Structural and functional characterization of three Type B and C chloramphenicol acetyltransferases from Vibrio species

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria

Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.

Emerging antibiotic resistance by various novel proteins/enzymes

BACKGROUND

The emergence and dissemination of antibiotic resistance represents a significant and ever-increasing global threat to human, animal, and environmental health. The explosive proliferation of resistance has ultimately been seen in all clinically used antibiotics. Infections caused by antibiotic-resistant bacteria have been associated with an estimated 4,950,000 deaths annually, with extremely limited therapeutic options and only a few new antibiotics under development. To combat this silent pandemic, a better understanding of the molecular mechanisms of antibiotic resistance is immensely needed, which not only helps to improve the efficacy of current drugs in clinical use but also design new antimicrobial agents that are less susceptible to resistance.

RESULTS

The past few years have witnessed a number of new advances in revealing the molecular mechanisms of AMR. Following five sophisticated mechanisms (efflux pump, antibiotics inactivation by enzymes, alteration of membrane permeability, target modification, and target protection), the roles of various novel proteins/enzymes in the acquisition of antibiotic resistance are constantly being described. They are widely used by clinical bacterial strains, playing a key role in the emergence of resistance.

CONCLUSION

While most of these have so far received less attention, expanding our understanding of these emerging resistance mechanisms is of crucial importance to combat the antibiotic resistance crisis in the world. This review summarizes recent advances in our knowledge of emerging resistance mechanisms in bacteria, providing an update on the current antibiotic resistance threats and encouraging researchers to develop critical strategies for overcoming the resistance.

The landscape of cell lineage tracing

Cell fate changes play a crucial role in the processes of natural development, disease progression, and the efficacy of therapeutic interventions. The definition of the various types of cell fate changes, including cell expansion, differentiation, transdifferentiation, dedifferentiation, reprogramming, and state transitions, represents a complex and evolving field of research known as cell lineage tracing. This review will systematically introduce the research history and progress in this field, which can be broadly divided into two parts: prospective tracing and retrospective tracing. The initial section encompasses an array of methodologies pertaining to isotope labeling, transient fluorescent tracers, non-fluorescent transient tracers, non-fluorescent genetic markers, fluorescent protein, genetic marker delivery, genetic recombination, exogenous DNA barcodes, CRISPR-Cas9 mediated DNA barcodes, and base editor-mediated DNA barcodes. The second part of the review covers genetic mosaicism, genomic DNA alteration, TCR/BCR, DNA methylation, and mitochondrial DNA mutation. In the final section, we will address the principal challenges and prospective avenues of enquiry in the field of cell lineage tracing, with a particular focus on the sequencing techniques and mathematical models pertinent to single-cell genetic lineage tracing, and the value of pursuing a more comprehensive investigation at both the spatial and temporal levels in the study of cell lineage tracing.

Molecular basis of the persistence of chloramphenicol resistance among Escherichia coli and Salmonella spp. from pigs, pork and humans in Thailand

This study aimed to investigate the potential mechanisms associated with the persistence of chloramphenicol (CHP) resistance in Escherichia coli and Salmonella enterica isolated from pigs, pork, and humans in Thailand. The CHP-resistant E. coli (n = 106) and Salmonella (n = 57) isolates were tested for their CHP susceptibility in the presence and absence of phenylalanine arginine β-naphthylamide (PAβN). The potential co-selection of CHP resistance was investigated through conjugation experiments. Whole genome sequencing (WGS) was performed to analyze the E. coli (E329, E333, and E290) and Salmonella (SA448, SA461, and SA515) isolates with high CHP MIC (32-256 μg/mL) and predominant plasmid replicon types. The presence of PAβN significantly reduced the CHP MICs (≥4-fold) in most E. coli (67.9%) and Salmonella (64.9%). Ampicillin, tetracycline, and streptomycin co-selected for CHP-resistant Salmonella and E. coli-transconjugants carrying cmlA. IncF plasmids were mostly detected in cmlA carrying Salmonella (IncFIIAs) and E. coli (IncFIB and IncF) transconjugants. The WGS analysis revealed that class1 integrons with cmlA1 gene cassette flanked by IS26 and TnAs1 were located on IncX1 plasmid, IncFIA(HI1)/HI1B plasmids and IncFII/FIB plasmids. IncFIA(HI1)/HI1B/Q1in SA448 contained catA flanked by IS1B and TnAs3. In conclusion, cross resistance through proton motive force-dependent mechanisms and co-selection by other antimicrobial agents involved the persistence of CHP-resistance in E. coli in this collection. Dissemination of CHP-resistance genes was potentially facilitated by mobilization via mobile genetic elements.

