How antibiotics cause antibiotic resistance

Genome-based assessment of antimicrobial resistance reveals the lineage specificity of resistance and resistance gene profiles in Riemerella anatipestifer from China

Riemerella anatipestifer (R. anatipestifer) is an important pathogen that causes severe systemic infections in domestic ducks, resulting in substantial economic losses for China's waterfowl industry. Controlling R. anatipestifer with antibiotics is extremely challenging due to its multidrug resistance. Notably, large-scale studies on antimicrobial resistance (AMR) and the corresponding genetic determinants in R. anatipestifer remain scarce. To solve this dilemma, more than 400 nonredundant R. anatipestifer isolates collected from 22 provinces in China between 1994 and 2021 were subjected to broth dilution antibiotic susceptibility assays, and their resistance-associated genetic determinants were characterized by whole-genome sequencing. While over 90% of the isolates was resistant to sulfamethoxazole, kanamycin, gentamicin, ofloxacin, norfloxacin, and trimethoprim, 88.48% of the isolates was resistant to the last-resort drug (tigecycline). Notably, R. anatipestifer resistance to oxacillin, norfloxacin, ofloxacin, and tetracycline was found to increase relatively over time. Genome-wide analysis revealed the alarmingly high prevalence of blaOXA-like (93.05%) and tet(X) (90.64%) genes and the uneven distribution of resistance genes among lineages. Overall, this study reveals a serious AMR situation regarding R. anatipestifer in China, with a high prevalence and high diversity of antimicrobial resistance genes, providing important data for the rational use of antibiotics in veterinary practice.IMPORTANCERiemerella anatipestifer (R. anatipestifer), an important waterfowl pathogen, has caused substantial economic losses worldwide, especially in China. Antimicrobial resistance (AMR) is a major challenge in controlling this pathogen. Although a few studies have reported antimicrobial resistance in R. anatipestifer, comprehensive data remain a gap. This study aims to address the lack of information on R. anatipestifer AMR and its genetic basis. By analyzing more than 400 isolates collected over two decades, this study reveals alarming levels of resistance to several antibiotics, including drugs of last resort. The study also revealed the lineage-specificity of resistance profiles and resistance gene profiles. Overall, this study provides new insights and updated data support for understanding AMR and its genetic determinants in R. anatipestifer.

Enhancing the antimicrobial activity of silver nanoparticles against ESKAPE bacteria and emerging fungal pathogens by using tea extracts

The sale of antibiotics and antifungals has skyrocketed since 2020. The increasing threat of pathogens like ESKAPE bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), which are effective in evading existing antibiotics, and yeasts like Candida auris or Cryptococcus neoformans is pressing to develop efficient antimicrobial alternatives. Nanoparticles, especially silver nanoparticles (AgNPs), are believed to be promising candidates to supplement or even replace antibiotics in some applications. Here, we propose a way to increase the antimicrobial efficiency of silver nanoparticles by using tea extracts (black, green, or red) for their synthesis. This allows for using lower concentrations of nanoparticles and obtaining the antimicrobial effect in a short time. We found that AgNPs synthesized using green tea extract (G-TeaNPs) are the most effective, causing approximately 80% bacterial cell death in Gram-negative bacteria within only 3 hours at a concentration of 0.1 mg mL-1, which is better than antibiotics. Ampicillin at the same concentration (0.1 mg mL-1) and within the same duration (3 h) causes only up to 40% decrease in the number of S. aureus and E. cloacae cells (non-resistant strains). The tested silver nanoparticles also have antifungal properties and are effective against C. auris and C. neoformans, which are difficult to eradicate using other means. We established that silver nanoparticles synthesized with tea extracts have higher antibacterial properties than silver nanoparticles alone. Such formulations using inexpensive tea extracts and lower concentrations of silver nanoparticles show a promising solution to fight various pathogens.

Copper and nanostructured anatase rutile and carbon coatings induce adaptive antibiotic resistance

Contaminated surfaces are vehicles for the spread of infectious disease-causing microorganisms. A strategy to prevent their spread is applying antimicrobial coatings to surfaces. Both nanostructured anatase rutile and carbon (NsARC), a TiO₂ formulation, and copper are examples of antimicrobial agents that are used in making or coating door handles and similar surfaces, to reduce microbial loads. Antimicrobial surfaces have been extensively tested for antimicrobial activity but not sublethal effects, such as exposure-associated multiple antibiotic resistance phenotypes usually caused by induction of efflux pump genes. The possibility of NsARC and copper inducing indicative efflux pump pathways was investigated by monitoring the expression of mScarlet fluorescent protein (FP) in two reporter strains of Escherichia coli. There was an increase in the expression of FP in the reporter strains exposed to NsARC and copper relative to the inert control composed of stainless steel. Furthermore we tested E. coli and Staphylococcus aureus following 8 h of exposure to NsARC for changes in resistance to selected antibiotics. E. coli that were exposed to NsARC became more susceptible to kanamycin but there was no significant change in susceptibility of S. aureus to any tested antibiotics. These findings suggests that even though NsARC and copper are antimicrobial, they also have some potential to cause unintended phenotypes.

New antimicrobial material NsARC based on TiO₂ compared to copper.

Both NsARC and copper induce efflux pump gene transcription.

Species-specific changes in antibiotic resistance from exposure to antimicrobial surface coatings.

