P E Varaldo

Università Politecnica delle Marche, Ancona, The Marches, Italy

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Publications (195)966.49 Total impact

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    ABSTRACT: Objectives: The objective of this study was to investigate the genetic environment of the cfr gene from two linezolid-resistant clinical isolates of Staphylococcus epidermidis from Italy. Methods: The two strains (SP1 and SP2) were phenotypically and genotypically characterized. Transferability of cfr was assessed by electrotransformation and conjugation. The genetic contexts of cfr were investigated by PCR mapping, sequencing and comparative sequence analyses. Results: SP1 and SP2 belonged to ST23 and ST83, respectively. In both strains, the cfr gene was located on a plasmid, which could be transferred to Staphylococcus aureus by transformation and conjugation. In isolate SP1, linezolid resistance mediated by mutations in 23S rRNA and the L3 ribosomal protein was also detected. pSP01, the cfr-carrying plasmid from strain SP1, had a larger number of additional resistance genes and was sequenced (76 991 bp). It disclosed a distinctive mosaic structure, with four cargo regions interpolated into a backbone 95% identical to that of S. aureus plasmid pPR9. Besides cfr, resistance genes distributed in the cargo regions included blaZ, lsa(B), msr(A) and aad, and a gene cluster for resistance to heavy metals. A closely related cfr plasmid (pSP01.1, ∼49 kb), differing from pSP01 by the lack of a large cargo region with some resistance genes, was detected in strain SP2. Conclusions: The conjugative multiresistance plasmid pSP01 is the first cfr-carrying plasmid to be sequenced in Italy. This is the first time cfr has been found: (i) in association with blaZ, msr(A) and heavy metal resistance genes; and (ii) in an S. epidermidis strain (SP2) belonging to ST83.
    Journal of Antimicrobial Chemotherapy 10/2015; DOI:10.1093/jac/dkv341 · 5.31 Impact Factor
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    ABSTRACT: Фm46.1 — a Streptococcus pyogenes bacteriophage carrying mef(A) and tet(O), respectively encoding resistance to macrolides (M phenotype) and tetracycline — is widespread in S. pyogenes but has not been reported outside this species. Фm46.1 is transferable in vitro among S. pyogenes isolates, but no information is available about its transferability to other Streptococcus species. We thus investigated Фm46.1 for its ability to be transduced in vitro to recipients of different Streptococcus species. Transductants were obtained from recipients of Streptococcus agalactiae, Streptococcus gordonii, and Streptococcus suis. Retransfer was always achieved, and from S. suis to S. pyogenes occurred at a much greater frequency than in the opposite direction. In transductants Фm46.1 retained its functional properties, such as inducibility with mitomycin C, presence both as a prophage and as a free circular form, and transferability. The transductants shared the same Фm46.1 chromosomal integration site as the donor, at the 3’ end of a conserved RNA uracil methyltransferase (rum) gene, which is an integration hotspot for a variety of genetic elements. No transfer occurred to recipients of Streptococcus pneumoniae, Streptococcus oralis, and Streptococcus salivarius, even though rum-like genes were also detected in the sequenced genomes of these species. A largely overlapping 18-bp critical sequence, where the site-specific recombination process presumably takes place, was identified in the rum genes of all recipients, including those of the species yielding no transductants. Growth assays to evaluate the fitness cost of Фm46.1 acquisition disclosed a negligible impact on S. pyogenes, S. agalactiae, and S. gordonii transductants and a noticeable fitness advantage in S. suis. The S. suis transductant also displayed marked overexpression of the autolysin-encoding gene atl.