Emerging resistome diversity in clinical Vibrio cholerae strains revealing their role as potential reservoirs of antimicrobial resistance

BACKGROUND

This is a unique and novel study delineating the genotyping and subsequent prediction of AMR determinants of Vibrio cholerae revealing the potential of contemporary strains to serve as precursors of severe AMR crisis in cholera.

METHODS AND RESULTS

Genotyping of representative strains, VC1 and VC2 was undertaken to characterize antimicrobial resistance genes (ARGs) against chloramphenicol, SXT, nalidixic acid and streptomycin against which they were found to be resistant by antibiogram analysis in our previous investigation. strAB, sxt, sul2, qace∆1-sul1 were detected by PCR. Genome annotation and identification of ARGs with WGS helped to detect the presence of almG, varG, strA (APH(3'')-Ib), strB (APH(6)-Id), sul2, catB9, floR, CRP, dfrA1 genes. Signatures of resistance determinants and protein domains involved in antimicrobial resistance, primarily, efflux of antibiotics were identified on the basis of 30-100% homology to reference proteins. These domains were predicted to be involved in other metabolic functions on the basis of 100% identity with 100% coverage with reference protein and nucleotide sequences and were predicted to be of a diverse taxonomic origin accentuating the influence of the microbiota on AMR acquisition. Sequence analysis of QRDR (quinolone resistance-determining region) revealed SNPs. Cytoscape v3.8.2 was employed to analyse protein-protein interaction of MDR proteins, MdtA and EmrD-2, with nodes of vital AMR pathways. Vital nodes involved in efflux of different classes of antibiotics were found to be absent in VC1 and VC2 justifying the sensitivity of these strains to most antibiotics.

CONCLUSIONS

The study helped to examine the resistome of VC isolated from recent outbreaks to understand the underlying reason of sensitivity to most antibiotics and also to characterize the ARGs in their genome. It revealed that VC is a reservoir of signatures of resistance determinants and serving as precursors for severe AMR crisis in cholera. This is the first study, to our knowledge, which has scrutinized and presented systematically, information on prospective domains which bear the potential of serving as AMR determinants in VC with the help of bioinformatic tools. This pioneering approach may help in the prediction of AMR landfalls and benefit epidemiological surveillance and early warning systems.

Characteristics and catalytic mechanism of a novel multifunctional oxidase, CpmO, for chloramphenicols degradation from Sphingobium sp. WTD-1

Chloramphenicols (CAPs) are ubiquitous emerging pollutants that threaten ecological environments and human health. Microbial and enzyme-based biodegradation strategies offer a cost-effective environmentally friendly approach for CAPs removal from contaminated sites. Here, CpmO, a novel multifunctional oxidase for CAP degradation was identified from the CAP-degrading strain Sphingobium sp. WTD-1. This enzyme was found to be responsible for both the oxidation of the C3-hydroxyl and oxidative cleavage of the C1-C2 bond of CAP, and the oxidative cleavage pathway of CAP was dominant. The catalytic efficiency of CpmO for CAP was 41.6 times that for thiamphenicol (TAP) under the optimal conditions (40 °C, pH 6.0). CpmO was identified as a member of the glucose-methanol-choline oxidoreductase family. Molecular docking and site-directed mutagenesis analysis indicated that CAP was connected to the key amino acid residues E231/E395, K277, and I273/A276 in CpmO through hydrogen bonding, nonclassical hydrogen bonding, and π-π stacking forces, respectively. The catalytic activities of the A276W, K277P, and E231S mutants were found to be 1.1 times, 6.4 times, and 13.2 times higher than that of the wild type, respectively. These findings provide genetic resources and theoretical guidance for future application in biotechnological and metabolic engineering efforts for the remediation of CAPs-contaminated environments.

