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1.  Influenza like Illness among Medical Residents Anticipates Influenza Diffusion in General Population: Data from a National Survey among Italian Medical Residents 
PLoS ONE  2016;11(12):e0168546.
The aim of this multicentre study was to assess incidence of influenza like illness (ILI) among Italian medical residents (MRs) during 2011–2012 influenza season, to detect variables associated with ILI and to compare estimated ILI incidence among MRs and general population. A cross-sectional survey was carried out throughout an anonymous questionnaire administered to all MRs attending the post-graduate medical schools of 18 Italian Universities. At the same time an analysis of the ILI incidence in the Italian general population was conducted through the Italian Influenza Surveillance Network. Of a total of 2,506 MRs, 1,191 (47.5%) reported at least one ILI episode. A higher proportion of ILIs was reported by MRs of Central (25.0% with ILI vs 20.2% without ILI) and Southern Italy (40.2% with ILI vs. 36.4 without ILI) compared to Northern Italy (34.8% with ILI vs. 43.4% without ILI) (p<0.001). Italian MRs had a higher cumulative incidence of ILIs (546.7 episodes per 1,000 vs. 75.9 episodes per 1,000) and an earlier peak (January 2012 vs. February 2012), compared to general population due to higher number of contacts in hospital setting. MRs reported a high rate of ILI infection probably in association with their working activities. These data suggest the need to offer an earlier influenza vaccination to HCWs than general population with the aim to both prevent ILI and its transmission to patients.
doi:10.1371/journal.pone.0168546
PMCID: PMC5173364  PMID: 27997602
2.  Evidence for Human Adaptation and Foodborne Transmission of Livestock-Associated Methicillin-Resistant Staphylococcus aureus 
We investigated the evolution and epidemiology of a novel livestock-associated methicillin-resistant Staphylococcus aureus strain, which colonizes and infects urban-dwelling Danes even without a Danish animal reservoir. Genetic evidence suggests both poultry and human adaptation, with poultry meat implicated as a probable source.
doi:10.1093/cid/ciw532
PMCID: PMC5091345  PMID: 27655995
MRSA; host adaptation; foodborne transmission; poultry; livestock
3.  Use of Cepheid Xpert Carba-R® for Rapid Detection of Carbapenemase-Producing Bacteria in Abdominal Septic Patients Admitted to Intensive Care Unit 
PLoS ONE  2016;11(8):e0160643.
Early institution of effective antibiotic therapy and source control are pivotal to improve survival of abdominal septic patients. Xpert® Carba-R is a real time polymerase chain reaction assay for rapid detection and differentiation of five genes (blaKPC, blaVIM, blaOXA-48, blaIMP-1, blaNDM) responsible for carbapenem resistance. We performed an observational study investigating the clinical usefulness and applicability of Xpert® Carba-R to detect carbapenem resistance in abdominal septic patients admitted to intensive care unit. We compared the results of Xpert® Carba-R with standard microbiological culture. We collected a set of two rectal/stomia swabs and two swabs from abdominal drainage fluid for each patient. We included 20 patients for a total of 45 comparisons between the two methods. In our clinical setting, the overall performance of Xpert® Carba-R for detection of carbapenem resistance in the presence of genes detectable and non-detectable by the method was: sensitivity 50% (95% CI 24.6–75.3); specificity 93.1% (95% CI 77.2–99.1); positive predictive value (PPV) 80% (95% CI 44.4–97.5); negative predictive value (NPV) 77.1% (95% CI 56.9–89.6). The inter-rater agreement was 0.47 (SE 0.14; 95% CI 0.20–0.74). When considering the only 5 mechanisms of resistance detected by both methods, the overall diagnostic performance was: sensitivity 100% (95% CI 69.1–100), specificity 94.2 (95% CI 80.8–99.3), PPV 83.3 (95% CI 59.6–97.9) and NPV 100% (95% CI 89.4–100). The inter-rater agreement was 0.88 (SE 0.08; 95% CI 0.71–1). Xpert® Carba-R may be considered an additional diagnostic tool for early diagnosis of carbapenem resistance in abdominal septic patients. Clinicians should be aware of their epidemiology before its introduction in the diagnostic protocol of their intensive care units.
doi:10.1371/journal.pone.0160643
PMCID: PMC4973873  PMID: 27490684
4.  Double Copies of blaKPC-3::Tn4401a on an IncX3 Plasmid in Klebsiella pneumoniae Successful Clone ST512 from Italy 
A carbapenem-resistant sequence type 512 (ST512) Klebsiella pneumoniae carbapenemase 3 (KPC-3)-producing K. pneumoniae strain showing a novel variant plasmid content was isolated in Palermo, Italy, in 2014. ST512 is a worldwide successful clone associated with the spread of blaKPC genes located on the IncFIIk pKpQIL plasmid. In our ST512 strain, the blaKPC-3 gene was unusually located on an IncX3 plasmid, whose complete sequence was determined. Two copies of blaKPC-3::Tn4401a caused by intramolecular transposition events were detected in the plasmid.
doi:10.1128/AAC.01886-15
PMCID: PMC4704230  PMID: 26525794
5.  A Snapshot on MRSA Epidemiology in a Neonatal Intensive Care Unit Network, Palermo, Italy 
Objectives: We performed a 1-year prospective surveillance study on MRSA colonization within the five NICUs of the metropolitan area of Palermo, Italy. The purpose of the study was to assess epidemiology of MRSA in NICU from a network perspective.