    Frontiers in Microbiology 01/2015; 5:1-9. DOI:10.3389/fmicb.2014.00746 · 3.99 Impact Factor
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    Marina Mingoia · Eleonora morici · Andrea Brenciani · Eleonora Giovanetti · Pietro Emanuele Varaldo ·
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    ABSTRACT: In streptococci mef(I) and catQ, two relatively uncommon macrolide and chloramphenicol resistance genes, respectively, are typically linked in a genetic module designated IQ module. Though variable, the module consistently encompasses, and is sometimes reduced to,a conserved ∼5.8-kb mef(I)-catQ fragment. The prototype IQ module was described in Streptococcus pneumoniae. IQ-like modules have subsequently been detected in Streptococcus pyogenes and in different species of viridans group streptococci, where mef(E) maybe found instead of mef(I). Three genetic elements, one carrying the prototype IQ module from S. pneumoniae and two carrying different, defective IQ modules from S. pyogenes, have recently been characterized. All are integrative and conjugative elements (ICEs) belonging to the Tn5253 family, and have been designated ICESpn529IQ, ICESpy029IQ and ICESpy005IQ, respectively. ICESpy029IQ and ICESpy005IQ were the first Tn5253 family ICEs to be described in S. pyogenes. A wealth of new information has been obtained by comparing their genetic organization, chromosomal integration, and transferability. The origin of the IQ module is unknown. The mechanism by which it spreads in streptococci is discussed.
    Frontiers in Microbiology 01/2015; 5:1-5. DOI:10.3389/fmicb.2014.00747 · 3.99 Impact Factor
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    ABSTRACT: The Gram-negative opportunistic pathogen, Klebsiella pneumoniae, is responsible for causing a spectrum of community-acquired and nosocomial infections and typically infects patients with indwelling medical devices, especially urinary catheters, on which this microorganism is able to grow as a biofilm. The increasingly frequent acquisition of antibiotic resistance by K. pneumoniae strains has given rise to a global spread of this multidrug-resistant pathogen, mostly at the hospital level. This scenario is exacerbated when it is noted that intrinsic resistance to antimicrobial agents dramatically increases when K. pneumoniae strains grow as a biofilm. This review will summarize the findings about the antibiotic resistance related to biofilm formation in K. pneumoniae.
    Pathogens 09/2014; 3(3):743-758. DOI:10.3390/pathogens3030743
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    ABSTRACT: The linkage between the macrolide efflux gene mef(I) and the chloramphenicol inactivation gene catQ was first described in Streptococcus pneumoniae (strain Spn529), where the two genes are located in a module designated IQ element. Subsequently, two different defective IQ elements were detected in Streptococcus pyogenes (strains Spy029 and Spy005). The genetic elements carrying the three IQ elements were characterized, and all were found to be Tn5253 family integrative and conjugative elements (ICEs). The ICE from S. pneumoniae (ICESpn529IQ) was sequenced, whereas the ICEs from S. pyogenes (ICESpy029IQ and ICESpy005IQ, the first Tn5253-like ICEs reported in this species) were characterized by PCR mapping, partial sequencing, and restriction analysis. ICESpn529IQ and ICESpy029IQ were found to share the intSp23FST81 integrase gene and an identical Tn916 fragment, whereas ICESpy005IQ has int5252 and lacks Tn916. All three ICEs were found to lack the linearized pC194 plasmid that is usually associated with Tn5253-like ICEs, and all displayed a single copy of a toxin-antitoxin operon that is typically contained in the direct repeats flanking the excisable pC194 region when this region is present. Two different insertion sites of the IQ elements were detected, one in ICESpn529IQ and ICESpy029IQ, and another in ICESpy005IQ. The chromosomal integration of the three ICEs was site specific, depending on the integrase (intSp23FST81 or int5252). Only ICESpy005IQ was excised in circular form and transferred by conjugation. By transformation, mef(I) and catQ were cotransferred at a high frequency from S. pyogenes Spy005 and at very low frequencies from S. pneumoniae Spn529 and S. pyogenes Spy029.
