Seroprevalence of emerging hepatitis E virus in patients with acute hepatitis between 2004 and 2018 in Csongrád County, Hungary.

OBJECTIVES: Hepatitis E virus (HEV) has recently become endemic in Europe, however, it is often a remnant neglected by clinicians as the causative agent of acute and chronic hepatitis and is often misdiagnosed as a drug-induced liver injury. The infection rate in European pig farms is estimated to be around 15-20%, therefore, the primary source of HEV infections might be poorly prepared pork meat. As HEV infections may occur more often in clinical practice than previously thought, the present paper aims to analyse the seroprevalence of HEV in patients with acute hepatitis over a period of 14 years in Csongrád County, Hungary. METHODS: The sera of 4,270 hepatitis patients collected between 2004-2018 were tested for cumulative anti-HEV IgG/IgM. Furthermore, 170 IgM positive sera were tested for the presence of viral RNA by RT-qPCR. RESULTS: Between 2012-2018, the cumulative seroprevalence has increased 9.18 times, and between 2013-2018, IgM prevalence has increased 12.49 times. Viral RNA was detectable in 12.35% of IgM positive sera. CONCLUSION: The present paper presents data showing that the seroprevalence of hepatitis E virus has increased markedly over the course of the last decade in Hungary and in other European countries as well. The exact reason behind this phenomenon is yet to be determined. To assess the dynamics and the reason for this increase in prevalence, pan-European, multicentre studies should be conducted.

Genomic insights into the origin of farming in the ancient Near East.

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

Changes in resistance pattern of ESKAPE pathogens between 2010 and 2020 in the clinical center of University of Szeged, Hungary.

The acronym ESKAPE stands for six antibiotic-resistant bacterial pathogens namely, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. Monitoring their resistance is an important task for clinical microbiology laboratories. Our aim was to analyze the resistance patterns of these bacteria over ten years in clinical samples of our department. We examined the sample types from which these pathogens were most frequently isolated. The incidence of tests with resistant results for each pathogen in aggregate and the most important subgroups of each was also analyzed. We have also intended to predict the local priorities amongst these pathogens. The results of 1,268,126 antibiotic susceptibility tests performed on a total of 70,099 isolates over this period were examined. Most strains were derived from urine, blood culture, trachea, vagina, wounds, and abscesses. Prevalence of ESKAPE bacteria increased between 2011 and 2020 however, the steepest intensifications were seen in the cases of K. pneumoniae and P. aeruginosa. The number of antibiotic susceptibility tests with resistant results has also increased over the decade but the most notable increase was detected in E. faecium and A. baumannii. Based on the calculation of antimicrobial resistance index for each pathogen, the most serious challenges for us at present are A. baumannii, P. aeruginosa, and E. faecium and their multi-resistant forms. The theoretical prediction of proportion of resistant tests between 2020 and 2030 in our care area draws attention to a worrying trend in the cases of vancomycin-resistant E. faecium and carbapenem-resistant A. baumannii strains.

Viral gene expression profile of goose haemorrhagic polyomavirus in susceptible primary cells.

Routine culturing of goose haemorrhagic polyomavirus (GHPV) is cumbersome, and limited data are available about its replication and gene expression profile. In this study, goose embryo fibroblast cells were infected with GHPV for temporal measurement of the viral genome copy number and mRNA levels with quantitative PCR. Accumulation of small and large tumour antigen-encoding mRNAs was detected as early as 9 hours post-infection (hpi), while high level expression of the capsid protein encoding VP1-VP3, and ORF-X mRNAs was first detected at 24 hpi. Elevation of GHPV genome copy number was noted at 48 hpi. The results indicate that the gene expression profile of GHPV is similar to that described for mammalian polyomaviruses.RESEARCH HIGHLIGHTS GHPV was propagated in culture of primary goose embryo fibroblast cells.The transcription commenced before the onset of viral DNA replication.The transcription patterns of GHPV and mammalian polyomaviruses were comparable.

Europhile Public vs Eurosceptic Governing Elite in Hungary?

The threat of an epidemic narrows the scope for political competition. As Fidesz's position within the EU has weakened significantly with the withdrawal from the European People's Party, and the COVID-19 crisis is generating serious social tensions, the questions seem to be more open in the spring of 2022 than during the previous three elections.

