{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T08:26:19Z","timestamp":1791361579465,"version":"4.3.1"},"reference-count":40,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T00:00:00Z","timestamp":1730419200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:sec><jats:title>Objectives<\/jats:title><jats:p>Ascites, often associated with critical pathologies such as liver cirrhosis or bowel perforation, can be complicated by fungal infection, increasing mortality especially in intensive care settings and demanding rapid diagnosis and adequate treatment. Traditional microbiological diagnostic methods have limited sensitivity in accurately identifying fungal pathogens in ascitic fluid. Alternative diagnostic methods may offer important insights to enable guiding of antifungal therapy and refining empirical treatment strategies. The objective of this study was to evaluate the potential of next-generation sequencing methods to identify specific fungal pathogens responsible for ascitic fluid infections.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We prospectively collected 50 ascitic fluid samples from ICU patients with suspected ascites infection. In addition to standard culture-based microbiological testing, an ascitic fluid aliquot underwent fungal DNA isolation and was analyzed by next-generation sequencing (NGS) methods for identification of fungal species.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Of 50 ascitic samples collected, five samples showed growth of <jats:italic>Candida<\/jats:italic> spp. in culture. After DNA isolation and ITS2 PCR, detectable amplification was achieved in 10 samples. Sequencing of the 50 patients\u2019 samples identified facultative pathogenic fungi in 19 patients. In 15 cases, culture alone would not have permitted the identification of all facultative pathogenic fungi. The identification of fungal DNA by sequencing was significantly associated with poor patient outcome and a number of clinical parameters.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Our results show a higher sensitivity for NGS-based diagnostic methods in the identification of ascitic fluid fungal infections compared to culture-based diagnostics. This may be beneficial especially for patients in a critical care setting, who have an increased prevalence of comorbidities and high mortality. The implementation of such methods in standard diagnosis will require increased standardization of the workflows and interpretation of the sequencing results with respect to patients\u2019 clinical picture.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fcimb.2024.1441805","type":"journal-article","created":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T06:10:34Z","timestamp":1730441434000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Enhancing ascitic fungal infection diagnosis through next-generation sequencing: a pilot study in surgical ICU patients"],"prefix":"10.3389","volume":"14","author":[{"given":"Sara","family":"Posadas-Cantera","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Negin","family":"Mehrbarzin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Wetzel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanna","family":"Goelz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lampros","family":"Kousoulas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Utzolino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Georg","family":"H\u00e4cker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed Tarek","family":"Badr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,11,1]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.15156\/BIO\/2938065","article-title":"Full UNITE+INSD dataset for Fungi. Version 18.07.2023. UNITE Community","author":"Abarenkov","year":"2023"},{"key":"B2","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"1246","DOI":"10.1053\/j.gastro.2010.06.019","article-title":"Infections in patients with cirrhosis increase mortality four-fold and should be used in determining prognosis","volume":"139","author":"Arvaniti","year":"2010","journal-title":"Gastroenterology."},{"key":"B4","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1128\/CMR.00091-13","article-title":"Molecular and nonmolecular diagnostic methods for invasive fungal infections","volume":"27","author":"Arvanitis","year":"2014","journal-title":"Clin. Microbiol. Rev."},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.01286","article-title":"Candida albicans and Candida dubliniensis Show Different Trailing Effect Patterns When Exposed to Echinocandins and Azoles","volume":"11","author":"Ayadi","year":"2020","journal-title":"Front. Microbiol."},{"key":"B6","unstructured":"FastQC A Quality Control tool for High Throughput Sequence Data"},{"key":"B7","doi-asserted-by":"publisher","first-page":"18224","DOI":"10.18632\/oncotarget.24804","article-title":"Increased gut permeability in cancer cachexia: mechanisms and clinical relevance","volume":"9","author":"Bindels","year":"2018","journal-title":"Oncotarget."},{"key":"B8","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1128\/JCM.01986-07","article-title":"Candida bracarensis Detected among Isolates of Candida glabrata by Peptide Nucleic Acid Fluorescence In Situ Hybridization: Susceptibility Data and Documentation of Presumed Infection","volume":"46","author":"Bishop","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1128\/JCM.02116-07","article-title":"Candida nivariensis, an emerging pathogenic fungus with multidrug resistance to antifungal agents","volume":"46","author":"Borman","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1111\/myc.2015.58.issue-7","article-title":"Spontaneous fungal peritonitis: a devastating complication of cirrhosis","volume":"58","author":"Bremmer","year":"2015","journal-title":"Mycoses."},{"key":"B11","doi-asserted-by":"publisher","first-page":"165rv13","DOI":"10.1126\/science.1222236","article-title":"Hidden killers: human fungal infections","volume":"4","author":"Brown","year":"2012","journal-title":"Sci. Transl. Med."},{"key":"B12","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"B13","doi-asserted-by":"publisher","first-page":"2650","DOI":"10.1007\/s00268-011-1305-2","article-title":"Candida peritonitis: an update on the latest research and treatments","volume":"35","author":"Carneiro","year":"2011","journal-title":"World J. Surg."},{"key":"B14","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1186\/s40168-018-0605-2","article-title":"Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data","volume":"6","author":"Davis","year":"2018","journal-title":"Microbiome."},{"key":"B15","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics."},{"key":"B16","doi-asserted-by":"publisher","first-page":"3459","DOI":"10.1128\/JCM.00727-07","article-title":"Catheter-related fungemia due to fluconazole-resistant candida nivariensis","volume":"45","author":"Fujita","year":"2007","journal-title":"J. Clin. Microbiol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"3226","DOI":"10.3390\/cells10113226","article-title":"Next- and third-generation sequencing outperforms culture-based methods in the diagnosis of ascitic fluid bacterial infections of ICU patients","volume":"10","author":"Goelz","year":"2021","journal-title":"Cells."