Prospective observational pilot study of the T2Resistance panel in the T2Dx system for detection of resistance genes in bacterial bloodstream infections.

Early initiation of antimicrobial therapy targeting resistant bacterial pathogens causing sepsis and bloodstream infections (BSIs) is critical for a successful outcome. The T2Resistance Panel (T2R) detects the following resistance genes within organisms that commonly cause BSIs directly from patient blood samples: blaKPC, blaCTXM-14/15, blaNDM/bla/IMP/blaVIM, blaAmpC, blaOXA, vanA, vanB, and mecA/mecC. We conducted a prospective study in two major medical centers for the detection of circulating resistance genes by T2R in patients with BSIs. T2R reports were compared to antimicrobial susceptibility testing (AST), phenotypic identification, and standard molecular detection assays. Among 59 enrolled patients, 25 resistance genes were identified: blaKPC (n = 10), blaNDM/bla/IMP/blaVIM (n = 5), blaCTXM-14/15 (n = 4), blaAmpC (n = 2), and mecA/mecC (n = 4). Median time-to-positive-T2R in both hospitals was 4.4 hours [interquartile range (IQR): 3.65-4.97 hours] in comparison to that for positive blood cultures with final reporting of AST of 58.34 h (IQR: 45.51-111.2 hours; P < 0.0001). The sensitivity of T2R to detect the following genes in comparison to AST was 100% for blaCTXM-14/15, blaNDM/bla/IMP/blaVIM, blaAmpC, mecA/mecC and 87.5% for blaKPC. When monitored for the impact of significant antimicrobial changes, there were 32 events of discontinuation of unnecessary antibiotics and 17 events of escalation of antibiotics, including initiation of ceftazidime/avibactam in six patients in response to positive T2R results for blaKPC. In summary, T2R markers were highly sensitive for the detection of drug resistance genes in patients with bacterial BSIs, when compared with standard molecular resistance detection systems and phenotypic identification assays while significantly reducing by approximately 90% the time to detection of resistance compared to standard methodology and impacting clinical decisions for antimicrobial therapy. IMPORTANCE: This is the first reported study to our knowledge to identify key bacterial resistance genes directly from the bloodstream within 3 to 5 hours in patients with bloodstream infections and sepsis. The study further demonstrated a direct effect in modifying initial empirical antibacterial therapy in response to T2R signal to treat resistant bacteria causing bloodstream infections and sepsis.

Accelerate Pheno™ system in sepsis by Gram-negative pathogens: four months of hospital experience.

This study reports our experience with the Accelerate PhenoTM system (ACC) to guide management of patients with sepsis by Gram-negative pathogens. A diagnostic workflow, based on pathogen and resistance genes detection or ACC testing, was applied to 33 patients. Clinical and microbiological data were recorded, and analysis of broad-spectrum agents sparing was performed. Antimicrobial susceptibility results by ACC were available for 28 of 33 patients (84.85%). Among 434 microorganism-antimicrobial combinations, categorical agreement was 97.93%, very major errors 0.23%, major errors 1.15%, and minor errors 0.69%. Time to report (mean ± SD) of ACC results was 27.14±6.90 h from sample collection, significantly shorter (p<0.001, Δ = 19.96 h, 95% CI: 24.71-15.22) than that of the standard method (47.10±11.92 h). A switch from empiric to targeted therapy was observed in 14 of 28 patients (50.0%), duration of empiric therapy was 37.73±19.87 h, with a saving of 5.45 piperacillin/tazobactam and 5.28 carbapenems prescribed daily doses. Considering patients in which de-escalation would have been theoretically feasible, 27.69 prescribed daily doses of piperacillin/tazobactam and 19.08 of carbapenems could had been spared, compared to standard methods. In conclusion, ACC could impact positively on the management of septic patients by Gram-negative pathogens.

Laboratory automation reduces time to report of positive blood cultures and improves management of patients with bloodstream infection.

