Metagenomic and genomic characterization of extrapulmonary Mycobacterium abscessus infections: a comparative cohort study

Abstract

Introduction

The incidence of Mycobacterium abscessus complex (MABC) infections is rising, becoming a major pathogen of nontuberculous mycobacteria responsible for pulmonary disease (PD) and extrapulmonary disease (ED). However, studies on the clinical characteristics of MABC-ED remain limited.

Methods

A 7-year retrospective analysis was conducted on MABC-ED cases at Zhongshan Hospital in Shanghai, China. We analyzed predisposing factors, clinical features, metagenomic sequencing (MS) results, drug susceptibility testing (DST), and genomic characteristics of MABC-ED patients, comparing the data with those of PD cases.

Results

Among 17 MABC-ED patients, 15 had predisposing risk factors and underlying conditions, with 2 of 3 patients with rheumatic disease showing poor prognosis. The diagnostic performance of metagenomic sequencing for MABC-ED was comparable to that for MABC-PD. However, MABC-ED samples exhibited distinct microbiome features and a more diverse mycobacterial community structure compared to PD. Resistance rates among extrapulmonary MABC isolates were observed as follows: 0% (amikacin), 20% (macrolides), 30% (linezolid), and 40% (cefoxitin). One case showed paradoxical results between erm (41) T28 sequevar and susceptibility phenotype. Genomic analysis revealed no specific dominant circulating clones (DCC) for MABC-ED isolates.

Conclusion

MABC-ED patients commonly present with risk factors and underlying diseases. Metagenomic sequencing diagnosis of MABC-ED poses challenges, and DST and whole genome sequencing data indicate diversity among MABC-ED isolates. Our study provides detailed data on MABC-ED, contributing to a better understanding of its disease characteristics.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-026-13117-9.

Introduction

Mycobacterium abscessus complex (MABC), a rapidly growing species of nontuberculous mycobacteria (NTM), has recently emerged as a major threat, particularly to individuals with cystic fibrosis (CF) in Western countries [1]. With intrinsic multidrug resistance, MABC is considered difficult to treat due to multi-antibiotic resistance for clinicians, and has attracted increasing attention from researchers [2]. While significant progress has been made in understanding pulmonary disease (PD) caused by MABC, challenges persist in the management of extrapulmonary disease (ED) [3].

Unlike PD, MABC-ED presents with diverse, non-specific manifestations (e.g., skin/soft tissue, joints, lymph nodes), leading to low clinical suspicion and frequent oversight. Furthermore, the extended turnaround time of culture hinders its utility for rapid pathogenic diagnosis. Additionally, the sampling procedure for ED diagnosis lacks standardized protocols, resulting in greater diagnostic uncertainty compared to PD. In the field of molecular diagnostics, our previous study [4] demonstrated that while metagenomic sequencing (MS) performs well as a non-targeted, broad-spectrum pathogen detection method, it exhibits lower sensitivity for NTM and requires more complex data interpretation.

The guidelines from the American Thoracic Society and Infectious Diseases Society of America recommended a shorter antibiotic duration (4–6 months) and higher cure rate in MABC-ED compared with PD [5]. Koh reported that this favorable outcome is partly due to the higher proportion of Mycobacterium abscessus subspecies massiliense (MAS) and macrolide susceptibility based on the erm gene [6]. However, Friedland’s report indicates that the severity and prognosis of MABC-ED vary significantly depending on host immune status and the organs involved [7]. Knowledge of precise management strategies for these infections remains limited.

Zhongshan Hospital, a comprehensive hospital with over 2,000 beds located in Shanghai, China, established a modern Infectious Diseases Department in 2016, focusing on bacterial and fungal infections. Since then, we have collected over 30 NTM-ED cases from various departments. Our previous research found that MABC-ED (42.4%) was the most common causative species in ED cases. In this study, we conducted a multifaceted investigation of MABC-ED cases to explore optimal management strategies.

