Article Figures & Data
Figures
- FIG. 1.
Maximum-likelihood tree of the 36 Ia nucleotide sequence types detected in E. coli isolates from human and nonhuman vertebrates living in Australia. In each label, the first number is the ST and the number in parentheses is the number of times the ST was observed, followed by the genetic groups of E. coli in which the ST was detected and finally if the ST co-occurred with the microcin V operon in the same strain. Bootstrap values are based on 500 replicates.
Tables
- TABLE 1.
Frequency of E. coli strains encoding colicin Ia, microcin V, or both bacteriocins, together with the predicted fraction of strains encoding both bacteriocins assuming that they randomly associatea
Source and group No. of isolates % Observed % Predicted, colicin Ia and microcin V P > χ2 Colicin Ia Microcin V Colicin Ia and microcin V Human A 90 4.4 3.3 6.6 1.1 <0.001 B1 51 9.8 7.8 2.0 1.1 0.575 B2 350 3.7 2.3 7.1 1.0 <0.001 D 128 4.7 2.7 3.1 0.4 <0.001 Animal A 93 2.2 1.1 0 <0.1 0.834 B1 272 6.2 1.8 1.1 <0.1 <0.001 B2 213 17.8 0.1 2.3 <0.1 <0.001 D 112 6.2 0 0 ↵ a Data presented are for strains isolated from humans and nonhuman vertebrates living in Australia with respect to the genetic group membership of the strains.
- TABLE 2.
Phenotypic and genotypic characteristics of plasmids encoding the bacteriocins colicin Ia and microcin V
Strain Colicin Ia Microcin V finO ST TraY type IncFII traT iroN iss sitA iutA Resistance profilea AE008 + − 10 − − − − − − − TMP SXT AM CE015 + − 14 R − + − + − − TMP SXT AM S PE006 + − 6 − − − − − − − TE SE016 + − 7 − − − − − − − AM TE C SE017 + − 20 − − − − − − − AM TE C AE013 + − 4 F + + − − − − TMP SXT S SPT CE003 + − 18 F + + − − − − TMP AM TE AE011 − + 5 F + + + + + − TMP SXT AM S TE CE014 − + 3 F + + + + + + TMP STX PE007 − + 5 F + + + + + − TMP STX S SE010 − + 5 F + + + + + − TMP STX H772 − + 15 F + + + + + + TE AE016 + + 8 F − + + + − − TMP STX CE004 + + 8 − − + + + + + TMP STX AM S TE K CE010 + + 12 − − + + + + + TMP STX AM S TE K PE001 + + 8 F − + + + + + TMP STX AM S PE002 + + 8 F − + + + + + AM TE PE004 + + 5 F − + + + + − TMP PE009 + + 19 F − + + + + + TMP STX AM S TE H053 + + 8 F − + + + + + TMP SXT AM S H070 + + 8 F − + + + + + TMP A S TE H073 + + 8 F − + + + + + TMP A S TE H111 + + 8 F − + + + + + SXT AM H112 + + 8 F − + + + + + AM TE H127 + + 11 F − + + + + + AM S TE H188 + + 8 F − + + + + + TMP SXT AM S TE K H190 + + 8 F − + + + + + TMP AM S TE K H461 + + 8 F − + + + + + AM S H549 + + 8 F − + + + + + TMP SXT AM S H098 + + 13 R + + + + − − S H100 + + 9 R + + + + − − TMP STX AM H314 + + 1 − + + + + − − AM S AE009 + + 17 R + + + + + + TMP STX AE010 + + 17 R + + + + + + TMP STX TE SE018 + + 5 F + + + + + − TE C ↵ a AM, ampicillin; C, chloramphenicol; K, kanamycin; S, streptomycin; SXT, sulfisoxazole; TE, tetracycline; TMP, trimethoprim.
- TABLE 3.
