Mycobacterium arupense sp. nov., a non-chromogenic bacterium isolated from clinical specimens

Abstract

Several Mycobacterium-like organisms related to the Mycobacterium terrae complex have been isolated from clinical samples. In the clinical microbiology laboratory, partial 16S rRNA gene sequencing (approximately the first 500 bp) rather than full 16S rRNA gene sequencing is often used to identify Mycobacterium species. Partial 16S rRNA gene sequence analysis revealed 100 % similarity between 65 clinical isolates and Mycobacterium sp. MCRO 6 (GenBank accession no. X93032). Even after sequencing the nearly full-length 16S rRNA gene, closest similarity was only 99?6 % to Mycobacterium nonchromogenicum ATCC 19530 T . Sequencing of the nearly full-length 16S rRNA gene, the 16S-23S internal transcribed spacer region and the hsp65 gene did not reveal genotypic identity with the type strains of M. nonchromogenicum, M. terrae or Mycobacterium triviale. Although sequence analysis suggested that these clinical isolates represented a novel species, mycolic acid analysis by HPLC failed to distinguish them from M. nonchromogenicum. Therefore, phenotypic analysis including growth characterization, antibiotic susceptibility testing and biochemical testing was performed. These strains from clinical samples should be recognized as representing a novel species of the genus Mycobacterium, for which the name Mycobacterium arupense sp. nov. is proposed. The type strain is AR30097 T (=ATCC BAA-1242 T =DSM 44942 T ).At the time of writing, the genus Mycobacterium comprises 119 species with validly published names, at least 30 of which have been described within the last 5 years (http:// www.bacterio.cict.fr/m/mycobacterium.html). Despite this rapid increase in the number of newly recognized Mycobacterium species, many additional Mycobacterium species remain to be formally described (Pauls et al., 2003;Tortoli, 2003;Turenne et al., 2004). Many of these unnamed species have been isolated from clinical specimens and need to be correctly characterized for appropriate patient management.In the clinical microbiology laboratory, phenotypic and biochemical testing may not identify Mycobacterium species accurately, as the results of these tests may be identical between different species or may vary depending on the growth conditions employed. Sequencing the 16S rRNA gene of Mycobacterium species has improved the speed and accuracy of identification (Cloud et al., 2002;Turenne et al., 2001;Patel et al., 2000). Sequencing additional targets such as the hsp65 gene and the 16S-23S internal transcribed spacer region 1 (ITS1) has increased our ability to describe novel Mycobacterium species (Turenne et al., 2004;Tortoli, 2003;Ringuet et al., 1999; Mohamed et al., 2005).The purpose of this study was to describe a Mycobacteriumlike organism that appears to be a genotypic match to Abbreviations: FL-HPLC, fluorescence detection HPLC; ITS1, internal transcribed spacer region 1; NTM, non-tuberculous mycobacteria.

Mycobacterium arupense, Mycobacterium heraklionense, and a Newly Proposed Species, “Mycobacterium virginiense” sp. nov., but Not Mycobacterium nonchromogenicum, as Species of the Mycobacterium terrae Complex Causing Tenosynovitis and Osteomyelitis

“…Two isolates (cases 4 and 5, Table 2) underwent complete 16S rRNA gene sequencing as well as secondary gene target sequencing as part of the original study describing M. arupense by Cloud et al in 2006 (28). One of these (AR 30097 T ) is the recognized type strain of M. arupense, and both isolates were a 100% match of the complete 16S rRNA gene to each other and other identified sputum isolates (28). In two other cases partial 16S rRNA gene sequencing was used, with 100% match to the type strain of M. arupense (cases 8 and 13) (31,35).…”

“…There have been approximately 34 additional case reports published since then, identified using nonmolecular methods (3-25), with 14 cases identified using molecular methods (26)(27)(28)(30)(31)(32)(33)(34)(35)(36) (Tables 1 and 2). With the exception of four isolates of M. arupense, including the original description of M. arupense (28), details of the methods and/or explicitly stating a 100% 16S rRNA gene sequence identity to recognized species for the remaining cases with molecular identifications have been absent (Table 2).…”

“…An additional eight new species have been validly published since 2006: Mycobacterium arupense (28), Mycobacterium kumamotonense (36), Mycobacterium heraklionense (1), Mycobacterium senuense (40), Mycobacterium minnesotense (41), My-cobacterium longobardum (1), Mycobacterium algericum (42), and Mycobacterium engbaekii (1). Two other MTC species have been described that currently have no standing in nomenclature: "Mycobacterium paraterrae" (43) and "Mycobacterium sinense" (44).…”

“…Almost all published cases of these 11 new species of the MTC have been respiratory except for the two previously mentioned isolates of M. arupense (including the type strain, ATCC BAA-1242), which were associated with tenosynovitis or hand infections (28). The distribution of these 11 newer species of the complex as well as the two established members (M. terrae and M. nonchromogenicum) among clinical isolates from synovial fluid, tissue, or bone based on DNA sequencing is not known.…”

Comparative evaluation of sequence analysis of 16S rRNA and rpoBgenes for identification of aquatic mycobacteria

“…In addition, the isolate of M. arupense was clustered with slowly growing mycobacteria in the rpoB gene analysis, while the 16S-based tree failed to produce this outcome. Mycobacterium arupense was recently described as an intermediate species, between slowly and rapidly growing mycobacteria (28). However, as it belongs to the M. terraelike group (29), it should be considered a slow-growing Mycobacterium.…”