Publications by authors named "Eleonora Cella"

116 Publications

SARS-CoV-2 Lineages and Sub-Lineages Circulating Worldwide: A Dynamic Overview.

Chemotherapy 2021 Mar 18:1-5. Epub 2021 Mar 18.

Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil,

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan, China, in early December 2019 has rapidly widespread worldwide, becoming one of the major global public health issues of the last centuries. Key Messages: Over the course of the pandemic, due to the advanced whole-genome sequencing technologies, an unprecedented amount of genomes have been generated, providing invaluable insights into the ongoing evolution and epidemiology of the virus during the pandemic. Therefore, this large amount of data played an important role in the SARS-CoV-2 mitigation and control strategies. Key Messages: The active monitoring and characterization of the SARS-CoV-2 lineages circulating worldwide is useful for a more specific diagnosis, better care, and timely treatment. In this review, a concise characterization of all the lineages and sub-lineages circulating and co-circulating across the world has been presented in order to determine the magnitude of the SARS-CoV-2 threat and to better understand the virus genetic diversity and its dispersion dynamics.
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http://dx.doi.org/10.1159/000515340DOI Listing
March 2021

Complete Genome Sequence of Exfoliative Toxin-Producing Staphylococcus aureus Strain MSSA_SSSS_01, Obtained from a Case of Staphylococcal Scalded-Skin Syndrome.

Microbiol Resour Announc 2021 Feb 11;10(6). Epub 2021 Feb 11.

Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA

Here, we announce the complete genome sequence of an exfoliative toxin-producing strain of sequence type 582 (ST582), isolated from a case of staphylococcal scalded-skin syndrome. The genome consists of a single circularized unitig with a total length of 2,792,190 bp carrying 2,699 genes. The genome is the basis for future epidemiological and genomic studies.
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http://dx.doi.org/10.1128/MRA.01335-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7883837PMC
February 2021

Epidemiology of Posterior Cruciate Ligament Reconstructions in Italy: A 15-Year Study.

J Clin Med 2021 Feb 1;10(3). Epub 2021 Feb 1.

Department of Orthopaedic and Trauma Surgery, Campus Bio-Medico University, Via Alvaro del Portillo, 200, Trigoria, 00128 Rome, Italy.

Background: The posterior cruciate ligament (PCL) is an essential element in knee stability. PCL reconstructions represent an under-investigated topic in the literature due to the rarity of this type of knee injury. This study aims to investigate the incidence of PCL reconstructive surgeries in Italy, following their trend during a 15-year period.

Methods: The National Hospital Discharge records (SDO) collected by the Italian Ministry of Health between January 2001 and October 2015 were analyzed. The database reports anonymous data comprising patients' ages, genders, International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes for diagnosis and intervention, census regions, regions of hospitalization, lengths of hospitalization and types of reimbursement.

Results: The overall incidence of PCL reconstructions in the Italian population during the study period was 0.46 surgeries per 100,000 inhabitants/year, ranging from 0.32 to 0.54. The median patient's age was 30 years old, and the male:female ratio was 5.3. PCL lesions were isolated in 39.7% of patients, while anterior cruciate ligament injuries were the most frequently associated lesions (31.1%).

Conclusions: The incidence of PCL reconstruction in Italy was low and stable during the study period. Young men are the category at the highest risk for these procedures. Given the paucity of epidemiological data on PCL reconstructions, this data may represent a reference for the current and foreseeable needs in PCL surgeries for countries sharing similar cultural context.
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http://dx.doi.org/10.3390/jcm10030499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7867089PMC
February 2021

Epidemiology of Anterior Cruciate Ligament Reconstruction Surgery in Italy: A 15-Year Nationwide Registry Study.

J Clin Med 2021 Jan 10;10(2). Epub 2021 Jan 10.

Department of Orthopaedic and Trauma Surgery, Campus Bio-Medico University, Via Alvaro del Portillo, 200, Trigoria, 00128 Rome, Italy.

There remains little information on the epidemiology of anterior cruciate ligament reconstruction (ACL-R), therefore, we performed an epidemiological evaluation on the ACL-R procedures performed in Italy from 2001 to 2015 to highlight potential disparities in access to healthcare. The National Hospital Discharge records (SDO) maintained at the Italian Ministry of Health were analyzed from 2001 to 2015; 248,234 ACL-Rs were performed in Italy over the 15-year study period in the adult population (starting from 15 years old), and the incidence rate per year in 100,000 persons ranged from 21.70 to 33.60 over the study period. The overall male/female ratio was 4.54. The length of hospitalization ranged from four days in 2001 to two days in 2015. Italy is historically divided into north, center, and south regions, and more than half of ACL-R surgery was performed in the north (67.2%); 95.2% of ACL-Rs were underwent in public institutions. The predicted model projected a slight growth in the number of ACL-Rs in the next 10 years (2016-2025). The number of ACL-R procedures increased in the adult population from 2001 to 2015. The ACL-R procedures were concentrated in the north of Italy, suggesting that efforts on regionalization of ACL-Rs should turn toward improving quality in hospitals in the south of Italy.
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http://dx.doi.org/10.3390/jcm10020223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7826510PMC
January 2021

Correction to: Epidemiology of Achilles tendon surgery in Italy: a nationwide registry study, from 2001 through 2015.

