. 2023 Feb 23;11:e14896. doi: 10.7717/peerj.14896

Table 2. Primers used for bacterial confirmation, AMR genotype, resistance determinants, virulence genes, and QRDRs detection.

Gene	Primer	Oligonucleotide sequences (5′–3′)	Amplicon size (bp)	Reference
Genus/species confirmation
*A. hydrophila*
aer	aer-F	CTACTTTTGCCGGCGAGCGG	953	Ahmed et al. (2018)
	aer-R	TGATTCCCGAAGGCACTCCC
ah	ah-F	GAAAGGTTGATGCCTAATACGTA	625	Ahmed et al. (2018)
	ah-R	CGTGCTGGCAACAAAGGACAG
*Salmonella*
invA*	invA-F	GTGAAATTATCGCCACGTTCGGGCAA	284	Kumar, Datta & Lalitha (2015)
	invA-R	TCATCGCACCGTCAAAGGAACC		Kumar, Datta & Lalitha (2015)
*V. cholerae*
ompW	ompW-F	CACCAAGAAGGTGACTTTATTGTG	588	Sathiyamurthy, Baskaran & Subbaraj (2013)
	ompW-R	GAACTTATAACCACCCGCG		Sathiyamurthy, Baskaran & Subbaraj (2013)
Resistance genes
bla _TEM	bla_TEM-F	GCGGAACCCCTATTT	964	Hasman et al. (2005)
	bla_TEM-R	TCTAAAGTATATATGAGTAAACTTGGTCTGAC		Hasman et al. (2005)
bla _SHV	bla_SHV-F	TTCGCCTGTGTATTATCTCCCTG	854	Hasman et al. (2005)
	bla_SHV-R	TTAGCGTTGCCAGTGYTG		Hasman et al. (2005)
bla _CTX−M	bla_CTX−M-F	CGATGTGCAGTACCAGTAA	585	Batchelor et al. (2005)
	bla_CTX−M-R	AGTGACCAGAATCAGCGG		Batchelor et al. (2005)
bla _NDM	bla_NDM-F	GGTTTGGCGATCTGGTTTTC	621	Pungpian et al. (2021)
	bla_NDM-R	CGGAATGGCTCATCACGATC		Pungpian et al. (2021)
bla _PSE	bla_PSE-F	GCAAGTAGGGCAGGCAATCA	422	Chuanchuen et al. (2008)
	bla_PSE-R	GAGCTAGATAGATGCTCACAA		Chuanchuen et al. (2008)
bla _OXA	bla_OXA-F	ACACAATACATATCAACTTCGC	813	Costa et al. (2006)
	bla_OXA-R	AGTGTGTGTTTAGAATGGTGATC		Costa et al. (2006)
sul1	sul1-F	CGGCGTGGGCTACCTGAACG	433	Khan et al. (2019)
	sul1-R	GCCGATCGCGTGAAGTTCCG		Khan et al. (2019)
sul2	sul2-F	CGGCATCGTCAACATAACCT	721	Khan et al. (2019)
	sul2-R	TGTGCGGATGAAGTCAGCTC		Khan et al. (2019)
sul3	sul3-F	CAACGGAAGTGGGCGTTGTGGA	244	Khan et al. (2019)
	sul3-R	GCTGCACCAATTCGCTGAACG		Khan et al. (2019)
qnrA	qnrA-F	AGAGGATTTCTCACGCCAGG	580	Cattoir et al. (2007)
	qnrA-R	TGCCAGGCACAGATCTTGAC		Cattoir et al. (2007)
qnrB	qnrB-F	GGMATHGAAATTCGCCACTG	264	Cattoir et al. (2007)
	qnrB-R	TTTGCYGYYCGCCAGTCGAAC		Cattoir et al. (2007)
qnrS	qnrS-F	GCAAGTTCATTGAACAGGGT	428	Cattoir et al. (2007)
	qnrS-R	TCTAAACCGTCGAGTTCGGCG		Cattoir et al. (2007)
ermB	ermB-F	AGACACCTCGTCTAACCTTCGCTC	640	Raissy et al. (2012)
	ermB-R	TCCATGTACTACCATGCCACAGG		Raissy et al. (2012)
dfrA1	dfrA1-F	GGAGTGCCAAAGGTGAACAGC	367	Shahrani, Dehkordi & Momtaz (2014)
	dfrA1-R	GAGGCGAAGTCTTGGGTAAAAAC		Shahrani, Dehkordi & Momtaz (2014)
dfrA12	dfrA12-F	TTCGCAGACTCACTGAGGG	330	Chuanchuen et al. (2008)
	dfrA12-R	CGGTTGAGACAAGCTCGAAT		Chuanchuen et al. (2008)
catA	catA-F	CCAGACCGTTCAGCTGGATA	454	Chuanchuen et al. (2008)
	catA-R	CATCAGCACCTTGTCGCCT		Chuanchuen et al. (2008)
catB	catB-F	CGGATTCAGCCTGACCACC	461	Chuanchuen et al. (2008)
	catB-R	ATACGCGGTCACCTTCCTG		Chuanchuen et al. (2008)
cmlA	cmlA-F	TGGACCGCTATCGGACCG	641	Chuanchuen et al. (2008)
	cmlA-R	CGCAAGACACTTGGGCTGC		Chuanchuen et al. (2008)
strA	strA-F	TGGCAGGAGGAACAGGAGG	405	Chuanchuen et al. (2008)
	strA-R	AGGTCGATCAGACCCGTGC		Chuanchuen et al. (2008)
strB	strB-F	GGCAGCATCAGCCTTATAATTT	470	Mala et al. (2017)
