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Highlights • EBV reactivation was observed in patients with COVID-19. • NK + and CD8 + T cell reduction was related to the severity of COVID-19 infection. • An increase of B cells in patients with severe symptoms was documented., Objectives The immunologic profile and opportunistic viral DNA increase were monitored in Italian patients with COVID-19 in order to identify markers of disease severity. Methods A total of 104 patients infected with SARS-CoV-2 were evaluated in the study. Of them, 42/104 (40.4%) were hospitalized in an intensive care unit (ICU) and 62/104(59.6%) in a sub-intensive care unit (SICU). Human cytomegalovirus (HCMV) and Epstein-Barr virus (EBV), Parvovirus B19 and Human Herpesvirus 6 virus reactivations were determined by real-time PCR, and lymphocyte subpopulation counts were determined by flow cytometry. Results Among opportunistic viruses, only EBV was consistently detected. EBV DNA was observed in 40/42 (95.2%) of the ICU patients and in 51/61 (83.6%) of the SICU patients. Comparing the two groups of patients, the EBV DNA median level among ICU patients was significantly higher than that observed in SICU patients. In parallel, a significant reduction of CD8 T cell and NK count in ICU patients as compared with SICU patients was observed (p

Currently, no consensus has been reached on the optimal blood compartment to be used for surveillance of cytomegalovirus (CMV) and Epstein-Barr virus (EBV) DNAemia. Although several comparative studies have been performed correlating CMV and EBV DNA loads in whole blood (WB) versus plasma, to our knowledge, no studies to date have analyzed the kinetics of both viruses in the 2 blood compartments. In this retrospective noninterventional multicenter cohort study, the kinetics of CMV and EBV DNA in 121 hematopoietic stem cell transplantation (HSCT) recipients were investigated by analyzing in parallel 569 and 351 paired samples from 80 and 58 sequential episodes of CMV and EBV DNAemia, respectively. Unlike previous studies, this study used a single automated molecular method that was CE-marked and Food and Drug Administration-approved for use in quantifying CMV and EBV DNA in both plasma and WB. Furthermore, the complete viral replication kinetics of all episodes (including both the ascending and the descending phases of the active infection) was examined in each patient. The previously observed overall correlation between CMV DNA levels in WB and plasma was confirmed (Spearman's ρ =.85; P

Highlights • Human enterovirus D68 (EV-D68) is a common cause of lower respiratory illness in pediatric age. • In most of the cases, EV-D68 is detected as a single infectious agent. • The circulation of EV-D68 B3 lineage has been proven in Italy during 2016. • The continuous global monitoring of epidemiology of EV-D68 should be improved., Background In recent years, several outbreaks due to Enterovirus D-68 (EV-D68) have been reported, and it was confirmed that the virus can cause upper and lower respiratory tract diseases and be associated with the development of neurological problems. Objectives The main aim of this research was to study the genetic characteristics of EV-D68 strains that were circulating in Italy identified during an outbreak of an EV-D68 infection that occurred in Italy during the period March-October 2016. Study design A retrospective study of the circulation of different types and subtypes of EV-D68 was performed. Nasopharyngeal swabs were collected from March 2016 through October 2016 in children admitted to the Emergency Room with respiratory diseases. Results Among 390 children, 22 (59.1% males; mean age 47 months) were found to be infected by EV-D68 and most of them were immunocompetent (72.7%). Pneumonia was diagnosed in 12 (54.5%) children. Phylogenetic analysis of the VP1 region showed that all the strains identified in this study belonged to clade B3. Within B3 subclade, the Italian EV-D68 strains were most closely related to strains detected in Southern China in 2015 as well as to strains detected in US and the Netherlands in 2016. Conclusions These results showed that EV-D68 infections are a common cause of lower respiratory illness in pediatric age. The circulation of one EV-D68 lineage has been proven in Italy and in the European region during 2016. However, further studies are required to investigate whether some strains or lineages may possess a higher affinity for the lower airway or central nervous system.