BMC Musculoskelet Disord 2020 Nov 10;21(1):728. Epub 2020 Nov 10.

Department of Orthopaedic and Trauma Surgery, Campus Bio-Medico University, Via Alvaro del Portillo, 200, Trigoria, 00128, Rome, Italy.

An amendment to this paper has been published and can be accessed via the original article.
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http://dx.doi.org/10.1186/s12891-020-03746-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7653848PMC
November 2020

Epidemiology of Achilles tendon surgery in Italy: a nationwide registry study, from 2001 through 2015.

BMC Musculoskelet Disord 2020 Oct 17;21(1):687. Epub 2020 Oct 17.

Department of Orthopaedic and Trauma Surgery, Campus Bio-Medico University, Via Alvaro del Portillo, 200, 00128 Trigoria, Rome, Italy.

Background: This study aims (1) to estimate the yearly number of Achilles tendon (AT) surgeries in Italy from 2001 to 2015 based on official hospitalization records; (2) to investigate the eventual presence of geographical variation in equity in access to AT surgery between three macroregions of Italy (North, Center and South); (3) to perform statistical projections of the number of AT procedure volumes and rates based on these data.

Methods: We analysed the National Hospital Discharge records (SDO) maintained at the Italian Ministry of Health for a 15-year period, from 2001 through 2015. These data are anonymous and include the patient's age (evaluated in the class of age), sex, census region, the region of hospitalization, length of the hospitalization, public or private reimbursement and diagnosis.

Results: During the 15-year study period, 118,652 AT repair were performed in Italy, whose peak of incidence was in 2010. More than half of AT repairs was performed in the North of Italy (52.1%), while 27.2% was performed in the South of Italy and 20.6% Center of Italy. The projection model predicted a slight growth of 2.65% in 2025 in comparison with 2015.

Conclusion: The current study provides detailed information about the national population-weighted incidence of AT surgery, distribution and projection. The peak of average age was 35-45 year. The majority of AT procedures was performed in the North of Italy. The projection model predicts a slight growth of AT surgery by 2025. Furthermore, this 15-year nationwide registry study shows that the age of incidence of AT injuries shifted from 30 to 40 to 35-45 years compared to the available literature. The higher prevalence of AT surgery was found in men during the working age. Moreover, a low rate of procedures in pediatric and elder age classes was observed.
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http://dx.doi.org/10.1186/s12891-020-03688-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7568369PMC
October 2020

Trends of anterior cruciate ligament reconstruction in children and young adolescents in Italy show a constant increase in the last 15 years.

Knee Surg Sports Traumatol Arthrosc 2020 Aug 8. Epub 2020 Aug 8.

Department of Orthopaedic and Trauma Surgery, Campus Bio-Medico University, Via Alvaro del Portillo, 200, 00128, Trigoria, Rome, Italy.

Purpose: The aim of this 15-year nationwide study was to investigate the trend in ACL reconstructive surgeries in patients younger than 15 years old in Italy, as well as their social and economic impact.

Materials And Methods: The National Hospital Discharge records (SDO) collected by the Italian Ministry of Health in the 15-year period between 2001 and 2015 were analyzed. This contains anonymous data including patients' age, gender, ICD-9-CM codes for diagnosis and intervention, census region, region of hospitalization, length of the hospitalization, and public or private reimbursement.

Results: 1,350 ACL reconstructions were performed in Italy in the population younger than 15 years old, with an incidence rate ranging from 0.16 to 2.04 procedures per 100,000 age-matched individuals. Similarly, the percentage of surgeries in 0-14 year old patients increased with respect to the total number of ACL reconstruction from 0.13% in 2001 to 0.95% in 2015. The age range 10-14 years is the most involved, accounting for 97.3% of surgeries recorded in the study period. The male:female ratio was 1.05 and most of these procedures were performed in the North of Italy (78.3%).

Conclusion: ACL reconstructions in patients aged 10-14 years are increasing constantly since 2001, and thus, specific actions aimed to define the best management strategy as well as national educational programs to prepare the future surgeons to this new reality are mandatory in the interest of the public health.

Level Of Evidence: Level III.
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http://dx.doi.org/10.1007/s00167-020-06203-1DOI Listing
August 2020

Draft Genome Sequence of sp. Strain CWR15, Isolated from a Gulf of Mexico Sponge.

Microbiol Resour Announc 2020 Mar 26;9(13). Epub 2020 Mar 26.

Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, USA

Here, we present the draft genome sequence of sp. strain CWR15, a bacterial symbiont of a Gulf of Mexico sponge. The genome consists of 35 contigs encoding 5,840 genes. The genome is the basis for future study and presents an underexplored taxonomy and biosynthetic potential.
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http://dx.doi.org/10.1128/MRA.00176-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7098904PMC
March 2020

High HIV-1 diversity in immigrants resident in Italy (2008-2017).

Sci Rep 2020 02 24;10(1):3226. Epub 2020 Feb 24.

National Center for the HIV/AIDS Research, Istituto Superiore di Sanità, Rome, Italy.

