WHO Fungal Priority Pathogens — Genome Metadata Report
Generated 2026-11-06 from NCBI Datasets
Download complete record-level data as CSV files. These companion files are generated alongside this report.
Per-record CSVs include both raw NCBI fields (host, isolation_source, host_disease, submitter, platform etc.) and a derived host_category column.
| Species | Priority | Total | With Location | With Date | With Both |
|---|---|---|---|---|---|
| Aspergillus fumigatus | Critical | 5,320 | 2,793 | 2,518 | 2,342 |
| Candida albicans | Critical | 4,832 | 3,181 | 3,131 | 3,025 |
| Candida auris | Critical | 34,334 | 31,412 | 32,371 | 31,241 |
| Candida parapsilosis | High | 1,963 | 1,646 | 984 | 984 |
| Candida tropicalis | High | 1,581 | 1,413 | 1,413 | 1,370 |
| Coccidioides spp. | Medium | 428 | 370 | 311 | 311 |
| Cryptococcus gattii | Medium | 397 | 318 | 146 | 146 |
| Cryptococcus neoformans | Critical | 6,862 | 3,946 | 3,201 | 3,107 |
| Eumycetoma agents | High | 97 | 89 | 92 | 89 |
| Fusarium spp. | High | 6,258 | 5,474 | 4,762 | 4,606 |
| Histoplasma spp. | High | 595 | 539 | 495 | 493 |
| Lomentospora prolificans | Medium | 20 | 20 | 17 | 17 |
| Mucorales | High | 2,430 | 775 | 616 | 615 |
| Nakaseomyces glabrata | High | 2,251 | 1,954 | 1,943 | 1,917 |
| Paracoccidioides spp. | Medium | 112 | 107 | 40 | 40 |
| Pichia kudriavzevii | Medium | 791 | 288 | 211 | 207 |
| Pneumocystis jirovecii | Medium | 12 | 8 | 4 | 3 |
| Scedosporium spp. | Medium | 38 | 32 | 25 | 23 |
| Talaromyces marneffei | Medium | 383 | 378 | 362 | 362 |
| Priority | Genomes | SRA WGS | Combined |
|---|---|---|---|
| Critical | 2,093 | 49,255 | 51,348 |
| High | 2,919 | 12,256 | 15,175 |
| Medium | 169 | 2,012 | 2,181 |
Combined assembled genomes and SRA WGS runs with geo_loc_name metadata from BioSample records.
Year-by-year counts of genome assemblies and SRA WGS runs, stacked by priority group or species. Default axis is collection year (the year the biological sample was taken), which reflects surveillance activity. Switch to release year to see when records were published to NCBI.
Where each species has actually been sampled, derived from the BioSample host, isolation_source and host_disease fields. Records are bucketed into coarse categories (human, animal, plant, environment, food, clinical_other, unknown). Raw NCBI values are preserved in the per-record CSV download.
