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Children are prone to bloodstream infections (BSIs), the rapid and accurate diagnosis of which is an unmet clinical need. The T2MR technology is a direct molecular assay for identification of BSI pathogens, which can help to overcome the limits of blood culture (BC) such as diagnostic accuracy, blood volumes required, and turnaround time. We analyzed results obtained with the T2Bacteria (648) and T2Candida (106) panels in pediatric patients of the Bambino Gesù Children’s Hospital between May 2018 and September 2020 in order to evaluate the performance of the T2Dx instrument with respect to BC. T2Bacteria and T2Candida panels showed 84.2% and 100% sensitivity with 85.9% and 94.1% specificity, respectively. The sensitivity and specificity of the T2Bacteria panel increased to 94.9% and 98.7%, respectively, when BC was negative but other laboratory data supported the molecular result. T2Bacteria sensitivity was 100% with blood volumes

Protozoa and helminths are responsible for several intestinal parasite infections (IPIs). Generally helminth infections are very unsafe but scarcely reported in high-income countries, while protozoa and helminth co-infections are usually reported in children living in inadequate hygienic-sanitary conditions and in rural areas. However, the impact of growing globalization, intense travelling, international adoptions and high levels of immigrants and refugees has significantly incremented the incidence of oro-faecal parasitosis in non endemic areas. Although most IPs clear without treatment when population, even children, emigrate from endemic to different geographical areas, some IPIs such as strongyloidiasis may persist for decades as subclinical infections or as low-grade disease with nonspecific clinical manifestations, unless to reappear under impairment conditions. Herein we report an unusual case of Giardia lamblia and Trichuris spp. chronic asymptomatic co-infection in a healthy adopted Romanian child, living in a Central Italy rural area, and an hidden case of Strongyloides stercoralis in an adopted Burundian child, resident in South Italy, long misdiagnosed as a recurrent undefined dermatitis. Our report suggests the need to review primary care practitioner guidelines and children's hospital procedures for appropriate IPIs screening and follow-up, hence providing new screening and prevention strategies, in agreement with international guidelines.

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.

Background Influenza 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. Methods A 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

Background: We describe methicillin-resistant Staphylococcus aureus (MRSA) nasal carriage at admission in patients admitted to a Department of Pediatrics. Methods: All patients received a nasal swab at admission. A questionnaire was administered and molecular genetics analyses were performed on all identified MRSA isolates. Results: We enrolled 785 patients, affected with both acute and chronic diseases. MRSA nasal colonization prevalence was 1.15% (CI: 0.5607%-2.093%). Methicillin-sensitive Staphylococcus aureus (MSSA) nasal colonization prevalence at admission was 19.75% (CI 17.07%-22.64%). Only one MRSA isolate carried the SCCmec V variant; all other isolates carried the SCCmecIV variant. Five out of 9 MRSA-colonized patients had an underlying condition. Antibiotic therapy in the previous 6 months was a protective factor for both MRSA (OR 0,66; 95% CI: 0,46-0,96) and MSSA (OR 0,65; 95% CI: 0,45-0,97) colonization. A tendency to statistical significance was seen in the association between hospitalization in the 6 months prior to admission and MRSA colonization at admission (OR 4,92; 95% CI: 0,97-24,83). No patient was diagnosed with an S. aureus infection during hospitalization. Conclusions: The majority of our MRSA colonizing isolates have community origins. Nevertheless, most MRSA-colonized patients had been hospitalized previously, suggesting that strains that circulate in the community also circulate in hospital settings. Further studies should elucidate the role of children with frequent contact with health care institutions in the circulation of antibiotic resistant strains between the hospital and the community.

