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. 2019 Dec 31;28:105066. doi: 10.1016/j.dib.2019.105066

Data on the link between genomic integration of IS1548 and lineage of the strain obtained by bioinformatic analyses of sequenced genomes of Streptococcus agalactiae available at the National Center for Biotechnology Information database

Sarah Khazaal a,b, Rim Al Safadi b, Dani Osman b, Aurélia Hiron a, Philippe Gilot a,∗
PMCID: PMC7096684  PMID: 32226814

Abstract

IS1548, a 1316-bp element of the ISAs1 family affects the expression of several genes of the opportunistic pathogen Streptococcus agalactiae. Furthermore, certain lineages of S. agalactiae are more frequently associated to particular diseases than other [1, 2]. We took advantage of the release of the genome sequences of a huge number of epidemiologically unrelated S. agalactiae strains of various origin to analyze the prevalence of IS1548 among S. agalactiae strains. To this end, S. agalactiae genome available at the National Center for Biotechnology Information (NCBI) database were blasted with IS1548 DNA sequences. A sequence type (ST), based on the allelic profile of seven housekeeping genes, was assigned to each strain possessing IS1548. These strains were then grouped into clonal complexes (CCs). The data obtained will give the opportunity to compare the sequenced genomes of S. agalactiae based on their lineage and/or possession of IS1548, and to select the corresponding strains for comparative experimental studies. The data is related to the research article « Dual and divergent transcriptional impact of IS1548 insertion upstream of the peptidoglycan biosynthesis murB gene of Streptococcus agalactiae” [2].

Keywords: Mobile genetic element, ISAs1 family, Multi locus sequence typing, Sequence type, Clonal complex, Population structure

Specifications Table

Subject Microbiology
Specific subject area Bacterial population structure and dynamics
Type of data Raw: Fig. 1, Fig. 2, Fig. 3, Fig. 4, Fig. 5, Fig. 6, Fig. 7, Fig. 8, Fig. 9
Raw: Table 1
How data were acquired BlastN program (https://blast.ncbi.nlm.nih.gov/)
MLST program (http://pubmlst.org/sagalactiae/)
goeBURST software (http://www.phyloviz.net/goeburst/)
Data format Raw
Parameters for data collection All the Streptococcus agalactiae genome sequences available as whole genome contigs or as complete genome sequences at the National Center for Biotechnology Information database on January 19, 2018 were analyzed
Description of data collection Bioinformatic analyses of the above cited genomes by the BlastN program, the MLST program and the goeBURST software
Data source location Institution: University of Tours
City/Town/Region: Tours
Country: France
Data accessibility With the article
Related research article Sarah Khazaal, Rim Al Safadi, Dani Osman, Aurelia Hiron, Philippe Gilot,
Dual and divergent transcriptional impact of IS1548 insertion upstream of the peptidoglycan biosynthesis murB gene of Streptococcus agalactiae, Gene, 720, https://doi.org/10.1016/j.gene.2019.144094
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Value of the Data
  • •

    As IS1548 plays a critical role in the evolution, the virulence and the host adaption ability of Streptococus agalactiae [1, 2], it is important to know which sequenced strains in the huge collection of the NCBI harbor (or not) this IS. It is also useful to know to which sequence type and clonal complex belong these strains as certain lineages of S. agalactiae are more frequently associated to particular diseases than other.

  • •

    Researchers involved in the study of: virulence and host adaptation mechanisms of S. agalactiae, of mobile genetic elements, of bacterial population structure and dynamics, and of S. agalactiae typing, can benefit from these data.

  • •

    The data gives the possibility to compare the sequenced genomes of Streptococcus agalactiae strains, available at the NCBI database, based on their lineage and/or possession of IS1548.

  • •

    The data allows the selection of sequenced strains based on their lineage and/or possession of IS1548 for comparative experimental studies.

