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Open Access Highly Accessed Research article

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)

John Kiiru123*, Patrick Butaye34, Bruno M Goddeeris25 and Samuel Kariuki1

Author Affiliations

1 Centre for Microbiology Research, Kenya Medical Research Institute, PO Box 19464-00202, Nairobi, Kenya

2 Department of Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 30, Heverlee, B-3001, Belgium

3 Veterinary and Agrochemical Research Centre, Groeselenberg 99, Ukkel, B-1180, Belgium

4 Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, University of Ghent, Salisburylaan 133, Merelbeke, 9820, Belgium

5 Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, University of Ghent, Salisburylaan 133, Merelbeke, 9820, Belgium

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BMC Microbiology 2013, 13:109  doi:10.1186/1471-2180-13-109

Published: 17 May 2013



We determined the prevalence and evidence for physical linkage amongst integrons, insertion sequences, Tn21 and Tn7 transposons in a collection of 1327 E. coli obtained over a 19-year period from patients in Kenya.


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 sul3 gene or IS26 or those containing the ISCR1 were only detected in multidrug resistant (MDR) strains. The dfrAs were the most common cassettes and their prevalence was: - dfrA1(28%), dfrA12(20%), dfA17(9%), dfrA7(9%), and dfrA16(5%). The aadA were the second most abundant cassettes and their prevalence was: - aadA1(25%), aadA2(21%), and aadA5(14%). Other cassettes occurred in lower prevalence of below 5%. Prevalence of Tn21, ISEcp1, ISCR1 and IS26 was 22%, 10%, 15%, and 7% respectively. Majority of Tn21 containing integrons carried a complete set of transposition genes while class 2 integrons were borne on Tn7 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 ISCR1. Close to 88% of blaTEM-52 were linked to IS26 while ≥ 80% of blaCTX-Ms and blaCMYs were linked to ISEcp1. Only a few studies have identified a blaCTX-M-9 containing an ISEcp1 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 J53 in mating experiments.


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.