Antibiotic resistance from two perspectives: man and microbe

In Vitro Probiotic and Antioxidant Potential of Lactococcus lactis subsp. cremoris LL95 and Its Effect in Mice Behaviour

The composition of intestinal microbiota is widely believed to not only affect gut health but also influence behaviour. This study aimed to evaluate the probiotic characteristics, antioxidant activity, and antidepressant- and anxiolytic-like activities of Lactococcus lactis subsp. cremoris LL95. This strain showed probiotic properties such as resistance in a simulated gastric tract model and survival at different concentrations of NaCl and bile salts. Moreover, antioxidant activity of LL95 was demonstrated through DPPH radical scavenging activity, scavenging of ABTS^•+ radical and ferric ion reducing antioxidant power (FRAP) assays. Female C57BL/6 mice received LL95 orally at a dose of 10⁹ UFC/day for 28 days. LL95 improved depressive- and anxiety-like behaviour, demonstrated by decreased immobility time in the tail suspension test and forced swim test and increased per cent of time spent in the open arms on the elevated plus maze. These findings indicate the potential antioxidant activity of LL95 and its role in behaviour, suggesting that probiotic may have therapeutic applications.

QSAR modeling: where have you been? Where are you going to?

Quantitative structure-activity relationship modeling is one of the major computational tools employed in medicinal chemistry. However, throughout its entire history it has drawn both praise and criticism concerning its reliability, limitations, successes, and failures. In this paper, we discuss (i) the development and evolution of QSAR; (ii) the current trends, unsolved problems, and pressing challenges; and (iii) several novel and emerging applications of QSAR modeling. Throughout this discussion, we provide guidelines for QSAR development, validation, and application, which are summarized in best practices for building rigorously validated and externally predictive QSAR models. We hope that this Perspective will help communications between computational and experimental chemists toward collaborative development and use of QSAR models. We also believe that the guidelines presented here will help journal editors and reviewers apply more stringent scientific standards to manuscripts reporting new QSAR studies, as well as encourage the use of high quality, validated QSARs for regulatory decision making.

Self-assembled squalenoylated penicillin bioconjugates: an original approach for the treatment of intracellular infections

We describe here new nanoparticles based on the bioconjugation of penicillin G to squalene in order to overcome severe intracellular infections by pathogen bacteria whose mechanism of resistance arises from the poor intracellular diffusion of several antibiotics. Two different squalene-penicillin G conjugates were synthesized (pH-sensitive and pH-insensitive), and their self-assembly as nanoparticles was investigated through morphology and stability studies. These nanoparticles had a size of 140 ± 10 nm (polydispersity index of 0.1) and a negative charge, and they did not display any supramolecular organization. Furthermore, they were found stable in water and in different culture medium. The cellular uptake and localization of these fluorescently labeled nanoparticles were explored on the macrophage cell line J774 by flow cytometry and confocal microscopy analysis. The squalenoylated nanoparticles were found to be cell internalized through clathrin-dependent and -independent endocytic pathways. Moreover, they induced an improved intracellular antibacterial activity on the facultative intracellular pathogen S. aureus, compared with free penicillin G, despite the absence of co-localization between the bacteria and the nanoparticles in the cells. This study suggests that the bioconjugation of an antibiotic to a squalene template could be a valuable approach for overcoming the antibiotic resistance due to intracellular bacterial infections.

Reporter phage and breath tests: emerging phenotypic assays for diagnosing active tuberculosis, antibiotic resistance, and treatment efficacy

The rapid and accurate diagnosis of active tuberculosis (TB) and its drug susceptibility remain a challenge. Phenotypic assays allow determination of antibiotic susceptibilities even if sequence data are not available or informative. We review 2 emerging diagnostic approaches, reporter phage and breath tests, both of which assay mycobacterial metabolism. The reporter phage signal, Green fluorescent protein (GFP) or β-galactosidase, indicates transcription and translation inside the recipient bacilli and its attenuation by antibiotics. Different breath tests assay, (1) exhaled antigen 85, (2) mycobacterial urease activity, and (3) detection by trained rats of disease-specific odor in sputum, have also been developed. When compared with culture, reporter phage assays shorten the time for initial diagnosis of drug susceptibility by several days. Both reporter phage and breath tests have promise as early markers to determine the efficacy of treatment. While sputum often remains smear and Mycobacterium tuberculosis DNA positive early in the course of efficacious antituberculous treatment, we predict that both breath and phage tests will rapidly become negative. If this hypothesis proves correct, phage assays and breath tests could become important surrogate markers in early bactericidal activity (EBA) studies of new antibiotics.

