Mixed infection of three nontuberculous mycobacteria species identified by metagenomic next-generation sequencing in a patient with peritoneal dialysis-associated peritonitis: a rare case report and literature review

Abstract

Background: Peritonitis caused by nontuberculous mycobacteria (NTM) is an infrequent but important complication in patients undergoing peritoneal dialysis (PD). There has been no report of mixed infections with multiple NTM. Peritoneal dialysis-associated peritonitis (PDAP) caused by Mycobacterium abscessus is more common than that caused by M. smegmatis and M. goodii.

Case presentation: This case concerns a patient with PDAP caused by gram-positive bacilli, which could not be identified at the species level in successive detections of initial peritoneal effluent. Later, M. smegmatis was detected with no sensitivity results in bacterial culture. However, metagenomic next-generation sequencing (mNGS) and first whole-genome sequences indicated that there were three species coexisting in the culture, including M. smegmatis (24,708 reads), M. abscessus (9224 reads), and M. goodii (8305 reads). This is the first case of PDAP with specific evidence that conventional detection methods isolated a poorly pathogenic NTM, whereas mNGS and first whole-genome sequences identified multiple NTM. Pathogenic bacteria might not be detected using conventional methods due to their lower abundance. This case report is the first description of mixed infections with more than two species of NTM during PDAP.

Conclusions: PDAP caused by multiple NTM is rare, and the diagnosis is difficult. When NTM are isolated by conventional tests in patients who are suspected of infection, clinicians should be vigilant, and further tests should be performed to determine the presence of rare or even previously unknown bacteria, for which the quantity is relatively low, but the pathogenicity is high. The rare pathogen may be a primary agent in causing such complications.

Keywords: Case report; Mixed infections; Nontuberculous mycobacteria; Peritoneal dialysis; Peritonitis.

Fig. 1

The diagnosis and treatment process of the patient and etiology testing. a Clinical course of the patient. LEV: levofloxacin; SCF: cefoperazone sulbactam; MFX: moxifloxacin; AMK: amikacin; CXT: cefoxitin; ab: abdominal dropsy; sp.: sputum; iv: intravenous; ip: intraperitoneal; ↙ means inject vancomycin 2 g into peritoneal cavity each time. b PCR results of three fragments for each of the three bacteria on agarose gel electrophoresis: NTC: No Template Control, S1: Target fragment 1 of Mycobacterium smegmatis which is 322 bp; S2: Target fragment 2 of Mycobacterium smegmatis which is 308 bp; S3: Target fragment 3 of Mycobacterium smegmatis which is 148 bp; G1: Target fragment 1 of Mycobacterium goodii which is 229 bp; G2: Target fragment 2 of Mycobacterium goodii which is 840 bp; G3: Target fragment 3 of Mycobacterium goodii which is 150 bp; A1: Target fragment 1 of Mycobacterium abscessus which is 1061 bp; A2: Target fragment 2 of Mycobacterium abscessus which is 320 bp; A3: Target fragment 3 of Mycobacterium abscessus which is 133 bp