Lincosamides, Streptogramins, Phenicols, and Pleuromutilins: Mode of Action and Mechanisms of Resistance

Co-occurrence and co-expression of antibiotic, biocide, and metal resistance genes with mobile genetic elements in microbial communities subjected to long-term antibiotic pressure: Novel insights from metagenomics and metatranscriptomics

The burgeoning of antibiotic resistance has emerged as a pressing global challenge. To gain a deeper understanding of the interactions between antibiotic resistance genes (ARGs), biocide and metal resistance genes (BRGs&MRGs), and mobile genetic elements (MGEs), this study utilized metagenomics and metatranscriptomics to investigate their co-occurrence and co-expression in two consortia subjected to long-term exposure to chloramphenicol and lincomycin. Long-term exposure to these antibiotics resulted in significant disparities in resistance profiles: ConsortiumCAP harbored 130 ARGs and 150 BRGs&MRGs, while ConsortiumLIN contained 57 ARGs and 32 BRGs&MRGs. Horizontal gene transfer (HGT) events were predicted at 125 and 300 instances in ConsortiumCAP and ConsortiumLIN, respectively, facilitating the emergence of multidrug-resistant bacteria, such as Caballeronia (10 ARGs, 2 BRGs&MRGs), Cupriavidus (2 ARGs, 10 BRGs&MRGs), and Bacillus (14 ARGs, 21 BRGs&MRGs). Chloramphenicol exposure significantly enriched genes linked to phenicol resistance (floR, capO) and co-expressed ARGs and BRGs&MRGs, while lincomycin exerted narrower effects on resistance genes. Additionally, both antibiotics modulated the expression of degradation genes and virulence factors, highlighting their role in altering bacterial substrate utilization and pathogenic traits. This study provides quantitative insights into the impact of antibiotics on microbial resistance profiles and functions at both DNA and RNA levels, highlighting the importance of reducing antibiotic pollution and limiting the spread of resistance genes in the environment.

Phenotypic and genotypic characteristics of macrolide, lacosamide, and streptogramin resistance in clinically resistant Streptococci and their correlation with reduced biocide susceptibility

BACKGROUND

Gram-positive Streptococci is a huge group of different species that are classified based on its hemolytic effect besides the C-substance in the cell wall. This study focuses on the investigation of the prevalence and genetic basis of resistance to macrolides, lincosamides, and streptogramins (MLS) in α- and β-hemolytic Streptococci.

METHODS

Streptococcal isolates were identified and their resistance was assessed to MLS antibiotics through phenotypic analysis and genotypic screening of resistance genes. Isolates were also tested for susceptibility to antiseptics/disinfectants. The correlation between high MLS antibiotic resistance and reduced susceptibility to biocides was assessed. Efflux pump activity in the most resistant isolates (to both MLS antibiotics and biocides) was investigated.

RESULTS

The susceptibility testing indicates an increasing resistance to MLS, particularly macrolides (erythromycin, azithromycin, and clarithromycin) and lincomycin. By screening the resistance, the most predominant phenotype is the constitutive (cMLS) one, while the erm genes, particularly ermB, are the most detected genotype. Furthermore, the esterase-encoding gene ereA is widely distributed in the streptococcal isolates. By evaluating the minimum inhibitory concentrations (MICs) to different biocides, there was a strong relation between the increased MIC values to both MLS antibiotics and tested biocides. This can be attributed mainly to the transferable ermB gene and the enhanced bacterial efflux.

CONCLUSIONS

A significant correlation exists between reduced biocide susceptibility and resistance to MLS antibiotics. Elevated efflux pump activity in MLS-resistant isolates suggests efflux mechanisms may contribute to dual resistance to antibiotics and biocides. However, cross-resistance is primarily driven by the horizontally transferable ermB gene, which confers resistance by targeting the 50S ribosomal subunit.

Genomic Characterization of Enterococcus casseliflavus Isolated from Beef Cows and Calves

Enterococcus species are used as One Health indicators of antimicrobial resistance (AMR) in humans, animals, and the environment. A surveillance study in beef cows and calves isolated Enterococcus casseliflavus along with E. faecium, E. faecalis, and E. hirae. Given the high prevalence of E. casseliflavus, we elected to characterize this species to better understand its role in the antimicrobial resistance of enterococci in cows and calves. Almost 12% of E. casseliflavus isolates exhibited multidrug resistance with the majority being resistant to lincomycin (99%), followed by quinupristin-dalfopristin (34%), ciprofloxacin (9.6%), tylosin (4.5%), erythromycin (2.7%), tetracycline (1.8%), tigecycline (1.5%), daptomycin (0.6%), streptomycin (0.3%), and kanamycin (0.3%). All E. casseliflavus were susceptible to chloramphenicol, penicillin, streptomycin, nitrofurantoin, gentamicin, and linezolid. Whole genome antimicrobial resistance gene profiling identified vanC-type intrinsic vancomycin resistance genes in all E. casseliflavus, with the vanC4XYT gene cluster being dominant (67%) followed by vanC2XYT (31%) and vanC3XYT (1.5%). Resistance genes for erythromycin (ermB) and tetracycline (tetM) were rarely identified (2.1% and 1.2%, respectively) within E. casseliflavus genomes. No resistance genes were identified to explain either the quinupristin-dalfopristin or ciprofloxacin resistance in these isolates. A core genome phylogenetic tree revealed two clades that exhibited no distinct association with the age of the host, time of sample collection, or the farm sampled. The open nature of the E. casseliflavus pan-genome highlighted its intraspecies diversity. These findings suggest that E. casseliflavus is likely a low-risk species in terms of contributing to antimicrobial resistance in the cow-calf sector.

Public health threat of antimicrobial resistance and virulence genes in Escherichia coli from human-chicken transmission in Egypt

Escherichia coli (E. coli) infections cause significant losses in the poultry industry and pose zoonotic risks due to rising antimicrobial resistance (AMR) and virulence factors. This study investigates E. coli prevalence, AMR, and virulence genes (papC, vgrG1, iss) in Egyptian chickens and farm workers. A total of 35 dead chickens from 14 flocks and 17 farm workers urine samples were examined bacteriologically to investigate E. coli presence followed by biochemical identification. Antimicrobial susceptibility testing was performed on 14 antibiotics using the disk diffusion method on Mueller-Hinton agar, following 'Clinical and Laboratory Standards Institute (CLSI) (2020) guidelines with Extended-spectrum β-lactamase (ESBL) activity evaluated via the Double Disc Synergy Test (DDST) with ceftazidime, cefotaxime, and their clavulanate combinations following CLSI protocols. virulence genes were detected through polymerase chain reaction (PCR) and phylogenetic analysis of the vgrG1 gene evaluated genetic relatedness between the chicken and human isolates. The study analysed 52 samples, identifying E. coli in 18 chicken organs (51.4%) and 11 human urine samples (64.7%), with no significant difference. various antimicrobic sensitivity profiles were identified phenotypically among all isolates in which 29 isolates, 58.6% were ESBL-producing, and 96.5% exhibited multidrug resistance (MDR), with chicken isolates showing higher resistance overall. virulence genes were detected in similar proportions across the isolates highlighting significant public health risks due to resistant and virulent E. coli. This study emphasized the public health risks of multidrug-resistant E. coli with virulence genes, highlighting potential zoonotic transmission and antibiotic use and food safety.

