Co-infections In COVID-19 Patients Research Articles

Evaluation of serum procalcitonin level as a biomarker for disease severity in Covid-19 patients: The experience of Mohammed VI University Hospital in Oujda.

The pandemic of coronavirus disease (Covid-19) has infected millions of individuals around the globe. The current study was aimed to evaluate the serum procalcitonin (PCT) level as a biomarker for bacterial co-infection and disease severity in Covid-19 patients. A total of 319 Covid-19 positive patients were examined in this study. Among the total individuals, 169 (53%) were male while 150 (47%) were female. Among the examined samples, 142 (44.5%) were hospitalized in Covid services, and 177(55.5%) were admitted in the intensive care unit (ICU). The mean PCT level for Covid-19 services patients was 0.58 ng/mL and for ICU patients was 7.84 ng/mL. The statistical analysis revealed that there was a significant association of PCT value and age (P<0,0001) while there was no association of gender and PCT value in COVID-19 patients (P=0.2745). Most Covid-19 patients have low PCT levels but elevated markers of inflammation such as C-reactive protein (CRP) on admission. It can be concluded that the serial PCT measurement could determine the prognosis of disease and presence of bacterial co-infection in Covid-19 patients. The main objective of our study is to determine the role of serum procalcitonin in the diagnosis and clinical management of patients with COVID-19 from Oriental Region of Morocco, also we evaluate the correlation between Procalcitonin and disease severity in COVID-19. We report the experience of the Moroccan Mohammed VI University Hospital of Oujda.

Secondary pulmonary infection and co-infection in elderly COVID-19 patients during the pandemics in a tertiary general hospital in Beijing, China.

Most people are infected with COVID-19 during pandemics at the end of 2022. Older patients were more vulnerable. However, the incidence of secondary bacterial, fungal or viral pulmonary infection and co-infection is not well described in elderly hospitalized COVID-19 patients. We retrospectively reviewed the medical records of all elderly (≥65 years) hospitalized patients with laboratory-confirmed COVID-19 from December 1, 2022 to January 31, 2023. Demographics, underlying diseases, treatments, and laboratory data were collected. Univariate and multivariate logistic regression models were used to explore the risk factors associated with secondary bacterial, fungal or viral pulmonary infection and co-infection. A total of 322 older patients with COVID-19 were enrolled. The incidence of secondary bacterial, fungal or viral pulmonary infection and co-infection was 27.3% (88/322) and 7.5% (24/322), respectively. The overall in-hospital mortality of all patients was 32.9% (106/322), and the in-hospital mortality among patients who acquired with secondary pulmonary infection and co-infection was 57.0% (57/100). A total of 23.9% (77/322) of patients were admitted to ICU within 48 h of hospitalization. The incidence of secondary pulmonary infection and co-infection among patients admitted to the ICU was 50.6% (39/77) and 13.0% (10/77), respectively. The overall in-hospital mortality of ICU patients was 48.1% (37/77), and the in-hospital mortality of ICU patients acquired with secondary pulmonary infection and co-infection was 61.4% (27/44). A total of 83.5% (269/322) of the included patients received empirical antibiotic therapy before positive Clinical Microbiology results. Influenza A virus (the vast majority were the H3N2 subtype) was the most common community acquired pathogen for co-infection. While A. baumannii, K. pneumoniae, and P. aeruginosa were the common hospital acquired pathogens for co-infection and secondary pulmonary infection. The incidence of Carbapenem-resistant Gram-negative bacilli (CR-GNB) infections was high, and the mortality reached 76.9%. Predictors of secondary pulmonary infection and co-infection were ICU admission within 48 h of hospitalization, cerebrovascular diseases, critical COVID-19, and PCT > 0.5 ng/mL. The prognosis for elderly hospitalized COVID-19 patients with secondary pulmonary infection or co-infection is poor. The inflammatory biomarker PCT > 0.5 ng/mL played an important role in the early prediction of secondary pulmonary infection and co-infection in COVID-19 patients.

Typing of Candida spp. from Colonized COVID-19 Patients Reveal Virulent Genetic Backgrounds and Clonal Dispersion.

