Predictors of Severity and Co-Infection Resistance Profile in COVID-19 Patients: First Report from Upper Egypt

Tracking Antibiotic Resistance Trends in Central Iran Amidst the COVID-19 Pandemic From 2021 to 2023: A Comprehensive Epidemiological Study

Background

The emergence of coronavirus disease in 2019 (COVID-19) appears to be having an impact on antibiotic resistance patterns. Specific circumstances during the COVID-19 era may have played a role in the spread of antimicrobial resistance (AMR). This study aimed to look at the changes in AMR patterns of Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii at Al-Zahra Hospital.

Materials and Methods

From March 2021 to January 2023, 3651 clinical samples were collected from patients hospitalized at Isfahan's Al-Zahra Hospital. The Clinical and Laboratory Standards Institute recommended procedures for detecting gram-negative bacteria and assessing antibiotic susceptibility were used. We divided the information into three years.

Results

Highest resistance rates were seen in A. baumannii to Ciprofloxacin (98.0%) and Ampicillin-Sulbactam (97.0%). For P. aeruginosa the resistance rate for Ceftazidime (36.1), Levofloxacin (37.8), and Meropenem (47.1) dropped seriously in 2022.

Conclusion

During the second year of the pandemic in central Iran, all three species studied showed rising rates of AMR. This can be attributable to two peaks within Iran on May 6, 2021 and August 27, 2021. The results of this study show that P. aeruginosa, K. pneumoniae, and A. baumannii bacteria in central Iran have a higher level of antibiotic resistance than previously studied strains before the pandemic.

Co-Infection of SARS-CoV-2 and Klebsiella pneumoniae: A Systematic Review and Meta-Analysis

The study aimed to assess the prevalence of COVID-19 and Klebsiella spp. coinfection across continents. Conducted following PRISMA guidelines, a systematic review utilized PubMed, Embase, SCOPUS, ScienceDirect, and Web of Science databases, searching for literature in English published from December 2019 to December 2022, using specific Health Sciences descriptors. A total of 408 records were identified, but only 50 were eligible, and of these, only 33 were included. Thirty-three references were analyzed to evaluate the correlation between COVID-19 and Klebsiella spp. infections. The tabulated data represented a sample group of 8741 coinfected patients. The findings revealed notable disparities in co-infection rates across continents. In Asia, 23% of individuals were infected with Klebsiella pneumoniae, while in Europe, the proportion of co-infected patients stood at 15%. Strikingly, on the African continent, 43% were found to be infected with Klebsiella pneumoniae, highlighting significant regional variations. Overall, the proportion of Klebsiella pneumoniae co-infections among COVID-positive individuals were determined to be 19%. Particularly concerning was the observation that 1 in 6 ICU coinfections was attributed to Klebsiella pneumoniae, indicating its substantial impact on patient outcomes and healthcare burden. The study underscores the alarming prevalence of co-infection between COVID-19 and Klebsiella pneumoniae, potentially exacerbating the clinical severity of patients and posing challenges to treatment strategies. These findings emphasize the importance of vigilant surveillance and targeted interventions to mitigate the adverse effects of bacterial coinfections in the context of the COVID-19 pandemic.

Hospital-acquired and ventilator-associated pneumonia caused by multidrug-resistant Gram-negative pathogens: Understanding epidemiology, resistance patterns, and implications with COVID-19

The ongoing spread of antimicrobial resistance has complicated the treatment of bacterial hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP). Gram-negative pathogens, especially those with multidrug-resistant profiles, including Escherichia coli, Klebsiella pneumoniae, Enterobacter spp., Pseudomonas aeruginosa, and Acinetobacter spp., are important culprits in this type of infections. Understanding the determinants of resistance in pathogens causing pneumonia is ultimately stressing, especially in the shadows of the COVID-19 pandemic, when bacterial lung infections are considered a top priority that has become urgent to revise. Globally, the increasing prevalence of these pathogens in respiratory samples represents a significant infection challenge, with major limitations of treatment options and poor clinical outcomes. This review will focus on the epidemiology of HAP and VAP and will present the roles and the antimicrobial resistance patterns of implicated multidrug-resistant (MDR) Gram-negative pathogens like carbapenem-resistant Acinetobacter baumannii (CRAB), carbapenem-resistant Pseudomonas aeruginosa (CRPA), carbapenem-resistant Enterobacterales (CRE), as well as colistin-resistant Gram-negative pathogens and extended-spectrum β-lactamase (ESBL)-producing Enterobacterales. While emerging from the COVID-19 pandemic, perspectives and conclusions are drawn from findings of HAP and VAP caused by MDR Gram-negative bacteria in patients with COVID-19.

Molecular Analysis of Carbapenem and Aminoglycoside Resistance Genes in Carbapenem-Resistant Pseudomonas aeruginosa Clinical Strains: A Challenge for Tertiary Care Hospitals

Carbapenem-resistant Pseudomonas aeruginosa (P. aeruginosa) strains have become a global threat due to their remarkable capability to survive and disseminate successfully by the acquisition of resistance genes. As a result, the treatment strategies have been severely compromised. Due to the insufficient available data regarding P. aeruginosa resistance from Pakistan, we aimed to investigate the resistance mechanisms of 249 P. aeruginosa strains by antimicrobial susceptibility testing, polymerase chain reaction for the detection of carbapenemases, aminoglycoside resistance genes, extended-spectrum beta-lactamases (ESBLs), sequence typing and plasmid typing. Furthermore, we tested silver nanoparticles (AgNPs) to evaluate their in vitro sensitivity against antimicrobial-resistant P. aeruginosa strains. We observed higher resistance against antimicrobials in the general surgery ward, general medicine ward and wound samples. Phenotypic carbapenemase-producer strains comprised 80.7% (201/249) with 89.0% (179/201) demonstrating genes encoding carbapenemases: blaNDM-1 (32.96%), blaOXA48 (37.43%), blaIMP (7.26%), blaVIM (5.03%), blaKPC-2 (1.12%), blaNDM-1/blaOXA48 (13.97%), blaOXA-48/blaVIM (1.68%) and blaVIM/blaIMP (0.56%). Aminoglycoside-modifying enzyme genes and 16S rRNA methylase variants were detected in 43.8% (109/249) strains: aac(6')-lb (12.8%), aac(3)-lla (12.0%), rmtB (21.1%), rmtC (11.0%), armA (12.8%), rmtD (4.6%), rmtF (6.4%), rmtB/aac(3)-lla (8.2%), rmtB/aac(6')-lla (7.3%) and rmtB/armA (3.6%). In total, 43.0% (77/179) of the strains coharbored carbapenemases and aminoglycoside resistance genes with 83.1% resistant to at least 1 agent in 3 or more classes and 16.9% resistant to every class of antimicrobials tested. Thirteen sequence types (STs) were identified: ST235, ST277, ST234, ST170, ST381, ST175, ST1455, ST1963, ST313, ST207, ST664, ST357 and ST348. Plasmid replicon types IncFI, IncFII, IncA/C, IncL/M, IncN, IncX, IncR and IncFIIK and MOB types F11, F12, H121, P131 and P3 were detected. Meropenem/AgNPs and Amikacin/AgNPs showed enhanced antibacterial activity. We reported the coexistence of carbapenemases and aminoglycoside resistance genes among carbapenem-resistant P. aeruginosa with diverse clonal lineages from Pakistan. Furthermore, we highlighted AgNP's potential role in handling future antimicrobial resistance concerns.

Predictive value of methicillin-resistant staphylococcus aureus nasal swab in patients with COVID-19 pneumonia and secondary bacterial pneumonia

OBJECTIVE

To determine the performance measures of admission methicillin-resistant Staphylococcus aureus (MRSA) nasal swabs for MRSA bacterial pneumonia in patients co-infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

METHODS

The study included patients admitted with SARS-CoV-2-positive nasopharyngeal specimens, MRSA nasal screens, and bacterial cultures to assess secondary MRSA pneumonia.

RESULTS

293 patients and 662 microbiological cultures evaluated. Overall, the specificity (91.8% [95% CI 88.6% to 95%]) and negative predictive value (NPV 97.4% [95% CI 95.4% - 99.3%]) of MRSA nasal swabs was high. However, the sensitivity (46.2%; 95% CI 19.1% to 73.3%) and positive predictive value (PPV 20.7%; 95% CI 59.5 - 35.4%) were low. Those patients in the MRSA nasal swab negative group had a shorter median duration of linezolid therapy.

CONCLUSIONS

SARS-CoV-2 infection doesn't reduce the specificity or negative predictive value of MRSA nasal swabs for secondary MRSA pneumonia.