	strB-R	GTGGATCCGTCATTCATTGTT		Mala et al. (2017)
tetA	tetA-F	GGCGGTCTTCTTCATCATGC	502	Khan et al. (2019)
	tetA-R	CGGCAGGCAGAGCAAGTAGA		Khan et al. (2019)
tetB	tetB-F	CGCCCAGTGCTGTTGTTGTC	615	Khan et al. (2019)
	tetB-R	CGCGTTGAGAAGCTGAGGTG		Khan et al. (2019)
tetD	tetD-F	AAACCATTACGGCATTCTGC	787	Kumai et al. (2005)
	tetD-R	GACCGGATACACCATCCATC		Kumai et al. (2005)
addA1	addA1-F	CTCCGCAGTGGATGGCGG	631	Chuanchuen et al. (2008)
	addA1-R	GATCTGCGCGCGAGGCCA		Chuanchuen et al. (2008)
addA2	addA2-F	CATTGAGCGCCATCTGGAAT	500	Chuanchuen et al. (2008)
	addA2-R	ACATTTCHCTCATCGCCGGC		Chuanchuen et al. (2008)
aac(3)IV	aac(3)IV-F	GTGTGCTGCTGGTCCACAGC	627	Stoll et al. (2012)
	aac(3)IV-R	AGTTGACCCAGGGCTGTCGC		Stoll et al. (2012)
aac(6′)-Ib	aac(6′)-Ib-F	TTGCGATGCTCTATGAGTGGCTA	482	Park et al. (2006)
	aac(6′)-lb-R	CTCGAATGCCTGGCGTGTTT		Park et al. (2006)
qepA	qepA- F	GCAGGTCCAGCAGCGGGTAG	199	Yamane et al. (2008)
	qepA- R	CTTCCTGCCCGAGTATCGTG		Yamane et al. (2008)
floR	floR-F	ATGGTGATGCTCGGCGTGGGCCA	800	Ying et al. (2019)
	floR-R	GCGCCGTTGGCGGTAACAGACACCGTGA		Ying et al. (2019)
mcr-1	mcr-1-F	AGTCCGTTTGTTCTTGTGGC	320	Rebelo et al. (2018)
	mcr-1-R	AGATCCTTGGTCTCGGCTTG		Rebelo et al. (2018)
mcr-2	mcr-2-F	CAAGTGTGTTGGTCGCAGTT	715	Rebelo et al. (2018)
	mcr-2-R	TCTAGCCCGACAAGCATACC		Rebelo et al. (2018)
mcr-3	mcr-3-F	AAATAAAAATTGTTCCGCTTATG	929	Rebelo et al. (2018)
	mcr-3-R	AATGGAGATCCCCGTTTTT		Rebelo et al. (2018)
mcr-4	mcr-4-F	TCACTTTCATCACTGCGTTG	1116	Rebelo et al. (2018)
	mcr-4-R	TTGGTCCATGACTACCAATG		Rebelo et al. (2018)
mcr-5	mcr-5-F	ATGCGGTTGTCTGCATTTATC	1644	Rebelo et al. (2018)
	mcr-5-R	TCATTGTGGTTGTCCTTTTCTG		Rebelo et al. (2018)
Integrons and integrative and conjugative elements
int1	int1-F	CCTGCACGGTTCGAATG	497	Kitiyodom et al. (2010)
	int1-R	TCGTTTGTTCGCCCAGC		Kitiyodom et al. (2010)
int2	int2-F	GGCAGACAGTTGCAAGACAA	247	Kitiyodom et al. (2010)
	int2-R	AAGCGATTTTCTGCGTGTTT		Kitiyodom et al. (2010)
int3	int3-F	CCGGTTCAGTCTTTCCTCAA	155	Kitiyodom et al. (2010)
	int3-R	GAGGCGTGTACTTGCCTCAT		Kitiyodom et al. (2010)
int _SXT	int_SXT-F	GCTGGATAGGTTAAGGGCGG	592	Kitiyodom et al. (2010)
	int_SXT-R	CTCTATGGGCACTGTCCACATTG		Kitiyodom et al. (2010)
Virulence genes
*A. hydrophila*
aero	aero-F	CACAGCCAATATGTCGGTGAAG	326	Ahmed et al. (2018)
	aero-R	GTCACCTTCTCGCTCAGGC		Ahmed et al. (2018)
hly	hly-F	CTATGAAAAAACTAAAAATAACTG	1500	Ahmed et al. (2018)
	hly-R	CAGTATAAGTGGGGAAATGGAAAG		Ahmed et al. (2018)
*V. cholerae*
hlyA	hlyA-F	GGCAAACAGCGAAACAAATACC	481	Imani et al. (2013)
	hlyA-R	CTCAGCGGGCTAATACGGTTTA		Imani et al. (2013)
ctx	ctx-F	CAGTCAGGTGGTCTTATGCCAAGAGG	167	Wong, You & Chen (2012)
	ctx-R	CCCACTAAGTGGGCACTTCTCAAACT		Wong, You & Chen (2012)
tcpA	tcpA-F	CACGATAAGAAAACCGGTCAAGAG	453	Singh, Isac & Colwell (2002)
	tcpA-R	CGAAAGCACCTTCTTTCACGTTG		Singh, Isac & Colwell (2002)
QRDR
gyrA	gyrA-F	GCTGAAGAGCTCCTATCTGG	436	Chuanchuen & Padungtod (2009)
	gyrA-R	GGTCGGCATGACGTCCGG		Chuanchuen & Padungtod (2009)
parC	parC-F	GTACGTGATCATGGATCGTG	390	Chuanchuen & Padungtod (2009)
	parC-R	TTCCTGCATGGTGCCGTCG

Notes.

Virulence gene of Salmonella.