Pier Sandro Cocconcelli

Università Cattolica del Sacro Cuore, Milano, Lombardy, Italy

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Publications (96)164.94 Total impact

  • Daniela Bassi · Edoardo Puglisi · Pier Sandro Cocconcelli ·
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    ABSTRACT: The environment of hard cheese encourages bacterial synergies and competitions along the ripening process, which might lead in defects such as clostridial blowing. In this study, Denaturing Gradient Gel Electrophoresis (DGGE), a quantitative Clostridium tyrobutyricum PCR and next-generation Illumina-based sequencing of 16S rRNA gene were applied to study 83 Grana Padano spoiled samples. The aim was to investigate the community of clostridia involved in spoilage, the ecological relationships with the other members of the cheese microbiota, and the effect of lysozyme. Three main genera were dominant in the analysed cheeses, Lactobacillus, Streptococcus and Clostridium, and the assignment at the species level was of 94.3% of 4,477,326 high quality sequences. C. tyrobutyricum and C. butyricum were the most prevalent clostridia. Hierarchical clustering based on the abundance of bacterial genera, revealed three main clusters: one characterized by the highest proportion of Clostridium, a second where Lactobacillus was predominant and the last, dominated by Streptococcus thermophilus. Ecological relationships among species were found: cheeses characterized by an high abundance of S. thermophilus and L. rhamnosus were spoiled by C. tyrobutyricum while, when L. delbrueckii was the most abundant Lactobacillus, C. butyricum was the dominant spoiling species. Lysozyme also shaped the bacterial community, reducing C. tyrobutyricum in favour of C. butyricum. Moreover, this preservative increased the proportion of L. delbrueckii and obligate heterofermentative lactobacilli and lowered L. helveticus and non-starter species, such as L. rhamnosus and L. casei. Copyright © 2015 Elsevier Ltd. All rights reserved.
    Food Microbiology 12/2015; 52:106-118. DOI:10.1016/j.fm.2015.07.004 · 3.33 Impact Factor

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    Simona Gazzola · Daniela Bassi · Pier Sandro Cocconcelli ·
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    ABSTRACT: It is known that the use of antibiotics in animal farming acts as selective pressure on bacterial populations, inducing the outgrowth of antimicrobial resistant (AMR) strains. Less information is available on the spread of these bacteria and of the AMR genes in the food chains and their fate and during food fermentation. Moreover, few data are available on the consumer exposure to AMR through foods. To investigate on it, we used two approaches: first the analysis AMR populations from milk and dairy fermented foods, then the use of genomics for the detection of AMR determinants in food associated bacteria. We focused on three antibiotics of human or veterinary importance: ampicillin, tetracycline and erythromycin. A total of 208 AMR strains were isolated from dairy products belonging the species Streptococcus lutatiensis, Lactobacillus salivarius, Lactococcus lactis, Enterococcus faecalis, Staphylococcus xylosus, Staphylococcus saprophyticus, Bacillus licheniformis, B. cereus Pseudomonas aeruginosa, Obesobacterium proteus, Hafnia alveae, Shigella spp, Escherichia coli, Klebsiella pneumonia and Proteus mirabilis. The genetic determinants responsible for resistance were identified and the mostr represented were ermB, ermC, tetM, and blaZ and genes for extended-spectrum β-lactamases. Multidrug resistant strains were isolated. The genomic analyses of species of Enterococcus, Lactobacillus, Streptococcus and Staphylococcus, targeted to the detection AMR genes and mobile elements, plasmids, transposons and ICE (integrative conjugative elements), revealed the presence of a scattered presence of AMR determinants, with a higher frequency in Enterococcus. These results highlight a risk associated to AMR bacteria in food and underline the emergency of deeper understanding the role of food AMR populations as risk factor for human health.
