Mycobacterium chimaera Genomics With Regard to Epidemiological and Clinical Investigations Conducted for an Open Chest Postsurgical Mycobacterium chimaera Infection Outbreak

Abstract

Background: Postsurgical infections due to Mycobacterium chimaera appeared as a novel nosocomial threat in 2015, with a worldwide outbreak due to contaminated heater-cooler units used in open chest surgery. We report the results of investigations conducted in France including whole-genome sequencing comparison of patient and heater-cooler unit isolates.

Methods: We sought M. chimaera infection cases from 2010 onwards through national epidemiological investigations in health care facilities performing cardiopulmonary bypass, together with a survey on good practices and systematic heater-cooler unit microbial analyses. Clinical and heater-cooler unit isolates were subjected to whole-genome sequencing analyzed with regard to the reference outbreak strain Zuerich-1.

Results: Only 2 clinical cases were shown to be related to the outbreak, although 23% (41/175) of heater-cooler units were declared positive for M. avium complex. Specific measures to prevent infection were applied in 89% (50/56) of health care facilities, although only 14% (8/56) of them followed the manufacturer maintenance recommendations. Whole-genome sequencing comparison showed that the clinical isolates and 72% (26/36) of heater-cooler unit isolates belonged to the epidemic cluster. Within clinical isolates, 5-9 nonsynonymous single nucleotide polymorphisms were observed, among which an in vivo mutation in a putative efflux pump gene was observed in a clinical isolate obtained for 1 patient on antimicrobial treatment.

Conclusions: Cases of postsurgical M. chimaera infections have been declared to be rare in France, although heater-cooler units were contaminated, as in other countries. Genomic analyses confirmed the connection to the outbreak and identified specific single nucleotide polymorphisms, including 1 suggesting fitness evolution in vivo.

Keywords: heater-cooler units (HCUs); mmpL; molecular epidemiology; nontuberculous mycobacteria (NTM).

Figure 1.

Overview of studied Mycobacterium chimaera isolates and their origin according to epidemiological investigations. Abbreviations: HCFs, health care facilities; HCU, heater-cooler unit; MAC, Mycobacterium avium complex; WGS, whole-genome sequencing. *Specific identification was not performed systematically for M. chimaera.

Figure 2.

Phylogenetic analysis of Mycobacterium chimaera isolates. A, Maximum parsimony tree (logarithmically scaled) built based on the 55 638 SNP positions found through comparison of the 75 genomes that were mapped to the reference genome (*) of M. chimaera ZUERICH-1. The 52 isolates, including Zuerich-1, belonging to group 1 are gathered in a green circle. B, Maximum parsimony tree (logarithmically scaled) built based on the 694 SNP positions found through comparison of the genomes that were mapped to the reference genome of M. chimaera ZUERICH-1. The number of SNP differences with regard to the epidemic strain M. chimaera ZUERICH-1 is indicated inside each circle. Isolates from HCU water samples are labeled in blue, isolates from clinical samples in purple, and isolates from clinical samples related to the outbreak in red. ^§Two isolates isolated from the same patient. Abbreviations: HCU, heater-cooler unit; SNP, single nucleotide polymorphism.

Figure 3.

Phylogenetic analysis of Mycobacterium chimaera isolates related to P2. Maximum parsimony tree (logarithmically scaled) built based on the 21 106 SNP positions mapped to the genome of M. chimaera ZUERICH-1 found through comparison of the 11 isolates related to patient P2. The number of SNP differences compared with patient P2’s isolate is indicated inside each circle. Isolates from HCU water samples are labeled in blue, and isolates from clinical samples related to the outbreak are labeled in red. Abbreviations: HCU, heater-cooler unit; SNP, single nucleotide polymorphism.