Evolution of Antibiotic Resistance in Surrogates of Francisella tularensis (LVS and Francisella novicida): Effects on Biofilm Formation and Fitness

Francisella tularensis, the causative agent of tularemia, is capable of causing disease in a multitude of mammals and remains a formidable human pathogen due to a high morbidity, low infectious dose, lack of a FDA approved vaccine, and ease of aerosolization. For these reasons, there is concern over the use of F. tularensis as a biological weapon, and, therefore, it has been classified as a Tier 1 select agent. Fluoroquinolones and aminoglycosides often serve as the first line of defense for treatment of tularemia. However, high levels of resistance to these antibiotics has been observed in gram-negative bacteria in recent years, and naturally derived resistant Francisella strains have been described in the literature. The acquisition of antibiotic resistance, either natural or engineered, presents a challenge for the development of medical countermeasures. In this study, we generated a surrogate panel of antibiotic resistant F. novicida and Live Vaccine Strain (LVS) by selection in the presence of antibiotics and characterized their growth, biofilm capacity, and fitness. These experiments were carried out in an effort to (1) assess the fitness of resistant strains; and (2) identify new targets to investigate for the development of vaccines or therapeutics. All strains exhibited a high level of resistance to either ciprofloxacin or streptomycin, a fluoroquinolone and aminoglycoside, respectively. Whole genome sequencing of this panel revealed both on-pathway and off-pathway mutations, with more mutations arising in LVS. For F. novicida, we observed decreased biofilm formation for all ciprofloxacin resistant strains compared to wild-type, while streptomycin resistant isolates were unaffected in biofilm capacity. The fitness of representative antibiotic resistant strains was assessed in vitro in murine macrophage-like cell lines, and also in vivo in a murine model of pneumonic infection. These experiments revealed that mutations obtained by these methods led to nearly all ciprofloxacin resistant Francisella strains tested being completely attenuated while mild attenuation was observed in streptomycin resistant strains. This study is one of the few to examine the link between acquired antibiotic resistance and fitness in Francisella spp., as well as enable the discovery of new targets for medical countermeasure development.

What drives changes in the virulence and antibiotic resistance of Vibrio harveyi in the South China Sea?

To understand the driving environmental factors in changes of bacterial virulence and antibiotic resistance, we determined the prevalence, antibiotic resistance and antibiotic resistance and virulence genes of Vibrio harveyi isolated from diseased marine fish in south coastal China. We isolated 2, 52 and 53 V. harveyi strains from Fujian, Hainan and Guangdong, respectively, and identified them by multilocus sequence analysis of 16S rRNA-toxR_Vh -rctB. Nine typical virulence genes were represented at a higher average in Hainan (7.39 ± 0.24) than in Guangdong (6.91 ± 0.28). Five atypical virulence genes were detected in some isolates. In particular, flaC and vvh were detected in more than 60% of isolates. Their average number was significantly higher in Hainan (2.30 ± 0.20) than in Guangdong (1.70 ± 0.10). Multidrug resistance was widespread with an average resistance to 4.57 ± 0.18 of 15 antibiotics. Both the average number of antibiotic resistance and antibiotic resistance genes were higher in Hainan (5.25 ± 0.27 and 1.11 ± 0.15, respectively) than in Guangdong (3.87 ± 0.21 and 0.75 ± 0.10, respectively). This study demonstrated that there were more virulence genes and greater drug resistance in Hainan than in Guangdong, suggesting that warmer temperature and antibiotics pollutants probably enhance antibiotic resistance and bacterial infection.

Prevalence of antibiotic-resistant Escherichia coli isolated from urban and agricultural streams in Canterbury, New Zealand

Baseline studies are needed to identify environmental reservoirs of non-pathogenic but associating microbiota or pathogenic bacteria that are resistant to antibiotics and to inform safe use of freshwater ecosystems in urban and agricultural settings. Mesophilic bacteria and Escherichia coli were quantified and isolated from water and sediments of two rivers, one in an urban and one in an agricultural area near Christchurch, New Zealand. Resistance of E. coli to one or more of nine different antibiotics was determined. Additionally, selected strains were tested for conjugative transfer of resistances. Despite having similar concentrations of mesophilic bacteria and E. coli, the rivers differed in numbers of antibiotic-resistant E. coli isolates. Fully antibiotic-susceptible and -resistant strains coexist in the two freshwater ecosystems. This study was the first phase of antibiotic resistance profiling in an urban setting and an intensifying dairy agroecosystem. Antibiotic-resistant E. coli may pose different ingestion and contact risks than do susceptible E. coli. This difference cannot be seen in population counts alone. This is an important finding for human health assessments of freshwater systems, particularly where recreational uses occur downstream.

Expression in Escherichia coli of novel recombinant hybrid antimicrobial peptide AL32-P113 with enhanced antimicrobial activity in vitro