    Antimicrobial Agents and Chemotherapy 07/2014; 58(10). DOI:10.1128/AAC.03638-14 · 4.48 Impact Factor
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    Carla Vignaroli · Alessio Mancini · Pietro E Varaldo ·

    Emerging Infectious Diseases 05/2014; 20(5):905-7. DOI:10.3201/eid2005.130934 · 6.75 Impact Factor
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    ABSTRACT: While most integrative and conjugative elements (ICEs) encode Tyr/Ser recombinases, two ICE families have recently been described (1) that rely on DDE transposases (2) for circularization and integration into the chromosome.…
    Antimicrobial Agents and Chemotherapy 01/2014; 58(4). DOI:10.1128/AAC.00048-14 · 4.48 Impact Factor
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    ABSTRACT: To investigate the distribution of erythromycin, tetracycline and chloramphenicol resistance mechanisms and determinants and the relevant genetic environments and elements in viridans group streptococci (VGS). A total of 263 VGS collected from routine throat swabs in 2010-12 and identified to the species level were studied. Antibiotic resistance determinants and the relevant genetic contexts and elements were determined using amplification and sequencing assays and restriction analysis. The investigation provided original information on the distribution of resistance mechanisms, determinants and genetic elements in VGS. Erythromycin-resistant isolates totalled 148 (56.3%; 37 belonging to the cMLS phenotype and 111 belonging to the M phenotype); there were 72 (27.4%) and 7 (2.7%) tetracycline- and chloramphenicol-resistant isolates, respectively. A number of variants of known genetic contexts and elements carrying determinants of resistance to these antibiotics were detected, including the mega element, Φ10394.4, Tn2009, Tn2010, the IQ element, Tn917, Tn3872, Tn6002, Tn916, Tn5801, a tet(O) fragment from ICE2096-RD.2 and ICESp23FST81. These findings shed new light on the distribution of antibiotic resistance mechanisms and determinants and their genetic environments in VGS, for which very few such data are currently available. The high frequency and broad variety of such elements supports the notion that VGS may be important reservoirs of resistance genes for the more pathogenic streptococci. The high rates of macrolide resistance confirm the persistence of a marked prevalence of resistant VGS in Europe, where macrolide resistance is, conversely, declining among the major streptococcal pathogens.
    Journal of Antimicrobial Chemotherapy 12/2013; 69(5). DOI:10.1093/jac/dkt495 · 5.31 Impact Factor
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    ABSTRACT: Tn5801, originally detected in Staphylococcus aureus Mu50, is a Tn916 family element where a unique int gene (int5801) replaces int916 and xis916. Among 62 tet(M)-positive tetracycline-resistant Streptococcus agalactiae isolates, 43 harbored Tn916 whereas 19 harbored a Tn5801-like element (Tn5801.Sag, ∼20.6 kb). Tn5801.Sag was characterized (PCR mapping, partial sequencing, chromosomal integration) and compared to other Tn5801-like elements. Similar to Tn5801 from S. aureus Mu50, tested in parallel, Tn5801.Sag was unable to undergo circularization and conjugal transfer.
    Antimicrobial Agents and Chemotherapy 07/2013; 57(9). DOI:10.1128/AAC.00521-13 · 4.48 Impact Factor
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    ABSTRACT: The unprecedented wealth of databases that have become available in the era of next-generation sequencing has considerably increased our knowledge of bacterial genetic elements (GEs). At the same time, the advent of single-cell based approaches has brought realization that unsuspected heterogeneity may occur in the bacterial population from a single colony. The increasing use of PCR-based techniques to study new GEs requires careful consideration of the possible different PCR targets associated with different subpopulations if incorrect or incomplete interpretations are to be avoided. In this commentary, confining ourselves to our direct experience, we illustrate some examples of PCR pitfalls that may be encountered while investigating GEs.
    05/2013; 3(3):e25255. DOI:10.4161/mge.25255
  • Claudio Palmieri · Marina Mingoia · Pietro E Varaldo ·

    Antimicrobial Agents and Chemotherapy 05/2013; 57(5):2440-1. DOI:10.1128/AAC.02548-12 · 4.48 Impact Factor
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    ABSTRACT: ICESp1116, responsible for erm(B)-mediated, inducible erythromycin resistance in Streptococcus pyogenes, was comprehensively characterized, and its chromosomal integration site was determined. It displayed a unique mosaic organization consisting of a scaffold, related to TnGallo1 from Streptococcus gallolyticus, with two inserted fragments separated by IS1216. One fragment, containing erm(B), displayed high-level identity to a portion of the S. pyogenes plasmid pSM19035; the other, containing a truncated tet(M) gene, displayed high-level identity to the right-hand portion of Clostridium difficile Tn5397.
