Coinfections in Patients Hospitalized with COVID-19: A Descriptive Study from the United Arab Emirates

The laboratory investigation, management, and infection prevention and control of Candida auris: a narrative review to inform the 2024 national guidance update in England

The emergent fungal pathogen Candida auris is increasingly recognised as an important cause of healthcare-associated infections globally. It is highly transmissible, adaptable, and persistent, resulting in an organism with significant outbreak potential that risks devastating consequences. Progress in the ability to identify C. auris in clinical specimens is encouraging, but laboratory diagnostic capacity and surveillance systems are lacking in many countries. Intrinsic resistance to commonly used antifungals, combined with the ability to rapidly acquire resistance to therapy, substantially restricts treatment options and novel agents are desperately needed. Despite this, outbreaks can be interrupted, and mortality avoided or minimised, through the application of rigorous infection prevention and control measures with an increasing evidence base. This review provides an update on epidemiology, the impact of the COVID-19 pandemic, risk factors, identification and typing, resistance profiles, treatment, detection of colonisation, and infection prevention and control measures for C. auris. This review has informed a planned 2024 update to the United Kingdom Health Security Agency (UKHSA) guidance on the laboratory investigation, management, and infection prevention and control of Candida auris. A multidisciplinary response is needed to control C. auris transmission in a healthcare setting and should emphasise outbreak preparedness and response, rapid contact tracing and isolation or cohorting of patients and staff, strict hand hygiene and other infection prevention and control measures, dedicated or single-use equipment, appropriate disinfection, and effective communication concerning patient transfers and discharge.

Candida auris Outbreaks: Current Status and Future Perspectives

Candida auris has been identified by the World Health Organization (WHO) as a critical priority pathogen on its latest list of fungi. C. auris infections are reported in the bloodstream and less commonly in the cerebrospinal fluid and abdomen, with mortality rates that range between 30% and 72%. However, no large-scale epidemiology studies have been reported until now. The diagnosis of C. auris infections can be challenging, particularly when employing conventional techniques. This can impede the early detection of outbreaks and the implementation of appropriate control measures. The yeast can easily spread between patients and in healthcare settings through contaminated environments or equipment, where it can survive for extended periods. Therefore, it would be desirable to screen patients for C. auris colonisation. This would allow facilities to identify patients with the disease and take appropriate prevention and control measures. It is frequently unsusceptible to drugs, with varying patterns of resistance observed among clades and geographical regions. This review provides updates on C. auris, including epidemiology, clinical characteristics, genomic analysis, evolution, colonisation, infection, identification, resistance profiles, therapeutic options, prevention, and control.

Methicillin resistant Staphylococcus aureus in the United Arab Emirates: a 12-year retrospective analysis of evolving trends

Introduction

Methicillin resistant Staphylococcus aureus (MRSA) is a major contributor to the global burden of antimicrobial resistance (AMR). As MRSA continues to evolve, the need for continued surveillance to evaluate trends remains crucial. This study was carried out to assess MRSA trends in the United Arab Emirates (UAE) based on analysis of data from the national AMR surveillance program.

Methods

We carried out a 12-year (2010-2021) retrospective analysis of MRSA demographic and microbiological data collected as part of the UAE national AMR surveillance program. Participating centers from across the country routinely submit AMR surveillance data collected by trained personnel to the National AMR Surveillance Committee, where data is analyzed using a unified WHONET platform. Data on non-duplicate isolates associated with clinical infections were obtained and included in the analysis.

Results

A total of 29,414 non-duplicate MRSA isolates associated with clinical infections were reported between 2010 and 2021 (2010: n = 259; 2021: n = 4,996). MRSA represented 26.4% of all S. aureus (n = 111,623) isolates identified during the study period. In 2010, among the S. aureus isolates with reported oxacillin testing, 21.9% (n/N = 259/1,181) were identified as MRSA and this showed an increase to 33.5% (n/N = 4,996/14,925) in 2021. Although there was variation in the distribution of MRSA across the seven emirates of the country, most had an upward trend. Patient demographics reflected a male preponderance, with most being adults and from the outpatient setting. Isolates were mostly from skin and soft tissue infection specimens (72.5%; n/N = 21,335/29,414). Among the inpatients (N = 8,282), a total of 3,313 MRSA isolates were from specimens obtained ≤ 48 h after admission indicative of community acquired infection. Increasing resistance trends were observed for most antibiotics including ciprofloxacin, levofloxacin, moxifloxacin, erythromycin, gentamicin, trimethoprim-sulfamethoxazole, and quinupristin/dalfopristin. Low levels of resistance (0.0-0.8%) were sustained for linezolid except for 2015, 2016, and 2017 with 2.5, 2.6, and 2.9%, respectively. No confirmed vancomycin resistance was reported.

