Population Genetics and the Emergence of Infectious Disease

Team members: Dr. Honour McCann, Christina Straub, Elena Colombi, Yeserin Yildirim
Collaborators: Dr. Matt Templeton, Dr. Erik Rikkerink, Dr. Steve Ritchie, Dr. Mark Thomas, Dr. Forest Rohwer, Dr. Frederic Bertels
Key publications: Wilner et al 2012 Am J Resp Cell Mol Biol, Kidd et al 2012 PLOS One, McCann et al 2013 PLOS Path, Whiteson et al 2014 Am J Resp Crit Care Med, Ritchie et al 2014 PLOS One.

Ecologists and evolutionists cannot help but be fascinated by diversity. The stunning array of diversity that evolves in experimental Pseudomonas populations got me hooked on the problem of diversity (its origin, maintenance and patterns of distribution). But in addition, during the course of a post doc at IVEM (now CEH) in Oxford (’91-’94), I began to work on natural populations of Pseudomonas from plants (mostly sugar beets). This work was largely descriptive and involved characterising strains using a variety of genotypic and phenotypic approaches. When writing one of these studies for publication (Microbiology 140, 2315) I realized that the ‘finger-printing’ approach did not provide any insight into the evolutionary processes causing the observed patterns of diversity — and this fascinated me. It was at this stage that my interest switched to population genetics: with estimates of allelic diversity it becomes possible to determine the contributions of various evolutionary processes (selection, drift, recombination, mutation and migration) to patterns of diversity.

Bernhard Haubold, one of my first PhD students, picked up the gauntlet and took a sample of Pseudomonas that I had collected (using an ecologically sound sampling strategy) from sugar beets at the Oxford University farm at Wytham and obtained a measure of allelic diversity at a number of different loci using multi-locus enzyme electrophoresis (how things have changed!). The ensuing analysis provided an eye-opening glimpse into the population structure of these bugs from both genetic and ecological perspectives (see Molecular Ecology 5, 747).

Toward the end of Bernhard’s thesis work it became feasible to obtain nucleotide sequence from multiple loci and we began a little of this, although I was not successful in attracting further funding, which effectively brought this work to an end. I was always disappointed by this — the sample collected at Wytham is probably one of the most ecologically signficant bacterial population samples ever collected (monthly samples (for six months) from a single field of sugar beets, collected at the level of individual leaves) and Bernhard’s analysis of just a single day using MLEE provided a wealth of insight: to have expanded the study to encompass the five additional sampling occasions and to have had nucleotide (rather than enzyme) data would have been fantastic. This comment made, we have, through collaborations with Dave Guttman, Rob Jackson and Dawn Arnold made some progress, although the sheer diversity encompassed in the Pseudomonas population has made primer design for multil-locus sequence analysis (MLSA) challenging.

Vibrios from sea anemones

On moving to NZ in 2003 I decided to reinvigorate my interests in population genetics and to combine this with a potentially fundable research area. There is much activity in the population genetics of pathogenic bacteria, but little work on the evolutionary emergence of pathogens where the focus of investigation is the non-pathogenic community from whence pathogens emerge. For a host of reasons I decided to target opportunistic marine bacteria belonging to the genus Vibrio(avoiding preconceived notions of supposed species divisions) and I decided to sample these from sea anemones (the beadlet anemone Actinia tenebrosa) at different levels of spatial scale. [A rather unique feature of the Auckland region means that it is possible to sample from two different oceans (Tasman and Pacific) — with the sampling sites separate by ~1,500 km — in the space of a couple of hours.]

With the help of Annabel Hurman we sequenced four different housekeeping loci from ~200 strains and also obtained sequence data from a phage receptor. I managed to convince Ed Fiel that it would be interesting to parallel this study in Britian: which he did. The data has been crunched and the picture that has emerged is extremely interesting. I hope soon to get the work written up.

