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Brucellosis is one of the most important zoonotic diseases in Greece, causing a significant burden on both human and animal vitality as well as economic loss. The present study was conducted from 2015 to 2022 on 711,415 serum samples by determining the seroepidemiology of Brucellosis among livestock in 24 geographical areas in Greece using the Rose Bengal Test (RBT) and the complement fixation test (CFT) and further performing genetic analysis of Brucella spp. by species-specific real-time PCR and MLVA Brucella analysis. A total of 3086 serum samples from goats, sheep, and cattle showed positive results using the RBT and CFT, and only strongly positive samples (n = 800) were preserved in the Βlood Bank of the Veterinary Laboratory of Brucellosis. From these, 212 sera samples were randomly selected for molecular and genetic analysis. The results indicated that the incidence rate of Brucellosis is higher in cattle herds in comparison with other animal species. Overall, 48 samples tested positive by real-time PCR, of which forty-seven of them were B. abortus and one was B. melitensis. Genetic analysis of two B. abortus samples revealed a common pattern, indicating two Bruce04, two Bruce18, four Bruce07, two Bruce09, three Bruce16, and four Bruce30 for both samples, which, interestingly, were not identical with the known genotypes in the public MLVA Brucella database. Our findings substantiate that animal Brucellosis remains a health issue in Greece, with a stable but apparent incidence rate, and further investigation is needed to fully characterize the newly identified Brucella strains in Greece.

Leishmania infantum is considered the predominant Leishmania species responsible for visceral leishmaniasis (VL) in Greece but limited molecular-typing-based studies have been performed so far. We retrospectively analyzed data and serum samples collected from 3661 individuals suspected for VL in a sixteen-year period, from 2005 to 2020, to study the seasonality and demographic characteristics of VL cases and to define the L. infantum genotypes circulating in the country. Serum samples were tested with immunofluorescence assay and/or molecular assay. qPCR Leishmania-positive samples were subjected to genotypic analysis based on polymorphisms in 12 microsatellite regions of the internal transcribed spacers (ITSs) 1 and 2. We diagnosed 219 definite (6%, sample with a positive molecular assay and/or antibody titer ≥ 1:400) and 230 probable (6.3%, sample with antibody titer between 1:100 and 1:200) VL cases. Data analysis revealed that amongst VL-definite cases, the age group (≥65) constitutes the most affected factor, since 36.9% of the VL cases belonged to this age group. Amongst the VL definite cases, the most frequently reported symptoms were fever (83%), splenomegaly (49%), and hepatomegaly (40%), but this was not the case for immunocompromised patients that developed non-typical symptoms of leishmaniasis. Although no statistically significant differences in the overall seasonality of VL cases were observed, February and June showed a significantly higher proportion of VL cases compared to August and December. Genotyping of ITS1 and ITS2 regions revealed that all VL cases belong to ITS type A of L. infantum. Our study provides epidemiological information on VL and demonstrates for the first time, providing genotypic data, the circulation of ITS type A L. infantum in Greece.

The genus Borrelia has been divided into Borreliella spp., which can cause Lyme Disease (LD), and Borrelia spp., which can cause Relapsing Fever (RF). The distribution of genus Borrelia has broadened due to factors such as climate change, alterations in land use, and enhanced human and animal mobility. Consequently, there is an increasing necessity for a One Health strategy to identify the key components in the Borrelia transmission cycle by monitoring the human-animal-environment interactions. The aim of this study is to summarize all accessible data to increase our understanding and provide a comprehensive overview of Borrelia distribution in the Mediterranean region. Databases including PubMed, Google Scholar, and Google were searched to determine the presence of Borreliella and Borrelia spp. in vectors, animals, and humans in countries around the Mediterranean Sea. A total of 3026 were identified and screened and after exclusion of papers that did not fulfill the including criteria, 429 were used. After examination of the available literature, it was revealed that various species associated with LD and RF are prevalent in vectors, animals, and humans in Mediterranean countries and should be monitored in order to effectively manage and prevent potential infections.

We present multiwavelength polarization measurements of the luminous blazar Mrk 501 over a 14 month period. The 2–8 keV X-ray polarization was measured with the Imaging X-ray Polarimetry Explorer (IXPE) with six 100 ks observations spanning from 2022 March to 2023 April. Each IXPE observation was accompanied by simultaneous X-ray data from NuSTAR, Swift/XRT, and/or XMM-Newton. Complementary optical–infrared polarization measurements were also available in the B , V , R , I , and J bands, as were radio polarization measurements from 4.85 GHz to 225.5 GHz. Among the first five IXPE observations, we did not find significant variability in the X-ray polarization degree and angle with IXPE. However, the most recent sixth observation found an elevated polarization degree at >3 σ above the average of the other five observations. The optical and radio measurements show no apparent correlations with the X-ray polarization properties. Throughout the six IXPE observations, the X-ray polarization degree remained higher than, or similar to, the R -band optical polarization degree, which remained higher than the radio value. This is consistent with the energy-stratified shock scenario proposed to explain the first two IXPE observations, in which the polarized X-ray, optical, and radio emission arises from different regions.

