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Background  We determined the prevalence and evidence for physical linkage amongst integrons, insertion sequences, Tn 21  and Tn 7  transposons in a collection of 1327  E. coli  obtained over a 19-year period from patients in Kenya.    Results  The prevalence of class 1 integrons was 35%, class 2 integrons were detected in 3 isolates but no isolate contained a class 3 integron. Integron lacking the 3’-CS or those linked to  sul 3 gene or IS 26  or those containing the IS CR 1 were only detected in multidrug resistant (MDR) strains. The  dfrAs  were the most common cassettes and their prevalence was: -  dfrA 1(28%),  dfrA 12(20%),  dfA 17(9%),  dfrA 7(9%), and  dfrA 16(5%). The  aadA  were the second most abundant cassettes and their prevalence was: -  aadA 1(25%),  aadA 2(21%), and  aadA 5(14%). Other cassettes occurred in lower prevalence of below 5%. Prevalence of Tn 21 , ISE cp 1, IS CR 1 and IS 26  was 22%, 10%, 15%, and 7% respectively. Majority of Tn 21  containing integrons carried a complete set of transposition genes while class 2 integrons were borne on Tn 7  transposon. The  qnrA  genes were detected in 34(3%) isolates while 19(1%) carried  qnrB . All  qnr  genes were in MDR strains carrying integrons containing the IS CR 1. Close to 88% of  bla   TEM- 52  were linked to IS 26  while ≥ 80% of  bla   CTX-M s  and  bla   CMYs   were linked to ISE cp 1. Only a few studies have identified a  bla   CTX-M -9  containing an ISE cp 1 element as reported in this study. Multiple genetic elements, especially those borne on  incIl ,  incFII , and  incL/M  plasmids, and their associated resistance genes were transferrable  en bloc  to  E. coli  strain J 53  in mating experiments.    Conclusions  This is the first detailed study on the prevalence of selected elements implicated in evolution of resistance determinants in a large collection of clinical  E. coli  in Africa. Proliferation of such strains carrying multiple resistance elements is likely to compromise the use of affordable and available treatment options for majority of poor patients in Africa. There is therefore a need to monitor the spread of these highly resistant strains in developing countries through proper infection control and appropriate use of antimicrobials.

bmc microbiology

Analysis for prevalence and physical linkages amongst integrons, ISEcp1, ISCR1, Tn21 and Tn7 encountered in Escherichia coli strains from hospitalized and non-hospitalized patients in Kenya during a 19-year period (1992–2011)