Detection of Viral and Bacterial Respiratory Pathogens Identified by Molecular Methods in COVID-19 Hospitalized Patients and Its Impact on Mortality and Unfavorable Outcomes

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.

Coinfection of SARS-CoV-2 with other respiratory pathogens in outpatients from Ecuador

Worldwide, the COVID-19 pandemic caused by SARS-CoV-2 has enormously impacted healthcare systems, especially in low and middle-income countries. Coinfections with respiratory pathogens in COVID-19 patients may contribute to worse outcomes. This study identified the presence of 12 viral coinfections and pneumococcal carriers among individuals with SARS-CoV-2 infection in outpatient and community settings in Ecuador. From January 2020 to November 2021, 215 nasopharyngeal and nasal swabs were taken from individuals who reported symptoms of COVID-19 or had known exposure to someone with confirmed or suspected COVID-19. One hundred fifty-eight tested positive for SARS-CoV-2 by RT-qPCR and coinfections were detected in 12% (19/158) of SARS-CoV-2-positive patients; the most frequent coinfection was with influenza A virus at 4.4% (7/158; 95% CI: 1.2-7.6), followed by respiratory syncytial virus with 3.1% (5/158; 95% CI: 0.4-5.8), and finally rhinovirus and human coronavirus NL63 with 1.2% (2/158). Pneumococcal carriage was detected in 3.7% (6/158; 95% CI: 0.76-6.64) of SARS-CoV-2 cases. Influenza B, adenovirus, human metapneumovirus (HMPV), parainfluenza virus types 1, 2, and 3, and human coronavirus HKU1 were undetected. To our knowledge, this is the first study of coinfection of SARS-CoV-2 and respiratory pathogens performed on outpatients in Latin America. The high proportion of outpatients with viral coinfections reported in our cohort allows us to suggest that testing for SARS-CoV-2 and other common respiratory pathogens should be carried out to ensure accurate diagnoses, prompt patient treatment, and appropriate isolation.

Using risk factors and markers to predict bacterial respiratory co-/superinfections in COVID-19 patients: is the antibiotic steward's toolbox full or empty?

BACKGROUND

Adequate diagnosis of bacterial respiratory tract co-/superinfection (bRTI) in coronavirus disease (COVID-19) patients is challenging, as there is insufficient knowledge about the role of risk factors and (para)clinical parameters in the identification of bacterial co-/superinfection in the COVID-19 setting. Empirical antibiotic therapy is mainly based on COVID-19 severity and expert opinion, rather than on scientific evidence generated since the start of the pandemic.

PURPOSE

We report the best available evidence regarding the predictive value of risk factors and (para)clinical markers in the diagnosis of bRTI in COVID-19 patients.

METHODS

A multidisciplinary team identified different potential risk factors and (para)clinical predictors of bRTI in COVID-19 and formulated one or two research questions per topic. After a thorough literature search, research gaps were identified, and suggestions concerning further research were formulated. The quality of this narrative review was ensured by following the Scale for the Assessment of Narrative Review Articles.

RESULTS

Taking into account the scarcity of scientific evidence for markers and risk factors of bRTI in COVID-19 patients, to date, COVID-19 severity is the only parameter which can be associated with higher risk of developing bRTI.

CONCLUSIONS

Evidence on the usefulness of risk factors and (para)clinical factors as predictors of bRTI in COVID-19 patients is scarce. Robust studies are needed to optimise antibiotic prescribing and stewardship activities in the context of COVID-19.

Imprinting of nanoparticles in thin films: Quo Vadis?

Nanomaterials, and especially nanoparticles, have been introduced to almost any aspect of our lives. This has caused increasing concern as to their toxicity and adverse effects on the environment and human health. The activity of nanoparticles, including their nanotoxicity, is not only a function of the material they are made of but also their size, shape, and surface properties. It is evident that there is an unmet need for simple approaches to the speciation of nanoparticles, namely to monitor and detect them based on their properties. An appealing method for such speciation involves the imprinting of nanoparticles in soft matrices. The principles of imprinting nanoparticles originate from the molecularly imprinted polymer (MIP) approach. This review summarizes the current status of this emerging field, which bridges between the traditional MIP approach and the imprinting of larger entities such as viruses and bacteria. The concepts of nanoparticle imprinting and the requirement of both physical and chemical matching between the nanoparticles and the matrix are discussed and demonstrated.