    Antimicrobial Agents and Chemotherapy 10/2012; 56(12). DOI:10.1128/AAC.01494-12 · 4.48 Impact Factor
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    ABSTRACT: The macrolide-aminoglycoside-streptothricin (MAS) element, an ∼4.2-kb insertion containing erm(B) and aphA3 resistance determinants, distinguishes Streptococcus pneumoniae transposon Tn1545/Tn6003 from Tn6002. Here, it is shown to be an unstable genetic element that, although it lacks recombinase genes, can exploit long, erm(B)-containing direct repeats acting as att sites for spontaneous excision that may result in loss. Consequent to excision, which is RecA independent, Tn1545/Tn6003 changes to Tn6002. In pneumococcal populations harboring Tn1545/Tn6003, the latter appears to coexist with Tn6002.
    Antimicrobial Agents and Chemotherapy 08/2012; 56(11):5994-7. DOI:10.1128/AAC.01487-12 · 4.48 Impact Factor
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    ABSTRACT: Mosaic tetracycline resistance determinants are a recently discovered class of hybrids of ribosomal protection tet genes. They may show different patterns of mosaicism, but their final size has remained unaltered. Initially thought to be confined to a small group of anaerobic bacteria, mosaic tet genes were then found to be widespread. In the genus Streptococcus, a mosaic tet gene [tet(O/W/32/O)] was first discovered in Streptococcus suis, an emerging drug-resistant pig and human pathogen. In this study, we report the molecular characterization of a tet(O/W/32/O) gene-carrying mobile element from an S. suis isolate. tet(O/W/32/O) was detected, in tandem with tet(40), in a circular 14,741-bp genetic element (39.1% G+C; 17 open reading frames [ORFs] identified). The novel element, which we designated 15K, also carried the macrolide resistance determinant erm(B) and an aminoglycoside resistance four-gene cluster including aadE (streptomycin) and aphA (kanamycin). 15K appeared to be an unstable genetic element that, in the absence of recombinases, is capable of undergoing spontaneous excision under standard growth conditions. In the integrated form, 15K was found inside a 54,879-bp integrative and conjugative element (ICE) (50.5% G+C; 55 ORFs), which we designated ICESsu32457. An ∼1.3-kb segment that apparently served as the att site for excision of the unstable 15K element was identified. The novel ICE was transferable at high frequency to recipients from pathogenic Streptococcus species (S. suis, Streptococcus pyogenes, Streptococcus pneumoniae, and Streptococcus agalactiae), suggesting that the multiresistance 15K element can successfully spread within streptococcal populations.
    Antimicrobial Agents and Chemotherapy 06/2012; 56(9):4697-702. DOI:10.1128/AAC.00629-12 · 4.48 Impact Factor
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    ABSTRACT: In ICESp2905, a widespread erm(TR)- and tet(O)-carrying genetic element of Streptococcus pyogenes, the two resistance determinants are contained in separate fragments inserted into a scaffold of clostridial origin. ICESp2905 (∼65.6 kb) was transferable not only in its regular form but also in a defective form lacking the erm(TR) fragment (ICESp2906, ∼53.0 kb). The erm(TR) fragment was also an independent integrative and conjugative element (ICE) (ICESp2907, ∼12.6 kb). ICESp2905 thus results from one ICE (ICESp2907) being integrated into another (ICESp2906).