Advances in the knowledge of the pathogenesis of SARS-CoV-2 allowed the survival of COVID-19 patients in intensive care units. However, due to the clinical characteristics of severe patients, they resulted in the appearance of colonization events. Therefore, we speculate that strains of Candida spp. isolated from COVID-19 patients have virulent genetic and phenotypic backgrounds involved in clinical worsening of patients. The aim of this work was to virutype Candida spp. strains isolated from colonized COVID-19 patients, analyze their genomic diversity, and establish clonal dispersion in care areas. The virulent potential of Candida spp. strains isolated from colonized COVID-19 patients was determined through adhesion tests and the search for genes involved with adherence and invasion. Clonal association was done by analysis of intergenic spacer regions. Six species of Candida were involved as colonizing pathogens in COVID-19 patients. The genotype analysis revealed the presence of adherent and invasive backgrounds. The distribution of clones was identified in the COVID-19 care areas, where C. albicans was the predominant species. Evidence shows that Candida spp. have the necessary genetic tools to be able colonize the lungs, and could be a possible causal agent of coinfections in COVID-19 patients. The detection of dispersion of opportunistic pathogens can be unnoticed by classical epidemiology. Epidemiological surveillance against opportunistic fungal pathogens in COVID-19 patients is an immediate need, since the findings presented demonstrate the potential virulence of Candida spp.

Prevalence and associated outcomes of coinfection between SARS-CoV-2 and influenza: a systematic review and meta-analysis

ObjectivesTo estimate the prevalence of influenza coinfection in COVID-19 patients and investigate its association with severe clinical outcomes. MethodsWe systematically searched the Web of Science, PubMed, Scopus, Embase, The Cochrane Library, and CNKI for studies published between January 01, 2020, and May 31, 2023. Meta-analysis was performed to estimate the pooled prevalence of coinfection and the impact on clinical outcomes. Systematic review registered in PROSPERO (CRD42023423113). ResultsA total of 95 studies involving 62,107 COVID-19 patients were included. The pooled prevalence of coinfection with influenza virus was 2.45% (95% confidence interval [CI]: 1.67-3.58%), with a high proportion of influenza A. Compared with mono-infected patients (COVID-19 only), the odds ratio (OR) for severe outcomes (including intensive care unit admission [OR = 2.20, 95% CI: 1.68-2.87, P < 0.001], mechanical ventilation support [OR = 2.73, 95% CI: 1.46-5.10, P = 0.002], and mortality [OR = 2.92, 95% CI: 1.16-7.30, P = 0.022]) was significantly higher among patients coinfected influenza A. ConclusionAlthough the prevalence of coinfection is low, coinfected patients are at higher risk of severe outcomes. Enhanced identification of both viruses, as well as individualized treatment protocols for coinfection, are recommended to reduce the occurrence of serious disease outcomes in the future.

Co-infection in COVID-19 patients performed microbiology detection: discovering multidrug resistant microorganisms increased during the COVID-19 pandemic in Shanghai, China

Co-infection in COVID-19 patients performed microbiology detection: discovering multidrug resistant microorganisms increased during the COVID-19 pandemic in Shanghai, China

Impact of antimicrobial stewardship in organisms causing nosocomial infection among COVID-19 critically ill adults

ObjectiveTo evaluate the implementation of an antibiotic stewardship program in critically ill COVID-19 patients and to establish risk factors for coinfection. Secondary objective was to analyze the evolution of the etiology of respiratory nosocomial infections. MethodsSingle-center observational cohort study of consecutive patients admitted to ICU due to COVID-19 pneumonia from March 2020 to October 2022. An antibiotic stewardship program was implemented at the end of the second wave. ResultsA total of 878 patients were included during 6 pandemic waves. Empirical antibiotic consumption decreased from the 96% of the patients during the first pandemic wave, mainly in combination (90%) to the 30% of the patients in the 6th pandemic wave most in monotherapy (90%). There were not differences in ICU and Hospital mortality between the different pandemic periods. In multivariate analysis, SOFA at admission was the only independent risk factor for coinfection in critically ill COVID-19 patients (OR 1,23 95%CI 1,14 to 1,35). Differences in bacterial etiology of first nosocomial respiratory infection were observed. There was a progressive reduction in Enterobacteriaceae and non- fermentative Gram Negative Bacilli as responsible pathogens, while methicillin-sensitive Staphylococcus aureus increased during pandemic waves. In the last wave, however, a trend to increase of potentially resistant pathogens was observed. ConclusionsImplementation of an antibiotic stewardship program was safe and not associated with worse clinical outcomes, being severity at admission the main risk factor for bacterial coinfection in covid-19 patients. A decline in potentially resistant pathogens was documented throughout the pandemic.

