Whole-genome sequencing and epidemiological analysis do not provide evidence for cross-transmission of mycobacterium abscessus in a cohort of pediatric cystic fibrosis patients

Abstract

Background: Mycobacterium abscessus has emerged as a major pathogen in cystic fibrosis (CF) patients and has been associated with poor clinical outcomes, particularly following lung transplant. We investigated the acquisition of this bacterium in a cohort of pediatric CF patients.

Methods: Demographic and patient location data were used to uncover epidemiological links between patients with genetically related strains of M. abscessus that had been previously typed by variable-number tandem repeat profiling. Whole-genome sequencing was applied to 27 M. abscessus isolates from the 20 patients in this cohort to provide definitive data on the genetic relatedness of strains.

Results: Whole-genome sequencing data demonstrated that M. abscessus isolates from 16 patients were unrelated, differing by at least 34 single-nucleotide polymorphisms (SNPs) from any other isolate, suggesting that independent acquisition events have occurred. Only 2 clusters of very closely related (<25 SNPs) isolates from different patients were seen. The first cluster contained 8 isolates, differing by a maximum of 17 SNPs, from a sibling pair who had intense exposure to each other both inside and outside the hospital. The second cluster contained 3 isolates, differing by a maximum of 24 SNPs, from 2 individuals with no apparent epidemiological links.

Conclusions: We have not demonstrated cross-transmission of M. abscessus within our hospital, except between 1 sibling pair. Alternative routes of acquisition of M. abscessus infection, in particular the environment, require further investigation.

Keywords: Mycobacterium abscessus; VNTR; cross-transmission; cystic fibrosis; whole-genome sequencing.

Figure 1.

Comparison of age of acquisition of Pseudomonas aeruginosa and Mycobacterium abscessus in cohort of pediatric cystic fibrosis patients. A, Age at first acquisition of P. aeruginosa in M. abscessus–negative patients (n = 122) vs age of acquisition of M. abscessus (P < .0001, Mann–Whitney U test). B, Age of acquisition of P. aeruginosa vs acquisition of M. abscessus in all 12 patients who acquired M. abscessus after first contact with hospital (P = .001, Wilcoxon signed-rank test). C, Time in years after first contact with hospital and first acquisition of P. aeruginosa vs acquisition of M. abscessus (n = 12; P = .002, Wilcoxon signed-rank test).

Figure 2.

Exposure of patients who first acquired Mycobacterium abscessus after contact with our center to other M. abscessus-infected patients. Exposure of patients who acquired M. abscessus subsp abscessus (MA) variable-number tandem repeat (VNTR) I (n = 3; A and D), MA VNTR II (n = 3; C and E), and MA VNTR unique strains (n = 5; C and F) to other patients already infected with MA VNTR I, VNTR II, VNTR unique, and M. abscessus subsp massiliense strains. A–C, Total number of bed-days on the same ward at the same time that each patient was with other M. abscessus-infected patients. C–E, Total number of outpatient episodes where patients were with other M. abscessus-infected patients. Abbreviation: OPD, outpatients department.

Figure 3.

A maximum likelihood tree based on single-nucleotide polymorphisms in shared regions from the whole genome of Mycobacterium abscessus isolates from this study (dark blue text) and from the study described by Bryant et al [10] (black text). Three major lineages representing the M. abscessus subsp massiliense, bolletti, and abscessus are shaded in orange, blue, and green, respectively. The scale bar represents the number of substitutions per site across 133 683 variable sites.

Figure 4.

Subtrees from the maximum likelihood tree in Figure 3 representing detailed views of 4 clades where >2 isolates from this study were clustered. Where there are groups of isolates only from the study by Bryant et al [10], these are collapsed and displayed as triangles because they do not represent new data. Isolates from this study are shown in dark blue, and those from the study described by Bryant et al in black. The scale bar represents the number of substitutions per site.