Table 7 Details on primers and PCR assays used for the detection of tick-borne pathogens in different tissues from rodents and ticks

Anaplasma phagocytophilum

RT

ApMsp2f

ATGGAAGGTAGTGTTGGTTATGGTATT

msp2 (77)

[81]

ApMsp2r

TTGGTCTTGAAGCGCTCGTA

ApMsp2p

FAM-TGGTGCCAGGGTTGA GCTTGAGATTG-BHQ1

Babesia spp.

C

BJ1

GTCTTGTAATTGGAATGATGG

18S rRNA (411–452)

[82]

BN2

TAGTTTATGGTTAGGACTACG

Bartonella spp.

C

Ba325s

CTTCAGATGATGATCCCA AGCCTTCTGGCG

16S-23S rRNA (ITS) (453–780)

[83]

Ba1100as

GAACCGACGACCCCCTGCTTGCAAAGC

Borrelia burgdorferi (s.l.)

RT

FlaF1a

AGCAAATTTAGGTGCTTTCCAA

P41 (96)

[84]

FlaR1

GCAATCATTGCCATTGCAGA

FlaProbe1

FAM-TGCTACAACCTCATCTG TCATTGTAGCATCTTTTATTTG-BBQ

MLST^a

cplAF1255

AAAGATAGATTTCTTCCAGAC

clpA (579)

[33, 85]

cplAR2104

GAATTTCATCTATTAAAAGCTTTC

clpXF403

GCTGCAGAGATGAATGTGCC

clpX (624)

clpXR1124

GATTGATTTCATATAACTCTTTTG

nifF1

ATGGATTTCAAACAAATAAAAAG

nifS (564)

nifR719

GATATTATTGAATTTCTTTTAAG

pepXF449

TTATTCCAAACCTTGCAATCC

pepX (570)

pepXR1115

GTTCCAATGTCAATAGTTTC

pyrF448

GATTGCAAGTTCTGAGAATA

pyrG (603)

pyrR1154

CAAACATTACGAGCAAATTC

recF917

CCCTTGTTGCCTTGCTTTC

recG (651)

recR1658

GAAAGTCCAAAACGCTCAG

rplfF40

TGGGTATTAAGACTTATAAGC

rplB (624)

rplR760

GCTGTCCCCAAGGAGACA

uvrF1434

GAAATTTTAAAGGAAATTAAAAGTAG

uvrA (570)

uvrR2111

CAAGGAACAAAAACATCTGG

“Candidatus Neoehrlichia mikurensis”

RT

NMikGroEL F2

CCTTGAAAATATAGCAAGATCAGGTAG

groEL (99)

[36, 38]

NMikGroEL rev1

CCACCACGTAACTTATTTAGCACTAAAG

NMikGroEL rev2

CCACCACGTAACTTATTTAGTACTAAAG

NMikGroEL-P2a

FAM-CCTCTACTAATTATTGCT GAAGATGTAGAAGGTGAAGC-BHQ1

Hepatozoon spp.

C

Hep-1f

CGCGAAATTACCCAATT

18S rRNA (660)

[63, 86]

Hep-2r

CAGACCGGTTACTTTYAGCAG

Rickettsia spp.

RT

Pan Rick gltA_2 for

ATAGGACAACCGTTTATTT

gltA (70)

[87]

Pan Rick gltA_2 rev

CAAACATCATATGCAGAAA

Pan Rick gltA_3 taq

6FAM-CCTGATAATTCGTTA GATTTTACCG–TMR

C^a

120–2788

AAACAATAATCAAGGTACTGT

OmpB (811)

[88]

120–3599

TACTTCCGGTTACAGCAAAGT