Methods: Transfer of patients between NICUs during 2014 was traced based on the annual hospital discharge records. In the period February 2014–January 2015, in the NICU B, at the University teaching hospital, nasal swabs from all infants were collected weekly, whereas in the other four NICUs (A, C, D, E) at 4 week-intervals of time. MRSA isolates were submitted to antibiotic susceptibility testing, SCCmec typing, PCR to detect lukS-PV and lukF-PV (lukS/F-PV) genes and the gene encoding the toxic shock syndrome toxin (TSST-1), multilocus variable number tandem repeat fingerprinting (MLVF), and multilocus sequence typing (MLST).
Results: In the period under study, 587 nasal swabs were obtained from NICU B, whereas 218, 180, 157, and 95 from NICUs A, C, D, and E, respectively. Two groups of NICUs at high prevalence and low prevalence of MRSA colonization were recognized. Overall, 113 isolates of MRSA were identified from 102 infants. Six MLVF types (A–F) were detected, with type C being subdivided into five subtypes. Five sequence types (STs) were found with ST22-IVa being the most frequent type in all NICUs. All the MRSA molecular subtypes, except for ST1-IVa, were identified in NICU B.
Conclusions: Our findings support the need to approach surveillance and infection control in NICU in a network perspective, prioritizing referral healthcare facilities.
doi:10.3389/fmicb.2016.00815
PMCID: PMC4882316  PMID: 27303395
MRSA; active surveillance; network approach; molecular typing; NICu
6.  Complete Genome Sequence of KPC-3- and CTX-M-15-Producing Klebsiella pneumoniae Sequence Type 307 
Genome Announcements  2016;4(2):e00213-16.
Klebsiella pneumoniae sequence type (ST) 307, carrying blaKPC-3, blaCTX-M-15, blaOXA-1, aac(6′)-Ib-cr, and qnrB1 genes, is replacing the predominant hyperepidemic ST258 clone in Italy. Whole-genome and complete plasmid sequencing of one ST307 strain was performed and new features were identified.
doi:10.1128/genomeA.00213-16
PMCID: PMC4824255  PMID: 27056222
7.  Design, Implementation, and Evaluation of the Adolescents and Surveillance System for the Obesity Prevention Project 
Medicine  2016;95(12):e3143.
Abstract
The Adolescents Surveillance System for Obesity prevention (ASSO) Project aimed at developing standardized and web-based tools for collecting data on adolescents’ obesity and its potential determinants. This has been implemented and piloted in the local area of Palermo city, Italy. The aim of the present study is to provide an overview of the Project's design, implementation, and evaluation, highlighting all the aspects for a potential scale-up of the surveillance system on the whole national territory and abroad, as a sustainable and effective source of data.
The overall structure and management, the ASSO-toolkit, the ASSO-NutFit software, and all developed and used procedures for recruiting, training, and data collecting/analyzing are addressed. An interim evaluation has been performed through a feasibility study; a final Project evaluation has been performed reporting the Strengths, Weaknesses, Opportunities, and Threats (SWOT) and the attributes that a surveillance system should have.
This article provides a detailed overview of the Project and highlights that ASSO can be considered a valid, logical, coherent, efficient, and sustainable surveillance system that is consistent with countries’ needs and priorities.
The system developed by the ASSO Project provides high-quality data and complies with several characteristics typical of a suitable surveillance system. It has a potential of being adopted within the National Health Service and other countries’ Health Services for monitoring adolescents’ obesity and its determinants, such as food intakes, behaviors, physical activity, and fitness profiles.
doi:10.1097/MD.0000000000003143
PMCID: PMC4998390  PMID: 27015195
8.  The Increasing Challenge of Multidrug-Resistant Gram-Negative Bacilli 
Medicine  2016;95(10):e3016.
Abstract
Colonization and infection by multidrug-resistant gram-negative bacilli (MDR GNB) in neonatal intensive care units (NICUs) are increasingly reported.
