A description of Mycobacterium chelonae subsp. gwanakae subsp. nov., a rapidly growing mycobacterium with a smooth colony phenotype due to glycopeptidolipids

Phylogenetic distribution of malonate semialdehyde decarboxylase (MSAD) genes among strains within the genus Mycobacterium: evidence of MSAD gene loss in the evolution of pathogenic mycobacteria

Despite the great diversity of malonate semialdehyde decarboxylases (MSADs), one of five subgroups of the tautomerase superfamily (TSF) found throughout the biosphere, their distribution among strains within the genus Mycobacterium remains unknown. In this study, we sought to investigate the phylogenetic distribution of MSAD genes of mycobacterial species via genome analysis of 192 different reference Mycobacterium species or subspecies retrieved from NCBI databases. We found that in a total of 87 of 192 strains (45.3%), MSAD-1 and MSAD-2 were distributed in an exclusive manner among Mycobacterium species except for 12 strains, including Mycobacterium chelonae members, with both in their genome. Of note, Mycobacterium strains better adapted to the host and of high virulence potential, such as the Mycobacterium tuberculosis complex, Mycobacterium leprae, Mycobacterium marinum, Mycobacterium ulcerans, and Mycobacterium avium subsp. paratuberculosis, had no orthologs of MSAD in their genome, suggesting MSAD loss during species differentiation in pathogenic slow-growing Mycobacterium. To investigate the MSAD distribution among strains of M. avium subspecies, the genome sequences of a total of 255 reference strains from the four subspecies of M. avium (43 of subspecies avium, 162 of subspecies hominissuis, 49 of subspecies paratuberculosis, and 1 of subspecies silvaticum) were further analyzed. We found that only 121 of 255 strains (47.4%) had MSADs in their genome, with none of the 49 M. avium subsp. paratuberculosis strains having MSAD genes. Even in 13 of 121 M. avium strains with the MSAD-1 gene in their genome, deletion mutations in the 98th codon causing premature termination of MSAD were found, further highlighting the occurrence of MSAD pseudogenization during species or subspecies differentiation of M. avium. In conclusion, our data indicated that there are two distinct types of MSADs, MSAD-1 and MSAD-2, among strains in the Mycobacterium genus, but more than half of the strains, including pathogenic mycobacteria, M. tuberculosis and M. leprae, have no orthologs in their genome, suggesting MSAD loss during host adaptation of pathogenic mycobacteria. In the future, the role of two distinct MSADs, MSAD-1 and MSAD-2, in mycobacterial pathogenesis or evolution should be investigated.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018

This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.

Short Signature rpoB Gene Sequence to Differentiate Species in Mycobacterium abscessus Group

Mycobacterium abscessus group (MAG) are rapidly growing acid-fast bacteria that consist of three closely related species: M. abscessus (Ma), M. bolletii (Mb), and M. massiliense (Mm). Differentiation of these species can be difficult but is increasingly requested owing to recent infectious outbreaks and their differential drug resistance. We developed a novel and rapid pyrosequencing method using short signature sequences (35 to 45 bp) at a hypervariable site in the rpoB gene to differentiate the three MAG species, along with M. chelonae (Mc), and M. immunogenum (Mi). This method was evaluated using 111 M. chelonae-abscessus complex (MCAC) isolates, including six reference strains. All isolates were successfully differentiated to the species level (69 Ma, four Mb, six Mm, 23 Mc, and nine Mi). The species identifications by this method had 100% agreement with Sanger sequencing as well as an in-silico rpoB typing method. This short signature sequencing (SSS) method is rapid (6 to 7 h), accurately differentiates MAG species, and is useful for informing antimicrobial therapy decision.

IMPORTANCEMycobacterium abscessus group (MAG) are rapidly growing acid-fast bacteria that include three species: M. abscessus, M. massiliense, and M. bolletii. These species are among the leading causes of nontuberculosis mycobacteria infections in humans but difficult to differentiate using commonly used methods. The differences of drug resistance among the species shape the treatment regimens and make it significant for them to be differentiated accurately and quickly. We developed and evaluated a novel short signature sequencing (SSS) method utilizing a gene called rpoB to differentiate the three MAG species, as well as other two species (M. chelonae and M. immunogenum). The identification results had 100% agreement with both the reference method of Sanger sequencing and rpoB typing method via a computer-simulated analysis. This SSS method was accurate and quick (6 to 7 h) for species differentiation, which will benefit patient care. The technology used for this method is affordable and easy to operate.

