[Show abstract][Hide abstract] ABSTRACT: Phylogenetic knowledge of the genus Mycobacterium is based on comparative analysis of their genetic sequences. The 16S rRNA has remained for many years the only target of such analyses, but in the last few years, other housekeeping genes have been investigated and the phylogeny based on their concatenated sequences become a standard. It is now clear that the robustness of the phylogenetic analysis is strictly related to the size of the genomic target used. Whole genome sequencing (WGS) is nowadays becoming widely accessible and comparatively cheap. It was decided, therefore, to use this approach to reconstruct the ultimate phylogeny of the genus Mycobacterium. Over 50 types of strains of the same number of species of Mycobacterium were sequenced using the Illumina HiSeq platform. The majority of the strains of which the whole sequence was already available in GenBank were excluded from this panel with the aim of maximizing the number of the species with genome available. Following assembling and annotation with proper software, the phylogenetic analysis was conducted with PhyloPhlAn and the pan-genome analysis pipeline. The phylogenetic three which emerged was characterized by a clear-cut distinction of slowly and rapidly growing species with the latter being more ancestral. The species of the Mycobacterium terrae complex occupied an intermediate position between rapid and slow growers. Most of the species revealed clearly related and occupied specific phylogenetic branches. Thanks to the WGS technology, the genus Mycobacterium is finally approaching its definitive location.
International Journal of Mycobacteriology. 11/2014; 4.
[Show abstract][Hide abstract] ABSTRACT: Carbapenem-resistant Acinetobacter baumannii (CRAb) are emerging worldwide as a public health problem in various settings. The aim of this study was to investigate the prevalence of CRAb isolates in Italy and to characterize their resistance mechanisms and genetic relatedness. A countrywide cross-sectional survey was carried out in 25 centers in mid-2011. CRAb isolates were reported from all participating centers, with an overall proportion of 45.7% and 22.2% among consecutive nonreplicate clinical isolates of A. baumannii from inpatients (n=508) and outpatients (n=63), respectively. Most of them were resistant to multiple antibiotics whereas all remained susceptible to colistin, with both MIC50 and MIC90 values ≤ 0.5 mg/L. Genes coding for carbapenemase production were identified by PCR and sequencing. OXA-23 enzymes (found in all centers) were by far the most common carbapenemases (81.7%), followed by OXA-58 oxacillinases (4.5%), that were found in 7 of 25 centers. In 6 cases, CRAb isolates carried both blaOXA-23-like and blaOXA-58-like genes. Rep-PCR technique, multiplex PCRs for group identification, and MLST were used to determine genetic relationships among representative isolates (n=55). Two different clonal lineages were identified, including a dominant clone of ST2 related to the international clone II (sequence groups SG1, SG4, and SG5) and a clone of ST78 (SG6) previously described in Italy. Overall, our results demonstrate that OXA-23 enzymes became the most prevalent carbapenemases and are now endemic in Italy. In addition, molecular typing profiles showed the presence of international and national clonal lineages in Italy.
Journal of clinical microbiology 06/2014; 52(8):3004-3010. · 4.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We investigated two consecutive Serratia marcescens (S. marcescens) outbreaks which occurred in a neonatal intensive care unit (NICU) of a tertiary level hospital in North Italy in a period of 10 years (January 2003-December 2012). Risk factors associated with S. marcescens acquisition were evaluated by a retrospective case-control study. A total of 21,011 clinical samples was examined: S. marcescens occurred in 127 neonates: 43 developed infection and 3 died. Seven clusters were recorded due to 12 unrelated clones which persisted for years in the ward, although no environmental source was found. The main epidemic clone A sustaining the first cluster in 2003 reappeared in 2010 as an extendedspectrum ?-lactamase (ESBL)-producing strain and supporting the second epidemic. Birth weight, gestational age, use of invasive devices and length of stay in the ward were significantly related to S. marcescens acquisition. The opening of a new ward for non-intensive care-requiring neonates, strict adherence to alcoholic hand disinfection, the timely identification and isolation of infected and colonized neonates assisted in containing the epidemics. Genotyping was effective in tracing the evolution and dynamics of the clones demonstrating their long-term persistence in the ward.
Serratia marcescens, Outbreak, Neonatal intensive care unit, Molecular epidemiology.
The New Microbiologica: official journal of the Italian Society for Medical Virology (SIVIM) 10/2013; 36(4):373-83. · 1.60 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: To identify the source of postnatal colonization with group B Streptococcus (GBS) and to evaluate the impact of intrapartum antibiotic prophylaxis (IAP) administration in newborn infant transmission.