We evaluated a multiplex PCR assay, the Seeplex Diarrhoea ACE detection, that simultaneously detects 15 enteric pathogens, including Salmonella spp., Shigella spp., Vibrio spp., toxin B producer Clostridium difficile, Campylobacter spp., Clostridium perfringens, Yersinia enterocolitica, Aeromonas spp., Escherichia coli O157:H7, verocytotoxin-producing Escherichia coli, adenovirus, Group A rotavirus, norovirus GI and GII, and astrovirus. We compared this assay with clinical methods routinely used in our laboratory, for detecting enteropathogens in stool samples collected from 245 paediatric patients with suspected infectious gastroenteritis. We recovered 61 bacterial pathogens and 121 enteric viruses with our laboratory assays, while we detected 78 bacteria and 167 viruses with the molecular assay. We calculated specificity and sensitivity for both methods after analysis of discordant results and demonstrated greater sensitivity for multiplex PCR than for our routine methods, with the exception of Salmonella spp. and toxigenic C. difficile detection. The multiplex PCR assay proved to be a reliable tool to directly detect the most common enteropathogens in stool samples but with some limitations.

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).

Major changes in medical, intensive care and organ transplantation practices are drastically increasing the risk of fungal opportunistic infections. We designed and set-up a MALDI-TOF MS-based assay to identify the most isolated and emerging therapy-refractory/uncommon fungi from cystic fibrosis (CF) and immunocompromised patients. Two-hundred and thirty isolates from 10 different genera (Aspergillus, Emericella, Fusarium, Geosmithia, Neosartorya, Penicillium, Pseudallescheria, Scedosporium, Talaromyces, Fomitopsis), investigated during routine diagnostic efforts, were correlated to 22 laboratory-adapted reference MALDI-TOF MS "proteomic phenotypes". A growth time-course at 30°C on Sabouraud agar medium was performed for the 22 "phenotypes" at 48, 72, 96 and 120h points. The best peptide extraction conditions for full recovery of conidia- or asci-producing multihyphal morph structures and the highest intra- and inter-class profiling correlation were identified for the 120h point spectra dataset, from which an engineered library derived (pre-analytical phase). Fingerprinting classifiers, selected by Wilcoxon/Kruskal-Wallis algorithm, were computed by Genetic Algorithm, Support Vector Machine, Supervised Neuronal Network and Quick Classifier model construction. MS identification (ID) of clinical isolates was referred to genotyping (GT) and, retrospectively, compared to routine morphotyping (MT) IDs (analytical phase). Proteomic phenotyping is revolutionizing diagnostic mycology as fully reflecting species/morph varieties but often overcoming taxonomic hindrance.

To evaluate the presence of Toxoplasma gondii in edible farmed shellfish, 1734 shellfish specimens i.e., 109 Crassostrea gigas (6 pools), 660 Mytilus galloprovincialis (22 pools), 804 Tapes decussatus (28 pools) and 161 Tapes philippinarum (6 pools), were collected from the Varano Lagoon (Apulia, Italy). Shellfish from 62 pools were subjected to two molecular techniques: a nested-PCR assay, and a fluorescent amplicon generation (FLAG) real-time PCR assay, both based on the multi-copy B1 target, were performed. One pooled sample of gills from C. gigas and one pooled sample of haemolymphs from T. decussatus were assessed as positive for T. gondii DNA by both techniques. The results demonstrated the presence of T. gondii in edible farmed C. gigas and T. decussatus and indicate that there may be a considerable health threat involved in eating contaminated raw shellfish.

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.

