Identification of emergent bla CMY-2 -carrying Proteus mirabilis lineages by whole-genome sequencing

Abstract

Whole-genome sequencing of 24 Proteus mirabilis isolates revealed the clonal expansion of two cefoxitin-resistant strains among patients with community-onset infection. These strains harboured bla CMY-2 within a chromosomally located integrative and conjugative element and exhibited multidrug resistance phenotypes. A predominant strain, identified in 18 patients, also harboured the PGI-1 genomic island and associated resistance genes, accounting for its broader antibiotic resistance profile. The identification of these novel multidrug-resistant strains among community-onset infections suggests that they are endemic to this region and represent emergent P. mirabilis lineages of clinical significance.

Keywords: ICE; PGI-1; Proteus mirabilis; blaCMY-2; genomics.

Fig. 1

Phylogenetic comparison of Irish Proteus mirabilis isolates with previously sequenced P. mirabilis strains. (A) A neighbour-joining tree was generated on the basis of concatenated sequences of seven conserved genes present in all strains (adk; PMI0375, fumC; PMI0891, gyrB; PMI1296, icd; PMI2184, mdh; PMI1732, purA; PMI3370 and recA; PMI3400). Sequences from 24 P. mirabilis isolates from this study and eight representative P. mirabilis whole-genome data sets; C05028 (ANBT00000000), WGLW4 (AMGU00000000), HI4320 (AM942759), ATCC29906 (ACLE01000000), ATCC7002 (JOVJ00000000), PR03 (AORN00000000), WGLW6 (AMGT00000000) and BB2000 (CP004022) were compared. Black bar indicates average nucleotide substitutions per site across the seven genes analysed (9 kb). To the right of the tree, under label CA, plus and minus symbols denote either community-acquired or hospital-associated infections, respectively, while subsequent columns ‘AC,’ ‘GN,’ ‘FX,’ ‘CZ,’ ‘CP’ and ‘TP’ indicate the resistance profile of each isolate to amoxicillin–clavulanic acid, gentamicin, cefoxitin, ceftazidime, ciprofloxacin and piperacillin–tazobactam, respectively. Colour indicates resistance level: black, full resistance; dark grey, intermediate resistance; light grey, susceptible. (B) Unrooted neighbour-joining tree of the observed 18-strain clonal cluster based on whole-genome comparisons across 3,207,626 called sites relative to the P. mirabilis HI4320 genome. Circles indicate genetically indistinguishable strains. Bar below the tree indicates length corresponding to one single-nucleotide variant.

Fig. 2

Observed mobile genetic elements associated with chromosomally integrated resistance genes among Proteus mirabilis strains identified in this study. Genetic environs (black) of detected resistance genes (white) among resistant P. mirabilis isolates are illustrated. Identified insertion sequences are highlighted in grey boxes. (A) Both strains harboured the described integrative and conjugative element (ICE) element ICEPmiJpn1, which was integrated between chromosomal genes PMI2422 (prfC) and PMI2949. The bla_CMY-2 gene was present within an ICE-embedded composite transposon flanked by IS10 elements, as observed in ICEPmiJpn1 (AB525688.1). The ICE observed in cluster I isolates also included three additional genes encoding hypothetical proteins (underlined), which are absent from previously described ICE elements in P. mirabilis. (B) Cluster I isolates harboured the aadA1 and dfrA1 genes associated within a Tn7-associated class 2 integron, chromosomally located between PMI3067 (glmS) and PMI3068. (C) PGI-1 genomic island was identified among cluster I isolates, chromosomally integrated between PMI3127 (hipB) and PMI3127 (trmE). Resistance genes identified within the PGI-1 region included aphA1b, bla_TEM-1, sul1, aadA2 and aadB, which were embedded among a mosaic of mobile genetic elements in the PGI-1 MDR region.