Nucleotide variation in a 527-bp fragment of the microcin V operon found in this study compared to previously published results (26)a
Variantb Nucleotide at position: 2 14 42 51 55 76 105 109 110 111 112 113 114 115 116 117 118 119 120 121 122 131 134 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 294 295 323 459 AF062847 (1) C G T T A T G T A A T G G G A T A G A A A G A - - - - - - - - - - - - - - - G C T A H030 (1) G A T T A T G T A A T G G G A T A G A A A A A - - - - - - - - - - - - - - - G C T G AF062845 (1) G G G C C G A T A A T G G G A T A G A A A A A - - - - - - - - - - - - - - - A T T A AF062849 (1) G G G C C G G T A A T G G G A T A G A A A A A - - - - - - - - - - - - - - - A T T A H368 (1) G G G T A T G T A A T G G G A T A G A A A A A - - - - - - - - - - - - - - - G C T G H781 (1) G G T T A T G - - - - - - - - - - - - - - A A - - - - - - - - - - - - - - - G C C G AF062844 (1) G G T T A T G T A A T G G G A T A G A A A A A - - - - - - - - - - - - - - - G C C G ECCVAC (52) G G T T A T G T A A T G G G A T A G A A A A A - - - - - - - - - - - - - - - G C T G B177 (1) G G T T A T G T A A T G G G A T A G A A A A G - - - - - - - - - - - - - - - G C T G H244 (2) G G T T A T G T A A T G G G A T A G A A A A G T G G G A T A A A A A G T A A G C T G AF062848 (1) G G T T A T G T A A T G G G A T A G A A A G A - - - - - - - - - - - - - - - G C T A - TABLE 4.
Population differentiation estimates (PhiPT) to determine the extent to which colicin Ia nucleotide sequence variation depended on the host group from which the strains were isolated or whether the strains also encoded microcin V
Comparisona PhiPT Probabilityb Ia animal vs Ia human 0.101 0.040 Ia animal vs IaV animal 0.480 0.001 Ia human vs IaV animal 0.386 0.002 Ia animal vs IaV human 0.292 0.001 Ia human vs IaV human 0.127 0.014 IaV animal vs IaV human 0.129 0.081 - TABLE 5.
Amino acid sequences of the colicin Ia variants detected in this study together with the human or nonhuman vertebrate sources from which the strains were isolated and whether the strains also encode microcin V
Strain Source Microcin V Varianta Nucleotide at position: 4 60 88 92 109 130 141 169 206 238 241 247 275 284 295 340 346 367 H190 Human + 3 (1) R G T I G R R H A A V A N A L A T E B439 Animal + 6 (1) R G T M A R R H A A V A N A P A T E B313 Animal + 14 (1) S G T M A R R H A A V A N A L A T E TA311 Animal + 16 (1) S G T M A R R H A A V A N A P A T E M550 Animal + 17 (2) S G T M A R R Y A A V A N A L A T E AE016 Human + 4 (1) R G T M A R R H A A V A N A L A T E H098 Human + 5 (1) R G T M A R R H A A V A N A P A S E H314 Human + 6 (7) R G T M A R R H A A V A N A P A T E H151 Human + 14 (12) S G T M A R R H A A V A N A L A T E H244 Human + 15 (1) S G T M A R R H A A V A N A P A S E PE002 Human + 16 (1) S G T M A R R H A A V A N A P A T E AE008 Human − 13 (1) S G T M A R R H A A V A K A P A T E CE015 Human − 15 (1) S G T M A R R H A A V A N A P A S E SE017 Human − 2 (2) R G A N G R R H A A V A N A P A S E H730 Human − 10 (2) R G T N G R R H A A V A N A P A T E H591 Human − 11 (1) R G T N G R R H A A V A N A P V S E H556 Human − 18 (1) S G T N G R Q H T A V A N A P A T E H468 Human − 19 (1) S G T N G R R H A A V A N A P A S E H422 Human − 21 (1) S G T N G R R H T A V A N A P A T E PE001 Human + 7 (2) R G T N G R R H A A V A N A L A T E H331 Human + 8 (2) R G T N G R R H A A V A N A P A S E PE004 Human + 9 (1) R G T N G R R H A A V A N A P A S K TA060 Animal − 1 (2) R G A N G H R H A A V A N A P A T E M411 Animal − 8 (1) R G T N G R R H A A V A N A P A S E TA026 Animal − 10 (3) R G T N G R R H A A V A N A P A T E R148 Animal − 12 (1) R G T N G R R H T A V A N A P A T E R529 Animal − 20 (1) S G T N G R R H T A I A N A P A T E TA261 Animal − 21 (3) S G T N G R R H T A V A N A P A T E B564 Animal − 22 (1) S G T N G R R H T A V A N T P A T E M008 Animal − 23 (1) S G T N G R R H T A V S N A P A T E M318 Animal − 24 (1) S G T N G R R H T V V A N A P A T E M028 Animal − 25 (1) S V T N G R R H T V V A N A P A T E ↵ a The number in parentheses is the number of times the variant was observed in that source population and in the presence or absence of microcin V.