Antibacterial Essential Oils as Adjuvants to Inhibit Antibiotic Resistance in Multidrug-resistant Bacteria

In order to contribute to the fight against the antibiotic resistance crisis, we used a dual-activity prospection strategy for natural product mixtures with antibiotic resistance modulating and antibacterial activities in the essential oils (EOs) of Artemisia ludoviciana, Lippia graveolens, and Cosmos bipinnatus against multidrug-resistant strains of Pseudomonas aeruginosa HIM-MR01, Staphylococcus aureus HIM-MR02, Enterococcus faecalis HIM-MR05, and Salmonella typhi HIM-MR06. The three EOs exerted antibacterial activity on the bacterial strains with minimum inhibitory concentrations (MICs) ranging from 0.1735 to 65.6263 µg/mL. When combined with antibiotics, the L. graveolens EO showed the highest resistance modulation for vancomycin (VA), nalidixic acid (NA), and chloramphenicol against S. aureus (MIC: 0.0347 µg/mL), E. faecalis (MIC: 0.0832 µg/mL), and P. aeruginosa (MIC: 0.0694 µg/mL). For the A. ludoviciana EO, resistance modulation was based on S. aureus-VA (MIC: 0.6525 µg/mL) and E. faecalis-NA (MIC: 0.3262 µg/mL). Thereby, C. bipinnatus EO did not show significant antibiotic resistance modulating activity. In conclusion, L. graveolens and A. ludoviciana EOs showed antibacterial activity and the greatest potential in inhibiting bacterial resistance to antibiotics. The dual activity of these EOs makes them a promising adjuvant in the treatment of diseases caused by multidrug-resistant pathogenic bacteria.

Acquired Bacterial Resistance to Antibiotics and Resistance Genes: From Past to Future

The discovery, commercialization, and regular administration of antimicrobial agents have revolutionized the therapeutic paradigm, making it possible to treat previously untreatable and fatal infections. However, the excessive use of antibiotics has led to develop resistance soon after their use in clinical practice, to the point of becoming a global emergency. The mechanisms of bacterial resistance to antibiotics are manifold, including mechanisms of destruction or inactivation, target site modification, or active efflux, and represent the main examples of evolutionary adaptation for the survival of bacterial species. The acquirement of new resistance mechanisms is a consequence of the great genetic plasticity of bacteria, which triggers specific responses that result in mutational adaptation, acquisition of genetic material, or alteration of gene expression, virtually producing resistance to all currently available antibiotics. Understanding resistance processes is critical to the development of new antimicrobial agents to counteract drug-resistant microorganisms. In this review, both the mechanisms of action of antibiotic resistance (AMR) and the antibiotic resistance genes (ARGs) mainly found in clinical and environmental bacteria will be reviewed. Furthermore, the evolutionary background of multidrug-resistant bacteria will be examined, and some promising elements to control or reduce the emergence and spread of AMR will be proposed.

Ethical bioprospecting and microbial assessments for sustainable solutions to the AMR crisis

Antimicrobial resistance (AMR) has been declared one of the top 10 global public health challenges of our age by the World Health Organization, and the World Bank describes AMR as a crisis affecting the finance, health, and agriculture sectors and a major threat to the attainment of Sustainable Development Goals. But what is AMR? It is a phenotype that evolves in microbes exposed to antimicrobial molecules and causes dangerous infections. This suggests that scientists and healthcare workers should be on the frontline in the search for sustainable solutions to AMR. Yet AMR is also a societal problem to be understood by everyone. This review aims to explore the need to address the problem of AMR through a coherent, international strategy with buy-in from all sectors of society. As reviewed here, the sustainable solutions to AMR will be driven by better understanding of AMR biology but will require more than this alone to succeed. Some advances on the horizon, such as the use of bacteriophage (phage) to treat AMR infections. However, many of the new technologies and new therapeutics to address AMR require access to biodiversity, where the custodians of that biodiversity-and the traditional knowledge required to access it-are needed as key partners in the scientific, clinical, biotechnological, and international ventures that would treat the problem of AMR and ultimately prevent its further evolution. Many of these advances will be built on microbial assessments to understand the extent of AMR in our environments and bioprospecting to identify microbes that may have beneficial uses. Genuine partnerships for access to this biodiversity and sharing of benefits accrued require a consideration of ethical practice and behavior. Behavior change is needed across all sectors of culturally diverse societies so that rapid deployment of solutions can be implemented for maximum effect against the impacts of AMR.

Photocatalytic Degradation of Lincosamides in the Presence of Commercial Pigments: Kinetics, Intermediates, and Predicted Ecotoxicity

Lincomycin belongs to the antibiotics commonly used in veterinary medicine. Its residues are easily spread in the environment because of its physicochemical properties, including resistance to biodegradation and good solubility in water. One of the effective methods for the removal of lincomycin from wastewater is the photocatalytic process, but it is not widely used due to the price of photocatalysts. The aim of this work was to compare the photocatalytic efficiency and the mechanism of lincomycin degradation initiated by UVa radiation in the presence of TiO2-P25 and ZnO, as well as in the presence of industrial pigments commonly used in construction and containing TiO2. Lincomycin was found to undergo efficient photocatalytic degradation in the presence of a commercial TiO2-P25 photocatalyst, industrial pigments containing only anatase, and in the presence of ZnO. On the contrary, industrial pigments containing only rutile or a mixture of rutile and anatase practically did not show any photocatalytic activity. The composition of the solutions after the degradation of lincomycin in the presence of TiO2-P25 and ZnO differed significantly. Most of the identified organic degradation products contained conserved pharmacophores, and some of them could have been highly ecotoxic.

In Vitro Synergistic Effect of Lefamulin with Doxycycline, Rifampin, and Quinupristin/Dalfopristin Against Enterococci

The widespread resistance of enterococci to many commonly used antimicrobial agents is a growing concern. Given that the current treatment options for enterococcal infections are limited, the discovery of new therapies, including combination therapies, is necessary. We evaluated double-drug combinations of lefamulin with doxycycline, rifampin, and quinupristin/dalfopristin for in vitro synergy against strains of Enterococcus faecium (E. faecium) and Enterococcus faecalis (E. faecalis) by using checkerboard and time-kill assays. In the checkerboard assay, the synergistic effect of lefamulin with doxycycline and rifampin was observed in 29 (85.3%) and 33 (97.1%) of the 34 different E. faecium strains tested, respectively. These combinations also showed synergistic effects against 17 (94.4%) of the 18 different vancomycin-resistant E. faecium strains. Among the 33 different E. faecalis strains, the combination of lefamulin with doxycycline, quinupristin/dalfopristin, and rifampin displayed synergistic effects in 31 (93.9%), 26 (78.8%), and 20 (60.6%) strains, respectively. No antagonism was observed in any of the combinations. The time-kill assay confirmed the synergistic effects of all these combinations. These synergistic combinations exhibited bacteriostatic activity. Although lefamulin is not currently used to treat enterococcal infections, we suggest that these combinations may serve as alternative drug regimens.

Antimicrobial Resistance in African Great Apes

BACKGROUND/OBJECTIVES

Antibiotic-resistant bacteria pose a significant global public health threat that demands serious attention. The proliferation of antimicrobial resistance (AMR) is primarily attributed to the overuse of antibiotics in humans, livestock, and the agro-industry. However, it is worth noting that antibiotic-resistant genes (ARGs) can be found in all ecosystems, even in environments where antibiotics have never been utilized. African great apes (AGAs) are our closest living relatives and are known to be susceptible to many of the same pathogens (and other microorganisms) as humans. AGAs could therefore serve as sentinels for human-induced AMR spread into the environment. They can potentially also serve as reservoirs for AMR. AGAs inhabit a range of environments from remote areas with little anthropogenic impact, over habitats that are co-used by AGAs and humans, to captive settings with close human-animal contacts like zoos and sanctuaries. This provides opportunities to study AMR in relation to human interaction. This review examines the literature on AMR in AGAs, identifying knowledge gaps.

RESULTS

Of the 16 articles reviewed, 13 focused on wild AGAs in habitats with different degrees of human presence, 2 compared wild and captive apes, and 1 study tested captive apes alone. Ten studies included humans working with or living close to AGA habitats. Despite different methodologies, all studies detected AMR in AGAs. Resistance to beta-lactams was the most common (36%), followed by resistance to aminoglycosides (22%), tetracyclines (15%), fluoroquinolones (10%), sulphonamides (5%), trimethoprim (5%), macrolide (3%), phenicoles (2%) and fosfomycin (1%).

