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Several rating definitions must be met following the envision's system. The envisioned system aims to develop the green building concept in the existing jetty building. These definitions are quality of life, leadership, resource allocation, nature, climate, and resilience. This sustainability is needed to initiate changes in the planning, design, and provision of sustainable infrastructure together with the company. This also applies to implementing long-term infrastructure investments that are more cost-effective, resource-efficient, and adaptable. The study uses a qualitative and quantitative method, where data is obtained by distributing questionnaires and simulating using Statistical Products and Solution Services (SPSS). The application of Value Engineering (VE) and Life Cycle Cost Analysis (LCCA) has been chosen by researchers on existing jetty buildings with the green jetty concept, with investment costs in economic green jetty buildings and a return on investment costs of less than four years. In achieving the ten most influential factors in improving cost performance in sustainable dock construction, the results of the SPSS simulation processing obtained the ten most influential factors, namely: Planning, Energy, Siting, Materials, Ecology, Community, Economy, Operation, and Maintenance Cost, Follow-up Inspection, and Labor Experience.

The MICE industry is considered one with high economic attractiveness for investors. Regulations and user requests for a new building are required to meet green building standards. The Green Building Council Indonesia issues Greenship's green building certification system. A minimum of 56 points is required for additional investment costs but will result in savings in operations to get a platinum rating. This paper aims to determine what factors are influential in optimising construction costs through the value engineering method to achieve a green building rating tool with life cycle costs using Structural Equation Modelling. The finding is that energy is the most influential factor in obtaining platinum rating certification, which requires value engineering and lifecycle cost analysis to achieve optimal investment costs with additional costs from 7,494% to 4,689%. The novelty of this research is that the selection of materials/machines and working methods of the green concept that saves energy needs to be carried out from the beginning of the design to achieve a feasible payback period for new investments, which will be the commitment of the owner to build a green MICE.

Mycobacterium marinum (M. marinum) is the most common causative bacteria of cutaneous non-tuberculous mycobacterial (NTM) infections, including fish tank granuloma. Treating M. marinum-caused infection takes longer than other NTM diseases because M. marinum is less susceptible to antimicrobial agents. A standard treatment regimen for M. marinum infection has not been established yet, and few in vivo experiments have been performed in mammals to evaluate the bactericidal effects of antimicrobials. In this study, we developed a noninvasive in vivo imaging method to assess the therapeutic efficacy of antimicrobials against M. marinum infection. The data obtained using fluorescent protein or bioluminescence from luciferase will offer valuable insights into bacteria visualization across various bacterial infections. Furthermore, through this imaging technique, we demonstrated that combining clarithromycin, rifampicin, ethambutol, and minocycline effectively cleared M. marinum from the footpad. Granulomas with necrotic abscesses formed on the footpad of M. marinum-infected mice, primarily due to neutrophils involved in the host's cell-mediated immune response. Inflammatory cytokine and chemokine levels significantly increased 7 days post-infection, aligning with the footpad swelling and granuloma formation observed in the untreated group. Interestingly, immune mediators and cells induced by M. marinum footpad infection were crucial factors associated with hypersensitivity and granuloma formation, as seen in pulmonary tuberculosis. This novel imaging analysis using a cutaneous NTM mouse model might be a powerful tool for the comprehensive analysis of mycobacterial infections., (© 2024. The Author(s).)

Japan is one of the rare non-tropical countries with documented cases of Buruli ulcer (BU). Mycobacterium ulcerans subsp. shinshuense has been identified as the causative agent. The first report of BU in Japan dates back to 1982, with sporadic reports thereafter. Recently, the number of cases has been on the increase, and 50 cases (57.7%) are from the past decade alone, out of a total of 87 cases reported to date. Japan's well-developed healthcare facilities play a crucial role in enabling detailed investigations and providing appropriate treatment for patients, contributing to a favorable prognosis. However, the rarity of the disease results in lack of awareness among healthcare professionals, leading to frequent delays in diagnosis. This article aims to offer an updated overview of BU cases in Japan and to raise awareness of BU among dermatologists and other healthcare professionals in a non-endemic setting., (© 2024 The Author(s). The Journal of Dermatology published by John Wiley & Sons Australia, Ltd on behalf of Japanese Dermatological Association.)

Buruli ulcer, caused by Mycobacterium (M.) ulcerans , is a neglected tropical disease (NTD) characterized by necrosis of the cutaneous tissue, predominantly affecting the limbs. The pathogenesis of this disease is mainly attributed to mycolactone, a lipid toxin produced by M. ulcerans . Here, we report the case of a 7-year-old Japanese girl who presented with worsening ulceration on her left forearm, extending to the elbow, following antimicrobial treatment. To evaluate disease progression, we used a mycolactone-specific lateral flow assay. The test yielded positive results in the advancing necrotic area, aiding in determining the extent of necessary debridement. After undergoing two debridement surgeries and receiving 38 weeks of antimicrobial treatment followed by skin grafting, the patient achieved cure. Timely diagnosis is imperative in avoiding prolonged treatment, highlighting the importance of readily available diagnostic point-of-care tests for Buruli ulcer. Moreover, detection of mycolactone not only can serve as a diagnostic tool for Buruli ulcer but also enables prediction of lesion spread and assessment of cure., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Dziedzom K. de Souza, Marco Biamonte, Gerd Pluschke, Rie R. Yotsu reports financial support was provided by Global Health Innovative Technology (GHIT) Fund (G2020-202). Yuji Miyamoto, Manabu Ato reports financial support was provided by Japan Agency for Medical Research and Development. Rie Yotsu is one of the guest editors for the Special Issue on Buruli Ulcer in the Journal of Clinical Tuberculosis and Other Mycobacterial Diseases. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors. Published by Elsevier Ltd.)

