Enzyme Inhibitors: The Best Strategy to Tackle Superbug NDM-1 and Its Variants

Novel partially reversible NDM-1 inhibitors based on the naturally occurring houttuynin

Discovering novel NDM-1 inhibitors is an urgent task for treatment of 'superbug' infectious diseases. In this study, we found that naturally occurring houttuynin and its sulfonate derivatives might be effective NDM-1 inhibitors with novel mechanism, i.e. the attribute of partially covalent inhibition of sulfonate derivatives of houttuynin against NDM-1. Primary structure-activity relationship study showed that both the long aliphatic side chain and the warhead of aldehyde group are vital for the efficiency against NDM-1. The homologs with longer chains (SNH-2 to SNH-5) displayed stronger inhibitory activities with IC50 range of 1.1-1.5 μM, while the shorter chain the weaker inhibition. Further synergistic experiments in cell level confirmed that all these 4 compounds (at 32 μg/mL) recovered the antibacterial activity of meropenem (MER) against E. coli BL21/pET15b-blaNDM-1.

Discovering NDM-1 inhibitors using molecular substructure embeddings representations

NDM-1 (New-Delhi-Metallo-β-lactamase-1) is an enzyme developed by bacteria that is implicated in bacteria resistance to almost all known antibiotics. In this study, we deliver a new, curated NDM-1 bioactivities database, along with a set of unifying rules for managing different activity properties and inconsistencies. We define the activity classification problem in terms of Multiple Instance Learning, employing embeddings corresponding to molecular substructures and present an ensemble ranking and classification framework, relaying on a k-fold Cross Validation method employing a per fold hyper-parameter optimization procedure, showing promising generalization ability. The MIL paradigm displayed an improvement up to 45.7 %, in terms of Balanced Accuracy, in comparison to the classical Machine Learning paradigm. Moreover, we investigate different compact molecular representations, based on atomic or bi-atomic substructures. Finally, we scanned the Drugbank for strongly active compounds and we present the top-15 ranked compounds.

Small-molecule inhibitors of bacterial-producing metallo-β-lactamases: insights into their resistance mechanisms and biochemical analyses of their activities

Antibiotic resistance (AR) remains one of the major threats to the global healthcare system, which is associated with alarming morbidity and mortality rates. The defence mechanisms of Enterobacteriaceae to antibiotics occur through several pathways including the production of metallo-β-lactamases (MBLs). The carbapenemases, notably, New Delhi MBL (NDM), imipenemase (IMP), and Verona integron-encoded MBL (VIM), represent the critical MBLs implicated in AR pathogenesis and are responsible for the worst AR-related clinical conditions, but there are no approved inhibitors to date, which needs to be urgently addressed. Presently, the available antibiotics including the most active β-lactam-types are subjected to deactivation and degradation by the notorious superbug-produced enzymes. Progressively, scientists have devoted their efforts to curbing this global menace, and consequently a systematic overview on this topic can aid the timely development of effective therapeutics. In this review, diagnostic strategies for MBL strains and biochemical analyses of potent small-molecule inhibitors from experimental reports (2020-date) are overviewed. Notably, N1 and N2 from natural sources, S3-S7, S9 and S10 and S13-S16 from synthetic routes displayed the most potent broad-spectrum inhibition with ideal safety profiles. Their mechanisms of action include metal sequestration from and multi-dimensional binding to the MBL active pockets. Presently, some β-lactamase (BL)/MBL inhibitors have reached the clinical trial stage. This synopsis represents a model for future translational studies towards the discovery of effective therapeutics to overcome the challenges of AR.

First Detection of blaNDM-1-Haboring IncHI2 Plasmid in Escherichia coli Strain Isolated from Goose in China

Carbapenem-resistant Enterobacteriaceae infections are among the most serious threats to human and animal health worldwide. Of the 1013 strains of Escherichia coli isolated and identified in 14 regions of China from 2007 to 2018, seven strains were resistant to meropenem and all were positive for bla_NDM. The seven New Delhi metallo-β-lactamase (NDM)-positive strains belonged to five different sequence types, indicating that most of the NDM-positive strains were nonclonal. An IncHI2 plasmid carrying the bla_NDM-1 element was identified in the C1147 strain from a goose source and reported for the first time, showing a specific structure. Conjugation experiments revealed that the IncHI2 plasmid was conjugatable, and the horizontal propagation of the plasmid led to the rapid propagation of NDM in the same and different strains. This study revealed that waterfowl, as a potential transmission factor for carbapenem-resistant bla_NDM-1, poses a threat to human health.

