Mycobacterium icosiumassiliensis sp. nov., a New Member in the Mycobacterium terrae Complex Isolated from Surface Water in Algeria

Djouadi, Lydia Neïla; Levasseur, Anthony; Khalil, Jacques Bou; Blanc-Taileur, Caroline; Asmar, Shady; Ghiloubi, Wassila; Natèche, Farida; Drancourt, Michel

doi:10.1007/s00284-016-1062-4

Cited by 14 publications

(8 citation statements)

References 37 publications

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“…The description of this taxon is as given by Djouadi et al ( 2016 ) for “ Mycobacterium icosiumassilensis” . The type strain is 8WA6 (= CSUR P1561 = DSM 100711).…”

Section: Discussionmentioning

confidence: 99%

Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera

2018

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The genus Mycobacterium contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of Mycobacterium species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus Mycobacterium, 136 core proteins for the phylum Actinobacteria and 8 other conserved proteins. Additionally, the overall genome similarity amongst the Mycobacterium species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus Mycobacterium at the highest level, which are designated as the “Tuberculosis-Simiae,” “Terrae,” “Triviale,” “Fortuitum-Vaccae,” and “Abscessus-Chelonae” clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the “Abscessus-Chelonae” clade forms the deepest branching lineage and does not form a monophyletic grouping with the “Fortuitum-Vaccae” clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all Mycobacterium species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus Mycobacterium and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus Mycobacterium into an emended genus Mycobacterium encompassing the “Tuberculosis-Simiae” clade, which includes all of the major human pathogens, and four novel genera viz. Mycolicibacterium gen. nov., Mycolicibacter gen. nov., Mycolicibacillus gen. nov. and Mycobacteroides gen. nov. corresponding to the “Fortuitum-Vaccae,” “Terrae,” “Triviale,” and “Abscessus-Chelonae” clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.

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“…The description of this taxon is as given by Djouadi et al ( 2016 ) for “ Mycobacterium icosiumassilensis” . The type strain is 8WA6 (= CSUR P1561 = DSM 100711).…”

Section: Discussionmentioning

confidence: 99%

Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera

2018

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“…JDM601 25 isolated in China, Mycobacterium longobardum 26 isolated in Italy, Mycobacterium heraklionense which ten isolates have been made in Greece, seven in Italy and six in India 26 , Mycobacterium minnesotense 27 isolated in northern Minnesota, USA., Mycobacterium paraterrae 28 isolated in Korea, M . icosiumassilensis 29 that we isolated in Algeria and M . virginiense 6,30 isolated in Virginia, USA (Table 6).…”

Section: Discussionmentioning

confidence: 95%

“…algericum GoatPulmonary lesionAlgeriaRGM 24 M . icosiumassiliensis LakeNdAlgeriaRGM 29 M . kumamotonense SputumPulmonary diseaseJapanSGM 22 « M .…”

Section: Discussionmentioning

confidence: 99%

“Mycobacterium mephinesia”, a Mycobacterium terrae complex species of clinical interest isolated in French Polynesia

Saad¹,

Phelippeau²,

Khoder³

et al. 2019

Sci Rep

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A 59-year-old tobacco smoker male with chronic bronchitis living in Taravao, French Polynesia, Pacific, presented with a two-year growing nodule in the middle lobe of the right lung. A guided bronchoalveolar lavage inoculated onto Löwenstein-Jensen medium yielded colonies of a rapidly-growing non-chromogenic mycobacterium designed as isolate P7213. The isolate could not be identified using routine matrix-assisted laser desorption ionization-time of flight-mass spectrometry and phenotypic and probe-hybridization techniques and yielded 100% and 97% sequence similarity with the respective 16S rRNA and rpoB gene sequences of Mycobacterium virginiense in the Mycobacterium terrae complex. Electron microscopy showed a 1.15 µm long and 0.38 µm large bacillus which was in vitro susceptible to rifampicin, rifabutin, ethambutol, isoniazid, doxycycline and kanamycin. Its 4,511,948-bp draft genome exhibited a 67.6% G + C content with 4,153 coding-protein genes and 87 predicted RNA genes. Genome sequence-derived DNA-DNA hybridization, OrthoANI and pangenome analysis confirmed isolate P7213 was representative of a new species in the M . terrae complex. We named this species “ Mycobacterium mephinesia ”.

