A variable-number tandem-repeat (VNTR) typing assay for the differentiation of Mycobacterium abscessus strains was developed. This assay showed complete reproducibility, locus stability, and a discriminatory power (Hunter-Gaston discriminatory index [HGDI] of 0.9563) that is superior to that of multilocus sequencing. It is a promising tool for the investigation of Mycobacterium abscessus epidemiology and nosocomial outbreaks.

Mycobacterium abscessus, a rapid-growing non-tuberculous mycobacterium, has been the cause of sporadic and outbreak infections world-wide. The subspecies in M. abscessus complex (M. abscessus, M. massiliense, and M. bolletii) are associated with different biologic and pathogenic characteristics and are known to be among the most frequently isolated opportunistic pathogens from clinical material. To date, the evolutionary forces that could have contributed to these biological and clinical differences are still unclear. We compared genome data from 243 M. abscessus strains downloaded from the NCBI ftp Refseq database to understand how the microevolutionary processes of homologous recombination and positive selection influenced the diversification of the M. abscessus complex at the subspecies level. The three subspecies are clearly separated in the Minimum Spanning Tree. Their MUMi-based genomic distances support the separation of M. massiliense and M. bolletii into two subspecies. Maximum Likelihood analysis through dN/dS (the ratio of number of non-synonymous substitutions per non-synonymous site, to the number of synonymous substitutions per synonymous site) identified distinct genes in each subspecies that could have been affected by positive selection during evolution. The results of genome-wide alignment based on concatenated locally-collinear blocks suggest that (a) recombination has affected the M. abscessus complex more than mutation and positive selection; (b) recombination occurred more frequently in M. massiliense than in the other two subspecies; and (c) the recombined segments in the three subspecies have come from different intra-species and inter-species origins. The results lead to the identification of possible gene sets that could have been responsible for the subspecies-specific features and suggest independent evolution among the three subspecies, with recombination playing a more significant role than positive selection in the diversification among members in this complex.

Objective Basal stem rot disease causes severe economic losses to oil palm production in South-east Asia and little is known on the pathogenicity of the pathogen, the basidiomyceteous Ganoderma boninense. Our data presented here aims to identify both the house-keeping and pathogenicity genes of G. boninense using Illumina sequencing reads. Description The hemibiotroph G. boninense establishes via root contact during early stage of colonization and subsequently kills the host tissue as the disease progresses. Information on the pathogenicity factors/genes that causes BSR remain poorly understood. In addition, the molecular expressions corresponding to G. boninense growth and pathogenicity are not reported. Here, six transcriptome datasets of G. boninense from two contrasting conditions (three biological replicates per condition) are presented. The first datasets, collected from a 7-day-old axenic condition provide an insight onto genes responsible for sustenance, growth and development of G. boninense while datasets of the infecting G. boninense collected from oil palm-G. boninense pathosystem (in planta condition) at 1 month post-inoculation offer a comprehensive avenue to understand G. boninense pathogenesis and infection especially in regard to molecular mechanisms and pathways. Raw sequences deposited in Sequence Read Archive (SRA) are available at NCBI SRA portal with PRJNA514399, bioproject ID.

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Mycobacterium massiliense is a rapidly growing mycobacterial species. The pathogenicity of this subspecies is not well known. We report here the annotated genome sequence of M. massiliense strain M18, which was isolated from a lymph node biopsy specimen from a Malaysian patient suspected of having tuberculous cervical lymphadenitis. Mycobacterium massiliense is one of three subspecies of M. abscessus, the other two being M. abscessus sensu stricto and M. bolletii (3,4,8). These subspecies are closely related genetically but exhibit different drug susceptibilities (3,7,9). Their differentiation depends mainly on DNA polymorphism in the rpoB, hsp65, sodA, recA, and secA genes or in the 16S-23S rRNA internal transcribed spacer (1,2,6,8).M. massiliense has been associated with pulmonary and soft tissue infections, including outbreaks of infections related to surgical procedures and medical devices (3, 7, 9). It has been reported to be susceptible to doxycycline and clarithromycin (3), in contrast to M. bolletii, which has been described as highly resistant to antimicrobial drugs, including clarithromycin (4).We sequenced the complete genome of M. massiliense M18 to further study phylogenetic relationships and the genetic factors responsible for pathogenicity. M. massiliense M18 was isolated from a lymph node biopsy specimen from a Malaysian patient who was investigated for cervical lymphadenitis. The biopsy specimen tissue showed granulomatous inflammation and acid-fast bacilli which grew on Lowenstein-Jensen medium within a week of incubation at 36°C. The identification of the isolate as M. massiliense was based on its hsp65 gene sequence, which was identical to that of the M. massiliense CIP 108297 reference strain, and its rpoB gene sequence, which showed an only 2-bp difference from the reference strain.To sequence the genome of M. massiliense M18, we used a shotgun sequencing method and Illumina Genome Analyzer 2X technology. A total of 19,111,625 Illumina sequencing reads were generated. These short sequences were assembled with Genomics Workbench 4.9, resulting in 34 contigs with the following quality measurements: an N25 contig size of 1,797,984 bp, an N50 contig size of 833,393 bp, and an N75 contig size of 218,930 bp. Automated annotation was done by using the Rapid Annotation and Subsystem Technology (RAST) server (5).The M. massiliense M18 genome sequence is 4,886,939 bp in length with 4,853 predicted coding sequences. There are 45 tRNAs and 3 rRNAs as predicted by the RAST pipeline. The automated annotation of this genome by the RAST server revealed that this genome may contain many genes encoding proteins that are categorized in the subsystem category of amino acids and derivatives (412 genes), followed by cofactors, vitamins, prosthetic groups, and pigments (324 genes). There are 37 genes encoding products that may be involved in virulence, disease, and defense, of which 24 are linked with resistance to antibiotics and toxic compounds and 13 are involved in invasion and intracellular resistance.Nucleo...