Global Spread Of Antibiotic Resistance Research Articles

Bacteriophage Infections of Biofilms of Health Care-Associated Pathogens: Klebsiella pneumoniae.

Members of the family Enterobacteriaceae, such as Klebsiella pneumoniae, are considered both serious and urgent public health threats. Biofilms formed by these health care-associated pathogens can lead to negative and costly health outcomes. The global spread of antibiotic resistance, coupled with increased tolerance to antimicrobial treatments in biofilm-associated bacteria, highlights the need for novel strategies to overcome treatment hurdles. Bacteriophages (phages), or viruses that infect bacteria, have reemerged as one such potential strategy. Virulent phages are capable of infecting and killing their bacterial hosts, in some cases producing depolymerases that are able to hydrolyze biofilms. Phage therapy does have its limitations, however, including potential narrow host ranges, development of bacterial resistance to infection, and the potential spread of phage-encoded virulence genes. That being said, advances in phage isolation, screening, and genome sequencing tools provide an upside in overcoming some of these limitations and open up the possibilities of using phages as effective biofilm control agents.

The Isolation of a Novel Streptomyces sp. CJ13 from a Traditional Irish Folk Medicine Alkaline Grassland Soil that Inhibits Multiresistant Pathogens and Yeasts

The World Health Organization recently stated that new sources of antibiotics are urgently required to stem the global spread of antibiotic resistance, especially in multiresistant Gram-negative bacteria. Although it was thought that many of the original sources of antibiotics were exhausted, innovative research has revealed promising new sources of antibiotic discovery in traditional medicine associated with Streptomyces. In this work we investigated the potential of a specific limestone grassland soil, associated with Irish folk medicine, as a new source of antimicrobial discovery. Using selective enrichment and isolation techniques on a limestone grassland soil sample obtained from Boho, West Fermanagh, we isolated Streptomyces sp. CJ13. This bacterium inhibited the growth of a broad range of pathogens in vitro including Gram positive Staphylococcus aureus (MRSA 43300) and Gram negative multiresistant Pseudomonas aeruginosa (PA01), as well as the anaerobic bacteria Propionibacterium acnes and the yeast Starmerella bombicola. Genome sequencing and phylogenetic analysis revealed Streptomyces sp. CJ13 to be closely related to an unclassified Streptomyces sp. MJM1172, Streptomyces sp. Mg1 and two species known as Streptomyces sp. ICC1 and ICC4 from a karst region in British Columbia. The closest type species to Streptomyces sp. CJ13 was Streptomyces lavendulae subspecies lavendulae. Analysis of Streptomyces sp. CJ13 whole genome sequence using the secondary metabolite prediction tool antiSMASH revealed similarities to several antibiotic gene synthesis clusters including salinichelin, mediomycin A, weishanmycin, combamide, heat stable antifungal factor and SAL-2242. These results demonstrate the potential of this alkaline grassland soil as a new resource for the discovery of a broad range of antimicrobial compounds including those effective against multiresistant Gram negative bacteria.

Epidemiologic, Phenotypic, and Structural Characterization of Aminoglycoside-Resistance Gene aac(3)-IV.

Aminoglycoside antibiotics are powerful bactericidal therapeutics that are often used in the treatment of critical Gram-negative systemic infections. The emergence and global spread of antibiotic resistance, however, has compromised the clinical utility of aminoglycosides to an extent similar to that found for all other antibiotic-drug classes. Apramycin, a drug candidate currently in clinical development, was suggested as a next-generation aminoglycoside antibiotic with minimal cross-resistance to all other standard-of-care aminoglycosides. Here, we analyzed 591,140 pathogen genomes deposited in the NCBI National Database of Antibiotic Resistant Organisms (NDARO) for annotations of apramycin-resistance genes, and compared them to the genotypic prevalence of carbapenem resistance and 16S-rRNA methyltransferase (RMTase) genes. The 3-N-acetyltransferase gene aac(3)-IV was found to be the only apramycin-resistance gene of clinical relevance, at an average prevalence of 0.7%, which was four-fold lower than that of RMTase genes. In the important subpopulation of carbapenemase-positive isolates, aac(3)-IV was nine-fold less prevalent than RMTase genes. The phenotypic profiling of selected clinical isolates and recombinant strains expressing the aac(3)-IV gene confirmed resistance to not only apramycin, but also gentamicin, tobramycin, and paromomycin. Probing the structure–activity relationship of such substrate promiscuity by site-directed mutagenesis of the aminoglycoside-binding pocket in the acetyltransferase AAC(3)-IV revealed the molecular contacts to His124, Glu185, and Asp187 to be equally critical in binding to apramycin and gentamicin, whereas Asp67 was found to be a discriminating contact. Our findings suggest that aminoglycoside cross-resistance to apramycin in clinical isolates is limited to the substrate promiscuity of a single gene, rendering apramycin best-in-class for the coverage of carbapenem- and aminoglycoside-resistant bacterial infections.

