Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria

Akinyemi, Kabiru Olusegun; Fakorede, Christopher Oladimeji; Linde, Jörg; Methner, Ulrich; Wareth, Gamal; Tomaso, Herbert; Neubauer, Heinrich

doi:10.1186/s12866-023-02901-1

Table 3 Distribution of Salmonella virulence genes clustered within several Salmonella pathogenicity Islands (SPIs) and plasmid operons from different source from Nigeria

From: Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria

Strain ID	Serovar	Num of virulence gene	Virulence loci	Virulence genes
19CS0245	Give	100	SPI-1 SPI-2, SPI-3 SPI-11SPI-5, SPI-24/CS54 fimbriae operon	ctdB, fae. faeD faeE sspH1*
19CS0246	Give	100	SPI-1 SPI-11 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	CtdB fae. faeD faeE sspH1*
19CS0247	Give	100	SPI-1 SPI-11 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	CtdB fae. faeD faeE sspH1*
19CS0248	Give	100	SPI-1 SPI-11 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	CtdB fae. faeD faeE sspH1*
19CS0249	Give	100	SPI-1 SPI-11 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	CtdB fae. faeD faeE sspH1*
19CS0250	Cotham	100	SPI-1 SPI-11 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	CtdB fae. faeD faeE pipB2*
19CS0251	Give	100	SPI-1 SPI-11 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE sspH1*
19CS0253	Typhimurium	116	SPI-1 Long polar fimbriae cluster, Plasmid encoded fimbriae cluster, Plasmid virulence Operon SPI-2 SPI-3 SPI-5 SPI-12 SPI-24/CS54 fimbriae operon	gogB grvA ipfA ipfB ipfC ipfD ipfE pefA pefB pefC pefD pipB2 rck sodC1 sopD2 spvB spvC spvR ssel.srfH sseK2 sspH2*
19CS0255	Senftenberg	101	SPI-1 Long polar fimbriae cluster SPI-3 SPI-5	ipfA ipfB ipfC ipfD ipfE pipB2 sopD2*
19CS0256	Typhimurium	116	SPI-1 SPI-2 SPI-3 Long polar fimbriae cluster, Plasmid encoded fimbriae cluster, Plasmid virulence Operon SPI-5 SPI-12 SPI-24/CS54 fimbriae operon	gogB grvA ipfA ipfB ipfC ipfD ipfE pefA pefB pefC pefD pipB2 rck sodC1 sopD2 spvB spvC spvR ssel.srfH sseK2 sspH2*
19CS0257	Abony	106	SPI-1 SPI-2 SPI-3 Long polar fimbriae cluster SPI-5 SPI-12 SPI-24/CS54 fimbriae operon	ipfA ipfB ipfC ipfD ipfE pipB2 shdA sodC1 sopD2 sseK2 sspH2*
19CS0258	Typhimurium	118	SPI-1 SPI-2 SPI-12 SPI-24/CS54 Long polar fimbriae cluster, Plasmid encoded fimbriae SPI-5iae cluster, Plasmid virulence Operon fimbriae operon	gogB grvA ipfA ipfB ipfC ipfD ipfE pefA pefB pefC pefD pipB2 rck shdA sodC1 sopD2 spvB spvC spvR ssel.srfH sseK2 sspH2 sspH1*
19CS0259	Give	100	SPI-1 SPI-11 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE sspH1*
19CS0260	Give	100	SPI-1 SPI-11 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE sspH1*
19CS0261	Give	100	SPI-1 SPI-11 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE sspH1*
19CS0262	Give	100	SPI-1 SPI-11 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	CtdB fae. faeD faeE sspH1*
19CS0263	Cotham	100	SPI-1 SPI-2 SPI-11 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0264	Give	100	SPI-1 SPI-11 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	CtdB fae. faeD faeE sspH1*
19CS0266	Give	100	SPI-1 SPI-11 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE sspH1*
19CS0267	Cotham	100	SPI-1 SPI-2 SPI-11 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0268	Give	100	SPI-1 SPI-11 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE sspH1*
19CS0269	Cotham	100	SPI-1 SPI-2 SPI-11 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0270	Mokola	102	SPI-1 SPI-2 SPI-3 SPI-5 SPI-12 SPI-24/CS54 fimbiae operon	entE pipB2 shdA sodC1 sopD2 sseK2 sspH2*