Conclusion

The increasing trend of MRSA isolates associated with clinical infections in the hospital and community settings is a concern. Continued monitoring including incorporation of genomic surveillance and infection control measures are recommended to stem the dissemination.

Coinfection and superinfection in ICU critically ill patients with severe COVID-19 pneumonia and influenza pneumonia: are the pictures different?

Background

Similar to influenza, coinfections and superinfections are common and might result in poor prognosis. Our study aimed to compare the characteristics and risks of coinfections and superinfections in severe COVID-19 and influenza virus pneumonia.

Methods

The data of patients with COVID-19 and influenza admitted to the intensive care unit (ICU) were retrospectively analyzed. The primary outcome was to describe the prevalence and pathogenic distribution of coinfections/ICU-acquired superinfections in the study population. The secondary outcome was to evaluate the independent risk factors for coinfections/ICU-acquired superinfections at ICU admission. Multivariate analysis of survivors and non-survivors was performed to investigate whether coinfections/ICU-acquired superinfections was an independent prognostic factor.

Results

In the COVID-19 (n = 123) and influenza (n = 145) cohorts, the incidence of coinfections/ICU-acquired superinfections was 33.3%/43.9 and 35.2%/52.4%, respectively. The most common bacteria identified in coinfection cases were Enterococcus faecium, Pseudomonas aeruginosa, and Acinetobacter baumannii (COVID-19 cohort) and A. baumannii, P. aeruginosa, and Klebsiella pneumoniae (influenza cohort). A significant higher proportion of coinfection events was sustained by Aspergillus spp. [(22/123, 17.9% in COVID-19) and (18/145, 12.4% in influenza)]. The COVID-19 group had more cases of ICU-acquired A. baumannii, Corynebacterium striatum and K. pneumoniae. A. baumannii, P. aeruginosa, and K. pneumoniae were the three most prevalent pathogens in the influenza cases with ICU-acquired superinfections. Patients with APACHE II ≥18, CD8+ T cells ≤90/μL, and 50 < age ≤ 70 years were more susceptible to coinfections; while those with CD8+ T cells ≤90/μL, CRP ≥120 mg/L, IL-8 ≥ 20 pg./mL, blood glucose ≥10 mmol/L, hypertension, and smoking might had a higher risk of ICU-acquired superinfections in the COVID-19 group. ICU-acquired superinfection, corticosteroid administration for COVID-19 treatment before ICU admission, and SOFA score ≥ 7 were independent prognostic factors in patients with COVID-19.

Conclusion

Patients with COVID-19 or influenza had a high incidence of coinfections and ICU-acquired superinfections. The represent agents of coinfection in ICU patients were different from those in the general ward. These high-risk patients should be closely monitored and empirically treated with effective antibiotics according to the pathogen.

Prevalence of secondary infections and association with mortality rates of hospitalized COVID-19 patients

BACKGROUND

ICU and other patients hospitalized with corona-virus disease 2019 (COVID-19) are more susceptible to secondary infections. Undetected secondary infections tend to have a severe clinical impact, associated with prolonged hospitalization and higher rates of inpatient mortality.

OBJECTIVES

Estimate the prevalence of secondary infections, determine the frequency of microbial species detected at different body sites, and measure the association between secondary infections and outcomes among hospitalized COVID-19 patients.

DESIGN

Cross-sectional analytical study.

SETTING

Tertiary care center in Riyadh PATIENTS AND METHODS: Data were collected through retrospective chart review of hospitalized COVID-19 patients >18 years old from March 2020 until May 2022 at King Saud University Medical City (27 months). Rates of secondary infections among hospitalized COVID-19 patients were described and data on clinical outcomes (intensive care admission, invasive management procedures and mortality) was collected.

MAIN OUTCOME MEASURES

Features and rates of infection and mortality.

SAMPLE SIZE

260 RESULTS: In total, 24.2% of the study population had secondary infections. However, only 68.8% of patients had secondary infection testing, from which 35.2% had a confirmed secondary infection. These patients had a significantly higher prevalence of diabetes mellitus (P<.0001) and cardiovascular diseases (P=.001). The odds of ICU admissions (63.3%) among secondarily infected patients was 8.4 times higher compared to patients with only COVID-19 infection (17.3%). Secondarily infected patients were more likely to receive invasive procedures (OR=5.068) and had a longer duration of hospital stay compared to COVID-19 only patients. Overall mortality was 16.2%, with a predominantly higher proportion among those secondarily infected (47.6% vs 6.1%) (OR=14.015). Bacteria were the most commonly isolated organisms, primarily from blood (23.3%), followed by fungal isolates, which were mostly detected in urine (17.2%). The most detected organism was Candida albicans (17.2%), followed by Escherichia coli (9.2%), Klebsiella pneumoniae (9.2%) and Pseudomonas aeruginosa (9.2%).

