{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T19:25:23Z","timestamp":1780773923217,"version":"3.54.1"},"reference-count":51,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,2,6]],"date-time":"2025-02-06T00:00:00Z","timestamp":1738800000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>Leishmaniasis, a protozoan disease caused by infection by <jats:italic>Leishmania<\/jats:italic>, is a critical issue in Asia, South America, East Africa, and North Africa. With 12 million cases globally, leishmaniasis is one of the most serious neglected tropical diseases worldwide. Direct identification of infected tissues is currently the primary method of diagnosis; however, the low sensitivity and inconvenience of microscopic examination in detecting amastigotes, parasitic manifestations of <jats:italic>Leishmania<\/jats:italic>, leads to the possibility of misdiagnosis, delayed diagnosis, and underdiagnosis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>With the development of metagenomic nextgeneration sequencing (mNGS) technology for pathogen identification, it is possible to detect specific nucleic acid sequences characteristic of <jats:italic>Leishmania<\/jats:italic> parasites, which opens new avenues for the more accurate diagnosis of leishmaniasis. In this study, we report two cases of leishmaniasis from Henan Province, China, in which <jats:italic>Leishmania<\/jats:italic> parasites were identified using mNGS technology, massively expediting diagnosis and treatment.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Our report demonstrates that the mNGS method is applicable to peripheral blood samples (PB), which are far more readily available in clinical settings, in addition to bone marrow aspirate samples (BM), which are traditionally used for diagnosis of visceral leishmaniasis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Our report validates the efficacy of mNGS technology as a rapid and accurate method of diagnosis for leishmaniasis.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fcimb.2025.1517046","type":"journal-article","created":{"date-parts":[[2025,2,6]],"date-time":"2025-02-06T07:10:03Z","timestamp":1738825803000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["Metagenomic next-generation sequencing assists in the diagnosis of visceral leishmaniasis in non-endemic areas of China"],"prefix":"10.3389","volume":"15","author":[{"given":"Rui","family":"Zhao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guilun","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin","family":"Xiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melinda","family":"Ji","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rongheng","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xudong","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,2,6]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12879-018-3394-0","article-title":"Double trouble: visceral leishmaniasis in twins after traveling to Tuscany\u2013a case report","volume":"18","author":"Adamczick","year":"2018","journal-title":"BMC Infect. Dis."},{"key":"B2","doi-asserted-by":"publisher","first-page":"e00048","DOI":"10.1128\/CMR.00048-18","article-title":"Recent development of visceral leishmaniasis treatments: successes, pitfalls, and perspectives","volume":"31","author":"Alves","year":"2018","journal-title":"Clin. Microbiol. Rev."},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2023.1197149","article-title":"Leishmania donovani visceral leishmaniasis diagnosed by metagenomics next-generation sequencing in an infant with acute lymphoblastic leukemia: a case report","volume":"11","author":"Chang","year":"2023","journal-title":"Front. Public Health"},{"key":"B4","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1111\/crj.13538","article-title":"Advantages and challenges of metagenomic sequencing for the diagnosis of pulmonary infectious diseases","volume":"16","author":"Chen","year":"2022","journal-title":"Clin. Respir. J."},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.528884","article-title":"Leishmaniasis diagnosis via metagenomic next-generation sequencing","volume":"10","author":"Chen","year":"2020","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"B7","doi-asserted-by":"publisher","first-page":"635","DOI":"10.16250\/j.32.1374.2022048","article-title":"Epidemiological investigation on a visceral leishmaniasis case in Zhengzhou city of Henan province","volume":"34","author":"Cheng","year":"2023","journal-title":"Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi."},{"key":"B8","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1097\/QCO.0000000000000194","article-title":"Leishmaniasis: treatment updates and clinical practice guidelines review","volume":"28","author":"Copeland","year":"2015","journal-title":"Curr. Opin. Infect. Dis."},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0006778","article-title":"Barriers to access to visceral leishmaniasis diagnosis and care among seasonal mobile workers in Western Tigray, Northern Ethiopia: A qualitative study","volume":"12","author":"Coulborn","year":"2018","journal-title":"PLoS Negl. Trop. Dis."