Genome Sequencing of a Neisseria gonorrhoeae Isolate of a Successful International Clone with Decreased Susceptibility and Resistance to Extended-Spectrum Cephalosporins

Abstract

eThe recent emergence of Neisseria gonorrhoeae strains with decreased susceptibility to extended-spectrum cephalosporins is a major concern globally. We sequenced the genome of an N. gonorrhoeae multiantigen sequence typing (NG-MAST) ST1407 isolate (SM-3) with decreased susceptibility and resistance to oral extended-spectrum cephalosporins. The isolate was cultured in 2008 in San Francisco, CA, and possessed mosaic penA allele XXXIV, which is associated with an international clone that possesses decreased susceptibility as well as resistance to oral extended-spectrum cephalosporins globally. The genome sequence of strain NCCP11945 was used as a scaffold, and our assembly resulted in 91 contigs covering 2,029,064 bp (91%; >150؋ coverage) of the genome. Numerous instances of suspected horizontal genetic transfer events with other Neisseria species were identified, and two genes, opa and txf, acquired from nongonococcal Neisseria species, were identified. Strains possessing mosaic penA alleles (n ‫؍‬ 108) and nonmosaic penA alleles (n ‫؍‬ 169) from the United States and Europe (15 countries), cultured in 2002 to 2009, were screened for the presence of these genes. The opa gene was detected in most (82%) penA mosaic-containing isolates (mainly from 2007 to 2009) but not in any penA nonmosaic isolates. The txf gene was found in all strains containing opa but also in several (18%) penA nonmosaic strains. Using opa and txf as genetic markers, we identified a strain that possesses mosaic penA allele XXXIV, but the majority of its genome is not genetically related to strain SM-3. This implies that penA mosaic allele XXXIV was transferred horizontally. Such isolates also possessed decreased susceptibility and resistance to oral extended-spectrum cephalosporins. These findings support that genetic screening for particular penA mosaic alleles can be a valuable method for tracking strains with decreased susceptibility as well as resistance to oral extended-spectrum cephalosporins worldwide and that screening using only NG-MAST may not be sufficient.

Utility of Specimens Positive for Neisseria gonorrhoeae by the Aptima Combo 2 Assay for Assessment of Strain Diversity and Antibiotic Resistance

“…Several reports have suggested that the resistant strains are largely clonal and contain specific PBP 2 mosaic patterns, such as type XXXIV (3). Sequence type 1407, based on the por and tbpB genes, has also been associated with ESC ds (14,15). In this study, we evaluated samples submitted for N. gonorrhoeae screening by the Aptima Combo 2 assay to determine if such samples can be used to establish circulating STs and antimicrobial susceptibility patterns.…”

Whole-genome sequencing of bacterial sexually transmitted infections

“…Urogenital LGV been identified in the genome of strain SM-3, associated with transfer of antibiotic resistance determinants [26]. A range of plasmids are associated with the strains of N. gonorrhoeae, from the small cryptic plasmid of 4.2 kb to larger conjugative plasmids which promote their own transfer between strains and may carry determinants of antibiotic resistance [8].…”

“…Four genome sequences of N. gonorrhoeae (2.2 Mb) are available for analysis [7,25,26], the most divergent strains being separated by 7331 SNPs (Table 1); a further 14 genomes exist in draft form (http://www.broadinstitute.org/). N. gonorrhoeae is naturally competent and able to take up exogenous DNA [27] which can be incorporated and used to shuffle novel functions into its genome.…”

Fluoroquinolone Resistance in Neisseria gonorrhoeae After Cessation of Ciprofloxacin Usage in San Francisco

“…net) and assigned allele and ST identities. Closely related STs (differing by <1% DNA sequence of the porB and tbpB gene) were grouped into genogroups, as previously described in Buono et al 22 and Hess et al 23 …”

“…These findings and other studies demonstrate that genetic-based surveillance, when combined with phenotypic surveillance, provides a powerful tool for public health efforts seeking to understand trends in drug resistance. 22,23,29 Therefore, it is vital to improve and continue the monitoring of GC antimicrobial susceptibility throughout the United States to delay the emergence of future drug-resistant strains. Such data can provide health departments with the information to make better strategic choices and policy decisions regarding surveillance and treatment of gonorrhea.…”