TABLE 2

Genomic mutations detected in the population of each pair of samples

SampleaMLSTTypeClassificationbLocus IDcFunctiondBLASTe
Mother 2ST23SNPNonsense (Q7X), fixedgbs1596Intermediary metabolismGlyoxalase
Mother 2ST23SNPSynonymous, fixedgbs0198Intermediary metabolismPolynucleotide phosphorylase, alpha chain
Mother 4ST17SNPMissense (K88E), polymorphicSAG0163_02655Information pathwaysSite-specific recombinase
Mother 9ST23IndelNoncodinghgbs0476 (3′ UTR)UnknownPutative membrane protein
Child 9ST23SNPMissense (R79H), polymorphicgbs1259Intermediary metabolismMetallo-beta-lactamase superfamily protein
Mother 10-1ST23SNPNoncoding, fixedgbs1986Cellular processesABC transporter
Child 11-2fST17IndelFrameshiftgbs1427Information pathwaysKH domain protein
Child 11-2fST17SNPMissense (A175D), fixedgbs1950Cellular processesPhosphate ABC transporter
Mother 12ST27SNPNoncoding, fixedgbs1946 (5′ UTR)Cellular processesGlucose-specific PTS enzyme IIABC
Child 12gST27SNPMissense (A49V), fixedgbs0668Intermediary metabolismd-lactate dehydrogenase
Child 12gST27SNPMissense (G814S), fixedgbs1038Cellular processesHypothetical ABC transporter permease
Child 12-1ST27SNPNoncoding, polymorphicgbs1946 (5′ UTR)Cellular processesGlucose-specific PTS enzyme IIABC
Child 12-1ST27IndelIn-frame deletionhgbs1377Intermediary metabolismHomocysteine S-methyltransferase
Child 12-1ST27IndelLarge deletionhUnknownPhage terminase
Child 12-2ST27SNPNoncoding, fixedgbs1672 (5′ UTR)Information pathwaysTwo-component response regulator (CovR)
Child 12-2ST27SNPMissense (R186K), fixedgbs0231Cellular processesEfflux protein
Mother 14ST17SNPNoncoding, fixedgbs0330 (5′ UTR)Information pathwaysTranscriptional regulator (MarR family)
Mother 14ST17SNPMissense (G30V), fixedgbs1234Cellular processesNeuD protein
Child 14ST17IndelDuplicationhgbs1958Information pathwaysTranscriptional regulator (MerR family)
Mother 15ST1IndelNoncodinghgbs0419 (5′ UTR)Intermediary metabolismGDXG lipolytic enzyme family protein
Mother 15ST1SNPMissense (I183T), fixedgbs1230Intermediary metabolismGlycerol-3-phosphate acyltransferase (PlsY)
Mother 15ST1SNPNoncoding, fixedUnknownAnaerococcus prevotii plasmid
Mother 18ST24SNPSynonymous, polymorphicgbs0189Cellular processesTrehalose-specific PTS enzyme IIABC
Mother 18ST24SNPMissense (P396S), polymorphicgbs1460Cellular processesPolysaccharide biosynthesis protein
Mother 19ST17SNPMissense (P80S), fixedgbs2047Information pathwaysRecA protein
Child 19gST17SNPNonsense (E96X), fixedgbs1159Intermediary metabolismPhosphotransacetylase
Child 19gST17SNPMissense (A115V), fixedgbs1672Information pathwaysTwo-component response regulator (CovR)
Child 19gST17IndelNoncodinghGBSCOH1_0416Cellular processesRib protein
  • a Sample of the corresponding pair in which the mutant allele was most frequently detected.

  • b Classification of the mutation detected. For nonsynonymous substitutions, the amino acid change is shown in parentheses. A mutation was considered fixed if at least 97% of the filtered reads supported the mutation in at least one of the samples of the pair (see Table S2 in the supplemental material). No frequency estimate was calculated for indels.

  • c Locus ID of the mutated gene: SAG0163_02655 corresponding to GBS MRI Z1-215 (GenBank accession no. NZ_ANET01000026), GBSCOH1_0416 corresponding to GBS COH1 (GenBank accession no. HG939456), and the rest corresponding to GBS NEM316 (GenBank accession no. AL732656).

  • d Functional category of each affected gene based on the SagaList database of NEM316.

  • e Annotation based on BLASTn homology search.

  • f Mutations were called by mapping against child 11-1.

  • g Mutations were detected in all child samples of the corresponding pair.

  • h No homology with any annotated GBS genomes in the NCBI database.