In the mean time this study has been expanded to incorporate vibrios from sea anemones (albeit different genera) from the Monterey coast (CA). In fact the study of the population structure of these bacteria now forms a significant portion of the practical work for students signed up on the Hopkins Microbiology Course.

This foray into vibrios has also resulted in the building of a super collaboration with Ned Ruby and his interests in the luminescent vibrios that colonize the light organ of the bobtail squid. There is so much that is interesting here — particularly the reasons for benevolence in an association that ought (one would predict) to evolve toward virulence — but we can’t seem to convince the funding agencies of this.

Staphylococcus and humans

There is nothing like working on bugs that kill people in terms of funding opportunities (and it goes without saying that it is nice to do something that others find worthwhile). In 2002 I met Mark Thomas, an infectious disease physician at the University of Auckland and we’ve explored ways ever since of building understanding of the genetic structure and evolution of Staphylococcus aureus in NZ and the broader South Pacific region where there are some very interesting and signfiicant issues — including the evolution of antibiotic resistance and the suggestion of local adaptation between bacteria and different ethnic groups (Maori and South Pacific Island peoples are disproportionately affected by S. aureus).

A couple of years ago Steve Ritchie (an infectious disease physician naive enough to want to undertake a PhD!) came along and showed much interest in learning some population genetics. Thanks to an HRC grant and more recently funding from the University of Auckland we have made real progress.

During his first year Steve assiduously (in a manner that would make an ecologist weep with delight) amassed a large collection of Staphylococcus aureus from both infected individuals (from his own clinic) and carriers (including random shopping mall customers). We’ve also been fortunate to have had interns throughout the South Pacific send us samples.

Steve has taken the standard S. aureus MLST scheme and re-designed primers so that we capture a greater spread of diversity. He’s got this new primer set up and running and we are nowing watching as the data comes on in (we are itching to analyze it).

Pseudomonas and kiwifruit

Modern agriculture remains vulnerable to significant losses caused by microbial pathogens, particularly where it relies on crops with limited genetic heterogeneity. The commercial cultivation of kiwifruit is largely reliant on the vegetative or clonal propagation of gold ‘Hort16A’ (A. chinensis) and green ‘Hayward’ (A. deliciosa) cultivars. Unlike most other crops, whose domestication began millennia ago, kiwifruit was domesticated less than a century ago. This presents us with the unusual opportunity to study the initial stages in the emergence of an agricultural pathogen. Our recent genomic and population analysis of more than 30 Psa strains has provided some insight into the origin and evolution this destructive infectious disease (McCann et al 2013 PLOS Path).

Kiwifruit outbreaks over the last three decades have been caused by distinct lineages of Psa. Each lineage of Psa exhibits little within-clade diversity, and patterns of polymorphism among Psa-V strains isolated during the recent global epidemic are consistent with the expansion and diversification of a single clone within the last decade (Figure 1).Evidence of between-clade recombination suggests the ancestors of each clade coexisted in a potentially non-agricultural source population. Outbreaks likely occurred as a result of transmission events from the source population, followed by selection in agricultural environments for host specialization. An isolate of Psa-V exhibits more rapid spread in ‘Hort16A’ compared to earlier Psa isolates, and an apparent tradeoff in systemic spread in ‘Hayward’ is suggestive of Psa-V specialization on ‘Hort16A’. The expansion in commercial cultivation of susceptible gold kiwifruit genotypes during the last decade may have exacerbated the severity of the latest outbreak. All lineages of Psa harbour unique repertoires of predicted virulence factors and toxins. Despite these differences, strains from the earlier outbreaks can grow to high levels in both cultivars.

The source population may be a reservoir of novel pathogen variants. Defining the population structure and host range of Psa isolated in wild and agricultural environments will clarify the evolutionary potential of this pathogen in response to disease control, and assist plant breeders in developing cultivars of kiwifruit with broad resistance to the pathogen population rather than a single strain.