The proportion of new diagnoses of HIV infection in immigrants residing in Italy raised from 11% in 1992 to 29.7% in 2018. To investigate the HIV clades circulating in this community a retrospective study was performed in 557 HIV-infected immigrants living in 12 Italian cities. Immigrants originated from East-Europe and Central-Asia (11.7%), North Africa and Middle East (7.3%), South and South-East Asia (7.2%), Latin America and the Caribbean (14.4%), and sub-Saharan Africa (59.4%). More than 87% of immigrants were on antiretroviral therapy (ART), although 26.6% of them were viremic. A 22.0% of immigrants had hepatitis (HBV and/or HCV) and/or tuberculosis. HIV phylogenetic analysis on sequences from 192 immigrants showed the presence of clades B (23.4%), G (16.1%), C (10.4%), A1 (9.4%), F1 (5.2%), D (1.6%) and Circulating Recombinant Forms (CRFs) (33.9%). CRF02_AG represented 72.3% of the total CRFs. Clusters between immigrants and Italian natives were also present. Drug resistance mutations to NRTI, NNRTI, and PI drug classes occurred in 29.1% of ART-treated and in 12.9% of ART-naïve individuals. These data highlight the need for tailored public health interventions in immigrants to avoid spreading in Italy of HIV genetic forms and ART-resistant variants, as well as HIV co-morbidities.
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http://dx.doi.org/10.1038/s41598-020-59084-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7039940PMC
February 2020

Whole genome sequencing of carbapenem-resistant : evolutionary analysis for outbreak investigation.

Future Microbiol 2020 02 14;15:203-212. Epub 2020 Feb 14.

Unit of Medical Statistics & Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy.

Carbapenemase-resistant represents a major concern in hospital setting. The evolutionary history of carbapenem-resistant strains was analyzed by core genome multilocus sequence typing and Bayesian phylogenesis by whole genomes sequencing. A great increase carbapenem-resistant causing blood stream infection was observed in the years 2015-2016. At multilocus sequence typing (MLST), they were prevalently ST512 and ST101. ST512 were core genome (cg)MLST 53, while ST101 mainly cgMLST453. The minimum-spanning tree, based on cgMLST, showed strains clustering based on the different STs. By Bayesian phylogenetic analysis, maximum clade credibility tree showed that strains were introduced in the year 2005 with the most probable location in the ICU ward. Two outbreaks by ST101 and ST512 strains with Tower T8 as the probable location were evidenced. Molecular epidemiology is a powerful tool to track the way of transmission of resistant bacteria within the hospital setting.
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http://dx.doi.org/10.2217/fmb-2019-0074DOI Listing
February 2020

Molecular epidemiology of HIV-1 infection in immigrant population in northern Italy.

Epidemiol Infect 2020 02 5;148:e19. Epub 2020 Feb 5.

Department of Mental Health and Public Medicine, Campania University Luigi Vanvitelli, Naples, Italy.

Human immunodeficiency virus-1 (HIV-1) is characterised by a vast genetic diversity classified into distinct phylogenetic strains and recombinant forms. We describe the HIV-1 molecular epidemiology and evolution of 129 consecutive HIV-1 positive migrants living in Milan (northern Italy). Polymerase gene sequences of 116 HIV-1 subtype-B positive patients were aligned with HIV-1 reference sequences (https://www.ncbi.nlm.nih.gov/) by using MAFFT alignment and edited by using Bioedit software. A maximum likelihood (ML) phylogenetic tree was performed by MEGA7 and was visualised by using FigTree v1.4.3. Of 129 migrants, 35 were born in Europe (28 in Eastern Europe), 70 in the Americas (67 in South America), 15 in Africa and nine in Asia; 76.4% were men who have sex with men (MSM). The serotype HIV-1-B prevailed (89.9%), followed by -C, -F1, -D and -A. Compared with 116 HIV-B patients, the 13 with HIV-non-B showed lower Nadir of CD4+ cell/mmc (P = 0.043), more frequently had sub Saharan origin (38.5 vs. 1.72%, P = 0.0001) and less frequently were MSM (40 vs. 74.5%, P = 0.02). The ML phylogenetic tree of the 116 HIV-1 subtype-B positive patients showed 13 statistically supported nodes (bootstrap > 70%). Most of the sequences included in these nodes have been isolated from male patients from the Americas and the most common risk factor was MSM. The low number of HIV-1 non-B subtype patients did not allow to perform this analysis. These results suggest a shift of HIV-1 prevention projects' focus and a continuous monitoring of HIV-1 molecular epidemiology among entry populations. Prevention efforts based on HIV molecular epidemiology may improve public health surveillance setting.
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http://dx.doi.org/10.1017/S0950268819002012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7019499PMC
February 2020

Exploring the genetic diversity of the 16S rRNA gene of in IBD and IBS.

Future Microbiol 2019 11 18;14:1497-1509. Epub 2019 Dec 18.

Unit of Medical Statistics & Molecular Epidemiology, University Campus Bio-Medico, Rome, Italy.

The human gastrointestinal tract harbors diverse, abundant microbiota and is involved in this community. The aim of this study is to characterize 16 new 16S ribosomal RNA sequences selected from a metagenomic database from stools of patients with irritable bowel syndrome (IBS), inflammatory bowel diseases and control (CTRLs) subjects by a phylogenetic approach. A phylogenetic approach was used to study the genetic diversity and SNPs in 16 16S ribosomal RNA sequences from stools of 107 individuals, 36 of which were patients affected by IBS, 30 by inflammatory bowel disease and 41 were CTRLs. Phylogenetic analysis confirmed the subdivision into different supported clusters. An increase of variability in IBS has been identified. The genetic variation combined to the relative abundance, contribute to the protective role of . Phylogenesis represent an additional approach to investigate genetic variability.
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http://dx.doi.org/10.2217/fmb-2019-0175DOI Listing
November 2019

Correction to: HBV molecular epidemiology and clinical condition of immigrants living in Italy.