Materials and methods

Patient data and samples

Medical records of NTM-ED patients treated at Zhongshan Hospital from 2016 to 2023 were screened using an electronic database. After excluding cases of non-MABC or failed species identification, and those not meeting the diagnostic criteria for MABC-ED [8], 17 patients were included in the study. All MABC-ED patients had their MABC infections confirmed by culture. Clinical characteristics, drug susceptibility test (DST), metagenomic sequencing testing and whole-genome sequencing (WGS) information were collected. Additionally, the MABC-PD data from our institution were employed for comparative assessment. This retrospective study was approved by the Ethical Committee of Zhongshan Hospital, Fudan University (approval number: B2020-411).

Culturing and DST

All tissue samples underwent standard processing methods, utilizing the MGIT (Mycobacteria Growth Indicator Tube) system for liquid enrichment and employing metagenomic next-generation sequencing (mNGS) for molecular diagnostics. The isolates were identified using matrix-assisted laser desorption/ionization-time of flight mass spectrometry. DST was performed using the Clinical and Laboratory Standards Institute recommended broth microdilution method for MABC [9].

Metagenomic sequencing testing and interpretation

Our metagenomic sequencing data were obtained from a rapid on-site platform in the hospital, where specimens were delivered to the lab bench almost immediately from the bedside. The high-quality reads were aligned to the human reference genome (hg19) via Burrows-Wheeler Alignment to remove the human-derived sequences. The remaining sequences were then mapped to current RefSeq database, which was downloaded from National Center Biotechnology Information (NCBI, http://ftp.ncbi.nlm.nih.gov/genomes/). The database used for this study contained 3446 bacterial species (including 127 mycobacterial species), 4152 viral taxa, 206 fungi, and 140 parasites associated with human diseases.

Interpretation of the metagenomic sequencing data largely relied on the findings of our previous study [9]. For commensal bacteria (such as Prevotella, Veillonella, and Candida), clinical significance is considered only when their relative abundance rate (RAR) exceeds 30% or is at least fourfold higher than that of any other microorganism. For putative pathogens (e.g., Acinetobacter baumannii, Enterobacteriaceae), both RAR > 10% and mapping reads number (MRN) > 6 are required. In contrast, for absolute pathogens such as Mycobacterium tuberculosis and Cryptococcus, as well as viruses, the diagnostic threshold is more sensitive, requiring only RAR > 1% at the species or genus level along with MRN > 6. Specifically for nontuberculous mycobacteria (NTM), a relative ranking criterion is applied, whereby detection within the top 10 at the bacterial genus level is considered positive [4].

Whole-genome sequencing and analysis

Mycobacterium samples were obtained from isolates of clinical specimens. Isolates were subcultured on solid media to obtain multiple colonies for sequencing. Using the Illumina HiSeq ×10 platform, quality-checked DNA samples were constructed with inserts of ~ 400 bp. Next, PE150 (pair-end) sequencing was performed with no less than 100× depth of coverage per sample.

Raw sequencing data were quality analyzed using FastQC [10] (https://github.com/s-andrews/FastQC). The obtained reads were assembled using SPAdes [11]. Macrolide and aminoglycoside resistance were predicted using the mab-ariba database [12], incorporating rrs gene mutations for aminoglycoside resistance detection. The core genome SNPs (single nucleotide polymorphism) was localized to the M. abscessus ATCC 19,977 reference genome (GenBank accession number GCA_000069185) using Snippy (https://github.com/tseemann/ Snippy), and Gubbins [13] was used to infer recombination sites. Phylogenetic trees were computed using RAxML [14], and (GTR)-GAMMA was used as a model to reconstruct maximum likelihood trees. and visualized and annotated using ggtree [15]. Using FastBAPS [16], clusters of samples were identified in the subspecies trees, referencing the dominant circulating clones strains from previous studies [17]. Beta diversity indexes were generated based on the Bray–Curtis algorithm to determine whether significant differences in microbiota existed between two groups, and were visualized using Principal Component Analysis (PCA).

Statistical analysis

Comparative analysis was conducted by Fisher exact test or Kruskal-Wallis test for variables where appropriate.

