Genomic Analysis of Cardiac Surgery-Associated Mycobacterium chimaera Infections, United States

Abstract

A surgical heater-cooler unit has been implicated as the source for Mycobacterium chimaera infections among cardiac surgery patients in several countries. We isolated M. chimaera from heater-cooler units and patient infections in the United States. Whole-genome sequencing corroborated a risk for these units acting as a reservoir for this pathogen.

Keywords: Mycobacterium chimaera; United States; bacteria; cardiac surgery; genomics; heater–cooler unit; nontuberculous mycobacteria; nosocomial infection; outbreak; tuberculosis and other mycobacteria.

Figure 1

Neighbor Net splitstree of Mycobacterium chimaera isolates: relationships between M. chimaera isolates (n = 124) mapped against the M. chimaera strain CDC 2015–22–71 heater–cooler unit (HCU) reference genome (18,190 single nucleotide polymorphisms [SNPs] in 3,815,639 core positions). Isolates were grouped with a threshold of <500 SNPs to the nearest cluster. Clustered HCU isolates, including the reference strain CDC 2015-22-71, comprise the HCU1 cluster (n = 112) and HCU2 (n = 3). Unclustered isolates include Australian (AUS) HCU isolates (n = 2), USA non-HCU isolates (n=8), and the type strain FI-01069. Scale bar indicates SNPs.

Figure 2

Maximum-likelihood phylogenetic relationships between HCU1 and US non-HCU–associated isolates (651 single-nucleotide polymorphisms [SNPs] in 4,024,718 core positions) as a circular phylogeny. From the center to the perimeter, colored circles indicate the country of origin, isolate source, and HCU genotype(s). Clinical isolate labels use country abbreviation: Australia (AUS), Denmark (DNK), Florence, Italy (FI), New Zealand (NZL), Switzerland (CHE), United Kingdom (GBR), United States (USA); HCU or PAT; isolate number. Non-HCU–associated isolates are from respiratory patients without a history of cardiac surgery. Suspected cases are isolates from blood or tissue samples collected from post–cardiac surgery patients; HCU are isolates collected from hospital HCUs (swabs, water, bioaerosols). Scale bar indicates SNPs. HCU, heater–cooler unit; PAT, suspected case-patient.