Table 2 Genes associated with patient case status

From: Combined comparative genomics and clinical modeling reveals plasmid-encoded genes are independently associated with Klebsiella infection

Gene	Annotation	Case frequency	Control frequency	Unadjusted			Adjusted for clinical variables		Mediation
Gene	Annotation	Case frequency	Control frequency	Odds ratio	P-value	Q-value**	Odds ratio	P-value**	Direct β	Direct P-value**	Indirect β	Indirect P-value**
aac(6')-Ib-cr5	fluoroquinolone-acetylating aminoglycoside 6'-N-acetyltransferase AAC(6')-Ib-cr5	0.176	0.006	30.68	0.0011	0.00131	52.41	0.0003	3.0601	0.0045	0.086	0.01
bla_OXA-1	oxacillin-hydrolyzing class D β-lactamase OXA-1	0.153	0.006	25.54	0.002	0.0053	49.29	0.0003	2.9698	0.0064	0.077	0.03
bla_CTX-M-15	class A extended-spectrum β-lactamase CTX-M-15	0.165	0.013	13.94	0.0007	0.0053	19.17	0.0004	2.3386	0.004	0.047	0.1567
group_13461	IS1380 family transposase ISEcp1	0.165	0.013	13.94	0.0007	0.0053	18.69	0.0003	2.482	0.0022	0.019	0.5833
group_13458	hypothetical protein	0.141	0.013	11.46	0.0018	0.01959	17.57	0.0006	2.0832	0.0112	0.034	0.3483
group_13460	hypothetical protein	0.153	0.013	12.69	0.0011	0.01065	16.73	0.0005	2.3118	0.0047	0.024	0.5217
group_13437	hypothetical protein	0.176	0.031	5.97	0.001	0.05505	7.28	0.0014	1.6137	0.0054	0.005	0.875
group_5875-tehA_2-group_10494*	HTH-type transcriptional regulatory protein GabR - tellurite-resistance protein TehA - hypothetical protein	0.129	0.025	5.65	0.004	0.1908	7.09	0.0029	1.8251	0.0053	0.007	0.8383
tnpR	transposon Tn3 resolvase	0.176	0.031	5.97	0.001	0.05505	6.24	0.0017	1.6379	0.0054	0.023	0.45
bla_TEM-1	class A broad-spectrum β-lactamase TEM-1	0.212	0.038	6.28	0.0002	0.01236	5.46	0.0009	1.6623	0.0021	0.035	0.1783
group_9575	tyrosine recombinase XerC	0.259	0.056	5.39	0.0001	0.0053	4.72	0.0019	1.3993	0.0044	0.048	0.05
group_13467	IS6 family transposase IS6100	0.224	0.044	5.75	0.0002	0.01093	4.58	0.0026	1.5338	0.003	0.023	0.4017
group_5455-sul2*	IS91 family transposase - sulfonamide-resistant dihydropteroate synthase Sul2	0.129	0.025	5.07	0.0077	0.1908	4.52	0.0258	2.0214	0.0053	−0.033	0.3617
group_13965	hypothetical protein	0.153	0.038	4.11	0.0066	0.16685	3.59	0.0264	1.0196	0.0806	0.074	0.01
group_9537	hypothetical protein	0.235	0.081	3.71	0.0009	0.13482	3.3	0.0035	1.0141	0.0216	0.049	0.025
group_13443	hypothetical protein	0.224	0.075	3.81	0.001	0.16685	3.23	0.005	1.0762	0.0178	0.06	0.0083
group_7606	hypothetical protein	0.141	0.025	6.26	0.0021	0.10991	3.07	0.0916	1.106	0.0975	0.097	0.0001
dgcE	hypothetical protein	0.341	0.138	3.37	0.0003	0.07663	3.06	0.0016	0.9197	0.0133	0.048	0.0083
aqpZ_2	aquaporin Z	0.247	0.094	3.96	0.0005	0.16685	2.97	0.0085	0.923	0.0385	0.074	0.0001
group_2409	ISL3 family transposase ISEc38	0.259	0.106	3.07	0.002	0.1908	2.67	0.0083	0.803	0.0487	0.05	0.01
pdeC_2	putative cyclic di-GMP phosphodiesterase PdeC	0.365	0.169	2.88	0.0008	0.10991	2.66	0.0026	0.7709	0.0296	0.041	0.015
sul1	sulfonamide-resistant dihydropteroate synthase Sul1	0.141	0.031	4.97	0.0037	0.17478	2.64	0.0939	1.102	0.0994	0.12	0.0001
qacEΔ1	quaternary ammonium compound efflux SMR transporter QacE Δ 1	0.153	0.031	5.46	0.0019	0.12853	2.63	0.1011	1.1732	0.0745	0.107	0.0001
arsD_1	arsenical resistance operon trans-acting repressor ArsD	0.318	0.144	3.19	0.0006	0.17478	2.62	0.0043	0.7263	0.0563	0.068	0.0001
group_774	hypothetical protein	0.459	0.25	2.55	0.0013	0.1391	2.55	0.0016	0.8601	0.0088	0.042	0.0033
group_7231	hypothetical protein	0.306	0.138	2.69	0.0032	0.16685	2.54	0.0071	0.7807	0.0373	0.026	0.1733
group_9530	hypothetical protein	0.459	0.238	2.64	0.0009	0.08496	2.38	0.0037	0.8449	0.0094	0.015	0.3533
ltrA	hypothetical protein	0.424	0.225	2.57	0.0013	0.16683	2.33	0.0051	0.7495	0.0229	0.037	0.015
group_9528	hypothetical protein	0.353	0.163	2.87	0.001	0.12853	2.31	0.0134	0.7418	0.0384	0.032	0.0917
group_622	hypothetical protein	0.482	0.269	2.71	0.0006	0.12566	2.24	0.0063	0.9086	0.0049	0.015	0.3683
group_4187	Antirestriction protein KlcA	0.424	0.219	2.54	0.0017	0.12566	2.24	0.0092	0.7747	0.0191	0.021	0.1983
umuD_2	Protein UmuD	0.6	0.369	2.42	0.0016	0.10991	2.1	0.0114	0.8272	0.0098	0.006	0.7
umuC_2	Protein UmuC	0.682	0.456	2.52	0.0012	0.10991	2.09	0.0141	0.8239	0.0107	0.006	0.71
group_2513	hypothetical protein	0.071	0.225	0.26	0.0038	0.16685	0.25	0.0031	−1.2577	0.0119	−0.02	0.3617

*Loci have identical presence/absence patterns across all sequenced isolates and are clustered for analysis.
**Bold text indicates significant results (unadjusted Q-value ≤ 0.2, P-value ≤ 0.01 after adjustment for clinical variables, and direct and/or indirect effect P-value ≤ 0.01).

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Table 2 Genes associated with patient case status

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