Identifying Predictors Associated with Risk of Death or Admission to Intensive Care Unit in Internal Medicine Patients with Sepsis: A Comparison of Statistical Models and Machine Learning Algorithms.

Background: Sepsis is a time-dependent disease: the early recognition of patients at risk for poor outcome is mandatory. Aim: To identify prognostic predictors of the risk of death or admission to intensive care units in a consecutive sample of septic patients, comparing different statistical models and machine learning algorithms. Methods: Retrospective study including 148 patients discharged from an Italian internal medicine unit with a diagnosis of sepsis/septic shock and microbiological identification. Results: Of the total, 37 (25.0%) patients reached the composite outcome. The sequential organ failure assessment (SOFA) score at admission (odds ratio (OR): 1.83; 95% confidence interval (CI): 1.41-2.39; p < 0.001), delta SOFA (OR: 1.64; 95% CI: 1.28-2.10; p < 0.001), and the alert, verbal, pain, unresponsive (AVPU) status (OR: 5.96; 95% CI: 2.13-16.67; p < 0.001) were identified through the multivariable logistic model as independent predictors of the composite outcome. The area under the receiver operating characteristic curve (AUC) was 0.894; 95% CI: 0.840-0.948. In addition, different statistical models and machine learning algorithms identified further predictive variables: delta quick-SOFA, delta-procalcitonin, mortality in emergency department sepsis, mean arterial pressure, and the Glasgow Coma Scale. The cross-validated multivariable logistic model with the least absolute shrinkage and selection operator (LASSO) penalty identified 5 predictors; and recursive partitioning and regression tree (RPART) identified 4 predictors with higher AUC (0.915 and 0.917, respectively); the random forest (RF) approach, including all evaluated variables, obtained the highest AUC (0.978). All models' results were well calibrated. Conclusions: Although structurally different, each model identified similar predictive covariates. The classical multivariable logistic regression model was the most parsimonious and calibrated one, while RPART was the easiest to interpret clinically. Finally, LASSO and RF were the costliest in terms of number of variables identified.

Remdesivir significantly reduces SARS-CoV-2 viral load on nasopharyngeal swabs in hospitalized patients with COVID-19: A retrospective case-control study.

Remdesivir is a broad-spectrum antiviral agent able to inhibit the RNA polymerase of SARS-CoV-2. At present, studies focusing on the effect of remdesivir on viral load (VL) are few and with contrasting results. Aim of the present study was to evaluate the effect of remdesivir on SARS-CoV-2 VL from nasopharyngeal swabs (cycle threshold criterion) in a sample of patients treated with the drug, compared with patients who did not receive the antiviral treatment. This retrospective analysis evaluated patients with (1) real-time polymerase chain reaction (RT-PCR) confirmed COVID-19 diagnosis and (2) availability of at least two positive nasopharyngeal swabs analysed with the same analytic platform (ORF target gene, Ingenius ELITe, ELITechGroup, Puteaux, France). Upper respiratory specimens from nasopharyngeal swabs were collected at admission (T0) and 7-14 days after treatment, upon clinical decision. A total of 27 patients treated with remdesivir (Group A) met the inclusion criteria and were compared with 18 patients (Group B) treated with standard care, matched for baseline clinical characteristics. At baseline, both remdesivir-treated and nontreated patients showed comparable VLs (21.73 ± 6.81 vs. 19.27 ± 5.24, p = 0.348). At the second swab, remdesivir-treated patients showed a steeper VL reduction with respect to controls (34.28 ± 7.73 vs. 27.22 ± 3.92; p < 0.001). Longitudinal linear model estimated a mean decrease in cycle threshold equal to 0.61 (SE: 0.09) per day in remdesivir-treated versus 0.33 (SE: 0.10) per day in remdesivir nontreated patients (p for heterogeneity = 0.045). The present study shows that the administration of remdesivir in hospitalized COVID-19 patients significantly reduces the VL on nasopharyngeal swabs.

Early Diagnosis and Antibiotic Treatment Combined with Multicomponent Hemodynamic Support for Addressing a Severe Case of Lemierre's Syndrome.

