Clinical Strains Research Articles

Genomic characterization and resistance features of Streptococcus agalactiae isolated from non-pregnant adults in Shandong, China

BackgroundStreptococcus agalactiae is a recognized pathogen that primarily affects infants and pregnant women. However, its increasingly important role in causing invasive infections among non-pregnant adults has become a significant health concern due to the severity and variety of its clinical impacts. MethodsNonduplicate S. agalactiae clinical strains associated with clinical infections (n = 139) were isolated from non-pregnant adults in Shandong, China. Antibiotic susceptibility testing, whole-genome sequencing and genomic analyses were conducted to characterize the genome and identify resistance features of these strains. ResultsThe strains exhibited universal susceptibility to penicillin, ampicillin, cefotaxime, meropenem, linezolid and vancomycin. Notably, high resistance rates were observed for erythromycin (91.4%), clindamycin (89.2%), levofloxacin (84.2%), tetracycline (54.0%) and, to a lesser extent, chloramphenicol (12.9%). Serotyping revealed seven serotypes and one non-typeable strain. Serotypes Ia, Ib, III and V predominated, representing 95.7% of the strains. Nineteen sequence types were categorized into seven clonal complexes, with CC10 being the most prevalent at 48.9%. The resistance genes mreA (100%), ermB (70.5%) and tetM (46.0%) were commonly detected. All the isolates carried at least one pilus backbone determinant and one alpha-like protein gene, with the PI-1+PI-2a and the bca gene being the most frequent at 84.2% and 54.7%, respectively. ConclusionsWhile S. agalactiae strains in non-pregnant adults retain sensitivity to β-lactam antibiotics, the elevated resistance to erythromycin, clindamycin, levofloxacin and tetracycline is concerning. Given the growing elderly population worldwide, the burden of S. agalactiae infections is significant. Continuous surveillance of serotype distribution and antibiotic resistance patterns is imperative for targeted prevention and therapeutic strategies.

Unravelling the genomic characteristics of a Klebsiella quasipneumoniae clinical isolate carrying blaNDM-1

ObjectiveDespite the increasing reports of blaNDM in Enterobacterales in Brazil, comprehensive whole genome sequencing (WGS) data remain scarce. To address this knowledge gap, our study focuses on the characterization of the genome of an New Delhi Metallo-β-lactamase (NDM)-1-producing Klebsiella quasipneumoniae subsp. quasipneumoniae (KQPN) clinical strain isolated in Brazil. MethodsThe antimicrobial susceptibility profile of the A-73.113 strain was performed by agar dilution or broth microdilution following the Brazilian Antimicrobial Susceptibility Testing Committee/European Committee on Antimicrobial Susceptibility Testing recommendations. WGS was performed using the Illumina® NextSeq platform and the generated reads were assembled using the SPAdes software. The sequences obtained were submitted to the bioinformatics pipelines to determine the sequence type, resistome, plasmidome, and virulome. ResultsThe A-73.113 strain was identified as KQPN and was susceptible to polymyxins (MICs, ≤0.25 µg/mL), tigecycline (MIC, 0.5 µg/mL), ciprofloxacin (MIC, 0.5 µg/mL), and levofloxacin (MIC, 1 µg/mL). WGS analysis revealed the presence of genes conferring resistance to β-lactams (blaNDM-1, blaCTX-M-15, blaOXA-9, blaOKP-A-5, blaTEM-1), aminoglycosides [aph(3′)-VI, aadA1, aac(6′)-Ib], and fluoroquinolones (oqxAB, qnrS1, aac(6′)-Ib-cr]. Additionally, the presence of the plasmid replicons Col(pHAD28), IncFIA(HI1), IncFIB(K) (pCAV1099-114), IncFIB(pQil), and IncFII(K), as well as virulence-encoding genes fimABCDEFGHIK (type 1 fimbria), pilW (type IV pili), iutA (aerobactin), entABCDEFS/fepABCDG/fes (Ent siderophores), iroE (salmochelin), and allABCDRS (allantoin utilization) was verified. Furthermore, we found that the A-73.113 strain belongs to ST1040. ConclusionsHere we report the genomic characteristics of an NDM-1-producing KQPN ST1040 strain isolated from blood cultures in Brazil. These data will enhance our comprehension of how this species contributes to the acquisition and dissemination of blaNDM-1 in Brazilian nosocomial settings.

