M kansasii

Clinical isolates (M. tuberculosis, M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, M. avium, M. intracellulare, M. kansasii, M. fortuitum, M. gordonae, M. smegmatis, M. scrofulaceum, and M. marinum) were obtained from Shanghai Pulmonary Hospital, Shanghai, China, and confirmed by 16S rRNA, rpoB, and hsp65 or whole-genome sequencing (12 (link)). Ten reference strains, M. tuberculosis H37Rv (ATCC 27294), M. abscessus subsp. abscessus (ATCC 19977), M. abscessus subsp. massiliense (CIP108297), M. avium (ATCC 25291), M. intracellulare (ATCC 13950), M. kansasii (ATCC 12478), M. xenopi (ATCC 19250), M. fortuitum (ATCC 6841), M. scrofulaceum (ATCC 19981), and M. marinum (ATCC 927), were purchased from the American Type Culture Collection (ATCC) (Manassas, VA, USA). All strains were cultured in Middlebrook 7H9 liquid medium and incubated at 37°C. Streptococcus pneumoniae, Haemophilus influenzae, Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii, Staphylococcus aureus, Klebsiella pneumoniae, and Nocardia asteroides were obtained from Shanghai Pulmonary Hospital, Shanghai, China, and cultured on blood agar plates.

A total of 10 NTM reference strains and 194 clinical, M. abscessus isolates were evaluated. The following reference strains: M. abscessus subsp. abscessus (ATCC 19977), M. avium (ATCC 25291), M. intracellulare (ATCC 13950), M. kansasii (ATCC 12478), M. fortuitum (ATCC 6841), M. gordonae (ATCC 14470), M. scrofulaceum (ATCC19981), M. peregrinum (ATCC700686), and M. xenopi (ATCC19250) were purchased from the American Type Culture Collection (ATCC; VA, United States). M. abscessus subsp. massiliense (CIP108297) was purchased from the Biological Resource Center of Institut Pasteur (CIP; Paris, France). Detailed information regarding the clinical isolates was provided in a previous study (Guo et al., 2020 (link)). All strains were grown at 37°C on Middlebrook 7H10 agar plates supplemented with 10% OADC and 0.2% glycerol, or with continuous shaking in Middlebrook 7H9 broth supplemented with 10% OADC and 0.05% Tween 80. Middlebrook 7H9 broth, M7H10 agar, cation-adjusted Mueller-Hinton II broth and OADC were purchased from Becton Dickinson and Company (NJ, United States).

Twelve NTM reference strains and 227 NTM clinical isolates (194 M. abscessus, 14 M. avium, 15 M. intracellulare, and 4 M. fortuitum) were evaluated. The reference strains, M. abscessus subsp. abscessus (ATCC 19977), M. smegmatis (ATCC 19420), M. avium (ATCC 25291), M. intracellulare (ATCC 13950), M. kansasii (ATCC 12478), M. fortuitum (ATCC 6841), M. gordonae (ATCC 14470), M. scrofulaceum (ATCC 19981), M. szulgai (ATCC 35799), M. xenopi (ATCC 19250), and M. peregrinum (ATCC 700686), were purchased from the American Type Culture Collection (VA, USA). M. abscessus subsp. massiliense (CIP 108297) was purchased from the Biological Resource Center of Institute Pasteur (Paris, France). The clinical isolates were obtained from the Shanghai Pulmonary Hospital from sputum and bronchoalveolar lavage fluid specimens of patients with NTM lung infections. All M. abscessus isolates were sequenced; the full genome sequence of each isolate was published and is available at DDBJ/ENA/GenBank (BioProject PRJNA488058, PRJNA448987, and PRJNA398137). All strains were grown at 37°C in Middlebrook 7H9 broth supplemented with 10% OADC or on Middlebrook 7H10 plates supplemented with 10% OADC.