The Assessment of Multiplex PCR in Identifying Bacterial Infections in Patients Hospitalized with SARS-CoV-2 Infection: A Systematic Review

Key performance evaluation of commercialized multiplex rRT-PCR kits for respiratory viruses: implications for application and optimization

Respiratory tract infections (RTIs) caused by viruses are prevalent and significant conditions in clinical settings. Accurate and effective detection is of paramount importance in the diagnosis, treatment, and prevention of viral RTIs. With technological advancements, multiplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assays have been developed and extensively adopted for the diagnosis of viral RTIs. Given the potential challenges in the detection performance of multiplex assays, this study evaluated the analytical sensitivity and competitive interference of the six most commonly used multiplex rRT-PCR kits for detection of respiratory viruses in China. The results revealed that the limits of detection were variable across the viruses and kits. Most of the evaluated multiplex kits demonstrated comparable or enhanced analytical sensitivity compared with singleplex kits for clinically significant viruses, including human adenovirus (HAdV)-3, HAdV-7, Omicron BA.5, H1N1pdm09, H3N2, B/Victoria, respiratory syncytial virus subtype A, and respiratory syncytial virus subtype B, whereas multiplex kits showed relatively less analytical sensitivity for human rhinovirus-B72, human metapneumovirus-A2, parainfluenza virus (PIV)-1, and PIV-3. In addition, most multiplex kits successfully identified co-infections when one analyte was present at a low concentration and another analyte was present at a high concentration.

IMPORTANCE

The complexity and severity of viral respiratory tract infections (RTIs) emphasize the pivotal role of precise diagnosis for viral RTIs in guiding effective public health responses and ensuring appropriate medical interventions, given the substantial population at risk. This study highlights the necessity and importance of evaluating the analytical validity of multiplex real-time reverse transcription polymerase chain reaction assays, offering valuable insights into their optimization and application.

Secondary Bacterial Infections in Critically Ill COVID-19 Patients Admitted in the Intensive Care Unit of a Tertiary Hospital in Romania

Background: The outbreak of the COVID-19 pandemic caught healthcare systems in many countries unprepared. Shortages of personnel, medicines, disinfectants, and intensive care unit (ICU) capacities, combined with inadvertent use of antibiotics and emergence of drug-resistant secondary infections, led to a surge in COVID-19-related mortality. Objective: We aimed to evaluate the prevalence of secondary bacterial infections and the associated antibiotic resistance in a temporary established ICU dedicated to COVID-19 patients. We also assessed the utility of clinical and routine laboratory data as predictors of secondary infections and mortality in these patients. Methods: We examined the medical records of 243 patients admitted to the COVID-19 Medical Support Unit of Târgu Mures, Romania, between 1 August 2020 and 31 January 2021. Results: Among the 243 patients admitted to the COVID-19 Medical Support Unit of Târgu Mures between 1 August 2020 and 31 January 2021, 59 (24.3%) presented secondary infections. Acinetobacter baumannii and Klebsiella pneumoniae were the most frequent isolates (31.1% and 18.9%, respectively), most of them multidrug resistant. Chronic obstructive pulmonary disease had a higher prevalence in patients who developed secondary infections (p = 0.012). Secondary infections were associated with longer stay in the ICU and with higher mortality (p = 0.006 and p = 0.038, respectively). Conclusions: Early identification of secondary infections and proper use of antibiotics are necessary to limit the spread of multidrug-resistant microorganisms in COVID-19 patients admitted in the ICU.

Rapid Molecular Diagnostics of Pneumonia Caused by Gram-Negative Bacteria: A Clinician's Review

With approximately half a billion events per year, lower respiratory tract infections (LRTIs) represent a major challenge for the global public health. Among LRTI cases, those caused by Gram-negative bacteria (GNB) are associated with a poorer prognostic. Standard-of-care etiologic diagnostics is lengthy and difficult to establish, with more than half of cases remaining microbiologically undocumented. Recently, syndromic molecular diagnostic panels became available, enabling simultaneous detection of tens of pathogen-related and antimicrobial-resistance genetic markers within a few hours. In this narrative review, we summarize the available data on the performance of molecular diagnostics in GNB pneumonia, highlighting the main strengths and limitations of these assays, as well as the main factors influencing their clinical utility. We searched MEDLINE and Web of Science databases for relevant English-language articles. Molecular assays have higher analytical sensitivity than cultural methods, and show good agreement with standard-of-care diagnostics regarding detection of respiratory pathogens, including GNB, and identification of frequent patterns of resistance to antibiotics. Clinical trials reported encouraging results on the usefulness of molecular assays in antibiotic stewardship. By providing early information on the presence of pathogens and their probable resistance phenotypes, these assays assist in the choice of targeted therapy, in shortening the time from sample collection to appropriate antimicrobial treatment, and in reducing unnecessary antibiotic use.