Results

Clinical characteristics of patients

The primary characteristics of the patients are summarized in Table 1. The majority were female (11/17), with a median age of 49 years (range 13–63 years). Most patients had underlying diseases or potential risk factors, including skin trauma (3/17), plastic-lipodissolve procedures (3/17), rheumatism (3/17), anti-IFN-γ auto-antibody syndrome (3/17) and others (2/17). Among the five cases with disseminated infections (case12, 13, 14, 15, 16), three patients had anti-IFN-γ auto-antibody syndrome, while the other two had diabetes and systemic lupus erythematosus (SLE), respectively. The duration of diagnosis varied widely, ranging from 1 to 36 months (median 3 months), as did the duration of chemotherapy (median,6 months; range 1–36 months). Some cases required a combination of surgical debridement and antimicrobial drugs (Fig. 1a and e).

Table 1.

Characteristics of the 17 patients of this report who presented extra-pulmonary infection caused by Mycobacterium abscessus

Comorbidity and probable exposure history		Participant No./Sex/Age	Infection site	Sample Type	culture	mNGS	Disease Duration at Time of Diagnostic	Duration of chemotherapy	*Treatment outcome
None		1/F/13	Vertebral body	tissue	+	+	1 m	11 m	Good
		2/F/65	Sinus	nasal swab	+	+	1 m	6 m	Poor
Trauma	scalpel treatment	3/M/46	Skin	pus	+	+	3 m	6 m	Good
	stray dog bite	4/F/49	skin+knee joint+inguinal lymph node	pus	+	-	1 m	6 m	Good
	scrub skin	5/M/44	Neck soft tissue	pus	+	+	3 m	4 m	Good
Plastic-lipodissolve		6/F/28	Skin	pus	+	+	3 m	6 m	Good
		7 F/25	Skin	pus	+	-	2 m	8 m	Poor
		8/F/37	Skin	pus	+	-	4 m	9 m	Good
		9/F/38	Skin	pus	+	+	2 m	Loss to follow-up
Rheumatism	AMD	10/M/49	Shoulder joint	pus	+	+	24 m	36 m	Poor
	RA	11/F/59	Right arm	pus	+	+	24 m	1 m	In treatment
	SLE	12/F/50	Vertebral body+multiple lymph nodes	lymph nodes	+	+	36 m	36 m	Poor
Anti-IFN-γ auto-antibody syndrome		13/M/33	Multiple lymph nodes	lymph nodes	+	+	3 m	1 m	In treatment
		14/F/63	Multiple lymph nodes	lymph nodes	+	+	24 m	12 m	Good
		15/F/62	Multiple lymph nodes+skin	lymph nodes	+	-	12 m	6 m	Good
Other	Diabetes	16/M/49	Multiple lymph nodes	lymph nodes	+	+	12 m	7 m	Good
	Advanced lung cancer	17/M/61	Thoracic cavity+mediastinal lymph nodes	lymph nodes	+	+	2 m	4 m	Poor

Abbreviations: F, female; M, male; RA, Rheumatoid Arthritis; SLE, Systemic Lupus Erythematosus; lymph nodes, peripheral lymph nodes

* Treatment outcome The prognosis of superficial infections such as those in the skin and soft tissues was assessed based on the resolution of infectious symptoms, while deep infections were evaluated through imaging follow-up

Fig. 1.

a, Axial T2-weighted magnetic resonance image (MRI) with contrast enhancement demonstrating infection and abscess of the L5-S1 vertebrae, intervertebral space, presacral, pelvic areas and right iliac in a 13-year-old girl. b, Axial T1-weighted MRI demonstrating signs suggestive of right sinusitis in a 65-year-old woman. c, Dog bite wound on the right lower leg and MRI demonstrating inflammation of the soft tissues with effusion in joint cavity in a 49-year woman. d, Skin injury at sites of lipolysis injection and MRI manifestation in a 38-year woman. e, Abscess formation at the foot acupuncture site and Positron Emission Tomography-Computed Tomography (PET-CT) presentation. f, PET-CT and representative images demonstrate disseminated infection in a patient with anti-IFN-γ autoantibody syndrome, involving both superficial and deep lymph nodes throughout the body as well as the skin

The majority of MABC-ED cases exhibited a good prognosis, while 4 out of 17 cases had poor outcome, particularly in those with rheumatism (case 10,12), elderly patients (case 2, Fig. 1b), and end-stage disease (case 17). Notably, patients with anti-IFN-γ auto-antibody syndrome showed favorable treatment outcomes (case 14 and 15, Fig. 1f), even when coupled with systemic infection and co-infection (e.g., Penicillium marneffei and varicella-zoster virus).

