ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data

BACKGROUND

Genomics-informed pathogen surveillance strengthens public health decision-making, playing an important role in infectious diseases' prevention and control. A pivotal outcome of genomics surveillance is the identification of pathogen genetic clusters and their characterization in terms of geotemporal spread or linkage to clinical and demographic data. This task often consists of the visual exploration of (large) phylogenetic trees and associated metadata, being time-consuming and difficult to reproduce.

RESULTS

We developed ReporTree, a flexible bioinformatics pipeline that allows diving into the complexity of pathogen diversity to rapidly identify genetic clusters at any (or all) distance threshold(s) or cluster stability regions and to generate surveillance-oriented reports based on the available metadata, such as timespan, geography, or vaccination/clinical status. ReporTree is able to maintain cluster nomenclature in subsequent analyses and to generate a nomenclature code combining cluster information at different hierarchical levels, thus facilitating the active surveillance of clusters of interest. By handling several input formats and clustering methods, ReporTree is applicable to multiple pathogens, constituting a flexible resource that can be smoothly deployed in routine surveillance bioinformatics workflows with negligible computational and time costs. This is demonstrated through a comprehensive benchmarking of (i) the cg/wgMLST workflow with large datasets of four foodborne bacterial pathogens and (ii) the alignment-based SNP workflow with a large dataset of Mycobacterium tuberculosis. To further validate this tool, we reproduced a previous large-scale study on Neisseria gonorrhoeae, demonstrating how ReporTree is able to rapidly identify the main species genogroups and characterize them with key surveillance metadata, such as antibiotic resistance data. By providing examples for SARS-CoV-2 and the foodborne bacterial pathogen Listeria monocytogenes, we show how this tool is currently a useful asset in genomics-informed routine surveillance and outbreak detection of a wide variety of species.

CONCLUSIONS

In summary, ReporTree is a pan-pathogen tool for automated and reproducible identification and characterization of genetic clusters that contributes to a sustainable and efficient public health genomics-informed pathogen surveillance. ReporTree is implemented in python 3.8 and is freely available at https://github.com/insapathogenomics/ReporTree .

Range-wide genetic structure and demographic history in the bat ectoparasite Cimex adjunctus

Background

Evolutionary histories of parasite and host populations are intimately linked such that their spatial genetic structures may be correlated. While these processes have been relatively well studied in specialist parasites and their hosts, less is known about the ecological and evolutionary consequences of relationships between generalist ectoparasites and their hosts. The aim of this study was to investigate the genetic structure and demographic history of a bat ectoparasite, Cimex adjunctus, whose host affinity is weak but the biology of the potential hosts have been well studied. This ectoparasite has been hypothesized to rely on its hosts for dispersal due to its low inherent dispersal potential. Here we describe genetic diversity and demographic history in C. adjunctus through most of its range in North America. We investigated variation at the cytochrome c oxidase 1 mitochondrial gene and nine microsatellite markers, and tested the prediction that genetic diversity in C. adjunctus is spatially structured. We also tested the prediction that demographic history in C. adjunctus is characterized by range and demographic expansion as a consequence of post-Pleistocene climate warming.

Results

We found stronger spatial structuring of genetic diversity in C. adjunctus than has been quantified in two of its hosts, but contrast in amount of variation explained by host association with different genetic markers (i.e., nuclear vs mitochondrial DNA). Also, C. adjunctus’ history is not primarily characterized by demographic and range expansion, as is the case with two of its key hosts.

Conclusions

Our study shows different patterns of genetic structure and demographic history in C. adjunctus than have been detected in two of its key hosts. Our results suggest an effect of a loose parasite-host relationship and anti-parasitism strategies on genetic structure and post-Pleistocene recovery of population size.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0839-1) contains supplementary material, which is available to authorized users.

Racial discrimination: how not to do it

The UNESCO Statements on Race of the early 1950s are understood to have marked a consensus amongst natural scientists and social scientists that 'race' is a social construct. Human biological diversity was shown to be predominantly clinal, or gradual, not discreet, and clustered, as racial naturalism implied. From the seventies social constructionists added that the vast majority of human genetic diversity resides within any given racialised group. While social constructionism about race became the majority consensus view on the topic, social constructionism has always had its critics. Sesardic (2010) has compiled these criticisms into one of the strongest defences of racial naturalism in recent times. In this paper I argue that Sesardic equivocates between two versions of racial naturalism: a weak version and a strong version. As I shall argue, the strong version is not supported by the relevant science. The weak version, on the other hand, does not contrast properly with what social constructionists think about 'race'. By leaning on this weak view Sesardic's racial naturalism intermittently gains an appearance of plausibility, but this view is too weak to revive racial naturalism. As Sesardic demonstrates, there are new arguments for racial naturalism post-Human Genome Diversity Project. The positive message behind my critique is how to be a social constructionist about race in the post-genomic era.