Direct molecular detection of a broad range of bacterial and viral organisms and Streptococcus pneumoniae vaccine serotypes in children with otitis media with effusion

Slinger, Robert; Duval, Melanie; Langill, Jonathan; Bromwich, Matthew; MacCormick, Johnna; Chan, Francis; Vaccani, Jean-Philippe

doi:10.1186/s13104-016-2040-4

Table 1 Real-time PCR assays for bacteria, viruses and Streptococcus pneumoniae serotypes

From: Direct molecular detection of a broad range of bacterial and viral organisms and Streptococcus pneumoniae vaccine serotypes in children with otitis media with effusion

Target	Forward primer	Reverse primer	Probe (all with MGB except^a)	Ref.
S. pneumoniae	acgcaatctagcagatga agca	tcgtgcgttttaattccagct	tgccgaaaacgcttgatacagggag^a	[19]
H. influenzae	ggttaaatatgccgatggtgttg	tgcatctttacgcacggtgta	ttgtgtacactccgttggtaaaagaacttgcac^a	[19]
A. otitidis	ctacgcatttcaccgctacac	ggggaagaacacggatagga	agtccgccagtttccaatgccgttcca^a	[10]^b
H. pylori	cgtggcaagcatgatccat	gggtatgcacggttacgagttt	tcaggaaacatcgcttcaatacccactt^a	[27]
M. catarrhalis	gtcaaacagctggaggtattgc	gacatgatgctcacctgctcta	atcgcaattgcaacttt	[28]
C. pneumoniae	cgcgaaggaccttacctgga	gtatctgtccttgcggaaagct	ctacagttgtcaaatacatgtc	[20]
M. pneumoniae	cgtggtgaagtgaaacatctcagtag	gcaagccctacaacccctatcta	atgataagtttggcctgttc	[20]
B. pertussis	catcaagcaccgctttaccc	tgttgggagttctggtaggtgtg	cttaccgcccacagac	[20]
B. parapertussis	gatatcaacgggtgacggatc	gcctgcacgttgctcgat	cagcaattggctgcagg	[20]
SP serotype 1	cgtgcggtaattgaagctatga	tgtggccccagcaactct	cttgcccttgtatagggt	[21]
SP serotype 3	ggtcagcagaaagtatgcattgg	tcgtttatccagggtctgatga	tattggatgtggtttatcgtgaag	[21]
SP serotype 4	cggcaggcaaaccaattat	catctcgttcgggactaaca	caggagatgctaaaata	[21]
SP serotype 5	ttacgggagtatcttatgtctttaatgg	cagcattccagtagcctaaaactaga	tctcagcaactctatttgg	[21]
SP serotype 6A	gctagagatggttccttcagttgat	catactctagtgcaaactttgcaaaat	ctggctcatgatagtt	[21]
SP serotype 6B	gctagagatggttccttcagttgat	catactctagtgcaaactttgcaaaat	actgtctcatgataatt	[21]
SP serotype 7F/A	aagcacagtgcgtgaacaat	aaaatctccctgtcccttcc	ctattccagaagaatctc	[21]
SP serotype 9 V/A	tggaatgggcaaagggtagta	tcggttccccaagattttctc	ttaatcatgctaacggctcat	[21]
SP serotype 14	cgactgaaatgtcactaggagaagat	aatacagtccatcaattactgcaatactc	attcgtttgccaatacttga	[21]
SP serotype 18C/B	ccctgaaactagttgggaaca	ttccaatcatcacccattaca	aaagtcagatgttaaagactac	[21]
SP serotype 19A	gctgtgtttatgggggttgg	agagacgtttaggctcatttgc	atgcaaaatgctcacctag	[21]
SP serotype 19F/B/C	aattcggtatttatgggagttgg	agagacgtttaggctcattagc	atgcaaaagtcaaatttaga	[21]
SP serotype 23F	ctgggccaagatatttaaaagagagt	aattccgcatcagagtatgcaa	ttgctcttcgaaaaatgt	[21]
RSV A	ctcaatttcctcacttctccagtgt	cttgattcctcggtgtacctctgt	cattatgcctaggccagcag	[20]
RSV B	ttcctaacttctcaagtgtggtccta	ctggtttcttggcgtacctctatac	tcccattatgcctagacct	[20]
Influenza A	ccccctcaaagccgagat	caagattggtcttgtctttagcca	ccatgagagcctcaagat	[20]
Influenza B	aatacggtggattaaacaaaagcaa	caggaggtctatatttggttccatt	catattgggcaatttccta	[20
HMPV A	cacctgagtgatttatcatacaagca	ttagcatacagaatttctccacacaa	acaccctcatcattgc	[20] MGB
HMPV B	caagaacaaatgtgacattgctgat	gaaaactgccgcacaacatttag	aagctgacagccatct	[20]
Rhinovirus	caagtaatggacagggtgtgaagag	ccaaagtagtcggtcccatcc	tccggcccctgaat	[20]
Enterovirus	gcccctgaatgcggctaa	ggaaacacggacacccaaagta	tctgcagcggaacc	[20]
Bocavirus	ggcagaattcagccatactcaaa	tctgggttagtgcaaaccatga	ccacagtcatcagacact	[20] MGB
Adenovirus	ccacggtggggtttctaaactt	cccagtggtcttacatgcacatc	tgcaccagacccgg	[20]
Coronavirus OC43	cgatgaggctattccgactaggt	ccttcctgagccttcaatatagtaacc	tccgcctggcacggt	[20]
Coronavirus 229E	ttccgacgtgctcgaacttt	ccaacacggttgtgacagtga	tcctgaggtcaatgca	[20]
Coronavirus HKU1	gccttgcgaatgaatgtgct	tgcatcaccactgctagtaccac	ttgctattatgttaagcctg	[20] MGB
Coronavirus NL63	ggaagcgtgttcctaccagaga	agcaagctgtggaaaacctttg	caaagcactgaataac	[20]
PIV1	acagatgaaattttcaagtgctactttagt	gcctcttttaatgccatattatcattaga	atggtaataaatcgactcgct	[20]
PIV 2	tgcatgttttataactactgatcttgctaa	gttcgagcaaaatggattatggt	actgtcttcaatggagatat	[20]
PIV 3	tgctgttcgatgccaacaa	attttatgctcctatctagtggaagaca	ttgctcttgctcctca	[20]
PIV 4	cctggagtcccatccaaagtaag	tgagactgttattttaagtgcatctatacg	tttgttgatcaagacaatac	[20]

RSV Respiratory syncytial virus; PIV Parainfluenza virus; HMPV human metapneumovirus; SP S. pneumoniae
^a Probes contained an internal quencher and no minor groove binder. All other probes contained a minor groove binder and no internal quencher
^b Primers from published reference, probe this study

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