Abstract
BackgroundWe evaluated the distribution of carbapenem and colistin resistance mechanisms of clinical E. coli and K. pneumoniae isolates from Iran.Methods165 non-duplicate non-consecutive isolates of K. pneumoniae and E. coli were collected from hospitalized patients admitted to Iran's tertiary care hospitals from September 2016 to August 2018. The isolates were cultured from different clinical specimens, including wound, urine, blood, and tracheal aspirates. Antibiotic susceptibility testing was performed by disc diffusion and microdilution method according to the Clinical and Laboratory Standards Institute (CLSI) guideline. The presence of extended spectrum β-lactamases (ESBLs) genes, carbapenemase genes, as well as fosfomycin resistance genes, and colistin resistance genes was also examined by PCR-sequencing. The ability of biofilm formation was assessed with crystal violet staining method. The expression of colistin resistance genes were measured by quantitative reverse transcription-PCR (RT-qPCR) analysis to evaluate the association between gene upregulation and colistin resistance. Genotyping was performed using the multi-locus sequencing typing (MLST).ResultsColistin and tigecycline were the most effective antimicrobial agents with 90.3% and 82.4% susceptibility. Notably, 16 (9.7%) isolates showed resistance to colistin. Overall, 33 (20%), 31 (18.8%), and 95 (57.6%) isolates were categorized as strong, moderate, and weak biofilm-producer, respectively. Additionally, blaTEM, blaSHV, blaCTX-M, blaNDM-1, blaOXA-48-like and blaNDM-6 resistance genes were detected in 98 (59.4%), 54 (32.7%), 77 (46.7%), 3 (1.8%), 17 (10.30%) and 3 (1.8%) isolates, respectively. Inactivation of mgrB gene due to nonsense mutations and insertion of IS elements was observed in 6 colistin resistant isolates. Colistin resistance was found to be linked to upregulation of pmrA-C, pmrK, phoP, and phoQ genes. Three of blaNDM-1 and 3 of blaNDM-6 variants were found to be carried by IncL/M and IncF plasmid, respectively. MLST revealed that blaNDM positive isolates were clonally related and belonged to three distinct clonal complexes, including ST147, ST15 and ST3299.ConclusionsThe large-scale surveillance and effective infection control measures are also urgently needed to prevent the outbreak of diverse carbapenem- and colistin-resistant isolates in the future.
Highlights
We evaluated the distribution of carbapenem and colistin resistance mechanisms of clinical E. coli and K. pneumoniae isolates from Iran
Bacterial isolates 165 non-duplicate non-consecutive isolates of E. coli and K. pneumoniae were collected from 73 (45.5%) females and 92 (54.5%) males admitted at five Iranian hospitals during the September 2016 to August 2018
Molecular analysis of colistin resistance The mcr-1, mcr-2, mcr-3, and mcr-4 genes were not found in any of the colistin-resistant isolates, we focused on other mechanisms of resistance, mgrB gene inactivation and the presence of the mutations in the pmrA, pmrB, phoP, and phoQ genes
Summary
We evaluated the distribution of carbapenem and colistin resistance mechanisms of clinical E. coli and K. pneumoniae isolates from Iran. Enterobacteriaceae are opportunistic pathogens that cause severe nosocomial infections, including urinary tract infections (UTIs), bloodstream infections, Sharahi et al Ann Clin Microbiol Antimicrob (2021) 20:32 abdominal infections, and ventilator-associated pneumonia [1, 2]. Escherichia coli and Klebsiella pneumoniae are two important members of Enterobacteriaceae that have the ability to develop resistance to various classes of antibiotics. Carbapenem antibiotics are recommended as the last-line therapy for MDR strains of K. pneumoniae and E. coli infections [1, 3]. Resistance to carbapenems in Enterobacteriaceae is mainly mediated by the production of carbapenem-hydrolyzing enzymes (carbapenemases), among which Klebsiella pneumoniae carbapenemase (KPC), metallo-β-lactamases (VIM, IMP, NDM), and OXA-48 type of enzymes are the most common. Mobile genetic elements, including plasmids, transposons, and integrons are involved in the dissemination of related encoding genes [5,6,7]
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