    3rd International Conference on Microbial Diversity, The Chellange of complexity; 10/2015
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    Simona Gazzola · Eleonora Sattin · Barbara Simionati · Pier Sandro Cocconcelli ·
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    ABSTRACT: Lactic acid bacteria (LAB) have been used to inhibit undesirable bacteria in ferment foods. Different studies showed how adjunct cultures are active against spoilage bacteria and pathogens in different foods. In cheese the spoilage can affect the shelf life of the product with smear on the cheese surface and packaging blowing. Recently cultured-independent methods, and in particular next generation sequencing (NGS), have been used to evaluate the complete microbiota in complex ecosystems and we applied this technique to better understand the microbial community in fresh cheese at the end of its shelf life. The cultivation based methods and NGS analysis over the shelf life period, showed that the spoilage microbiota at 8°C and 14°C is composed of primarily by species of Enterobacteriaceae and Moraxellaceae. To limit the outgrowth of these bacteria we tested in in vitro cheese model 13 different lactic acid bacteria (LAB). Three out of 13 bacteria, namely Lactobacillus rhamnosus RH05, L. sakei LK04 and Carnobacterium maltoaromaticum CNB04, were the most effective in inhibiting Gram negative bacteria and so they were assessed in industrial trials either alone or in combination. Soft cheese with and without adjunct cultures were prepared and stored at 8°C and 14°C until the end of the shelf life. Traditional counting colonies and next generation sequencing demonstrated that the use of adjunct cultures reduces the growth of spoilage microbiota at both temperatures of storage. In particular during industrial experiments Carnobacterium maltoaromaticum CNB04 showed the most evident activity against psychotropic spoilage microbes.
    3rd International Conference on Microbial Diversity, The Chellange of complexity, Perugia; 10/2015
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    Simona Gazzola · Daniela Bassi · Cecilia Fontana · Pier Sandro Cocconcelli ·

    EFSA’s 2nd Scientific Conference Shaping the Future of Food Safety, Together; 10/2015
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    Daniela Bassi · Cecilia Fontana · Simona Gazzola · Pier Sandro Cocconcelli ·
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    ABSTRACT: Objectives Recent improvements in the quality, efficiency and cost of next generation sequencing (NGS) technologies have led to a revolution in the study of a great number of bacterial genomes. Aim of this work is to highlight how NGS might provide a tool for deeper understanding of bacteria intentionally introduced in the food chain and that require an authorization by risk managers. To reach this goal, whole genome sequencing together with the sequence comparison among different strains was applied in the risk assessment process, highlighting the presence of putative genes involved in virulence and antimicrobial resistances. Materials and Methods. A total of 22 strains belonging to different species of lactic acid bacteria (LAB) used as human and animal probiotics, silage and food starter cultures, belonging to the species Lactobacillus rhamnosus, L. plantarum, L. helveticus, L. casei, Streptococcus thermophilus, Lactococcus lactis, Staphylococcus epidermidis and Enterococcus faecium, were subjected to genome analysis. Sequencing was made using an Illumina Genome Analyzer Hiseq1000. Quality reader filter and assembly was performed using Velvet 1.2.08. Functional annotations were performed with Manatee and RAST. KEGG was used to reconstruct biochemical pathways. Antimicrobial resistance genes and genes coding for putative virulence factors were detected using ResFinder 2.0, PatogenFinder, VirulenceFinder, VFDB and MvirDB databases. Phylogenomic approaches were used to assign enterococcal strain to the commensal or clinical clade. Results. Strains of LAB species belonging or not to the EFSA QPS list were studied. NGS technique provided relevant information on these bacterial strains. Data deriving from genome annotation showed a great variability in the genome sizes and number of genes among the analyzed species. The comparative sequence analysis added new insights in the metabolic pathways and safety features. Genes coding for antibiotic resistances were detected in strains of Lactobacillus and Enterococcus and virulence factors in strain of E. faecium and Staphylococcus epidermidis. Conclusions. The interpretation of the sequence information constitutes an essential approach to perform the risk assessment of strains intentionally introduced in the food chain. Moreover, it allows the study of bacterial biodiversity, genetic drift, to reconstruct the biochemical pathways and to analyze the phylogenetic relationship among strains and species.
    Shaping the future of food safety, together EFSA conference 2015, Milan; 10/2015
  • Pier Sandro Cocconcelli · Chiara Corbo · Daniela Bassi ·

    Laboratorio Expo. The many faces of sustainability, Annali della Fondazione Feltrinelli edited by Salvatore Veca, 10/2015: pages 199-212; Giangiacomo Feltrinelli Editore., ISBN: 9788807990700
  • Pier Sandro Cocconcelli · Daniela Bassi · Chiara Corbo ·

    Poverty Eradication: Access to Land, Access to Food, Edited by Simona Beretta, Sara Balestri, 09/2015: pages 103-113; EduCatt.