Development of two multiplex PCR assays for rapid detection of eleven Gram-negative bacteria in children with septicemia

AimThis study aimed to develop a multiplex PCR assay for simultaneous detection of major Gram-negative etiologies of septicemia and evaluate its performance.MethodsMultiplex PCR (mPCR) assays were developed targeting 11 bacterial strains. Species-specific primers were confirmed using known clinical isolates and standard strains. Gradient PCR was performed on each primer against its target bacterial gene to determine its optimal amplification condition. The minimum detectable DNA concentration of the two assays was evaluated by adjusting bacterial DNA concentration to 100 ng/μL and, tenfold serially diluting it up to 10 pg/μL with DNAse-free water. The diagnostic accuracy of mPCR assays was established by subjecting the assays to 60 clinical blood samples.ResultsTwo mPCR assays were developed. Optimal primer annealing temperature of 55 °C was established and utilized in the final amplification conditions. The assays detected all targeted bacteria, with a 100 pg minimum detectable DNA concentration. Pathogens were not detected directly from whole blood, but after 4 h and 8 h of incubation, 41% (5/12) and 100% (12/12) of the bacteria were detected in culture fluids, respectively. The assays also identified Salmonella spp. and Klebsiella pneumoniae co-infections and extra pathogens (1 E. coli and 2 K. pneumoniae) compared with culture. The sensitivity and specificity of the mPCR were 100.0% (71.7–100.0) and 98.0% (90.7–99.0), respectively. The area under the ROC curve was 1.00 (1.00–1.00).ConclusionsThe mPCR assays demonstrated substantial potential as a rapid tool for septicemia diagnosis alongside the traditional blood culture method. Notably, it was able to identify additional isolates, detect co-infections, and efficiently detect low bacterial DNA loads with high sensitivity, implying its value in enhancing efficiency of diagnosis of septicemia.

Rapid discrimination methods for clinical and environmental strains of Aeromonas hydrophila and A. veronii biovar sobria using the N-terminal sequence of the flaA gene and investigation of antimicrobial resistance.

Although the genus Aeromonas inhabits the natural environment, it has also been isolated from hospital patient specimens as a causative agent of Aeromonas infections. However, it is not known whether clinical strains live in the natural environment, and if these strains have acquired antimicrobial resistance. In this study, we performed the typing of flagellin A gene (flaA) of clinical and environmental strains of Aeromonas hydrophila and A. veronii biovar sobria using Polymerase Chain Reaction (PCR) assay with newly designed primers. Detection rates of the clinical and environmental flaA types of A. hydrophila were 66.7% and 88.2%, and the corresponding rates for A. veronii biovar sobria were 66.7% and 90.9%. The PCR assays could significantly discriminate between clinical and environmental strains of both species in approximately 4 h. Also, among the 63 clinical Aeromonas strains used, only one extended-spectrum β-lactamase-producing bacteria, no plasmid-mediated quinolone resistance bacteria, and only four multidrug-resistant bacteria were detected. Therefore, the PCR assays could be useful for the rapid diagnosis of these Aeromonas infections and the monitoring of clinical strain invasion into water-related facilities and environments. Also, the frequency of drug-resistant Aeromonas in clinical isolates from Okinawa Prefecture, Japan, appeared to be low.

Monophasic variant of Salmonella Typhimurium 4,[5],12:i:- outbreak: an investigation by the Competent Authority.

Foodborne diseases represent a significant public health issue, regarding both collective health and the economy, with implications for healthcare costs and agribusiness. This paper shows the description and results of the investigation of a Salmonella enterica subsp. enterica foodborne outbreak that occurred in the Marche Region (Italy) in 2022, which was linked to the consumption of a roasted pork product (porchetta). As part of the outbreak investigations discussed in this article, molecular analysis to evaluate the genomic correlation between clinical, food, and environmental origin strains was carried out. All Salmonella strains of different origins were serotyped as monophasic variant of Salmonella Typhimurium with an antibiotic-resistance pattern and an allelic profile such as to define the "cluster strain" allowing the correlation between clinical and food/environmental strains, definitively confirmed by whole genome sequencing analysis. Following the laboratory evidence, corrective measures at the porchetta processing plant and at the retail stores involved were carried out by the Local Animal Based Food Hygiene Service. The results of this study show that effective intervention is only possible if efficient data exchange, standardized procedures, and staff training are guaranteed. The latter aspect also concerns the food business operator, who must take appropriate measures to minimize the risk.