Prevalence of asymptomatic strongyloidiasis co-infection in COVID-19 patients residing in endemic areas

BackgroundFatal forms of strongyloidiasis, hyperinfection syndrome (HS) and disseminated strongyloidiasis (DS), are caused by exaggerated autoinfection of the intestinal nematode, Strongyloides stercoralis (S. stercoralis). Corticosteroids, frequently administered to patients with severe COVID-19, can transform chronic asymptomatic strongyloidiasis into the above-mentioned fatal diseases. This study aimed to investigate the prevalence of strongyloidiasis in COVID-19 patients receiving corticosteroids in a hypoendemic region.MethodsThe present cross-sectional study enrolled 308 COVID-19 patients admitted to two hospitals in Ahvaz and Abadan in the southwest of Iran between 2020 and 2022. A real-time reverse transcription polymerase chain reaction (RT-PCR) test and chest computed tomography (CT) scan were employed to detect and monitor the disease’s severity in the patients, respectively. All patients were evaluated for IgG/IgM against S. stercoralis using Enzyme-linked immunosorbent assay (ELISA) test. Subsequently, individuals with a positive ELISA test were confirmed using parasitological methods, including direct smear and agar plate culture (APC).ResultsThe patients were between 15 and 94 years old, with a mean age of 57.99 ± 17.4 years. Of the 308 patients, 12 (3.9%) had a positive ELISA test, while 296 (96.1%) had negative results. Three of the 12 patients with a positive ELISA result died, and three failed to provide a stool sample. To this end, only six cases were examined parasitologically, in which S. stercoralis larvae were observed in five patients. Significant differences were found between S. stercoralis infection with sex (p = 0.037) and age (p = 0.027). Binary regression analysis revealed that strongyloidiasis was positively associated with sex (odds ratio [OR]: 5.137; 95% confidence interval [CI]: 1.107–23.847), age (OR: 5.647; 95% CI 1.216–26.218), and location (OR: 3.254; 95% CI: 0.864–12.257).ConclusionsOur findings suggest that screening for latent strongyloidiasis in COVID-19 patients in endemic areas using high-sensitivity diagnostic methods, particularly ELISA, before receiving suppressive drugs should be given more consideration.

Strongyloides coinfection in COVID-19 patients treated with corticosteroids: A systematic review.

The COVID-19 pandemic linked to the virus SARS-CoV-2, which began in China, affected ∼765 million people as of 30 April 2023. The widespread use of corticosteroids for the symptomatic treatment of COVID-19 could lead to the reactivation of infections of opportunistic pathogens, including Strongyloides. We sought to determine the clinical symptoms and demographic characteristics of SARS-CoV-2-Strongyloides co-infection, particularly in patients with severe disease and being treated with immunosuppressive drugs. To do this, we undertook a systematic review of the literature, and searched public accessible scientific databases-the Web of Science, Scopus, PubMed/Medline and Embase -for eligible studies (1 December 2019 to 30 August 2022). The review protocol is registered in PROSPERO (CRD42022377062). Descriptive statistical analyses were used to present the clinical and laboratory parameters of the co-infection; for this, we calculated prevalence using the following formula: positive cases/total number of cases×100. Of a total of 593 studies identified, 17 studies reporting 26 co-infected patients met the criteria for inclusion in this review. The median age of these patients was 55.14years. Most of cases (53.8%) were treated with dexamethasone, followed by methylprednisolone (26.9%). Eighteen of 26 patients were immigrants living in European countries or the USA; most of these immigrants originated from Latin America (58%) and South-East Asia (11%). The commonest symptoms of co-infection were abdominal pain (50%), fever (46.1%), dyspnoea (30.7%) and cough (30.7%), and frequently reported laboratory findings were high absolute eosinophil count (38.4%), high white blood cell count (30.7%), high C-reactive protein (23.0%) and high neutrophil count (19.2%). Two of the 26 patients (7.7%) had fatal outcomes. Most of the SARS-CoV-2-Strongyloides coinfected cases were immigrants living in developed countries, emphasising the need for clinicians in these countries to be aware of clinical and laboratory parameters associated with such co-infections, as well as the key importance of rapid and accurate diagnostic tests for timely and effective diagnosis and patient management.