We present X-ray polarimetry observations from the Imaging X-ray Polarimetry Explorer (IXPE) of three low spectral peak and one intermediate spectral peak blazars, namely 3C 273, 3C 279, 3C 454.3, and S5 0716+714. For none of these objects was IXPE able to detect X-ray polarization at the 3 σ level. However, we placed upper limits on the polarization degree at ∼10%–30%. The undetected polarizations favor models where the X-ray band is dominated by unpolarized photons upscattered by relativistic electrons in the jets of blazars, although hadronic models are not completely eliminated. We discuss the X-ray polarization upper limits in the context of our contemporaneous multiwavelength polarization campaigns.

Borreliosis (Lyme disease) is a zoonosis, mediated to humans and small mammals through specific vectors (ticks), with increasing global incidence. It is associated with a variety of clinical manifestations and can, if not promptly recognized and left untreated, lead to significant disability. In Europe, the main Borrelia species causing disease in humans are Borrelia burgdorferi s.s., Borrelia afzelii, Borrelia garinii, and Borrelia spielmanii. The Ixodes ricinus tick is their principal vector. Although Lyme disease is considered endemic in the Balkan region and Turkey, and all three main Lyme pathogens have been detected in ticks collected in these countries, autochthonous Lyme disease remains controversial in Greece. We report a case of aseptic meningitis associated with antibody seroconversion against Borrelia afzelii in a young female patient from the prefecture of Thasos without any relevant travel history. The patient presented with fever and severe headache, and the cerebrospinal fluid examination showed lymphocytic pleocytosis. Serum analysis was positive for specific IgG antibodies against Borrelia afzelii. In the absence of typical erythema migrans, serological evidence of infection is required for diagnosis. Although atypical in terms of clinical presentation, the seasonality and geographical location of potential disease transmission in the reported patient should raise awareness among clinicians for a still controversial and potentially underreported emerging infectious disease in Greece.

We obtained fecal samples from migrant children

Introduction. Cat scratch disease (CSD) is the most common cause of bacterial infectious lymphadenopathy, especially in children, but its diagnosis still remains challenging. Serological assays are widely applied due to their simplicity and the non-invasive sampling. However, these techniques present several limitations, including not well-defined antigen preparation, assay conditions and cutoff titers, severe cross-reactions with other species and organisms, and the notably ranging seroprevalence in the normal population. The objective of this study is to review the literature in order to determine the best diagnostic procedure for the diagnosis of CSD. Methods. Databases including PubMed, Medline, Google Scholar, and Google were searched to determine the best diagnostic procedure for the diagnosis of CSD. A total of 437 papers were identified and screened, and after exclusion of papers that did not fulfill the including criteria, 63 papers were used. Results. It was revealed that sensitivities of serological assays varied from 10% to 100%. Indeed, more than half of the studies reported a sensitivity lower than 70%, while 71% of them had a sensitivity lower than 80%. Moreover, specificities of serological assays ranged from 15% to 100%, with 25 assays reporting a specificity lower than 90%. Conclusion. It is considered that molecular assays should be the gold standard technique for CSD confirmation, and physicians are reinforced to proceed to lymph node biopsy in suspicious CSD cases.

The lower-energy peak of the spectral energy distribution of blazars has commonly been ascribed to synchrotron radiation from relativistic particles in the jets. Despite the consensus regarding jet emission processes, the particle acceleration mechanism is still debated. Here, we present the first X-ray polarization observations of PG 1553+113, a high-synchrotron-peak blazar observed by the Imaging X-ray Polarimetry Explorer (IXPE). We detect an X-ray polarization degree of (10 ± 2)% along an electric-vector position angle of ψ _X = 86° ± 8°. At the same time, the radio and optical polarization degrees are lower by a factor of ∼3. During our IXPE pointing, we observed the first orphan optical polarization swing of the IXPE era, as the optical angle of PG 1553+113 underwent a smooth monotonic rotation by about 125°, with a rate of ∼17° day ^–1 . We do not find evidence of a similar rotation in either radio or X-rays, which suggests that the X-ray and optically emitting regions are separate or, at most, partially cospatial. Our spectropolarimetric results provide further evidence that the steady-state X-ray emission in blazars originates in a shock-accelerated and energy-stratified electron population.

We report the first >99% confidence detection of X-ray polarization in BL Lacertae. During a recent X-ray/ γ -ray outburst, a 287 ks observation (2022 November 27–30) was taken using the Imaging X-ray Polarimetry Explorer (IXPE), together with contemporaneous multiwavelength observations from the Neil Gehrels Swift observatory and XMM-Newton in soft X-rays (0.3–10 keV), NuSTAR in hard X-rays (3–70 keV), and optical polarization from the Calar Alto and Perkins Telescope observatories. Our contemporaneous X-ray data suggest that the IXPE energy band is at the crossover between the low- and high-frequency blazar emission humps. The source displays significant variability during the observation, and we measure polarization in three separate time bins. Contemporaneous X-ray spectra allow us to determine the relative contribution from each emission hump. We find >99% confidence X-ray polarization ${{\rm{\Pi }}}_{2\mbox{--}4\mathrm{keV}}={21.7}_{-7.9}^{+5.6} \% $ and electric vector polarization angle ψ _2–4keV = −28.°7 ± 8.°7 in the time bin with highest estimated synchrotron flux contribution. We discuss possible implications of our observations, including previous IXPE BL Lacertae pointings, tentatively concluding that synchrotron self-Compton emission dominates over hadronic emission processes during the observed epochs.