Optimization of antibacterial peptides by genetic algorithms and cheminformatics

Pathogens resistant to available drug therapies are a pressing global health problem. Short, cationic peptides represent a novel class of agents that have lower rates of drug resistance than derivatives of current antibiotics. Previously, we created a software system utilizing artificial neural networks that were trained on quantitative structure-activity relationship descriptors calculated for a total of 1400 synthetic peptides for which antibacterial activity was determined. Using the trained system, we correctly identified additional peptides with activity of 94% accuracy; active peptides were 47 of the top rated 50 peptides chosen from an in silico library of nearly 100,000 sequences. Here, we report a method of generating candidate peptide sequences using the heuristic evolutionary programming method of genetic algorithms (GA), which provided a large (19-fold) improvement in identification of novel antibacterial peptides. Approximately 0.50% of peptides evaluated during the GA method were classified as highly active, while only 0.026% of the nearly 100,000 sequences we previously screened were classified as highly active. A selection of these peptides was tested in vitro and activities reported here. While GA significantly improves the possibility of identifying candidate peptides, we encountered important pitfalls to this method that should be considered when using GA.

Interaction of an antimicrobial peptide with membranes: experiments and simulations with NKCS

We used Monte Carlo simulations and biophysical measurements to study the interaction of NKCS, a derivative of the antimicrobial peptide NK-2, with a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) membrane. The simulations showed that NKCS adsorbed on the membrane surface and the dominant conformation featured two amphipathic helices connected by a hinge region. We designed two mutants in the hinge to investigate the interplay between helicity and membrane affinity. Simulations with a Leu-to-Pro substitution showed that the helicity and membrane affinity of the mutant (NKCS-[LP]) decreased. Two Ala residues were added to NKCS to produce a sequence that is compatible with a continuous amphipathic helix structure (NKCS-[AA]), and the simulations showed that the mutant adsorbed on the membrane surface with a particularly high affinity. The circular dichroism spectra of the three peptides also showed that NKCS-[LP] is the least helical and NKCS-[AA] is the most. However, the activity of the peptides, determined in terms of their antimicrobial potency and influence on the temperature of the transition of the lipid to hexagonal phase, displayed a complex behavior: NKCS-[LP] was the least potent and had the smallest influence on the transition temperature, and NKCS was the most potent and had the largest effect on the temperature.

Reduced susceptibility to amoxicillin of oral streptococci following amoxicillin exposure

As antibiotic pressure often triggers bacterial resistance, the use of short-duration therapies is increasingly recommended. The objective of the present study was to evaluate both the clinical efficiency and the impact on oral streptococci of a 3 day versus a 7 day amoxicillin therapy for odontogenic infection requiring tooth extraction. On day 0, patients were randomly assigned to a 3 day or 7 day amoxicillin treatment. The tooth was extracted on day 2 and the post-operative follow-up was carried out on day 9. Oral flora was collected on days 0, 9 and 30, and the susceptibility of the streptococci to amoxicillin was determined. The results showed that treatment with amoxicillin for 3 or 7 days had a similar clinical efficiency, and also induced similar selection of oral streptococci with reduced susceptibility to amoxicillin, suggesting that the selection of strains with reduced susceptibility to amoxicillin is a rapid phenomenon, appearing even with short-duration therapies.

Identification of novel antibacterial peptides by chemoinformatics and machine learning

The rise of antibiotic resistant pathogens is one of the most pressing global health issues. Discovery of new classes of antibiotics has not kept pace; new agents often suffer from cross-resistance to existing agents of similar structure. Short, cationic peptides with antimicrobial activity are essential to the host defenses of many organisms and represent a promising new class of antimicrobials. This paper reports the successful in silico screening for potent antibiotic peptides using a combination of QSAR and machine learning techniques. On the basis of initial high-throughput measurements of activity of over 1400 random peptides, artificial neural network models were built using QSAR descriptors and subsequently used to screen an in silico library of approximately 100,000 peptides. In vitro validation of the modeling showed 94% accuracy in identifying highly active peptides. The best peptides identified through screening were found to have activities comparable or superior to those of four conventional antibiotics and superior to the peptide most advanced in clinical development against a broad array of multiresistant human pathogens.

An enhanced miniaturized assay for antimicrobial prospecting

Bioprospecting for novel antimicrobials increasingly relies on extremely small samples unsuitable for conventional bulk extraction and assay. We developed a microtitre plate assay for minimal amounts of test materials which is rapid, extremely sensitive, allows time-course analysis and reduces false negatives. Developed for the analyses of antimicrobial sensitivity and resistance, the technique is appropriate for assays where source materials are scarce.

