Analysis of the nasopharyngeal microbiome and respiratory pathogens in COVID-19 patients from Saudi Arabia

Background Infection with SARS-CoV-2 may perturb normal microbiota, leading to secondary infections that can complicate the viral disease. The aim of this study was to probe the alteration of nasopharyngeal (NP) microbiota in the context of SARS-CoV-2 infection and obesity and to identify other respiratory pathogens among COVID-19 cases that may affect patients' health. Methods A total of 107 NP swabs, including 22 from control subjects and 85 from COVID-19 patients, were processed for 16 S amplicon sequencing. The respiratory pathogens causing secondary infections were identified by RT-PCR assay, using a kit that contained specific primers and probes combinations to amplify 33 known respiratory pathogens. Results No significant (p>0.05) difference was observed in the alpha and beta diversity analysis, but specific taxa differed significantly between the control and COVID-19 patient groups. Genera of Sphingomonas, Kurthia, Microbacterium, Methylobacterium, Brevibacillus, Bacillus, Acinetobacter, Lactococcus, and Haemophilus was significantly abundant (p<0.05) in COVID-19 patients compared with a healthy control group. Staphylococcus was found in relatively high abundance (35.7%) in the COVID-19 patient groups, mainly those treated with antibiotics. A relatively high percentage of Streptococcus was detected in COVID-19 patient groups with obesity or other comorbidities. Respiratory pathogens, including Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Salmonella species, along with Pneumocystis jirovecii fungal species were detected by RT-PCR mainly in the COVID-19 patients. Klebsiella pneumoniae was commonly found in most of the samples from the control and COVID-19 patients. Four COVID-19 patients had viral coinfections with human adenovirus, human rhinovirus, enterovirus, and human parainfluenza virus 1. Conclusions Overall, no substantial difference was observed in the predominant NP bacterial community, but specific taxa were significantly changed between the healthy control and COVID-19 patients. Comparatively, an increased number of respiratory pathogens were identified in COVID-19 patients, and NP colonization by K. pneumoniae was probably occurring in the local population.

Analysis of the nasopharyngeal microbiome and respiratory pathogens in COVID-19 patients from Saudi Arabia.

BACKGROUND: Infection with SARS-CoV-2 may perturb normal microbiota, leading to secondary infections that can complicate the viral disease. The aim of this study was to probe the alteration of nasopharyngeal (NP) microbiota in the context of SARS-CoV-2 infection and obesity and to identify other respiratory pathogens among COVID-19 cases that may affect patients' health. METHODS: A total of 107 NP swabs, including 22 from control subjects and 85 from COVID-19 patients, were processed for 6S amplicon sequencing. The respiratory pathogens causing secondary infections were identified by RT-PCR assay, using a kit that contained specific primers and probes combinations to amplify 33 known respiratory pathogens. RESULTS: No significant (p > 0.05) difference was observed in the alpha and beta diversity analysis, but specific taxa differed significantly between the control and COVID-19 patient groups. Genera of Sphingomonas, Kurthia, Microbacterium, Methylobacterium, Brevibacillus, Bacillus, Acinetobacter, Lactococcus, and Haemophilus was significantly abundant (p < 0.05) in COVID-19 patients compared with a healthy control group. Staphylococcus was found in relatively high abundance (35.7 %) in the COVID-19 patient groups, mainly those treated with antibiotics. A relatively high percentage of Streptococcus was detected in COVID-19 patient groups with obesity or other comorbidities. Respiratory pathogens, including Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Salmonella species, along with Pneumocystis jirovecii fungal species were detected by RT-PCR mainly in the COVID-19 patients. Klebsiella pneumoniae was commonly found in most of the samples from the control and COVID-19 patients. Four COVID-19 patients had viral coinfections with human adenovirus, human rhinovirus, enterovirus, and human parainfluenza virus 1. CONCLUSIONS: Overall, no substantial difference was observed in the predominant NP bacterial community, but specific taxa were significantly changed between the healthy control and COVID-19 patients. Comparatively, an increased number of respiratory pathogens were identified in COVID-19 patients, and NP colonization by K. pneumoniae was probably occurring in the local population.

Features and Outcomes of Confirmed COVID-19 Patients Presenting to the Emergency Department.