CONCLUSIONS

While several studies suggest a correlation between increased human contact and higher AMR in AGAs, resistance was also found in relatively pristine habitats. While AGAs clearly encounter bacteria resistant to diverse antibiotics, significant gaps remain in understanding the underlying processes. Comparative studies using standardized methods across different sites would enhance our understanding of the origin and distribution of AMR in AGAs.

Novel pleuromutilin derivatives conjugated with phenyl-sulfide and boron-containing moieties as potent antibacterial agents against antibiotic-resistant bacteria

In response to the escalating threat of microbial resistance, a series of novel pleuromutilin derivatives, conjugated with phenyl-sulfide and boron-containing moieties, were designed and synthesized. Most derivatives, especially 14b and 16b, demonstrated significant efficacy against Gram-positive bacteria, including multidrug-resistant strains, as well as pleuromutilin-resistant strains. Compound 16b showed high stability in the liver microsomes of rats and humans, along with acceptable tolerance in vitro and in vivo. Additionally, compound 16b exhibited promising efficacy in MRSA-infected mouse models. Our data highlight the potential of conjugated pleuromutilin derivatives as valuable agents against drug-resistant bacteria.

Mechanism of staphylococcal resistance to clinically relevant antibiotics

Staphylococcus aureus, a notorious pathogen with versatile virulence, poses a significant challenge to current antibiotic treatments due to its ability to develop resistance mechanisms against a variety of clinically relevant antibiotics. In this comprehensive review, we carefully dissect the resistance mechanisms employed by S. aureus against various antibiotics commonly used in clinical settings. The article navigates through intricate molecular pathways, elucidating the mechanisms by which S. aureus evades the therapeutic efficacy of antibiotics, such as β-lactams, vancomycin, daptomycin, linezolid, etc. Each antibiotic is scrutinised for its mechanism of action, impact on bacterial physiology, and the corresponding resistance strategies adopted by S. aureus. By synthesising the knowledge surrounding these resistance mechanisms, this review aims to serve as a comprehensive resource that provides a foundation for the development of innovative therapeutic strategies and alternative treatments for S. aureus infections. Understanding the evolving landscape of antibiotic resistance is imperative for devising effective countermeasures in the battle against this formidable pathogen.

A Lincomycin-Specific Antibody Was Developed Using Hapten Prediction, and an Immunoassay Was Established to Detect Lincomycin in Pork and Milk

Prolonged consumption of animal-derived foods containing high levels of lincomycin (LIN) residues can adversely impact human health. Therefore, it is essential to develop specific antibodies and immunoassay methods for LIN. This study utilized computational chemistry to predict the efficacy of LIN haptens prior to chemical synthesis, with subsequent confirmation obtained through an immunization experiment. A hybridoma cell line named LIN/1B11 was established, which is specific to LIN. The optimized indirect competitive enzyme-linked immunosorbent assay (ic-ELISA) method exhibited high specificity for detecting LIN residues, with an IC50 value of 0.57 ± 0.03 µg/kg. The method effectively detected LIN residues in pork and milk samples, achieving a limit of detection (LOD) ranging from 0.81 to 1.20 µg/kg and a limit of quantification (LOQ) ranging from 2.09 to 2.29 µg/kg, with recovery rates between 81.9% and 108.8%. This study offers a valuable tool for identifying LIN residues in animal-derived food products. Furthermore, the efficient hapten prediction method presented herein improves antibody preparation efficiency and provides a simple method for researchers in screening haptens.

Enterococci as a One Health indicator of antimicrobial resistance

The rapid increase of antimicrobial-resistant bacteria in humans and livestock is concerning. Antimicrobials are essential for the treatment of disease in modern day medicine, and their misuse in humans and food animals has contributed to an increase in the prevalence of antimicrobial-resistant bacteria. Globally, antimicrobial resistance is recognized as a One Health problem affecting humans, animals, and environment. Enterococcal species are Gram-positive bacteria that are widely distributed in nature. Their occurrence, prevalence, and persistence across the One Health continuum make them an ideal candidate to study antimicrobial resistance from a One Health perspective. The objective of this review was to summarize the role of enterococci as an indicator of antimicrobial resistance across One Health sectors. We also briefly address the prevalence of enterococci in human, animal, and environmental settings. In addition, a 16S RNA gene-based phylogenetic tree was constructed to visualize the evolutionary relationship among enterococcal species and whether they segregate based on host environment. We also review the genomic basis of antimicrobial resistance in enterococcal species across the One Health continuum.

Recent development and fighting strategies for lincosamide antibiotic resistance

SUMMARYLincosamides constitute an important class of antibiotics used against a wide range of pathogens, including methicillin-resistant Staphylococcus aureus. However, due to the misuse of lincosamide and co-selection pressure, the resistance to lincosamide has become a serious concern. It is urgently needed to carefully understand the phenomenon and mechanism of lincosamide resistance to effectively prevent and control lincosamide resistance. To date, six mobile lincosamide resistance classes, including lnu, cfr, erm, vga, lsa, and sal, have been identified. These lincosamide resistance genes are frequently found on mobile genetic elements (MGEs), such as plasmids, transposons, integrative and conjugative elements, genomic islands, and prophages. Additionally, MGEs harbor the genes that confer resistance not only to antimicrobial agents of other classes but also to metals and biocides. The ultimate purpose of discovering and summarizing bacterial resistance is to prevent, control, and combat resistance effectively. This review highlights four promising strategies, including chemical modification of antibiotics, the development of antimicrobial peptides, the initiation of bacterial self-destruct program, and antimicrobial stewardship, to fight against resistance and safeguard global health.

Decoding antimicrobial resistance: unraveling molecular mechanisms and targeted strategies

Antimicrobial resistance poses a significant global health threat, necessitating innovative approaches for combatting it. This review explores various mechanisms of antimicrobial resistance observed in various strains of bacteria. We examine various strategies, including antimicrobial peptides (AMPs), novel antimicrobial materials, drug delivery systems, vaccines, antibody therapies, and non-traditional antibiotic treatments. Through a comprehensive literature review, the efficacy and challenges of these strategies are evaluated. Findings reveal the potential of AMPs in combating resistance due to their unique mechanisms and lower propensity for resistance development. Additionally, novel drug delivery systems, such as nanoparticles, show promise in enhancing antibiotic efficacy and overcoming resistance mechanisms. Vaccines and antibody therapies offer preventive measures, although challenges exist in their development. Non-traditional antibiotic treatments, including CRISPR-Cas systems, present alternative approaches to combat resistance. Overall, this review underscores the importance of multifaceted strategies and coordinated global efforts to address antimicrobial resistance effectively.

Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update

Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.

Synthesis, Antibacterial Effects, and Toxicity of Licochalcone C

Drug-resistant bacteria constitute a big barrier against current pharmacotherapy. Efforts are urgent to discover antibacterial drugs with novel chemical and biological features. Our work aimed at the synthesis, evaluation of antibacterial effects, and toxicity of licochalcone C (LCC), a naturally occurring chalcone. The synthetic route included six steps, affording a 10% overall yield. LCC showed effects against Gram-positive bacteria (MIC = 6.2-50.0 µg/mL), Mycobacterium species (MIC = 36.2-125 µg/mL), and Helicobacter pylori (MIC = 25 µg/mL). LCC inhibited the biofilm formation of MSSA and MRSA, demonstrating MBIC50 values of 6.25 μg/mL for both strains. The investigations by fluorescence microscopy, using PI and SYTO9 as fluorophores, indicated that LCC was able to disrupt the S. aureus membrane, similarly to nisin. Systemic toxicity assays using Galleria mellonella larvae showed that LCC was not lethal at 100 µg/mL after 80 h treatment. These data suggest new uses for LCC as a compound with potential applications in antibacterial drug discovery and medical device coating.

Therapeutic effects of lincomycin and level of drug degradation in broiler tissues after treatment

Background and Aim

Lincomycin is an antibiotic used in broiler farming and is commonly combined with other substances to achieve synergistic and complementary effects on the antibacterial spectrum and mechanism. We developed a specific high-performance liquid chromatography (HPLC) method to measure lincomycin levels in broiler tissues. This study aimed to determine the lincomycin level in tissues and compare it with the minimum inhibitory concentration (MIC) and maximum residue limit (MRL) of certain pathogenic bacteria.

