Table 3.

Phage resistance mutations arising during experimental communities with and without phage

Population	Isolate ID	U136BR	tolC mutation†	TET MIC (μg/mL)‡	LPS mutation	CST MIC (ng/mL)§	Other genes with mutations¶
Populations evolved with phage U136B present
+1	AB277	+	IS5 insertion at 190/1,482 nt	0.25	−	200	narZ C292S (TGC→AGC)
+2	AB279	+	Y283D (TAT→GAT)	2.00	−	200
+3	AB281	+	IS5 insertion coding 190/1,482 nt	0.25	−	200
+4	AB283	+	21 bp duplication at 259/1,482 nt	2.00	−	250	ryjB (novel sRNA, function unknown), T→G at 62/90 nt
+5	AB285	+	IS5 insertion at 194/1,482 nt	0.25	−	200
+6	AB287	+	G75V (GGC→GTC)	2.00	−	250
+7	AB289	+	Δ1 bp at 1,066/1,482 nt	0.25	−	200
+8	AB291	+	E110* (GAA→TAA)	0.25	−	200
+9	AB293	+	IS5 insertion at 190/1,482 nt	0.25	−	250	arsC and yhiS Δ1,421 bp at 3,643,975, IS5-mediated
+10	AB295	+	E339* (GAA→TAA)	0.25	−	250
Populations evolved without phage U136B present
−1	AB278	−	−	2.00	−	200
−2	AB280	−	−	2.00	−	200	bglH IS5 (–) +4 bp at 1244/1617 nt
−3	AB282	−	−	2.00	−	250
−4	AB284	−	−	2.00	−	250
−5	AB286	−	−	2.00	−	200
−6	AB288	−	−	2.00	−	200	metE L19M (CTG→ATG)
−7	AB290	−	−	2.00	−	200
−8	AB292	−	−	2.00	−	250
−9	AB294	−	−	2.00	−	250	lplT 24 bp duplication at 229/1194 nt
−10	AB296	−	−	2.00	−	250

Control MIC values for BW25113 and tolC mutant are from the same dataset reported in Table 2.

^†A “Δ” indicates deletion of indicated base pairs or gene. An asterisk indicates a point mutation resulting in a stop codon. Values in parentheses indicate either single substitutions or the location of either a stop codon or IS element insertion within coding sequences. Underlined bases indicate single substitutions; nt, indicates nucleotide.

^‡Tetracycline (TET) concentrations tested were 0.125, 0.25, 0.5, 1.0, 2.0, and 4.0 μg/mL, so the discrete value listed may be greater than the actual MIC but not more than the next highest value tested. Values are the mode of three to four replicates tested for each strain.

^§Colistin (CST) concentrations tested were 12.5, 25, 50, 100, 150, 200, 250, 300, 350, and 400 ng/mL, so the discrete value listed may be greater than the actual MIC but not more than the next highest value tested. Values are the mode of two replicates tested for each mutant.

^¶narZ: nitrate reductase 2 (NRZ), alpha subunit; ryiB: novel small RNA (sRNA), function unknown; arsC: arsenate reductase; yhiS: putative uncharacterized protein; bglH is a cryptic carbohydrate-specific OMP gene; metE is a 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase gene; lplT is a lysophospholipid transporter gene.