Current Updates on Mycobacterial Taxonomy, 2018 to 2019

This minireview provides an updated overview of taxonomic changes for the genus Mycobacterium, with a focus on new species identified from humans or those associated with human disease for the period of 2018 to 2019.

MmpL3 Inhibition: A New Approach to Treat Nontuberculous Mycobacterial Infections

Outside of Mycobacterium tuberculosis and Mycobacterium leprae, nontuberculous mycobacteria (NTM) are environmental mycobacteria (>190 species) and are classified as slow- or rapid-growing mycobacteria. Infections caused by NTM show an increased incidence in immunocompromised patients and patients with underlying structural lung disease. The true global prevalence of NTM infections remains unknown because many countries do not require mandatory reporting of the infection. This is coupled with a challenging diagnosis and identification of the species. Current therapies for treatment of NTM infections require multidrug regimens for a minimum of 18 months and are associated with serious adverse reactions, infection relapse, and high reinfection rates, necessitating discovery of novel antimycobacterial agents. Robust drug discovery processes have discovered inhibitors targeting mycobacterial membrane protein large 3 (MmpL3), a protein responsible for translocating mycolic acids from the inner membrane to periplasm in the biosynthesis of the mycobacterial cell membrane. This review focuses on promising new chemical scaffolds that inhibit MmpL3 function and represent interesting and promising putative drug candidates for the treatment of NTM infections. Additionally, agents (FS-1, SMARt-420, C10) that promote reversion of drug resistance are also reviewed.

Efficacy and Mechanisms of Flavonoids against the Emerging Opportunistic Nontuberculous Mycobacteria

Nontuberculous mycobacteria (NTM) are the causative agent of severe chronic pulmonary diseases and is accountable for post-traumatic wound infections, lymphadenitis, endometritis, cutaneous, eye infections and disseminated diseases. These infections are extremely challenging to treat due to multidrug resistance, which encompasses the classical and existing antituberculosis agents. Hence, current studies are aimed to appraise the antimycobacterial activity of flavonoids against NTM, their capacity to synergize with pharmacological agents and their ability to block virulence. Flavonoids have potential antimycobacterial effects at minor quantities by themselves or in synergistic combinations. A cocktail of flavonoids used with existing antimycobacterial agents is a strategy to lessen side effects. The present review focuses on recent studies on naturally occurring flavonoids and their antimycobacterial effects, underlying mechanisms and synergistic effects in a cocktail with traditional agents.

Non-tuberculous mycobacteria and the rise of Mycobacterium abscessus

Infections caused by non-tuberculous mycobacteria (NTM) are increasing globally and are notoriously difficult to treat due to intrinsic resistance of these bacteria to many common antibiotics. NTM are diverse and ubiquitous in the environment, with only a few species causing serious and often opportunistic infections in humans, including Mycobacterium abscessus. This rapidly growing mycobacterium is one of the most commonly identified NTM species responsible for severe respiratory, skin and mucosal infections in humans. It is often regarded as one of the most antibiotic-resistant mycobacteria, leaving us with few therapeutic options. In this Review, we cover the proposed infection process of M. abscessus, its virulence factors and host interactions and highlight the commonalities and differences of M. abscessus with other NTM species. Finally, we discuss drug resistance mechanisms and future therapeutic options. Taken together, this knowledge is essential to further our understanding of this overlooked and neglected global threat.

Genome-based taxonomic revision detects a number of synonymous taxa in the genus Mycobacterium

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.

Current significance of the Mycobacterium chelonae-abscessus group

Organisms of the Mycobacterium chelonae-abscessus group can be significant pathogens in humans. They produce a number of diseases including acute, invasive and chronic infections, which may be difficult to diagnose correctly. Identification among members of this group is complicated by differentiating at least eleven (11) known species and subspecies and complexity of identification methodologies. Treatment of their infections may be problematic due to their correct species identification, antibiotic resistance, their differential susceptibility to the limited number of drugs available, and scarcity of susceptibility testing.

Nontuberculous mycobacteria: Insights on taxonomy and evolution

Seventy years have passed since Ernest H. Runyon presented a phenotypic classification approach for nontuberculous mycobacteria (NTM), primarily as a starting point in trying to understand their clinical relevance. From numerical taxonomy (biochemical testing) to 16S rRNA gene sequencing to whole genome sequencing (WGS), our understanding of NTM has also evolved. Novel species are described at a rapid pace, while taxonomical relationships are re-defined in large part due to the accessibility of WGS. The evolutionary course of clonal complexes within species is better known for some NTM and less for others. In contrast with M. tuberculosis, much is left to learn about NTM as a whole.