We present polarization measurements in the 2–8 keV band from blazar 1ES 0229+200, the first extreme high synchrotron peaked source to be observed by the Imaging X-ray Polarimetry Explorer (IXPE). Combining two exposures separated by about two weeks, we find the degree of polarization to be Π _X = 17.9% ± 2.8% at an electric-vector position angle ψ _X = 25.°0 ± 4.°6 using a spectro-polarimetric fit from joint IXPE and XMM-Newton observations. There is no evidence for the polarization degree or angle varying significantly with energy or time on both short timescales (hours) or longer timescales (days). The contemporaneous polarization degree at optical wavelengths was >7× lower, making 1ES 0229+200 the most strongly chromatic blazar yet observed. This high X-ray polarization compared to the optical provides further support that X-ray emission in high-peaked blazars originates in shock-accelerated, energy-stratified electron populations, but is in tension with many recent modeling efforts attempting to reproduce the spectral energy distribution of 1ES 0229+200, which attribute the extremely high energy synchrotron and Compton peaks to Fermi acceleration in the vicinity of strongly turbulent magnetic fields.

The SARS-CoV-2 infection was previously associated with the expression of the dopamine biosynthetic enzyme L-Dopa decarboxylase (DDC). Specifically, a negative correlation was detected between DDC mRNA and SARS-CoV-2 RNA levels in in vitro infected epithelial cells and the nasopharyngeal tissue of COVID-19 patients with mild/no symptoms. However, DDC, among other genes related to both DDC expression and SARS-CoV-2-infection (ACE2, dACE2, EPO), was upregulated in these patients, possibly attributed to an orchestrated host antiviral response. Herein, by comparing DDC expression in the nasopharyngeal swab samples of severe/critical to mild COVID-19 cases, we showed a 20 mean-fold reduction, highlighting the importance of the expression of this gene as a potential marker of COVID-19 severity. Moreover, we identified an association of SARS-CoV-2 infection with the expression of key catecholamine biosynthesis/metabolism-related genes, in whole blood samples from hospitalized patients and in cultured cells. Specifically, viral infection downregulated the biosynthetic part of the dopamine pathway (reduction in DDC expression up to 7.5 mean-fold), while enhanced the catabolizing part (increase in monoamine oxidases A and B expression up to 15 and 10 mean-fold, respectively) in vivo, irrespectively of the presence of comorbidities. In accordance, dopamine levels in the sera of severe cases were reduced (up to 3.8 mean-fold). Additionally, a moderate positive correlation between DDC and MAOA mRNA levels (r = 0.527, p < 00001) in the blood was identified upon SARS-CoV-2-infection. These observations were consistent to the gene expression data from SARS-CoV-2-infected Vero E6 and A549 epithelial cells. Furthermore, L-Dopa or dopamine treatment of infected cells attenuated the virus-derived cytopathic effect by 55% and 59%, respectively. The SARS-CoV-2 mediated suppression of dopamine biosynthesis in cell culture was, at least in part, attributed to hypoxia-like conditions triggered by viral infection. These findings suggest that L-Dopa/dopamine intake may have a preventive or therapeutic value for COVID-19 patients.

(1) Background: Surfaces have been implicated in the transmission of infections. We aimed to assess how effective an usnic-acid-containing self-decontaminating coating was on the surfaces of the Athens underground metro. (2) Methods: Two samples were collected from each of 60 surfaces of a station and a wagon before the application of the coating and 9 and 20 days after, and they were tested for bacteria, fungi, and SARS-CoV-2 using conventional microbiological and molecular methods. Bacteria and fungi growth were expressed in colony forming units (CFUs)/102cm2. (3) Results: Before the application of the coating, 50% of the samples tested positive for the targeted microbes: 91.7% for bacteria, 18.3% for fungi, and 8.3% for SARS-CoV-2. After nine days, 3.3% of the samples tested positive for bacteria and 6.6% after 20 days. The average amount of bacteria before the coating was applied was 8.5 CFU/102cm2 compared to 0 and 0 CFU/102cm2 after application (100% and 95% reduction); all samples collected after the application were negative for SARS-CoV-2 and fungi (100% reduction). (4) Conclusion: An usnic-acid-containing self-decontaminating coating was highly effective in eliminating bacterial, fungal, and SARS-CoV-2 contamination of surfaces in the underground metro.

Underdiagnosis of Coxiella burnetii infections in Greece is possible because of lack of awareness by physicians, and most suspected cases are in patients with no bovine contact. We found serologic evidence of C. burnetii infection throughout Greece and identified a new C. burnetii genotype in the aortic valve of a patient with Q fever endocarditis.

