[Downloaded free from http://www.ijmyco.org on Friday, January 29, 2021, IP: 197.46.112.30] Original Article An Overview of Pulmonary Infections due to Rapidly Growing Mycobacteria in South Asia and Impressions from a Subtropical Region Kamal Shrivastava1, Chanchal Kumar1, Anupriya Singh1, Anshika Narang1, Astha Giri1, Naresh Kumar Sharma1, Shraddha Gupta1, Varsha Chauhan1, Jayanthi Gunasekaran1, Viswesvaran Balasubramanian2, Anil Chaudhry3, Rupak Singla4, Rajendra Prasad2, Mandira Varma-Basil1 Departments of 1Microbiology and 2Pulmonary Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, 3Department of Pulmonary Medicine, Rajan Babu Institute of Pulmonary Medicine and Tuberculosis, 4Department of TB and Respiratory Diseases, National Institute of Tuberculosis and Respiratory Diseases, Delhi, India Abstract Background: Rapidly growing mycobacteria (RGM) comprise nearly half of the validated species of nontuberculous mycobacteria (NTM) and have been reported to have a higher incidence in Asia as compared to Europe and America. There is limited information on RGM infections from South Asia. Hence, the present study aimed to ascertain the incidence of pulmonary infections due to RGM in Delhi and to review the status of available information on the prevalence of RGM in South Asia, a region endemic for tuberculosis. Methods: We analyzed 933 mycobacterial isolates obtained from pulmonary samples in Delhi and performed species identification by polymerase chain reaction (PCR)-restriction analysis (restriction fragment length polymorphism) and line probe assay. Drug susceptibility testing (DST) was performed by broth microdilution method. We also reviewed reports available on pulmonary infections in South Asia, attributed to RGM. Results: Of the 933 mycobacterial isolates studied, NTM were identified in 152 (16.3%). Of these, 65/152 (42.8%) were RGM comprising Mycobacterium fortuitum (34/65; 52.3%), Mycobacterium abscessus (25/65; 38.5%), Mycobacterium chelonae (3/65; 4.61%), Mycobacterium mucogenicum (2/65; 3.1%), and Mycobacterium smegmatis (1/65; 1.5%). On applying the American Thoracic Society/Infectious Diseases Society of America guidelines, 11/25 (44%) M. abscessus, 3/3 (100%) M. chelonae, and both isolates of M. mucogenicum were found to be clinically relevant. DST revealed that maximum susceptibility of the RGM was seen to linezolid, clarithromycin, and amikacin. Conclusions: Of the RGM isolated in the present study, 16/65 (24.6%) were found to be clinically relevant. Hence, it is important to recognize these organisms as potential pathogens to identify patients with RGM disease to initiate appropriate therapy. Keywords: India, nontuberculous mycobacteria, rapidly growing mycobacteria, rapidly growing mycobacteria pulmonary infections, South Asia Submitted: 15-Nov-2019 Accepted: 23-Nov-2019 Published: 06-Mar-2020 INTRODUCTION favors the formation of biofilms, accounting for their resistance to antibiotics and commonly used disinfectants.[5] Dispersal Rapidly growing mycobacteria (RGM) are ubiquitous of the organisms from biofilms may also be a source of organisms isolated from soil, dust, rocks, and water and are characterized by visible growth on solid media within Address for correspondence: Dr. Mandira Varma‑Basil, 7 days.[1] Although generally of low virulence, RGM Department of Microbiology, Vallabhbhai Patel Chest Institute, especially, Mycobacterium abscessus, Mycobacterium University of Delhi, Delhi ‑ 110 007, India. E‑mail: [email protected] fortuitum, Mycobacterium chelonae, and Mycobacterium mucogenicum, are being increasingly seen to cause a wide ORCID: spectrum of diseases including pulmonary, skin, soft tissue, and https://orcid.org/0000‑0001‑5562‑015X disseminated infections.[1-4] Moreover, the high hydrophobicity of RGM, and other nontuberculous mycobacteria (NTM), This is an open access journal, and articles are distributed under the terms of the Creative Commons Attribution‑NonCommercial‑ShareAlike 4.0 License, which allows others to Access this article online remix, tweak, and build upon the work non‑commercially, as long as appropriate credit Quick Response Code: is given and the new creations are licensed under the identical terms. Website: For reprints contact: [email protected] www.ijmyco.org How to cite this article: Shrivastava K, Kumar C, Singh A, Narang A, DOI: Giri A, Sharma NK, et al. An overview of pulmonary infections due to 10.4103/ijmy.ijmy_179_19 rapidly growing mycobacteria in South Asia and impressions from a subtropical region. Int J Mycobacteriol 2020;9:62-70. 62 © 2020 International Journal of Mycobacteriology | Published by Wolters Kluwer - Medknow [Downloaded free from http://www.ijmyco.org on Friday, January 29, 2021, IP: 197.46.112.30] Shrivastava, et al.: RGM infections in South Asia nosocomial infection in patients through water pipes or other articles, we extracted the following data using a data devices.