Phenotype-genotype correlations among carbapenem-resistant Enterobacterales recovered from four Egyptian hospitals with the report of SPM carbapenemase

BACKGROUND: Carbapenem-resistant Enterobacterales (CRE), currently listed by the World Health Organization (WHO) as top priority critical pathogens, are a major global menace to human health. In low- and middle-income countries (LMICs) the threat is mounting fueled by selective pressures caused by antibiotic abuse and inadequate diagnostic resources. METHODS: This study phenotypically and genotypically characterized carbapenem resistance among 115 Enterobacterales isolates including 76 Klebsiella (K.) pneumoniae, 19 Escherichia (E.) coli, 14 Shigella (S.) sonnei, 5 Enterobacter (E.) cloacae, and 1 Proteus (P.) mirabilis. RESULTS: Ninety-three isolates (80.9%) were carbapenem-resistant with an alarming 57.5% carbapenem non-susceptibility in isolates collected from the outpatient department. Molecular characterization of the carbapenemases (CPases) encoding genes showed that bla(NDM) (80.5%) was the most prevalent; it was detected in 62 isolates (54 K. pneumoniae, 6 E. coli and 2 S. sonnei), followed by bla(VIM) (36.4%) which was observed in 28 isolates (24 K. pneumoniae, 3 E. coli and 1 E. cloacae). Other CPases included bla(KPC) (28.6%; in 20 K. pneumoniae, 1 E. coli and 1 S. sonnei), bla(OXA-48) (26%; in 17 K. pneumoniae, 1 E. coli,1 E. cloacae and 1 P. mirabilis), bla(IMP) (6.5%; in 5 K. pneumoniae) and bla(SPM) (1.3%; in K. pneumoniae). Notably more than half of the Enterobacterales isolates (54.5%) co-harboured more than one CPase-encoding gene. Co-existence of bla(NDM) and bla(VIM) genes was the most dominant (31.2%), followed by association of bla(NDM) and bla(KPC) (24.7%), then bla(VIM) and bla(KPC) (13%). Moreover, the effects of different genotypes on meropenem MIC values were assessed, and a statistically significant difference between the genotype (Ambler classes A and B) and the genotype (Ambler classes B and D) was recorded. CONCLUSION: The current findings may serve for a better understanding of the context of CRE in Egypt, associated drivers and CPases. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13756-022-01061-7.