Predictors of mortality among inpatients in COVID-19 treatment centers in the city of Butembo, North Kivu, Democratic Republic of Congo

Determining the risk factors for severe disease and death among hospitalized Covid-19 patients is critical to optimize health outcomes and health services efficiency, especially in resource-constrained and humanitarian settings. This study aimed to identify the predictors of mortality of Covid-19 patients in North Kivu province in the Democratic Republic of Congo.A retrospective cohort study was conducted in 6 Covid-19 treatment centers in the city of Butembo from 1 January to 31 December 2021. The time to event (death), the outcome variable, was visualized by Kaplan-Meier curves and the log-rank test was used to confirm differences in trends. Cox regression was used for all the predictors in the bivariate analysis and multivariate analysis was done using predictors found statistically significant in the bivariate analysis. The following variables were considered for inclusion to the Cox regression model: Age, Sex, Disease length, Treatment site, History of at least one co-morbidity, Body mass index, Stage according to SpO2 and the NEWS-modified score.Among the 303 participants (mean age of 53 years), the fatality rate was 33.8 deaths per 1000 patient-days. Four predictors were independently associated with inpatient death: age category (≥ 60 years) (adjusted HR: 9.90; 95% CI: 2.68-36.27), presence of at least one comorbidity (adjusted HR: 11.39; 95% CI: 3.19-40.71); duration of illness of > 5 days before hospitalization (adjusted HR:1.70, 95% CI: 1.04-2.79) and peripheral capillary oxygen saturation (SpO2) < 90% (adjusted HR = 14.02, 95% CI: 2.23-88.32). In addition to advanced age, comorbidity, and length of disease before hospitalization, ambient air SpO2 measured by healthcare providers using low-tech, affordable and relatively accessible pulse oximetry could inform the care pathways of Covid-19 inpatients in resource-challenged health systems in humanitarian settings.

Bacterial respiratory infections in patients with COVID-19: A retrospective study from a tertiary care center in Lebanon

BACKGROUND

Despite multiple reports of increased incidence of bacterial respiratory tract infections following COVID-19 globally, the microbiology is not yet fully elucidated. In this study, we describe the microbiology of bacterial infections and the prevalence of multidrug resistant organisms (MDROs) in hospitalized COVID-19 patients with community-acquired pneumonia (CAP), and hospital-acquired pneumonia (HAP) which includes both non-ventilated hospital acquired pneumonia (NVHAP) and ventilator-associated pneumonia (VAP). To our knowledge, this is the first study that compares the microbiology of VAP and NVHAP in COVID-19 patients.

METHODS

This is a longitudinal retrospective cohort study conducted at the American University of Beirut Medical Center (AUBMC), a tertiary-care centre in Lebanon. Adult patients with confirmed COVID-19 and concurrent bacterial respiratory infections with an identifiable causative organism who were hospitalized between March 2020 and September 2021 were included. Bacterial isolates identified in hospital-acquired pneumonia (HAP) were divided into 3 groups based on the time of acquisition of pneumonia after admission: hospital day 3-14, 15-28 and 29-42.

RESULTS

Out of 1674 patients admitted with COVID-19, 159 (9.5%) developed one or more respiratory infections with an identifiable causative organism. Overall, Gram-negative bacteria were predominant (84%) and Stenotrophomonas maltophilia was the most common pathogen, particularly in HAP. Among 231 obtained isolates, 59 (26%) were MDROs, seen in higher proportion in HAP, especially among patients with prolonged hospital stay (> 4 weeks). Non-fermenter Gram-negative bacilli (NFGNB) (OR = 3.52, p-value<0.001), particularly S. maltophilia (OR = 3.24, p-value = 0.02), were significantly more implicated in VAP compared to NVHAP.

CONCLUSIONS

NFGNB particularly S. maltophilia were significantly associated with COVID-19 VAP. A high rate of bacterial resistance (25%), especially among Gram-negative bacteria, was found which may compromise patients' outcomes and has important implications in guiding therapeutic decisions in COVID-19 patients who acquire bacterial respiratory infections.

Effects of awake-prone positioning on oxygenation and physiological outcomes in non-intubated patients with COVID-19: A randomized controlled trial

BACKGROUND

Prone positioning is a well-known supportive approach for increasing oxygenation and reducing mortality in non-COVID-19 patients with moderate to severe acute respiratory distress syndrome. However, studies highlighting the effects of proning in patients with COVID-19 are limited.

AIM

To investigate the effects of awake-prone positioning (APP) on oxygenation and physiological outcomes in non-intubated patients with COVID-19.

STUDY DESIGN

A randomized controlled trial was carried out with two parallel groups at 1:1 ratio. Adult awake non-intubated patients with confirmed COVID-19, non-rebreathing face mask or continuous positive airway pressure, PaO2 /FiO2 ratio ≤150 mmHg were randomly assigned to the APP group or control group. The control group was subjected to conventional positioning interventions. Outcome measures were PaO2 /FiO2 ratio, ROX index, PaO2 , PaCO2 , SaO2 , respiratory rate, blood pressure, and shock index. These parameters were recorded immediately before positioning, 10 min after patient positioning, and 1 h after patient positioning.

RESULTS

Of 115 patients assessed for eligibility, 82 were randomized to the APP group or control group (41 patients in each group). The use of APP for non-intubated patients with COVID-19 resulted in statistically significant improvements in oxygenation parameters, that is, SpO2 , PaO2 /FiO2 , ROX index, PaO2 , and SaO2 , at the three study time points (p = .000, .007, .000, .011, and .000 respectively). The SpO2 was increased to 92.15 ± 2.735 mmHg for the APP group versus 88.17 ± 4.847 for the control group after 1 h of patients' positioning. The PaO2 /FiO2 ratio increased in the APP group before proning compared with 1 h after proning (79.95 ± 22.508 vs. 98.91 ± 34.44) respectively. APP improved the SpO2 , PaO2 /FiO2 , ROX index, PaO2 , and SaO2 values for the APP group, representing an increase of 5.85%, 23.71%, 30.79%, 22.59%, and 5.26%, respectively.

CONCLUSION

Awake proning in non-intubated patients with COVID-19 showed marked improvement in oxygenation and physiological parameters.

RELEVANCE TO CLINICAL PRACTICE

This study provides evidence for critical care nurses to implement APP in non-intubated patients with COVID-19 to improve oxygenation and physiological parameters, as it was tolerated by most of the patients without serious adverse events.

Isolation of Carbapenem and Colistin Resistant Gram-Negative Bacteria Colonizing Immunocompromised SARS-CoV-2 Patients Admitted to Some Libyan Hospitals

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a devastating effect, globally. We describe, for the first time, the occurrence of carbapenem-resistant bacteria colonizing SARS-CoV-2 patients who developed hospital-associated infections with carbapenemase-producing, Gram-negative bacteria at some isolation centers of SARS-CoV-2 in the eastern part of Libya. In total, at first, 109 samples were collected from 43 patients, with the samples being recovered from oral (n = 35), nasal (n = 45), and rectal (n = 29) cavities. Strain identification was performed via matrix assisted laser desorption ionization-time of flight (MALDI-TOF). Antibiotic susceptibility testing was carried out on Mueller-Hinton agar, using the standard disk diffusion method. MIC determination was confirmed via E-TEST and microdilution standard methods. A molecular study was carried out to characterize the carbapenem and colistin resistance in Gram-negative bacterial strains. All of the positive results were confirmed via sequencing. Klebsiella pneumoniae (n = 32), Citrobacter freundii (n = 21), Escherichia coli (n = 7), and Acinetobacter baumannii (n = 21) were the predominant isolated bacteria. Gram-negative isolates were multidrug-resistant and carried different carbapenem resistance-associated genes, including NDM-1 (56/119; 47.05%), OXA-48 (15/119; 12.60%), OXA-23 (19/119; 15.96%), VIM (10/119; 8.40%), and the colistin resistance mobile gene mcr-1 (4/119; 3.36%). The overuse of antimicrobials, particularly carbapenem antibiotics, during the SARS-CoV-2 pandemic has led to the emergence of multidrug-resistant bacteria, mainly K. pneumoniae, A. baumannii, and colistin-resistant E. coli strains. Increased surveillance as well as the rational use of carbapenem antibiotics and, recently, colistin are required to reduce the propagation of multidrug-resistant strains and to optimally maintain the efficacy of these antibiotics. IMPORTANCE In this work, we describe, for the first time, the occurrence of carbapenem-resistant bacteria colonizing COVID-19 patients who developed hospital-associated infections with carbapenemase-producing, Gram-negative bacteria at some isolation centers of COVID-19 in the eastern part of Libya. Our results confirmed that the overuse of antimicrobials, such as carbapenem antibiotics, during the COVID-19 pandemic has led to the emergence of multidrug-resistant bacteria, mainly K. pneumoniae and A. baumannii, as well as colistin resistance.

