Genomic Analysis of a Hospital-Associated Outbreak of Mycobacterium abscessus: Implications on Transmission

Abstract

Whole-genome sequencing (WGS) has recently been used to investigate acquisition of Mycobacterium abscessus. Investigators have reached conflicting conclusions about the meaning of genetic distances for interpretation of person-to-person transmission. Existing genomic studies were limited by a lack of WGS from environmental M. abscessus isolates. In this study, we retrospectively analyzed the core and accessory genomes of 26 M. abscessus subsp. abscessus isolates collected over 7 years. Clinical isolates (n = 22) were obtained from a large hospital-associated outbreak of M. abscessus subsp. abscessus, the outbreak hospital before or after the outbreak, a neighboring hospital, and two outside laboratories. Environmental M. abscessus subsp. abscessus isolates (n = 4) were obtained from outbreak hospital water outlets. Phylogenomic analysis of study isolates revealed three clades with pairwise genetic distances ranging from 0 to 135 single-nucleotide polymorphisms (SNPs). Compared to a reference environmental outbreak isolate, all seven clinical outbreak isolates and the remaining three environmental isolates had highly similar core and accessory genomes, differing by up to 7 SNPs and a median of 1.6% accessory genes, respectively. Although genomic comparisons of 15 nonoutbreak clinical isolates revealed greater heterogeneity, five (33%) isolates had fewer than 20 SNPs compared to the reference environmental isolate, including two unrelated outside laboratory isolates with less than 4% accessory genome variation. Detailed genomic comparisons confirmed environmental acquisition of outbreak isolates of M. abscessus subsp. abscessus. SNP distances alone, however, did not clearly differentiate the mechanism of acquisition of outbreak versus nonoutbreak isolates. We conclude that successful investigation of M. abscessus subsp. abscessus clusters requires molecular and epidemiologic components, ideally complemented by environmental sampling.

Keywords: Mycobacterium abscessus; hospital outbreak; infection prevention; nontuberculous mycobacteria; whole-genome sequencing.

FIG 1

Phylogenomic analysis of study cohort including outbreak and control M. abscessus subsp. abscessus isolates. (A) Genome-wide SNP data from study isolates with genetic inclusion criteria (n = 26) and isolates without genetic inclusion criteria (n = 22) were analyzed using the neighbor-joining (NJ) method. The x axis represents SNP distance. Outgroup isolates of M. abscessus subsp. massiliense (*) and M. abscessus subsp. bolletii (**) were included. The clade with the previously described “dominant circulating clone,” including the M. abscessus subsp. abscessus type strain ATCC 19977^T, is labeled in yellow. (B) Study isolates with genetic inclusion criteria were analyzed in detail. Sample categories are designated shapes, and color-coded labels are indicated for environmental (red) and within outbreak (brown) isolates. Bootstrap support values from 100 replicate searches are shown on selected nodes (values of >50), and three genetic clades are labeled. Suspected U.S. state of acquisition is given in parentheses. Abbreviations: AO, after outbreak; BO, before outbreak; C, clinical; E, environmental; NH, neighboring hospital; OL, outside laboratory; P, phase of outbreak.

FIG 2

Genomic similarities of M. abscessus subsp. abscessus isolates in the study cohort by isolate categories. (A) Genome-wide SNP distances relative to a reference environmental strain collected during phase 1 of the outbreak (P1-E1) are shown on the y axis by sample categories (x axis). The previously described 20-bp SNP threshold is shown as a red dashed line. (B) Accessory genome variation for all isolates compared to P1-E1 is shown on the y axis as percent accessory genes. Sample categories are indicated on the x axis. The percent accessory gene threshold (4%) that includes 90% of clinical outbreak isolates is shown as a blue dashed line. (C) Integrated scatterplot of core genome SNPs versus percent accessory genes relative to P1-E1. Samples are color coded by sample category, and threshold lines are indicated as for panels A and B. Abbreviations: AO, after outbreak; BO, before outbreak; C, clinical; E, environmental; NH, neighboring hospital; OL, outside laboratory; P, phase of outbreak.

FIG 3

Clustering of M. abscessus subsp. abscessus study isolates by accessory genes. Accessory genes (n = 1,766) identified among study isolates (n = 26) were analyzed by hierarchical cluster analysis using a Euclidean distance metric. The dendrogram on the left shows the clustering pattern of isolates (rows) based on gene content, and the heat map illustrates the presence (blue) or absence (light yellow) of accessory genes (columns). Suspected U.S. state of acquisition is given in parentheses. Abbreviations: AO, after outbreak; BO, before outbreak; C, clinical; E, environmental; NH, neighboring hospital; OL, outside laboratory; P, phase of outbreak.