Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica

Liao, Jingqiu; Orsi, Renato Hohl; Carroll, Laura M.; Kovac, Jasna; Ou, Hongyu; Zhang, Hailong; Wiedmann, Martin

doi:10.1186/s12862-019-1457-5

BMC Ecology and Evolution

Table 3 Serotype-associated core genes undergoing positive selection specifically on AMR S. Dublin, S. Newport or S. Typhimurium ancestral branches

From: Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica

Gene	Ln L MA1^a	Ln L MA^b	p value^c	FDR^d	Function^e	ω^f	proportion of sites under pos. Selection(%)^g
S. Dublin branch
Cluster_1190	− 7073.691	− 7048.222	0.000	0.000	autotransporter outer membrane beta-barrel domain-containing protein	569.327	5.984
Cluster_1721	− 1052.362	− 1038.860	0.000	0.000	dipeptidase E	999.000	1.364
Cluster_1900	−2015.241	−2004.734	0.000	0.002	bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase	999.000	0.526
Cluster_2035	− 2457.111	− 2446.938	0.000	0.002	flagellar M-ring protein FliF	999.000	0.482
Cluster_3324	−778.864	− 771.694	0.000	0.032	fimbrial protein StiA	999.000	0.804
S. Newport branch
Cluster_831	− 1041.959	− 1024.731	0.000	0.000	ABC transporter ATP-binding protein	999.000	3.724
Cluster_875	−844.370	− 826.859	0.000	0.000	CaiF/GrlA family transcriptional regulator	999.000	4.986
Cluster_1190	− 7071.499	− 7051.968	0.000	0.000	autotransporter outer membrane beta-barrel domain-containing protein	999.000	6.661
Cluster_1461	− 4112.903	− 4103.963	0.000	0.003	2-oxoglutarate dehydrogenase E1 component	999.000	0.113
Cluster_1538	− 2076.594	− 2066.164	0.000	0.001	invasin	999.000	0.295
Cluster_1678	−2008.961	−2001.754	0.000	0.019	hypothetical protein	204.362	0.829
Cluster_3346	− 1744.612	− 1726.105	0.000	0.000	hypothetical protein	999.000	11.655
Cluster_3368	− 4010.845	− 3976.156	0.000	0.000	outer membrane protein assembly factor BamA	836.419	3.378
S. Typhimurium branch
Cluster_476	−1969.539	− 1933.139	0.000	0.000	porin	859.863	7.172
Cluster_1190	− 7076.553	−7037.396	0.000	0.000	autotransporter outer membrane beta-barrel domain-containing protein	252.954	7.072
Cluster_1216	− 2790.059	− 2781.805	0.000	0.008	maltodextrin glucosidase	999.000	0.764
Cluster_1756	− 2830.518	− 2823.397	0.000	0.024	glutamine--fructose-6-phosphate aminotransferase	828.247	0.394
Cluster_2234	−1998.702	−1990.410	0.000	0.008	tryptophan permease	999.000	1.035
Cluster_2311	− 3370.510	− 3358.161	0.000	0.000	E3 ubiquitin--protein ligase	171.701	1.404
Cluster_2757	− 2077.394	− 2068.717	0.000	0.008	D-serine/D-alanine/glycine transporter	106.317	1.691

^aLn L MA1; Lognormal likelihood score for the null hypothesis that sites evolved following neutral model in the serotype ancestral branch
^bLn L MA; Lognormal likelihood score for the alternative hypothesis that sites evolved under positive selection in the serotype ancestral branch
^cThe test statistic was calculated as 2[(−Ln L MA1) - (−Ln L MA)]
^dThis column indicates the p-value after a FDR (False Discovery Rate) correction was carried out to correct for multiple comparison
^e“Function” represents the gene function provided by the NCBI Prokaryotic Genome Annotation Pipeline
^fω, average dN/dS value for codon sites under positive selection. dN is the number of nonsynonymous changes divided by the number of nonsynonymous sites. dS is the number of synonymous changes divided by the number of synonymous sites. ω = 999.000 represent infinite values as dS = 0
^gproportion of codon sites under positive selection

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ISSN: 2730-7182

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