The study was performed in small built-up areas belonging to the district of Echrarda (35° 07’ 08’’ Nord, 10° 01’ 49’’ Est), South part of Kairouan Governorate, Tunisia. The selection of small cluster of houses hosted dogs was based on the knowledge of recent ZCL confirmed diagnosis, while in the whole district and incidence of 96.7 cases/100,000 Ha was reported [14]. The area is characterized by a rural, semi-arid environment. The registered population is 27,518 (2014) on 330 km2, while there is scarce information on the dogs’ population. Fifty-one dogs, 31 males, 20 females, with an estimated age ranging between 1–12 years were recruited, based on the compliance of the owners to join the anti-rabies vaccination campaign. After the vaccine administration, the owners were informed about the possibility to submit the dogs to further sampling for Leishmania spp. diagnosis, informed consent was obtained from all participants. Dogs were submitted to clinical examination by filling a clinical form, and sampled for blood, popliteal lymph node (LN) aspirate, skin punch biopsy and conjunctival swab. Blood samples (3 mL) were obtained by peripheral veins, then divided in two aliquots respectively in empty and EDTA coated tubes, for serum, plasma and buffy coat (BC) collection. Lymph node aspiration was performed by one of the two popliteal lymph node, skin biopsy was obtained by punching the surface between neck and ear, with a 1 mm punch biopsy. Conjunctival swabs were performed by both lower eyelids but processed together. The collected materials were stored in 1.5 ml tubes. Samples collection was performed following the Good Clinical Practice medical procedures, in accordance with the international guidelines for animal welfare. Tubes were kept at 4°C until the arrival at laboratory. Blood was centrifuged 10 min at 2500 rpm, to separate red cells, BC and plasma. Plasmas were stored at − 20◦ until serological analysis; BC, LN aspirates, skin biopsy samples and conjunctival swabs were stored at − 20◦ until DNA extraction. Serological diagnosis was performed by ELISA (Enzyme linked immunosorbent assay) ID Screen Leishmaniasis Indirect Test® kit (ID vet, Innovative diagnostics, France), the same used in a previous study [6]. Briefly, Optical densities were read at 450 nm (ELISA plate reader Anthos®, Bristol, England). Results were expressed as percentages plasmas whose results were between 40% and 50% and designated by manufacturer as “doubtful” were tested by an indirect immunofluorescence antibodies test (IFAT) using spot slides sensitized by L. infantum promastigotes; a threshold of 1:100 defining seropositivity. Additional serological test was performed on Leishmania spp. Samples, to detect possible co-infections with other canine vector borne diseases (CVBDs). Antibodies to Anaplasma phagocytophilum/Anaplasma platys, Borrelia burgdorferi, Ehrlichia canis/Erlichia ewingii, and antigens to Dirofilaria immitis were detected by SNAP 4Dx Plus test (IDEXX Laboratories, Westbrook, Maine, US).
