Prevalence and phylogeny of Chlamydiae and hemotropic mycoplasma species in captive and free-living bats

Fritschi, Janine; Marti, Hanna; Seth-Smith, Helena M. B.; Aeby, Sébastien; Greub, Gilbert; Meli, Marina L.; Hofmann-Lehmann, Regina; Mühldorfer, Kristin; Stokar-Regenscheit, Nadine; Wiederkehr, Danja; Pilo, Paola; Van Den Broek, Peggy Rüegg-; Borel, Nicole

doi:10.1186/s12866-020-01872-x

BMC Microbiology

Table 3 Primers and probes used in the present study

From: Prevalence and phylogeny of Chlamydiae and hemotropic mycoplasma species in captive and free-living bats

PCR method*	Gene target & amplicon size	Name	Sequence (5′ – 3′)	Reference
Chlam23S-qPCR	23S rRNA, 111 bp	Ch23S-F	CTGAAACCAGTAGCTTATAAGCGGT	Ehricht et al. 2006 [37]
		Ch23S-R	ACCTCGCCGTTTAACTTAACTCC
		Ch23S-p	6-FAM-CTCATCATGCAAAAGGCACGCCG-TAMRA
23SIG-PCR	23S rRNA signature sequence, 700 bp	U23-F	GATGCCTTGGCATTGATAGGCGATGAAGGA	Everett et al. 1999 [4, 36]
23SIG-PCR	23S rRNA signature sequence, 700 bp	23SIG-R	TGGCTCATCATGCAAAAGGCA	Everett et al. 1999 [4, 36]
16S-IGF/IGR-PCR	16S rRNA, 278 bp	16S-IGF	GATGAGGCATGCAAGTCGAACG	Pospischil et al. 2012 [39]; Blumer et al. 2007 [40]
16S-IGF/IGR-PCR	16S rRNA, 278 bp	16S-IGR	CCAGTGTTGGCGGTCAATCTCTC	Pospischil et al. 2012 [39]; Blumer et al. 2007 [40]
16S-pan-qPCR^a 16S-pan-PCR^b	16S rRNA, 200 bp^a,b	16S-panCh-F^a,b	CCGCAACACTGGGACT	Lienard et al. 2011 [41]^a, Hokynar et al. 2016^b [32]
		16S-panCh-R^a,b	GGAGTTAGCCGGTGCTTCTTTAC
		16S-panCh^a	6-FAM-CTACGGGAGGCTGCAGTCGAGAATC-BHQ1
	sequencing primers^a	panFseq^a	CCAACACTGGGACTGAGA
	sequencing primers^a	panRseq^a	GCCGGTGCTTCTTTAC
eGFP-qPCR	eGFP, 177 bp	eGFP-1-F	GACCACTACCAGCAGAACAC	Blumer et al. 2011 [38]
		eGFP-10-R	CTTGTACAGCTCGTCCATGC
		eGFP-Hex	VIC-AGCACCCAGTCCGCCCTGAGCA-none
Hemoplasma SYBR Green qPCR	16S rRNA	Mhae_sybr.359f	AGCAATACCATGTGAACGATGAA	Willi et al. 2009 [42]
		Mcocc_sybrF	AGCAATGCCATGTGAACGATGAA
		Mhae_sybr.432r	TGGCACATAGTTTGCTGTCACTT
		Cmhae_Sybr.493r	GCTGGCACATAGTTAGCTGTCACT
Mhf-like qPCR	16S rRNA, 114 bp	Group_Mhf_fwd	GGAGCGGTGGAATGTGTAG	Tasker et al. 2010 [43]
		Group_Mhf_rev	GGGGTATCTAATCCCATTTGC
		Group_Mhf_probe	6-FAM-TYAAGAACACCAGAGGCGAAGGCG-BHQ1
CMmh-like qPCR	16S rRNA, 139 bp	Group_CMhm_fwd	GGGGCCAAGTCAAGTCATC	Tasker et al. 2010 [43]
		Group_CMhm_rev	GCGAATTGCAGCCTTTTATC
		Group_CMhm_probe	YYE-TACCATTGTAGCACGTTYGCAGCCC-BHQ1
HemMycop41/938-PCR	16S rRNA, 871 bp	HemMycop16S-41 s	GYATGCMTAAYACATGCAAGTCGARCG	Mascarelli et al. 2014 [21]
HemMycop41/938-PCR	16S rRNA, 871 bp	HemMycop16S-938as	CTCCACCACTTGTTCAGGTCCCCGTC	Mascarelli et al. 2014 [21]
HemMycop322/1420-PCR	16S rRNA, 1030 bp	HemMycop16S-322 s	GCCCATATTCCTACGGGAAGCAGCAGT	Mascarelli et al. 2014 [21]
HemMycop322/1420-PCR	16S rRNA, 1030 bp	HemMycop16S-1420as	GTTTGACGGGCGGTGTGTACAAGACC	Mascarelli et al. 2014 [21]

*conventional PCR (PCR), real-time PCR (qPCR)
^{a & b}PCRs performed according to the respective labeled reference, using the respective labeled primers

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ISSN: 1471-2180

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