    Antimicrobial Agents and Chemotherapy 01/2012; 56(1):591-4. DOI:10.1128/AAC.05352-11 · 4.48 Impact Factor
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    Claudio Palmieri · Pietro E Varaldo · Bruna Facinelli ·
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    ABSTRACT: Streptococcus suis, a major porcine pathogen, has been receiving growing attention not only for its role in severe and increasingly reported infections in humans, but also for its involvement in drug resistance. Recent studies and the analysis of sequenced genomes have been providing important insights into the S. suis resistome, and have resulted in the identification of resistance determinants for tetracyclines, macrolides, aminoglycosides, chloramphenicol, antifolate drugs, streptothricin, and cadmium salts. Resistance gene-carrying genetic elements described so far include integrative and conjugative elements, transposons, genomic islands, phages, and chimeric elements. Some of these elements are similar to those reported in major streptococcal pathogens such as Streptococcus pyogenes, Streptococcus pneumoniae, and Streptococcus agalactiae and share the same chromosomal insertion sites. The available information strongly suggests that S. suis is an important antibiotic resistance reservoir that can contribute to the spread of resistance genes to the above-mentioned streptococci. S. suis is thus a paradigmatic example of possible intersections between animal and human resistomes.
    Frontiers in Microbiology 11/2011; 2:235. DOI:10.3389/fmicb.2011.00235 · 3.99 Impact Factor
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    Carla Vignaroli · Caterina Rinaldi · Pietro E Varaldo ·

    Antimicrobial Agents and Chemotherapy 05/2011; 55(5):2495-6; author reply 296-7. DOI:10.1128/AAC.00224-11 · 4.48 Impact Factor
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    Marina Mingoia · Emily Tili · Esther Manso · Pietro E Varaldo · Maria Pia Montanari ·
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    ABSTRACT: Several drug resistances in Streptococcus pneumoniae are associated with mobile genetic elements, which are loosely subdivided into a group of smaller (18- to 27-kb) and a group of larger (>50-kb) elements. While the elements of the former group, which typically carry the tetracycline resistance determinant tet(M) and whose prototype is Tn916 (18 kb), have been studied extensively, the larger elements, whose prototype is Tn5253 (∼65.5 kb), are not as well explored. Tn5253 is a composite structure consisting of two independent conjugative transposons, Tn5251 (which is virtually identical to Tn916) and Tn5252 (∼47.5 kb), with the former inserted into the latter. Tn5252, which so far has only partially been sequenced, carries an integrase gene, driving its site-specific insertion into the host cell genome, and the chloramphenicol resistance cat(pC194) determinant. This study investigated 20 clinical isolates of S. pneumoniae, which were selected on the basis of cat(pC194)-mediated chloramphenicol resistance. All 20 isolates harbored a Tn5253-like element. The composite elements (some of which have been completely sequenced) demonstrated considerable heterogeneity that stemmed from a dual variability: in the Tn5252-like element, due primarily to differences in the integrase gene but also to differences in cargo genes and in the overall genetic organization, and in the Tn916-like element, with the possible involvement, besides Tn916, of a number of Tn916 family pneumococcal elements carrying different erythromycin resistance genes. In mating experiments, only one composite element, containing a less typical Tn916 family element, appeared to be nonmobile. Being part of a Tn5253-like composite element may confer on some Tn916-like transposons, which are apparently nontransferable as independent genetic elements, the ability to be mobilized.
    Antimicrobial Agents and Chemotherapy 03/2011; 55(4):1453-9. DOI:10.1128/AAC.01087-10 · 4.48 Impact Factor
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    ABSTRACT: The genetic support for tet(W), an emerging tetracycline resistance determinant, was studied in two strains of Streptococcus suis, SsCA and SsUD, both isolated in Italy from patients with meningitis. Two completely different tet(W)-carrying genetic elements, sharing only a tet(W)-containing segment barely larger than the gene, were found in the two strains. The one from strain SsCA was nontransferable, and aside from an erm(B)-containing insertion, it closely resembled a genomic island recently described in an S. suis Chinese human isolate in sequence, organization, and chromosomal location. The tet(W)-carrying genetic element from strain SsUD was transferable (at a low frequency) and, though apparently noninducible following mitomycin C treatment, displayed a typical phage organization and was named ΦSsUD.1. Its full sequence was determined (60,711 bp), the highest BLASTN score being Streptococcus pyogenes Φm46.1. ΦSsUD.1 exhibited a unique combination of antibiotic and heavy metal resistance genes. Besides tet(W), it contained a MAS (macrolide-aminoglycoside-streptothricin) fragment with an erm(B) gene having a deleted leader peptide and a cadC/cadA cadmium efflux cassette. The MAS fragment closely resembled the one recently described in pneumococcal transposons Tn6003 and Tn1545. These resistance genes found in the ΦSsUD.1 phage scaffold differed from, but were in the same position as, cargo genes carried by other streptococcal phages. The chromosome integration site of ΦSsUD.1 was at the 3′ end of a conserved tRNA uracil methyltransferase (rum) gene. This site, known to be an insertional hot spot for mobile elements in S. pyogenes, might play a similar role in S. suis.