COVID-19 and Respiratory Virus Co-Infections: A Systematic Review of the Literature

Τhe COVID-19 pandemic highly impacted the circulation, seasonality, and morbidity burden of several respiratory viruses. We reviewed published cases of SARS-CoV-2 and respiratory virus co-infections as of 12 April 2022. SARS-CoV-2 and influenza co-infections were reported almost exclusively during the first pandemic wave. It is possible that the overall incidence of SARS-CoV-2 co-infections is higher because of the paucity of co-testing for respiratory viruses during the first pandemic waves when mild cases might have been missed. Animal models indicate severe lung pathology and high fatality; nevertheless, the available literature is largely inconclusive regarding the clinical course and prognosis of co-infected patients. Animal models also indicate the importance of considering the sequence timing of each respiratory virus infection; however, there is no such information in reported human cases. Given the differences between 2020 and 2023 in terms of epidemiology and availability of vaccines and specific treatment against COVID-19, it is rational not to extrapolate these early findings to present times. It is expected that the characteristics of SARS-CoV-2 and respiratory virus co-infections will evolve in the upcoming seasons. Multiplex real-time PCR-based assays have been developed in the past two years and should be used to increase diagnostic and infection control capacity, and also for surveillance purposes. Given that COVID-19 and influenza share the same high-risk groups, it is essential that the latter get vaccinated against both viruses. Further studies are needed to elucidate how SARS-CoV-2 and respiratory virus co-infections will be shaped in the upcoming years, in terms of impact and prognosis.

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

Bacterial infection can occur in patients hospitalized with SARS-CoV-2 in various conditions, resulting in poorer outcomes, such as a higher death rate. This current systematic review was conducted in order to assess the efficiency of multiplex PCR in detecting bacterial infections in hospitalized COVID-19 patients, as well as to analyze the most common bacterial pathogens and other factors that interfere with this diagnosis. The research was conducted using four electronic databases (PubMed, Taylor&Francis, Web of Science, and Wiley Online Library). Out of 290 studies, nine were included in the systematic review. The results supported the use of multiplex PCR in detecting bacteria, considering its high sensitivity and specificity rates. The most common bacterial pathogens found were Klebsiella pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae, and Haemophilus influenzae. The median age at admission was 61.5 years, and the majority of patients were men (70.3%), out of a total of 1553 patients. The proportion of ICU admission was very high, with a pooled proportion of 52.6% over the analyzed studies, and an average duration of hospitalization of 13 days. The mortality rate was proportionally high, as was the rate of ICU admission, with a pooled mortality of 24.9%. It was discovered that 65.2% of all patients used antibiotics before admission, with or without medical prescription. Antibiotic treatment should be considered consciously, considering the high risks of developing antibiotic resistance.

Bacterial profiles and their antibiotic resistance background in superinfections caused by multidrug-resistant bacteria among COVID-19 ICU patients from southwest Iran

This study investigated the bacterial causes of superinfections and their antibiotic resistance pattern in severe coronavirus disease 2019 (COVID-19) patients admitted to the intensive care unit (ICU) of Razi Hospital in Ahvaz, southwest Iran. In this cross-sectional study, endotracheal tube (ETT) secretion samples of 77 intubated COVID-19 patients, confirmed by reverse transcription-quantitative polymerase chain reaction, were investigated by standard microbiology test and analytical profile index kit. Antibiotic susceptibility testing was performed by disc diffusion. The presence of Haemophilus influenzae and Mycoplasma pneumoniae was investigated by the polymerase chain reaction (PCR). Using culture and PCR methods, 56 (72.7%) of the 77 COVID-19 patients (mean age of 55 years, 29 male and 27 female) had superinfections. Using culture, 67 isolates including 29 (43.2%) Gram-positive and 38 (56.7%) Gram-negative bacteria (GNB) were identified from 49 COVID-19 patients. The GNB were more predominant than the Gram-positive pathogens. Klebsiella pneumoniae (28.4%, n = 19/67) was the most common isolate followed by Staphylococcus aureus (22.4%, n = 15/67). Using PCR, 10.4% (8/77) and 11.7% (9/77) of ETT secretion specimens had H. influenzae and M. pneumoniae amplicons, respectively. Gram-positive and Gram-negative isolates showed high resistance rates (>70.0%) to majority of the tested antibiotics including fluoroquinolone, carbapenems, and cephalosporins and 68.7% (46/67) of isolates were multidrug-resistant (MDR). This study showed a high frequency rate of superinfections by MDR bacteria among COVID-19 patients in southwest Iran. The prevention of long-term consequences caused by COVID-19, demands continuous antibiotic surveillance particularly in management of bacterial superinfections.

