Next-generation approaches to understand and combat the antibiotic resistome

Design, synthesis, and evaluation of amphiphilic sofalcone derivatives as potent Gram-positive antibacterial agents

New antimicrobial agents are urgently needed to overcome drug-resistant bacterial infections. Here we describe the design, synthesis and evaluation of a new class of amphiphilic sofalcone compounds as antimicrobial peptidomimetics. The most promising compound 14, bearing two arginine residues, showed poor hemolytic activity, low cytotoxicity, and excellent antimicrobial activity against Gram-positive bacteria, including MRSA. Compound 14, had good stability in various salt conditions, killed bacteria rapidly by directly disrupting bacterial cell membranes and was slow at developing bacterial resistance. Additionally, compound 14 exhibited effective in vivo efficacy in the murine model of bacterial keratitis caused by Staphylococcus aureus ATCC29213. Our studies suggested that compound 14 possessed promising potential to be used as a novel antimicrobial agent to combat drug-resistant Gram-positive bacteria.

Acquired Genetic Elements that Contribute to Antimicrobial Resistance in Frequent Gram-Negative Causative Agents of Healthcare-Associated Infections

Antimicrobial resistance (AMR) is a worldwide public health problem that reduces therapeutic options and increases the risk of death. The causative agents of healthcare-associated infections (HAIs) are drug-resistant microorganisms of the nosocomial environment, which have developed different mechanisms of AMR. The hospital-associated microbiota has been proposed to be a reservoir of genes associated with AMR and an environment where the transfer of genetic material among organisms may occur. The ESKAPE group (Enterococcus faecalis and Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter aerogenes and Escherichia coli) is a frequent causative agents of HAIs. In this review, we address the issue of acquired genetic elements that contribute to AMR in the most frequent Gram-negative of ESKAPE, with a focus on last resort antimicrobial agents and the role of transference of genetic elements for the development of AMR.

Subsistence and complexity of antimicrobial resistance on a community-wide level

There are a multitude of resistance strategies that microbes can apply to avoid inhibition by antimicrobials. One of these strategies is the enzymatic modification of the antibiotic, in a process generally termed inactivation. Furthermore, some microorganisms may not be limited to the mere inactivation of the antimicrobial compounds. They can continue by further enzymatic degradation of the compounds' carbon backbone, taking nutritional and energetic advantage of the former antibiotic. This driving force to harness an additional food source in a complex environment adds another level of complexity to the reasonably well-understood process of antibiotic resistance proliferation on a single cell level: It brings bioprotection into play at the level of microbial community. Despite the possible implications of a resistant community in a host and a lurking antibiotic failure, knowledge of degradation pathways of antibiotics and their connections is scarce. Currently, it is limited to only a few families of antibiotics (e.g. β-lactams and sulfonamides). In this article, we discuss the fluctuating nature of the relationship between antibiotic resistance and the biodegradation of antibiotics. This distinction mainly depends on the genetic background of the microbe, as general resistance genes can be recruited to function in a biodegradation pathway.

Epidemiological Study on Prevalence, Serovar Diversity, Multidrug Resistance, and CTX-M-Type Extended-Spectrum β-Lactamases of Salmonella spp. from Patients with Diarrhea, Food of Animal Origin, and Pets in Several Provinces of China

A total of 2,283 Salmonella isolates were recovered from 18,334 samples, including samples from patients with diarrhea, food of animal origin, and pets, across 5 provinces of China. The highest prevalence of Salmonella spp. was detected in chicken meats (39.3%, 486/1,237). Fifteen serogroups and 66 serovars were identified, with Salmonella enterica serovars Typhimurium and Enteritidis being the most dominant. Most (85.5%, 1,952/2,283) isolates exhibited resistance to ≥1 antimicrobial, and 56.4% were multidrug resistant (MDR). A total of 222 isolates harbored extended-spectrum β-lactamases (ESBLs), and 200 of these were of the CTX-M type and were mostly detected in isolates from chicken meat and turtle fecal samples. Overall, eight blaCTX-M genes were identified, with blaCTX-M-65, blaCTX-M-123, blaCTX-M-14, blaCTX-M-79, and blaCTX-M-130 being the most prevalent. In total, 166 of the 222 ESBL-producing isolates had amino acid substitutions in GyrA (S83Y, S83F, D87G, D87N, and D87Y) and ParC (S80I), while the plasmid-mediated quinolone resistance (PMQR)-encoding genes oqxA, oqxB, qepA, qnrB, and qnrS were detected in almost all isolates. Of the 15 sequence types (STs) identified in the 222 ESBLs, ST17, ST11, ST34, and ST26 ranked among the top 5 in number of isolates. Our study revealed considerable serovar diversity and a high prevalence of the co-occurrence of MDR determinants, including CTX-M-type ESBLs, quinolone resistance-determining region (QRDR) mutations, and PMQR genes. This is the first report of CTX-M-130 Salmonella spp. from patients with diarrhea and QRDR mutations from turtle fecal samples. Our study emphasizes the importance of actions, both in health care settings and in the veterinary medicine sector, to control the dissemination of MDR, especially the CTX-M-type ESBL-harboring Salmonella isolates.

Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase

Metallo-β-lactamases (MBLs) degrade a broad spectrum of β-lactam antibiotics, and are a major disseminating source for multidrug resistant bacteria. Despite many biochemical studies in diverse MBLs, molecular understanding of the roles of residues in the enzyme's stability and function, and especially substrate specificity, is lacking. Here, we employ deep mutational scanning (DMS) to generate comprehensive single amino acid variant data on a major clinical MBL, VIM-2, by measuring the effect of thousands of VIM-2 mutants on the degradation of three representative classes of β-lactams (ampicillin, cefotaxime, and meropenem) and at two different temperatures (25°C and 37°C). We revealed residues responsible for expression and translocation, and mutations that increase resistance and/or alter substrate specificity. The distribution of specificity-altering mutations unveiled distinct molecular recognition of the three substrates. Moreover, these function-altering mutations are frequently observed among naturally occurring variants, suggesting that the enzymes have continuously evolved to become more potent resistance genes.

