Mycobacterium saopaulense sp. nov., a rapidly growing mycobacterium closely related to members of the Mycobacterium chelonae–Mycobacterium abscessus group

Abstract

Five isolates of non-pigmented, rapidly growing mycobacteria were isolated from three patients and, in an earlier study, from zebrafish. Phenotypic and molecular tests confirmed that these isolates belong to the Mycobacterium chelonae-Mycobacterium abscessus group, but they could not be confidently assigned to any known species of this group. Phenotypic analysis and biochemical tests were not helpful for distinguishing these isolates from other members of the M. chelonae-M. abscessus group. The isolates presented higher drug resistance in comparison with other members of the group, showing susceptibility only to clarithromycin. The five isolates showed a unique PCR restriction analysis pattern of the hsp65 gene, 100 % similarity in 16S rRNA gene and hsp65 sequences and 1-2 nt differences in rpoB and internal transcribed spacer (ITS) sequences. Phylogenetic analysis of a concatenated dataset including 16S rRNA gene, hsp65, and rpoB sequences from type strains of more closely related species placed the five isolates together, as a distinct lineage from previously described species, suggesting a sister relationship to a group consisting of M. chelonae, Mycobacterium salmoniphilum, Mycobacterium franklinii and Mycobacterium immunogenum. DNA-DNA hybridization values .70 % confirmed that the five isolates belong to the same species, while values ,70 % between one of the isolates and the type strains of M. chelonae and M. abscessus confirmed that the isolates belong to a distinct species. The polyphasic characterization of these isolates, supported by DNA-DNA hybridization results, demonstrated that they share characteristics with M. chelonae-M. abscessus members, but constitute a different species, for which the name Mycobacterium saopaulense sp. nov. is proposed. The type strain is EPM 10906 T (5CCUG 66554 T 5LMG 28586 T 5INCQS 0733 T ).Abbreviations: DDH, DNA-DNA hybridization; ITS, internal transcribed spacer; PFGE, pulsed-field gel electrophoresis; PRA, PCR restriction analyses.The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence of strains EPM 10906 T , EPM 10695, IAL 3785, JAN1 and JAN2 are KM973037, KM973036, KM973038, DQ866774 and DQ866775, respectively; for the hsp65 sequence are KM973026, KM973025, KM973027, DQ866786 and DQ866787, respectively; for the rpoB sequence are KM973029, KM973028, KM973030, KM973031 and KM973032, respectively; and for the internal transcribed spacer (ITS) sequence are KM973034, KM973033, KM973035, DQ866774 and DQ866775, respectively.Three supplementary tables and a supplementary figure are available with the online Supplementary Material.

Recommendations for Health Monitoring and Reporting for Zebrafish Research Facilities

“…There are more than 170 recognized Mycobacterium spp., including both infectious and noninfectious environmental species, which may be found in zebrafish systems and have the potential to cause disease in fish and/or human handlers. [25][26][27] Immunosuppressed handlers are particularly at risk. Seven different species have been reported to be pathogenic in zebrafish, including M. chelonae, M. marinum, M. haemophilum, M. abscessus, M. fortuitum and M. peregrinum and M. saopaulense.…”

“…Seven different species have been reported to be pathogenic in zebrafish, including M. chelonae, M. marinum, M. haemophilum, M. abscessus, M. fortuitum and M. peregrinum and M. saopaulense. 25,26 These mycobacterial species are facultative pathogens that can both proliferate in the system biofilms and infect immunocompetent zebrafish. 25,27 Two of these, M. marinum and M. haemophilum, are slowly growing mycobacteria that cause obvious clinical disease and mortality in infected colonies.…”

“…34 M. abscessus is very close phylogenetically to M. chelonae, and similarly produces predominantly subclinical infections; the recently described M. saopaulense also belongs to this group. 26 M. fortuitum is a widely distributed species associated with chronic subclinical granulomatous infections. 35 M. peregrinum is relatively uncommon and is usually subclinical, 36 although a high mortality epizootic has also been reported in association with this species.…”

Whole-Genome Sequences of Four Strains Closely Related to Members of the Mycobacterium chelonae Group, Isolated from Biofilms in a Drinking Water Distribution System Simulator

“…These rapidly growing nontuberculous mycobacteria (NTM) are opportunistic pathogens with the ability to form biofilms on the surface of DWDS (3). Furthermore, this complex has been implicated in invasive infections in immunocompromised hosts and is represented by M. chelonae , M. abscessus , M. immunogenum , M. salmoniphilum , M. franklinii , and M. saopaulense (4–10). Little information is available about the resilience of NTM in DWDS and the potential to cause public health problems (11, 12).…”

“…ANI calculations were performed using the online calculator available from EzGenome (http://www.ezbiocloud.net/ezgenome/ani). Furthermore, a comparative analysis of the rpoB , recA , and sodA genes revealed <95.04% ± 0.05% sequence homology with representatives of the M. chelonae-M. abscessus complex (6–10). Genomic comparison confirmed that these isolates belong to the M. chelonae group but may constitute a different subspecies.…”