Diagnostic concordance between BioFire® FilmArray® Pneumonia Panel and culture in patients with COVID-19 pneumonia admitted to intensive care units: the experience of the third wave in eight hospitals in Colombia

Background

The detection of coinfections is important to initiate appropriate antimicrobial therapy. Molecular diagnostic testing identifies pathogens at a greater rate than conventional microbiology. We assessed both bacterial coinfections identified via culture or the BioFire® FilmArray® Pneumonia Panel (FA-PNEU) in patients infected with SARS-CoV-2 in the ICU and the concordance between these techniques.

Methods

This was a prospective study of patients with SARS-CoV-2 who were hospitalized for no more than 48 h and on mechanical ventilation for no longer than 24 h in 8 ICUs in Medellín, Colombia. We studied mini-bronchoalveolar lavage or endotracheal aspirate samples processed via conventional culture and the FA-PNEU. Coinfection was defined as the identification of a respiratory pathogen using the FA-PNEU or cultures. Serum samples of leukocytes, C-reactive protein, and procalcitonin were taken on the first day of intubation. We analyzed the empirical antibiotics and the changes in antibiotic management according to the results of the FA-PNEUM and cultures.

Results

Of 110 patients whose samples underwent both methods, FA-PNEU- and culture-positive samples comprised 24.54% versus 17.27%, respectively. Eighteen samples were positive in both techniques, 82 were negative, 1 was culture-positive with a negative FA-PNEU result, and 9 were FA-PNEU-positive with negative culture. The two bacteria most frequently detected by the FA-PNEU were Staphylococcus aureus (37.5%) and Streptococcus agalactiae (20%), and those detected by culture were Staphylococcus aureus (34.78%) and Klebsiella pneumoniae (26.08%). The overall concordance was 90.1%, and when stratified by microorganism, it was between 92.7 and 100%. The positive predictive value (PPV) was between 50 and 100% and were lower for Enterobacter cloacae and Staphylococcus aureus. The negative predictive value (NPV) was high (between 99.1 and 100%); MecA/C/MREJ had a specificity of 94.55% and an NPV of 100%. The inflammatory response tests showed no significant differences between patients whose samples were positive and negative for both techniques. Sixty-one patients (55.45%) received at least one dose of empirical antibiotics.

Conclusions

The overall concordance was 90.1%, and it was between 92.7% and 100% when stratified by microorganisms. The positive predictive value was between 50 and 100%, with a very high NPV.

Methicillin-resistant Staphylococcus aureus lung infection in coronavirus disease 2019: how common?

PURPOSE OF REVIEW

Some patients with coronavirus disease 2019 (COVID-19) may develop pulmonary bacterial coinfection or superinfection, that could unfavorably impact their prognosis.

RECENT FINDINGS

The exact burden of methicillin-resistant Staphylococcus aureus (MRSA) lung infection in peculiar populations such as patients with COVID-19 remains somewhat elusive, possibly because of wide heterogeneity in methods and endpoints across studies.

SUMMARY

There was important heterogeneity in the retrieved literature on the epidemiology of MRSA lung infection in patients with COVID-19, both when considering all other bacteria as the denominator (relative prevalence ranging from 2% to 29%) and when considering only S. aureus as the denominator (relative prevalence ranging from 11% to 65%). Overall, MRSA is among the most frequent causative agents of pulmonary infection in patients with COVID-19. Improving our ability to rapidly reach etiological diagnosis of bacterial lung infection in COVID-19 patients remains fundamental if we are to improve the rates of appropriate antibiotic therapy in patients with COVID-19 and concomitant/superimposed MRSA infection, at the same time avoiding antibiotic overuse in line with antimicrobial stewardship principles.

Epidemiology and Drug Resistance of Neonatal Bloodstream Infection Pathogens in East China Children's Medical Center From 2016 to 2020

Introduction

To analyze the pathogen distribution and drug resistance of newborns with bloodstream infection (BSI) to help clinicians choose the appropriate empirical antibiotic therapy for clinical infection control.

Methods

A total of 707 neonatal BSI cases were retrospectively analyzed. The bacteria in blood culture-positive samples were cultured, identified, and analyzed for drug sensitivity by routine methods. Statistical software was used to compare and analyze the basic data, pathogenic information, and drug resistance of the main bacteria.