Infection 2020 Feb;48(1):147

Section of Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania Luigi Vanvitelli, Via L. Armanni 5, 80131, Naples, Italy.

The original version of this article unfortunately contained a mistake. The name of the author Mara Caroprese was rendered wrongly. The correct name is shown above.
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http://dx.doi.org/10.1007/s15010-019-01365-8DOI Listing
February 2020

Transmitted drug resistance mutations and trends of HIV-1 subtypes in treatment-naïve patients: A single-centre experience.

J Glob Antimicrob Resist 2020 03 10;20:298-303. Epub 2019 Sep 10.

Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy. Electronic address:

Objectives: Transmitted drug resistance (TDR) and HIV-1 genetic diversity may affect treatment efficacy and clinical outcomes. Here we describe the circulating viral subtypes and estimate the prevalence of drug resistance among antiretroviral therapy (ART)-naïve patients attending Sapienza University Hospital (Rome, Italy) from 2006-2017.

Methods: Genotypic resistance testing (GRT) was performed on 668 ART-naïve patients for integrase (n = 52), protease and reverse transcriptase (n = 668) sequences.

Results: Twenty-one different HIV-1 subtypes and circulating recombinant forms (CRFs) were identified. Subtype B was the most common (67.1%), followed by CRF02_AG (8.4%), and subtypes C and F (both 6.0%). A significantly increase in the proportion of non-B strains (P < 0.001) and the rate of non-Italian patients was observed over time. The overall prevalence of TDR was 9.4% (NRTI, 4.2%; NNRTI, 5.8%; and PI, 1.0%) and was higher in subtype B strains. Transmitted INSTI mutations (Q148H and G140S) responsible for high-level resistance to raltegravir and elvitegravir and intermediate resistance to dolutegravir and bictegravir were found, for the first time, in two individuals. Minor or accessory INSTI mutations were detected in 17.3% of patients. No significant decrease in the prevalence of TDR was documented over time.

Conclusion: The significant increase in non-B subtypes suggests that the molecular epidemiology of HIV-1 is changing. Detection of a major INSTI mutation in two ART-naïve patients highlights the importance of performing GRT before commencing treatment. This finding and the lack of a significant reduction in TDRs underline the importance of continuous surveillance of resistance mutations.
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http://dx.doi.org/10.1016/j.jgar.2019.08.024DOI Listing
March 2020

Phylogenetic Analysis of Multi-Drug Resistant Strains From Duodenoscope Biofilm: Microbiological Surveillance and Reprocessing Improvements for Infection Prevention.

Front Public Health 2019 6;7:219. Epub 2019 Aug 6.

Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy.

Duodenoscopes have been described as potential vehicles of patient-to-patient transmission of multi-drug resistant organisms. Carbapenem-resistant duodenoscope related infections have been described by the Center for Disease Control and the US Food and Drug Administration consequently to outbreaks occurring in the United States. These evidences suggested that improved microbiological surveillance and endoscope design optimization could represent valid tools to improve infection control. At this aim, in this study an example of duodenoscope microbiological surveillance and reprocessing improvement analyzing strains component of bacterial biofilm by phylogenetic analysis has been proposed. From September 2016 to December 2017, duodenoscope instruments were subjected to microbial surveillance by post-reprocessing cultures of liquid collected by internal channels of instruments after injection and aspiration cycles and membrane filtration. During surveillance seventeen , of which 10/17 (58.8%) MDR and KPC strains were collected from duodenoscope instruments plus one MDR strain from the rectal swab performed before ERCP procedure in an inpatient. The surveillance allowed evidencing potential failure of reprocessing procedure and performing consequent reprocessing improvements including the contaminated instruments quarantine until their negativity. Phylogenetic analysis of whole genome sequence of duodenoscope strains plus inpatients MDR strains, showed intermixing between duodenoscopes and inpatients, as evidenced by minimum spanning tree and time-scale Maximum Clade Credibility tree. In minimum spanning tree, three groups have been evidenced. Group I including strains, isolated from inpatients before microbiological surveillance adoption; group II including intermixed strains isolated from inpatients and strains isolated from duedonoscopes and group III including strains exclusively from duedonoscope instruments. In the Maximum Credibility Tree, a statistically supported cluster including two strains from duedonoscope instruments and one strains isolated from an inpatient was showed. From the first microbiologic surveillance performed on September 2016 and after the reprocessing improvement adoption, none MDR or susceptible strain was isolated in the following surveillance periods. In conclusion, these results should encourage hospital board to perform microbiological surveillance of duodenoscopes as well as of patients, by rectal swabs culture, and rapid molecular testing for antimicrobial resistance before any endoscopic invasive procedure.
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http://dx.doi.org/10.3389/fpubh.2019.00219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6691149PMC
August 2019

Fecal and Mucosal Microbiota Profiling in Irritable Bowel Syndrome and Inflammatory Bowel Disease.