A Comparative Study of Bacterial Infections Between COVID-19 and Non-COVID-19 Patients With Respect to Different Isolates and Their Antibiotic Sensitivity Pattern

Background Following the pandemic caused by SARS-CoV-2, the emergence of and following the pandemic has required major modifications to healthcare systems and frameworks. Antimicrobials have more than a few potential roles in managing COVID-19. Experimental cures for the treatment of SARS-CoV-2 are being explored. The availability of limited data suggests that nosocomial infections are associated with a higher risk of death and severity of COVID-19. To fill this knowledge gap, we conducted a study to assess the spectrum of bacteriological isolates in different samples from COVID-19 patients. Our study aimed to evaluate the antibiotic resistance pattern of these bacterial isolates and compare the spectrum of bacteriological isolates in different samples and their antibiotic sensitivity pattern between COVID-19 and non-COVID-19 patients. Methodology An observational cross-sectional, partly retrospective, and partly prospective study was carried out in the bacteriology section of the Department of Microbiology, Indira Gandhi Institute of Medical Sciences (IGIMS), Patna, Bihar, for a total duration of six months from February 2021 to July 2021. The profile of pathogens isolated from 105 clinical samples from COVID-19 patients was studied. To detect COVID-19, RT-PCR was performed. All clinical specimens (urine, blood, pus, respiratory sample, etc.) were processed and cultured on different media to support the growth of the bacteria as per our standard operating procedures (SOP) for bacteriology samples. Antimicrobial susceptibility testing was carried out based on the Clinical and Laboratory Standards Institute. Results A total of 105 clinical samples were received in the bacteriology section of the Department of Microbiology, IGIMS, Patna, Bihar, from admitted COVID-19 patients. The mean age of study participants was 51.57 ± 14.76 years, and males (66.7%, 70/105) were more than females (33.3%, 35/105). The majority of the patients were 91 out of 105 (86.67%) from the ward and 14 from the ICU (13.33%). Of the total samples tested, 62 (59%) were urine samples, 26 (24.8%) were respiratory specimens, 13 (12.4%) were pus samples, 3 (2.9%) were body fluids, and 1 (1%) were tissue samples. Among the total pathogen isolates (n=57) obtained from patients with SARS-CoV-2 admitted to the ward and ICU, 56.14% (32) were gram-negative, 26.31% (15) were Candida, and 17.54% (10) were gram-positive pathogens. The most isolated pathogen was Escherichia coli (39.02%, 16/41) followed by Klebsiella pneumoniae (29.26%, 12/41), Acinetobacter baumannii (7.31%, 3/41), and Enterobacter cloacae (2.43%, 1/41). Enterococcus spp. as gram-positive bacteria were isolated in 21.95% (9/41) of patients. Among the gram-negative bacteria (Enterobacterales), the highest resistance was seen in ampicillin (100%,29/29). For non-Enterobacterales, the highest resistance was seen in ceftriaxone (66.66%,2/3). Enterococcus spp. showed maximum ciprofloxacin, and gentamicin (high level) resistance was 100% (9/9). Conclusion Secondary infections with resistant pathogens in COVID-19 patients highlight the importance of antimicrobial management programs focused on the optimal selection of empirical treatments based on culture reports.

Fungal-Bacterial Co-Infections and Super-Infections among Hospitalized COVID-19 Patients: A Systematic Review

This study systematically reviewed fungal-bacterial co-infections and super-infections among hospitalized COVID-19 patients. A PRISMA systematic search was conducted. On September 2022, Medline, PubMed, Google Scholar, PsychINFO, Wiley Online Library, NATURE, and CINAHL databases were searched for all relevant articles published in English. All articles that exclusively reported the presence of fungal-bacterial co-infections and super-infections among hospitalized COVID-19 patients were included. Seven databases produced 6937 articles as a result of the literature search. Twenty-four articles met the inclusion criteria and were included in the final analysis. The total number of samples across the studies was 10,834, with a total of 1243 (11.5%) patients admitted to the intensive care unit (ICU). Of these patients, 535 underwent mechanical ventilation (4.9%), 2386 (22.0%) were male, and 597 (5.5%) died. Furthermore, hospitalized COVID-19 patients have a somewhat high rate (23.5%) of fungal-bacterial co-infections and super-infections. Moreover, for SARS-CoV-2 patients who have a chest X-ray that suggests a bacterial infection, who require immediate ICU admission, or who have a seriously immunocompromised condition, empiric antibiotic therapy should be taken into consideration. Additionally, the prevalence of co-infections and super-infections among hospitalized COVID-19 patients may have an impact on diagnosis and treatment. It is crucial to check for fungal and bacterial co-infections and super-infections in COVID-19 patients.

ESKAPE and Beyond: The Burden of Coinfections in the COVID-19 Pandemic

The ESKAPE group constitute a threat to public health, since these microorganisms are associated with severe infections in hospitals and have a direct relationship with high mortality rates. The presence of these bacteria in hospitals had a direct impact on the incidence of healthcare-associated coinfections in the SARS-CoV-2 pandemic. In recent years, these pathogens have shown resistance to multiple antibiotic families. The presence of high-risk clones within this group of bacteria contributes to the spread of resistance mechanisms worldwide. In the pandemic, these pathogens were implicated in coinfections in severely ill COVID-19 patients. The aim of this review is to describe the main microorganisms of the ESKAPE group involved in coinfections in COVID-19 patients, addressing mainly antimicrobial resistance mechanisms, epidemiology, and high-risk clones.

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.

Multidrug-Resistant Acinetobacter baumannii Infections in the United Kingdom versus Egypt: Trends and Potential Natural Products Solutions

Acinetobacter baumannii is a problematic pathogen of global concern. It causes multiple types of infection, especially among immunocompromised individuals in intensive care units. One of the most serious concerns related to this pathogen is its ability to become resistant to almost all the available antibiotics used in clinical practice. Moreover, it has a great tendency to spread this resistance at a very high rate, crossing borders and affecting healthcare settings across multiple economic levels. In this review, we trace back the reported incidences in the PubMed and the Web of Science databases of A. baumannii infections in both the United Kingdom and Egypt as two representative examples for countries of two different economic levels: high and low-middle income countries. Additionally, we compare the efforts made by researchers from both countries to find solutions to the lack of available treatments by looking into natural products reservoirs. A total of 113 studies reporting infection incidence were included, with most of them being conducted in Egypt, especially the recent ones. On the one hand, this pathogen was detected in the UK many years before it was reported in Egypt; on the other hand, the contribution of Egyptian researchers to identifying a solution using natural products is more notable than that of researchers in the UK. Tracing the prevalence of A. baumannii infections over the years showed that the infections are on the rise, especially in Egypt vs. the UK. Further concerns are linked to the spread of antibiotic resistance among the isolates collected from Egypt reaching very alarming levels. Studies conducted in the UK showed earlier inclusion of high-throughput technologies in the tracking and detection of A. baumannii and its resistance than those conducted in Egypt. Possible explanations for these variations are analyzed and discussed.

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.

The Intriguing Carbapenemases of Pseudomonas aeruginosa: Current Status, Genetic Profile, and Global Epidemiology

Worldwide, Pseudomonas aeruginosa remains a leading nosocomial pathogen that is difficult to treat and constitutes a challenging menace to healthcare systems. P. aeruginosa shows increased and alarming resistance to carbapenems, long acknowledged as last-resort antibiotics for treatment of resistant infections. Varied and recalcitrant pathways of resistance to carbapenems can simultaneously occur in P. aeruginosa, including the production of carbapenemases, broadest spectrum types of β-lactamases that hydrolyze virtually almost all β-lactams, including carbapenems. The organism can produce chromosomal, plasmid-encoded, and integron- or transposon-mediated carbapenemases from different molecular classes. These include Ambler class A (KPC and some types of GES enzymes), class B (different metallo-β-lactamases such as IMP, VIM, and NDM), and class D (oxacillinases with carbapenem-hydrolyzing capacity like OXA-198) enzymes. Additionally, derepression of chromosomal AmpC cephalosporinases in P. aeruginosa contributes to carbapenem resistance in the presence of other concomitant mechanisms such as impermeability or efflux overexpression. Epidemiologic and molecular evidence of carbapenemases in P. aeruginosa has been long accumulating, and reports of their existence in different geographical areas of the world currently exist. Such reports are continuously being updated and reveal emerging varieties of carbapenemases and/or new genetic environments. This review summarizes carbapenemases of importance in P. aeruginosa, highlights their genetic profile, and presents current knowledge about their global epidemiology.

