Complete Genome Sequences of African Salmonella enterica Serovar Enteritidis Clinical Isolates Associated with Bloodstream Infection

Perez-Sepulveda, Blanca; Predeus, Alexander V.; Fong, Wai Yee; Parry, Christopher M.; Cheesbrough, J.; Wigley, Paul; Feasey, Nicholas; Hinton, Jay C. D.

doi:10.1128/mra.01452-20

Cited by 7 publications

(24 citation statements)

References 17 publications

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“…The browsers show the transposon insertion profiles for the chromosome and plasmid of S. Enteritidis (pSENV in P125109; pSEN-BT and pRGI00316 in D7795). To yield maximum biological insight from the transposon mutagenesis experiment, we employed our recent re-annotation of the coding genes and non-coding sRNA genes of P125109 and D7795 [15], which was derived from a comparative genomic approach that identified all the annotated genes of S. Typhimurium ST19 [52] and S. Typhimurium ST313 [53] that were carried by the two S. Enteritidis strains (Materials and Methods).…”

Section: Resultsmentioning

confidence: 99%

“…We compared the interaction of S. Enteritidis GEC P125109 and CEAC D7795 with RAW 264.7 macrophages, together with two additional S. Enteritidis strains, A1636 and CP255. A1636 is a GEC isolate from Africa, while CP255 belongs to the same Central/Eastern African clade as D7795 that originated from the Democratic Republic of Congo [9,15]. ΔphoPQ deletion mutants were constructed in P125109 and D7795 by λ Red recombineering as negative controls for the infection studies.…”

Section: Resultsmentioning

confidence: 99%

“…The annotated complete long-read-based genome assemblies of S. Enteritidis P125109 and D7795 are available in the National Center for Biotechnology Information (NCBI) Assembly database (accession numbers SAMN16552335GCA_015240635.1 [P125109] and SAMN16552336GCA_015240855.1 [D7795]) [15]. Orthologues between the S. Enteritidis and other Salmonella strains presented in this study were identified using the pipeline described at https://github.com/apredeus/multi-bacpipe.…”

Section: Methodsmentioning

confidence: 99%

“…Experimental validation of these candidates by individual gene deletion mutation will be necessary to verify a role in intra-macrophage replication. P125109 ID = P125109 locus tags from re-annotation [15]; SEN ID = S. Enteritidis identifiers; D23580 = S. Typhimurium ST313 strain D23580; LT2 = S. Typhimurium ST19 strain LT2 D7795 ID = D7795 locus tags from re-annotation [15]; SEN ID = S. Enteritidis identifiers; D23580 = S. Typhimurium ST313 strain D23580; LT2 = S. Typhimurium ST19 strain LT2…”

Section: Candidate Novel Macrophage Fitness Genes That Were Unique To...mentioning

confidence: 99%

“…P125109 was isolated from an outbreak of human food poisoning in the United Kingdom in 1988 [12][13][14], while D7795 was isolated from blood culture from a Malawian child in 2000 [9]. The genome sequences of P125109 and D7795 were published in 2008 [12] and 2016 [9], respectively, and were recently reannotated and improved with long-read sequencing [15].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and Global Epidemic pathovariants of Salmonella Enteritidis

Fong

Canals

Predeus

et al. 2022

Preprint

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Salmonella Enteritidis is the second most common serovar associated with iNTS disease in sub-Saharan Africa. Previously, genomic and phylogenetic characterisation of S. Enteritidis isolates from human bloodstream led to the discovery of the Western African and Central/Eastern African (CEAC) clades, which were distinct from the gastroenteritis- associated Global Epidemic clade (GEC). The African S. Enteritidis clades have unique genetic signatures that include genomic degradation, novel prophage repertoires and multidrug resistance, but the molecular basis for the enhanced propensity of African S. Enteritidis to cause bloodstream infection is poorly understood. We used transposon insertion sequencing to identify the genetic determinants of the GEC representative strain P125109 and the CEAC representative strain D7795 for growth in three in vitro conditions (LB or minimal NonSPI2 and InSPI2 growth media), and for survival and replication in RAW 264.7 murine macrophages. We identified 207 in vitro-required genes that were common to both S. Enteritidis strains and also required by S. Typhimurium, S. Typhi and Escherichia coli, and 63 genes that were only required by individual S. Enteritidis strains. Similar types of genes were required by both P125109 and D7795 for optimal growth in particular media. Screening the transposon libraries during macrophage infection identified 177 P125109 and 201 D7795 genes that contribute to bacterial survival and replication in mammalian cells. The majority of these genes have proven roles in Salmonella virulence. Our analysis also revealed candidate strain-specific macrophage fitness genes, some of which represent potential novel Salmonella virulence factors.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Candidate Novel Macrophage Fitness Genes That Were Unique To...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and Global Epidemic pathovariants of Salmonella Enteritidis