CONCLUSION

Secondary infections were prevalent among hospitalized COVID-19 patients. Secondarily infected patients had longer hospital stay, higher odds of ICU admission, mortality, and invasive procedures.

LIMITATION

Single-center study, retrospective design and small sample size.

CONFLICT OF INTEREST

None.

Investigation of antimicrobial resistance patterns and molecular typing of Pseudomonas aeruginosa isolates among Coronavirus disease-19 patients

BACKGROUND

Pseudomonas aeruginosa is a common co-infecting pathogen recognized among COVID-19 patients. We aimed to investigate the antimicrobial resistance patterns and molecular typing of Pseudomonas aeruginosa isolates among Coronavirus disease-19 patients.

METHODS

Between December 2020 and July 2021, 15 Pseudomonas aeruginosa were isolated from COVID-19 patients in the intensive care unit at Sina Hospital in Hamadan, west of Iran. The antimicrobial resistance of the isolates was determined by disk diffusion and broth microdilution methods. The double-disk synergy method, Modified Hodge test, and polymerase chain reaction were utilized to detect Pseudomonas aeruginosa extended spectrum beta-lactamase and carbapenemase producers. Microtiter plate assay was performed to evaluate the biofilm formation ability of the isolates. The isolates phylogenetic relatedness was revealed using the multilocus variable-number tandem-repeat analysis method.

RESULTS

The results showed Pseudomonas aeruginosa isolates had the most elevated resistance to imipenem (93.3%), trimethoprim-sulfamethoxazole (93.3%), ceftriaxone (80%), ceftazidime (80%), gentamicin (60%), levofloxacin (60%), ciprofloxacin (60%), and cefepime (60%). In the broth microdilution method, 100%, 100%, 20%, and 13.3% of isolates showed resistance to imipenem, meropenem, polymyxin B, and colistin, respectively. Ten (66.6%) isolates were identified as multiple drug resistance. Carbapenemase enzymes and extended spectrum beta-lactamases were identified in 66.6% and 20% of the isolates, respectively and the biofilm formation was detected in 100% of the isolates. The blaOXA-48, blaTEM, blaIMP, blaSPM, blaPER, blaVEB, blaNDM, blaSHV, and blaCTX-M genes were detected in 100%, 86.6%, 86.6%, 40%, 20%, 20%, 13.3%, 6.6%, and 6.6% of the isolates, respectively. The blaVIM, blaGIM, blaGES, and blaMCR-1 genes were not identified in any of the isolates. The MLVA typing technique showed 11 types and seven main clusters and most isolates belong to cluster I, V and VII.

CONCLUSION

Due to the high rate of antimicrobial resistance, as well as the genetic diversity of Pseudomonas aeruginosa isolates from COVID-19 patients, it is indispensable to monitor the antimicrobial resistance pattern and epidemiology of the isolates on a regular basis.

Antimicrobial resistance in patients with COVID-19: a systematic review and meta-analysis

BACKGROUND

Frequent use of antibiotics in patients with COVID-19 threatens to exacerbate antimicrobial resistance. We aimed to establish the prevalence and predictors of bacterial infections and antimicrobial resistance in patients with COVID-19.

METHODS

We did a systematic review and meta-analysis of studies of bacterial co-infections (identified within ≤48 h of presentation) and secondary infections (>48 h after presentation) in outpatients or hospitalised patients with COVID-19. We searched the WHO COVID-19 Research Database to identify cohort studies, case series, case-control trials, and randomised controlled trials with populations of at least 50 patients published in any language between Jan 1, 2019, and Dec 1, 2021. Reviews, editorials, letters, pre-prints, and conference proceedings were excluded, as were studies in which bacterial infection was not microbiologically confirmed (or confirmed via nasopharyngeal swab only). We screened titles and abstracts of papers identified by our search, and then assessed the full text of potentially relevant articles. We reported the pooled prevalence of bacterial infections and antimicrobial resistance by doing a random-effects meta-analysis and meta-regression. Our primary outcomes were the prevalence of bacterial co-infection and secondary infection, and the prevalence of antibiotic-resistant pathogens among patients with laboratory-confirmed COVID-19 and bacterial infections. The study protocol was registered with PROSPERO (CRD42021297344).