| Species | Top hosts (count) | Top isolation sources (count) |
|---|---|---|
| Aspergillus fumigatus | Homo sapiens (1221); Environmental (13); Anas platyrhynchos (9); Larus smithsonianus (6); Branta canadensis (6); Broad-winged hawk (4); Haliaeetus leucocephalus (4); Leucophaeus atricilla (4); Mareca americana (3); Strigops habroptila (2); Osprey (2); Pregrine falcon (2); Cygnus buccinator (2); Agricultural fields (2); Artemisia annua (1) | soil (448); sputum (306); air - outside (283); Environmental,soil (226); laboratory cross (195); clinical laboratory sample (98); not available (55); feces (41); Grapes (34); clinical (32); compost sample at golf course (31); lung (30); wheat (25); Laboratory (25); BAL (25) |
| Candida albicans | Homo sapiens (2428); Laboratory (8); Quercus petraea (6); Quercus robur (3); Mus musculus (2); Sturnus vulgaris (2); Mus musculus strain C57BL/6 (1); Not required. (1); Struthio camelus (1); Anser anser (1); Cairina moschata (1); natural / free-living (1) | blood (334); human; superficial (277); saliva (221); Laboratory (126); in vitro (121); evolved (117); bloodstream (104); human; invasive (68); Vagina (65); Mouth (48); evolution experiment (48); evolved in 0.7ug/mL fluconazole (47); Oropharanyx (40); Vaginal (33); Mouse stool (32) |
| Candida auris | Homo sapiens (32047); environment (25); Homo sapiens (male) (6); dog (5); Environment (5); Homo sapiens (female) (2); laboratory evolved (2); Dog (2); Dolphin (1); Canis lupus familiaris (1) | urine (4492); blood (4179); axilla/groin (1555); Axilla/Groin (1378); Swab of axilla and groin (1370); other (1047); wound (936); Swab_Skin (877); skin (568); sputum (564); wastewater (561); Axilla and groin (556); Axilla and Groin (519); SWAB_SKIN (516); Axilla and groin swab (445) |
| Candida parapsilosis | Homo sapiens (1682); "Homo sapiens" (3); Olea europaea (2); Cynomolgus macaque (2); lab strain (1) | blood (619); Clinic (354); Clinical environment (125); clinical sample (115); Human gut (72); Patient sample (69); Blood culture (40); CRISPR-Cas9 manipulated (29); clinical isolate (22); Tissue (20); gut (20); feces (18); urine (14); Biospy (12); swab (10) |
| Candida tropicalis | Homo sapiens (1143); Melanotus villosus (1) | clinical (529); blood (257); urine (100); Oropharynx (including sputum/BAL/swab) (91); seawater (63); Beach soil (62); sputum (56); feces (28); freshwater (16); soil (11); Mudbank soil (10); mangrove soil (7); not available (6); Patient with candidemia (6); CVC (6) |
| Coccidioides spp. | Homo sapiens (252); Macaca nemestrina (13); Mus musculus (1); Canis lupus familiaris (1) | Laboratory mixed culture (18); lungs (13); soil (10); sputum (8); Tissue (6); human (6); Laboratory mutant strain (5); BAL (4); CSF (3); Bronchial washing (3); lung (3); Bronchial Washing (3); lung tissue (3); Tissue/Lung (3); Synovial fluid (2) |
| Cryptococcus gattii | Homo sapiens (167); Cryptococcus gattii (50); Eucalyptus camaldulensis (1) | clinical (52); CSF (33); environmental (4); Environment (3); clinical sample (2); Human CSF (2); CSF, HIV- (2); soil (2); Lung Biopsy (2); woody debris of Eucalyptus tereticornis (1); eucalyptus tree (1); unidentified tree (1); plant (1); veterinary (1); clinical, HIV- (1) |
| Cryptococcus neoformans | Homo sapiens (2018); Culture (390); Environmental (82); Humans (24); pigeon (16); Cockatoo (9); mopane (8); Pigeon (7); eucalyptus (4); Eucalyptus (2); Mopane tree (2); Oak tree (2); Homosapiens (2); clinical sample (2); Eucalyptus tereticornis (1) | laboratory (383); Site of infection (284); CSF /HIV+ (269); CSF (247); Crossing of laboratory and clinical strain (243); clinical (185); cerebrospinal fluid (145); Laboratory experiment (142); Laboratory (101); cerebrospinal fluid (CSF) (88); Frozen stock (82); Tree (82); Lab experiment (74); laboratory strain (63); Laboratory stock (60) |
| Eumycetoma agents | Homo sapiens (87) | foot (22); not available (8); Lt foot (8); Mycetoma (4); tissue biopsy (4); Rt foot (4); Mycetoma patient (3); patient (3); Both feet (3); Right foot (3); Left foot, mycetoma (2); Rt leg & knee (2); Left foot (2); Foot (1); hand (1) |
