Delineating Mycobacterium abscessus population structure and transmission employing high-resolution core genome multilocus sequence typing

Abstract

Mycobacterium abscessus is an emerging multidrug-resistant non-tuberculous mycobacterium that causes a wide spectrum of infections and has caused several local outbreaks worldwide. To facilitate standardized prospective molecular surveillance, we established a novel core genome multilocus sequence typing (cgMLST) scheme. Whole genome sequencing data of 1991 isolates were employed to validate the scheme, re-analyze global population structure and set genetic distance thresholds for cluster detection and taxonomic identification. We confirmed and amended the nomenclature of the main dominant circulating clones and found that these also correlate well with traditional 7-loci MLST. Dominant circulating clones could be linked to a corresponding reference genome with less than 250 alleles while 99% of pairwise comparisons between epidemiologically linked isolates were below 25 alleles and 90% below 10 alleles. These thresholds can be used to guide further epidemiological investigations. Overall, the scheme will help to unravel the apparent global spread of certain clonal complexes and as yet undiscovered transmission routes.

The small non-coding RNA B11 regulates multiple facets of Mycobacterium abscessus virulence

“…Examination of three additional sets of publicly available clinical M . abscessus genome sequences totaling 750 patients revealed 17 additional isolates with B11 mutations ( S4 and S5 Tables), indicating a similar frequency of B11 mutations as observed in the Danish and Irish datasets (~2.3–2.5%) [ 63 – 70 ]. While some additional loop mutants were observed, the B11 del1 and B11 ins1 mutations described above were two of the three most prevalent types.…”

The problem of Mycobacterium abscessus complex: multi-drug resistance, bacteriophage susceptibility and potential healthcare transmission

“…Further bioinformatics comparison ( File S4 ) of our samples with all the DCC1 strains ( n = 330) used in a previous paper [ 24 ] showed most strains having a high number of SNPs difference compared with our database, with none showing a difference of <10 SNPs with any samples in our collection.…”

“…The produced phylogenetic tree was visualized using FigTree and iTOL [ 22 ]. DCCs were identified by analysing genetic distances to reference strains as defined previously [ 7 , 23 , 24 ].…”

“…The phylogeny of 90 M. abscessus strains with reference strains is shown and each is assigned to dominant circulating clones (DCC1–DDC7) as defined previously [ 7 ]. Strains chosen to represent previously characterized dominant circulating clones are the following: ATCC19977 for DCC1, GD54 for DCC2, G220 and JHN_AB_0023_1 for DCC3, 976 for DCC4, 1100 for DCC5, A47 for DCC6 and FLAC047 for DCC7 as performed in previous studies [ 24 ]. Strain subspecies designations are shown ( massiliense, bolletii, abscessus ).…”

Epidemiological Investigation of Hospital Transmission of Corynebacterium striatum Infection by Core Genome Multilocus Sequence Typing Approach

“…Therefore, it is necessary to define an “outbreak threshold” based on cgMLST to identify strains from the same outbreak and closely related isolates and to investigate the nosocomial spread of C. striatum . According to previous research on outbreak investigation based on cgMLST, the number of allelic differences among outbreak-related strains is generally less than 40, as isolates from the same outbreak are very closely related ( 35 – 41 ). Therefore, the clustering efficiency of 1 and 40 allelic differences is measured by calculating the Dunn index (DI) ( 42 ) (Fig.…”