Synthesis of Bioactive Nickel Nanoparticles Using Bacterial Strains from an Antarctic Consortium.

Marine microorganisms have been demonstrated to be an important source for bioactive molecules. In this paper we report the synthesis of Ni nanoparticles (NiSNPs) used as reducing and capping agents for five bacterial strains isolated from an Antarctic marine consortium: Marinomonas sp. ef1, Rhodococcus sp. ef1, Pseudomonas sp. ef1, Brevundimonas sp. ef1, and Bacillus sp. ef1. The NiSNPs were characterized by Ultraviolet-visible (UV-vis) spectroscopy, Dynamic Light Scattering (DLS), Transmission Electron Microscopy (TEM), X-ray diffraction (XRD) and Fourier Transform Infrared (FTIR) spectroscopic analysis. The maximum absorbances in the UV-Vis spectra were in the range of 374 nm to 422 nm, corresponding to the Surface plasmon resonance (SPR) of Nickel. DLS revealed NiSNPs with sizes between 40 and 45 nm. All NiSNPs were polycrystalline with a face-centered cubic lattice, as revealed by XRD analyses. The NiSNPs zeta potential values were highly negative. TEM analysis showed that the NiSNPs were either spherical or rod shaped, well segregated, and with a size between 20 and 50 nm. The FTIR spectra revealed peaks of amino acid and protein binding to the NiSNPs. Finally, all the NiSNPs possess significant antimicrobial activity, which may play an important role in the management of infectious diseases affecting human health.

Machine learning algorithms in sepsis.

Sepsis remains a significant global health challenge due to its high mortality and morbidity, compounded by the difficulty of early detection given its variable clinical manifestations. The integration of machine learning (ML) into laboratory medicine for timely sepsis identification and outcome forecasting is an emerging field of interest. This comprehensive review assesses the current body of research on ML applications for sepsis within the realm of laboratory diagnostics, detailing both their strengths and shortcomings. An extensive literature search was performed by two independent investigators across PubMed and Scopus databases, employing the keywords "Sepsis," "Machine Learning," and "Laboratory" without publication date limitations, culminating in January 2023. Each selected study was meticulously evaluated for various aspects, including its design, intent (diagnostic or prognostic), clinical environment, demographics, sepsis criteria, data gathering period, and the scope and nature of features, in addition to the ML methodologies and their validation procedures. Out of 135 articles reviewed, 39 fulfilled the criteria for inclusion. Among these, the majority (30 studies) were focused on devising ML algorithms for diagnosis, fewer (8 studies) on prognosis, and one study addressed both aspects. The dissemination of these studies across an array of journals reflects the interdisciplinary engagement in the development of ML algorithms for sepsis. This analysis highlights the promising role of ML in the early diagnosis of sepsis while drawing attention to the need for uniformity in validating models and defining features, crucial steps for ensuring the reliability and practicality of ML in clinical setting.

Synthesis of Bioactive Silver Nanoparticles Using New Bacterial Strains from an Antarctic Consortium.

In this study, we report on the synthesis of silver nanoparticles (AgNPs) achieved by using three bacterial strains Rhodococcus, Brevundimonas and Bacillus as reducing and capping agents, newly isolated from a consortium associated with the Antarctic marine ciliate Euplotes focardii. After incubation of these bacteria with a 1 mM solution of AgNO3 at 22 °C, AgNPs were synthesized within 24 h. Unlike Rhodococcus and Bacillus, the reduction of Ag+ from AgNO3 into Ag0 has never been reported for a Brevundimonas strain. The maximum absorbances of these AgNPs in the UV-Vis spectra were in the range of 404 nm and 406 nm. EDAX spectra showed strong signals from the Ag atom and medium signals from C, N and O due to capping protein emissions. TEM analysis showed that the NPs were spherical and rod-shaped, with sizes in the range of 20 to 50 nm, and they were clustered, even though not in contact with one another. Besides aggregation, all the AgNPs showed significant antimicrobial activity. This biosynthesis may play a dual role: detoxification of AgNO3 and pathogen protection against both the bacterium and ciliate. Biosynthetic AgNPs also represent a promising alternative to conventional antibiotics against common nosocomial pathogens.