Metagenomic sequencing performance comparison of MABC-ED and MABC-PD

A total of 17 extrapulmonary and 42 pulmonary specimens, including sputum and bronchoalveolar lavage fluid (BALF), were analyzed. As shown in Fig. 2a, the metagenomic sequencing positivity rates for MABC-ED and MABC-PD were 69% and 74%, respectively (p = 0.847). Notably, prior to metagenomic sequencing testing, some patients in this study were misdiagnosed with conditions such as tuberculosis (cases 1 and 14), common bacterial infections (case 2, 3 and 6), multiple myeloma (case12) and lymphoma (case 15). This underscores the importance of the metagenomic sequencing technique for diagnosing MABC-ED in patients with atypical symptoms.

Fig. 2.

Performance comparison of metagenomic sequencing in MABC-ED (n=17) and MABC-PD (n=42). Metagenomic sequencing -based information was compared in terms of detection rate (a), MABC burden (b) bacteriome structure by PCA and Mann-Whitney U test (c) and Mycobacteriome structure excluding MABC (d). The Y-axis indicates species relative abundance. MABC, Mycobacterium abscessus complex; PCA, Principal Component Analysis; PD, Pulmonary Disease; ED, Extrapulmonary Disease; SMRNG, Strict Mapping Reads Number of Genus; ns, no significant difference

In line with our previous study, parameters such as strict mapping read number genus (SMRNG) and relative abundance rate (RAR) were used as semiquantitative measures for pathogen burden. SMRNG refers to converting the mapping reads number (MRN) into the number of sequences per 200,000 reads. RAR is calculated as RAR = (MRN × 10^6 / genome size) / Σ (MRN × 10^6 / genome size) [4]. There was no significant difference in MABC SMRNG (p = 0.84) and RAR (p = 0.24) between ED and PD groups (Fig. 2b).

Distinguishable bacteriome between MABC-ED and MABC-PD

To determine whether bacterial distribution differed between the ED and PD groups, we compared beta-diversity using PCA. The bacterial community compositions differed significantly between the two groups (PERMANOVA, 999 permutations, P = 0.001). Additionally, comparison of the bacteria composition at the genera level revealed a higher RAR of Ralstonia (p = 0.001), Bradyrhizobium (p < 0.001), and Burkholderia (p = 0.014) in MABC-ED patients, while MABC-PD patients had relatively higher levels of airway-colonizing bacteria (Fig. 2c).

Although MABC may be pathogenic, many other NTM species are usually non-pathogenic and commonly identified from the environment. Therefore, we next examined the variation in mycobacteriome characteristic based on metagenomic sequencing results. Our findings indicated that MABC-ED samples had higher microbial biomass and a more diverse mycobacterial community structure compared to PD samples (Fig. 2d).

DST results and genetic analyses between MABC-ED and MABC-PD

Since 2020, DST of NTM has been available at our hospital. Ten out of 17 cases were further studied for minimum inhibitory concentration (MIC) distribution. The MIC range and the MIC50 and MIC90 values of each antimicrobial agent for MABC isolates are shown in Table 2. For clarithromycin, 20% of MABC-ED isolates showed inducible resistance, with MIC90 values at day 5 and day 14 being 0.5 µg/mL and 8 µg/mL, respectively. Amikacin and cefoxitin exhibited resistance rates of 0% and 40%, respectively, with MIC90 values of 8 mg/L for amikacin and 128 mg/L for cefoxitin. MABC also showed notably high resistance levels to antibiotics including imipenem (60%), moxifloxacin (90%), ciprofloxacin (90%), doxycycline (90%) and sulfamethoxazole (90%). Comparatively, MABC-ED appeared more susceptible to clarithromycin than MABC-PD (CLA5-MIC, p = 0.45; CLA14-MIC, p = 0.002), while exhibiting more resistance to other drugs. Aggregated MIC distributions of clarithromycin, moxifloxacin, linezolid, amikacin, imipenem and tigecycline in MABC-ED are presented in Fig. 3a.