One year cross-sectional study in adult and neonatal intensive care units reveals the bacterial and antimicrobial resistance genes profiles in patients and hospital surfaces

Several studies have shown the ubiquitous presence of bacteria in hospital surfaces, staff, and patients. Frequently, these bacteria are related to HAI (healthcare-associated infections) and carry antimicrobial resistance (AMR). These HAI-related bacteria contribute to a major public health issue by increasing patient morbidity and mortality during or after hospital stay. Bacterial high-throughput amplicon gene sequencing along with identification of AMR genes, as well as whole genome sequencing (WGS), are biotechnological tools that allow multiple-sample screening for a diversity of bacteria. In this paper, we used these methods to perform a one-year cross sectional profiling of bacteria and AMR genes in adult and neonatal intensive care units (ICU and NICU) in a Brazilian public, tertiary hospital. Our results showed high abundances of HAI-related bacteria such as S. epidermidis, S. aureus, K. pneumoniae, A. baumannii complex, E. coli, E. faecalis, and P. aeruginosa in patients and hospital surfaces. Most abundant AMR genes detected throughout ICU and NICU were mecA, blaCTX-M-1 group, blaSHV-like, and blaKPC-like. We found that NICU environment and patients were more widely contaminated with pathogenic bacteria than ICU. Patient samples, despite the higher bacterial load, have lower bacterial diversity than environmental samples in both units. Finally, we also identified contamination hotspots in the hospital environment showing constant frequencies of bacterial and AMR contamination throughout the year. Whole genome sequencing (WGS), 16S rRNA oligotypes, and AMR identification allowed a high-resolution characterization of the hospital microbiome profile.

Survey of drug resistance associated gene mutations in Mycobacterium tuberculosis, ESKAPE and other bacterial species

Tuberculosis treatment includes broad-spectrum antibiotics such as rifampicin, streptomycin and fluoroquinolones, which are also used against other pathogenic bacteria. We developed Drug Resistance Associated Genes database (DRAGdb), a manually curated repository of mutational data of drug resistance associated genes (DRAGs) across ESKAPE (i.e. Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) pathogens, and other bacteria with a special focus on Mycobacterium tuberculosis (MTB). Analysis of mutations in drug-resistant genes listed in DRAGdb suggested both homoplasy and pleiotropy to be associated with resistance. Homoplasy was observed in six genes namely gidB, gyrA, gyrB, rpoB, rpsL and rrs. For these genes, drug resistance-associated mutations at codon level were conserved in MTB, ESKAPE and many other bacteria. Pleiotropy was exemplified by a single nucleotide mutation that was associated with resistance to amikacin, gentamycin, rifampicin and vancomycin in Staphylococcus aureus. DRAGdb data also revealed that mutations in some genes such as pncA, inhA, katG and embA,B,C were specific to Mycobacterium species. For inhA and pncA, the mutations in the promoter region along with those in coding regions were associated with resistance to isoniazid and pyrazinamide respectively. In summary, the DRAGdb database is a compilation of all the major MTB drug resistance genes across bacterial species, which allows identification of homoplasy and pleiotropy phenomena of DRAGs.

Durable Antibacterial Cotton Fabrics Based on Natural Borneol-Derived Anti-MRSA Agents

Borneol, a natural extract with unique bicyclic monoterpene structure, has attracted increasing attention due to its broad-spectrum antibacterial properties via membrane disruption mechanism. However, the negligible water solubility of borneol limits its antibacterial efficiency. Herein, borneol-based water-soluble antibacterial agents are designed and synthesized to combat multi-drug resistant bacteria. The integration of borneol with hydrophilic poly(N,N-dimethylethyl methacrylate) (PDMAEMA) polymer chains boosts the antibacterial capability of borneol against Gram-negative, Gram-positive, and even multi-drug resistant bacteria. Methicillin-resistant Staphylococcus aureus (MRSA) are completely killed upon treatment with 50 µg mL^-1 of borneol-based polymers and Escherichia coli are annihilated at 39 µg mL^-1 . It is further demonstrated that the borneol-based antibacterial agents can be grafted onto cotton fabrics as a nonleaching antibacterial agent, which have higher sustained antibacterial activity than cotton fabrics coated with the commercial quaternary ammonium finishing agents (AEM 5700). The functionalized fabrics with excellent bactericidal activity, especially against MRSA, may have great potential applications in managing hospital-acquired infections.

A kinase bioscavenger provides antibiotic resistance by extremely tight substrate binding

Microbial communities are self-controlled by repertoires of lethal agents, the antibiotics. In their turn, these antibiotics are regulated by bioscavengers that are selected in the course of evolution. Kinase-mediated phosphorylation represents one of the general strategies for the emergence of antibiotic resistance. A new subfamily of AmiN-like kinases, isolated from the Siberian bear microbiome, inactivates antibiotic amicoumacin by phosphorylation. The nanomolar substrate affinity defines AmiN as a phosphotransferase with a unique catalytic efficiency proximal to the diffusion limit. Crystallographic analysis and multiscale simulations revealed a catalytically perfect mechanism providing phosphorylation exclusively in the case of a closed active site that counteracts substrate promiscuity. AmiN kinase is a member of the previously unknown subfamily representing the first evidence of a specialized phosphotransferase bioscavenger.

Horizontal Gene Transfer: From Evolutionary Flexibility to Disease Progression

Flexibility in the exchange of genetic material takes place between different organisms of the same or different species. This phenomenon is known to play a key role in the genetic, physiological, and ecological performance of the host. Exchange of genetic materials can cause both beneficial and/or adverse biological consequences. Horizontal gene transfer (HGT) or lateral gene transfer (LGT) as a general mechanism leads to biodiversity and biological innovations in nature. HGT mediators are one of the genetic engineering tools used for selective introduction of desired changes in the genome for gene/cell therapy purposes. HGT, however, is crucial in development, emergence, and recurrence of various human-related diseases, such as cancer, genetic-, metabolic-, and neurodegenerative disorders and can negatively affect the therapeutic outcome by promoting resistant forms or disrupting the performance of genome editing toolkits. Because of the importance of HGT and its vital physio- and pathological roles, here the variety of HGT mechanisms are reviewed, ranging from extracellular vesicles (EVs) and nanotubes in prokaryotes to cell-free DNA and apoptotic bodies in eukaryotes. Next, we argue that HGT plays a role both in the development of useful features and in pathological states associated with emerging and recurrent forms of the disease. A better understanding of the different HGT mediators and their genome-altering effects/potentials may pave the way for the development of more effective therapeutic and diagnostic regimes.

Tetracycline-inactivating enzymes from environmental, human commensal, and pathogenic bacteria cause broad-spectrum tetracycline resistance

Tetracycline resistance by antibiotic inactivation was first identified in commensal organisms but has since been reported in environmental and pathogenic microbes. Here, we identify and characterize an expanded pool of tet(X)-like genes in environmental and human commensal metagenomes via inactivation by antibiotic selection of metagenomic libraries. These genes formed two distinct clades according to habitat of origin, and resistance phenotypes were similarly correlated. Each gene isolated from the human gut encodes resistance to all tetracyclines tested, including eravacycline and omadacycline. We report a biochemical and structural characterization of one enzyme, Tet(X7). Further, we identify Tet(X7) in a clinical Pseudomonas aeruginosa isolate and demonstrate its contribution to tetracycline resistance. Lastly, we show anhydrotetracycline and semi-synthetic analogues inhibit Tet(X7) to prevent enzymatic tetracycline degradation and increase tetracycline efficacy against strains expressing tet(X7). This work improves our understanding of resistance by tetracycline-inactivation and provides the foundation for an inhibition-based strategy for countering resistance.

