Risk factors and molecular characterization of carbapenem resistant Escherichia coli recovered from a tertiary hospital in Fujian, China from 2021 to 2023

Abstract Background There is a serious public health concern regarding the emergence of carbapenem-resistant Escherichia coli (CREC). The purpose of this study is to identify the molecular characterization and risk factors of CREC in Fujian province, China. Methods A total of 48 CREC isolates were collected from various clinical samples. The strains were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS). Susceptibility to antibiotics was determined by the standard broth microdilution method. Polymerase chain reaction (PCR) was used to screen common drug resistance genes. Multilocus sequence typing (MLST) was used to type isolates. RT-qPCR was used to detect gene expression of acrA, acrB, and tolC. Conjugation assays were used to analyze the transferability of plasmids carrying mcr-1 or bla NDM. Risk factors for CREC infection were identified by logistic regression analysis. Results 48 CREC strains were collected, with 81.25% producing carbapenemase (CP-CREC), and 18.75% were not producing carbapenemase (no-CP-CREC). They belonged to 21 sequence type (STs) and five unknown STs. Perianal swabs were the main sample type, with 25 patients found to have hematological malignancies. All isolates of CP-CREC were found to contain bla NDM (bla NDM−5 (n = 32), bla NDM−1 (n = 5), bla NDM−4 (n = 1), and bla NDM−13 (n = 1)), among which one isolate co-existence bla NDM−5 and bla OXA−48. Two bla NDM-positive strains, specifically bla NDM−5 and bla NDM−4, were found to co-habor mcr-1 with ST617. Conjugation assays confirmed that bla NDM−1, bla NDM−13, and most bla NDM−5(68.75%, 22/32) could be transferred between E. coli strains. Four of the 9 non-CP-CREC isolates had deletions in ompC and ompF with bla CTX−M production, while the other five showed high expression of acrA, acrB, and tolC. Antibiotics usage, antifungal treatment, detection of other pathogens (prior to CREC infection), and respiratory disease were identified as independent risk factors for CREC infection. The area under the receiver operating characteristic curve for the scoring system was 0.937. Youden’s index, with sensitivity and specificity of 0.96 and 0.78, was maximal when 2 points were scored. Conclusions In CP-CREC, carbapenem resistance is caused primarily by multiple types of bla NDM, while non-CP-CREC is caused by loss of porin protein or high expression of efflux pumps coupled with carrying bla CTX−M. CREC isolates were highly diverse in terms of ST, with a total of 21 STs identified. Here, we first describe a clinical strain of CREC from China both mcr-1 and bla NDM −4 with ST617. An easy-to-use scoring system was developed to diagnose CREC infections.