Using PacBio Sequencing, Scientists Find No Evidence of Horizontal Gene Transfer in Haitian Cholera Strain
Wednesday, July 3, 2013
A new analysis from public health scientists has found that the cholera strain responsible for the 2010 outbreak in Haiti has a limited ability to add to its genetic repertoire through horizontal gene transfer.
The paper, “Evolutionary Dynamics of Vibrio cholerae O1 Following a Single-Source Introduction to Haiti,” from lead author Lee Katz and senior author Cheryl Tarr, both from the US Centers for Disease Control and Prevention, came out this week in mBio, a journal published by the American Society for Microbiology.
Because the 2010 epidemic represents the first known arrival of cholera in Haiti, the outbreak served as an unusual opportunity to study the pathogen from a single point of origin and its subsequent evolution as it spread across the country.
The CDC scientists, together with collaborators at the Public Health Agency of Canada, Mount Sinai School of Medicine, Georgia Institute of Technology, and others, sequenced several cholera isolates from different regions and different stages of the outbreak. Nine of those isolates, plus a reference genome, were sequenced to near-closure on the PacBio® platform.
The data corroborate earlier findings that grouped the Haitian isolates with strains found in Nepal. In Haiti, however, the pathogen showed little in the way of evolution, adopting no new genes or genomic regions through the usual mechanism of horizontal gene transfer, the scientists report. They note that the strain is “severely impaired for transformation”; in addition to the lack of acquired genes in any of the isolates’ genomes, the bacteria failed in lab tests to take up new genetic material through traditional mechanisms.
“A pangenome analysis showed nearly homogeneous genomic content, with no evidence of gene acquisition among Haiti isolates,” the authors write. They add, “It is well accepted that [horizontal gene transfer] is a major force driving evolution in bacteria, including Vibrio; thus, the lack of HGT observed in our study might be surprising.”
The authors also made note of a technical challenge in their work: pulsed-field gel electrophoresis, useful at the outset to verify that the outbreak was caused by a single strain, in time was no longer able to confirm the single founder theory. This issue was addressed by switching to whole genome sequencing for bacterial analysis, making comprehensive surveillance more effective and conclusive.
Read the full paper here.