| Fusarium spp. | Cicer arietinum (591); rice (339); wheat (230); Triticum aestivum (222); Solanum lycopersicum (216); Homo sapiens (167); Humulus lupulus (147); Avena sativa (103); winegrape (102); Fragaria x ananassa (100); Sugarcane (87); Lactuca sativa (87); Zea mays (73); Cucumis melo (61); Glycine max (55) | progeny of sexual cross in laboratory (238); stem (157); wheat (70); Soft wheat (69); rice field (68); Pseudostem (65); soil (64); Wheat field (56); isolates were obtained from the sugarcane leaves with leaf scald symptoms in Yunnan (53); Winter Wheat Head (52); Tissue (38); Soybean grain (36); culture (35); Persea americana (31); Enza Pel (28) |
| Histoplasma spp. | Homo sapiens (500); Felis catus (10); Canis lupus (6); ND (5); Didelphis virginiana (1); Rattus norvegicus (1); Wild mice (1); Canis lupus familiares (1) | blood (13); Bronchial washing (10); bone marrow (8); BAL (7); lymph node (5); soil (5); sputum (4); the sample came from strain G217B with spontaneous chromosome rearrangement during laboratory passage from frozen stocks (3); bronchoalveolar lavage (3); patients (2); Blood culture (2); Skin biopsy (2); Body (1); right adrenal gland from a male Taiwanese patient with histoplasmosis having traveled to the USA and China within the last 3 years (1); Respiratory, Lower, Bronchoalveolar Lavage (1) |
| Lomentospora prolificans | Homo sapiens (20) | patient (7); bronchoalveolar lavage fluid from cystic fibrosis patient at Johns Hopkins Hospital (4); sputum (2); Sinus (1) |
| Mucorales | Homo sapiens (255); Theobroma grandiflorum (4); Ipomoea batatas (4); Ficus carica (3); Passiflora edulis (3); soil (2); Black gram (1); Prunus persica L. (1); wheat (1); Gallus gallus (1); Yongchuan douchi (1); tobacco (1); rabbit (1); Ground Nuts (1); Pear (1) | culture (69); environmental (57); wild (54); Environment (48); feces (29); Maxillary sinus (21); Nasal crust (13); soil (11); bird dung (11); Westerdijk Fungal Biodiversity Institute culture collection strain (9); domesticated (8); sputum (6); air (6); Middle turbinate (5); clinical (5) |
| Nakaseomyces glabrata | Homo sapiens (1903) | blood (1099); Caspofungin induced isolate (60); human (59); in-vitro evolution in YPD (57); stool (36); urine (34); in vitro experimental evolution under fluconazole (32); Ascites (22); Laboratory (21); Mouth (19); Adaptive evolution experiments for thermotolerance, derived from a founding population consisting of MH-CgG and MH-CgY (18); seawater (18); vaginal (14); GI (13); feces (12) |
| Paracoccidioides spp. | Homo sapiens (67); Dasypus novemcinctus (7) | Biopsy (21); Human, PCM (13); Human, chronic PCM (10); Mouth Biopsy (6); Mesenteric Lymph node (5); chronic PCM (4); PCM (4); D. novemcinctus (armadillo) (4); tongue biopsy (3); soil (2); Lymph none aspirate (2); spleen (1); liver (1); Nasal Biopsy (1); C. centralis (armadillo) (1) |
| Pichia kudriavzevii | Homo sapiens (186); Grape (2); Microbial (2); Zingiber officinale (2); environmental (2); Cepaea nemoralis (1); Bos taurus (1); Baijiu fermentation culture (1); cheese (1) | blood (66); fermented food (32); feces (21); laboratory (12); Cocoa bean heap fermentation (6); grape skin (5); fermented masau fruits (4); membranes filtration cranberry juice processing environment (4); urine (4); Oropharyngeal (3); sputum (3); lab strain (2); NRRL Collection (2); floor (2); Baking (2) |
| Pneumocystis jirovecii | Homo sapiens (9) | bronchoalveolar lavage (2); Lungs (2); host broncho alveolar lavage (1); Bronchoalveolar lavage fluid (1); bronchalveolar lavage (1) |
| Scedosporium spp. | Homo sapiens (22); Hypericum maculatum (2) | sputum (5); Subcutaneous tissue (3); Ear tissue (3); Landfill soil (2); root (2); Industrial wastewater (2); soil contaminated with PAHs (2); Eye type, Cornea, Right (2); Left Sinus (1); bronchoalveolar lavage (1); Frontal Lobe (1); soil (1); Pancreatic Pseudocyst (1); respiratory secretions (1); Bronchial wash (1) |
| Talaromyces marneffei | Homo sapiens (370); Rhizomys sinensis (3); Animal (2); bamboo rat (2) | Blood or Skin (335); blood (13); bone marrow/blood (3); blood of an AIDS patient (2); Rhizomys cinensis (2); fiber-supporting mirror (2); Maharaj Nakorn Chiang Mai Hospital, Chiang Mai, Thailand (2); rainforest (1); balf (1); sputum (1) |
Who has been depositing genomes and SRA runs for each species. Genome submitter is taken from BioSample owner.name with assembly-level submitter as fallback. SRA submitter is the SUBMISSION center_name. Top 10 per species, combined across genomes and SRA.