The impact on time to results (TTR) and clinical decisions was evaluated for mono-microbial positive blood cultures (BC) processed using the BD Kiestra Work Cell Automation (WCA) system. Positive BC were processed by the WCA system by full-automatic subculture on solid media and digital imaging after 8 h of incubation (8-h method) followed by identification (ID) and antimicrobial susceptibility testing (AST). To evaluate the accuracy of the 8-h method, ID and AST from 8-h and overnight incubated colonies were compared for the same organisms. To evaluate its clinical impact, results from 102 BC processed by the 8-h method (cases) were compared with those from 100 BC processed by overnight incubation method (controls) in a comparable period. Identification after 8-h and overnight incubation gave concordant results in 101/102 (99.0%) isolates. Among a total of 1379 microorganism-antimicrobial combinations, categorical agreement was 99.4% (1371/1379); no very major error, 7 major errors, and one minor error were observed. TTR in cases (32.8 h ± 8.3 h) was significantly (p < 0.001) shorter than in controls (55.4 h ± 13.3 h). A significant reduction was observed for duration of empirical therapy (cases 54.8 h ± 23.3 h vs controls 86.9 h ± 34.1 h, p < 0.001) and 30-day crude mortality rate (cases 16.7% vs controls 29.0%, p < 0.037). Automation and 8-h digital reading of plates from positive BC, followed by ID and AST, greatly reduce TTR and shorten the duration of antimicrobial empiric therapy, possibly improving outcome in patients with mono-microbial bloodstream infections.

Orbital Infiltration in a Patient with Waldenström Macroglobulinemia: Need for Multidisciplinary Approach and Comparison with the Literature.

The use of specific inhibitory drugs of intracellular signalling pathways (such as Bruton-Kinase inhibitors) for the treatment of Waldenström's macroglobulinaemia (WM) is a recognised risk factor for Aspergillus spp. infections. The overlapping clinical manifestations of the two diseases may require the involvement of different medical specialities. We describe the clinical course of a patient with pulmonary and encephalic aspergillosis, with concomitant orbital infiltration, which represented a difficult diagnosis: the case required a multidisciplinary approach to define the ocular lesions and an in-depth study of the literature.

Latent Tuberculosis Infection and COVID-19: Analysis of a Cohort of Patients from Careggi University Hospital (Florence, Italy).

Data regarding the relationship between coronavirus disease (COVID-19) and active or latent tuberculosis (TB) are discordant. We conducted a retrospective study examining the impact of latent tuberculosis infection (LTBI) on the clinical progression of COVID-19 patients. We selected 213 patients admitted with COVID-19 in a tertiary-level Italian hospital (February-December 2020), who underwent a QuantiFERON-TB test (QFT) and/or chest radiological exam. The population was divided into three groups: (i) QFT negative and without radiological TB sequelae (Neg); (ii) QFT positive and without radiological TB sequelae (Pos); (iii) radiological TB sequelae regardless of QFT result (Seq). In-hospital mortality and oro-tracheal intubation (OTI) showed significantly higher results in the Seq group (Seq 50% vs. Pos 13.3% vs. Neg 9.3%, p < 0.001; Seq 16.7% vs. Pos 6.7% vs. Neg 4.9%, p = 0.045). Considering the Pos and Seq groups' patients as the population with defined LTBI, in-hospital mortality (20/51, 39.2%) and OTI risk (7/51, 13.7%) were statistically higher with respect to patients without LTBI (in-hospital mortality: 15/162, 9.3%, p < 0.001; OTI risk: 8/162, 4.9%, p = 0.023), respectively. Multivariate analysis showed that radiological sequelae and the Charlson Comorbidity Index (CCI) were significantly associated with higher mortality rate; despite the higher CCI of Seq population, we cannot exclude the correlation between COVID-19 in-hospital mortality and the presence of radiological TB sequelae.

Characteristics of COVID-19 vaccinated and unvaccinated patients admitted to Careggi University Hospital, Florence, Italy.

More than 11.5 billion COVID-19 vaccine doses have been administered around the world. Although vaccine effectiveness for severe infections is reported to be 89.0%, breakthrough infections are common and may lead to severe outcome in fragile population. We conducted a real-world observational study on 420 COVID-19 admitted patients from July 2021 to January 2022 in a tertiary level Italian hospital. We collected patient's vaccination and SARS-CoV-2 serological status, SARS-CoV-2 treatments, oxygen supports, intensive (ICU) and subintensive (sub-ICU) care unit admissions, length of staying (LoS) and in-hospital mortality. One-hundred-seventy-two vaccinated and 248 unvaccinated patients were admitted during the study period. Vaccinated group (Vg) had a significantly more elevated Charlson Comorbidity Index than Unvaccinated group (UVg), and no statistical differences were found in terms of in-hospital mortality, LoS or ICU and sub-ICU admissions. Among Vg, anti-S antibodies were detected in 86.18% of patients (seropositives). Vaccinated seronegative patients' in-hospital mortality was significantly higher than vaccinated seropositive patients (33.33% vs 10.69%, p = 0.0055): in particular, mortality rate in 45-69 years old population was higher in vaccinated seronegative group, and comparable in patients ≥ 70 years old. No differences in terms of outcome were registered between Vg and UVg, taking into account that Vg was considerably older and with more comorbidities. In line with other recent observations, higher mortality rate was evidenced for seronegative vaccinated patients. Primary prophylaxis and early treatments result to be necessary, especially for older and immunosuppressed populations.