We conducted a 5-year prospective cohort surveillance study in a tertiary NICU of the hospital “Paolo Giaccone,” Palermo, Italy. Our objectives were to describe incidence and trends of MDR GNB colonization and the characteristics of the most prevalent organisms and to identify the risk factors for colonization. Demographic, clinical, and microbiological data were prospectively collected. Active surveillance cultures (ASCs) were obtained weekly. Clusters of colonization by extended spectrum β-lactamase (ESBL) producing Escherichia coli and Klebsiella pneumoniae were analyzed by conventional and molecular epidemiological tools.
During the study period, 1152 infants were enrolled in the study. Prevalences of colonization by MDR GNB, ESBL-producing GNB and multiple species/genera averaged, respectively, 28.8%, 11.7%, and 3.7%. Prevalence and incidence density of colonization by MDR GNB and ESBL-producing GNB showed an upward trend through the surveillance period. Rates of ESBL-producing E coli and K pneumoniae colonization showed wide fluctuations peaking over the last 2 years. The only independent variables associated with colonization by MDR GNB and ESBL-producing organisms and multiple colonization were, respectively, the days of NICU stay (odds ratio [OR] 1.041), the days of exposure to ampicillin–sulbactam (OR 1.040), and the days of formula feeding (OR 1.031). Most clusters of E coli and K pneumoniae colonization were associated with different lineages. Ten out of 12 clusters had an outborn infant as their index case.
Our study confirms that MDR GNB are an increasing challenge to NICUs. The universal once-a-week approach allowed us to understand the epidemiology of MDR GNB, to timely detect new clones and institute contact precautions, and to assess risk factors. Collection of these data can be an important tool to optimize antimicrobials use and control the emergence and dissemination of resistances in NICU.
doi:10.1097/MD.0000000000003016
PMCID: PMC4998898  PMID: 26962817
9.  Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing 
The Open Microbiology Journal  2016;10:176-182.
Background:
Francisella tularensis (F. tularensis) is the etiological microorganism for tularemia. There are different forms of tularemia such as respiratory tularemia. Respiratory tularemia is the most severe form of tularemia with a high rate of mortality; if not treated. Therefore, traditional microbiological tools and Polymerase Chain Reaction (PCR) are not useful for a rapid, reliable, accurate, sensitive and specific diagnosis. But, DNA microarray technology does. DNA microarray technology needs to appropriate microarray probe designing.
Objective:
The main goal of this original article was to design suitable long oligo microarray probes for detection and identification of F. tularensis.
Method:
For performing this research, the complete genomes of F. tularensis subsp. tularensis FSC198, F. tularensis subsp. holarctica LVS, F. tularensis subsp. mediasiatica, F. tularensis subsp. novicida (F. novicida U112), and F. philomiragia subsp. philomiragia ATCC 25017 were studied via NCBI BLAST tool, GView and PanSeq Servers and finally the microarray probes were produced and processed via AlleleID 7.7 software and Oligoanalyzer tool, respectively.
Results:
In this in silico investigation, a number of long oligo microarray probes were designed for detecting and identifying F. tularensis. Among these probes, 15 probes were recognized as the best candidates for microarray chip designing.
Conclusion:
Calibrated microarray probes reduce the biasis of DNA microarray technology as an advanced, rapid, accurate and cost-effective molecular diagnostic tool with high specificity and sensitivity. Professional microarray probe designing provides us with much more facility and flexibility regarding preparation of a microarray diagnostic chip.
doi:10.2174/1874285801610010176
PMCID: PMC5204066  PMID: 28077973
Bioinformatics; DNA microarray; Dry lab; Francisella tularensis; Probe designing; Tularemia
10.  Bloodstream infections in intensive care unit patients: distribution and antibiotic resistance of bacteria 
Bloodstream infections (BSIs) are among the leading infections in critically ill patients. The case-fatality rate associated with BSIs in patients admitted to intensive care units (ICUs) reaches 35%–50%. The emergence and diffusion of bacteria with resistance to antibiotics is a global health problem. Multidrug-resistant bacteria were detected in 50.7% of patients with BSIs in a recently published international observational study, with methicillin resistance detected in 48% of Staphylococcus aureus strains, carbapenem resistance detected in 69% of Acinetobacter spp., in 38% of Klebsiella pneumoniae, and in 37% of Pseudomonas spp. Prior hospitalization and antibiotic exposure have been identified as risk factors for infections caused by resistant bacteria in different studies. Patients with BSIs caused by resistant strains showed an increased risk of mortality, which may be explained by a higher incidence of inappropriate empirical therapy in different studies. The molecular genetic characterization of resistant bacteria allows the understanding of the most common mechanisms underlying their resistance and the adoption of surveillance measures. Knowledge of epidemiology, risk factors, mechanisms of resistance, and outcomes of BSIs caused by resistant bacteria may have a major influence on global management of ICU patients. The aim of this review is to provide the clinician an update on BSIs caused by resistant bacteria in ICU patients.
doi:10.2147/IDR.S48810
PMCID: PMC4536838  PMID: 26300651
bloodstream infections; multidrug resistant; antibiotic; intensive care unit; MDR; ICU
11.  An Update of the Evolving Epidemic of blaKPC Carrying Klebsiella pneumoniae in Sicily, Italy, 2014: Emergence of Multiple Non-ST258 Clones 
PLoS ONE  2015;10(7):e0132936.
