Matrix-assisted laser desorption ionization-time of flight mass spectrometry has emerged as a rapid, cost-effective alternative for bacterial species identification. Identifying 60 blind-coded nonfermenting bacteria samples, this international study (using eight laboratories) achieved 98.75% interlaboratory reproducibility. Only 6 of the 480 samples were misidentified due to interchanges (4 samples) or contamination (1 sample) or not identified because of insufficient signal intensity (1 sample).Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a fast and costeffective alternative for bacterial species identification in microbiology. On the basis of mass analysis of the protein composition of a bacterial cell, which is assumed to be characteristic for each bacterial species, it is possible to determine the species within few minutes, starting from whole cells, cell lysates, or crude bacterial extracts (2, 3, 5, 6). The proof of principle of MALDI-TOF MS for bacterial species identification was shown a decade ago (2, 5, 6); however, due to low reproducibility, it has not been widely adopted in clinical microbiology. We have recently shown that use of a larger mass range for detection (2,000 to 20,000 Da), dedicated analysis software for spectral pattern matching, and a highquality reference database of spectra generated from qualitycontrolled culture collection strains resulted in accurate species identifications, with high intralaboratory reproducibility (7). For interlaboratory reproducibility, there are only very limited data available (8, 10). We therefore evaluated the interlaboratory reproducibility for MALDI-TOF MS-based species identification in a multicenter study, applying the above-described MALDI-TOF MS improvements.(

BackgroundInfluenza is a major public health issue worldwide. It is characterized by episodes of infection that involve hundreds of millions of people each year. Since that in the seasons 2010–2011 and 2011–2012 the circulation of FLUB was decreasing we evaluated the clinical presentation, demographic characteristics, admitting department, and length of stay in children who contracted influenza admitted to Bambino Gesù Children’s Hospital, during the 2012–2013 influenza season, with the aim to establish if the recover of FLUB was associated to a clinical worsening, in comparison with those due to FLUA.MethodsA total of 133 respiratory specimens, collected from patients with symptoms of respiratory tract infections, positive for the Influenza A and B viruses (FLUA and B) were subtyped. Comparisons between the FLUA and FLUB groups were performed with the one-way ANOVA for continuous parametric variables, the Mann-Whitney test for non-parametric variables, or the Chi-Square test or Fisher’s exact test (if cells <5) for categorical variables.Results87.09 % of the FLUA isolates were the H1N1 subtype and 12.90 % were H3N2. Among the FLUB isolates, 91.54 % were the B/Yamagata/16/88 lineage and 8.45 % were the B/Victoria/02/87 lineage. The largest number of FLUA/H1N1 cases was observed in children less than 1 years old, while the B/Yamagata/16/88 lineage was most prevalent in children 3–6 years old. Fever was a common symptom for both FLUA and B affected patients. However, respiratory symptoms were more prevalent in patients affected by FLUA. The median length of stay in the hospital was 5 days for FLUA and 3 days for FLUB.ConclusionsThe clinical features correlated to different Influenza viruses, and relevant subtypes, were evaluated concluding that the increasing of FLUB in the season 2012–2013 was without any dramatic change in clinical manifestation. Our findings suggest, finally, that a stronger commitment to managing patients affected by FLUA is required, as the disease is more severe than FLUB.

Proteomics is particularly suitable for characterising human pathogens with high life cycle complexity, such as fungi. Protein content and expression levels may be affected by growth states and life cycle morphs and correlate to species and strain variation. Identification and typing of fungi by conventional methods are often difficult, time-consuming and frequently, for unusual species, inconclusive. Proteomic phenotypes from MALDI-TOF MS were employed as analytical and typing expression profiling of yeast, yeast-like species and strain variants in order to achieve a microbial proteomics population study. Spectra from 303 clinical isolates were generated and processed by standard pattern matching with a MALDI-TOF Biotyper (MT). Identifications (IDs) were compared to a reference biochemical-based system (Vitek-2) and, when discordant, MT IDs were verified with genotyping IDs, obtained by sequencing the 25-28S rRNA hypervariable D2 region. Spectra were converted into virtual gel-like formats, and hierarchical clustering analysis was performed for 274 Candida profiles to investigate species and strain typing correlation. MT provided 257/303 IDs consistent with Vitek-2 ones. However, amongst 26/303 discordant MT IDs, only 5 appeared "true". No MT identification was achieved for 20/303 isolates for incompleteness of database species variants. Candida spectra clustering agreed with identified species and topology of Candida albicans and Candida parapsilosis specific dendrograms. MT IDs show a high analytical performance and profiling heterogeneity which seems to complement or even outclass existing typing tools. This variability reflects the high biological complexity of yeasts and may be properly exploited to provide epidemiological tracing and infection dispersion patterns.

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The human gut has been continuously exposed to a broad spectrum of intestinal organisms, including viruses, bacteria, fungi, and parasites (protozoa and worms), over millions of years of coevolution, and plays a central role in human health. The modern lifestyles of Western countries, such as the adoption of highly hygienic habits, the extensive use of antimicrobial drugs, and increasing globalisation, have dramatically altered the composition of the gut milieu, especially in terms of its eukaryotic “citizens.” In the past few decades, numerous studies have highlighted the composition and role of human intestinal bacteria in physiological and pathological conditions, while few investigations exist on gut parasites and particularly on their coexistence and interaction with the intestinal microbiota. Studies of the gut “parasitome” through “omic” technologies, such as (meta)genomics, transcriptomics, proteomics, and metabolomics, are herein reviewed to better understand their role in the relationships between intestinal parasites, host, and resident prokaryotes, whether pathogens or commensals. Systems biology–based profiles of the gut “parasitome” under physiological and severe disease conditions can indeed contribute to the control of infectious diseases and offer a new perspective of omics-assisted tropical medicine.

We evaluated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) Biotyper as a tool for the identification of anaerobic bacteria compared with 500 base-pair (bp) 16S ribosomal ribonucleic acid (rRNA) gene sequencing analysis, which is considered to be the "gold standard" method. A total of 484 anaerobic bacteria were retrieved from the clinical specimens of 318 pediatric patients. Molecular identification resulted in 18 genera and 51 species. The most prevalent genus was Clostridium (76.85 %), with 70 % C. difficile isolates. The concordance and sensitivity determined by MALDI-TOF MS for C. difficile, the most prevalent species isolated, was 94.08 %, whereas the specificity was 100 %. For the other anaerobes, the sensitivity and specificity were 94.07 % and 81.82 %, respectively, with a concordance of 93.15 %. Low performance was observed for Propionibacterium acnes and Fusobacterium nucleatum, for which a dedicated pretreatment procedure should likely be set up. MALDI-TOF MS was shown to be a valid alternative for the fast and reliable identification of the most clinically relevant anaerobic bacteria; moreover, it is less time-consuming, the cost for reagents is minimized, and it does not require dedicated personnel.