Table 3.
Overview of the Molecular Methods Used for Screening Rodent Samples for Zoonotic Agents
| Pathogen | Tissue | Method | Target | Reference |
|---|---|---|---|---|
| Puumala virus | Lung | Conventional RT-PCR | Partial S segment (760 bp) | Essbauer et al. 2006 |
| Dobrava–Belgrade virus | Lung | Conventional RT-PCR | Partial L segment | Klempa et al. 2006 |
| Tula virus | Lung | Conventional RT-PCR and direct sequencing |
Partial S segment (760 bp) | Essbauer et al. 2006 |
| Lymphocytic choriomeningitis virus | Spleen | Conventional RT-PCR | Partial Lassavirus L gene | Coulybaly-N‘Golo et al. 2011, Vieth et al. 2007 |
| Orthopox virus (OPV)a | Liver | Real-time PCR | Partial hemagglutinin gene | Qiagen-Artus Orthopox LC PCR Kit; Olson et al. 2004 |
| Leptospira spp. | Kidney | Conventional PCR | Partial flaB (563-bp fragment) | Gravekamp et al.1993 |
| Partial secY (285-bp fragment) | Bal et al. 1994, Levett et al. 2005 | |||
| Partial lipl (423-bp fragment) | Haake et al. 2000, Mayer-Scholl et al. 2011 | |||
| Borrelia spp. | Skin | Nested conventional PCR and direct sequencing | Partial 16S rRNA (600 bp) | Richter et al. 2006, 2013 |
| Rickettsia spp. | Skin | Screening real-time PCR | Partial gltA | Wölfel et al. 2006, Schex et al. 2011 |
| Conventional PCR | Partial ompB | |||
| Bartonella spp. | Spleen | Real-time screening PCR | Partial rpoB (78 bp) | This paperb |
| Conventional confirmatory PCR and direct sequencing | ITS (419–565 bp) | Maggi and Breitschwerdt 2005 | ||
| Coxiella burnetii | Liver | Screening real-time PCR | Partial IS1111 | Schrader et al. 2000 |
| Nested conventional PCR | Partial com1 | Zhang et al. 1998 | ||
| Toxoplasma gondii | Brain | Conventional PCR | 529-bp repeat | Reischl et al. 2003, Homan et al. 2000, this paperc |
Detects OPV including also cowpox virus (CPXV).
With QuantiFast Probe PCR kit (Qiagen) according to the manufacturers' protocol using primers BART F1(5′-AGA AGA GTT TGT TGT TTG CC), BART F2 (5′-AGA AGA GTT TGT TGT TTG TC), BART R (5′-GAA ACA TCC ATC AAA TCA ACA TG) and LNA probe BART-P (5′-FAM- AAA CTT CAC CAG CAT GA-BHQ1.
Primers TOX-8 (0.5 μM) in combination with Tox5 (0.5 μM) were used with the Dynazyme II F-501L polymerase (Finzyme, Espoo, Finland). Cycling was performed at 94°C for 1 min, followed by 35 cycles of 60°C for 1 min, 72°C for 1 min, and 94°C for 1 min, and a final extension at 72°C for 10 min.
FAM, 6-carboxyfluorescein; BHQ1, black hole quencher 1.