Table 2.

Results of drug susceptibility testing against MABC

	MABC-ED(n = 10)				MABC-PD(n = 43)
	MIC a range	MIC50a	MIC90a	% resistantb	MIC a range	MIC50a	MIC90a	% resistantb
Clarithromycin, day5	0.06-1	0.12	0.5	0	0.06-16	0.25	2	5.6%
Clarithromycin, day14	0.06-8	0.12	8	20%	0.06-16	8	16	54.6%
Amikacin	2–8	4	8	0	1–16	4	8	0
Linezolid	2–32	8	32	30%	1–32	8	8	18.9%
Cefoxitin	16–128	64	128	40%	4-128	32	128	16.8%
Imipenem	8–64	32	64	60%	2–64	16	64	46.2%
Tobramycin	4–16	8	16	no breakpoint	2–16	8	16	no breakpoint
Tigecycline	0.25-2	0.25	0.5	no breakpoint	0.06-1	0.5	1	no breakpoint
Ciprofloxacin	2–4	4	4	90%	0.5-4	4	4	69.9%
Moxifloxacin	2–8	8	8	90%	0.5-8	4	8	73.4%
Doxycycline	0.5–16	16	16	90%	0.12-16	16	16	89.5%
Sulfamethoxazole	1–8	8	8	90%	1–8	8	8	79.7%

a. MIC, minimum inhibitory concentration (µg/mL); MIC50/90 = MIC required to inhibit the growth of 50% and 90% of the strains, respectively.

b. Breakpoint values are referenced from the Clinical and Laboratory Standards Institute (CLSI) recommendations (clarithromycin, 8 µg/mL; amikacin, 64 µg/mL; cefoxitin, 128 µg/mL; imipenem, 32 µg/mL; linezolid, 32 µg/mL; ciprofloxacin, 4 µg/mL; moxifloxacin, 4 µg/mL; doxycycline, 8 µg/mL༛Sulfamethoxazole, 4 µg/mL)

Fig. 3.

Distribution of MIC and erm(41) genes. a. Distribution of antibiotic MIC in 10 MABC-ED cases. b. Concordance between erm(41) gene mutations and phenotypic drug susceptibility in 6 MABC-ED cases with whole gene sequencing information. Black labels indicate gene truncation or mutation. MIC, Minimum Inhibitory Concentration; CLA, Clarithromycin; AMK, Amikacin; FOX, Cefoxitin; CFX: Cefoxitin; IMI, Imipenem; LZD, Linezolid; TGC, Tigecycline; MOX, Moxifloxacin; CIP, Ciprofloxacin; DOX, Doxycycline;MIN, Minocycline; SMZ, Sulfamethoxazole; TOB, Tobramycin; S, susceptible; I, intermittent; R, resistant. Dotted vertical lines indicate breakpoints of “intermittent”, solid lines of “resistant” according to the Clinical and Laboratory Standards Institute (CLSI)

Genetic analyses of 9 isolates from 6 patients were conducted in the present study. Analysis of drug resistance genes revealed that our strains had no mutations in the rrl and rrs genes, and the results for the erm(41) gene are shown in Fig. 3b. Four MABC isolates were not susceptible to clarithromycin, all without the T28C mutation in the erm(41) gene. Among the other 5 susceptible isolates, four were consistent with genetic results, such as having a truncated erm(41) gene or the T28C mutation. The remaining isolate from a disseminated infection case (case16) showed T28 sequevar, harboring numerous other mutations in erm(41) gene. Notably, longitudinal studies in case 2 revealed a transversion in the C28 sequevar in the fourth month of therapy and failed culture conversion. The patient underwent seven months of intermittent and ineffective antimicrobial therapy due to intolerance to several antimicrobials and prolonged intravenous infusions.

Whole genome sequencing and analysis

Whole genome analysis was conducted on 9 MABC-ED and 56 MABC-PD isolates to construct a phylogenetic tree (Fig. 4). The genomes of PD and ED strains were evenly distributed throughout the phylogenetic tree, with no distinct clustering observed for either group.

Fig. 4.

Phylogenetic tree based on whole-genome in MABC-PD (n = 56) and MABC-ED (n = 9) isolates included in the study. The tip legend in the phylogenetic tree represents the naming of strains in our MABC strain library. Strains labeled with “case” indicate MABC-ED isolates from this study. DCC, Dominant Circulating Clone; ABS1, non-DCC cluster belong to Abscessus Mycobacterium; NON-DCC, no cluster

Among the ED strains, eight were identified as M. abscessus subspecies, while one was identified as M. massiliense subspecies. Eight out of the nine MABC-ED strains belonged to dominant circulating clones, specifically DCC4, DCC5 and DCC6. The remaining strain was part of a local cluster, ABS1 (Fig. 4).

Discussion

Pulmonary disease (PD) is the most common manifestation of NTM infections, but NTM can also cause localized infection of the skin, bones and soft tissues, as well as disseminated infections in patients with severely compromised immune systems. The current ATS/IDSA guidelines review these alternate manifestations but do not specifically address the diagnosis and treatment of NTM-ED. Among the 190 species of NTM, the incidence of MABC infections is on the rise and poses significant challenges due to high antimicrobial resistance [2]. Many previous studies have not differentiated the infection sites of MABC and have included a wide range of management strategies.

Due to the relatively limited research on MABC-ED, its management usually mirrored lessons learned from MABC-PD and other NTM infections. This study is the first to focus on a comparison of MABC-PD and MABC-ED, in terms of clinical characteristics, metagenomic sequencing diagnosis and WGS analysis.

Timely diagnosis and treatment are crucial to prevent multifocal infections and irreversible tissue damage in MABC-ED. The advancement of molecular diagnostic techniques, particularly MS, has accelerated the detection of MABC [18]. Our findings indicate that MABC-ED samples, compared to MABC-PD, exhibited a more diverse and abundant array of environmental NTM species. This aligns with our previous study, which demonstrated that NTM is one of the most challenging pathogens to detect by metagenomic sequencing [4]. Additionally, extrapulmonary metagenomic sequencing is more easily influenced by environmental NTM. Samples from both non-sterile sites (e.g., skin and soft tissues) and theoretically sterile sites (e.g., lymph nodes, joints) are susceptible to contamination with skin-colonizing flora during collection, which may compromise the accuracy of NGS for species-level identification. In our previous study, we attempted to incorporate baseline mycobacteriome information into the bioinformatics pipeline to enhance the specificity of metagenomic sequencing in airway samples. Our current study suggests that baseline mycobacteriome data from extrapulmonary samples is essential for improving standardized interpretation criteria of metagenomic sequencing in MABC-ED patients.

MABC is traditionally considered resistant to multiple antibiotics, and data supporting effective drugs or regimens are very limited. It remains unclear whether antimicrobial susceptibility differs between ED and PD, which is critical for establishing chemotherapy principles. Our isolates showed 100% susceptibility to amikacin in both ED and PD. However, amikacin is an intravenous drug associated with risks of ototoxicity and nephrotoxicity, limiting its use. In this study, macrolides appeared to have a higher susceptibility rate in ED compared to PD in day14, suggesting that ED patients may benefit more from this class of drugs. Although linezolid showed higher resistance in ED (30%) compared to PD (18.9%), it remains a potentially ideal option for ED treatment due to its high drug concentration in bone and tissue. Oral medications such as moxifloxacin, doxycycline and sulfamethoxazole, demonstrated general resistance in both ED and PD patients, consistent with studies from Korea [6]. According to ATS/IDSA guidelines, strains of MABC subsp. abscessus and MABC subsp. bolletii have an erm(41) gene that may predict inducible resistance to macrolides, whereas MABC subsp. massiliense harbors a truncated erm(41) gene resulting in macrolide susceptibility [19]. Interestingly, one case (case14) in our research indicated paradoxical result between T28C sequevar and macrolides inducible resistance, with various other erm(41) gene mutations such as A120G, T159C, and A238G. The findings suggest that the resistance genes recommended by the guidelines do not fully correspond with the phenotypic resistance. Additional genes on erm and rrl, and possibly others beyond these loci, might also affect resistance. Thus, exploring MABC’s resistance genes remains a formidable task.

