Challenges in the Identification of Environmental Bacterial Isolates from a Pharmaceutical Industry Facility by 16S rRNA Gene Sequences

Microbial contamination is a critical challenge for the pharmaceutical industry, especially in thermosensitive sterile products, and can compromise their quality and safety. The accurate identification of microorganisms is essential to trace sources of contamination and adopt corrective measures. Although MALDI-TOF MS technology has revolutionized this process, its database limitations necessitate the use of complementary methods, such as sequencing 16S rRNA genes, housekeeping genes, and, in some cases, the entire genome. Advances in sequencing have expanded genomic taxonomy, increasing the accuracy of bacterial identification. The integration of these approaches significantly improves the reliability of identification, overcoming the limitations of isolated methods.