Mycobacterium tuberculosis and Mycobacterium leprae have remained, for many years, the primary species of the genus Mycobacterium of clinical and microbiological interest. The other members of the genus, referred to as nontuberculous mycobacteria (NTM), have long been underinvestigated. In the last decades, however, the number of reports linking various NTM species with human diseases has steadily increased and treatment difficulties have emerged. Despite the availability of whole genome sequencing technologies, limited effort has been devoted to the genetic characterization of NTM species. As a consequence, the taxonomic and phylogenetic structure of the genus remains unsettled and genomic information is lacking to support the identification of these organisms in a clinical setting. In this work, we widen the knowledge of NTMs by reconstructing and analyzing the genomes of 41 previously uncharacterized NTM species. We provide the first comprehensive characterization of the genomic diversity of NTMs and open new venues for the clinical identification of opportunistic pathogens from this genus.
The activity of Eucalyptus globulus essential oil was determined for 120 isolates of Streptococcus pyogenes, 20 isolates of S. pneumoniae, 40 isolates of S. agalactiae, 20 isolates of Staphylococcus aureus, 40 isolates of Haemophilus influenzae, 30 isolates of H. parainfluenzae, 10 isolates of Klebsiella pneumoniae, 10 isolates of Stenotrophomonas maltophilia and two viruses, a strain of adenovirus and a strain of mumps virus, all obtained from clinical specimens of patients with respiratory tract infections. The cytotoxicity was evaluated on VERO cells by the MTT test. The antibacterial activity was evaluated by the Kirby Bauer paper method, minimum inhibitory concentration, and minimum bactericidal concentration. H. influenzae, parainfluenzae, and S. maltophilia were the most susceptible, followed by S. pneumoniae. The antiviral activity, assessed by means of virus yield experiments titered by the end-point dilution method for adenovirus, and by plaque reduction assay for mumps virus, disclosed only a mild activity on mumps virus.
The aim of this study was to examine the cytotoxicity and the antibacterial effects of a variety of essential oils on major respiratory tract pathogens. The cytotoxicity of 13 essential oils was evaluated on Vero cells. The antibacterial activity was evaluated by the Kirby Bauer paper method, minimum inhibitory and bactericidal concentration against Streptococcus pyogenes, agalactiae, pneumoniae and Klebsiella pneumoniae, Haemophilus influenzae, Staphylococcus aureus and Stenotrophomonas maltophilia isolated from clinical specimens. The antibiotic sensitivity of these isolates was examined. Some oils showed inhibition of bacterial growth against most of the organisms examined. Cinnamon and thyme showed the strongest action followed by clove. The results reported in this paper indicate that thyme can be considered as a potential antimicrobial agent for the treatment of some respiratory tract infections in man.
Although commercially available DNA probes for identification of mycobacteria have been investigated with large numbers of strains, nothing is known about the ability of these probes to identify less frequently encountered species. We analyzed, with INNO LiPA MYCOBACTERIA (Innogenetics) and with GenoType Mycobacterium (Hein), 317 strains, belonging to 136 species, 61 of which had never been assayed before. INNO LiPA misidentified 20 taxa, the majority of which cross-reacted with the probes specific for Mycobacterium fortuitum and the Mycobacterium avium-Mycobacterium intracellulare-Mycobacterium scrofulaceum group. GenoType misidentified 28 taxa, most of which cross-reacted with M. intracellulare and M. fortuitum probes; furthermore, eight species were not recognized as members of the genus Mycobacterium. Among 54 strains investigated with AccuProbe (Gen-Probe), cross-reactions were detected for nine species, with the probes aiming at the M. avium complex being most involved in cross-reactions.