Antimicrobial resistance genes in raw milk for human consumption

The increasing prevalence of antimicrobial resistance (AMR) is a significant threat to global health. More and more multi-drug-resistant bacterial strains cause life-threatening infections and the death of thousands of people each year. Beyond disease control animals are often given antibiotics for growth promotion or increased feed efficiency, which further increase the chance of the development of multi-resistant strains. After the consumption of unprocessed animal products, these strains may meet the human bacteriota. Among the foodborne and the human populations, antimicrobial resistance genes (ARGs) may be shared by horizontal gene transfer. This study aims to test the presence of antimicrobial resistance genes in milk metagenome, investigate their genetic position and their linkage to mobile genetic elements. We have analyzed raw milk samples from public markets sold for human consumption. The milk samples contained genetic material from various bacterial species and the in-depth analysis uncovered the presence of several antimicrobial resistance genes. The samples contained complete ARGs influencing the effectiveness of acridine dye, cephalosporin, cephamycin, fluoroquinolone, penam, peptide antibiotics and tetracycline. One of the ARGs, PC1 beta-lactamase may also be a mobile element that facilitates the transfer of resistance genes to other bacteria, e.g. to the ones living in the human gut.

Integrated metagenomic and metatranscriptomic profiling reveals differentially expressed resistomes in human, chicken, and pig gut microbiomes

Gut microbiota is a reservoir of antibiotic resistance genes (ARGs). Yet, limited information is available regarding the presence (metagenomic DNA level) and expression profiles (metatranscriptomic RNA level) of ARGs in gut microbiota. Here, we used both metagenomic and metatranscriptomic approaches to comprehensively reveal the abundance, diversity, and expression of ARGs in human, chicken, and pig gut microbiomes in China. Based on deep sequencing data and ARG databases, a total of 330 ARGs associated with 21 antibiotic classes were identified in 18 human, chicken, and pig fecal samples. Metatranscriptomic analysis revealed that 49.4, 66.5, and 56.6% of ARGs identified in human, chicken, and pig gut microbiota, respectively, were expressed, indicating that a large proportion of ARGs were not transcriptionally active. Further analysis demonstrated that transcript abundance of tetracycline, aminoglycoside, and beta-lactam resistance genes was mainly contributed by acquired ARGs. We also found that various biocide, chemical, and metal resistance genes were actively transcribed in human and animal guts. The combination of metagenomic and metatranscriptomic analysis in this study allowed us to specifically link ARGs to their transcripts, providing a comprehensive view of the prevalence and expression of ARGs in gut microbiota. Taken together, these data deepen our understanding of the distribution, evolution, and dissemination of ARGs and metal resistance genes in human, chicken, and pig gut microbiota.

An alternative approach to the synthesis of the three fragments of anachelin H

The synthesis of the fully protected peptide, polyketide and alkaloid fragments of anachelin H is presented. The peptide fragment was prepared using a liquid phase peptide synthesis; the polyketide fragment was synthetized using a cross metathesis and an intramolecular oxa-Michael reaction as the key steps to introduce the desired stereochemistry; finally, the alkaloid fragment was obtained by an oxidative cyclization of a catechol derivative using potassium ferricyanide. The synthesis of all fragments was based on the use of natural amino acids as sources of asymmetry. The independent synthesis of the three fragments should allow more efficient biological studies on the fragments instead of the whole natural product. Experiments to illustrate the coupling of fragments and the effectiveness of the convergent strategy are also described.

Light-Excited Antibiotics for Potentiating Bacterial Killing via Reactive Oxygen Species Generation

The irrational or excessive use of antibiotics causes the emergence of bacterial resistance, making antibiotics less effective or ineffective. As the number of resistant antibiotics increases, it is crucial to develop new strategies and innovative approaches to potentiate the efficacy of existing antibiotics. In this paper, we report that some existing antibiotics can produce reactive oxygen species (ROS) directly under light irradiation. Thus, a novel antibacterial photodynamic therapy (PDT) strategy is proposed by using existing antibiotics for which the activities are potentiated via light-activation. This antibiotic-based PDT strategy can achieve efficient bacteria killing with a low dosage of antibiotics, indicating that bacterial killing can be enhanced by the light-irradiated antibiotics. Moreover, the specific types of ROS produced by different antibiotics under light irradiation were studied for better elucidation of the antibacterial mechanism. The findings can extend the application of existing antibiotics and provide a promising strategy for treatment of bacterial infections and even cancers.

Coevolution of host-plasmid pairs facilitates the emergence of novel multidrug resistance

Multidrug resistance (MDR) of pathogens is an ongoing public health crisis exacerbated by the horizontal transfer of antibiotic resistance genes via conjugative plasmids. Factors that stabilize these plasmids in bacterial communities contribute to an even higher incidence of MDR, given the increased likelihood that a host will already contain a plasmid when it acquires another through conjugation. Here, we show one such stabilizing factor is host-plasmid coevolution under antibiotic selection, which facilitated the emergence of MDR via two distinct plasmids in communities consisting of Escherichia coli and Klebsiella pneumoniae once antibiotics were removed. In our system, evolution promoted greater stability of a plasmid in its coevolved host. Further, pleiotropic effects resulted in greater plasmid persistence in both novel host-plasmid combinations and, in some cases, multi-plasmid hosts. This evolved stability favoured the generation of MDR cells and thwarted their loss within communities with multiple plasmids. By selecting for plasmid persistence, the application of antibiotics may promote MDR well after their original period of use.

Metatranscriptomics Reveals Antibiotic-Induced Resistance Gene Expression in the Murine Gut Microbiota

Antibiotic resistance is a current and expanding threat to the practice of modern medicine. Antibiotic therapy has been shown to perturb the composition of the host microbiome with significant health consequences. In addition, the gut microbiome is known to be a reservoir of antibiotic resistance genes. Work has demonstrated that antibiotics can alter the collection of antibiotic resistance genes within the microbiome through selection and horizontal gene transfer. While antibiotics also have the potential to impact the expression of resistance genes, metagenomic-based pipelines currently lack the ability to detect these shifts. Here, we utilized a dual sequencing approach combining shotgun metagenomics and metatranscriptomics to profile how three antibiotics, amoxicillin, doxycycline, and ciprofloxacin, impact the murine gut resistome at the DNA and RNA level. We found that each antibiotic induced broad, but untargeted impacts on the gene content of the resistome. In contrast, changes in ARG transcript abundance were more targeted to the antibiotic treatment. Doxycycline and amoxicillin induced the expression of tetracycline and beta-lactamase resistance genes, respectively. Furthermore, the increased beta-lactamase resistance gene transcripts could contribute to an observed bloom of Bacteroides thetaiotaomicron during amoxicillin treatment. Based on these findings, we propose that the utilization of a dual sequencing methodology provides a unique capacity to fully understand the response of the resistome to antibiotic perturbation. In particular, the analysis of transcripts reveals that the expression and utilization of resistance genes is far narrower than their abundance at the genomic level would suggest.

