Primer Blind Spots: Underrepresentation of ESKAPE Pathogens from Developing Regions in 16S rRNA Targeted Sequencing

Abstract

Targeted 16S rRNA sequencing is stalwart of microbial profiling and diagnostics, but its reliance on some "universal" primers introduces bias. In this in-silico study, we investigated how well these primers capture ESKAPE pathogens by screening multiple databases and found that a considerable fraction showed suboptimal primer binding, suggesting that amplification and identification may be compromised. Notably, these strains were disproportionately associated with isolates from developing countries, underscoring the risk of primer bias in global surveillance.