Characterization of the genomic sequence of a novel CRESS DNA virus identified in Eurasian jay (Garrulus glandarius).

Circular replication associated protein (Rep)-encoding ssDNA (CRESS DNA) viruses have diverse genomic architecture and are widely distributed in different ecosystems. In this study we characterized the complete genomic sequence of a novel circovirus-like virus, Garrulus glandarius associated circular virus-1 (GgaCV-1). The genome size (1971 nt) and other features (the nonanucleotide, rolling circle replication motif and SF3 helicase motif) are also reminiscent of circoviruses. Similar genomes with uni-directionally localized and overlapping rep and cap genes are typical of type V CRESS DNA viruses that were identified in invertebrates and environmental samples of aquatic ecosystems. GgaCV-1 showed the highest aa identity with partial rep sequences detected in bat feces (77%) and with the rep (54%) and cap (42%) of Lake Sarah-associated circular virus-23 of New Zealand freshwater mussel origin. A dietary origin for GgaCV-1 could not be excluded as the virus was detected in the cloacal swab specimen of an Eurasian jay. Further studies may help to reveal the linkage among variable organisms regarding virus transmission.

Genome sequence of a mallard duck origin cyclovirus, DuACyV-1.

The genome sequence of a novel avian cyclovirus is described in this study. The genome size and orientation of predicted genes was similar to those described in other vertebrate and insect origin cycloviruses. The greatest genome sequence identity was shared with a dragonfly cyclovirus (nt, 60.6%). Phylogenetic analysis showed marginal relatedness with another avian cyclovirus, the chicken associated cyclovirus 1. In contrast, along a short fragment of the replication-associated protein coding gene (rep) (spanning nt 1240-1710) the duck origin cyclovirus was very similar to human origin and honey bee origin rep sequences (human - TN4, 98%; honey bee - hb10, 100%). Related cyclovirus strains existing amongst various animal species living in diverse ecosystems and separated by large geographic distances show the need for additional studies to better understand the ecology and epidemiology of cycloviruses.

Molecular genetic investigations on Balantidium ctenopharyngodoni Chen, 1955, a parasite of the grass carp (Ctenopharyngodon idella).

Balantidium ctenopharyngodoni is a common ciliate in Hungary, infecting the hindgut of grass carp (Ctenopharyngodon idella), a cyprinid fish of Chinese origin. Although data have already been presented on its occasional pathogenic effect on the endothelium of the host, generally it is a harmless inhabitant of the gut. Phylogenetic analysis of the 18S rDNA and ITS fragments of this protozoan proved that it is in the closest phylogenetic relationship with endocommensalist and symbiont ciliates of mammals feeding on large volumes of green forage, in a similar way as Balantidium spp. known from algae-eating marine fishes.

Coding-complete sequencing classifies parrot bornavirus 5 into a novel virus species.

In this study, we determined the sequence of the coding region of an avian bornavirus detected in a blue-and-yellow macaw (Ara ararauna) with pathological/histopathological changes characteristic of proventricular dilatation disease. The genomic organization of the macaw bornavirus is similar to that of other bornaviruses, and its nucleotide sequence is nearly identical to the available partial parrot bornavirus 5 (PaBV-5) sequences. Phylogenetic analysis showed that these strains formed a monophyletic group distinct from other mammalian and avian bornaviruses and in calculations performed with matrix protein coding sequences, the PaBV-5 and PaBV-6 genotypes formed a common cluster, suggesting that according to the recently accepted classification system for bornaviruses, these two genotypes may belong to a new species, provisionally named Psittaciform 2 bornavirus.

Sequence and phylogenetic analysis identifies a putative novel gyrovirus 3 genotype in ferret feces.

The genomic sequence of a novel gyrovirus (GyV) 3 strain was detected from the fecal sample of a pet ferret. The length (2,359 nt) and the basic genomic structure of this strain was very similar to that of the single known GyV3 reference strain, whereas the genome sequence identity between the two strains was only 76 %. Similarly, moderate sequence homology was found within the predicted protein coding regions, VP1 (nt, 72 %; aa, 76 %), VP2 (nt, 84 %; aa, 85 %), and VP3 (nt, 85 %; aa, 73 %). Sequence identities were lower when comparing our strain with other GyV species (48-65 % genome-wide nt identity). Phylogenetic analysis of the coding regions clustered the ferret origin GyV3 strain within Clade A. Although the available whole genomic sequence of novel GyVs permits limited conclusions to be drawn regarding the classification of the Hungarian GyV3 strain, our data indicate that this novel strain may be considered as a new genotype within GyV3. Further investigations are needed to reveal the genetic diversity and biological properties of newly described members of the Gyrovirus genus.