Safety and Efficacy of Outpatient Treatments for COVID-19: Real-Life Data from a Regionwide Cohort of High-Risk Patients in Tuscany, Italy (the FEDERATE Cohort).

Early COVID-19 treatments can prevent progression to severe disease. However, real-life data are still limited, and studies are warranted to monitor the efficacy and tolerability of these drugs. We retrospectively enrolled outpatients receiving early treatment for COVID-19 in 11 infectious diseases units in the Tuscany region of Italy between 1 January and 31 March 2022, when Omicron sublineages BA.1 and BA.2 were circulating. Eligible COVID-19 patients were treated with sotrovimab (SOT), remdesivir (RMD), nirmatrelvir/ritonavir (NRM/r), or molnupiravir (MOL). We gathered demographic and clinical features, 28-day outcomes (hospitalization or death), and drugs tolerability. A total of 781 patients (median age 69.9, 66% boosted for SARS-CoV-2) met the inclusion criteria, of whom 314 were treated with SOT (40.2%), 205 with MOL (26.3%), 142 with RMD (18.2%), and 120 with NRM/r (15.4%). Overall, 28-day hospitalization and death occurred in 18/781 (2.3%) and 3/781 (0.3%), respectively. Multivariable Cox regression showed that patients receiving SOT had a reduced risk of meeting the composite outcome (28-day hospitalization and/or death) in comparison to the RMD cohort, while no significant differences were evidenced for the MOL and NRM/r groups in comparison to the RMD group. Other predictors of negative outcomes included cancer, chronic kidney disease, and a time between symptoms onset and treatment administration > 3 days. All treatments showed good safety and tolerability, with only eight patients (1%) whose treatment was interrupted due to intolerance. In the first Italian multicenter study presenting real-life data on COVID-19 early treatments, all regimens demonstrated good safety and efficacy. SOT showed a reduced risk of progression versus RMD. No significant differences of outcome were observed in preventing 28-day hospitalization and death among patients treated with RMD, MOL, and NRM/r.

Accuracy and Impact on Patient Management of New Tools for Diagnosis of Sepsis: Experience with the T2 Magnetic Resonance Bacteria Panel.

The rapid and accurate identification of pathogens responsible for sepsis is essential for prompt and effective antimicrobial therapy. Molecular technologies have been developed to detect the most common causative agents, with high sensitivity and short time to result (TTR). T2 Bacteria Panel (T2), based on a combination of PCR and T2 magnetic resonance, can identify directly in blood samples Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterococcus faecium, and Acinetobacter baumannii pathogens. This study evaluates the role of T2 in the diagnosis of sepsis and its impact on patient management, specifically in terms of TTR and the switch from empirical to directed therapy, comparing results of blood culture (BC) and T2 assay in 82 patients with sepsis. T2 significantly improved the detection of the causative agents of sepsis. For pathogens included in the panel, T2 sensitivity was 100% (95% CI 86.3-100.0), significantly higher than that of BC (54.8%, 95% CI 36.0-72.7). The TTR (median, IQR) of positive T2 (3.66 h, 3.59-4.31) was significantly shorter than that of the positive BC (37.58 h, 20.10-47.32). A significant reduction in the duration of empiric therapy and an increase in the percentage of patients with switched therapy was observed in patients with a positive T2 result. In conclusion, T2 can shorten and improve the etiological diagnosis of sepsis with a positive impact on patient management.

Direct Testing for KPC-Mediated Carbapenem Resistance from Blood Samples Using a T2 Magnetic Resonance Based Assay.

Molecular-based carbapenem resistance testing in Gram-negative bacterial bloodstream infections (BSIs) is currently limited because of the reliance on positive blood culture (BC) samples. The T2Resistance™ panel may now allow the detection of carbapenemase- and other ß-lactamase encoding genes directly from blood samples. We detected carbapenem resistance genes in 11 (84.6%) of 13 samples from patients with BC-documented BSIs (10 caused by KPC-producing Klebsiellapneumoniae and 1 caused by VIM/CMY-producing Citrobacter freundii). Two samples that tested negative for carbapenem resistance genes were from patients with BC-documented BSIs caused by KPC-producing K. pneumoniae who were receiving effective antibiotic therapy. In conclusion, our findings suggest that the T2Resistance™ panel can be a reliable tool for diagnosing carbapenem-resistant Gram-negative bacterial BSIs.