A prospective, longitudinal study evaluated GBS colonization in 160 mother-baby pairs. Specimens were collected from the time of delivery to 8 weeks post-partum, from rectum, vagina, and milk of mothers, and from throat and rectum of neonates. Women were grouped according to their GBS status at discharge from the hospital: culture-positive carriers (n = 83), culture-negative carriers (n = 26), and noncarriers (n = 51). Newborns were considered colonized if GBS was yielded from at least 1 site.
A total of 35 (21.9%) neonates were colonized; 30 were born to culture-positive carriers, 2 to culture-negative carriers, and 3 to noncarriers. Infants of culture-positive carriers exposed to IAP were less likely to be colonized (15/57 vs 15/26, P = .01), or heavily colonized, (7/57 vs 9/26, P = .04). Of all newborns, those exposed to IAP and discharged GBS-free from hospital, often became colonized subsequently (12/57 vs 1/26, P = .09). Molecular typing analysis (available for 30 of 32 carrier mothers and their infants) confirmed an identical strain of GBS in all mother-baby pairs. Six of 83 culture-positive carrier mothers had a positive milk culture. Their respective neonates all were heavily colonized.
Newborns exposed to IAP and GBS-free at hospital discharge subsequently acquire GBS from their mothers. Culture-positive milk is associated with heavy neonatal colonization.
The Journal of pediatrics 07/2013; · 4.02 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: PURPOSE: The aim of this prospective observational study was to evaluate in patients with sepsis not requiring intensive care unit admission the relationship between the levels of endotoxin activity assay (EAA) early after sepsis recognition and the risk of development of organ dysfunction (OD). METHODS: Endotoxin activity assay levels were drawn immediately after sepsis identification (baseline) and at 6, 24, and 48 hours postbaseline in 50 patients with signs of sepsis of a duration of less than 24 hours. An EAA 0.60 units or greater was considered as highly elevated. RESULTS: Logistic regression showed independent association between EAA levels at baseline and the appearance of new OD (adjusted odd ratio, 2.41; 95% confidence interval, 1.18-4.90; P < .05). Fifteen patients (30%) who developed new OD after baseline had at least 1 EAA level 0.60 or greater. The adjusted linear regression analysis showed that across the 4 time points, EAA levels were significantly higher in patients who developed new OD (0.11; 95% confidence interval, 0.01-0.20; P < .05). CONCLUSIONS: Endotoxin activity assay levels 0.60 or greater early after sepsis diagnosis in patients not requiring intensive care unit admission predict risk of development of new organ dysfunction. High EAA levels in the first 48 hours of recognition of sepsis are also predictive of risk of deterioration.
Journal of critical care 04/2013; · 2.13 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: TO THE EDITOR: Legionella pneumophila serogroups (SGs) 1-16 cause pneumonia in humans. Although SG 1 is the serogroup most commonly associated with disease (1), we report a case of community-acquired legionellosis caused by SG 11.
[Show abstract][Hide abstract] ABSTRACT: Fusarium is an opportunistic fungal pathogen which is emerging as a significant cause of morbidity and mortality in immunocompromised hosts. We present a rare case of F. verticillioides fungemia that occurred in a patient who underwent a second orthotopic liver transplantation for chronic rejection and completely responded to treatment with voriconazole.
[Show abstract][Hide abstract] ABSTRACT: Mucorales-specific T cells were investigated in 28 hematologic patients during the course of their treatment. Three developed proven invasive mucormycosis (IM), 17 had infections of known origin but other than IM, and 8 never had fever during the period of observation. Mucorales-specific T cells could be detected only in patients with IM, both at diagnosis and throughout the entire course of the IM, but neither before nor for long after resolution of the infection. Such T cells predominantly produced IL-4, IFN-γ, IL-10, and to a lesser extent IL-17 and belonged to either CD4(+) or CD8(+) subsets. The specific T cells that produced IFN-γ were able to directly induce damage to Mucorales hyphae. None of the 25 patients without IM had Mucorales-specific T cells. Specific T cells contribute to human immune responses against fungi of the order Mucorales and could be evaluated as a surrogate diagnostic marker of IM.