Introduction: Fusobacterium necrophorum is an anaerobic Gram negative bacillus highly virulent, responsible, usually in children or adolescents, of localized abscesses and pharynx, as well as severe systemic infections, called Lemierre syndrome. Methods: A 15 year old child came to the emergency department (ED) of Bambino Gesù Children Hospital. Physicians prescribed chemicalphysical examination on blood and liquor, blood cultures for aerobic and anaerobic bacteria and for fungi (BD Ped Plus, lytic Ana, Micosis), microbiological culture on liquor (CSF) and on the swab from the right outer ear. Results: On chemical examination, liquor appears cloudy, with 309 mg/dl of total proteins, glucose undetectable,WBC 11,160 mmc, 92% of neutrophils. Hyperleukocytosis was detected also on the emocrome (WBC 21x103/μl, 92% neutrophils). No bacterial antigens were detected. CSF culture resulted negative for aerobic bacteria, even after 48 hours of incubation. After 24 hours of inoculation, the blood culture for anaerobic bacteria resulted positive and, Fusobacterium necrophorum was isolated and identified, by genomic sequencing, after 24 hours growth on Schaedler medium. Microbiological culture of the right outer ear swab, highlighted only Corynebacterium spp. After 6 days from admission, the patient died for meningitis. Conclusion:This event has shown the severity of infection by F. necrophorum and, at the same time, the underestimation of this germ in the spectrum of etiologic agents responsible for meningitis.The only microbiological indication was obtained from the anaerobes bacteria blood culture. Following this episode our working procedures for what concerns liquor samples management was modified, including routinely the investigation for anaerobic bacteria. Presumably this episode of meningitis has originated from a F. necrophorum otitis of the right ear, unfortunately not microbiologically confirmed.The anaerobic bacteria should always be considered as potentially responsible of meningitis, especially when ear infections or pharyngeal abscesses precede or accompany the onset of symptoms.

Recent data have shown that a functional NO-cGMP signalling system plays an important role during development and seems to be operative early during the differentiation of embryonic stem cells. The intriguing possibility exists that this role can be evolutionarily conserved between vertebrates and invertebrates. In this paper, we have analyzed the effect of NO-cGMP pathway on the regeneration process in Hydra vulgaris, the most primitive invertebrate possessing a nervous system. Our results indicate that NO production increased during Hydra regeneration. The NOS inhibitor L-NAME reduced the regenerative process and the same effect was obtained by treatment with either the specific guanylate cyclase inhibitor ODQ or the protein kinase G (PKG) inhibitor KT-5823. In contrast, the regeneration process was increased by treating decapitated Hydra with the NO donor NOC-18. Furthermore, we found that cell proliferation was also increased by treating decapitated Hydra with the NO donor NOC-18 and reduced by treatment with the NOS inhibitor L-NAME. Our results strongly suggest that the NO-cGMP-PKG pathway is involved in the control of the proliferative-differentiative patterns of developing and regenerating structures in cnidarians as well as bilaterians.

Background: Bacterial biofilms identified in various medical devices used in otorhinolaryngology, including tympanostomy tubes, voice prostheses, and cochlear implants, can directly colonise mucosal tissues. The upper airways seem to be at high risk for this type of colonisation. Chronic and/or recurrent upper airway infections may be related to the complex structural and biochemical (quorum sensing) organisation of the biofilm which interferes with the activity of antibiotics (including those with proven in vitro efficacy), thus promoting the establishment of a chronic infection eradicable only by surgical treatment. Biofilm formation plays a role in upper respiratory infections: it not only explains the resistance of these infections to antibiotic therapy but it also represents an important element that contributes to the maintenance of a chronic inflammatory reaction.Objectives: To document the presence of biofilms in surgical tissue specimens from patients with recurrent infection diseases, and identify their possible role in the chronicity of these infectious processes.Method: We examined 32 surgical specimens from the upper respiratory tract (tonsils, adenoids, mucosa from the ethmoid and maxillary sinuses) of 28 patients (20 adults, eight children) with upper airway infections that had persisted despite repeated treatment with anti-inflammatory agents and antibiotics with demonstrated in vitro efficacy. Tissues were cultured using conventional methods and subjected to scanning electron microscopy for detection of biofilm formation.Results: Over 80 per cent (26/32; 81.3 per cent) of the tissue specimens were culture-positive. Bacterial biofilms (associated in most cases with coccoid bacteria) were observed in 65.6 per cent of the tissue samples.