},{"key":"B10","first-page":"75","article-title":"Immunopathological changes in HIV-Leishmania co-infection","volume":"39","author":"Da-Cruz","year":"2006","journal-title":"Rev Soc Bras Med Trop"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgph.0002557","article-title":"Developments in Leishmaniasis diagnosis: A patent landscape from 2010 to 2022","volume":"3","author":"De Avelar","year":"2023","journal-title":"PLoS Glob Public Health"},{"key":"B12","doi-asserted-by":"publisher","first-page":"8105","DOI":"10.1007\/s00253-020-10846-y","article-title":"Recent advances and new strategies in Leishmaniasis diagnosis","volume":"104","author":"De Brito","year":"2020","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1016\/j.jare.2021.09.012","article-title":"Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections","volume":"38","author":"Diao","year":"2022","journal-title":"J. Adv. Res."},{"key":"B14","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1093\/cid\/cix807","article-title":"Long-term clinical outcomes in visceral leishmaniasis\/human immunodeficiency virus\u2013coinfected patients during and after pentamidine secondary prophylaxis in Ethiopia: a single-arm clinical trial","volume":"66","author":"Diro","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0007900","article-title":"Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent","volume":"13","author":"Domagalska","year":"2019","journal-title":"PLoS Negl. Trop. Dis."},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0121418","article-title":"Visceral leishmaniasis and immunocompromise as a risk factor for the development of visceral leishmaniasis: a changing pattern at the hospital for tropical diseases, London","volume":"10","author":"Fletcher","year":"2015","journal-title":"PLoS One"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.922894","article-title":"A case report of two kala-azar cases in China diagnosed by metagenomic next-generation sequencing","volume":"13","author":"Gao","year":"2022","journal-title":"Front. Microbiol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"432","DOI":"10.4314\/ovj.v8i4.13","article-title":"Zoonotic impact and epidemiological changes of leishmaniasis in Ethiopia","volume":"8","author":"Gebremichael","year":"2018","journal-title":"Open Vet. J."},{"key":"B19","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1186\/s13071-022-05524-z","article-title":"Laboratory diagnostics for human Leishmania infections: a polymerase chain reaction-focussed review of detection and identification methods","volume":"15","author":"Gow","year":"2022","journal-title":"Parasites Vectors"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES2013.18.29.20535","article-title":"The burden of visceral leishmaniasis in Italy from 1982 to 2012: a retrospective analysis of the multi-annual epidemic that occurred from 1989 to 2009","volume":"18","author":"Gramiccia","year":"2013","journal-title":"Euro Surveill."},{"key":"B21","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1016\/s0190-9622(96)80121-6","article-title":"Leishmaniasis","volume":"34","author":"Grevelink","year":"1996","journal-title":"J. Am. Acad. Dermatol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/2049-9957-3-10","article-title":"Historical experience in the elimination of visceral leishmaniasis in the plain region of Eastern and Central China","volume":"3","author":"Guan","year":"2014","journal-title":"Infect. Dis. Poverty"},{"key":"B23","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/j.ijid.2020.05.056","article-title":"A case of pediatric visceral leishmaniasis-related hemophagocytic lymphohistiocytosis diagnosed by mNGS","volume":"97","author":"Guo","year":"2020","journal-title":"Int. J. Infect. Dis."},{"key":"B24","doi-asserted-by":"publisher","first-page":"668","DOI":"10.1080\/1040841X.2019.1681933","article-title":"mNGS in clinical microbiology laboratories: on the road to maturity","volume":"45","author":"Han","year":"2019","journal-title":"Crit. Rev. Microbiol."},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofac511","article-title":"The value of metagenomic next-generation sequencing in leishmaniasis diagnosis: a case series and literature review","volume":"9","author":"Han","year":"2022","journal-title":"Open Forum Infect. Dis."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0005889","article-title":"Towards elimination of visceral leishmaniasis in the Indian subcontinent\u2014Translating research to practice to public health","volume":"11","author":"Hirve","year":"2017","journal-title":"PLoS Negl Trop Dis"},{"key":"B27","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1101\/gr.5969107","article-title":"MEGAN analysis of metagenomic data","volume":"17","author":"Huson","year":"2007","journal-title":"Genome Res."},{"key":"B28","first-page":"1124","author":"Jiang","year":""},{"key":"B29","doi-asserted-by":"publisher","first-page":"W5","DOI":"10.1093\/nar\/gkn201","article-title":"NCBI BLAST: a better web interface","volume":"36","author":"Johnson","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"B30","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows\u2013Wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2022.1044043","article-title":"Case report: Application of metagenomic next-generation sequencing in the diagnosis of visceral leishmaniasis and its treatment evaluation","volume":"9","author":"Liang","year":"2023","journal-title":"Front. Med. (Lausanne)"},{"key":"B32","doi-asserted-by":"publisher","first-page":"9903","DOI":"10.12998\/wjcc.v9.i32.9903","article-title":"Next-generation sequencing technology for diagnosis and efficacy evaluation of a patient with visceral leishmaniasis: a case report","volume":"9","author":"Lin","year":"2021","journal-title":"World J Clin Cases"},{"key":"B33","doi-asserted-by":"publisher","first-page":"147","DOI":"10.2147\/HIV.S93789","article-title":"Leishmaniasis-HIV coinfection: current challenges","volume":"8","author":"Lindoso","year":"2016","journal-title":"HIV AIDS (Auckl)"},{"key":"B34","doi-asserted-by":"publisher","first-page":"193","DOI":"10.2147\/HIV.S143929","article-title":"Visceral leishmaniasis and HIV coinfection: current perspectives","volume":"10","author":"Lindoso","year":"2018","journal-title":"HIV AIDS (Auckl)"},{"key":"B35","doi-asserted-by":"publisher","first-page":"987","DOI":"10.1128\/CMR.00080-14","article-title":"Visceral leishmaniasis in China: an endemic disease under control","volume":"28","author":"Lun","year":"2015","journal-title":"Clin. Microbiol. Rev."