},{"key":"B18","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1007\/s10096-013-1953-2","article-title":"Spontaneous fungal peritonitis: a severe complication in patients with advanced liver cirrhosis","volume":"33","author":"Hwang","year":"2014","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"B19","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1111\/j.1574-6941.2012.01437.x","article-title":"New primers to amplify the fungal ITS2 region \u2013 evaluation by 454-sequencing of artificial and natural communities","volume":"82","author":"Ihrmark","year":"2012","journal-title":"FEMS Microbiol. Ecol"},{"key":"B20","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1016\/j.funbio.2015.04.007","article-title":"DNA barcoding of fungi causing infections in humans and animals","volume":"120","author":"Irinyi","year":"2016","journal-title":"Fungal Biol."},{"key":"B21","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1093\/mmy\/myv008","article-title":"International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database\u2014the quality controlled standard tool for routine identification of human and animal pathogenic fungi","volume":"53","author":"Irinyi","year":"2015","journal-title":"Med. Mycol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"3100","DOI":"10.3390\/jcm12093100","article-title":"Clinical characteristics and early diagnosis of spontaneous fungal peritonitis\/fungiascites in hospitalized cirrhotic patients with ascites: A case\u2013control study","volume":"12","author":"Jiang","year":"2023","journal-title":"J. Clin. Med."},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.02903","article-title":"A new age in molecular diagnostics for invasive fungal disease: are we ready","volume":"10","author":"Kidd","year":"2020","journal-title":"Front. Microbiol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"5112","DOI":"10.1128\/AEM.01043-13","article-title":"Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the miseq illumina sequencing platform","volume":"79","author":"Kozich","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"3390","DOI":"10.1021\/acs.chemrev.0c00199","article-title":"Antifungal drug resistance: molecular mechanisms in candida albicans and beyond","volume":"121","author":"Lee","year":"2021","journal-title":"Chem. Rev."},{"key":"B26","doi-asserted-by":"publisher","first-page":"1033","DOI":"10.1007\/s40121-021-00422-w","article-title":"Spontaneous fungal ascites infection in patients with cirrhosis: an analysis of 10 cases","volume":"10","author":"Li","year":"2021","journal-title":"Infect. Dis. Ther."},{"key":"B27","doi-asserted-by":"publisher","first-page":"2228","DOI":"10.1097\/01.CCM.0000087326.59341.51","article-title":"Intensive care unit management of intra-abdominal infection","volume":"31","author":"Marshall","year":"2003","journal-title":"Crit. Care Med."},{"key":"B28","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1093\/clinids\/23.3.486","article-title":"Emergence of antibiotic-resistant bacteria in cases of peritonitis after intraabdominal surgery affects the efficacy of empirical antimicrobial therapy","volume":"23","author":"Montravers","year":"1996","journal-title":"Clin. Infect. Dis."},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.151663","article-title":"Customization of a DADA2-based pipeline for fungal internal transcribed spacer 1 (ITS1) amplicon data sets","volume":"7","author":"Rolling","year":"2022","journal-title":"JCI Insight"},{"key":"B30","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1056\/NEJM199402033300508","article-title":"Care of patients with ascites","volume":"330","author":"Runyon","year":"1994","journal-title":"N Engl. J. Med."},{"key":"B31","doi-asserted-by":"publisher","first-page":"D20","DOI":"10.1093\/nar\/gkaa892","article-title":"Database resources of the national center for biotechnology information","volume":"50","author":"Sayers","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B32","doi-asserted-by":"publisher","first-page":"6241","DOI":"10.1073\/pnas.1117018109","article-title":"Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi","volume":"109","author":"Schoch","year":"2012","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B33","doi-asserted-by":"publisher","first-page":"596","DOI":"10.4254\/wjh.v11.i7.596","article-title":"Spontaneous fungal peritonitis: Micro-organisms, management and mortality in liver cirrhosis-A systematic review","volume":"11","author":"Tariq","year":"2019","journal-title":"World J. Hepatol."},{"key":"B34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3897\/mycokeys.10.4852","article-title":"Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi","volume":"10","author":"Tedersoo","year":"2015","journal-title":"MycoKeys."},{"key":"B35","doi-asserted-by":"publisher","first-page":"1256688","DOI":"10.1126\/science.1256688","article-title":"Global diversity and geography of soil fungi","volume":"346","author":"Tedersoo","year":"2014","journal-title":"Science"},{"key":"B36","doi-asserted-by":"publisher","first-page":"2323","DOI":"10.1001\/jama.2009.1754","article-title":"International study of the prevalence and outcomes of infection in intensive care units","volume":"302","author":"Vincent","year":"2009","journal-title":"JAMA."},{"key":"B37","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1007\/s00423-010-0727-x","article-title":"Intestinal ischemia\/reperfusion: microcirculatory pathology and functional consequences","volume":"396","author":"Vollmar","year":"2011","journal-title":"Langenbecks Arch. Surg."},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2023.1275405","article-title":"Longitudinal dynamics of gut bacteriome and mycobiome interactions pre- and post-visceral surgery in Crohn\u2019s disease","volume":"13","author":"Wetzel","year":"2024","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B39","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-98141-3","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2009"},{"key":"B40","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00268-020-05380-x","article-title":"Appropriate source control and antifungal therapy are associated with improved survival in critically ill surgical patients with intra-abdominal candidiasis","volume":"44","author":"Yan","year":"2020","journal-title":"World J. Surg."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2024.1441805\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,1]],"date-time":"2024-11-01T06:10:40Z","timestamp":1730441440000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2024.1441805\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,1]]},"references-count":40,"alternative-id":["10.3389\/fcimb.2024.1441805"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2024.1441805","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,1]]},"article-number":"1441805"}}