Non-tuberculosis Mycobacterial Pulmonary Disease Caused by Mycobacterium kiyosense, a New Species

Abstract

Non-tuberculosis mycobacterial (NTM) pulmonary disease (NTM-PD) is quite common, and newly identified species are being reported increasingly frequently thanks to advances in identification technologies. A 56-year-old woman had mild sputum production showed bronchiectasis with multiple small nodules, consistent with NTM-PD, on chest computed tomography. Mycobacterial species were isolated from the specimens; however, conventional methods could not identify the species. We conducted whole-genome sequencing and identified the NTM isolates as Mycobacterium kiyosense, a species newly registered in 2023 from Japan. She was diagnosed with NTM-PD caused by M. kiyosense and received watchful waiting.

Introduction

The incidence of non-tuberculosis mycobacteria pulmonary disease (NTM-PD) is increasing in many countries as it becomes a more common disease (1). There are approximately 200 species and subspecies in the genus Mycobacteria, and the identification of presumed new species is also increasing with improvements in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and genome analysis techniques (2,3).

We herein report the first case of NTM-PD caused by a newly recognized species, Mycobacterium kiyosense (4).

Case Report

A 56-year-old immunocompetent woman was referred to our hospital because of abnormal chest radiograph findings obtained during a medical checkup. She had mild sputum production, normal vital signs, and no specific medical history. The laboratory data were nonspecific, and her serum level of antibody against the glycopeptidolipid (GPL) core antigen was <0.50 U/mL. Chest radiography revealed multiple nodular shadows in the middle to lower lung fields of the left lung. Chest computed tomography (CT) revealed small centrilobular nodules and bronchiectasis with consolidation in the left lingular and lower lobes (Figure). Although mycobacteria were cultured twice from her sputum, the species could not be identified by conventional methods, such as polymerase chain reaction (PCR) tests for M. avium and M. intracellulare or MALDI-TOF MS. We performed a DNA-DNA hybridization assay (16S rRNA analysis; BML, Tokyo, Japan) and revealed that this mycobacterium showed high homology to M. asiaticum (99.51%), M. vicinigordonae (99.28%), and M. gordonae (99.09%) but could not be precisely identified at the species level.

Figure.

Radiological presentation of a 56-year-old woman. Chest X-ray showed multiple nodular shadows in the middle to lower lung field of the left lung. Chest computed tomography showed small centrilobular nodules and bronchiectasis with consolidation in the left lingular and lower lobe consistent with NTM-PD.

Because the multiple nodular shadows were slightly worsened on CT performed three months later, we collected bronchial lavage using a bronchoscope. Drug susceptibility testing was performed using BrothMIC NTM (Kyokuto Pharmaceutical Industrial, Tokyo, Japan). The mycobacteria isolated from the bronchial lavage fluid had the same drug susceptibility as those isolated from sputum (Table 1), indicating that these were the same unidentified species. Finally, we performed whole-genome sequencing (WGS) of both isolates at the Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, and revealed that the unidentified mycobacteria had 99.9% genomic similarity to M. kiyosense as measured by the average nucleotide identity (ANI) index (5) (Table 2). The patient met the clinical and microbiological criteria for the diagnosis of NTM-PD (1); therefore, we diagnosed her with NTM-PD caused by M. kiyosense. There is no evidence-based treatment for this species, and her clinical symptoms have not worsened. Therefore, we are carefully performing watchful waiting.

Table 1.

Results of Drug Susceptibility Tests.

Drugs	Specimen
	Bronchial lavage fluid MIC (mg/mL)	Sputum MIC (mg/mL)
Ethambutol hydrochloride (EB)	0.5	0.5
Kanamycin monosulfate (KM)	2.0	2.0
Rifampicin (RFP)	≤0.03	≤0.03
Rifabutin (RBT)	0.15	0.15
Levofloxacin hydrate (LVFX)	0.25	0.25
Clarithromycin (CAM)	0.06	0.06
Ethionamide (TH)	4.0	4.0
Amikacin sulfate (AMK)	2.0	2.0
Streptomycin sulfate (SM)	0.5	0.5

Table 2.

Results of the ANI Analysis.

Bronchial lavage fluid
Species		ANI (%)
Mycobacterium sp. 20KCMC460 (Mycobacterium kiyosense)		99.9194
Mycobacterium sp. IWGMT90018-18076 (Mycobacterium kiyosense)		99.8727
Mycobacterium vicinigordonae		86.8728
Mycobacterium paragordonae		82.7476
Mycobacterium avium		82.4237
Mycobacterium gordonae		82.1585
Mycobacterium avium subsp. paratuberculosis		82.0074
Mycobacterium sp. MAC_011194_8550		81.9907
Mycobacterium avium subsp. hominissuis		81.9535
Mycobacterium timonense		81.9463
Sputum
Species		ANI (%)
Mycobacterium sp. 20KCMC460 (Mycobacterium kiyosense)		99.9331
Mycobacterium sp. IWGMT90018-18076 (Mycobacterium kiyosense)		99.8875
Mycobacterium vicinigordonae		86.8402
Mycobacterium paragordonae		82.8064
Mycobacterium avium		82.4187
Mycobacterium gordonae		82.173
Mycobacterium bouchedurhonense		82.0403
Mycobacterium avium subsp. hominissuis		82.0128
Mycobacterium timonense		81.954
Mycobacterium sp. MAC_011194_8550		81.9528

ANI: average nucleotide identity

The ANI values were calculated using FastANI with ‘-fragLen 1000’ option (5).

Discussion

With advances in bacterial isolation and genomic analysis techniques, new species of NTM have been continuously reported, and as of July 2023, 196 NTM species have been identified worldwide (6). Not all NTM are pathogenic to immunocompetent humans. Notably, the present case met the clinical and bacteriological criteria for the diagnosis of NTM-PD (1), and this is the first report of NTM-PD caused by M. kiyosense.

M. kiyosense was identified and reported in Japan in June 2023 (4). Prior to being identified as this species, it was detected in several samples in Japan and is considered a non-pathogenic M. gordonae complex (7). M. gordonae has been suggested to have subtypes based on minute differences in housekeeping genes. Fukano et al. clearly highlighted the differences between M. gordonae and M. kiyosense based on the results of a phylogenetic tree of the 16S rRNA gene, WGS analysis, and ANI analysis (4). They revealed that only M. kiyosense contains the virulence factor mgtC, whereas the other members of M. gordonae complex do not contain it. mgtC has been reported to play an important role in intramacrophage growth in intracellular pathogens such as M. tuberculosis (8). Therefore, M. kiyosense is thought to have different biological characteristics and virulence from other species of M. gordonae complex, and our report supports this hypothesis. Interestingly, this case was a middle-aged immunocompetent woman whose radiographic findings were similar to those of NTM-PD caused by M. intracellulare avium complex.

Our patient was highly susceptible to clarithromycin, rifampicin, rifabutin, levofloxacin, and ethambutol (EB). In contrast, a previous report showed M. kiyosense is moderately resistant to EB (4). No standard treatment regimen has been established, as M. kiyosense has only recently been identified. If the clinical symptoms and/or imaging findings worsen in this case, we plan to start multiple-drug therapy carefully based on the results of these drug sensitivity tests.

To our knowledge, this is the first case of NTM-PD caused by M. kiyosense. NTM-PD caused by an unidentified Mycobacterium species may include diseases caused by this species. To elucidate the clinical course and establish treatment regimens for M. kiyosense, more cases need to be accumulated and analyzed in the future.

The authors state that they have no Conflict of Interest (COI).