Moreover, our WGS data revealed that MABC-ED strains belonged to DCC 4–6 rather than DCC 1, which is predominant in MABC-PD patients from western countries [17]. These findings indicate that ED isolates are phylogenetically diverse and distributed across various DCCs, reflecting a wide genetic diversity within the MABC species complex.

MABC-ED almost always presents in patients with underlying immunodeficiency, which may be acquired or genetic. The host immune response aims to reduce infection and clear pathogens, but MABC can adaptively evolve and alter normal host pathways to survive immune stress. The outcome of MABC-ED is determined by complex interactions among the pathogen, host, and treatment factors. Drug susceptibility alone may not precisely predict treatment outcomes. Our understanding of the immune characteristics in MABC-ED patients remains limited, with clear immunosuppression observed in only a subset of cases. In this study, we elaborated underlying disease or possible risk factors of participants. It’s notable that rheumatic patients appeared to have poorer prognosis despite prolonged chemotherapy, whereas patients with anti-IFN-γ auto-antibody syndrome were usually cured after antimicrobial treatment. A particularly interesting case in our cohort involved a patient with sinusitis, who had no obvious risk factors but experienced treatment failure and developed macrolide-resistant mutations within the lineage after four months of chemotherapy. The disappointing outcome in this case may be attributed to the patient’s advanced age (65 years) and drug intolerance. Our study enhances our understanding of the relationships among these elements. Beside the development of novel antimicrobial agents and bacteriophages, host-directed therapy also holds promise for improving the prognosis of MABC-ED.

Conclusion

This study is the first to compare MABC-PD and MABC-ED in mainland China. MS results from MABC-ED patients exhibited greater mycobacterial diversity, complicating their interpretation. MABC-ED isolates suggested greater resistance to non-macrolide drugs, and rheumatism was potentially linked to poorer prognosis. WGS data revealed significant diversity among MABC-ED isolates. Our study offers insights and future directions for MABC-ED research.

Supplementary Information

Below is the link to the electronic supplementary material.

Abbreviations

MABC

Mycobacterium abscessus complex

NTM

Nontuberculous mycobacteria

DCC

Dominant Circulating Clone

CF

Cystic fibrosis

PD

Pulmonary Disease

ED

Extrapulmonary Disease

MS

Metagenomic sequencing

DST

Drug susceptibility testing

MAS

Mycobacterium abscessus subspecies massiliense

WGS

Whole genome sequencing

MGIT

Mycobacteria growth indicator tube

mNGS

Next-generation sequencing

BALF

Bronchoalveolar lavage fluid

SMRNG

Strict mapping read number genus

RAR

Relative abundance rate

MIC

Minimum inhibitory concentration

CLSI

Clinical and Laboratory Standards Institute

Author contributions

Y. C. wrote the original draft and completed visualization, methodology, investigation, data curation and conceptualization. R. B., W. J., X. Y. and L. Q. collaborated on investigation and data curation. J. P., Y. Y., J. S., T. F., Y. M.,C. Z. assisted in data curation. Q. M. and B. H. took part in writing review & editing, methodology, funding acquisition and conceptualization. B. H. also accomplished supervision. All authors have approved the final version of manuscript.

Funding

This work was supported by the Shanghai Hospital Development Center Foundation (SHDC22024315).

Data availability

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

Declarations

Ethics approval and consent to participate

The study was approved by the Ethical Committee of Zhongshan Hospital, Fudan University (approval number: B2020-411). All study participants had informed consent. Informed consent was obtained from all subjects and/or their legal guardian(s).

Consent for publication

Written informed consent for publication was obtained from all participants and/or their legal guardians.

Competing interests

The authors declare no competing interests.