Viral Population Heterogeneity and Fluctuating Mutational Pattern during a Persistent SARS‐CoV‐2 Infection in an Immunocompromised Patient

Literature offers plenty of cases of immunocompromised patients, who develop chronic and severe SARS‐CoV‐2 infections. The aim of this study is to provide further insight into SARS-CoV‐2 evolutionary dynamic taking into exam a subject suffering from follicular lymphoma, who developed a persistent infection for over 7 months. Eight nasopharyngeal swabs were obtained, and were analyses by qRT‐PCR for diagnostic purposes. All of them were considered eligible (Ct < 30) for NGS sequencing. Sequence analysis showed that all sequences matched the B.1.617.2 AY.122 lineage, but they differed by few mutations identifying three genetically similar subpopulations, which evolved during the course of infection, demonstrating that prolonged replication is paralleled with intra‐host virus evolution. These evidences support the hypothesis that SARS‐CoV‐2 adaptive capacities are able to shape a heterogeneous viral population in the context of immunocompromised patients. Spill‐over of viral variants with enhanced transmissibility or immune escape capacities from these subjects is plausible

Molecular Approach for the Laboratory Diagnosis of Periprosthetic Joint Infections

The incidence of total joint arthroplasty is increasing over time since the last decade and expected to be more than 4 million by 2030. As a consequence, the detection of infections associated with surgical interventions is increasing and prosthetic joint infections are representing both a clinically and economically challenging problem. Many pathogens, from bacteria to fungi, elicit the immune system response and produce a polymeric matrix, the biofilm, that serves as their protection. In the last years, the implementation of diagnostic methodologies reduced the error rate and the turn-around time: polymerase chain reaction, targeted or broad-spectrum, and next-generation sequencing have been introduced and they represent a robust approach nowadays that frees laboratories from the unique approach based on culture-based techniques

Can diaphragmatic ultrasonography performed during the T-tube trial predict weaning failure? The role of diaphragmatic rapid shallow breathing index

Background: The rapid shallow breathing index (RSBI), which is the ratio between respiratory rate (RR) and tidal volume (VT), is one of the most widely used indices to predict weaning outcome. Whereas the diaphragm plays a fundamental role in generating VT, in the case of diaphragmatic dysfunction the inspiratory accessory muscles may contribute. If this occurs during a weaning trial, delayed weaning failure is likely since the accessory muscles are more fatigable than the diaphragm. Hence, we hypothesised that the traditional RSBI could be implemented by substituting VT with the ultrasonographic evaluation of diaphragmatic displacement (DD). We named the new index the diaphragmatic-RSBI (D-RSBI). The aim of this study was to compare the ability of the traditional RSBI and D-RSBI to predict weaning failure in ready-to-wean patients. Methods: We performed a prospective observational study. During a T-tube spontaneous breathing trial (SBT) we simultaneously evaluated right hemidiaphragm displacement (i.e., DD) by using M-mode ultrasonography as well as the RSBI. Outcome of the weaning attempt, length of mechanical ventilation, length of intensive care unit and hospital stay, and hospital mortality were recorded. Receiver operator characteristic (ROC) curves were used to evaluate the diagnostic accuracy of D-RSBI and RSBI. Results: We enrolled 51 patients requiring mechanical ventilation for more than 48 h who were ready to perform a SBT. Most of the patients, 34 (66 %), were successfully weaned from mechanical ventilation. When considering the 17 patients that failed the weaning attempt, 11 (64 %) had to be reconnected to the ventilator during the SBT, three (18 %) had to be re-intubated within 48 h of extubation, and three (18 %) required non-invasive ventilation support within 48 h of extubation. The areas under the ROC curves for D-RSBI and RSBI were 0.89 and 0.72, respectively (P = 0.006). Conclusions: D-RSBI (RR/DD) was more accurate than traditional RSBI (RR/VT) in predicting the weaning outcome. Trial registration: Our clinical trial was retrospectively registered with ClinicalTrials.gov (identifier: NCT02696018). ClinicalTrials.gov processed our record on 25 February 2016