Constructing and deconstructing the bacterial cell wall

The history of modern medicine cannot be written apart from the history of the antibiotics. Antibiotics are cytotoxic secondary metabolites that are isolated from Nature. The antibacterial antibiotics disproportionately target bacterial protein structure that is distinct from eukaryotic protein structure, notably within the ribosome and within the pathways for bacterial cell-wall biosynthesis (for which there is not a eukaryotic counterpart). This review focuses on a pre-eminent class of antibiotics-the β-lactams, exemplified by the penicillins and cephalosporins-from the perspective of the evolving mechanisms for bacterial resistance. The mechanism of action of the β-lactams is bacterial cell-wall destruction. In the monoderm (single membrane, Gram-positive staining) pathogen Staphylococcus aureus the dominant resistance mechanism is expression of a β-lactam-unreactive transpeptidase enzyme that functions in cell-wall construction. In the diderm (dual membrane, Gram-negative staining) pathogen Pseudomonas aeruginosa a dominant resistance mechanism (among several) is expression of a hydrolytic enzyme that destroys the critical β-lactam ring of the antibiotic. The key sensing mechanism used by P. aeruginosa is monitoring the molecular difference between cell-wall construction and cell-wall deconstruction. In both bacteria, the resistance pathways are manifested only when the bacteria detect the presence of β-lactams. This review summarizes how the β-lactams are sensed and how the resistance mechanisms are manifested, with the expectation that preventing these processes will be critical to future chemotherapeutic control of multidrug resistant bacteria.

La batalla contra las superbacterias: No más antimicrobianos, no hay ESKAPE

La resistencia a los antimicrobianos es uno de los más grandes retos de la medicina moderna. Durante la última década, un grupo de seis bacterias han probado no sólo su capacidad para relativamente “escapar” de los efectos de casi cualquier antimicrobiano, sino también por ser la causa principal de las infecciones hospitalarias. Estos organismos en conjunto se les conoce como ESKAPE, siglas que derivan de la primera letra de la categoría taxonómica género, o sea, del nombre científico de cada una de estas bacterias (Enterococcus spp, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa y Enterobacter spp.). La presente revisión tiene como objetivo describir los principales mecanismos de resistencia asociados a este grupo de bacterias y el impacto que han tenido en el desarrollo de nuevas estrategias antimicrobianas.

Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes

The current epidemic of antibiotic resistance has been facilitated by the wide and rapid horizontal dissemination of antibiotic resistance genes (ARGs) in microbial communities. Indeed, ARGs are often located on plasmids, which can efficiently shuttle genes across diverse taxa. While the existence conditions of plasmids have been extensively studied in a few model bacterial populations, their fate in complex bacterial communities is poorly understood. Here, we coupled plasmid transfer assays with serial growth experiments to investigate the persistence of the broad-host-range IncP-1 plasmid pKJK5 in microbial communities derived from a sewage treatment plant. The cultivation conditions combined different nutrient and oxygen levels, and were non-selective and non-conducive for liquid-phase conjugal transfer. Following initial transfer, the plasmid persisted in almost all conditions during a 10-day serial growth experiment (equivalent to 60 generations), with a transient transconjugant incidence up to 30%. By combining cell enumeration and sorting with amplicon sequencing, we mapped plasmid fitness effects across taxa of the microbial community. Unexpected plasmid fitness benefits were observed in multiple phylotypes of Aeromonas, Enterobacteriaceae, and Pseudomonas, which resulted in community-level plasmid persistence. We demonstrate, for the first time, that plasmid fitness effects across community members can be estimated in high-throughput without prior isolation. By gaining a fitness benefit when carrying plasmids, members within complex microbial communities might have a hitherto unrecognised potential to maintain plasmids for long-term community-wide access.

RNA polymerase mutations cause cephalosporin resistance in clinical Neisseria gonorrhoeae isolates

Increasing Neisseria gonorrhoeae resistance to ceftriaxone, the last antibiotic recommended for empiric gonorrhea treatment, poses an urgent public health threat. However, the genetic basis of reduced susceptibility to ceftriaxone is not completely understood: while most ceftriaxone resistance in clinical isolates is caused by target site mutations in penA, some isolates lack these mutations. We show that penA-independent ceftriaxone resistance has evolved multiple times through distinct mutations in rpoB and rpoD. We identify five mutations in these genes that each increase resistance to ceftriaxone, including one mutation that arose independently in two lineages, and show that clinical isolates from multiple lineages are a single nucleotide change from ceftriaxone resistance. These RNA polymerase mutations cause large-scale transcriptional changes without altering susceptibility to other antibiotics, reducing growth rate, or deranging cell morphology. These results underscore the unexpected diversity of pathways to resistance and the importance of continued surveillance for novel resistance mutations.

Wastewater discharge drives ARGs spread in the coastal area: A case study in Hangzhou Bay, China

The distribution of 14 ARGs, intI1, and 16S rDNA were analysed in 4 wastewater treatment plants (WWTPs), 2 effluent receiving areas (ERAs), and Hangzhou Bay (HZB). The results showed that each integrated WWTP (IWWTP) received higher abundance of ARGs than pharmaceutical WWTPs (PWWTPs), and IWWTPs removed ARGs more efficiently than PWWTPs. The WWTP effluents greatly contributed to the ARGs pollution in the water environments of the ERAs and HZB, and the total abundance of the ARGs displayed a distance decay pattern. In coastal sediments, more ARGs were accumulated in remote sites. The correlation analysis showed that the occurrence of ARGs was more related to 16S rDNA and intI1 in the WWTPs. Three macrolides resistance genes (ermB, mphA, and vatB) had strong correlations with 16S rDNA and intI1 in all the sample groups. Our study clearly reveals the link between land WWTPs discharge and emerging pollution of ARGs in coastal environments.

Gut Resistome After Oral Antibiotics in Preschool Children in Burkina Faso: A Randomized, Controlled Trial

We evaluated the effect of systemic antibiotics (azithromycin, amoxicillin, cotrimoxazole, or placebo) on the gut resistome in children aged 6 to 59 months. Azithromycin and cotrimoxazole led to an increase in macrolide and sulfonamide resistance determinants. Resistome expansion can be induced with a single course of antibiotics.