Vaccination is an important factor in public health. The recombinant bacillus Calmette Guérin (rBCG) vaccine, which expresses foreign antigens, is expected to be a superior vaccine against infectious diseases. Here, we report a new recombination platform in which the BCG Tokyo strain is transformed with nucleotide sequences encoding foreign protein fused with the MPB70 immunogenic protein precursor. By RNA-sequencing, mpb70 was found to be the most transcribed among all known genes of BCG Tokyo. Small oligopeptide, namely, polyhistidine tag, was able to be expressed in and secreted from rBCG through a process in which polyhistidine tag fused with intact MPB70 were transcribed by an mpb70 promoter. This methodology was applied to develop an rBCG expressing the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2. Immunoblotting images and mass spectrometry data showed that RBD was also secreted from rBCG. Sera from mice vaccinated with the rBCG showed a tendency of weak neutralizing capacity. The secretion was retained even after a freeze-drying process. The freeze-dried rBCG was administered to and recovered from mice. Recovered rBCG kept secreting RBD. Collectively, our recombination platform offers stable secretion of foreign antigens and can be applied to the development of practical rBCGs., (© 2024 The Societies and John Wiley & Sons Australia, Ltd.)

Diagnosis of non-tuberculous mycobacterial (NTM) infection is difficult due to low sensitivity and time-consuming laboratory tests. Current serological assays fail in tropical countries due to high antibody background. This study aimed to investigate an appropriate method for detecting anti-glycopeptidolipid (GPL)-core antibodies to diagnose NTM infection in Thailand. Heparinized plasma samples were collected from 20 patients with NTM-pulmonary disease (NTM-PD) and 22 patients with disseminated NTM (dNTM) for antibody detection by ELISA. The results were compared with those from patients with tuberculosis, other bacterial pulmonary infections and healthy controls. Among the different antibody isotypes, anti-GPL-core IgA exhibited the highest suitability. Therefore, anti-GPL-core IgA and its subclass IgA2 were further investigated. A significant increase in antibody levels was observed during the active infection stage, whereas NTM-PD with culture conversion at the 6-month follow-up showed reduced IgA levels. The diagnostic cut-off for IgA and IgA2 was newly defined as 1.4 and 1.0 U/ml, respectively. Using our IgA cut-off, the sensitivity and specificity for diagnosing NTM-PD were 77.3% and 81.4%, respectively. The new IgA cut-off demonstrated significantly improved specificity compared to the manufacturer's cut-off. Thus, serological detection of anti-GPL-core IgA, with a cut-off of 1.4 U/ml, can be a valuable tool for supporting NTM diagnosis in Thailand., (© 2023. The Author(s).)

Non-tuberculosis mycobacterial (NTM) diseases are steadily increasing in prevalence and mortality worldwide. Mycobacterium avium and M. intracellulare, the two major pathogens of NTM diseases, are resistant to antibiotics, and chlorine, necessitating their capacity to survive in natural environments (e.g. soil and rivers) and disinfected municipal water. They can also form biofilms on artificial surfaces to provide a protective barrier and habitat for bacilli, which can cause refractory systemic disseminated NTM disease. Therefore, preventing biofilm formation by these pathogens is crucial; however, not many in vivo experimental systems and studies on NTM biofilm infection are available. This study develops a mouse model of catheter-associated systemic disseminated disease caused by M. intracellulare that reproduces the pathophysiology of catheter-associated infections observed in patients undergoing peritoneal dialysis. In addition, the bioluminescence system enabled noninvasive visualization of the amount and distribution of bacilli in vivo and conveniently examine the efficacy of antimicrobials. Furthermore, the cellulose-based biofilms, which were extensively formed in the tissue surrounding the catheter insertion site, reduced drug therapy effectiveness. Overall, this study provides insights into the cause of the drug resistance of NTM and may guide the development of new therapies for NTM diseases., (© 2023. Springer Nature Limited.)

