Overview of the filtering process within the amr.watch workflow applied to public genomes of priority bacterial pathogens available in the International Nucleotide Sequence Database Collaboration (INSDC) databases. The genome data are filtered in a series of steps, depicted from left to right in the table, with the numbers in each column representing a subset of those from the previous column.

For the pathogens that are grouped together, we initially accept genomes annotated in the ENA with any of the corresponding taxonomy IDs from the same group and use the Speciator assignments in subsequent processing.

Pathogen	ENA entries (run accessions)	Illumina paired-end entries	Filtered entries¹	Entries with geotemporal data²	Entries available for download in SRA	Entries associated with unique samples³	Assembled genomes	Genomes with correct species	Genomes that passed QC	Genomes with collection date post-2010	Last updated
All Pathogens	1,735,084	1,532,749	1,505,140	883,048	873,491	840,277	812,359	792,304	771,139	706,413
A. baumannii	50,534	41,142	39,003	26,609	26,152	25,336	25,025	24,660	24,232	22,696	12/1/2025
C. coli	174,733	169,844	166,796	113,227	111,992	111,391	109,140	33,662	32,398	31,267	11/30/2025
C. jejuni	174,733	169,844	166,796	113,227	111,992	111,391	109,140	73,696	70,398	67,886	11/30/2025
E. cloacae complex	22,024	19,437	19,029	14,507	14,401	13,168	12,807	12,386	11,755	11,295	12/1/2025
E. faecium	44,505	42,551	42,228	26,611	26,598	25,524	25,339	25,086	24,744	23,495	11/30/2025
E. coli	629,048	523,467	517,130	294,161	292,931	281,835	273,338	235,587	231,500	211,915	12/1/2025
S. flexneri								13,705	13,286	12,505	12/1/2025
S. sonnei								15,724	15,270	14,290	12/1/2025
H. influenzae	18,616	17,309	17,242	8,385	8,360	8,075	7,443	7,426	7,262	6,646	11/30/2025
K. pneumoniae	129,805	113,149	108,459	70,698	69,308	63,831	61,992	59,744	58,012	55,951	12/1/2025
N. gonorrhoeae	81,499	77,482	77,362	51,928	51,928	48,683	45,562	45,155	43,078	42,294	12/8/2025
P. aeruginosa	85,171	62,352	59,881	31,724	31,559	30,428	28,644	28,280	27,360	25,644	11/30/2025
Salmonella Typhi	130,384	121,575	120,507	93,850	93,627	91,604	90,285	9,127	8,955	6,917	12/1/2025
Salmonella Typhimurium								28,285	27,555	25,379	12/1/2025
Salmonella Enteritidis								48,780	47,902	46,220	12/1/2025
S. aureus	184,201	167,602	161,408	93,964	89,532	85,662	81,727	80,297	77,866	66,111	11/30/2025
S. pneumoniae	184,564	176,839	176,095	57,384	57,103	54,740	51,057	50,704	49,566	35,902	11/30/2025

Entries (runs) are filtered to include only those with two FASTQ files, ≥20x mean coverage (via assessment of the "base_count" field) and those associated with a single sample accession.
Entries (runs) are filtered to include those with a collection date that is decodable to at least the year and a sampling location that is decodable to at least the country level.
Entries (runs) are filtered to ensure only one run per sample accession is included (selecting the run with the highest number of bases via assessment of the "base_count" field).