Antimicrobial resistance of Klebsiella pneumoniae stool isolates circulating in Kenya

Abstract

We sought to determine the genetic and phenotypic antimicrobial resistance (AMR) profiles of commensal Klebsiella spp. circulating in Kenya by testing human stool isolates of 87 K. pneumoniae and three K. oxytoca collected at eight locations. Over one-third of the isolates were resistant to ≥3 categories of antimicrobials and were considered multidrug-resistant (MDR). We then compared the resistance phenotype to the presence/absence of 238 AMR genes determined by a broad-spectrum microarray and PCR. Forty-six genes/gene families were identified conferring resistance to β-lactams (ampC/blaDHA, blaCMY/LAT, blaLEN-1, blaOKP-A/OKP-B1, blaOXA-1-like family, blaOXY-1, blaSHV, blaTEM, blaCTX-M-1 and blaCTX-M-2 families), aminoglycosides (aac(3)-III, aac(6)-Ib, aad(A1/A2), aad(A4), aph(AI), aph3/str(A), aph6/str(B), and rmtB), macrolides (mac(A), mac(B), mph(A)/mph(K)), tetracyclines (tet(A), tet(B), tet(D), tet(G)), ansamycins (arr), phenicols (catA1/cat4, floR, cmlA, cmr), fluoroquinolones (qnrS), quaternary amines (qacEΔ1), streptothricin (sat2), sulfonamides (sul1, sul2, sul3), and diaminopyrimidines (dfrA1, dfrA5, dfrA7, dfrA8, dfrA12, dfrA13/21/22/23 family, dfrA14, dfrA15, dfrA16, dfrA17). This is the first profile of genes conferring resistance to multiple categories of antimicrobial agents in western and central Kenya. The large number and wide variety of resistance genes detected suggest the presence of significant selective pressure. The presence of five or more resistance determinants in almost two-thirds of the isolates points to the need for more effective, targeted public health policies and infection control/prevention measures.

Whole genome sequencing snapshot of multi-drug resistant Klebsiella pneumoniae strains from hospitals and receiving wastewater treatment plants in Southern Romania

“…Similar to other studies, the most prevalent tetracyclines resistance genes were tetA and tetD [58].…”

“…Chloramphenicol resistance was mainly related to the presence of catB and catA genes, followed by cmIA5. Although cmr genes are reported by some studies as the most frequently found in clinical K. pneumoniae isolates [58], it was not present in the selected strains.…”

Antibiotic sensitivity pattern for non-beta lactam antibiotics and carbapenems in extended-spectrum beta-lactamase (ESBL) producing uropathogens versus non-ESBL producing uropathogens

“…8,20 Non-ESBL producers showed a sensitivity of 85.1% to gentamicin which is therefore a reasonable option for intravenous therapy. Within the group of non-ESBL producers, only about half of the isolates were sensitive to nalidixic acid while more than 3/4 th of isolates were sensitive to other tested antibiotics (nitrofurantoin, nalidixic acid, ciprofloxacin, norfloxacin and gentamicin).…”

“…E. coli and Klebsiella species, produce β-lactamases with an extended spectrum of activity. 8,9,10 ESBL producers are resistant to the penicillins including the first, second and third-generation cephalosporins and aztreonam but not to the cephamycins or carbapenems. Even though such organisms are known to occur in nosocomial settings, they have become a threat to the community as well.…”

A Survey of Antimicrobial Resistance Determinants in Category A Select Agents, Exempt Strains, and Near-Neighbor Species

“…The ARDM v.3.1 has a total of four subarrays (two pairs of identical subarrays, 2240 probes/ subarray). The subarrays are based on two previous versions-ARDM v.2 (238 AMR determinants) [27,53,54], and ARDM v.3 (542 AMR determinants) [28]-and was re-designed to remove non-relevant or redundant content and emphasize AMR-related content from Select Agents. Each microarray slide could therefore analyze two samples (each sample = two subarrays).…”