Nontuberculous mycobacterial infections are generally believed to be independently acquired from the environment. Although person-to-person transmission of nontuberculous mycobacteria, especially Mycobacterium abscessus subsp. massiliense , is a serious concern among individuals with cystic fibrosis (CF), evidence of its spread among patients without CF has never been established. We unexpectedly found a number of M. abscessus subsp. massiliense cases among patients without CF in a hospital. This study aimed to define the mechanism of M. abscessus subsp. massiliense infection among patients who were ventilator dependent and without CF who had progressive neurodegenerative diseases in our long-term care wards from 2014 to 2018 during suspected nosocomial outbreaks. We conducted whole-genome sequencing of M. abscessus subsp. massiliense isolates from 52 patients and environmental samples. Potential opportunities for in-hospital transmission were analyzed using epidemiological data. M. abscessus subsp. massiliense was isolated from one air sample obtained near a patient without CF who was colonized with M. abscessus subsp. massiliense but not from other potential sources. Phylogenetic analysis of the strains from these patients and the environmental isolate revealed clonal expansion of near-identical M. abscessus subsp. massiliense isolates, with the isolates generally differing by fewer than 22 single nucleotide polymorphisms (SNPs). Approximately half of the isolates differed by fewer than nine SNPs, indicating interpatient transmission. Whole-genome sequencing revealed a potential nosocomial outbreak among patients who were ventilator dependent and without CF. IMPORTANCE The isolation of M. abscessus subsp. massiliense from the air, but not from environmental fluid samples, may suggest airborne transmission. This was the first report to demonstrate person-to-person transmission of M. abscessus subsp. massiliense , even among patients without CF. M. abscessus subsp. massiliense may spread among patients who are ventilator dependent without CF through direct or indirect in-hospital transmission. The current infection control measures should address potential transmission among patients without CF, particularly in facilities that treat patients who are ventilator dependent and patients with preexisting chronic pulmonary diseases, such as CF., Competing Interests: The authors declare no conflict of interest.

Accurate point-of-care testing (POCT) is critical for managing tuberculosis (TB). However, current antibody-based diagnosis shows low specificity and sensitivity. To find proper antigen candidates for TB diagnosis by antibodies, we assessed IgGs responsiveness to Mycobacterium tuberculosis proteins in pulmonary TB (PTB) patients. We employed major secreted proteins, such as Rv1860, Ag85C, PstS1, Rv2878c, Ag85B, and Rv1926c that were directly purified from M. tuberculosis. In the first screening, we found that IgG levels were significantly elevated in PTB patients only against Rv1860, PstS1, and Ag85B among tested antigens. However, recombinant PstS1 and Ag85B from Escherichia coli (E. coli) couldn't distinguish PTB patients and healthy controls (HC). Recombinant Rv1860 was not checked due to its little expression. Then, the 59 confirmed PTB patients from Soetomo General Academic Hospital, Surabaya, Indonesia, and 102 HC were tested to Rv1860 and Ag85B only due to the low yield of the PstS1 from M. tuberculosis. The ROC analysis using native Ag85B and Rv1860 showed an acceptable area under curve for diagnosis, which is 0.812 (95% CI 0.734-0.890, p < 0.0001) and 0.821 (95% CI 0.752-0.890, p < 0.0001). This study indicates that taking consideration of native protein structure is key in developing TB's POCT by antibody-based diagnosis., (© 2023. Springer Nature Limited.)

Corynebacterium ulcerans is a closely related bacterium to the diphtheria bacterium C. diphtheriae, and some C. ulcerans strains produce toxins that are similar to diphtheria toxin. C. ulcerans is widely distributed in the environment and is considered one of the most harmful pathogens to livestock and wildlife. Infection with C. ulcerans can cause respiratory or nonrespiratory symptoms in patients. Recently, the microorganism has been increasingly recognized as an emerging zoonotic agent of diphtheria-like illness in Japan. To clarify the overall clinical characteristics, treatment-related factors, and outcomes of C. ulcerans infection, we analyzed 34 cases of C. ulcerans that occurred in Japan during 2001-2020. During 2010-2020, the incidence rate of C. ulcerans infection increased markedly, and the overall mortality rate was 5.9%. It is recommended that adults be vaccinated with diphtheria toxoid vaccine to prevent the spread of this infection.