Antibiotic-resistant pathogens have become a major public health problem worldwide. New discoveries and strategies as regards antibiotic drug development are urgently in need for curing infected patients. Antimicrobial peptides (AMPs) are short cationic peptides that play important roles in innate immune system with a broad spectrum of antimicrobial activity. Recently, hybrid AMPs have been reported to increase antimicrobial activity, stability, and in vivo half-life. In the present study, a gene encoding for AL32-P113 hybrid peptide consisting of two truncated active forms of human LL-37 and histatin-5 (Hst-5) was commercially constructed, cloned into pTXB-1 commercial plasmid, and expressed in E. coli BL21 (DE3). To increase the yield of target protein expression, IPTG concentration, time and temperature were optimized. The results indicate that AL32-P113-intein fusion protein with 33.7 kDa was expressed mostly in inclusion form and estimated to be 20% of the total protein. After chitin affinity purification, 5.7-kDa of AL32-P113 peptide was separated with an average concentration of 12.1 mg per litre of bacterial culture and over 86% purity. The minimum inhibitory concentration (MIC) was evaluated for antimicrobial activity determination of recombinant AL32-P113 compared to synthetic peptides, LL-37, Hst-5, and L31-P113. The results implied that both hybrid peptides exhibited potent antimicrobial activity against gram-negative bacteria and yeast cells whereas the L31-P113 peptide possessed approximately four times greater antimicrobial activity in gram-positive bacteria than parent LL-37. An increasing of undesired hemolysis of these hybrid peptides toward human red cells was also observed when red blood cell hemolytic assay was performed. Several factors including charge and secondary structure predicted by public software were utilized for explanation of the antimicrobial potency of both hybrid peptides. This study proved that hybrid peptides show broader and more potent antimicrobial ability against pathogens and they could be applied as a therapeutic approach for topical treatment of microbial infection in the future.

Herbicide ingredients change Salmonella enterica sv. Typhimurium and Escherichia coli antibiotic responses

Herbicides are frequently released into both rural and urban environments. Commercial herbicide formulations induce adaptive changes in the way bacteria respond to antibiotics. Salmonella enterica sv. Typhimurium and Escherichia coli were exposed to common co-formulants of formulations, and S. enterica sv. Typhimurium was exposed to active ingredients dicamba, 2,4-D and glyphosate to determine what ingredients of the commercial formulations caused this effect. Co-formulants Tween80 and carboxymethyl cellulose induced changes in response, but the pattern of the responses differed from the active ingredients, and effect sizes were smaller. A commercial wetting agent did not affect antibiotic responses. Active ingredients induced changes in antibiotic responses similar to those caused by complete formulations. This occurred at or below recommended application concentrations. Targeted deletion of efflux pump genes largely neutralized the adaptive response in the cases of increased survival in antibiotics, indicating that the biochemistry of induced resistance was the same for formulations and specific ingredients. We found that glyphosate, dicamba, and 2,4-D, as well as co-formulants in commercial herbicides, induced a change in susceptibility of the potentially pathogenic bacteria E. coli and S. enterica to multiple antibiotics. This was measured using the efficiency of plating (EOP), the relative survival of the bacteria when exposed to herbicide and antibiotic, or just antibiotic, compared to survival on permissive media. This work will help to inform the use of non-medicinal chemical agents that induce changes in antibiotic responses.

Sublethal exposure to commercial formulations of the herbicides dicamba, 2,4-dichlorophenoxyacetic acid, and glyphosate cause changes in antibiotic susceptibility in Escherichia coli and Salmonella enterica serovar Typhimurium

Biocides, such as herbicides, are routinely tested for toxicity but not for sublethal effects on microbes. Many biocides are known to induce an adaptive multiple-antibiotic resistance phenotype. This can be due to either an increase in the expression of efflux pumps, a reduced synthesis of outer membrane porins, or both. Exposures of Escherichia coli and Salmonella enterica serovar Typhimurium to commercial formulations of three herbicides-dicamba (Kamba), 2,4-dichlorophenoxyacetic acid (2,4-D), and glyphosate (Roundup)-were found to induce a changed response to antibiotics. Killing curves in the presence and absence of sublethal herbicide concentrations showed that the directions and the magnitudes of responses varied by herbicide, antibiotic, and species. When induced, MICs of antibiotics of five different classes changed up to 6-fold. In some cases the MIC increased, and in others it decreased. Herbicide concentrations needed to invoke the maximal response were above current food maximum residue levels but within application levels for all herbicides. Compounds that could cause induction had additive effects in combination. The role of soxS, an inducer of the AcrAB efflux pump, was tested in β-galactosidase assays with soxS-lacZ fusion strains of E. coli. Dicamba was a moderate inducer of the sox regulon. Growth assays with Phe-Arg β-naphtylamide (PAβN), an efflux pump inhibitor, confirmed a significant role of efflux in the increased tolerance of E. coli to chloramphenicol in the presence of dicamba and to kanamycin in the presence of glyphosate. Pathways of exposure with relevance to the health of humans, domestic animals, and critical insects are discussed.

IMPORTANCE

Increasingly common chemicals used in agriculture, domestic gardens, and public places can induce a multiple-antibiotic resistance phenotype in potential pathogens. The effect occurs upon simultaneous exposure to antibiotics and is faster than the lethal effect of antibiotics. The magnitude of the induced response may undermine antibiotic therapy and substantially increase the probability of spontaneous mutation to higher levels of resistance. The combination of high use of both herbicides and antibiotics in proximity to farm animals and important insects, such as honeybees, might also compromise their therapeutic effects and drive greater use of antibiotics. To address the crisis of antibiotic resistance requires broadening our view of environmental contributors to the evolution of resistance.

Application of a phosphite dehydrogenase gene as a novel dominant selection marker for yeasts

The use of antibiotic resistance markers in the commercial application of genetically modified microorganisms is limited due to restrictions on the release of antibiotics and their resistance genes to the environment. To avoid contamination by other microorganisms, the development of a dominant selection marker with low environmental risks is still needed. Here we demonstrated a new selection system for Schizosaccharomyces pombe and Saccharomyces cerevisiae using a bacterial phosphite dehydrogenase gene (ptxD). A Sz. pombe transformant carrying ptxD under a strong promoter or on a multicopy plasmid grew on a minimal medium containing phosphite (Pt) as a sole source of phosphorus. To adapt this system to S. cerevisiae strains, codon optimization of ptxD was necessary. The codon-optimized ptxD system appeared effective in not only laboratorial but also industrial S. cerevisiae strains that are diploid or polyploid. Since Pt is a safe and inexpensive chemical, ptxD could be used as a novel dominant selection marker applicable on an industrial scale.