| Species | Priority | Top submitter (count) | 2nd | 3rd | 4th | 5th |
|---|---|---|---|---|---|---|
| Aspergillus fumigatus | Critical | University of Birmingham (638) | Leibniz-HKI (504) | Imperial College London (391) | NORWEGIAN VETERINARY INSTITUTE (313) | UMass Amherst (302) |
| Candida albicans | Critical | Institut Pasteur (772) | SRG (380) | Chinese Center for Disease Control and Prevention (370) | Shanghai Tenth People's Hospital (304) | TEL AVIV UNIVERSITY (291) |
| Candida auris | Critical | UPHL_ID (5419) | NVSPHL (4730) | MDH_CSL (2629) | cdc-ncezid-mdb (2405) | MDHHS-GS (2145) |
| Candida parapsilosis | High | University College Dublin (375) | First Affiliated Hospital of Sun Yat-sen University (182) | Shenzhen Institute of Advanced Technology Chinese Academy of Science (125) | Memorial Sloan Kettering Cancer Center (123) | Fundacion para la Investigacion Biomedica del Hospital Gregorio Maranon (115) |
| Candida tropicalis | High | Peking Union Medical College Hospital (459) | Fudan University (291) | Vallabhbhai Patel Chest Institute (133) | Institute of Clinical Pathology and Medical Research (83) | Canisius-Wilhelmina Hospital (82) |
| Coccidioides spp. | Medium | University of California, San Francisco (96) | Translational Genomics Institute (74) | TGen North (68) | University of Utah (50) | Northern Arizona University (36) |
| Cryptococcus gattii | Medium | Broad Institute (109) | TGen North (63) | Chinese Academy of Science (50) | University of Exeter (39) | BI (34) |
| Cryptococcus neoformans | Critical | Broad Institute (1298) | Duke University (891) | BI (807) | Shanghai Tenth People's Hospital (644) | Oxford University Clinical Research Unit (415) |
| Eumycetoma agents | High | cdc-ncezid-mdb (68) | Umm Al Qura University (6) | ErasmusMC (4) | EBI (4) | Medical Mycology Research Center, Chiba University (3) |
| Fusarium spp. | High | Cook Lab - University of California at Davis (588) | Wageningen University and Research (564) | CSIRO (329) | University of Amsterdam (292) | University of Warmia and Mazury in Olsztyn (255) |
| Histoplasma spp. | High | University of California, San Francisco (251) | University of North Carolina at Chapel Hill (104) | University of Brasilia (62) | Centers for Disease Control and Prevention (48) | National Institute For Communicable Diseases (33) |
| Lomentospora prolificans | Medium | Johns Hopkins University (10) | Murdoch University (7) | University of Maryland, Baltimore (3) | — | — |
| Mucorales | High | JGI (1361) | Duke University School of Medicine (129) | UMIGS (87) | Institution of Microbiology (67) | J Craig Venter Institute (57) |
| Nakaseomyces glabrata | High | cdc-ncezid-mdb (312) | Peking union medical college hospital (250) | Public Health Agency of Canada (149) | University of Pittsburgh School of Medicine (105) | Chonnam National University Medical School and Chonnam National University Hospital (89) |
| Paracoccidioides spp. | Medium | Northern Arizona University (31) | BI (31) | University of North Carolina at Chapel Hill (22) | University of Brasilia (7) | Broad Institute of MIT and Harvard (5) |
| Pichia kudriavzevii | Medium | JGI (461) | Fudan university (86) | University College Dublin (35) | McMaster University (28) | Broad Institute (21) |
| Pneumocystis jirovecii | Medium | National Institutes Of Health (3) | BI (3) | Broad Institute (2) | NIH (2) | EBI (1) |
| Scedosporium spp. | Medium | The Kids Research Institute Australia (6) | University of Maryland, Baltimore (6) | INAIL-DIT, Research Area (4) | University of the Sunshine Coast (3) | LUNAM - Angers University (2) |
| Talaromyces marneffei | Medium | Broad Institute (345) | Chongqing Public Health Medical Center (15) | The First Affiliated Hospital of Guangxi Medical University (4) | The Hong Kong Polytechnic University (3) | Guangzhou Eighth People's Hospital, Guangzhou Medical University (2) |
Each submitter is classified into one of seven categories (public health agency, hospital / clinical, university, research institute, agriculture, commercial, other) using the curated keyword tables in classifiers.toml. The chart answers a different question to the sampling-context one: not where the pathogen came from biologically, but what kind of organisation is generating the data.
