Abstract:The rise of multi-drug resistance in bacterial pathogens is one of the grand challenges facing medical science. A major concern is the speed of development of β-lactamase-mediated resistance in Gram-negative species, thus putting at risk the efficacy of the most recently approved antibiotics and inhibitors, including carbapenems and avibactam, respectively. New strategies to overcome resistance are urgently required, which will ultimately be facilitated by a deeper understanding of the mechanisms that regulate… Show more
“…In simulations of carbapenem acylenzyme complexes, committor analysis identifies the conformation of the Trp105 loop as one factor differentiating so-called “permissive” conformations (in which the β-lactam acylenzyme carbonyl occupies the oxyanion hole and the deacylating water is present) from “non-permissive” conformations with the carbonyl outside the oxyanion hole and the deacylating water absent [74]. In multiple-replica parallel tempering metadynamics simulations, that access timescales not available through conventional methodologies, unliganded KPC is shown to undergo motions of active site regions, including Trp105 and the omega-loop containing Glu166, that are related to hydrophobic networks in the individual α and α/β domains and that direct interactions with substrates [75]. Experimental studies of site-directed mutants support these findings by identifying Trp105 as a determinant of KPC activity [71].…”
The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g.,
Escherichia coli
) and non-fermenting organisms (e.g.,
Pseudomonas aeruginosa
). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.
“…In simulations of carbapenem acylenzyme complexes, committor analysis identifies the conformation of the Trp105 loop as one factor differentiating so-called “permissive” conformations (in which the β-lactam acylenzyme carbonyl occupies the oxyanion hole and the deacylating water is present) from “non-permissive” conformations with the carbonyl outside the oxyanion hole and the deacylating water absent [74]. In multiple-replica parallel tempering metadynamics simulations, that access timescales not available through conventional methodologies, unliganded KPC is shown to undergo motions of active site regions, including Trp105 and the omega-loop containing Glu166, that are related to hydrophobic networks in the individual α and α/β domains and that direct interactions with substrates [75]. Experimental studies of site-directed mutants support these findings by identifying Trp105 as a determinant of KPC activity [71].…”
The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g.,
Escherichia coli
) and non-fermenting organisms (e.g.,
Pseudomonas aeruginosa
). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.
“…Thus, ESBLs confer multiresistance to these antibiotics and related oxyimino-beta lactams, which play an important role in antibiotic resistance in E. coli . KPC is another key enzyme in MDR, due to its ability to hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins and penicillins [26]. Interestingly, ESBL gene were not detected by VITEK 2 Compact System, highlighting its flaws in clinical setting.Fig.…”
Background
Multidrug resistance is a growing global public health threat with far more serious consequences than generally anticipated. In this study, we investigated the antibiotic resistance and genomic traits of a clinical strain of
Escherichia coli
LCT-EC001.
Results
LCT-EC001 was resistant to 16 kinds of widely used antibiotics, including fourth-generation cephalosporins and carbapenems. In total, up to 68 determinants associated with antibiotic resistance were identified, including 8 beta-lactamase genes (notably producing ESBLs and KPCs), 31 multidrug efflux system genes, 6 outer membrane transport system genes, 4 aminoglycoside-modifying enzyme genes, 10 two-component regulatory system genes, and 9 other enzyme or transcriptional regulator genes, covering nearly all known drug-resistance mechanisms in
E. coli
. More than half of the resistance genes were located close to mobile genetic elements, such as plasmids, transposons, genomics islands, and insertion sequences. Phylogenetic analysis revealed that this strain may have evolved from
E. coli
K-12 but is a completely new MLST type.
Conclusions
Antibiotic resistance was extremely severe in
E. coli
LCT-EC001, mainly due to mobile genetic elements that allowed the gain of a large quantity of resistance genes. The antibiotic resistance genes of
E. coli
LCT-EC001 can probably be transferred to other bacteria. To the best of our knowledge, this is the first report of a strain of
E. coli
which has such a large amount of antibiotic resistance genes. Apart from providing an
E. coli
reference genome with an extremely high multidrug-resistant background for future analyses, this work also offers a strategy for investigating the complement and characteristics of genes contributing to drug resistance at the whole-genome level.
Electronic supplementary material
The online version of this article (10.1186/s13099-019-0298-5) contains supplementary material, which is available to authorized users.
“…Nosocomial pathogens having multidrug resistance (MDR) or pandemic drug resistance (PDR) traits usually represent a paradigm in pathogenesis and responsible for life-threatening diseases in human 54,55 . The non-judicial usage of available antibiotics remains as the main reason for the crisis of having significant and effective antibiotic against resistance pathogens [8][9][10] .…”
A Kashmir Himalayan (India) soil isolate, Streptomyces sp. SM01 was subjected to small scale fermentation for the production of novel antimicrobials, picolinamycin (SM1). The production has been optimized which found to be maximum while incubated in AIA medium (pH 7) for 7 days at 30 °C. Seven days grew crude cell-free culture media (50 µL) showed a larger zone of inhibition against Staphylococcus aureus compared to streptomycin (5 µg) and ampicillin (5 µg). Extraction, purification, and chemical analysis of the antimicrobial component has been proved to be a new class of antibiotic with 1013 dalton molecular weight. We have named this new antibiotic as picolinamycin for consisting picolinamide moiety in the center of the molecule and produced by a Streptomyces sp. In general, the antimicrobial potency of this newly characterized antibiotic found to be higher against Gram-positive organisms than the tested Gram-negative organisms. The MIC of this antimicrobial compound was found to be 0.01 µg/ml for tested Gram-positive organisms and 0.02 to 5.12 µg/ml for Gram-negative organisms. Furthermore, it showed strong growth impairments of several multidrug resistance (MDR) strains, including methicillin-resistant strains of Staphylococci and Enterococci with the MIC value of 0.04 to 5.12 µg/ml and MDR (but methicillin-sensitive) strains of S. aureus with the MIC value of 0.084 µg/ml. It also showed anti-mycobacterial potential in higher concentrations (MIC is 10.24 µg/ml). Picolinamycin however did not show toxicity against tested A549 human cell line indicating that the spectrum of its activity limited within bacteria only. About one out of ten patients are acquiring nosocomial infection as hospitals are the principal source of multidrug-resistant (MDR) pathogens 1. The most formidable MDR pathogens are methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE); vancomycin-resistant S. aureus (VRSA) and principal Gram-negative bacteria involved in nosocomial infection like Klebsiella pneumoniae, Acinetobacter baumanni, Pseudomonas aeruginosa, Enterobacter sp. which generally are also resistant against major existing antibiotics such as second-generation cephalosporin, fluoroquinolones, penicillin in combination with beta-lactamase inhibitor, third-generation cephalosporin and carbapenem 2-8. Non-judicial use of antibiotics is thought to be the major factor for antimicrobial resistance 8-10. More than 100,000 tons of antibiotics have been manufactured annually to combat pathogens 2. However most of the clinically used antibiotics against nosocomial bacteria remain ineffective due to their acquired resistance 11-14. From January 2000 to October 2019, only 44 compounds under 7 novel classes have been introduced in clinical pipeline 15. Among these 27 compounds are synthetic, 14 are derivative of natural product and 3 are from other sources. However the antimicrobials of natural origin are very rare, but these are found to be most suitable against multidrug resistance (MDR) bacteria, as the...
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