Human lactoferrin increases Helicobacter pylori internalisation into AGS cells

Helicobacter pylori has high global infection rates and can cause other undesirable clinical manifestations such as duodenal ulcer (DU) and gastric cancer (GC). Frequencies of re-infection after therapeutic clearance and rates of DU versus GC vary geographically and differ markedly between developed and developing countries, which suggests additional factors may be involved. The possibility that, in vivo, lactoferrin (Lf) may play a subtle role in modulating micronutrient availability or bacterial internalisation with implications for disease etiology is considered. Lf is an iron binding protein produced in mammals that has antimicrobial and immunomodulatory properties. Some bacteria that regularly colonise mammalian hosts have adapted to living in high Lf environments and we investigated if this included the gastric pathogen H. pylori. We found that H. pylori was able to use iron from fully iron-saturated human Lf (hLf) whereas partially iron-saturated hLf (apo) did not increase H. pylori growth. Instead, apo-hLf increased adherence to and internalisation of bacteria into cultured epithelial cells. By increasing internalisation, we speculate that apo-human lactoferrin may contribute to H. pylori's ability to persistence in the human stomach, an observation that potentially has implications for the risk of H. pylori-associated disease.

Comparative genomic assessment of novel broad-spectrum targets for antibacterial drugs

Single and multiple resistance to antibacterial drugs currently in use is spreading, since they act against only a very small number of molecular targets; finding novel targets for anti-infectives is therefore of great importance. All protein sequences from three pathogens (Staphylococcus aureus, Mycobacterium tuberculosis and Escherichia coli O157:H7 EDL993) were assessed via comparative genomics methods for their suitability as antibacterial targets according to a number of criteria, including the essentiality of the protein, its level of sequence conservation, and its distribution in pathogens, bacteria and eukaryotes (especially humans). Each protein was scored and ranked based on weighted variants of these criteria in order to prioritize proteins as potential novel broad-spectrum targets for antibacterial drugs. A number of proteins proved to score highly in all three species and were robust to variations in the scoring system used. Sensitivity analysis indicated the quantitative contribution of each metric to the overall score. After further analysis of these targets, tRNA methyltransferase (trmD) and translation initiation factor IF-1 (infA) emerged as potential and novel antimicrobial targets very worthy of further investigation. The scoring strategy used might be of value in other areas of post-genomic drug discovery.

Allele fixation in a dynamic metapopulation: founder effects vs refuge effects

The fixation of mutant alleles has been studied with models assuming various spatial population structures. In these models, the structure of the metapopulation that we call the "landscape" (number, size and connectivity of subpopulations) is often static. However, natural populations are subject to repetitive population size variations, fragmentation and secondary contacts at different spatiotemporal scales due to geological, climatic and ecological processes. In this paper, we examine how such dynamic landscapes can alter mutant fixation probability and time to fixation. We consider three stochastic landscape dynamics: (i) the population is subject to repetitive bottlenecks, (ii) to the repeated alternation of fragmentation and fusion of demes with a constant population carrying capacity, (iii) idem with a variable carrying capacity. We show by deriving a variance, a coalescent and a harmonic mean population effective size, and with simulations that these landscape dynamics generate repetitive founder effects which counteract selection, thereby decreasing the fixation probability of an advantageous mutant but accelerate fixation when it occurs. For models (ii) and (iii), we also highlight an antagonistic "refuge effect" which can strongly delay mutant fixation. The predominance of either founder effects or refuge effects determines the time to fixation and mainly depends on the characteristic time scales of the landscape dynamics.

Selective solid-phase extraction of amoxicillin and cephalexin from urine samples using a molecularly imprinted polymer

In this paper we describe, for the first time, a molecularly imprinted polymer (MIP) for the antibiotic amoxicillin (AMX), synthesised by a noncovalent molecular imprinting approach and used to extract AMX selectively from urine samples. The MIP was applied as a molecularly selective sorbent in molecularly imprinted SPE (MISPE) in an off-line mode, where it showed useful cross-selectivity for a structurally related antibiotic, cephalexin (CPX). By using a MISPE protocol, the MIP was able to selectively extract both AMX and CFX from 5 mL of water spiked with 10 mg/L with recoveries of 75 and 78% for AMX and CFX, respectively. When applied to real samples (urine) at clinically relevant concentrations, recoveries from 2 mL of human urine spiked with 20 mg/L decreased slightly to 65 and 63% for AMX and CFX, respectively. To demonstrate further the selectivity of the MIP obtained, a comparison with commercially available SPE cartridges was performed. Improvements in the retention of both AMX and CFX on the MIP were obtained relative to the commercially available cartridges, and the MISPE extracts were considerably cleaner, due to molecularly selective analyte binding by the MIP.

The fixation of locally beneficial alleles in a metapopulation

Extinction, recolonization, and local adaptation are common in natural spatially structured populations. Understanding their effect upon genetic variation is important for systems such as genetically modified organism management or avoidance of drug resistance. Theoretical studies on the effect of extinction and recolonization upon genetic variance started appearing in the 1970s, but the role of local adaptation still has no good theoretical basis. Here we develop a model of a haploid species in a metapopulation in which a locally adapted beneficial allele is introduced. We study the effect of different spatial patterns of local adaptation, and different metapopulation dynamics, upon the fixation probability of the beneficial allele. Controlling for the average selection pressure, we find that a small area of positive selection can significantly increase the global probability of fixation. However, local adaptation becomes less important as extinction rate increases. Deme extinction and recolonization have a spatial smoothing effect that effectively reduces spatial variation in fitness.