Antibiotics Usage and Resistance among Patients with Severe Acute Respiratory Syndrome Coronavirus 2 in the Intensive Care Unit in Makkah, Saudi Arabia

Antibiotic resistance is a global health and development threat, especially during the Severe Acute Respiratory Syndrome Coronavirus 2 (COVID-19) pandemic. Therefore, the current study was conducted to describe antibiotic usage and resistance among patients with COVID-19 in the intensive care unit (ICU) in Makkah, Saudi Arabia. In this cross-sectional study, only patients with positive COVID-19 status (42 patients) admitted to the ICU at the King Faisal Hospital were selected using a census sampling method. The susceptibility test of bacteria was carried out according to the standard protocol. The identified strains were tested in-vitro against several antibiotics drugs. Statistical analysis was performed using SPSS version 24. A total of 42 patients were included, with a mean age of 59.35 ± 18 years. Of them, 38.1% were males, and 61.9% were females. 35.7% have blood group O +. For age and blood groups, statistically significant associations were found between males and females, with p-values = 0.037 and 0.031, respectively. A large percentage (42.7%) of the obtained samples contained Klebsiella Pneumoniae; all bacteria were multidrug-resistance bacteria. Furthermore, 76.2% of bacteria were resistant to Ampicillin, 66.7% were resistant to Ciprofloxacin, 64.3% were resistant to Levofloxacin, 57.1% were resistant to Imipenem, and 57.1% were resistant to Moxifloxacin. On the contrary, among the 40 examined antibiotics, the effective antibiotics were Daptomycin, Linezolid, Mupirocin, Synercid, Teicoplanin, Vancomycin, and Nitrofurantoin. Our study demonstrates that antibiotic resistance is highly prevalent among ICU patients with COVID-19 at the King Faisal Hospital. Additionally, all bacteria were multidrug-resistance bacteria. Therefore, this high prevalence should be seriously discussed and urgently considered.

Bacterial and Fungal Superinfections in COVID-19 Patients Hospitalized in an Intensive Care Unit from Timișoara, Romania

PURPOSE

Critically ill patients hospitalized in the intensive care unit (ICU) have an increased infection risk. The aim of this study was to determine the bacterial and fungal superinfections rate in Coronavirus disease 2019 (COVID-19) patients stationed in the ICU, identify risk factors associated with their development and to determine whether superinfection plays a role in patients' outcome in this population.

PATIENTS AND METHODS

In this retrospective, non-interventional, single centre, cohort study, medical records of 302 consecutive patients with SARS-COV-2 pneumonia admitted into the COVID-19 ICU of the largest university hospital from Western Romania between October 2020 and May 2021, were reviewed, of whom 236 patients met the inclusion criteria.

RESULTS

One hundred and nineteen patients developed a superinfection ≥48 h after being admitted to the hospital. Superinfection rate in the ICU was 50.42%. Coagulase-negative Staphylococci (CoNS) and Enterococcus spp. were predominantly isolated from blood cultures, while Acinetobacter baumannii, Staphylococcus aureus and Candida spp. from tracheobronchial aspirates. Significant independent risk factors regarding bacterial/fungal superinfection in COVID-19 patients were obtained for the following variables: number of days of central venous catheter (HR = 1.13 [1.07-1.20], p < 0.001) and prior administration of corticosteroids (HR = 2.80 [1.33-5.93], p = 0.007). Four independent predictive risk factors were associated with unfavorable outcome: age (HR = 1.07 [95% CI 1.03-1.12], p = 0.001); Carmeli Score (HR = 6.09 [1.18-31.50], p = 0.031); body mass index (HR = 1.11 [1.02-1.21], p = 0.011) and the presence of a central venous catheter (HR = 6.49 [1.93-21.89], p = 0.003).

CONCLUSION

The superinfection rate in COVID-19 patients was high in this study group. Exogenous risk factors were associated with superinfection more than endogenous factors. Only a small percentage of uninfected COVID-19 patients were not prescribed antibiotics during their hospitalization, raising serious concerns regarding the judicious prescribing of antibiotics in viral infections.

Which patients bring the most costs for hospital? A study on the cost determinants among COVID-19 patients in Iran

Background

Accurate information on the cost determinants in the COVID-19 patients could provide policymakers a valuable planning tool for dealing with the future COVID-19 crises especially in the health systems with limited resources.

Objectives

This study aimed to determine the factors affecting direct medical cost of COVID-19 patients in Hamadan, the west of Iran.

Methods

This study considered 909 confirmed COVID-19 patients with positive real-time reverse-transcriptase polymerase-chain-reaction test which were hospitalized from 1 March to 31 January 2021 in Farshchian (Sina) hospital in Hamadan, Iran. A checklist was utilized to assess the relationship of demographic characteristics, clinical presentation, medical laboratory findings and the length of hospitalization to the direct hospitalization costs in two groups of patients (patients with hospitalization ≤ 9 days and > 9 days). Statistical analysis was performed using chi-square, median test and multivariable quantile regression model at 0.05 significance levels with Stata 14 software program.

Results

The median cost of hospitalization in patients was totally 134.48 dollars (Range: 19.19–2397.54) and respectively 95.87 (Range: 19.19–856.63) and 507.30 dollars (Range: 68.94–2397.54) in patients with hospitalization ≤ 9 days and > 9 days. The adjusted estimates presented that in patients with 9 or less hospitalization days history of cardiovascular disease, wheezing pulmonary lung, SPO2 lower than 90%, positive CRP, LDH higher than 942 U/L, NA lower than 136 mEq/L, lymphosite lower than 20% and patients with ICU experience had significantly positive relationship to the median of cost. Moreover, in patients with more than 9 hospitalization days, history of cardiovascular disease and ICU experience was statistically positive association and age older than 60 years and WBC lower than 4.5 mg/dL had statistically negative relationship to the median of hospitalization cost.

Conclusion

As the length of hospital stay, which can be associated with the severity of the disease, increases, health systems become more vulnerable in terms of resource utilization, which in turn can challenge their responsiveness and readiness to meet the specialized treatment needs of individuals.

The Associations of Iron Related Biomarkers with Risk, Clinical Severity and Mortality in SARS-CoV-2 Patients: A Meta-Analysis

The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is spreading rapidly around the world and has led to millions of infections and deaths. Growing evidence indicates that iron metabolism is associated with COVID-19 progression, and iron-related biomarkers have great potential for detecting these diseases. However, the results of previous studies are conflicting, and there is not consistent numerical magnitude relationship between those biomarkers and COVID-19. Thereby, we aimed to integrate the results of current studies and to further explore their relationships through a meta-analysis. We searched peer-reviewed literature in PubMed, Scopus and Web of Science up to 31 May 2022. A random effects model was used for pooling standard mean difference (SMD) and the calculation of the corresponding 95% confidence interval (CI). I2 was used to evaluate heterogeneity among studies. A total of 72 eligible articles were included in the meta-analysis. It was found that the ferritin levels of patients increased with the severity of the disease, whereas their serum iron levels and hemoglobin levels showed opposite trends. In addition, non-survivors had higher ferritin levels (SMD (95%CI): 1.121 (0.854, 1.388); Z = 8.22 p for Z < 0.001; I2 = 95.7%, p for I2 < 0.001), lower serum iron levels (SMD (95%CI): −0.483 (−0.597, −0.368), Z = 8.27, p for Z < 0.001; I2 = 0.9%, p for I2 =0.423) and significantly lower TIBC levels (SMD (95%CI): −0.612 (−0.900, −0.324), Z = 4.16, p for Z < 0.001; I2 = 71%, p for I2 = 0.016) than survivors. This meta-analysis demonstrates that ferritin, serum iron, hemoglobin and total iron banding capacity (TIBC) levels are strongly associated with the risk, severity and mortality of COVID-19, providing strong evidence for their potential in predicting disease occurrence and progression.

Prevalence of Fungal Drug Resistance in COVID-19 Infection: a Global Meta-analysis

Purpose

Secondary bacterial or fungal infections are one of the most important medical complications among patients with Coronavirus Disease 2019 (COVID-19). The emergence of multidrug-resistant (MDR) candida can cause many problems such as treatment failure, adverse clinical outcomes, and even disease outbreaks. This systematic review and meta-analysis aims to investigate the prevalence and outcomes of fungal drug-resistant in COVID-19 patients.

Methods

PubMed, Embase, Scopus, Cochrane Library, and Web of Science databases were searched for peer reviewed-articles published in English up to May 20, 2021. Heterogeneity across studies was evaluated using Cochrane’s Q test and the I² index. The pooled point prevalence and their corresponding 95% confidence intervals (CIs) were considered to estimate the prevalence of fungal drug resistance infection in COVID-19 patients.