Although leprosy (Hansen's disease) is one of the oldest known diseases, the pathogenicity of Mycobacterium leprae ( M. leprae ) remains enigmatic. Indeed, the cell wall components responsible for the immune response against M. leprae are as yet largely unidentified. We reveal here phenolic glycolipid-III (PGL-III) as an M. leprae -specific ligand for the immune receptor Mincle. PGL-III is a scarcely present trisaccharide intermediate in the biosynthetic pathway to PGL-I, an abundant and characteristic M. leprae glycolipid. Using activity-based purification, we identified PGL-III as a Mincle ligand that is more potent than the well-known M. tuberculosis trehalose dimycolate. The cocrystal structure of Mincle and a synthetic PGL-III analogue revealed a unique recognition mode, implying that it can engage multiple Mincle molecules. In Mincle-deficient mice infected with M. leprae , increased bacterial burden with gross pathologies were observed. These results show that PGL-III is a noncanonical ligand recognized by Mincle, triggering protective immunity., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Scotochromogenic slow-growing mycobacteria were isolated from the sputum or bronchoalveolar lavage fluid of 12 patients in Japan. From a comparison of the whole-genome sequences, the representative strain IWGMT90018-18076 T and the unknown strains obtained from the patients were found to represent a novel species related to the Mycobacterium gordonae complex. The average nucleotide identity values of IWGMT90018-18076 T with Mycobacterium vicinigordonae , Mycobacterium paragordonae and M. gordonae were 86.7, 82.5 and 82.2 %, respectively. The genome size of the representative strain IWGMT90018-18076 T was approximately 6.3 Mbp, and the genomic DNA G+C content was 67.1 %. The major fatty acid methyl esters were C 16 : 0 (37.71 %), C 18 : 1 ω9 c (29.5 %) and C 16 : 1 ω7 c (10.32 %). In this study, we performed phylogenetic analyses, physiological and biochemical characteristic tests, drug susceptibility tests and fatty acid profiling of the clinical isolates. On the basis of the results obtained, we propose that the unknown clinical isolates represent a novel species, ' Mycobacterium kiyosense sp. nov,' with the type strain being IWGMT90018-18076 T (=JCM 34837 T =KCTC 49725 T ).

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., Competing Interests: All authors reported no potential conflicts of interest., (© 2023 The Authors.)

Background: This study assessed longitudinal national data on mortality due to nontuberculous mycobacteriosis (NTMosis) and bronchiectasis and the association between the two diseases., Methods: We analysed the national death statistics of Japan from 1970 to 2015. The International Classification of Disease (ICD) codes were used to extract the relevant data. Crude mortality, age-adjusted mortality and standardised mortality rates were calculated using vital statistics and the population in 2000. We also identified domestic publications related to NTMosis and bronchiectasis with an internet-based search system., Results: The total number of bronchiectasis-related deaths remained at the same level, which was approximately 1000, for 45 years, although the number of deaths has consistently decreased in males but increased in females since the mid-1990s. A substantial increasing trend in females was also observed for NTMosis in the same period. The age-adjusted mortality data showed an increase in mortality in women due to NTMosis and confirmed the trend in bronchiectasis in women. The patterns in the number of domestic reports showed a recent slight increase in bronchiectasis and a marked increase in NTMosis., Conclusions: The trends in bronchiectasis-related mortality differed by sex. The epidemiological trends in the two diseases were associated, especially in elderly females since the mid-1990s. It is suggested that pulmonary NTMosis without pre-existing bronchiectasis might be a leading cause of postinfectious bronchiectasis in Japan., Competing Interests: Conflict of interest: K. Morimoto reports grants from AMED during the study, JSPS KAKENHI and lecture fees from INSMED outside the submitted work. T. Asakura reports grants from JSPS KAKENHI and AMED outside the submitted work. Y. Tanaka reports personal fees from Nippon Boehringer Ingelheim Co, Ltd, outside the submitted work. M. Ato reports grants from AMED outside the submitted work. N. Hasegawa reports grants from AMED and JSPS KAKENHI, and lecture fees from INSMED outside the submitted work. K. Iwai, T. Yoshiyama, M. Ito, F. Uesugi, T. Osawa, K. Furuuchi, A. Kurahsima, K. Fujiwara, K. Shoji, Y. Shiraishi, S. Mitarai, and K. Ohta declare that they have no competing interests., (Copyright ©The authors 2023.)

Objectives: Leprosy, or Hansen's disease was a major public health problem in Japan in the early 20th century. Today, the number of new cases has decreased significantly. We aimed to investigate the trends of leprosy in Japan over the past 73 years and the challenges faced in recent years., Methods: We assessed the data on newly registered cases of leprosy from 1947 to 2020., Results: A total of 10,796 newly registered cases of leprosy were reported during the study period, of which 7573 were registered in mainland Japan, 2962 in Okinawa, and 250 were of foreign origin. Most autochthonous cases were born before 1950 in mainland Japan and before 1975 in Okinawa. The number of nonautochthonous cases surpassed that of autochthonous cases in 1992. Nonautochthonous cases originated from 26 countries, particularly Brazil and the Philippines. Three cases of antimicrobial resistance have been detected among nonautochthonous cases since 2004., Conclusion: Our data suggest that ongoing transmission of leprosy likely ceased in the 1940s in mainland Japan and in the 1970s in Okinawa. With the recent rise of nonautochthonous cases with globalization, continuous surveillance and efforts to maintain leprosy services within the country are necessary even after reaching the state of elimination., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Tuberculosis (TB) and COVID-19 have become significant health problems globally, especially in countries with high prevalence. Therefore, this research aims to examine all possibilities and predict the impact of TB-SARS-CoV-2 co-infection to anticipate the cascade effect of both diseases in all sectors. The conceptual strategy of the algorithm in TB-COVID-19 is needed to create an integrated management system. It includes the stages of early detection with accurate and effective methods, as well as the synchronization of TB-COVID-19 health services, starting from primary health facilities to secondary and tertiary referral centers. The algorithm in TB-COVID-19 is crucial to prepare future strategies for PTB co-infection viral respiratory infections other than SARS-CoV-2, ILI, ARI, and SARI. Since the implementation involves all health services, there is a need to integrate the governance of TB-COVID-19 and other comorbidities in good health services based on research and multicentre design.