The antibiotic resistome: the nexus of chemical and genetic diversity

Over the millennia, microorganisms have evolved evasion strategies to overcome a myriad of chemical and environmental challenges, including antimicrobial drugs. Even before the first clinical use of antibiotics more than 60 years ago, resistant organisms had been isolated. Moreover, the potential problem of the widespread distribution of antibiotic resistant bacteria was recognized by scientists and healthcare specialists from the initial use of these drugs. Why is resistance inevitable and where does it come from? Understanding the molecular diversity that underlies resistance will inform our use of these drugs and guide efforts to develop new efficacious antibiotics.

Environment arrays: a possible approach for predicting changes in waterborne bacterial disease potential

Current molecular techniques for identifying bacteria in water have proven useful, but they are not reliably predictive of impending disease outbreaks. Genomics-based approaches will help to detect the presence of pathogens quickly and well before they grow into a population that poses a risk to public health. We suggest that genomics is only one component of the toolbox that will be needed to identify emerging waterborne threats. We propose a methodology beyond genomics, based on activity in the mobile genome. This approach makes use of a new device called an environment array. The array will depend upon the same research necessary for genomics-based detection, but will not require an a priori knowledge of virulence genes. Environment arrays are assembled from molecular profiles of the infectious elements that transfer between bacteria. The advantage of the array is that it monitors the activity of the mobile genome, rather than the presence of particular DNA sequences. Environmental arrays should thus be many times more sensitive than traditional hybridization or PCR-based techniques that target already-known DNA sequences. Mobile elements are known to respond to new environmental conditions that may correlate with a chemical contamination or the bloom of bacterial pathogens, potentially allowing for a much broader application in detecting unknown or unanticipated biological and chemical contaminants.

Static recipient cells as reservoirs of antibiotic resistance during antibiotic therapy

How does taking the full course of antibiotics prevent antibiotic resistant bacteria establishing in patients? We address this question by testing the possibility that horizontal/lateral gene transfer (HGT) is critical for the accumulation of the antibiotic-resistance phenotype while bacteria are under antibiotic stress. Most antibiotics prevent bacterial reproduction, some by preventing de novo gene expression. Nevertheless, in some cases and at some concentrations, the effects of most antibiotics on gene expression may not be irreversible. If the stress is removed before the bacteria are cleared from the patients by normal turnover, gene expression restarts, converting the residual population to phenotypic resistance. Using mathematical models we investigate how static recipients of resistance genes carried by plasmids accumulate resistance genes, and how specifically an environment cycling between presence and absence of the antibiotic uniquely favors the evolution of horizontally mobile resistance genes. We found that the presence of static recipients can substantially increase the persistence of the plasmid and that this effect is most pronounced when the cost of carriage of the plasmid decreases the cell's growth rate by as much as a half or more. In addition, plasmid persistence can be enhanced even when conjugation rates are as low as half the rate required for the plasmid to persist as a parasite on its own.

Kinetic properties of four plasmid-mediated AmpC beta-lactamases

The heterologous production in Escherichia coli, the purification, and the kinetic characterization of four plasmid-encoded class C beta-lactamases (ACT-1, MIR-1, CMY-2, and CMY-1) were performed. Except for their instability, these enzymes are very similar to the known chromosomally encoded AmpC beta-lactamases. Their kinetic parameters did not show major differences from those obtained for the corresponding chromosomal enzymes. However, the K(m) values of CMY-2 for cefuroxime, cefotaxime, and oxacillin were significantly decreased compared to those of the chromosomal AmpC enzymes. Finally, the susceptibility patterns of different E. coli hosts producing a plasmid- or a chromosome-encoded class C enzyme toward beta-lactam antibiotics are mainly due to the overproduction of the beta-lactamase in the periplasmic space of the bacteria rather than to a specific catalytic profile of the plasmid-encoded beta-lactamases.

A rapid method combining immunofluorescence and flow cytometry for improved understanding of competitive interactions between lactic acid bacteria (LAB) and methicillin-resistant S. aureus (MRSA) in mixed culture

The increasing frequency of methicillin-resistant Staphylococcus aureus (MRSA) infections in hospital and community settings highlights the need for effective anti-MRSA agents that will not contribute to the growing problem of antibiotic resistance. Lactic acid bacteria (LAB) are known to exclude various pathogens through multiple mechanisms. In vitro models studying interactions of pathogens and LAB in mixed cultures use selective agar plates to quantify changes in target populations. We applied commercially available S. aureus-specific polyclonal antibodies conjugated with fluorescein isothiocyanate (FITC) for this purpose, producing a bright green signal that clearly differentiates S. aureus from LAB species when mixed cultures are analyzed by flow cytometry and fluorescent microscopy. Flow cytometry of mixed cultures revealed a much larger population of MRSA cells than was detectable using selective agar plates. To our knowledge, this is the first time immunofluorescent flow cytometry has been applied to the study of competitive exclusion in mixed bacterial populations over time.

