TarBase-v9.0 extends experimentally supported miRNA-gene interactions to cell-types and virally encoded miRNAs.

TarBase is a reference database dedicated to produce, curate and deliver high quality experimentally-supported microRNA (miRNA) targets on protein-coding transcripts. In its latest version (v9.0, https://dianalab.e-ce.uth.gr/tarbasev9), it pushes the envelope by introducing virally-encoded miRNAs, interactions leading to target-directed miRNA degradation (TDMD) events and the largest collection of miRNA-gene interactions to date in a plethora of experimental settings, tissues and cell-types. It catalogues ∼6 million entries, comprising ∼2 million unique miRNA-gene pairs, supported by 37 experimental (high- and low-yield) protocols in 172 tissues and cell-types. Interactions are annotated with rich metadata including information on genes/transcripts, miRNAs, samples, experimental contexts and publications, while millions of miRNA-binding locations are also provided at cell-type resolution. A completely re-designed interface with state-of-the-art web technologies, incorporates more features, and allows flexible and ingenious use. The new interface provides the capability to design sophisticated queries with numerous filtering criteria including cell lines, experimental conditions, cell types, experimental methods, species and/or tissues of interest. Additionally, a plethora of fine-tuning capacities have been integrated to the platform, offering the refinement of the returned interactions based on miRNA confidence and expression levels, while boundless local retrieval of the offered interactions and metadata is enabled.

Intubation Decision Based on Illness Severity and Mortality in COVID-19: An International Study.

OBJECTIVES: To evaluate the impact of intubation timing, guided by severity criteria, on mortality in critically ill COVID-19 patients, amidst existing uncertainties regarding optimal intubation practices. DESIGN: Prospective, multicenter, observational study conducted from February 1, 2020, to November 1, 2022. SETTING: Ten academic institutions in the United States and Europe. PATIENTS: Adults (≥ 18 yr old) confirmed with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and hospitalized specifically for COVID-19, requiring intubation postadmission. Exclusion criteria included patients hospitalized for non-COVID-19 reasons despite a positive SARS-CoV-2 test. INTERVENTIONS: Early invasive mechanical ventilation (EIMV) was defined as intubation in patients with less severe organ dysfunction (Sequential Organ Failure Assessment [SOFA] < 7 or Pa o2 /F io2 ratio > 250), whereas late invasive mechanical ventilation (LIMV) was defined as intubation in patients with SOFA greater than or equal to 7 and Pa o2 /F io2 ratio less than or equal to 250. MEASUREMENTS AND MAIN RESULTS: The primary outcome was mortality within 30 days of hospital admission. Among 4464 patients, 854 (19.1%) required mechanical ventilation (mean age 60 yr, 61.7% male, 19.3% Black). Of those, 621 (72.7%) were categorized in the EIMV group and 233 (27.3%) in the LIMV group. Death within 30 days after admission occurred in 278 patients (42.2%) in the EIMV and 88 patients (46.6%) in the LIMV group ( p = 0.28). An inverse probability-of-treatment weighting analysis revealed a statistically significant association with mortality, with patients in the EIMV group being 32% less likely to die either within 30 days of admission (adjusted hazard ratio [HR] 0.68; 95% CI, 0.52-0.90; p = 0.008) or within 30 days after intubation irrespective of its timing from admission (adjusted HR 0.70; 95% CI, 0.51-0.90; p = 0.006). CONCLUSIONS: In severe COVID-19 cases, an early intubation strategy, guided by specific severity criteria, is associated with a reduced risk of death. These findings underscore the importance of timely intervention based on objective severity assessments.

Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population.