Materials and Methods

Three groups of broiler chickens were involved in the study (n = 20 in each group): A control group without lincomycin treatment and two groups (each further divided into two sub-groups) that received oral lincomycin at a dose of 1 g/10 kg of body weight daily for 7 and 14 consecutive days. Tissue samples were collected from each group 1 day and 1 week after lincomycin administration (ALA). This study validated the development of a technique for analyzing drug level degradation in tissues using HPLC. Descriptive and statistical analyses were performed for drug levels to assess their therapeutic value and safety based on lincomycin MIC of certain pathogenic bacteria and MRL.

Results

The method validation resulted in linear regression and coefficient of determination for tissues with r2 > 0.99, with a recovery rate of 90%-110%, precision as the coefficient of variation 15%, and specificity with no peak overlap for lincomycin. The limits of detection for the liver and kidney were 0.01 μg/g, 0.05 μg/g, and 0.1 μg/g for the breast muscle and all tissues. Administration of lincomycin for 7 and 14 days resulted in therapeutic value concentrations. Lincomycin levels in the liver and kidney of ALA exceeded the MRL, whereas breast muscles were below the MRL for a week of ALA treatment.

Conclusion

Administration of lincomycin for 7 and 14 consecutive days resulted in therapeutic value; however, after a week, most tissues showed high drug concentrations that exceeded the MRL. It is necessary to carefully consider the prolonged therapeutic dose of lincomycin in broilers. Antibiotic therapy must be guided in such a way as to protect the product from harmful residues.

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.

Targeting Iron - Respiratory Reciprocity Promotes Bacterial Death

Discovering new bacterial signaling pathways offers unique antibiotic strategies. Here, through an unbiased resistance screen of 3,884 gene knockout strains, we uncovered a previously unknown non-lytic bactericidal mechanism that sequentially couples three transporters and downstream transcription to lethally suppress respiration of the highly virulent P. aeruginosa strain PA14 - one of three species on the WHO's 'Priority 1: Critical' list. By targeting outer membrane YaiW, cationic lacritin peptide 'N-104' translocates into the periplasm where it ligates outer loops 4 and 2 of the inner membrane transporters FeoB and PotH, respectively, to suppress both ferrous iron and polyamine uptake. This broadly shuts down transcription of many biofilm-associated genes, including ferrous iron-dependent TauD and ExbB1. The mechanism is innate to the surface of the eye and is enhanced by synergistic coupling with thrombin peptide GKY20. This is the first example of an inhibitor of multiple bacterial transporters.

Virulence genes, resistome and mobilome of Streptococcus suis strains isolated in France

Streptococcus suis is a leading cause of infection in pigs, causing extensive economic losses. In addition, it can also infect wild fauna, and can be responsible for severe infections in humans. Increasing antimicrobial resistance (AMR) has been described in S. suis worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs). This contributes to their dissemination by horizontal gene transfer. A collection of 102 strains isolated from humans, pigs and wild boars in France was subjected to whole genome sequencing in order to: (i) study their genetic diversity, (ii) evaluate their content in virulence-associated genes, (iii) decipher the mechanisms responsible for their AMR and their association with MGEs, and (iv) study their ability to acquire extracellular DNA by natural transformation. Analysis by hierarchical clustering on principal components identified a few virulence-associated factors that distinguish invasive CC1 strains from the other strains. A plethora of AMR genes (n=217) was found in the genomes. Apart from the frequently reported erm(B) and tet(O) genes, more recently described AMR genes were identified [vga(F)/sprA, vat(D)]. Modifications in PBPs/MraY and GyrA/ParC were detected in the penicillin- and fluoroquinolone-resistant isolates respectively. New AMR gene-MGE associations were detected. The majority of the strains have the full set of genes required for competence, i.e for the acquisition of extracellular DNA (that could carry AMR genes) by natural transformation. Hence the risk of dissemination of these AMR genes should not be neglected.

Antimicrobial resistance characteristics and phylogenetic relationships of pleuromutilin-resistant Enterococcus isolates from different environmental samples along a laying hen production chain

Antimicrobial resistance in the laying hen production industry has become a serious public health problem. The antimicrobial resistance and phylogenetic relationships of the common conditional pathogen Enterococcus along the laying hen production chain have not been systematically clarified. 105 Enterococcus isolates were obtained from 115 environmental samples (air, dust, feces, flies, sewage, and soil) collected along the laying hen production chain (breeding chicken, chick, young chicken, and commercial laying hen). These Enterococcus isolates exhibited resistance to some clinically relevant antibiotics, such as tetracycline (92.4%), streptomycin (92.4%), and erythromycin (91.4%), and all strains had multidrug resistance phenotypes. Whole genome sequencing characterized 29 acquired antibiotic resistance genes (ARGs) that conferred resistance to 11 classes of antibiotics in 51 pleuromutilin-resistant Enterococcus isolates, and lsa(E), which mediates resistance to pleuromutilins, always co-occurred with lnu(B). Alignments with the Mobile Genetic Elements database identified four transposons (Tn554, Tn558, Tn6261, and Tn6674) with several ARGs (erm(A), ant(9)-la, fex(A), and optrA) that mediated resistance to many clinically important antibiotics. Moreover, we identified two new transposons that carried ARGs in the Tn554 family designated as Tn7508 and Tn7492. A complementary approach based on conventional multi-locus sequence typing and whole genome single nucleotide polymorphism analysis showed that phylogenetically related pleuromutilin-resistant Enterococcus isolates were widely distributed in various environments on different production farms. Our results indicate that environmental contamination by antimicrobial-resistant Enterococcus requires greater attention, and they highlight the risk of pleuromutilin-resistant Enterococcus and ARGs disseminating along the laying hen production chain, thereby warranting effective disinfection.

Biotransformation-coupled mutasynthesis for the generation of novel pristinamycin derivatives by engineering the phenylglycine residue

Streptogramins are the last line of defense antimicrobials with pristinamycin as a representative substance used as therapeutics against highly resistant pathogenic bacteria. However, the emergence of (multi)drug-resistant pathogens renders these valuable antibiotics useless; making it necessary to derivatize compounds for new compound characteristics, which is often difficult by chemical de novo synthesis due to the complex nature of the molecules. An alternative to substance derivatization is mutasynthesis. Herein, we report about a mutasynthesis approach, targeting the phenylglycine (Phg) residue for substance derivatization, a pivotal component of streptogramin antibiotics. Mutasynthesis with halogenated Phg(-like) derivatives altogether led to the production of two new derivatized natural compounds, as there are 6-chloropristinamycin I and 6-fluoropristinamycin I based on LC-MS/MS analysis. 6-Chloropristinamycin I and 6-fluoropristinamycin I were isolated by preparative HPLC, structurally confirmed using NMR spectroscopy and tested for antimicrobial bioactivity. In a whole-cell biotransformation approach using an engineered E. coli BL21(DE3) pET28-hmo/pACYC-bcd-gdh strain, Phg derivatives were generated fermentatively. Supplementation with the E. coli biotransformation fermentation broth containing 4-fluorophenylglycine to the pristinamycin mutasynthesis strain resulted in the production of 6-fluoropristinamycin I, demonstrating an advanced level of mutasynthesis.

Phylogenomics analysis of multidrug-resistant Elizabethkingia anophelis in industrial wastewater treatment plant

AIMS

This study investigated the phylogenetic relatedness of multidrug-resistant Elizabethkingia anophelis recovered from an industrial wastewater treatment plant (WWTPi).

METHODS AND RESULTS

The wastewater samples were plated in brain heart infusion agar (4 mg/L ceftazidime, 8 mg/L meropenem, and 2 mg/L polimixin). Four isolates recovered from four stages of WWTPi (influent, aeration, decantation, and treated effluent) were identified and evaluated of susceptibility profiles in the VITEK 2 system. These strains identified as E. meningoseptica were confirmed to be E. anophelis by whole genomic sequencing (Miseq-Illumina) and showed antimicrobial resistance genes of β-lactams, aminoglycosides, and tetracycline's classes. The ribosomal multilocus sequence typing showed that they belong to the rST 65620 together with clinical strains. The phylogenomic tree revealed the similarity of our strains to those belonging to sublineage 11 and the single nucleotide polymorphism analysis confirmed that they belong to a single clade.

