Transcriptional Analysis of IncFrepB-Mediated blaOXA-48-Positive Plasmid Characterized from Escherichia coli ST448

Prevalence and genomic insights of carbapenem resistant and ESBL producing Multidrug resistant Escherichia coli in urinary tract infections

Urinary tract infections are a common condition affecting people globally, with multidrug-resistant (MDR) Escherichia coli (E. coli) being a major causative agent. Antimicrobial susceptibility profiling was performed using the VITEK 2 automated system for 1254 E. coli isolates, revealing that 831(66.2%) isolates were determined as MDR E. coli. A significant resistance pattern was observed for nalidixic acid (86.04%), ampicillin (74.16%), ticarcillin (70.73%), cefalotin (65.23%), cefixime (62.68%), ciprofloxacin (55.18%), ceftriaxone (53.75%), amoxicillin-clavulanic acid (22.81%), ertapenem (7.18%), and fosfomycin (2.23%). Whole Genome Sequencing of Carbapenem-resistant E. coli (CREC)-CREC 3 (ST405), CREC 4 (ST448), and CREC 5 (ST167) was performed to determine genomic characteristics. CREC 3, CREC 4, and CREC 5 belong to the phylogroup D, B1, and A, respectively. The NDM-5 gene was common in all three isolates, with CTX-M-15 being present in CREC 3 and CREC 4. Virulence factors of CREC 3 (fliC, shuA), CREC 4 (spaS), CREC 5 (iucA, papH, papG, iucB, yigF), and plasmids (IncFIA, IncFIB) were identified to be significant. The use of pangenome analysis enhances our understanding of resistance traits of isolates ST167, ST405, and ST448, offering valuable insights into comparative genomics of uropathogenic MDR E. coli.

High Prevalence of Carbapenem-Resistant Enterobacterales Producing OXA-48 among Carbapenem-Resistant Isolates in a Regional Hospital in Central Taiwan

In response to the increasing number of carbapenem-resistant Enterobacterales (CRE), we investigated carbapenemase-producing Klebsiella pneumoniae and non-K. pneumoniae epidemiology and genetics. We collected 76 clinical Enterobacterales and 4 stool surveillance Escherichia coli isolates resistant to ertapenem or imipenem. Using polymerase chain reaction (PCR) and DNA sequencing, we assessed carbapenemases, extended-spectrum β-lactamases, and AmpC β-lactamases. Molecular typing via pulsed-field gel electrophoresis (PFGE) and conjugation experiments were conducted to examine resistance gene transfer. Among the 80 isolates, 96.2% harbored at least one carbapenemase gene, with blaOXA-48 in 87.5%. KPC-2 and IMP-8 carbapenemases were found in 15.0 and 22.5% of the isolates, respectively, with 27.5% having 2 or more carbapenemase genes. The PFGE analysis revealed the presence of diverse genotypes. PCR-based plasmid replicon typing identified IncA/C as the most prevalent type among K. pneumoniae isolates (26/29), and IncF and IncFIB among E. coli isolates (22/28). Conjugal transfer was successful for plasmids encoding OXA-48, CTX-M-3, CTX-M-14, CMY-2, and other β-lactamases, except the KPC-2 gene. In conclusion, our study highlights high carbapenemase prevalence in CRE, primarily OXA-48. Multiple carbapenemases within strains were common, and PFGE showed diverse patterns in these carbapenem-resistant isolates.

The Characteristics of Extended-Spectrum β-Lactamases (ESBLs)-Producing Escherichia coli in Bloodstream Infection

Background

Bloodstream infection (BSI) is a common type of infection frequently diagnosed in clinics. The emergence and spread of ESBLs-producing Escherichia coli (E. coli) has emerged as one of the biggest challenges in global community health.

Methods

The production of ESBLs was determined by the composite disk diffusion method. The expression of the various resistance and virulence genes were detected by PCR and sequencing. Multi-locus sequence typing (MLST) and phylogenetic groups were used for the classification. The transfer of resistant plasmids was determined by conjugation assay. The statistical differences were analyzed using Statistical Product and Service Solutions (SPSS) version 23.0.

