AbstractThis study sought to investigate the occurrence and subsequently to characterize extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae from urban and rural stagnant water samples during the wet season (December to February) in several regions of northern Tunisia. From 56 stagnant water samples, 14 ESBL-producing Enterobacteriaceae were recovered, including 9 Escherichia coli, 3 Klebsiella pneumoniae, and 2 K. oxytoca. Most isolates were multidrug-resistant, with ESBL production primarily encoded by blaCTX-M-15 (n = 8) and blaCTX-M-1 (n = 4) followed by blaCTX-M-55 (n = 1) and blaTEM-26 (n = 1). One K. pneumoniae isolate co-harbored blaKPC and blaCTX-M-15 genes. Class 1 integrons were detected in 4 isolates, however, sul1, sul2, and aac(6′)-Ib-cr genes were detected in eleven, two, and four isolates, respectively. The nine E. coli isolates belonged to seven sequence types namely, B2/ST131 (3 isolates), A/ST164, A/ST10, A/ST224, A/ST38, A/ST155, and A/ST69 (each of them one isolate). The three K. pneumoniae isolates were assigned to three sequence types: ST101, ST405 (harboring CTX-M-15 and KPC), and ST1564. Overall, the phenotypic and genotypic traits of collected isolates mirror the molecular epidemiology of ESBL-producing enterobacteria in Tunisia and highlight the potential role of stagnant water in both urban and rural areas as a reservoir of ESBL-producing Enterobacteriaceae.

AbstractAntimicrobial disinfectants have been extensively used to control hospital-acquired infections worldwide. Prolonged exposure to bacteria could promote resistance to antimicrobial disinfectants. This study evaluated the antimicrobial activity of four commonly used disinfectants; triclosan, chlorhexidine digluconate, benzalkonium chloride, and formaldehyde against Acinetobacter baumannii clinical isolates. This study also determined the prevalence and association of efflux pumps encoding genes qacE, qacED1, emrA, and aceI with tolerance to disinfectants. A total of 100 A. baumannii isolates were included in the current study. The antimicrobial disinfectants' minimum inhibitory concentration (MIC) was determined using an agar dilution method. Genes involved in resistance to disinfectants were investigated by PCR method. The benzalkonium chloride MICs ranged between 32 and 128 μg mL−1, chlorhexidine digluconate 8–64 μg mL−1, triclosan 1–32 μg mL−1, and formaldehyde 128 μg mL−1. Overall, the highest MIC90 value was identified for formaldehyde (128 μg mL−1), followed by benzalkonium chloride and chlorhexidine digluconate (64 μg mL−1, each one) and triclosan (4 μg mL−1). In the present study, the qacE, qacED1, emrA, and aceI genes were found in 91%, 55%, 100%, and 88% of isolates, respectively. The qacG gene was not identified in our A. baumannii isolates. The qacED1 gene was associated with higher MICs for all disinfectants tested (P < 0.05), while the qacE and aceI genes were associated with higher MICs for benzalkonium chloride and chlorhexidine. This study indicated that triclosan is the most effective disinfectant against A. baumannii isolates.

AbstractHepatitis C virus (HCV) can cause both acute and chronic hepatitis infections. Gaziantep is located southeast part of Turkey and has a border with Syria. More than 400,000 Syrian refugees live in Gaziantep. The aim of this study was to evaluate distribution of HCV genotypes among Syrian patients and in people who inject drugs.Serum samples form 1,628 individuals (786 female, 842 male) which were sent to our laboratory for genotyping between January 2013 and December 2022, were analyzed retrospectively. Three different HCV genotyping assays (Qiagen, RTA and Abbott) were used during the 10-year study period.Out of the 1,628 patients, genotype 1 was detected in 51.5%, genotype 3 in 21.4%, genotype 4 in 20%, genotype 5 in 4.6%, genotype 2 in 1.3%. Mixed genotype was found in 20 patients. Of the patients, 1,143 were Turkish patients and among those patients genotype 1 (66.8%) was the most common genotype followed by genotype 3 (29%). Among Syrian patients (n = 477), genotype 4 (64.2%) was predominant genotype followed by genotype 1 and genotype 5. Genotype 3 was detected in 277 (79.6%) prisoners. All of them were male and probably the main source of HCV infection was intravenous drug abuse. While genotypes 1 and 4 were common in females, genotypes 1 and 3 were common in males.In the future genotype 3 may become an increasing problem due to the persons who inject drugs. Less frequent genotypes such as 4 and 5 may become more frequent due to Syrian patients.