Fong

Canals

Predeus

et al. 2022

Preprint

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Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and global epidemic pathovariants of Salmonella enterica Enteritidis

et al. 2023

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Salmonella enterica Enteritidis is the second most common serovar associated with invasive non-typhoidal Salmonella (iNTS) disease in sub-Saharan Africa. Previously, genomic and phylogenetic characterization of S . enterica Enteritidis isolates from the human bloodstream led to the discovery of the Central/Eastern African clade (CEAC) and West African clade, which were distinct from the gastroenteritis-associated global epidemic clade (GEC). The African S . enterica Enteritidis clades have unique genetic signatures that include genomic degradation, novel prophage repertoires and multi-drug resistance, but the molecular basis for the enhanced propensity of African S . enterica Enteritidis to cause bloodstream infection is poorly understood. We used transposon insertion sequencing (TIS) to identify the genetic determinants of the GEC representative strain P125109 and the CEAC representative strain D7795 for growth in three in vitro conditions (LB or minimal NonSPI2 and InSPI2 growth media), and for survival and replication in RAW 264.7 murine macrophages. We identified 207 in vitro-required genes that were common to both S . enterica Enteritidis strains and also required by S . enterica Typhimurium, S . enterica Typhi and Escherichia coli , and 63 genes that were only required by individual S . enterica Enteritidis strains. Similar types of genes were required by both P125109 and D7795 for optimal growth in particular media. Screening the transposon libraries during macrophage infection identified 177 P125109 and 201 D7795 genes that contribute to bacterial survival and replication in mammalian cells. The majority of these genes have proven roles in Salmonella virulence. Our analysis uncovered candidate strain-specific macrophage fitness genes that could encode novel Salmonella virulence factors.

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Isolation and characterisation of bacteriophages with activity against invasive non-typhoidalSalmonellacausing bloodstream infection in Malawi

Rodwell

Wenner

Pulford

et al. 2021

Preprint

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In recent years, novel lineages of invasive non-typhoidal Salmonella (iNTS) serovars Typhimurium and Enteritidis have been identified in patients with bloodstream infection in sub-Saharan Africa. Here, we isolated and characterised 32 phages capable of infecting S. Typhimurium and S. Enteritidis, from water sources in Malawi and the UK. The phages were classified in three major phylogenetic clusters that were geographically distributed. In terms of host range, Cluster 1 phages were able to infect all bacterial hosts tested, whereas Clusters 2 and 3 had a more restricted profile. Cluster 3 contained two sub-clusters, and 3.b contained the most novel isolates. This study represents the first exploration of the potential for phages to target the lineages of Salmonella that are responsible for bloodstream infections in sub-Saharan Africa.

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Complete Genome Sequences of African Salmonella enterica Serovar Enteritidis Clinical Isolates Associated with Bloodstream Infection

Abstract: We report the complete genome sequencing and annotation of four Salmonella enterica serovar Enteritidis isolates, two that are representative of the Central/Eastern African clade (CP255 and D7795) and two of the Global Epidemic clade (A1636 and P125109).

Cited by 7 publications

References 17 publications

Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and Global Epidemic pathovariants of Salmonella Enteritidis

Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and Global Epidemic pathovariants of Salmonella Enteritidis

Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and global epidemic pathovariants of Salmonella enterica Enteritidis

Isolation and characterisation of bacteriophages with activity against invasive non-typhoidalSalmonellacausing bloodstream infection in Malawi

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