Genetic diversity of Salmonella Paratyphi A isolated from enteric fever patients in Bangladesh from 2008 to 2018

Abstract

Background: The proportion of enteric fever cases caused by Salmonella Paratyphi A is increasing and may increase further as we begin to introduce typhoid conjugate vaccines (TCVs). While numerous epidemiological and genomic studies have been conducted for S. Typhi, there are limited data describing the genomic epidemiology of S. Paratyphi A in especially in endemic settings, such as Bangladesh.

Principal findings: We conducted whole genome sequencing (WGS) of 67 S. Paratyphi A isolated between 2008 and 2018 from eight enteric disease surveillance sites across Bangladesh. We performed a detailed phylogenetic analysis of these sequence data incorporating sequences from 242 previously sequenced S. Paratyphi A isolates from a global collection and provided evidence of lineage migration from neighboring countries in South Asia. The data revealed that the majority of the Bangladeshi S. Paratyphi A isolates belonged to the dominant global lineage A (67.2%), while the remainder were either lineage C (19.4%) or F (13.4%). The population structure was relatively homogenous across the country as we did not find any significant lineage distributions between study sites inside or outside Dhaka. Our genomic data showed presence of single point mutations in gyrA gene either at codon 83 or 87 associated with decreased fluoroquinolone susceptibility in all Bangladeshi S. Paratyphi A isolates. Notably, we identified the pHCM2- like cryptic plasmid which was highly similar to S. Typhi plasmids circulating in Bangladesh and has not been previously identified in S. Paratyphi A organisms.

Significance: This study demonstrates the utility of WGS to monitor the ongoing evolution of this emerging enteric pathogen. Novel insights into the genetic structure of S. Paratyphi A will aid the understanding of both regional and global circulation patterns of this emerging pathogen and provide a framework for future genomic surveillance studies.

Fig 1. Geographical distrbution of S. Paratyphi A lineages in each study site of Bangladesh.

Map of Bangladesh showing the lineage distribution at each of the eight study sites across Bangladesh (Direct base layer link for Bangladesh and Dhaka map available athttps://geodash.gov.bd/layers/geonode:level_1_administrative_areas and https://geodash.gov.bd/layers/geonode:dhaka_administrative_boundaries respectively, maps sourced from https://geodash.gov.bd and modified by using ArcGIS10.8.1 software). Pie charts at each site depict the lineage distribution. The number of S. Paratyphi A positive cases (n) at each study site are also shown in the key.

Fig 2. Global population structure of Bangladesh S. Paratyphi A with AMR genes and plasmid replicons presence heatmap.

Maximum-likelihood phylogenetic tree of 309 S. Paratyphi A genome sequences from the global collection including Bangladeshi isolates from this study. The coloured heatmap shows country, lineages, AMR genes, mutations in the QRDR and acrB genes, plasmid replicons for each isolate; see legend for colours.

Fig 3. The local evolutionary history of the pHCM2 plasmid in Bangladesh.

(A) Unrooted of maximum likelihood whole pHCM2 phylogeny including S. Paratyphi A isolates from this study and S. Typhi, S. Paratyphi B variant Java from previous studies in Bangladesh (B) Maximum likelihood of pHCM2 phylogeny including only S. Paratyphi A and Typhi isolates. The coloured heatmap shows species and year of collection for each isolate.