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    ABSTRACT: Coagulase-negative staphylococci (CoNS) belong to saprophytic microbiota on the skin and mucous membranes of warm-blooded animals and humans, but are also isolated from foodstuffs such as meat, cheese, and milk. In other circumstances, some CoNS can act as pathogens. Thus the presence of CoNS may not be an immediate danger to public health, but can become a risk factor. In particular antibiotic-resistant genes could be transferred to other potentially pathogenic microorganisms. Furthermore, CoNS are known to be strong biofilm producers and this is also a risk factor for public health.The aim of the present work was to determine the genotypic and phenotypic profiles of 106 CoNS belonging to four different species isolated from five different Italian cheeses for the presence of some adhesion and virulence features. In order to verify a possible correlation between the formation of biofilm and staphylococcal virulence factors, we checked the presence of adhesin genes by PCR and we investigated the ability of these strains to make biofilm at different temperatures. Furthermore, in some conditions, we analyzed surface proteins and autolytic pattern of selected strains. In conclusion, we checked the presence of norA and mecA genes responsible for fluoroquinolones and methicillin resistance, respectively. We found resistant genes in a proportion of the food isolates in amounts of 9.4% (mecA) and 5.7% (norA). These data support the importance to continuously examine the microbiota not only for the creation of a database but also to safeguard public health. © The Author(s) 2015.
    International journal of immunopathology and pharmacology 08/2015; 28(3). DOI:10.1177/0394632015593236 · 1.62 Impact Factor
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    Daniela Bassi · Edoardo Puglisi · Pier Sandro Cocconcelli ·
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    ABSTRACT: In the last decades, the inoculum of high counts of suitable microorganisms, defined as starter cultures, has become a widely adopted approach in the production of fermented foods. Here, we reviewed the recent works about the use of selected cultures or the exploitation of indigenous microbiota in the production of dry fermented sausages and dairy products. We found that the scientific literature is well consistent in indicating a significant advantage in the use of selected and natural starter cultures (SSC and NSC) as compared to adventitious microbiota (AM) in terms of acidification, sensory traits and acceptability of final ripened products, as well as in the control of undesired microorganisms. Anyway, a thorough understanding of the interactions at ecological level between the introduced strains and the autochthonous microbial communities is a challenge that needs to be addressed in the near future.
    03/2015; 2. DOI:10.1016/j.cofs.2015.03.002
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    Cecilia Fontana · Pier S. Cocconcelli · Graciela Vignolo · Lucila Saavedra ·
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    ABSTRACT: The ability to inhibit the growth of Listeria cells and the presence of bacteriocin encoding genes was examined in 115 LAB strains isolated from Argentinean vacuum-packaged beef and different traditional fermented sausages. Lactobacillus (L) sakei, Lactobacillus (L) curvatus and Enterococcus (E) faecium showed a great inhibition of all Listeria strains evaluated while Pediococcus (P) acidilactici and Lactobacillus (L) plantarum demonstrated a limited or absent antilisterial activity. Both L. curvatus and L. sakei carried the sppA, sppQ and sapA structural genes, encoding for sakacin P, sakacin Q and curvacin A bacteriocins, respectively. Whilst L. curvatus exhibited a higher occurrence of these genes, L. sakei strains were more effective at inhibiting Listeria (L) strains, Listeria monocytogenes UC8159 and Listeria innocua 7 being the most sensitive to these bacteriocins. Among analyzed E. faecium strains, the wide distribution of entA, entB and entP genes accounted for the high antilisterial activity particularly observed against L. monocytogenes FBUNT. The structural gene plantEF was mostly present in Lactobacillus plantarum strains and no pedA gene was found in P. acidilactici evaluated strains. The antilisterial potential of L. sakei and E. faecium offers great possibilities for the meat industry as biopreservative cultures, although more studies are needed in order to conclude about this issue.