FINDINGS

We included 148 studies of 362  976 patients, which were done between December, 2019, and May, 2021. The prevalence of bacterial co-infection was 5·3% (95% CI 3·8-7·4), whereas the prevalence of secondary bacterial infection was 18·4% (14·0-23·7). 42 (28%) studies included comprehensive data for the prevalence of antimicrobial resistance among bacterial infections. Among people with bacterial infections, the proportion of infections that were resistant to antimicrobials was 60·8% (95% CI 38·6-79·3), and the proportion of isolates that were resistant was 37·5% (26·9-49·5). Heterogeneity in the reported prevalence of antimicrobial resistance in organisms was substantial (I2=95%).

INTERPRETATION

Although infrequently assessed, antimicrobial resistance is highly prevalent in patients with COVID-19 and bacterial infections. Future research and surveillance assessing the effect of COVID-19 on antimicrobial resistance at the patient and population level are urgently needed.

FUNDING

WHO.

SMART: A Swing-Assisted Multiplexed Analyzer for Point-of-Care Respiratory Tract Infection Testing

Respiratory tract infections such as the ongoing coronavirus disease 2019 (COVID-19) has seriously threatened public health in the last decades. The experience of fighting against the epidemic highlights the importance of user-friendly and accessible point-of-care systems for nucleic acid (NA) detection. To realize low-cost and multiplexed point-of-care NA detection, a swing-assisted multiplexed analyzer for point-of-care respiratory tract infection testing (SMART) was proposed to detect multiple respiratory tract pathogens using visible loop-mediated isothermal amplification. By performing hand-swing movements to generate acceleration force to distribute samples into reaction chambers, the design of the SMART system was greatly simplified. By using different format of chips and integrating into a suitcase, this system can be applied to on-site multitarget and multi-sample testing. Three targets including the N and Orf genes of SARS-CoV-2 and the internal control were simultaneously analyzed (limit of detection: 2000 copies/mL for raw sample; 200 copies/mL for extracted sample). Twenty-three clinical samples with eight types of respiratory bacteria and twelve COVID-19 clinical samples were successfully detected. These results indicate that the SMART system has the potential to be further developed as a versatile tool in the diagnosis of respiratory tract infection.

The Epidemiological Pattern, Resistance Characteristics and Clinical Outcome of Enterobacter cloacae: Recent Updates and Impact of COVID-19 Pandemic

OBJECTIVES

E. cloacae is an opportunistic organism that causes serious infections, particularly in immuno-compromised and hospitalized patients, along with the emergence of resistance traits. The COVID-19 pandemic has impacted the epidemiological pattern and resistance traits of E. cloacae infections as well as those of other bacteria. The study aims to assess the epidemiological patterns, resistance characteristics and clinical outcomes of E. cloacae in Saudi Arabia and the impact of the COVID-19 pandemic.

METHODS

King Fahad Medical City in Riyadh provided the data between January 2019 and December 2021 for the retrospective study of 638 isolates of E. cloacae. The clinical outcome of an E. cloacae infection was also determined by collecting and statistically analyzing the clinical records of 153 ICU patients.

RESULTS

The total percentage of resistant E. cloacae isolates decreased from 48.36% in 2019 to 38% in 2020 and 37.6% in 2021. The overall mortality rate among ICU patients was 40.5%, with an adult age group having a substantial relative risk value of 1.37.

CONCLUSION

E. cloacae is a prevalent nosocomial infection in which adult age is a significant risk factor for mortality. Moreover, this study emphasizes the importance of comparing E. cloacae resistance trends before and throughout the pandemic period in order to better understand the bacteria's behaviour.

Bacterial coinfection and antibiotic resistance in hospitalized COVID-19 patients: a systematic review and meta-analysis

Background

There were a few studies on bacterial coinfection in hospitalized COVID-19 patients worldwide. This systematic review aimed to provide the pooled prevalence of bacterial coinfection from published studies from 2020 to 2022.

Methods

Three databases were used to search the studies, and 49 studies from 2,451 identified studies involving 212,605 COVID-19 patients were included in this review.