[Show abstract][Hide abstract] ABSTRACT: Bloodstream infections due to Staphylococcus aureus (BSI) are serious infections both in hospitals and in the community, possibly leading to infective endocarditis (IE). The use of glycopeptides has been recently challenged by various forms of low-level resistance. This study evaluated the distribution of MSSA and MRSA isolates from BSI and IE in 4 Italian hospitals, their antibiotic susceptibility--focusing on the emergence of hVISA--and genotypic relationships. Our results demonstrate that the epidemiology of MRSA is changing versus different STs possessing features between community-acquired (CA)- and hospital-acquired (HA)-MRSA groups; furthermore, different MSSA isolated from BSI and IE were found, with the same backgrounds of the Italian CA-MRSA. The hVISA phenotype was very frequent (19.5%) and occurred more frequently in isolates from IE and in both the MSSA and MRSA strains. As expected, hVISA were detected in MRSA with vancomycin minimum inhibitory concentrations (MICs) of 1-2 mg/l, frequently associated with the major SCCmec I and II nosocomial clones; this phenotype was also detected in some MSSA strains. The few cases of MR-hVISA infections evaluated in our study demonstrated that 5 out of 9 patients (55%) receiving a glycopeptide, died. Future studies are required to validate these findings in terms of clinical impact.
European Journal of Clinical Microbiology 08/2011; 31(5):739-45. · 3.02 Impact Factor
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[Show abstract][Hide abstract] ABSTRACT: Four strains isolated in the last 15 years were revealed to be identical in their 16S rRNA gene sequences to MCRO19, the sequence of which was deposited in GenBank in 1995. In a polyphasic analysis including phenotypic and genotypic features, the five strains (including MCRO19), which had been isolated in four European countries, turned out to represent a unique taxonomic entity. They are scotochromogenic slow growers and are genetically related to the group that included Mycobacterium simiae and 15 other species. The novel species Mycobacterium europaeum sp. nov. is proposed to accommodate these five strains. Strain FI-95228(T) ( = DSM 45397(T) = CCUG 58464(T)) was chosen as the type strain. In addition, a thorough revision of the phenotypic and genotypic characters of the species related to M. simiae was conducted which leads us to suggest the denomination of the 'Mycobacterium simiae complex' for this group.
International Journal of Systematic and Evolutionary Microbiology 07/2011; 61(Pt 7):1606-11. · 2.79 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We report on the first detection of the NDM-1 carbapenemase in Italy, in Escherichia coli isolated in October 2009. Prolonged colonization and relapsing infection by NDM-1-positive E. coli were observed in a patient (index case) with an indirect epidemiological link with areas of endemicity. Transient colonization was apparently observed in another patient linked with the index case.
Journal of clinical microbiology 04/2011; 49(7):2755-8. · 4.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Diagnosing pleural tuberculosis (plTB) might be difficult due to limited sensitivity of conventional microbiology tools. As M. tuberculosis (MTB)-specific T cells are recruited into pleural space in plTB, their detection may provide useful clinical information. To this aim, in addition to standard diagnostic tests, we used the QuantiFERON-TB Gold In-Tube (QFT-IT) test in blood and pleural effusion (PE) samples from 48 patients with clinical suspicion of plTB, 18 (37.5%) of whom had confirmed plTB. Four of them (22.2%) tested positive with a nucleic acid amplification test for MTB. The tuberculin skin test was positive in most confirmed plTB cases (88.9%). Positive QFT-IT tests were significantly more frequent in patients with confirmed plTB, as compared to patients with an alternative diagnosis, both in blood (77.7 vs 36.6%, p=0.006) and in PE samples (83.3% vs 46.6%, p=0.02). In addition, both blood and PE MTB-stimulated IFN-gamma levels were significantly higher in plTB patients (p=0.03 and p=0.0049 vs non-plTB, respectively). In blood samples, QFT-IT had 77.8% sensitivity and 63.3% specificity, resulting in 56.0% positive (PPV) and 82.6% negative (NPV) predictive values. On PE, QFT-IT sensitivity was 83.3% and specificity 53.3% (PPV 51.7% and NPV 84.2%). The optimal AUC-derived cut-off for MTB-stimulated pleural IFN-gamma level was 3.01 IU/mL (77.8% sensitivity, 80% specificity, PPV 68.4% and NPV 82.8%). These data suggest that QFT-IT might have a role in ruling out plTB in clinical practice.
International journal of immunopathology and pharmacology 01/2011; 24(1):159-65. · 2.51 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The Legionnaires’ disease is a major issue in the healthcare because it ranks among the emerging infectious diseases in our country,
particularly those caused by Legionella pneumophila serogroup 1. The severity of the infection is related to several factors including the
virulence of the bacterium and the immune status of patient. Since the clinical diagnosis of Legionella infections or pneumonia with different
etiology is extremely difficult, the use of new diagnostic techniques in rapid identification plays a key role. The aim of our study was to
evaluate the performance of a new immunochromatographic assay can detect and identify strains of Legionella spp. from the cultures.