Background
In Italy, Klebsiella pneumoniae carbapenemase producing K. pneumoniae (KPC-Kp) strains are highly endemic and KPC producing CC258 is reported as the widely predominating clone. In Palermo, Italy, previous reports have confirmed this pattern. However, recent preliminary findings suggest that an epidemiological change is likely ongoing towards a polyclonal KPC-Kp spread. Here we present the results of molecular typing of 94 carbapenem non susceptible K. pneumoniae isolates detected during 2014 in the three different hospitals in Palermo, Italy.
Methods and Results
Ninety-four consecutive, non replicate carbapenem non susceptible isolates were identified in the three largest acute general hospitals in Palermo, Italy, in the six-month period March-August 2014. They were characterized by PCR for β-lactam, aminoglycoside and plasmid mediated fluoroquinolone resistance genetic determinants. The mgrB gene of the colistin resistant isolates was amplified and sequenced. Clonality was assessed by pulsed field gel electrophoresis and multilocus sequence typing. Eight non-CC258 sequence types (STs) were identified accounting for 60% of isolates. In particular, ST307 and ST273 accounted for 29% and 18% of isolates. CC258 isolates were more frequently susceptible to gentamicin and non-CC258 isolates to amikacin. Colistin non susceptibility was found in 42% of isolates. Modifications of mgrB were found in 32 isolates.
Conclusions
Concurrent clonal expansion of some STs and lateral transmission of genetic resistance determinants are likely producing a thorough change of the KPC-Kp epidemiology in Palermo, Italy. In our setting mgrB inactivation proved to substantially contribute to colistin resistance. Our findings suggest the need to continuously monitor the KPC-Kp epidemiology and to assess by a nationwide survey the possible shifting towards a polyclonal epidemic.
doi:10.1371/journal.pone.0132936
PMCID: PMC4503429  PMID: 26177547
12.  Phenotypic and Molecular Epidemiology of Acinetobacter calcoaceticus baumannii Complex Strains Spread at Nemazee Hospital of Shiraz, Iran 
Background
Acinetobacter calcoaceticus baumannii (ACB) complex are Gram-negative opportunistic bacteria with low virulence properties. Their resistance to antibiotics has become a matter of concern in hospital infections.
Objectives
The present study aimed to determine the prevalence and antimicrobial susceptibility of ACB isolates collected from the Nemazee hospital of Shiraz. In addition, Pulsed Field Gel Electrophoresis (PFGE) was used to determine the genetic patterns of these strains.
Patients and Methods
In this cross-sectional study, 93 strains of ACB complex were isolated from patients of Nemazee hospital, Shiraz, Iran. The antibiotic susceptibility patterns of the isolates to the following 15 antibiotics were determined: gentamicin, ticarcillin, ceftazidime, co-trimoxazole, imipenem, piperacillin tazobactam, amikacin, aztreonam, sulbactam, meropenem, tobramycin, cefotaxime, ceftriaxone, colistin, polymyxin B. Pulsed Field Gel Electrophoresis was used to determine the clonal relationship of these strains.
Results
Most of the isolates were found to be resistant to cefotaxime, co-trimoxazole, ceftriaxone, aztreonam, ceftazidime and ticarcillin (90%), and the least resistance was observed to colistin and polymyxin B. Among the 93 tested samples, 35 antimicrobial susceptibility patterns and 47 PFGE patterns were obtained.
Conclusions
High resistance to antibiotics was observed among the strains of ACB complex and the least resistance was towards colistin and polymyxin B, indicating that these antibiotics could be effective for treatment, in case there is no other choice. Using PFGE, the similarity between some strains of Acinetobacter was determined, which indicated epidemics in different parts of the hospital; such epidemics can in turn lead to increased incidence of Acinetobacter infections.
doi:10.5812/jjm.8(5)2015.19180
PMCID: PMC4548468  PMID: 26322204
Acinetobacter baumannii; Drug Resistance; Electrophoresis, Gel, Pulsed-Field
14.  Comparative validity of the ASSO–Food Frequency Questionnaire for the web-based assessment of food and nutrients intake in adolescents 
Food & Nutrition Research  2015;59:10.3402/fnr.v59.26216.
Background
A new web-based food frequency questionnaire (the ASSO–FFQ) was developed within the ASSO Project funded by the Italian Ministry of Health.