A 20-year-old man was admitted to the intensive care unit for septic shock due to Lemierre's syndrome. It is a rare syndrome that manifests as an upper respiratory infection, although systemic involvement, severe coagulopathy, and multi-organ failure can dangerously complicate the clinical picture. In this syndrome, sepsis-related neuroendocrine dysregulation and microcirculation impairment can have a rapid deleterious progression. Consequently, proper diagnosis, early source control, and appropriate antibiotics administration are mandatory to improve the prognosis. The intensive treatment is aimed at limiting organ damage through hemodynamic optimization. Remarkably, in septic shock due to Lemierre's syndrome, hemodynamic optimization can be achieved through the synergic effect of norepinephrine, argipressin, and hydrocortisone.

VOC 202012/01 Variant Is Effectively Neutralized by Antibodies Produced by Patients Infected before Its Diffusion in Italy.

The coronavirus disease 2019 (Covid-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and presents a global health emergency that needs urgent intervention. Viruses constantly change through mutation, and new variants of a virus are expected to occur over time. In the United Kingdom (UK), a new variant called B.1.1.7 has emerged with an unusually large number of mutations. The aim of this study is to evaluate the level of protection of sera from 12 patients infected and later healed in Apulia Region (Italy) with Covid-19 between March and November 2020, when the English variant was not circulating in this territory yet, against the new VOC 202012/01 variant by seroneutralization assay. The sera of patients had already been tested before, using a virus belonging to the lineage B.1 and showed an antibody neutralizing titer ranging between 1:160 and 1:320. All the 12 sera donors confirmed the same titers of neutralizing antibodies obtained with a strain belonging to the lineage B.1.1.7 (VOC 202012/01). These data indicate that antibodies produced in subjects infected with variants of Sars-CoV-2 strain before the appearance of the English one, seem to have a neutralizing power also against this variant.

Genomic epidemiology of Klebsiella pneumoniae in Italy and novel insights into the origin and global evolution of its resistance to carbapenem antibiotics.

Klebsiella pneumoniae is at the forefront of antimicrobial resistance for Gram-negative pathogenic bacteria, as strains resistant to third-generation cephalosporins and carbapenems are widely reported. The worldwide diffusion of these strains is of great concern due to the high morbidity and mortality often associated with K. pneumoniae infections in nosocomial environments. We sequenced the genomes of 89 K. pneumoniae strains isolated in six Italian hospitals. Strains were selected based on antibiotypes, regardless of multilocus sequence type, to obtain a picture of the epidemiology of K. pneumoniae in Italy. Thirty-one strains were carbapenem-resistant K. pneumoniae carbapenemase producers, 29 were resistant to third-generation cephalosporins, and 29 were susceptible to the aforementioned antibiotics. The genomes were compared to all of the sequences available in the databases, obtaining a data set of 319 genomes spanning the known diversity of K. pneumoniae worldwide. Bioinformatic analyses of this global data set allowed us to construct a whole-species phylogeny, to detect patterns of antibiotic resistance distribution, and to date the differentiation between specific clades of interest. Finally, we detected an ∼ 1.3-Mb recombination that characterizes all of the isolates of clonal complex 258, the most widespread carbapenem-resistant group of K. pneumoniae. The evolution of this complex was modeled, dating the newly detected and the previously reported recombination events. The present study contributes to the understanding of K. pneumoniae evolution, providing novel insights into its global genomic characteristics and drawing a dated epidemiological scenario for this pathogen in Italy.

Twenty years of surveillance of Invasive Meningococcal Diseases in Puglia, Italy.

INTRODUCTION: The study aims to investigate the change in the burden of disease and the microbiological characteristics of Invasive Meningococcal Disease (IMD) in Puglia in comparison with overall incidence from 1994 through 2014. METHODS: Data are gathered in the frame of the National Surveillance System coordinated by the National Reference Laboratory (NRL) of the Istituto Superiore di Sanità. RESULTS: In Puglia, from 1994 through 2014, the average incidence of IMD was 0.2 per 100 000 inhabitants, below the national average value (0.33). IMD cases tended to be older than the other cases reported in Italy (median age 19 vs 16). The case-fatality rate was 20.4% in Puglia vs 13.3% in Italy. Serogroups B and C were most frequently identified. Serogroups C and Y presented a fairly clonal pattern, whereas serogroup B was genetically rather heterogeneous. CONCLUSION: Surveillance systems are critical in monitoring any change in the epidemiology of IMD.