The 19 fungal entities from the WHO Fungal Priority Pathogens List (2022) are queried, grouped into Critical (4), High (7), and Medium (8) priority. For genus-level entries (e.g. Histoplasma spp.), the genus name is queried. For Mucorales, the order name is used. For eumycetoma agents, multiple causative genera are queried (Madurella, Medicopsis, Falciformispora, Trematosphaeria). Where NCBI taxonomy has been updated (e.g. Candida glabrata → Nakaseomyces glabrata), both old and new names are queried and results deduplicated by accession.
Genome assembly metadata is retrieved using the NCBI Datasets CLI (datasets summary genome taxon). Fields extracted per assembly: accession, organism name, taxonomy ID, release date, assembly level, submitter, and BioSample attributes (collection date, geographic location, host, isolation source). Both GenBank and RefSeq assemblies are included.
Sequencing read metadata is retrieved from the NCBI Sequence Read Archive (SRA) via E-utilities (esearch + efetch). Runs are filtered to library_source=GENOMIC and library_strategy=WGS to include only whole-genome sequencing data. BioSample attributes (collection date, geo_loc_name, host, isolation_source, host_disease), the SUBMISSION center_name, the LIBRARY block (strategy, source, selection), and the PLATFORM block (platform, instrument_model) are extracted from the inline sample metadata in the SRA XML. Placeholder values (missing, not collected, not applicable, unknown, etc.) are treated as absent.
Each record's BioSample host, isolation_source and host_disease values are joined and matched against keyword lists to assign one of seven coarse categories: human, animal, plant, environment, food, clinical_other (healthcare-associated surfaces and devices), unknown. Both the raw NCBI strings and the derived category are kept in the per-record CSV downloads.
For each record (genome or SRA), "With Location" indicates a non-empty geo_loc_name BioSample attribute; "With Date" indicates a non-empty collection_date; "With Both" requires both fields present. The data availability table can be filtered by source (Genomes only, SRA only, or combined).
Geographic distribution: The geo_loc_name field is parsed to extract the country (text before the first colon), mapped to ISO 3166-1 alpha-3 codes, and displayed on a Natural Earth 110m equirectangular projection with a log-scale colour gradient. Combined genome + SRA data.
Genomes over time: Year-by-year counts of genome assemblies and SRA WGS runs. Default axis is collection_date (year), stacked by species (default) or priority group. A toggle switches to release_date for the publication view.
Sampling context: Stacked bars per species using the derived host category, with a toggle for absolute counts vs proportions. Raw host and isolation_source values are listed in the per-species table.
Submitting centres: Top submitting organisation per species, ranked by total record count (genomes + SRA). For genomes, the BioSample owner.name is preferred over the assembly-level submitter because RefSeq assemblies have a constant "National Center for Biotechnology Information" submitter that masks the original depositor. For SRA, the SUBMISSION center_name is used.
unknown bucket; sanity-check using the raw values in the per-record CSV.