Observational study of factors associated with morbidity and mortality from COVID-19 in Lebanon, 2020-2021.

BACKGROUND: The COVID-19 pandemic claimed millions of lives worldwide without clear signs of abating despite several mitigation efforts and vaccination campaigns. There have been tremendous interests in understanding the etiology of the disease particularly in what makes it severe and fatal in certain patients. Studies have shown that COVID-19 patients with kidney injury on admission were more likely to develop severe disease, and acute kidney disease was associated with high mortality in COVID-19 hospitalized patients. METHODS: This study investigated 819 COVID-19 patients admitted between January 2020-April 2021 to the COVID-19 ward at a tertiary care center in Lebanon and evaluated their vital signs and biomarkers while probing for two main outcomes: intubation and fatality. Logistic and Cox regressions were performed to investigate the association between clinical and metabolic variables and disease outcomes, mainly intubation and mortality. Times were defined in terms of admission and discharge/fatality for COVID-19, with no other exclusions. RESULTS: Regression analysis revealed that the following are independent risk factors for both intubation and fatality respectively: diabetes (p = 0.021 and p = 0.04), being overweight (p = 0.021 and p = 0.072), chronic kidney disease (p = 0.045 and p = 0.001), and gender (p = 0.016 and p = 0.114). Further, shortness of breath (p<0.001), age (p<0.001) and being overweight (p = 0.014) associated with intubation, while fatality with shortness of breath (p<0.001) in our group of patients. Elevated level of serum creatinine was the highest factor associated with fatality (p = 0.002), while both white blood count (p<0.001) and serum glutamic-oxaloacetic transaminase levels (p<0.001) emerged as independent risk factors for intubation. CONCLUSIONS: Collectively our data show that high creatinine levels were significantly associated with fatality in our COVID-19 study patients, underscoring the importance of kidney function as a main modulator of SARS-CoV-2 morbidity and favor a careful and proactive management of patients with elevated creatinine levels on admission.

Trends of Multidrug-Resistant Pathogens, Difficult to Treat Bloodstream Infections, and Antimicrobial Consumption at a Tertiary Care Center in Lebanon from 2015-2020: COVID-19 Aftermath.

INTRODUCTION: We studied the trend of antimicrobial resistance and consumption at Saint George Hospital University Medical Center (SGHUMC), a tertiary care center in Beirut, Lebanon, with a focus on the SARS-CoV-2 pandemic. MATERIALS AND METHODS: We calculated the isolation density/1000 patient-days (PD) of the most isolated organisms from 1 January 2015-31 December 2020 that included: E. coli (Eco), K. pneumoniae (Kp), P. aeruginosa (Pae), A. baumannii (Ab), S. aureus (Sau), and E. faecium (Efm). We considered March-December 2020 a surrogate of COVID-19. We considered one culture/patient for each antimicrobial susceptibility and excluded Staphylococcus epidermidis, Staphylococcus coagulase-negative, and Corynebacterium species. We analyzed the trends of the overall isolates, the antimicrobial susceptibilities of blood isolates (BSI), difficult-to-treat (DTR) BSI, carbapenem-resistant Enterobacteriaceae (CRE) BSI, and restricted antimicrobial consumption as daily-defined-dose/1000 PD. DTR implies resistance to carbapenems, beta-lactams, fluoroquinolones, and additional antimicrobials where applicable. RESULTS AND DISCUSSION: After applying exclusion criteria, we analyzed 1614 blood cultures out of 8314 cultures. We isolated 85 species, most commonly Eco, at 52%. The isolation density of total BSI in 2020 decreased by 16%: 82 patients were spared from bacteremia, with 13 being DTR. The isolation density of CRE BSI/1000 PD decreased by 64% from 2019 to 2020, while VREfm BSI decreased by 34%. There was a significant decrease of 80% in Ab isolates (p-value < 0.0001). During COVID-19, restricted antimicrobial consumption decreased to 175 DDD/1000 PD (p-value < 0.0001). Total carbapenem consumption persistently decreased by 71.2% from 108DDD/1000 PD in 2015-2019 to 31 DDD/1000 PD in 2020. At SGHUMC, existing epidemics were not worsened by the pandemic. We attribute this to our unique and dynamic collaboration of antimicrobial stewardship, infection prevention and control, and infectious disease consultation.

Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant.

INTRODUCTION: The SARS-CoV-2 pandemic has been associated with the occurrence since summer 2020 of several viral variants that overlapped or succeeded each other in time. Those of current concern harbor mutations within the spike receptor binding domain (RBD) that may be associated with viral escape to immune responses. In our geographical area a viral variant we named Marseille-4 harbors a S477 N substitution in this RBD. MATERIALS AND METHODS: We aimed to implement an in-house one-step real-time reverse transcription-PCR (qPCR) assay with a hydrolysis probe that specifically detects the SARS-CoV-2 Marseille-4 variant. RESULTS: All 6 cDNA samples from Marseille-4 variant strains identified in our institute by genome next-generation sequencing (NGS) tested positive using our Marseille-4 specific qPCR, whereas all 32 cDNA samples from other variants tested negative. In addition, 39/42 (93 %) respiratory samples identified by NGS as containing a Marseille-4 variant strain and 0/26 samples identified as containing non-Marseille-4 variant strains were positive. Finally, 2018/3960 (51%) patients SARS-CoV-2-diagnosed in our institute, 10/277 (3.6 %) respiratory samples collected in Algeria, and none of 207 respiratory samples collected in Senegal, Morocco, or Lebanon tested positive using our Marseille-4 specific qPCR. DISCUSSION: Our in-house qPCR system was found reliable to detect specifically the Marseille-4 variant and allowed estimating it is involved in about half of our SARS-CoV-2 diagnoses since December 2020. Such approach allows the real-time surveillance of SARS-CoV-2 variants, which is warranted to monitor and assess their epidemiological and clinical characterics based on comprehensive sets of data.