Antibiotic survey ofLactococcus lactisstrains to six antibiotics by Etest, and establishment of new susceptibility-resistance cut-off values

In order to establish cut-off values forLactococcus lactisto six antibiotics to distinguish susceptible and intrinsically resistant strains from those having acquired resistances, the minimum inhibitory concentration (MIC) of tetracycline, erythromycin, clindamycin, streptomycin, chloramphenicol and vancomycin was determined in 93 differentLc. lactisstrains using the Etest. These bacterial strains were originally isolated from dairy and animal sources in widely separated geographical locations. Cut-offs were defined on the basis of the distribution of the MICs frequency of the studied antibiotics, which in the absence of acquired determinants should approach to a normal statistical distribution. In general, the new cut-off values proposed in this study are higher than previously defined (European Commission, 2005. The EFSA Journal 223, 1–12). Based on these new values, all the strains tested were susceptible to erythromycin, chloramphenicol and vancomycin, and 79 susceptible to all six antibiotics. However, 11 strains (around 12%) were considered resistant to tetracycline (six of which had been identified after screening of a large collection of lactococci strains for tetracycline resistance) and five (5·4%) resistant to streptomycin. Of these, two fish isolates proved to be resistance to both tetracycline and streptomycin. From the tetracycline resistant strains,tet(M) and mosaictet(L/S) genes were amplified by PCR, demonstrating they harboured acquired antibiotic resistance determinants.

AMPer: a database and an automated discovery tool for antimicrobial peptides

MOTIVATION

Increasing antibiotics resistance in human pathogens represents a pressing public health issue worldwide for which novel antibiotic therapies based on antimicrobial peptides (AMPs) may offer one possible solution. In the current study, we utilized publicly available data on AMPs to construct hidden Markov models (HMMs) that enable recognition of individual classes of antimicrobials peptides (such as defensins, cathelicidins, cecropins, etc.) with up to 99% accuracy and can be used for discovering novel AMP candidates.

RESULTS

HMM models for both mature peptides and propeptides were constructed. A total of 146 models for mature peptides and 40 for propeptides have been developed for individual AMP classes. These were created by clustering and analyzing AMP sequences available in the public sources and by consequent iterative scanning of the Swiss-Prot database for previously unknown gene-coded AMPs. As a result, an additional 229 additional AMPs have been identified from Swiss-Prot, and all but 34 could be associated with known antimicrobial activities according to the literature. The final set of 1045 mature peptides and 253 propeptides have been organized into the open-source AMPer database.

AVAILABILITY

The developed HMM-based tools and AMP sequences can be accessed through the AMPer resource at http://www.cnbi2.com/cgi-bin/amp.pl

In vitro antimicrobial and resistance-modifying activities of aqueous crude khat extracts against oral microorganisms

OBJECTIVES

To assess antimicrobial activities of aqueous crude khat (Catha edulis) extracts against a panel of oral microorganisms and to test their ability to modify bacterial resistance to tetracycline and penicillin in vitro.

DESIGN

Lyophilized aqueous extracts were prepared from three khat cultivars. The agar dilution method of the NCCLS was used to test the extracts, at concentrations of 20-1.25 mg/ml, against 33 oral strains. MIC was defined as the lowest concentration at which there was no visible growth. Slight growth was defined as marked growth reduction (MGR). The E-test was used to determine the MICs of tetracycline and penicillin-G for three resistant strains in absence and presence of a sub-MIC of the khat extracts (5mg/ml).

RESULTS

Eighteen strains (55%) were sensitive to the extracts (MICs 5-20 mg/ml). Most of these were periodontal pathogens with Porphyromonas gingivalis and Tannerella forsythensis being the most susceptible (MIC 5-10mg/ml). Veillonella parvula, Actinomyces israelii and some streptococci were not sensitive. Except for Lactobacillus acidophilus that showed MGR at 1mg/ml, cariogenic species were neither sensitive. The extracts were active against Streptococcus pyogenes (MIC 10-20 mg/ml) but not against Candida albicans and Staphylococcus aureus. The presence of the khat extracts at a sub-MIC resulted in a 2-4-fold potentiation of the tested antibiotics against the resistant strains.

CONCLUSIONS

Khat has water-soluble constituents possessing selective antibacterial activity against oral bacteria. There is preliminary evidence for presence of an antibiotic resistance-modifying component. Further investigation is needed to identify the active components and assess their clinical relevance.

