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. 2016 Nov 30;2(11):e000092.
doi: 10.1099/mgen.0.000092. eCollection 2016 Nov.

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

Laura Maria Francisca Kuijpers  1   2 , Simon Le Hello  3 , Nizar Fawal  3 , Laetitia Fabre  3 , Mathieu Tourdjman  4 , Muriel Dufour  5 , Dara Sar  6 , Chun Kham  6 , Thong Phe  6 , Erika Vlieghe  1   7 , Christiane Bouchier  8 , Jan Jacobs  1   2 , François-Xavier Weill  3
Affiliations

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

Laura Maria Francisca Kuijpers et al. Microb Genom. .

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.

Keywords: Cambodia; Salmonella Paratyphi A; resistance; whole genome sequencing.

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Figures

Fig. 1.
Fig. 1.
Enteric fever cases at SHCH, Phnom Penh, Cambodia, and in travellers returning to France from Cambodia, 2008–2015. The numbers of blood culture-confirmed cases of enteric fever (only the first isolate per patient was included) at SHCH and the numbers of confirmed cases in migrants or travellers returning to France from Cambodia during the 2008–2015 period are shown.
Fig. 2.
Fig. 2.
Timed phylogeny for 4810 SNPs in 159 Salmonella Paratyphi A genomes. A maximum clade credibility tree generated by BEAST 1.8 (exponential clock rate and Bayesian skyline population models) is shown, providing information about the geographical origin, antimicrobial resistance phenotype (AMR type), gyrA mutation encoding resistance to nalidixic acid and lineages of the genomes. The different clades (C1 to C5) of lineage C are also indicated. The tips of the tree are coloured according to the geographical origin of the genomes. The abbreviations used for the antibiotics are as follows: AMP, ampicillin; NAL, nalidixic acid; STR, streptomycin; SXT, trimethoprim/sulfamethoxazole. AMPR indicates resistance to AMP. NALR indicates resistance to NAL, which was associated with decreased susceptibility to ciprofloxacin (MIC in the range 0.125–1 mg l−1).
Fig. 3.
Fig. 3.
Representative XbaI-PFGE profiles of Salmonella Paratyphi A isolates. The 10 different XbaI–PFGE profiles obtained from the analysis of 51 Salmonella Paratyphi A isolates are shown. Lanes 1, 6, 11 and 15, S. enterica serotype Braenderup H9812 used as a molecular size marker (M) (band sizes in kb); lane 2, C5 isolate 4416 (XParaA_001); lane 3, C3 isolate 201300701 (XParaA_009); lane 4, C5 isolate 201404185 (XParaA_011); lane 5, C4 isolate 201304008 (XParaA_002); lane 7, A isolate 03–2557 (XParaA_003); lane 8, C4 isolate 201301308 (XParaA_004); lane 9, C5 isolate 201311858 (XParaA_005); lane 10, A isolate 201400552 (XParaA_006); lane 12, C4 isolate 201403926 (XParaA_007); lane 13, C5 isolate 99–7427 (XParaA_001); and lane 14, C5 isolate 5288/46 (XParaA_010).
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Data Bibliography

    1. Salmonella enterica subsp. enterica serovar Choleraesuis strain SC-B67 complete genome: GenBank accession number AE017220.
    1. Salmonella enterica subsp. enterica serovar Dublin strain CT_02021853 complete genome: GenBank accession number CP001144.
    1. Salmonella enterica subsp. enterica serovar Enteritidis strain P125109 complete genome: GenBank accession number AM933172.
    1. Salmonella enterica subsp. enterica serovar Gallinarum strain 287/91 complete genome: GenBank accession number AM933173.
    1. Salmonella enterica subsp. enterica serovar Heidelberg strain SL476 complete genome: GenBank accession number CP001120.

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