The recurrence of multi-drug resistant (MDR) pathogens to the latest antibiotics and the limited development of new antibacterial agents have reduced the options for the treatment of severe infections. The reintroduction of old antibiotics, such as colistin, represents an effective strategy, since the latest antibiotics are over-consumed and ineffective against MDR pathogens. In 2015, Liu (Lancet Infect Dis 16:161-168, 2016) reported Escherichia coli (E. coli) isolates carrying plasmid-mediated colistin resistance gene mcr-1. The first of mcr-1 positive colistin-resistant (col-R) E. coli from a human blood culture was observed in 2012 in Latin America, while in Italy was reported for the first time by our center in 2016. The present study aimed to describe the prevalence of mcr-1 positive col-R strains in E. coli-related bloodstream infection among patients hospitalized in Fondazione IRCCS Policlinico San Matteo in Pavia, Italy, from 2012 to 2018, including the three cases already published.All col-R E. coli strains isolated from blood cultures collected during the study period were analyzed. The minimal inhibitory concentration of colistin was determined using broth microdilution and detection of mcr-1 and mcr-2 genes was performed by PCR. The sequence type of E. coli mcr-1 positive was determined according to Multilocus sequence typing.Out of 1557 samples, 14 strains (0.90%) were col-R. and positive for the presence of the mcr-1 gene, with no mcr-2 detected. The most common ST was ST10 (n = 3), followed by ST410 (n = 2). The remaining strains exhibited different MLST profiles, indicating that they were genetically unrelated.Proper reporting of the presence of mcr-1 genes is an essential component to anticipate the spread of colistin resistance. This public health issue is particularly alarming in Italy due to the consistent circulation of MDR bacteria.

Human adenoviruses (HAdVs) cause a wide spectrum of clinical syndromes, depending on species and types, from mild respiratory infections to deadly pneumonia: in particular, severe infections occur in immunocompromised patients. In this report, we describe the case of a 36 years-old woman admitted to our intensive care unit (ICU) with severe respiratory distress syndrome caused by adenovirus pneumonia, that required invasive respiratory support (mechanical ventilation and extracorporeal membrane oxygenation). Molecular assays detected the virus in respiratory and plasma specimen and sequencing procedure identified HAdV type 4. Patient improved after cidofovir administration. Leukopenia and subsequent bacterial infection occurred, but the patient recovered completely and was discharged from the hospital after 54days.

El objetivo de este trabajo fue evaluar el efecto de la aplicación de efluentes líquidos porcinos sobre la productividad del cultivo de maíz y diversas propiedades químicas y físicas de un Argiudol del centro de Santa Fe. Para ello se realizó un experimento a campo donde se aplicaron tres dosis de efluente en un diseño en bloques completamente aleatorizado con tres repeticiones. No se registraron variaciones en el número de plantas entre el inicio y el fin del ensayo. La productividad del cultivo se incrementó marcadamente por la adición del efluente lográndose la mayor respuesta en grano con la dosis intermedia. Las propiedades químicas del suelo mostraron cambios debido a la adición de efluentes porcinos mientras que las físicas, a excepción de la resistencia mecánica, no sufrieron cambios significativos. Se considera necesario realizar nuevos ensayos para monitorear fundamentalmente las propiedades químicas para minimizar riesgos de contaminación del suelo y toxicidad sobre las plantas. The aim of this paper was to assess the effect of the swine effluent application on the corn production and some chemical and physical properties of an Argiudoll of the center of Santa Fe. A field experiment was carried out applying three rates of swine liquid effluent in a randomized complete block design with three replications. No changes were observed on crop density from the the beginning to the end of the experiment. The crop productivity increased notably due to the swine effluent application and the highest yield was obtained with the intermediate rate. Soil chemical properties showed some changes related to swine effluent application while the physical properties did not show significant changes, with the exception of soil mechanical resistance. More research and continuous monitoring of the soil chemical properties are needed in order to minimize potential risks of environmental contamination and toxicity over plants. and continuous monitoring of the soil chemical properties are needed in order to minimize potential risks of environmental contamination and toxicity over plants. Fil: Micheloud, H.. Universidad Nacional del Litoral. Facultad de Ciencias Agrarias; Argentina Fil: Carrizo, Maria Eugenia. Universidad Nacional del Litoral. Facultad de Ciencias Agrarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Santa Fe. Instituto de Agrobiotecnologia del Litoral; Argentina Fil: Alesso, Carlos Agustín. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Santa Fe. Instituto de Agrobiotecnologia del Litoral; Argentina Fil: Girello, G.. Universidad Nacional del Litoral. Facultad de Ciencias Agrarias; Argentina Fil: Capeletti, M.. Universidad Nacional del Litoral. Facultad de Ciencias Agrarias; Argentina Fil: Imhoff, Silvia del Carmen. Universidad Nacional del Litoral. Facultad de Ciencias Agrarias; Argentina

Sustained virologic response rates have increased dramatically following direct acting antiviral (DAA) therapy in chronic HCV infection. However, resistance-associated substitutions (RASs) may occur either prior to DAA or following drug exposure. The aim of this study was to determine RASs in DAA treatment-failing patients and the role of RASs in failure treatment. Six hundred and twenty HCV patients were evaluated. Direct sequencing of HCV genes was performed at breakthrough in all 31 patients failing DAAs, and in 19 baseline patients. Deep sequencing analysis was performed in 15/19 baseline patients. RASs were detected at breakthrough in 17/31 patients and at baseline in 11/19 patients, although, only 8/19 patients carried RASs associated with the prescribed regimen. Deep sequencing analysis showed RASs at baseline in 10/15 treatment-failing patients. No significant difference was observed with the Sanger sequencing. Treatment failure in the 14/31 patients without RASs was associated with suboptimal treatment. In 54.8% of treatment-failing patients one of the causes of failure might be the presence of RASs. In the majority of patients with RASs, mutations were present at baseline. Direct resistance test is advocated before treatment and at breakthrough in order to optimize retreatment regimens.

