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bioRxiv2022

Whole genome-based characterization of multi-drug resistant Enterobacter and Klebsiella aerogenes isolates from Lebanon

BackgroundEnterobacter spp. are rod-shaped Gram-negative opportunistic pathogens belonging to Enterobacterales. This study aimed at the molecular and genomic characterization of multi-drug resistant Enterobacter spp. isolates recovered from hospitalized patients in a tertiary care hospital in Lebanon. MaterialsA total of 59 Enterobacter spp. clinical isolates consisting of 41 carbapenem-resistant and 18 susceptible by E-test were included in this study. Genotypic identification through whole-genome sequencing was performed and confirmed in silico. Resistance and plasmid profiles were studied using ResFinder4.0 and Plasmid-Finder2.1. Multi-locus sequence typing (MLST) was used to determine the isolates clonality. ResultsANI identified and confirmed that 47 (80%) isolates were E. hormaechei, 11 (18%) were Klebsiella aerogenes and 1 (2%) was an E. cloacae. Carbapenem-resistance was detected among 41 isolates all showing an MIC90 of [≥] 32 {micro}g/ml for ertapenem, imipenem, and meropenem. blaNDM-1 (58.5%), blaACT-16 (54%), and blaOXA-1 (54%) were the most common detected {beta}-lactamases, while blaCTX-M-15 gene (68%) was the main detected extended-spectrum {beta}-lactamase (ESBL) encoding gene. Chromosomal ampC gene, carbapenemase encoding genes, and porin modifications were among the detected carbapenem resistance determinants. The carbapenemase encoding genes were linked to three well-defined plasmid Inc groups, IncFII/IncFIB, IncX3, and IncL. MLST typing revealed the diversity within the studied isolates, with ST114 being the most common amongst the studied E. hormaechei. ConclusionThe spread of carbapenem-resistant isolates in clinical settings in Lebanon is a serious challenge. Screening and continuous monitoring through WGS analysis could effectively limit the dissemination of drug-resistant isolates in hospitalized patients. ImportanceDrug resistance is an increasing global public health threat that involves most disease-causing organisms and antimicrobial drugs. Drug-resistant organisms spread in healthcare settings, and resistance to multiple drugs is common. Our study demonstrated the mechanisms leading to resistance against the last resort antimicrobial agents among members of the Enterobacteriaceae family. The spread of carbapenem-resistant bacteria in clinical settings is a serious challenge. Screening and continuous monitoring could effectively limit the dissemination of drug-resistant isolates in hospitalized patients.

genomics↗

bioRxiv2021

Fitness effects of CTX-M-15-encoding IncF plasmids on their native Escherichia coli ST131 H30Rx hosts

ObjectivesThe objective of this study was to investigate effects of large CTX-M-15-encoding IncF plasmids on the fitness of their native E. coli ST131 H30Rx hosts in order to understand possible plasmid-host coevolution. MethodsWe selected five E. coli ST131 H30Rx strains of diverse origin, each carrying a multireplicon IncF plasmid encoding the gene blaCTX-M-15. The plasmid was eliminated from each isolate by displacement using an incompatible plasmid vector pMDP5_cureEC958. Whole-genome sequencing (WGS) was performed to obtain complete chromosome and plasmid sequences of wild-type isolates and to detect chromosomal mutations in plasmid-free strains. Competition assays were conducted to determine the relative fitness of plasmid-free clones compared to the corresponding wild-type isolates. ResultsWe were able to successfully eliminate the IncF plasmids from all of the wild-type strains using the curing vector pMDP5_cureEC958. The chromosomes of plasmid-free clones contained zero to six point mutations. Plasmid-free strains of three isolates showed no significant difference in relative fitness compared to the corresponding plasmid-free strains. In the two remaining isolates, the plasmids produced a small but significant fitness cost. ConclusionWe conclude that IncF plasmids produce moderate fitness effects in their E. coli ST131 H30Rx hosts. This fitness compatibility is likely to promote the maintenance of antibiotic resistance in this worrisome E. coli lineage.

evolutionary biology↗