Objective
The aim of the present study is to assess the validity of the ASSO–FFQ at food groups, energy, and nutrients level.
Design and subjects
The validation study compared the ASSO–FFQ against a weighted food record (WFR) measuring foods, beverages and supplements intake, compiled during the week following the ASSO–FFQ administration. Ninety-two subjects aged 14–17, recruited from secondary schools in Palermo (Italy), completed the ASSO–FFQ and WFR. The intake of 24 food groups, energy, and 52 nutrients were taken as main outcomes. Tests for paired observations, Spearman and Pearson’s correlation coefficients (cc), kappa statistics and classification in quintiles, Bland–Altman plots and multiple regressions, on untransformed and transformed data were used for the statistical analysis.
Results
High cc (≥0.40) were found for soft drinks, milk, tea/coffee, vegetables, and lactose; fair energy-adjusted cc (0.25–0.40) for water, alcoholic drinks, breakfast cereals, fishery products, savory food, fruit juice, eggs, and 19 nutrients. The subjects classified in the same or adjacent quintile for food groups ranged from 40% (alcoholic drinks) to 100% (dried fruit); for energy and nutrients from 43% (phosphorus, thiamin, niacin) to 77% (lactose). Mean differences were not significant for water, soft drinks, meat, sweets, animal fats, milk and white bread, and vitamin B12 and folate. Limits of Agreement were broad for all food groups and nutrients. School, gender, alcohol consumption and between meals mainly affected most food groups’ intake differences. Gender stratification showed females had increased Pearson’s cc for energy and 28 nutrients, such as almost all fats, carbohydrates, vitamins and minerals.
Conclusions
The ASSO–FFQ could be applied in epidemiological studies for the assessment of dietary consumption in adolescents to adequately rank food, energy and nutrient intakes at a group level.
doi:10.3402/fnr.v59.26216
PMCID: PMC4400301  PMID: 25882537
food frequency questionnaire; intake; nutrient; adolescent; validation; validity
15.  Assessment of the microbiological quality of fresh produce on sale in Sicily, Italy: preliminary results 
Background
Fresh produce occupies an increasingly important place in the human food supply because of its health-promoting nutritional properties. Most fresh produce is eaten raw or after minimal processing and, consequently, pathogen contamination can represent a serious health risk. There has been an increase in foodborne outbreaks and cases associated with fresh produce, but literature data about the prevalence of pathogen contamination are inconsistent. This study was undertaken to assess the hygienic quality and the prevalence of the most common bacterial pathogens in fresh produce sold in retail markets in Sicily. A total of 125 samples of different types of vegetables were examined by standardized microbiological methods.
Results
The aerobic mesophilic count ranged between 2 log and 7 log cfu g−1 and the Enterobacteriaceae counts between < 1 log and 6 log cfu g−1, with statistically significant differences between unprocessed and minimally processed products (p < 0.05). Escherichia coli was detected only in leaf vegetables at a concentration of 2 log - 3 log cfu g−1. Enterococci were found at a concentration of 2 log - 4 log cfu g−1. Coagulase positive Staphylococci and sulphite-reducing Clostridia were not detected in any sample. Three samples tested positive for Listeria monocytogenes, Yersinia enterocolitica and Salmonella veneziana.
Conclusion
Our study provides updated data on the microbiological quality of retail vegetables and confirms the need to implement strategies to increase microbial safety of fresh produce.
doi:10.1186/s40709-015-0026-3
PMCID: PMC4389663  PMID: 25984508
Fresh produce; Vegetables; Food safety; Hygiene quality; Foodborne pathogens
16.  The web-based ASSO-food frequency questionnaire for adolescents: relative and absolute reproducibility assessment 
Nutrition Journal  2014;13:119.
Background
A new food frequency questionnaire (FFQ) has been recently developed within the Italian Adolescents and Surveillance System for the Obesity prevention (ASSO) Project; it was found to be appropriate for ranking adolescents in food and nutrient levels of intake. The aim of this study was to assess the relative and absolute reproducibility of the ASSO-FFQ for 24 food groups, energy and 52 nutrients.
Methods
A test-retest study was performed on two ASSO-FFQs administered one month apart of each other to 185 adolescents, aged 14–17 and attending secondary schools in Palermo (Italy). Wilcoxon test assessed differences in median daily intakes between the two FFQs. Agreement was evaluated by quintiles comparison and weighted kappa. Intraclass Correlation Coefficients (ICC) and Bland-Altman method assessed the relative and absolute reliability respectively.
