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

Laura Maria Francisca Kuijpers,Mathieu Tourdjman,Nizar Fawal,Jan Jacobs,Christiane Bouchier,Erika Vlieghe,Laetitia Fabre,Chun Kham,François-Xavier Weill,Dara Sar,Simon Le Hello,Muriel Dufour,Thong Phe

doi:10.1099/mgen.0.000092

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.

Highlights

Salmonella enterica serotypes Typhi (Salmonella Typhi) and Paratyphi A (Salmonella Paratyphi A) are Gram-negative bacteria confined to human hosts
During the 2008–2012 period, enteric fever in patients attending the Sihanouk Hospital Centre of HOPE (SHCH) and in travellers returning from Cambodia to France was caused mostly by Salmonella Typhi (Fig. 1)
12 cases of Salmonella Paratyphi A infection were identified among patients attending the SHCH, and only 1 such case was reported in a traveller returning from Cambodia to France

Summary

Introduction

Salmonella enterica serotypes Typhi (Salmonella Typhi) and Paratyphi A (Salmonella Paratyphi A) are Gram-negative bacteria confined to human hosts They can invade the bloodstream, causing typhoid and paratyphoid fever (known together as ‘enteric fever’). The number of Salmonella Paratyphi A infections has been increasing steadily over the last 20 years, and it is estimated that there are six million cases of paratyphoid fever annually (Newton et al, 2016). This increase is most apparent in Asia, where Salmonella Paratyphi A accounts for 14 % (Indonesia) to 64 % (South-East China) of enteric fever cases (Ochiai et al, 2005). International travellers returning from countries in which Salmonella Paratyphi A is endemic are increasingly being infected with this bacterium, which accounted for 31 % of imported cases of enteric fever in the European Union in 2011 (ECDC, 2013)

Methods

Results

Conclusion