Quantitative and Fast Sterility Assurance Testing of Surfaces by Enumeration of Germinable Endospores

A fast Endospore Germinability Assay (EGA) was validated with traditional plate counts to enumerate single endospore germination events for monitoring surface sterilization. The assay is based on a time-gated luminescence microscopy technique enabling visualization and enumeration of individual germinating endospores. Germinating endospores release calcium dipicolinate to form highly luminescent terbium dipicolinate complexes surrounding each germinating endospore. EGA and heterotrophic plate counting (HPC) were used to evaluate the swab/rinse recovery efficiency of endospores from stainless steel surfaces. EGA and HPC results were highly correlated for endospore recovery from stainless steel coupons inoculated with range of 1,000 endospores per coupon down to sterility. Dosage-dependent decrease of surface endospore germinability were observed in dry heat, UV irradiation, oxygen plasma and vaporized hydrogen peroxide treatments, measured with EGA and HPC. EGA is a fast and complementary method to traditional HPC for quantitative sterility assurance testing of surfaces. This work introduces and validates a 15-minute or faster assay for germinable endospores to complement the conventional lengthy, culture-based surface sterility validation, which is critical in hospitals, food and pharmaceutical industries to help minimize nosocomial infection, food spoilage, and pharmaceutical contamination.

Implications of indoor microbial ecology and evolution on antibiotic resistance

The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide "healthy" building design.

Emerging antibacterial nanomedicine for enhanced antibiotic therapy

This review highlights the different mechanisms of current nano-antibiotic systems for combatting serious antibiotic resistance of bacteria.

Efficient Bacteria Killing by Cu2WS4 Nanocrystals with Enzyme-like Properties and Bacteria-Binding Ability

Antibacterial agents with high antibacterial efficiency and bacteria-binding capability are highly desirable. Herein, we describe the successful preparation of Cu₂WS₄ nanocrystals (CWS NCs) with excellent antibacterial activity. CWS NCs with small size (∼20 nm) achieve more than 5 log (>99.999%) inactivation efficiency of both Staphylococcus aureus (Gram-positive) and Escherichia coli (Gram-negative) at low concentration (<2 μg mL^-1) with or without ambient light, which is much better than most of the reported antibacterial nanomaterials (including Ag, TiO₂, etc.) and even better than the widely used antibiotics (vancomycin and daptomycin). Antibacterial mechanism study showed that CWS NCs have both enzyme-like (oxidase and peroxidase) properties and selective bacteria-binding ability, which greatly facilitate the production of reactive oxygen species to kill bacteria. Animal experiments further indicated that CWS NCs can effectively treat wounds infected with methicillin-resistant Staphylococcus aureus (MRSA). This work demonstrates that CWS NCs have the potential as effective antibacterial nanozymes for the treatment of bacterial infection.

Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes

Identification of the nucleotide sequences encoding antibiotic resistance elements and determination of their association with antibiotic resistance are critical to improve surveillance and monitor trends in antibiotic resistance. Current methods to study antibiotic resistance in various environments rely on extensive deep sequencing or laborious culturing of fastidious organisms, both of which are heavily time-consuming operations. An accurate and sensitive method to identify both rare and common resistance elements in complex metagenomic samples is needed. Referencing the sequences in the Comprehensive Antibiotic Resistance Database, we designed a set of 37,826 probes to specifically target over 2,000 nucleotide sequences associated with antibiotic resistance in clinically relevant bacteria. Testing of this probe set on DNA libraries generated from multidrug-resistant bacteria to selectively capture resistance genes reproducibly produced higher numbers of reads on target at a greater length of coverage than shotgun sequencing. We also identified additional resistance gene sequences from human gut microbiome samples that sequencing alone was not able to detect. Our method to capture the resistome enables a sensitive means of gene detection in diverse environments where genes encoding antibiotic resistance represent less than 0.1% of the metagenome.

The resistome and genomic reconnaissance in the age of malaria elimination

Malaria is an infectious disease caused by parasitic protozoa in the Plasmodium genus. A complete understanding of the biology of these parasites is challenging in view of their need to switch between the vertebrate and insect hosts. The parasites are also capable of becoming highly motile and of remaining dormant for decades, depending on the stage of their life cycle. Malaria elimination efforts have been implemented in several endemic countries, but the parasites have proven to be resilient. One of the major obstacles for malaria elimination is the development of antimalarial drug resistance. Ineffective treatment regimens will fail to remove the circulating parasites and to prevent the local transmission of the disease. Genomic epidemiology of malaria parasites has become a powerful tool to track emerging drug-resistant parasite populations almost in real time. Population-scale genomic data are instrumental in tracking the hidden pockets of Plasmodium in nationwide elimination efforts. However, genomic surveillance data can be useful in determining the threat only when combined with a thorough understanding of the malarial resistome – the genetic repertoires responsible for causing and potentiating drug resistance evolution. Even though long-term selection has been a standard method for drug target identification in laboratories, its implementation in large-scale exploration of the druggable space in Plasmodium falciparum, along with genome-editing technologies, have enabled mapping of the genetic repertoires that drive drug resistance. This Review presents examples of practical use and describes the latest technology to show the power of real-time genomic epidemiology in achieving malaria elimination.

Summary: This Review discusses the challenges in malaria elimination and how implementation of national-scale genomic surveillance programmes in combination with resistome analyses could provide a powerful solution.

Introduction of NGS in Environmental Surveillance for Healthcare-Associated Infection Control

The hospital environment significantly contributes to the onset of healthcare associated infections (HAIs), representing the most frequent and severe complications related to health care. The monitoring of hospital surfaces is generally addressed by microbial cultural isolation, with some performance limitations. Hence there is need to implement environmental surveillance systems using more effective methods. This study aimed to evaluate next-generation sequencing (NGS) technologies for hospital environment microbiome characterization, in comparison with conventional and molecular methods, in an Italian pediatric hospital. Environmental samples included critical surfaces of randomized rooms, surgical rooms, intensive care units and delivery rooms. The resistome of the contaminating population was also evaluated. NGS, compared to other methods, detected with higher sensitivity the environmental bacteria, and was the only method able to detect even unsearched bacteria. By contrast, however, it did not detect mycetes, nor it could distinguish viable from dead bacteria. Microbiological and PCR methods could identify and quantify mycetes, in addition to bacteria, and PCR could define the population resistome. These data suggest that NGS could be an effective method for hospital environment monitoring, especially if flanked by PCR for species identification and resistome characterization, providing a potential tool for the control of HAI transmission.