AbstractAim of this study was to explore molecular characteristics and resistance mechanisms of carbapenem-resistant Raoultella ornithinolytica (CR-ROR) isolated from patients in a hospital in China. Three CR-ROR strains were collected and bacterial identification was done by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) Vitek-MS and by digital DDH analysis. VITEK 2 compact system and Kirby-Bauer (K–B) disk diffusion were used for antimicrobial susceptibility testing. Whole genome sequencing was carried out using the Illumina platform NovaSeq sequencer. Abricate software was used for the prediction of antibiotic resistance genes of three CR-ROR strains. The phylogenetic tree was constructed through genome SNPs to investigate the genetic relationship of three CR-ROR strains. Three CR-ROR (WF1357, WF2441, and WF3367) strains were collected in this study. Two strains were isolated from neurosurgery (WF1357 and WF2441), and one was isolated from pulmonology department (WF3367). All strains harboured multiple antibiotic resistance genes. Two strains (WF1357, WF2441) carried the blaNDM-1 gene, one of the strains (WF3367) carried the blaKPC-2 gene. Three CR-RORs were resistant to different antimicrobial agents including carbapenems. The three CR-ROR strains collected in this study and 51 CR-ROR strain genomes downloaded from NCBI, were divided into six evolutionary groups (A-F). In this study, three CR-ROR strains were found to have a higher level of resistance to antibacterial agents and carried multiple antibiotic resistance genes. The CR-ROR strains carrying multiple antibacterial resistant genes require the stringent monitoring to avoid the spread of multidrug-resistant bacterial strains.

Increase in antibiotic resistance in Staphylococcus aureus isolated from ear infection is a serious public health problem. The objective of this investigation was to determine the antibacterial resistance profile and genetic variability of the S. aureus isolated from adult patients with otitis externa (OE) and otitis media (OM) infections, Tehran- Iran. The disk diffusion was employed to detect the susceptibility of 45 S. aureus strains. Biofilm production was evaluated by microtiter plate assay. Genetic diversity of the isolates was determined by staphylococcal cassette SCCmec, spa, and MLST techniques. Resistance to mupirocin and vancomycin were identified in 40 and 2.2% of isolates. Out of the 45 S. aureus isolates, 41 (91.2%) strains were considered as positive biofilm strains at different levels. According to our results, S. aureus isolated from OM (44.4%, 20/45) were including CC8/ST239-SCCmecIII corresponded to spa types t860, t030, t037, t234, t421 (70%, 14/20) and CC/ST30-SCCmecIV corresponded to spa types t605 and t019 (30%, 6/20) while S. aureus isolated from OE (55.6%, 25/45) were including CC/ST30-SCCmecIV corresponded to spa types t605, t345 and t1130 (52%, 13/25), CC/ST22-SCCmecIV corresponded to spa type t790 (20%, 5/25), CC8/ST8-SCCmecIV corresponded to spa type t008 (16%,4/25), and CC/ST45-SCCmecIV corresponded to spa types t004 and t038 (12%, 3/25). This study highlighted genetic variability and strong biofilm formation ability among our isolates revealing its crucial role in enhancing the resistance of this bacteria to drugs. Thus, it is necessary to continue the epidemiological analysis to improve the control of ear infections related to S. aureus.