Front Microbiol 2019 17;10:1655. Epub 2019 Jul 17.

Unit of Digestive Disease, Campus Bio-Medico University, Rome, Italy.

An imbalance in the bacterial species resulting in the loss of intestinal homeostasis has been described in inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS). In this prospective study, we investigated whether IBD and IBS patients exhibit specific changes in richness and distribution of fecal and mucosal-associated microbiota. Additionally, we assessed potential 16S rRNA gene amplicons biomarkers for IBD, IBS, and controls (CTRLs) by comparison of taxonomic composition. The relative abundance of bacteria, at phylum and genus/species levels, and the bacterial diversity were determined through 16S rRNA sequence-based fecal and mucosal microbiota analysis. Linear discriminant analysis effect size (LEfSe) was used for biomarker discovery associated to IBD and IBS as compared to CTRLs. In fecal and mucosal samples, the microbiota richness was characterized by a microbial diversity reduction, going from CTRLs to IBS to IBD. β-diversity analysis showed a clear separation between IBD and CTRLs and between IBD and IBS with no significant separation between IBS and CTRLs. β-diversity showed a clear separation between mucosa and stool samples in all the groups. In IBD, there was no difference between inflamed and not inflamed mucosa. Based upon the LEfSe data, the and Ruminococcaceae were identified as the most differentially abundant bacterial taxa in CTRLs. Erysipelotrichi was identified as potential biomarker for IBS, while Gammaproteobacteria, , and Enterococcaceae for IBD. This study provides an overview of the alterations of microbiota and may aid in identifying potential 16S rRNA gene amplicons mucosal biomarkers for IBD and IBS.
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http://dx.doi.org/10.3389/fmicb.2019.01655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6650632PMC
July 2019

The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review.

J Med Virol 2019 10 12;91(10):1707-1724. Epub 2019 Jul 12.

Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy.

In the last decade, the phylogenetic approach is recurrent in molecular evolutionary analysis. On 12 May, 2019, about 2 296 213 papers are found, but typing "phylogeny" or "epidemiology AND phylogeny" only 199 804 and 20 133 are retrieved, respectively. Molecular epidemiology in infectious diseases is widely used to define the source of infection as so as the ancestral relationships of individuals sampled from a population. Coalescent theory and phylogeographic analysis have had scientific application in several, recent pandemic events, and nosocomial outbreaks. Hepatitis viruses and immunodeficiency virus (human immunodeficiency virus) have been largely studied. Phylogenetic analysis has been recently applied on Polyomaviruses so as in the more recent outbreaks due to different arboviruses type as Zika and chikungunya viruses discovering the source of infection and the geographic spread. Data on sequences isolated by the microorganism are essential to apply the phylogenetic tools and research in the field of infectious disease phylodinamics is growing up. There is the need to apply molecular phylogenetic and evolutionary methods in areas out of infectious diseases, as translational genomics and personalized medicine. Lastly, the application of these tools in vaccine strategy so as in antibiotic and antiviral researchers are encouraged.
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http://dx.doi.org/10.1002/jmv.25526DOI Listing
October 2019

Baseline haematological and biochemical reference values for healthy male adults from Mali.

Pan Afr Med J 2019 4;32. Epub 2019 Jan 4.

Migrant Health Research Organisation (Mi-HeRO), Centro di Ricerca Sulla Salute delle Popolazioni Mobili e Globale, Italy; Department of Public Health and Infectious Diseases, Sapienza University of Rome, Policlinico Umberto I, Rome, Italy.

Introduction: Haematological reference values are very important for diagnostic orientation and treatment decision. The aim of this study was to establish haematological reference values for Malian healthy adults.

Methods: A cross-sectional study including 161 male Malians aged between 19 and 54 years old was performed. Median and reference ranges were calculated for haematological and biochemical parameters. Parametric student's t-test was used to determine any statistically significant differences by age, smoker status, body mass index (BMI) and occupation. Ranges were further compared with those reported for other African, Afro-American and Caucasian populations.

Results: Increased levels of MCV, MCH, PLT and EOS were found in younger Malians who had abnormal BMI and altered platelets parameters. Notably, significantly lower eosinophil and monocyte counts were observed in Malians compared to Europeans The smoking status did not seem to directly affect RIs.

Conclusion: This is the first study to determine normal laboratory parameters in Malian adult males. Our results underscore the necessity of establishing region-specific clinical reference ranges that would allow clinicians and practitioners to manage laboratory tests, diagnosis and therapies. These data are useful not only for the management of patients in Mali, but also to support European and American clinicians in the health management of asylum seekers and migrants from Mali.
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http://dx.doi.org/10.11604/pamj.2019.32.5.12797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6492302PMC
May 2019

The transmission dynamic of Madariaga Virus by bayesian phylogenetic analysis: Molecular surveillance of an emergent pathogen.

Microb Pathog 2019 Jul 25;132:80-86. Epub 2019 Apr 25.

Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy.

