A couple of months ago, my institution hosted a one-day symposium on phylogenetics. One of the speakers was John Avise, a member of the National Academy of Sciences and the individual generally credited with originating the field of phylogeography. His talk and those of two other speakers were focused on subjects most typically regarded as part of biology, not medicine. However, the fourth lecturer on the program applied some of the same methods and patterns of thought to the interactions between HIV and its human hosts, thereby illustrating the potential relevance of phylogenetic analysis to matters of clinical significance. A recent paper in Science (Harris et al., 2010) provides another such example.

Methicillin-resistant Staphylococcus aureus (MRSA) is a pathogen of major significance in many countries. According to Maryn McKenna (2010), author of a recent book on this pathogen, there are almost 19,000 deaths and almost 370,000 hospitalizations annually attributable to MRSA infections in the United States. The yearly total costs for these infections are estimated to be in the billions of dollars.

Harris et al. apply high-resolution genotyping using the Illumina Genome Analyzer to map single-nucleotide polymorphisms (SNPs) as well as insertions and deletions (indels) to a reference genome. This approach provides information on a much broader sample of the genome than the previous technique of choice for characterization of pathogen genomes, multilocus sequence typing (MLST). The genomic variation identified by Harris et al. was used in analyzing the spread, both on a global scale and also on the scale of a single hospital, of the MRSA lineage known as sequence type 239 (ST239).

Where MLST focuses on a small number of loci encoding enzymes involved in intermediary metabolism and that are unlikely to fully or directly reflect genomic changes associated with the acquisition of antibiotic resistance or new modes or extents of virulence (Aziz and Nizet, 2010), the genotyping approach employed by Harris et al. addresses genetic alterations in both what Aziz and Nizet refer to as the core genome (which would include the loci normally assessed in MLST) and what these authors refer to as the accessory genome, i.e. loci contained in mobile genetic elements (MGE; e.g., bacteriophages, transposons, plasmids). MGE are commonly acquired through horizontal gene transfer, and it is frequently through the acquisition of MGE that bacteria begin to express new forms of antibiotic resistance and new modes of virulence.

The authors of the study suggest that the origin of ST239 was most likely in Europe in the mid to late 1960’s. Key evidence supporting the initiation of ST239 to Europe was that isolates from Europe were substantially more diverse, genetically, than those from South America or Southeast Asia. In addition, the results of genotyping a group of isolates from a hospital in northeast Thailand permitted the identification of the specific wards from which the lineage began its local spread. Finally, the investigation provided an estimate of the mutation rate in ST239 as well as data suggestive of the role of antibiotic use in focusing the evolution of ST239 with respect to antibiotic resistance.

The approach of Harris and colleagues, or related methods, will presumably be applied to an expanding list of other pathogens in the coming years. As high-throughput DNA sequencing becomes more effective and less expensive per unit, improved abilities to characterize the origins of pathogen strains, their pathways of transmission, and the genetic origins of both resistance to therapeutic agents and virulence mechanisms are reasonably to be expected.

References

Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, Chantratita N, Gardete
S, Tavares A, Day N, Lindsay JA, Edgeworth JD, de Lencastre H, Parkhill J,
Peacock SJ, Bentley SD. Evolution of MRSA during hospital transmission and
intercontinental spread. Science. 2010 Jan 22;327(5964):469-74. PubMed PMID:
20093474; PubMed Central PMCID: PMC2821690.

McKenna, M. Backing away from the MRSA crisis. Los Angeles Times, April 11, 2010.http://www.latimes.com/news/opinion/commentary/la-oe-mckenna11-2010apr11,0,4271481.story

Aziz RK, Nizet V. Pathogen microevolution in high resolution. Sci Transl Med.
2010 Jan 27;2(16):16ps4.