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1. Data description

One hundred and twenty-one S. agalactiae strains with IS1548 positive blastN similarity finding were identified among the 911 strains whose genomes where sequenced and available at the NCBI database on January 19, 2018 [2]. The dataset comprises the analysis of the Multi Locus Sequence type of these strains with the MLST program (Table 1) and their classification in clonal complex with the goeburst software (Fig. 1, Fig. 2, Fig. 3, Fig. 4, Fig. 5, Fig. 6, Fig. 7, Fig. 8, Fig. 9), respectively.

Table 1.

Raw data of the Multi Locus Sequence Typing profiles of Streptococcus agalactiae strains possessing IS1548, obtained by submitting their sequenced genomes to the MLST databasea.

Strain adhP pheS atr glnA sdhA glcK tkt ST
351521 1 1 3 1 1 2 2 2
418136 1 1 3 2 2 2 2 19
446329 1 1 3 2 2 2 2 19
0506A_35_952 13 3 1 3 1 1 1 22
112469214_isolate1 13 3 1 3 1 1 1 22
2603V/R 1 1 3 2 2 2 9 110
357_SAGA 13 3 1 3 1 1 1 22
986_SAGA 156 1 3 2 2 2 2 853
B37VS 1 1 43 2 2 2 2 335
B41VS 116 1 4 1 3 3 2 652
B81VD 1 1 3 4 2 5 2 106
B848 1 1 3 2 2 2 2 19
B96V 2 1 1 2 1 1 1 17
BE-PW-051 1 1 3 2 2 2 2 19
BE-PW-095 1 1 3 2 2 2 2 19
BG-NI-012 1 1 3 2 2 2 2 19
BSU167 1 1 3 2 2 2 2 19
BSU174 10 1 12 1 3 2 2 41
BSU188 5 4 6 3 2 1 3 23
BSU442 13 3 1 3 1 1 1 22
BSU447 1 1 3 2 2 2 2 19
BV3L5 1 1 3 2 2 2 9 110
CCUG 19094 1 1 3 2 2 2 2 19
CCUG 24810 1 1 3 2 2 2 2 19
CCUG 37737 1 1 3 2 2 2 2 19
CCUG 37738 1 1 3 2 2 2 2 19
CCUG 37741 1 1 3 2 2 2 2 19
CCUG 37742 1 1 3 2 2 2 2 19
CCUG 44077 1 1 2 1 1 2 2 1
CCUG 44104 1 1 3 2 2 2 2 19
CCUG 45061 1 1 3 2 2 2 2 19
CZ-NI-002 1 1 3 2 2 2 2 19
CZ-NI-003 1 1 3 2 2 2 2 19
DE-NI-007 1 1 3 2 2 2 2 19
DE-NI-041 1 1 3 4 2 5 2 106
DE-NI-042 1 1 3 2 2 2 2 19
DK-NI-011 1 1 3 2 2 2 2 19
DK-PW-060 1 1 3 2 2 2 2 19
DK-PW-066 1 1 3 2 2 2 2 19
DK-PW-162 1 1 3 2 2 2 2 19
DML120817 1 1 3 2 2 2 2 19
ES-PW-008 1 1 3 2 2 2 2 19
ES-PW-033 1 1 3 2 2 2 2 19
ES-PW-063 1 1 3 2 2 2 2 19
ES-PW-085 1 1 3 2 2 2 2 19
ES-PW-118 1 1 3 2 2 2 2 19