Biogenic Synthesis of Copper Nanoparticles Using Bacterial Strains Isolated from an Antarctic Consortium Associated to a Psychrophilic Marine Ciliate: Characterization and Potential Application as Antimicrobial Agents.

In the last decade, metal nanoparticles (NPs) have gained significant interest in the field of biotechnology due to their unique physiochemical properties and potential uses in a wide range of applications. Metal NP synthesis using microorganisms has emerged as an eco-friendly, clean, and viable strategy alternative to chemical and physical approaches. Herein, an original and efficient route for the microbial synthesis of copper NPs using bacterial strains newly isolated from an Antarctic consortium is described. UV-visible spectra of the NPs showed a maximum absorbance in the range of 380-385 nm. Transmission electron microscopy analysis showed that these NPs are all monodispersed, spherical in nature, and well segregated without any agglomeration and with an average size of 30 nm. X-ray powder diffraction showed a polycrystalline nature and face centered cubic lattice and revealed characteristic diffraction peaks indicating the formation of CuONPs. Fourier-transform infrared spectra confirmed the presence of capping proteins on the NP surface that act as stabilizers. All CuONPs manifested antimicrobial activity against various types of Gram-negative; Gram-positive bacteria; and fungi pathogen microorganisms including Escherichia coli, Staphylococcus aureus, and Candida albicans. The cost-effective and eco-friendly biosynthesis of these CuONPs make them particularly attractive in several application from nanotechnology to biomedical science.

Machine learning models predicting multidrug resistant urinary tract infections using "DsaaS".

BACKGROUND: The scope of this work is to build a Machine Learning model able to predict patients risk to contract a multidrug resistant urinary tract infection (MDR UTI) after hospitalization. To achieve this goal, we used different popular Machine Learning tools. Moreover, we integrated an easy-to-use cloud platform, called DSaaS (Data Science as a Service), well suited for hospital structures, where healthcare operators might not have specific competences in using programming languages but still, they do need to analyze data as a continuous process. Moreover, DSaaS allows the validation of data analysis models based on supervised Machine Learning regression and classification algorithms. RESULTS: We used DSaaS on a real antibiotic stewardship dataset to make predictions about antibiotic resistance in the Clinical Pathology Operative Unit of the Principe di Piemonte Hospital in Senigallia, Marche, Italy. Data related to a total of 1486 hospitalized patients with nosocomial urinary tract infection (UTI). Sex, age, age class, ward and time period, were used to predict the onset of a MDR UTI. Machine Learning methods such as Catboost, Support Vector Machine and Neural Networks were utilized to build predictive models. Among the performance evaluators, already implemented in DSaaS, we used accuracy (ACC), area under receiver operating characteristic curve (AUC-ROC), area under Precision-Recall curve (AUC-PRC), F1 score, sensitivity (SEN), specificity and Matthews correlation coefficient (MCC). Catboost exhibited the best predictive results (MCC 0.909; SEN 0.904; F1 score 0.809; AUC-PRC 0.853, AUC-ROC 0.739; ACC 0.717) with the highest value in every metric. CONCLUSIONS: the predictive model built with DSaaS may serve as a useful support tool for physicians treating hospitalized patients with a high risk to acquire MDR UTIs. We obtained these results using only five easy and fast predictors accessible for each patient hospitalization. In future, DSaaS will be enriched with more features like unsupervised Machine Learning techniques, streaming data analysis, distributed calculation and big data storage and management to allow researchers to perform a complete data analysis pipeline. The DSaaS prototype is available as a demo at the following address: https://dsaas-demo.shinyapps.io/Server/.

Horizontal gene transfer and silver nanoparticles production in a new Marinomonas strain isolated from the Antarctic psychrophilic ciliate Euplotes focardii.