BackgroundThere are few studies about the presence of murine typhus in Greece. Our objective was to conduct a large scale retrospective investigation to determine the clinical and epidemiological features of patients diagnosed with murine typhus in Greece.Methodology/principal findingsFrom 2012 to 2019 serum samples from hospitalized patients and outpatients throughout Greece suspected for murine typhus infection were tested by immunofluorescence assay for Rickettsia typhi. Immunofluorescence positive samples obtained since 2016 were also tested by qPCR targeting R. typhi. Clinical and epidemiological data were retrospectively collected for the patients with confirmed murine typhus. Overall, we tested 5,365 different patients and, in total, 174 patients from all geographic regions of Greece were diagnosed with murine typhus. The most frequently reported sign or symptom was fever (89%), followed by headache (84%) and rash (81%). The classical triad of fever, headache, and rash was present in 72% of patients during their illness. Severe infections with complications including acute renal failure or septic shock were not recorded. The majority of cases (81%) occurred during May-October and peaked in June and September. Most of patients (81%) infected in Athens, recalled that their only activity the last weeks before symptoms onset was swimming on the beach and 59% of them also reported an insect bite while sunbathing.Conclusions/significanceOur results may reflect the reemergence of murine typhus in Greece and we highlight the importance of awareness of this difficult-to-recognize undifferentiated febrile illness.

L-Dopa decarboxylase (DDC) is the most significantly co-expressed gene with ACE2, which encodes for the SARS-CoV-2 receptor angiotensin-converting enzyme 2 and the interferon-inducible truncated isoform dACE2. Our group previously showed the importance of DDC in viral infections. We hereby aimed to investigate DDC expression in COVID-19 patients and cultured SARS-CoV-2-infected cells, also in association with ACE2 and dACE2. We concurrently evaluated the expression of the viral infection- and interferon-stimulated gene ISG56 and the immune-modulatory, hypoxia-regulated gene EPO. Viral load and mRNA levels of DDC, ACE2, dACE2, ISG56 and EPO were quantified by RT-qPCR in nasopharyngeal swab samples from COVID-19 patients, showing no or mild symptoms, and from non-infected individuals. Samples from influenza-infected patients were analyzed in comparison. SARS-CoV-2-mediated effects in host gene expression were validated in cultured virus-permissive epithelial cells. We found substantially higher gene expression of DDC in COVID-19 patients (7.6-fold; p = 1.2e-13) but not in influenza-infected ones, compared to non-infected subjects. dACE2 was more elevated (2.9-fold; p = 1.02e-16) than ACE2 (1.7-fold; p = 0.0005) in SARS-CoV-2-infected individuals. ISG56 (2.5-fold; p = 3.01e-6) and EPO (2.6-fold; p = 2.1e-13) were also increased. Detected differences were not attributed to enrichment of specific cell populations in nasopharyngeal tissue. While SARS-CoV-2 virus load was positively associated with ACE2 expression (r≥0.8, p

In-depth understanding of the immune response provoked by SARS-CoV-2 infection is necessary, as there is a great risk of reinfection and a difficulty in achieving herd immunity due to a decline in both antibody concentration and avidity. Avidity testing, however, could overcome variability in the immune response associated with sex or clinical symptoms, and thus differentiate between recent and past infections. In this context, here, we analyzed SARS-CoV-2 antibody kinetics and avidity in Greek hospitalized (26%) and non-hospitalized (74%) COVID-19 patients (N = 71) in the course of up to 15 months after their infection to improve the accuracy of the serological diagnosis in dating the onset of the infection. The results showed that IgG-S1 levels decline significantly at four months (p = 0.0239) in both groups of patients and are higher in hospitalized ones (up to 2.1-fold, p < 0.001). Additionally, hospitalized patients’ titers drop greatly and are equalized to non-hospitalized ones only at a time-point of twelve to fifteen months. Antibody levels of women in total remain more stable months after infection, compared to men. Furthermore, we examined the differential maturation of IgG avidity after SARS-CoV-2 infection, showing an incomplete maturation of avidity that results in a plateau at four months after infection. We also defined 38.2% avidity (sensitivity: 58.9%, specificity: 90.91%) as an appropriate “cut-off” that could be used to determine the stage of infection before avidity reaches a plateau.

The gut microbiota is often affected by the dietary and lifestyle habits of the host, resulting in a better efficacy that favors energy harvesting from the consumed food. Our objective was to characterize the composition of gut microbiota in adult Saudis and investigate possible association with lifestyle and dietary practices. Feces from 104 Saudi volunteers (48% males) were tested for microbiota by sequencing the V3-V4 region of bacterial 16S ribosomal RNA (rRNA). For all participants, data were collected related to their lifestyle habits and dietary practices. The relative abundance (RA) of Fusobacteria was significantly higher in normal weight Saudis (P = 0.005, false discovery rate-FDR = 0.014). Individuals who consumed more coffee presented marginally significant more RA of Fusobacteria (P = 0.02, FDR = 0.20) in their gut microbiota compared to those reporting low or no coffee intake, but the RA of Fusobacteria was significantly higher in smokers compared to non-smokers (P = 0.009, FDR = 0.027). The RA of Fusobacteria was also significantly higher in those reporting daily consumption of bread (P = 0.005, FDR = 0.015). At the species level, the gut microbiota of people who consumed coffee was dominated by Bacteroides thetaiotaomicron followed by Phascolarctobacterium faecium and Eubacterium rectale. Similarly, the gut microbiota of smokers was also enriched by B. thetaiotaomicron and Lactobacillus amylovorus. Smoking cessation, bread and coffee consumption induce changes in the intestinal microbial composition of Saudis. This indicates the significance of diet and lifestyle practices in the determination of the composition of the gut microbiota, which could possibly lead later to changes in metabolic profile and weight.