Results

The random-effects inverse-variance model determined that the pooled prevalence of bacterial coinfection in hospitalized COVID-19 patients was 26.84% (95% CI [23.85-29.83]). The pooled prevalence of isolated bacteria for Acinetobacter baumannii was 23.25% (95% CI [19.27-27.24]), Escherichia coli was 10.51% (95% CI [8.90-12.12]), Klebsiella pneumoniae was 15.24% (95% CI [7.84-22.64]), Pseudomonas aeruginosa was 11.09% (95% CI [8.92-13.27]) and Staphylococcus aureus (11.59% (95% CI [9.71-13.46])). Meanwhile, the pooled prevalence of antibiotic-resistant bacteria for extended-spectrum beta-lactamases producing Enterobacteriaceae was 15.24% (95% CI [7.84-22.64]) followed by carbapenem-resistant Acinetobacter baumannii (14.55% (95% CI [9.59-19.52%])), carbapenem-resistant Pseudomonas aeruginosa (6.95% (95% CI [2.61-11.29])), methicillin-resistant Staphylococcus aureus (5.05% (95% CI [3.49-6.60])), carbapenem-resistant Enterobacteriaceae (4.95% (95% CI [3.10-6.79])), and vancomycin-resistant Enterococcus (1.26% (95% CI [0.46-2.05])).

Conclusion

All the prevalences were considered as low. However, effective management and prevention of the infection should be considered since these coinfections have a bad impact on the morbidity and mortality of patients.

Essential Fitness Repertoire of Staphylococcus aureus during Co-infection with Acinetobacter baumannii In Vivo

Staphylococcus aureus represents a major human pathogen that is frequently involved in polymicrobial infections. However, the prevalence and role of co-infectious microbes on the pathogenesis and fitness essentiality of S. aureus in vivo remain largely unknown. In this study, we firstly performed a retrospective surveillance of 760 clinical samples and revealed a notable predominance of co-infection with S. aureus and Acinetobacter baumannii. The high-density S. aureus transposon mutant library coupled to transposon insertion sequencing (Tn-Seq) further identified a core set of genes enriched in metabolism of inorganic ions, amino acids, and carbohydrates, which are essential for infection and tissue colonization of S. aureus in the murine systemic infection model. Notably, we revealed a differential requirement of fitness factors for S. aureus in tissue-specific (liver and kidney) and infection-type-specific manner (mono- and co-infection). Co-infection with A. baumannii dramatically altered the fitness requirements of S. aureus in vivo; 49% of the mono-infection fitness genes in S. aureus strain Newman were converted to non-essential, and the functionality of ATP-binding cassette (ABC) transporters was significantly elicited during co-infection. Furthermore, the number of genes essential during co-infection (503) outnumbers the genes essential during mono-infection (362). In addition, the roles of 3 infection-type-specific genes in S. aureus during mono-infection or co-infection with A. baumannii were validated with competitive experiments in vivo. Our data indicated a high incidence and clinical relevance of S. aureus and A. baumannii co-infection, and provided novel insights into establishing antimicrobial regimens to control co-infections. IMPORTANCE Polymicrobial infections are widespread in clinical settings, which potentially correlate with increased infection severity and poor clinical outcomes. Staphylococcus aureus is a formidable human pathogen that causes a variety of diseases in polymicrobial nature. Co-infection and interaction of S. aureus have been described with limited pathogens, mainly including Pseudomonas aeruginosa, Candida albicans, and influenza A virus. Thus far, the prevalence and role of co-infectious microbes on the pathogenesis and fitness essentiality of S. aureus in vivo remain largely unknown. Understanding the polymicrobial composition and interaction, from a community and genome-wide perspective, is thus crucial to shed light on S. aureus pathogenesis strategy. Here, our findings demonstrated, for the first time, that a high incidence rate and clinical relevance of co-infection was caused by S. aureus and Acinetobacter baumannii, illustrating the importance of polymicrobial nature in investigating S. aureus pathogenesis. The infection-type-specific genes likely serve as potential therapeutic targets to control S. aureus infections, either in mono- or co-infection situation, providing novel insights into the development of antimicrobial regimens to control co-infections.

Bacterial co-infections and antimicrobial resistance associated with the Coronavirus Disease 2019 infection

Bacterial co-infections are typically associated with viral respiratory tract infections and pose a significant public health problem around the world. COVID-19 infection damages tissues lining the respiratory track and regulates immune cells/cytokines leading to microbiome dysbiosis and facilitating the area to be colonized by pathogenic bacterial agents. There have been reports of different types of bacterial co-infection in COVID-19 patients. Some of these reports showed despite geographical differences and differences in hospital settings, bacterial co-infections are a major cause of morbidity and mortality in COVID-19 patients. The inappropriate use of antibiotics for bacterial infections, particularly broad-spectrum antibiotics, can also further complicate the infection process, often leading to multi drug resistance, clinical deterioration, poor prognosis, and eventually death. To this end, researchers must establish a new therapeutic approach to control SARS-CoV-2 and the associated microbial coinfections. Hence, the aim of this review is to highlight the bacterial co-infection that has been recorded in COVID-19 patients and the status of antimicrobial resistance associated with the dual infections.