Results

Eight eligible articles were included in our meta-analysis. The number of COVID-19 patients with fungal co-infection varied from 5 to 35 among selected studies. The overall pooled prevalence of fungal drug resistance among patients with co-infections of fungal and COVID-19 was 69% (95% CI: 37%, 94%) by using a random-effects model. In terms of specific species, the pooled meta-analysis for Candida Auris was estimated to be 100% (95%CI: 98%, 100%; I² = 0%), for Multi-Candida 59% (95%CI: 38%, 79%; I² = 12.5%), and for Aspergillus 15% (95%CI: 0%, 42%; I² = 0%).

Conclusion

Our study shows the high prevalence of fungal drug resistance in COVID-19 patients and emphasizes the need to strengthen antimicrobial stewardship programs, close monitoring for treatment failure, and the emergence of resistance upon treatment.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12281-022-00439-9.

Correlation between Multidrug Resistance Infection with Clinical Outcomes of Critically ill Patients with COVID-19 Admitted to an Intensive Care at RSUP Dr. M. Djamil in Indonesia

BACKGROUND: Approximately 14–50% of severe COVID-19 patients are admitted to the Intensive Care Unit (ICU) that acquires a multidrug-resistant bacterial infection (MDR) and worsens clinical outcomes of patients. AIM: We aim to determine the increased risk of MDR infection in the ICU including large-spectrum antibiotic administration, invasive procedure performance (mechanical ventilation), and clinical outcomes of patient. METHODS: We analyzed 227 patients with a primary diagnosis of COVID-19 on mechanical ventilation who were admitted to ICU COVID-19 RSUP Dr. M. Djamil from 2020 to 2021. Demographic information, sputum culture results, intubation, and clinical outcomes were all collected in the medical records for this retrospective cohort study. Patients who were hospitalized for <48 h in the ICU were excluded from the study. An independent t-test and a Chi-square test were used to analyze the data. RESULTS: In sixty patients (26.4%), bacteria were found in the sputum culture, 40 patients (66.7%) of them were MDR. The most common bacteria found was Acinetobacter baumanii (35%) followed by Klebsiella pneumonia (21.7%). There is a significant relationship between MDR (p-value 0.000) and intubation (p-value, 000) to clinical outcomes of patients (improvement or death). There is a significant relationship between intubation and MDR (p-value 0.009). CONCLUSION: MDR patient status affected the outcomes of COVID-19 patients in the ICU. Patients with MDR were more likely to have a poor clinical outcome.

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.

Predictors and microbiology of respiratory and bloodstream bacterial infection in patients with COVID-19: living rapid review update and meta-regression

BACKGROUND

The prevalence of bacterial infection in patients with COVID-19 is low, however, empiric antibiotic use is high. Risk stratification may be needed to minimize unnecessary empiric antibiotic use.

OBJECTIVE

To identify risk factors and microbiology associated with respiratory and bloodstream bacterial infection in patients with COVID-19.

DATA SOURCES

We searched MEDLINE, OVID Epub and EMBASE for published literature up to 5 February 2021.

STUDY ELIGIBILITY CRITERIA

Studies including at least 50 patients with COVID-19 in any healthcare setting.

METHODS

We used a validated ten-item risk of bias tool for disease prevalence. The main outcome of interest was the proportion of COVID-19 patients with bloodstream and/or respiratory bacterial co-infection and secondary infection. We performed meta-regression to identify study population factors associated with bacterial infection including healthcare setting, age, comorbidities and COVID-19 medication.

RESULTS

Out of 33 345 studies screened, 171 were included in the final analysis. Bacterial infection data were available from 171 262 patients. The prevalence of co-infection was 5.1% (95% CI 3.6-7.1%) and secondary infection was 13.1% (95% CI 9.8-17.2%). There was a higher odds of bacterial infection in studies with a higher proportion of patients in the intensive care unit (ICU) (adjusted OR 18.8, 95% CI 6.5-54.8). Female sex was associated with a lower odds of secondary infection (adjusted OR 0.73, 95% CI 0.55-0.97) but not co-infection (adjusted OR 1.05, 95% CI 0.80-1.37). The most common organisms isolated included Staphylococcus aureus, coagulase-negative staphylococci and Klebsiella species.

CONCLUSIONS

While the odds of respiratory and bloodstream bacterial infection are low in patients with COVID-19, meta-regression revealed potential risk factors for infection, including ICU setting and mechanical ventilation. The risk for secondary infection is substantially greater than the risk for co-infection in patients with COVID-19. Understanding predictors of co-infection and secondary infection may help to support improved antibiotic stewardship in patients with COVID-19.

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.

Antimicrobial resistance (AMR) in COVID-19 patients: a systematic review and meta-analysis (November 2019-June 2021)

BACKGROUND

Pneumonia from SARS-CoV-2 is difficult to distinguish from other viral and bacterial etiologies. Broad-spectrum antimicrobials are frequently prescribed to patients hospitalized with COVID-19 which potentially acts as a catalyst for the development of antimicrobial resistance (AMR).

OBJECTIVES

We conducted a systematic review and meta-analysis during the first 18 months of the pandemic to quantify the prevalence and types of resistant co-infecting organisms in patients with COVID-19 and explore differences across hospital and geographic settings.

METHODS

We searched MEDLINE, Embase, Web of Science (BioSIS), and Scopus from November 1, 2019 to May 28, 2021 to identify relevant articles pertaining to resistant co-infections in patients with laboratory confirmed SARS-CoV-2. Patient- and study-level analyses were conducted. We calculated pooled prevalence estimates of co-infection with resistant bacterial or fungal organisms using random effects models. Stratified meta-analysis by hospital and geographic setting was also performed to elucidate any differences.

RESULTS

Of 1331 articles identified, 38 met inclusion criteria. A total of 1959 unique isolates were identified with 29% (569) resistant organisms identified. Co-infection with resistant bacterial or fungal organisms ranged from 0.2 to 100% among included studies. Pooled prevalence of co-infection with resistant bacterial and fungal organisms was 24% (95% CI 8-40%; n = 25 studies: I2 = 99%) and 0.3% (95% CI 0.1-0.6%; n = 8 studies: I2 = 78%), respectively. Among multi-drug resistant organisms, methicillin-resistant Staphylococcus aureus, carbapenem-resistant Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and multi-drug resistant Candida auris were most commonly reported. Stratified analyses found higher proportions of AMR outside of Europe and in ICU settings, though these results were not statistically significant. Patient-level analysis demonstrated > 50% (n = 58) mortality, whereby all but 6 patients were infected with a resistant organism.

CONCLUSIONS

During the first 18 months of the pandemic, AMR prevalence was high in COVID-19 patients and varied by hospital and geography although there was substantial heterogeneity. Given the variation in patient populations within these studies, clinical settings, practice patterns, and definitions of AMR, further research is warranted to quantify AMR in COVID-19 patients to improve surveillance programs, infection prevention and control practices and antimicrobial stewardship programs globally.

Science, Technology, and Innovation Response to the COVID-19 Pandemic

The COVID-19 pandemic has caused deep changes all over the world. Great efforts to stop the spread of the contagious are still under actions in economy, social works, STI through many activities. The study highlights the Egyptian efforts in the STI sector for facing the pandemic effects. Conceptual and methodology framework of the study is built up and discussed. Egyptian government emergency response package greatly minimized its effects. Also, HEI's policies suggested an innovation framework to strengthen the Egyptian market. STI institutions in both MOHESR and MOHP worked on the effects of drugs clinical trials, vaccine manufacturing, and therapeutic approaches. Internationally recognized publications in Egyptian top universities and research centers focused on many topics including the effect of drugs and antibiotics on the infected patients with the virus for efficient therapy, the genetic development of the virus in Egypt, monitoring of the extent possibilities for the formation of collective immunity in Egyptians, the movement of antibodies in their bodies, and many other activities.

Does dengue and COVID-19 co-infection have worse outcomes? A systematic review of current evidence

In dengue-endemic regions, the co-infection with SARS-CoV-2 and dengue is a significant health concern. Therefore, we performed a literature search for relevant papers in seven databases on 26 Spetember 2021. Out of 24 articles, the mortality rate and intensive care unit (ICU) admission were 19.1% and 7.8%, respectively. The mean hospital stay was 11.4 days. In addition, we identified two pregnancies with dengue and COVID-19 co-infection; one ended with premature rupture of membrane and intrauterine growth restriction fetus, while the other one ended with maternal mortality and intrauterine fetal death. COVID-19 and dengue co-infection had worse outcomes regarding mortality rates, ICU admission, and prolonged hospital stay. Thus, wise-decision management approaches should be adequately offered to these patients to enhance their outcomes. Establishing an early diagnosis might be the answer to reducing the estimated significant burden of these conditions.