Results
Significant difference (p < 0.05) in median intakes was found only for bread substitutes, savoury food, water, soft drinks, carbohydrates and sugar. The subjects classified into the same or adjacent quintiles for food groups ranged from 62% (white bread) to 91% (soft drinks); for energy and nutrients from 64% (polyunsaturated fatty acids) to 90% (ethanol). Mean values of weighted kappa were 0.47 and 0.48, respectively for food groups and nutrients. Fair to good ICC values (>0.40) were assessed for thirteen food groups, energy and forty-three nutrients. Limits of Agreement were narrow for almost all food groups and all nutrients.
Conclusions
The ASSO-FFQ is a reliable instrument for estimating food groups, energy and nutrients intake in adolescents.
Electronic supplementary material
The online version of this article (doi:10.1186/1475-2891-13-119) contains supplementary material, which is available to authorized users.
doi:10.1186/1475-2891-13-119
PMCID: PMC4320587  PMID: 25518876
Food frequency questionnaire; Reproducibility; Adolescent; Nutrient; Intake
17.  Molecular epidemiology of tuberculosis in Sicily, Italy: what has changed after a decade? 
BMC Infectious Diseases  2014;14:602.
Background
We aimed to investigate the molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) isolates in the province of Palermo, Sicily, Italy, by characterizing 183 isolates identified in the years 2004–2012. A comparison with 104 MTBC strains identified in the same geographic area in the years 1994–2000 was also carried out.
Methods
One hundred eighty-three MTBC isolates identified in Palermo, Italy, in the years 2004–2012 were analyzed by spoligotyping and the 24 mycobacterial interspersed repetitive unit (MIRU)-variable-number tandem-repeat (VNTR) method typing. Susceptibility testing to streptomycin, isoniazid, rifampin and ethambutol was also performed. Furthermore, the spoligotyping dataset obtained from 104 MTBC isolates identified from 1994 to 2000 was reanalyzed. Distribution into lineages and clustering of isolates in the two periods was compared.
Results
One hundred seventy-seven out of the 183 isolates of MTBC submitted to molecular typing were fully characterized. Of these, 108 were from Italian-born and 69 from foreign-born individuals. Eleven different lineages and 35 families-subfamilies were identified with the most represented lineages being Haarlem (26.5%), T (19.2%), LAM (13.6%) and S (8.5%). Except for the Haarlem lineage, where isolates from foreign-born patients were overrepresented, the distribution of isolates in the families belonging to the Euro-American clone reflected the proportions of the two subpopulations. A total of 27 (15.2%) strains were clustered and three clusters were mixed. Approximately 25% of the 183 MTBC isolates under study proved to be resistant to at least one antiTB drug, with only three isolates categorized as multidrug resistant (MDR). When MTBC isolates identified in the years 1994–2000 were reanalyzed, lineages T (30.8%), LAM (29.8%), Haarlem (16.3%) and S (13.5%) proved to be predominant. No MTBC isolates belonging to CAM, U, CAS, Turkish and Ural lineages were identified.
Conclusions
A wide heterogeneity was detected among the MTBC strains isolated in the years 2004–2012. Six lineages were not present among the isolates of the period 1994–2000. Comparison between distribution of lineages in the two consecutive periods depicts rapid and deep changes in the TB epidemiology in Palermo, Italy. An universal and continued laboratory-based surveillance of TB in Sicily is required.
doi:10.1186/s12879-014-0602-4
PMCID: PMC4241219  PMID: 25407589
Tuberculosis; Sicily; Epidemiology; Spoligotyping; MIRU-VNTR
19.  Protein supplements consumption: a comparative study between the city centre and the suburbs of Palermo, Italy 
Background
Protein supplements are extensively used among commercial gym users and athletes. Although demographic information amongst such consumption has been poorly investigated. The aim of this study is to compare protein supplement consumption in commercial gym users, both from the city centre and the suburbs of Palermo, Italy.
Methods
A face-to-face questionnaire has been administered to 561 subjects. 207 from the city centre (CC) and 354 from the suburbs (SB) of Palermo, Italy. Protein supplement consumption, frequency of use and association with other dietary supplements has been investigated. Subsequently frequency distribution has been used for demographic assessment.
Results
30% of commercial gym users from the CC and 28.8% from the SB use protein supplements. The majority of these subjects are men (69.5% from the CC and 93.1 from the SB). Frequency of use differs from the two areas showing a mode of 7 days per week consumption for the CC while a mode of 5 days per week consumption is showed for the SB. Interestingly, the association between protein supplements and other dietary supplements also differs between CC and SB. A combined use between proteins, amino acids and creatine is showed in the CC whilst proteins and amino acids or creatine are used alone in the SB.