Emergence of a VIM-1 MBL and CTX-M-15 ESbL-producing Klebsiella pneumoniae clone from acute and rehabilitation hospitals in Italy.

We report the emergence of VIM-1 MBL and CTX-M-15-producing K. pneumoniae isolates collected from patients at two acute care hospitals (I.R.C.C.S. "S. Matteo" and "Casa Sollievo della Sofferenza" Hospital) and a long-term rehabilitation facility in Northern Italy (I.R.C.C.S. "S. Maugeri"). Between February 2007 and October 2008, 30 K. pneumoniae strains showing decreased susceptibility to carbapenems were collected. PCR and sequencing experiments revealed the presence of blaVIM-1 gene in 14/30 isolates. All the above isolates carried the blaSHV-5 determinant as well; interestingly, 8/14 VIM positive isolates were also CTX-M-1- like producers. VIM-1 positive strains were present in all hospitals. PFGE genomic profiles of the 14/30 isolates showed that 2 different clones, A and B, were responsible for outbreaks. The coexistence in the same bacterial cell of compatible plasmids carrying epidemiologically important emerging resistance genes, such as MBLs and CTX-Ms, is worrisome since it could predict the generation and spread of pan-resistant bacteria and the consequent treatment option limitations that can lead to significant morbidity and mortality. Control measures should be applied to detect MBL-producing strains and to contrast the vertical and plasmidic diffusion of carbapenem-resistant K. pneumoniae in acute care and rehabilitation facilities.

Cranial and spinal subdural empyema.

Subdural empyema represents a loculated suppuration between the dura and the arachnoid. It has been described either intracranially or in the spinal canal, the latter localization being quite rare. It is a rare but serious illness with a declining mortality rate but rather frequent neurological sequelae. Morbidity and mortality in intracranial and spinal subdural empyema directly relate to the delay in diagnosis and therapy. The epidemiology, etiology, pathophysiology and symptoms of spinal subdural empyema and cranial subdural empyema are somewhat different, but brain and spinal subdural empyema are not always two different entities. An adequate treatment strategy should be selected on a case-by-case basis, especially for patients with a massive CNS involvement, where management represents a challenge.

Nosocomial outbreak caused by multidrug-resistant Pseudomonas aeruginosa producing IMP-13 metallo-beta-lactamase.

An outbreak of Pseudomonas aeruginosa showing a multidrug-resistant (MDR) phenotype (including carbapenems, ceftazidime, cefepime, gentamicin, tobramycin, and fluoroquinolones) was observed, during a 5-month period, in a general intensive care unit of a large tertiary care and clinical research hospital in southern Italy. The outbreak involved 15 patients, with a total of 87 isolates, mostly from lower respiratory tract specimens. Analysis of isolates involved in the outbreak revealed production of metallo-beta-lactamase (MBL) activity, and genotyping by pulsed-field gel electrophoresis of genomic DNA digested by SpeI revealed clonal relatedness among isolates. Molecular analysis of the MBL determinant showed the presence of a bla(IMP-13) gene carried on a gene cassette inserted in a class 1 integron which also contained an aacA4 aminoglycoside resistance cassette encoding an AAC(6')-Ib enzyme. The bla(IMP-13)-containing integron and its genetic environment appeared to be similar to those found in P. aeruginosa isolates producing IMP-13 from a hospital in Rome. The bla(IMP-13) gene was not transferable by conjugation and was apparently carried on the chromosome. The outbreak was coincidental with a shortage of nursing personnel, and resolution was apparently associated with reinstatement of nursing personnel and reinforcement of general infection control practices within the intensive care unit. To our best knowledge this is the first description of a nosocomial outbreak of relatively large size caused by an IMP-producing gram-negative pathogen in Europe.