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Table 1 Biomolecular method used for pathogen identification, target genes, primers, probes and references.

From: Occurrence and identification of risk areas of Ixodes ricinus-borne pathogens: a cost-effectiveness analysis in north-eastern Italy

Species

method

gene

primers

Nucleotide sequence (5'- 3')

Amplicon

size (bp)c

Ref.

Ixodes

PCR

16S ribosomal RNA

F-16sIxodes

AAAAAAATACTCTAGGGATAACAGCGTAA

97

[12]

(extraction control)

  

R-16sIxodes

ACCAAAAAAGAATCCTAATCCAACA

  
   

16s-Ixodes-Probe

TTTTGGATAGTTCATATAGATAAAATAGTTTGC GACCTCG

  

B. burgdorferi s.l.

real time PCR (duplex)

23S-rRNA

Bb23Sf

CGAGTCTTAAAAGGGCGATTTAGT

75

[14]

   

Bb23Sr

GCTTCAGCCTGGCCATAAATAG

  
   

Bb23Sp-FAM

AGATGTGGTAGACCCGAAGCCGAGTG

  

A. phagocytophilum

real time PCR (duplex)

msp2

ApMSP2f

ATGGAAGGTAGTGTTGGTTATGGTATT

77

[14]

   

ApMSP2r

TTGGTCTTGAAGCGCTCGTA

  
   

ApMSP2p-HEX

TGGTGCCAGGGTTGAGCTTGAGATTG

  

B. burgdorferi s.l.

PCR

flagellin

FLA1

AGAGCAACTTACAGACGAAATTAAT

482

[16]

   

FLA2

CAAGTCTATTTTGGAAAGCACCTAA

  

A. phagocytophilum

PCR

msp2

msp2-3f

CCAGCGTTTAGCAAGATAAGAG

334

[15]

   

msp2-3r

GMCCAGTAACAACATCATAAGC

  

TBEv

rRT-PCR

3' non-coding region

F-TBE 1

GGGCGGTTCTTGTTCTCC

67

[12]

   

R-TBE 1

ACACATCACCTCCTTGTCAGACT

  
   

TBE-Probe-WT

TGAGCCACCATCACCCAGACACA

  

TBEv

nested PCR

non-structural protein NS5

FSM-1

GAGGCTGAACAACTGCACGA

357

[13]

   

FSM-2

GAACACGTCCATTCCTGATCT

  
  

non-structural protein NS5

FSM-1i

ACGGAACGTGACAAGGCTAG

251

 
   

FSM-2i

GCTTGTTACCATCTTTGGAG

  

Rickettsia spp.

PCR

citrate synthase

RpCS.877p

GGGGGCCTGCTCACGGCGG

381

[17]

   

RpCS1258n

ATTGCAAAAAGTACAGTGAACA

  

Cand. N. mikurensis

PCR

groEL

NM-128s

AACAGGTGAAACACTAGATAAGTCCAT

1024

[19]

   

NM-1152as

TTCTACTTTGAACATTTGAAGAATTACTAT

  

Babesia/Theileria

PCR

18S rRNA

RLB-F2

GACACAGGGAGGTAGTGACAA

400

[18]

   

RLB-R2

CTAAGAATTTCACCTCTGACAGT

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