Due to the rise of bacteria that are resistant to multiple drugs, treating infections in burn wounds has become a worldwide problem. It is important to find new ways to treat these infections. Lipid-based drug delivery systems have emerged as a promising type of carrier for antibiotics as well as antibacterial agents, such as antimicrobial peptides and nucleic acids, for wound infections. To this end, the current study assessed the antibacterial effects and wound healing properties of vancomycin-loaded solid lipid nanoparticles (SLN) against methicillin-resistant Staphylococcus aureus (MRSA) surgical wound infections. vancomycin-SLN was synthesized by double emulsion solvent evaporation techniques, and then in vitro antibacterial activity was evaluated by well diffusion and broth microdilution methods. A surgical wound was inflicted on 36 male rats; the infection was caused by MRSA, and free vancomycin and vancomycin-SLN were topically applied. Particle size, PDI, zeta potential, drug loading, and encapsulation efficiency of the optimum vancomycin-SLN were 350 ± 24 nm, 0.402 ± 0.014, -16.3 ± 2.5 mV, 13.9 ± 1.4%, and 92.14 ± 3.1%, respectively. In vitro antibacterial assays showed lower MICs for free vancomycin and killed bacteria more efficiently than vancomycin-SLN. However, the synthesized nanoparticles indicated long-term antibacterial activity against MRSA. Animals that were treated with vancomycin-SLN showed the best wound healing procedure. Treatment of rats with vancomycin-SLN increased re-epithelialization and decreased granulation tissue development, as seen by histological analysis. Antibiotic-loaded SLN could not only manage wound infection but also enhance wound healing. Therefore, this kind of treatment should be considered by scientists as an applicable treatment for wounds.

Pseudomonas aeruginosa is one of the major infectious agents in burn patients. Globally, high rates of antimicrobial resistance in P. aeruginosa have been reported, which is a cause of concern. The objective of this study was to determine the rate of resistance to carbapenems in P. aeruginosa isolates recovered from burn patients in Tunisia, to search genes encoding for carbapenemases and to determine their epidemiological markers (serotypes). A retrospective study was conducted in the Burn Intensive Care Unit (BICU) of the Trauma and Burn Centre of Ben Arous, Tunisia, and P.aeruginosa isolates collected from burn patients, from January to December 2018 were investigated. Carbapenemase screening was performed by Carbapenem Inactivation Method (CIM) and by EDTA-disk test for all carbapenem resistant isolates. Genes encoding carbapenemases (blaVIM, blaIMP, blaGES, blaNDM, and blaKPC) were investigated by PCR and selected carbapenemase genes were sequenced. During the study period, 104 non duplicated P. aeruginosa isolates were recovered. Most of them were isolated from skin samples (45.1%) and blood culture (22.1%) and belonged to O:11 (19.2%), O:12, and O:5 (12.5%, each) serotypes. High rates of resistance were observed for carbapenems (64.4%). Among the 67 carbapenem resistant isolates, 58 (86.5%) harbored blaVIM gene and 55 (82%) blaGES gene; in addition, 48 (71.6%) co-harbored blaVIM and blaGES genes. After sequencing, the blaVIM-2 and blaGES-5 gene variants were identified in seven randomly selected isolates. To the best of our knowledge, this is the first description of P. aeruginosa simultaneously harboring blaVIM-2 and blaGES-5 genes.