    Food Control 01/2015; 47:53–59. DOI:10.1016/j.foodcont.2014.06.021 · 2.81 Impact Factor
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    ABSTRACT: The diversity of lactic acid bacteria (LAB) associated with chicha, a traditional maize-based fermented alcoholic beverage from Northwestern Argentina, was analyzed using culture-dependent and culture-independent approaches. Samples corresponding to 10 production steps were obtained from two local producers at Maimará (chicha M) and Tumbaya (chicha T). Whereas by culture-dependent approach a few number of species (Lactobacillus plantarum and Weissella viridescens in chicha M, and Enterococcus faecium and Leuconostoc mesenteroides in chicha T) were identified, a higher quantitative distribution of taxa was found in both beverages by pyrosequencing. The relative abundance of OTUs was higher in chicha M than in chicha T; six LAB genera were common for chicha M and T: Enterococcus, Lactococcus, Streptococcus, Weissella, Leuconostoc and Lactobacillus while Pediococcus only was detected in chicha M. Among the 46 identified LAB species, those of Lactobacillus were dominant in both chicha samples, exhibiting the highest diversity, whereas Enterococcus and Leuconostoc were recorded as the second dominant genera in chicha T and M, respectively. Identification at species level showed the predominance of Lb. plantarum, Lactobacillus rossiae, Leuconostoc lactis and W. viridescens in chicha M while Enterococcus hirae, E. faecium, Lc. mesenteroides and Weissella confusa predominated in chicha T samples. In parallel, when presumptive LAB isolates (chicha M: 146; chicha T: 246) recovered from the same samples were identified by ISR-PCR and RAPD-PCR profiles, species-specific PCR and 16S rRNA gene sequencing, most of them were assigned to the Leuconostoc genus (Lc. mesenteroides and Lc. lactis) in chicha M, Lactobacillus, Weissella and Enterococcus being also present. In contrast, chicha T exhibited the presence of Enterococcus and Leuconostoc, E. faecium being the most representative species. Massive sequencing approach was applied for the first time to study the diversity and evolution of microbial communities during chicha manufacture. Although differences in the LAB species profile between the two geographically different chicha productions were observed by culturing, a larger number for predominant LAB species as well as other minorities were revealed by pyrosequencing. The fine molecular inventory achieved by pyrosequencing provided more precise information on LAB population composition than culture-dependent analysis processes. Copyright © 2014 Elsevier B.V. All rights reserved.
    International Journal of Food Microbiology 12/2014; 198C:9-18. DOI:10.1016/j.ijfoodmicro.2014.12.027 · 3.08 Impact Factor
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    Fabrizio Cappa · Nicoleta Suciu · Marco Trevisan · Susanna Ferrari · Edoardo Puglisi · Pier Sandro Cocconcelli ·
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    ABSTRACT: Glaciers are important ecosystems, hosting bacterial communities that are adapted to cold conditions and scarcity of available nutrients. Several works focused on the composition of bacterial communities in glaciers and on the long-range atmospheric deposition of pollutants in glaciers, but it is not clear yet if ski resorts can represent a source of point pollution in near-by glaciers, and if these pollutants can influence the residing bacterial communities. To test these hypotheses, 12 samples were analyzed in Madaccio Glacier, in a 3200 m a.s.l. from two areas, one undisturbed and one close to a summer ski resort that is active since the 1930s. Chemical analyses found concentrations up to 43 ng L− 1 for PCBs and up to 168 μg L− 1 for PAHs in the contaminated area: these values are significantly higher than the ones found in undisturbed glaciers because of long-range atmospheric deposition events, and can be explained as being related to the near-by ski resort activities. Isolation of strains on rich medium plates and PCR-DGGE analyses followed by sequencing of bands allowed the identification of a bacterial community with phylogenetic patterns close to other glacier environments, with Proteobacteria and Actinobacteria the mostly abundant phyla, with Acidobacteria, Firmicutes and Cyanobacteria also represented in the culture-independent analyses. A number of isolates were identified by molecular and biochemical methods as phylogenetic related to known xenobiotic-degrading strains: glaciers subjected to chemical contamination can be important reservoirs of bacterial strains with potential applications in bioremediation.
