Evolution of high-level resistance during low-level antibiotic exposure

Antivirulence DsbA inhibitors attenuate Salmonella enterica serovar Typhimurium fitness without detectable resistance

Inhibition of the DiSulfide Bond (DSB) oxidative protein folding machinery, a major facilitator of virulence in Gram‐negative bacteria, represents a promising antivirulence strategy. We previously developed small molecule inhibitors of DsbA from Escherichia coli K‐12 (EcDsbA) and showed that they attenuate virulence of Gram‐negative pathogens by directly inhibiting multiple diverse DsbA homologues. Here we tested the evolutionary robustness of DsbA inhibitors as antivirulence antimicrobials against Salmonella enterica serovar Typhimurium under pathophysiological conditions in vitro. We show that phenylthiophene DsbA inhibitors slow S. Typhimurium growth in minimal media, phenocopying S. Typhimurium isogenic dsbA null mutants. Through passaging experiments, we found that DsbA inhibitor resistance was not induced under conditions that rapidly induced resistance to ciprofloxacin, an antibiotic commonly used to treat Salmonella infections. Furthermore, no mutations were identified in the dsbA gene of inhibitor‐treated S. Typhimurium, and S. Typhimurium virulence remained susceptible to DsbA inhibitors. Our work demonstrates that under in vitro pathophysiological conditions, DsbA inhibitors can have both antivirulence and antibiotic action. Importantly, our finding that DsbA inhibitors appear to be evolutionarily robust offers promise for their further development as next‐generation antimicrobials against Gram‐negative pathogens.

Impact of high precipitation and temperature events on the distribution of emerging contaminants in surface water in the Mid-Atlantic, United States

Extreme weather events induced by climate change have potential to impact water quality and have received increasing attention from surface water source management perspectives. However, it remains unclear how such phenomenon may influence concentration of emerging contaminants (ECs) in surface water that are vital source of irrigation. In the present study, we investigated the impact of high precipitation and ambient temperature on the distribution of ECs in surface water samples (N = 250) from Mid-Atlantic region, collected between 2016 and 2018. We analyzed the water samples using a liquid chromatography tandem mass spectrometry (LC-MS/MS) based method. We then investigated how the detection frequencies and concentrations of ten emerging contaminants were influenced by high precipitation and temperature events in the previous day or 7 days prior to the sampling events using a generalized additive model (GAM). We observed that heavy rainfalls occurring within 24 h before sampling increased the concentration/likelihood of detection of the ECs in surface waters, likely due to surface runoffs, remobilization from soil/sediment and sewage overflows. The impact of high precipitation during previous seven days varied across chemicals. Likewise, the detection frequency and concentration of most analytes increased with increasing temperature, in previous day of sampling event, likely due to enhanced solubility in water. Long-term high temperature events appeared to decrease the detection of the most tested ECs probably due to enhanced degradation. However, the potential risk of unknown degradation products cannot be ignored. Our results indicate potential decline of water quality after extreme weather events which may have implications for water source management under changing climate.

Evolution of Antibiotic Tolerance Shapes Resistance Development in Chronic Pseudomonas aeruginosa Infections

Over the past decades, pan-resistant strains of major bacterial pathogens have emerged and have rendered clinically available antibiotics ineffective, putting at risk many of the major achievements of modern medicine, including surgery, cancer therapy, and organ transplantation. A thorough understanding of processes leading to the development of antibiotic resistance in human patients is thus urgently needed.

The widespread use of antibiotics promotes the evolution and dissemination of resistance and tolerance mechanisms. To assess the relevance of tolerance and its implications for resistance development, we used in vitro evolution and analyzed the inpatient microevolution of Pseudomonas aeruginosa, an important human pathogen causing acute and chronic infections. We show that the development of tolerance precedes and promotes the acquisition of resistance in vitro, and we present evidence that similar processes shape antibiotic exposure in human patients. Our data suggest that during chronic infections, P. aeruginosa first acquires moderate drug tolerance before following distinct evolutionary trajectories that lead to high-level multidrug tolerance or to antibiotic resistance. Our studies propose that the development of antibiotic tolerance predisposes bacteria for the acquisition of resistance at early stages of infection and that both mechanisms independently promote bacterial survival during antibiotic treatment at later stages of chronic infections.

Antibiotics in a wastewater matrix at environmentally relevant concentrations affect coexisting resistant/sensitive bacterial cultures with profound impact on advanced oxidation treatment

Antibiotic resistance containment strategies at wastewater treatment plants need to be supported by a firm knowledge on the behavior of resistant bacteria within a diverse microbial population in the presence of trace amount of antibiotics. In this study via investigating the population dynamics of resistant/sensitive Staphylococcus aureus co-cultures in several model wastewater matrix systems, valuable insights were obtained into the effect of trace amount of antibiotics (piperacillin and erythromycin) on bacteria, and into the suitability of advanced oxidation treatment (electron beam irradiation) as a remediation measure. It appears that environmentally relevant concentration levels of the antibiotic present in a wastewater matrix leads to a shift in the population in favor of the sensitive subtype, presumably on account of triggering protective biochemical processes in the resistant mutant, which confer no selective advantage since the sensitive strain remains unaffected in this concentration range. The impact of these conditions on the population dynamics can be diminished by using advanced oxidation treatment, considering that degradation products from the wastewater matrix constituents (such as humic acid) might also have an effect. Furthermore, it became also apparent that the presence of trace amount of antibiotics while triggers biological processes in the resistant subtype, concomitantly makes the bacteria more sensitive towards the attack of free radicals during advanced oxidation treatment. The behavior of resistant bacteria under environmental conditions at the cellular and population level clearly merits more attention.