Molecular detection and characterization of human gyroviruses identified in the ferret fecal virome.

The recently described novel gyroviruses may infect chickens and/or humans; however, their pathogenic potential is unknown. In our metagenomic investigation, we detected many of the novel gyroviruses in the fecal viromes of ferrets with lymph node and organ enlargement. The complete genomic sequences of selected gyrovirus strains showed 90.7-99.4 % similarity to homologous reference gyrovirus strains. This study did not demonstrate an association between gyrovirus shedding from ferrets and the observed background disease; however, it provides evidence for genetic diversity among gyroviruses and raises the possibility that pet ferrets may transmit gyroviruses to heterologous hosts, e.g., humans.

Infection and colonization by Stenotrophomonas maltophilia: antimicrobial susceptibility and clinical background of strains isolated at a tertiary care centre in Hungary.

BACKGROUND: Stenotrophomonas maltophilia is an important opportunistic, mainly nosocomial pathogen that emerged in the last decades worldwide. Due to its inherent extended antibiotic resistance, therapeutic options are strongly limited. New resistance mechanisms in S. maltophilia make antibiotic therapy even more difficult. The aim of our study was to investigate the antimicrobial resistance of S. maltophilia isolates collected in our laboratory and to reveal related clinical background. METHOD: Consecutive non-duplicate S. maltophilia isolates (n = 160) were collected in a three-year period. Conventional methods, automated identification system and MALDI-TOF MS was used for identification, ERIC-PCR for genetic relationship analysis and broth microdilution method to determine the susceptibility for trimethoprim/sulfamethoxazole (SXT), ciprofloxacin, levofloxacin, moxifloxacin, colistin, doxycycline and tigecycline. Clinical final reports were used retrospectively to collect clinical information. RESULTS: ERIC-PCR revealed large heterogeneity. Trimethoprim/sulfamethoxazole, moxifloxacin and levofloxacin were found to be the most effective agents with MIC50/MIC90 0.5/1, 0.25/1, 1/2 mg/l, respectively. Seventy percent of patients with S. maltophilia infection were treated in intensive care units. All-cause mortality rate was 45%. Nearly 70% of the isolates were collected from polymicrobial infections/colonizations. CONCLUSIONS: Trimethoprim/sulfamethoxazole is the most potent antibiotic agent against S. maltophilia. In case of SXT hypersensitivity, intolerance or resistance, fluoroquinolones are alternative therapeutic options. Missing clinical breakpoints, consensus antibiotic susceptibility testing guidelines and clinical trials make the interpretation of antibiotic susceptibility testing results difficult. The indirect pathogenicity of S. maltophilia in polymicrobial infections or colonizations has to be taken into consideration.

Prescription of Rifampicin for Staphylococcus aureus Infections Increased the Incidence of Corynebacterium striatum with Decreased Susceptibility to Rifampicin in a Hungarian Clinical Center.

Several reports have suggested a role for Corynebacterium striatum as an opportunistic pathogen. The authors have conducted a retrospective study at the Clinical Center of the University of Szeged, Hungary, between 2012 and 2021 that revealed significantly increased rifampicin resistance in this species. This work aimed to investigate the reasons behind this phenomenon. The data were collected corresponding to the period between 1 January 2012 and 31 December 2021 at the Department of Medical Microbiology, University of Szeged. To characterize the resistance trends, the antibiotic resistance index was calculated for each antibiotic in use. Fourteen strains with different resistance patterns were further analyzed with Fourier-transform infrared spectroscopy using the IR Biotyper®. The decline in C. striatum sensitivity to rifampicin seen during the COVID-19 pandemic may have been attributable to the use of Rifadin® to treat concomitant Staphylococcus aureus infections. The fact that the IR Biotyper® typing method revealed that the rifampicin-resistant C. striatum strains were closely related supports this hypothesis. The IR Biotyper® infrared spectroscopy proved to be a modern and fast method to support effective antimicrobial stewardship programs.