CONCLUSIONS

To the best of our knowledge, this is the first study reporting the persistence of multidrug-resistant E. anophelis sublineage 11 along the wastewater treatment.

Structural conservation of antibiotic interaction with ribosomes

The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron-microscopy structures of 17 distinct compounds from six different antibiotic classes bound to the bacterial ribosome at resolutions ranging from 1.6 to 2.2 Å. The improved resolution enables a precise description of antibiotic-ribosome interactions, encompassing solvent networks that mediate multiple additional interactions between the drugs and their target. Our results reveal a high structural conservation in the binding mode between antibiotics with the same scaffold, including ordered water molecules. Water molecules are visualized within the antibiotic binding sites that are preordered, become ordered in the presence of the drug and that are physically displaced on drug binding. Insight into RNA-ligand interactions will facilitate development of new antimicrobial agents, as well as other RNA-targeting therapies.

Multi-Host Pathogen Staphylococcus aureus-Epidemiology, Drug Resistance and Occurrence in Humans and Animals in Poland

Staphylococcus aureus is a drug resistant pathogen with zoonotic potential commonly isolated from humans and animals. The aim of this study was to compare the occurrence of drug resistance, resistance genes, sequence types (STs), and genotypes of S. aureus isolated from humans, livestock, and wildlife in eastern Poland. A high percentage of isolates resistant to penicillin (63%), erythromycin (39%), clindamycin (37%), tetracycline (31%), and methicillin (MRSA-19%), an intermediate resistant to vancomycin (VISA-13%), and a multidrug resistant (MDR-39%) was obtained. Multilocus sequence typing analysis showed the presence of 35 different STs (with dominance ST 15, ST 45, ST 7, and ST 582 in human, and ST 398 and ST 8139 in porcine and cattle isolates, respectively), including 9 new ones that had never been reported before (ST 8133-8141). Identical genotypic patterns were detected among porcine and cattle isolates as well as from humans and cattle. A high percentage of MDR, MRSA, and VISA in humans and livestock combined with the presence of the same genotypes among S. aureus isolated from human and cattle indicates the circulation of strains common in the region and their zoonotic potential. There is a need to develop new strategies to counteract this phenomenon according to the One Health policy.

Phytochemicals as Antimicrobials: Prospecting Himalayan Medicinal Plants as Source of Alternate Medicine to Combat Antimicrobial Resistance

Among all available antimicrobials, antibiotics hold a prime position in the treatment of infectious diseases. However, the emergence of antimicrobial resistance (AMR) has posed a serious threat to the effectiveness of antibiotics, resulting in increased morbidity, mortality, and escalation in healthcare costs causing a global health crisis. The overuse and misuse of antibiotics in global healthcare setups have accelerated the development and spread of AMR, leading to the emergence of multidrug-resistant (MDR) pathogens, which further limits treatment options. This creates a critical need to explore alternative approaches to combat bacterial infections. Phytochemicals have gained attention as a potential source of alternative medicine to address the challenge of AMR. Phytochemicals are structurally and functionally diverse and have multitarget antimicrobial effects, disrupting essential cellular activities. Given the promising results of plant-based antimicrobials, coupled with the slow discovery of novel antibiotics, it has become highly imperative to explore the vast repository of phytocompounds to overcome the looming catastrophe of AMR. This review summarizes the emergence of AMR towards existing antibiotics and potent phytochemicals having antimicrobial activities, along with a comprehensive overview of 123 Himalayan medicinal plants reported to possess antimicrobial phytocompounds, thus compiling the existing information that will help researchers in the exploration of phytochemicals to combat AMR.

Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR

Genome-encoded antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F subfamily (ARE-ABCFs) mediate intrinsic resistance in diverse Gram-positive bacteria. The diversity of chromosomally-encoded ARE-ABCFs is far from being fully experimentally explored. Here we characterise phylogenetically diverse genome-encoded ABCFs from Actinomycetia (Ard1 from Streptomyces capreolus, producer of the nucleoside antibiotic A201A), Bacilli (VmlR2 from soil bacterium Neobacillus vireti) and Clostridia (CplR from Clostridium perfringens, Clostridium sporogenes and Clostridioides difficile). We demonstrate that Ard1 is a narrow spectrum ARE-ABCF that specifically mediates self-resistance against nucleoside antibiotics. The single-particle cryo-EM structure of a VmlR2-ribosome complex allows us to rationalise the resistance spectrum of this ARE-ABCF that is equipped with an unusually long antibiotic resistance determinant (ARD) subdomain. We show that CplR contributes to intrinsic pleuromutilin, lincosamide and streptogramin A resistance in Clostridioides, and demonstrate that C. difficile CplR (CDIF630_02847) synergises with the transposon-encoded 23S ribosomal RNA methyltransferase Erm to grant high levels of antibiotic resistance to the C. difficile 630 clinical isolate. Finally, assisted by uORF4u, our novel tool for detection of upstream open reading frames, we dissect the translational attenuation mechanism that controls the induction of cplR expression upon an antibiotic challenge.

Molecular mechanisms of antibiotic resistance revisited

Antibiotic resistance is a global health emergency, with resistance detected to all antibiotics currently in clinical use and only a few novel drugs in the pipeline. Understanding the molecular mechanisms that bacteria use to resist the action of antimicrobials is critical to recognize global patterns of resistance and to improve the use of current drugs, as well as for the design of new drugs less susceptible to resistance development and novel strategies to combat resistance. In this Review, we explore recent advances in understanding how resistance genes contribute to the biology of the host, new structural details of relevant molecular events underpinning resistance, the identification of new resistance gene families and the interactions between different resistance mechanisms. Finally, we discuss how we can use this information to develop the next generation of antimicrobial therapies.

Characterization of Linezolid-Analogue L3-Resistance Mutation in Staphylococcus aureus

In a previous study, a linezolid analogue, called 10f, was synthesized. The 10f molecule has an antimicrobial activity comparable to that of the parental compound. In this study, we isolated a Staphylococcus aureus (S. aureus) strain resistant to 10f. After sequencing the 23S rRNA and the ribosomal proteins L3 (rplC) and L4 (rplD) genes, we found that the resistant phenotype was associated with a single mutation G359U in rplC bearing to the missense mutation G120V in the L3 protein. The identified mutation is far from the peptidyl transferase center, the oxazolidinone antibiotics binding site, thus suggesting that we identified a new and interesting example of a long-range effect in the ribosome structure.

Inhibition of Erythromycin and Erythromycin-Induced Resistance among Staphylococcus aureus Clinical Isolates

The increasing incidence of erythromycin and erythromycin-induced resistance to clindamycin among Staphylococcus aureus (S. aureus) is a serious problem. Patients infected with inducible resistance phenotypes may fail to respond to clindamycin. This study aimed to identify the prevalence of erythromycin and erythromycin-induced resistance and assess for potential inhibitors. A total of 99 isolates were purified from various clinical sources. Phenotypic detection of macrolide-lincosamide-streptogramin B (MLSB)-resistance phenotypes was performed by D-test. MLSB-resistance genes were identified using PCR. Different compounds were tested for their effects on erythromycin and inducible clindamycin resistance by broth microdilution and checkerboard microdilution methods. The obtained data were evaluated using docking analysis. Ninety-one isolates were S. aureus. The prevalence of constitutive MLSB, inducible MLSB, and macrolide-streptogramin (MS) phenotypes was 39.6%, 14.3%, and 2.2%, respectively. Genes including ermC, ermA, ermB, msrA, msrB, lnuA, and mphC were found in 82.6%, 5.8%, 7.7%, 3.8%, 3.8%, 13.5%, and 3.8% of isolates, respectively. Erythromycin resistance was significantly reduced by doxorubicin, neomycin, and omeprazole. Quinine, ketoprofen, and fosfomycin combated and reversed erythromycin/clindamycin-induced resistance. This study highlighted the significance of managing antibiotic resistance and overcoming clindamycin treatment failure. Doxorubicin, neomycin, omeprazole, quinine, ketoprofen, and fosfomycin could be potential inhibitors of erythromycin and inducible clindamycin resistance.