Coinfections in intensive care units. Has anything changed with Covid-19 pandemia?

Since December 2019, the Coronavirus disease 2019, caused by severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2), has spread from China, becoming a pandemic. Bacterial and fungal co-infections may lead to increase in COVID-19 severity with a decrease in patients survive. The aim of this work was to evaluate bacterial and fungal co-infections in COVID-19 patients admitted to ICU in comparison with patients recovered in ICU in pre-COVID-19 era in order to understand whether the pandemic had changed the incidence of overinfections in patients admitted to ICU. In fact, the epidemiological data should guide the choice of empirical therapy. During pandemic, AOUC Policlinico of Bari organized dedicated ICUs for patient with SARS-CoV-2. Blood cultures, urine, and tracheobronchial aspirate were included in the analysis. Specimens of 1905 patients were analysed in this work. Comparing clinical isolates prevalence by material and COVID-19 vs. non-COVID-19 patients statistically significant differences were detected for A. baumannii complex, Aspergillus fumigatus, Escherichia coli, Haemophilus influenzae and Serratia marcescens isolated from tracheobronchial aspirates; C. albicans from urine samples, A. baumannii complex, Enterococcus faecalis and Enterococcus faecium isolated from blood culture. Although the organisms isolated in COVID-19 patients are consistent with those frequently associated with healthcare associated infection, our data suggest a particular prevalence in COVID-19 patients of A. baumannii, Stenotrophomonas maltophilia and Aspergillus spp. in the respiratory tract, C. albicans in urine and A. baumannii, E. faecalis and E. faecium in blood cultures.

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.

Viral reactivations and co-infections in COVID-19 patients: a systematic review

BackgroundViral reactivations and co-infections have been reported among COVID-19 patients. However, studies on the clinical outcomes of different viral reactivations and co-infections are currently in limit. Thus, the primary purpose of this review is to perform an overarching investigation on the cases of latent virus reactivation and co-infection in COVID-19 patients to build collective evidence contributing to improving patient health. The aim of the study was to conduct a literature review to compare the patient characteristics and outcomes of reactivations and co-infections of different viruses.MethodsOur population of interest included confirmed COVID-19 patients who were diagnosed with a viral infection either concurrently or following their COVID-19 diagnosis. We extracted the relevant literature through a systematic search using the key terms in the online databases including the EMBASE, MEDLINE, Latin American Caribbean Health Sciences Literature (LILACS), from inception onwards up to June 2022. The authors independently extracted data from eligible studies and assessed the risk of bias using the Consensus-based Clinical Case Reporting (CARE) guidelines and the Newcastle–Ottawa Scale (NOS). Main patient characteristics, frequency of each manifestation, and diagnostic criteria used in studies were summarized in tables.ResultsIn total, 53 articles were included in this review. We identified 40 reactivation studies, 8 coinfection studies, and 5 studies where concomitant infection in COVID-19 patients was not distinguished as either reactivation or coinfection. Data were extracted for 12 viruses including IAV, IBV, EBV, CMV, VZV, HHV-1, HHV-2, HHV-6, HHV-7, HHV-8, HBV, and Parvovirus B19. EBV, HHV-1, and CMV were most frequently observed within the reactivation cohort, whereas IAV and EBV within the coinfection cohort. In both reactivation and coinfection groups, patients reported cardiovascular disease, diabetes, and immunosuppression as comorbidities, acute kidney injury as complication, and lymphopenia and elevated D-dimer and CRP levels from blood tests. Common pharmaceutical interventions in two groups included steroids and antivirals.ConclusionOverall, these findings expand our knowledge on the characteristics of COVID-19 patients with viral reactivations and co-infections. Our experience with current review indicates a need for further investigations on virus reactivation and coinfection among COVID-19 patients.

Mucormycosis: Issues, Pathophysiology, Diagnosis and Treatment

Mucormycosis (Black fungus) is an infection caused by opportunistic fungi of order Mucorales affecting the immune-compromised individuals. Cases of Aspergillus and Candida (White fungus) were also reported. The cases of fungal co-infection in COVID-19 patients are increasing globally affecting mainly diabetic patients and individuals that have undergone corticosteroid therapy. Iron metabolism and hypoxia plays an important role in pathophysiology of this disease. Mucormycosis causes thrombosis of blood vessels hindering the blood circulation causing black discoloration of affected site. Histopathological examination of specimen is the most effective way of its diagnosis. Surgical removal of affected site is the best treatment practice in rhino-orbital and cutaneous cases whereas lipid formulation of Amphotericin B is effective in other forms of fungal infection.

