The under investigated facet of the COVID-19 pandemic: Molecular analysis of secondary bacterial infections at a COVID dedicated intensive care unit within a tertiary care center in Lebanon

Abstract

BackgroundThe coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. Secondary bacterial infections are associated with unfavorable outcomes in respiratory viral infections. This study aimed at determining the prevalence of secondary bacterial infections in COVID-19 patients admitted at a tertiary medical center in Lebanon.MethodologyFrom May till November, 2020, a total of 26 Gram-negative isolates were recovered from 16 patients during the course of their COVID-19 infection with Escherichia coli being the most prevalent. The isolates were assessed for their antimicrobial susceptibility by broth microdilution against 19 antimicrobial agents from different classes. Whole genome sequencing of 13 isolates allowed the mining of antimicrobial resistance (AMR) determinants as well as mobile genetic elements and sequence types (ST). Finally, broth microdilution with three different efflux pump inhibitors [theobromine, conessine and PheArg-β-naphthylamide (PAβN)] was done.ResultsAntimicrobial susceptibility testing showed that out of the 26 Gram-negative isolates, 1 (4%) was extensively drug resistant and 14 (54%) were multi-drug resistant (MDR). Whole genome sequencing results revealed a plethora of AMR determinants among the 13 sequenced isolates. Moreover, the 9 Enterobacterales and 4 Pseudomonas aeruginosa sequenced isolates belonged to 9 and 2 different ST, respectively. Using a variety of efflux pump inhibitors we demonstrated that only PAβN had a significant effect when combined with levofloxacin, and the latter regained its activity against two P. aeruginosa isolates.ConclusionThe identification of carbapenem and colistin resistant Gram-negative bacilli causing secondary bacterial infections in critical patients diagnosed with COVID-19 should be of high concern. Additionally, it is crucial to monitor and track AMR, post-COVID pandemic, in order to better understand the effect of this disease on AMR exacerbation.

Emergence ofAcinetobacter baumanniiInternational Clone 10 predominantly found in the Middle East

“…We identified a total of 110 ST158 Pas isolates in the literature by querying the PubMed® database for biomedical literature (https://pubmed.ncbi.nlm.nih.gov/) [18][19][20][21][22][23][24][25][26][27][28][29][30] We compiled whole-genome sequencing data for 60 of the ST158 Pas isolates. Of these, 17…”

“…All 60 isolates underwent short-read sequencing, of which 46 were completed by Université de Sherbrooke (this study), 3 by co-authors [19][20][21] and 11 by previous studies 18,[22][23][24][25][26][27][28][29][30] . For all the 46 in-house sequenced isolates, DNA isolation, library construction and genome sequencing were performed according to the manufacturer's instructions.…”