Acquisition of Ciprofloxacin Resistance Among an Expanding Clade of β-Lactamase-Positive, Serogroup Y Neisseria meningitidis in the United States

Abstract

Background: Penicillin and ciprofloxacin are important for invasive meningococcal disease (IMD) management and prevention. IMD cases caused by penicillin- and ciprofloxacin-resistant Neisseria meningitidis containing a ROB-1 β-lactamase gene (blaROB-1) and a mutated DNA gyrase gene (gyrA) have been recently reported in the United States.

Methods: We examined 2097 meningococcal genomes collected through US population-based surveillance from January 2011 to February 2020 to identify IMD cases caused by strains with blaROB-1- or gyrA-mediated resistance. Antimicrobial resistance was confirmed phenotypically. The US isolate genomes were compared to non-US isolate genomes containing blaROB-1. Interspecies transfer of ciprofloxacin resistance was assessed by comparing gyrA among Neisseria species.

Results: Eleven penicillin- and ciprofloxacin-resistant isolates were identified after December 2018; all were serogroup Y, sequence type 3587, clonal complex (CC) 23, and contained blaROB-1 and a T91I-containing gyrA allele. An additional 22 penicillin-resistant, blaROB-1- containing US isolates with wild-type gyrA were identified from 2013 to 2020. All 33 blaROB-1-containing isolates formed a single clade, along with 12 blaROB-1-containing isolates from 6 other countries. Two-thirds of blaROB-1-containing US isolates were from Hispanic individuals. Twelve additional ciprofloxacin-resistant isolates with gyrA T91 mutations were identified. Ciprofloxacin-resistant isolates belonged to 6 CCs and contained 10 unique gyrA alleles; 7 were similar or identical to alleles from Neisseria lactamica or Neisseria gonorrhoeae.

Conclusions: Recent IMD cases caused by a dual resistant serogroup Y suggest changing antimicrobial resistance patterns in the United States. The emerging dual resistance is due to acquisition of ciprofloxacin resistance by β-lactamase-containing N. meningitidis. Routine antimicrobial resistance surveillance will effectively monitor resistance changes and spread.

Keywords: Neisseria meningitides; antibiotic resistance; ciprofloxacin; meningococcal disease; β-lactamase.

Figure 1.

Temporal (A) and geographic (B) distribution of Neisseria meningitidis isolates with β-lactamase activity (red: contain the bla_ROB-1 gene), ciprofloxacin resistance (blue: T91I or T91F mutations in gyrA), or both (purple) in the United States. States are labeled with the number of isolates identified with each resistance profile. *2020 only includes isolates collected through February 14^th, 2020.

Figure 2.

Phylogeny of Neisseria meningitidis isolates containing bla_ROB-1 and others with the same sequence types (ST-3587, 15379 or 13034) available in the PubMLST database as of April 21, 2020, based on a core genome alignment with recombinant regions removed. Isolates are labeled with the year and country of collection. Colored bars to the right of the phylogeny indicate the presence of antimicrobial resistance markers: penA mosaic allele (yellow), bla_ROB-1 (red), and gyrA T91I (blue). The scale bar is 10⁻⁵ substitutions per site. Branches with bootstrap percentages over 70% are labeled. The tree is rooted on a ST-23 isolate collected in the USA in 2003.

Figure 3.

Neighbor-net of 177 gyrA gene fragments containing the QRDR. Alleles with ciprofloxacin resistance-associated mutations are marked in blue (T91F) or red (T91I). Filled circles indicate T91F and T91I alleles that were present among the 2,097 invasive meningococcal isolates collected in the United States between January 1^st, 2011 and February 14^th, 2020. Open circles indicate additional T91F and T91I alleles from 18,249 N. meningitidis isolates in the PubMLST database. Colored “X”s indicate T91F and T91I alleles that were only identified in isolates from other species in the PubMLST database: 4,354 N. gonorrhoeae, 363 N. lactamica, 39 N. cinerea, 33 N. subflava, 22 N. mucosa, and 21 N. polysaccharea. Allele numbers detected in US isolates are written adjacent to filled circles, with allele 242 from bla_ROB-1-containing isolates in bold. Black circles indicate clusters in the network that contain all moderate frequency alleles (>1%) for the named species. Scale bar represents 1% sequence divergence and only sequences present in the PubMLST database, as of April 21, 2020, are shown.