Characterization of Salmonella phage of the genus Kayfunavirus isolated from sewage infecting clinical strains of Salmonella enterica.

The emergence of multi-drug resistance in Salmonella, causing food-borne infections, is a significant issue. With over 2,600 serovars in in Salmonella sp., it is crucial to identify specific solutions for each serovar. Phage therapy serves as an alternate treatment option. In this study, vB_SalP_792 phage was obtained from sewage, forming plaques in eight out of 13 tested clinical S. enterica isolates. Transmission electron microscopy (TEM) examination revealed a T7-like morphotype. The phage was characterized by its stability, life cycle, antibiofilm, and lytic ability in food sources. The phage remains stable throughout a range of temperatures (-20 to 70°C), pH levels (3-11), and in chloroform and ether. It also exhibited lytic activity within a range of MOIs from 0.0001 to 100. The life cycle revealed that 95% of the phages attached to their host within 3 min, followed by a 5-min latent period, resulting in a 50 PFU/cell burst size. The vB_SalP_792 phage genome has a dsDNA with a length of 37,281 bp and a GC content of 51%. There are 42 coding sequences (CDS), with 24 having putative functions and no resistance or virulence-related genes. The vB_SalP_792 phage significantly reduced the bacterial load in the established biofilms and also in egg whites. Thus, vB_SalP_792 phage can serve as an effective biocontrol agent for preventing Salmonella infections in food, and its potent lytic activity against the clinical isolates of S. enterica, sets out vB_SalP_792 phage as a successful candidate for future in vivo studies and therapeutical application against drug-resistant Salmonella infections.

Identification of Bioactive Compounds of Streptomyces spp. Isolated from Qom Lake Sediments and Evaluation of its Antimicrobial Activity against Pseudomonas aeruginosa

Background: Marine sediments are rich sources for isolating active secondary metabolites from microorganisms. Among the microorganisms, Actinomycetes are highly important due to the production of various chemical compounds in a wide range of biological activities, such as antibacterial activity. Streptomyces is the most important genera in the family of Actinomycetes. As a member of this group, it has great potential in the production of secondary metabolites such as antibiotics, enzymes, herbicides, anti-carcinogenic, and other useful compounds. Objective: This study aims to identify bioactive compounds of Streptomyces isolated from sediments of the Salt Lake of Qom and to study their antimicrobial properties against standard strains of Pseudomonas aeruginosa. Methods: In this study, 20 samples were collected from a depth of 5 to 15-20 cm of sediment in the Salt Lake of Qom. Pure cultivations were then provided from these samples. This study used starch casein agar (SCA) to isolate streptomyces, and 35 Streptomyces were isolated. The disc diffusion method was used to explore the antimicrobial properties of Streptomyces against clinical strains of Pseudomonas aeruginosa and strains standard of Pseudomonas aeruginosa PTCC 1310. Results: Seven strains, including SCA3 SCB1, SCB4, SCB8, SCC15, SCC18, and SCC28 strains, had antimicrobial properties. In this study, the results show that SCC15 with the halo diameter of 17, 17, 15, and 19 contains the best antibacterial properties against clinical strains 1, 2 and 3 of Pseudomonas aeruginosa and Pseudomonas aeruginosa PTCC 1310. among the 16 peaks observed by GC/MS to identify bioactive compounds of Streptomyces, it was found that Bis (2-ethyl hexyl) phthalate, with 69.06 percent, had the highest peak production, which reflects the importance of phthalates in microbial activities. Conclusion: According to the results, the Salt Lake of Qom was one of the sources of Streptomyces. In addition, the isolated Streptomyces had antimicrobial properties against Pseudomonas aeruginosa isolates. It was also found that phthalate was the most bioactive substance of Streptomyces isolated.

Variable Surface Antigens of Plasmodium falciparum: Protein Families with Divergent Roles.

