Glutamic acid at position 152 and serine at position 191 are key residues required for the metallo-β-lactamase activity of NDM-7

Conserved ancillary residues situated proximally to the VIM-2 active-site affect its metallo β-lactamase activity

Verona-integron-metallo-β-lactamase (VIM-2) is one of the most widespread class B β-lactamase responsible for β-lactam resistance. Although active-site residues help in metal binding, the residues nearing the active-site possess functional importance. Here, to decipher the role of such residues in the activity and stability of VIM-2, the residues E146, D182, N210, S207, and D213 were selected through in-silico analyses and substituted with alanine using site-directed mutagenesis. The effects of substitution mutations were assessed by comparing the changes in β-lactam susceptibility pattern of Escherichia coli host cell expressing VIM-2 and its mutated proteins. VIM-2_N210A enhanced the susceptibility of the host by ∼4-8 folds against penicillins and cephalosporins, while the expression of VIM-2_D182A radically increased the susceptibility of host. However, expression of VIM-2_E146A reduced the susceptibility of host by 2-fold. Further, proteins were purified to homogeneity, and VIM_N210A and VIM_D182A displayed reduced thermal stability than VIM-2. Moreover, in vitro catalytic efficiencies of VIM-2_D182A were drastically reduced against all the β-lactams tested whereas the same were moderately reduced for VIM-2_N210A. Conversely, the catalytic efficiency was marginally altered for VIM_E146A. Overall, we infer that both N210A and D182A substitutions negatively affect the performance of VIM-2 by influencing substrate specificity and stability, respectively.

Occurrence of blaNDM-1, blaNDM-5, blaNDM-7, and blaKPC-2 genes in clinical isolates of enterobacterales with high genetic variability, from colonization and infection in patients with or without COVID-19, from a hospital in Brazil

AIMS

This study aimed to investigate the presence of beta-lactams resistance genes and the clonal relationship of clinical isolates of Enterobacterales obtained from patients with and without COVID-19, in a hospital in northeastern Brazil.

METHODS AND RESULTS

The study analyzed 45 carbapenem-resistant clinical isolates using enterobacterial repetitive intergenic consensus (ERIC-PCR), PCR, and amplicon sequencing to detect resistance genes (blaKPC, blaGES, blaNDM, blaVIM, and blaIMP). The main species were Klebsiella pneumoniae, Serratia marcescens, and Proteus mirabilis. Detected genes included blaNDM (46.66%), blaKPC (35.55%), and both (17.79%). ERIC-PCR showed multiclonal dissemination and high genetic variability. The main resistance gene was blaNDM, including blaNDM-5 and blaNDM-7.

CONCLUSIONS

The presence of Enterobacterales carrying blaKPC and blaNDM in this study, particularly K. pneumoniae, in infections and colonizations of patients with COVID-19 and non-COVID-19, highlights genetic variability and resistance to carbapenems observed in multiple species of this order.

Two non-active site residues W165 and L166 prominently influence the beta-lactam hydrolytic ability of OXA-23 beta-lactamase

Dissemination of class D OXA-type carbapenemases is one of the significant causes of beta-lactam resistance in Gram-negative bacteria. The amino acid residues present near the active site are involved in hydrolytic mechanism of class D carbapenemases, though it is not identified in OXA-23. Here, with the help of site-directed mutagenesis, we aimed to explicate the importance of the residues W165, L166 and V167 of the possible omega loop and residue D222 in the short β5-β6 loop on the activity of OXA-23. All the residues were substituted with alanine. The resultant proteins were assayed for the changes in activity in E. coli cells and purified for in vitro activity, and stability assessment. E. coli cells harboring OXA-23_W165A and OXA-23_L166A, individually, exhibited a significant decrease in resistance towards beta-lactam antibiotics as compared to OXA-23. Further, purified OXA-23_W165A and OXA-23_L166A imparted about >4-fold decrease in catalytic efficiency and displayed reduced thermal stability as compared to OXA-23. Bocillin-FL binding assay revealed that W165A substitution results in improper N-carboxylation of K82, leading to deacylation deficient OXA-23. Therefore, we infer that the residue W165 maintains the integrity of N-carboxylated lysine (K82) of OXA-23 and the residue L166 might be responsible for properly orientating the antibiotic molecules.

