Molecular Characterization of Extended-Spectrum β-Lactamase–Producing Escherichia coli and Klebsiella pneumoniae Among the Pediatric Population in Qatar
Andrés Pérez‐López, Sathyavathi Sundararaju, Hassan Al Mana, Kin Ming Tsui, Mohammad R. Hasan, Mohammed Suleiman, Mohammed Janahi, Eman Al Maslamani, Patrick Tang
Abstract
Introduction: Although extended-spectrum β-lactamase (ESBL)-producing Enterobacterales are a public health problem in the Arabian Peninsula, data on the molecular characteristic of their antimicrobial resistance determinants in children is limited. Aim: To determine the molecular characteristics of ESBL-producing Escherichia coli and Klebsiella pneumoniae in the pediatric population of Qatar. Methods: Whole-genome sequencing (WGS) was performed on ESBL-producing E. coli and K. pneumoniae isolates recovered from screening and clinical specimens from pediatric patients at Sidra Medicine in Doha from January to December 2018. Results: A total of 327 ESBL producers were sequenced: 254 E. coli and 73 K. pneumoniae. Non-susceptibility rates to non-beta-lactam antibiotics for both species were: 18.1% and 30.1% for gentamicin, 0.8% and 4.1% for amikacin, 41.3% and 41.1% for ciprofloxacin, and 65.8% and 76.1% for co-trimoxazole. The most common sequence types (ST) were ST131 (16.9%), ST38 and ST10 (8.2 % each) in E. coli and ST307 (9.7%), ST45 and ST268 (6.9% each) in K. pneumoniae. CTX-M type ESBL were found in all but one isolate, with CTX-M-15 accounting for 87.8%. Among other beta lactamases, TEM-1B and OXA-1 were co-produced in 41% and 19.6% of isolates. The most common plasmid-mediated quinolone resistance genes co-carried were qnr A/B/E/S (45.3%). Ninety percent of gentamicin non-susceptible isolates harbored genes encoding AAC(3) enzymes, mainly aac(3)-IIa. Only 2 of 57 isolates harboring aac(6’)-Ib-cr were non-susceptible to amikacin. Chromosomal mutations in genes encoding DNA gyrase and topoisomerase IV enzymes were detected in 96.2% fluoroquinolone-non-susceptible E. coli and 26.7% fluoroquinolone-non-susceptible K. pneumoniae. Conclusions: Our data show that CTX-M enzymes are largely the most prevalent ESBLs in children in Qatar with a predominance of CTX-M-15. Carbapenem-sparing options to treat ESBL infections are limited given the frequent co-production of OXA-1 and TEM-1B enzymes and co-resistance to antibiotic classes other than β-lactams.