Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes

Abstract

Many pathogens that caused devastating disease throughout human history, such as Yersinia pestis, Mycobacterium tuberculosis, and Mycobacterium leprae, remain problematic today. Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously understudied resource. This minireview brings together example studies which have utilized ancient DNA, individual historical isolates (both extant and dead) and collections of historical isolates. The studies span human history and highlight the contribution that sequencing and analysis of historical bacterial genomes have made to a wide variety of fields. From providing retrospective diagnosis, to uncovering epidemiological pathways and characterizing genetic diversity, there is clear evidence for the utility of historical isolate studies in understanding disease today. Studies utilizing historical isolate collections, such as those from the National Collection of Type Cultures, the American Type Culture Collection, and the Institut Pasteur, offer enhanced insight since they typically span a wide time period encompassing important historical events and are useful for the investigating the phylodynamics of pathogens. Furthermore, historical sequencing studies are particularly useful for looking into the evolution of antimicrobial resistance, a major public health concern. In summary, although there are limitations to working with historical bacterial isolates, especially when utilizing ancient DNA, continued improvement in molecular and sequencing technologies and the resourcefulness of investigators mean this area of study will continue to expand and contribute to the understanding of pathogens.

Setting the standard: multidisciplinary hallmarks for structural, equitable and tracked antibiotic policy

“…Rising numbers of point prevalence studies and whole-genome sequencing are enhancing our knowledge of drivers and variations of AMR over time and in different areas across the world. [48][49][50][51] However, our wider understanding of the evolutionary factors underlying AMR levels is still fragmentary as is our understanding of which stewardship interventions might make how much of a difference: in some cases like targeted 1950s antibiotic prescription bans at St Bartholomew's Hospital in London 52 or Denmark's 1990s ban of lower-dosed avoparcin and tylosin animal growth promoters, reducing selection pressure by a specific type of drug usage led to a marked reduction, but not a complete disappearance, of correlating AMR. 53 54 In other cases, antibiotic reductions may take years to manifest in terms of reduced AMR-as highlighted by the UK's 2019 ESPAUR report and experiences in Scandinavian countries.…”

Human biology and ancient DNA: exploring disease, domestication and movement

“…M€ uhlemann et al 2018a, 2018b), a more detailed picture of the role these microbes played in our evolution is gradually developing. The role of aDNA will be crucial in shining a light on not just where and when these microorganisms became human pathogens, but also in revealing how they have evolved to exploit human biology and behaviour (Bennett and Baker 2019;Rascovan et al 2019). Ham et al (2019) examine patterns of Neanderthal allele variation in modern humans in order to explore hypotheses for selective pressures.…”

Temporal GWAS identifies a widely distributed putative adhesin contributing to pathogen success in Shigella spp

“…Historical isolate collections provide an invaluable resource with which to make unique insights into long-term trends in pathogen evolution and epidemiology, and evaluate the impact of major historical events, e.g. the clinical introduction of antimicrobials, on bacterial evolution [15]. Advances in both sequencing technologies and sampling strategies have allowed previously inaccessible historical bacterial DNA to be investigated, revealing a plethora of unique insights, such as those gained from the first isolate accessioned into the National Collection of Type Cultures (NCTC) [16].…”