Use of whole genome sequencing to complement characterisation of a typhoid fever outbreak among a Marshallese community: Oklahoma, 2015

Abstract

Typhoid fever is an illness caused by Salmonella enterica serotype Typhi. In developing regions, it affects an estimated 20 million people annually, causing 200 000 deaths. Although uncommon, cases occur in the USA each year, predominantly due to international travel. During February 2015, the Oklahoma State Department of Health (OSDH) detected an outbreak of typhoid fever among residents of northwestern Oklahoma. OSDH conducted case-patient interviews to identify the source and symptomatic contacts. Whole genome sequencing (WGS) was performed to characterise the genetic relatedness of isolates among the four outbreak-associated pulsed-field gel electrophoresis (PFGE) patterns. We identified 38 cases, 25 confirmed and 13 probable, in two states. WGS revealed a 0–10 single-nucleotide polymorphism variation between isolates. Although we were unable to determine the source, almost all case-patients were members of the Marshallese community that attended a common event in Oklahoma, or were contacts to a confirmed case. This is the largest outbreak of typhoid fever in the USA since 1989, and first to apply WGS to complement interpretation of PFGE results during a typhoid fever outbreak investigation. This investigation illustrates the potential risk of outbreaks among communities comprised of international populations from regions where typhoid fever remains endemic.

Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa

“…We detected from 0 to 28 pairwise SNP differences among the 12 putative epidemiologic linkages and 3 instances of repeat positive cultures from the same individual collected ~1 month apart ( Table 4 ). Relatedness criteria of 10 SNPs or less [ 40 ] would encompass 13/15 (86.7%) linkages, and 12/13 were within ≤4 SNPs, a suggested cutoff for Salmonella enterica [ 41 ]. Future studies to characterize S .…”

“…We detected from 0 to 28 pairwise SNP differences among the 12 putative epidemiologic linkages and 3 instances of repeat positive cultures from the same individual collected ~1 month apart (Table 4). Relatedness criteria of 10 SNPs or less [40] would encompass 13/15 (86.7%) linkages, and 12/13 were within �4 SNPs, a suggested cutoff for Salmonella enterica [41]. Future studies to characterize S. Typhi population diversity in acute infections and asymptomatic carriers by sequencing and comparing multiple colonies obtained from stool cultures collected over time, as has been completed for other enteric pathogens [42], could aid in establishing appropriate thresholds for SNP-based relatedness among S. Typhi isolates for cluster identification.…”

Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from 13,000SalmonellaTyphi genomes

“…Nearly all those contacted responded, and are included as Consortium authors on this study. The exceptions, where authors did not respond to email inquiries, were: (i) one genome reported from Malaysia (Ahmad et al, 2017) and n=133 draft genomes reported from India (Katiyar et al, 2020), which were excluded as sequence reads were not available in NCBI; and (ii) n=39 genomes reported in studies of travel-associated or local outbreaks (Burnsed et al, 2019;Hao et al, 2020;Shin et al, 2021), which were included as raw sequence data and sufficient metadata were publicly available. A further n=850 genomes sequenced by US Centers for Disease Control and Prevention and available in NCBI were excluded from analysis because travel history was unknown and most US cases are travel-associated.…”

Typhoid Outbreaks, 1989–2018: Implications for Prevention and Control

“…The most commonly implemented intervention, described in 17 (65%) of 26 outbreaks, was improving WASH infrastructure, including building a new water tower, repair of unsanitary latrines and toilets, and rehabilitation of fecally contaminated boreholes. 38,51,[57][58][59] Other measures to improve drinking water, implemented in 14 (54%) outbreaks, 32,38,39,44,47,49,57,[59][60][61][62][63][64][65] were described as improving water quality which included providing alternative drinking water sources and distribution of chlorine products for water disinfection in the household, point of use, point of water collection, or at the municipal water source. Efforts to increase health education were described in 15 (58%) outbreaks.…”