DNA was extracted from 51 buffy coat, lymph node and skin biopsy samples, using the DNeasy Blood & Tissue kit (Qiagen, Leipzig, Germany) according to the manufacturer’s instructions. Moreover, DNA was extracted from 51 conjunctival swabs, using the Leishmania Screen Glow (Avantech Group, Angri, Italy) following the protocol described by Maurelli et al. [15]. Three different PCR protocols were used for amplification of DNA samples: i) qPCR to amplify a region of the minicircle kinetoplast DNA (kDNA) [16] was used to analyze all the DNA extracted (total = 200 DNA samples); ii) nested-PCR to amplify the small subunit ribosomal RNA (SSUrRNA)[17] ; iii) end-point PCR to amplify the Internal Transcribed Spacer 1 (ITS-1) region [18]. These last two protocols (endpoint and nested were used in order to confirm positive results obtained by qPCR and to characterize the Leishmania species. Briefly, for qPCR a PCR mix was prepared in a final volume of 20 µL, containing 1X Bio-Rad Universal Master Mix (Bio-Rad, USA), 0.3 mM of each specific primer (LEISH-1 5’-GGCGTTCTGCGAAAACCG-3’; LEISH-2 5’-AAAATGGCATTTTCGGGCC-3’), 0.25 mM of probe (5’-FAM-TGGGTGCAGAAATCCCGTTCA-3’-BHQ1) and 2 µL of extracted DNA was prepared. Each amplification was performed in duplicate. To prepare a standard curve, a serial dilution of a positive sample, provided by the National Reference Center for Leishmaniosis (CReNaL), consisting of equivalents of DNA from 1 × 106 cells to 1 cell per amplified sample, was prepared. A negative control was added for each run to verify contaminations. The thermal cycling conditions included a 10 min denaturation at 95°C and 40 cycles of 95°C for 15 sec and 60°C for 35 sec. The reactions were performed in a CFX96 (Bio-Rad, USA). To quantify parasite burdens, cycle threshold (Ct) values obtained for each test sample were compared with those obtained for the corresponding standard curve. For SSUrRNA amplification, a first PCR mix was prepared in a final volume of 50 µL, containing 1X EmeraldAmp® GT PCR mix (Takara, France), 25 pmol/ µL of each specific primer (R221 5’-GGTTCCTTTCCTGATTTACG-3’; R332 5’-GGCCGGTAAAGGCCGAATAG-3’) and 5 µL of extracted DNA. DNA samples of Leishmania was used as positive controls. The thermal cycling conditions included 5 min denaturation at 94°C and 35 cycles of 94°C for 30 sec, 60°C for 30 sec, 72°C for 30 sec and a final extension at 72°C for 5 min. The reaction was performed in a T100 (Bio-Rad, USA). The nested-PCR was prepared in a final volume of 50 µL, containing 1X EmeraldAmp® GT PCR mix (Takara, France), 25 pmol/µL of each specific primer (R223 5’-TCCCATCGCAACCTCGGTT- 3’; R333 5’-AAAGCGGGCGCGGTGCTG-3’) and 5 µL of DNA amplified with the first PCR. DNA samples of Leishmania was used as positive controls. The thermal cycling conditions included 5 min denaturation at 94°C and 35 cycles of 94°C for 30 sec, 65°C for 30 sec, 72°C for 30 sec and a final extension at 72°C for 5 min. The reaction was performed in a T100 (Bio-Rad, USA). The PCR products obtained from the nested-PCR were detected on a 2% ethidium bromide-stained low melting agarose gel (Bio-Rad, USA). Bands were cut from the gel under UV exposure, and the amplified DNAs were purified by QIAquick Gel Extraction KIT (Qiagen, Germany). The purified PCR products were sequenced, and the obtained sequences, in both forward and reverse directions, were analysed using the Chromas version 2.6.6 software and compared with sequences present in GenBank, using BLASTn system and ClustalW. For ITS-1 amplification, a PCR mix was prepared in a final volume of 50 µL, containing 1X EmeraldAmp® GT PCR mix (Takara, France), 0.50 mM of each specific primer (LITSR 5’-CTGGATCATTTTCCGATG-3’; L5.8S 5’-TGATACCACTTATCGCACTT-3’) and 5 µL of extracted DNA. DNA samples of Leishmania was used as positive controls. The thermal cycling conditions included 4 min denaturation at 95°C and 36 cycles of 95°C for 40 sec, 53°C for 30 sec, 72°C for 1 min and a final extension at 72°C for 6 min. The reaction was performed in a T100 (Bio-Rad, USA). The PCR products were detected on a 2% ethidium bromide-stained low melting agarose gel (Bio-Rad, USA). Bands were cut from the gel under UV exposure, and the amplified DNAs were purified by QIAquick Gel Extraction KIT (Qiagen, Germany). The purified PCR products were sequenced, and the obtained sequences, in both forward and reverse directions, were analysed using the Chromas version 2.6.6 software and compared with sequences present in GenBank, using BLASTn system and ClustalW.