Conclusions
A considerable number of commercial gym users take protein supplements alone or combined (mainly creatine and amino-acids). Demographic differences are shown between frequency of use and combined use of other dietary supplements. We emphasize on the importance of the dissemination of scientifically based information about supplementation in this environment.
doi:10.1186/2052-1847-6-29
PMCID: PMC4118305  PMID: 25089201
Protein consumption; Dietary supplements; Demographic assessment
20.  Protein supplementation and dietary behaviours of resistance trained men and women attending commercial gyms: a comparative study between the city centre and the suburbs of Palermo, Italy 
Background
It is anecdotally recognized that commercial gym users assume supplements in order to improve performance or health. However, dietary behaviours of people and athletes attending commercial gyms have been poorly studied. The exact amount and frequency of dietary supplements consumption are still needed to be investigated. The main purpose of this study is to understand the quantity and quality of food intake, as well as dietary supplementation in people attending commercial gyms. Secondly to compare the city centre and the suburbs of Palermo, Italy.
Methods
A face-to-face questionnaire was administered to 561 subjects, 207 from the city centre (CC) and 354 from the suburbs (SB) of Palermo, Italy. Frequency of protein supplements use and association with dietary behaviours were investigated. Subsequently, the frequency distribution was used for demographic assessment.
Results
Frequency of protein consumption was similar in both groups (30% for CC and 28.8% for SB). Males show greater consumption percentages than females (30.5% in males and 6.9% in females). Milk and chicken are the most frequently consumed foods. Data show that non-supplement users (NSU) consume significantly more snacks and bakery products than supplement users (SU) (P < 0.001). While, SU consume significantly higher quantities of vegetables, nuts, fresh fish, eggs and canned tuna (P < 0.001). SU consume less low protein food and higher protein foods than NSU. No differences were found between CC and SB.
Conclusions
Protein consumption among commercial gym users is 30% for the CC and 28.8% for the SB. Significant differences were found between CC and SB females, underlining an interesting discrepancy, indicating to dietary supplement industries regarding regional implications. Subjects that use protein supplements also consume larger quantities of high protein food compared to NSU. NSU also eat higher proportions of unhealthy food compared to SU.
doi:10.1186/1550-2783-11-30
PMCID: PMC4073191  PMID: 24976800
Dietary behaviour; Protein project; Protein supplements; Questionnaire; Gym
21.  Methicillin-Resistant Staphylococcus aureus Colonization: A Three-Year Prospective Study in a Neonatal Intensive Care Unit in Italy 
PLoS ONE  2014;9(2):e87760.
Background
Methicillin resistant Staphylococcus aureus (MRSA) is a major etiological agent of infection in neonatal intensive care units (NICUs). Routes of entry of this organism can be different and the transmission pathway complex. Colonized neonates are the main endogenous reservoir.
Methods and Results
We conducted a prospective three-year study on MRSA colonization recruiting 722 neonates admitted between 2009 and 2012. Nasal swabs were cultured weekly and MRSA isolates were submitted to molecular typing. The annual incidence density of acquisition of MRSA ranged from a maximum of 20.2 cases for 1000 patient-days during the first year to a minimum of 8.8 cases in the second one to raise again up to 13.1 cases during the third year. The mean weekly colonization pressure fluctuated from 19.1% in the first year to 13.4% in the second year and 16.8% in the third year. It significantly correlated with the number of MRSA acquisitions in the following week. Overall, 187 (25.9%) subjects tested positive for MRSA. A non multiresistant, tst positive, ST22-MRSA-IVa spa t223 strain proved to be endemic in the NICU, being identified in 166 (88.8%) out of 187 colonized neonates. Sporadic or epidemic occurrence of other strains was detected.
Conclusions
An MRSA strain belonging to the tst1 positive, UK-EMRSA-15/ “Middle Eastern Variant” appeared to be endemic in the NICU under investigation. During the three-year period, substantial changes occurred in case-mix of patients moving towards a higher susceptibility to MRSA colonization. The infection control procedures were able to decrease the colonization rate from more than 40% to approximately 10%, except for an outbreak due to a CA-MRSA strain, ST1-MRSA-IVa, and a transient increase in the colonization prevalence rate coincident with a period of substantial overcrowding of the ward. Active surveillance and molecular typing contributed to obtain a reliable picture of the MRSA dissemination in NICU.
doi:10.1371/journal.pone.0087760
PMCID: PMC3914835  PMID: 24505312
22.  Rapid Differentiation between Livestock-Associated and Livestock-Independent Staphylococcus aureus CC398 Clades 
PLoS ONE  2013;8(11):e79645.