The First Report of Escherichia coli and Klebsiella pneumoniae Strains That Produce Both NDM-5 and OXA-181 in Jiangsu Province, China

Objective

The aim of this study was to analyze the genetic characteristics of three Enterobacteriaceae strains (one strain of Escherichia coli and two strains of Klebsiella pneumoniae) that produce both the NDM-5 and OXA-181 carbapenemases in pediatric patients.

Methods

Carbapenem-resistant Enterobacteriaceae (CRE) strains were collected from the Children's Hospital Affiliated to Nanjing Medical University in 2022. Resistance genes were detected by PCR. CRE strains that produced both the bla_NDM-5 and bla_OXA-181 genes were further characterized by antimicrobial susceptibility testing, multilocus sequence typing (MLST), plasmid conjugation assay, S1 nuclease-PFGE, Southern blotting and whole-genome sequencing.

Results

Three Enterobacteriaceae strains carrying both the bla_NDM-5 and bla_OXA-181 resistance genes were screened. MLST results showed that the strain of Escherichia coli carrying both bla_NDM-5 and bla_OXA-181 was ST410; the two strains of Klebsiella pneumoniae with both bla_NDM-5 and bla_OXA-181 were ST2601 and ST759. Conjugation assays showed that the plasmids harboring the bla_NDM-5 and bla_OXA-181 genes were self-transmissible. S1-PFGE and Southern blotting showed that the bla_NDM-5 and bla_OXA-181 genes were located on the plasmid with the size of about 60kb~. The genotyping results showed that the plasmid types were ColKP3 and IncX3.

Conclusion

This is the first report of Enterobacteriaceae strains that produce both NDM-5 and OXA-181 isolated from pediatric patients in China. Active infection control measures are urgently needed to prevent the spread of bacteria in children.

The activity and mechanism of vidofludimus as a potent enzyme inhibitor against NDM-1-positive E. coli

New Delhi metallo-β-lactamase-1 (NDM-1) is the most important and prevalent enzyme among all metallo-β-lactamases. NDM-1 can hydrolyze almost all-available β-lactam antibiotics including carbapenems, resulting in multidrug resistance, which poses an increasing clinical threat. However, there is no NDM-1 inhibitor approved for clinical treatment. Therefore, identifying a novel and potential enzyme inhibitor against NDM-1-mediated infections is an urgent need. In this study, vidofludimus was identified as a potential NDM-1 inhibitor by structure-based virtual screening and an enzyme activity inhibition assay. Vidofludimus significantly inhibited NDM-1 hydrolysis activity with a significant dose-dependent effect. When the vidofludimus concentration was 10 μg/ml, the inhibition rate and 50% inhibitory concentration were 93.3% and 13.8 ± 0.5 μM, respectively. In vitro, vidofludimus effectively restored the antibacterial activity of meropenem against NDM-1-positive Escherichia coli (E. coli), and the minimum inhibitory concentration of meropenem was decreased from 64 μg/ml to 4 μg/ml, a 16-fold reduction. The combination of vidofludimus and meropenem showed a significant synergistic effect with a fractional inhibitory concentration index of 0.125 and almost all the NDM-1-positive E. coli were killed within 12 h. Furthermore, the synergistic therapeutic effect of vidofludimus and meropenem in vivo was evaluated in mice infected with NDM-1 positive E. coli. Compared with the control treatment, vidofludimus combined with meropenem significantly improved the survival rate of mice infected with NDM-1-positive E. coli (P < 0.05), decreased the white blood cell count, the bacterial burden and inflammatory response induced by NDM-1-positive E. coli (P < 0.05), and alleviated histopathological damage in infected mice. It was demonstrated by molecular dynamic simulation, site-directed mutagenesis and biomolecular interaction that vidofludimus could interact directly with the key amino acids (Met67, His120, His122 and His250) and Zn²⁺ in the active site of NDM-1, thereby competitively inhibiting the hydrolysis activity of NDM-1 on meropenem. In summary, vidofludimus holds promise as anNDM-1 inhibitor, and the combination of vidofludimus and meropenem has potential as a therapeutic strategy for NDM-1-mediated infections.