Correlation between Exogenous Compounds and the Horizontal Transfer of Plasmid-Borne Antibiotic Resistance Genes.

The global spread of antibiotic resistance has posed a serious threat to public healthcare and undermined decades of progress made in the fight against bacterial infections. It has been demonstrated that the lack of novel effective antibiotics and rapid spread of antibiotic resistance genes via horizontal transfer in the ecosystem are mainly responsible for this crisis. Notably, plasmid-mediated horizontal transfer of antibiotic resistance genes (ARGs) is recognized as the most dominant dissemination pathway of ARGs in humans, animals and environmental settings. Antibiotic selective pressure has always been regarded as one of the crucial contributors to promoting the dissemination of antibiotic resistance through horizontal gene transfer (HGT). However, the roles of exogenous compounds and particularly non-antibiotic drugs in the spread of ARGs are still underappreciated. In this review, we first summarize the major pathways of HGT in bacteria, including conjugation, transformation, transduction and vesiduction. Subsequently, an overview of these compounds capable of promoting the HGT is presented, which guides to the formulation of more reasonable dosing regimens and drug residue standards in clinical practice. By contrast, these compounds that display an inhibition effect on HGT are also highlighted, which provides a unique strategy to minimize the spread of ARGs. Lastly, we discuss the implementations and challenges in bringing these HGT inhibitors into clinical trials.

Deep Functional Profiling Facilitates the Evaluation of the Antibacterial Potential of the Antibiotic Amicoumacin.

The global spread of antibiotic resistance is forcing the scientific community to find new molecular strategies to counteract it. Deep functional profiling of microbiomes provides an alternative source for the discovery of novel antibiotic producers and probiotics. Recently, we implemented this ultrahigh-throughput screening approach for the isolation of Bacillus pumilus strains efficiently producing the ribosome-targeting antibiotic amicoumacin A (Ami). Proteomics and metabolomics revealed essential insight into the activation of Ami biosynthesis. Here, we applied omics to boost Ami biosynthesis, providing the optimized cultivation conditions for high-scale production of Ami. Ami displayed a pronounced activity against Lactobacillales and Staphylococcaceae, including methicillin-resistant Staphylococcus aureus (MRSA) strains, which was determined using both classical and massive single-cell microfluidic assays. However, the practical application of Ami is limited by its high cytotoxicity and particularly low stability. The former is associated with its self-lactonization, serving as an improvised intermediate state of Ami hydrolysis. This intramolecular reaction decreases Ami half-life at physiological conditions to less than 2 h, which is unprecedented for a terminal amide. While we speculate that the instability of Ami is essential for Bacillus ecology, we believe that its stable analogs represent attractive lead compounds both for antibiotic discovery and for anticancer drug development.

Sewage from Airplanes Exhibits High Abundance and Diversity of Antibiotic Resistance Genes.

