Abstract
Introduction
Identification of the causative pathogen in musculoskeletal infection is critical as it directs further treatment. Fracture-related infection is often associated with ‘no growth’ in standard culture. We investigated the efficiency of two alternate methods to identify the causative pathogen, namely extended bacterial culture and 16Sr RNA gene sequence analysis with next generation sequencing (NGS) in ‘culture negative’ fracture related infections.
Method
Patients were diagnosed as having fracture related infection based on the MSIS criteria (n=120). All patients had samples taken for culture and sensitivity. All samples which were culture negative by standard culture methods formed the study group. These samples were subjected to further extended culture in both aerobic and anaerobic medium for 14 days to improve recovery of pathogens. Further, DNA isolated from implants from a sub-group of these culture negative patients were subjected to 16SrRNA gene amplification followed by Sanger sequencing. Subsequent sequencing analysis was performed using the Illumina NGS platform which identified and detected the most abundant genera/species present in those samples more precisely.
Result
57 culture negative samples formed the study group. Eight samples (14%) converted to positivity after 14 days of culture. Bacteroides fragilis was the commonest yield. 14 samples underwent 16SrRNA gene amplification followed by Sanger sequencing. Acinetobacter baumannii, Enterococcus faecalis, Pseudomonas aeruginosa were identified as common pathogens. Next generation sequencing (n=12) not only identified common pathogens like as Staphylococcus, Acinetobacter baumannii, but also many uncultivable species.
Conclusion
Positive results from extended bacterial culture are about 15%. The delay in definite identification of pathogens in extended culture may be critical in certain clinical situations. Molecular methods are quicker and have additional yield in culture negative infections. The exact role of all microorganisms identified by molecular methods in the pathogenesis of infection is unknown.