18F-FDG PET/CT impact on testicular tumours clinical management

PURPOSE: Testicular tumour is the most common malignancy in young men. The diagnostic work-up is mainly based on morphological imaging. The aim of our study was to evaluate the clinical impact of (18)F-FDG PET/CT in patients with testicular tumour. METHODS: We retrospectively evaluated all patients studied by (18)F-FDG PET/CT at our centre. Inclusion criteria were: pathological confirmation of testicular tumour, contrast-enhanced CT scan performed within a month of the PET/CT scan, and clinical/imaging follow-up performed at the Oncology Unit of our hospital. Overall, 56 patients were enrolled and 121 PET/CT scans were evaluated. (18)F-FDG PET/CT was performed following standard procedures and the results were compared with clinical, imaging and follow-up data. Clinicians were contacted to inquire whether the PET/CT scan influenced the patient's management. Answers were scored as follows: start/continue chemotherapy or radiotherapy, indication for surgery of secondary lesions, and clinical surveillance. RESULTS: On a scan basis, 51 seminoma and 70 nonseminoma (NS) cases were reviewed. Of the 121 cases. 32 were found to be true-positive, 74 true-negative, 8 false-positive and 6 false-negative by PET/CT. PET/CT showed good sensitivity and specificity for seminoma lesion detection (92% and 84%, respectively), but its sensitivity was lower for NS forms (sensitivity and specificity 77% and 95%, respectively). The PET/CT scan influenced the clinical management of 47 of 51 seminomas (in 6 chemotherapy was started/continued, in 3 radiotherapy was started/continued, in 2 surgery of secondary lesions was performed, and in 36 clinical surveillance was considered appropriate), and 59 of 70 NS (in 18 therapy/surgery was started/continued, and in 41 clinical surveillance was considered appropriate). CONCLUSION: Our preliminary data demonstrate the potential usefulness of PET/CT for the assessment of patients with testicular tumour. It provides valuable information for the clinical management, particularly for clinical surveillance, post-therapy assessment and when relapse is suspected

Effect of the Pandemic Outbreak on ICU-Associated Infections and Antibiotic Prescription Trends in Non-COVID19 Acute Respiratory Failure Patients

Background: The COVID-19 pandemic had a relevant impact on the organization of intensive care units (ICU) and may have reduced the overall compliance with healthcare-associated infections (HAIs) prevention programs. Invasively ventilated patients are at high risk of ICU-associated infection, but there is little evidence regarding the impact of the pandemic on their occurrence in non-COVID-19 patients. Moreover, little is known of antibiotic prescription trends in the ICU during the first wave of the pandemic. The purpose of this investigation is to assess the incidence, characteristics, and risk factors for ICU-associated HAIs in a population of invasively ventilated patients affected by non-COVID-19 acute respiratory failure (ARF) admitted to the ICU in the first wave of the COVID-19 pandemic, and to evaluate the ICU antimicrobial prescription strategies. Moreover, we compared HAIs and antibiotic use to a cohort of ARF patients admitted to the ICU the year before the pandemic during the same period. Methods: this is a retrospective, single-centered cohort study conducted at S. Anna University Hospital (Ferrara, Italy). We enrolled patients admitted to the ICU for acute respiratory failure requiring invasive mechanical ventilation (MV) between February and April 2020 (intra-pandemic group, IP) and February and April 2019 (before the pandemic group, PP). We excluded patients admitted to the ICU for COVID-19 pneumonia. We recorded patients’ baseline characteristics, ICU-associated procedures and devices. Moreover, we evaluated antimicrobial therapy and classified it as prophylactic, empirical or target therapy, according to the evidence of infection at the time of prescription and to the presence of a positive culture sample. We compared the results of the two groups (PP and IP) to assess differences between the two years. Results: One hundred and twenty-eight patients were screened for inclusion and 83 patients were analyzed, 45 and 38 in the PP and I group, respectively. We found a comparable incidence of HAIs (62.2% vs. 65.8%, p = 0.74) and multidrug-resistant (MDR) isolations (44.4% vs. 36.8% p= 0.48) in the two groups. The year of ICU admission was not independently associated with an increased risk of developing HAIs (OR = 0.35, 95% CI 0.16–1.92, p = 0.55). The approach to antimicrobial therapy was characterized by a significant reduction in total antimicrobial use (21.4 ± 18.7 vs. 11.6 ± 9.4 days, p = 0.003), especially of target therapy, in the IP group. Conclusions: ICU admission for non-COVID-19 ARF during the first wave of the SARS-CoV-2 pandemic was not associated with an increased risk of ICU-associated HAIs. Nevertheless, ICU prescription of antimicrobial therapy changed and significantly decreased during the pandemic