We isolated a novel bacterial strain from a prokaryotic consortium associated to the psychrophilic marine ciliate Euplotes focardii, endemic of the Antarctic coastal seawater. The 16S rDNA sequencing and the phylogenetic analysis revealed the close evolutionary relationship to the Antarctic marine bacterium Marinomonas sp. BSw10506 and the sub antarctic Marinomonas polaris. We named this new strain Marinomonas sp. ef1. The optimal growth temperature in LB medium was 22 °C. Whole genome sequencing and analysis showed a reduced gene loss limited to regions encoding for transposases. Additionally, five genomic islands, e.g. DNA fragments that facilitate horizontal gene transfer phenomena, were identified. Two open reading frames predicted from the genomic islands coded for enzymes belonging to the Nitro-FMN-reductase superfamily. One of these, the putative NAD(P)H nitroreductase YfkO, has been reported to be involved in the bioreduction of silver (Ag) ions and the production of silver nanoparticles (AgNPs). After the Marinomonas sp. ef1 biomass incubation with 1 mM of AgNO3 at 22 °C, we obtained AgNPs within 24 h. The AgNPs were relatively small in size (50 nm) and had a strong antimicrobial activity against twelve common nosocomial pathogenic microorganisms including Staphylococcus aureus and two Candida strains. To our knowledge, this is the first report of AgNPs biosynthesis by a Marinomonas strain. This biosynthesis may play a dual role in detoxification from silver nitrate and protection from pathogens for the bacterium and potentially for the associated ciliate. Biosynthetic AgNPs also represent a promising alternative to conventional antibiotics against common pathogens.

Synthesis of Bioactive Silver Nanoparticles by a Pseudomonas Strain Associated with the Antarctic Psychrophilic Protozoon Euplotes focardii.

The synthesis of silver nanoparticles (AgNPs) by microorganisms recently gained a greater interest due to its potential to produce them in various sizes and morphologies. In this study, for AgNP biosynthesis, we used a new Pseudomonas strain isolated from a consortium associated with the Antarctic marine ciliate Euplotes focardii. After incubation of Pseudomonas cultures with 1 mM of AgNO3 at 22 °C, we obtained AgNPs within 24 h. Scanning electron (SEM) and transmission electron microscopy (TEM) revealed spherical polydispersed AgNPs in the size range of 20-70 nm. The average size was approximately 50 nm. Energy dispersive X-ray spectroscopy (EDS) showed the presence of a high intensity absorption peak at 3 keV, a distinctive property of nanocrystalline silver products. Fourier transform infrared (FTIR) spectroscopy found the presence of a high amount of AgNP-stabilizing proteins and other secondary metabolites. X-ray diffraction (XRD) revealed a face-centred cubic (fcc) diffraction spectrum with a crystalline nature. A comparative study between the chemically synthesized and Pseudomonas AgNPs revealed a higher antibacterial activity of the latter against common nosocomial pathogen microorganisms, including Escherichia coli, Staphylococcus aureus and Candida albicans. This study reports an efficient, rapid synthesis of stable AgNPs by a new Pseudomonas strain with high antimicrobial activity.

Antibiotic activity of the antioxidant drink effective Microorganism-X (EM-X) extracts against common nosocomial pathogens: an in vitro study.

EM-X is a mixed consortium of beneficial microorganisms of natural occurrence (lactic bacteria, yeast and photosynthetic bacteria). The aim of this study is to evaluate the antimicrobial activity in-vitro of EM-X to the principal pathogens isolated in clinical settings and to understand if it could be a suitable adjuvant to synthetic antibiotics. According the World Health Organization we performed antimicrobial assays to the main pathogens usually found in hospital wards. After antimicrobial testing, EM-X has been shown to be most effective at a concentration of 40 mg/ml four time concentrated than the commercial original solution (10 mg/ml). The EM-X antimicrobial action, although effective against bacteria, has proved to be ineffective against the candida genus. This active range of concentration (mg/ml) may prove a very weak action of EM, but further investigations will be done to separate the active substances form the inactive ones in this complex mixture.

Differences between Community - and Hospital - acquired urinary tract infections in a tertiary care hospital.