Objective: To evaluate the presence of wiper epitheliopathy in patients with blepharospasm and/or hemifacial spasm before and 4 weeks after routine treatment with botulinum toxin., Methods: Prospective study comprising 31 eyes of 20 patients with neurological diagnosis of hemifacial spasm (9 eyes of 9 patients) and essential blepharospasm (22 eyes of 11 patients). Various ocular surface parameters were assessed before and 4 weeks after infiltration with botulinum toxin using the OSDI questionnaire, Schirmer's test, tear break-up time (BUT), fluorescein and lissamine green staining assessed with the Oxford test and the degree of involvement of the palpebral wiper., Results: 100% of the patients had palpebral wiper involvement before (30% mild and 70% moderate) and after toxin treatment (100% mild). 75% of patients had mild-normal OSDI before treatment, after treatment it was 80%. The BUT was 7.2 ± 0.2 sg before and 7.5 ± 0.7 sg after treatment. Schirmer's test was 11.4 ± 5.5 and 12.5 ± 5.5 mm before and after treatment. The Oxford test was initially pathological in 69.3% of patients, after 4 weeks it was pathological in only 54%., Conclusion: Wiper epitheliopathy is present in 100% of patients with blepharospasm and/or hemifacial spasm. The main pathophysiological mechanism that triggers it in these patients is the increase in the coefficient of friction, as tear volume and stability are normal., (Copyright © 2022 Sociedad Española de Oftalmología. Published by Elsevier España, S.L.U. All rights reserved.)

Mycobacterium abscessus (M. abscessus) is a highly antimicrobial-resistant pathogen that causes refractory pulmonary disease. Recently, the possibility of M. abscessus cross-transmission among cystic fibrosis (CF) patients has been reported. CF is rare in Asia, but M. abscessus pulmonary disease is common. Therefore, we investigated the possibility of M. abscessus cross-transmission in a Japanese hospital setting. Of 104 M. abscessus isolates, 25 isolates from 24 patients were classified into four clusters based on their variable number of tandem repeat profiles and were subjected to whole-genome sequencing (WGS). The epidemiological linkages among our patients were investigated by integrating the WGS data of previously reported nosocomial outbreak-related M. abscessus clinical isolates in the United Kingdom and the United States. Eight transmissible clusters (TCs) were identified. The United Kingdom and United States isolates were assigned to four clusters (TC1, TC2, TC5, and TC8) and one cluster (TC3), respectively. A total of 12 isolates from our hospital belonged to 4 clusters (TC4, TC5, TC6, and TC7). Epidemiological linkage analysis inferred direct or indirect transmission between patients in our hospital in TC4 and TC5 but not in TC6 and TC7. In TC5, the single nucleotide polymorphism distance between isolates from Japanese and United Kingdom patients was less than 21; however, there was no contact. This study revealed that genetically closely related isolates exist, even in non-CF patients. However, the transmission route remains unclear, and further research is warranted to clarify whether cross-transmission is involved. IMPORTANCE Although the possibility of Mycobacterium abscessus (M. abscessus) cross-transmission in cystic fibrosis (CF) patients has often been reported, it is not clear whether similar events have occurred in Asian non-CF patients. Whole-genome sequencing analysis of M. abscessus isolates from Fukujuji Hospital in Japan indicated that genetically closely related M. abscessus isolates exist. In addition, according to epidemiological linkage analysis, some clusters were suspected of direct or indirect transmission between patients within our hospital. However, the transmission route of M. abscessus remains unclear, because interestingly, one cluster showed a single nucleotide polymorphism distance of less than 21 from the United Kingdom isolates, but no epidemiological linkage was identified.

Mycobacterium abscessus complex (MABC) is a group of emerging, highly antimicrobial-resistant non-tuberculous mycobacteria. Specific MABC clones are spreading globally in patients with cystic fibrosis (CF); however, associated genomic epidemiology is lacking in East Asia, with very few patients with CF. Here, we investigated MABC populations derived from non-CF patients in Japan and Taiwan. Analysis of whole-genome sequencing data of 220 MABC isolates revealed that 112, 105, and 3 were M. abscessus subsp. abscessus (ABS), M. abscessus subsp. massiliense (MAS), and M. abscessus subsp. bolletii (BOL), respectively. Moreover, >50% of ABS and >70% of MAS were related to four predominant clones in the region. Known mutations conferring macrolide resistance were rare (1.4%) and were not enriched in the predominant clones. Conversely, the macrolide-susceptible erm (41) T28C mutation was significantly enriched in one predominant ABS clone. The most predominant ABS clone was genetically related to the previously described dominant circulating clone (DCC)1 in patients with CF, whereas no isolates were related to DCC2; isolates related to DCC3 were not necessarily predominant in our sample set. We found that the erm (41) T28C mutants spread globally, and some of them reacquired the functional erm (41) gene through both point mutation and recombination. This study revealed predominant MABC clones in Japan and Taiwan and their relationship with the globally superadding clones in the patient community with CF. Our study provides insights into the genetic characteristics of globally dominant and area-specific strains isolated from patients with or without CF and differences between globally spread and regionally specific strains. IMPORTANCE Members of Mycobacterium abscessus complex (MABC) are frequently isolated from patients. Studies have reported that predominant clones of MABC (known as dominant circulating clones; DCCs) are distributed worldwide and transmitted from humans to humans in patients with cystic fibrosis (CF). However, associated genomic epidemiology has not yet been conducted in East Asia, including Japan and Taiwan, where there are only a few patients with CF. Using whole-genome sequencing data derived from non-CF patients in Japan and Taiwan, we revealed prevalent clones and the incidence of macrolide resistance-associated mutations in the MABC population in this region. We also clarified the associations between these predominant clones and DCCs in the global CF patient community. Our results would assist further studies in elucidating the genetic characteristics of strains isolated from patients with or without CF, the differences between globally spread and regionally specific strains, and the adaptive evolution of MABC within the host.

