Table 2.

WGS reads of non- A . pleuropneumoniae bacterial species used in this study

Species	No. of samples (n=66)	SRA run accession no.
Porcine bacterial pathogens	46	–
“Actinobacillus porcitonsillarum”*	2	ERR200086, ERR200087
Actinobacillus suis *	4	SRR5184352, SRR5189134, SRR5189141, SRR5189321
Bordetella bronchiseptica	5	SRR931866, SRR942675, SRR9614213, SRR9614214, SRR9614215
Escherichia coli *	5	SRR10099931, SRR10099940, SRR10099946, SRR11647626, SRR9619978
Glaesserella parasuis	5	ERR175964, ERR176010, ERR176017, ERR225607, ERR270808
Mycoplasma hyopneumoniae	5	SRR7601664, SRR7601670, SRR7601671, SRR7601681, SRR7601682
Pasteurella multocida	5	SRR13148928, SRR13148936, SRR13148937, SRR13148946, SRR13148947
Salmonella enterica serovar Choleraesuis	5	ERR1777400, ERR1777414, ERR1777421, ERR1777449, ERR1777457
Salmonella enterica serovar Typhimurium	5	SRR2015698, SRR2015925, SRR2075991, SRR8291813, SRR9879548
Streptococcus suis	5	SRR4431635, SRR4431639, SRR4431646, SRR4431671, SRR5177695
Others	20	–
Aggregatibacter actinomycetemcomitans *,†	3	SRR12066794, SRR3170532, SRR3947678
Bordetella pertussis *,†	5	SRR11855995, SRR12105040, SRR5080696, SRR8689258, SRR9118293
Mannheimia haemolytica *,‡	5	SRR3749365, SRR3749458, SRR3750210, SRR3767545, SRR3775504
Moraxella bovis *.‡	2	SRR11012145, SRR7431214
Proteus vulgaris *,†	5	ERR4014498, ERR4014630, SRR10728100, SRR13191024, SRR13191127

*RTX toxin-producing bacteria.

†Human pathogens.

‡Bovine pathogens.