A large-scale, whole-genome comparison of Canadian Neisseria gonorrhoeae isolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While some N. gonorrhoeae multiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaic penA alleles, followed in 2000/2001 with the penA mosaic X allele and then in 2007 with ST1407 strains with the penA mosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated with penA mosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections. N eisseria gonorrhoeae is a Gram-negative diplococcus bacterium that causes gonorrhea infections. Gonorrhea is the second most reported bacterial sexually transmitted infection (STI) in Canada, with reported cases increasing from 15.5 per 100,000 in 1997 to 36.2 per 100,000 in 2012 (1), and approximately 106 million cases are estimated annually worldwide (2). N. gonorrhoeae bacteria have developed resistance against sulfonamides, penicillins, tetracyclines, and fluoroquinolones (3, 4), and current treatment options now include third-generation extended-spectrum cephalosporins (ESC), namely, cefixime (CFM) and ceftriaxone (CRO) (5). MIC creep has seen the modal MIC values rise between 2001 and 2010 in Canada from 0.016 g/ml to 0.125 g/ml and 0.063 g/ml for CFM and CRO, respectively (6). These results coincide with recent clinical reports of treatment failures to primarily CFM monotherapy in Canada (7,8) and additional global reports of high-level CRO MICs in isolates from Japan and Europe (9-13). Furthermore, isolates with decreased susceptibility to cephalosporins and coresistance to azithromycin (AZM), a recommended cotherapy (5), have recently been identified in Canada (14).Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) and resistance to AZM have been attributed to several molecular mechanisms. The primary mechanism for ESC-DS is modification of the ...