Effects of fluid and drinking on pneumonia mortality in older adults: A systematic review and meta-analysis

Background and aims

Methods

Results

Conclusions

Global data analysis and risk factors associated with morbidity and mortality of COVID-19

This review was focused on global data analysis and risk factors associated with morbidity and mortality of coronavirus disease 2019 from different countries, including Bangladesh, Brazil, China, Central Eastern Europe, Egypt, India, Iran, Pakistan, and South Asia, Africa, Turkey and UAE. Male showed higher confirmed and death cases compared to females in most of the countries. In addition, the case fatality ratio (CFR) for males was higher than for females. This gender variation in COVID-19 cases may be due to males' cultural activities, but similar variations in the number of COVID-19 affected males and females globally. Variations in the immune system can illustrate this divergent risk comparatively higher in males than females. The female immune system may have an edge to detect pathogens slightly earlier. In addition, women show comparatively higher innate and adaptive immune responses than men, which might be explained by the high density of immune-related genes in the X chromosome. Furthermore, SARS-CoV-2 viruses use angiotensin-converting enzyme 2 (ACE2) to enter the host cell, and men contain higher ACE2 than females. Therefore, males may be more vulnerable to COVID-19 than females. In addition, smoking habit also makes men susceptible to COVID-19. Considering the age-wise distribution, children and older adults were less infected than other age groups and the death rate. On the contrary, more death in the older group may be associated with less immune system function. In addition, most of these group have comorbidities like diabetes, high pressure, low lungs and kidney function, and other chronic diseases. Due to the substantial economic losses and the numerous infected people and deaths, research examining the features of the COVID-19 epidemic is essential to gain insight into mitigating its impact in the future and preparedness for any future epidemics.

Lessons learned in stroke care during COVID-19 pandemic and preparing for future pandemics in the MENA+ region: A consensus statement from the MENA+-SINO

BACKGROUND

COVID-19 pandemic has negatively impacted stroke care services at multiple levels. There was a decline in acute stroke admissions. Fewer interventions have been performed. Increased "door-to-needle times and "door-to-groin puncture" during this pandemic. These factors combined have led to declining in the favoured outcomes of stroke patients' globally. Yet this pandemic permits an opportunity for higher preparedness for future pandemics.

OBJECTIVES AND METHODS

This paper aims to shed light on the main lessons learned in the field of stroke care during the first wave of COVID-19 pandemic. Here we are presenting proposals and initiatives for better preparedness in future similar emergencies. These proposals are based primarily on literature review of COVID-19 publications, as well as the first-hand experience gained during the first wave at the regional level. In addition to the consensus and collective ride of stroke experts in the Middle East North Africa Stroke and Interventional Neurotherapies Organization (MENA+-SINO) and interaction and collaboration with international stroke specialists from the Stroke World Organization (WSO), European Stroke Organization (ESO) and stroke and COVID-19 papers authors.

CONCLUSION

Stroke care is very complex, particularly in the initial hours after onset of symptoms. A successful outcome requires very close collaboration between clinical personnel from multiple specialties. Preparedness for future pandemics requires the improvement of care plans that allow for rapid assessment of stroke patients and ensuring that regular 'mock exercises' familiarize quintessential services that care for the stroke patients.

A nomogram predicting severe COVID-19 based on a large study cohort from China

BACKGROUND

The use of accurate prediction tools and early intervention are important for addressing severe coronavirus disease 2019 (COVID-19). However, the prediction models for severe COVID-19 available to date are subject to various biases. This study aimed to construct a nomogram to provide accurate, personalized predictions of the risk of severe COVID-19.

METHODS

This study was based on a large, multicenter retrospective derivation cohort and a validation cohort. The derivation cohort consisted of 496 patients from Jiangsu Province, China, between January 10, 2020, and March 15, 2020, and the validation cohort contained 105 patients from Huangshi, Hunan Province, China, between January 21, 2020, and February 29, 2020. A nomogram was developed with the selected predictors of severe COVID-19, which were identified by univariate and multivariate logistic regression analyses. We evaluated the discrimination of the nomogram with the area under the receiver operating characteristic curve (AUC) and the calibration of the nomogram with calibration plots and Hosmer-Lemeshow tests.

RESULTS

Three predictors, namely, age, lymphocyte count, and pulmonary opacity score, were selected to develop the nomogram. The nomogram exhibited good discrimination (AUC 0.93, 95% confidence interval [CI] 0.90-0.96 in the derivation cohort; AUC 0.85, 95% CI 0.76-0.93 in the validation cohort) and satisfactory agreement.

CONCLUSIONS

The nomogram was a reliable tool for assessing the probability of severe COVID-19 and may facilitate clinicians stratifying patients and providing early and optimal therapies.

Predictors of severity and development of critical illness of Egyptian COVID-19 patients: A multicenter study

Objectives

We conducted the present multicenter, retrospective study to assess the epidemiological, clinical, laboratory, and radiological characteristics associated with critical illness among patients with COVID-19 from Egypt.

Methods

The present study was a multicenter, retrospective study that retrieved the data of all Egyptian cases with confirmed COVID-19 admitted to hospitals affiliated to the General Organization for Teaching Hospitals and Institutes (GOTHI) through the period from March to July 2020. The diagnosis of COVID-19 was based on a positive reverse transcription-polymerase chain reaction (RT-PCR) laboratory test.

Results

This retrospective study included 2724 COVID-19 patients, of whom 423 (15.52%) were critically ill. Approximately 45.86% of the critical group aged above 60 years, compared to 39.59% in the non-critical group (p = 0.016). Multivariate analysis showed that many factors were predictors of critically illness, including age >60 years (OR = 1.30, 95% CI [1.05, 1.61], p = 0.014), low oxygen saturation (OR = 0.93, 95% CI [0.91, 0.95], p<0.001), low Glasgow coma scale (OR = 0.75, 95% CI [0.67, 0.84], p<0.001), diabetes (OR = 1.62, 95% CI [1.26, 2.08], p<0.001), cancer (OR = 2.47, 95% CI [1.41, 4.35], p = 0.002), and serum ferritin (OR = 1.004, 95% CI [1.0003, 1.008], p = 0.031).

Conclusion

In the present report, we demonstrated that many factors are associated with COVID-19 critical illness, including older age groups, fatigue, elevated temperature, increased pulse, lower oxygen saturation, the preexistence of diabetes, malignancies, cardiovascular disease, renal diseases, and pulmonary disease. Moreover, elevated serum levels of ALT, AST, and ferritin are associated with worse outcomes. Further studies are required to identify independent predictors of mortality for patients with COVID-19.

Co-infection of ST2IP carbapenem-resistant Acinetobacter baumannii with SARS-CoV-2 in the patients admitted to a Tehran tertiary referral hospital

BACKGROUND

Carbapenem-resistant Acinetobacter baumannii (CRAB) is among the most concerning cause of healthcare-associated infections (HAI) due to its high level of antibiotic resistance and high mortality. In the era of the COVID-19 pandemic, the key priority of infection control committees is to contain the dissemination of antibiotic resistant Gram-negative bacteria. Here, we aimed to timely recognize the emergence of CRAB in COVID-19 cases admitted to the wards of a tertiary referral hospital and to identify the genetic relatedness of the isolates.

METHODS

From 30 March to 30 May 2020, a total of 242 clinical samples from COVID-19 cases were screened for CRAB isolates using standard microbiologic and antibiotic susceptibility tests. The PCRs targeting oxa23, oxa24, oxa58, blaTEM and blaNDM-1 genes were performed. Two multiplex PCRs for identifying the global clones (GC) of A. baumannii were also performed. The sequence type of CRABs was determined using Institut Pasteur (IP) multilocus sequence typing (MLST) scheme.

RESULTS

Eighteen CRAB isolates were recovered from COVID-19 patients with the mean age of 63.94 ± 13.8 years. All but 4 COVID-19 patients co-infected with CRAB were suffering from an underlying disease. Death was recorded as the outcome in ICUs for 9 (50%) COVID-19 patients co-infected with CRAB. The CRAB isolates belong to GC2 and ST2IP and carried the oxa23 carbapenem resistance gene.

CONCLUSION

This study demonstrated the co-infection of CRAB isolates and SARS-CoV-2 in the patients admitted to different ICUs at a referral hospital in Tehran. The CRAB isolates were found to belong to ST2IP, share the oxa23 gene and to have caused several outbreaks in the wards admitting COVID-19 patients.

