Occurrence of Salmonella enterica and Escherichia coli in raw chicken and beef meat in northern Egypt and dissemination of their antibiotic resistance markers

Moawad, Amira A.; Hotzel, Helmut; Awad, Omnia; Tomaso, Herbert; Neubauer, Heinrich; Hafez, Hafez M.; El-Adawy, Hosny

doi:10.1186/s13099-017-0206-9

Gut Pathogens

Table 3 PCR primers, their sequences and amplification targets used in this study

From: Occurrence of Salmonella enterica and Escherichia coli in raw chicken and beef meat in northern Egypt and dissemination of their antibiotic resistance markers

Primer	Sequence (5′–3′)	Amplicon size (bp)	Amplification target	References
E. coli, Salmonella enterica and Salmonella serovar identification
ECO-f	GAC CTC GGT TTA GTT CAC AGA	585	E. coli	[67]
ECO-r	CAC ACG CTG ACG CTG ACC A	585	E. coli	[67]
OMPCF	ATC GCT GAC TTA TGC AAT CG	204	Salmonella genus	[68]
OMPCR	CGG GTT GCG TTA TAG GTC TG	204	Salmonella genus	[68]
ENTF	TGT GTT TTA TCT GAT GCA AGA GG	304	S. Enteritidis	[68]
ENTR	TGA ACT ACG TTC GTT CTT CTG G	304	S. Enteritidis	[68]
TYPHF	TTG TTC ACT TTT TAC CCC TGA A	401	S. Typhimurium	[68]
TYPHR	CCC TGA CAG CCG TTA GAT ATT	401	S. Typhimurium	[68]
β-Lactamases
TEM-F	ATA AAA TTC TTG AAG ACG AAA	1080	bla _TEM	[69]
TEM-R	GAC AGT TAC CAA TGC TTA ATC	1080	bla _TEM	[69]
OXA-F	TCA ACT TTC AAG ATC GCA	591	bla _OXA	[69]
OXA-R	GTG TGT TTA GAA TGG TGA	591	bla _OXA	[69]
OXA-F-2	ATT AAG CCC TTT ACC AAA CCA		Whole bla _OXA	[69]
OXA-R-2	AAG GGT TGG GCG ATT TTG CCA		Whole bla _OXA	[69]
OXA-23-F	GAT CGG ATT GGA GAA CCA GA	501	bla _OXA-23	[25]
OXA-23-R	ATT TCT GAC CGC ATT TCC AT	501	bla _OXA-23	[25]
CTX-M-F	CGC TTT GCG ATG TGC AG	550	bla _CTX-M	[69]
CTX-M-R	ACC GCG ATA TCG TTG GT	550	bla _CTX-M	[69]
CTX-M-F2	CCA GAA TAA GGA ATC CCA TG		Whole bla _CTX-M	[69]
CTX-M-R2	GCC GTC TAA GGC GAT AAA C		Whole bla _CTX-M	[69]
CMY-F	GAC AGC CTC TTT CTC CAC A	1007	bla _CMY	[69]
CMY-R	TGG AAC GAA GGC TAC GTA	1007	bla _CMY	[69]
CMY-F2	ACG GAA CTG ATT TCA TGA TG		Whole bla _CMY	[69]
CMY-R2	GAA AGG AGG CCC AAT ATC CT		Whole bla _CMY	[69]
SHV-F	TTA TCT CCC TGT TAG CCA CC	795	bla _SHV	[69]
SHV-R	GAT TTG CTG ATT TCG CTC GG	795	bla _SHV	[69]
Integrons
5′-CS	GGC ATC CAA GCA GCA AG	152	Class 1 integron	[69]
3′-CS	AAG CAG ACT TGA CCT GA	152	Class 1 integron	[69]
hep74	CGG GAT CCC GGA CGG CAT GCA CGA TTT GTA	491	Class 2 integron	[69]
hep51	GAT GCC ATC GCA AGT ACG AG	491	Class 2 integron	[69]
Plasmid-mediated quinolone resistance gene
qnrA-F	ATT TCT CAC GCC AGG ATT TG	516	qnrA	[69]
qnrA-R	GAT CGG CAA AGG TTA GGT CA	516	qnrA	[69]
qnrB-F	GAT CGT GAA AGC CAG AAA GG	469	qnrB	[69]
qnrB-R	ACG ATG CCT GGT AGT TGT CC	469	qnrB	[69]
qnrS-F	ACG ACA TTC GTC AAC TGC AA	417	qnrS	[69]
qnrS-R	TAA ATT GGC ACC CTG TAG GC	417	qnrS	[69]
Plasmid-mediated colistin resistance gene
CLR5-F	CGG TCA GTC CGT TTG TTC	308	mcr-1	[24]
CLR5-R	CTT GGT CGG TCT GTA GGG	308	mcr-1	[24]

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ISSN: 1757-4749

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