We have isolated a strain that we believe is identical to strain IWGMT90018-an unidentified nontuberculous mycobacterium (NTM) species published in 1981-and named it IWGMT90018-18076. Here, we report its complete chromosomal genome sequence. This study will help us understand the diversity and pathogenicity of NTM.

Introduction: Rhabdophis snakes, which include 27 species, are rear-fanged venomous snakes that are widely distributed from India to East Asia and Russia. Severe envenomation by R. tigrinus (Yamakagashi snake) in Japan and R. subminiatus in Southeast Asia has been reported. The epidemiology of R. tigrinus bites, such as geographical features, the incidence, and changes in the number of bites over time have not been comprehensively examined. Hence, we intended to clarify the epidemiological features of R. tigrinus bites through a careful review of scientific data over the last 50 years in Japan. Methods: Patient records of R. tigrinus bites between 1971 and 2020 at the Japan Snake Institute were examined retrospectively. The following were ascertained: patient characteristics, clinical symptoms, laboratory data, treatment-related factors, and hospital mortality. These variables were compared in the antivenom and the without-antivenom groups. Results: Over the 50-year study period, 43 R. tigrinus bites, including five fatal cases, were encountered. Severe cases of R. tigrinus bites have been treated with antivenom since 1985; however, fatalities occurred in 2006 and 2020. R. tigrinus bite cases have been well-distributed in the western part of Japan since 2000. The mortality rate in the antivenom group was significantly lower in the patient group that was not administered the antivenom (0 vs. 23.8%, p = 0.048). Conclusion: This study clarified the epidemiology of R. tigrinus bites in Japan over a 50-year period. Almost all severe cases of R. tigrinus bites have been treated with the antivenom in the current situation, and fatalities occurred in cases not treated with the antivenom. It is important to diagnose R. tigrinus bites in the early phase of the clinical course. The antivenom, the definitive treatment for R. tigrinus bites, is an unapproved drug. Hence, approval needs to be obtained for the drug., Competing Interests: KM was employed by company KM Biologics Co., Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Hifumi, Sakai, Yamamoto, Morokuma, Otani, Takahashi and Ato.)

Mycobacterium tuberculosis, the causative agent of tuberculosis, possess flavin-dependent thymidylate synthase, ThyX. Since thyX is absent in humans and was shown to be essential for M. tuberculosis normal growth, ThyX is thought to be an attractive novel TB drug target. This study assessed thyX essentiality in Mycobacterium bovis BCG strains using CRISPR interference based gene silencing and found that thyX is not essential in an M. bovis BCG Tokyo derivative strain. A thyX deletion mutant strain was successfully constructed from that strain, which reinforces the non-essentiality of thyX under a certain genetic background., (© 2021 The Societies and John Wiley & Sons Australia, Ltd.)

Mycobacterium avium subsp. hominissuis (MAH) is one of the most important agents causing non-tuberculosis mycobacterial infection in humans and pigs. There have been advances in genome analysis of MAH from human isolates, but studies of isolates from pigs are limited despite its potential source of infection to human. Here, we obtained 30 draft genome sequences of MAH from pigs reared in Japan. The 30 draft genomes were 4,848,678-5,620,788 bp in length, comprising 4652-5388 coding genes and 46-75 (median: 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., Competing Interests: The authors declare that they have no competing interests., (© The Author(s) 2021.)

Mycobacterium leprae is the predominant cause of leprosy worldwide, and its genotypes can be classified into four single-nucleotide polymorphism (SNP) types and 16 subtypes. Determining M. leprae drug resistance and genotype is typically done by PCR and Sanger DNA sequencing, which require substantial effort. Here, we describe a rapid method involving multiplex PCR in combination with nested amplification and next-generation sequence analysis that allows simultaneous determination of M. leprae drug resistance and SNP genotype directly from clinical specimens. We used this method to analyze clinical samples from two paucibacillary, nine multibacillary, and six type-undetermined leprosy patients. Regions in folP1 , rpoB , gyrA , and gyrB that determine drug resistance and those for 84 SNP-InDels in the M. leprae genome were amplified from clinical samples and their sequences determined. The results showed that seven samples were subtype 1A, three were 1D, and seven were 3K. Three samples of the subtype 3K had folp1 mutation. The method may allow more rapid genetic analyses of M. leprae in clinical samples.

