Genome sequencing of a Neisseria gonorrhoeae isolate of a successful international clone with decreased susceptibility and resistance to extended-spectrum cephalosporins

Abstract

The 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.

Fig 1

Chromosomal positions of the major features reported in the manuscript. GR stands for genomic rearrangements and shows the locations of the 10 rearrangements reported in Tables 1 and 2. HM stands for high-mutation-density region and shows the locations of these 10 regions, as reported in Table 3. In addition, the location of the penA gene is shown, along with the two loci used to determine the NG-MAST sequence type: porB and tbpB.

Fig 2

Phylogenetic trees based on the porB allele of penA mosaic, opacity factor-positive strains (n = 83). DNAml was used to generate maximum likelihood trees.

Fig 3

Graphical representations of genetic maps of the two discordant strain types investigated in detail in our study, ST5895 and ST4252. The genetic markers examined are displayed on the circular bacterial chromosome with relative positioning (see also Table S5 in the supplemental material). Genetic markers in red have alleles that match strain SM-3, while genetic markers in black have alleles that match cephalosporin-susceptible strains. Since the genomic location of the opacity factor is not known, its presence or absence is denoted underneath the relevant strain type.