title: Genomic analysis ofSalmonella entericaserotype Paratyphi A during an outbreak in Cambodia, 2013-2015.
abstract: In 2013, an unusual increase in the number ofSalmonella entericaserotype Paratyphi A (SalmonellaParatyphi 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 theseSalmonellaParatyphi 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.
authors.affiliation: 1​Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.|2​Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium.
authors.forename: Laura Maria Francisca
authors.initials: LMF
authors.lastname: Kuijpers
authors.affiliation: 3​Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, France.
authors.forename: Simon
authors.initials: S
authors.lastname: Le Hello
authors.affiliation: 3​Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, France.
authors.forename: Nizar
authors.initials: N
authors.lastname: Fawal
authors.affiliation: 3​Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, France.
authors.forename: Laetitia
authors.initials: L
authors.lastname: Fabre
authors.affiliation: 4​Santé Publique France, Direction des Maladies Infectieuses, Saint-Maurice, France.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Tourdjman
authors.affiliation: 5​Institute of Environmental Science and Research Limited, NCBID, Wallaceville, New Zealand.
authors.forename: Muriel
authors.initials: M
authors.lastname: Dufour
authors.affiliation: 6​Sihanouk Hospital Centre of HOPE, Phnom Penh, Cambodia.
authors.forename: Dara
authors.initials: D
authors.lastname: Sar
authors.affiliation: 6​Sihanouk Hospital Centre of HOPE, Phnom Penh, Cambodia.
authors.forename: Chun
authors.initials: C
authors.lastname: Kham
authors.affiliation: 6​Sihanouk Hospital Centre of HOPE, Phnom Penh, Cambodia.
authors.forename: Thong
authors.initials: T
authors.lastname: Phe
authors.affiliation: 1​Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.|7​Department of Tropical Diseases, University Hospital Antwerp, Antwerp, Belgium.
authors.forename: Erika
authors.initials: E
authors.lastname: Vlieghe
authors.affiliation: 8​Institut Pasteur, Plate-forme Génomique (PF1), Paris, France.
authors.forename: Christiane
authors.initials: C
authors.lastname: Bouchier
authors.affiliation: 1​Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.|2​Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Jacobs
authors.affiliation: 3​Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, France.
authors.forename: François-Xavier
authors.initials: FX
authors.lastname: Weill
mesh_terms: D000349:Africa; D001208:Asia; D002160:Cambodia / Q000453:epidemiology; D004196:Disease Outbreaks; D024881:Drug Resistance, Bacterial; D005060:Europe; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D006801:Humans; D010284:Paratyphoid Fever / Q000453:epidemiology / Q000382:microbiology*; D012482:Salmonella paratyphi A / Q000145:classification / Q000187:drug effects / Q000235:genetics*; D065288:Serogroup
keywords: Cambodia; Salmonella Paratyphi A; resistance; whole genome sequencing