Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses

Abstract

ObjectivesShigella sonnei is a globally important diarrhoeal pathogen tracked through the surveillance network PulseNet Latin America and Caribbean (PNLA&C), which participates in PulseNet International. PNLA&C laboratories use common molecular techniques to track pathogens causing foodborne illness. We aimed to demonstrate the possibility and advantages of transitioning to whole genome sequencing (WGS) for surveillance within existing networks across a continent where S. sonnei is endemic.MethodsWe applied WGS to representative archive isolates of S. sonnei (n = 323) from laboratories in nine PNLA&C countries to generate a regional phylogenomic reference for S. sonnei and put this in the global context. We used this reference to contextualise 16 S. sonnei from three Argentinian outbreaks, using locally generated sequence data. Assembled genome sequences were used to predict antimicrobial resistance (AMR) phenotypes and identify AMR determinants.ResultsS. sonnei isolates clustered in five Latin American sublineages in the global phylogeny, with many (46%, 149 of 323) belonging to previously undescribed sublineages. Predicted multidrug resistance was common (77%, 249 of 323), and clinically relevant differences in AMR were found among sublineages. The regional overview showed that Argentinian outbreak isolates belonged to distinct sublineages and had different epidemiologic origins.ConclusionsLatin America contains novel genetic diversity of S. sonnei that is relevant on a global scale and commonly exhibits multidrug resistance. Retrospective passive surveillance with WGS has utility for informing treatment, identifying regionally epidemic sublineages and providing a framework for interpretation of prospective, locally sequenced outbreaks.

Whole Genome Sequencing of Antimicrobial-Resistant Shigella sonnei Associated with Infection Acquired from International and Domestic Settings Reveals Gene Allelic Variants that Predict Global Lineages

“…As mentioned previously, there were differences in the types of AMR seen between the two lineages found in the collection; only Lineage III isolates carried resistance to quinolones and macrolides, the two drugs of major concern especially in the United States. This observation has been seen in previous literature, as Lineage III S. sonnei have been found to harbor more AMR genotypes when compared to other lineages (8, 9, 29, 31, 32). In regards to quinolone resistance, which has been a primary focus especially in international S. sonnei studies, Lineage III S. sonnei isolates appear to solely carry chromosomal mutations linked to quinolone resistance.…”

“…Previous studies of S. sonnei that have investigated phylogenetic segmentation align with the original analysis performed by Holt et al; all S . sonnei appear to cluster into the Global Lineages (8, 9, 29, 31, 32). The original study, however, did not contain Shigella from the United States, so lineage characterization of isolates originating from the United States was not performed until Chung The et al examined a collection of quinolone-resistant S. sonnei which included a few isolates from the United States (32).…”

“…When using additional S. sonnei sequences to test the lineage prediction alleles, S. sonnei III. ERR200550 was part of a large collection of S. sonnei from Latin America investigated by Baker et al to examine via WGS, and coincidentally, this sequence was one of a number of genomes that segmented into the newly described Global Lineage V (31). This observation aligns isolate ERR200550 appeared to carry a unique pattern of Lineage II and III specific alleles and related SNPs (Table 3).…”

Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity

“…Phylogenetic trees based on core genome SNPs were constructed with Parsnp v.1.2 [55]. To include contextualization of the position of the isolates sequenced in this study relative to the main lineages of EIEC and S. sonnei and the phylogenetic groups (PG) of S. flexneri randomly selected genomes from each lineage or phylogenetic group were included in the phylogenetic tree [3,19,22,56,57]. Details of these representatives and their accession numbers are depicted in Additional file 5.…”

Ciprofloxacin facilitates the transfer of XDR plasmids from commensalE. coliinto epidemic fluoroquinolone-resistantShigella sonnei

“…Unlike other Shigella, S. sonnei exists as a single serotype and has a population structure encompassing five lineages, of which lineage III successfully disseminated globally from the 1970s onwards. A key event facilitating the success of this lineage was the acquisition of a multi-drug resistance (MDR) phenotype, which distinguishes this population 5,6 . Antimicrobials are important for Shigella treatment and disease control, and the World Health Organization (WHO) currently recommends ciprofloxacin (fluoroquinolone) as a first-line treatment, followed by pivmecillinam (beta-lactam), ceftriaxone (cephalosporin), and azithromycin (macrolide) as alternatives 7 .…”