Antimicrobial resistance pattern of avian pathogenic Escherichia coli with detection of extended-spectrum β-lactamase-producing isolates in broilers in east Algeria

Background and Aim: Avian pathogenic Escherichia coli (APEC) is the causative agent of colibacillosis, one of the most prevalent bacterial diseases responsible for significant economic losses in the poultry industry worldwide. This study aimed to assess the antimicrobial resistance (AMR) patterns of APEC isolates recovered from poultry in east Algeria and estimate the prevalence of extended-spectrum β-lactamase (ESBL)-producing isolates. Materials and Methods: In the slaughterhouse of Batna City (Algeria), livers indicating colibacillosis were sampled from 204 suspected carcasses with growth retardation and generalized congestion. Escherichia coli isolation and identification were performed on MacConkey agar using conventional methods and the API 20E system. Antimicrobial resistance susceptibility was tested by the disk diffusion method according to the Clinical Laboratory Standards Institute Guidelines. Extended-spectrum β-lactamase detection was carried out using the double-disk confirmation test. Results: One hundred sixty E. coli isolates were recovered (one isolate per sample). Avian pathogenic Escherichia coli isolates showed high levels of resistance to ampicillin and tetracycline (100%), nalidixic acid (95%), ofloxacin (93.75%), doxycycline (91.87), ciprofloxacin (87.50%), trimethoprim/sulfamethoxazole (62.50%), gentamycin (32.50%), chloramphenicol (27.50%), amoxicillin/clavulanic acid (16.25%), colistin (14.37%), and nitrofurantoin (10.62%). All strains were multidrug-resistant to at least three antibiotics, and more than half (52.52%) of the isolates were resistant to at least seven antibiotics. All isolates were susceptible to ceftriaxone, ceftazidime, and aztreonam. Two E. coli isolates were ESBL producers (1.25%). Conclusion: Avian pathogenic Escherichia coli resistance to most antimicrobial agents used in poultry may lead to antimicrobial therapy failure. Keywords: antimicrobial resistance, avian pathogenic Escherichia coli, broilers, colibacillosis, Eastern Algeria, extended-spectrum β-lactamase.

Clinical Resistant Strains of Enterococci and Their Correlation to Reduced Susceptibility to Biocides: Phenotypic and Genotypic Analysis of Macrolides, Lincosamides, and Streptogramins

Enterococci are troublesome nosocomial, opportunistic Gram-positive cocci bacteria showing enhanced resistance to many commonly used antibiotics. This study aims to investigate the prevalence and genetic basis of antibiotic resistance to macrolides, lincosamides, and streptogramins (MLS) in Enterococci, as well as the correlation between MLS resistance and biocide resistance. From 913 clinical isolates collected from King Khalid Hospital, Hail, Saudi Arabia, 131 isolates were identified as Enterococci spp. The susceptibility of the clinical enterococcal isolates to several MLS antibiotics was determined, and the resistance phenotype was detected by the triple disk method. The MLS-involved resistance genes were screened in the resistant isolates. The current results showed high resistance rates to MLS antibiotics, and the constitutive resistance to all MLS (cMLS) was the most prevalent phenotype, observed in 76.8% of resistant isolates. By screening the MLS resistance-encoding genes in the resistant isolates, the erythromycin ribosome methylase (erm) genes that are responsible for methylation of bacterial 23S rRNA were the most detected genes, in particular, ermB. The ereA esterase-encoding gene was the most detected MLS modifying-encoding genes, more than lnuA (adenylation) and mphC (phosphorylation). The minimum inhibitory concentrations (MICs) of commonly used biocides were detected in resistant isolates and correlated with the MICs of MLS antibiotics. The present findings showed a significant correlation between MLS resistance and reduced susceptibility to biocides. In compliance with the high incidence of the efflux-encoding genes, especially mefA and mefE genes in the tolerant isolates with higher MICs to both MLS antibiotics and biocides, the efflux of resistant isolates was quantified, and there was a significant increase in the efflux of resistant isolates with higher MICs as compared to those with lower MICs. This could explain the crucial role of efflux in developing cross-resistance to both MLS antibiotics and biocides.

The emergence of novel macrolide resistance island in Macrococcus caseolyticus and Staphylococcus aureus of food origin

Food-derived Staphylococcaceae species with severe antimicrobial resistance, especially Staphylococcus aureus, is a major threat to public health. Macrococcus caseolyticus (M. caseolyticus) is a member of the Staphylococcaceae family which plays a vital role in fermented products and disease causation in animals. In our previous study, several Staphylococcus aureus antibiotic-resistant island msr (SaRI_msr) were found in multidrug-resistant S. aureus. In this study, novel SaRI_msr, SaRI_msr-III emerged from S. aureus. Another novel SaRI_msr-like further emerged in M. caseolyticus from food. These isolates' prevalence and genetic environment were investigated and characterized to understand the distribution and transmission of these novel SaRI_msr strains. All SaRI_msr-positive S. aureus isolates exhibited a multidrug resistance (MDR) phenotype, within which a series of antimicrobial resistance genes (ARGs) and virulence factor genes (VFs) were identified. In addition, three SaRI_msr types, SaRI_msr-I (15.1 kb), SaRI_msr-II (16-17 kb), and SaRI_msr-III (18 kb) carrying mef(D)-msr(F), were identified in these isolates' chromosomes. SaRI_msr-(I-III) contains a site-specific integrase gene int and operon mef(D)-msr(F). SaRI_msr-III has an additional orf3-orf4-IS30 arrangement downstream of mef(D) and msr(F). Moreover, the SaRI_msr-like and macrolide-resistant transposon Tn6776 forming a novel mosaic structure coexisted in one M. caseolyticus isolate. Within this mosaic structure, the macrolide-resistant genes mef(D)-msr(F) were absent in SaRI_msr-like, whereas an operon, mef(F)-msr(G), was identified in Tn6776. The SaRI_msr-(I-III) and SaRI_msr-like structure were inserted into the rpsI gene encoding the 30S ribosomal protein S9 in the chromosome. Excision and cyclisation of SaRI_msr-III, SaRI_msr-like, operon mef(D)-msr(F), and orf3-orf4-IS30 arrangements were confirmed using two-step PCR. This study is the first to report MDR S. aureus harbouring novel SaRI_msr-III and M. caseolyticus containing novel mosaic structures isolated from retail foods. Similar SaRI_msr-type resistant islands' occurrence and propagation in Staphylococcaceae species require continuous monitoring and investigation.

An in-house 45-plex array for the detection of antimicrobial resistance genes in Gram-positive bacteria

Identifying antimicrobial resistance (AMR) genes and determining their occurrence in Gram-positive bacteria provide useful data to understand how resistance can be acquired and maintained in these bacteria. We describe an in-house bead array targeting AMR genes of Gram-positive bacteria and allowing their rapid detection all at once at a reduced cost. A total of 41 AMR probes were designed to target genes frequently associated with resistance to tetracycline, macrolides, lincosamides, streptogramins, pleuromutilins, phenicols, glycopeptides, aminoglycosides, diaminopyrimidines, oxazolidinones and particularly shared among Enterococcus and Staphylococcus spp. A collection of 124 enterococci and 62 staphylococci isolated from healthy livestock animals through the official Belgian AMR monitoring (2018-2020) was studied with this array from which a subsample was further investigated by whole-genome sequencing. The array detected AMR genes associated with phenotypic resistance for 93.0% and 89.2% of the individual resistant phenotypes in enterococci and staphylococci, respectively. Although linezolid is not used in veterinary medicine, linezolid-resistant isolates were detected. These were characterized by the presence of optrA and poxtA, providing cross-resistance to other antibiotics. Rarer, vancomycin resistance was conferred by the vanA or by the vanL cluster. Numerous resistance genes circulating among Enterococcus and Staphylococcus spp. were detected by this array allowing rapid screening of a large strain collection at an affordable cost. Our data stress the importance of interpreting AMR with caution and the complementarity of both phenotyping and genotyping methods. This array is now available to assess other One-Health AMR reservoirs.