The Menace of Candida auris Epidemic Amidst the COVID-19 Pandemic: A Systematic Review

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the causative agent for the Coronavirus Disease 2019 (COVID-19) pandemic, has sparked a medical emergency worldwide. With the rise in COVID-19 infections and an eventual increase in hospitalized critically ill patients, a trend of bacterial, fungal, and viral superinfection has been noted. One important agent of co-infection identified is Candida auris. Due to its multidrug-resistant nature and easy transmissibility, C. auris is difficult to manage in COVID-positive patients. Patients with comorbidities, immunosuppressive states, intubated and on ventilators are more likely to contract the fungal infection. Therefore, it is essential to the first screen, diagnose, and isolate patients with C. auris infection and manage and treat them while preventing the spread of the disease. Failure to recognize and prevent its spread may lead to an eventual epidemic or even a pandemic during the current COVID-pandemic, which the exhausted healthcare system can most definitely not handle. This systematic review investigates the prevalence of C. auris, its pathophysiology, diagnosis, prevention, and treatment during the COVID-19 pandemic.

Fungal Infection in Co-infected Patients With COVID-19: An Overview of Case Reports/Case Series and Systematic Review

Fungal co-infections are frequent in patients with coronavirus disease 2019 (COVID-19) and can affect patient outcomes and hamper therapeutic efforts. Nonetheless, few studies have investigated fungal co-infections in this population. This study was performed to assess the rate of fungal co-infection in patients with COVID-19 as a systematic review. EMBASE, MEDLINE, and Web of Science were searched considering broad-based search criteria associated with COVID-19 and fungal co-infection. We included case reports and case series studies, published in the English language from January 1, 2020 to November 30, 2021, that reported clinical features, diagnosis, and outcomes of fungal co-infection in patients with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Totally, 54 case reports and 17 case series were identified, and 181 patients (132 men, 47 women, and 2 not mentioned) co-infected with COVID-19 and fungal infection enrolled. The frequency of fungal co-infection among patients with COVID-19 was 49.7, 23.2, 19.8, 6.6, and 0.5% in Asia, America, Europe, Africa, and Australia, respectively. Diabetes (59.6%) and hypertension (35.9%) were found as the most considered comorbidities in COVID-19 patients with fungal infections. These patients mainly suffered from fever (40.8%), cough (30.3%), and dyspnea (23.7%). The most frequent findings in the laboratory results of patients and increase in C-reactive protein (CRP) (33.1%) and ferritin (18.2%), and lymphopenia (16%) were reported. The most common etiological agents of fungal infections were Aspergillus spp., Mucor spp., Rhizopus spp., and Candida spp. reported in study patients. The mortality rate was 54.6%, and the rate of discharged patients was 45.3%. Remdesivir and voriconazole were the most commonly used antiviral and antifungal agents for the treatment of patients. The global prevalence of COVID-19-related deaths is 6.6%. Our results showed that 54.6% of COVID-19 patients with fungal co-infections died. Thus, this study indicated that fungal co-infection and COVID-19 could increase mortality. Targeted policies should be considered to address this raised risk in the current pandemic. In addition, fungal infections are sometimes diagnosed late in patients with COVID-19, and the severity of the disease worsens, especially in patients with underlying conditions. Therefore, patients with fungal infections should be screened regularly during the COVID-19 pandemic to prevent the spread of the COVID-19 patients with fungal co-infection.

Global Prevalence and Subgroup Analyses of Coronavirus Disease (COVID-19) Associated Candida auris infections (CACa): A Systematic Review and Meta-Analysis

Background

Increased hospitalisation rates in the Coronavirus disease 19 (COVID‐19) era lead to a new wave of hospital‐acquired infections such as emerging multidrug‐resistant Candida auris. We aimed to evaluate and estimate the global prevalence of coronavirus‐associated C. auris infection (CACa).

Methods

We searched related databases between December 2019 and April 2022 for studies that reported data about CACa. Meta‐analysis was performed using MedCalc software version 20.104 according to the DerSimonian and Laird method applying the random‐effects model. We evaluated heterogeneity using the χ²‐based Q statistic (significant for p‐value < .1) and the I² statistic (>75% indicative of ‘notable’ heterogeneity). Moreover, if possible, an odds ratio (OR) analysis was performed for eligible data.

