From blood and skin biopsies from the Connecticut site, DNA was extracted using the Qiagen DNeasy Tissue Kit (Qiagen, Valencia, CA) as described. 27 (
link) For ticks collected at the Connecticut site, DNA was extracted from individual nymphal
I. scapularis following Beati and Keirans for the 2002 collection. 28 (
link) For ticks collected at several locations in 2004–2007 collections, total DNA was extracted using ammonium hydroxide (NH
4OH). For this procedure, ticks were incubated for 2 h in 5 μL of 1.4 mol/L NH
4OH at 22°C and crushed with a plastic pipette tip. To this was added 95 μL distilled H
2O before a second incubation at 95°C for 30 minutes. Material was centrifuged to separate tick debris from DNA solution, and the supernatant was transferred to clean vials containing 1 μL of 100 mmol/L EDTA and stored at −20°C.
In addition to the DNA extracts from blood, tissue, and ticks described above, two other sets of DNA samples, which were extracted from ticks by the method of Beati and Keirans, 28 (
link) were available for examination: (1) flat nymphs that were derived from engorged larvae removed from captured mammals at the Connecticut field site, as described by Hanincova and others, 29 (
link) and (2) flat larvae and nymphs of laboratory-reared
P. leucopus, which were infected with
B. miyamotoi, as described. 12 (
link)
DNA extracts were subjected to quantitative multiplex real-time PCR (qPCR), as described, 15 (
link),16 (
link),30 (
link) with two probes hybridizing to a region of the 16S rDNA that differed between
B. burgdorferi and
B. miyamotoi. Results were expressed as the number of spirochete cells per tick or volume of blood or tissue. Forward and reverse primers were, respectively, 5′GCTGTAAACGATGCACACTTGGT and 5′GGCGGCACACTTAACACGTTAG. The corresponding dye-labeled probes were 6FAM-TTCGGTACTA ACTTTTAGTTAA and VIC-CGGTACTAACCTTTCGAT TA with 3′ ends modified with a minor groove binding protein (Applied Biosystems, Foster City, CA). The reaction was performed in 25-μL volume in single tubes or wells at a final concentration of 900 nmol/L for each primer and 200 nmol/L for each probe. 15 (
link) The final concentration of EDTA was < 0.1 mmol/L. The PCR conditions were 50°C for 2 minutes and 95°C for 10 minutes, followed by 45 cycles of 95°C for 15 seconds and 63°C for 60 seconds on an Applied Biosystems 7300 Real-Time PCR apparatus for the 2002 and 2004 samples and a Rotor-Gene RG-3000 apparatus (Corbett Research, San Francisco, CA) for the 2005–2007 samples. The DNA extractions, PCR reaction preparations, and analysis of the products were carried out in three separated laboratory rooms. To monitor for contamination, negative controls were included with all DNA extraction and PCR procedures.
DNA standards were the same for each experiment: strain B31 (ATCC 35210) for
B. burgdorferi and strain HS1 (ATCC 35209) of
B. hermsii for the uncultivable
B. miyamotoi.15 (
link)
B. hermsii and
B. miyamotoi have identical sequences for the regions of the primers and probe.
Borrelia species cells were grown in BSK II medium at 34°C and harvested as described. 31 (
link) With DNA standards, the qPCR assays with each probe set was linear with a
R2 ≥ 0.99 over a range of 1–10
6 spirochetes per reaction. The linear regression coefficients (95% confidence intervals [CIs]) for
Ct values on log-transformed cell counts were −3.31 (−3.40 to −3.28) for
B. burgdorferi and −3.40 (−3.52 to −3.28) for the
B. hermsii surrogate (
P > 0.05). Samples with estimated spirochete counts of less than one per tick or biopsy specimen were considered negative.
The identities of the
Borrelia species in 100 random samples scored by qPCR as
B. burgdorferi were confirmed by PCR of the 16S–23S intergenic spacer region (IGR) with species-specific primers. 8 (
link),15 (
link),32 (
link) Random samples scored as
B. miyamotoi or
B. burgdorferi by qPCR were confirmed by direct sequencing of the IGR on a CEQ 8000 capillary sequencer (Beckman Coulter, Fullerton, CA).
Barbour A.G., Bunikis J., Travinsky B., Hoen A.G., Diuk-Wasser M.A., Fish D, & Tsao J.I. (2009). Niche Partitioning of Borrelia burgdorferi and Borrelia miyamotoi in the Same Tick Vector and Mammalian Reservoir Species. The American journal of tropical medicine and hygiene, 81(6), 1120-1131.