    Antimicrobial Agents and Chemotherapy 02/2011; 55(2):631-6. DOI:10.1128/AAC.00965-10 · 4.48 Impact Factor
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    ABSTRACT: In Streptococcus pyogenes, inducible erythromycin (ERY) resistance is due to posttranscriptional methylation of an adenine residue in 23S rRNA that can be encoded either by the erm(B) gene or by the more recently described erm(TR) gene. Two erm(TR)-carrying genetic elements, showing extensive DNA identities, have thus far been sequenced: ICE10750-RD.2 (∼49 kb) and Tn1806 (∼54 kb), from tetracycline (TET)-susceptible strains of S. pyogenes and Streptococcus pneumoniae, respectively. However, TET resistance, commonly mediated by the tet(O) gene, is widespread in erm(TR)-positive S. pyogenes. In this study, 23 S. pyogenes clinical strains with erm(TR)-mediated ERY resistance—3 TET susceptible and 20 TET resistant—were investigated. Two erm(TR)-carrying elements sharing only a short, high-identity erm(TR)-containing core sequence were comprehensively characterized: ICESp1108 (45,456 bp) from the TET-susceptible strain C1 and ICESp2905 (65,575 bp) from the TET-resistant strain iB21. While ICESp1108 exhibited extensive identities to ICE10750-RD.2 and Tn1806, ICESp2905 showed a previously unreported genetic organization resulting from the insertion of separate erm(TR)- and tet(O)-containing fragments in a scaffold of clostridial origin. Transferability by conjugation of the erm(TR) elements from the same strains used in this study had been demonstrated in earlier investigations. Unlike ICE10750-RD.2 and Tn1806, which are integrated into an hsdM chromosomal gene, both ICESp1108 and ICESp2905 shared the chromosomal integration site at the 3′ end of the conserved rum gene, which is an integration hot spot for several mobile streptococcal elements. By using PCR-mapping assays, erm(TR)-carrying elements closely resembling ICESp1108 and ICESp2905 were shown in the other TET-susceptible and TET-resistant test strains, respectively.
    Antimicrobial Agents and Chemotherapy 02/2011; 55(5):2106-12. DOI:10.1128/AAC.01378-10 · 4.48 Impact Factor

Publication Stats

4k Citations
966.49 Total Impact Points


  • 2000-2015
    • Università Politecnica delle Marche
      • • Department of Biomedical Sciences and Public Health
      • • Department of Biomedical Sciences
      Ancona, The Marches, Italy
    • University of Florence
      Florens, Tuscany, Italy
    • Università degli Studi di Trieste
      Trst, Friuli Venezia Giulia, Italy
  • 1999-2007
    • University of Camerino
      Camerino, The Marches, Italy
  • 2006
    • University of Naples Federico II
      Napoli, Campania, Italy
  • 2003
    • University of Washington Seattle
      • Department of Pathology
      Seattle, Washington, United States
  • 1993-2002
    • Catholic University of the Sacred Heart
      • Institute of Microbiology
      Milano, Lombardy, Italy
  • 2001
    • Istituto Superiore di Sanità
      • Department of Infectious, Parasitic and Immune-mediated Diseases
      Roma, Latium, Italy
  • 1992-2000
    • Università degli Studi di Siena
      Siena, Tuscany, Italy
  • 1979-1991
    • Università degli Studi di Genova
      • Sezione di Microbiologia
      Genova, Liguria, Italy
  • 1989
    • CRO Centro di Riferimento Oncologico di Aviano
      Aviano, Friuli Venezia Giulia, Italy