In Silico Analysis of Extremophilic Bacteria Isolated from Food-Service Environments in Lahore

Abstract

Background: Food-service surfaces in dense urban settings act as reservoirs for Enterobacteriaceae, and routine alkaline sanitation may select for pH-tolerant organisms. Enterobacter bugandensis has emerged as a multidrug-resistant pathogen, yet its recovery from food-contact surfaces in South Asian settings remains poorly characterised. Objective: To isolate alkali-tolerant bacteria from high-contact dining surfaces in Lahore, Pakistan, and computationally evaluate the haemolysin-coregulated protein (Hcp) of the Type VI secretion system and the heme transporter ChuA as candidate inhibitor targets. Methods: In this cross-sectional laboratory-based study, sterile swabs were collected from high-contact surfaces in thirty restaurants. Isolates were recovered on nutrient agar, screened across pH 7–10, and characterised by staining, biochemical profiling, and bidirectional 16S rRNA Sanger sequencing. Phylogeny was inferred in MEGA X. Hcp and ChuA were modelled by SWISS-MODEL and validated by Ramachandran and MolProbity analysis. Binding pockets were predicted by PrankWeb. Three matrix metalloprotease inhibitors were docked into Hcp and five heme analogues into ChuA using CB-Dock2 (AutoDock Vina), ranked by predicted binding energy. Results: A dominant alkali-tolerant Gram-negative bacillus grew sustainably at pH 10. Biochemical profile matched Enterobacter; 16S rRNA BLASTn returned closest identity to Enterobacter bugandensis (96.12%). The Hcp model achieved GMQE 0.92 with 98.39% favoured Ramachandran residues. Ilomastat returned the most favourable Hcp binding energy (–6.3 kcal/mol), engaging R26, D25, and Y99. Mn(III) and Ru(III) protoporphyrin IX both yielded –7.4 kcal/mol against ChuA, though template and ligand-identity limitations restrict interpretation. Conclusion: An alkali-tolerant Enterobacter closely related to E. bugandensis persisted on routinely cleaned dining surfaces, indicating that conventional sanitation may inadequately eliminate clinically relevant Enterobacteriaceae. Ilomastat emerged as a candidate Hcp inhibitor; ChuA findings require re-validation. Routine molecular surveillance of food-contact surfaces is warranted.