Results

Our meta‐analysis includes ten eligible studies, including 1942 patients hospitalised with COVID‐19; 129 were C. auris cases. The overall pooled prevalence of CACa was estimated at 5.7%. The mortality rate of CACa was estimated at 67.849%. Hypertension was the most prevalent comorbidity (59.374%), followed by diabetes mellitus (52.898%) and cardiovascular diseases (31.392%). Men with a prevalence rate of 80.012% were 3.27 (OR) times more prone to getting infected by C. auris.

Conclusion

We concluded that the prevalence of C. auris infections decreased during the COVID‐19 pandemic and the prevalence gradient changed from Asia to America. Unfortunately, there are many descriptive studies with duplicate content in the field of epidemiology of C. auris infections which are increasing every day. We suggest further non‐descriptive studies to accurately establish the cause‐and‐effect relationships between C. auris and COVID‐19 infections.

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.

Bacterial and fungal co-infection is a major barrier in COVID-19 patients: A specific management and therapeutic strategy is required

Microbial co-infections are another primary concern in patients with coronavirus disease 2019 (COVID-19), yet it is an untouched area among researchers. Preliminary data and systematic reviews only show the type of pathogens responsible for that, but its pathophysiology is still unknown. Studies show that these microbial co-infections are hospital-acquired/nosocomial infections, and patients admitted to intensive care units with invasive mechanical ventilation are highly susceptible to it. Patients with COVID-19 had elevated inflammatory cytokines and a weakened cell-mediated immune response, with lower CD4⁺ T and CD8⁺ T cell counts, indicating vulnerability to various co-infections. Despite this, there are only a few studies that recommend the management of co-infections.

The Collateral Effects of COVID-19 Pandemic on the Status of Carbapenemase-Producing Pathogens

The serious challenge of antimicrobial resistance continues to threaten public health and lingers in the era of the coronavirus disease 2019 (COVID-19), declared pandemic by the World Health Organization. While the pandemic has triggered the importance of infection control practices and preventive measures such as physical distancing, hand hygiene, travel reduction and quarantine, the ongoing alarm of antimicrobial resistance seems to accompany the pandemic too. Antimicrobial resistance has been fostered during COVID-19, possibly due to high rate of empirical antibiotic utilization in COVID-19 patients, increased use of biocides, and the disruption of proper healthcare for other conditions. Specifically, carbapenemase-producing Gram-negative bacteria have shown to cause secondary bacterial infections in patients hospitalized for COVID-19. Clinical and microbiological evidence of such infections is accumulating in different parts of the world. With the resilient nature of carbapenemases, their association with mortality, and the limited treatment options available, concerns regarding this group of antibiotic-hydrolyzing enzymes during the pandemic are expected to upsurge. While the additional burden carbapenemases exert on healthcare is worrisome, it remains hidden or abandoned among the various health consequences of the pandemic. The purpose of this minireview is to shed a light on carbapenemase-associated infections during such unprecedented time of COVID-19. A focused insight shall be made into carbapenemases, their implications for COVID-19 patients, and the features and consequences of co-infection, with a review of available evidence from pertinent literature. The importance of increased surveillance for carbapenemase-producers and optimizing their management in relation to the pandemic, shall be addressed as well.

Enhanced endocytosis elevated virulence and severity of SARS-CoV-2 due to hyperglycemia in type 2 diabetic patients

Diabetes mellitus is a metabolic disease that causes hyperglycemia. In COVID-19 patients the severity of the disease depends on myriad factors but diabetes mellitus is the most important comorbidity. The current review was conducted to investigate the virulence of SARS-CoV-2 and disease severity of COVID-19 in type 2 diabetes mellitus patients and relevant treatment. The literature published in PubMed, Scopus, Web of Science, and Google Scholar was reviewed up to September 2021. The keywords including SARS-CoV-2, type 2 diabetes mellitus in COVID-19, hyperglycemia in COVID-19, opportunistic infections in type 2 diabetes mellitus and COVID-19 were used in different combinations. Hyperglycemic individuals over-express ACE-2 receptors in the lungs thus increasing the SARS-CoV-2 susceptibility and replication. Although dipeptidyl peptidase-4 plays an important role in glucose homeostasis, additionally it also stimulates the production of proinflammatory cytokines such as IL-6 and TNF-α creating a cytokine storm. Cytokine storm might be responsible for respiratory insufficiency in severe COVID-19 patients. Type 2 diabetes mellitus is associated with immunosuppression and the patients are prone to get many opportunistic infections. Type 2 diabetes mellitus patients with severe COVID-19 have lymphopenia. Moreover, in type 2 diabetes mellitus patients the neutrophils exhibit decreased chemotaxis, hydrogen peroxide production, and phagocytosis. Reduction in lymphocyte count and defective neutrophil capacity renders them with COVID-19 susceptible to opportunistic bacterial and fungal infections increasing the mortality rate. The opportunistic bacterial infections in COVID-19 patients were due to Staphylococcus aureus, Streptococcus pneumonia, and coagulase-negative Staphylococci, E. coli, Pseudomonas aeruginosa, and Klebsiella sp. In COVID-19 patients with type 2 diabetes mellitus, mucormycosis was found to be the most common fungal infection with a higher predilection to males. Hyperglycemia in COVID-19 patients with type 2 diabetes mellitus enhances the SARS-CoV-2 replication with an adverse outcome. A strong correlation exists between the poor prognosis of COVID-19 and type 2 diabetes mellitus. Proper glycemic control in COVID-19 patients with diabetes mellitus might lessen the severity of the disease.

