Analysis of β-lactamase phenotypes and carriage of selected β-lactamase genes among <it>Escherichia coli</it> strains obtained from Kenyan patients during an 18-year period

<p>Abstract</p> <p>Background</p> <p>Although β-lactam antibiotics are heavily used in many developing countries, the diversity of β-lactamase genes (<it>bla</it>) is poorly understood. We screened for major β-lactamase phenotypes and diversity of <it>bla</it> genes among 912 <it>E. coli</it> strains isolated from clinical samples obtained between 1992 and 2010 from hospitalized and non-hospitalized patients.</p> <p>Results</p> <p>None of the isolates was resistant to carbapenems but 30% of all isolates were susceptible to cefepime, cephamycins and piperacillin-tazobactam. Narrow spectrum β-lactamase (NSBL) phenotype was observed in 278 (30%) isolates that contained <it>bla</it>_{<it>TEM</it>-1} (54%) or <it>bla</it>_{<it>SHV</it>-1} (35%) or both (11%). Extended Spectrum β-lactamase (ESBL) phenotype was detected in 247 (27%) isolates which carried <it>bla</it>_{<it>CTX-M</it>-14} (29%), <it>bla</it>_{<it>CTX-M</it>-15} (24%), <it>bla</it>_{<it>CTX-M</it>-9} (2%), <it>bla</it>_{<it>CTX-M</it>-8} (4%), <it>bla</it>_{<it>CTX-M</it>-3} (11%), <it>bla</it>_{<it>CTX-M</it>-1} (6%), <it>bla</it>_{<it>SHV</it>-5} (3%), <it>bla</it>_{<it>SHV</it>-12} (5%), and <it>bla</it>_{<it>TEM-52</it>} (16%). Complex Mutant TEM-like (CMT) phenotype was detected in 220 (24%) isolates which carried <it>bla</it>_{<it>TEM</it>-125} (29%), while <it>bla</it>_{<it>TEM</it>-50}, <it>bla</it>_{<it>TEM</it>-78}, <it>bla</it>_{<it>TEM</it>-109}, <it>bla</it>_{<it>TEM −</it>152} and <it>bla</it>_{<it>TEM</it>-158} were detected in lower frequencies of between 7% and 11%. Majority of isolates producing a combination of CTX-M-15 + OXA-1 + TEM-1 exhibited resistance phenotypes barely indistinguishable from those of CMT-producers. Although 73 (8%) isolates exhibited Inhibitor Resistant TEM-like (IRT) phenotype, <it>bla</it>_{<it>TEM</it>-103} was the only true IRT-encoding gene identified in 18 (25%) of strains with this phenotype while the rest produced a combination of TEM-1 + OXA-1. The pAmpCs-like phenotype was observed in 94 (10%) isolates of which 77 (82%) carried <it>bla</it>_{<it>CMY</it>-2} while 18% contained <it>bla</it>_{<it>CMY</it>-1.}</p> <p>Isolates from urine accounted for 53%, 53%, 74% and 72% of strains exhibiting complex phenotypes such as IRT, ESBL, CMT or pAmpC respectively. On the contrary, 55% isolates from stool exhibited the relatively more susceptible NSBL-like phenotype. All the phenotypes, and majority of the <it>bla</it> genes, were detected both in isolates from hospitalized and non-hospitalized patients but complex phenotypes were particularly common among strains obtained between 2000 and 2010 from urine of hospitalized patients.</p> <p>Conclusions</p> <p>The phenotypes and diversity of <it>bla</it> genes in <it>E. coli</it> strains implicated in clinical infections in non-hospitalized and hospitalized patients in Kenya is worryingly high. In order to preserve the efficacy of β-lactam antibiotics, culture and susceptibility data should guide therapy and surveillance studies for β-lactamase-producers in developing countries should be launched.</p>