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Paratyphi A outbreak in Cambodia, 2013-2015

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

PROVIDER: PRJEB12224 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1197530_1.fastq.gz	Fastqsanger.gz
	ERR1197530_2.fastq.gz	Fastqsanger.gz
	ERR1197640_1.fastq.gz	Fastqsanger.gz
	ERR1197640_2.fastq.gz	Fastqsanger.gz
	ERR1197650_1.fastq.gz	Fastqsanger.gz

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

Project description: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.

| S-EPMC5320704 | biostudies-literature

Genomic comparisons of Salmonella enterica serovar Paratyphi A isolates

Project description:Comparative genomic analysis of a temporally and locally diverse set of S. enterica ssp I sv Paratyphi A isolates Keywords: ordered

2004-07-21 | E-GEOD-1500 | biostudies-arrayexpress

Enteric fever in Phnom Penh, Cambodia

Project description:The clinical and microbiological characteristics of enteric fever in Cambodia, 2008-2015

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Genomic comparisons of Salmonella enterica serovar Paratyphi A isolates

Project description:Comparative genomic analysis of a temporally and locally diverse set of S. enterica ssp I sv Paratyphi A isolates Keywords: ordered

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Ebola virus glycoprotein variant with increased infectivity for human cells dominated the 2013-2016 outbreak

Project description:The unprecedented magnitude of the 2013-2016 Makona Ebola virus (M-EBOV) epidemic likely resulted from multiple epidemiologic factors that set it apart from previous outbreaks. Nonetheless, genetic adaptations that distinguish M-EBOV from previous isolates may also have contributed to the scale of the epidemic. Of particular interest is a M-EBOV glycoprotein (GP) variant, GP-A82V, that was first detected at the inflection point of the 2013-2016 outbreak - when the number of cases increased exponentially - and which completely supplanted the earlier M-EBOV sequence. We found that, as compared with the earlier strain, GP-A82V increased the ability of M-EBOV to fuse with and infect cells of primate origin, including human blood dendritic cells, without altering innate immune signaling in target cells. Residue 82 is located at the NPC1-binding site on M-EBOV GP and the increased infectivity of GP-A82V was restricted to cells from species in which the NPC1 orthologue bears primate-defining residues at the critical interface. We utilized HIV-derived lentiviral vectors pseudotyped with founder and A82V containing M-EBOV GPs to explore the potential that this modification alters how human monocyte-derived dendritic cells (MDDCs) respond to EBOV GP stimulation.

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Phylogenomic investigation of an outbreak of fluoroquinolone-resistant Salmonella enterica serovar Paratyphi A in Phnom Penh, Cambodia.

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ParaA epidemic Cambodia 2014

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Project description:Epidemiologic information is key when interpreting whole genome sequence data – lessons learned from the genomic analysis of the largest German Legionella pneumophila outbreak (Warstein, 2013)

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High-throughput gene expression profiling of Salmonella enterica serovar Paratyphi A in the blood of bacteremic patients in Bangladesh

Project description:In this work, we applied an RNA analysis method, Selective Capture of Transcribed Sequences (SCOTS), and cDNA hybridization-microarray technology to identify S. Paratyphi A transcripts expressed by bacteria in the blood of three patients in Bangladesh. In total, we detected 1798 S. Paratyphi A mRNAs expressed in the blood of infected humans (43.9% of the ORFeome). Of these, we identified 868 in at least two patients, and 315 in all three patients. S. Paratyphi A transcripts identified in at least two patients encode proteins involved in energy metabolism, nutrient and iron acquisition, vitamin biosynthesis, stress responses, oxidative stress resistance, and pathogenesis. A number of detected transcripts are expressed from PhoP and SlyA-regulated genes associated with intra-macrophage survival, genes contained within Salmonella Pathogenicity Islands (SPIs) 1-4, 6, 10, 13, and 16, as well as RpoS-regulated genes. The largest category of identified transcripts are those encoding proteins with unknown function. When comparing level of bacterial mRNA detection using in vivo samples collected from infected patients to samples from in vitro grown organisms, we found significant differences for 347, 391, and 456 S. Paratyphi A transcripts in each of three individual patients (approximately 9.7% of the ORFeome). Of these, expression of 194 transcripts (4.7% of ORFs) was concordant in two or more patients, and 41 in all patients. Genes encoding these transcripts are contained within SPI-1, 3, 6 and 10, are PhoP-regulated genes, are involved in energy metabolism, nutrient acquisition, drug resistance, or are uncharacterized genes. Using quantitative RT-PCR, we confirmed increased gene expression in vivo for a subset of genes identified in our analyses. We compared transcriptional profiles of S. Paratyphi A from the blood of infected humans to S. Paratyphi A grown in vitro. Replicates and dye-swaps were performed.

2010-09-06 | E-GEOD-22958 | biostudies-arrayexpress

Transcriptional responses in whole blood of healthy adult volunteers experimentally challenged with S. Paratyphi

Project description:This studies describes the transcriptional response in whole blood derived from healthy adult volunteers experimentally infected with S. Paratyphi A. Samples were collected at pre-challenge baseline (Group: CTRL), at day 7 after challenge in those participants who stayed well over 14 days following challenge (Group: suspected Enteric Fever - sEF). Participants who developed signs of enteric fever were sampled at the time of inititiation of antibiotics (Group: EF).In this group diagnosis was confirmed by blood culture positive for S. Paratyphi (SPT). Antibiotic therapy commenced at time of diagnosis or at day 14 after challenge in those who did not develop symptoms. The clinical results of this study have been published in: Dobinson et al. Evaluation of the Clinical and Microbiological Response to Salmonella Paratyphi A Infection in the First Paratyphoid Human Challenge Model. Clin Infect Dis. 2017 Apr 15;64(8):1066-1073.

2019-09-02 | GSE114033 | GEO

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