Complete molecular genome analyses of equine rotavirus A strains from different continents reveal several novel genotypes and a largely conserved genotype constellation.

In this study, the complete genome sequences of seven equine group A rotavirus (RVA) strains (RVA/Horse-tc/GBR/L338/1991/G13P[18], RVA/Horse-wt/IRL/03V04954/2003/G3P[12] and RVA/Horse-wt/IRL/04V2024/2004/G14P[12] from Europe; RVA/Horse-wt/ARG/E30/1993/G3P[12], RVA/Horse-wt/ARG/E403/2006/G14P[12] and RVA/Horse-wt/ARG/E4040/2008/G14P[12] from Argentina; and RVA/Horse-wt/ZAF/EqRV-SA1/2006/G14P[12] from South Africa) were determined. Multiple novel genotypes were identified and genotype numbers were assigned by the Rotavirus Classification Working Group: R9 (VP1), C9 (VP2), N9 (NSP2), T12 (NSP3), E14 (NSP4), and H7 and H11 (NSP5). The genotype constellation of L338 was unique: G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11. The six remaining equine RVA strains showed a largely conserved genotype constellation: G3/G14-P[12]-I2/I6-R2-C2-M3-A10-N2-T3-E2/E12-H7, which is highly divergent from other known non-equine RVA genotype constellations. Phylogenetic analyses revealed that the sequences of these equine RVA strains are related distantly to non-equine RVA strains, and that at least three lineages exist within equine RVA strains. A small number of reassortment events were observed. Interestingly, the three RVA strains from Argentina possessed the E12 genotype, whereas the three RVA strains from Ireland and South Africa possessed the E2 genotype. The unusual E12 genotype has until now only been described in Argentina among RVA strains collected from guanaco, cattle and horses, suggesting geographical isolation of this NSP4 genotype. This conserved genetic configuration of equine RVA strains could be useful for future vaccine development or improvement of currently used equine RVA vaccines.

Mammal extinction facilitated biome shift and human population change during the last glacial termination in East-Central Europe.

The study of local extinction times, together with the associated environmental and human population changes in the last glacial termination, provides insights into the causes of mega- and microfauna extinctions. In East-Central (EC) Europe, groups of Palaeolithic humans were present throughout the last glacial maximum, but disappeared suddenly around 15,200 cal BP. In this study cave sediment profiles dated using radiocarbon techniques and a large set of mammal bones dated directly by AMS 14C were used to determine local extinction times. These were, in turn, compared to changes in the total megafauna population of EC Europe derived from coprophilous fungi, the Epigravettian population decline, quantitative climate models, pollen and plant macrofossil inferred climate, as well as to biome reconstructions. The results suggest that the population size of large herbivores decreased in the area after 17,700 cal BP, when temperate tree abundance and warm continental steppe cover both increased in the lowlands. Boreal forest expansion started around 16,200 cal BP. Cave sediments show the decline of narrow-headed vole and arctic lemming populations specifically associated with a tundra environment at the same time and the expansion of the common vole, an inhabitant of steppes. The last dated appearance of arctic lemming was at ~ 16,640 cal BP, while that of the narrow-headed vole at ~ 13,340, and the estimated extinction time of woolly mammoth was either at 13,830 (GRIWM) or 15,210 (PHASE), and reindeer at 11,860 (GRIWM) or 12,550 cal BP (PHASE). The population decline of the large herbivore fauna slightly preceded changes in terrestrial vegetation, and likely facilitated it via a reduction in the intensity of grazing and the concomitant accumulation of plant biomass. Furthermore, it is possible to conclude that the Late Epigravettian population had high degree of quarry-fidelity; they left the basin when these mammals vanished.

Comparison of four PCR and two point of care assays used in the laboratory detection of SARS-CoV-2.