The aim of this retrospective study was to highlight the differences in antibiotic resistance between Hospital-acquired and Community-acquired urinary tract infections (UTIs). Antimicrobial UTIs resistance data were collected from March 2011 to March 2018. Uropathogens were identified from 41,715 patients using routine laboratory methods. Differences in antibiotic resistance between Hospital and Community (non-hospitalized) patients were statistically validated. Odds ratio (OR) and p-values was used to determine whether a particular exposure (hospitalization) was a risk factor for a particular outcome (higher antibiotic resistance). We reported a general increase of unnecessary urine cultures in both community and hospital patients. The most representative microorganism isolated from Community (58.2%) and Hospital (47.6%) was E. coli. UTIs causative bacteria in hospitalized patients was more than twice as resistant to Trimetoprim/sulphamethoxazole (OR 2.26) and Imipenem (OR 2.56), for Gram-positive and Gram-negative, respectively, than in Community patients. Nitrofurantoin was the only agent without differences in resistance rate between community and hospital UTIs. Therefore, physicians could use it as a definitive therapy for uncomplicated cystitis and as a prophylactic agent for recurrent uncomplicated cystitis. With this work we provided a general protocol applicable by physicians to select the most suitable, if necessary, UTIs empiric treatment.

CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design.

BACKGROUND: The study of cell metabolism is becoming central in several fields such as biotechnology, evolution/adaptation and human disease investigations. Here we present CiliateGEM, the first metabolic network reconstruction draft of the freshwater ciliate Tetrahymena thermophila. We also provide the tools and resources to simulate different growth conditions and to predict metabolic variations. CiliateGEM can be extended to other ciliates in order to set up a meta-model, i.e. a metabolic network reconstruction valid for all ciliates. Ciliates are complex unicellular eukaryotes of presumably monophyletic origin, with a phylogenetic position that is equal from plants and animals. These cells represent a new concept of unicellular system with a high degree of species, population biodiversity and cell complexity. Ciliates perform in a single cell all the functions of a pluricellular organism, including locomotion, feeding, digestion, and sexual processes. RESULTS: After generating the model, we performed an in-silico simulation with the presence and absence of glucose. The lack of this nutrient caused a 32.1% reduction rate in biomass synthesis. Despite the glucose starvation, the growth did not stop due to the use of alternative carbon sources such as amino acids. CONCLUSIONS: The future models obtained from CiliateGEM may represent a new approach to describe the metabolism of ciliates. This tool will be a useful resource for the ciliate research community in order to extend these species as model organisms in different research fields. An improved understanding of ciliate metabolism could be relevant to elucidate the basis of biological phenomena like genotype-phenotype relationships, population genetics, and cilia-related disease mechanisms.

A three-year study entailing molecular characterization and epidemiology of Clostridium difficile in an Italian tertiary care hospital.

In Italy, there are limited studies on the molecular epidemiology of Clostridium difficile, possibly due to insufficient laboratory diagnostic capacity, low awareness and lack of high-quality surveillance systems. The aim of this study was to evaluate the diffusion of C. difficile in a tertiary care hospital and to genotype all the collected strains in order for hospital staff to take corrective action. All specimens were subjected to a CDI diagnostic algorithm. This included highly specific toxin PCRs and multilocus sequence typing (MLST) to obtain clear, unequivocal genotypization. During a three-year study period, as part of routine C. difficile testing, 711 stool samples were collected from 522 patients to detect the presence of toxigenic genes. After testing, 106 different samples were identified as toxigenic. The proportions of non-toxigenic and toxigenic isolates were respectively 8.7% (62/711) and 14.9% (106/711). The most infection findings in wards for toxigenic strains were in Internal Medicine (56), followed by Neurology (11) and Gastroenterology (11). Three novel sequence types (STs) were found. The two most prevalent STs in wards were clade 1 ST-378 (40) and clade 1 ST-379 (33). Other healthcare-acquired strains were clade 4 ST-37 (11) and clade 5 ST-11 (7). Two STs, namely clade 3 ST-5 (10) and clade 1 ST-380 (5), were isolated among external patients. To prevent an increase in outbreak probability, an active surveillance programme combined with proper hand hygiene, environmental cleaning and contact precautions should be implemented.

A Real-World Setting Study: Which Glucose Meter Could Be the Best for POCT Use? An Easy and Applicable Protocol During the Hospital Routine.

