The aim of this study is to evaluate opportunistic pathogenic bacteria of the genus Pseudomonas in anthropogenically impacted bathing waters, primarily focusing on bathing ponds. The findings include the detection of these bacteria, their susceptibility to selected antibiotics, and the determination of the Exotoxin A (exoA) gene using PCR method. P. aeruginosa was present in most samples, albeit in low concentrations (1-14 CFU/100 mL). The presence of P. otitidis, which is associated with ear infection, in this type of bathing water, was not rare (up to 90 CFU/100 mL). This species would not be detected by the standard methods, including tests on acetamid medium, used for P. aeruginosa in water. The isolated strains of P. otitidis lack the exoA gene and exhibited higher resistance to meropenem compared to P. aeruginosa.
- MeSH
- ADP Ribose Transferases genetics MeSH
- Anti-Bacterial Agents * pharmacology MeSH
- Drug Resistance, Bacterial MeSH
- Bacterial Proteins genetics MeSH
- Bacterial Toxins genetics MeSH
- Pseudomonas aeruginosa Exotoxin A MeSH
- Exotoxins genetics MeSH
- Virulence Factors genetics MeSH
- Microbial Sensitivity Tests * MeSH
- Water Microbiology * MeSH
- Polymerase Chain Reaction MeSH
- Pseudomonas * genetics isolation & purification classification drug effects MeSH
- Ponds * microbiology MeSH
- Publication type
- Journal Article MeSH
BackgroundDuring the COVID-19 pandemic, non-pharmaceutical interventions (NPIs) such as social distancing, lockdowns and enhanced hygiene led to a decrease in respiratory pathogens. However, as NPIs were relaxed, a resurgence in several respiratory pathogens was observed including one local Chlamydia pneumoniae outbreak in Switzerland, prompting the need for a better understanding of C. pneumoniae epidemiology.AimTo assess temporal and geographical variations in C. pneumoniae detection before, during and after the COVID-19 pandemic.MethodsData on C. pneumoniae PCR detection ratios (number of positive tests/ total number of tests) across pre-pandemic (2018-2019), pandemic (2020-2022) and post-pandemic (2023) periods were collected via a global survey disseminated through various professional networks.ResultsC. pneumoniae detection ratios were analysed across 28 sites (27 in Europe, one in Taiwan) in 2023 (Dataset A, n = 172,223 tests) and 20 sites from 2018 to 2023 (Dataset B, n = 693,106 tests). Twenty-seven sites were laboratories (hospital or clinical) and one a surveillance system (Denmark). A significant decrease in detection ratios was observed during the pandemic period (from 1.05% to 0.23%, p < 0.001). In 2023, detection ratios increased to 0.28% (p < 0.002). Notable regional variations were found, with statistically significant increases in detection ratios at six sites located in Switzerland and Slovenia, where ratios ranged from 0.52% to 3.25%.DiscussionThe study highlights how NPIs influenced C. pneumoniae epidemiology, with reduced detection during the pandemic and partial resurgence afterwards. Regional variations suggest differing NPI impacts and underscore the need for continued surveillance.
- MeSH
- Chlamydophila pneumoniae * isolation & purification genetics MeSH
- COVID-19 * epidemiology MeSH
- Chlamydophila Infections * epidemiology diagnosis MeSH
- Humans MeSH
- Pandemics MeSH
- Polymerase Chain Reaction MeSH
- SARS-CoV-2 MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Europe MeSH
- Taiwan MeSH
BackgroundOn 29 January 2024, the European Centre for Disease Prevention and Control distributed an alert about a metronidazole-resistant Clostridioides difficile outbreak of PCR ribotype (RT) 955 in England.AimWe aimed to investigate the presence of RT955 in Czech, Slovak and Polish C. difficile isolates and evaluate different culture media for detecting its metronidazole resistance.MethodsIsolates with binary toxin genes identified as 'unknown' by the WEBRIBO PCR ribotyping database up to 2023 were re-analysed after adding the RT955 profile to the database. The RT955 isolates were characterised by whole genome sequencing and tested for susceptibility to 15 antimicrobials.ResultsWe did not find RT955 in Czech (n = 6,661, 2012-2023) and Slovak (n = 776, 2015-2023) isolates, but identified 13 RT955 cases (n = 303, 2021-2023) in three hospitals in Poland. By whole genome multilocus sequence typing, 10 isolates clustered into one clonal complex including a sequence of United Kingdom strain ERR12670107, and shared similar antimicrobial resistance genes/mutations. All 13 isolates were resistant to ciprofloxacin/moxifloxacin, erythromycin/clindamycin and ceftazidime. All isolates had a mutation in the nimB gene promoter and in NimB (Tyr130Ser and Leu155Ile). The metronidazole resistance was detected in all isolates using brain-heart-infusion agar supplemented with haemin and Chocolate agar. Results were discrepant with the European Committee on Antimicrobial Susceptibility Testing-recommended Fastidious anaerobe agar and Brucella blood agar.ConclusionThe identification of clonally related haem-dependent metronidazole-resistant C. difficile RT955 in multiple hospitals indicates a need for prospective surveillance to estimate its prevalence in Europe.