Recent molecular diagnostic methods have significantly improved the diagnosis of viral pneumonia in intensive care units (ICUs). It has been observed that 222G/N changes in the HA gene of H1N1pdm09 are associated with increased lower respiratory tract (LRT) replication and worse clinical outcome. In the present study, the frequency of respiratory viruses was assessed in respiratory samples from 88 patients admitted to 16 ICUs during the 2014–2015 winter-spring season in Lombardy. Sixty-nine out of 88 (78.4%) patients were positive for a respiratory viral infection at admission. Of these, 57/69 (82.6%) were positive for influenza A (41 A/H1N1pdm09 and 15 A/H3N2), 8/69 (11.6%) for HRV, 2/69 (2.9%) for RSV and 2/69 (2.9%) for influenza B. Phylogenetic analysis of influenza A/H1N1pdm09 strains from 28/41 ICU-patients and 21 patients with mild respiratory syndrome not requiring hospitalization, showed the clear predominance of subgroup 6B strains. The median influenza A load in LRT samples of ICU patients was higher than that observed in the upper respiratory tract (URT) (p

Background Acute gastroenteritis is a common cause of morbidity and mortality in humans worldwide. The rapid and specific identification of infectious agents is crucial for correct patient management. However, diagnosis of acute gastroenteritis is usually performed with diagnostic panels that include only a few pathogens. In the present bicentric study, the diagnostic value of FilmArray™ GI panels was assessed in unformed stool samples of patients with acute gastroenteritis and in a series of samples collected from pediatric patients with heamorragic diarrhea. The clinical performance of the FilmArray™ gastrointestinal (GI) panel was assessed in 168 stool samples collected from patients with either acute gastroenteritis or hemorragic diarrhea. Samples showing discordant results between FilmArray and routine methods were further analyzed with an additional assay. Results Overall, the FilmArray™ GI panel detected at least one potential pathogen in 92/168 (54.8%) specimens. In 66/92 (71.8%) samples, only one pathogen was detected, while in 26/92 (28.2%) multiple pathogens were detected. The most frequent pathogens were rotavirus 13.9% (22/168), Campylobacter 10.7% (18/168), Clostridium difficile 9.5% (16/168), and norovirus 8.9% (15/168). Clostridium difficile was identified only in patients with acute gastroenteritis (p

We describe a case of severe swine influenza A(H1N1) virus infection in an immunocompetent middle-aged man in October 2016 in Italy who had only indirect exposure to pigs. The patient developed a severe acute distress respiratory syndrome which was successfully supported by extracorporeal membrane oxygenation and treated with antiviral therapy. The sole risk factor for influenza was a body mass index > 30 kg/m2. After a month of hospitalisation, the patient was discharged in good health.

Enterovirus 68 (EV-D68) was associated with mild to severe respiratory infections. In the last 4 years, circulation of different EV-D68 strains has been documented worldwide. In this study, the phylogenetic characterization of nine EV-D68 strains identified in patients in the 2010–2012 period and 12 additional EV-D68 Italian strains previously identified in 2008 in Italy was described. From January 2010 to December 2012, a total of 889 respiratory specimens from 588 patients stayed or visited at the Fondazione IRCCS Policlinico San Matteo were positive for HRV or HEV. Extracted nucleic acids were amplified by one-step RT-PCR with primer specific for VP1 region of EV-D68 and purified positive PCR products were directly sequenced. Overall, 9/3736 (0.24%) patients were EV-D68 positive. Of these, 7/9 (77.8%) were pediatric and two (22.2%) were adults. Five out of seven (71.4%) pediatric patients had lower respiratory tract infection with oxygen saturation

The coding sequences of five human enterovirus (HEV)-C genotype 105 strains recovered in Italy, Romania and Burundi from patients with upper and lower respiratory tract infections were analysed and phylogenetically compared with other circulating HEV-C strains. The EV-C105 was closely related to EV-C109 and EV-C118 strains. The European strains were similar to other circulating EV-C105 strains, while the two African EV-C105 clustered in separate bootstrap-supported (>0.90) branches of the P2 and P3 region trees. Minor inconsistencies in the clustering pattern of EV-C105 in the capsid region (P1) and non-capsid region (P3) suggest that recombination may have occurred in EV-C105 group B viruses. In conclusion, phylogenetic analysis revealed the circulation of two distinct EV-C105 lineages in Europe and Africa. A different pattern of evolution could be hypothesized for the two EV-C105 lineages.