β-Lactam potentiators to re-sensitize resistant pathogens: Discovery, development, clinical use and the way forward

β-lactam antibiotics are one of the most widely used and diverse classes of antimicrobial agents for treating both Gram-negative and Gram-positive bacterial infections. The β-lactam antibiotics, which include penicillins, cephalosporins, monobactams and carbapenems, exert their antibacterial activity by inhibiting the bacterial cell wall synthesis and have a global positive impact in treating serious bacterial infections. Today, β-lactam antibiotics are the most frequently prescribed antimicrobial across the globe. However, due to the widespread use and misapplication of β-lactam antibiotics in fields such as human medicine and animal agriculture, resistance to this superlative drug class has emerged in the majority of clinically important bacterial pathogens. This heightened antibiotic resistance prompted researchers to explore novel strategies to restore the activity of β-lactam antibiotics, which led to the discovery of β-lactamase inhibitors (BLIs) and other β-lactam potentiators. Although there are several successful β-lactam-β-lactamase inhibitor combinations in use, the emergence of novel resistance mechanisms and variants of β-lactamases have put the quest of new β-lactam potentiators beyond precedence. This review summarizes the success stories of β-lactamase inhibitors in use, prospective β-lactam potentiators in various phases of clinical trials and the different strategies used to identify novel β-lactam potentiators. Furthermore, this review discusses the various challenges in taking these β-lactam potentiators from bench to bedside and expounds other mechanisms that could be investigated to reduce the global antimicrobial resistance (AMR) burden.

Distribution and driving factors of antibiotic resistance genes in treated wastewater from different types of livestock farms

Treated wastewater from livestock farms is an important reservoir for antibiotic resistance genes (ARGs), and is a main source of ARGs in the environment. However, the distribution and driving factors of ARGs in treated wastewater from different types of livestock farms are rarely reported. In this study, treated wastewater from 69 large-scale livestock farms of different types, including broiler, layer, and pig farms, was collected, and 11 subtypes of ARGs, 2 mobile genetic elements (MGEs) and bacterial community structure were analyzed. The results revealed detection rates of NDM-1 and mcr-1 of 90 % and 43 %, respectively, and the detection rates of other ARGs were 100 %. The relative abundance of ARGs, such as tetA, tetX and strB, in broiler farms was significantly higher than that in layer farms, but the bacterial α diversity was significantly lower than that in other farm types. Furthermore, although the treatment process had a greater impact on the physicochemical properties of the treated wastewater than the livestock type, livestock type was the main factor affecting the bacterial community in the treated wastewater. The analysis of potential host bacteria of ARGs revealed significant differences in the host bacteria of ARGs in treated wastewater from different types of livestock farms. The host bacteria of ARGs in broiler farms mainly belonged to Actinobacteria, layer farms mainly belonged to Proteobacteria, and pig farms mainly belonged to Firmicutes. Additionally, redundancy analysis showed that the distribution of ARGs may have resulted from the combination of multiple driving factors in different types of livestock farms, among which tnpA and NH₄⁺-N were the main influencing factors. This study revealed multiple driving factors for the distribution of typical ARGs in treated wastewater from different types of livestock farms, providing basic data for the prevention and control of ARG pollution in agricultural environments.

Emergence of a Salmonella Rissen ST469 clinical isolate carrying blaNDM-13 in China

New Delhi metallo-β-lactamase-13 (NDM-13) is an NDM variant that was first identified in 2015 and has not been detected in Salmonella species prior to this study. Here we describe the first identification of a Salmonella Rissen strain SR33 carrying bla_NDM-13. The aim of this study was to molecularly characterize SR33’s antimicrobial resistance and virulence features as well as investigate the genetic environment of bla_NDM-13. The Salmonella Rissen SR33 strain was isolated from a patient with fever and diarrhea. SR33 belonged to ST469, and it was found to be multidrug-resistant (MDR) and to carry many virulence genes. Phylogenetic analysis showed that SR33 shared a close relationship with most of the Chinese S. Rissen ST469 strains. bla_NDM-13 was located in a transmissible IncI1 plasmid pNDM13-SR33. Sequence analysis of bla_NDM-13-positive genomes downloaded from GenBank revealed that a genetic context (ΔISAba125-bla_NDM-13-ble_MBL-trpF) and a hybrid promoter (consisting of −35 sequences provided by ISAba125 and −10 sequences) were conserved. ISAba125 was truncated by IS1294 in three plasmids carrying bla_NDM-13, including pNDM13-SR33. To our knowledge, this is the first report of bla_NDM-13 carried by Salmonella. The emergence of bla_NDM-13 in a clinical MDR S. Rissen ST469 strain highlights the critical need for monitoring and controlling the dissemination of bla_NDM-13. bla_NDM-13 carried by a transmissible IncI1 plasmid may result in an increased risk of bla_NDM-13 transmission. IS1294 may be involved in the movement of bla_NDM-13.