Prediction of Pasteurella multocida serotypes based on whole genomic sequences
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Prediction of Pasteurella multocida serotypes based on whole genomic sequences. / Christensen, Henrik; Sajid, Sajid Mahmood; Bisgaard, Magne; Magistrali, Chiara Francesca; Massacci, Francesca Romana; Liman, Martin; Menke, Theresa; Bischoff, Henning; Olsen, John E.
In: Veterinary Microbiology, Vol. 271, 109492, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Prediction of Pasteurella multocida serotypes based on whole genomic sequences
AU - Christensen, Henrik
AU - Sajid, Sajid Mahmood
AU - Bisgaard, Magne
AU - Magistrali, Chiara Francesca
AU - Massacci, Francesca Romana
AU - Liman, Martin
AU - Menke, Theresa
AU - Bischoff, Henning
AU - Olsen, John E.
N1 - Publisher Copyright: © 2022 The Authors
PY - 2022
Y1 - 2022
N2 - The serotypes of Pasteurella multocida were predicted based on whole genomic sequences (WGS) with specific genes of the capsular and liposaccharide (LPS) outer core polysaccharide regions as targets. A total of 56 strains were whole genomic sequenced and in addition all assembled genomes from NCBI were included for comparison. BIGSdb (Bacterial Isolate Genome Sequence Database) was installed on a Linux server and targets for capsular types A, B, D, E and F were defined as gene sequences of hyaD, bcbD, dcbF, ecbJ and fcbD, respectively and targets for LPS groups 1, 2, 3, 4, 5, 6, 7 and 8 were defined as gene sequences of pcgB, nctA, gatF, latB, rmlA, nctB, ppgB and natG, respectively. The serotypes of P. multocida were predicted from WGS by designating the capsular type and LPS group as well as subtype alleles to isolates. Comparisons between WGS predictions of capsular types and classical phenotypic typing showed correspondence in 87 % of cases whereas comparisons of WGS predictions of LPS groups to phenotypic typing corresponded for 82 % of the strains. In total 93 % and 94 % of the strains available with WGS could be capsular and LPS group typed, respectively. The server is free to access from https://ivsmlst.sund.ku.dk.
AB - The serotypes of Pasteurella multocida were predicted based on whole genomic sequences (WGS) with specific genes of the capsular and liposaccharide (LPS) outer core polysaccharide regions as targets. A total of 56 strains were whole genomic sequenced and in addition all assembled genomes from NCBI were included for comparison. BIGSdb (Bacterial Isolate Genome Sequence Database) was installed on a Linux server and targets for capsular types A, B, D, E and F were defined as gene sequences of hyaD, bcbD, dcbF, ecbJ and fcbD, respectively and targets for LPS groups 1, 2, 3, 4, 5, 6, 7 and 8 were defined as gene sequences of pcgB, nctA, gatF, latB, rmlA, nctB, ppgB and natG, respectively. The serotypes of P. multocida were predicted from WGS by designating the capsular type and LPS group as well as subtype alleles to isolates. Comparisons between WGS predictions of capsular types and classical phenotypic typing showed correspondence in 87 % of cases whereas comparisons of WGS predictions of LPS groups to phenotypic typing corresponded for 82 % of the strains. In total 93 % and 94 % of the strains available with WGS could be capsular and LPS group typed, respectively. The server is free to access from https://ivsmlst.sund.ku.dk.
KW - Capsular encoding gene region
KW - LPS outer core polysaccharide encoding
KW - MLST
KW - Multilocus, gene sequence typing
U2 - 10.1016/j.vetmic.2022.109492
DO - 10.1016/j.vetmic.2022.109492
M3 - Journal article
C2 - 35714528
AN - SCOPUS:85131966431
VL - 271
JO - Veterinary Microbiology
JF - Veterinary Microbiology
SN - 0378-1135
M1 - 109492
ER -
ID: 313495061