Half of the public sequence data on WHO's priority fungi is one species.

fungi.watch tracks assembled genomes and sequencing runs on NCBI for the 19 pathogens on the WHO list. Reporting includes who is sequencing what, where samples come from, and how much of the metadata are available.

Explore the data How it is built

Top-down photograph of a petri dish with white, cream and green fungal colonies growing on amber agar

Total records: 68,780
Assembled genomes: 5,181
SRA WGS runs: 63,599
Species groups: 19
Countries: 126

A handful of species dominate the data.

Candida auris accounts for 50.0% of the 68,780 assembly and SRA run records shown here, much of it deposited by public health laboratories. At the other end, Pneumocystis jirovecii has 12 records in total.

Critical
4 species
74.8%
2,093 genomes
49,331 SRA runs
High
7 species
22.1%
2,919 genomes
12,256 SRA runs
Medium
8 species
3.2%
169 genomes
2,012 SRA runs

Widely different reported metadata

Combined genomes and SRA runs per species, with the share of records that carry a location and a collection date. Mucorales and Pichia kudriavzevii have both for only about a quarter of their records.

Candida auris
34,410
Place
92%
Date
94%
Cryptococcus neoformans
6,862
Place
58%
Date
47%
Fusarium spp.
6,258
Place
87%
Date
76%
Aspergillus fumigatus
5,320
Place
53%
Date
47%
Candida albicans
4,832
Place
66%
Date
65%
Mucorales
2,430
Place
32%
Date
25%
Nakaseomyces glabrata
2,251
Place
87%
Date
86%
Candida parapsilosis
1,963
Place
84%
Date
50%
Candida tropicalis
1,581
Place
89%
Date
89%
Pichia kudriavzevii
791
Place
36%
Date
27%
Histoplasma spp.
595
Place
91%
Date
83%
Coccidioides spp.
428
Place
86%
Date
73%
Cryptococcus gattii
397
Place
80%
Date
37%
Talaromyces marneffei
383
Place
99%
Date
95%
Paracoccidioides spp.
112
Place
96%
Date
36%
Eumycetoma agents
97
Place
92%
Date
95%
Scedosporium spp.
38
Place
84%
Date
66%
Lomentospora prolificans
20
Place
100%
Date
85%
Pneumocystis jirovecii
12
Place
67%
Date
33%

Explore metadata completeness across all species

Geography

Where isolates were sampled

Country of origin parsed from the location field, shaded on a log scale so a few heavily sampled countries do not hide the rest.

Show

Hover a country

135,370 recordsNo mapped records

Timeline

Genomes over time

Assemblies and sequencing runs by the year the sample was collected, or by the year the record was released.

Year type

Group by

373 records collected before 1990 are not shown.

Critical
High
Medium

Where the isolates come from

Derived from BioSample host, isolation source and host disease fields.

Candida auris
Almost entirely a hospital organism
32,123 of 34,410 records list Homo sapiens as host, mostly urine, blood and axilla/groin swabs, with 561 wastewater samples.
Fusarium spp.
Sampled from fields, not patients
Top hosts are chickpea (591), rice (339) and wheat (230). Only 167 records come from humans.
Cryptococcus neoformans
Lab strains blur the picture
Frequently reported isolation sources include laboratory crosses, frozen stocks, experimental samples and cerebrospinal fluid from patients.
Eumycetoma agents
Small, but complete
Of 97 records, 87 report a human host and 92 report a collection date.

Explore sampling context across all species

Who is depositing

The leading submitting centre for a few species, genomes and SRA runs combined.

Candida auris
5,439
UPHL_ID
Public health laboratories dominate, followed by NVSPHL (4,730) and MDH_CSL (2,629).
Cryptococcus neoformans
1,298
Broad Institute
Research institutes lead, with Duke University (891) close behind.
Candida albicans
772
Institut Pasteur
A spread of universities and hospitals, no single dominant depositor.
Mucorales
1,361
JGI
One genome-sequencing centre accounts for over half of all records.

Explore submitting centres across all species

Methods

Built from NCBI with automatic updates

A short description of the pipeline and the caveats worth knowing before you cite a number from this page.

Species selection

The 19 entities on the WHO Fungal Priority Pathogens List (2022) are queried. Where NCBI taxonomy has been renamed, such as Candida glabrata to Nakaseomyces glabrata, both names are searched and results deduplicated by accession.

Assembled genomes

Assembly metadata comes from the NCBI Datasets CLI, including GenBank and RefSeq. We extract accession, taxonomy, release date, assembly level, submitter and BioSample attributes.

SRA WGS runs

Read metadata is pulled through E-utilities and filtered to library_source GENOMIC and library_strategy WGS. Placeholders such as "missing" or "not collected" are treated as absent.

Host categorisation

Host, isolation source and host disease are matched against keyword lists to assign human, animal, plant, environment, food, clinical other or unknown. Raw NCBI strings are always kept.

Read before you cite

SRA counts for genus-level queries may include non-pathogenic species in the genus.
Geographic parsing is approximate. Sub-national locations without a country prefix can be missed.
Collection dates vary in precision, and only the year is used in temporal charts.
Host categories rely on keyword matching against free text, so ambiguous records land in unknown.
Submitter names are not curated; one organisation can appear under several aliases.
Some NCBI assemblies are suppressed or superseded but still returned by the Datasets CLI.

Half of the public sequence data on WHO's priority fungi is one species.

A handful of species dominate the data.

Critical

High

Medium

Widely different reported metadata

Where isolates were sampled

Genomes over time

Where the isolates come from

Almost entirely a hospital organism

Sampled from fields, not patients

Lab strains blur the picture

Small, but complete

Who is depositing

Built from NCBI with automatic updates

Read before you cite

Download the underlying tables