Evaluation of Lumipulse® G SARS-CoV-2 antigen assay automated test for detecting SARS-CoV-2 nucleocapsid protein (NP) in nasopharyngeal swabs for community and population screening.

OBJECTIVES: To compare the Lumipulse® SARS-CoV-2 antigen test with the gold standard real-time reverse transcription-polymerase chain reaction (RT-PCR) for diagnosis of SARS-CoV-2 infection and to evaluate its role in screening programs. METHODS: Lumipulse® SARS-CoV-2 antigen assay was compared with the gold standard RT-PCR test in a selected cohort of 226 subjects with suspected SARS-CoV-2 infection, and its accuracy was evaluated. Subsequently, the test was administered to a real-life screening cohort of 1738 cases. ROC analysis was performed to explore test features and cutoffs. All tests were performed in the regional reference laboratory in Umbria, Italy. RESULTS: A 42.0% positive result at RT-PCR was observed in the selected cohort. The Lumipulse® system showed 92.6% sensitivity (95% CI 85.4-97.0%) and 90.8% specificity (95% CI 84.5-95.2%) at 1.24 pg/mL optimal cutoff. In the screening cohort, characterized by 5.2% prevalence of infection, Lumipulse® assay showed 100% sensitivity (95% CI 96.0-100.0%) and 94.8% specificity (95% CI 93.6-95.8%) at 1.645 pg/mL optimal cutoff; the AUC was 97.4%, NPV was 100% (95% CI 99.8-100.0%) and PPV was 51.1% (95% CI 43.5-58.7%). CONCLUSIONS: The Lumipulse® SARS-CoV-2 antigen assay can be safely employed in the screening strategies in small and large communities and in the general population.

Accelerate Pheno™ blood culture detection system: a literature review.

Accelerate Pheno™ (ACC) is a fully automated system providing rapid identification of a panel of bacteria and yeasts, and antimicrobial susceptibility testing of common bacterial pathogens responsible for bloodstream infections and sepsis. Diagnostic accuracy for identification ranges from 87.9 to 100%, and antimicrobial susceptibility testing categorical agreement is higher than 91%. The present review includes peer-reviewed studies on ACC published to date. Both interventional and hypothetical studies evidenced the potential positive clinical role of ACC in the management and therapy of patients with bloodstream infections and sepsis, due to the important reduction in time to report, suggesting a crucial impact on the therapeutic management of these patients, provided the presence of a hospital antimicrobial stewardship program, a 24/7 laboratory operating time and a strict collaboration between clinical microbiologist and clinician. Further prospective multicenter studies are necessary to explore the impact of this system on mortality, length of stay and spread of multidrug-resistant organisms.

Measurement and prediction of antimicrobial resistance in bloodstream infections by ESKAPE pathogens and Escherichia coli.

OBJECTIVES: This study aimed to evaluate a cumulative antimicrobial resistance index (ARI) as a possible key outcome measure of antimicrobial stewardship programmes (ASPs) and a tool to predict the antimicrobial resistance (AMR) trend. METHODS: Antimicrobial susceptibility for Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli (ESKAPEEc) pathogens recovered from blood cultures during a 5-year period (2014-2018) was analysed to obtain a cumulative ARI. For each antibiotic tested, a score of 0, 0.5 or 1 was assigned for susceptibility, intermediate resistance or resistance, respectively, and the ARI was calculated by dividing the sum of these scores by the number of antibiotics tested. Cumulative ARIs of ESKAPEEc micro-organisms were compared and a mathematical prediction model for AMR trend was obtained. RESULTS: In total, 1858 ESKAPEEc isolates were included in the study. The cumulative ESKAPEEc mean ARI increased significantly from 0.200 ± 0.01 in 2014 to 0.276 ± 0.02 in 2018 (P < 0.001). In multivariable regression analysis, factors significantly associated with ARI ≥ 0.5 were E. faecium, K. pneumoniae, P. aeruginosa and A. baumannii infection (P < 0.001) and infection occurring after 2014 (P < 0.05). Based on the prediction model obtained, in the absence of any interventional measure, a tendency to pandrug resistance of the ESKAPEEc group could be expected in the next 8-15 years. CONCLUSION: The ARI could be a useful tool to measure the impact of ASPs on AMR. The increasing incidence of AMR among ESKAPEEc organisms underscores the needing for ASPs.