Prevalence and Molecular Characterization of Carbapenem resistance Gram negative bacilli among hospitalized patients in Khartoum state

Background Carbapenems are broad-spectrum β-lactam antibiotics widely prescribed for the treatment of multidrug-resistant gram negative bacilli in systemic infections. In the past ten years the Carbapenem resistance among gram-negative bacilli is rapidly expanding across nosocomial infection isolates. This study was conducted to determine the prevalence and to characterize Carbapenem resistance genes among Gram negative bacilli (GNB) isolated from patients treated in hospitals in Khartoum state, Sudan.Methods A cross-sectional laboratory based study was conducted over six months at the microbiology department in Soba University Hospital and Institute of Endemic Diseases, University of Khartoum. A total of 206 GNB isolates from different clinical specimens were analyzed for carbapenem resistance genes using phenotypic tests and affirmed by genes detection. Multiplex PCR was performed for each strain to detect the carbapenemase genes, including those encoding the NDM-, VIM-, and IMP -type Metallo-beta-lactamases, the class A KPC-type carbapenemases, and the class D OXA-48 enzyme. In addition to CTXM, TEM and SHV. DNA sequencing and bioinformatics analysis were used to detect genes subtypes.Results Of 206 isolates, 171 (83%) positive phenotypically and 121 (70.7%) from 171 isolates were confirmed for present one or more carbapenemase gene. NDM-types were the most predominant genes, blaNDM 107(88.4%), followed by blaIMP 7 (5.7%), blaOXA-48 5(4.1%), blaVIM 2 (1.6%) and blaKPC 0 (0%). Co- resistance genes with NDM producing Gram-negative bacilli were detected in 87 (81.3%) of all NDM positive isolates. Correlation between phenotypic and genotypic resistance was observed (P- value < 0.001). Carbapenemase genes were mostly detected in the K. pneumoniae 70 (42.6%), followed by P. aeruginosa 33 (20%), A. baumannii 30 (18.2%) and E. coli with 18 strains (10.9%). NDM-1 was detected in 75 isolates (70%), other subtypes of NDM were identified by sequencing were NDM- 5 and NDM-6.Conclusions The prevalence of carbapenemase producing bacilli was fond to be high in Khartoum hospitals. NDM was found to be the most prevalent carbapenemase genes among clinical isolates and belong to Indian lineage. For prevention infection control and regular surveillance must be enhanced.