Francesco Messina
@inmi.it
Scopus Publications
Scopus Publications
Angela Cannas, Ornella Butera, Antonio Mazzarelli, Francesco Messina, Antonella Vulcano, Mario Pasquale Parracino, Gina Gualano, Fabrizio Palmieri, Antonino Di Caro, Carla Nisii,et al.
MDPI AG
Over the past years, Tuberculosis (TB) control strategies have been effective in reducing drug-resistant (DR) TB globally; however, a wider implementation of new diagnostic strategies, such as Whole genome sequencing (WGS), would be critical for further improvement. The aim of this study, based on WGS of Mycobacterium tuberculosis (MTB) strains isolated in a TB referral center over 6 years, was to evaluate the efficacy of this methodology in improving therapy guidance for clinicians and in improving the understanding of the epidemiology of TB transmission. WGS was performed in addition to pDST on 1001 strains consecutively isolated between January 2016 and December 2021; the results allowed us to improve the quality of data on resistance and to identify possible clusters of transmission. Prediction of rifampicin-resistant (RR) or multi-drug-resistant TB strains (MDR-TB, defined as resistance to at least rifampicin and isoniazid) was obtained for 50 strains (5%). Mutations predictive of an MDR isolate were further characterized, and Ser450Leu and Ser315Thr were found to be the most frequent mutations in rpoB and katG genes, respectively. Discordances between WGS and phenotypic drug susceptibility testing (pDST) were found in few strains, and their impact on clinical decisions and outcome was addressed. The introduction of WGS in our Institute improved our diagnostic routine, allowing accurate patient management, and was a valid instrument for epidemiological investigations and infection control.
Angela Cannas, Antonella Campanale, Daniela Minella, Francesco Messina, Ornella Butera, Carla Nisii, Antonio Mazzarelli, Carla Fontana, Lucia Lispi, Francesco Maraglino,et al.
MDPI AG
Background: From 2013 onwards, a large outbreak of Mycobacterium chimaera (MC) invasive infection, which was correlated with the use of contaminated heater–cooler units (HCUs) during open chest surgery, was reported from all over the world. Here, we report the results of the epidemiological and molecular investigations conducted in Italy after the alarm raised about this epidemic event. Methods: MC strains isolated from patients or from HCU devices were characterized by genomic sequencing and molecular epidemiological analysis. Results: Through retrospective epidemiological analysis conducted between January 2010 and December 2022, 40 possible cases of patients infected with MC were identified. Thirty-six strains isolated from these patients were analysed by whole genome sequencing (WGS) and were found to belong to the genotypes 1.1 or 1.8, which are the genotypes correlated with the outbreak. Most of the cases presented with prosthetic valve endocarditis, vascular graft infection or disseminated infection. Among the cases found, there were 21 deaths. The same analysis was carried out on HCU devices. A total of 251 HCUs were found to be contaminated by MC; genotypes 1.1 or 1.8 were identified in 28 of those HCUs. Conclusions: To ensure patients’ safety and adequate follow-up, clinicians and general practitioners were made aware of the results and public health measures, and recommendations were issued to prevent further cases in the healthcare settings. The Italian Society of Cardiac Surgery performed a national survey to assess the incidence of HCU-related MC prosthetic infections in cardiac surgery. No cases were reported after HCU replacement or structural modification and disinfection and possibly safe allocation outside surgical rooms.
Anna Niarakis, Marek Ostaszewski, Alexander Mazein, Inna Kuperstein, Martina Kutmon, Marc E. Gillespie, Akira Funahashi, Marcio Luis Acencio, Ahmed Hemedan, Michael Aichem,et al.
Frontiers Media SA
IntroductionThe COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. MethodsExtensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors.ResultsResults revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19. DiscussionThe key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.
Martina Rueca, Simone Lanini, Emanuela Giombini, Francesco Messina, Concetta Castilletti, Giuseppe Ippolito, Maria Rosaria Capobianchi, and Maria Beatrice Valli
Springer Science and Business Media LLC
Abstract Background The aim of this study was to characterize the genome of a recombinant Enterovirus associated with severe and fatal nosocomial infection; it was typed as Echovirus 11 (E-11) according to the VP1 gene. Enterovirus infection is generally asymptomatic and self-limited, but occasionally it may progress to a more severe clinical manifestation, as in the case described here. Recombination plays a crucial role in the evolution of Enteroviruses (EVs) and has been recognized as the main driving force behind the emergence of epidemic strains associated with severe infection. Therefore, it is of utmost importance to monitor the circulation of recombinant strains for surveillance purposes. Methods Enterovirus-RNA was detected in the serum and liver biopsy of patients involved in the nosocomial cluster by commercial One-Step qRT-PCR method and the Enterovirus strains were isolated in vitro. The EVs typing was determined by analyzing the partial-length of the 5′UTR and VP1 sequences with the web-based open-access Enterovirus Genotyping Tool Version 0.1. The amplicons targeting 5′UTR, VP1 and overlapping fragments of the entire genome were sequenced with the Sanger method. Phylogenetic analysis was performed comparing the VP1 and the full-genome sequences of our strains against an appropriate reference set of Enterovirus prototypes of the Picornaviridae genera and species retrieved from the Enterovirus Genotyping Tool. Recombination analysis was performed using RDP4 software. Results The Neighbor-Joining tree of the VP1 gene revealed that the 4 patients were infected with an identical molecular variant of Echovirus 11 (E-11). While the phylogenetic and the RDP4 analysis of the full-genome sequences provided evidence that it was a chimeric strain between an E-11 and a Coxsackievirus B (CV-B). Conclusions The chimeric structure of the E-11 genome might have contributed to the severe infection and epidemic feature of the strain, but further biological characterizations are needed. The evidence reported in this study, highlights the limit of typing techniques based on the VP1 gene, as they fail to identify the emergence of recombinant strains with potentially more pathogenic or epidemic properties, thus providing only partial information on the epidemiology and pathogenesis of Enteroviruses.
F. Bisognin, F. Messina, O. Butera, C. Nisii, A. Mazzarelli, S. Cristino, M. R. Pascale, G. Lombardi, A. Cannas, and P. Dal Monte
American Society for Microbiology
Our manuscript focuses on interventions to reduce waterborne disease transmission, improve sanitation, and control infection. Sanitary water can be contaminated by nontuberculous Mycobacteria, including M. chimaera , a causative agent of invasive infections in immunocompromised patients.
Daniele Pietrucci, Adelaide Teofani, Marco Milanesi, Bruno Fosso, Lorenza Putignani, Francesco Messina, Graziano Pesole, Alessandro Desideri, and Giovanni Chillemi
MDPI AG
In recent years, the involvement of the gut microbiota in disease and health has been investigated by sequencing the 16S gene from fecal samples. Dysbiotic gut microbiota was also observed in Autism Spectrum Disorder (ASD), a neurodevelopmental disorder characterized by gastrointestinal symptoms. However, despite the relevant number of studies, it is still difficult to identify a typical dysbiotic profile in ASD patients. The discrepancies among these studies are due to technical factors (i.e., experimental procedures) and external parameters (i.e., dietary habits). In this paper, we collected 959 samples from eight available projects (540 ASD and 419 Healthy Controls, HC) and reduced the observed bias among studies. Then, we applied a Machine Learning (ML) approach to create a predictor able to discriminate between ASD and HC. We tested and optimized three algorithms: Random Forest, Support Vector Machine and Gradient Boosting Machine. All three algorithms confirmed the importance of five different genera, including Parasutterella and Alloprevotella. Furthermore, our results show that ML algorithms could identify common taxonomic features by comparing datasets obtained from countries characterized by latent confounding variables.
Anna Camporesi, Annalisa De Silvestri, Veronica Diotto, Stefania Ferrario, Laura Eccher, Alessandra De Ferrari, Francesco Messina, Gloria Pelizzo, Davide Mileto, Valeria Calcaterra,et al.
Frontiers Media SA
Reliable testing methods for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in children are essential to allow normal activities. Diagnosis of SARS-CoV-2 infection is currently based on real-time reverse transcriptase-polymerase chain reaction (RT-PCR) performed on nasopharyngeal (NP) swabs; concerns have been raised regarding NP swab accuracy in children to detect the virus because of potential lack of cooperation of the patients or due to general uncertainties about concordance between high and low respiratory tract specimens in children. The aim of the study (IRB approval: ST/2020/405) is to prospectively compare RT-PCR results on NP and tracheo-bronchial aspirate (TA) in children admitted to the hospital for surgery or admitted to the Pediatric Intensive Care Unit (PICU) of a tertiary children hospital in Milano, Italy, during a peak of COVID-19 infections in the city. A total of 385 patients were enrolled in the study: 364 from surgical theater and 21 from PICU. Two patients (0.5%) tested positive on TA and were negative on NP; both cases occurred in November 2020, during a peak of infection in the city. Specificity of NP swab was.995 (95% CI: 0.980–0.999). Two patients with positive NP swabs tested negative on TA.ConclusionOur study shows that the specificity of SARS-CoV-2 RT-PCR on TA swab, compared to results of SARS-CoV-2 RT-PCR on NP, was very high for negative cases in our pediatric cohort during a period of high epidemiological pressure.
Francesca Colavita, Silvia Meschi, Cesare Ernesto Maria Gruber, Martina Rueca, Francesco Vairo, Giulia Matusali, Daniele Lapa, Emanuela Giombini, Gabriella De Carli, Martina Spaziante,et al.
Frontiers Media SA
BackgroundVaccines for coronavirus disease 2019 (COVID-19) are proving to be very effective in preventing severe illness; however, although rare, post-vaccine infections have been reported. The present study focuses on virological and serological features of 94 infections that occurred in Lazio Region (Central Italy) between 27 December 2020, and 30 March 2021, after one or two doses of mRNA BNT162b2 vaccine.MethodsWe evaluated clinical features, virological (viral load; viral infectiousness; genomic characterisation), and serological (anti-nucleoprotein Ig; anti-Spike RBD IgG; neutralising antibodies, nAb) characteristics of 94 post-vaccine infections at the time of diagnosis. Nasopharyngeal swabs (NPSs) and serum samples were collected in the framework of the surveillance activities on SARS-CoV-2 variants established in Lazio Region (Central Italy) and analysed at the National Institute for Infectious Diseases “L. Spallanzani” in Rome.ResultsThe majority (92.6%) of the post-vaccine infections showed pauci/asymptomatic or mild clinical course, with symptoms and hospitalisation rate significantly less frequent in patients infected after full vaccination course as compared to patients who received a single dose vaccine. Although differences were not statistically significant, viral loads and isolation rates were lower in NPSs from patients infected after receiving two vaccine doses as compared to patients with one dose. Most cases (84%) had nAb in serum at the time of infection diagnosis, which is a sub-group of vaccinees, were found similarly able to neutralise Alpha and Gamma variants. Asymptomatic individuals showed higher nAb titres as compared to symptomatic cases (median titre: 1:120 vs. 1:40, respectively). Finally, the proportion of post-vaccine infections attributed either to Alpha and Gamma variants was similar to the proportion observed in the contemporary unvaccinated population in the Lazio region, and mutational analysis did not reveal enrichment of a defined set of Spike protein substitutions depending on the vaccination status.ConclusionOur study conducted using real-life data, emphasised the importance of monitoring vaccine breakthrough infections, through the characterisation of virological, immunological, and clinical features associated with these events, in order to tune prevention measures in the next phase of the COVID-19 pandemic.
Martina Rueca, Emanuela Giombini, Francesco Messina, Barbara Bartolini, Antonino Di Caro, Maria Rosaria Capobianchi, and Cesare EM Gruber
JMIR Publications Inc.
Background Early sequencing and quick analysis of the SARS-CoV-2 genome have contributed to the understanding of the dynamics of COVID-19 epidemics and in designing countermeasures at a global level. Objective Amplicon-based next-generation sequencing (NGS) methods are widely used to sequence the SARS-CoV-2 genome and to identify novel variants that are emerging in rapid succession as well as harboring multiple deletions and amino acid–changing mutations. Methods To facilitate the analysis of NGS sequencing data obtained from amplicon-based sequencing methods, here, we propose an easy-to-use SARS-CoV-2 genome assembler: the Easy-to-use SARS-CoV-2 Assembler (ESCA) pipeline. Results Our results have shown that ESCA could perform high-quality genome assembly from Ion Torrent and Illumina raw data and help the user in easily correct low-coverage regions. Moreover, ESCA includes the possibility of comparing assembled genomes of multisample runs through an easy table format. Conclusions In conclusion, ESCA automatically furnished a variant table output file, fundamental to rapidly recognizing variants of interest. Our pipeline could be a useful method for obtaining a complete, rapid, and accurate analysis even with minimal knowledge in bioinformatics.
Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta‐Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab,et al.
EMBO
Marek Ostaszewski , Anna Niarakis , Alexander Mazein, Inna Kuperstein , Robert Phair , Aurelio Orta-Resendiz , Vidisha Singh , Sara Sadat Aghamiri , Marcio Luis Acencio , Enrico Glaab , Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Crist obal Monraz G omez, Julia Somers , Matti Hoch , Shailendra Kumar Gupta , Julia Scheel, Hanna Borlinghaus, Tobias Czauderna , Falk Schreiber, Arnau Montagud , Miguel Ponce de Leon , Akira Funahashi , Yusuke Hiki, Noriko Hiroi , Takahiro G Yamada, Andreas Dr€ager , Alina Renz, Muhammad Naveez , Zsolt Bocskei , Francesco Messina , Daniela Börnigen , Liam Fergusson, Marta Conti, Marius Rameil , Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E Ackerman, Jason E Shoemaker, Jeremy Zucker , Kristie Oxford, Jeremy Teuton , Ebru Kocakaya , Gökçe Ya gmur Summak , Kristina Hanspers, Martina Kutmon , Susan Coort, Lars Eijssen, Friederike Ehrhart , D A B Rex , Denise Slenter , Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff-Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan , Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel , Rupsha Fraser, Vera Ortseifen , Silvia Marchesi , Piotr Gawron, Ewa Smula, Laurent Heirendt , Venkata Satagopam, Guanming Wu, Anders Riutta , Martin Golebiewski , Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W Overall , Dieter Maier, Angela Bauch , Benjamin M Gyori , John A Bachman , Carlos Vega , Valentin Grou es, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna , Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas , Marina Esteban-Medina, Maria Pe~ na-Chilet, Kinza Rian, Tom a s Helikar , Bhanwar Lal Puniya , Dezso Modos , Agatha Treveil , Marton Olbei , Bertrand De Meulder , Stephane Ballereau, Aur elien Dugourd, Aur elien Naldi , Vincent No€el, Laurence Calzone, Chris Sander , Emek Demir, Tamas Korcsmaros , Tom C Freeman, Franck Aug e , Jacques S Beckmann , Jan Hasenauer , Olaf Wolkenhauer, Egon L Willighagen, Alexander R Pico, Chris T Evelo , Marc E Gillespie , Lincoln D Stein, Henning Hermjakob , Peter D’Eustachio , Julio Saez-Rodriguez , Joaquin Dopazo , Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray , Rudi Balling , Reinhard Schneider & the COVID-19 Disease Map Community
Chiara Montaldo, Francesco Messina, Isabella Abbate, Manuela Antonioli, Veronica Bordoni, Alessandra Aiello, Fabiola Ciccosanti, Francesca Colavita, Chiara Farroni, Saeid Najafi Fard,et al.
Springer Science and Business Media LLC
Abstract Background Omics data, driven by rapid advances in laboratory techniques, have been generated very quickly during the COVID-19 pandemic. Our aim is to use omics data to highlight the involvement of specific pathways, as well as that of cell types and organs, in the pathophysiology of COVID-19, and to highlight their links with clinical phenotypes of SARS-CoV-2 infection. Methods The analysis was based on the domain model, where for domain it is intended a conceptual repository, useful to summarize multiple biological pathways involved at different levels. The relevant domains considered in the analysis were: virus, pathways and phenotypes. An interdisciplinary expert working group was defined for each domain, to carry out an independent literature scoping review. Results The analysis revealed that dysregulated pathways of innate immune responses, (i.e., complement activation, inflammatory responses, neutrophil activation and degranulation, platelet degranulation) can affect COVID-19 progression and outcomes. These results are consistent with several clinical studies. Conclusions Multi-omics approach may help to further investigate unknown aspects of the disease. However, the disease mechanisms are too complex to be explained by a single molecular signature and it is necessary to consider an integrated approach to identify hallmarks of severity.
Alessandra Vergori, , Patrizia Lorenzini, Alessandro Cozzi-Lepri, Davide Roberto Donno, Gina Gualano, Emanuele Nicastri, Fabio Iacomi, Luisa Marchioni, Paolo Campioni,et al.
Springer Science and Business Media LLC
AbstractProphylactic low molecular weight heparin (pLMWH) is currently recommended in COVID-19 to reduce the risk of coagulopathy. The aim of this study was to evaluate whether the antinflammatory effects of pLMWH could translate in lower rate of clinical progression in patients with COVID-19 pneumonia. Patients admitted to a COVID-hospital in Rome with SARS-CoV-2 infection and mild/moderate pneumonia were retrospectively evaluated. The primary endpoint was the time from hospital admission to orotracheal intubation/death (OTI/death). A total of 449 patients were included: 39% female, median age 63 (IQR, 50–77) years. The estimated probability of OTI/death for patients receiving pLMWH was: 9.5% (95% CI 3.2–26.4) by day 20 in those not receiving pLMWH vs. 10.4% (6.7–15.9) in those exposed to pLMWH; p-value = 0.144. This risk associated with the use of pLMWH appeared to vary by PaO2/FiO2 ratio: aHR 1.40 (95% CI 0.51–3.79) for patients with an admission PaO2/FiO2 ≤ 300 mmHg and 0.27 (0.03–2.18) for those with PaO2/FiO2 > 300 mmHg; p-value at interaction test 0.16. pLMWH does not seem to reduce the risk of OTI/death mild/moderate COVID-19 pneumonia, especially when respiratory function had already significantly deteriorated. Data from clinical trials comparing the effect of prophylactic vs. therapeutic dosage of LMWH at various stages of COVID-19 disease are needed.
Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta‐Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab,et al.
EMBO
We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS‐CoV‐2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large‐scale community effort to build an open access, interoperable and computable repository of COVID‐19 molecular mechanisms. The COVID‐19 Disease Map (C19DMap) is a graphical, interactive representation of disease‐relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph‐based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS‐CoV‐2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID‐19 or similar pandemics in the long‐term perspective.
Francesco Messina, Emanuela Giombini, Chiara Montaldo, Ashish Arunkumar Sharma, Antonio Zoccoli, Rafick-Pierre Sekaly, Franco Locatelli, Alimuddin Zumla, Markus Maeurer, Maria R. Capobianchi,et al.
Springer Science and Business Media LLC
AbstractIn the last months, many studies have clearly described several mechanisms of SARS-CoV-2 infection at cell and tissue level, but the mechanisms of interaction between host and SARS-CoV-2, determining the grade of COVID-19 severity, are still unknown. We provide a network analysis on protein–protein interactions (PPI) between viral and host proteins to better identify host biological responses, induced by both whole proteome of SARS-CoV-2 and specific viral proteins. A host-virus interactome was inferred, applying an explorative algorithm (Random Walk with Restart, RWR) triggered by 28 proteins of SARS-CoV-2. The analysis of PPI allowed to estimate the distribution of SARS-CoV-2 proteins in the host cell. Interactome built around one single viral protein allowed to define a different response, underlining as ORF8 and ORF3a modulated cardiovascular diseases and pro-inflammatory pathways, respectively. Finally, the network-based approach highlighted a possible direct action of ORF3a and NS7b to enhancing Bradykinin Storm. This network-based representation of SARS-CoV-2 infection could be a framework for pathogenic evaluation of specific clinical outcomes. We identified possible host responses induced by specific proteins of SARS-CoV-2, underlining the important role of specific viral accessory proteins in pathogenic phenotypes of severe COVID-19 patients.
Francesco Messina, Chiara Montaldo, Isabella Abbate, Manuela Antonioli, Veronica Bordoni, Giulia Matusali, Alessandra Sacchi, Emanuela Giombini, Gian Fimia, Mauro Piacentini,et al.
MDPI AG
Complex systems are inherently multilevel and multiscale systems. The infectious disease system is considered a complex system resulting from the interaction between three sub-systems (host, pathogen, and environment) organized into a hierarchical structure, ranging from the cellular to the macro-ecosystem level, with multiscales. Therefore, to describe infectious disease phenomena that change through time and space and at different scales, we built a model framework where infectious disease must be considered the set of biological responses of human hosts to pathogens, with biological pathways shared with other pathologies in an ecological interaction context. In this paper, we aimed to design a framework for building a disease model for COVID-19 based on current literature evidence. The model was set up by identifying the molecular pathophysiology related to the COVID-19 phenotypes, collecting the mechanistic knowledge scattered across scientific literature and bioinformatic databases, and integrating it using a logical/conceptual model systems biology. The model framework building process began from the results of a domain-based literature review regarding a multiomics approach to COVID-19. This evidence allowed us to define a framework of COVID-19 conceptual model and to report all concepts in a multilevel and multiscale structure. The same interdisciplinary working groups that carried out the scoping review were involved. The conclusive result is a conceptual method to design multiscale models of infectious diseases. The methodology, applied in this paper, is a set of partially ordered research and development activities that result in a COVID-19 multiscale model.
Carolina Venditti, Ornella Butera, Marcello Meledandri, Maria Pia Balice, Giulio Cesare Cocciolillo, Carla Fontana, Silvia D'Arezzo, Chiara De Giuli, Mario Antonini, Alessandro Capone,et al.
Elsevier BV
OBJECTIVES
To analyse the strains collected during a one-year survey of ceftazidime-avibactam (CZA)-resistant KPC-producing Klebsiella pneumoniae (KPC-Kp), in order to investigate the molecular mechanisms potentially responsible for their resistant phenotype.
METHODS
Clinical KPC-Kp isolates were collected from 31 patients in 6 different hospitals in Rome. For 8/31 patients, an additional strain grown before the start of treatment was also available, bringing the total of isolates studied to 39. Antimicrobial susceptibility was determined by automated system, broth microdiluition and E-test as appropriate. In silico analysis of acquired resistance genes was achieved by whole-genome sequencing, while MLST and core genome multi locus sequence typing (cgMLST) were employed for molecular typing. Mutations associated with CZA resistance were identified by Sanger sequencing of the blaKPC gene. Possible mutations in OmpK35 and OmpK36 outer membrane proteins were also investigated.
RESULTS
Molecular analyses highlighted the circulation of the ST512, 101 and 307 high-risk clones; 26/31 carried a mutated KPC variant, 5/31 a wild-type KPC-3. Among the KPC variants detected, 11 were different mutations within the blaKPC-3 gene, 4 of which were novel mutational changes.
CONCLUSIONS
Different mutations including single amino-acid substitutions, insertions or deletions within the blaKPC gene were found in 26/31 CZA -resistant KPC-Kp strains belonging to high-risk clones circulating in Italy. Of note, in 14/31 cases the isolates displayed resistance to both CZA and carbapenems, raising the alarm for the possible selection of a multi-drug-resistant phenotype.
Giulia Matusali, Francesca Colavita, Daniele Lapa, Silvia Meschi, Licia Bordi, Pierluca Piselli, Roberta Gagliardini, Angela Corpolongo, Emanuele Nicastri, Andrea Antinori,et al.
MDPI AG
SARS-CoV-2 serum neutralization assay represents the gold standard for assessing antibody-mediated protection in naturally infected and vaccinated individuals. In the present study, 662 serum samples collected from February 2020 to January 2021 from acute and convalescent COVID-19 patients were tested to determine neutralizing antibody (NAb) titers using a microneutralization test (MNT) for live SARS-CoV-2. Moreover, anti-SARS-CoV-2 IgG, IgA, and IgM directed against different viral antigens were measured by high-throughput automated platforms. We observed higher levels of NAbs in elderly (>60 years old) individuals and in patients presenting acute respiratory distress syndrome. SARS-CoV-2 NAbs develop as soon as five days from symptom onset and, despite a decline after the second month, persist for over 11 months, showing variable dynamics. Through correlation and receiver operating characteristic (ROC) curve analysis, we set up a testing algorithm, suitable for the laboratory workload, by establishing an optimal cutoff value of anti-SARS-CoV-2 IgG for convalescent plasma donors to exclude from MNT samples foreseen to have low/negative NAb titers and ineligible for plasma donation. Overall, MNT, although cumbersome and not suitable for routine testing of large sample sizes, remains the reference tool for the assessment of antibody-mediated immunity after SARS-CoV-2 infection. Smart testing algorithms may optimize the laboratory workflow to monitor antibody-mediated protection in COVID-19 patients, plasma donors, and vaccinated individuals.
Annalisa Mondi, Patrizia Lorenzini, Concetta Castilletti, Roberta Gagliardini, Eleonora Lalle, Angela Corpolongo, Maria Beatrice Valli, Fabrizio Taglietti, Stefania Cicalini, Laura Loiacono,et al.
Elsevier BV
Background
Few data about predictors and outcomes associated with prolonged SARS-CoV-2 RNA shedding (VS) are available.
Methods
Retrospective study including all patients admitted with COVID-19 in an Italian reference hospital for infectious diseases between March 1 and July 1, 2020. Predictors of viral clearance (VC) and prolonged VS from upper respiratory tract were assessed by Poisson regression and logistic regression analyses. The causal relation between duration of VS and probability of clinical outcomes was evaluated through inverse probability weighted Cox model.
Results
536 subjects were included. Median duration of VS from symptoms onset was 18 days (IQR 12-26). The estimated 30-day probability of VC was 70.2% (95%CI:65-75). At multivariable analysis, patients with comorbidities (aIRR = 0.88, p = 0.004), lymphopenia at hospital admission (aIRR = 0.75, p = 0.032) and with moderate/severe respiratory disease (aIRR = 0.42, p < 0.001) had a lower chance of achieving VC. The development of moderate/severe respiratory failure (aOR = 2.65, p = 0.003), a delayed hospital admission after symptoms onset (aOR = 1.18, p < 0.001), having baseline comorbidities (aOR = 1.25, p = 0.019) and D-dimer >1000 ng/mL at admission (aOR = 1.76, p = 0.035) independently predicted prolonged VS. The achievement of VC doubled the chance of clinical recovery (aHR = 2.17, p < 0.001) and reduced the probability of death/mechanical ventilation (aHR = 0.36, p = 0.002).
Conclusions
In this study, severity of respiratory disease, comorbidities, delayed hospital admission and inflammatory markers negatively predicted the achievement of VC, which resulted to be associated to better clinical outcomes. These findings highlight the importance of prompt hospitalization of symptomatic patients, especially in presence of signs of severity or comorbidities.
Martina Rueca, Antonino Di Caro, Cesare Ernesto Maria Gruber, Francesco Messina, Emanuela Giombini, Maria Beatrice Valli, Eleonora Lalle, Simone Lanini, Francesco Vairo, Maria Rosaria Capobianchi,et al.
Frontiers Media SA
We report phylogenetic and mutational analysis by NGS of six SARS-CoV-2 strains from patients flying from Bangladesh to Italy (July 2020). Data suggest that no further circulation of such imported strains occurred in Italy, stating the efficacy of early screening at the point of entry and supporting the importance of molecular epidemiology in monitoring the efficacy of control measures.
Martina Spaziante, Carolina Venditti, Ornella Butera, Francesco Messina, Antonino Di Caro, Gilda Tonziello, Simone Lanini, Maria Adriana Cataldo, and Vincenzo Puro
Informa UK Limited
Introduction New Delhi metallo-β-lactamase producing Klebsiella pneumoniae (NDM-Kpn) strains have been causing healthcare-associated infections worldwide. The aim of this study was to describe the molecular mechanisms of antimicrobial resistance and to analyze the clonality of NDM-Kpn isolates collected between January 2019 and June 2020 from patients admitted to hospitals from the Lazio region, Italy. Methods We performed a retrospective cohort study. Whole-genome sequencing (WGS) was performed on all NDM-Kpn strains; clonality and genetic relationships were further investigated. Results During the surveillance period, 17 NDM-Kpn isolates were obtained from 17 patients admitted to seven different hospitals. Eight different sequence types (STs) were detected: ST147 (n = 4), ST383 (n = 4), ST15 (n = 3), ST11 (n = 2), ST17 (n = 1), ST29 (n = 1), ST307 (n = 1) and the newly identified ST4853 (n = 1). Genetic relationships were further investigated by the WGS-based core genome MLST (cgMLST) scheme, and 5 cluster types (CTs) were identified. Whereas a substantial overall heterogeneity among isolates was detected (8 different STs were identified out of 17 isolates), the strains within each cluster showed a very high level of genome similarity. Discussion Our study highlights the key role of surveillance, which allowed taking a picture of a part of the NDM-Kpn strains circulating in Italy, adding further insight into their molecular features.
Marek Ostaszewski, Alexander Mazein, Marc E. Gillespie, Inna Kuperstein, Anna Niarakis, Henning Hermjakob, Alexander R. Pico, Egon L. Willighagen, Chris T. Evelo, Jan Hasenauer,et al.
Springer Science and Business Media LLC
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Marek Ostaszewski, Alexander Mazein, Marc E. Gillespie, Inna Kuperstein, Anna Niarakis, Henning Hermjakob, Alexander R. Pico, Egon L. Willighagen, Chris T. Evelo, Jan Hasenauer,et al.
Springer Science and Business Media LLC
Researchers around the world join forces to reconstruct the molecular processes of the virus-host interactions aiming to combat the cause of the ongoing pandemic.
Francesca Colavita, Daniele Lapa, Fabrizio Carletti, Eleonora Lalle, Francesco Messina, Martina Rueca, Giulia Matusali, Silvia Meschi, Licia Bordi, Patrizia Marsella,et al.