Objective This study is aimed to determine whether there is a correlation between demographic characteristics, symptoms, initial vital signs, laboratory findings, and clinical outcome(s) of patients with coronavirus disease 2019 (COVID-19). Methods This descriptive, single-center study retrospectively reviewed data from the medical records of patients confirmed with COVID-19 in a tertiary academic center in Jeddah, Saudi Arabia, between March and June 2020. Results The present study enrolled 1039 patients (mean age ± SD, 45.16 ± 19.33 years) suffering from COVID-19, of whom 60.9% were not known to have any medical illnesses. The most common comorbidity was cardiovascular disease (27.8%). Patients with advanced age (p < 0.001), cardiovascular disease (p < 0.001), diabetes mellitus (p = 0.003), asthma (p = 0.008), renal disease (p = 0.020), fever (p = 0.002), dyspnea (p < 0.001), tachypnea (p < 0.001), low albumin (p < 0.001), low alkaline phosphatase levels (p = 0.008), high C-reactive protein (p = 0.003), high fibrinogen (p = 0.047), and high lactate levels (p = 0.015) were more likely to be admitted. Conclusions Patients with increased age, multiple comorbidities, and unstable initial vital signs at emergency department presentation experienced a more severe course of COVID-19 and required admission.

The Role of Demographic, Clinical, and Laboratory Characteristics in Predicting the In-Hospital Outcomes of Patients With COVID-19.

Objective In this study, we aimed to analyze the role of initial patient characteristics obtained at admission (including sociodemographic, clinical, and laboratory findings) in predicting the outcomes in patients with coronavirus disease 2019 (COVID-19). Methods This descriptive, retrospective cohort study included all hospital-admitted COVID-19-confirmed cases at a tertiary academic center in Jeddah, the Kingdom of Saudi Arabia (KSA), from March to June 2020. A total of 656 patients with a mean age of 50 ± 19.4 years were included. Results Of all the patients recruited, 19.3% required ICU admission, and 19% required mechanical ventilation. The majority (79.9%) of the patients recovered from COVID-19 and were discharged, while 20.1% of them died. Patients with advanced age (p=0.005), male sex (p=0.009), low platelet counts (p=0.015), low hemoglobin levels (p=0.004), low albumin levels (p=0.003), high alkaline phosphatase levels (p=0.002), high blood urea nitrogen levels (p<0.001), and high lactate dehydrogenase levels (p<0.001) were more likely to die. Conclusion Based on our findings, it can be inferred that mortality in COVID-19 is highly associated with advanced age and male gender, low platelet counts, low hemoglobin levels, low albumin levels, high alkaline phosphatase levels, high blood urea nitrogen levels, high lactate dehydrogenase levels, tachypnea, and requirement for mechanical ventilation.

Variation in COVID-19 Disease Severity and Clinical Outcomes Between Different ABO Blood Groups.

The primary objective of this study was to explore whether coronavirus disease 2019 (COVID-19) severity and outcomes varied between different ABO blood groups. This retrospective study included 363 COVID-19 confirmed patients who had their blood group recorded in the hospital medical records, from March to June 2020. Data representing demographics, clinical features, vital signs, laboratory findings, and COVID-19 outcomes were collected. Multivariate logistic regression was used for analysis and the results were adjusted for sociodemographic, clinical, and laboratory variables. The patients' mean age was 50 ± 17.8 years. Of the 363 patients, 30% were blood group A, 22.3% were blood group B, 8.8% were blood group AB, and 38.8% were blood group O. Bivariate analysis showed that patients with blood group AB were more likely to be free of any medical disease (65.6%) compared to other blood groups (p = 0.007). Fever was the most common presenting complaint (66.7%), and it did not significantly vary with changes in ABO blood groups (p = 0.230). Regarding laboratory characteristics, only C-reactive protein (CRP) levels were significantly associated with the blood groups, with high levels seen in blood groups A, B, and O (p = 0.036). In multivariate analysis, variations in emergency department (ED) disposition, requirement of intensive care unit care, and requirement of mechanical ventilation were not statistically significant among the different ABO blood groups. Furthermore, no correlation was found between hospital death and the different ABO blood groups. In conclusion, COVID-19 is most prevalent among patients with blood group O and least prevalent among those with blood group AB. No particular blood group had worse COVID-19 disease severity and outcomes than other blood groups. Therefore, we believe that ABO blood grouping should not be used as a major assessment tool for COVID-19 disease severity and outcome, and other known risk factors should be investigated.