Results

The 5-year average positive rate of neonatal blood culture was 2.50%. The number of specimens submitted for inspection in 2020 significantly decreased. The top five infectious pathogens with the highest proportion were coagulase-negative Staphylococcus (67.35%), of which Staphylococcus epidermidis had the highest proportion (31.26%), followed by Escherichia coli (12.87%), Klebsiella pneumoniae (9.05%), Streptococcus agalactiae (8.63%), and Staphylococcus aureus (3.25%). Gram-positive (G+) bacteria were dominant, accounting for 69.45%. The main G+ bacteria had a higher rate of resistance to erythromycin and penicillin G. The main Gram-negative (G-) bacteria had a high resistance rate to a variety of antibacterial drugs, especially cephalosporin antibiotics. The overall resistance of K. pneumoniae was higher than that of E. coli. The top two fungi detected were Candida parapsilosis and Candida albicans. C. parapsilosis did not appear to be resistant to antibiotics, while C. albicans was resistant to multiple antibiotics. The type of microbial infection had a statistically significant difference in the positive rate among the age at delivery and wards (p < 0.05). There were significant differences in the detection of fungi among these groups (p < 0.05). The positive rate of G+ bacteria in the term newborns was significantly higher than that in the preterm newborns (p < 0.05). Preterm newborns are more susceptible to pneumonia.

Conclusion

G+ bacteria are the main pathogens of neonatal BSI. Preterm newborns are more likely to be infected with G- bacteria. E. coli and K. pneumoniae are the most common G- bacteria, and both have a high resistance rate to a variety of antibacterial drugs. According to the distribution characteristics and drug resistance, it is very important to select antibiotics reasonably.

SARS-CoV-2-Legionella Co-Infections: A Systematic Review and Meta-Analysis (2020-2021)

Legionnaires' Disease (LD) is a severe, sometimes fatal interstitial pneumonia due to Legionella pneumophila. Since the inception of the SARS-CoV-2 pandemic, some contradictory reports about the effects of lockdown measures on its epidemiology have been published, but no summary evidence has been collected to date. Therefore, we searched two different databases (PubMed and EMBASE) focusing on studies that reported the occurrence of LD among SARS-CoV-2 cases. Data were extracted using a standardized assessment form, and the results of such analyses were systematically reported, summarized, and compared. We identified a total of 38 articles, including 27 observational studies (either prospective or retrospective ones), 10 case reports, and 1 case series. Overall, data on 10,936 SARS-CoV-2 cases were included in the analyses. Of them, 5035 (46.0%) were tested for Legionella either through urinary antigen test or PCR, with 18 positive cases (0.4%). A pooled prevalence of 0.288% (95% Confidence Interval (95% CI) 0.129-0.641), was eventually calculated. Moreover, detailed data on 19 co-infections LD + SARS-CoV-2 were obtained (males: 84.2%; mean age: 61.9 years, range 35 to 83; 78.9% with 1 or more underlying comorbidities), including 16 (84.2%) admissions to the ICU, with a Case Fatality Ratio of 26.3%. In summary, our analyses suggest that the occurrence of SARS-CoV-2-Legionella infections may represent a relatively rare but not irrelevant event, and incident cases are characterized by a dismal prognosis.

Current pharmacotherapy for methicillin-resistant Staphylococcus aureus (MRSA) pneumonia

INTRODUCTION

Currently, several antibiotics are active against methicillin-resistant Staphylococcus aureus (MRSA) and can be used for the treatment of pneumonia. They show great variability in terms of antibiotic class, indication, pharmacodynamic/pharmacokinetic properties, type of available formulations, spectrum of activity against bacteria other than MRSA, and toxicity profile.

AREAS COVERED

In this narrative review, the authors discuss the characteristics of currently available agents for the treatment of MRSA pneumonia.

EXPERT OPINION

The availability of different agents with anti-MRSA activity, and approved for the treatment of pneumonia can allow a personalized approach for any given patient based on the severity of the disease, the setting of occurrence, the patient's baseline risk of toxicity and drug interactions, and the possibility of oral therapy whenever early discharge or outpatient treatment are possible. Although some gray areas still remain, like the lack of high certainty evidence on the efficacy of some old agents and on the precise role of companion agents with toxin inhibitory activity in the case of necrotizing pneumonia, the frequent availability of different treatment choices, each with peculiar characteristics, is already allowing an important step toward a precision medicine approach for the treatment of MRSA pneumonia.