Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens.

Phage therapy is gaining increasing interest in the fight against critically antibiotic-resistant nosocomial pathogens. However, the narrow host range of bacteriophages hampers the development of broadly effective phage therapeutics and demands precision approaches. Here, we combine large-scale phylogeographic analysis with high-throughput phage typing to guide the development of precision phage cocktails targeting carbapenem-resistant Acinetobacter baumannii, a top-priority pathogen. Our analysis reveals that a few strain types dominate infections in each world region, with their geographical distribution remaining stable within 6 years. As we demonstrate in Eastern Europe, this spatiotemporal distribution enables preemptive preparation of region-specific phage collections that target most local infections. Finally, we showcase the efficacy of phage cocktails against prevalent strain types using in vitro and animal infection models. Ultimately, genomic surveillance identifies patients benefiting from the same phages across geographical scales, thus providing a scalable framework for precision phage therapy.

Favipiravir does not improve viral clearance in mild to moderate COVID-19 - A systematic review and meta-analysis of randomized controlled trials.

Purpose: Favipiravir has been used in the therapy of COVID-19, including patients with mild to moderate symptoms in certain countries. The aim of our systematic review and meta-analysis was to investigate its efficacy and safety in mild-to-moderate COVID-19 infections. Methods: The PubMed, Embase, Web of Science, and Cochrane databases were systematically reviewed for articles reporting the results of randomized controlled trials published until January 6, 2023, resulting in the identification of 20 eligible studies. Results: There were no significant differences in viral clearance time (HR = 1.20, p = 0.09) compared to those without favipiravir therapy. However, in the subgroup analyses, favipiravir treatment significantly increased viral clearance by 59 % (HR = 1.59, p < 0.01) and 42 % (HR = 1.42, p < 0.01], I2 = 20 %) compared to the comparator group in patients with moderate severity of COVID-19 and in the inpatient care setting, respectively. Favipiravir had no beneficial effects in the case of patients with mild symptoms and treated in ambulatory care. Conclusions: The use of favipiravir is questionable in the treatment of outpatients with COVID-19 with mild symptoms. Moderate beneficial effects in the case of patients with moderate symptoms and inpatients should be treated with care due to the limitations of the analysed trials.

Image-based and machine learning-guided multiplexed serology test for SARS-CoV-2.

We present a miniaturized immunofluorescence assay (mini-IFA) for measuring antibody response in patient blood samples. The method utilizes machine learning-guided image analysis and enables simultaneous measurement of immunoglobulin M (IgM), IgA, and IgG responses against different viral antigens in an automated and high-throughput manner. The assay relies on antigens expressed through transfection, enabling use at a low biosafety level and fast adaptation to emerging pathogens. Using severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the model pathogen, we demonstrate that this method allows differentiation between vaccine-induced and infection-induced antibody responses. Additionally, we established a dedicated web page for quantitative visualization of sample-specific results and their distribution, comparing them with controls and other samples. Our results provide a proof of concept for the approach, demonstrating fast and accurate measurement of antibody responses in a research setup with prospects for clinical diagnostics.

Impact of the COVID-19 Pandemic on Ambulatory Care Antibiotic Use in Hungary: A Population-Based Observational Study.

The COVID-19 pandemic and related restrictions have potentially impacted the use of antibiotics. We aimed to analyze the use of systemic antibiotics (J01) in ambulatory care in Hungary during two pandemic years, to compare it with pre-COVID levels (January 2015-December 2019), and to describe trends based on monthly utilization. Our main findings were that during the studied COVID-19 pandemic period, compared to the pre-COVID level, an impressive 23.22% decrease in the use of systemic antibiotics was detected in ambulatory care. A significant reduction was shown in the use of several antibacterial subgroups, such as beta-lactam antibacterials, penicillins (J01C, -26.3%), and quinolones (J01M, -36.5%). The trends of antibiotic use moved in parallel with the introduction or revoking of restriction measures with a nadir in May 2020, which corresponded to a 55.46% decrease in use compared to the previous (pre-COVID) year's monthly means. In general, the systemic antibiotic use (J01) was lower compared to the pre-COVID periods' monthly means in almost every studied pandemic month, except for three months from September to November in 2021. The seasonal variation of antibiotic use also diminished. Active agent level analysis revealed an excessive use of azithromycin, even after evidence of ineffectiveness for COVID-19 emerged.

Antibiotic use in elderly patients in ambulatory care: A comparison between Hungary and Sweden.