BACKGROUND: Expression quantitative trait loci (eQTL) studies provide insights into regulatory mechanisms underlying disease risk. Expanding studies of gene regulation to underexplored populations and to medically relevant tissues offers potential to reveal yet unknown regulatory variants and to better understand disease mechanisms. Here, we performed eQTL mapping in subcutaneous (S) and visceral (V) adipose tissue from 106 Greek individuals (Greek Metabolic study, GM) and compared our findings to those from the Genotype-Tissue Expression (GTEx) resource. RESULTS: We identified 1,930 and 1,515 eGenes in S and V respectively, over 13% of which are not observed in GTEx adipose tissue, and that do not arise due to different ancestry. We report additional context-specific regulatory effects in genes of clinical interest (e.g. oncogene ST7) and in genes regulating responses to environmental stimuli (e.g. MIR21, SNX33). We suggest that a fraction of the reported differences across populations is due to environmental effects on gene expression, driving context-specific eQTLs, and suggest that environmental effects can determine the penetrance of disease variants thus shaping disease risk. We report that over half of GM eQTLs colocalize with GWAS SNPs and of these colocalizations 41% are not detected in GTEx. We also highlight the clinical relevance of S adipose tissue by revealing that inflammatory processes are upregulated in individuals with obesity, not only in V, but also in S tissue. CONCLUSIONS: By focusing on an understudied population, our results provide further candidate genes for investigation regarding their role in adipose tissue biology and their contribution to disease risk and pathogenesis.

Circulating suPAR associates with severity and in-hospital progression of COVID-19.

BACKGROUND: COVID-19 disease progression is characterized by hyperinflammation and risk stratification may aid in early aggressive treatment and advanced planning. The aim of this study was to assess whether suPAR and other markers measured at hospital admission can predict the severity of COVID-19. METHODS: The primary outcome measure in this international, multi-centre, prospective, observational study with adult patients hospitalized primarily for COVID-19 was the association of WHO Clinical Progression Scale (WHO-CPS) with suPAR, ferritin, CRP, albumin, LDH, eGFR, age, procalcitonin, and interleukin-6. Admission plasma suPAR levels were determined using the suPARnostic® ELISA and suPARnostic® Turbilatex assays. RESULTS: Seven hundred and sixty-seven patients, 440 (57.4%) males and 327 (42.6%) females, were included with a median age of 64 years. Log-suPAR levels significantly correlated with WHO-CPS score, with each doubling of suPAR increasing the score by one point (p < .001). All the other markers were also correlated with WHO-CPS score. Admission suPAR levels were significantly lower in survivors (7.10 vs. 9.63, 95% CI 1.47-3.59, p < .001). A linear model (SALGA) including suPAR, serum albumin, serum lactate dehydrogenase, eGFR, and age can best estimate the WHO-CPS score and survival. Combining all five parameters in the SALGA model can improve the accuracy of discrimination with an AUC of 0.80 (95% CI: 0.759-0.836). CONCLUSIONS: suPAR levels significantly correlated with WHO-CPS score, with each doubling of suPAR increasing the score by one point. The SALGA model may serve as a quick tool for predicting disease severity and survival at admission.

Prevalence of human papillomavirus and subtype distribution in male partners of women with cervical intraepithelial neoplasia (CIN): a systematic review.

BACKGROUND: Human Papillomavirus (HPV) infection is estimated to be the most common sexually transmitted infection. The present systematic review summarizes data regarding the prevalence of HPV and the distribution of subtypes in heterosexual male partners of women, who were diagnosed with any grade of cervical intraepithelial neoplasia (CIN). METHODS: We conducted a systematic review of the literature by Medline and Google Scholar databases using the terms "Human Papillomavirus" or "HPV" plus "men" or "male partners" or "women with CIN". We included original published English-language articles published from 1/1/2000 until 1/1/2018 that had screened male partners of women with CIN using HPV DNA testing. We excluded studies that they overlapped with other included studies or were unrelated to the study subject. RESULTS: We included a total of 12 publications, which reported the prevalence of HPV in free-clinical signs male partners of women with CIN. The largest proportion of the studies were from South America (seven studies), and the rest from Europe. The mean age of participants was 35.18 + - 3.47 years. HPV prevalence ranged from 12.9 to 86%; the total HPV prevalence among the studies was 49.1%, while ten out twelve studies (83.3%) demonstrated prevalence > 20%. Between the studies, the distribution of HPV subtypes varied on the basis of the method used, on the population and on the geographic region. A great variety of subtypes were detected, including 6, 11, 16, 18, 31, 33, 40, 42, 45, 51, 52, 53, 54, 56, 57, 58, 59, 61, 62, 66, 68, 81 and 83. In six studies the HPV 16 was the most frequent, while in two others the HPV 6 and HPV 83. CONCLUSIONS: Until now, there are not precise screening or surveillance guidelines for the management of partners of women with CIN. This population is frequently colonized by various HPV subtypes and therefore need to be screened in an effort to reduce the infection in both sexes. The screening test could include detection/identification of HPV subtypes by a molecular assay, followed by peniscopy only in the positive cases.