Seeing the global emergence and the lack of a definitive cure for COVID-19, it is essential to find the most sensitive and specific detection method to identify infected patients in a timely manner. Our paper aims to compare the clinical sensitivity of different commercial RT-qPCR (Genesig, 1copy, DNA-Techonolgy and Charité primer-probe sets), isothermal PCR (Ustar Isothermal Amplification-Real Time Fluorescent Assay) and immunochromatographic antigen detection (BIOCREDIT COVID-19 Ag) assays developed to use in laboratory diagnosis of COVID-19. A total of 119 nasopharyngeal swab specimens were collected from symptomatic patients. A subset of samples, positive with two RT-qPCR assays were then tested with isothermal PCR and rapid antigen tests. Of the 119 specimens, 65 were positive by at least two PCR assays. All PCR assays showed substantial or perfect match, although some variations in the clinical performance was observed. Of the 37 and 32 remnant nasopharyngeal samples positive by RT-qPCR, respectively, three were positive by the BIOCREDIT COVID-19 Ag and 14 were detected by the isothermal amplification assay. In conclusion, in the clinical settings we recorded that each of the RT-qPCR assays was superior to other test formats, in particular, the routine use of the DNA-technology assay is recommended. Although alternative recommendations exist, we belive that the use of isothermal amplifiaction assays and antigen rapid tests for COVID-19 diagnosis can only serve as adjuncts while awaiting the PCR result because of their high false-negative rate.

Unexpected Diversity of Yeast Species in Esophageal Mycosis of Waterfowls.

This study was performed to evaluate the diversity and prevalence of yeasts associated with esophageal mycosis in domestic ducks and geese. Fungi were isolated from esophageal lesions of dead animals sent for microbiologic laboratory diagnosis. Species identification using a culture-dependent method was carried out by sequencing of the internal transcribed spacer (ITS)1-5.8S rRNA-ITS2 region. The most frequently isolated yeast was Candida albicans (43.1%) followed by Saccharomyces cerevisiae (17.6%), Candida kefyr (11.7%), Kazachstania bovina (11.7%), Candida lambica (3.9%), and single isolates (1.9%) representing Candida inconspicua, Candida rugosa, Candida pelliculosa, Candida krusei, Magnusiomyces capitatus, and Trichosporon asahii. Our results indicate that a number of potentially pathogenic yeast species can be isolated from esophageal mycosis of waterfowls, but additional studies are needed to make conclusions regarding their possible etiologic role in disease.

Occurrence and genetic diversity of CRESS DNA viruses in wild birds: a Hungarian study.

Circoviruses, cycloviruses and other circular, replication-associated protein-encoding single stranded (CRESS) DNA viruses have been detected in a variety of animal taxa. In this study, cloacal swab samples (n = 90) were examined for CRESS DNA viruses from 31 wild bird species living at various aquatic sites in Hungary to identify possible reservoirs of viruses pathogenic to domestic poultry. A total of 30 (33.3%) specimens tested positive with pan-CRESS DNA virus specific PCR. Goose circovirus (GoCV), Duck associated cyclovirus 1 (DuACyV-1) and Garrulus glandarius associated circular virus 1 (GgaCV-1) were detected in nine, three and two different bird species, respectively. Selected specimens were subjected to whole genome sequencing. The obtained sequence data revealed conserved gene structure within the identified virus species and detected homologous (within GoCV) and possible heterologous recombination (within DuACyV-1) events. Results presented here provide new information on the genomic diversity and evolution of selected CRESS DNA viruses.

Publisher Correction: Occurrence and genetic diversity of CRESS DNA viruses in wild birds: a Hungarian study.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

[Summary and lessons of the European and Hungarian measles situation]. / Az európai és a magyarországi kanyaróhelyzet összefoglalása és tanulságai.

Measles is one of the most serious preventable infectious diseases, which in our country were among the rare diseases in the last 10 to 20 years. One of the reasons for this is that the Hungarian population born after 1969 was vaccinated in almost 99 percent. The other reason is that in the period prior to vaccination era, the often-occurring measles epidemics left life-long immunity in the affected persons. Thus, natural and artificial immunizations provided extensive herd immunity. However, the ongoing measles epidemics in Europe have highlighted the fact that the symptoms and differential diagnosis related to measles have been relegated to the negligible category for the last 20 years. In addition to reviewing the consequences of the European measles pandemics in Hungary, the purpose of this paper is to revise and summarize the clinical and laboratory knowledge required to establish a definitive epidemiological control of measles. Orv Hetil. 2019; 160(20): 767-773.