title: Insertion site and distribution of a genomic island conferring DNA phosphorothioation in the Mycobacterium abscessus complex.
abstract: Nearly half of US clinical isolates of the emerging pathogen Mycobacterium abscessus were reported to exhibit smeared DNA during PFGE. This DNA degradation (Dnd) phenotype results from DNA phosphorothioation, a sulfur modification found in other bacteria and conferred by dnd genes located on mobile elements. Putative dnd genes are located on a 19.6 kbp genomic island (GI) in the M. abscessus type strain ATCC 19977. We confirmed that ATCC 19977(T) is Dnd-positive by PFGE and we developed a PCR assay to predict Dnd phenotype. Dnd-positive strains generated an amplicon from dndC whereas Dnd-negative strains generated a bridge amplicon that spanned the GI insertion site, indicating they lacked the entire 'Dnd-GI'. Comparative analyses of sequences from the bridge amplicon with ATCC 19977(T) revealed the Dnd-GI is flanked by 22 bp repeats in M. abscessus sensu stricto and inserted downstream of a tRNA-Ala gene and between inverted repeats. Regions flanking the Dnd-GI were highly conserved within the M. abscessus complex. Bioinformatics studies suggest the Dnd-GI inserted independently into a strain of Mycobacterium massiliense and that other species of mycobacteria also have dnd genes, supporting reports that the Dnd phenotype is common among actinomycetes. Within the M. abscessus complex, Dnd-positive clinical isolates were primarily M. abscessus sensu stricto, and tandem repeat typing indicated these isolates were highly related, confirming previous PFGE studies and revealing a widespread family of strains with significance in human disease.
authors.affiliation: Department of Microbiology, The University of Texas Health Science Center at Tyler, 11937 U.S. Highway 271, Tyler, TX, USA.
authors.forename: Susan T
authors.initials: ST
authors.lastname: Howard
authors.affiliation: Department of Microbiology, The University of Texas Health Science Center at Tyler, 11937 U.S. Highway 271, Tyler, TX, USA.
authors.forename: Kristopher L
authors.initials: KL
authors.lastname: Newman
authors.affiliation: Mycobacteria/Nocardia Laboratory, The University of Texas Health Science Center at Tyler, 11937 U.S. Highway 271, Tyler, TX, USA.|Department of Microbiology, The University of Texas Health Science Center at Tyler, 11937 U.S. Highway 271, Tyler, TX, USA.
authors.forename: Steven
authors.initials: S
authors.lastname: McNulty
authors.affiliation: Mycobacteria/Nocardia Laboratory, The University of Texas Health Science Center at Tyler, 11937 U.S. Highway 271, Tyler, TX, USA.|Department of Microbiology, The University of Texas Health Science Center at Tyler, 11937 U.S. Highway 271, Tyler, TX, USA.
authors.forename: Barbara A
authors.initials: BA
authors.lastname: Brown-Elliott
authors.affiliation: Mycobacteria/Nocardia Laboratory, The University of Texas Health Science Center at Tyler, 11937 U.S. Highway 271, Tyler, TX, USA.|Department of Microbiology, The University of Texas Health Science Center at Tyler, 11937 U.S. Highway 271, Tyler, TX, USA.
authors.forename: Ravikiran
authors.initials: R
authors.lastname: Vasireddy
authors.affiliation: Mycobacteria/Nocardia Laboratory, The University of Texas Health Science Center at Tyler, 11937 U.S. Highway 271, Tyler, TX, USA.|Department of Microbiology, The University of Texas Health Science Center at Tyler, 11937 U.S. Highway 271, Tyler, TX, USA.
authors.forename: Linda
authors.initials: L
authors.lastname: Bridge
authors.affiliation: Mycobacteria/Nocardia Laboratory, The University of Texas Health Science Center at Tyler, 11937 U.S. Highway 271, Tyler, TX, USA.|Department of Microbiology, The University of Texas Health Science Center at Tyler, 11937 U.S. Highway 271, Tyler, TX, USA.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Wallace
mesh_terms: D002876:Chromosomes, Bacterial; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D016521:Electrophoresis, Gel, Pulsed-Field; D023061:Gene Order; D044404:Genomic Islands; D008969:Molecular Sequence Data; D009161:Mycobacterium / Q000235:genetics* / Q000378:metabolism*; D016133:Polymerase Chain Reaction; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D013873:Thionucleotides / Q000378:metabolism*
chemical_list: D004269:DNA, Bacterial; D013873:Thionucleotides