Airplane sanitary facilities are shared by an international audience. We hypothesized the corresponding sewage to be an extraordinary source of antibiotic-resistant bacteria (ARB) and resistance genes (ARG) in terms of diversity and quantity. Accordingly, we analyzed ARG and ARB in airplane-borne sewage using complementary approaches: metagenomics, quantitative polymerase chain reaction (qPCR), and cultivation. For the purpose of comparison, we also quantified ARG and ARB in the inlets of municipal treatment plants with and without connection to airports. As expected, airplane sewage contained an extraordinarily rich set of mobile ARG, and the relative abundances of genes were mostly increased compared to typical raw sewage of municipal origin. Moreover, combined resistance against third-generation cephalosporins, fluorochinolones, and aminoglycosides was unusually common (28.9%) among Escherichia coli isolated from airplane sewage. This percentage exceeds the one reported for German clinical isolates by a factor of 8. Our findings suggest that airplane-borne sewage can effectively contribute to the fast and global spread of antibiotic resistance.

Global Spread of Antibiotic Resistance Renders Current Antibiotics Infective

Global Spread of Antibiotic Resistance Renders Current Antibiotics Infective

High diversity and rapid spatial turnover of integron gene cassettes in soil.

Integrons are genetic elements that promote rapid adaptation in bacteria by capturing exogenous, mobile gene cassettes. Recently, a subset of gene cassettes has facilitated the global spread of antibiotic resistance. However, outside clinical settings, very little is known about their diversity and spatial ecology. To address this question, we sequenced integron gene cassettes from soils sampled across Australia and Antarctica. We recovered 44 970 open reading frames that encoded 27 215 unique proteins, representing an order of magnitude more cassettes than previous sequencing efforts. We found that cassettes have extremely high local richness, significantly greater than previously predicted, with estimates ranging from 4000 to 18 000 unique cassettes per 0.3 g of soil. We show that cassettes have a heterogeneous distribution across space, and that they exhibit rapid turnover with distance. Similarity between samples drops to between 0.1% and 10% at distances of as little as 100 m. Together, these data provide key insights into the ecology and size of the gene cassette metagenome.

Experimental Epidemiology of Antibiotic Resistance: Looking for an Appropriate Animal Model System.

Antibiotic resistance is recognized as one of the major challenges in public health. The global spread of antibiotic resistance is the consequence of a constant flow of information across multi-hierarchical interactions, involving cellular (clones), subcellular (resistance genes located in plasmids, transposons, and integrons), and supracellular (clonal complexes, genetic exchange communities, and microbiotic ensembles) levels. In order to study such multilevel complexity, we propose to establish an experimental epidemiology model for the transmission of antibiotic resistance with the cockroach Blatella germanica. This paper reports the results of five types of preliminary experiments with B. germanica populations that allow us to conclude that this animal is an appropriate model for experimental epidemiology: (i) the composition, transmission, and acquisition of gut microbiota and endosymbionts; (ii) the effect of different diets on gut microbiota; (iii) the effect of antibiotics on host fitness; (iv) the evaluation of the presence of antibiotic resistance genes in natural- and lab-reared populations; and (v) the preparation of plasmids harboring specific antibiotic resistance genes. The basic idea is to have populations with higher and lower antibiotic exposure, simulating the hospital and the community, respectively, and with a certain migration rate of insects between populations. In parallel, we present a computational model based on P-membrane computing that will mimic the experimental system of antibiotic resistance transmission. The proposal serves as a proof of concept for the development of more-complex population dynamics of antibiotic resistance transmission that are of interest in public health, which can help us evaluate procedures and design appropriate interventions in epidemiology.

Fitness Costs of Plasmids: a Limit to Plasmid Transmission.

Plasmids mediate the horizontal transmission of genetic information between bacteria, facilitating their adaptation to multiple environmental conditions. An especially important example of the ability of plasmids to catalyze bacterial adaptation and evolution is their instrumental role in the global spread of antibiotic resistance, which constitutes a major threat to public health. Plasmids provide bacteria with new adaptive tools, but they also entail a metabolic burden that, in the absence of selection for plasmid-encoded traits, reduces the competitiveness of the plasmid-carrying clone. Although this fitness reduction can be alleviated over time through compensatory evolution, the initial cost associated with plasmid carriage is the main constraint on the vertical and horizontal replication of these genetic elements. The fitness effects of plasmids therefore have a crucial influence on their ability to associate with new bacterial hosts and consequently on the evolution of plasmid-mediated antibiotic resistance. However, the molecular mechanisms underlying plasmid fitness cost remain poorly understood. Here, we analyze the literature in the field and examine the potential fitness effects produced by plasmids throughout their life cycle in the host bacterium. We also explore the various mechanisms evolved by plasmids and bacteria to minimize the cost entailed by these mobile genetic elements. Finally, we discuss potential future research directions in the field.