    Science of The Total Environment 11/2014; s 497–498:50–59. DOI:10.1016/j.scitotenv.2014.07.094 · 4.10 Impact Factor
  • Simona Gazzola · Sotirios Vasileiadis · Pier Sandro Cocconcelli ·
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    ABSTRACT: Staphylococcus epidermidis is a major nosocomial pathogen involved in medical device infections but it is also a common inhabitant of healthy human skin and it can be frequently found in fermented foods of animal origin. We performed genomic studies such as MLST, core-genome and pan-genome analyses on Staphylococcus epidermidis UC 7032, a strain isolated from cured pork meat. This strain may be a risk for consumers in that it is resistant up to 32 mg l -1 of vancomycin and produces enterotoxins. It is classified in the agr group II and harbors genes coding for protein with adhesive function, involved in the first phase of biofilm formation (atlE), in catheter-associated infections (fbe) and the Bap homologue biofilm-associated protein (bhp). The 38,48 % of total chromosome length represents the putative chromosomal parts identified as horizontally transferred and three different prophage. This food strain showed also the presence of a plasmid, the insertion element IS1272 and other putative virulence factors, such as arginine catabolic mobile element ACME, the phenol-soluble modulin (PMSs) with a multiple function in biofilm development and in evasion of immune system. Moreover it contains sepA and sspA genes involved in degradation of fibrinogen and probably responsible of tissue damage; dtlABCD (D-alanylation of theicoic acids), mprF (phosphatidylglycerol lysyltransferase); graR and graS involved in Aps system. These genomic information support the phenotypic observations, thus S. epidermidis UC7032 shows characteristics of clinical strains. Inconsistent with this, MLST analysis classified UC7032 close to the ST407, a sequence type of S. epidermidis strains isolated from healthy subject, and phylogenomic studies, based on the analysis of the core genome, grouped UC7032 among the commensal isolates (group B). In conclusion the genomic analysis proved relevant information on the safety of bacteria within the natural communities of fermented meats.
    Fermented Meat, Valencia; 10/2014
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    Ester Pietta · Maria Camila Montealegre · Jung Hyeob Roh · Pier Sandro Cocconcelli · Barbara E Murray ·
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    ABSTRACT: During a study to investigate the evolution of ampicillin resistance in Enterococcus faecium, we observed that a number of E. faecium strains, mainly from the recently described subclade A2, showed PBP5 sequences in between PBP5-S and PBP5-R. These hybrid PBP5-S/R patterns reveal a progression of amino acid changes from the S form to the R form of this protein; however, these changes do not strictly correlate with changes in ampicillin MICs. © 2014, American Society for Microbiology. All Rights Reserved.
    Antimicrobial Agents and Chemotherapy 09/2014; 58(11). DOI:10.1128/AAC.03648-14 · 4.48 Impact Factor
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    ABSTRACT: Peatlands are archives of extreme importance for the assessment of past ecological, environmental and climatic changes. The importance as natural archives is even greater in the case of ombrotrophic peat bogs, where the only inputs are atmospheric in origin. Here we integrated previously published physical and chemical results regarding the solid and liquid phase of peat with a biomolecular microbiological approach to assess the relationships between chemistry and microbial biodiversity along a Swiss bog profile corresponding to approximately 2,000 years of peat formation. The structure of bacterial and archaeal communities was assessed through a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach followed by sequencing of PCR-DGGE bands of interest. Both chemical and microbiological data showed a differentiation of properties along the peat profile, with three major zones identified. Both bacterial and archaeal profiles clustered according to the depth (i.e., age) of samples. Among bacteria, Acidobacteria were recovered primarily in the first layers of the profile, whereas methanogenic archaea were more commonly recovered in the deepest part of the core, corresponding to the occurring anoxic conditions. Finally, a number of sequences had low homologies with known species, especially in bacteria: this points to an almost unknown microbial community adapted to the extreme conditions of peat bogs, which are acidic, rich in dissolved organic C, and predominantly anoxic.