Abstract Background Most studies on the human microbiota have analyzed stool samples, although a large proportion of the absorption of nutrients takes place in upper gut tract. We collected samples from different locations along the entire gastrointestinal tract from six patients who had simultaneously undergone upper endoscopy and colonoscopy, to perform a comprehensive analysis using culturomics with matrix assisted laser desorption ionisation - time of flight (MALDI-TOF) identification and by metagenomics targeting the 16S ribosomal ribonucleic acid (rRNA) gene. Results Using culturomics, we isolated 368 different bacterial species, including 37 new species. Fewer species were isolated in the upper gut: 110 in the stomach and 106 in the duodenum, while 235 were isolated from the left colon (p

Autotaxin (ATX; ENPP2) is a secreted lysophospholipase D catalyzing the extracellular production of lysophosphatidic acid (LPA), a pleiotropic signaling phospholipid. Genetic and pharmacologic studies have previously established a pathologic role for ATX and LPA signaling in pulmonary injury, inflammation, and fibrosis. Here, increased ENPP2 mRNA levels were detected in immune cells from nasopharyngeal swab samples of COVID-19 patients, and increased ATX serum levels were found in severe COVID-19 patients. ATX serum levels correlated with the corresponding increased serum levels of IL-6 and endothelial damage biomarkers, suggesting an interplay of the ATX/LPA axis with hyperinflammation and the associated vascular dysfunction in COVID-19. Accordingly, dexamethasone (Dex) treatment of mechanically ventilated patients reduced ATX levels, as shown in two independent cohorts, indicating that the therapeutic benefits of Dex include the suppression of ATX. Moreover, large scale analysis of multiple single cell RNA sequencing datasets revealed the expression landscape of ENPP2 in COVID-19 and further suggested a role for ATX in the homeostasis of dendritic cells, which exhibit both numerical and functional deficits in COVID-19. Therefore, ATX has likely a multifunctional role in COVID-19 pathogenesis, suggesting that its pharmacological targeting might represent an additional therapeutic option, both during and after hospitalization.

Anti-SARS-CoV-2 spike RBD (receptor-binding domain) IgG antibody levels were monitored in 1643 volunteer healthcare workers of Eginition, Evangelismos, and Konstantopoulio General Hospitals (Athens, Greece), who underwent vaccination with two doses of COVID-19 BNT162b2 mRNA vaccine (Pfizer) and had no history of SARS-CoV-2 infection. Venous blood was collected 20–30 days after the second vaccine dose and anti-RBD IgG levels were determined using CMIA SARS-CoV-2 IgG II Quant (Abbott) on ARCHITECT i System or ADVIA Centaur SARS-CoV-2 IgG (Siemens) on Centaur XP platform. From the total population of 1643 vaccinees (533 M/1110 F; median age = 49; interquartile range-IQR = 40–56), 1636 (99.6%) had anti-SARS-CoV-2 IgG titers above the positivity threshold of the assay used. One-Way ANOVA Kruskal-Wallis H test showed a statistically significant difference in the median of antibody titers between the different age groups (p < 0.0001). Consistently, Spearman’s correlation coefficient (r) for IgGs and age as continuous variables was −0.2380 (p = 1.98 × 10−17). Moreover, antibody titers were slightly higher by 1.2-mean fold (p = 3 × 10−6) in the total female population of the three hospitals (median = 1594; IQR = 875–2584) as compared to males (median = 1292; IQR = 671.9–2188). The present study supports that BNT162b2 vaccine is particularly effective in producing high anti-SARS-CoV-2 IgG levels in healthy individuals, and this humoral response is age- and gender-dependent.

Empyema of acalculous gallbladder in the setting of salmonellosis represents an extremely rare and life-threatening clinical condition in adults. In this unique case report, we deal with a previously healthy patient who developed acalculous cholecystitis and empyema due to infection by Salmonella. He underwent explorative laparotomy in emergency setting, and cholecystectomy was performed due to his toxic clinical condition. Empyema of gallbladder was revealed and cultures were collected. A combination of antibiotics (ciprofloxacin and metronidazole) was set, and the patient was discharged 8 days after the surgical operation in good condition. It has to be highlighted that acalculous cholecystitis is a rare entity, mostly at critically ill patients, and treatment options depend on clinical condition, risk factors, and etiology. To our knowledge, this is the first case report dealing with acalculous cholecystitis with empyema due to salmonellosis up to date. Although it is extremely rare, high index of suspicion is needed by the operating surgeon in order to avoid unfavorable outcomes.

