{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:48:44Z","timestamp":1787010524405,"version":"build-2736575974"},"reference-count":60,"publisher":"Microbiology Society","issue":"10","license":[{"start":{"date-parts":[[2020,10,1]],"date-time":"2020-10-01T00:00:00Z","timestamp":1601510400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Institut Pasteur"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,10,1]]},"abstract":"<jats:p>\n                    Although several studies have investigated genetic diversity of\n                    <jats:italic>Leishmania infantum<\/jats:italic>\n                    in North Africa, genome-wide analyses are lacking. Here, we conducted comparative analyses of nuclear and mitochondrial genomes of seven\n                    <jats:italic>L<\/jats:italic>\n                    .\n                    <jats:italic>infantum<\/jats:italic>\n                    isolates from Tunisia with the aim to gain insight into factors that drive genomic and phenotypic adaptation. Isolates were from cured (\n                    <jats:italic>n<\/jats:italic>\n                    =4) and recurrent (\n                    <jats:italic>n<\/jats:italic>\n                    =3) visceral leishmaniasis (VL) cases, originating from northern (\n                    <jats:italic>n<\/jats:italic>\n                    =2) and central (\n                    <jats:italic>n<\/jats:italic>\n                    =5) Tunisia, where respectively stable and emerging VL foci are observed. All isolates from relapsed patients were from Kairouan governorate (Centre); one showing resistance to the anti-leishmanial drug Meglumine antimoniate. Nuclear genome diversity of the isolates was analysed by comparison to the\n                    <jats:italic>L. infantum<\/jats:italic>\n                    JPCM5 reference genome. Kinetoplast maxi and minicircle sequences (1 and 59, respectively) were extracted from unmapped reads and identified by\n                    <jats:sc>blast<\/jats:sc>\n                    analysis against public data sets. The genome variation analysis grouped together isolates from the same geographical origins. Strains from the North were very different from the reference showing more than 34 587 specific single nucleotide variants, with one isolate representing a full genetic hybrid as judged by variant frequency. Composition of minicircle classes within isolates corroborated this geographical population structure. Read depth analysis revealed several significant gene copy number variations correlating with either geographical origin (amastin and Hsp33 genes) or relapse (CLN3 gene). However, no specific gene copy number variation was found in the drug-resistant isolate. In contrast, resistance was associated with a specific minicircle pattern suggesting\n                    <jats:italic>Leishmania<\/jats:italic>\n                    mitochondrial DNA as a potential novel source for biomarker discovery.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.000444","type":"journal-article","created":{"date-parts":[[2020,9,25]],"date-time":"2020-09-25T10:24:23Z","timestamp":1601029463000},"source":"Crossref","is-referenced-by-count":14,"title":["Nuclear and mitochondrial genome sequencing of North-African Leishmania infantum isolates from cured and relapsed visceral leishmaniasis patients reveals variations correlating with geography and phenotype"],"prefix":"10.1099","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4078-7413","authenticated-orcid":false,"given":"Giovanni","family":"Bussotti","sequence":"first","affiliation":[{"name":"Institut Pasteur, INSERM U1201, Unit\u00e9 de Parasitologie mol\u00e9culaire et Signalisation, D\u00e9partement des Parasites et Insectes vecteurs, 25 Rue du Dr Roux, 75015 Paris, France"},{"name":"Institut Pasteur, Hub Bioinformatique et biostatistique, 28 Rue du Dr Roux, 75015 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9988-3250","authenticated-orcid":false,"given":"Alia","family":"Benkahla","sequence":"additional","affiliation":[{"name":"Laboratoire de recherche, LR 16IPT09, Bioinformatique, Biomath\u00e9matiques et Biostatistiques, Institut Pasteur de Tunis, Universit\u00e9 Tunis El-Manar, 13 Place Pasteur, Tunis, Tunisie"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8448-0720","authenticated-orcid":false,"given":"Fakhri","family":"Jeddi","sequence":"additional","affiliation":[{"name":"Laboratoire de Parasitologie et Mycologie M\u00e9dicale, CHU de Nantes, Nantes, France"},{"name":"Laboratoire de Parasitologie, H\u00f4pital de la Timone, Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2443-114X","authenticated-orcid":false,"given":"Oussama","family":"Souia\u00ef","sequence":"additional","affiliation":[{"name":"Laboratoire de recherche, LR 16IPT09, Bioinformatique, Biomath\u00e9matiques et Biostatistiques, Institut Pasteur de Tunis, Universit\u00e9 Tunis El-Manar, 13 Place Pasteur, Tunis, Tunisie"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karim","family":"Aoun","sequence":"additional","affiliation":[{"name":"Laboratoire de recherche, LR 16IPT06, Parasitoses m\u00e9dicales, Biotechnologies et Biomol\u00e9cules, Institut Pasteur de Tunis, Universit\u00e9 Tunis El-Manar, 13 Place Pasteur, Tunis, Tunisie"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0256-2029","authenticated-orcid":false,"given":"Gerald F.","family":"Sp\u00e4th","sequence":"additional","affiliation":[{"name":"Institut Pasteur, 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