Rifaximin, a poorly absorbed antibiotic: pharmacology and clinical potential

Rifaximin (4-deoxy-4'-methylpyrido[1',2'-1,2]imidazo- [5,4-c]-rifamycin SV) is a synthetic antibiotic designed to modify the parent compound, rifamycin, in order to achieve low gastrointestinal (GI) absorption while retaining good antibacterial activity. Both experimental and clinical pharmacology clearly show that this compound is a nonsystemic antibiotic with a broad spectrum of antibacterial action covering Gram-positive and Gram-negative organisms, both aerobes and anaerobes. Being virtually nonabsorbed, its bioavailability within the GI tract is rather high with intraluminal and fecal drug concentrations that largely exceed the minimal inhibitory concentration values observed in vitro against a wide range of pathogenic organisms. The GI tract represents, therefore, the primary therapeutic target and GI infections the main indication. The appreciation of the pathogenic role of gut bacteria in several organic and functional GI diseases has increasingly broadened its clinical use, which is now extended to hepatic encephalopathy, small intestine bacterial overgrowth, inflammatory bowel disease and colonic diverticular disease. Potential indications include the irritable bowel syndrome and chronic constipation, Clostridium difficile infection and bowel preparation before colorectal surgery. Because of its antibacterial activity against the microorganism and the lack of strains with primary resistance, some preliminary studies have explored the rifaximin potential for Helicobacter pylori eradication. Oral administration of this drug, by getting rid of enteric bacteria, could also be employed to achieve selective bowel decontamination in acute pancreatitis, liver cirrhosis (thus preventing spontaneous bacterial peritonitis) and nonsteroidal anti-inflammatory drug (NSAID) use (lessening in that way NSAID enteropathy). This antibiotic has, therefore, little value outside the enteric area and this will minimize both antimicrobial resistance and systemic adverse events. Indeed, the drug proved to be safe in all patient populations, including young children. Although rifaximin has stood the test of time, it still attracts the attention of both basic scientists and clinicians. As a matter of fact, with the advancement of the knowledge on microbial-gut interactions in health and disease novel indications and new drug regimens are being explored. Besides widening the clinical use, the research on rifaximin is also focused on the synthesis of new derivatives and on the development of original formulations designed to expand the spectrum of its clinical use.

MRSA – what is it, and how do we deal with the problem?

Methicillin-resistant Staphylococcus aureus (MRSA) has become a serious nosocomial pathogen, and more recent reports in the scientific literature underscore the potential issues with emerging community-MRSA. MRSA is reported to be involved in > 50% of hospital S. aureus infections, more in the intensive care unit (ICU) than the non-ICU, and increases in multi-drug resistant MRSA and increasingly virulent MRSA have been reported. Together with its broad-based beta-lactam resistance, MRSA often possesses a multi-drug resistance genotype, including cephalosporins, aminoglycosides, fluoroquinolones, and macrolide resistances. MRSA has now emerged as the predominant nosocomial Gram-positive pathogen, and it has a high rate of morbidity and mortality. Action must be taken to contain and eradicate MRSA through a combination of infection control, the development of novel anti-MRSA agents, development of vaccines and other non-traditional approaches of intervention.

MRSA: status and prospects for therapy? An evaluation of key papers on the topic of MRSA and antibiotic resistance

Methicillin-resistant Staphylococcus aureus (MRSA) is a serious nosocomial pathogen, and a related community-sourced MRSA is emerging. MRSA has evolved to become the major S. aureus phenotype in the hospital, emerging from just 30 to over 60% of the S. aureus population over the past 15 years. Together with its beta-lactam resistance, MRSA possesses multi-drug resistance genotype, including quinolones, macrolides and sulfonamides. MRSA has now emerged as the predominant nosocomial Gram-positive pathogen, and it has a high rate of mortality. Action must be taken to contain and eradicate MRSA through a combination of infection control and the development of novel anti-MRSA agents and vaccines.

LC–MS/MS determination in rabbit plasma of the main photoproduct of RLP068/Cl, a cationic sensitizer proposed for photodynamic therapy (PDT) of microbial infections

The clinical development of a sensitizer for photodynamic therapy (PDT) requires the structural identification of the photoproducts and their quantification in biological fluids and tissues. We describe the LC-MS identification of the most important photoproducts of a cationic phthalocyanine sensitizer (RLP068/Cl) and a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the determination of the main photoproduct (the cationic phthalimide derivative 3-[(1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl)oxy]-N,N,N-trimethylbenzenaminium chloride) in rabbit plasma. The tri-deuterated product was used as co-eluting internal standard. The cationic photoproduct was isolated from plasma samples by protein precipitation with perchloric acid in methanol (7%, v/v). HPLC step was performed on a Phenomenex Synergi Hydro-RP column (20 mm x 2.0 mm, 2 microm particles) with a mobile phase of 0.5% (v/v) aqueous TFA/methanol (85:15, v/v). Flow rate was 0.2 mL/min and 40 microL injection were performed. Run time was 10 min. Detection was achieved by means of a Bruker Esquire 3000+ ion trap mass spectrometer equipped with an ESI source working in positive mode. A multiple reaction monitoring method following the transitions 297.1 --> 282.1 for the analyte and 300.1 --> 282.1+285.1 for the internal standard was used. The analytical method was validated over the concentration range 0.46-91.2 ng/mL and lower limits of detection (LLOD) and quantification (LLOQ) respectively of 0.2 and 0.5 ng/mL were found.