterium avium complex. While it has characteristic features of an environmental bacterium, it also shows a high pathogenic potential with the presence of a wide variety of putative genes related to bacterial virulence and shares very similar pathogenomic profiles with the known pathogenic mycobacterial species...
2016: PloS One
https://read.qxmd.com/read/27028886/trehalose-polyphleates-are-produced-by-a-glycolipid-biosynthetic-pathway-conserved-across-phylogenetically-distant-mycobacteria
#20
Sophie Burbaud, Françoise Laval, Anne Lemassu, Mamadou Daffé, Christophe Guilhot, Christian Chalut
Mycobacteria synthesize a variety of structurally related glycolipids with major biological functions. Common themes have emerged for the biosynthesis of these glycolipids, including several families of proteins. Genes encoding these proteins are usually clustered on bacterial chromosomal islets dedicated to the synthesis of one glycolipid family. Here, we investigated the function of a cluster of five genes widely distributed across non-tuberculous mycobacteria. Using defined mutant analysis and in-depth structural characterization of glycolipids from wild-type or mutant strains of Mycobacterium smegmatis and Mycobacterium abscessus, we established that they are involved in the formation of trehalose polyphleates (TPP), a family of compounds originally described in Mycobacterium phlei...
February 18, 2016: Cell Chemical Biology
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