Object of our study was to analyze the carriage of resistance genes in carbapenem-resistant Raoultella planticola (CRRP) by whole genome sequencing (WGS). Three strains of CRRP (named WF0027, WF3597 and WF3648) were collected for clinical analysis and susceptibility of antimicrobial agents was determined. The WGS of three strains was done by Illumina platform and strain identification was performed by average nucleotide identity, and the antibiotic resistance genes carried by the three strains were detected by ABRicate software. Whole genome data of 46 CRRP strains were downloaded from the National Center for Biotechnology Information (NCBI) database, and the evolutionary tree was constructed by genomic single nucleotide polymorphism together with this study strains. Antimicrobial susceptibility testing revealed that WF3597 and WF3648 were susceptible to tigecycline and colistin, while exhibited resistance to 24 antimicrobial agents. WF0027 was resistant to 18 antimicrobial agents. A total of 25 resistance genes were identified using ABRicate software. WF0027 carried blaIMP-8, whereas WF3597 and WF3648 carried blaNDM-1 carbapenem resistance gene. As predicted by the PlasmidFinder, WF3597 and WF3648 carried one plasmid IncFII(p14)_1_p14, whereas WF0027 carried five plasmids. Evolutionary tree results show all strains are clustered into six groups, the strains WF3597 and WF3648 belonged to the same evolutionary group (E clade) and WF0027 belonged to the F clade. Three CRRP strains in our study carried carbapenem resistance genes (blaNDM-1 or blaIMP-8) and were resistant to multiple antimicrobial agents, posing a significant challenge for clinical treatment.

The study aimed to investigate prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKP) blood culture isolates and their susceptibility to two new antibiotics, imipenem/relebactam and ceftazidime/avibactam. Out of 765 isolates recovered from blood cultures in a tertiary care hospital in Serbia between 2020 and 2023, 143 non-repetitive K. pneumoniae strains were included in this study. Minimum inhibitory concentration (MIC) values of the examined antimicrobial drugs was determined byVITEK 2 system, MIC test strip (imipenem/relebactam and ceftazidime/avibactam), and broth microdilution method (tigecycline and colistin). Carbapenemase-encoding genes (blaKPC, blaOXA-48-like, blaNDM, blaVIM, blaIMP) were detected using a multiplex-PCR assay, the BioFire-Blood Culture Identification 2-panel. This closed molecular assay is designed for the BioFire® FilmArray® system, enabling automated sample preparation, amplification, detection, and analysis (bioMérieux, France). Results revealed that K. pneumoniae was the most common isolate from blood cultures in 2022. The prevalence of K. pneumoniae was about 11.6% in 2020 and 2021, while in 2022 it raised to over 30%. Also, the frequency of CRKP increased from 11.76% in 2020, through 15.29% in 2021 to 72.94% in 2022. The majority of CRKP carried blaOXA-48-like (60.0%), followed by blaKPC (16.47%), and blaNDM (8.24%) genes, while 14.12% harboured both blaOXA-48-like and blaNDM genes. Only 25.88% of CRKP isolates were resistant to ceftazidime/avibactam, while 51.76% were resistant to imipenem/relebactam and colistin. The rapid spread of CRKP is particularly concerning because therapeutic options are limited to a few antibiotics. While imipenem/relebactam and colistin showed similar antimicrobial activity against CRKP clinical isolates, ceftazidime/avibactam proved to be the most effective antibiotic.

Irreversible pulpitis is an inflammation of the tooth pulp caused by an opportunity-driven invasion of the pulp space by oral microbiota typically prevalent in the oral cavity. Microbial organisms are extensively recognised to be the fundamental cause of endodontic infections and treatment failures. Previously, bacterial species responsible for these infections were largely recognised using conventional microbial culture techniques, lending credence to the widely held belief that anaerobic Gram-negative bacteria frequently enter the pulp space and trigger endodontic infections. The advent of novel technologies grants the advantage of detecting and studying microbial populations via an amalgamation of the modern "Omics" techniques and meticulous bioinformatics analysis, additionally detecting the metatranscriptome, metaproteome and metabolome along with the metagenome. Amongst these analytical strategies, metagenomic analyses are essentially pragmatic for investigating the oral microbiome. Metagenomics favor not only assessment of microbial composition in diseased conditions, but also contributes to detection of novel, potentially pathogenic species inclusive of non-viable bacteria. The present review describes current knowledge of root canal microbiome, including its composition and functional attributes, the novel strategies available for detection of microbiome as well as challenges associated and provides some crucial pointers for areas of future research.