Madariaga Virus (MADV) is an emergent Alphavirus of the eastern equine encephalitis virus (EEEV) strain complex causing epizootic epidemics. In this study the genetic diversity and the transmission dynamics of Madariaga virus has been investigated by Bayesian phylogenetics and phylodynamic analysis. A database of 32 sequences of MADV group structural polyprotein were downloaded from GenBank, aligned manually edited by Bioedit Software. ModelTest v. 3.7 was used to select the simplest evolutionary model that adequately fitted the sequence data. Neighbor-joining tree was generated using MEGA7. The phylogenetic signal of the dataset was tested by the likelihood mapping analysis. The Bayesian phylogenetic tree was built using BEAST. Selective pressure analysis revealed one positive selection site. The phylogenetic trees showed two main clusters. In particular, Lineage II showed an epizootic infection in monkeys and Lineage III, including 2 main clusters (IIIa and IIIB), revealing an epizootic infection in humans in Haiti and an epizootic infection in humans in Venezuela during the 2016, respectively. The Bayesian maximum clade credibility tree and the time of the most common recent ancestor estimates, showed that the root of the tree dated back to the year 346 with the probable origin in Brazil. Gene flow analysis revealed viral exchanges between different neighbor countries of South America. In conclusion, Bayesian phylogenetic and phylodynamic represent useful tools to follow the transmission dynamic of emergent pathogens to prevent new epidemics spreading worldwide.
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http://dx.doi.org/10.1016/j.micpath.2019.04.039DOI Listing
July 2019

Correction to: Efficacy of radiofrequency ablation in autonomous functioning thyroid nodules. A systematic review and meta-analysis.

Rev Endocr Metab Disord 2019 Mar;20(1):45

Department of Nuclear Medicine and Thyroid Centre, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.

The authors of this paper declare that their correct family and first names and their correct affiliations are shown in this correction paper.
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http://dx.doi.org/10.1007/s11154-019-09499-8DOI Listing
March 2019

Efficacy of radiofrequency ablation in autonomous functioning thyroid nodules. A systematic review and meta-analysis.

Rev Endocr Metab Disord 2019 03;20(1):37-44

Department of Nuclear Medicine and Thyroid Centre, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.

Whether thermal ablation is effective to treat toxic thyroid nodules (TTN) is still unknown. Aim of this review was to achieve more robust evidence on the efficacy of radiofrequency ablation (RFA) in treating TTN in terms of TSH normalization, thyroid scintiscan, and volume reduction rate (VRR). A comprehensive literature search of PubMed/Medline and Scopus was performed in November 2018 to retrieve published studies. Original papers reporting TTN treated by RFA and later followed-up were eligible. Excluded were: articles not within this field, articles with unclear data, overlapping series, case/series reports. Discordances were solved in a final collegial meeting. Information was collected concerning population features, treatment procedure, follow-up, cases with TSH normalization, cases with scintiscan normalization, VRR of nodules. Pooled prevalence of patients with TSH or scintiscan normalization, and pooled VRR over time were calculated. For statistical analysis, the random-effects model was used. Eight articles published between 2008 and 2018 were included. The overall number of AFTN treated by RFA was 205. Five studies used a single session of treatment. The time of follow-up ranged from six to 24 months. The pooled rate of patients with TSH normalization was 57%. The pooled rate of patients with scintigraphically proven optimal response was 60%. The pooled VRR at 1 year was 79%. Baseline nodules volume was associated with the rate of TSH normalization. In conclusion, a moderate efficacy of RFA in treating TTN was found, and this can represent a solid starting point in this field.
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http://dx.doi.org/10.1007/s11154-019-09487-yDOI Listing
March 2019

Diffuse maculopapular rash: A family cluster during the last Chikungunya virus epidemic in Italy.

Clin Case Rep 2018 Dec 22;6(12):2322-2325. Epub 2018 Oct 22.

Unit of Medical Statistics and Molecular Epidemiology University Campus Bio-Medico of Rome Rome Italy.

A family cluster of father, mother, and daughter with Chikungunya virus (CHIKV) infection was diagnosed during last epidemic in Italy. In temperate area, during the summer season, clinicians should consider CHIKV infection in the differential diagnosis of patients with fever, maculopapular rash, polyarthralgia, and conjunctival erythema.
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http://dx.doi.org/10.1002/ccr3.1831DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6293132PMC
December 2018

Genetic diversity in the env V1-V2 region of proviral quasispecies from long-term controller MHC-typed cynomolgus macaques infected with SHIVSF162P4cy.

J Gen Virol 2018 12 12;99(12):1717-1728. Epub 2018 Oct 12.

1​National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161 Rome, Italy.

Intra-host evolution of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) has been shown by viral RNA analysis in subjects who naturally suppress plasma viremia to low levels, known as controllers. However, little is known about the variability of proviral DNA and the inter-relationships among contained systemic viremia, rate of reservoir reseeding and specific major histocompatibility complex (MHC) genotypes, in controllers. Here, we analysed the proviral DNA quasispecies of the env V1-V2 region, in PBMCs and in anatomical compartments of 13 long-term controller monkeys after 3.2 years of infection with simian/human immunodeficiency virus (SHIV)SF162P4cy. A considerable variation in the genetic diversity of proviral quasispecies was present among animals. Seven monkeys exhibited env V1-V2 proviral populations composed of both clusters of identical ancestral sequences and new variants, whereas the other six monkeys displayed relatively high env V1-V2 genetic diversity with a large proportion of diverse novel sequences. Our results demonstrate that in SHIVSF162P4cy-infected monkeys there exists a disparate pattern of intra-host viral diversity and that reseeding of the proviral reservoir occurs in some animals. Moreover, even though no particular association has been observed between MHC haplotypes and the long-term control of infection, a remarkably similar pattern of intra-host viral diversity and divergence was found within animals carrying the M3 haplotype. This suggests that in animals bearing the same MHC haplotype and infected with the same virus, viral diversity follows a similar pattern with similar outcomes and control of infection.
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http://dx.doi.org/10.1099/jgv.0.001159DOI Listing
December 2018

Human hepatitis E virus circulation in Bulgaria: Deep Bayesian phylogenetic analysis for viral spread control in the country.