Omicron Sub-Lineage BA.5 and Recombinant XBB Evasion from Antibody Neutralisation in BNT162b2 Vaccine Recipients

The recent emergence of a number of new SARS-CoV-2 variants resulting from recombination between two distinct parental lineages or sub-lineages within the same lineage has sparked the debate regarding potential enhanced viral infectivity and immune escape. Among these, XBB, recombinant of BA.2.10 and BA.2.75, has caused major concern in some countries due to its rapid increase in prevalence. In this study, we tested XBB escape capacity from mRNA-vaccine-induced (BNT162b2) neutralising antibodies compared to B.1 ancestral lineage and another co-circulating variant (B.1.1.529 BA.5) by analysing sera collected 30 days after the second dose in 92 healthcare workers. Our data highlighted an enhanced and statistically significant immune escape ability of the XBB recombinant. Although these are preliminary results, this study highlights the importance of immune escape monitoring of new and forthcoming variants and of the reformulation of existing vaccines

Evaluation of STANDARDTM M10 SARS-CoV-2, a Novel Cartridge-Based Real-Time PCR Assay for the Rapid Identification of Severe Acute Respiratory Syndrome Coronavirus 2

Since the beginning of the pandemic, SARS-CoV-2 has caused problems for all of world’s population, not only in terms of deaths but also in terms of overloading healthcare facilities in all countries. Diagnosis is one of the key aspects of controlling the spread of SARS-CoV-2, and among the current molecular techniques, real-time PCR is considered as the gold standard. The availability of tests that allow for the rapid and accurate identification of SARS-CoV-2 is therefore of considerable importance. Moreover, if these tests allow for even minimal intervention by the operator, any risk of contamination is reduced. In this study, the performances of the new STANDARDTM M10 SARS-CoV-2 (SD Biosensor Inc., Suwon, Korea) rapid molecular test, which incorporates the above-mentioned features, were characterized. The clinical and analytical performances measured by testing different variants circulating in Italy of STANDARDTM M10 SARS-CoV-2 were compared to the test already on the market and recognized as the gold standard: Xpert Xpress SARS-CoV-2 (Cepheid, Sunnyvale, CA, USA). The results obtained between the two tests are largely comparable, suggesting that STANDARDTM M10 SARS-CoV-2 can be used with excellent results in the fight against the global spread of SARS-CoV-2

Genomic and Temporal Analysis of Deletions Correlated to qRT-PCR Dropout in N Gene in Alpha, Delta and Omicron Variants

Since the first SARS-CoV-2 outbreak, mutations such as single nucleotide polymorphisms (SNPs) and insertion/deletions (INDELs) have changed and characterized the viral genome sequence, structure and protein folding leading to the onset of new variants. The presence of those alterations challenges not only the clinical field but also the diagnostic demand due to failures in gene detection or incompleteness of polymerase chain reaction (PCR) results. In particular, the analysis of understudied genes such as N and the investigation through whole-genome next generation sequencing (WG-NGS) of regions more prone to mutate can help in the identification of new or reacquired mutations, with the aim of designing robust and long-lasting primers. In 48 samples of SARS-CoV-2 (including Alpha, Delta and Omicron variants), a lack of N gene amplification was observed in the genomes analyzed through WG-NGS. Three gene regions were detected hosting the highest number of SNPs and INDELs. In several cases, the latter can interfere deeply with both the sensitivity of diagnostic methodologies and the final protein folding. The monitoring over time of the viral evolution and the reacquisition among different variants of the same mutations or different alterations within the same genomic positions can be relevant to avoid unnecessary consumption of resources