Farming Practice Influences Antimicrobial Resistance Burden of Non-Aureus Staphylococci in Pig Husbandries

Non-aureus staphylococci (NAS) are ubiquitous bacteria in livestock-associated environments where they may act as reservoirs of antimicrobial resistance (AMR) genes for pathogens such as Staphylococcus aureus. Here, we tested whether housing conditions in pig farms could influence the overall AMR-NAS burden. Two hundred and forty porcine commensal and environmental NAS isolates from three different farm types (conventional, alternative, and organic) were tested for phenotypic antimicrobial susceptibility and subjected to whole genome sequencing. Genomic data were analysed regarding species identity and AMR gene carriage. Seventeen different NAS species were identified across all farm types. In contrast to conventional farms, no AMR genes were detectable towards methicillin, aminoglycosides, and phenicols in organic farms. Additionally, AMR genes to macrolides and tetracycline were rare among NAS in organic farms, while such genes were common in conventional husbandries. No differences in AMR detection existed between farm types regarding fosfomycin, lincosamides, fusidic acid, and heavy metal resistance gene presence. The combined data show that husbandry conditions influence the occurrence of resistant and multidrug-resistant bacteria in livestock, suggesting that changing husbandry practices may be an appropriate means of limiting the spread of AMR bacteria on farms.

Development of a novel core genome MLST scheme for tracing multidrug resistant Staphylococcus capitis

Staphylococcus capitis, which causes bloodstream infections in neonatal intensive care units, is a common cause of healthcare-associated infections. Thus, a standardized high-resolution typing method to document the transmission and dissemination of multidrug-resistant S. capitis isolates is required. We aimed to establish a core genome multilocus sequence typing (cgMLST) scheme to surveil S. capitis. The cgMLST scheme was defined based on primary and validation genome sets and tested with outbreaks of linezolid-resistant isolates and a validation set. Phylogenetic analysis was performed to investigate the population structure and compare it with the result of cgMLST analysis. The S. capitis population consists of 1 dominant, NRCS-A, and 4 less common clones. In this work, a multidrug-resistant clone (L clone) with linezolid resistance is identified. With the features of type III SCCmec and multiple copies of mutations of G2576T and C2104T in the 23S rRNA, the L clone has been spreading silently across China.

Staphylococcus capitis is a common causative agent of bloodstream infections in neonatal intensive care units, with multidrug resistant isolates complicating treatment. Authors aimed to establish a core genome multilocus sequence typing (cgMLST) scheme to document the transmission and dissemination of multidrug-resistant S. capitis isolates.

How Streptococcus suis escapes antibiotic treatments

Streptococcus suis is a zoonotic agent that causes sepsis and meningitis in pigs and humans. S. suis infections are responsible for large economic losses in pig production. The lack of effective vaccines to prevent the disease has promoted the extensive use of antibiotics worldwide. This has been followed by the emergence of resistance against different classes of antibiotics. The rates of resistance to tetracyclines, lincosamides, and macrolides are extremely high, and resistance has spread worldwide. The genetic origin of S. suis resistance is multiple and includes the production of target-modifying and antibiotic-inactivating enzymes and mutations in antibiotic targets. S. suis genomes contain traits of horizontal gene transfer. Many mobile genetic elements carry a variety of genes that confer resistance to antibiotics as well as genes for autonomous DNA transfer and, thus, S. suis can rapidly acquire multiresistance. In addition, S. suis forms microcolonies on host tissues, which are associations of microorganisms that generate tolerance to antibiotics through a variety of mechanisms and favor the exchange of genetic material. Thus, alternatives to currently used antibiotics are highly demanded. A deep understanding of the mechanisms by which S. suis becomes resistant or tolerant to antibiotics may help to develop novel molecules or combinations of antimicrobials to fight these infections. Meanwhile, phage therapy and vaccination are promising alternative strategies, which could alleviate disease pressure and, thereby, antibiotic use.

Transcriptomic analysis of Staphylococcus equorum KM1031 from the high-salt fermented seafood jeotgal under chloramphenicol, erythromycin and lincomycin stresses

Staphylococcus equorum strain KM1031 is resistant to chloramphenicol, erythromycin and lincomycin. To shed light on the genetic factors underlying these antibiotic resistances, we determined the global gene expression profile of S. equorum KM1031 using RNA sequencing. During chloramphenicol, erythromycin and lincomycin treatment, 8.3% (183/2,336), 16.0% (354/2,336), and 2.9% (63/2,336) of S. equorum KM1031 genes exhibited significant differences in expression, respectively. These three antibiotics upregulated genes related to efflux and downregulated genes related to transporters. Antibiotic treatment also upregulated osmoprotectant-related genes involved in salt tolerance. To identify specific genes functionally related to antibiotic resistance, we compared the genome of strain KM1031 with those of three S. equorum strains that are sensitive to these three antibiotics. We identified three genes of particular interest: an antibiotic biosynthesis monooxygenase gene (abm, AWC34_RS01805) related to chloramphenicol resistance, an antibiotic ABC transporter ATP-binding protein gene (msr, AWC34_RS11115) related to erythromycin resistance, and a lincosamide nucleotydyltransferase gene (lnuA, AWC34_RS13300) related to lincomycin resistance. These genes were upregulated in response to the corresponding antibiotic; in particular, msr was upregulated more than fourfold by erythromycin treatment. Finally, the results of RNA sequencing were validated by quantitative real-time PCR. This transcriptomic analysis provides genetic evidence regarding antibiotic stress responses of S. equorum strain KM1031.

The Mechanism of Bacterial Resistance and Potential Bacteriostatic Strategies

Bacterial drug resistance is rapidly developing as one of the greatest threats to human health. Bacteria will adopt corresponding strategies to crack the inhibitory effect of antibiotics according to the antibacterial mechanism of antibiotics, involving the mutation of drug target, secreting hydrolase, and discharging antibiotics out of cells through an efflux pump, etc. In recent years, bacteria are found to constantly evolve new resistance mechanisms to antibiotics, including target protective protein, changes in cell morphology, and so on, endowing them with multiple defense systems against antibiotics, leading to the emergence of multi-drug resistant (MDR) bacteria and the unavailability of drugs in clinics. Correspondingly, researchers attempt to uncover the mystery of bacterial resistance to develop more convenient and effective antibacterial strategies. Although traditional antibiotics still play a significant role in the treatment of diseases caused by sensitive pathogenic bacteria, they gradually lose efficacy in the MDR bacteria. Therefore, highly effective antibacterial compounds, such as phage therapy and CRISPER-Cas precision therapy, are gaining an increasing amount of attention, and are considered to be the treatments with the moist potential with regard to resistance against MDR in the future. In this review, nine identified drug resistance mechanisms are summarized, which enhance the retention rate of bacteria under the action of antibiotics and promote the distribution of drug-resistant bacteria (DRB) in the population. Afterwards, three kinds of potential antibacterial methods are introduced, in which new antibacterial compounds exhibit broad application prospects with different action mechanisms, the phage therapy has been successfully applied to infectious diseases caused by super bacteria, and the CRISPER-Cas precision therapy as a new technology can edit drug-resistant genes in pathogenic bacteria at the gene level, with high accuracy and flexibility. These antibacterial methods will provide more options for clinical treatment, and will greatly alleviate the current drug-resistant crisis.

Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp

Since antibiotic resistance is often associated with a fitness cost, bacteria employ multi-layered regulatory mechanisms to ensure that expression of resistance factors is restricted to times of antibiotic challenge. In Bacillus subtilis, the chromosomally-encoded ABCF ATPase VmlR confers resistance to pleuromutilin, lincosamide and type A streptogramin translation inhibitors. Here we show that vmlR expression is regulated by translation attenuation and transcription attenuation mechanisms. Antibiotic-induced ribosome stalling during translation of an upstream open reading frame in the vmlR leader region prevents formation of an anti-antiterminator structure, leading to the formation of an antiterminator structure that prevents intrinsic termination. Thus, transcription in the presence of antibiotic induces vmlR expression. We also show that NusG-dependent RNA polymerase pausing in the vmlR leader prevents leaky expression in the absence of antibiotic. Furthermore, we demonstrate that induction of VmlR expression by compromised protein synthesis does not require the ability of VmlR to rescue the translational defect, as exemplified by constitutive induction of VmlR by ribosome assembly defects. Rather, the specificity of induction is determined by the antibiotic's ability to stall the ribosome on the regulatory open reading frame located within the vmlR leader. Finally, we demonstrate the involvement of (p)ppGpp-mediated signalling in antibiotic-induced VmlR expression.

Detection of the optrA Gene Among Polyclonal Linezolid-Susceptible Isolates of Enterococcus faecalis Recovered from Community Patients

Dispersion of transferable oxazolidinone resistance genes among enterococci poses a serious problem to human health. Prompt detection of bacteria carrying these genes is crucial to avoid their spread to multidrug-resistant bacteria. The aim of the study was to describe the presence of optrA-positive isolates among enterococci in a Spanish hospital, and to determine their genetic context and location through whole genome sequencing. All enterococci recovered in a Spanish hospital (Hospital El Bierzo; HEB) from February to December 2018 (n = 443), with minimal inhibitory concentrations (MICs) to linezolid (LZD) ≥4 mg/L, were tested by polymerase chain reaction for the presence of cfr, optrA, and poxtA transferable genes. Only four Enterococcus faecalis isolates (0.9%) had LZD MICs ≥4 mg/L and none of them was positive for cfr or poxtA genes. However, the optrA gene was detected in three isolates collected from urine samples of community patients, whose genomes were sequenced and subjected to bioinformatics analysis. These isolates belonged to different clones: ST7, ST480, and ST585. In these three isolates, the optrA gene was located on plasmids, associated with IS1216 in different arrays. In one isolate, the optrA plasmid coexists with a second plasmid, which carried multiple resistance genes for different classes of antibiotics. Detection of optrA-positive E. faecalis isolates in the community is a matter of concern. The spread of these bacteria into hospital settings, particularly in those, such as the HEB, where vancomycin-resistant enterococci are endemic, should be avoided, to preserve the efficacy of the last-resort oxazolidinones.

Campylobacter Species, Microbiological Source Tracking and Risk Assessment of Bacterial pathogens

Campylobacter species continue to remain critical pathogens of public health interest. They are responsible for approximately 500 million cases of gastroenteritis per year worldwide. Infection occurs through the consumption of contaminated food and water. Microbial risk assessment and source tracking are crucial epidemiological strategies to monitor the outbreak of campylobacteriosis effectively. Various methods have been proposed for microbial source tracking and risk assessment, most of which rely on conventional microbiological techniques such as detecting fecal indicator organisms and other novel microbial source tracking methods, including library-dependent microbial source tracking and library-independent source tracking approaches. However, both the traditional and novel methods have their setbacks. For example, while the conventional techniques are associated with a poor correlation between indicator organism and pathogen presence, on the other hand, it is impractical to interpret qPCR-generated markers to establish the exact human health risks even though it can give information regarding the potential source and relative human risk. Therefore, this article provides up-to-date information on campylobacteriosis, various approaches for source attribution, and risk assessment of bacterial pathogens, including next-generation sequencing approaches such as shotgun metagenomics, which effectively answer the questions of potential pathogens are there and in what quantities.

Synthetic oxepanoprolinamide iboxamycin is active against Listeria monocytogenes despite the intrinsic resistance mediated by VgaL/Lmo0919 ABCF ATPase

Background

Listeriosis is a food-borne disease caused by the Gram-positive Bacillota (Firmicute) bacterium Listeria monocytogenes. Clinical L. monocytogenes isolates are often resistant to clinically used lincosamide clindamycin, thus excluding clindamycin as a viable treatment option.

Objectives

We have established newly developed lincosamide iboxamycin as a potential novel antilisterial agent.

Methods

We determined MICs of the lincosamides lincomycin, clindamycin and iboxamycin for L. monocytogenes, Enterococcus faecalis and Bacillus subtilis strains expressing synergetic antibiotic resistance determinants: ABCF ATPases that directly displace antibiotics from the ribosome and Cfr, a 23S rRNA methyltransferase that compromises antibiotic binding. For L. monocytogenes strains, either expressing VgaL/Lmo0919 or lacking the resistance factor, we performed time-kill kinetics and post-antibiotic effect assays.

Results

We show that the synthetic lincosamide iboxamycin is highly active against L. monocytogenes and can overcome the intrinsic lincosamide resistance mediated by VgaL/Lmo0919 ABCF ATPase. While iboxamycin is not bactericidal against L. monocytogenes, it displays a pronounced post-antibiotic effect, which is a valuable pharmacokinetic feature. We demonstrate that VmlR ABCF of B. subtilis grants significant (33-fold increase in MIC) protection from iboxamycin, while LsaA ABCF of E. faecalis grants an 8-fold protective effect. Furthermore, the VmlR-mediated iboxamycin resistance is cooperative with that mediated by the Cfr, resulting in up to a 512-fold increase in MIC.

Conclusions

While iboxamycin is a promising new antilisterial agent, our findings suggest that emergence and spread of ABCF ARE variants capable of defeating next-generation lincosamides in the clinic is possible and should be closely monitored.

A Review: Antimicrobial Therapy for Human Pythiosis

Human pythiosis is associated with poor prognosis with significant mortality caused by Pythium insidiosum. Antimicrobials’ in vitro and in vivo results against P. insidiosum are inconsistent. Although antimicrobials are clinically useful, they are not likely to achieve therapeutic success alone without surgery and immunotherapy. New therapeutic options are therefore needed. This non-exhaustive review discusses the rationale antimicrobial therapy, minimum inhibitory concentrations, and efficacy of antibacterial and antifungal agents against P. insidiosum. This review further provides insight into the immunomodulating effects of antimicrobials that can enhance the immune response to infections. Current data support using antimicrobial combination therapy for the pharmacotherapeutic management of human pythiosis. Also, the success or failure of antimicrobial treatment in human pythiosis might depend on the immunomodulatory effects of drugs. The repurposing of existing drugs is a safe strategy for anti-P. insidiosum drug discovery. To improve patient outcomes in pythiosis, we suggest further research and a deeper understanding of P. insidiosum virulence factors, host immune response, and host immune system modification by antimicrobials.

Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

Alteration of antibiotic binding sites through modification of ribosomal RNA (rRNA) is a common form of resistance to ribosome-targeting antibiotics. The rRNA-modifying enzyme Cfr methylates an adenosine nucleotide within the peptidyl transferase center, resulting in the C-8 methylation of A2503 (m8A2503). Acquisition of cfr results in resistance to eight classes of ribosome-targeting antibiotics. Despite the prevalence of this resistance mechanism, it is poorly understood whether and how bacteria modulate Cfr methylation to adapt to antibiotic pressure. Moreover, direct evidence for how m8A2503 alters antibiotic binding sites within the ribosome is lacking. In this study, we performed directed evolution of Cfr under antibiotic selection to generate Cfr variants that confer increased resistance by enhancing methylation of A2503 in cells. Increased rRNA methylation is achieved by improved expression and stability of Cfr through transcriptional and post-transcriptional mechanisms, which may be exploited by pathogens under antibiotic stress as suggested by natural isolates. Using a variant that achieves near-stoichiometric methylation of rRNA, we determined a 2.2 Å cryo-electron microscopy structure of the Cfr-modified ribosome. Our structure reveals the molecular basis for broad resistance to antibiotics and will inform the design of new antibiotics that overcome resistance mediated by Cfr.