J Med Virol 2019 01 24;91(1):132-138. Epub 2018 Sep 24.

Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy.

Hepatitis E virus (HEV) infection in Bulgaria is endemic, as demonstrated by the seroprevalence of antibody against the virus in the general population and by the high prevalence of clinical cases registered. In this study, a deep Bayesian phylogenetic analysis has been performed to provide information on the genetic diversity and the spread of HEV genotypes in Bulgaria. Three different data sets of HEV virus was built for genotyping by the maximum likelihood method, for evolutionary rate estimated by Bayesian Markov Chain Monte Carlo approach, for demographic history investigation and for selective pressure analysis. The evolutionary rate for genotype 3e, was 351 × 10 substitution/site/year (95% highest posterior density [95% HPD]: 145 × 10 -575 × 10 ). The root of the time to the most recent common ancestor of the Bayesian maximum clade credibility tree of HEV 3e genotype corresponded to 1965 (HPD 95% 1949-1994). The Bulgarian sequences mainly clustered in the main clade (clade A). The monophyletic clade included all Bulgarian genotype 3e sequences. The demographic history showed a slight growth from 1995 to 2000, followed by a sort of bottleneck in 2010s, a peak in 2011 and a new growth to 2015. Selection pressure analysis did not show sites under positive pressure but 64 statistically significant sites under negative selection. Molecular epidemiological surveillance by Bayesian phylogeny of HEV virus can contribute to trace the way of human infection after contact with swine source directly or heating meat improving public health control.
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http://dx.doi.org/10.1002/jmv.25296DOI Listing
January 2019

MALDI-TOF MS Identification and Clustering Applied to Species in Nosocomial Setting.

Front Microbiol 2018 14;9:1885. Epub 2018 Aug 14.

Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy.

microorganisms cause important bacterial infections in humans. Recently, carbapenem resistant isolates carrying the KPC gene were described and their clonal transmission in different nosocomial outbreaks reported. In this study, the relative numbers of species, their antimicrobial susceptibility along 3 years of observation and the identification ability of the two most common MALDI-TOF platforms were evaluated. A clustering analysis was performed to identify changes in the microbial population within the nosocomial environment. were identified using two platforms (MALDI-TOF Biotyper and VITEK MS). Antimicrobial susceptibility was tested by Vitek2 Compact and MIC and MIC was evaluated using GraphPad software. Clustering analysis was performed by MALDI-TOF and a dendrogram was built with both platforms and compared. The most frequent species isolated were and with a gradual increase of in 2017. MALDI-TOF platforms showed a very good sensitivity and specificity except for identification that was reliable only by MALDI-TOF MS Biotyper. An increase of resistance for , confirmed by the isolation of extended spectrum beta-lactamase (ESBL) strains and the emergence of multidrug-resistant (MDR) and carbapenem resistant strains, was observed. A clonal route of transmission involving general surgery and geriatric wards was evidenced as previously described for MDR strains in the same nosocomial setting. These data represent an important source of information about the spreading of in the nosocomial environment.
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http://dx.doi.org/10.3389/fmicb.2018.01885DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6102349PMC
August 2018

Multi-drug resistant Pseudomonas aeruginosa nosocomial strains: Molecular epidemiology and evolution.

Microb Pathog 2018 Oct 19;123:233-241. Epub 2018 Jul 19.

Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy.

Pseudomonas aeruginosa causes a wide variety of nosocomial infections. In the study, phylogenetic, selective pressure analysis and homology modelling were applied to oprD efflux pump gene with the aim to characterize multi-drug resistant strains circulating in the nosocomial setting, their transmission dynamics and ongoing evolution. One hundred ninety-three consecutive inpatients with Pseudomonas aeruginosa infection were enrolled at the University Campus Bio-Medico of Rome, between January 2015 and December 2016. oprD gene was sequenced in 20 nosocomial multi-drug resistant P. aeruginosa strains. Phylogeographic, selective pressure, residue conservation analysis and homology modelling were performed. Clinical epidemiological data were extracted from patient medical records. Multi-drug resistant strains accounted for the 36% of total strains and were responsible of 20 cases of nosocomial infections. P. aeruginosa infections occurred prevalently in the West area, especially at the location IIIW and in the Geriatric ward. The time of the most recent common ancestor indicated that strains could have been introduced in the hospital since the end of the year 2009 with the most probable location in general surgery ward. By selective pressure analysis, 29 positions under diversifying selection have been identified and mapped onto the OprD model. Most of the observed residue substitutions are predicted to be destabilizing and some of them occurred in the Loops 2 and 3 that are involved in solute selection and carbapenem susceptibility. The molecular and evolutionary analysis of Multi-drug resistant strains circulating in the nosocomial setting may provide useful insights into the epidemiology and the mechanisms leading to resistance, contributing to infection control improvement.
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http://dx.doi.org/10.1016/j.micpath.2018.07.020DOI Listing
October 2018

HIV-2 Infection in a Migrant from Gambia: The History of the Disease Combined with Phylogenetic Analysis Revealed the Real Source of Infection.