Staphylococcus aureus clonal complex 398 (CC398) isolates cluster into two distinct phylogenetic clades based on single-nucleotide polymorphisms (SNPs) revealing a basal human clade and a more derived livestock clade. The scn and tet(M) genes are strongly associated with the human and the livestock clade, respectively, due to loss and acquisition of mobile genetic elements. We present canonical single-nucleotide polymorphism (canSNP) assays that differentiate the two major host-associated S. aureus CC398 clades and a duplex PCR assay for detection of scn and tet(M). The canSNP assays correctly placed 88 S. aureus CC398 isolates from a reference collection into the human and livestock clades and the duplex PCR assay correctly identified scn and tet(M). The assays were successfully applied to a geographically diverse collection of 272 human S. aureus CC398 isolates. The simple assays described here generate signals comparable to a whole-genome phylogeny for major clade assignment and are easily integrated into S. aureus CC398 surveillance programs and epidemiological studies.
doi:10.1371/journal.pone.0079645
PMCID: PMC3828327  PMID: 24244535
23.  KPC - 3 Klebsiella pneumoniae ST258 clone infection in postoperative abdominal surgery patients in an intensive care setting: analysis of a case series of 30 patients 
BMC Anesthesiology  2013;13:13.
Background
Abdominal surgery carries significant morbidity and mortality, which is in turn associated with an enormous use of healthcare resources. We describe the clinical course of 30 Intensive Care Unit (ICU) patients who underwent abdominal surgery and showed severe infections caused by Klebsiella pneumoniae sequence type (ST) 258 producing K. pneumoniae carbapenemase (KPC-Kp). The aim was to evaluate risk factors for mortality and the impact of a combination therapy of colistin plus recommended regimen or higher dosage of tigecycline.
Methods
A prospective assessment of severe monomicrobial KPC-Kp infections occurring after open abdominal surgery carried out from August 2011 to August 2012 in the same hospital by different surgical teams is presented. Clinical and surgical characteristics, microbiological and surveillance data, factors associated with mortality and treatment regimens were analyzed. A combination regimen of colistin with tigecycline was used. A high dose of tigecycline was administered according to intra-abdominal abscess severity and MICs for tigecycline.
Results
The mean age of the patients was 56.6 ± 15 and their APACHE score on admission averaged 22.72. Twenty out of 30 patients came from the surgical emergency unit. Fifteen patients showed intra-abdominal abscess, eight anastomotic leakage, four surgical site infection (SSI) and three peritonitis. The overall crude ICU mortality rate was 40% (12 out of 30 patients). Twelve of the 30 patients were started on a combination treatment of high-dose tigecycline and intravenous colistin. A significantly lower mortality rate was observed among those patients compared to patients treated with approved dose of tigecycline plus colistin. No adverse events were reported with high doses of tigecycline.
Conclusions
Critically-ill surgical patients are prone to severe post-surgical infectious complications caused by KPC-Kp. Timely microbiological diagnosis and optimizing antibiotic dosing regimens are essential to prevent worse outcomes. Further studies and well-controlled clinical trials are needed to define the optimal treatment of infections by KPC-Kp and, more generally, carbapenem-resistant bacteria.
doi:10.1186/1471-2253-13-13
PMCID: PMC3737059  PMID: 23822218
Klebsiella pneumoniae; Carbapenemase; Abdominal surgery
24.  The occurrence of extended-spectrum β-lactamase producing Shigella spp. in Tehran, Iran 
Iranian Journal of Microbiology  2013;5(2):108-112.
Background and Objectives
The emergence of extended-spectrum β-lactamase (ESBL)-producing Shigella spp. is of increasing clinical concern specially in children worldwide. The aim of this study was to investigate the occurrence of extended-spectrum β-lactamase producing Shigella spp. in Tehran, Iran
Materials and Methods
The study included all Shigella isolates recovered from pediatric patients aged less than 12 years admitted to a major pediatric hospital in Tehran, Iran, from 2008 to 2010. Bacterial identification, antimicrobial susceptibility testing, extended spectrum β-lactamases (ESBLs) screening and confirmatory tests were performed according to the standard guidelines. Conjugal transfer experiments and plasmid analysis were also carried out. Polymerase chain reaction and sequencing were used to identify the genetic determinants responsible for ESBL production.
Results
Four out of 55 Shigella isolates, including three S. sonnei and one S. flexneri, showed an ESBL-positive phenotype. Plasmid transfer of the ESBL phenotype was successful for the S. flexneri isolate only. By PCR and sequencing, one S. sonnei isolate tested positive for the CMY-59 gene, while the other two S. sonnei and the S. flexneri isolates tested positive for the bla TEM-1 and bla CTX-M-15 genes.
Conclusion
We found the prevalence of ESBL producing Shigella isolates was higher than detection rates observed in many other countries. Our finding raise concerns about the dissemination of ESBL among the strains of endemic S. sonnei throughout the country, because this species is now the most frequently isolated Shigella species in Iran and shigellosis by such strains in the community can pose a significant threat to patients and presents a challenge for disease management.
PMCID: PMC3696844  PMID: 23825726
ESBLs; Shigella spp; Antibiotic resistance

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