    Biology and Fertility of Soils 07/2014; 50(5):815-826. DOI:10.1007/s00374-014-0902-2 · 3.40 Impact Factor
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    ABSTRACT: Matsoni, a traditional Georgian fermented milk, has variable quality and stability besides a short shelf-life (72-120 h at 6 °C) due to inadequate production and storage conditions. To individuate its typical traits as well as select and exploit autochthonous starter cultures to standardize its overall quality without altering its typicality, we carried out a thorough physico-chemical, sensorial and microbial characterization of traditional Matsoni. A polyphasic approach, including a culture-independent (PCR-DGGE) and two PCR culture-dependent methods, was employed to study the ecology of Matsoni. Overall, the microbial ecosystem of Matsoni resulted largely dominated by Streptococcus (S.) thermophilus and Lactobacillus (Lb.) delbrueckii subsp. bulgaricus. High loads of other lactic acid bacteria species, including Lb. helveticus, Lb. paracasei and Leuconostoc (Leuc.) lactis were found to occur as well. A selected autochthonous multiple strain culture (AMSC) composed of one Lb. bulgaricus, one Lb. paracasei and one S. thermophilus strain, applied for the pilot-scale production of traditional Matsoni, resulted the best in terms of enhanced shelf-life (one month), sensorial and nutritional quality without altering its overall typical quality. This AMSC is at disposal of SMEs who need to exploit and standardize the overall quality of this traditional fermented milk, preserving its typicality.
    Food Microbiology 04/2014; 38:179-91. DOI:10.1016/j.fm.2013.09.004 · 3.33 Impact Factor
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    ABSTRACT: Red stripe is a bacterial disease of sugarcane causing important economic losses in Argentina that affects 30 % of the milling stems and consequently the juice quality. In this study, sugarcane leaves exhibiting red stripe symptoms were sampled in the 2008–09 growing season from 13 different sugarcane producing areas of Tucumán and Salta (northwest of Argentina). To achieve the identification and characterization of the causal agent of red stripe, bacterial isolation was performed. Species-specific PCR using Oaf1/Oar1 primers allowed the amplification of a fragment of 550 bp from approximately 50 % of the isolates; 16S rDNA sequences analysis displayed a similarity greater than 99 % with Acidovorax avenae subsp. avenae. By means of RAPD-PCR the presence of at least four different biotypes among the analyzed isolates was detected. Results of pathogenicity test allowed us to confirm A. avenae subsp. avenae as the pathogenic agent for red stripe. This study constitutes the first report on the identification and molecular characterization of this plant pathogen from the Argentina sugarcane production areas. The genetic diversity observed among A. avenae is an important factor to be considered to improve an accurate diagnosis and/or the selection of sugarcane tolerant clones.
    European Journal of Plant Pathology 11/2013; 137(3). DOI:10.1007/s10658-013-0263-y · 1.49 Impact Factor
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    ABSTRACT: Staphylococcus epidermidis strain UC7032 was isolated from ready-to-eat cured meat and is heteroresistant to glycopeptide antibiotics. The draft whole-genome analysis revealed that this strain shows common characteristics typical of strains that are involved in nosocomial infections.
    Genome Announcements 08/2013; 1(5). DOI:10.1128/genomeA.00709-13
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    ABSTRACT: Clostridium tyrobutyricum is considered the main agent of late-blowing defect in the production of hard cheese. Here, we described the draft genome sequences and annotation of C. tyrobutyricum strain UC7086, which was isolated from Grana Padano cheese with blowing defect, and C. tyrobutyricum DSM 2637 type strain in a comparative study.
    Genome Announcements 06/2013; 1(4). DOI:10.1128/genomeA.00614-13

Publication Stats

2k Citations
164.94 Total Impact Points


  • 2011-2015
    • Università Cattolica del Sacro Cuore
      Milano, Lombardy, Italy
  • 1984-2015
    • Catholic University of the Sacred Heart
      • Institute of Microbiology
      Milano, Lombardy, Italy
  • 2008
    • Instituto Universitario de Tecnología de Valencia
      Valencia, Carabobo, Venezuela
  • 2006
    • Catholic University of Louvain
      • Institute of Life Sciences
      Louvain-la-Neuve, WAL, Belgium
  • 2005
    • University of Groningen
      • Department of Molecular Genetics
      Groningen, Province of Groningen, Netherlands
  • 2001
    • University of Bologna
      • Department of Agricultural Sciences DipSA
      Bolonia, Emilia-Romagna, Italy