AIDS Res Hum Retroviruses 2018 12 15;34(12):1090-1094. Epub 2018 Aug 15.

Unit of Medical Statistic and Moelcular Epidemiology, University Campus Bio-Medico, Rome, Italy.

Human immunodeficiency virus type 2 (HIV-2) infection prevalence is increasing in some European countries. The increasing migratory flow from countries where HIV-2 is endemic has facilitated the spread of the virus into Europe and other regions. We describe a case of HIV-2 infection in a migrant individual in the Asylum Seekers Centre (ASC) in Italy. The patient's virus was sequenced and found to be a typical HIV-2 genotype A virus. Bayesian evolutionary analysis revealed that the HIV-2 sequence from migrant dated back to 1986 in a subcluster, including sequences from Guinea Bissau. This was coherent with the history of the migrant who lived in Guinea Bissau from his birth until 1998 when he was 13 years old. Monitoring for HIV-2 infection in migrants from western Africa is necessary using adequate molecular tools to improve the diagnosis and understand the real origin of infection.
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http://dx.doi.org/10.1089/AID.2018.0112DOI Listing
December 2018

Hepatitis E virus genotypes and subgenotypes causing acute hepatitis, Bulgaria, 2013-2015.

PLoS One 2018 7;13(6):e0198045. Epub 2018 Jun 7.

Viral Hepatitis and Oncovirus and Retrovirus Diseases Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.

Background: In industrialized areas of the world, including Europe, Hepatitis E Virus (HEV) is considered an emerging pathogen. In fact, autochthonous cases caused by HEV genotype 3 (HEV-3) are increasingly reported. Several studies described the human HEV-3 subtypes and strains circulating in West Europe countries; in contrast, very little is known about the HEV strains responsible for acute hepatitis E in countries of East Europe/Balkans, such as Bulgaria.

Methods And Findings: Anti-HEV IgM positive serum samples (n = 103) from acute hepatitis cases (2013-2015) from all over Bulgaria were analysed for HEV RNA by Real-Time PCR. Viremia was detected in 90/103 samples. A fragment of the viral genome (ORF-2 region) was amplified by nested PCR from 76/90 viremic samples, leading to a sequence in 64 of them. Genotyping by phylogenetic analysis with standard reference sequences showed HEV-1 in 1/64 cases, HEV-3 in 63/64. Subtyping of HEV-3 sequences showed 3e (39/63, 62%), 3f (n = 15/63, 24%) and 3c (n = 8/63, 13%) subtypes; in one case the sequence subtype was uncertain and classified as 3hi. In the phylogenetic tree, most 3e sequences grouped in two well distinct clusters (A and B), each one with very low intragroup genetic distances. In contrast, 3f and 3c were interspersed with reference sequences and showed lower tendency to cluster and/or higher intragroup distances. Geographically, while 3f and 3c were scattered throughout the country, 3e was restricted to the South-West area, with most cases in two towns about 40 kilometres apart from each other.

Conclusions: Most acute hepatitis E cases in Bulgaria are caused by HEV-3, subtypes 3e, 3f and 3c. Circulation of 3e appears quite different from 3f and 3c, with 3e restricted to the South-West area while 3f and 3c diffused over the country. The factors underlying the observed molecular and geographical differences remain to be investigated.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0198045PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991722PMC
December 2018

HBV molecular epidemiology and clinical condition of immigrants living in Italy.

Infection 2018 Aug 23;46(4):523-531. Epub 2018 May 23.

Section of Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania Luigi Vanvitelli, Via L. Armanni 5, 80131, Naples, Italy.

Introduction: We investigated 170 HBsAg-positive immigrants living in Italy for 1-7 years to ascertain whether they may have become infected in the host country.

Methods: Of 2032 adult immigrants interviewed, 1727 (85%) voluntarily adhered to a screening program for bloodborne or sexually transmitted infections. HBsAg was detected in 170 (9.8%) screened immigrants who completed the diagnostic, clinical and therapeutic process at the nearest clinic of infectious diseases. HBV molecular biology was performed applying a homemade technology. Phylogenetic signal of the datasets was obtained by a likelihood-mapping analysis using TreePuzzle.

Results: Of the 170 HBsAg-positive immigrants, 133 were inactive carriers, 29 had chronic hepatitis and 8 compensated cirrhosis. HBV genotype was identified in 109 of the 113 HBV-DNA-positive immigrants and HBV-genotype-E predominated (68.9%). Of these 109, 6 (5.5%) subjects showed an HBV genotype absent or extremely rare in their native country: HBV-genotype-E in three from Eastern Europe and in one from Sri Lanka, possibly acquired from other immigrants from sub-Saharan countries, HBV-genotype-D1 in one from Burkina Faso and one from Senegal, possibly acquired in Italy.

Conclusion: The data suggest that immigrants may acquire HBV infection in Italy and, therefore, HBV vaccination programs should be extended to all immigrants living in Italy.
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http://dx.doi.org/10.1007/s15010-018-1153-1DOI Listing
August 2018