Molecular characterization and PCR-based replicon typing of multidrug resistant Shigella sonnei isolates from an outbreak in Thimphu, Bhutan

Ruekit, Sirigade; Wangchuk, Sonam; Dorji, Tshering; Tshering, Kinzang Pem; Pootong, Piyarat; Nobthai, Panida; Serichantalergs, Oralak; Poramathikul, Kamonporn; Bodhidatta, Ladaporn; Mason, Carl Jeffries

doi:10.1186/1756-0500-7-95

Table 1 PCR primer sequence

From: Molecular characterization and PCR-based replicon typing of multidrug resistant Shigella sonnei isolates from an outbreak in Thimphu, Bhutan

Primer	Sequence (5’-3’)	Location	Annealing temperature (°C)	Product size (bp)	Reference
IntF	GGCATCCAAGCAGCAAGC	5’-CS of class 1 integrons	58	varied	[17]
IntB	AAGCAGACTTGACCTGAT	3’-CS of class 1 integrons	58	varied	[17]
IntI2L	GTAGCAAACGAGTGACGAAATG	intI2	58	789	[17]
IntI2R	CACGGATATGCGACAAAAAGGT	intI2	58	789	[17]
IntI2CaF	GATAAAAACAGCCTGACCTCTTC	intI2	58	2433	[17]
IntI2CaR	CCCACTTGACATCTCATCAATAC	3’ region of class 2 integrons	58	2433	[17]
ST.GYRA1	TGTCCGAGATGGCCTGAAGC	DNA gyrase A	55	470	[18]
ST.GYRA12	CGTTGATGACTTCCGTCAG	DNA gyrase A	55	470	[18]
mphA F	AACTGTACGCACTTGC	macrolide 2’-phosphotransferase	50	837	[19]
mphA R	GGTACTCTTCGTTACC	macrolide 2’-phosphotransferase	50	837	[19]
Multiplex 1
B/O_F	GCGGTCCGGAAAGCCAGAAAAC	RNAI	60	159	[15]
B/O_R	TCTGCGTTCCGCCAAGTTCGA	RNAI	60	159	[15]
FIC_F	GTGAACTGGCAGATGAGGAAGG	repA2	60	262	[15]
FIC_R	TTCTCCTCGTCGCCAAACTAGAT	repA2	60	262	[15]
A/C_F	GAGAACCAAAGACAAAGACCTGGA	repA	60	465	[15]
A/C_R	ACGACAAACCTGAATTGCCTCCTT	repA	60	465	[15]
P_F	CTATGGCCCTGCAAACGCGCCAGAAA	iterons	60	534	[15]
P_R	TCACGCGCCAGGGCGCAGCC	iterons	60	534	[15]
T_F	TTGGCCTGTTTGTGCCTAAACCAT	repA	60	750	[15]
T_R	CGTTGATTACACTTAGCTTTGGAC	repA	60	750	[15]
Multiplex 2
K/B_F	GCGGTCCGGAAAGCCAGAAAAC	RNAI	60	160	[15]
K/B_R	TCTTTCACGAGCCCGCCAAA	RNAI	60	160	[15]
W_F	CCTAAGAACAACAAAGCCCCCG	repA	60	242	[15]
W_R	GGTGCGCGGCATAGAACCGT	repA	60	242	[15]
FIIA_F	CTGTCGTAAGCTGATGGC	repA	60	270	[15]
FIIA_R	CTCTGCCACAAACTTCAGC	repA	60	270	[15]
FIA_F	CCATGCTGGTTCTAGAGAAGGTG	iterons	60	462	[15]
FIA_R	GTATATCCTTACTGGCTTCCGCAG	iterons	60	462	[15]
FIB_F	GGAGTTCTGACACACGATTTTCTG	repA	60	702	[15]
FIB_R	CTCCCGTCGCTTCAGGGCATT	repA	60	702	[15]
Y_F	AATTCAAACAACACTGTGCAGCCTG	repA	60	765	[15]
Y_R	GCGAGAATGGACGATTACAAAACTTT	repA	60	765	[15]
Multiplex 3
I1_F	CGAAAGCCGGACGGCAGAA	RNAI	60	139	[15]
I1_R	TCGTCGTTCCGCCAAGTTCGT	RNAI	60	139	[15]
Frep_F	TGATCGTTTAAGGAATTTTG	RNAI/repA	60	270	[15]
Frep_R	GAAGATCAGTCACACCATCC	RNAI/repA	60	270	[15]
X_F	AACCTTAGAGGCTATTTAAGTTGCTGAT	ori γ	60	376	[15]
X_R	TGAGAGTCAATTTTTATCTCATGTTTTAGC	ori γ	60	376	[15]
HI1_F	GGAGCGATGGATTACTTCAGTAC	parA-parB	60	471	[15]
HI1_R	TGCCGTTTCACCTCGTGAGTA	parA-parB	60	471	[15]
N_F	GTCTAACGAGCTTACCGAAG	repA	60	559	[15]
N_R	GTTTCAACTCTGCCAAGTTC	repA	60	559	[15]
HI2_F	TTTCTCCTGAGTCACCTGTTAACAC	iterons	60	644	[15]
HI2_R	GGCTCACTACCGTTGTCATCCT	iterons	60	644	[15]
L/M_F	GGATGAAAACTATCAGCATCTGAAG	repA, B, C	60	785	[15]
L/M_R	CTGCAGGGGCGATTCTTTAGG	repA, B, C	60	785	[15]
oricolE_F	GTTCGTGCATACAGTCCA	ColE plasmids	60	187	[16]
oricolE_R	GGCGAAACCCGACAGGAC	ColE plasmids	60	187	[16]
IncR_F	TCGCTTCATTCCTGCTTCAGC	IncR plasmids	60	251	[16]
IncR_R	GTGTGCTGTGGTTATGCCTCA	IncR plasmids	60	251	[16]
IncU_F	TCACGACACAAGCGCAAGGG	IncU plasmids	60	843	[16]
IncU_R	TCATGGTACATCTGGGCGC	IncU plasmids	60	843	[16]

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ISSN: 1756-0500

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