Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru

Background Multidrug-resistant tuberculosis poses a major threat to the success of tuberculosis control programs worldwide. Understanding how drug-resistant tuberculosis evolves can inform the development of new therapeutic and preventive strategies. Methods Here, we use novel genome-wide analysis techniques to identify polymorphisms that are associated with drug resistance, adaptive evolution and the structure of the phylogenetic tree. A total of 471 samples from different patients collected between 2009 and 2013 in the Lima suburbs of Callao and Lima South were sequenced on the Illumina MiSeq platform with 150bp paired-end reads. After alignment to the reference H37Rv genome, variants were called using standardized methodology. Genome-wide analysis was undertaken using custom written scripts implemented in R software. Results High quality homoplastic single nucleotide polymorphisms were observed in genes known to confer drug resistance as well as genes in the Mycobacterium tuberculosis ESX secreted protein pathway, pks12, and close to toxin/anti-toxin pairs. Correlation of homoplastic variant sites identified that many were significantly correlated, suggestive of epistasis. Variation in genes coding for ESX secreted proteins also significantly disrupted phylogenetic structure. Mutations in ESX genes in key antigenic epitope positions were also found to disrupt tree topology. Conclusion Variation in these genes have a biologically plausible effect on immunogenicity and virulence. This makes functional characterization warranted to determine the effects of these polymorphisms on bacterial fitness and transmission.

[1]  S Niemann,et al.  Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a TBNET/RESIST-TB consensus statement. , 2016, The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease.

[2]  Julian Parkhill,et al.  Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data , 2016, bioRxiv.

[3]  M. Kendall,et al.  Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution , 2015, bioRxiv.

[4]  Tal Galili,et al.  dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering , 2015, Bioinform..

[5]  Michelle Kendall,et al.  Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution , 2015, bioRxiv.

[6]  C. Dye,et al.  Transmission of Multidrug-Resistant and Drug-Susceptible Tuberculosis within Households: A Prospective Cohort Study , 2015, PLoS medicine.

[7]  Nalin Rastogi,et al.  The Association between Mycobacterium Tuberculosis Genotype and Drug Resistance in Peru , 2015, PloS one.

[8]  Jolyon Holdstock,et al.  Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples , 2015, Journal of Clinical Microbiology.

[9]  Nathan D. Price,et al.  The DNA-binding network of Mycobacterium tuberculosis , 2015, Nature Communications.

[10]  S. Molin,et al.  Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis , 2014, Nature Genetics.

[11]  Jayarama,et al.  The coffee genome provides insight into the convergent evolution of caffeine biosynthesis , 2014, Science.

[12]  D. Weiner,et al.  Multivalent TB vaccines targeting the esx gene family generate potent and broad cell-mediated immune responses superior to BCG , 2014, Human vaccines & immunotherapeutics.

[13]  Derrick E. Wood,et al.  Kraken: ultrafast metagenomic sequence classification using exact alignments , 2014, Genome Biology.

[14]  Hiroki Ando,et al.  A silent mutation in mabA confers isoniazid resistance on Mycobacterium tuberculosis , 2014, Molecular microbiology.

[15]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[16]  Jukka Corander,et al.  Evolution and transmission of drug resistant tuberculosis in a Russian population , 2014, Nature Genetics.

[17]  Razvan Sultana,et al.  Genomic Analysis Identifies Targets of Convergent Positive Selection in Drug Resistant Mycobacterium tuberculosis , 2013, Nature Genetics.

[18]  P. Provero,et al.  Genome-wide signatures of convergent evolution in echolocating mammals , 2013, Nature.

[19]  J. Pedrosa,et al.  Evidence for diversifying selection in a set of Mycobacterium tuberculosis genes in response to antibiotic- and nonantibiotic-related pressure. , 2013, Molecular biology and evolution.

[20]  Christopher J. Marx,et al.  Good Codons, Bad Transcript: Large Reductions in Gene Expression and Fitness Arising from Synonymous Mutations in a Key Enzyme , 2012, Molecular biology and evolution.