Increase in antibiotic resistance in diabetic foot infections among peruvian patients: a single-center cross-sectional study

Background

Diabetic foot is one of the most significant complications in individuals with diabetes and is closely associated with lower limb amputation. The antibiotic susceptibility patterns of these bacterial isolates play a critical role in guiding effective treatment strategies We aimed to determine the most common bacterial agents causing diabetic foot infections in a tertiary-care hospital in Peru.

Methods

Clinical and microbiological data were collected from 181 patients diagnosed with diabetic foot infections and positive microbiological culture results. All the samples were analyzed with the Vitek 2 compact system and the cut-off points were defined with the CLSI M100 guide. The data were segregated based on mono-microbial or poly-microbial cultures, bacterial types, and antibiotic susceptibility profiles.

Results

A total of 32 bacterial species were identified, predominantly Gram-negative (63%). The most frequent bacterial agents isolated were Staphylococcus aureus (19.9%), Escherichia coli (12.2%), Pseudomonas aeruginosa (8.3%), and Proteus vulgaris (6.6%). These bacteria commonly exhibited resistance to Ampicillin, Ciprofloxacin, Levofloxacin, Trimethoprim-sulfamethoxazole, and Cefuroxime. E. coli showed the highest antibiotic resistance (19 antibiotics), while Gentamicin, Tobramycin, and Levofloxacin demonstrated the highest sensitivity against the most prevalent bacteria. Gram-negative bacteria also exhibited notable antibiotic-susceptibility to Meropenem, Piperacillin/tazobactam, and Amikacin. Regarding the presence of Extended-Spectrum Beta-Lactamase, 54 isolates tested positive, with 35 (64.8%) and 14 (42.4%) of these being S. aureus and E. coli.

Conclusions

Bacterial agents causing diabetic foot infections pose a constant concern, particularly due to the increasing antibiotic resistance observed. This difficulty in treating the condition contributes to a higher risk of amputation and mortality. Further research on bacterial susceptibility is necessary to determine appropriate dosages for pharmacological treatment and to prevent the overuse of antibiotics.

Sex differences in coronavirus disease 2019 myocarditis

Myocarditis is frequently caused by viral infections, but animal models that closely resemble human disease suggest that virus-triggered autoimmune disease is the most likely cause of myocarditis. Myocarditis is a rare condition that occurs primarily in men under age 50. The incidence of myocarditis rose at least 15x during the COVID-19 pandemic from 1-10 to 150-400 cases/100,000 individuals, with most cases occurring in men under age 50. COVID-19 vaccination was also associated with rare cases of myocarditis primarily in young men under 50 years of age with an incidence as high as 50 cases/100,000 individuals reported for some mRNA vaccines. Sex differences in the immune response to COVID-19 are virtually identical to the mechanisms known to drive sex differences in myocarditis pre-COVID based on clinical studies and animal models. The many similarities between COVID-19 vaccine-associated myocarditis to COVID-19 myocarditis and non-COVID myocarditis suggest common immune mechanisms drive disease.

COVID-19 and Laboratory Markers from Romanian Patients-A Narrative Review

COVID-19 has significantly impacted the whole world, and Romania was no exception. Biomarkers play a crucial role in understanding and managing the disease. However, research regarding laboratory analyses for patients with COVID-19 is fairly limited. For detection, PCR testing is still considered the golden standard, while antibodies are still useful for monitoring both patients and their vaccination status. In our country, biomarkers such as CRP, LDH, transaminases, cardiac, and iron markers have been used to assess the status of patients and even predict illness outcome. CRP, IL-6, LDH, FER, fibrinogen, creatinine, and vitamin D levels have been associated with increased severity, risk of ICU admission, and death. Cardiac markers and D-dimers are also good predictors, but their role seems more important in patients with complications. HDL cholesterol and BUN levels were also suggested as potential biomarkers. Hematological issues in SARS-CoV-2 infections include neutrophilia, lymphopenia and their ratio, while PCT, which is a marker of bacterial infections, is better to be used in patients with co- or supra-infections. The current research is a narrative review that focuses on the laboratory results of Romanian COVID-19 patients. The goal of this article is to provide an update on the research on biomarkers and other laboratory tests conducted inside the borders of Romania and identify gaps in this regard. Secondly, options for further research are discussed and encouraged.