Background: The spatiotemporal profiling of molecular transmission clusters (MTCs) using viral genomic data can effectively identify transmission networks in order to inform public health actions targeting SARS-CoV-2 spread. Methods: We used whole genome SARS-CoV-2 sequences derived from ten European regions belonging to eight countries to perform phylogenetic and phylodynamic analysis. We developed dedicated bioinformatics pipelines to identify regional MTCs and to assess demographic factors potentially associated with their formation. Results: The total number and the scale of MTCs varied from small household clusters identified in all regions, to a super-spreading event found in Uusimaa-FI. Specific age groups were more likely to belong to MTCs in different regions. The clustered sequences referring to the age groups 50–100 years old (y.o.) were increased in all regions two weeks after the establishment of the lockdown, while those referring to the age group 0–19 y.o. decreased only in those regions where schools’ closure was combined with a lockdown. Conclusions: The spatiotemporal profiling of the SARS-CoV-2 MTCs can be a useful tool to monitor the effectiveness of the interventions and to reveal cryptic transmissions that have not been identified through contact tracing.

Bacteria genetically related to Coxiella burnetii have been found in ticks. Using molecular techniques, we detected Coxiella-like bacteria, here named Candidatus Coxiella massiliensis, in skin biopsy samples and ticks removed from patients with an eschar. This organism may be a common agent of scalp eschar and neck lymphadenopathy after tick bite.

Objectives: Asymptomatic faecal carriage of Tropheryma whipplei, the agent of Whipple's disease, is reported among sewage workers. However, the potential development of such carriage is unknown. A 7-year follow-up of T. whipplei-carrying sewage workers is reported. Methods: Nineteen sewage workers previously detected as faecal carriers of T. whipplei were followed to ascertain the chronicity of their carriage. Faeces were tested by molecular assays using quantitative real-time PCR specifically targeting T. whipplei. Serological anti-T. whipplei Western blotting was also performed. Results: Seventy-nine percent (15/19) of workers exhibited a strong immune response against T. whipplei. Among these, five were followed for more than 1 year. Four maintained a strong response, with three carrying the same strain and one becoming negative. The fifth exhibited a decreased immune response, a negative faeces result, and subsequent carriage of another strain. Three individuals with low immune responses were also followed. Two never developed a response, with one carrying the same strain and one becoming negative and then positive with another strain; the third developed a strong response and became negative. Conclusions: Chronic T. whipplei carriers appear to be protected against reinfection, but those with low or decreasing antibody levels may be re-colonized by another strain.

To further characterize human infections caused by Rickettsia sibirica mongolitimonae, we tested skin biopsy and swab samples and analyzed clinical, epidemiologic, and diagnostic characteristics of patients with a rickettsiosis. The most common (38%) indigenous species was R. sibirica mongolitimonae. Significantly more cases of R. sibirica mongolitimonae infection occurred during spring and summer.

Objectives: Q fever has been reported throughout the African continent. The objective of this study was to detect the presence of Coxiella burnetii in febrile patients from Africa. Methods: Blood samples from febrile and non-febrile patients from six African countries and from France were investigated retrospectively for Q fever infection by molecular assays targeting the IS1111 and IS30A spacers. Results: We tested 1888 febrile patients from Senegal, Mali, Tunisia, Algeria, Gabon, and Morocco and found one male adult patient (0.3%) infected with C. burnetii in Algeria and six positive patients (0.5%) in Senegal. For one patient from Senegal we determined that the infection was caused by C. burnetii genotype 35. In Senegal, more patients were infected with C. burnetii in Keur Momar Sarr (p = 0.002) than in the other locations. Blood samples taken from 500 (51% males) non-febrile people from Senegal and France were all negative. Conclusions: The installation of point-of-care laboratories in rural Africa can be a very effective tool for studying the epidemiology of many infectious diseases.

As worldwide vectors of human infectious diseases, ticks are considered to be second only to mosquitoes. Each tick species has preferred environmental conditions and biotopes that determine its geographic distribution, the pathogens it vectors, and the areas that pose risk for tick-borne diseases. Researchers have identified an increasing number of bacterial pathogens that are transmitted by ticks, including Anaplasma, Borrelia, Ehrlichia, and Rickettsia spp. Recent reports involving humans and canines suggest that ticks should be considered as potential vectors of Bartonella spp. To strengthen this suggestion, numerous molecular surveys to detect Bartonella DNA in ticks have been conducted. However, there is little evidence that Bartonella spp. can replicate within ticks and no definitive evidence of transmission by a tick to a vertebrate host.

Few studies have tested the small intestine microbiota in humans, where most nutrient digestion and absorption occur. Here, our objective was to examine the duodenal microbiota between obese and normal volunteers using metagenomic techniques.We tested duodenal samples from five obese and five normal volunteers using 16S rDNA V6 pyrosequencing and Illumina MiSeq deep sequencing. The predominant phyla of the duodenal microbiota were Firmicutes and Actinobacteria, whereas Bacteroidetes were absent. Obese individuals had a significant increase in anaerobic genera (p < 0.001) and a higher abundance of genes encoding Acyl-CoA dehydrogenase (p = 0.0018) compared to the control group. Obese individuals also had a reduced abundance of genes encoding sucrose phosphorylase (p = 0.015) and 1,4-alpha-glucan branching enzyme (p = 0.05). Normal weight people had significantly increased FabK (p = 0.027), and the glycerophospholipid metabolism pathway revealed the presence of phospholipase A1 only in the control group (p = 0.05).The duodenal microbiota of obese individuals exhibit alterations in the fatty acid and sucrose breakdown pathways, probably induced by diet imbalance.