Biochar accelerates the removal of tetracyclines and their intermediates by altering soil properties

Tetracyclines accumulation in soil environment potentially threatens agroecosystem safety. Interestingly, biochar could clean up organic pollutants, but to what extent biochar affects the removal of tetracyclines is unknown. To investigate it, five types of biochars derived from cow manure (CMB) and other four plant materials were respectively added into soils contaminated with a mixture of tetracycline, oxytetracycline, and chlortetracycline for 60-day incubation in the dark. Three parent tetracyclines and their corresponding intermediates (epitetracycline, anhydrotetracycline, epianhydrotetracycline, epioxytetracycline, epichlortetracycline, and demethylchlortetracycline) were respectively determined and named as TTCs, OTCs and CTCs. Obtained results showed biochar especially CMB could effectively remove the antibiotics (P < 0.05). Compared to control, the removal rate of TTCs, OTCs and CTCs respectively increased by up to 10.86%, 10.29% and 10.12% in CMB-added soil. The increased removal rate of the antibiotics after biochar addition was due to the increasing accessibilities for degrading microorganisms via the elevating electrical conductivity. Moreover, biochar addition might stimulate these microbial activities through the increase of C and N supplement. Our results indicate biochar accelerates the removal of tetracyclines and their intermediates by altering soil properties and thus increasing the antibiotics accessibilities, which provide insights into how biochar accelerates the removal for these antibiotics.

Structural Requirements of N-alpha-Mercaptoacetyl Dipeptide (NAMdP) Inhibitors of Pseudomonas Aeruginosa Virulence Factor LasB: 3D-QSAR, Molecular Docking, and Interaction Fingerprint Studies

The zinc metallopeptidase Pseudomonas elastase (LasB) is a virulence factor of Pseudomonas aeruginosa (P. aeruginosa), a pathogenic bacterium that can cause nosocomial infections. The present study relates the structural analysis of 118 N-alpha-mercaptoacetyl dipeptides (NAMdPs) as LasB inhibitors. Field-based 3D-QSAR and molecular docking methods were employed to describe the essential interactions between NAMdPs and LasB binding sites, and the chemical features that determine their differential activities. We report a predictive 3D-QSAR model that was developed according to the internal and external validation tests. The best model, including steric, electrostatic, hydrogen bond donor, hydrogen bond acceptor, and hydrophobic fields, was found to depict a three-dimensional map with the local positive and negative effects of these chemotypes on the LasB inhibitory activities. Furthermore, molecular docking experiments yielded bioactive conformations of NAMdPs inside the LasB binding site. The series of NAMdPs adopted a similar orientation with respect to phosphoramidon within the LasB binding site (crystallographic reference), where the backbone atoms of NAMdPs are hydrogen-bonded to the LasB residues N112, A113, and R198, similarly to phosphoramidon. Our study also included a deep description of the residues involved in the protein-ligand interaction patterns for the whole set of NAMdPs, through the use of interaction fingerprints (IFPs).

Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome

Hospitalized preterm infants receive frequent and often prolonged exposures to antibiotics because they are vulnerable to infection. It is not known whether the short-term effects of antibiotics on the preterm infant gut microbiota and resistome persist after discharge from neonatal intensive care units. Here, we use complementary metagenomic, culture-based and machine learning techniques to study the gut microbiota and resistome of antibiotic-exposed preterm infants during and after hospitalization, and we compare these readouts to antibiotic-naive healthy infants sampled synchronously. We find a persistently enriched gastrointestinal antibiotic resistome, prolonged carriage of multidrug-resistant Enterobacteriaceae and distinct antibiotic-driven patterns of microbiota and resistome assembly in extremely preterm infants that received early-life antibiotics. The collateral damage of early-life antibiotic treatment and hospitalization in preterm infants is long lasting. We urge the development of strategies to reduce these consequences in highly vulnerable neonatal populations.

Constructing antibacterial polymer nanocapsules based on pyridine quaternary ammonium salt

Excessive use of antibiotics accelerates the development and spread of drug-resistant strains, which is a huge challenge for the field of medical health worldwide. Quaternary ammonium salt polymers are considered to be membrane-active bactericidal groups with vast potential to control bacterial infections and inhibit drug resistance. Herein, we report on the creative synthesis and characterization of novel antimicrobial polymer nanocapsules based on pyridine quaternary ammonium salt. The antimicrobial polymer nanocapsules were formed by reaction of C₃ symmetrical rigid monomer 2,4,6‑tris(4‑pyridyl)‑1,3,5‑triazine (TPT) and a flexible linker 1,2‑dibromoethane. The polymer nanocapsule was constructed as a cationic hollow sphere composed of a two-dimensional sheet whose main chain was formed by the pyridine quaternary ammonium salt, and a part of the bromide ion was adsorbed on the sphere. This hollow nanocapsule was characterized in detail by DLS, SEM, TEM, AFM, EDS and EA. When the cationic polymer nanocapsules are close to the Gram-negative Escherichia coli, the negatively charged phospholipid molecules in the bacterial membrane are attracted to the cationic surface and lead to rupture of cells. SEM confirmed the breakage of Escherichia coli membranes. The minimum inhibitory concentration was found to be 0.04 mg/mL, and the minimum bactericidal concentration was 0.1 mg/mL. Our experiments demonstrated that the adsorption of negatively charged phospholipid molecules on the surface of the pyridine quaternary ammonium salt polymer can kill Gram-negative bacteria without inserting quaternary ammonium salt hydrophobic groups into the cell membrane.

Metagenomics: aid to combat antimicrobial resistance in diarrhea

Antimicrobial resistance (AMR) has emerged as an obstacle in the supple administration of antimicrobial agents to critical diarrheal patients. Most diarrheal pathogens have developed resistance against the major classes of antibiotics commonly used for assuaging diarrheal symptoms. Antimicrobial resistance develops when pathogens acquire antimicrobial resistance genes (ARGs) through genetic recombination from commensals and pathogens. These are the constituents of the complex microbiota in all ecological niches. The recombination events may occur in the environment or in the gut. Containment of AMR can be achieved through a complete understanding of the complex and diverse structure and function of the microbiota. Its taxonomic entities serve as focal points for the dissemination of antimicrobial resistance genetic determinants. Molecular methods complemented with culture-based diagnostics have been historically implemented to document these natural events. However, the advent of next-generation sequencing has revolutionized the field of molecular epidemiology. It has revolutionized the method of addressing relevant problems like diagnosis and surveillance of infectious diseases and the issue of antimicrobial resistance. Metagenomics is one such next-generation technique that has proved to be a monumental advancement in the area of molecular taxonomy. Current understanding of structure, function and dysbiosis of microbiota associated with antimicrobial resistance was realized due to its conception. This review describes the major milestones achieved due to the advent and implementation of this new technique in the context of antimicrobial resistance. These achievements span a wide panorama from the discovery of novel microorganisms to invention of translational value.

