Biology subjects

Ato, M.

Publications and source records attributed to Ato, M..

6 recordsLinked to original sources

bioRxiv2026

A novel recombinant BCG vaccine using a mycobacteriophage promoter shows improved protection against tuberculosis

The limited efficacy of conventional bacillus Calmette-Guerin (BCG) vaccination against adult pulmonary tuberculosis highlights the need for improved vaccine strategies. Genome integration can overcome the plasmid instability of recombinant BCG, but we hypothesized that this approach would be constrained by reduced transcriptional activity of conventional promoters when present as a single genomic copy. Here we identified P79, a mycobacteriophage-derived promoter that sustains high-level expression from a single genomic locus and used it to construct a genome-integrated recombinant BCG, termed LRC-BCG. LRC-BCG secretes the HSP70-MMPII fusion antigen flanked by the PEST sequences, maintained stable antigen expression over serial passages, and induced strong activation of macrophages and dendritic cells in vitro. In vivo, LRC-BCG inhibited Mycobacterium tuberculosis multiplication more effectively than conventional BCG, even at low doses. These findings demonstrate the feasibility of using P79 for stable genome-integrated recombinant BCG and support LRC-BCG as a promising tuberculosis vaccine candidate.

microbiology↗

bioRxiv2025

Plasmid-mediated macrolide resistance among rapidly growing mycobacteria in Japan

ObjectivesThe spread of a transmissible plasmid carrying the 23S rRNA methylase gene erm(55), which confers inducible macrolide resistance in rapidly growing mycobacteria (RGM), has raised significant clinical concerns. The aim of this study was to investigate the prevalence of erm(55)-carrying plasmids in clinically isolated RGM strains in Japan. MethodsIn total, 607 RGM clinical isolates, representing 32 species or complexes, collected between 2019 and 2023 in Japan were examined. To detect the presence of erm(55)-carrying plasmids, we conducted PCR screening, minimum inhibitory concentration testing for clarithromycin, and whole-plasmid genome sequencing. Comparative genomic analyses were performed to characterise the plasmids. ResultsAmong the 607 RGM isolates, 0.8% (5/607) possessed the plasmid with the erm(55) gene and exhibited inducible macrolide resistance, with ratios of 100% (1/1) in Mycobacterium murale, 50% (3/6) in M. obuense, and 0.8% (1/125) in M. chelonae. The erm(55)-carrying plasmids ranged from 126,187 to 170,220 bp in size. Pairwise BLASTn comparisons of the erm(55)-carrying plasmids showed weighted percent identity values ranging from 99.5% to 99.9%, with query and subject coverage values ranging from 74.2% to 100%. All erm(55) sequences (813 bp) were identical and located within a horizontal gene transfer region. ConclusionsThis study confirmed the presence of macrolide-resistant RGMs related to the erm(55)-carrying plasmid in Japan, although the overall prevalence remains low. These findings emphasise the need to consider plasmid-mediated resistance when treating infections caused by the RGM species.

microbiology↗

bioRxiv2022

Unique genomic sequences in novel Mycobacterium avium subsp. hominissuis lineage enabled fine scale tracing the transmission route during pig movement

Mycobacterium avium subsp. hominissuis (MAH) is one of the most prevalent mycobacteria causing non-tuberculous mycobacterial disease in humans and animals. Of note, MAH is a major cause of mycobacterial granulomatous mesenteric lymphadenitis outbreaks in pig populations. To determine the precise source of infection of MAH in a pig farm and to clarify the epidemiological relationship among pig, human and environmental MAH lineages, we collected 50 MAH isolates from pigs reared in Japan and determined draft genome sequences of 30 isolates. A variable number of tandem repeat analysis revealed that most pig MAH isolates in Japan were closely related to North American, European and Russian human isolates but not to those from East Asian human and their residential environments. Historical recombination analysis revealed that most pig isolates could be classified into SC2/4 and SC3, which contain MAH isolated from pig, European human and environmental isolates. Half of the isolates in SC2/4 had many recombination events with MAH lineages isolated from humans in East Asia. To our surprise, four isolates belonged to a new lineage (SC5) in the global MAH population. Members of SC5 had few footprints of inter-lineage recombination in the genome, and carried 80 unique genes, most of which were located on lineage specific-genomic islands. Using unique genetic features, we were able to trace the putative transmission route via their host pigs. Together, we clarify the possibility of species-specificity of MAH in addition to local adaptation. Our results highlight two transmission routes of MAH, one exposure on pig farms from the environment and the other via pig movement. Moreover, our study also warns that the evolution of MAH in pigs is influenced by MAH from patients and their residential environments, even if the MAH are genetically distinct. HighlightsO_LIVariable number of tandem repeat analysis of Mycobacterium avium subsp. hominissuis (MAH) isolated from pigs (n=50) were conducted. C_LIO_LIDraft genome sequences of MAH (n=30) and genome analysis were conducted. C_LIO_LIPig MAHs were genetically far from East Asian human isolates and close to those of Western countries. C_LIO_LINovel MAH lineage which were transmitted farms by pig movement was found. C_LIO_LIHuman MAH isolates influenced the evolution of pig isolates. C_LI