Malaria caused by Plasmodium falciparum (Pf) is an illness that contributes significantly to the global health burden. Pf makes significant alterations to the host cell to meet its metabolic demands and escape the immune response of the host. These include the export of a large number of parasite proteins to the infected Red Blood Cells (iRBC). Variable Surface Antigens (VSAs), which are highly polymorphic protein families with important roles in immune evasion, form an important component of the exported proteins. A total of five protein families constitute the VSAs, viz. PfEMP1 (Pf erythrocyte membrane protein 1), RIFIN (repetitive interspersed family), STEVOR (sub-telomeric open reading frame), SURFIN (surface-associated interspersed gene family), and PfMC-2TM (Pf Maurer's cleft two transmembrane). With orthologues present in various simian-infecting species, VSAs take up a variety of domain topologies and organizational structures while exhibiting differential expressions throughout the parasite life cycle. Their expression varies across clinical isolates and laboratory strains, which suggests their crucial role in host cell survival and defense. Members of VSAs are reported to contribute significantly to disease pathogenesis through immune evasion processes like cytoadherence, iRBC sequestration in the host vasculature, rosetting, reduced erythrocyte deformability, and direct immunosuppression. In this study, we have gathered information on various aspects of VSAs, like their orthologues, domain architecture, surface topology, functions and interactions, and three-dimensional structures, while emphasizing discoveries in the field. Considering the vast repertoire of Plasmodial VSAs with new emergent functions, a lot remains unknown about these families and, hence, malaria biology.

Secretion of 2,4 di-tertbutylphenol by a new Pseudomonas strain SBMCH11: A tert-butyl substituted phenolic compound displayed antibacterial efficacy

Pseudomonas sp. SBMCH11 was newly isolated from maritime soil samples which was identified by morphological, biochemical, and 16S rRNA gene sequencing. The isolated Pseudomonas sp. SBMCH11 had significant antibacterial activity against clinical bacterial strains including Pseudomonas aeruginosa and Staphylococcus aureus. Subsequently, high concentrations of antibacterial substances were achieved by optimizing the following parameters: pH (7.0), carbon (1 %), nitrogen sources (casein 0.2 %), NaCl (10 %), and incubation time (120 hrs). Furthermore, the extracted component from the Pseudomonas sp. SBMCH11 was shown to have a significant inhibitory effect on tested clinical pathogens. On the other hand, the extracted compound was confirmed as 2,4 di-tertbutylphenol (2,4 DTBP) by GC–MS with a molecular weight of 206.5 Daltons. Based on these findings, the isolated 2,4 DTBP could be recognized as a promising bioactive molecule for further antibacterial medication development. Compounds identified in the maritime environment from microorganisms, especially Pseudomonas sp. SBMCH11 could be regarded as a potential bio-factory for the synthesis of antibacterial compounds to suppress large numbers of pathogenic bacteria in the natural environment.

Characterization of Acinetobacter baumannii at a tertiary hospital in Guangzhou: a genomic and clinical study

Acinetobacter baumannii (AB) infections have become a global public health concern due to the continued increase in the incidence of infection and the rate of resistance to carbapenems. This study aimed to investigate the genomic features of AB strains recovered from a tertiary hospital and assess the clinical implications of the findings. A total of 217 AB strains were collected between 2016 and 2018 at a tertiary hospital in Guangzhou, with 183 (84.33%) being carbapenem-resistant AB (CRAB), with the main mechanism being the carriage of the blaOXA-23 gene. The overall mortality rate of patients caused by such strains was 15.21% (n = 33). Artificial lung ventilation and the use of meropenem were mortality risk factors in AB-infected patients, while KL2 AB infection was negatively associated. Core genome multilocus sequence typing and clustering analysis were performed on the integrated AB genome collection from the NCBI database and this study to illustrate the population structure among China. The results revealed diverse core genome profiles (n = 17) among AB strains from China, and strains from this single hospital exhibited most of the core genome profiles (n = 13), suggesting genetic variability within the hospital and transmission across the country. These findings show that the high transmission potential of the CRAB strains and meropenem usage that confers a selective advantage of CRAB clinically are two major factors that pose significant challenges to the effective clinical management of AB infections. Understanding the genetic features and transmission patterns of clinical AB strains is crucial for the effective control of infections caused by this pathogen.

Laser-induced 2D/0D graphene-nanoceria freestanding paper-based films for on-site hydrogen peroxide monitoring in no-touch disinfection treatments

