Identification of Nonserotypeable Shigella Spp. Using Genome Sequencing: A Step Forward

Figures & data

Figure 1.  Serogroup distribution of Shigella from feces specimens over 5 years (2011–2015).

Figure 2.  Antimicrobial susceptibility trend of serotypeable and nonserotypeable Shigella spp. over 5 years (2011–2015).

Table 1.  Comparative analysis of SpeciesFinder, KmerFinder, gyrB sequence and O-antigen gene sequence based identification of nonserotypeable Shigella.

Isolate ID	Manual analysis using PATRIC	Center for Genomic Epidemiology		BLAST gyrB sequence analysis	Sequence types
		SpeciesFinder	KmerFinder
FC1	S. boydii	S. boydii	S. boydii	S. boydii	145
FC2	S. boydii	S. boydii	S. boydii	S. boydii	145
FC3	S. boydii	Matching failed	S. boydii	S. boydii	243
FC4	S. boydii	Matching failed	S. boydii	S. boydii	145
FC5	S. boydii	Matching failed	S. boydii	S. boydii	145
FC6	S. boydii	S. boydii	S. boydii	S. boydii	145
FC7	S. boydii	S. boydii	S. boydii	S. boydii	145
FC8	S. boydii	S. boydii	S. boydii	S. boydii	145
FC9	S. boydii	S. boydii	S. boydii	S. boydii	145
FC10	S. flexneri 2a	S. flexneri	S. flexneri	S. flexneri	245
FC11	S. flexneri 2a	S. flexneri	S. flexneri	S. flexneri	245
FC12	S. flexneri 2a	S. flexneri	S. flexneri	S. flexneri	245
FC13	S. dysenteriae	Matching failed	S. boydii	S. boydii^†	148
FC14	S. dysenteriae	S. boydii	S. boydii	S. boydii^†	148
FC15	S. dysenteriae	S. boydii	S. boydii	S. boydii^†	148
FC16	S. dysenteriae	S. boydii	S. boydii	S. boydii^†	148
FC17	S. dysenteriae	S. boydii	S. boydii	S. boydii^†	148
FC18	–	Matching failed	S. boydii	S. boydii	243
FC19	–	Matching failed	S. boydii	S. boydii^†	148
FC20	–	S. boydii	S. boydii	S. boydii^†	148
FC21	–	E. coli	E. coli	E. coli	6199
FC22	–	E. coli	E. coli	E. coli	6199
FC23	–	E. coli	E. coli	E. coli	6270

† Isolates with only 99% identity.

Table 2.  Genomic characteristics of nonserotypeable Shigella (n = 23).

Isolate ID	Total size (bp)	Antimicrobial resistance profile	ResFinder	VirulenceFinder	PlasmidFinder	Accession
FC1	4511440	SXT-NAL	strA, strB, aadA1, sul2, dfrA1	iha, senB, ipaD, virF	IncFII	MDDI00000000
FC2	4669256	AMP-SXT	strA, strB, blaTEM1B, qnrS1, sul2, tetA, dfrA14	virF, ipaD, senB, ipaH, iha	IncFII, IncFIB	MDDH00000000
FC3	4553246	SXT-NAL-FIX	aadA1, sul1, tetA, dfrA1, dfrA4	virF, capU, ipaD, ipfA, senB, iha	IncA/C2, IncFII	MDGW00000000
FC4	4561671	–	–	iha, capU, ipaD, sigA,senB, virF	IncFII	MDJL00000000
FC5	4579536	AMP-SXT-NAL	–	iha, capU, sigA, ipaD, senB, virF	IncFII	MIIV00000000
FC6	4556438	AMP-SXT	strA, strB, blaTEM-1B, qnrS1, sul2, tetA, dfrA14	iha, capU, sigA, ipaD, senB, virF	IncFII, IncFIB	MINP00000000
FC7	4514218	SXT-NAL-NOR	aadA1, dfrA1	senB, ipaD, iha, virF, capU, sigA	IncFII	MINQ00000000
FC8	4512137	SXT	aadA1, dfrA1	senB, ipaD, virF, iha, capU, sigA	IncFII	MINR00000000
FC9	4622022	AMP-SXT-NAL^†	strA.strB, blaTEM-1B, qnrS1, sul2, dfrA14	iha, capU, sigA, ipaD, senB, virF	IncFII, IncFIB	MINU00000000
FC10	4378269	AMP-SXT-NAL-NOR^†	strA, strB, aadA1, blaOXA-1, sul2, tetB, dfrA1	ipfA, pic, sigA	–	MDJJ00000000
FC11	4309816	AMP-SXT	–	ipfA	–	MECX00000000
FC12	4411934	AMP-SXT-NAL-NOR^†	strA, strB, blaOXA1, sul2, tetB, dfrA1	ipaH, ipfA, pic, sigA	–	MDJI00000000
FC13	4558192	NAL-TAX	strA, strB, aadA1, sul2, tetB, dfrA1	capU, virF, ipaD, sigA, senB, ipfA, iha	IncFII	MECW00000000
FC14	4561234	SXT	aadA1, blaOXA-1, tetB, dfrA1	capU, ipaD, sigA, senB, iha, ipfA, virF	IncFII	MIIX00000000
FC15	4655758	NAL	tetB, dfrA1	capU, ipaD, senB, ipfA, sigA, iha, virF	IncFII	MIIY00000000
FC16	4575582	AMP-NAL-TAX	aadA1, blaOXA-1, tetB, dfrA1	capU, virF, ipaD, sigA, senB, ipfA, iha	IncFII	MINS00000000
FC17	4561447	AMP-NAL-TAX	aadA1, blaOXA-1, tetB, dfrA1	capU, ipaD, iha, sigA,senB, ipfA, virF	IncFII	MINT00000000
FC18	4502544	AMP-SXT-NAL	strA, strB, aadA1, blaTEM-1B, qnrS1, sul2, dfrA1	ipfA, capU, ipaD, virF, senB, iha, sigA	IncN, IncFII	MDJK00000000
FC19	4458457	AMP-SXT-NAL	strA, strB, blaTEM-1B, qnrS1, sul2, dfrA14	capU, ipaD, sigA,senB, iha, ipfA, virF	IncFII, IncFIB	MECT00000000
FC20	4651491	AMP-SXT-NAL	strA, strB, aadA1, blaOXA-1, sul2, tetB, dfrA1	capU, ipaD, iha, sigA, senB, ipfA, virF	IncFII	MINV00000000
FC21	5432092	–	dfrA5, sul1	senB, sat, capU, iha, ipfA	IncFII, Col(BS512), ColpVC, IncFIB, IncB/O/K/Z	MDES00000000
FC22	5416583	NAL-TAX	dfrA5, sul1	senB, iha, sat, capU, ipfA	IncFII, IncFIB, Col(BS512), IncB/O/K/Z. Col156	MDDJ00000000
FC23	4664034	NAL	–	–	IncX1	MECV00000000

† Intermediate susceptible.

Figure 3.  Phylogenetic tree was constructed using maximum likelihood method of nucleotide sequences of gyrB genes for the study isolates.

Table 3.  16S rRNA sequence similarity within Shigella species.

Organism	S. dysenteriae	S. boydii	S. sonnei	S. flexneri	S. flexneri 5a
S. dysenteriae	100
S. boydii	98.72	100
S. sonnei	98.79	99.4	100
S. flexneri	99.06	99.66	99.73	100
S. flexneri 5a	98.86	99.47	99.68	99.8	100