[21]  Stephen D. Bentley,et al.  Microevolution of extensively drug-resistant tuberculosis in Russia. , 2012, Genome research.

[22]  Thibaut Jombart,et al.  adegenet 1.3-1: new tools for the analysis of genome-wide SNP data , 2011, Bioinform..

[23]  J. Rougemont,et al.  Comparative Genomics of esx Genes from Clinical Isolates of Mycobacterium tuberculosis Provides Evidence for Gene Conversion and Epitope Variation , 2011, Infection and Immunity.

[24]  Klaus Peter Schliep,et al.  phangorn: phylogenetic analysis in R , 2010, Bioinform..

[25]  F. Balloux,et al.  Discriminant analysis of principal components: a new method for the analysis of genetically structured populations , 2010, BMC Genetics.

[26]  Stefan Niemann,et al.  MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria , 2010, Nucleic Acids Res..

[27]  Julian Parkhill,et al.  Evolution of MRSA During Hospital Transmission and Intercontinental Spread , 2010, Science.

[28]  J. Cox,et al.  Comprehensive Functional Analysis of Mycobacterium tuberculosis Toxin-Antitoxin Systems: Implications for Pathogenesis, Stress Responses, and Evolution , 2009, PLoS genetics.

[29]  V. Arcus,et al.  The vapBC operon from Mycobacterium smegmatis is an autoregulated toxin-antitoxin module that controls growth via inhibition of translation. , 2009, Journal of molecular biology.

[30]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[31]  George M Church,et al.  Tuberculosis Drug Resistance Mutation Database , 2009, PLoS medicine.

[32]  J. Piatigorsky.  A Genetic Perspective on Eye Evolution: Gene Sharing, Convergence and Parallelism , 2008, Evolution: Education and Outreach.

[33]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[34]  M. James,et al.  The molecular structure of Rv1873, a conserved hypothetical protein from Mycobacterium tuberculosis, at 1.38 A resolution. , 2006, Acta crystallographica. Section F, Structural biology and crystallization communications.

[35]  A. R. Escombe,et al.  Microscopic-Observation Drug-Susceptibility Assay for the Diagnosis of TB , 2008 .

[36]  Nalin Rastogi,et al.  Proposal for Standardization of Optimized Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis , 2006, Journal of Clinical Microbiology.

[37]  Alexandros Stamatakis,et al.  Phylogenetic models of rate heterogeneity: a high performance computing perspective , 2006, Proceedings 20th IEEE International Parallel & Distributed Processing Symposium.

[38]  Loren H. Rieseberg,et al.  Parallel genotypic adaptation: when evolution repeats itself , 2005, Genetica.

[39]  M. Cynamon,et al.  The Largest Open Reading Frame (pks12) in the Mycobacterium tuberculosis Genome Is Involved in Pathogenesis and Dimycocerosyl Phthiocerol Synthesis , 2003, Infection and Immunity.

[40]  T. Ottenhoff,et al.  Epitope Mapping of the Immunodominant Antigen TB10.4 and the Two Homologous Proteins TB10.3 and TB12.9, Which Constitute a Subfamily of the esat-6 Gene Family , 2002, Infection and Immunity.

[41]  D. Berg,et al.  Rapid, Efficient Detection and Drug Susceptibility Testing of Mycobacterium tuberculosis in Sputum by Microscopic Observation of Broth Cultures , 2000, Journal of Clinical Microbiology.

[42]  S. Cole,et al.  Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays , 1999, Molecular microbiology.

[43]  D van Soolingen,et al.  Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology , 1997, Journal of clinical microbiology.

[44]  B. Efron,et al.  Bootstrap confidence levels for phylogenetic trees. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[45]  B. Efron,et al.  Bootstrap confidence levels for phylogenetic trees. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Stefan Niemann,et al.  Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes , 2011 .

[47]  James E Gomez,et al.  M. tuberculosis persistence, latency, and drug tolerance. , 2004, Tuberculosis.