A one-shot CO2 laser-based strategy to generate conductive reduced graphene oxide (rGO) decorated with nanoceria (nCe) is proposed. The 2D/0D rGO-nCe films, integrated as catalytic sensing layers in paper-based sensors, were employed for on-site monitoring of indoor fogging treatments against Listeria monocytogenes (Lm), a ubiquitous pathogenic bacterium. The rGO-nCe laser-assisted synthesis was optimized to preserve the rGO film morphological and electron-transfer features and simultaneously integrate catalytic nCe. The films were characterized by microscopical (SEM), spectroscopical (EDX, Raman, and FTIR), and electrochemical techniques. The most performing film was integrated into a nitrocellulose substrate, and the complete sensor was assembled via a combination of xurography and stencil printing. The rGO-nCe sensor's catalytic activity was proved toward the detection of H2O2, obtaining sensitive determination (LOD = 0.3 µM) and an extended linear range (0.5–1500 µM). Eventually, the rGO-nCe sensor was challenged for the real-time continuous monitoring of hydrogen peroxide aerosol during no-touch fogging treatment conducted following the EU’s recommendation for biocidal product use. Treatment effectiveness was proved toward three Lm strains characterized by different origins, i.e., type strain ATCC 7644, clinical strain 338, and food strain 641/6II. The sensor allows for discrimination and quantification treatments at different environmental biocidal amounts and fogging times, and correlates with the microbiological inhibition, promoting the proposed sensor as a useful tool to modulate and monitor no-touch treatments.Graphical

Dynamic evolution of ceftazidime-avibactam resistance from a single patient through the IncX3_NDM-5 plasmid transfer and blaKPC mutation

The rapid dissemination of carbapenem-resistant Enterobacterales (CRE) especially carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a great threat to global public health. Ceftazidime-avibactam, a novel β-lactam/β-lactamase inhibitor combination, has been widely used due to its excellent antibacterial activity against KPC-producing K. pneumoniae. However, several resistance mechanisms have been reported since its use. Here, we conducted a series of in vitro experiments to reveal and demonstrate the dynamic evolution of ceftazidime-avibactam resistance including interspecies IncX3_NDM-5 plasmid transfer between Enterobacter cloacae and K. pneumoniae and blaKPC mutation from blaKPC-2 to blaKPC-33. Through the analysis of conjugation frequency and fitness cost, the IncX3_NDM-5 plasmid in this study showed strong transmissibility and stability in E. coli EC600 and clinical strain K. pneumoniae 5298 as recipient strain. With increasing ceftazidime-avibactam concentration, the conjugation frequency remained at 10-3-10-5, while the mutation frequency of K. pneumoniae 5298 was 10-6-10-8 at the same concentration. Further plasmid analysis (the IncX3_NDM plasmid from this study and other 658 plasmids from the NCBI database) revealed the diverse origin and genetic structure of blaNDM-5 carrying plasmids. E. coli (42.9%), China (43.9%), IncX3 (66.6%) are the most common strains, regions, and Inc types respectively. By analysing of genetic environment detected in IncX3 plasmids, the dominant structures (168/258, 65.1%) were identified: ISKox3-IS26-blaNDM-5-IS5-ISAba125-Tn3000-Tn3. In additon, several structural variations were found in the core gene structure. In conclusion, the high fitness and transmissibility of the IncX3_NDM-5 plasmids were noteworthy. More importantly, the diverse ceftazidime-avibactam resistance mechanisms including blaNDM-5 tranfer and blaKPC-2 mutation highlighted the importance of the continuous monitoring of antimicrobial susceptibility and carbapenemases subtype during ceftazidime-avibactam treatment.

River waters in Greece: A reservoir for clinically relevant extended-spectrum-β-lactamases-producing Escherichia coli

In the current study, the genotypic characteristics such as antimicrobial resistance and virulence genes, and plasmid replicons and phenotypic characteristics such as biofilm formation and antimicrobial resistance of 87 extended-spectrum beta-lactamase (ESBL)-producing E. coli (ESBL-Ec) isolated from 7 water bodies in northern Greece were investigated. Our data show a high prevalence (60.0 %) of ESBL-Ec in surface waters that exhibit high genetic diversity, suggesting multiple sources of their transmission into the aquatic environment. When evaluating the antimicrobial resistance of isolates, wide variation in their resistance profiles has been detected, with all isolates being multi-drug resistant (MDR). Regarding biofilm formation capacity and phylogenetic groups, the majority (54.0 %, 47/87) of ESBL-Ec were classified as no biofilm producers mainly assigned to phylogroup A (35.6 %; 31/87), followed by B2 (26.5 %; 23/87). PCR screening showed that a high proportion of the isolates tested positive for the blaCTX-M-1 group genes (69 %, 60/87), followed by blaTEM (55.2 %, 48/87), blaOXA (25.3 %, 22/87) and blaCTX-M-9 (17.2 %, 15/87). A subset of 28 ESBL-Ec strains was further investigated by applying whole genome sequencing (WGS), and among them, certain clinically significant sequence types were identified, such as ST131 and ST10. The corresponding in silico analysis predicted all these isolates as human pathogens, while a significant proportion of WGS-ESBL-Ec were assigned to extraintestinal pathogenic E. coli (ExPEC; 32.1 %), and urinary pathogenic E. coli (UPEC; 28.6 %) pathotypes. Comparative phylogenetic analysis, showed that the genomes of the ST131-O25:H4-H30 isolates are genetically linked to the human clinical strains. Here, we report for the first time the detection of a plasmid-mediated mobile colistin resistance gene in ESBL-Ec in Greece isolated from an environmental source. Overall, this study underlines the role of surface waters as a reservoir for antibiotic resistance genes and for presumptive pathogenic ESBL-Ec.