A global reemergence of human enterovirus 68 (EV-D68) associated with severe respiratory illness occurred in 2014. We developed and validated an EV-D68-specific real-time reverse transcription-PCR (RT-PCR) for the detection of EV-D68 in respiratory samples. The rapid diagnosis of EV-D68 may contribute to better management of EV-D68 infections.

HIV, tuberculosis (TB) and TB/HIV co-infection prevalences were assessed in prisons PI and PII in Itirapina, SP, Brazil. This retrospective study was performed by consulting the records of diagnostic assays carried out at the Instituto Adolfo Lutz (IAL) Rio Claro Laboratory from January 2003 to December 2010. Culture for TB was performed on 24.3 % (1,375 samples) of PI and 25.8 % (3,332 samples) of PII, and HIV serology in 32.0 % (1,810 samples) of PI and 20.4 % (2,634 samples) of PII. There were 177 (4.0 %) HIV positive samples, 157 (3.3 %) positive culture for mycobacteria, and 16 (11.5 %) for TB/HIV. The prevalences of TB were 2.8 % and 3.6 % (p=0.160) for PI and PII respectively; of HIV, 2.1 % and 5.3 % (p

Radionuclides take a major role in guidelines of environmental agencies/national organizations of countries worldwide. In Brazil, CNEN-Comissao Nacional de Energia Nuclear is responsible for managing all subjects related to nuclear energy in the country. Thus, laboratories employing radionuclides for the development of their activities must submit a “Radioprotection Plan” to CNEN in order to get an operation license. Such plan must indicate that the laboratory is exempt of risks to the people involved and designed to fit all related environmental aspects. This was the case of LABIDRO-Hydrochemical and Isotopes Laboratory that belongs to IGCE-Geosciences and Exact Sciences Institute from UNESP – the University of the State of Sao Paulo “Julio de Mesquita Filho”, located at Rio Claro city, Sao Paulo State, Brazil. The total monthly activity of the radionuclides utilized during the laboratorial activities held at LABIDRO corresponds to 0.01 μCi. This paper describes all information provided by LABIDRO in order to get the CNEN license. The LABIDRO plan also showed the expected radioactive waste released when the experiments take place and CNEN decided that it fits the guidelines established by Brazilian legislation. Therefore, LABIDRO received its license for utilizing radionuclides, which is valid until September 2016.

In the diagnosis of pulmonary tuberculosis, sputum bacilloscopy was standardized by the WHO for slide preparation, staining, and reading the smear. The Brazilian Ministry of Health adopted this standardization for staining and reading, but the smear was extended to 2/3 of the slide, different to the elliptical format recommended by the WHO. This study aimed at comparing the two smear techniques by evaluating the sensitivity and specificity, preparation and reading times, and biosafety issues. Eight regional laboratories of the Adolfo Lutz Institute participated. Over three months, slides were prepared for 356 sputum samples using the two techniques. Reading of slides employed semi-quantitative counts using bacilloscopy index scale as recommended by the WHO and Brazilian Ministry of Health. The sensitivity of the elliptical smear was 97.0%, specificity 97.5%, accuracy 97.2%, and error 2.8%. Agreement of classification according to the scale was: 80.7% for rare BAAR, 83.7% for 1+, 89.8% for 2+, 90.9% for 3+ and 97.5% for negative cases (Kappa=0.87 p

The establishment of gut microbiota is reportedly aberrant in newborns admitted to neonatal intensive care units (NICUs), with detrimental long-term health impacts. Here, we vertically tracked the developing gut bacterial communities of newborns hosted in an NICU during an outbreak sustained by ESBL Klebsiella pneumoniae and compared colonized and non-colonized patients. Most communities were highly variable from one sampling point to the next, and dominated by few taxa, often Proteobacteria and Enterobacteriaceae, with marked interindividual variability. This picture was retrieved independently of colonization status or clinical covariates. Our data support the emerging idea of preterm infants as a population in which no defined microbial signatures are clearly associated to clinical status. Instead, the strong pressure of the nosocomial environment, antibiotics and, in this case, the ongoing outbreak, possibly drive the evolution of microbiota patterns according to individual conditions, also in non-colonized patients.

We describe two cases of Zika virus infection involving an Italian patient returning from the Dominican Republic and his wife, who remained in Italy and had not travelled to Zika virus endemic areas in the previous months. The infection was transmitted through unprotected sexual intercourse after the man's return to Italy.