Antimicrobial Resistance Patterns and Genetic Basis of Extended Spectrum β-Lactamases in Faecal Escherichia coli Isolated from Severely Malnourished and Non-Malnourished Children Attending Mbagathi District Hospital, Nairobi

Abstract

Severely malnourished children have increased risk of severe infections and are therefore more likely to use antimicrobial agents. This could in turn present a strong selection pressure for the emergence and spread of multidrug resistant (MDR) strains. In this case-control, hospital-based study, 109 E. coli isolates were obtained from both severely malnourished and non-malnourished children. Higher resistances were observed in severely malnourished children to cefpodoxime, cefepime, ceftazidime, cefotaxime, amoxicilin/clavulanic acid, ciprofloxacin, nalidixic acid, chloramphenicol, and gentamicin than in non-malnourished children. Severely malnourished children were 8.2 times more likely to carry ESBL-producers than non-malnourished children (P < 0.0001, O.R - 8.2254, C.I - 3.6374 to 18.6003). blaCTX-M was present in 25 (49%) and 6 (75%) among Cases and Controls respectively. Among the 31 CTX-M producers, 30 (97%) carried blaCTX-M-15. Also blaCTX-M-15 occurred in combination with blaTEM-1 and blaOXA-1 in 10 (32 %) isolates. Other bla alleles detected alongside blaCTX-M-15 but rarely reported globally were blaTEM-33 1(3%) and blaTEM-158 1(3%). ST131 clones were present in 12 (39%) of the CTX-M-15 isolates. This study also identified a novel ST4481 clone and has been deposited in the Warwick database. This study reports the first occurrence of CTX-M-15-producing E. coli strains from Mbagathi District Hospital belonging to ST131, ST405, ST44, ST205, ST1642, ST1722, ST617, ST38, ST1675, ST648 and ST167, ST940 and a newly submitted ST4481. ST4481 has not been associated with CTX-M-15 enzymes anywhere else in the world. This study provides proof that ST131 strains with CTX-M-15 enzymes are indeed widespread. Isolates from non-malnourished children only fit into few ST-clones (ST405, ST940 and ST131) while ambiguity was observed in ST clones from malnourished children.