Genomic Differences Associated with Resistance and Virulence in Pseudomonas aeruginosa Isolates from Clinical and Environmental Sites.

Pseudomonas aeruginosa is a pathogen that causes healthcare-associated infections (HAIs) worldwide. It is unclear whether P. aeruginosa isolated from the natural environment has the same pathogenicity and antimicrobial resistance potential as clinical strains. In this study, virulence- and resistance-associated genes were compared in 14 genomic sequences of clinical and environmental isolates of P. aeruginosa using the VFDB, PATRIC, and CARD databases. All isolates were found to share 62% of virulence genes related to adhesion, motility, secretion systems, and quorum sensing and 72.9% of resistance genes related to efflux pumps and membrane permeability. Our results indicate that both types of isolates possess conserved genetic information associated with virulence and resistance mechanisms regardless of the source. However, none of the environmental isolates were associated with high-risk clones (HRCs). These clones (ST235 and ST111) were found only in clinical isolates, which have an impact on human medical epidemiology due to their ability to spread and persist, indicating a correlation between the clinical environment and increased virulence. The genomic variation and antibiotic susceptibility of environmental isolates of P. aeruginosa suggest potential biotechnological applications if obtained from sources that are under surveillance and investigation to limit the emergence and spread of antibiotic resistant strains.

Evaluation of Automated Disk Diffusion Antimicrobial Susceptibility Testing Using Radian® In-Line Carousel

Antimicrobial susceptibility testing (AST) by disk diffusion provides an accurate image of bacterial growth, enabling the detection of culture purity, heterogeneous growth, and antibiotic interactions. However, this manual method is time-consuming and visual interpretation is prone to errors. To overcome these disadvantages, the Radian® In-Line Carousel (Copan, Brescia, Italy) was launched, which is a WASPLab® module dedicated to full automation of (pre)-analytical steps as well as interpretation of disk diffusion AST. However, until now, no evaluation of Radian® against manual disk diffusion has been performed. We assessed the categorical agreement (CA) between standardized disk diffusion (reference method) and Radian® using EUCAST 2021 breakpoints. We tested 135 non-duplicate strains, selected from the National EUCAST challenge panel, clinical strains, and external quality controls. The strains included Enterobacterales (n = 63), Enterococcus faecalis (n = 3), Enterococcus faecium (n = 10), Pseudomonas aeruginosa (n = 16), Staphylococcus aureus (n = 19), coagulase-negative staphylococci (n = 4), and Streptococcus spp. (n = 20). Furthermore, we explored antibiotic disk thermolability in the WASP Radian® carousel by testing 10 ATCC® strains up to 7 days. The observed CA was 95.3%, 96.3%, 93.8%, 97.3% and 98.0% for Enterobacterales, Enterococcus spp., P. aeruginosa, Staphylococcus spp. and Streptococcus spp., respectively, resulting in an acceptable overall CA for all groups. (Very) major error rates were ≤ 5% for all antibiotics. Antibiotic disk thermostability was confirmed up to 4 days in the WASP Radian® In-Line Carousel. The Radian® In-Line Carousel provides a fully automated solution for accurate disk diffusion AST, reducing workload and improving standardization and traceability. In addition, our study demonstrated the thermostability of antibiotic disks up to 4 days in the WASP Radian® In-Line Carousel.

Investigation of the Affinity of Aptamers for Bacteria by Surface Plasmon Resonance Imaging Using Nanosomes.