Involvement of the non-active site Residues in the Catalytic Activity of NDM-4 Metallo beta-lactamase

The rise of New Delhi metallo beta-lactamase (NDM) producing bacteria imposes a significant threat to the treatment of bacterial infections due to their broad spectrum against beta-lactams. The activity of metallo beta-lactamases is affected by active site residues as well as residues near the active site. Therefore, we aimed to identify the amino acid residues around the active site of NDM-4 which influence its function. To achieve that, seven substitution mutations (S191A, D192A, S213A, K216A, S217A, D223A and D225A) of NDM-4 were generated through site-directed mutagenesis. Out of these, expression of NDM-4_D192A and NDM-4_S217A in Escherichia coli cells increased the beta-lactam susceptibility as compared to NDM-4. Further, proteins were purified to assess the effect of substitution mutations on zinc content, in vitro catalytic efficiency, and stability of NDM-4. The catalytic efficiency was reduced for these mutants (D192A and S217A) towards beta-lactam substrates, while the thermal stability remained insubstantial as compared to NDM-4. However, the purified NDM-4_D192A exhibited altered zinc content. In silico studies reveal that these changes might be the outcomes of alterations in hydrogen bonding networks and substrate interactions. Taken together, we infer that the D192 and the S217 residues play a substantial role in the activity of NDM-4.

Deciphering the role of residues in the loops nearing the active site of OXA-58 in imparting beta-lactamase activity

The existence of OXA-58 carbapenemase alone or in combination with other beta-lactam resistance factors poses significant beta-lactam resistance. The exact mechanism of action of OXA type beta-lactamases is debatable due to the involvement of multiple residues within or outside the active site. In the present work, we have elucidated the relative role of residues present in the putative omega (W169, L170, K171) and β6-β7 (A226 and D228) loops on the activity of OXA-58 by substituting into alanine (and aspartate for A226) through site-directed mutagenesis. E. coli cells harbouring OXA-58, substituted at the putative omega loop, manifest a significant decrease in the beta-lactam resistance profile than that of the cells expressing OXA-58. Further, a reduction in the catalytic efficiency is observed for the purified variants of OXA-58 carrying individual substitutions in the putative omega loop than that of OXA-58. However, the addition of NaHCO₃ (for carbamylation of K86) increases catalytic efficiency of the individual protein as revealed by nitrocefin hydrolysis assay and steady state kinetics. Moreover, W169A and K171A substitutions show significant effects on the thermal stability of OXA-58. Therefore, we conclude that the putative omega loop residues W169, L170 and K171, individually, have significant role in the activity and stability of OXA-58, mostly by stabilising carbamylated lysine of active site.

Penicillin Binding Proteins and β-Lactamases of Mycobacterium tuberculosis: Reexamination of the Historical Paradigm

Penicillin binding proteins (PBPs) have been extensively studied due to their importance to the physiology of bacterial cell wall peptidoglycan and as targets of the most widely used class of antibiotics, the β-lactams. The existing paradigm asserts that PBPs catalyze the final step of peptidoglycan biosynthesis, and β-lactams inhibit their activities. According to this paradigm, a distinct enzyme class, β-lactamases, exists to inactivate β-lactams. This paradigm has been the basis for how bacterial diseases are treated with β-lactams. We tested whether this historical view accurately reflects the relationship between β-lactams and the PBPs and the β-lactamase, BlaC, of Mycobacterium tuberculosis. BlaC was the major inactivator of the cephalosporin subclass of β-lactams. However, the PBPs PonA1 and PonA2 inactivated penicillins and carbapenems more effectively than BlaC. These findings demonstrate that select M. tuberculosis PBPs are effective at inactivating several β-lactams. Lesser-known PBPs, DacB, DacB1, DacB2, and Rv2864c, a putative PBP, were comparably more resistant to inhibition by all β-lactam subclasses. Additionally, Rv1730c exhibited low affinity to most β-lactams. Based on these findings, we conclude that in M. tuberculosis, BlaC is not the only source of inactivation of β-lactams. Therefore, the historical paradigm does not accurately describe the relationship between β-lactams and M. tuberculosis. IMPORTANCE M. tuberculosis, the causative agent of tuberculosis, kills more humans than any other bacterium. β-lactams are the most widely used class of antibiotics to treat bacterial infections. Unlike in the historical model that describes the relationship between β-lactams and M. tuberculosis, we find that M. tuberculosis penicillin binding proteins are able to inactivate select β-lactams with high efficiency.

Evolving trends of New Delhi Metallo-betalactamse (NDM) variants: A threat to antimicrobial resistance

The rapid emergence of carbapenemase producing Gram-negative bacterial strains exhibit broad-spectrum β-lactam resistance, especially New Delhi metallo-β-lactamase (NDM-1). It is a major public health threat as it catalyses the hydrolysis of a vast variety of β-lactam antibiotics, including carbapenems, which is the last choice for physicians to treat infections. NDM-1 and its variants are continuously spreading worldwide, in spite of constant efforts to control. Its clinical treatment remains challenging due to continuous evolution of new variants. A thorough structural study of all variants is required to develop new and effective inhibitors. This review focuses on the dissemination, position of substitution and carbapenemases activity of all the 28 NDM variants so far reported.