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

Background: Microbial contamination is a significant challenge for the pharmaceutical sector, especially for heat-sensitive sterile products. This contamination can alter the physical and chemical properties of pharmaceutical products, compromising quality and safety. Correct bacterial identification is essential for tracing sources of contamination and implementing preventive and corrective measures. Matrix-Assisted Laser Desorp-tion Ionization-Time of Flight/Mass Spectrometry (MALDI-TOF MS) technology has revolutionized microbial identification, but there are limitations in the databases, re-quiring additional analyses, such as sequencing of the 16S rRNA and housekeeping genes and/or whole genome sequencing. Objectives: This review explores the challenges of identifying bacterial contaminants in the pharmaceutical industry using 16S rRNA gene sequences. Additional sequencing of housekeeping genes can be useful for differ-entiating bacteria at the species level. Advances in DNA sequencing technology have expanded genomic taxonomy, allowing for more accurate bacterial classification. This study aims to demonstrate how the combination of these methods increases the accuracy of bacterial identification. Conclusions and future directions: MALDI-TOF MS is widely used in the pharmaceutical sector for bacterial identification. A public database of spectral profiles of environmental bacterial isolates would be essential for bacterial identification and information exchange between institutions. Complementary methods, such as 16S rRNA and housekeeping genes sequencing, can provide reliable bacterial identification and allow the expansion of the MALDI-TOF MS database. Advances in genomic taxonomy have enabled the development of genomic taxonomy tools to im-prove bacterial identification. The combination of multiple methods provides greater precision and overcomes the limitations of single-gene approaches.