The cell-SELEX method enables efficient selection of aptamers that bind whole bacterial cells. However, after selection, it is difficult to determine their binding affinities using common screening methods because of the large size of the bacteria. Here we propose a simple surface plasmon resonance imaging method (SPRi) for aptamer characterization using bacterial membrane vesicles, called nanosomes, instead of whole cells. Nanosomes were obtained from membrane fragments after mechanical cell disruption in order to preserve the external surface epitopes of the bacterium used for their production. The study was conducted on Bacillus cereus (B. cereus), a Gram-positive bacterium commonly found in soil, rice, vegetables, and dairy products. Four aptamers and one negative control were initially grafted onto a biochip. The binding of B. cereus cells and nanosomes to immobilized aptamers was then compared. The use of nanosomes instead of cells provided a 30-fold amplification of the SPRi signal, thus allowing the selection of aptamers with higher affinities. Aptamer SP15 was found to be the most sensitive and selective for B. cereus ATCC14579 nanosomes. It was then truncated into three new sequences (SP15M, SP15S1, and SP15S2) to reduce its size while preserving the binding site. Fitting the results of the SPRi signal for B. cereus nanosomes showed a similar trend for SP15 and SP15M, and a slightly higher apparent association rate constant kon for SP15S2, which is the truncation with a high probability of a G-quadruplex structure. These observations were confirmed on nanosomes from B. cereus ATCC14579 grown in milk and from the clinical strain B. cereus J066. The developed method was validated using fluorescence microscopy on whole B. cereus cells and the SP15M aptamer labeled with a rhodamine. This study showed that nanosomes can successfully mimic the bacterial membrane with great potential for facilitating the screening of specific ligands for bacteria.

System proteinase/inhibitors in the pathogenesis of experimental kidney tuberculosis

BACKGROUND: Damage to the kidney parenchyma of various origins is associated with the accumulation of extracellular matrix proteins, the regulation of which involves the matrix metalloproteinase/inhibitor system. AIM: To evaluate the pathogenetic role of the proteinase/blood inhibitor system in experimental renal tuberculosis. MATERIAL AND METHODS: When modeling the process, a clinical strain 5582 of the Beijing genotype with multidrug resistance of mycobacteria was used. The study was conducted on 20 rabbits, divided into three groups: the first (n=6) included infected untreated animals; in the second (n=7) and third (n=7) anti-tuberculosis therapy was administered orally for 18.5 weeks; in the third, treatment was carried out in combination with a single injection of autologous mesenchymal stem cells into the ear vein. Blood levels of matrix metalloproteinases-1 and -9, tissue inhibitor of metalloproteinases-1, cystatin C and neutrophil elastase were determined. Morphological changes in the kidney parenchyma at the end of the experiment were assessed using 26 indicators, including tubulointerstitial and vascular changes. The median and interquartile ranges were calculated, the Kruskal–Wallis test, analysis of covariance, and the projective classification method were used. RESULTS: The progression of kidney tuberculosis was accompanied by a significant increase in the level of neutrophil elastase by 1.9 times, matrix metalloproteinase-9 by 2.2 times, and cystatin C by 1.5 times compared to the initial level. The treatment carried out in the second and third groups contributed to the normalization of these indicators. The concentrations of matrix metalloproteinase-1 and tissue inhibitor of metalloproteinase-1 in all three groups did not change relative to the baseline level. Covariance analysis showed that in the pathogenesis of renal tuberculosis changes in matrix metalloproteinase-1 (p=0.003), matrix metalloproteinase-9 (p=0.002), tissue inhibitor of metalloproteinases-1 (p=0.01) and cystatin C (p=0.0001) were primarily associated with vascular changes, found in all study groups. A linear combination containing three morphological characteristics allowed us to identify differences between the three groups with 90% accuracy. CONCLUSION: Renal tuberculosis, caused by a multidrug-resistant pathogen, is characterized by an imbalance in the proteinase/inhibitor system and impaired renal function, the degree of which is associated with the morphological characteristics of vascular and tubulointerstitial changes.