Background: The elderly use antibiotics frequently due to their increasing infection susceptibility. Given the high and increasing proportion of elderly in the population, their antibiotic use is substantial. Objective: This study aimed to compare antibiotic use in the elderly in the ambulatory care sector between Hungary and Sweden. Methods: This retrospective, descriptive, cross-national, comparative study included antibacterial use data from the Hungarian National Health Insurance Fund and the Swedish eHealth Agency. Antibiotic use (anatomical therapeutical chemical: J01) was expressed as the number of prescriptions/1000 inhabitants/year or month and was further stratified by age and sex. Results: Antibiotic exposure was higher in the Hungarian elderly population (649.8 prescriptions/1000 inhabitants/year) compared to its Swedish counterparts (545.0 prescriptions/1000 inhabitants/year). Hungary had a similar scale of antibacterial exposure across all elderly age subgroups, with different trends in males and females, while Sweden had a stepwise increase in antibiotic exposure by age in both sexes. The seasonal fluctuation was high in Hungary and reached a peak of 80.7 prescriptions/1000 inhabitants/month in January 2017, while even antibiotic use was detected throughout the year in Sweden. The pattern of antibiotic use in the elderly considerably differed between the two countries. Penicillin and beta-lactamase combinations, such as co-amoxiclav, were more frequently used in Hungary than in Sweden (19.08% vs 1.83% of corresponding total ambulatory antibiotic use). Likewise, quinolones were more commonly used in Hungary than in Sweden (34.53% vs. 9.98). The elderly in Sweden were mostly prescribed narrow spectra penicillins (26.71% vs. 0.29% in Hungary). Conclusion: This cross-national comparison revealed important differences in all aspects of antibiotic use in the elderly between the two countries. The identical scale and pattern of antibiotic use cannot be anticipated due to the poorer health status of the Hungarian elderly population. However, the substantial differences indicate some room for improvement in the antibiotic prescription for the Hungarian elderly.

Prescribing Patterns and Variations of Antibiotic Use for Children in Ambulatory Care: A Nationwide Study.

The aim of this study was to analyse characteristics of paediatric antibiotic use in ambulatory care in Hungary. Data on antibiotics for systemic use dispensed to children (0-19 years) were retrieved from the National Health Insurance Fund. Prescribers were categorised by age and specialty. Antibiotic use was expressed as the number of prescriptions/100 children/year or month. For quality assessment, the broad per narrow (B/N) ratio was calculated as defined by the European Surveillance of Antimicrobial Consumption (ESAC) network. Paediatric antibiotic exposure was 108.28 antibiotic prescriptions/100 children/year and was the highest in the age group 0-4 years. Sex differences had heterogenous patterns across age groups. The majority of prescriptions were issued by primary care paediatricians (PCP). The use of broad-spectrum agents dominated, co-amoxiclav alone being responsible for almost one-third of paediatric antibiotic use. Elderly physicians tended to prescribe less broad-spectrum agents. Seasonal variation was found to be substantial: antibiotic prescribing peaked in January with 16.6 prescriptions/100 children/month, while it was the lowest in July with 4 prescriptions/100 children/month. Regional variation was prominent with an increasing west to east gradient (max: 175.6, min: 63.8 prescriptions/100 children/year). The identified characteristics of paediatric antibiotic use suggest that prescribing practice should be improved.

The characteristics and trends of Hungarian outpatient antibiotic use (2010­2019) / Az antibiotikum ambuláns alkalmazásának jellemzoi és tendenciái Magyarországon (2010-2019).