Algorithms for the selection of etiotropic therapy for bacterial infection of the upper respiratory tract in children

The article tells about the etiology of acute tonsillitis, pharyngitis, sinusitis and acute otitis media in children; there is data on the sensitivity of the bacterial pathogens of the infectious and inflammatory diseases of the respiratory tract to the most commonly prescribed antibiotics. The focus is on the global spread of antibiotic resistance of pathogens and questions of restraining its further acceleration. Approaches to the rational use of antibiotics for bacterial infections of the upper respiratory tract are discussed. Benefits of antibiotics in dispersible tablets are demonstrated. Algorithms for the primary selection of antibiotics for acute bacterial tonsillitis, pharyngitis, sinusitis and acute otitis media in children are suggested.

Subinhibitory Concentrations of Disinfectants Promote the Horizontal Transfer of Multidrug Resistance Genes within and across Genera.

The greater abundances of antibiotic resistance genes (ARGs) in point-of-use tap and reclaimed water than that in freshly treated water raise the question whether residual disinfectants in distribution systems facilitate the spread of ARGs. This study investigated three widely used disinfectants (free chlorine, chloramine, and hydrogen peroxide) on promoting ARGs transfer within Escherichia coli strains and across genera from Escherichia coli to Salmonella typhimurium. The results demonstrated that subinhibitory concentrations (lower than minimum inhibitory concentrations [MICs]) of these disinfectants, namely 0.1-1 mg/L Cl2 for free chlorine, 0.1-1 mg/L Cl2 for chloramine, and 0.24-3 mg/L H2O2, led to concentration-dependent increases in intragenera conjugative transfer by 3.4-6.4, 1.9-7.5, and 1.4-5.4 folds compared with controls, respectively. By comparison, the intergenera conjugative frequencies were slightly increased by approximately 1.4-2.3 folds compared with controls. However, exposure to disinfectants concentrations higher than MICs significantly suppressed conjugative transfer. This study provided evidence and insights into possible underlying mechanisms for enhanced conjugative transfer, which involved intracellular reactive oxygen species formation, SOS response, increased cell membrane permeability, and altered expressions of conjugation-relevant genes. The results suggest that certain oxidative chemicals, such as disinfectants, accelerate ARGs transfer and therefore justify motivations in evaluating disinfection alternatives for controlling antibiotic resistance. This study also triggers questions regarding the potential role of environmental chemicals in the global spread of antibiotic resistance.

Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping.

Bacterial plasmids are extensively involved in the rapid global spread of antibiotic resistance. We here present an assay, based on optical DNA mapping of single plasmids in nanofluidic channels, which provides detailed information about the plasmids present in a bacterial isolate. In a single experiment, we obtain the number of different plasmids in the sample, the size of each plasmid, an optical barcode that can be used to identify and trace the plasmid of interest and information about which plasmid that carries a specific resistance gene. Gene identification is done using CRISPR/Cas9 loaded with a guide-RNA (gRNA) complementary to the gene of interest that linearizes the circular plasmids at a specific location that is identified using the optical DNA maps. We demonstrate the principle on clinically relevant extended spectrum beta-lactamase (ESBL) producing isolates. We discuss how the gRNA sequence can be varied to obtain the desired information. The gRNA can either be very specific to identify a homogeneous group of genes or general to detect several groups of genes at the same time. Finally, we demonstrate an example where we use a combination of two gRNA sequences to identify carbapenemase-encoding genes in two previously not characterized clinical bacterial samples.