A Rapid and Robust DNA Extraction Method for PCR-Based Diagnosis of V. cholerae

Cholera, caused by _V. cholerae_, needs rapid diagnosis because of its threat for rapid spread. Recent molecular diagnosis by PCR assay is more advantageous than the conventional methods. The bottleneck in PCR diagnosis lies in the delay in template DNA extraction of _V. cholerae_, which is the basic requirement. This study describes a simple, less expensive, and rapid template DNA extraction method to lessen the total time for PCR diagnosis of _V. cholerae._ To obtain template DNA, our method involves boiling of _V. cholerae_ suspension in distilled water (takes 18-24 hours) instead of boiling the suspension in broth medium, which is a lengthy process (takes 72 hours). The validation of our template DNA was conducted using 40 _V. cholerae_ O1 strains that were confirmed previously, and its usefulness was checked on 20 clinical strains of _V. cholerae_ O1 isolated from acute diarrhea patients; results were compared with those of conventional template DNA. The analysis of our template DNA in simplex and quadruplex PCR assays revealed the presence of _ctxA_, _tcpA _(El Tor), _rfb _(O1), _ToxR_, _ctxB_, _zot_, _ace,rst _, and _OmpW _genes in _V. cholerae _O1. The comparison of the results of PCR assays using the template DNA from both sources showed equal results and matched correctly. The sensitivity of our template DNA was 1.5x103 CFU per assay. Our template DNA extraction method is simple, less expensive, and rapid, and it can be employed for early diagnosis of _V. cholerae_ during outbreaks, in research laboratories, and in hospital setups where infrastructures are available.

Harmol used for the treatment of herpes simplex virus induced keratitis.

Herpes simplex virus type 1 (HSV-1) infection of the eyes results in herpes simplex keratitis (HSK), which has led to vision loss and even blindness in patients. However, the rate of drug resistance in HSV is on the rise; therefore, new antiviral agents with sufficient safety profiles must be developed. At present, we assessed the anti-HSV-1 activity of 502 natural compounds and their ability to reduce the HSV-1-induced cytopathic effect. We chose harmol for further studies because it exhibited the highest antiviral activity. We found that harmol inhibited both HSV-1F and HSV-1/153 (a clinical drug-resistant strain) replication, with an EC50 of 9.34 µM and 5.84 µM, respectively. Moreover, harmol reduced HSV-1 replication in corneal tissues and viral progeny production in tears, and also alleviated early corneal surface lesions related to HSK. For example, harmol treatment preserved corneal thickness and nerve density in HSK mice. Interestingly, harmol also showed a promising antiviral effect on HSV-1/153 induced HSK in mouse model. Furthermore, harmol combined with acyclovir (ACV) treatment showed a greater antiviral effect than either one alone in vitro. Therefore, harmol may be a promising therapeutic agent for managing HSK.

Comparison of testing methods assessing the in vitro efficacy of the combination of aztreonam with avibactam on multidrug-resistant Gram-negative bacilli

BackgroundAztreonam-avibactam (ATM-AVI) combination shows promising effectiveness on most carbapenemase-producing Gram-negatives, yet standardized antibiotic susceptibility testing (AST) methods for evaluating the combination in clinical laboratories is lacking. We aimed to evaluate different ATM-AVI AST approaches.Methods96 characterized carbapenem-resistant clinical isolates belonging to 9 Enterobacterales (EB; n = 80) and P. aeruginosa (PA; n = 16) species, including 90 carbapenemase producers and 72 strains resistant to both CAZ-AVI and ATM, were tested. Paper disk elution (DE; Bio-Rad) and E-test gradient strips stacking (SS; bioMérieux) were performed for the ATM + CAZ-AVI combination. MIC Test Strip (MTS; Liofilchem) was evaluated for ATM-AVI MIC determination. Results were interpreted applying ATM clinical breakpoints of the EUCAST guidelines and compared to the broth microdilution method (Sensititre, Thermofisher).ResultsAccording to broth microdilution method, 93% of EB and 69% of PA were tested susceptible to ATM-AVI. The synergistic effect of ATM-AVI was of 95% for EB, but of only 17% for PA. The MTS method yielded higher categorical and essential agreement (CA/EA) rates for both EB (89%/91%) and PA (94%/94%) compared to SS, where the rates were 87%/83% for EB and 81%/81% for PA. MTS and SS yielded 2 and 3 major discrepancies, respectively, while 3 very major discrepancies each were observed for both methods. Concerning the DE method, CA reached 91% for EB and 81% for PA, but high number of very major discrepancies were observed for EB (n = 6; 8%) and for PA (n = 3; 19%).ConclusionsThe ATM-AVI association displayed excellent in vitro activity against highly resistant clinical Enterobacterales strains. MTS method offers accurate ATM-AVI AST results, while the SS method might serve as better alternative then DE method in assessing the efficacy of ATM + CAZ-AVI combination. However, further investigation is needed to confirm the methods' ability to detect ATM-AVI resistance.