CTX-M ?-LACTAMASE–PRODUCING ESCHERICHIA COLI IN SUDAN TERTIARY HOSPITALS: DETECTION GENOTYPES VARIANTS AND BIOINFORMATICS ANALYSIS

Abstract

Background: Extended spectrum ?-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) constitute an emerging public-health concern. Consider that ESBL genes type CTX-M types has been increased significantly in most parts of the world.  Few data are available on the CTX-M variants circulating in Sudan. Objective: This study used polymerase chain reaction (PCR) and bioinformatics tools to identify blaCTX-M and its variants for Extended-spectrum ?-lactamase (ESBLs) producing clinical isolates of Escherichia coli (E. coli) obtained from hospitals in Khartoum-Sudan. Methods: A total of 216 non-repetitive isolates were selected during 2007-2018. The phenotypic identification of ESBL production was confirmed according to CLSI guidelines. CTX-M genotype was analyzed by uniplex PCRs reactions subsequently sequences performed later sequences were analyzed using bioinformatics tools with nBLAST program, multiple alignments to determine CTX-M  genotype  variants . Nucleotide sequences were submitted to Gen Bank and accession numbers were obtained. Result:  ESBL phenotype among 212 confirmed E.coli isolates was   (34.9% of 212,n=74).  (62.2% of 74, n=46) strains carried bla CTX-M genes, CTX-M genotype variants identified in this study as followed: blaCTX-M-15 gene was the most prevalent one (78.6%) followed by blaCTX 90 (14.3%) and CTX-M55 (7.1%),

Conclusion: This study reveled high ESBL occurrence among E.coli isolates, with CTX-M 15 the predominant variants and highlights the incidence of CTX-M-55 for the first time from Sudan.

Keywords:    E. coli, PCR, ESBLs, CTX-M, Sudan, bioinformatics