Diversity of Bacterial Clones and Plasmids of NDM-1 Producing Escherichia coli Clinical Isolates in Central Greece.

The objective of the present study was to genetically characterize ten NDM-1 producing Escherichia coli isolates, recovered from patients in a hospital in Central Greece during the period 2017 to 2021.The isolates were studied by whole genome sequencing to obtain multi-locus sequencing typing (MLST), identification of blaNDM1-environment, resistome and plasmid content. MLST analysis showed the presence of eight sequence types: ST46* (two isolates), ST46, ST744, ST998, ST410, ST224, ST4380, ST683 and ST12 (one isolate each). Apart of the presence of blaNDM-1, the isolates carried a combination of various to ß-lactams encoding resistance genes: blaTEM-1B, blaCTX-15, blaOXA-1, blaVIM-1, blaSHV-5, blaOXA-16, blaOXA-10 and blaVEB-1. Additionally, plurality of resistance genes to aminoglycosides, macrolides, rifamycin, phenicols, sulfonamides and tetracycline was detected. The presence of multiple replicons was observed, with predominance of IncFII and IncFIB. Analysis of blaNDM-1 genetic environment of the isolates showed that seven had 100% identity with the pS-3002cz plasmid (Accession Number KJ 958927), two with the pB-3002cz plasmid (Accession Number KJ958926) and one with the pEc19397-131 plasmid (Accession Number MG878866). Τhis latter plasmid was derived by the fusion of two, previously identified, plasmids, pAMPD2 and pLK75 (Accession Numbers CP078058 and KJ440076, respectively). The diversity of clones and plasmids of NDM-1 producing E. coli isolated from patients in Greece indicates a continuous horizontal gene transfer.

Detection of Zoonotic Gastrointestinal Pathogens in Dairy Sheep and Goats by Using FilmArray® Multiplex-PCR Technology.

The objectives of this study were (a) to detect gastrointestinal pathogens in faecal samples of sheep and goats using the FilmArray® GI Panel and (b) to evaluate factors that were associated with their presence. Faecal samples from ewes or does in 70 sheep flocks and 24 goat herds in Greece were tested for the presence of 22 gastrointestinal pathogens by means of the BioFire® FilmArray® Gastrointestinal (GI) Panel. The most frequently detected pathogens were Shiga-like toxin-producing Escherichia coli stx1/stx2 (94.7% of farms), Giardia lamblia (59.6%), and Campylobacter spp. (50.0% of farms). Other pathogens detected were Cryptosporidium spp., Salmonella spp., enterotoxigenic E. coli lt/st, Yersinia enterocolitica, E. coli O157, Rotavirus A, Shigella/enteroinvasive E. coli, and Plesiomonasshigelloides. There was a difference in the prevalence of detection of pathogens between sheep and goat farms only for Salmonella spp.: 18.3% versus 0.0%, respectively. Mixed infections were detected in 76 farms (80.9% of farms), specifically 57 sheep flocks and 19 goat herds, with on average, 2.5 ± 0.1 pathogens detected per farm. The body condition score of ewes in farms, in which only one pathogen was detected in faecal samples, was significantly higher than that of ewes in farms, in which at least two pathogens were detected: 2.55 ± 0.11 versus 2.31 ± 0.04. In sheep flocks, the number of pathogens in faecal samples was significantly higher in farms with semi-extensive management. In goat herds, the number of pathogens in faecal samples was positively correlated with average precipitation and inversely correlated with temperature range in the respective locations.

Zoonotic Problems Reported by Sheep and Goat Farmers and Factors Potentially Contributing to the Occurrence of Brucellosis among Them.