Bacterial co-infection in Covid-19 patients visiting a tertiary care hospital in Maharashtra

Background and objectives: Several patients with SARS-CoV-2 infection presents with bacterial co-infection. The aim of the present study was to determine the bacteria responsible for co-infection in Covid-19 infected patients visiting a tertiary care hospital of Maharashtra, India. Material and methods: A cross sectional study was conducted for 3 months at tertiary care center. Covid-19 patients attending the hospital were included in the study. All the specimens were collected either at the time of admission at outdoor or within 24-48 hours of admission. All the specimens were processed for culture and antibiotic susceptibility testing as per institutional policy and standard methods. Results: Total 200 samples were collected out of which 98 (49%) patients were diagnosed with bacterial co-infection. Majority of cases with bacterial co-infection were above 21 years of age. Culture was positive in 80%, 66.7%, 49.2% and 38.8% of tracheal aspirate, pus, blood and urine samples respectively. Out of 98 cases of bacterial co-infection, 62.2% and 37.8% had infection with Gram negative and positive bacteria respectively. Most common organism isolated was Klebsiella pneumoniae (20.4%) followed by Enterococcus species (14.3%). Over 70% of Klebsiella pneumoniae isolates were resistant to aminoglycosides, cephalosporins, fluroquinolones and carbapenems while 100% Acinetobacter was resistant to all antimicrobials tested. Among 57 Of the Gram negative isolates, 5 and 24 isolates were positive for ESBL carbapenemase respectively. Conclusion: The study revealed that bacterial co-infection was present in considerable proportion of Covid-19 patients and the organisms responsible were resistant to several antimicrobial agents. IMC J Med Sci. 2023; 17(2):006. DOI: https://doi.org/10.55010/imcjms.17.016 *Correspondence: Sahjid Mukhida, Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, India-411018. E-mail: drssmukhida@rediffmail.com

No sign of Rotavirus co-infection in COVID-19 patients with gastrointestinal symptoms.

The main goal of the present study is to investigate the incidence of Rotavirus co-infection in COVID-19 patients. Fecal samples of COVID-19 patients with gastrointestinal symptoms which had positive PCR- were collected from Abadan's hospital, Iran during the period December 2020 to January 2021. Samples were analyzed by RT-PCR to determine the presence of Rotavirus. Finally, the total samples size of 37 were included in this study. The mean age of patients was 48.22 years. Abdominal pain alone was detected in 48.65% of the patients. At least one gastrointestinal symptom was detected in all of the patients. Diarrhea and fever were seen in 13.51% and 59.46% of patients, respectively. Nausea and vomiting were seen in 5.41% of the patients. RT-PCR showed no infection of Rotavirus among the patients. Gastrointestinal symptoms related to COVID-19 are common. More studies is need among these patients groups for investigate co-infection with other fecal viral shedding carries, due to a worse prognosis and its association with disease severity.

Bacterial Co-infections and Susceptibility patterns among admitted COVID 19 patients during 3rd wave of pandemic, in a Tertiary Care Hospital. Lahore.

Objective: To check the Bacterial Co-infections and Susceptibility patterns among admitted COVID-19 patients during 3rd wave of pandemic. Study Design: Descriptive Cross Sectional study. Setting: Department of Microbiology, Combined Military Hospital Lahore Pakistan. Period: May 2021 to August 2021. Material &amp; Methods: Six hundred and twelve COVID-19 positive patients having positive bacterial cultures were processed, Antibiotic susceptibility testing was done by Kirby-Bauer diffusion technique, all antibiotics were reported using breakpoints recommended in clinical and laboratory standards institute (CLSI 2021). Results: Out of 612 patients, 348 (56.9%) were male and 264 (43.2%) were female. Mean age of the patients was 57.2 ± 14.4 years with a range of 22 to 89 years. Bacterial coinfection was present in 70.4% of the patients. Gram negative bacteria (94.4%) were more prevalent in COVID-19 patients as compared to gram positive isolates (5.6%). Antibiotic sensitivity pattern of Staphylococcus aureus showed a high resistance against penicillin, ampicillin, tetracycline and doxycycline. Conclusion: Our study reported a high prevalence of bacterial coinfections in COVID-19 patients infected during the third wave of pandemic. A high percentage of gram negative species were identified in our study population, this could be due to the suppression in the immunity of individuals due to severity of COVID-19 infection and already present Antimicrobial resistance.

