OXA β-lactamases

Abstract

The OXA β-lactamases were among the earliest β-lactamases detected; however, these molecular class D β-lactamases were originally relatively rare and always plasmid mediated. They had a substrate profile limited to the penicillins, but some became able to confer resistance to cephalosporins. From the 1980s onwards, isolates of Acinetobacter baumannii that were resistant to the carbapenems emerged, manifested by plasmid-encoded β-lactamases (OXA-23, OXA-40, and OXA-58) categorized as OXA enzymes because of their sequence similarity to earlier OXA β-lactamases. It was soon found that every A. baumannii strain possessed a chromosomally encoded OXA β-lactamase (OXA-51-like), some of which could confer resistance to carbapenems when the genetic environment around the gene promoted its expression. Similarly, Acinetobacter species closely related to A. baumannii also possessed their own chromosomally encoded OXA β-lactamases; some could be transferred to A. baumannii, and they formed the basis of transferable carbapenem resistance in this species. In some cases, the carbapenem-resistant OXA β-lactamases (OXA-48) have migrated into the Enterobacteriaceae and are becoming a significant cause of carbapenem resistance. The emergence of OXA enzymes that can confer resistance to carbapenems, particularly in A. baumannii, has transformed these β-lactamases from a minor hindrance into a major problem set to demote the clinical efficacy of the carbapenems.

FIG 1

Maximum likelihood amino acid tree of the OXA-type β-lactamases found in Acinetobacter species. For enzymes for which a designation was not available, the species and strain designation are used instead. Due to its large size, the OXA-51 enzyme group has been collapsed so that the other enzyme groups can be more easily seen. Relationships between the OXA-51-like enzymes are shown in Fig. 5. The tree was implemented in SeaView version 4.2.5 (172) with PhyML using a Le and Gascuel (LG) model (173). Support was estimated by using approximate likelihood ratio tests, the results of which label the branches. The tree was visualized by using FigTree version 1.3.1 (http://tree.bio.ed.ac.uk/) and is midpoint rooted.

FIG 2

Molecular surface models of the active-site cleft of the OXA-51-like enzymes. Structural models were created by using the online protein homology/analogy recognition engine (phyre) (http://www.sbg.bio.ic.ac.uk/∼phyre/), using the crystal structure for OXA-40/24 reported by Santillana et al. (38) as a backbone. Using local numbering, structures were viewed in Swiss-PdbViewer DeepView version 4 (http://spdbv.vital-it.ch/). (A) View down the active-site cleft of OXA-66 with the active-site serine 80 (red) and an isoleucine at position 129 (blue); (B) view down the active-site cleft of OXA-83 with the active-site serine 80 (red) and a leucine at position 129 (blue); (C) view down the active-site cleft of OXA-66 (from the opposite orientation to panels A and B) with the active-site serine 80 (red) and a leucine at position 167 (blue); (D) view down the active-site cleft of OXA-82 with the active-site serine 80 (red) and a valine at position 167 (blue).

FIG 3

Molecular surface models of the active-site cleft of OXA-66 (A) and OXA-40 (B), showing the absence of a hydrophobic bridge in OXA-66. Using local numbering, the active-site serine 80 is shown in red. (A) Leucine 110 is in yellow, phenylalanine 111 is in blue, and tryptophan 222 is in pink; (B) tyrosine 112 is in blue, and methionine 223 is in pink.

FIG 4

Regions of the OXA-51-like enzymes with evidence of selection. π_N/π_S, ratio of nonsynonymous to synonymous polymorphisms, with a ratio of >1 providing evidence for positive selection. Ratios were calculated with DNAsp version 5 (174) in sliding windows 50 nucleotides long, with a step size of 10 nucleotides. The horizontal gray line indicates a π_N/π_S ratio of 1; red boxes indicate predicted active-site elements (38); blue boxes indicate predicted sites involved in specificity for the carbapenems (38); orange boxes indicate predicted sites involved in dimer formation (50); blue arrows indicate regions where a π_N/π_S ratio could not be determined, as these regions contained only nonsynonymous polymorphisms; purple boxes indicate α-helices; green boxes indicate β-sheets; the red arrow indicates the active-site serine; orange stars indicate the location of residues forming the hydrophobic bridge in OXA-40 (38); and the bracket indicates the location of the Ω-loop.

FIG 5

Maximum likelihood nucleotide tree of the bla_OXA-51-like genes intrinsic to A. baumannii. For enzymes for which a designation was not available, the strain designation or gene accession number (http://www.ncbi.nlm.nih.gov/) is used instead. The tree was implemented in SeaView version 4.2.5 (172) with PhyML using a general time-reversible (GTR) model (173). Support was estimated by using approximate likelihood ratio tests, the results of which label the branches. The tree was visualized by using FigTree version 1.3.1 (http://tree.bio.ed.ac.uk/) and is midpoint rooted. The gene coding for the enzyme representative of global clone 1 isolates, OXA-66, is highlighted in red; the gene for OXA-69, representative of global clone 2 isolates, is highlighted in blue; and the gene for OXA-71, representative of global clone 3 isolates, is highlighted in pink. Colored arrows represent genes or branches containing polymorphisms that are observed in more than one position within the tree. The arrows are color coded by the amino acid position in the enzyme that the location of the polymorphism codes for and are labeled with the amino acid change from the consensus that results from the polymorphism. *, except for OXA-223 and OXA-242; **, except for OXA-242.

FIG 6

Mobile genetic elements associated with bla_OXA genes. Commonly occurring features are color coded. (A and B) See reference ; (C) see reference ; (D) see reference ; (E) see reference ; (F) see reference ; (G) see reference ; (H) see reference ; (I) see reference ; (J) ISAba1 upstream of the bla_OXA-51-like gene (78) and on one occasion found downstream as well (dashed box), see reference ; (K) see reference ; (L) see reference ; (M) see reference ; (N) see reference ; (O) see reference ; (P) see reference ; (Q) see reference ; (R) see reference ; (S) see reference ; (T) see reference ; (U) see reference ; (V) see reference ; (W) see reference ; (X and Y) see reference ; (Z) see reference ; (AA) see reference ; (AB) see reference ; (AC) see reference ; (AD) see reference ; (AE) see reference ; (AF) see reference ; (AG) see reference ; (AH) see reference ; (AI) see reference ; (AJ) see reference ; (AK) see reference ; (AL) see reference .