The study aimed to investigate the occurrence of zoonotic problems reported by dairy small ruminant farmers in Greece and to study potential associations with socio-demographic characteristics of the farmers and management practices applied in the farms. A countrywide investigation was performed in 325 sheep and 119 goat farms in the 13 administrative regions of Greece. The selected farms were visited and interviews were conducted with respective farmers. The occurrence of zoonotic problems in the farmers was recorded. A total biosecurity score (0−6) was devised, based on biosecurity practices followed in farms. Sixty-seven farmers (15.10%, 95% confidence intervals (CI): 12.1−18.7%) reported experiencing a zoonotic problem. Most of the farmers (n = 57) (85.1%, 95% CI: 74.76−91.7%, of those with a zoonotic problem) (12.8%, 95% CI: 10.0−16.3%, of all) reported that the zoonotic problem had been brucellosis. Odds ratio for the occurrence of brucellosis in goat farmers was 1.879 (95% CI: 1.051−3.359) compared to the occurrence of the infection in sheep farmers (p = 0.033). For the outcome 'occurrence of brucellosis' in sheep farmers, the application of hand-milking, the availability of a separate lambing area and the presence of cats in the farm emerged as significant (p < 0.01); for the same outcome in goat farmers, only the availability of a separate kidding area emerged as significant (p = 0.001). The mean biosecurity score in farms in the continental area of the country was significantly higher than in the islands: 3.45 ± 0.05 versus 2.76 ± 0.28, respectively (p = 0.006), whilst there was also a significantly higher score in farms, where the farmer reported occurrence of brucellosis: 3.68 ± 0.15 versus 3.34 ± 0.06 in farms, where the farmer did not report such an incident (p = 0.042). In farms, where the above predictors prevail, farmers should be warned of an increased potential risk for human infection and biosecurity measures should be implemented and tightened.

Isolation of Listeria ivanovii from Bulk-Tank Milk of Sheep and Goat Farms-From Clinical Work to Bioinformatics Studies: Prevalence, Association with Milk Quality, Antibiotic Susceptibility, Predictors, Whole Genome Sequence and Phylogenetic Relationships.

A cross-sectional study was performed in 325 sheep and 119 goat dairy farms in Greece. Samples of bulk-tank milk were examined by standard microbiological techniques for Listeria spp. Listeria monocytogenes was isolated from one (0.3%) and Listeria ivanovii from three (0.9%) sheep farms. No associations between the isolation of L. monocytogenes or L. ivanovii and milk quality were found. No resistance to antibiotics was identified. Three variables emerged as significant predictors of isolation of the organism: the presence of pigs, low average relative humidity and a high number of ewes on the farm. The three L. ivanovii isolates were assessed in silico for identification of plasmids, prophages, antibiotic resistance genes, virulence factors, CRISPRs and CAS genes. Phylogenetic analysis using the core genome revealed that the three strains belonged to the L. ivanovii subsp. ivanovii branch and were especially close to the PAM 55 strain. All strains of the branch appeared to be very similar, with the distance between them being small.

Clostridioides difficile as a Dynamic Vehicle for the Dissemination of Antimicrobial-Resistance Determinants: Review and In Silico Analysis.

The present paper is divided into two parts. The first part focuses on the role of Clostridioides difficile in the accumulation of genes associated with antimicrobial resistance and then the transmission of them to other pathogenic bacteria occupying the same human intestinal niche. The second part describes an in silico analysis of the genomes of C. difficile available in GenBank, with regard to the presence of mobile genetic elements and antimicrobial resistance genes. The diversity of the C. difficile genome is discussed, and the current status of resistance of the organisms to various antimicrobial agents is reviewed. The role of transposons associated with antimicrobial resistance is appraised; the importance of plasmids associated with antimicrobial resistance is discussed, and the significance of bacteriophages as a potential shuttle for antimicrobial resistance genes is presented. In the in silico study, 1101 C. difficile genomes were found to harbor mobile genetic elements; Tn6009, Tn6105, CTn7 and Tn6192, Tn6194 and IS256 were the ones more frequently identified. The genes most commonly harbored therein were: ermB, blaCDD, vanT, vanR, vanG and vanS. Tn6194 was likely associated with resistance to erythromycin, Tn6192 and CTn7 with resistance to the ß-lactams and vancomycin, IS256 with resistance to aminoglycoside and Tn6105 to vancomycin.