Are bacterial coinfections really rare in COVID-19 intensive care units?

ObjectivesThere are limited data about nosocomial coinfections of COVID-19 cases monitored in the intensive care unit. This study aims to investigate coinfections in COVID-19 patients followed in an intensive care unit of a university hospital.MethodsThis study analyzed retrospectively the data of coinfections of 351 COVID-19 patients in the period 28.02.2020–15.01.2021 in a tertiary care intensive care unit in a university hospital.ResultsBacterial coinfections were present in 216 of the 351 cases. One hundred and thirty of these cases were evaluated as nosocomial infections. On the third day the Sequential Organ Failure Assessment Score, usage of invasive mechanical ventilation and presence of septic shock were significantly higher in the coinfected group. The neutrophil/lymphocyte ratio, polymorphonuclear leukocyte count, procalcitonin, ferritin, and blood urea nitrogen values were significantly higher in the coinfection group. White blood cells (WBC) (OR: 1.075, 95% CI 1.032–1.121, p = 0.001) and ICU hospitalization day (OR: 1.114, 95% CI 1.063–1.167, p < 0.001) were found to be independent risk factors for coinfection in the multivariate logistic regression analysis. The rates of hospitalization day on the day of arrival, the 21st day, as well as total mortality (p = 0.004), were significantly higher in the coinfected group.ConclusionBacterial coinfections of COVID-19 patients in the intensive care unit remain a problem. Identifying the infectious agent, classifying colonizations and infections, and using the proper treatment of antibiotics are of great importance in the case management of COVID-19 patients in the intensive care unit.

Transcriptome analysis reveals increased abundance and diversity of opportunistic fungal pathogens in nasopharyngeal tract of COVID-19 patients.

We previously reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiomes (bacteria, archaea and commensal respiratory viruses) with inclusion of pathobionts. This study aimed to assess the possible changes in the abundance and diversity of resident mycobiome in the nasopharyngeal tract (NT) of humans due to SARS-CoV-2 infections. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected for RNA-sequencing followed by taxonomic profiling of mycobiome. Our analyses indicate that SARS-CoV-2 infection significantly increased (p < 0.05, Wilcoxon test) the population and diversity of fungi in the NT with inclusion of a high proportion of opportunistic pathogens. We detected 863 fungal species including 533, 445, and 188 species in COVID-19, Recovered, and Healthy individuals, respectively that indicate a distinct mycobiome dysbiosis due to the SARS-CoV-2 infection. Remarkably, 37% of the fungal species were exclusively associated with SARS-CoV-2 infection, where S. cerevisiae (88.62%) and Phaffia rhodozyma (10.30%) were two top abundant species. Likewise, Recovered humans NT samples were predominated by Aspergillus penicillioides (36.64%), A. keveii (23.36%), A. oryzae (10.05%) and A. pseudoglaucus (4.42%). Conversely, Nannochloropsis oceanica (47.93%), Saccharomyces pastorianus (34.42%), and S. cerevisiae (2.80%) were the top abundant fungal species in Healthy controls nasal swabs. Importantly, 16% commensal fungal species found in the Healthy controls were not detected in either COVID-19 patients or when they were cured from COVID-19 (Recovered). We also detected several altered metabolic pathways correlated with the dysbiosis of fungal mycobiota in COVID-19 patients. Our results suggest that SARS-CoV-2 infection causes significant dysbiosis of mycobiome and related metabolic functions possibly play a determining role in the progression of SARS-CoV-2 pathogenesis. These findings might be helpful for developing mycobiome-based diagnostics, and also devising appropriate therapeutic regimens including antifungal drugs for prevention and control of concurrent fungal coinfections in COVID-19 patients.