The polarised emission from active galactic nuclei (AGN) jets carries information about the physical conditions at the emitting plasma elements, while its temporal evolution probes the physical processes that introduce variability and dynamically modify the local conditions. Here we present the analysis of multi-frequency radio linear and circular polarisation datasets with the aim of exactly quantifying the conditions in blazar jets. Our analysis includes both the careful treatment of observational datasets and numerical modelling for the reproduction of synthetic polarisation curves that can be compared to the observed ones. In our approach, the variability is attributed to traveling shocks. The emission from the cells of our jet model is computed with radiative transfer of all Stokes parameters. The model also accounts for Faraday effects which map the low-energy particle populations. We present two extreme cases in terms of the significance of Faraday conversion in the production of circular polarisation. As we show, in both regimes the model gives a realistic reproduction of the observed emission.

To determine the presence of Bartonella quintana in head and body lice from persons in different locations in Ethiopia, we used molecular methods. B. quintana was found in 19 (7%) genotype C head lice and in 76 (18%) genotype A body lice. B. quintana in head lice was positively linked to altitude (p = 0.014).

Cat-scratch disease is seasonal in the United States and Japan; but no data are available from Europe. To assess the seasonality of the disease in France, we analyzed lymph node biopsy specimens collected during 1999–2009. Most (87.5%) cases occurred during September–April and peaked in December.

During the past 2 years, we identified live Bartonella henselae in the primary inoculation sites of 3 patients after a cat scratch. Although our data are preliminary, we report that a cutaneous swab of the skin lesion from a patient in the early stage of cat-scratch disease can be useful for diagnosis of the infection.

Radio polarimetry is an invaluable tool to investigate the physical conditions and variability processes in active galactic nuclei (AGN) jets. However, detecting their linear and circular polarization properties is a challenging endeavor due to their low levels and possible depolarization effects. We have developed an end-to-end data analysis methodology to recover the polarization properties of unresolved sources with high accuracy. It has been applied to recover the linear and circular polarization of 87 AGNs measured by the F-GAMMA program from July 2010 to January 2015 with a mean cadence of 1.3 months. Their linear polarization was recovered at four frequencies between 2.64 and 10.45 GHz and the circular polarization at 4.85 and 8.35 GHz. The physical conditions required to reproduce the observed polarization properties and the processes which induce their variability were investigated with a full-Stokes radiative transfer code which emulates the synchrotron emission of modeled jets. The model was used to investigate the conditions needed to reproduce the observed polarization behavior for the blazar 3C 454.3, assuming that the observed variability is attributed to evolving internal shocks propagating downstream.

S5 0716+714 is a well known BL Lac object, and one of the brightest and most active blazars. The discovery in the Very High Energy band (VHE, E > 100 GeV) by MAGIC happened in 2008. In January 2015, the source went through the brightest optical state ever observed, triggering MAGIC follow-up and a VHE detection with ∼ 13 σ significance (ATel ♯ 6999 ). Rich multiwavelength coverage of the flare allowed us to construct the broad-band spectral energy distribution of S5 0716+714 during its brightest outburst. In this work, we will present the preliminary analysis of MAGIC and Fermi-LAT data of the flaring activity in January and February 2015 for the HE (0.1 < HE < 300 GeV) and VHE band, together with radio (Metsähovi, OVRO, VLBA, Effelsberg), sub-millimeter (SMA), optical (Tuorla, Perkins, Steward, AZT-8+ST7, LX-200, Kanata), X-ray and UV (Swift-XRT and UVOT), in the same time-window and discuss the time variability of the multiwavelength light curves during this impressive outburst.

BACKGROUND: Isolation of Rickettsia species from skin biopsies may be replaced by PCR. We evaluated culture sensitivity compared to PCR based on sampling delay and previous antibiotic treatment. METHODOLOGY/PRINCIPAL FINDINGS: Skin biopsies and ticks from patients with suspected Rickettsia infection were screened for Rickettsia spp. using qPCR, and positive results were amplified and sequenced for the gltA and ompA genes. Immunofluorescence for spotted fever group rickettsial antigens was done for 79 patients. All skin biopsies and only ticks that tested positive using qPCR were cultured in human embryonic lung (HEL) fibroblasts using the centrifugation-shell vial technique. Patients and ticks were classified as definitely having rickettsioses if there was direct evidence of infection with a Rickettsia sp. using culture or molecular assays or in patients if serology was positive. Data on previous antibiotic treatments were obtained for patients with rickettsiosis. Rickettsia spp. infection was diagnosed in 47 out of 145 patients (32%), 41 by PCR and 12 by culture, whereas 3 isolates were obtained from PCR negative biopsies. For 3 of the patients serology was positive although PCR and culture were negative. Rickettsia africae was the most common detected species (n = 25, [17.2%]) and isolated bacterium (n = 5, [3.4%]). The probability of isolating Rickettsia spp. was 12 times higher in untreated patients and 5.4 times higher in patients from our hometown. Rickettsia spp. was amplified in 24 out of 95 ticks (25%) and we isolated 7 R. slovaca and 1 R. raoultii from Dermacentor marginatus. CONCLUSIONS/SIGNIFICANCE: We found a positive correlation between the bacteria copies and the isolation success in skin biopsies and ticks. Culture remains critical for strain analysis but is less sensitive than serology and PCR for the diagnosis of a Rickettsia infection.

