Phenotypic markers misclassify isolates of Salmonella typhimurium as S. typhi, but were correctly identified by whole genome sequencing during a septicemia study in western Kenya

Antimicrobial resistance (AMR) is a rising global health threat and estimated to cause 700,000 deaths annually. Although blood cultures (BCs) are the reference standard to diagnose bloodstream infections and inference of antimicrobial susceptibility testing (AST), the method could fail to differentiate bacteria with similar biochemical characteristics. This study evaluated the utility of whole genome sequencing (WGS) in complimenting BCs in bacteria identification and assessing AMR. Blood samples came from septicemic patients attending county referral hospitals in western Kenya and around the Lake Victoria region. BCs and AST were performed on BD Bactec 9050 and Phoenix 100 respectively. Out of the 960 BCs, 17 had uncontaminated growth and were evaluated by WGS on the Oxford Nanopore PromethION platform. BD Phoenix system identified the 17 bacteria isolates as: 4 Escherichia coli, 8 Salmonella enterica serovar Typhi, 1 unspeciated Salmonella, 3 Staphylococcus aureus and 1 Streptococcus pneumoniae. WGS results differed from BCs in identifying Salmonella species, with WGS identifying the species as Salmonella enterica serovar Typhimurium. Conversely, WGS detected AMR genes in bacteria that AST had classified as susceptible. In conclusion, we caution that BCs may not be providing correct identity of Salmonella species. The observed discrepancies between phenotypic and genotypic markers of drug resistance highlight the challenges in interpreting and predicting the functional utility of AMR genes.