Computational protocol: Genetic diversity and virulence of novel sequence types of Streptococcus suis from diseased and healthy pigs in China

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Protocol publication

[…] Bacteria were grown overnight at 37°C in Todd-Hewitt Broth (THB) and genomic DNA was then isolated using a TIANamp bacterial DNA kit (TIANGEN, China). For MLST (), the DNA fragments of seven housekeeping genes, including aroA, cpn60, dpr, gki, mutS, recA, and thrA, were amplified by PCR. Both DNA strands were sequenced with PCR primers on ABI-3700 sequencer. DNA sequences were aligned using MUSCLE Version 3.8 (). The alleles and the ST number of each isolate were determined by querying the S. suis MLST database . Clonal complexes were identified and the overall population structure was determined using the eBURST software (). Two different STs sharing six of the seven loci constituted a single-locus variant (SLV). A double-locus variant (DLV) contained two STs that differed in two loci but share the same other loci. A triple-locus variant (TLV) included two STs that differed in three loci. A clonal complex was composed of at least three STs with only SLVs. Two STs belonging to the same group with SLV were called a doublet. The remaining STs that did not contain SLV with other STs were termed singletons. The founders (ancestry types) of CCs were predicted with 1,000 re-samplings for bootstrap. […]

Pipeline specifications

Software tools MUSCLE, BURST
Applications WGS analysis, Nucleotide sequence alignment
Organisms Streptococcus suis, Sus scrofa, Mus musculus
Diseases Meningitis, Pierre Robin Syndrome, Drug-Related Side Effects and Adverse Reactions