title: Whole genome sequencing of Mycobacterium tuberculosis reveals slow growth and low mutation rates during latent infections in humans.
abstract: Very little is known about the growth and mutation rates of Mycobacterium tuberculosis during latent infection in humans. However, studies in rhesus macaques have suggested that latent infections have mutation rates that are higher than that observed during active tuberculosis disease. Elevated mutation rates are presumed risk factors for the development of drug resistance. Therefore, the investigation of mutation rates during human latency is of high importance. We performed whole genome mutation analysis of M. tuberculosis isolates from a multi-decade tuberculosis outbreak of the New Zealand Rangipo strain. We used epidemiological and phylogenetic analysis to identify four cases of tuberculosis acquired from the same index case. Two of the tuberculosis cases occurred within two years of exposure and were classified as recently transmitted tuberculosis. Two other cases occurred more than 20 years after exposure and were classified as reactivation of latent M. tuberculosis infections. Mutation rates were compared between the two recently transmitted pairs versus the two latent pairs. Mean mutation rates assuming 20 hour generation times were 5.5 X 10(-10) mutations/bp/generation for recently transmitted tuberculosis and 7.3 X 10(-11) mutations/bp/generation for latent tuberculosis. Generation time versus mutation rate curves were also significantly higher for recently transmitted tuberculosis across all replication rates (p = 0.006). Assuming identical replication and mutation rates among all isolates in the final two years before disease reactivation, the u 20 hr mutation rate attributable to the remaining latent period was 1.6 × 10(-11) mutations/bp/generation, or approximately 30 fold less than that calculated during the two years immediately before disease. Mutations attributable to oxidative stress as might be caused by bacterial exposure to the host immune system were not increased in latent infections. In conclusion, we did not find any evidence to suggest elevated mutation rates during tuberculosis latency in humans, unlike the situation in rhesus macaques.
authors.affiliation: Department of Medicine, Rutgers-New Jersey Medical School, Newark, New Jersey, United States of America.
authors.forename: Roberto
authors.initials: R
authors.lastname: Colangeli
authors.affiliation: Department of Biological Sciences, University of Waikato, Hamilton, New Zealand.
authors.forename: Vic L
authors.initials: VL
authors.lastname: Arcus
authors.affiliation: Department of Biological Sciences, University of Waikato, Hamilton, New Zealand.
authors.forename: Ray T
authors.initials: RT
authors.lastname: Cursons
authors.affiliation: Department of Biological Sciences, University of Waikato, Hamilton, New Zealand.
authors.forename: Ali
authors.initials: A
authors.lastname: Ruthe
authors.affiliation: Respiratory Research Unit, Waikato Hospital, Hamilton, New Zealand.
authors.forename: Noel
authors.initials: N
authors.lastname: Karalus
authors.affiliation: Department of Pathology, Waikato Hospital, Hamilton, New Zealand.
authors.forename: Kathy
authors.initials: K
authors.lastname: Coley
authors.affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America.
authors.forename: Shannon D
authors.initials: SD
authors.lastname: Manning
authors.affiliation: Department of Preventive Medicine, Rutgers-New Jersey Medical School, Newark, New Jersey, United States of America.
authors.forename: Soyeon
authors.initials: S
authors.lastname: Kim
authors.affiliation: Department of Medicine, Rutgers-New Jersey Medical School, Newark, New Jersey, United States of America.
authors.forename: Emily
authors.initials: E
authors.lastname: Marchiano
authors.affiliation: Department of Medicine, Rutgers-New Jersey Medical School, Newark, New Jersey, United States of America.
authors.forename: David
authors.initials: D
authors.lastname: Alland
mesh_terms: D004196:Disease Outbreaks; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D055985:Latent Tuberculosis / Q000453:epidemiology* / Q000382:microbiology*; D009154:Mutation; D059645:Mutation Rate; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics*; D009520:New Zealand / Q000453:epidemiology; D010802:Phylogeny; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide