Publications by authors named "Monica Pecorari"

38 Publications

Legionella antibiotic susceptibility testing: is it time for international standardization and evidence-based guidance?

Authors:
Edward Portal Ghislaine Descours Christophe Ginevra Massimo Mentasti Baharak Afshar Meera Chand Jessica Day Fedoua Echahidi Laura Franzin Valeria Gaia Christian Lück Alaeddine Meghraoui Jacob Moran-Gilad Maria Luisa Ricci Gerard Lina Søren Uldum Jonas Winchell Robin Howe Kathryn Bernard Owen B Spiller Victoria J Chalker Sophie Jarraud Catherine Ahlen Ibrahim Al Hashmi Görel Allestam Junko Amemura-Maekawa Sabina Andersson Jette Marie Bangsborg Sheila Bararossa Laetitia Beraud Kathryn Bernard Paola Borella Petra Brandsema Jacob P Bruin Andrea Buzzigoli Rosa Cano Beatrice Casini Giuseppe Celenza Vicki Chalker Samuel Collins Sebastian Crespi Rotger Maria Luisa Cristina Sandra Cristino Sophia David Birgitta de Jong Jeroen den Boer Fedoua Echahidi Pernille Landsbo Elverdal Haluk Erdogan Sjoerd Euser Laura Franzin Norman K Fry Valeria Gaia Marian Garcia-Nuñez Christophe Ginevra Elsa Filipa Pasmal de Ameida Concalves Paula Gonçalves Tiscar Graells Fernandez Antonella Grottola Nicole Gysin Timothy G Harrison Manfred Höfle Sophie Jarraud Charlotte Svaerke Jorgensen Carol Joseph Björn Slott Kanto Darja Kese Louise Kindingstad Daniela Emilia Klingenberg Mehmet Kösekul Natalia Kozak-Muiznieks Fumiaki Kura Jaana Kusnetsov Sandra Lai Susanne Lee John Vincent Lee Diane Lindsay Christian Lück Marcel Leuscher Wilco van der Lugt Maria Teresa Marques Marisa Meacci Alaeddine Meghraoui Massimo Mentasti Silja Mentula Antonija Mikrut Josep Modol Ginny Moore Jacob Moran-Gilad Matilda Morin Selin Nar Otgun Olav Bjarte Nataas Neda Nezam Abadi Katarzyna Pancer Monica Pecorari Maria Luisa Pedro-Botet Carmen Pelaz Markus Petzold Nicholas Pissarides Edward A R Portal Miriam Ramliden Brian Raphael Kate Reddington Maria Luisa Ricci Emmanuel Robesyn Sandrine Roisin Fabio Rumpianesi Henri Saenz Maria Scaturro Johanna Schalk Graf Simone Stine Skotte Bjerregaard Anna Maria Spagnolo Owen B Spiller Anna Stjarne Aspelund Christina Wild Svarrer Igor Tartakovshiy Kate Templeton Soren Uldum Enrico Veschetti James Walker France Wallet Guenther Wewalka Catherine Whapham Anika Wunderlich Ingrid Wybo

J Antimicrob Chemother 2021 Feb 20. Epub 2021 Feb 20.

Centre National de Reference des Legionelles, Hospices Civils de Lyon, University de Lyon, Lyon, France.

Legionella pneumophila, a Gram-negative bacillus, is the causative agent of Legionnaire's disease, a form of severe community-acquired pneumonia. Infection can have high morbidity, with a high proportion of patients requiring ICU admission, and up to 10% mortality, which is exacerbated by the lack of efficacy of typical empirical antibiotic therapy against Legionella spp. The fastidious nature of the entire Legionellaceae family historically required inclusion of activated charcoal in the solid medium to remove growth inhibitors, which inherently interferes with accurate antimicrobial susceptibility determination, an acknowledged methodological shortfall, now rectified by a new solid medium that gives results comparable to those of microbroth dilution. Here, as an international Legionella community (with authors representing various international reference laboratories, countries and clinical stakeholders for diagnosis and treatment of legionellosis), we set out recommendations for the standardization of antimicrobial susceptibility testing methods, guidelines and reference strains to facilitate an improved era of antibiotic resistance determination.
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http://dx.doi.org/10.1093/jac/dkab027DOI Listing
February 2021

Cytomegalovirus reactivation after hematopoietic stem cell transplant with CMV-IG prophylaxis: A monocentric retrospective analysis.

J Med Virol 2021 Feb 12. Epub 2021 Feb 12.

Section of Hematology, Department of Medical and Surgical Sciences, Azienda Ospedaliero-Universitaria di Modena, University of Modena and Reggio Emilia, Modena, Italy.

Human cytomegalovirus (CMV) represents the most common viral infection after hematopoietic stem cell transplant (HSCT), mainly occurring as reactivation from latency in seropositive patients, with a different prevalence based on the extent and timing of seroconversion in a specific population. Here, we retrospectively analyzed a cohort of patients who underwent HSCT at our Institution between 2013 and 2018, all of whom were prophylactically treated with CMV-IG (Megalotect Biotest®), to define the incidence and clinical outcomes of CMV reactivation and clinically significant infection. CMV infection occurred in 69% of our patient series, mainly resulting from reactivation, and CMV clinically significant infection (CS-CMVi) occurred in 48% of prophylactically treated patients. CMV infection and CS-CMVi impacted neither on relapse incidence nor on overall survival nor on relapse-free survival. Moreover, a very low incidence of CMV end-organ disease was documented. CMV-IG used alone as prophylactic therapy after HSCT does not effectively prevent CMV reactivation.
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http://dx.doi.org/10.1002/jmv.26861DOI Listing
February 2021

Subjects with blood group O are not at lower risk to acquire SARS-CoV-2 infection.

Vox Sang 2020 Dec 16. Epub 2020 Dec 16.

Immuno-Hematology and Transfusion Medicine Unit, Azienda Ospedaliero-Universitaria di Modena and University of Modena and Reggio Emilia, Modena, Italy.

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http://dx.doi.org/10.1111/vox.13062DOI Listing
December 2020

Long-term maintenance of virologic suppression in native and migrant HIV-1 naïve patients: an Italian cohort study.

AIDS Care 2020 Nov 10:1-8. Epub 2020 Nov 10.

Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.

Little is known about long-term maintenance of virologic suppression in HIV migrants in Italy. The study aims to compare virologic failure rates and associated factors among antiretroviral therapy (ART)-naïve migrants and natives enrolled in the ARCA database since 2007 who achieved virologic suppression within 18 months from the beginning of the ART. Kaplan-Meier method assessed the probability of virologic suppression and failure. Cox regression model was used for multivariate analysis. Of 2515 patients, 2020 (80.3%) were Italian, 286 (10.6%) migrants from low-income countries, of whom 201 (75.0%) from Africa, and 227 (9.0%) from high-income-countries. The median follow-up was 4.5 years (IQR 2.5-7). No difference was observed in the time of achievement of virological suppression in the three groups (log-rank:  = 0.5687). Higher probability of virologic failure was observed in Africans compared to Italians, to patients from high-income-countries and from low-income-countries other than Africans (Log-rank =  < 0.001). In the adjusted analysis, a higher virologic failure risk was found in Africans only compared to Italians. [HR 4.01; 95% CI 2.44-6.56,  < 0.001]. In Italy, African migrants are less likely to maintain virologic suppression compared to natives and other migrants. Targeted interventions could be needed for foreigners, especially for Africans.
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http://dx.doi.org/10.1080/09540121.2020.1839011DOI Listing
November 2020

A Retrospective Whole-Genome Sequencing Analysis of Carbapenem and Colistin-Resistant Nosocomial Strains Isolated during an MDR Surveillance Program.

Antibiotics (Basel) 2020 May 12;9(5). Epub 2020 May 12.

Department of Surgery, Medicine, Dentistry, and Morphological Sciences with Transplant Surgery, Oncology, and Regenerative Medicine Relevance, University of Modena and Reggio Emilia, Via Del Pozzo 71, 41124 Modena, Italy.

Multidrug-resistant (MDR ), in particular carbapenem-resistant (CR-), has become endemic in Italy, where alarming data have been reported on the spread of colistin-resistant CR- (CRCR-). During the period 2013-2014, 27 CRCR- nosocomial strains were isolated within the Modena University Hospital Policlinico (MUHP) multidrug resistance surveillance program. We retrospectively investigated these isolates by whole-genome sequencing (WGS) analysis of the resistome, virulome, plasmid content, and core single nucleotide polymorphisms (cSNPs) in order to gain insights into their molecular epidemiology. The in silico WGS analysis of the resistome revealed the presence of genes, such as , related to the phenotypically detected resistances to carbapenems. Concerning colistin resistance, the plasmidic genes were not detected, while known and new genetic variations in , , and were found. The virulome profile revealed the presence of type-3 fimbriae, capsular polysaccharide, and iron acquisition system genes. The detected plasmid replicons were classified as , , , , and types. The cSNPs genotyping was consistent with the multi locus sequence typing (MLST) and with the distribution of mutations related to colistin resistance genes. In a nosocomial drug resistance surveillance program, WGS proved to be a useful tool for elucidating the spread dynamics of CRCR- nosocomial strains and could help to limit their diffusion.
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http://dx.doi.org/10.3390/antibiotics9050246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7277725PMC
May 2020

Pretreatment HIV drug resistance and treatment failure in non-Italian HIV-1-infected patients enrolled in ARCA.

Antivir Ther 2020 ;25(2):61-71

Department of Biomedical Sciences and Human Oncology, Clinic of Infectious Diseases, University of Bari Medical School, Bari, Italy.

Background: An increase in pretreatment drug resistance (PDR) to first-line antiretroviral therapy (ART) in low-income countries has been recently described. Herein we analyse the prevalence of PDR and risk of virological failure (VF) over time among migrants to Italy enrolled in ARCA.

Methods: HIV-1 sequences from ART-naive patients of non-Italian nationality were retrieved from ARCA database from 1998 to 2017. PDR was defined by at least one mutation from the reference 2009 WHO surveillance list.

Results: Protease/reverse transcriptase sequences from 1,155 patients, mainly migrants from sub-Saharan Africa (SSA; 42%), followed by Latin America (LA; 25%) and Western countries (WE; 21%), were included. PDR was detected in 8.6% of sequences (13.1% versus 5.8% for B and non-B strains, respectively; P<0.001). 2.1% of patients carried a PDR for protease inhibitors (PIs; 2.1% versus 2.3%; P=0.893), 3.9% for nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs; 6.8% versus 2.1%; P<0.001) and 4.3% for non-nucleoside/nucleotide reverse transcriptase inhibitors (NNRTIs; 6.3% versus 3.1%; P=0.013). Overall, prevalence of PDR over the years remained stable, while it decreased for PIs in LA (P=0.021) and for NRTIs (P=0.020) among migrants from WE. Having more than one class of PDR (P=0.015 versus absence of PDR), higher viral load at diagnosis (P=0.008) and being migrants from SSA (P=0.001 versus WE) were predictive of VF, while a recent calendar year of diagnosis (P<0.001) was protective for VF.

Conclusions: PDR appeared to be stable over the years in migrants to Italy enrolled in ARCA; however, it still remains an important cause of VF together with viral load at diagnosis.
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http://dx.doi.org/10.3851/IMP3349DOI Listing
January 2020

No impact of previous NRTIs resistance in HIV positive patients switched to DTG+2NRTIs under virological control: Time of viral suppression makes the difference.

Antiviral Res 2019 12 17;172:104635. Epub 2019 Oct 17.

III Infectious Disease Unit, ASST-FBF-Sacco, Milan, Italy; Department of Biomedical and Clinical Sciences DIBIC L. Sacco, University of Milan, Milan, Italy.

The accumulation of drug-resistance mutations on combined antiretroviral regimens (ART) backbone could affect the virological efficacy of the regimen. Our aim was to assess the impact of previous drug resistance to nucleoside reverse transcriptase inhibitors (NRTIs) on the probability of virological failure (VF) in patients, under virological control, who switched to dolutegravir (DTG)+2NRTIs regimens. All HIV-1 positive drug-experienced patients who started a regimen composed by DTG+2NRTIs [abacavir/lamivudine or tenofovir disoproxil fumarate (TDF) or tenofovir alafenamide (TAF)/emtricitabine (FTC)] in the ARCA collaborative group with HIV-RNA <50 cp/mL were included in the analysis. Patients with a previous VF to integrase inhibitors were excluded. The impact of single and combined NRTIs mutations on the probability of VF (defined as 2 consecutive HIV-RNA >50 copies/mL or one HIV-RNA >1000 copies/mL) was assessed by Kaplan Meier curves. A multivariable Cox regression analysis was constructed to assess factors potentially related to VF. Five hundred and eighty-eight patients were included in the analysis with a median time of viral suppression before the switch of 37 months (IQR 12-78), of whom 148 (25.2%) had at least one previous NRTIs resistance mutation. In the multivariable model no association was observed between NRTIs mutations and VF. Conversely, the duration of viral suppression before switch resulted associated with a lower risk of VF (for 1 month increase, adjusted Hazard Ratio 0.98, 95%CI 0.96-0.99; p=0.024). Previous NRTIs mutations appeared to have no impact on the risk of VF in patients switched to DTG+2NRTIs, whereas a longer interval on a controlled viremia decreased significantly the risk of VF.
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http://dx.doi.org/10.1016/j.antiviral.2019.104635DOI Listing
December 2019

Genome-based taxonomic revision detects a number of synonymous taxa in the genus Mycobacterium.

Infect Genet Evol 2019 11 26;75:103983. Epub 2019 Jul 26.

Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy.

The aim of this study was to clarify the taxonomic status of named species within the genus Mycobacterium. The analysis of genomes belonging to 174 taxa (species or subspecies) of the genus Mycobacterium was conducted using both the Average Nucleotide Identity and the Genome to Genome Distance. A number of synonymous taxa were detected. The list of synonyms includes: two subspecies of M. chelonae (M. chelonae subsp. bovis and M. chelonae subsp. gwanakae), two subspecies of M. fortuitum (M. fortuitum subsp. fortuitum and M. fortuitum subsp. acetamidolyticum), four subspecies of M. avium (M. avium subsp. avium, M. avium subsp. silvaticum, M. avium subsp. paratuberculosis and "M. avium subsp. hominissuis"), two couples of subspecies of M. intracellulare (M. intracellulare subsp. intracellulare/M. intracellulare subsp. paraintracellulare and M. intracellulare subsp. chimaera/M. intracellulare subsp. yongonense), the species M. austroafricanum and M. vanbaalenii, the species M. senegalense and M. conceptionense, the species M. talmoniae and M. eburneum and the species M. marinum, M. ulcerans and M. pseudoshottsii. Furthermore one species were reclassified as subspecies of another mycobacterium: M. lepraemurium was reclassified as a subspecies of M. avium (M. avium subsp. lepraemurium). The updates to nomenclature are proposed basing on the priority of names according the Code of nomenclature of prokaryotes. For two species (M. bouchedurhonense and M. marseillense) the loss of standing in nomenclature is proposed because of unavailability of respective type strains in culture collections.
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http://dx.doi.org/10.1016/j.meegid.2019.103983DOI Listing
November 2019

Pneumocystosis as a Complication of H1N1 Influenza A Infection in an HIV-Positive Patient on Effective cART.

Open Forum Infect Dis 2019 Apr 7;6(4):ofz105. Epub 2019 Mar 7.

Infectious Diseases Unit, University of Modena and Reggio Emilia, Modena, Italy.

H1N1 influenza A virus can affect the immune system, causing lymphopenia. This might be of great concern for HIV individuals undergoing effective antireroviral therapy (cART). We report the first confirmed case of H1N1-induced AIDS and pneumonia in an HIV-positive woman on effective cART since 2006.
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http://dx.doi.org/10.1093/ofid/ofz105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6453522PMC
April 2019

Improvement of Legionnaires' disease diagnosis using real-time PCR assay: a retrospective analysis, Italy, 2010 to 2015.

Euro Surveill 2018 Dec;23(50)

Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.

AimTo evaluate real-time PCR as a diagnostic method for Legionnaires' disease (LD). Detection of DNA is among the laboratory criteria of a probable LD case, according to the European Centre for Disease Prevention and Control, although the utility and advantages, as compared to culture, are widely recognised.MethodsTwo independent laboratories, one using an in-house and the other a commercial real-time PCR assay, analysed 354 respiratory samples from 311 patients hospitalised with pneumonia between 2010-15. The real-time PCR reliability was compared with that of culture and urinary antigen tests (UAT). Concordance, specificity, sensitivity and positive and negative predictive values (PPV and NPV, respectively) were calculated.ResultsOverall PCR detected eight additional LD cases, six of which were due to (Lp) non-serogroup 1. The two real-time PCR assays were concordant in 99.4% of the samples. Considering in-house real-time PCR as the reference method, specificity of culture and UAT was 100% and 97.9% (95% CI: 96.2-99.6), while the sensitivity was 63.6% (95%CI: 58.6-68.6) and 77.8% (95% CI: 72.9-82.7). PPV and NPV for culture were 100% and 93.7% (95% CI: 91.2-96.3). PPV and NPV for UAT were 87.5% (95% CI: 83.6-91.4) and 95.8% (95% CI: 93.5-98.2).ConclusionRegardless of the real-time PCR assay used, it was possible to diagnose LD cases with higher sensitivity than using culture or UAT. These data encourage the adoption of PCR as routine laboratory testing to diagnose LD and such methods should be eligible to define a confirmed LD case.
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http://dx.doi.org/10.2807/1560-7917.ES.2018.23.50.1800032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299505PMC
December 2018

Impact of the M184V Resistance Mutation on Virological Efficacy and Durability of Lamivudine-Based Dual Antiretroviral Regimens as Maintenance Therapy in Individuals With Suppressed HIV-1 RNA: A Cohort Study.

Open Forum Infect Dis 2018 Jun 15;5(6):ofy113. Epub 2018 May 15.

Infectious Diseases Unit, AOU Senese, Siena, Italy.

Background: Dual therapy (DT) with boosted protease inhibitors (bPIs) plus lamivudine has been shown to be superior to bPI monotherapy in virologically suppressed patients despite previous selection of the lamivudine resistance M184V mutation. We compared the virological efficacy of lamivudine-based DT in patients with and without a history of M184V detection.

Methods: We retrospectively analyzed patients with HIV-RNA ≤50 copies/mL switching to DT with at least 1 previous resistance genotype in the ARCA database. Time to virological failure (VF; HIV-RNA ≥200 copies/mL or 2 consecutive HIV-RNA >50 copies/mL) and to treatment discontinuation (TD) was analyzed by survival analysis.

Results: Four hundred thirty-six patients switching to lamivudine plus bPIs (70%) or integrase inhibitors (30%) were included. Patients with M184V (n = 87) were older, had lower nadir CD4+ cell count, longer duration of antiretroviral therapy and of virologic suppression, and higher rate of hepatitis C virus infection compared with patients without M184V. The 3-year probability of remaining free from VF was 91.9% (95% confidence interval [CI], 86.6-97.2) without M184V and 87.8% (95% CI, 78.4-97.2) with M184V ( = .323). The time to TD did not differ between groups. Multivariate analysis adjusting for baseline variables differing between groups also did not detect M184V as being associated with VF or TD; however, the 3-year probability of remaining free of viral blips (isolated HIV-RNA 51-199 copies/mL) was 79.8% (95% CI, 67.8%-91.8%) with M184V vs 90.1% (95% CI, 84.0%-96.2%) without M184V ( = .016).

Conclusions: Previous selection of M184V did not increase the risk of VF or TD with lamivudine-based DT but was associated with a higher probability of viral blips.
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http://dx.doi.org/10.1093/ofid/ofy113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6016422PMC
June 2018

Prevalence of Usutu and West Nile virus antibodies in human sera, Modena, Italy, 2012.

J Med Virol 2018 10 6;90(10):1666-1668. Epub 2018 Jun 6.

Scientific Department, Army Medical Center, Roma, Italy.

A collection of 3069 human sera collected in the area of the municipality of Modena, Emilia Romagna, Italy, was retrospectively investigated for specific antibodies against Usutu (USUV) and West Nile viruses (WNV). All the samples resulting positive using a preliminary screening test were analyzed with the plaque reduction neutralization test. Overall, 24 sera were confirmed as positive for USUV (0.78%) and 13 for WNV (0.42%). The results suggest that in 2012, USUV was circulating more than WNV in North-eastern Italy.
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http://dx.doi.org/10.1002/jmv.25230DOI Listing
October 2018

The new phylogeny of the genus Mycobacterium: The old and the news.

Infect Genet Evol 2017 12 11;56:19-25. Epub 2017 Oct 11.

Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy. Electronic address:

Background: Phylogenetic studies of bacteria have been based so far either on a single gene (usually the 16S rRNA) or on concatenated housekeeping genes. For what concerns the genus Mycobacterium these approaches support the separation of rapidly and slowly growing species and the clustering of most species in well-defined phylogenetic groups. The advent of high-throughput shotgun sequencing leads us to revise conventional taxonomy of mycobacteria on the light of genomic data. For this purpose we investigated 88 newly sequenced species in addition to 60 retrieved from GenBank and used the Average Nucleotide Identity pairwise scores to reconstruct phylogenetic relationships within this genus.

Results: Our analysis confirmed the separation of slow and rapid growers and the intermediate position occupied by the M. terrae complex. Among the rapid growers, the species of the M. chelonae-abscessus complex belonged to the most ancestral cluster. Other major clades of rapid growers included the species related to M. fortuitum and M. smegmatis and a large grouping containing mostly environmental species rarely isolated from humans. The members of the M. terrae complex appeared as the most ancestral slow growers. Among slow growers two deep branches led to the clusters of species related to M. celatum and M. xenopi and to a large group harboring most of the species more frequently responsible of disease in humans, including the major pathogenic mycobacteria (M. tuberculosis, M. leprae, M. ulcerans). The species previously grouped in the M. simiae complex were allocated in a number of sub-clades; of them, only the one including the species M. simiae identified the real members of this complex. The other clades included also species previously not considered related to M. simiae. The ANI analysis, in most cases supported by Genome to Genome Distance and by Genomic Signature-Delta Difference, showed that a number of species with standing in literature were indeed synonymous.

Conclusions: Genomic data revealed to be much more informative in comparison with phenotype. We believe that the genomic revolution enabled by high-throughput shotgun sequencing should now be considered in order to revise the conservative approaches still informing taxonomic sciences.
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http://dx.doi.org/10.1016/j.meegid.2017.10.013DOI Listing
December 2017

Persistent intestinal bleeding due to severe CMV-related thrombocytopenia in a preterm newborn.

J Matern Fetal Neonatal Med 2018 May 11;31(9):1246-1249. Epub 2017 Apr 11.

a Dipartimento Integrato Materno-Infantile , Terapia Intensiva Neonatale, Azienda Ospedaliero-Universitaria Policlinico , Modena , Italy.

The optimal threshold for neonatal platelet transfusions in sick newborns is still uncertain. We report a congenital cytomegalovirus (CMV) infection in a premature neonate with severe thrombocytopenia who subsequently presented with necrotizing enterocolitis and intestinal bleeding. The baby recovered after platelet transfusions were discontinued and the therapy was switched from intravenous ganciclovir to oral valganciclovir. We discuss both measures, speculating on the key role of platelet transfusions.
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http://dx.doi.org/10.1080/14767058.2017.1312331DOI Listing
May 2018

Genomic characterization of Nontuberculous Mycobacteria.

Sci Rep 2017 03 27;7:45258. Epub 2017 Mar 27.

Centre for Integrative Biology, University of Trento, Trento, Italy.

Mycobacterium tuberculosis and Mycobacterium leprae have remained, for many years, the primary species of the genus Mycobacterium of clinical and microbiological interest. The other members of the genus, referred to as nontuberculous mycobacteria (NTM), have long been underinvestigated. In the last decades, however, the number of reports linking various NTM species with human diseases has steadily increased and treatment difficulties have emerged. Despite the availability of whole genome sequencing technologies, limited effort has been devoted to the genetic characterization of NTM species. As a consequence, the taxonomic and phylogenetic structure of the genus remains unsettled and genomic information is lacking to support the identification of these organisms in a clinical setting. In this work, we widen the knowledge of NTMs by reconstructing and analyzing the genomes of 41 previously uncharacterized NTM species. We provide the first comprehensive characterization of the genomic diversity of NTMs and open new venues for the clinical identification of opportunistic pathogens from this genus.
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http://dx.doi.org/10.1038/srep45258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5366915PMC
March 2017

Characterization of 17 strains belonging to the Mycobacterium simiae complex and description of Mycobacterium paraense sp. nov.

Int J Syst Evol Microbiol 2015 Feb 8;65(Pt 2):656-662. Epub 2014 Dec 8.

Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy.

Fourteen mycobacterial strains isolated from pulmonary samples of independent patients in the state of Pará (Brazil), and three strains isolated in Italy, were characterized using a polyphasic approach. Thorough genetic investigation, including whole-genome sequencing, demonstrated that the strains belong to the M. simiae complex, being most closely related to Mycobacterium interjectum. For 14 of the strains, evidence emerged supporting their inclusion in a previously unreported species of the genus Mycobacterium, for which the name Mycobacterium paraense sp. nov. is proposed (type strain, IEC26(T) = DSM 46749(T) = CCUG 66121(T)). The novel species is characterized by slow growth, unpigmented or pale yellow scotochromogenic colonies, and a HPLC mycolic acid profile different from other known mycobacteria. In different genetic regions, high sequence microheterogeneity was detected.
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http://dx.doi.org/10.1099/ijs.0.068395-0DOI Listing
February 2015

Serratia marcescens in a neonatal intensive care unit: two long-term multiclone outbreaks in a 10-year observational study.

New Microbiol 2013 Oct 1;36(4):373-83. Epub 2013 Oct 1.

Department to Integrated Activity of Laboratory Medicine, Modena, Italy.

We investigated two consecutive Serratia marcescens (S. marcescens) outbreaks which occurred in a neonatal intensive care unit (NICU) of a tertiary level hospital in North Italy in a period of 10 years (January 2003-December 2012). Risk factors associated with S. marcescens acquisition were evaluated by a retrospective case-control study. A total of 21,011 clinical samples was examined: S. marcescens occurred in 127 neonates: 43 developed infection and 3 died. Seven clusters were recorded due to 12 unrelated clones which persisted for years in the ward, although no environmental source was found. The main epidemic clone A sustaining the first cluster in 2003 reappeared in 2010 as an extended spectrum ?-lactamase (ESBL)-producing strain and supporting the second epidemic. Birth weight, gestational age, use of invasive devices and length of stay in the ward were significantly related to S. marcescens acquisition. The opening of a new ward for non-intensive care-requiring neonates, strict adherence to alcoholic hand disinfection, the timely identification and isolation of infected and colonized neonates assisted in containing the epidemics. Genotyping was effective in tracing the evolution and dynamics of the clones demonstrating their long-term persistence in the ward.
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October 2013

Lack of evidence for an association between seminoma and human papillomavirus infection using GP5+/GP6+ consensus primers.

J Med Virol 2013 Jan 16;85(1):105-9. Epub 2012 Oct 16.

Microbiology and Virology Unit, Policlinico Hospital, Modena, Italy.

Testicular germ cell tumors account for about 1% of all cancers. The incidence of these tumors is increasing and they represent the most common solid malignancies of young men aged 15-40 years with seminoma being one of the most common histotype. Pathogenesis of testicular germ cell tumors remains unknown and, although cryptorchidism is considered the main risk factor, there is evidence of an association with environmental and genetic risk factors. Human papillomaviruses (HPV) are a family of DNA viruses and represent a major risk factor for cervical cancer. In addition, they have been associated with other human non-malignant and malignant diseases, including breast and head and neck cancer. HPV sequences have been detected throughout the male lower genitourinary tract as well as in seminal fluid and an increased testicular tumorigenesis has been reported in HPV transgenic mice. Aim of this study was to evaluate the potential involvement of HPV in human testicular tumorigenesis. Real-time PCR employing GP5+/GP6+ consensus HPV primers was used to examine the presence of HPV sequences in a subset of human seminoma (n = 61) and normal testicles (n = 23). None of the specimens tested displayed the presence of HPV DNA. These findings do not support an association between HPV and human seminoma and warrant further studies to assess definitively the role of these viruses in human testicular tumorigenesis.
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http://dx.doi.org/10.1002/jmv.23431DOI Listing
January 2013

Performance of 2 commercial real-time polymerase chain reaction assays for the detection of Aspergillus and Pneumocystis DNA in bronchoalveolar lavage fluid samples from critical care patients.

Diagn Microbiol Infect Dis 2012 Jun 12;73(2):138-43. Epub 2012 Apr 12.

Dipartimento di Scienze di Sanità Pubblica, Università di Modena e Reggio Emilia, Modena, Italy.

This article investigates the performance of 2 commercial real-time polymerase chain reaction (PCR) assays, MycAssay™ Aspergillus (Myc(Asp)Assay) and MycAssay™ Pneumocystis (Myc(PCP)Assay), on the ABI 7300 platform for the detection of Aspergillus (Asp) or Pneumocystis jirovecii (Pj) DNA in bronchoalveolar lavage (BAL) samples from 20 patients. Operationally, patients enrolled were clustered into 3 groups: invasive aspergillosis group (IA, 7 patients), Pj pneumonia group (PCP, 8 patients), and negative control group (5 patients). All the IA patients were Myc(Asp)Assay positive, whereas 12 non-IA patients returned negative PCR results. Furthermore, 7 of 8 PCP patients were Myc(PCP)Assay positive, while 9 non-PCP patients were PCR negative. In conclusion, these data provide an early indication of the effectiveness of both the Myc(Asp)Assay and Myc(PCP)Assay on the ABI 7300 platform for the detection of either Asp or Pj DNA in BAL from patients with deep fungal infections.
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http://dx.doi.org/10.1016/j.diagmicrobio.2012.03.001DOI Listing
June 2012

Mucorales-specific T cells emerge in the course of invasive mucormycosis and may be used as a surrogate diagnostic marker in high-risk patients.

Blood 2011 Nov 19;118(20):5416-9. Epub 2011 Sep 19.

Section of Haematology, Department of Oncology, Haematology and Respiratory Diseases, University of Modena and Reggio Emilia, Modena, Italy;

Mucorales-specific T cells were investigated in 28 hematologic patients during the course of their treatment. Three developed proven invasive mucormycosis (IM), 17 had infections of known origin but other than IM, and 8 never had fever during the period of observation. Mucorales-specific T cells could be detected only in patients with IM, both at diagnosis and throughout the entire course of the IM, but neither before nor for long after resolution of the infection. Such T cells predominantly produced IL-4, IFN-γ, IL-10, and to a lesser extent IL-17 and belonged to either CD4(+) or CD8(+) subsets. The specific T cells that produced IFN-γ were able to directly induce damage to Mucorales hyphae. None of the 25 patients without IM had Mucorales-specific T cells. Specific T cells contribute to human immune responses against fungi of the order Mucorales and could be evaluated as a surrogate diagnostic marker of IM.
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http://dx.doi.org/10.1182/blood-2011-07-366526DOI Listing
November 2011

A novel methodology for large-scale phylogeny partition.

Nat Commun 2011 24;2:321. Epub 2011 May 24.

Clinic of Infectious Diseases, Catholic University of the Sacred Heart, Rome, Italy.

Understanding the determinants of virus transmission is a fundamental step for effective design of screening and intervention strategies to control viral epidemics. Phylogenetic analysis can be a valid approach for the identification of transmission chains, and very-large data sets can be analysed through parallel computation. Here we propose and validate a new methodology for the partition of large-scale phylogenies and the inference of transmission clusters. This approach, on the basis of a depth-first search algorithm, conjugates the evaluation of node reliability, tree topology and patristic distance analysis. The method has been applied to identify transmission clusters of a phylogeny of 11,541 human immunodeficiency virus-1 subtype B pol gene sequences from a large Italian cohort. Molecular transmission chains were characterized by means of different clinical/demographic factors, such as the interaction between male homosexuals and male heterosexuals. Our method takes an advantage of a flexible notion of transmission cluster and can become a general framework to analyse other epidemics.
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http://dx.doi.org/10.1038/ncomms1325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6045912PMC
August 2011

Usutu virus in Italy: an emergence or a silent infection?

Vet Microbiol 2011 Aug 12;151(3-4):264-74. Epub 2011 Apr 12.

Istituto G. Caporale, Teramo, Italy.

A two year study (2008-2009) was carried out to monitor the Usutu virus (USUV) circulation in Italy. Sentinel horses and chickens, wild birds and mosquitoes were sampled and tested for the presence of USUV and USUV antibodies within the WND National Surveillance plan. Seroconversion evidenced in sentinel animals proved that in these two years the virus has circulated in Tuscany, Emilia Romagna, Veneto and Friuli Venezia Giulia regions. In Veneto USUV caused a severe blackbird die-off disease involving at least a thousand birds. Eleven viral strains were detected in organs of 9 blackbirds (52.9%) and two magpies (0.5%) originating from Veneto and Emilia Romagna regions. USUV was also detected in a pool of Culex pipiens caught in Tuscany. According to the alignment of the NS5 partial sequences, no differences between the Italian USUV strains isolated from Veneto, Friuli and Emilia Romagna regions were observed. The Italian North Eastern strain sequences were identical to those of the strain detected in the brain of a human patient and shared a high similarity with the isolates from Vienna and Budapest. Conversely, there were few differences between the Italian strains which circulated in the North Eastern regions and the USUV strain detected in a pool of C. pipiens caught in Tuscany. A high degree of similarity at both nucleotide and amino acid level was also found when the full genome sequence of the Italian North Eastern isolate was compared with that of the strains circulating in Europe. The North Eastern Italian strain sequence exhibited 97% identity to the South African reference strain SAAR-1776. The deduced amino acid sequences of the Italian strain differed by 10 and 11 amino-acids from the Budapest and Vienna strains, respectively, and by 28 from the SAAR-1776 strain. According to this study two strains of USUVs are likely to have circulated in Italy between 2008 and 2009. They have developed strategies of adaptation and evolution to spread into new areas and to become established.
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http://dx.doi.org/10.1016/j.vetmic.2011.03.036DOI Listing
August 2011

Low rate of virological failure and maintenance of susceptibility to HIV-1 protease inhibitors with first-line lopinavir/ritonavir-based antiretroviral treatment in clinical practice.

J Med Virol 2010 Dec;82(12):1996-2003

Clinic of Infectious Diseases, Catholic University of Sacred Heart, Rome, Italy.

Protease inhibitor (PI)-resistant HIV-1 has hardly ever been detected at failed boosted PI-based first-line antiretroviral regimens in clinical trials. However, this phenomenon has not been investigated in clinical practice. To address this gap, data from patients starting a first-line lopinavir/ritonavir (LPV/rtv)-based therapy with available baseline HIV-1 RNA load, a viral genotype and follow-up viral load after 3 and 6 months of treatment were extracted from the Italian Antiretroviral Resistance Cohort Analysis (ARCA) observational database. Based on survival analysis, 39 (7.1%) and 43 (7.8%) of the 548 examined patient cases had an HIV-1 RNA >500 and >50 copies/ml, respectively, after 6 months of treatment. Cox proportional hazard models detected baseline HIV-1 RNA (RH 1.79, 95%CI 1.10-2.92 per 1-log(10) increase, P=0.02) and resistance to the nucleoside backbone (RH 1.04, 95%CI 1.02-1.06 per 10-point increase using the Stanford HIVdb algorithm, P<0.001) as independent predictors of HIV-1 RNA at >500 copies/ml, but not at the >50 copies/ml cutoff criteria. Higher baseline viral load, older patient age, heterosexual route of infection and use of tenofovir/emtricitabine were predictors of failure at month 3 using the 50-copy and/or 500-copy threshold. Resistance to LPV/rtv did not occur or increase in any of the available 36 follow-up HIV-1 genotypes. Resistance to the nucleoside backbone (M184V) developed in four cases. Despite the likely differences in patient population and adherence, both the low rate of virological failure and the lack of development of LPV/rtv resistance documented in clinical trials are thus confirmed in clinical practice.
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http://dx.doi.org/10.1002/jmv.21927DOI Listing
December 2010

Performance of genotypic tropism testing in clinical practice using the enhanced sensitivity version of Trofile as reference assay: results from the OSCAR Study Group.

New Microbiol 2010 Jul;33(3):195-206

University of Rome Tor Vergata, Department of Experimental Medicine, Roma, Italy.

Objective: The goal of the OSCAR programme is to evaluate the performances of genotypic HIV-1 tropism testing in clinical practice using the enhanced sensitivity version of Trofile (ESTA) as reference-assay.