There are few epidemiological and clinical studies about the presence of cat scratch disease (CSD) on the island of Crete. The objective of this study was to analyze a large number of patients with suspected CSD to define the frequency of Bartonella infections in Crete. From January 2005 to October 2008, we studied patients with suspected CSD from hospitals in Crete. Sera of the referred patients were tested by immunofluorescence assay (IFA). For some patients, we also received lymph nodes and blood samples that we tested for the presence of Bartonella henselae by molecular assays. Overall, we tested 507 serum samples and we found 56 (11%) cases of CSD. PCR assay was positive for 2 patients; one had a B. henselae positive lymph node and the other a positive whole blood sample. Significantly more CSD cases (62.5%, 35 of 56) were reported in children than in infants and adults (P

BACKGROUND: Gut microbiota play a major role in digestion and energy conversion of nutrients. Antibiotics, such as avoparcin (a vancomycin analogue), and probiotics, such as Lactobacillus species, have been used to increase weight in farm animals. We tested the effect of antibiotics given for infective endocarditis (IE) on weight gain (WG). METHODOLOGY/PRINCIPAL FINDINGS: Forty-eight adults with a definite diagnosis of bacterial IE (antibiotic group) were compared with forty-eight age-matched controls without IE. Their body mass index (BMI) was collected at one month before the first symptoms and one year after hospital discharge. The BMI increased significantly and strongly in vancomycin-plus-gentamycin-treated patients (mean [+/-SE] kg/m(2), +2.3 [0.9], p = 0.03), but not in controls or in patients treated with other antibiotics. Seventeen patients had a BMI increase of >or=10%, and five of the antibiotic group developed obesity. The treatment by vancomycin-plus-gentamycin was an independent predictor of BMI increase of >or=10% (adjusted OR, 6.7; 95% CI, 1.37-33.0; p = 0.02), but not treatment with other antibiotics. Weight gain was particularly high in male patients older than 65 who did not undergo cardiac surgery. Indeed, all three vancomycin-treated patients with these characteristics developed obesity. CONCLUSIONS/SIGNIFICANCE: A major and significant weight gain can occur after a six-week intravenous treatment by vancomycin plus gentamycin for IE with a risk of obesity, especially in males older than 65 who have not undergone surgery. We speculate on the role of the gut colonization by Lactobacillus sp, a microorganism intrinsically resistant to vancomycin, used as a growth promoter in animals, and found at a high concentration in the feces of obese patients. Thus, nutritional programs and weight follow-up should be utilized in patients under such treatment.

BACKGROUND: A bacterial role in the obesity pandemic has been suspected based on the ingestion of probiotics that can modify the gut flora. The objective of our study was to determine if increased Lactobacillus sp. in the gut flora of newborn broiler chicks and ducks could result in weight gain increase. METHODOLOGY: Female broiler chicks (Gallus gallus domesticus) and ducks (Anas platyrhynchos domestica) were separated into one control and two experimental groups, and inoculated once or twice with 4x10(10)Lactobacillus spp. per animal in PBS, or with PBS alone. Fecal samples were collected before and at 24 hours, 2, 4, 8, 16 and 30 days after the inoculation. DNA was extracted from the stools, and qPCR assays were performed on a MX3000 system for the detection and quantification of Lactobacillus sp., Bacteroidetes and Firmicutes, using a quantification plasmid. Animals were measured and sacrificed 60 days after the beginning of the experiment, and livers were collected and measured. PRINCIPAL FINDINGS: Chicks inoculated once and twice with Lactobacillus weighed 10.2% (p = 0.0162) and 13.5% (p = 0.0064) more than the control group animals, respectively. Similarly, ducks inoculated once and twice weighed 7.7% (p = 0.05) and 14% (p = 0.035) more than those in the control group, respectively. Liver mass was also significantly higher in inoculated animals compared to the control group. Inoculation with Lactobacillus sp. increased the DNA copies of Lactobacillus spp. and Firmicutes in the stools. Bacteroidetes remained stable, and only the second Lactobacillus sp. inoculation significantly decreased its population in chicks. The ratio of DNA copies of Firmicutes to those of Bacteroidetes increased to as much as 6,4 in chicks and 8,3 in ducks. CONCLUSIONS: Differences in the intestinal microbiota may precede weight increase, as we found that an increase of Lactobacillus sp. in newborn ducks and chicks preceded the development of weight gain.