Community-acquired Klebsiella pneumoniae – Its Virulence and Antimicrobial Resistance Genes Complement in Participants Presenting for COVID-19 Testing in Lagos State, Nigeria

Background and Objective: The COVID-19 pandemic brought about significant health, economic, and security challenges during its outbreak in late 2019. Accurate diagnosis and differentiation from other respiratory infections are crucial for effective management. Klebsiella pneumoniae, a known respiratory pathogen, presents symptoms similar to COVID-19, complicating diagnosis and treatment. This study emphasizes the importance of screening for K. pneumoniae in individuals presenting with COVID-19-like symptoms to achieve proper patient management. Methods: In this cross-sectional study, a total of 269 nasopharyngeal swabs were collected from individuals at a COVID-19 testing center in Yaba, Lagos. Standard laboratory procedures were employed for the isolation of K. pneumoniae using MacConkey and Eosin Methylene Blue agars, characterization was done with specific biochemical tests, and antibiotic susceptibility testing using the disc diffusion method. Polymerase chain reaction was used to detect species-specific, virulence, and antimicrobial resistance genes. Results: Among the participants, 11.2% tested positive for COVID-19, 7.8% for Klebsiella species, and 0.74% for both. Specifically, 5.24% were positive for the K. pneumoniae-specific gene, PfPr1. Antibiotic susceptibility ranged from 30.4% to 82.6%, with sensitivities to cephalosporins (47.8%), carbapenems (65.3%), and ciprofloxacin (34.8%). Notably, all isolates were resistant to macrolides and glycopeptides. Of the 14 K. pneumoniae isolates, 7 harbored virulence genes: 4 were positive for mrkD (28.6%) and 3 for K2 (21.4%). In addition, 12 isolates carried antimicrobial resistance genes: 10 were positive for blaTEM (71.4%) and 2 for blaSHV (14.3%). Conclusion and Implication for Translation: The detection of virulence factors and antimicrobial resistance genes, including those conferring resistance to last-resort antibiotics, in community-acquired K. pneumoniae isolates highlights the potential for severe clinical outcomes and increased healthcare burden. The emergence of these multidrug-resistant strains in community settings underscores the critical need for routine surveillance of K. pneumoniae, particularly in the context of coinfections with Severe Acute Respiratory Syndrome Coronavirus-2 and the implementation of comprehensive antimicrobial stewardship programs to mitigate the spread and impact of resistant pathogens. This will lead to improved case management in the event of a new wave of COVID-19 infection.