Detection of mixed Neisseria gonorrhoeae infections in clinical samples using whole genome sequence data

Mixed infection is defined as the infection of a host with more than one strain or genotype, and the identification of mixed gonococcal infections was historically based on the non-clonal structure of Neisseria gonorrhoeae... [ view full abstract ]

Mixed infection is defined as the infection of a host with more than one strain or genotype, and the identification of mixed gonococcal infections was historically based on the non-clonal structure of Neisseria gonorrhoeae populations or the use of single genetic markers. As the etiological agent responsible for the sexually transmitted infection gonorrhea, N. gonorrhoeae is the second most common notifiable infection in the United States, and approximately 78 million new gonorrhea cases were estimated globally in 2012. Considering the emergence of multidrug resistant gonococcal isolates worldwide, failure to address the implications of mixed gonococcal infections could lead to treatment failures and the transmission of resistant strains. In this study, laboratory sampling techniques were combined with whole genome sequencing methods to detect the presence of mixed infections in clinical N. gonorrhoeae samples that were collected from 48 male patients. Multiple colonies from each sample (N = 488) were isolated and sequenced, and genomic variation and phylogenetic analyses were used to identify secondary strains within putative mixed infections. Five (10%) putative mixed infections were detected based on SNP differences and phylogenetic results. The results support the presence of mixed gonococcal infections and provide data that will inform the development of future N. gonorrhoeae diagnostic methods and treatment guidelines.