Superbugs and antibiotics in the newborn

Antibiotic resistance has become an urgent and global issue, with 700,000 deaths attributable to multidrug-resistance occurring each year worldwide. The overuse of antibiotics, both in animal industry and in clinical settings, and the generated selective pressure, are the main factors implicated in the emergence of resistant strains. The Centers for Disease Control and Prevention (CDC) have pointed out that more than half of hospital patients receive an antibiotic during their stay, and nearly a third receive a broad-spectrum antibiotic. In neonatal units, previous antibiotic exposure to third-generation cephalosporin and carbapenem were identified as independent risk factors for infection caused by multi-drug resistant strains. While resistant ‘superbugs’ emerge, the arsenal to fight these microorganisms is progressively shrinking, as the number of newly discovered antibiotics approved by the Food and Drug administration each year is dropping. In face of global spread of antibiotic resistance and of the limited development of new drugs, policies and rules are under study by agencies (CDC, World Health Organization) and governments, in order to: i) facilitate and foster the discovery of new antibiotic compounds; ii) develop new, alternative therapies able to potentiate or modulate the host immune response or to abrogate the resistance and virulence factors in the microorganisms; and iii) prevent the emergence of resistance through antibiotic stewardship programs, educational programs, and reduction of antibiotic use in livestock; the field of neonatal medicine will need its own, newborn-tailored, antibiotic stewardship programs to be implemented in the NICUs. Proceedings of the 11th International Workshop on Neonatology and Satellite Meetings · Cagliari (Italy) · October 26th-31st, 2015 · From the womb to the adultGuest Editors: Vassilios Fanos (Cagliari, Italy), Michele Mussap (Genoa, Italy), Antonio Del Vecchio (Bari, Italy), Bo Sun (Shanghai, China), Dorret I. Boomsma (Amsterdam, the Netherlands), Gavino Faa (Cagliari, Italy), Antonio Giordano (Philadelphia, USA)

Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India.

BackgroundInternational travel contributes to the spread of antibiotic resistant bacteria over the world. Most studies addressing travel-related changes in the faecal flora have focused on specific mobile resistance genes, or depended on culturing of individual bacterial isolates. Antibiotic resistance can, however, also spread via travellers colonized by bacteria carrying chromosomal antibiotic resistance mutations, but this has received little attention so far. Here we aimed at exploring the abundance of chromosomal quinolone resistance mutations in Escherichia communities residing in the gut of Swedish travellers, and to determine potential changes after visiting India. Sweden is a country with a comparably low degree of quinolone use and quinolone resistance, whereas the opposite is true for India.MethodsMassively parallel amplicon sequencing targeting the quinolone-resistance determining region of gyrA and parC was applied to total DNA extracted from faecal samples. Paired samples were collected from 12 Swedish medical students before and after a 4–15 week visit to India. Twelve Indian residents were included for additional comparisons. Methods known resistance mutations were common in Swedes before travel as well as in Indians, with a trend for all mutations to be more common in the Indian sub group. There was a significant increase in the abundance of the most common amino acid substitution in GyrA (S83L, from 44 to 72 %, p = 0.036) in the samples collected after return to Sweden. No other substitution, including others commonly associated with quinolone resistance (D87N in GyrA, S80I in ParC) changed significantly. The number of distinct genotypes encoded in each traveller was significantly reduced after their visit to India for both GyrA (p = 0.0020) and ParC (p = 0.0051), indicating a reduced genetic diversity, similar to that found in the Indians.ConclusionsInternational travel can alter the composition of the Escherichia communities in the faecal flora, favouring bacteria carrying certain resistance mutations, and, thereby, contributes to the global spread of antibiotic resistance. A high abundance of specific mutations in Swedish travellers before visiting India is consistent with the hypothesis that these mutation have no fitness cost even in the absence of an antibiotic selection pressure.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0574-6) contains supplementary material, which is available to authorized users.

Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA

Aminoglycosides are potent, broad spectrum, ribosome-targeting antibacterials whose clinical efficacy is seriously threatened by multiple resistance mechanisms. Here, we report the structural basis for 30S recognition by the novel plasmid-mediated aminoglycoside-resistance rRNA methyltransferase A (NpmA). These studies are supported by biochemical and functional assays that define the molecular features necessary for NpmA to catalyze m(1)A1408 modification and confer resistance. The requirement for the mature 30S as a substrate for NpmA is clearly explained by its recognition of four disparate 16S rRNA helices brought into proximity by 30S assembly. Our structure captures a "precatalytic state" in which multiple structural reorganizations orient functionally critical residues to flip A1408 from helix 44 and position it precisely in a remodeled active site for methylation. Our findings provide a new molecular framework for the activity of aminoglycoside-resistance rRNA methyltransferases that may serve as a functional paradigm for other modification enzymes acting late in 30S biogenesis.

The End of the Golden Age of Antibiotics?

The discovery of a substance with antibacterial properties was expected to permanently diminish the occurrence of bacterial infections posing a threat to health and life. Since the discovery of penicillin many new groups of antibiotics have been introduced into treatment of disease in people and animals, but their excessive and frequently unjustified use, and most importantly, incorrect dosage, have led to numerous unanticipated problems in contemporary human and veterinary medicine. The most serious of these is the continually increasing number of bacteria resistant to commonly used antibiotics, including drugs of last resort. This phenomenon currently affects all species of microbes, as well as all antibiotics. This situation necessitates strict adherence to the principles of safe and effective antibiotic therapy, regular monitoring of antibiotic resistance in bacteria isolated from animals intended for food production, as well as from pets, wild animals and their living environments, and a search for new ways of fighting bacteria. Strategies should also include efforts aimed at an international ban on the use of antibiotics as growth stimulators in animals, and the development of practices in animal husbandry that reduce the risk of emergence of antibiotic resistance. It is also essential to increase research potential in such areas as genetic improvement of animals aimed at identifying markers associated with enhanced innate resistance to pathogens; the search for new antimicrobial agents; determination of the role of bacteria occurring in animal husbandry in the transmission of antibiotic resistance to bacterial flora in humans and the associated potential risk; and other strategies for preventing and controlling infectious diseases in animals. I was inspired to write these few paragraphs by an article by Alan P. Johnson and Neil Woodford published in the Journal of Medical Microbiology (2013), 62, 499-513., entitled “Global spread of antibiotic resistance: the example of New Delhi metallo-β-lactamase (NDM)-mediated carbapenem resistance”. The information presented by the authors illustrating the speed with which resistance genes can spread all over the world confirms the alarming growth of the problem, which affects public health on a global scale and whose resolution requires international cooperation.

Overcoming and containing bacterial resistance: appropriate antibiotic use in community-acquired RTIs

The global spread of antibiotic resistance is driving the need for more thoughtful antibiotic prescribing. This paper reviews the principles of appropriate antibiotic therapy for community-acquired respiratory tract infections. Appropriate therapy options include: prescribing antibiotics only when they are beneficial to the patient; using agents that target the likely pathogens, taking into account local resistance patterns and risk factors for infection by resistant pathogens while not affecting the bowel flora and other nonrespiratory organisms; and using a dosing schedule and treatment duration that optimizes efficacy, tolerability and adherence to treatment.

Prevention of pneumococcal disease in children. Pneumococcal conjugate vaccines: their use globally could have a major impact on public health

Pneumococcal disease is a major cause of morbidity and mortality in infants and young children worldwide. New pneumococcal conjugate vaccines include 7 to 11 serotypes, which are the most common cause of paediatric disease in most parts of the world. The efficacy of a 7-valent conjugate vaccine was 97.4% (95% CI, 82.7-99.9) against invasive pneumococcal disease, and 57% (95% CI, 44-67) against otitis media, caused by vaccine serotypes. Evidence shows that the vaccine has the potential to prevent pneumonia. Pneumococcal conjugate vaccination has also been shown to reduce nasopharyngeal carriage of vaccine serotypes (particularly serotypes associated with antibiotic resistance). Thus widespread use of pneumococcal conjugate vaccine could substantially reduce the burden of invasive disease and would have the potential to control the global spread of antibiotic resistance in pneumococci. It is important that these highly effective vaccines should be made available to children in the developing countries.