Problems in monitoring horizontal gene transfer in field trials of transgenic plants

Transgenic crops are approved for release in some countries, while many more countries are wrestling with the issue of how to conduct risk assessments. Controls on field trials often include monitoring of horizontal gene transfer (HGT) from crops to surrounding soil microorganisms. Our analysis of antibiotic-resistant bacteria and of the sensitivity of current techniques for monitoring HGT from transgenic plants to soil microorganisms has two major implications for field trial assessments of transgenic crops: first, HGT from transgenic plants to microbes could still have an environmental impact at a frequency approximately a trillion times lower than the current risk assessment literature estimates the frequency to be; and second, current methods of environmental sampling to capture genes or traits in a recombinant are too insensitive for monitoring evolution by HGT. A model for HGT involving iterative short-patch events explains how HGT can occur at high frequencies but be detected at extremely low frequencies.

Synthesis and preliminary evaluation of some pyrazine containing thiazolines and thiazolidinones as antimicrobial agents

A series of N'-[3,4-disubstituted-1,3-thiazol-2(3H)-ylidene]-2-(pyrazin-2-yloxy)acetohydrazide 11-66 and N'-[(2Z)-3-(4-bromophenyl)-4-oxo-1,3-thiazolidin-2-ylidene]-2-(pyrazin-2-yloxy)acetohydrazide 68-74 were synthesized using appropriate synthetic route. The entire test compounds 11-66 and 68-74 were assayed in vitro for antibacterial activity against two different strains of Gram-negative (E. coli and S. typhi), Gram-positive (S. aureus and B. subtilis) bacteria and the antimycobacterial activity was evaluated against H(37)Rv strain of Mycobacterium tuberculosis. The minimum inhibitory concentration (MIC) was determined for test compounds and for reference standards. The test compounds showed significant antibacterial and antimycobacterial activity against the microbial strains used, when tested in vitro. In general, pyrazine ring and substituted thiazoline ring are essential for antimicrobial activity. Among the compounds tested, compounds 11, 12 and 40 were found to be most potent. The toxicity of most potent compounds 11, 12 and 40 were determined using hemolytic assay and minimal hemolytic concentration (MHCs) were determined. The test compounds were found to be nontoxic up to a dose level of 250 microg/mL.

Synthesis and screening of a molecularly imprinted polymer library targeted for penicillin G

A library of molecularly imprinted polymers (MIPs) was synthesized by radical bulk polymerization using the beta-lactam antibiotic penicillin G as the template. Diversity of the library was obtained by combining various functionalized monomers and cross-linkers and by varying the stoichiometry and the concentration of the components in the prepolymerization mixtures. The library was screened for selectivity to penicillin G by a radioligand binding assay and was compared to a corresponding control library. The best MIP candidate, showing the highest selectivity for penicillin G, was prepared from methacrylic acid and trimethylolpropane trimethacrylate as the functionalized monomer and cross-linker, respectively. Cross-reactivity studies with other beta-lactam antibiotics showed a low cross-reactivity of penicillin V (15%), ampicillin (16%), and amoxicillin (19%). Nafcillin and oxacillin showed less cross-reactivity (<1%). Cross-reaction with a cephalosporin antibiotic (cephapirin) and structurally nonrelated antibiotics (chloramphenicol, tetracycline, dapsone, and erythromycin) was less than 0.01%.

Serotyping and antibiotic resistance profiling of Salmonella in feedlot and nonfeedlot beef cattle

As part of a larger study to assess risk factors associated with hide and carcass contamination of beef cattle during transport to slaughter, a total of 281 salmonellae were isolated from 1,050 rectal, hide, carcass, and environmental samples. For feedlot cattle, salmonellae were recovered from 4.0% of rectal samples, 37.5% of hide samples, 19.0% of carcass samples, and 47.4% of environmental samples. For nonfeedlot cattle, salmonellae were recovered from 10.9% of rectal samples, 37.5% of hide samples, 54.2% of carcass samples, and 50.0% of environmental samples. Overall, the five serotypes most commonly associated with feedlot cattle and their environment were Salmonella Anatum (18.3% of the isolates), Salmonella Kentucky (17.5%), Salmonella Montevideo (9.2%), Salmonella Senftenberg (8.3%), and Salmonella Mbandaka (7.5%). The five serotypes most commonly associated with nonfeedlot cattle and their environment were Salmonella Kentucky (35.4%), Salmonella Montevideo (21.7%). Salmonella Cerro (7.5%), Salmonella Anatum (6.8%), and Salmonella Mbandaka (5.0%). Antimicrobial susceptibility testing of all of the isolates associated with feedlot cattle revealed that 21.7% were resistant to tetracycline, compared with 11.2% of the isolates associated with nonfeedlot cattle. None of the other isolates from feedlot cattle were resistant to any of other antimicrobial agents tested, whereas 6.2% of nonfeedlot cattle isolates were resistant to more than four of the antimicrobial agents tested.

Stress-based identification and classification of antibacterial agents: second-generation Escherichia coli reporter strains and optimization of detection

Escherichia coli strains bearing single-copy fusions between the lacZ reporter gene and the cspA, ibp, or P3rpoH stress promoters offer a simple means to detect sublethal concentrations of antibacterial agents interfering with prokaryotic translation or cell envelope integrity while simultaneously providing information on the mechanism of action of the test compound (A. A. Bianchi and F. Baneyx, Appl. Environ. Microbiol. 65:5023-5027, 1999). Here, we expand the usefulness of this system by (i) demonstrating that a fusion between the SOS-inducible sulA promoter and lacZ is a highly specific probe for the detection of antimicrobial agents that ultimately interfere with DNA replication, (ii) showing that inactivation of the tolC gene allows efficient detection of very low concentrations of model antibiotics (including aminoglycosides) whereas polymyxin B-mediated outer membrane permeabilization facilitates the identification of intermediate concentrations of hydrophobic compounds, and (iii) validating the potential of detector strains and sensitization strategies for high-throughput screening using a reproducible and internally consistent 96-well microplate assay.