The aim of this retrospective study is to evaluate the reliability and robustness of six glucose meters for point-of-care testing in our wards using a brand-new protocol. During a 30-days study period a total of 50 diabetes patients were subjected to venous blood sampling and glucose meter blood analysis. The results of six glucose meters were compared with our laboratory reference assay. GlucoMen Plus (Menarini) with the 82% of acceptable results was the most robust glucose meter. Even if the Passing-Bablok analysis demonstrates the presence of constant systematic errors and the Bland-Altman test highlighted a possible overestimation, the surveillance error grid analysis showed that this glucose meter can be used safely. We proved that portable glucose meters are not always reliable in routinely clinical settings.

Retrospective analysis of nosocomial infections in an Italian tertiary care hospital.

Nosocomial infections are one of the leading causes of morbidity and mortality in hospitalized patients. Studies of their prevalence in single institutions can reveal trends over time and help to identify risk factors. The aim of this study was to investigate the nosocomial infections trend and identify the prevalence of predominant bacterial microorganisms and their drug resistance patterns in an Italian tertiary care hospital. Infections were classified according to the Centres for Disease Control and Prevention definitions. A retrospective study was carried out from March 2011 to June 2014, based on the bacterial isolate reports of a hospital located in Central Italy. During the 40-month study period, a total of 1547 isolates were obtained from 1046 hospitalized patients and tested for their antibiotic sensitivity. The most common isolates belonged to the Enterobacteriaceae family (61.7%), followed by Enterococcus species (12.4%), Pseudomonas species (10.7%) and S. aureus (10.0%). The incidence density rate of nosocomial infections was 7.4 per 1000 patient days, with a significant difference among the 3 annual infection rates (P<0.001). The highest infection prevalence rate was found in Internal Medicine Unit (41.3%), followed by Intensive Care Units (12.4%), Surgical Units (9.0%,) and Cardiology (7.1%).

Listeria monocytogenes meningitis in an immunocompromised patient.

This report describes a case of meningitis caused by Listeria monocytogenes in a stem cell transplant recipient on immunosuppressive therapy for cutaneous chronic graft-versus host disease. A 59-year-old woman had undergone allogeneic stem cell transplantation (from a matched unrelated donor) 13 months previously for chronic lymphocytic leukemia. She was on regular hematologic follow-up. Though her previous malignancy has been in remission, she was immunosuppressed due to the pharmacological treatment. We describe a meningitis caused by a typical food-borne pathogen, dangerous in patients with impaired cell-mediated immunity. Moreover the bacterium had a multidrug resistance, a rare characteristic in clinical listeriosis. Rapid diagnosis and treatment are key factors in these cases. We chose ampicillin and rifampicin that allowed a complete resolution of the clinical manifestations.

Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences.

We report the characterization of the bacterial consortium associated to Euplotes focardii, a strictly psychrophilic marine ciliate that was maintained in laboratory cultures at 4 °C after its first isolation from Terra Nova Bay, in Antarctica. By Illumina genome analyser, we obtained 11,179 contigs of potential prokaryotic origin and classified them according to the NCBI's prokaryotic attributes table. The majority of these sequences correspond to either Bacteroidetes (16 %) or Proteobacteria (78 %). The latter were dominated by gamma- (39 %, including sequences related to the pathogenic genus Francisella), and alpha-proteobacterial (30 %) sequences. Analysis of the Pfam domain family and Gene Ontology term variation revealed that the most frequent terms that appear unique to this consortium correspond to proteins involved in "transmembrane transporter activity" and "oxidoreductase activity". Furthermore, we identified genes that encode for enzymes involved in the catabolism of complex substance for energy reserves. We also characterized members of the transposase and integrase superfamilies, whose role in bacterial evolution is well documented, as well as putative antifreeze proteins. Antibiotic treatments of E. focardii cultures delayed the cell division of the ciliate. To conclude, our results indicate that this consortium is largely represented by bacteria derived from the original Antarctic sample and may contribute to the survival of E. focardii in laboratory condition. Furthermore, our results suggest that these bacteria may have a more general role in E. focardii survival in its natural cold and oxidative environment.