Measurably evolving pathogens in the genomic era

Abstract

Current sequencing technologies have created unprecedented opportunities for studying microbial populations. For pathogens with comparatively low per-site mutation rates, such as DNA viruses and bacteria, whole-genome sequencing can reveal the accumulation of novel genetic variation between population samples taken at different times. The concept of “measurably evolving populations” and related analytical approaches have provided powerful insights for fast-evolving RNA viruses, but their application to other pathogens is still in its infancy. Here we argue that previous distinctions between slow- and fast-evolving pathogens become blurred once evolution is assessed at a genome-wide scale and we highlight important analytical challenges to be overcome in order to infer pathogen population dynamics from genomic data.

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

“…This definitely shows a clear RD pattern with lesser near-clades and LD at this microevolutionary level. This shows also that the 'measurably evolving pathogen' approach (Biek et al, 2015) can now be applied to eukaryotic micropathogens: the epidemiology of these organisms can be followed in recent times through WGS and time-serial samplings.…”

“…It exhibits a clear microclustering (RD pattern), although the most recent common ancestor is estimated to be dated to the year 1959 only (Wong et al, 2015). This shows that 'measurably evolving pathogens' (Biek et al, 2015), that is, pathogens whose epidemiology can be followed up through WGS and time-serial samplings, are not only limited to fastevolving viruses but also concern bacteria (Wong et al, 2015) and even parasitic protozoa (Imamura et al, 2016).…”

Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis

“…The increased availability of whole-genome sequences has shifted the limits of measurably evolving pathogens to also encompass bacteria (20), including Mtb (13, 21), despite its relatively slow substitution rate compared with most other bacterial pathogens (22). Here we applied phylodynamic methods, calibrated with sampling dates (tip-dating), to a collection of Mtb isolates from Europe and southeast and central Asia.…”

Genomic Analysis of Bacterial Outbreaks

“…These methods can accommodate strict and relaxed clock models, different demographic regimes, as well as variation in rates among lineages, thus allowing the estimation of relevant evolutionary parameters from organisms with different natural and evolutionary histories. Most often they are applied to rapidly evolving organisms, collectively known as measurably evolving populations (Drummond et al, 2003;Biek et al, 2015), which mainly include viruses along with some bacteria. But the methods are also valid for more slowly evolving organisms with sampling dates different enough as to provide estimates of the evolutionary rate.…”

“…On the long run, many of these transient variants will have disappeared and evolutionary rates are reduced correspondingly. This negative correlation has to be taken into account when comparing rates across studies, even for the same species, and in the inference of other evolutionary parameters (Biek et al, 2015).…”