TABLE 3

Exceptions to the inclusion/exclusion criteria used for Shigella serotypinga

Gene markerFunction and useSerotypeDescription of exceptionNo. of strains with exception (accession number of strains)No. of strains examined
ipaH_CConserved virulence gene Shigella/EIEC inclusion markerS. boydii 13Absent3 (SRR4178425, SRR4181329, SRR4181518)3
EclacYLactose permease Shigella exclusion markerS. boydii 9Full-length lacY4 (CP026836.1, SRR4180506, SRR6760302, SRR8186698)7
373-bp 5′ end of lacY3 (SRR4176997, SRR4180898, SRR4181342)
S. boydii 15lacY with 72-bp deletion at 5′ end3 (ASM296813v1 [GCF_002968135.1], SRR4179879, SRR8186662)3
S. dysenteriae 1366- to 475-bp 5′ end of lacY8 (CP000034, CP006736, DRR015930, SRR1811629, SRR5330538, SRR6373753, SRR8186696, SRR8186588)8
S. sonnei270-bp 5′ end of lacY21 (CP000038.1, CP023645.1, ERR1762061, ERR1762062, SRR4180904, SRR6927290, SRR6954223, SRR6982834, SRR7013788, SRR7013790, SRR7013792, SRR7013793, SRR7013794, SRR7013797, SRR7013799, SRR8186598, SRR8186617, SRR8186670, SRR8186671, SRR8186733, SRR8186738)22
No lacY1 (SRR6927273)
cadALysine decarboxylase, Shigella exclusion markerS. boydii 11Full-length cadA4 (CP026846.1, SRR4176974, SRR4180810, SRR4180822)5
258-bp 3′ end of cadA1 (DRR015925)
S. dysenteriae 1Full-length cadAb8 (see above for accession numbers)8
S. dysenteriae 8Full-length cadA6 (CP026827.1, DRR015992, SRR2994193, SRR8186616, SRR8186618, SRR8186667)6
S. dysenteriae 10127- to 171-bp 3′ end of cadA3 (CP026831.1, DRR015994, SRR8186726)3
S. sonneiFull-length cadAc22 (see above for accession numbers)22
Ss_methylasePutative (DNA) methylase, S. sonnei-specific markerS. dysenteriae 10Full-length Ss_methylase3 (see above for accession numbers)3
EIECFull-length Ss_methylase2 (DRR015801, SRR5330536)14
  • a Gene markers ipaH, EclacY, cadA, and Ss_methylase were examined from the genomes of 53 Shigella serotypes and EIEC. Serotypes displaying a genotype(s) that is an exception to the rule for Shigella/EIEC inclusion/exclusion, description of the exception, number of strains with the exception, accession numbers of the isolates, and total number of strains examined are listed.

  • b The full-length cadA in the S. dysenteriae 1 genome has a 4-bp deletion and the gene product is prematurely truncated.

  • c The full-length cadA in the S. sonnei genome is disrupted by two insertional elements and the gene product is prematurely truncated.