ES-PW-156 1 1 3 2 2 2 2 19
FSL F2-338 13 3 1 3 1 1 1 22
FSL S3-003 1 1 3 2 2 2 2 19
FSL S3-005 13 3 1 3 1 1 1 22
FSL S3-268 13 3 1 3 1 1 1 22
FSL S3-337 1 1 3 2 2 2 2 19
GB00092 1 1 3 2 2 2 2 19
GB00174 13 3 1 3 1 1 1 22
GB00264 9 1 4 1 3 3 2 10
GB00543 1 1 3 2 2 2 7 36
GB00561 1 1 3 2 2 2 2 19
GB00653 10 1 4 1 3 3 2 12
GB00663 1 1 3 2 2 2 2 19
GB00864 9 1 4 1 3 3 2 10
GB00865 1 1 3 2 2 2 2 19
GB00884 1 1 3 2 2 2 2 19
GB00904 1 1 3 2 2 2 2 19
GB00923 1 1 3 3 2 2 2 175
GB00929 1 1 3 2 2 2 2 19
GB00975 13 3 1 3 1 1 1 22
GB00984 1 1 3 2 2 2 2 19
GB01004 13 3 1 3 1 1 1 22
GB-NI-007 1 1 3 2 2 2 2 19
GB-NI-011 1 1 3 2 2 2 2 19
GB-NI-014 13 3 1 3 1 1 1 22
GB-NI-015 1 1 3 2 2 2 2 19
GB-PW-035 1 1 3 2 2 2 2 19
GB-PW-041 1 1 3 2 2 2 2 19
GB-PW-049 1 1 3 2 2 2 2 19
GB-PW-051 1 1 3 2 2 2 2 19
GB-PW-067 10 1 4 1 3 3 2 12
GB-PW-087 1 1 3 2 2 2 2 19
GB-PW-088 1 1 3 2 2 2 2 19
GBS1-NY 13 3 1 3 1 1 1 22
GBS2-NM 13 3 1 3 1 1 1 22
GBS6 13 3 1 3 1 1 1 22
GBS11 1 1 3 2 2 2 2 19
Gottschalk 1003A 1 1 3 2 2 2 2 19
H002 1 1 110 2 2 2 2 928
IMMI_409 1 1 3 2 2 2 2 19
IT-NI-036 1 1 5 4 1 4 6 26
IT-NI-037 1 1 5 4 1 4 6 26
LMG 15089 1 1 3 2 2 2 2 19
LMG 15093 1 1 3 2 2 2 9 110
Madagascar-IP-47 9 1 4 1 3 3 2 10
MC627 13 3 1 3 1 1 1 22
MC628 1 1 3 2 2 2 2 19
MC632 13 3 1 3 1 1 1 22
MC633 13 3 1 3 1 1 1 22
MC634 13 3 1 3 1 1 1 22
ML41151 1 1 4 2 2 3 2 328
Mother12 1 1 3 4 2 2 2 27
MRI Z1-022 32 1 3 2 2 2 2 121
PSS_7568 1 1 3 2 2 2 2 19
PSS_7632a 1 1 3 2 2 2 2 19
RBH01 1 1 3 2 2 2 2 19
RBH03 1 1 3 2 2 2 2 19
RBH04 1 1 3 2 2 2 2 19
RBH06 13 3 1 3 1 1 1 22
RBH11 1 1 3 2 2 2 2 19
RBH12 1 1 3 2 2 2 2 19
S10-201 1 1 3 2 2 2 2 19
Sag158 1 1 3 2 2 2 2 19
SG-M25 1 1 3 2 2 2 2 19
SH0334 1 1 3 2 2 2 2 19
SH0655 10 1 4 2 3 3 2 286
SH1370 1 1 2 1 1 2 2 1
SH3601 1 1 3 2 2 2 2 19
ST 610 13 40 6 65 3 52 50 610
ST 612 111 40 6 65 3 52 51 612
ST 613 111 40 67 65 3 52 51 613
ST 615 13 40 6 65 3 52 51 615
ST 617 13 40 68 65 3 52 51 617
ST 618 111 40 69 65 3 52 51 618
USS-107 1 1 3 2 18 2 2 182
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a