- MeSH
- Anti-Bacterial Agents * pharmacology MeSH
- Drug Resistance, Bacterial * genetics MeSH
- Clostridioides difficile * genetics drug effects isolation & purification classification MeSH
- Disease Outbreaks MeSH
- Clostridium Infections * epidemiology microbiology drug therapy MeSH
- Humans MeSH
- Metronidazole * pharmacology MeSH
- Microbial Sensitivity Tests MeSH
- Multilocus Sequence Typing MeSH
- Polymerase Chain Reaction MeSH
- Ribotyping * MeSH
- Whole Genome Sequencing MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Czech Republic MeSH
- Poland MeSH
- Slovakia MeSH
Chronic bronchitis is increasingly reported as a healthcare challenge in clinical settings partially due to the disease's bad prognosis and unresponsiveness to therapy, including the ineffectiveness of glucocorticoids. The ineffectiveness could have a link with genetic polymorphism of receptor genes resulting in inappropriate glucocorticoid pharmacodynamics. We sought to identify the role of gene polymorphism in the response of patients with chronic bronchitis to prednisolone therapy. To do so, a total of 60 newly diagnosed chronic bronchitis patients enrolled in the present study. Prednisolone at a dose of 30mg/day for two weeks was given and respiratory parameters [forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), and FEV1/FVC were measured before and after therapy. Blood samples were withdrawn for genetic profiling of genes involved in glucocorticoids pharmacodynamics, including BCII (rs41423247), N363S (rs56149945), and ER22/23EK (rs6189/rs6190) measured for their homozygous versus heterozygous gene splice variants.Results: Gene splice variants for BCII (rs41423247), N363S (rs56149945), and ER22/23EK (rs6189/rs6190) homozygous (73.3%, 98.7%, and 95%) represented a higher percentage than heterozygous (26.7%, 1.7%, and 5%). The respiratory parameters FEV1, FVC, and FEV1/FVC have shown significantly (p<0.05) better values at baseline in homozygous versus heterozygous, correspondingly, the responsiveness to therapy has shown significantly (p<0.05) better values in homozygous versus heterozygous.Conclusion: The study has provided a good template for genetic behaviour toward individualised medicine in our locality providing that these genes could be a cornerstone for discovering issues related to the pharmacodynamics profiling of drugs in clinical settings.