Spatiotemporal dynamics of multidrug resistant bacteria on intensive care unit surfaces

Bacterial pathogens that infect patients also contaminate hospital surfaces. These contaminants impact hospital infection control and epidemiology, prompting quantitative examination of their transmission dynamics. Here we investigate spatiotemporal and phylogenetic relationships of multidrug resistant (MDR) bacteria on intensive care unit surfaces from two hospitals in the United States (US) and Pakistan collected over one year. MDR bacteria isolated from 3.3% and 86.7% of US and Pakistani surfaces, respectively, include common nosocomial pathogens, rare opportunistic pathogens, and novel taxa. Common nosocomial isolates are dominated by single lineages of different clones, are phenotypically MDR, and have high resistance gene burdens. Many resistance genes (e.g., blaNDM, blaOXA carbapenamases), are shared by multiple species and flanked by mobilization elements. We identify Acinetobacter baumannii and Enterococcus faecium co-association on multiple surfaces, and demonstrate these species establish synergistic biofilms in vitro. Our results highlight substantial MDR pathogen burdens in hospital built-environments, provide evidence for spatiotemporal-dependent transmission, and demonstrate potential mechanisms for multi-species surface persistence.

Antimicrobial resistance in water in Latin America and the Caribbean: a scoping review protocol

OBJECTIVE

The objective of this scoping review is to identify and map existing evidence of antimicrobial resistance (AMR) in water in Latin America and the Caribbean (LAC), while also identifying the gaps in AMR information in the region in eight themes of interest.

INTRODUCTION

Antimicrobial resistance is a public health concern that has gained increasing global awareness. Concerns have been raised toward the importance of the environment's role in the dissemination of clinically relevant AMR. Although studies on AMR have been conducted, the reality of the role of the environment in the LAC region has not been studied.

INCLUSION CRITERIA

Articles that examine AMR in water in the LAC region will be considered for inclusion. Antimicrobial resistance will be defined as a natural process that arises when the microorganisms that cause infection (e.g. bacteria) survive exposure to a drug that would normally kill them or stop their growth. The search will focus on eight themes of interest, as defined in the protocol, relating to the presence of resistant microorganisms in water sources and reported negative health effects. Qualitative and quantitative studies will be considered for inclusion. Reviews and gray literature will be excluded.

METHODS

The proposed scoping review will be conducted in accordance with the JBI methodology for scoping reviews. A search for published literature will be performed in PubMed, Web of Science and Scopus. Independent screening of articles will be performed by examining the abstracts and then the full texts, utilizing pre-defined inclusion and exclusion criteria. Data for specific variables will be extracted, and descriptive examination will be performed.

Microbial diversity and antibiotic resistome in swine farm environments

Swine feedlots are recognized as a reservoir of antibiotic resistance genes (ARGs). However, the microbiome and antibiotic resistome in swine wastewater and its impact on receiving environments remain to be further explored by culture independent metagenomics. We investigated the microbial diversity of swine wastewater and the receiving environments in three swine farms by 16S rRNA gene sequencing. Metagenomic sequencing was utilized to further study the antibiotic resistome in the different depths of soils in vegetable fields, which had been fertilized with swine wastewater for at least 24 years. The 16S rRNA gene sequencing showed that the microbiome of the well water, fishpond, vegetables and the field soils was affected by the respective swine farms. Significant positive correlations were found between 20 ARGs and 41 genus of bacteria across all environmental samples. The metagenomic sequencing showed that a total of 79 types of ARGs were found in soil cores (at depth of 0-20 cm, 20-40 cm and 40-70 cm) and the irrigation water (swine wastewater). Antibiotics were detected in vertical soil profiles and wastewater. Compared with the vegetable fields without animal manure application, the soils irrigated with swine wastewater harbored higher diversity of ARGs and contained higher concentrations of antibiotics. Co-occurrence of integron-related scaffolds was found in different depths of soil cores and the swine wastewater. The results suggest that environmental microbiome was changed under the impact of swine farms, and long-term manure/wastewater application have resulted in the accumulation of ARGs in deeper soils Prudent use of antibiotics and reasonable management of animal wastes in livestock feedlots should therefore be considered to reduce the dissemination of antibiotic resistance to the environment.

Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria

Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.

Characterization of the Microbial Resistome in Conventional and "Raised Without Antibiotics" Beef and Dairy Production Systems

Metagenomic investigations have the potential to provide unprecedented insights into microbial ecologies, such as those relating to antimicrobial resistance (AMR). We characterized the microbial resistome in livestock operations raising cattle conventionally (CONV) or without antibiotic exposures (RWA) using shotgun metagenomics. Samples of feces, wastewater from catchment basins, and soil where wastewater was applied were collected from CONV and RWA feedlot and dairy farms. After DNA extraction and sequencing, shotgun metagenomic reads were aligned to reference databases for identification of bacteria (Kraken) and antibiotic resistance genes (ARGs) accessions (MEGARes). Differences in microbial resistomes were found across farms with different production practices (CONV vs. RWA), types of cattle (beef vs. dairy), and types of sample (feces vs. wastewater vs. soil). Feces had the greatest number of ARGs per sample (mean = 118 and 79 in CONV and RWA, respectively), with tetracycline efflux pumps, macrolide phosphotransferases, and aminoglycoside nucleotidyltransferases mechanisms of resistance more abundant in CONV than in RWA feces. Tetracycline and macrolide–lincosamide–streptogramin classes of resistance were more abundant in feedlot cattle than in dairy cow feces, whereas the β-lactam class was more abundant in dairy cow feces. Lack of congruence between ARGs and microbial communities (procrustes analysis) suggested that other factors (e.g., location of farms, cattle source, management practices, diet, horizontal ARGs transfer, and co-selection of resistance), in addition to antimicrobial use, could have impacted resistome profiles. For that reason, we could not establish a cause–effect relationship between antimicrobial use and AMR, although ARGs in feces and effluents were associated with drug classes used to treat animals according to farms’ records (tetracyclines and macrolides in feedlots, β-lactams in dairies), whereas ARGs in soil were dominated by multidrug resistance. Characterization of the “resistance potential” of animal-derived and environmental samples is the first step toward incorporating metagenomic approaches into AMR surveillance in agricultural systems. Further research is needed to assess the public-health risk associated with different microbial resistomes.

Genomic and Metagenomic Approaches for Predictive Surveillance of Emerging Pathogens and Antibiotic Resistance

Antibiotic-resistant organisms (AROs) are a major concern to public health worldwide. While antibiotics have been naturally produced by environmental bacteria for millions of years, modern widespread use of antibiotics has enriched resistance mechanisms in human-impacted bacterial environments. Antibiotic resistance genes (ARGs) continue to emerge and spread rapidly. To combat the global threat of antibiotic resistance, researchers must develop methods to rapidly characterize AROs and ARGs, monitor their spread across space and time, and identify novel ARGs and resistance pathways. We review how high-throughput sequencing-based methods can be combined with classic culture-based assays to characterize, monitor, and track AROs and ARGs. Then, we evaluate genomic and metagenomic methods for identifying ARGs and biosynthetic pathways for novel antibiotics from genomic data sets. Together, these genomic analyses can improve surveillance and prediction of emerging resistance threats and accelerate the development of new antibiotic therapies to combat resistance.