Sequence type (ST), alcohol dehydrogenase gene (adhP), phenylalanine tRNA synthetase gene (pheS), amino acid transporter gene (atr), glutamine synthetase gene (glnA), serine dehydratase gene (sdhA), glucose kinase gene (glcK) and transketolase gene (tkt). Multi Locus Sequence Typing (MLST) database at https://pubmlst.org/sagalactiae/.

Fig. 1.

Fig. 1

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Raw data of the goeBURST analysis of the sequence types of strains possessing IS1548: Clonal Complex 1.

Fig. 2.

Fig. 2

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Raw data of the goeBURST analysis of the sequence types of strains possessing IS1548: Clonal Complex 7.

Fig. 3.

Fig. 3

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Raw data of the goeBURST analysis of the sequence types of strains possessing IS1548: Clonal Complex 10 and 12.

Fig. 4.

Fig. 4

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Raw data of the goeBURST analysis of the sequence types of strains possessing IS1548: Clonal Complex 17.

Fig. 5.

Fig. 5

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Raw data of the goeBURST analysis of the sequence types of strains possessing IS1548: Clonal Complex 19.

Fig. 6.

Fig. 6

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Raw data of the goeBURST analysis of the sequence types of strains possessing IS1548: Clonal Complex 22.

Fig. 7.

Fig. 7

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Raw data of the goeBURST analysis of the sequence types of strains possessing IS1548: Clonal Complex 23.

Fig. 8.

Fig. 8

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Raw data of the goeBURST analysis of the sequence types of strains possessing IS1548: Clonal Complex 27.

Fig. 9.

Fig. 9

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Raw data of the goeBURST analysis of the sequence types of strains possessing IS1548: Clonal Complex 615.

2. Experimental design, materials, and methods

The list of the S. agalactiae strains analyzed is available in Table S1 of reference [2]. Sequences of the genomes of these strains were available as whole genome contigs or as complete genome sequences at the NCBI database on January 19, 2018 (https://www.ncbi.nlm.nih.gov/genome/genomes/186?). Strains with an IS1548 genomic insertion were identified by blasting these genomes with the IS1548 DNA sequences described in Ref. [2]. To this end, the nucleotide collection (nr/nt) and the whole-genome shotgun contigs (wgs) databases of S. agalactiae (taxid:1311) were screened with the blastN program optimized for highly similar sequences (megablast). The algorithm parameters were defined as followed: maximum number of aligned sequences to display: 1000; parameters for short input sequences automatically adjusted; expect threshold: 10; word size: 28; maximum matches in a query range: 0; match/mismatch scores: 1,-2; gap costs: linear; filter for low complexity region activated; mask for lookup table only activated. S. agalactiae strains with an IS1548 positive blastN similarity finding were typed by Multi Locus Sequence Typing (MLST). Seven housekeeping genes were analyzed: alcohol dehydrogenase gene (adhP), phenylalanine tRNA synthetase gene (pheS), amino acid transporter gene (atr), glutamine synthetase gene (glnA), serine dehydratase gene (sdhA), glucose kinase gene (glcK) and transketolase gene (tkt). A sequence type, based on the allelic profile of these housekeeping genes, was assigned to each strain by submitting the complete genome sequence or all of the contigs sequences of each strain to the Streptococcus agalactiae MLST database (http://pubmlst.org/sagalactiae/, [3], Table 1). Identified MLST types were then assigned to clonal complexes defined by the goeBURST algorithm (http://www.phyloviz.net/goeburst/, [4], Fig. 1, Fig. 2, Fig. 3, Fig. 4, Fig. 5, Fig. 6, Fig. 7, Fig. 8, Fig. 9) with the ST1 to ST1193 MLST profiles available at the MLST database (https://pubmlst.org/bigsdb?db=pubmlst_sagalactiae_seqdef&page=downloadProfiles&scheme_id=1). A goeBURST clonal complex was defined as all allelic profiles sharing six identical alleles with at least one other member of the group.

Acknowledgments

SK was supported by PhD fellowships of the Lebanese University and AZM & SAADÉ and of the Lebanese Association for Scientific Research (LASeR). This publication made use of the PubMLST website (https://pubmlst.org/) developed by Keith Jolley and sited at the University of Oxford. The development of that website was funded by the Wellcome Trust.

Footnotes

Appendix A

Supplementary data to this article can be found online at https://doi.org/10.1016/j.dib.2019.105066.

Conflict of Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Appendix A. Supplementary data

The following is the Supplementary data to this article:

Multimedia component 1
mmc1.xml (371B, xml)

References

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Supplementary Materials

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