[1] In fact, it has been reported that hospital-acquired extraction sheet: research setting, study period, population infections due to NTM are most commonly associated with tested and numbers, NTM species isolated, method for NTM RGM.[6] However, due to their ubiquitous nature, isolation of identification, prevalence of pulmonary NTM isolation/disease, RGM from clinical specimens does not necessarily indicate HIV coinfection rate, and risk factors for NTM acquisition. At NTM disease and was until recently, often ignored. The recent least two authors reviewed each article. progress in the development of rapid molecular methods Data analysis in clinical microbiology has led to increased isolation and In estimating country-level and overall prevalence of NTM identification of these organisms from clinical specimens.[3,4,7] in South Asia, a pooled estimate was computed based on Consequently, a number of new species have been identified the reported prevalence. We checked all retrieved articles and some species previously considered to be contaminants, for application of the American Thoracic Society (ATS) are now recognized as pathogens.[8] With increasing awareness diagnostic criteria for clinically relevant RGM and recorded of the importance of RGM, clinicians are facing challenges the proportion of patients meeting these criteria and NTM while treating patients with RGM infection, especially if the species responsible for infection. RGM has been recently identified as a pathogen. Reporting the rapidly growing mycobacteria associated Species-level identification of RGM is recommended as the with pulmonary infections in Delhi, India susceptibility pattern varies among different species.[8] Since conventional biochemical tests are time-consuming and Clinical specimens and mycobacterial isolates cumbersome, laboratorians rely on molecular methods of A total of 933 isolates were obtained from patients suspected identification such as polymerase chain reaction restriction of suffering from pulmonary mycobacterial disease between analysis (PRA), line probe assay (LPA), and sequencing of January 2014 and April 2019 at the Department of Microbiology, hsp65 or16s rRNA. Furthermore, most RGM are resistant to Vallabhbhai Patel Chest Institute, Delhi, India, after approval first-line antituberculous drugs. In fact, M. abscessus is the from the Institutional ethical committee. The patients had most difficult to treat. Hence, drug susceptibility has been reported to the outpatient unit of Vallabhbhai Patel Chest Institute, recommended for all RGM found to be clinically relevant.[2,9] Rajan Babu Institute of Pulmonary Medicine and TB of Delhi, or National Institute of TB and Respiratory Diseases, Delhi, India. Although reports on the incidence of RGM infection are The clinical isolates obtained were characterized by their colony increasing, most of the reports come from industrialized morphology on Lowenstein–Jensen medium and were subjected nations of the world.[2,10] There is still a paucity of data on RGM to biochemical identification by niacin, nitrate reduction, and infections from South Asia, a region that is also endemic for semi-quantitative catalase tests.[14] Further characterization of tuberculosis (TB).[11,12] Here, we report our experience with the isolates was performed by PRA of the hsp65 gene using the RGM associated with pulmonary infections in Delhi, India, and enzymes NruI and BamHIas previously described.[15] present an overview of clinically significant RGM identified in South Asia, to understand the extent of awareness of these Species identification by line probe assay pathogens in this region. Species identification of the isolates identified as NTM was performed by GenoType Mycobacterium CM/AS (Hain Lifescience GmbH, Germany). METHODS Literature search Sanger sequencing Species identification of a subset of the clinical isolates A review of the reports on RGM in South Asia was conducted in was confirmed by Sanger sequencing of heat-shock accordance with PRISMA guidelines.[13] The overall aim of this protein-65 (hsp65) gene in an Applied Biosystems Automated review was to determine the prevalence of clinically significant Sequencer (Ocimum Biosolutions, Bengaluru, India). RGM in patients with pulmonary infection in South Asia. Sequences were identified by similarity using Blastn We included Afghanistan, Bangladesh, Bhutan, Nepal, India, available at National Center for Biotechnology Information Pakistan, Sri Lanka, and the Maldives in the South Asian region. (NCBI) (www.blast.ncbi.nlm.nih.gov/blast.cgi). Species We searched PubMed, Scopus, EMBASE,