- MeSH
- Bronchitis, Chronic * diagnosis genetics MeSH
- Glucocorticoids pharmacology MeSH
- Humans MeSH
- Polymerase Chain Reaction methods MeSH
- Polymorphism, Genetic genetics MeSH
- Prednisolone pharmacology therapeutic use MeSH
- Protein Isoforms genetics MeSH
- Receptors, Glucocorticoid * genetics drug effects MeSH
- Respiratory Function Tests methods MeSH
- Check Tag
- Humans MeSH
- Publication type
- Clinical Study MeSH
- Research Support, Non-U.S. Gov't MeSH
BACKGROUND: Filoviruses, including Ebola and Marburg viruses, cause severe hemorrhagic fever in humans and primates. These viruses pose significant threats to public health, making rapid and sensitive detection critical for controlling outbreaks. We developed and validated a hemi-nested generic PanFilo assay to detect all Ebola virus species, Marburg viruses, and recently discovered bat filoviruses. This assay was deployed to 15 European laboratories and evaluated through testing of eight non-infectious samples. OBJECTIVES: Laboratories were asked to determine the detection limit of positive controls and test all samples using the assay provided. The deployed assay enables direct Nanopore sequencing of PCR products, by using tagged primers during the second round of PCR. Sequencing of the samples was carried out on a voluntary basis. RESULTS: Multicenter validation revealed a 95 % limit of detection of 5309 RNA copies/μL for Ebola, 10,273 copies/μL for Marburg, and 2145 copies/μL for Mengla virus. In an implementation quality assessment, 93.3 % (84/90) of samples containing filovirus RNA were correctly identified and 100 % (30/30) of filovirus-negative samples were correctly identified. Thirteen laboratories sequenced PCR products, with nine identifying all positive samples correctly. CONCLUSION: The assay enables rapid and reliable detection of filoviruses, with sequencing capabilities for identifying both known and novel variants. This assay might be used for detection during the initial phase of an emerging filovirus outbreak, before a specific assay has been developed. However, our distribution across 15 laboratories revealed variability challenges due to reagents, human performance, and sequencing capacity, emphasizing the need for more training and standardization.
- MeSH
- Molecular Diagnostic Techniques methods MeSH
- Hemorrhagic Fever, Ebola * diagnosis virology MeSH
- Humans MeSH
- Limit of Detection MeSH
- Marburg Virus Disease * diagnosis virology MeSH
- Polymerase Chain Reaction * methods MeSH
- RNA, Viral genetics MeSH
- Sensitivity and Specificity MeSH
- Ebolavirus * isolation & purification genetics MeSH
- Marburgvirus * isolation & purification genetics MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Multicenter Study MeSH
- Validation Study MeSH
- Geographicals
- Europe MeSH
Článek se zaměřuje na rutinně nekultivovatelné treponemové infekce, které i nadále představují celosvětový problém. Pojednává o současných poznatcích v oblasti molekulární genetiky a zdůrazňuje důležitost implementace aktuálních výzkumů do dermatovenerologie. Soustředí se na využití metody PCR v diagnostice a propojení klinické medicínské praxe s vědeckými poznatky v oblasti molekulární genetiky u treponemových infekcí.
The article deals with routinely uncultivable treponemal infections that continue to be a global problem. The current knowledge in the field of molecular genetics is presented and the importance of implementing current research into dermatovenerology is emphasized. The article focuses on the use of the PCR method in diagnosis as well as on linking clinical medical practice with scientific knowledge in the field of molecular genetics in treponemal infections.
Whippleova choroba (WD) je vzácné multisystémové onemocnění způsobené aktinomycetou Tropheryma whipplei s varia- bilním klinickým průběhem. V prodromálním stadiu se typicky projevuje artralgiemi, v symptomatickém stadiu pacienti nejčastěji trpí gastrointestinálními projevy (chronický průjem, abdominalgie, váhový úbytek). Základem diagnostiky je endoskopická biopsie duodena. Definitivním potvrzením diagnózy je v současnosti PCR. Léčba je založena na dlouhodobé antibiotické terapii. Tato kazuistika pojednává o 65leté ženě s nově diagnostikovanou WD s těžkou malnutricí, u které se manifestovaly revmatologické a hematologické projevy, a popisuje naši terapeutickou a nutriční intervenci.
Whipple's Disease (WD) is a rare multisystem disorder caused by the actinomycete Tropheryma whipplei, characterized by a diverse clinical presentation. The prodromal stage is often characterized by arthralgia, while the symptomatic stage predominantly manifests with gastrointestinal symptoms such as chronic diarrhea, abdominal pain, and weight loss. Duodenal biopsy remains the cornerstone of diagnosis, with PCR analysis providing a definitive confirmation. Treatment involves long-term antibiotic therapy. This case report describes a 65-year-old woman newly diagnosed with WD, presenting with severe malnutrition and notable rheumatological and hematological symptoms, outlining our therapeutic and nutritional interventions.