Egypt's COVID-19 Recent Happenings and Perspectives: A Mini-Review

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected countries across the world. While the zoonotic aspects of SARS-CoV-2 are still under investigation, bats and pangolins are currently cited as the animal origin of the virus. Several types of vaccines against COVID-19 have been developed and are being used in vaccination drives across the world. A number of countries are experiencing second and third waves of the pandemic, which have claimed nearly four million lives out of the 180 million people infected globally as of June 2021. The emerging SARS-CoV-2 variants and mutants are posing high public health concerns owing to their rapid transmissibility, higher severity, and in some cases, ability to infect vaccinated people (vaccine breakthrough). Here in this mini-review, we specifically looked at the efforts and actions of the Egyptian government to slow down and control the spread of COVID-19. We also review the COVID-19 statistics in Egypt and the possible reasons behind the low prevalence and high case fatality rate (CFR%), comparing Egypt COVID-19 statistics with China (the epicenter of COVID-19 pandemic) and the USA, Brazil, India, Italy, and France (the first countries in which the numbers of patients infected with COVID-19). Additionally, we have summarized the SARS-CoV-2 variants, vaccines used in Egypt, and the use of medicinal plants as preventive and curative options.

Acinetobacter baumannii Infections in Times of COVID-19 Pandemic

The COVID-19 pandemic has generated an overuse of antimicrobials in critically ill patients. Acinetobacter baumannii frequently causes nosocomial infections, particularly in intensive care units (ICUs), where the incidence has increased over time. Since the WHO declared the COVID-19 pandemic on 12 March 2020, the disease has spread rapidly, and many of the patients infected with SARS-CoV-2 needed to be admitted to the ICU. Bacterial co-pathogens are commonly identified in viral respiratory infections and are important causes of morbidity and mortality. However, we cannot neglect the increased incidence of antimicrobial resistance, which may be attributed to the excess use of antimicrobial agents during the COVID-19 pandemic. Patients with COVID-19 could be vulnerable to other infections owing to multiple comorbidities with severe COVID-19, prolonged hospitalization, and SARS-CoV-2-associated immune dysfunction. These patients have acquired secondary bacterial infections or superinfections, mainly bacteremia and urinary tract infections. This review will summarize the prevalence of A. baumannii coinfection and secondary infection in patients with COVID-19.

Secondary bacterial infections and antimicrobial resistance in COVID-19: comparative evaluation of pre-pandemic and pandemic-era, a retrospective single center study

PURPOSE

In this study, we aimed to evaluate the epidemiology and antimicrobial resistance (AMR) patterns of bacterial pathogens in COVID-19 patients and to compare the results with control groups from the pre-pandemic and pandemic era.

METHODS

Microbiological database records of all the COVID-19 diagnosed patients in the Ege University Hospital between March 15, 2020, and June 15, 2020, evaluated retrospectively. Patients who acquired secondary bacterial infections (SBIs) and bacterial co-infections were analyzed. Etiology and AMR data of the bacterial infections were collected. Results were also compared to control groups from pre-pandemic and pandemic era data.

RESULTS

In total, 4859 positive culture results from 3532 patients were analyzed. Fifty-two (3.59%) patients had 78 SBIs and 38 (2.62%) patients had 45 bacterial co-infections among 1447 COVID-19 patients. 22/85 (25.88%) patients died who had bacterial infections. The respiratory culture-positive sample rate was 39.02% among all culture-positive samples in the COVID-19 group. There was a significant decrease in extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (8.94%) compared to samples from the pre-pandemic (20.76%) and pandemic era (20.74%) (p = 0.001 for both comparisons). Interestingly, Acinetobacter baumannii was the main pathogen in the respiratory infections of COVID-19 patients (9.76%) and the rate was significantly higher than pre-pandemic (3.49%, p < 0.002) and pandemic era control groups (3.11%, p < 0.001).

CONCLUSION

Due to the low frequency of SBIs reported during the ongoing pandemic, a more careful and targeted antimicrobial prescription should be taken. While patients with COVID-19 had lower levels of ESBL-producing Enterobacterales, the frequency of multidrug-resistant (MDR) A. baumannii is higher.

Bacterial co-infection in patients with SARS-CoV-2 in the Kingdom of Bahrain

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic presents a significant challenge to the medical profession, increasing in the presence of microbial co-infection. Bacterial and Fungal co-infections increase the risk of morbidity and mortality in patients with COVID-19.

AIM

To study the bacterial profile in patients with COVID-19 who needed admission to receive treatment in the main centres concerned with managing COVID-19 disease in the Kingdom of Bahrain.

METHODS

The study was a retrospective observational analysis of the bacterial profile and the bacterial resistance in patients with confirmed COVID-19 disease who needed admission to receive treatment in the main centres assigned to manage patients with COVID-19 disease in the Kingdom of Bahrain from February to October 2020. We used the electronic patients' records and the microbiology laboratory data to identify patients' demographics, clinical data, microbial profile, hospital or community-acquired, and the outcomes.

RESULTS

The study included 1380 patients admitted with confirmed COVID-19 disease during the study period. 51% were admitted from February to June, and 49% were admitted from July to October 2020, with a recurrence rate was 0.36%. There was a significant increase in bacterial and fungal co-infection in the second period compared to the first period. The most common isolated organisms were the gram-negative bacteria (mainly Klebsiella pneumoniae, Pseudomonas aeruginosa, multi-drug resistant Acinetobacter baumannii, and Escherichia coli), the gram-positive bacteria (mainly coagulase negative Staphylococci, Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus) and fungaemia (Candida galabrata, Candida tropicalis, Candida albicans, Aspergillus fumigatus, Candida parapsilosis, Aspergillus niger). The hospital-acquired infection formed 73.8%, 61.6%, 100% gram-negative, gram-positive and fungaemia. Most of the hospital-acquired infection occurred in the second period with a higher death rate than community-acquired infections.

CONCLUSION

Bacterial and fungal co-infections in patients admitted with confirmed COVID-19 disease pose higher morbidity and mortality risks than those without co-infections. We should perform every effort to minimize these risks.

Bacterial co-infection in patients with SARS-CoV-2 in the Kingdom of Bahrain

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic presents a significant challenge to the medical profession, increasing in the presence of microbial co-infection. Bacterial and Fungal co-infections increase the risk of morbidity and mortality in patients with COVID-19.

AIM

To study the bacterial profile in patients with COVID-19 who needed admission to receive treatment in the main centres concerned with managing COVID-19 disease in the Kingdom of Bahrain.

METHODS

The study was a retrospective observational analysis of the bacterial profile and the bacterial resistance in patients with confirmed COVID-19 disease who needed admission to receive treatment in the main centres assigned to manage patients with COVID-19 disease in the Kingdom of Bahrain from February to October 2020. We used the electronic patients’ records and the microbiology laboratory data to identify patients’ demographics, clinical data, microbial profile, hospital or community-acquired, and the outcomes.

RESULTS

The study included 1380 patients admitted with confirmed COVID-19 disease during the study period. 51% were admitted from February to June, and 49% were admitted from July to October 2020, with a recurrence rate was 0.36%. There was a significant increase in bacterial and fungal co-infection in the second period compared to the first period. The most common isolated organisms were the gram-negative bacteria (mainly Klebsiella pneumoniae, Pseudomonas aeruginosa, multi-drug resistant Acinetobacter baumannii, and Escherichia coli), the gram-positive bacteria (mainly coagulase negative Staphylococci, Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus) and fungaemia (Candida galabrata, Candida tropicalis, Candida albicans, Aspergillus fumigatus, Candida parapsilosis, Aspergillus niger). The hospital-acquired infection formed 73.8%, 61.6%, 100% gram-negative, gram-positive and fungaemia. Most of the hospital-acquired infection occurred in the second period with a higher death rate than community-acquired infections.

CONCLUSION

Bacterial and fungal co-infections in patients admitted with confirmed COVID-19 disease pose higher morbidity and mortality risks than those without co-infections. We should perform every effort to minimize these risks.

Epidemiology of Systemic Mycoses in the COVID-19 Pandemic

The physiopathologic characteristics of COVID-19 (high levels of inflammatory cytokines and T-cell reduction) promote fungal colonization and infection, which can go unnoticed because the symptoms in both diseases are very similar. The objective of this work was to study the current epidemiology of systemic mycosis in COVID-19 times. A literature search on the subject (January 2020–February 2021) was performed in PubMed, Embase, Cochrane Library, and LILACS without language restrictions. Demographic data, etiological agent, risk factors, diagnostic methods, antifungal treatment, and fatality rate were considered. Eighty nine publications were found on co-infection by COVID-19 and pneumocystosis, candidiasis, aspergillosis, mucormycosis, coccidioidomycosis, or histoplasmosis. In general, the co-infections occurred in males over the age of 40 with immunosuppression caused by various conditions. Several species were identified in candidiasis and aspergillosis co-infections. For diagnosis, diverse methods were used, from microbiological to molecular. Most patients received antifungals; however, the fatality rates were 11–100%. The latter may result because the clinical picture is usually attributed exclusively to SARS-CoV-2, preventing a clinical suspicion for mycosis. Diagnostic tests also have limitations beginning with sampling. Therefore, in the remainder of the pandemic, these diagnostic limitations must be overcome to achieve a better patient prognosis.