From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways

Novel drug targets are required in order to design new defenses against antibiotic-resistant pathogens. Comparative genomics provides new opportunities for finding optimal targets among previously unexplored cellular functions, based on an understanding of related biological processes in bacterial pathogens and their hosts. We describe an integrated approach to identification and prioritization of broad-spectrum drug targets. Our strategy is based on genetic footprinting in Escherichia coli followed by metabolic context analysis of essential gene orthologs in various species. Genes required for viability of E. coli in rich medium were identified on a whole-genome scale using the genetic footprinting technique. Potential target pathways were deduced from these data and compared with a panel of representative bacterial pathogens by using metabolic reconstructions from genomic data. Conserved and indispensable functions revealed by this analysis potentially represent broad-spectrum antibacterial targets. Further target prioritization involves comparison of the corresponding pathways and individual functions between pathogens and the human host. The most promising targets are validated by direct knockouts in model pathogens. The efficacy of this approach is illustrated using examples from metabolism of adenylate cofactors NAD(P), coenzyme A, and flavin adenine dinucleotide. Several drug targets within these pathways, including three distantly related adenylyltransferases (orthologs of the E. coli genes nadD, coaD, and ribF), are discussed in detail.

Gene transfer between Salmonella enterica serovar Typhimurium inside epithelial cells

Virulence and antibiotic resistance genes transfer between bacteria by bacterial conjugation. Conjugation also mediates gene transfer from bacteria to eukaryotic organisms, including yeast and human cells. Predicting when and where genes transfer by conjugation could enhance our understanding of the risks involved in the release of genetically modified organisms, including those being developed for use as vaccines. We report here that Salmonella enterica serovar Typhimurium conjugated inside cultured human cells. The DNA transfer from donor to recipient bacteria was proportional to the probability that the two types of bacteria occupied the same cell, which was dependent on viable and invasive bacteria and on plasmid tra genes. Based on the high frequencies of gene transfer between bacteria inside human cells, we suggest that such gene transfers occur in situ. The implications of gene transfer between bacteria inside human cells, particularly in the context of antibiotic resistance, are discussed.

Syntheses of Curcumin Bioconjugates and Study of Their Antibacterial Activities against beta-Lactamase-Producing Microorganisms

In the present study curcumin bioconjugates, viz. di-O-glycinoylcurcumin (I), di-O-glycinoyl-C(4)-glycylcurcumin (II), 5'-deoxy-5'-curcuminylthymidine (5'-cur-T) (IV), and 2'-deoxy-2'-curcuminyluridine (2'-cur-U) (V) have been synthesized and characterized by elemental analysis and (1)H NMR. The turmeric peptide (Tp) was isolated from the aqueous turmeric extract of the turmeric rhizome. The antibacterial activity of these four bioconjugates and also of the turmeric peptide and sodium salt of curcumin (III) have been tested particularly for beta-lactamase-producing microorganisms.

Low-level antibacterial resistance: a gateway to clinical resistance

The huge amount of antibiotic substances released in the human environment has probably resulted in an acceleration in the rate of bacterial evolution. It is to note that most interactions between chemotherapeutic agents and microbial populations occur at very low antibiotic concentrations. Thus, natural selection is expected to act on very small increases in the bacterial ability to resist to antibiotic inhibitory effects. On the other hand, there is a wealth of mechanisms to resist to these low antibiotic concentrations. The progressive enrichment in low-level resistant populations favours secondary selections for more specific and effective mechanisms of resistance, particularly in treated patients. These adaptations may have a biological cost in the absence of antibiotics, but frequently compensatory mutations occur, minimizing such genetic burden. In this way, a phenomenon of directional selection takes place, with low possibilities of return to susceptibility. Moreover, low antibiotic concentrations are not only able to select low-level antibiotic resistant variants, but may produce a substantial stress in bacterial populations, that eventually influences the rate of genetic variation and the diversity of adaptive responses. More attention should be devoted to the mechanisms of low-level resistance in microorganisms, as they can serve as stepping stones to develop high level, clinically relevant resistance. These mechanisms should be identified early in the development of drugs in order to adapt the therapeutic strategies (for instance dosage) to minimize the selection of low-level resistant variants, as frequently they emerge by means of concentration-specific selection. At the same time, conventional susceptibility testing should probably be able to detect low-level resistance, and not only clinically-relevant resistance. We should be vigilant of the evolutionary trends of microorganisms; for that a purpose, knowledge of the biology and epidemiology of low-level resistance is becoming a real need.

Discovery through total synthesis: a retrospective on the himastatin problem

A total synthesis of a structure proposed for himastatin was accomplished. The non-identity of the fully synthetic material with himastatin necessitated a revision of the assigned structure. Confirmation of the revised stereostructure was subsequently confirmed through total synthesis. Among the achievements during this effort were i) stereospecific routes to both anti-cis and syn-cis pyrrolindoline substructures; ii) a practical synthesis to 5-hydroxypiperazic acid in enantiomerically pure form; iii) a Stille coupling leading to a complex bi-indole moiety, and iv) efficient protecting group management throughout the evolving depsipeptide domain. The outlines for a biological pharmacophore have been delineated. The alternating D- and L-substituents in the 6-mer as well as the biaryl linkage connecting the two identical subunits are critical for maintaining biological activity. This pattern is simulated in another antibiotic, and suggests a possible structural trend for future SAR investigations.

Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids

Postsegregational killing (PSK) systems consist of a tightly linked toxin-antitoxin pair. Antitoxin must be continually produced to prevent the longer lived toxin from killing the cell. PSK systems on plasmids are widely believed to benefit the plasmid by ensuring its stable vertical inheritance. However, experimental tests of this "stability" hypothesis were not consistent with its predictions. We suggest an alternative hypothesis to explain the evolution of PSK: that PSK systems have been selected through benefiting host plasmids in environments where plasmids must compete during horizontal reproduction. In this "competition" hypothesis, success of PSK systems is a consequence of plasmid-plasmid competition, rather than from an adaptive plasmid-host relationship. In support of this hypothesis, a plasmid-encoded parDE PSK system mediated the exclusion of an isogenic DeltaparDE plasmid. An understanding of how PSK systems influence plasmid success may provide insight into the evolution of other determinants (e.g., antibiotic resistance and virulence) also rendering a cell potentially dependent on an otherwise dispensable plasmid.

Molecular strategies for overcoming antibiotic resistance in bacteria

Overuse of antibiotics in humans and livestock has led to the rapid evolution of bacteria that are resistant to multiple drugs such that even vancomycin, the drug of last resort, is no longer effective against some strains. Apart from the discovery and exploitation of the natural peptide antimicrobial agents that form part of the innate immune systems of plants and animals, there have been few new antibiotics developed in recent years. Here we review strategies designed to exploit recent advances in molecular biology, including recombinant DNA technology, molecular modelling and genomics to develop new antibacterial agents that overcome antibiotic resistance.

Do antibiotics maintain antibiotic resistance?

Important human pathogens resistant to antibiotics result from the human use of antibiotics. Does this imply that reducing their usage or removing antibiotics from medicine and agriculture will restore the effectiveness of these drugs? The authors argue that resistance evolution and susceptibility evolution are not, in a sense, just different sides of the same coin. Resistance genes acquire new functions and the initial costs of resistance can evolve into advantages. Decreasing drug use might not replace a fundamental change in drug design to avoid the evolution of resistant, and encourage the evolution of susceptible, microorganisms.

New hypotheses on the material nature of horizontally mobile genes

The evolutionary history of organisms is often assumed to be recorded in the structure of important molecules, such as DNA sequences. Whereas the structure of these molecules does sometimes affirm other evidence of ancestry, like fossil records, it sometimes does not. Horizontal gene transfer can distort perceptions of ancestry. Determining the impact of horizontal gene transfer on evolution has been limited by the crude tools available to detect it. Physical and genetic vectors are now known to conduct genes between organisms, even between biological kingdoms of organisms. The effects are being noticed in important molecules preserved in the genomes of organisms. This article will review the systematic bias in using molecular morphology, like DNA sequences, to infer ancestry and how this bias is the unavoidable result of the way that experimental genetics itself evolved. We present the novel hypothesis that genes usually called epigenes, like methylation patterns and prions, are infectiously transferred, sometimes using DNA as a vector, but not as a gene.

Protease inhibitors. Part 7. Inhibition of Clostridium histolyticum collagenase with sulfonylated derivatives of L-valine hydroxamate

Sulfonylated L-valine hydroxamate derivatives were obtained by reaction of alkyl/arylsulfonyl halides with the title amino acid, followed by treatment with benzyl chloride, and conversion of the COOH moiety to the CONHOH group. Other derivatives were obtained by reaction of N-benzyl-L-valine with arylisocyanates, arylsulfonylisocyanates or benzoylisothiocyanate, followed by the similar conversion of the COOH into the CONHOH moiety, with hydroxylamine in the presence of carbodiimides. The obtained compounds were assayed as inhibitors of the Clostridium histolyticum collagenase, ChC (EC 3.4.24.3), a zinc enzyme which degrades triple helical collagen. The hydroxamate derivatives were generally 100-500 times more active than the corresponding carboxylates. In the series of synthesized derivatives, substitution patterns leading to best ChC inhibitors were those involving perfluoroalkylsulfonyl- and substituted-arylsulfonyl moieties, such as pentafluorophenylsulfonyl; 3- and 4-protected-aminophenylsulfonyl-; 3- and 4-carboxyphenylsulfonyl-; 3-trifluoromethylphenylsulfonyl; or 1- and 2-naphthyl among others. Similarly to the matrix metalloproteinase hydroxamate inhibitors, ChC inhibitors of the type reported here must incorporate hydrophobic moieties at the P(2') and P(3') subsites, in order to achieve tight binding to the enzyme. Such compounds might lead to drugs useful in the treatment corneal bacterial keratitis.

Transfer of conjugative plasmids and bacteriophage lambda occurs in the presence of antibiotics that prevent de novo gene expression

Plasmids transferred between bacteria prevented from expressing genes by the presence of bacteriostatic antibiotics. Whereas it has long been known that de novo gene expression is not required in donor cells for conjugation, the observations reported here extend the autonomy of plasmid transfer to the early events of establishment in recipients. In addition, this phenomenon was extended to bacteriophage lambda.

Integrated bacterial genomics for the discovery of novel antimicrobials

Sequencing of bacterial genomes has been progressing with breathtaking speed. Currently, the genomes of 23 bacterial species are sequenced, with approximately 40 more sequencing projects in progress. Industrial research is now facing the challenge of translating this information efficiently into drug discovery. This review will summarize the impact of bacterial genomics, bioinformatics and second-generation genomic technologies on target identification, assay development, lead optimization and compound characterization.