Sinus bradycardia is associated with poor outcome in critically ill patients with COVID-19 due to the B.1.1.7 Lineage.

The progress of COVID-19 from moderate to severe may be precipitous, while the characteristics of the disease are heterogenous. The aim of this study was to describe the development of sinus bradycardia in critically ill patients with COVID-19 and its association with outcome in outbreak due to the SARS-CoV-2 B.1.1.7 Lineage. We leveraged the multi-center SuPAR in Adult Patients With COVID-19 (SPARCOL) study and identified patients who required admission to intensive care unit (ICU). Inclusion criteria were: (a) adult (≥18 years old) patients hospitalized primarily for COVID-19; (b) a confirmed SARS-CoV-2 infection diagnosed through reverse transcriptase polymerase chain reaction test of nasopharyngeal or oropharyngeal samples; and (c) at least one blood sample collected at admission and stored for suPAR, hs-CRP, and ferritin testing. All patients had continuous heart rate monitoring during hospitalization. In total, 81 patients were included. Of them, 17 (21 %) and 64 (79 %) were intubated and admitted to the ICU during the first and second wave, respectively. Two (12 %) and 62 (97 %) developed bradycardia before ICU admission, respectively (p < 0.001). Patients with bradycardia had increased suPAR (p < 0.001) and hs-CRP level (p < 0.001). Infusion of isoprenaline and/or noradrenaline was necessary to maintain an adequate rate and peripheral perfusion in all patients. Mortality was significantly higher in patients with bradycardia (p < 0.001). In conclusion, bradycardia was associated with poor outcome. As B.1.1.7 variant strain is spreading more rapidly in many countries, our findings help in the identification of patients who may require early admission to ICU.

Prevalence, Patterns, Association with Biofilm Formation, Effects on Milk Quality and Risk Factors for Antibiotic Resistance of Staphylococci from Bulk-Tank Milk of Goat Herds.

The objectives of this work were to study the prevalence and the patterns of antibiotic resistance of staphylococcal isolates from bulk-tank milk of goat herds across Greece, to assess possible associations of the presence of antibiotic resistance with the quality of milk in these herds and to evaluate herd-related factors potentially associated with the presence of antibiotic resistance among these staphylococcal isolates. A cross-sectional study was performed on 119 goat herds in Greece. Bulk-tank milk samples were collected for bacteriological examination; staphylococcal isolates were evaluated for resistance to 20 antibiotics. Oxacillin-resistant, resistant to at least one antibiotic, and multi-resistant staphylococcal isolates were recovered from 5.0%, 30.3%, and 16.0% of herds, respectively. Of 80 isolates, 7.5% were resistant to oxacillin, 50.0% were resistant to at least one antibiotic and 27.5% were multi-resistant. Resistance was seen more frequently among coagulase-negative staphylococci (59.3%) than among Staphylococcus aureus (23.8%). Resistance was more frequent against penicillin and ampicillin (41.3% of isolates) and fosfomycin (27.5%). No association was found with biofilm formation by staphylococci. For recovery of oxacillin-resistant isolates, the presence of working staff in the herds emerged as a significant factor; respective factors for the isolation of staphylococci resistant to at least one antibiotic were part-time farming and high (>10) number of systemic disinfections in the farm annually. The same three factors concurrently were also identified to be significant for the recovery of multi-resistant isolates.

Antibiotic Resistance of Staphylococci from Bulk-Tank Milk of Sheep Flocks: Prevalence, Patterns, Association with Biofilm Formation, Effects on Milk Quality, and Risk Factors.