Strain belonging to an emerging, virulent sublineage of ST131 Escherichia coli isolated in fresh spinach, suggesting that ST131 may be transmissible through agricultural products

Food contamination with pathogenic Escherichia coli can cause severe disease. Here, we report the isolation of a multidrug resistant strain (A23EC) from fresh spinach. A23EC belongs to subclade C2 of ST131, a virulent clone of Extraintestinal Pathogenic E. coli (ExPEC). Most A23EC virulence factors are concentrated in three pathogenicity islands. These include PapGII, a fimbrial tip adhesin linked to increased virulence, and CsgA and CsgB, two adhesins known to facilitate spinach leaf colonization. A23EC also bears TnMB1860, a chromosomally-integrated transposon with the demonstrated potential to facilitate the evolution of carbapenem resistance among non-carbapenemase-producing enterobacterales. This transposon consists of two IS26-bound modular translocatable units (TUs). The first TU carries aac(6')-lb-cr, bla OXA-1, ΔcatB3, aac(3)-lle, and tmrB, and the second one harbors bla CXT-M-15. A23EC also bears a self-transmissible plasmid that can mediate conjugation at 20°C and that has a mosaic IncF [F(31,36):A(4,20):B1] and Col156 origin of replication. Comparing A23EC to 86 additional complete ST131 sequences, A23EC forms a monophyletic cluster with 17 other strains that share the following four genomic traits: (1) virotype E (papGII+); (2) presence of a PAI II536-like pathogenicity island with an additional cnf1 gene; (3) presence of chromosomal TnMB1860; and (4) frequent presence of an F(31,36):A(4,20):B1 plasmid. Sequences belonging to this cluster (which we named "C2b sublineage") are highly enriched in septicemia samples and their associated genetic markers align with recent reports of an emerging, virulent sublineage of the C2 subclade, suggesting significant pathogenic potential. This is the first report of a ST131 strain belonging to subclade C2 contaminating green leafy vegetables. The detection of this uropathogenic clone in fresh food is alarming. This work suggests that ST131 continues to evolve, gaining selective advantages and new routes of transmission. This highlights the pressing need for rigorous epidemiological surveillance of ExPEC in vegetables with One Health perspective.

Antibiotic resistance in ocular bacterial infections: an integrative review of ophthalmic chloramphenicol

INTRODUCTION

Chloramphenicol is a broad-spectrum antibiotic widely used for treating ophthalmic infections, but concerns about rising bacterial resistance to chloramphenicol have been observed due to its frequent use as an over-the-counter medication. This review assessed the common ophthalmic bacterial pathogens, their chloramphenicol resistance mechanisms, and rates of drug resistance.

METHODS

PubMed and Google Scholar databases were searched for relevant publications from the years 2000 to 2022, bordering on ophthalmic bacterial infections, chloramphenicol susceptibility profiles, and drug resistance mechanisms against chloramphenicol. A total of 53 journal publications met the inclusion criteria, with data on the antibiotic susceptibility profiles available in 44 of the reviewed studies, which were extracted and analyzed.

RESULTS

The mean resistance rates to chloramphenicol from antibiotic susceptibility profiles varied between 0% and 74.1%, with the majority of the studies (86.4%) showing chloramphenicol resistance rates below 50%, and more than half (23 out of 44) of the studies showed resistance rates lower than 20%. The majority of the publications (n = 27; 61.4%) were from developed nations, compared to developing nations (n = 14; 31.8%), while a fraction (n = 3; 6.8%) of the studies were regional cohort studies in Europe, with no country-specific drug resistance rates. No pattern of cumulative increase or decrease in ophthalmic bacterial resistance to chloramphenicol was observed.