Coinfections with Bacteria, Fungi, and Respiratory Viruses in Patients with SARS-CoV-2: A Systematic Review and Meta-Analysis

Background: Coinfection with bacteria, fungi, and respiratory viruses in SARS-CoV-2 is of particular importance due to the possibility of increased morbidity and mortality. In this meta-analysis, we calculated the prevalence of such coinfections. Methods: Electronic databases were searched from 1 December 2019 to 31 March 2021. Effect sizes of prevalence were pooled with 95% confidence intervals (CIs). To minimize heterogeneity, we performed sub-group analyses. Results: Of the 6189 papers that were identified, 72 articles were included in the systematic review (40 case series and 32 cohort studies) and 68 articles (38 case series and 30 cohort studies) were included in the meta-analysis. Of the 31,953 SARS-CoV-2 patients included in the meta-analysis, the overall pooled proportion who had a laboratory-confirmed bacterial infection was 15.9% (95% CI 13.6–18.2, n = 1940, 49 studies, I² = 99%, p < 0.00001), while 3.7% (95% CI 2.6–4.8, n = 177, 16 studies, I² = 93%, p < 0.00001) had fungal infections and 6.6% (95% CI 5.5–7.6, n = 737, 44 studies, I² = 96%, p < 0.00001) had other respiratory viruses. SARS-CoV-2 patients in the ICU had higher co-infections compared to ICU and non-ICU patients as follows: bacterial (22.2%, 95% CI 16.1–28.4, I² = 88% versus 14.8%, 95% CI 12.4–17.3, I² = 99%), and fungal (9.6%, 95% CI 6.8–12.4, I² = 74% versus 2.7%, 95% CI 0.0–3.8, I² = 95%); however, there was an identical other respiratory viral co-infection proportion between all SARS-CoV-2 patients [(ICU and non-ICU) and the ICU only] (6.6%, 95% CI 0.0–11.3, I² = 58% versus 6.6%, 95% CI 5.5–7.7, I² = 96%). Funnel plots for possible publication bias for the pooled effect sizes of the prevalence of coinfections was asymmetrical on visual inspection, and Egger’s tests confirmed asymmetry (p values < 0.05). Conclusion: Bacterial co-infection is relatively high in hospitalized patients with SARS-CoV-2, with little evidence of S. aureus playing a major role. Knowledge of the prevalence and type of co-infections in SARS-CoV-2 patients may have diagnostic and management implications.

Multidrug Resistence Prevalence in COVID Area

Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, is often complicated by severe acute respiratory syndrome. The new coronavirus outbreak started in China in December 2019 and rapidly spread around the world. The high diffusibility of the virus was the reason for the outbreak of the pandemic viral disease, reaching more than 100 million infected people globally by the first three months of 2021. In the various treatments used up to now, the use of antimicrobial drugs for the management, especially of bacterial co-infections, is very frequent in patients admitted to intensive care. In addition, critically ill patients with SARS-CoV-2 infection are subjected to prolonged mechanical ventilation and other therapeutic procedures often responsible for developing hospital co-infections due to multidrug-resistant bacteria. Co-infections contribute to the increase in the morbidity-mortality of viral respiratory infections. We performed this study to review the recent articles published on the antibiotic bacterial resistance and viruses to predict risk factors of coronavirus disease 2019 and to assess the multidrug resistance in patients hospitalized in the COVID-19 area.

A Pandemic within Other Pandemics. When a Multiple Infection of a Host Occurs: SARS-CoV-2, HIV and Mycobacterium tuberculosis

By the middle of 2021, we are still immersed in the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The concurrence of this new pandemic in regions where human immunodeficiency virus (HIV) and tuberculosis (TB) infections possess the same epidemiological consideration, has arisen concerns about the prognosis, clinical management, symptomatology, and treatment of patients with triple infection. At the same time, healthcare services previously devoted to diagnosis and treatment of TB and HIV are being jeopardized by the urgent need of resources and attention for COVID-19 patients. The aim of this review was to collect any article considering the three conditions (HIV, TB, and SARS-CoV-2), included in PubMed/Medline and published in the English language since the beginning of the COVID-19 pandemic. We focused on detailed descriptions of the unusual cases describing the three co-infections. Eighty-four out of 184 publications retrieved met our inclusion criteria, but only three of them reported cases (five in total) with the three concomitant infections. The clinical evolution, management, and therapy of all of them were not different from mild/severe cases with exclusive COVID-19; the outcome was not worse either, with recovery for the five patients. Cases of patients with COVID-19 besides HIV and TB infections are scarce in literature, but studies deliberately embracing the triple infection as a priori inclusion criterion should be carried out in order to provide a complete understanding of joint influence.

Carbapenem-Resistant Klebsiella pneumoniae Infections in ICU COVID-19 Patients-A Scoping Review

Introduction: The spread of multidrug-resistant pathogens is a serious problem and challenge for the whole medical community. Carbapenem-resistant Klebsiella pneumoniae (CRKP) infections in immunocompromised patients have a severe course and may be fatal. Increasingly, these bacteria are exhibiting resistance to carbapenem antibiotics, which have been used as so-called drugs of last resort. The emergence of the new coronavirus and the pandemic that it has caused require changes to protect against the spread of the new SARS-CoV-2. These changes paradoxically may contribute to the spread of other infections. Methods: PubMed, Cochrane Library databases were searched using relevant keywords. A literature review of carbapenem-resistant Klebsiella pneumoniae infection in patients hospitalized for COVID-19 was conducted according to PRISMA recommendations. A written review protocol was not prepared. Results: 1016 studies in scientific databases were searched. After rejecting duplicate studies, 964 results were obtained. Inclusion and exclusion criteria were then applied, and studies were qualitatively analyzed. Finally, 11 studies were included in the review. The results of infected patients were from six countries. The prevalence of CRKP in Covid-19 patients ranged from 0.35–53%. The majority of CRKP infected patients were male (85%), with a mean age of 61 years. Among isolates, the predominant genes were KPC, OXY-48, CTX-M, TEM, NDM and SHV. Conclusion: The results presented in our review indicate the necessity of paying attention to carbapenem-resistant Klebsiella pneumoniae infections in patients with COVID-19. In order to prevent the increase of bacterial resistance, rational antibiotic therapy should be used, as well as continuous control and surveillance of hospital infections caused by multidrug-resistant organisms.

Prevalence and outcomes of co-infection and superinfection with SARS-CoV-2 and other pathogens: A systematic review and meta-analysis

INTRODUCTION

The recovery of other pathogens in patients with SARS-CoV-2 infection has been reported, either at the time of a SARS-CoV-2 infection diagnosis (co-infection) or subsequently (superinfection). However, data on the prevalence, microbiology, and outcomes of co-infection and superinfection are limited. The purpose of this study was to examine the occurrence of co-infections and superinfections and their outcomes among patients with SARS-CoV-2 infection.

PATIENTS AND METHODS

We searched literature databases for studies published from October 1, 2019, through February 8, 2021. We included studies that reported clinical features and outcomes of co-infection or superinfection of SARS-CoV-2 and other pathogens in hospitalized and non-hospitalized patients. We followed PRISMA guidelines, and we registered the protocol with PROSPERO as: CRD42020189763.

RESULTS

Of 6639 articles screened, 118 were included in the random effects meta-analysis. The pooled prevalence of co-infection was 19% (95% confidence interval [CI]: 14%-25%, I2 = 98%) and that of superinfection was 24% (95% CI: 19%-30%). Pooled prevalence of pathogen type stratified by co- or superinfection were: viral co-infections, 10% (95% CI: 6%-14%); viral superinfections, 4% (95% CI: 0%-10%); bacterial co-infections, 8% (95% CI: 5%-11%); bacterial superinfections, 20% (95% CI: 13%-28%); fungal co-infections, 4% (95% CI: 2%-7%); and fungal superinfections, 8% (95% CI: 4%-13%). Patients with a co-infection or superinfection had higher odds of dying than those who only had SARS-CoV-2 infection (odds ratio = 3.31, 95% CI: 1.82-5.99). Compared to those with co-infections, patients with superinfections had a higher prevalence of mechanical ventilation (45% [95% CI: 33%-58%] vs. 10% [95% CI: 5%-16%]), but patients with co-infections had a greater average length of hospital stay than those with superinfections (mean = 29.0 days, standard deviation [SD] = 6.7 vs. mean = 16 days, SD = 6.2, respectively).

CONCLUSIONS

Our study showed that as many as 19% of patients with COVID-19 have co-infections and 24% have superinfections. The presence of either co-infection or superinfection was associated with poor outcomes, including increased mortality. Our findings support the need for diagnostic testing to identify and treat co-occurring respiratory infections among patients with SARS-CoV-2 infection.