Rationale: Nontuberculous mycobacteria (NTM) are environmental mycobacteria that can cause a chronic progressive lung disease. Although epidemiological data indicate potential genetic predisposition, its nature remains unclear., Objectives: We aimed to identify host susceptibility loci for Mycobacterium avium complex (MAC), the most common NTM pathogen., Methods: This genome-wide association study (GWAS) was conducted in Japanese patients with pulmonary MAC and healthy controls, followed by genotyping of candidate single-nucleotide polymorphisms (SNPs) in another Japanese cohort. For verification by Korean and European ancestry, we performed SNP genotyping., Results: The GWAS discovery set included 475 pulmonary MAC cases and 417 controls. Both GWAS and replication analysis of 591 pulmonary MAC cases and 718 controls revealed the strongest association with chromosome 16p21, particularly with rs109592 (p=1.64×10 -13 , OR 0.54), which is in an intronic region of the calcineurin-like EF-hand protein 2 ( CHP2 ). Expression quantitative trait loci analysis demonstrated an association with lung CHP2 expression. CHP2 was expressed in the lung tissue in pulmonary MAC disease. This SNP was associated with the nodular bronchiectasis subtype. Additionally, this SNP was significantly associated with the disease in patients of Korean (p=2.18×10 -12 , OR 0.54) and European (p=5.12×10 -03 , OR 0.63) ancestry., Conclusions: We identified rs109592 in the CHP2 locus as a susceptibility marker for pulmonary MAC disease., Competing Interests: Conflict of interest: H. Namkoong reports grants from JSPS (JSPS KAKENHI grant number 15H06590), AMED (2019 US-Japan Collaborative Proposal 28863) and NIAID/CBER Intramural Tuberculosis Research Initiative (FY19 Start-up support from CAN 8020315), during the conduct of the study. Conflict of interest: Y. Omae reports grants from JSPS KAKENHI (18K15041), during the conduct of the study. Conflict of interest: T. Asakura reports grants from JSPS, outside the submitted work. Conflict of interest: M. Ishii reports grants from JSPS KAKENHI (18H02821, 18K19566), outside the submitted work. Conflict of interest: S. Suzuki reports grants from JSPS, outside the submitted work. Conflict of interest: K. Morimoto reports grants from AMED (2019 US-Japan Collaborative Proposal 28863), during the conduct of the study; personal fees for consultancy from INSMED, outside the submitted work. Conflict of interest: Y. Kawai has nothing to disclose. Conflict of interest: K. Emoto has nothing to disclose. Conflict of interest: A.J. Oler has nothing to disclose. Conflict of interest: E.P. Szymanski has nothing to disclose. Conflict of interest: M. Yoshida reports grants from JSPS (grant-in-aid for young scientists (B), JSPS KAKENHI grant number 17K16066), during the conduct of the study. Conflict of interest: S. Matsuda has nothing to disclose. Conflict of interest: K. Yagi has nothing to disclose. Conflict of interest: I. Hase has nothing to disclose. Conflict of interest: T. Nishimura reports grants from JSPS KAKENHI (16K09942), outside the submitted work. Conflict of interest: Y. Sasaki reports grants from JSPS (JSPS KAKENHI grant number 15H06590), during the conduct of the study. Conflict of interest: T. Asami has nothing to disclose. Conflict of interest: T. Shiomi has nothing to disclose. Conflict of interest: H. Matsubara has nothing to disclose. Conflict of interest: H. Shimada has nothing to disclose. Conflict of interest: J. Hamamoto reports grants from JSPS KAKENHI (19K08610), outside the submitted work. Conflict of interest: B.W. Jhun reports grants from AMED (2019 US-Japan Collaborative Proposal 28863), during the conduct of the study. Conflict of interest: S-Y. Kim has nothing to disclose. Conflict of interest: H.J. Huh has nothing to disclose. Conflict of interest: H-H. Won has nothing to disclose. Conflict of interest: M. Ato reports grants from Japan Agency for Medical Research and Development, during the conduct of the study. Conflict of interest: K. Kosaki reports grants from Japan Agency for Medical Research and Development (AMED), outside the submitted work. Conflict of interest: T. Betsuyaku reports grants from JSPS KAKENHI and Japan Agency for Medical Research and Development (AMED), outside the submitted work. Conflict of interest: K. Fukunaga reports grants from JSPS KAKENHI and Japan Agency for Medical Research and Development (AMED), outside the submitted work. Conflict of interest: A. Kurashima reports personal fees for consultancy from Insmed, during the conduct of the study. Conflict of interest: H. Tettelin reports grants from NIAID (contract number HHSN272200900009CJSPS), during the conduct of the study. Conflict of interest: H. Yanai has nothing to disclose. Conflict of interest: S. Mahasirimongkol has nothing to disclose. Conflict of interest: K.N. Olivier reports non-financial support from AIT Therapeutics, non-financial support from Insmed, outside the submitted work. Conflict of interest: Y. Hoshino reports grants from The Japan Agency for Medical Research and Development/Japan International Cooperation Agency (AMED), during the conduct of the study (JP18fk0108043 and JP18fk0108075). Conflict of interest: W-J. Koh reports grants from National Research Foundation of Korea (grant number NRF-2018R1A2A1A05018309), during the conduct of the study. Conflict of interest: S.M. Holland has nothing to disclose. Conflict of interest: K. Tokunaga reports grants from Japan Agency for Medical Research and Development (grant-in-aid for research JP17km0405205h0002), during the conduct of the study. Conflict of interest: N. Hasegawa reports grants from Japan Agency for Medical Research and Development(AMED), during the conduct of the study; grants from JSPS KAKENHI, personal fees for consultancy from INSMED, outside the submitted work., (The content of this work is not subject to copyright. Design and branding are copyright ©ERS 2021. For commercial reproduction rights and permissions contact permissions@ersnet.org.)