Fungal Infections Identified with Multiplex PCR in Severe COVID-19 Patients during Six Pandemic Waves

Background and Objectives: With an increasing number of severe COVID-19 cases presenting with secondary fungal infections, this study aimed to determine the prevalence of fungal co-infections in severe COVID-19 patients across the six waves, identify the most common fungal pathogens associated with severe COVID-19, and explore any potential links between patient characteristics, therapeutic strategies, and the prevalence and type of fungal infection. Materials and Methods: A retrospective analysis was conducted on severe COVID-19 patients admitted to the Infectious Diseases and Pulmonology Hospital, "Victor Babes", Romania, between March 2020 and August 2022. Samples were collected from respiratory specimens, blood, and urine, after which a standard nucleic acid extraction protocol was employed. Patients were divided into groups with and without fungal infections, identified using multiplex PCR. The groups were compared based on demographic data, comorbidities, pandemic wave number, and clinical outcomes. Results: Out of 288 patients, 96 (33.3%) had fungal infections, with Candida spp. being the most common. Patients with fungal infections had higher rates of obesity (35.4% vs. 21.4%, p = 0.010) and a higher Charlson comorbidity index (CCI > 2) (37.5% vs 25.0%, p = 0.027). Ventilator use was significantly higher in the fungal infection group (45.8% vs. 18.8%; p < 0.001), as was ICU admission (39.6% vs. 26.6%; p = 0.024) and mortality (32.3% vs 12.0%; p < 0.001). The distribution of different fungal species varied across the pandemic waves, with no statistical significance (p = 0.209). The mortality risk notably increased with the degree of drug resistance (OR for three or more drug resistances = 6.71, p < 0.001). The second, fourth, and fifth pandemic waves were significantly associated with higher mortality risk (OR = 3.72, 3.61, and 4.08, respectively, all p < 0.001). Aspergillus spp. and Mucor spp. infections were significantly associated with increased mortality risk (OR = 4.61 and 6.08, respectively, both p < 0.001). Conclusions: Our study indicates a significant presence of fungal co-infections among severe COVID-19 patients that is associated with increased morbidity and mortality, particularly in patients with drug-resistant infections. These findings underline the necessity for comprehensive diagnostic approaches and tailored treatment strategies in managing COVID-19 patients, especially during specific pandemic waves and in patients with particular fungal infections. Further research is required to understand the implications of these co-infections and their management.

One biomarker does not fit all: tailoring anti-infective therapy through utilization of procalcitonin and other specific biomarkers

INTRODUCTION

Considering the ongoing increase in antibiotic resistance, the importance of judicious use of antibiotics through reduction of exposure is crucial. Adding procalcitonin (PCT) and other biomarkers to pathogen-specific tests may help to further improve antibiotic therapy algorithms and advance antibiotic stewardship programs to achieve these goals.

AREAS COVERED

In recent years, several trials have investigated the inclusion of biomarkers such as PCT into clinical decision-making algorithms. For adult patients, findings demonstrated improvements in the individualization of antibiotic treatment, particularly for patients with respiratory tract infections and sepsis. While most trials were performed in hospitals with central laboratories, point-of-care testing might further advance the field by providing a cost-effective and rapid diagnostic tool in upcoming years. Furthermore, novel biomarkers including CD-64, presepsin, Pancreatic stone and sTREM-1, have all shown promising results for increased accuracy of sepsis diagnosis. Availability of these markers however is currently still limited and there is insufficient evidence for their routine use in clinical care.

EXPERT OPINION

In addition to new host-response markers, combining such biomarkers with pathogen-directed diagnostics present a promising strategy to increase algorithm accuracy in differentiating between bacterial and viral infections. Recent advances in microbiologic testing using PCR or nucleic amplification tests may further improve the diagnostic yield and promote more targeted pathogen-specific antibiotic therapy.

Post-Severe-COVID-19 Cardiopulmonary Rehabilitation: A Comprehensive Study on Patient Features and Recovery Dynamics in Correlation with Workout Intensity

The aftermath of severe COVID-19 frequently involves considerable cardiopulmonary damage, necessitating rehabilitation. This study aimed to evaluate the impact of COVID-19 on cardiopulmonary health and assess the effectiveness of various rehabilitative interventions. Conducted between September 2021 and September 2022, this prospective study included patients who had been diagnosed with severe COVID-19 and admitted at the "Victor Babes" Infectious Diseases and Pulmonology Hospital, Timisoara, Romania. The patients were stratified into low- and high-intensity rehabilitation groups. The rehabilitation protocols were individually tailored, and the patient recovery was closely monitored over a 3-month period. Our cohort comprised 84 patients, with a mean age of 56.3 years for the low-intensity group (n = 42) and 53.1 years for the high-intensity group (n = 42). Both groups showed significant improvements in the lung injury area, need for oxygen supplementation, ejection fraction, systolic pulmonary artery pressure, and forced vital capacity. Additionally, considerable enhancements were observed in maximal voluntary ventilation, FEV1, FEV1/FVC ratio, peak expiratory flow, and forced expiratory flow at 25-75%. The work intensity also demonstrated substantial improvements from the initial testing to the 3-month mark in both groups. This study provides evidence that personalized, targeted rehabilitation strategies can improve long-term cardiopulmonary health in patients recovering from severe COVID-19, proving both low-intensity and high-intensity training as sufficient to improve heart and lung function if performed correctly and over a relatively short duration of 3 months. The study findings underscore the importance of implementing comprehensive cardiopulmonary rehabilitation protocols in the care of post-COVID-19 patients and highlight the value of stratified rehabilitation intensity based on individual patient dynamics and recovery features.