Összefoglaló. Bevezetés: Az antibiotikumok észszeru alkalmazása kulcsfontosságú a hatékonyságuk megorzésében és a néhol kritikus méreteket ölto antibiotikumrezisztencia visszaszorításában. Célkituzés: A hazai ambuláns antibiotikumfelhasználás jellemzoinek, trendjeinek bemutatása. Módszer: A 2010 és 2019 közötti idoszakra vonatkozó, dobozszámban kifejezett ambuláns szisztémás antibiotikumfelhasználási adatokat - a WHO 2019. évi indexe alapján - "defined daily dose" (DDD - napi átlagdózis) egységbe konvertáltuk. Standardizált technikai egységünk a DDD/1000 fo/nap volt (DID). Az antibiotikumfelhasználás értékelésére nemzetközileg elfogadott minoségi indikátorokat alkalmaztunk. Eredmények: Az antibiotikumfelhasználás mértéke kismértéku ingadozást mutatott (min.: 12,9 DID, max.: 14,7 DID), viszont a szezonális ingadozás a teljes megfigyelt idoszakban jelentos mértéku volt. A széles versus szuk spektrumú béta-laktámok és makrolidek felhasználási hányadosa évrol évre tovább emelkedett (2010: 13,3 vs. 2019: 71,6), a fluorokinolonok alkalmazási aránya továbbra is meghatározó (2010: 14,3%, 2019: 14,5%). A vizsgált 12 minoségi indikátor közül a tanulmány nyitó évében 4, a tanulmány záró évében 6 indikátor esetében a legkedvezotlenebbül teljesíto európai országok közé tartoztunk. Megbeszélés: A hazai antibiotikumalkalmazás mértéke európai mérce szerint nem magas, de csökkentésére látszik lehetoség; mintázata szuboptimális, és az évek során kedvezotlen irányba változott. Következtetés: A kapott antibiotikumfelhasználási adatok s azok értelmezése alapján rendkívül sürgeto morális kötelesség a szakmai és hatósági intervenciókra épülo hazai antibiotikumstratégia és -akcióterv mielobbi kidolgozása, implementálása. Orv Hetil. 2022; 163(4): 140-149. INTRODUCTION: Prudent antibiotic use is an important tool to preserve their effectiveness as well as reverse and confine antibiotic resistance. OBJECTIVE: To evaluate the trends and characteristics of Hungarian outpatient antibiotic use. METHODS: Crude, package level antibiotic sales data for the period 2010-2019 were converted into DDD (defined daily dose) and were standardized for 1000 inhabitants and per year (ATC-DDD index, version 2019). Internationally validated drug-specific quality indicators were used to evaluate antibiotic use. RESULTS: The scale of antibiotic use was stagnating with minimal fluctuation (min.: 12.9 DID, max.: 14.7 DID), and with high intra-year seasonality index. The ratio of the consumption of broad to narrow spectrum beta-lactams and macrolides increased gradually from year to year (2010: 13.3 vs. 2019: 71.6) and the relative consumption of fluoroquinolones is still remarkable (2010: 14.3%, 2019: 14.5%). Out of the twelve surveyed drug-specific quality indicators in the first and last year of analysis, we were ranked among the weakest European countries in the case of four and six indicators, respectively. DISCUSSION: The scale of Hungarian outpatient antibiotic use is not high, in European comperison, but has some reserve capacity for reduction. The pattern of Hungarian antibiotic use is suboptimal and had further decreased quality through the years. CONCLUSION: Based on the recorded data of antibiotic use and their interpretation, the development of national antibiotic strategy (including both professional and authority interventions) is a pressing moral obligation. Orv Hetil. 2021; 163(4): 140-149.

Impaired cytoplasmic domain interactions cause co-assembly defect and loss of function in the p.Glu293Lys KNCJ2 variant isolated from an Andersen-Tawil syndrome patient.

AIMS: Subunit interactions at the cytoplasmic domain interface (CD-I) have recently been shown to control gating in inward rectifier potassium channels. Here we report the novel KCNJ2 variant p.Glu293Lys that has been found in a patient with Andersen-Tawil syndrome type 1 (ATS1), causing amino acid substitution at the CD-I of the inward rectifier potassium channel subunit Kir2.1. Neither has the role of Glu293 in gating control been investigated nor has a pathogenic variant been described at this position. This study aimed to assess the involvement of Glu293 in CD-I subunit interactions and to establish the pathogenic role of the p.Glu293Lys variant in ATS1. METHODS AND RESULTS: The p.Glu293Lys variant produced no current in homomeric form and showed dominant-negative effect over wild-type (WT) subunits. Immunocytochemical labelling showed the p.Glu293Lys subunits to distribute in the subsarcolemmal space. Salt bridge prediction indicated the presence of an intersubunit salt bridge network at the CD-I of Kir2.1, with the involvement of Glu293. Subunit interactions were studied by the NanoLuc® Binary Technology (NanoBiT) split reporter assay. Reporter constructs carrying NanoBiT tags on the intracellular termini produced no bioluminescent signal above background with the p.Glu293Lys variant in homomeric configuration and significantly reduced signals in cells co-expressing WT and p.Glu293Lys subunits simultaneously. Extracellularly presented reporter tags, however, generated comparable bioluminescent signals with heteromeric WT and p.Glu293Lys subunits and with homomeric WT channels. CONCLUSIONS: Loss of function and dominant-negative effect confirm the causative role of p.Glu293Lys in ATS1. Co-assembly of Kir2.1 subunits is impaired in homomeric channels consisting of p.Glu293Lys subunits and is partially rescued in heteromeric complexes of WT and p.Glu293Lys Kir2.1 variants. These data point to an important role of Glu293 in mediating subunit assembly, as well as in gating of Kir2.1 channels.