Pathogenesis of Respiratory Viral and Fungal Coinfections

Individuals suffering from severe viral respiratory tract infections have recently emerged as "at risk" groups for developing invasive fungal infections. Influenza virus is one of the most common causes of acute lower respiratory tract infections worldwide. Fungal infections complicating influenza pneumonia are associated with increased disease severity and mortality, with invasive pulmonary aspergillosis being the most common manifestation. Strikingly, similar observations have been made during the current coronavirus disease 2019 (COVID-19) pandemic. The copathogenesis of respiratory viral and fungal coinfections is complex and involves a dynamic interplay between the host immune defenses and the virulence of the microbes involved that often results in failure to return to homeostasis. In this review, we discuss the main mechanisms underlying susceptibility to invasive fungal disease following respiratory viral infections. A comprehensive understanding of these interactions will aid the development of therapeutic modalities against newly identified targets to prevent and treat these emerging coinfections.

Evaluation of Bacterial Coinfection and Antibiotic Resistance in Patients with COVID-19 Under Mechanical Ventilation

Patients with confirmed SARS-CoV-2 are principally at risk of emerging superinfections, particularly those caused by Gram-negative bacteria. Therefore, in this retrospective cohort study, we investigated the presence of bacteria in endotracheal aspirate samples in severe COVID-19 patients under mechanical ventilation between 20 February 2020 and 21 September 2020 in Mazandaran Heart Center Hospital, Iran. Outcomes were compared between ICU patients with confirmed SARS-CoV-2 (corona group) and those who suffer from other disease (non-corona group). Out of 38 subjects who met the diagnostic criteria for ventilator-associated pneumonia (VAP) in ICU, 22 and 16 patients in corona and non-corona groups, respectively, were enrolled in the study. Hospital length of stay in 27% of case in corona group was > 10 days. Also, SOFA score was > 10 in 64% and 25% of corona and non-corona groups, respectively (P < 0.05). Moreover, the number of death was significantly higher among corona patients (45%) than non-corona group (6%) in ICU (P < 0.05). Acinetobacter spp. were the most common bacteria in nine corona patients (41%) that were 100% resistant to amikacin, gentamycin, cefixime, and imipenem antibiotics. The prevalence of antibiotic resistance among pathogens isolated from patients with COVID-19 under mechanical ventilation in ICU highlighted the importance of preventing coinfections caused by this pathogen, suggesting an essential standardized approach to antibiotic stewardship in patients with COVID-19 for successful treatment.

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.

Empirical antibiotic usage and bacterial superinfections in patients with COVID-19 in Japan: A nationwide survey by the Japanese Respiratory Society

An internet questionnaire survey for investigating empirical antibiotic usage and bacterial superinfections in patients with coronavirus disease-2019 (COVID-19) in Japan was conducted among the chief physicians of respiratory disease departments of 715 Japanese Respiratory Society-certified hospitals using Google Forms between January 28, 2021 and February 28, 2021. Responses to the questionnaire survey were obtained from 198 of 715 hospitals (27.6%). The survey revealed that the complication incidences of community-acquired pneumonia; hospital-acquired pneumonia, including ventilator-associated pneumonia; and sepsis were 2.86, 5.59, and 0.99%, respectively, among patients with moderate/severe and critical COVID-19. Bacterial co-infection and secondary infection rarely affected patients with COVID-19 in Japan, and the isolated pathogens were not specific to these patients. Moreover, the anti-inflammatory effects of macrolides for COVID-19 were not observed in several studies. These results might be useful in clinical practice for COVID-19.