Oxford University Press (OUP)
Abstract Background The pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains unclear. We report the detection of viral RNA from different anatomical districts and the antibody profile in the first 2 COVID-19 cases diagnosed in Italy. Methods We tested for SARS-CoV-2 RNA clinical samples, either respiratory and nonrespiratory (ie, saliva, serum, urine, vomit, rectal, ocular, cutaneous, and cervico-vaginal swabs), longitudinally collected from both patients throughout the hospitalization. Serological analysis was carried out on serial serum samples to evaluate IgM, IgA, IgG, and neutralizing antibody levels. Results SARS-CoV-2 RNA was detected since the early phase of illness, lasting over 2 weeks in both upper and lower respiratory tract samples. Virus isolate was obtained from acute respiratory samples, while no infectious virus was rescued from late respiratory samples with low viral RNA load, collected when serum antibodies had been developed. Several other specimens came back positive, including saliva, vomit, rectal, cutaneous, cervico-vaginal, and ocular swabs. IgM, IgA, and IgG were detected within the first week of diagnosis, with IgG appearing earlier and at higher titers. Neutralizing antibodies developed during the second week, reaching high titers 32 days after diagnosis. Conclusions Our longitudinal analysis showed that SARS-CoV-2 RNA can be detected in different body samples, which may be associated with broad tropism and different spectra of clinical manifestations and modes of transmission. Profiling antibody response and neutralizing activity can assist in laboratory diagnosis and surveillance actions.
Francesco Vairo, Martin Aimè Coussoud-Mavoungou, Francine Ntoumi, Concetta Castilletti, Lambert Kitembo, Najmul Haider, Fabrizio Carletti, Francesca Colavita, Cesare Gruber, Marco Iannetta,et al.
MDPI AG
The Republic of Congo (RoC) declared a chikungunya (CHIK) outbreak on 9 February 2019. We conducted a ONE-Human-Animal HEALTH epidemiological, virological and entomological investigation. Methods: We collected national surveillance and epidemiological data. CHIK diagnosis was based on RT-PCR and CHIKV-specific antibodies. Full CHIKV genome sequences were obtained by Sanger and MinION approaches and Bayesian tree phylogenetic analysis was performed. Mosquito larvae and 215 adult mosquitoes were collected in different villages of Kouilou and Pointe-Noire districts and estimates of Aedes (Ae.) mosquitos’ CHIKV-infectious bites obtained. We found two new CHIKV sequences of the East/Central/South African (ECSA) lineage, clustering with the recent enzootic sub-clade 2, showing the A226V mutation. The RoC 2019 CHIKV strain has two novel mutations, E2-T126M and E2-H351N. Phylogenetic suggests a common origin from 2016 Angola strain, from which it diverged around 1989 (95% HPD 1985–1994). The infectious bite pattern was similar for 2017, 2018 and early 2019. One Ae. albopictus pool was RT-PCR positive. The 2019 RoC CHIKV strain seems to be recently introduced or be endemic in sylvatic cycle. Distinct from the contemporary Indian CHIKV isolates and in contrast to the original Central-African strains (transmitted by Ae. aegypti), it carries the A226V mutation, indicating an independent adaptive mutation in response to vector replacement (Ae. albopictus vs Ae. aegypti).
Martina Rueca, Barbara Bartolini, Cesare Ernesto Maria Gruber, Antonio Piralla, Fausto Baldanti, Emanuela Giombini, Francesco Messina, Luisa Marchioni, Giuseppe Ippolito, Antonino Di Caro,et al.
MDPI AG
We report whole-genome and intra-host variability of SARS-Cov-2 assessed by next generation sequencing (NGS) in upper (URT) and lower respiratory tract (LRT) from COVID-19 patients. The aim was to identify possible tissue-specific patterns and signatures of variant selection for each respiratory compartment. Six patients, admitted to the Intensive Care Unit, were included in the study. Thirteen URT and LRT were analyzed by NGS amplicon-based approach on Ion Torrent Platform. Bioinformatic analysis was performed using both realized in-house and supplied by ThermoFisher programs. Phylogenesis showed clade V clustering of the first patients diagnosed in Italy, and clade G for later strains. The presence of quasispecies was observed, with variants uniformly distributed along the genome and frequency of minority variants spanning from 1% to ~30%. For each patient, the patterns of variants in URT and LRT were profoundly different, indicating compartmentalized virus replication. No clear variant signature and no significant difference in nucleotide diversity between LRT and URT were observed. SARS-CoV-2 presents genetic heterogeneity and quasispecies compartmentalization in URT and LRT. Intra-patient diversity was low. The pattern of minority variants was highly heterogeneous and no specific district signature could be identified, nevertheless, analysis of samples, longitudinally collected in patients, supported quasispecies evolution.