Results

A total of 60 strains of ESBLs-producing E. coli were collected. The resistance genes that were identified included bla _CTX-M, bla _TEM, bla _SHV, bla _OXA-1 and mcr-1. The most common one was the bla _CTX-M including bla _CTX-M-27 (n = 16), bla _CTX-M-14 (n = 15), bla _CTX-M-15 (n = 11), bla _CTX-M-55 (n = 14) and bla _CTX-M-65 (n = 5). A total of 31 STs were detected, and the most abundant among which was ST131 (n = 16, 26.7%). Most of the E. coli (n = 46, 76.7%) belonged to the groups B2 and D. And some virulence genes were related to the classification of the E. coli. Among them, the detection rates of hek/hra, kpsMII and papGII-III in groups B2 and D were higher than those in groups A and B1. The detection rates of cnf1, iucC and papGII-III in ST131 were higher than those in non-ST131. And the distributions of hek/hra, iroN, iucC, kpsMII and papGII-III were related to the bla _CTX-M subtypes. Finally, most bacterial (n = 32, 53.3%) resistance genes could be transferred between the bacteria by plasmids, especially IncFIB.

Conclusion

ESBLs-producing E. coli in BSI exhibited had high resistance rates and carried a variety of virulence factors (VFs). This is necessary to strengthen the monitoring of ESBLs-producing isolates in the medical environment.

Screening and Characterization of Multidrug-Resistant Enterobacterales among Hospitalized Patients in the African Archipelago of Cape Verde

This study aimed to investigate, for the first time, the occurrence and characteristics of extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacterales in Cape Verde. A total of 98 inpatients hospitalized at Hospital Universitário Agostinho Neto were screened for rectal colonization. All ESBL- and carbapenemase-producing isolates were tested for antimicrobial susceptibility and characterized by multilocus sequence typing. Mating-out assay followed by PCR-based replicon typing were performed to characterize the plasmids harboring carbapenemase encoding genes. A large proportion of patients carried ESBL- or carbapenemase-producing Enterobacterales (56% and 6%, respectively). Among 93 ESBL-producing isolates, there were mainly Klebsiella pneumoniae (58%) and Escherichia coli (37%). Five different ESBLs were detected, with CTX-M-15 being highly predominant (92%). Six carbapenemase-producing isolates (five E. coli and one K. pneumoniae) were recovered, and all of the OXA-48-like type (four OXA-181, one OXA-48, and one OXA-244). The bla_OXA-48 gene was located on an IncFI-type plasmid, the bla_OXA-181 gene on IncFI or IncX3 plasmids, and the bla_OXA-244 gene was found to be chromosomally located. The five carbapenemase-producing E. coli isolates belonged to five distinct sequence types. This study overall showed a very high prevalence of ESBL-producing Enterobacterales, as well as the emergence of carbapenemase producers in this hospital.

High Prevalence and Fitness of IncFrepB Carrying qnrS1 in Hypervirulent Klebsiella pneumoniae Isolates

Objective: This study aimed to reveal the prevalence and fitness of qnrS1-carrying plasmids in hypervirulent Klebsiella pneumoniae (hvKP) isolates. Materials and Methods: Two hundred ninety-nine hvKP strains carrying qnrS1 were collected and screened for resistance genes using PCR and sequencing. The location of qnrS1 and rmpA2 was identified by Southern blotting. The transferability and fitness of qnrS1-carrying plasmids were analyzed by conjugation experiments and plasmid stability assay. Result: In 299 hvKP isolates, the most frequently detected capsular serotype was K64 (81.9%, 245/299), followed by K1 (4.7%, 14/299) and K2 (3.7%, 11/299). All K64-hvKP were sequence type (ST) 11. The qnrS1 and rmpA2 gene mainly was located on the ∼70-210 kb IncFrepB and ∼170-220 kb IncFIB plasmid, respectively. QnrS1-carrying plasmids could be transferred into Escherichia coli J53. However, the plasmid was transferred at a low rate of 13.4% (40/299). The 40 donor isolates belong to 4 STs-ST11, ST700, ST592, and ST86, and none contains the CRISPR-Cas loci. CRISPR-Cas loci were mainly found in ST23 K. pneumoniae. The relative fitness (RF) of qnrS1-carrying plasmids in ST86 and ST11 (cotransfer with bla_TEM-1 genes) was more than one and enhanced during cultivation, especially in ST86. However, the RF of qnrS1-carrying plasmids in ST592 and ST700 showed a high fitness cost. Whole-genome sequencing showed that the qnrS1-carrying plasmids in ST86 harbored more maintenance modules (SOS inhibitor protein psiB, parA, and parB partition systems) and insertion sequence (IS) elements (IS91, IS481-like, IS1380), indicating that the qnrS1-carrying plasmid in ST86 is more stable than the other types of qnrS1-carrying plasmids. Conclusion: QnrS1-carrying IncFrepB plasmids were highly prevalent and show polymorphism in hvKP strains. The qnrS1-carrying IncFrepB plasmid in ST86 hvKP should be highlighted due to its remarkable adaptability advantages.