19CS0271	Cotham	100	SPI-1 SPI-2 SPI-11 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0272	Cotham	100	SPI-1 SPI-2 SPI-11 SPI-3 SP1-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0273	Mokola	102	SPI-1 SPI-2 SPI-3 SPI-5 SPI-12 SPI-24/CS54 fimbriae operon	entE pipB2 shdA sodC1 sopD2 sseK2 sspH2*
19CS0274	Cotham	100	SPI-1 SPI-2SPI-11 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0275	Cotham	100	SPI-1 SPI-2SPI-11 SPI-3 SPI-5 f SPI-24/CS54 imbriae operon	ctdB fae. faeD faeE pipB2*
19CS0276	Mokola	102	SPI-1 SPI-2 SPI-3 SPI-5 SPI-12 SPI-24/CS54 fimbriae operon	entE pipB2 shdA sodC1 sopD2 sseK2 sspH2*
19CS0277	Cotham	100	SPI-1 SPI-2SPI-11 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0278	Cotham	100	SPI-1 SPI-2 SPI-11 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0279	Cotham	100	SPI-1 SPI-2 SPI-11 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0280	Give	100	SPI-1 SPI-2SPI-11 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE sspH1*
19CS0281	Mokola	100	SPI-1 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	entE pipB2 shdA sodC1 sopD2*
19CS0282	Mokola	102	SPI-1 SPI-2 SPI-3 SPI-5 SPI-12 SPI-24/CS54 fimbriae operon	entE pipB2 shdA sodC1 sopD2 sseK2 sspH2*
19CS0283	Cotham	100	SPI-1 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0284	Cotham	100	SPI-1 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0285	Cotham	100	SPI-1 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0286	Typhimurium	116	SPI-1 SPI- SPI-3 2 Long polar fimbriae cluster, Plasmid encoded fimbriae cluster, Plasmid virulence Operon SPI-5 SPI-12 SPI-24/CS54 fimbriae operon	gogB grvA ipfA ipfB ipfC ipfD ipfE pefA pefB pefC pefD pipB2 rck sodC1 sopD2 spvB spvC spvR ssel.srfH sseK2 sspH2*
19CS0287	Mokola	101	SPI-1 SPI-2 SPI-3 SPI-5 SPI-12 SPI-24/CS54 fimbriae operon	entE pipB2 shdA sodC1 sopD2 sspH2*
19CS0288	Cotham	100	SPI-1 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0289	Give	100	SPI-1 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE sodC1 sopD2 sspH1 sspH1*
19CS0290	Abony	106	SPI-1 SPI-2 SPI-3 SPI-24/CS54 Long polar fimbriae cluster SPI-5 fimbriae operon	ipfA ipfB ipfC ipfD ipfE pipB2 shdA sseK2 sspH2*
19CS0291	Cotham	100	SPI-1 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0292	Cotham	100	SPI-1 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE pipB2*
19CS0293	Give	100	SPI-1 SPI-2 SPI-3 SPI-5 SPI-24/CS54 fimbriae operon	ctdB fae. faeD faeE sspH1*
19CS0294	Abony	106	SPI-1 SPI-2 SPI-3 SPI-12 SPI-24/CS54 Long polar fimbriae cluster SPI-5 fimbriae operon	ipfA ipfB ipfC ipfD ipfE pipB2 shdA sodC1 sopD2 sseK2 sspH2*
19CS0295	Abony	106	SPI-1 SPI-2 SPI-3 SPI-12 SPI-24/CS54 Long polar fimbriae cluster SPI-5 fimbriae operon	ipfA ipfB ipfC ipfD ipfE pipB2 shdA sodC1 sopD2 sseK2 sspH2*
GCF0000069452ASM694v2	LT2	117	SPI-1 SPI-2 SPI-3 SPI-5 SPI-12 SPI-24/CS54 Long polar fimbriae cluster, Plasmid encoded fimbriae cluster, Plasmid virulence Operon fimbriae operon	gogB grvA ipfA ipfB ipfC ipfD ipfE pefA pefB pefC pefD pipB2 rck sodC1 sopD2 SshdA spvB spvC spvR ssel.srfH sseK2 sspH2*

*Represents the following 95 virulence genes: avrA csgA csgB csgC csgD csgE csgF csgG entA entB fepC fepG fimC fimD fimF fimH fimI invA invB invC invE invF invG invH invI invJ mgtB mgtC mig.14 misL ompA orgA orgB orgC pipB prgH prgI prgJ prgK ratB sicA sicP sifA sifB sinH sipA.sspA sipB.sspB sipC.sspC sipD slrP sopA sopB.sigD sopD sopE2 spaO spaP spaQ spaR spaS spiC.ssaB sptP ssaC ssaD ssaE ssaG ssaH ssaI ssaJ ssaK ssaL ssaM ssaN ssaO ssaP ssaQ ssaR ssaS ssaT ssaU ssaV sscA sscB sseA sseB sseC sseD sseE sseF sseG sseJ sseK1 sseL steA steB steC
3° 24’ 23.2128’’ E. (Longitude)

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ISSN: 1471-2180

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