The aim of this study was to clarify the taxonomic status of named species within the genus Mycobacterium. The analysis of genomes belonging to 174 taxa (species or subspecies) of the genus Mycobacterium was conducted using both the Average Nucleotide Identity and the Genome to Genome Distance. A number of synonymous taxa were detected. The list of synonyms includes: two subspecies of M. chelonae (M. chelonae subsp. bovis and M. chelonae subsp. gwanakae), two subspecies of M. fortuitum (M. fortuitum subsp. fortuitum and M. fortuitum subsp. acetamidolyticum), four subspecies of M. avium (M. avium subsp. avium, M. avium subsp. silvaticum, M. avium subsp. paratuberculosis and "M. avium subsp. hominissuis"), two couples of subspecies of M. intracellulare (M. intracellulare subsp. intracellulare/M. intracellulare subsp. paraintracellulare and M. intracellulare subsp. chimaera/M. intracellulare subsp. yongonense), the species M. austroafricanum and M. vanbaalenii, the species M. senegalense and M. conceptionense, the species M. talmoniae and M. eburneum and the species M. marinum, M. ulcerans and M. pseudoshottsii. Furthermore one species were reclassified as subspecies of another mycobacterium: M. lepraemurium was reclassified as a subspecies of M. avium (M. avium subsp. lepraemurium). The updates to nomenclature are proposed basing on the priority of names according the Code of nomenclature of prokaryotes. For two species (M. bouchedurhonense and M. marseillense) the loss of standing in nomenclature is proposed because of unavailability of respective type strains in culture collections.
Mycobacterium europaeum sp. nov., a scotochromogenic species related to the Mycobacterium simiae complex Four strains isolated in the last 15 years were revealed to be identical in their 16S rRNA gene sequences to MCRO19, the sequence of which was deposited in GenBank in 1995. In a polyphasic analysis including phenotypic and genotypic features, the five strains (including MCRO19), which had been isolated in four European countries, turned out to represent a unique taxonomic entity. They are scotochromogenic slow growers and are genetically related to the group that included Mycobacterium simiae and 15 other species. The novel species Mycobacterium europaeum sp. nov. is proposed to accommodate these five strains. Strain FI-95228 T (5DSM 45397 T 5CCUG 58464 T ) was chosen as the type strain. In addition, a thorough revision of the phenotypic and genotypic characters of the species related to M. simiae was conducted which leads us to suggest the denomination of the 'Mycobacterium simiae complex' for this group.A unique genetic signature characterizes a limited number of slowly growing non-tuberculous mycobacteria; it is represented by a 12 nt deletion in the 16S rRNA gene starting at Escherichia coli position 459. About 20 years ago, when genetic sequencing of the 16S rRNA gene began to be used for the taxonomic characterization of mycobacteria, Mycobacterium simiae appeared to be the only slowly growing mycobacterial species presenting the aforesaid deletion (Rogall et al., 1990; Kirschner et al., 1993b). Mycobacterium interjectum (Springer et al., 1993) was the first species to be newly described that was recognized to share this genetic marker with M. simiae and, in subsequent years, the group of M. simiae-like organisms has steadily extended and includes 16 species at present (Böttger et al., 1993;Fanti et al., 2004;Floyd et al., 1996Floyd et al., , 2000Haas et al., 1997;Karassova et al., 1965;Levi et al., 2003;Meier et al., 1993; Pourahmad et al., 2008;Selvarangan et al., 2004;Springer et al., 1993Springer et al., , 1996b
Fourteen mycobacterial strains isolated from pulmonary samples of independent patients in the state of Pará (Brazil), and three strains isolated in Italy, were characterized using a polyphasic approach. Thorough genetic investigation, including whole-genome sequencing, demonstrated that the strains belong to the M. simiae complex, being most closely related to Mycobacterium interjectum. For 14 of the strains, evidence emerged supporting their inclusion in a previously unreported species of the genus Mycobacterium, for which the name Mycobacterium paraense sp. nov. is proposed (type strain, IEC26 T 5DSM 46749 T 5CCUG 66121 T ). The novel species is characterized by slow growth, unpigmented or pale yellow scotochromogenic colonies, and a HPLC mycolic acid profile different from other known mycobacteria. In different genetic regions, high sequence microheterogeneity was detected.The mycobacteria related to Mycobacterium simiae constitute, at the time of writing, the largest group or complex within the genus Mycobacterium. The group actually includes 17 officially recognized species (Tortoli et al., 2011).Seventeen strains sharing phenotypic and genotypic characteristics consistent with this complex were isolated, in many cases repeatedly (39 isolations in total), from 16 patients with pulmonary symptoms. Most of such mycobacteria were found during the reidentification (by means of DNA sequencing) of clinical isolates, which, with PCR Restriction Analysis (PRA), had either been previously identified as Mycobacterium asiaticum, or had presented unknown PRA-patterns (da Costa et al., 2010). The genetic sequences of these strains showed a high degree of similarity, with Mycobacterium interjectum (Springer Abbreviations: ITS, internal transcribed spacer; SNPs, single nucleotide polymorphisms.
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