Genomic analysis of cardiac surgery-associated Mycobacterium chimaera infections in Italy

Abstract

One hundred and twenty-two Mycobacterium chimaera strains isolated in Italy from cardiac surgery-related patients, cardiac surgery-unrelated patients and from heater-cooler units, were submitted to whole-genome sequencing and to subsequent SNP analysis. All but one strains isolated from cardiac surgery-related patients belonged to Subgroup 1.1 (19/23) or Subgroup 1.8 (3/23). Only 28 out of 79 strains isolated from heater-cooler units belonged to groupings other than 1.1 and 1.8. The strains isolated from cardiac surgery-unrelated patients were instead distributed across the phylogenetic tree. Our data, the first on isolates from Italy, are in agreement with a recent large genomic study suggesting a common source, represented by strains belonging to Subgroups 1.1 and 1.8, of cardiac surgery-related Mycobacterium chimaera infections. The strains belonging to groupings other than 1.1 and 1.8 isolated from heather-cooler units evidently resulted from contaminations at hospital level and had no share in the Mycobacterium chimaera outbreak. One Mycobacterium chimaera strain investigated in this study proved distant from every previously known Mycobacterium chimaera Groups (1, 2, 3 and 4) and we propose to assign to a novel group, named "Group 5".

Fig 1. Maximum parsimony tree built from 348 SNP positions of the 108 group1 isolates mapped to the genome of M. chimaera DSM44623 in logarithmic scale.

The M. chimaera genomes from HCUs, patients and Published genome data are indicated in different colours. The two major outbreak subgroups 1.1, 1.8 and also other subgroups are indicated by red labels. A cut-off of 5 SNPs was used to collapse the branches. For this analysis, we combined all group 1 isolates from our study with five other published genomes from LivaNova HCUs, water supply at production site and Maquet HCU production site. We excluded isolates for which a mixed strain population was detected based on signature SNPs [4].

Fig 2. NeighborNet splitstree tree.

NeighborNet splitstree tree built from 60570 SNP positions of representative M. chimaera genomes belonging to Groups 1, 2, 3 and 4, supporting the presence of a previously unreported grouping we named Group 5.