},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1590\/0074-02760190253","article-title":"Where, when, and how the diagnosis of human visceral leishmaniasis is defined: answers from the Brazilian control program","volume":"114","author":"Luz","year":"2019","journal-title":"Mem Inst Oswaldo Cruz"},{"key":"B37","article-title":"Leishmaniasis","volume-title":"StatPearls","author":"Maxfield","year":"2024"},{"key":"B38","doi-asserted-by":"publisher","first-page":"831","DOI":"10.1101\/gr.238170.118","article-title":"Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid","volume":"29","author":"Miller","year":"2019","journal-title":"Genome Res."},{"key":"B39","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1093\/qjmed\/hct116","article-title":"Current diagnosis and treatment of visceral leishmaniasis","volume":"8","author":"Mondal","year":"2010","journal-title":"QJM"},{"key":"B40","doi-asserted-by":"publisher","first-page":"1856","DOI":"10.1017\/S0031182014000134","article-title":"Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections","volume":"141","author":"Pallen","year":"2014","journal-title":"Parasitology"},{"key":"B41","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1101\/gr.278550.123","article-title":"Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites","volume":"34","author":"Reis-Cunha","year":"2024","journal-title":"Genome Res."},{"key":"B42","doi-asserted-by":"publisher","first-page":"863","DOI":"10.1093\/bioinformatics\/btr026","article-title":"Quality control and preprocessing of metagenomic datasets","volume":"27","author":"Schmieder","year":"2011","journal-title":"Bioinformatics"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2021.764142","article-title":"Metagenomic analysis identifying a rare Leishmania infection in an adult with AIDS","volume":"11","author":"Song","year":"2021","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"497","DOI":"10.21037\/atm-22-1351","article-title":"A case report and literature review: diagnosis and treatment of human immunodeficiency virus coinfected with visceral leishmania by metagenomic next-generation sequencing in China","volume":"10","author":"Tang","year":"2022","journal-title":"Ann. Transl. Med."},{"key":"B45","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1093\/trstmh\/trae009","article-title":"Spatial-temporal distribution of visceral leishmaniasis in Rio de Janeiro, Brazil, 2001\u20132020: expansion and challenges","volume":"118","author":"Vasconcelos","year":"2024","journal-title":"Trans. R Soc. Trop. Med. Hyg"},{"key":"B46","doi-asserted-by":"publisher","first-page":"957","DOI":"10.4269\/ajtmh.18-0042","article-title":"Antigen detection in urine for noninvasive diagnosis and treatment monitoring of visceral leishmaniasis in human immunodeficiency virus coinfected patients: an exploratory analysis from Ethiopia","volume":"99","author":"Vogt","year":"2018","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"B47","doi-asserted-by":"publisher","first-page":"2532","DOI":"10.1021\/acssensors.8b00759","article-title":"Ligand-capped ultrapure metal nanoparticle sensors for the detection of cutaneous leishmaniasis disease in exhaled breath","volume":"3","author":"Welearegay","year":"2018","journal-title":"ACS sens"},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.3390\/tropicalmed8060318","article-title":"Reemergence of visceral leishmaniasis in Henan province","volume":"8","author":"Yang","year":"2023","journal-title":"China Trop. Med. Infect. Dis."},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.1095072","article-title":"Case report: Diagnosis of visceral leishmaniasis using metagenomic next-generation sequencing and bone marrow smear","volume":"12","author":"Zhang","year":"2022","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B50","doi-asserted-by":"publisher","first-page":"e52","DOI":"10.1111\/ijlh.13103","article-title":"The role of bone marrow metagenomics next-generation sequencing to differential diagnosis among visceral leishmaniasis, histoplasmosis, and talaromycosis marneffei","volume":"42","author":"Zhang","year":"2020","journal-title":"Int. J. Lab. Hematol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"625","DOI":"10.46234\/ccdcw2020.173","article-title":"Visceral leishmaniasis\u2014China, 2015\u2013 2019","volume":"2","author":"Zhou","year":"2020","journal-title":"China CDC Wkly"}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2025.1517046\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,6]],"date-time":"2025-02-06T07:10:08Z","timestamp":1738825808000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2025.1517046\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,6]]},"references-count":51,"alternative-id":["10.3389\/fcimb.2025.1517046"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2025.1517046","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,6]]},"article-number":"1517046"}}