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“…Ziehl-Neelsen-positive colonies were subsequently identified by sequencing PCR-amplified DNA. Genomic DNA was extracted using BIOROBOT EZ1 and the Qiagen Genomic DNA Extraction kit (Qiagen, Courtaboeuf, France) as previously described 49 . Sterile PBS was used as a negative control for extraction.…”

Section: Methodsmentioning

confidence: 99%

Mycobacteria fecal shedding in wild boars (Sus scrofa), South-eastern France

Fellag

Drancourt

Marié³

et al. 2019

Preprint

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11The recent recrudescence of tuberculosis in cattle has implicated wild boar as a 12 reservoir and vector of this disease, which led to the investigation of fecal shedding of 13 the causative Mycobacterium bovis. In the Provence region of France, wild boars are 14 very abundant, and the current study was carried out to assess the presence of 15 tuberculous and nontuberculous mycobacteria in feces of wild boar population. W e 16 developed an original protocol allowing the fast isolation of mycobacteria by 17 combining a 1%-chlorhexidine decontamination of fecal matter with culture on MOD9 18 medium. Colonies were identified by matrix-assisted laser desorption/ionization time-19 of-flight mass spectrometry, combined with DNA sequencing. This protocol yielded 20 no tuberculous mycobacteria among ninety-nine wild boar fecal samples collected in 21 the Provence region. However, non-tuberculous mycobacteria were isolated from five 22 samples (5.05%), including Mycobacterium peregrinum, Mycobacterium vaccae and 23 Mycobacterium setense, the last species being previously unreported in the wild 24 boar; in addition to two positive samples for Nocardia spp. In conclusion, wild boars 25 in southeastern France are not shedding tuberculosis agents, but they could 26 constitute a reservoir of human non-tuberculous mycobacteriosis in selected 27 populations directly exposed to wild boars.28 29 Bovine tuberculosis is a zoonosis due to Mycobacterium bovis (M. bovis) affecting 30 both livestock and wild mammals 1 . Bovine tuberculosis is a contagious infection of 31 significant health and economic importance and eradication programs have been 32 implemented in a number of developed countries 1,2 . These programs yielded a 33 remarkable reduction of the incidence of the disease 1,3 . 34 However, the wide distribution of M. bovis in wildlife is a major obstacle to the 35 eradication of tuberculosis in cattle 2,3 . In numerous countries, bovine tuberculosis is 36 maintained by multi-host systems involving cattle and wild mammals 2-4 . While the 37 role of the red deer (Cervus elaphus) remains controversial 3 , the European badger 38 (Meles meles) in Great Britain and Ireland and the wild boar (Sus scrofa) in the 39 Iberian Peninsula are acknowledged reservoirs for M. bovis 3,5 . The later species is 40 also recognized as a host for other Mycobacterium tuberculosis complex, including 41 Mycobacterium microti 6 and Mycobacterium caprae 7 . In addition, non-tuberculous 42 mycobacteria that are widely distributed in the environment are not uncommon in wild 43 boars, where they were isolated from lymph nodes 8 and feces 9,10 . These non-44 tuberculous mycobacteria have been identified as emerging human pathogens, 45 especially in immunocompromised patients 11,12 . 46 Accordingly, naturally infected wild boars excrete M. bovis mycobacteria by oro-47 nasal and digestive routes, with inocula above 10 3 colony-forming units (CFU)/g 13 . 48 Furthermore, it has been shown that M. bovis can persist in soil for several months 14 . 49 Interaction...

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Mycobacterium icosiumassiliensis sp. nov., a New Member in the Mycobacterium terrae Complex Isolated from Surface Water in Algeria

Cited by 14 publications

References 37 publications

Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera

Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera

“Mycobacterium mephinesia”, a Mycobacterium terrae complex species of clinical interest isolated in French Polynesia

Mycobacteria fecal shedding in wild boars (Sus scrofa), South-eastern France

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