Genomic analysis of Salmonella enterica serotype Paratyphi A during an outbreak in Cambodia, 2013–2015

Abstract

In 2013, an unusual increase in the number of Salmonella enterica serotype Paratyphi A (Salmonella Paratyphi A) infections was reported in patients in Phnom Penh, Cambodia, and in European, American and Japanese travellers returning from Cambodia. Epidemiological investigations did not identify a common source of exposure. To analyse the population structure and genetic diversity of these Salmonella Paratyphi A isolates, we used whole-genome sequencing on 65 isolates collected from 1999 to 2014: 55 from infections acquired in Cambodia and 10 from infections acquired in other countries in Asia, Africa and Europe. Short-read sequences from 80 published genomes from around the world and from 13 published genomes associated with an outbreak in China were also included. Pulsed-field gel electrophoresis (PFGE) was performed on a subset of isolates. Genomic analyses were found to provide much more accurate information for tracking the individual strains than PFGE. All but 2 of the 36 isolates acquired in Cambodia during 2013–2014 belonged to the same clade, C5, of lineage C. This clade has been isolated in Cambodia since at least 1999. The Chinese outbreak isolates belonged to a different clade (C4) and were resistant to nalidixic acid, whereas the Cambodian outbreak isolates displayed pan-susceptibility to antibiotics. Since 2014, the total number of cases has decreased, but there has been an increase in the frequency with which nalidixic acid-resistant C5 isolates are isolated. The frequency of these isolates should be monitored over time, because they display decreased susceptibility to ciprofloxacin, the first-choice antibiotic for treating paratyphoid fever.

Global phylogenomics of multidrug resistant Salmonella enterica serotype Kentucky ST198

“…AST was performed on all 97 S. Kentucky ST198 isolates using the disk diffusion method with a panel of 32 antimicrobial agents (Bio-Rad, Marnes-La-Coquette, France) as described previously (24). The minimum inhibitory concentrations (MICs) of ceftriaxone, ceftazidime, imipenem, ertapenem, meropenem, ciprofloxacin, azithromycin, and tigecycline were also determined by Etests (AB Biodisk, Solna, Sweden Table S1.…”

Laboratory and Molecular Surveillance of Paediatric Typhoidal Salmonella in Nepal: Antimicrobial Resistance and Implications for Vaccine Policy

“…To characterize and analyse the genomes of the 66 S. Paratyphi A strains, a similar bioinformatic process was adopted using S. Paratyphi A AKU_12601 27 (accession no: FM200053) as the reference genome to create an alignment with another selected 176 isolates from previous studies 28–30 , for global context resulting in an alignment of 5,277 SNPs in a total of 242 S. Paratyphi isolates, with alleles from S. Typhi CT18 22 (accession no: AL515582) included as an outgroup to root the tree.…”

When ‘substandard’ is the standard, who decides what is appropriate? Exploring healthcare provision in Cambodia

“…Phnom Penh, the capital of Cambodia, is a rapidly economically expanding city, although poverty and communicable diseases remain important issues (Clarke et al, 2016). In 2012-2015 a community outbreak of Salmonella Paratyphi A infections occurred in Phnom Penh, affecting large numbers of local residents and international travelers (Kuijpers et al, 2016). As an estimated 1.55 million people live in Phnom Penh, of whom approximately 82% have access to improved sanitation facilities such as a piped sewer system and a septic tank (Davies et al, 2015), a qualitative study was warranted to investigate potential social and environmental drivers of this outbreak (Kuijpers et al, 2018(Kuijpers et al, , 2016.…”