Evaluation of INNO-LiPA mycobacteria v2 assay for identification of rapidly growing mycobacteria

Misidentification of Mycobacterium smegmatis as Mycobacterium fortuitum by DNA line probe assay

Optimal management of infection with mycobacterial species requires accurate identification down to complex/species level due to variations in outcomes. Over the last few decades, there have been significant advances in laboratory diagnostics with development of newer and rapid molecular methods. Here we describe a case of Mycobacterium smegmatis that was misidentified as Mycobacterium fortuitum by DNA line probe assay.

Whole-Genome Sequencing Analysis to Identify Infection with Multiple Species of Nontuberculous Mycobacteria

Mixed infection with multiple species of nontuberculous mycobacteria (NTM) is difficult to identify and to treat. Current conventional molecular-based methods for identifying mixed infections are limited due to low specificity. Here, we evaluated the utility of whole-genome sequencing (WGS) analysis to detect and identify mixed NTM infections. Analytical tools used included PubMLST, MetaPhlAn3, Kraken2, Mykrobe-Predictor and analysis of heterozygous SNP frequencies. The ability of each to identify mixed infections of NTM species was compared. Sensitivity was tested using 101 samples (sequence sets) including 100 in-silico simulated mixed samples with various proportions of known NTM species and one sample of known mixed NTM species from a public database. Single-species NTM control samples (155 WGS samples from public databases and 15 samples from simulated reads) were tested for specificity. Kraken2 exhibited 100% sensitivity and 98.23% specificity for detection and identification of mixed NTM species with accurate estimation of relative abundance of each species in the mixture. PubMLST (99% and 96.47%) and MetaPhlAn3 (95.04% and 83.52%) had slightly lower sensitivity and specificity. Mykrobe-Predictor had the lowest sensitivity (57.42%). Analysis of read frequencies supporting single nucleotide polymorphisms (SNPs) could not detect mixed NTM samples. Clinical NTM samples (n = 16), suspected on the basis of a 16S-23S rRNA gene sequence-based line-probe assay (LPA) to contain more than one NTM species, were investigated using WGS-analysis tools. This identified only a small proportion (37.5%, 6/16 samples) of the samples as mixed infections and exhibited only partial agreement with LPA results. LPAs seem to be inadequate for detecting mixed NTM species infection. This study demonstrated that WGS-analysis tools can be used for diagnosis of mixed infections with different species of NTM.

A Case of Surgical Site Infection Caused by Mycobacterium fortuitum, following Herniorrhaphy

Rapidly Growing Mycobacteria (RGM) are opportunistic pathogens found in the environment. Mycobacterium fortuitum, M. chelonae and M.abscessus are the important human pathogens of this group. They cause wound infections, disseminated cutaneous disease, pulmonary infection in patients with cystic fibrosis or bronchiectasis, bone and joint infections and keratitis. Infections due to these Non-Tuberculous Mycobacteria (NTM) are increasingly reported. Post laparoscopic wound infections, mesh site infections and other surgical site infections due to M. fortuitum and M. chelonae have been reported. Usually wound infections due to atypical mycobacteria have delayed onset and do not respond to conventional antibiotics. Identification of RGM can be done by a set of cumbersome biochemical tests, High Performance Liquid Chromatography (HPLC), molecular methods using DNA probes or by Polymerase Chain Reaction (PCR). We here report a case of post-herniorrhaphy wound infection due to M. fortuitum which was identified by molecular method (HAIN mycobacterial species system). This case report underscores the importance of examining Ziehl-Neelsen (ZN) stain of all exudates with sterile culture on day one for non fastidious bacteria. Timely identification can lead to prompt therapy of patients preventing further complications.

Pulmonary infection caused by Mycobacterium neoaurum: the first case in Korea

Mycobacterium neoaurum is rapidly growing mycobacteria that can cause human infections. It commonly causes bloodstream infections in immunocompromised hosts, and unlike other mycobacteria species, it rarely causes pulmonary infections. We confirmed the first pulmonary infection case in Korea caused by M. neoaurum using full-length 16S rRNA gene sequencing.