Methods: HIV-1 coreceptor-usage was assessed using plasma samples from 406 HIV-1 infected patients by ESTA and by gp120 V3 population-sequencing followed by Geno2pheno (set at a False Positive Rate [FPR] of 10% and 5%).

Results: ESTA was successful in 365 (89.9%) samples indicating R5 in 254 (69.6%), and DM/X4 in 111 (30.4% of samples (104 [28.5%] DM and 7 [1.9%] X4). Genotypic-testing successfully assessed viral tropism for all 406 samples, including the 41 with undetermined result by ESTA. Genotypic-tropism testing at a FPR of 5% and 10% was 81.1% and 78.4% concordant with ESTA, respectively. Despite a sensitivity of 48.7% and 55.9% at a FPR of 5% and 10%, respectively, a high concordance (specificity: 95.3% for FPR of 5% and 88.2% for FPR of 10%) between genotypic-tropism testing and ESTA was reached in the detection of R5-tropic viruses.

Conclusion: Our results are in line with other European studies, and support the routine use of genotypic tropism testing in clinical-settings for monitoring of HIV-1 infected patients candidate to or failing CCR5-antagonists.
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July 2010

Mycobacterium europaeum sp. nov., a scotochromogenic species related to the Mycobacterium simiae complex.

Int J Syst Evol Microbiol 2011 Jul 6;61(Pt 7):1606-1611. Epub 2010 Aug 6.

Laboratory of Microbiology and Virology, Modena University Hospital, Modena, Italy.

Four strains isolated in the last 15 years were revealed to be identical in their 16S rRNA gene sequences to MCRO19, the sequence of which was deposited in GenBank in 1995. In a polyphasic analysis including phenotypic and genotypic features, the five strains (including MCRO19), which had been isolated in four European countries, turned out to represent a unique taxonomic entity. They are scotochromogenic slow growers and are genetically related to the group that included Mycobacterium simiae and 15 other species. The novel species Mycobacterium europaeum sp. nov. is proposed to accommodate these five strains. Strain FI-95228(T) ( = DSM 45397(T)  = CCUG 58464(T)) was chosen as the type strain. In addition, a thorough revision of the phenotypic and genotypic characters of the species related to M. simiae was conducted which leads us to suggest the denomination of the 'Mycobacterium simiae complex' for this group.
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http://dx.doi.org/10.1099/ijs.0.025601-0DOI Listing
July 2011

Organising pneumonia mimicking invasive fungal disease in patients with leukaemia.

Eur J Haematol 2010 Jul 9;85(1):76-82. Epub 2010 Feb 9.

Department of Oncology, Haematology and Respiratory Diseases, Section of Haematology, University of Modena and Reggio Emilia, Azienda Ospedaliero-Universitaria Policlinico, Modena, Italy.

Clinical charts from 63 consecutive highly immunocompromised haematologic patients presenting with pulmonary nodular lesions on CT scan, classified as either probable or possible invasive fungal disease (IFD) according to the revised EORTC/MSG classification, were retrospectively studied. Histopathological analysis of lung tissues, available for 23 patients, demonstrated proven IFD in 17 cases (14 invasive aspergillosis and 3 invasive zygomycosis), diffuse alveolar damage in one and organising pneumonia (OP) in five cases. In the OP cases, three of which have been defined as probable IFD according to EORTC/MSG classification, extensive immunohistochemical, molecular and immunological analyses for fungi were negative. Our case descriptions extend the notion that OP may be encountered as a distinct histopathological entity in pulmonary nodular lesions in patients with leukaemia with probable/possible IFD.
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http://dx.doi.org/10.1111/j.1600-0609.2010.01427.xDOI Listing
July 2010

Commercial DNA probes for mycobacteria incorrectly identify a number of less frequently encountered species.

J Clin Microbiol 2010 Jan 11;48(1):307-10. Epub 2009 Nov 11.

Regional Reference Center for Mycobacteria, Piastra dei Servizi, A. O. U. Careggi, viale Morgagni 85, 50134 Florence, Italy.

Although commercially available DNA probes for identification of mycobacteria have been investigated with large numbers of strains, nothing is known about the ability of these probes to identify less frequently encountered species. We analyzed, with INNO LiPA MYCOBACTERIA (Innogenetics) and with GenoType Mycobacterium (Hein), 317 strains, belonging to 136 species, 61 of which had never been assayed before. INNO LiPA misidentified 20 taxa, the majority of which cross-reacted with the probes specific for Mycobacterium fortuitum and the Mycobacterium avium-Mycobacterium intracellulare-Mycobacterium scrofulaceum group. GenoType misidentified 28 taxa, most of which cross-reacted with M. intracellulare and M. fortuitum probes; furthermore, eight species were not recognized as members of the genus Mycobacterium. Among 54 strains investigated with AccuProbe (Gen-Probe), cross-reactions were detected for nine species, with the probes aiming at the M. avium complex being most involved in cross-reactions.
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http://dx.doi.org/10.1128/JCM.01536-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812265PMC
January 2010

Splenic hyalohyphomycosis, molecularly and immunologically consistent with invasive aspergillosis, in a patient with acute lymphoblastic leukemia.

Am J Hematol 2010 Mar;85(3):188-9

Department of Oncology, Hematology and Respiratory Diseases, University of Modena and Reggio Emilia, Azienda Ospedaliera-Universitaria Policlinico, Modena, Italy.

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http://dx.doi.org/10.1002/ajh.21438DOI Listing
March 2010