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The Mycobacterium phlei Genome: Expectations and Surprises.

ABSTRACT: Mycobacterium phlei, a nontuberculosis mycobacterial species, was first described in 1898-1899. We present the complete genome sequence for theM. phlei CCUG21000(T)type strain and the draft genomes for four additional strains. The genome size for all five is 5.3 Mb with 69.4% Guanine-Cytosine content. This is ?0.35 Mbp smaller than the previously reported M. phlei RIVM draft genome. The size difference is attributed partly to large bacteriophage sequence fragments in theM. phlei RIVM genome. Comparative analysis revealed the following: 1) A CRISPR system similar to Type 1E (cas3) in M. phlei RIVM; 2) genes involved in polyamine metabolism and transport (potAD,potF) that are absent in other mycobacteria, and 3) strain-specific variations in the number of ?-factor genes. Moreover,M. phlei has as many as 82 mce(mammalian cell entry) homologs and many of the horizontally acquired genes in M. phlei are present in other environmental bacteria including mycobacteria that share similar habitat. Phylogenetic analysis based on 693 Mycobacterium core genes present in all complete mycobacterial genomes suggested that its closest neighbor is Mycobacterium smegmatis JS623 and Mycobacterium rhodesiae NBB3, while it is more distant toM. smegmatis mc2 155.

SUBMITTER: Das S

PROVIDER: S-EPMC4860684 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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The Mycobacterium phlei Genome: Expectations and Surprises.

Das Sarbashis S Pettersson B M Fredrik BM Behra Phani Rama Krishna PR Ramesh Malavika M Dasgupta Santanu S Bhattacharya Alok A Kirsebom Leif A LA

Genome biology and evolution 20160408 4

Mycobacterium phlei, a nontuberculosis mycobacterial species, was first described in 1898-1899. We present the complete genome sequence for theM. phlei CCUG21000(T)type strain and the draft genomes for four additional strains. The genome size for all five is 5.3 Mb with 69.4% Guanine-Cytosine content. This is ≈0.35 Mbp smaller than the previously reported M. phlei RIVM draft genome. The size difference is attributed partly to large bacteriophage sequence fragments in theM. phlei RIVM genome. Com ...[more]

PMID: 26941228

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Project description:Background: We have previously reported the results of a prospective multi-institutional study on the efficacy of MCNA in patients who recurred after intravesical BCG treatment [1]. Since that publication, a new standardized definition for BCG-unresponsiveness has been established [2]. Objective: We re-analyzed the oncologic outcomes following intravesical MCNA in patients classified as BCG-unresponsive according to the new definition. Methods: For this analysis, we focused on the enrolled patients who satisfied the requirements for BCG Unresponsiveness: i.e. adequate BCG treatment (at least 5/6 induction and 2/3 maintenance instillations) and high grade tumor within 6 months of prior BCG. Treatment course included 6 weekly intravesical instillations of 8 mg MCNA followed by 3 weekly instillations at months 3, 6, 12, 18, and 24. Followup assessments included cystoscopy, urine cytology and biopsy. Patients absent of high grade disease confirmed by central review of biopsy were deemed disease-free. Results: Of the 129 patients enrolled, 94 (68 CIS with/without papillary tumors, 26 papillary only tumors) fit the criteria for the new BCG Unresponsive definition. Overall, disease free survival (DFS) for all BCG unresponsive patients was 48.9% (95% CI 38.0-59.0%) at 6 months, 34.8% (95% CI 24.7-45%) at 1 year and 28.3% (15.7-34.3%) at 2 years post induction. In the group with papillary tumors, DFS measured at months 6, 12, and 24 were: 61.2% (38.2-77.8%), 61.2(38.2-77.8%), and 50.1% (27.5-69%). In the CIS-containing group, the corresponding DFS were: 44.8% (32.3-56.4%), 26.5% (16.3-37.9%), and 16.6% (8.6-26.9%), respectively. Conclusions: For patients who are BCG Unresponsive, MCNA has the potential to render 26.5% of patients with CIS and 61.2% of patients with papillary tumors disease-free for at least 1 year with an intact bladder. The higher efficacy noted in the true BCG-unresponsive cohort than was previously reported with all-comers emphasizes the importance of having clearly defined criteria for clinical trials investigating new intravesical therapies after BCG failure.

Dataset Information

The Mycobacterium phlei Genome: Expectations and Surprises.

Publications

The Mycobacterium phlei Genome: Expectations and Surprises.

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