microbiology↗

bioRxiv2021

Genomic features of Mycobacterium avium subsp. hominissuis isolated from pigs in Japan.

Mycobacterium avium subsp. hominissuis (MAH) is one of the most important agents causing non-tuberculosis mycobacterial infection in humans and pigs. Genome analysis on MAH of human isolates has been proceeding, however, those of pigs are limited despite its potential source of infection to human. In the current study, we obtained 30 draft genome sequences of MAH of pigs reared in Japan. The 30 draft genomes consisted of 4,848,678 - 5,620,788 bp length, 4,652 - 5,388 coding genes and 46 - 75 (Med: 47) tRNAs. All isolates had restriction modification associated genes and 185 - 222 predicted virulence genes. Two isolates had tRNA arrays and one isolate had a clustered regularly interspaced short palindromic repeat (CRISPR) region. Our results will be useful for evaluation of the ecology of MAH by providing a foundation for genome-based epidemiological studies.

microbiology↗

bioRxiv2020

A Novel DNA Chromatography Method to Distinguish M. abscessus Subspecies and Macrolide Susceptibility

RationaleThe clinical impact of infection with Mycobacterium abscessus complex (MABC), a group of emerging non-tuberculosis mycobacteria (NTM), is increasing. Mycobacterium abscessus subsp. abscessus/bolletii frequently shows natural resistance to macrolide antibiotics, whereas Mycobacterium abscessus subsp. massiliense is generally susceptible. Therefore, rapid and accurate discrimination of macrolide-susceptible MABC subgroups is required for effective clinical decisions about macrolide treatments for MABC infection. ObjectivesTo develop a simple and rapid diagnostic that can identify MABC isolates showing macrolide susceptibility. MethodsWhole genome sequencing (WGS) was performed for 148 clinical or environmental MABC isolates from Japan to identify genetic markers that can discriminate three MABC subspecies and the macrolide-susceptible erm(41) T28C sequevar. Using the identified genetic markers, we established PCR based- or DNA chromatography-based assays. Validation testing was performed using MABC isolates from Taiwan. Measurements and Main ResultsWe identified unique sequence regions that could be used to differentiate the three subspecies. Our WGS-based phylogenetic analysis indicated that M. abscessus carrying the macrolide-susceptible erm(41) T28C sequevar were tightly clustered, and identified 11 genes that were significantly associated with the lineage for use as genetic markers. To detect these genetic markers and the erm(41) locus, we developed a DNA chromatography method that identified three subspecies, the erm(41) T28C sequevar and intact erm(41) for MABC in a single assay within one hour. The agreement rate between the DNA chromatography-based and WGS-based identification was 99.7%. ConclusionsWe developed a novel, rapid and simple DNA chromatography method for identification of MABC macrolide susceptibility with high accuracy.

microbiology↗

bioRxiv2020

Diversification of the restriction modification system of Streptococcus pyogenes through its acquisition of mobile elements

Restriction-modification (RM) systems are typically regarded as "primitive immune systems" in bacteria. The roles of methylation in gene regulation, segregation, and mismatch repair are increasingly recognized. To analyze methyltransferase (MTase) diversity in Streptococcus pyogenes, we compared the RM system distribution in eight new complete genome sequences obtained here and in the database-deposited complete genome sequences of 51 strains. The MTase gene distribution showed that type I MTases often change DNA sequence specificity via switching target recognition domains between strains. The type II MTases in the included strains fell into two groups: a prophage-dominant one and a CRISPR-dominant one. Some highly variable type II MTases were found in the prophage region, suggesting that MTases acquired from phage DNA can generate methylome diversity. Additionally, to investigate the possible contribution of DNA methylation to phenotype, we compared the methylomes and transcriptomes from the four most closely related strains, the results of which suggest that phage-derived methylases possibly regulate the methylome, and, hence, regulate expression levels in S. pyogenes. Our findings will benefit further experimental work on the relationship between virulence genes and pathogenicity in S. pyogenes.

microbiology↗