Mycobacterium bovis BCG has been the only practical vaccine for tuberculosis. However, BCG cannot fully prevent adult pulmonary tuberculosis. Therefore, the improvement of BCG vaccine is necessary. We previously produced recombinant (r) BCG (BCG-PEST) for the better control of tuberculosis. BCG-PEST was developed by introducing PEST-Heat Shock Protein (HSP)70-Major Membrane Protein (MMP)-II-PEST fusion gene into urease-deficient rBCG using antibiotic-resistant gene for the selection of rBCG. HSP70-MMPII fusion protein is highly immunogenic and PEST sequence was added to enhance processing of the fusion protein. Although BCG-PEST effectively inhibited intrapulmonary growth of Mycobacterium tuberculosis (MTB), BCG with antibiotic-resistant gene is not appropriate for human use. Therefore, we produced antibiotic-resistant gene-free rBCG. We generated leucine-biosynthetic gene (leuD)-deficient BCG and introduced the fusion gene with leuD as the selection marker and named this rBCG as BCG-LeuPH. BCG-LeuPH activated human naïve T cells of both CD4 and CD8 subsets and efficiently inhibited aerosol-challenged MTB in mice. These results indicate that leuD can replace antibiotic-resistant gene for the selection of vaccine candidates of rBCG for human use., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Background: The clinical impact of infection with Mycobacterium (M.) abscessus complex (MABC), a group of emerging non-tuberculosis mycobacteria (NTM), is increasing. M. abscessus subsp. abscessus/bolletii frequently shows natural resistance to macrolide antibiotics, whereas M. 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. We aimed to develop a simple and rapid diagnostic that can identify MABC isolates showing macrolide susceptibility., Methods: Whole 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., Finding: We 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%., Interpretation: We developed a novel, rapid and simple DNA chromatography method for identification of MABC macrolide susceptibility with high accuracy., Funding: AMED, JSPS KAKENHI., Competing Interests: Declaration of Competing Interest Mitsunori Yoshida, Sotaro Sano, Shigehiko Miyamoto and Yoshihiko Hoshino are listed on a pending patent in Japan for the DNA chromatography methodology to distinguish MABC and identify macrolide susceptibility (JP2020–066277 and JP2020–066306). Dr. Morimoto and Dr Kurashima report personal fees as Consultant of INSMED, outside the submitted work. The other authors have nothing to disclose under this manuscript., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

Mycobacterium avium subspecies hominissuis (MAH) is a pathogen that causes various non-tuberculous mycobacterial diseases in humans and animals worldwide. Among the genus, MAH is characterized by relatively slow growth. Here, we isolated a rapidly growing variant of the MAH 104 strain. The variant strain (named N104) exhibited an enhanced growth rate and higher motility compared to the parent MAH 104 strain (P104). Whole-genome sequencing analysis of N104 revealed the loss of the stop codon of MAV&#95;RS14660 due to a single nucleotide replacement, resulting in the substitution of the codon for tryptophan. Notably, exclusion of the stop codon ligated the open reading frames and caused the fusion of two adjacent proteins. A revertant parent strain, in which a mutation was introduced to restore the stop codon, revealed that elimination of the stop codon in MAV&#95;RS14660 was responsible for the N104 phenotype. Furthermore, we analysed the phenotypes of the parent and mutated strains by determining the functions of the MAV&#95;RS14660 and MAV&#95;RS14655 coding regions flanking the stop codon. The mutant strains, expected to express a fusion protein, exhibited increased resistance to antimicrobial drugs and exogenous copper toxicity compared to that of the parent strains. These findings suggest that the fusion of the MAV&#95;RS14660 - and MAV&#95;RS14655 -encoding regions in the mutant N104 strain could be related to the modified functions of these intrinsic proteins.