The objectives of this work were to study prevalence and characteristics of resistance to antibiotics of staphylococcal isolates from the bulk-tank milk of sheep flocks across Greece, to assess possible associations of the presence of antibiotic resistance with the quality of milk in these flocks and to evaluate flock-related factors potentially associated with antibiotic resistance among these isolates. A cross-sectional study was performed in 325 sheep flocks in Greece. Bulk-tank milk samples were collected for bacteriological examination; staphylococcal isolates were evaluated for resistance to 20 antibiotics. Oxacillin-resistant staphylococcal isolates, isolates resistant to any antibiotic, and multi-resistant isolates were recovered from 8.0%, 30.5%, and 12.0% of flocks, respectively. Of 232 isolates, 11.6% were resistant to oxacillin, 46.1% were resistant to at least one antibiotic, and 16.4% were multi-resistant. Resistance was seen more frequently among coagulase-negative (50.6%) than among Staphylococcus aureus (31.5%) isolates. Resistance was more frequent against penicillin and ampicillin (34.1% of isolates), clindamycin (17.7%), and fosfomycin (14.2%). An association was found between biofilm formation by staphylococci and resistance to fosfomycin. For recovery of oxacillin-resistant isolates, the lack of experience by farmers emerged as a significant factor; respective factors for the isolation of staphylococci resistant to any antibiotic or multi-resistant isolates were the early stage of the lactation period (0th-1st month) and the intensive management system applied in the flocks, respectively.

Do smoking and human papilloma virus have a synergistic role in the development of head and neck cancer? A systematic review and meta-analysis.

PURPOSE: Head and neck squamous cell carcinoma (HNSCC), arising from the squamous epithelium, is the most common head and neck cancer (HNC). Smoking and alcohol are well known risk factors for HNSCC, while some high-risk human papilloma virus (HPV) subtypes were specifically identified as a high-risk factors for developing oropharyngeal squamous cell carcinoma (OPSCC). In this study, we have conducted a systematic review and meta-analysis in order to investigate the possible synergistic role of smoking and HPV in the development of HNSCC. METHODS: We conducted a systematic search in two online databases PubMed and Cochrane Library, searching for studies published between 2010-2018. Sixteen studies met the inclusion criteria; a total of 2161 patients were included, comprising 1470 HPV-negative and 691 HPV-positive, respectively. RESULTS: The number of smokers between HPV-positive HNSCC patients (group A) and HPV-negative HNSCC patients (group B) was compared. We have found that smokers in HPV-positive group were statistically significantly less than smokers in HPV-negative group (OR=0.33 with 95% CI 0.18, 0.61). The test for overall effect was Z =3.61 (p=0.0003). CONCLUSION: Smoking is less common in HPV positive group than in HPV negative group, and so probably smoking does not play a major role in the pathogenesis of HPV-positive HNSCC as in the pathogenesis of HPV-negative HNSCC.

MLSB-Resistant Staphylococcus aureus in Central Greece: Rate of Resistance and Molecular Characterization.

The aim of the present study was to determine the rate and mechanisms of resistance to macrolides, lincosamides, and streptogramin B (MLSB) antibiotics of Staphylococcus aureus collected in Central Greece. Of the 2,893 S. aureus collected during 2012-2017, 1,161 isolates (40.2%) exhibited resistance to at least one of the MLSB agents. The rate of erythromycin resistance was statistically significantly higher in methicillin-resistant S. aureus (MRSA) (58.6%) than in methicillin-sensitive S. aureus (MSSA) isolates (20.7%) (p = 0.002). Two hundred seventy-five representative MLSB-resistant S. aureus, including 81 MSSA and 194 MRSA isolates, were further studied. Thirty-eight MSSA isolates carried ermC, 26 MSSA were positive for ermA, whereas 17 isolates carried msrA gene. Among MRSA, the ermA gene was identified in the majority of the isolates (n = 153). Thirty-seven MRSA isolates carried ermC; three isolates carried msrA, whereas the remaining MRSA was positive for two genes (ermA and ermC). Phylogenetic analysis showed that ST225, which belongs to CC5, was the most prevalent, accounting for 137 MRSA isolates. Higher genetic diversity was found in the group of MSSA isolates, which comprised of 13 sequence types. Whole-genome sequencing data showed that all ermA-positive S. aureus, with the exception of one ST398 isolate, harbored the ermA-carrying Tn554 transposon integrated into their chromosomes. Furthermore, Illumina sequencing followed by polymerase chain reaction screening identified that ermC, which was identified in a polyclonal population of MSSA and MRSA isolates, was carried by small plasmids, like pNE131. These findings highlighted the important role of high-risk clones and of mobile elements carrying resistance genes in the successful dissemination of MLSB-resistant staphylococci.