CONCLUSIONS

Chloramphenicol is still active against ophthalmic bacterial infections and is suitable as a topical antibiotic for ophthalmic infections. However, concerns remain about the drug becoming unsuitable in the long run due to some proof of high drug resistance rates.

Deciphering a novel chloramphenicols resistance mechanism: Oxidative inactivation of the propanediol pharmacophore

Expanding knowledge about new types of antibiotic resistance genes is of great significance in dealing with the global antibiotic resistance crisis. Herein, a novel oxidoreductase capO was discovered to be responsible for oxidative inactivation of chloramphenicol and thiamphenicol. The antibiotic resistance mechanism was comprehensively deciphered using multi-omics and multiscale computational approaches. A 66,383 bp DNA fragment carrying capO was shared among four chloramphenicol-resistant strains, and the co-occurrence of capO with a mobile genetic element cluster revealed its potential mobility among different taxa. Metagenomic analysis of 772 datasets indicated that chloramphenicol was the crucial driving factor for the development and accumulation of capO in activated sludge bioreactors treating antibiotic production wastewater. Therefore, we should pay sufficient attention to its possible prevalence and transfer to pathogens, especially in some hotspot environments contaminated with high concentrations of chloramphenicols. This finding significantly expands our knowledge boundary about chloramphenicols resistance mechanisms.

Nanobiotics against antimicrobial resistance: harnessing the power of nanoscale materials and technologies

Given the spasmodic increment in antimicrobial resistance (AMR), world is on the verge of “post-antibiotic era”. It is anticipated that current SARS-CoV2 pandemic would worsen the situation in future, mainly due to the lack of new/next generation of antimicrobials. In this context, nanoscale materials with antimicrobial potential have a great promise to treat deadly pathogens. These functional materials are uniquely positioned to effectively interfere with the bacterial systems and augment biofilm penetration. Most importantly, the core substance, surface chemistry, shape, and size of nanomaterials define their efficacy while avoiding the development of AMR. Here, we review the mechanisms of AMR and emerging applications of nanoscale functional materials as an excellent substitute for conventional antibiotics. We discuss the potential, promises, challenges and prospects of nanobiotics to combat AMR.

Aquatic environments: A Potential Source of Antimicrobial-Resistant Vibrio spp

Vibrio spp. are associated with water and seafood-related outbreaks worldwide. They are naturally present in aquatic environments such as seawater, brackish water and freshwater environments. These aquatic environments serve as the main reservoirs of antimicrobial-resistant genes and promote the transfer of antimicrobial-resistant bacterial species to aquatic animals and humans through the aquatic food chain. Vibrio spp. are known as etiological agents of cholera and non-cholera Vibrio infections in humans and animals. Antimicrobial-resistant Vibrio species have become a huge threat in regard to treating Vibrio infections in aquaculture and public health. Most of the Vibrio spp. possess resistance towards the commonly used antimicrobials, including β-lactams, aminoglycosides, tetracyclines, sulfonamides, quinolones and macrolides. The aim of this review is to summarize the antimicrobial resistance properties of Vibrio spp. isolated from aquatic environments to provide awareness about potential health risks related to Vibrio infections in aquaculture and public health.

Virulence and Antibiotic Resistance Characteristics of Vibrio Isolates From Rustic Environmental Freshwaters

