An Overview on Phenotypic and Genotypic Characterisation of Carbapenem-Resistant Enterobacterales

Abstract

Improper use of antimicrobials has resulted in the emergence of antimicrobial resistance (AMR), including multi-drug resistance (MDR) among bacteria. Recently, a sudden increase in Carbapenem-resistant Enterobacterales (CRE) has been observed. This presents a substantial challenge in the treatment of CRE-infected individuals. Bacterial plasmids include the genes for carbapenem resistance, which can also spread to other bacteria to make them resistant. The incidence of CRE is rising significantly despite the efforts of health authorities, clinicians, and scientists. Many genotypic and phenotypic techniques are available to identify CRE. However, effective identification requires the integration of two or more methods. Whole genome sequencing (WGS), an advanced molecular approach, helps identify new strains of CRE and screening of the patient population; however, WGS is challenging to apply in clinical settings due to the complexity and high expense involved with this technique. The current review highlights the molecular mechanism of development of Carbapenem resistance, the epidemiology of CRE infections, spread of CRE, treatment options, and the phenotypic/genotypic characterisation of CRE. The potential of microorganisms to acquire resistance against Carbapenems remains high, which can lead to even more susceptible drugs such as colistin and polymyxins. Hence, the current study recommends running the antibiotic stewardship programs at an institutional level to control the use of antibiotics and to reduce the spread of CRE worldwide.

Assessment of Phenotypic Testing by mCIM with eCIM for Determination of the type of Carbapenemase Produced by Carbapenem-resistant Enterobacterales

“…Among the 53 CRE in our study, Klebsiella pneumoniae was the most predominant species, representing 69.8%, followed by E. coli (28.3%) and Klebsiella oxytoca (1.9%). Similarly, in Turkey, Baran and Aksu reported that the most common CRE species was Klebsiella pneumoniae (38.12 %), followed by E. coli (7.18 %) and Klebsiella oxytoca (0.55 %) 35 . On the contrary, a study in Nigeria reported that the most common CRE species were K. oxytoca 41%, then K. pneumoniae 32% and E. coli 27% 36 .…”

Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection

“…This could be problematic when trying to detect chromosomal AMR genes. Nonetheless, the most prevalent BSI causative antimicrobial resistance strains (MRSA, Vancomycin-Resistant Enterococcus , Multidrug-Resistant Enterobacteriaceae , Extended-Spectrum β-Lactamase (ESBL) gram-negative species or Carbapenem-Resistant Enterobacterales [ 56 ]), generally have plasmid-mediated resistant mechanisms [ 71 – 75 ]. Because of the low coverage obtained in two of the genes present on the plasmid ( aac6’-lb-cr and catB4 ), these were misidentified as closely related genes: aac(6’)-lb-W104R, aac(6’)-lb-D181Y, aac(6’)-lb-AKT and catB3 .…”

Characterization of blaNDM-19-producing IncX3 plasmid isolated from carbapenem-resistant Escherichia coli and Klebsiella pneumoniae

“…Carbapenem-resistant Enterobacterales (CRE) are a major concern in the community and in healthcare settings [ 1 ]. Among the carbapenamases, NDM, with the exception of aztreonam, mediates resistance to all β-lactam antibiotics [ 2 ].…”