Tracking Carbapenem-Producing Klebsiella pneumoniae Outbreak in an Intensive Care Unit by Whole Genome Sequencing

The presence of carbapenem-producing Klebsiella pneumoniae (CP-Kp) is a serious threat to the control of nosocomial infections. Plasmid-mediated horizontal transfer of the resistance gene makes it difficult to control hospital-acquired CP- Kp infections. Nine CP- Kp strains were isolated during an outbreak in the intensive care unit of Shanghai Huashan hospital in east China. We conducted a retrospective study to identify the origin and route of transmission of this CP-Kp outbreak. Whole-genome sequencing (WGS) analysis was performed on 9 clinical isolates obtained from 8 patients, and the results were compared to clinical and epidemiological records. All isolates were ST11 CP-Kp. Single-nucleotide polymorphisms and the presence and structure of plasmids indicated that this CP-Kp outbreak had different origins. These 9 isolates were partitioned into two clades according to genetic distance. Four plasmids, CP002474.1, CP006799.1, CP018455.1, and CP025459.1, were detected among the 9 isolates. The plasmid phylogeny and antibiotic resistance (AR) gene profile results were consistent with the sequencing results. We found that two clades of CP-Kp were responsible for this nosocomial outbreak and demonstrated the transmission route from two index patients. Plasmid carriage and phylogeny are a useful tool for identifying clades involved in disease transmission.

Microbicide surface nano-structures

The prevention of infectious diseases is a global challenge where multidrug-resistant bacteria or "superbugs" pose a serious threat to worldwide public health. Microtopographic surfaces have attracted much attention as they represent a biomimetic and nontoxic surface antibacterial strategy to replace biocides. The antimicrobial effect of such natural and biomimetic surface nanostructures involves a physical approach which eradicates bacteria via the structural features of the surfaces without any release of biocides or chemicals. These recent developments present a significant proof-of-concept and a powerful tool in which cellular adhesion and death caused by a physical approach, can be controlled by the micro/nanotopology of such surfaces. This represents an innovative direction of development of clean, effective and nonresistant antimicrobial surfaces. The minireview will cover novel approaches for the construction of nanostructures on surfaces in order to create antimicrobial surface in an environmentally friendly, nontoxic manner.

Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution

Antibiotics are powerful drugs used in the treatment of bacterial infections. The inappropriate use of these medicines has driven the dissemination of antibiotic resistance (AR) in most bacteria. Pseudomonas aeruginosa is an opportunistic pathogen commonly involved in environmental- and difficult-to-treat hospital-acquired infections. This species is frequently resistant to several antibiotics, being in the "critical" category of the WHO's priority pathogens list for research and development of new antibiotics. In addition to a remarkable intrinsic resistance to several antibiotics, P. aeruginosa can acquire resistance through chromosomal mutations and acquisition of AR genes. P. aeruginosa has one of the largest bacterial genomes and possesses a significant assortment of genes acquired by horizontal gene transfer (HGT), which are frequently localized within integrons and mobile genetic elements (MGEs), such as transposons, insertion sequences, genomic islands, phages, plasmids and integrative and conjugative elements (ICEs). This genomic diversity results in a non-clonal population structure, punctuated by specific clones that are associated with significant morbidity and mortality worldwide, the so-called high-risk clones. Acquisition of MGEs produces a fitness cost in the host, that can be eased over time by compensatory mutations during MGE-host coevolution. Even though plasmids and ICEs are important drivers of AR, the underlying evolutionary traits that promote this dissemination are poorly understood. In this review, we provide a comprehensive description of the main strategies involved in AR in P. aeruginosa and the leading drivers of HGT in this species. The most recently developed genomic tools that allowed a better understanding of the features contributing for the success of P. aeruginosa are discussed.

Antibiotic resistance genes attenuated with salt accumulation in saline soil

Salt accumulation on the surface of the soil layer driven by the strong evaporation is a natural phenomenon that usually happens in the dry season, particularly on the coastal lands reclaimed from tidal flats. However, the influence of salt accumulation on the distribution profile of antibiotic resistance genes (ARGs) and mobile gene elements (MGEs) remains unclear. In this study, we sampled a wild saline soil where the salt accumulation was frequently observed to investigate the vertical distribution profiles of ARGs and MGEs. The results showed that an increasing gradient of ARGs and MGEs was observed from the top to deep layer with the decreasing of electrical conductivity (EC1:5 values) indicating the salt-influenced attenuation of ARGs in the saline soil. The competing test suggested that the attenuation of ARGs in response to salinity gradient was attributable to the elimination of the ARG-harboring plasmids, due to the reduction of the relative fitness of plasmid-harboring strains. Additionally, the network analyses showed that the attenuation of ARGs might be associated with decreased abundance of Actinobacteria. Overall, this study identifies that salinity as an abiotic stress could re-shape the distribution of ARGs, which may influence the dissemination of ARGs in the environment.

Bystander Selection for Antimicrobial Resistance: Implications for Patient Health

Antimicrobial therapy promotes resistance emergence in target infections and in off-target microbiota. Off-target resistance emergence threatens patient health when off-target populations are a source of future infections, as they are for many important drug-resistant pathogens. However, the health risks of antimicrobial exposure in off-target populations remain largely unquantified, making rational antibiotic stewardship challenging. Here, we discuss the contribution of bystander antimicrobial exposure to the resistance crisis, the implications for antimicrobial stewardship, and some novel opportunities to limit resistance evolution while treating target pathogens.

Crossroads of Antibiotic Resistance and Biosynthesis

The biosynthesis of antibiotics and self-protection mechanisms employed by antibiotic producers are an integral part of the growing antibiotic resistance threat. The origins of clinically relevant antibiotic resistance genes found in human pathogens have been traced to ancient microbial producers of antibiotics in natural environments. Widespread and frequent antibiotic use amplifies environmental pools of antibiotic resistance genes and increases the likelihood for the selection of a resistance event in human pathogens. This perspective will provide an overview of the origins of antibiotic resistance to highlight the crossroads of antibiotic biosynthesis and producer self-protection that result in clinically relevant resistance mechanisms. Some case studies of synergistic antibiotic combinations, adjuvants, and hybrid antibiotics will also be presented to show how native antibiotic producers manage the emergence of antibiotic resistance.