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 onethird 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.