title: Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients.
abstract: In the context of advanced immunosuppression, M. tuberculosis is known to cause detectable mycobacteremia. However, little is known about the intra-patient mycobacterial microevolution and the direction of seeding between the sputum and blood compartments.
  
  
  
  From a diagnostic study of HIV-infected TB patients, 51 pairs of concurrent blood and sputum M. tuberculosis isolates from the same patient were available. In a previous analysis, we identified a subset with genotypic concordance, based on spoligotyping and 24 locus MIRU-VNTR. These paired isolates with identical genotypes were analyzed by whole genome sequencing and phylogenetic analysis.
  
  
  
  Of the 25 concordant pairs (49 % of the 51 paired isolates), 15 (60 %) remained viable for extraction of high quality DNA for whole genome sequencing. Two patient pairs were excluded due to poor quality sequence reads. The median CD4 cell count was 32 (IQR; 16-101)/mm(3) and ten (77 %) patients were on ART. No drug resistance mutations were identified in any of the sequences analyzed. Three (23.1 %) of 13 patients had SNPs separating paired isolates from blood and sputum compartments, indicating evidence of microevolution. Using a phylogenetic approach to identify the ancestral compartment, in two (15 %) patients the blood isolate was ancestral to the sputum isolate, in one (8 %) it was the opposite, and ten (77 %) of the pairs were identical.
  
  
  
  Among HIV-infected patients with poor cellular immunity, infection with multiple strains of M. tuberculosis was found in half of the patients. In those patients with identical strains, whole genome sequencing indicated that M. tuberculosis intra-patient microevolution does occur in a few patients, yet did not reveal a consistent direction of spread between sputum and blood. This suggests that these compartments are highly connected and potentially seed each other repeatedly.
authors: Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda. willyssengooba@gmail.com.|Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium. willyssengooba@gmail.com.|Department of Global Health and Amsterdam, Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands. willyssengooba@gmail.com.
authors: Willy
authors: W
authors: Ssengooba
authors: Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium.|Division of Infectious Diseases, New York University, New York, NY, USA.
authors: Bouke C
authors: BC
authors: de Jong
authors: Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda.
authors: Moses L
authors: ML
authors: Joloba
authors: Department of Global Health and Amsterdam, Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.|KNCV Tuberculosis Foundation, The Hague, Netherlands.
authors: Frank G
authors: FG
authors: Cobelens
authors: Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium.
authors: Conor J
authors: CJ
authors: Meehan
mesh_terms: D017088:AIDS-Related Opportunistic Infections / Q000382:microbiology; D000328:Adult; D015373:Bacterial Typing Techniques / Q000379:methods; D001769:Blood / Q000382:microbiology* / Q000821:virology; D019143:Evolution, Molecular; D005260:Female; D016680:Genome, Bacterial; D005838:Genotype; D015658:HIV Infections / Q000150:complications / Q000382:microbiology*; D015497:HIV-1; D006801:Humans; D020071:Interspersed Repetitive Sequences; D008297:Male; D008875:Middle Aged; D018598:Minisatellite Repeats; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods; D013183:Sputum / Q000382:microbiology*; D014376:Tuberculosis / Q000150:complications / Q000382:microbiology*; D055815:Young Adult
keywords: Ancestral; Concurrent sputum and blood M. tuberculosis; Intra-patient; Microevolution