- MeSH
- Ceftriaxone administration & dosage therapeutic use MeSH
- Humans MeSH
- Malnutrition etiology MeSH
- Polymerase Chain Reaction MeSH
- Aged MeSH
- Tropheryma MeSH
- Whipple Disease * diagnosis drug therapy pathology MeSH
- Check Tag
- Humans MeSH
- Aged MeSH
- Female MeSH
- Publication type
- Case Reports MeSH
Background: Stenotrophomonas infections are becoming more widespread around the world and can be counted as a "newly emerging pathogen of concern". The present study aimed to detect a variety of Stenotrophomonas species (S. maltophilia) using specific 23S rRNA gene primers and investigate their multi-drug resistance potential.Methods: This study includes 375 clinical samples from different clinical sources 175 from males and 200 from females collected from Mosul City Hospital. Identification of Stenotrophomonas was conducted through multiple steps including culturing methods, molecular methods in addition to some biochemical tests 11(3%) of isolates belonged to Stenotrophomonas maltophilia. The isolates understudy were tested for their ability to resist 10 different antibiotics using the Kirby-Bauer disk diffusion method.Results: The resistance rate to amoxicillin, gentamicin, and amikacin (100%), cefixime (91%), imipenem (64%), meropenem(55%), Azithromycin (36%), nalidixic acid and trimethoprim (18%), ciprofloxacin(0%). The virulence factors of S. maltophilia siderophores were found in all (11) isolates belonging to S. maltophilia at a percentage (100%). The result of PCR assay using specific primers designed for detecting 23S rRNA genes of S. maltophilia gives amplification for 11 isolates from 14 suspected isolates. Nucleic acid sequencing for the 23S rRNA gene shows that all isolates belong to S. maltophilia with a similarity rate (91-99) in NCBI.Because the 23S rRNA gene sequence in Stenotrophomonas species shows more variety in this location this study used specific 23S rRNA gene primers to identify S. maltophilia.Conclusion: The study used phenotypic and molecular diagnostic techniques to isolate the bacteria, including the S rRNA23 gene. The results emphasize the need for increased vigilance in hospitals to prevent the spread of antibiotic-resistant bacteria and the development of new treatment strategies.
- MeSH
- Drug Resistance, Microbial genetics MeSH
- Drug Resistance, Bacterial genetics MeSH
- Cross Infection genetics microbiology MeSH
- Clinical Studies as Topic methods MeSH
- Humans MeSH
- Microbiological Techniques methods MeSH
- Polymerase Chain Reaction methods MeSH
- RNA, Ribosomal, 23S * analysis genetics MeSH
- Siderophores analysis genetics MeSH
- Stenotrophomonas maltophilia * genetics pathogenicity MeSH
- Check Tag
- Humans MeSH
We designed and synthesized a set of four 2'-deoxyribonucleoside 5'-O-triphosphates (dNTPs) bearing cationic substituents (protonated amino, methylamino, dimethylamino and trimethylammonium groups) attached to position 5 of pyrimidines or position 7 of 7-deazapurines through hex-1-ynyl or propargyl linker. These cationic dNTPs were studied as substrates in enzymatic synthesis of modified and hypermodified DNA using KOD XL DNA polymerase. In primer extension (PEX), we successfully obtained DNA containing one, two, three, or (all) four modified nucleotides, each bearing a different cationic modification. The cationic dNTPs were somewhat worse substrates compared to previously studied dNTPs bearing hydrophobic or anionic modifications, but the polymerase was still able to synthesize sequences up to 73 modified nucleotides. We also successfully combined one cationic modification with one anionic and two hydrophobic modifications in PEX. In polymerase chain reaction (PCR), we observed exponential amplification only in the case of one cationic modification, while the combination of more cationic nucleotides gave either very low amplification or no PCR product. The hypermodified oligonucleotides prepared by PEX were successfully re-PCRed and sequenced by Sanger sequencing. Biophysical studies of hybridization, denaturation, and circular dichroism spectroscopy showed that the presence of cationic modifications increases the stability of duplexes.
- MeSH
- Deoxyribonucleotides metabolism chemistry MeSH
- DNA-Directed DNA Polymerase * metabolism chemistry MeSH
- DNA * chemistry biosynthesis metabolism MeSH
- Cations * chemistry MeSH
- Polymerase Chain Reaction MeSH
- Purines chemistry biosynthesis MeSH
- Pyrimidines chemistry MeSH
- Publication type
- Journal Article MeSH
