IMPACTT Microbiome @IMPACTT@qoto.org

The White–Kauffmann–Le Minor (WKL) scheme is the most widely used Salmonella typing scheme for reporting the disease prevalence of the enteric pathogen. With the advent of whole-genome sequencing (WGS), in silico methods have increasingly replaced traditional serotyping due to reproducibility, speed and coverage. However, despite integrating genomic-based typing by in silico serotyping tools such as SISTR, in silico serotyping in certain contexts remains ambiguous and insufficiently informative. Specifically, in silico serotyping does not attempt to resolve polyphyly. Furthermore, in spite of the widespread acknowledgement of polyphyly from genomic studies, the prevalence of polyphyletic serovars is not well characterized. Here, we applied a genomics approach to acquire the necessary resolution to classify genetically discordant serovars and propose an alternative typing scheme that consistently reflect natural Salmonella populations. By accessing the unprecedented volume of bacterial genomic data publicly available in GenomeTrakr and PubMLST databases (>180 000 genomes representing 723 serovars), we characterized the global Salmonella population structure and systematically identified putative non-monophyletic serovars. The proportion of putative non-monophyletic serovars was estimated higher than previous reports, reinforcing the inability of antigenic determinants to depict the complexity of Salmonella evolutionary history. We explored the extent of genetic diversity masked by serotyping labels and found significant intra-serovar molecular differences across many clinically important serovars. To avoid false discovery due to incorrect in silico serotyping calls, we cross-referenced reported serovar labels and concluded a low error rate in in silico serotyping. The combined application of clustering statistics and genome-wide association methods demonstrated effective characterization of stable bacterial populations and explained functional differences. The collective methods adopted in our study have practical values in establishing genomic-based typing nomenclatures for an entire microbial species or closely related subpopulations. Ultimately, we foresee an improved typing scheme to be a hybrid that integrates both genomic and antigenic information such that the resolution from WGS is leveraged to improve the precision of subpopulation classification while preserving the common names defined by the WKL scheme.

In times of a public health emergency, lawyers and ethicists play a key role in ensuring that government responses, such as travel restrictions, are both legally and ethically justified. However, when travel bans were imposed in a broadly discriminatory manner against southern African countries in response to the Omicron SARS-CoV-2 variant in late 2021, considerations of law, ethics or science did not appear to guide politicians’ decisions. Rather, these bans appeared to be driven by fear of contagion and electoral blowback, economic motivations and inherently racist assumptions about low-income and middle-income countries (LMICs). With a new pandemic treaty and amendments to the WHO’s International Health Regulations (IHR) on the near-term horizon, ethics and international law are at a key inflection point in global health governance. Drawing on examples of bordering practices to contain contagion in the current pandemic and in the distant past, we argue that the current IHR is not adequately constructed for a just and equitable international response to pandemics. Countries impose travel restrictions irrespective of their need or of the health and economic impact of such measures on LMICs. While the strengthening and reform of international laws and norms are worthy pursuits, we remain apprehensive about the transformative potential of such initiatives in the absence of collective political will, and suggest that in the interim, LMICs are justified in seeking strategic opportunities to play the same stark self-interested hardball as powerful states.