The study investigated the occurrence of antimicrobial resistance genes and virulence determinants in Vibrio species recovered from different freshwater sheds in rustic milieu. A total of 118 Vibrio isolates comprising Vibrio fluvialis (n=41), Vibrio mimicus (n=40) and V. vulnificus (n=37) was identified by amplification of ToxR, vmh and hsp60 genes. The amplification of virulence genes indicated that V. mimicus (toxR, zot, ctx, VPI, and ompU) genes were detected in 12.5%, 32.5%, 45%, 37.5% and 10% respectively. V. fluvialis genes (stn, hupO and vfh) were harboured in 48.8%, 14.6% and 19.5% isolates congruently. The other virulence genes that include vcgC and vcgE were observed in 63.1% and 29% of isolates belonging to V. vulnificus. With the exceptions of imipenem, meropenem and ciprofloxacin, most isolates exhibited more than 50% resistance to antibiotics. The antimicrobial resistance was more prevalent for polymyxin B (100%), azithromycin (100%) and least in ciprofloxacin (16.1%). Multiple antibiotic resistance index range was 0.3 and 0.8 with most isolates showing MARI of 0.8. The blaTEM, AmpC, blaGES, blaIMP, blaOXA-48 and blaKPC genes were detected in 53.3%, 42%, 29.6%, 16.6%, 15%, 11.3% and 5.6% of the isolates. Non-beta lactamases such as streptomycin resistance (aadA and strA), gentamicin resistance (aphA1) and quinolone resistance gene (qnrVC) were found in 5.2%, 44.3%, 26% and 2.8%. Chloramphenicol resistance genes (cmlA1 and catII) were found in 5.2% and 44.3% among the isolates. Our findings reveal the presence of antimicrobial resistance genes and virulent Vibrio species in aquatic environment which can have potential risk to human and animal's health.

Structural characterization of a Type B chloramphenicol acetyltransferase from the emerging pathogen Elizabethkingia anophelis NUHP1

Elizabethkingia anophelis is an emerging multidrug resistant pathogen that has caused several global outbreaks. E. anophelis belongs to the large family of Flavobacteriaceae, which contains many bacteria that are plant, bird, fish, and human pathogens. Several antibiotic resistance genes are found within the E. anophelis genome, including a chloramphenicol acetyltransferase (CAT). CATs play important roles in antibiotic resistance and can be transferred in genetic mobile elements. They catalyse the acetylation of the antibiotic chloramphenicol, thereby reducing its effectiveness as a viable drug for therapy. Here, we determined the high-resolution crystal structure of a CAT protein from the E. anophelis NUHP1 strain that caused a Singaporean outbreak. Its structure does not resemble that of the classical Type A CATs but rather exhibits significant similarity to other previously characterized Type B (CatB) proteins from Pseudomonas aeruginosa, Vibrio cholerae and Vibrio vulnificus, which adopt a hexapeptide repeat fold. Moreover, the CAT protein from E. anophelis displayed high sequence similarity to other clinically validated chloramphenicol resistance genes, indicating it may also play a role in resistance to this antibiotic. Our work expands the very limited structural and functional coverage of proteins from Flavobacteriaceae pathogens which are becoming increasingly more problematic.

Structural and functional characterization of three Type B and C chloramphenicol acetyltransferases from Vibrio species

Chloramphenicol acetyltransferases (CATs) were among the first antibiotic resistance enzymes identified and have long been studied as model enzymes for examining plasmid-mediated antibiotic resistance. These enzymes acetylate the antibiotic chloramphenicol, which renders it incapable of inhibiting bacterial protein synthesis. CATs can be classified into different types: Type A CATs are known to be important for antibiotic resistance to chloramphenicol and fusidic acid. Type B CATs are often called xenobiotic acetyltransferases and adopt a similar structural fold to streptogramin acetyltransferases, which are known to be critical for streptogramin antibiotic resistance. Type C CATs have recently been identified and can also acetylate chloramphenicol, but their roles in antibiotic resistance are largely unknown. Here, we structurally and kinetically characterized three Vibrio CAT proteins from a nonpathogenic species (Aliivibrio fisheri) and two important human pathogens (Vibrio cholerae and Vibrio vulnificus). We found all three proteins, including one in a superintegron (V. cholerae), acetylated chloramphenicol, but did not acetylate aminoglycosides or dalfopristin. We also determined the 3D crystal structures of these CATs alone and in complex with crystal violet and taurocholate. These compounds are known inhibitors of Type A CATs, but have not been explored in Type B and Type C CATs. Based on sequence, structure, and kinetic analysis, we concluded that the V. cholerae and V. vulnificus CATs belong to the Type B class and the A. fisheri CAT belongs to the Type C class. Ultimately, our results provide a framework for studying the evolution of antibiotic resistance gene acquisition and chloramphenicol acetylation in Vibrio and other species.