PS-C16-11: PREVALENCE AND HOSPITAL OUTCOME OF BACTERIAL CO-INFECTION IN RESPIRATORY TRACT SPECIMEN AMONG COVID 19 PATIENTS WITH SARS-COV-2 PNEUMONIA

Introduction: COVID-19, a zoonotic disease caused by the novel coronavirus SARS-CoV-2, is a highly transmittable pathogenic viral infection, infecting millions of people globally. Guidelines recommendthe use of empiric antimicrobials based on clinical judgment, patient host factors and local epidemiology in patients suspected or confirmed severe COVID-19. However, current evidence does not support a high rate of bacterial respiratory co-infections in patients with SARS-COV-2 infection. At present, there is no known study regarding the prevalence of bacterial co-infection in COVID-19 patients in the Philippines Methods: This research is a cross-sectional hospital-based study that utilized hospital electronic and printed medical records, chest radiograph and microbiologic results. All respiratory specimen bacteriologic results for the year 2020 and 2021 were collected from the hospital laboratory unit followed by review of the hospital electronic records, printed medical records and chest radiograph results. Data were analyzed using Two-tailed Z-test for significance test for proportions and Chi-square test. Results: Among 100 subjects, only 22% (n = 22) of the subjects were found to have bacterial isolates. the only demographic that is dependent with presence of bacterial infection is gender. The three most common bacterial isolate among COVID confirmed patients are Klebsiella pneumoniae (n = 9), Pseudomonas aeruginosa (n = 5), and Acinetobacter baumannii (n = 3). Although the most common bacterial isolate is Klebsiella pneumoniae, the most common bacterial co-infection in patients who died are Acinetobacter baumannii (n = 2, 29%)and Pseudomonas aeruginosa (n = 2, 29%). Conclusion: The prevalence of bacterial co-infection among COVID confirmed patients is relatively low, hence appropriate guidelines regarding antibiotic use should be formed taking into consideration local data on antimicrobial resistance.

PROCALCITONINA COMO FERRAMENTA DE GERENCIAMENTO DE ANTIMICROBIANOS EM PACIENTES COM COVID-19

ABSTRACT Objective: to investigate the relationship between procalcitonin in the differential diagnosis of bacterial coinfection in COVID-19 patients. Method: a cross-sectional retrospective study conducted between February and March 2021 in the Intensive Care Unit of a public hospital from southern Brazil by filling in a form. Descriptive statistical analyses were performed, as well as of association between variables. Results: of the 231 patients, 28.14% presented infection (63.20% in the lungs), 25% had bacteria isolated, 77.49% used antimicrobials and, in 14.72% of the cases, procalcitonin &gt; 2 ng/mL. There was a significant association between antimicrobial use and infection (p=0.001), isolation of bacteria (p&lt;0.001), topography of the infection (p&lt;0.001) and procalcitonin values (p&lt;0.001). Procalcitonin use showed an association with bacterial infection (p&lt;0.001), isolation of bacteria (p&lt;0.001), antimicrobial use (p=0.001) and death (p&lt;0.001). Conclusion: procalcitonin can reduce empirical antimicrobial use and stimulate detection and identification of pathogens, taking into account the clinical and epidemiological data.

Diagnosis of Legionnaires' Disease Assisted by Next-Generation Sequencing in a Patient with COVID-19.

Coinfection in COVID-19 patients is associated with worsening outcome. Among patients with COVID-19, Legionella pneumophila, a common cause of pneumonia, has been reported as a co-occurring respiratory infection. A nonspecific clinical presentation, however, makes an early diagnosis difficult. Bronchoalveolar lavage fluid was collected from a patient suffering from COVID-19 and presenting with pneumonia and sent for metagenomic analysis. Differential abundance analysis was carried out by comparing each taxon reads per million between the bronchoalveolar lavage fluid sample and the negative control. Two replicates of metagenomic sequencing were conducted on bronchoalveolar lavage fluid samples. Within each replicated sequencing, one negative control was sequenced for comparison of taxon abundance in the BALF sample. In both replicates, Legionella pneumophila was the only taxon with significantly higher abundance when compared with the negative control. PCR of the bronchoalveolar further confirmed the presence of L. pneumophila. Several studies have estimated that the incidence of Legionnaires' disease co-infection in patients with COVID-19 infection is approximately 0% to 1.5%. There are some common characteristics of COVID-19 and co-infection with Legionnaires' disease, making it difficult to diagnose bacterial infection early. The diagnosis of these cases is important due to the different treatments used. Current diagnostic tests for Legionnaires' disease include conventional culture, urinary antigen for L. pneumophila serogroup 1, polymerase chain reaction, direct fluorescent antibody stain, and paired serology. The current study demonstrated that metagenomics is a promising approach that facilitated the diagnosis of Legionnaires' disease.