Alternative, environmentally conscious approaches for removing antibiotics from wastewater treatment systems

Prevalence of antibiotic resistance in the environment is of critical concern from a public health perspective, with many human impacted environments showing increased incidence of antibiotic resistant bacteria. Wastewater treatment environments are of particular interest due to their high levels of antibiotic residuals, which can select for antibiotic resistance genes in bacteria. However, wastewater treatment plants are generally not designed to remove antibiotics from collected waste, and many of the currently proposed methods are unsafe for environmental use. This has prompted researchers to identify alternative environmentally safe methods for removing antibiotics from wastewater to be used in parallel with conventional wastewater treatment, as it is a potential strategy towards the mitigation of environmental antibiotic resistance selection. This paper reviews several methods developed to absorb and/or degrade antibiotics from aqueous solutions and wastewater biosolids, which includes ligninolytic fungi and ligninolytic enzymes, algae-driven photobioreactors and algae-activated sludge, and organically-sourced biochars.

Real-time tracking of bacterial membrane vesicles reveals enhanced membrane traffic upon antibiotic exposure

Membrane vesicles are ubiquitous carriers of molecular information. A broad understanding of the biological functions of membrane vesicles in bacteria remains elusive because of the imaging challenges during real-time in vivo experiments. Here, we provide a quantitative analysis of the motion of individual vesicles in living microbes using fluorescence microscopy, and we show that while vesicle free diffusion in the intercellular space is rare, vesicles mostly disperse along the bacterial surfaces. Most remarkably, when bacteria are challenged with low doses of antibiotics, vesicle production and traffic, quantified by instantaneous vesicle speeds and total traveled distance per unit time, are significantly enhanced. Furthermore, the enhanced vesicle movement is independent of cell clustering properties but rather is associated with a reduction of the density of surface appendages in response to antibiotics. Together, our results provide insights into the emerging field of spatial organization and dynamics of membrane vesicles in microcolonies.

Antibiotic resistance: turning evolutionary principles into clinical reality

Antibiotic resistance is one of the major challenges facing modern medicine worldwide. The past few decades have witnessed rapid progress in our understanding of the multiple factors that affect the emergence and spread of antibiotic resistance at the population level and the level of the individual patient. However, the process of translating this progress into health policy and clinical practice has been slow. Here, we attempt to consolidate current knowledge about the evolution and ecology of antibiotic resistance into a roadmap for future research as well as clinical and environmental control of antibiotic resistance. At the population level, we examine emergence, transmission and dissemination of antibiotic resistance, and at the patient level, we examine adaptation involving bacterial physiology and host resilience. Finally, we describe new approaches and technologies for improving diagnosis and treatment and minimizing the spread of resistance.

To give or not to give antibiotics is not the only question

In a 1945 Nobel Lecture, Sir Alexander Fleming warned against the overuse of antibiotics, particularly in response to public pressure. In the subsequent decades, evidence has shown that bacteria can become resistant to almost any available molecule. One key question is how the emergence and dissemination of resistant bacteria or resistance genes can be delayed. Although some clinicians remain sceptical, in this Personal View, we argue that the prescription of fewer antibiotics and shorter treatment duration is just as effective as longer regimens that remain the current guideline. Additionally, we discuss the fact that shorter antibiotic treatments exert less selective pressure on microorganisms, preventing the development of resistance. By contrast, longer treatments associated with a strong selective pressure favour the emergence of resistant clones within commensal organisms. We also emphasise that more studies are needed to identify the optimal duration of antibiotic therapy for common infections, which is important for making changes to the current guidelines, and to identify clinical biomarkers to guide antibiotic treatment in both hospital and ambulatory settings.

Prokaryotic life finds a way: insights from evolutionary experimentation in bacteria

While evolution proceeds through the generation of random variant alleles, the application of selective pressures can select for subsets of mutations that confer fitness-improving physiological benefits. This, in essence, defines the process of adaptive evolution. The rapid replication rate of bacteria has allowed for the design of experiments to study these processes over a reasonable timeframe within a laboratory setting. This has been greatly assisted by advances in tractability of diverse microorganisms, next generation sequencing technologies and bioinformatic analysis pipelines. Examining the processes by which organisms adapt their genetic code to cope with sub-optimal growth conditions has yielded a wealth of molecular insight into diverse biological processes. Here we discuss how the study of adaptive evolutionary trajectories in bacteria has allowed for improved understanding of stress responses, revealed important insight into microbial physiology, allowed for the production of highly optimised strains for use in biotechnology and increased our knowledge of the role of genomic plasticity in chronic infections.

Mapping the Role of AcrAB-TolC Efflux Pumps in the Evolution of Antibiotic Resistance Reveals Near-MIC Treatments Facilitate Resistance Acquisition

Antibiotic resistance has become a major public health concern as bacteria evolve to evade drugs, leading to recurring infections and a decrease in antibiotic efficacy. Systematic efforts have revealed mechanisms involved in resistance. Yet, in many cases, how these specific mechanisms accelerate or slow the evolution of resistance remains unclear. Here, we conducted a systematic study of the impact of the AcrAB-TolC efflux pump on the evolution of antibiotic resistance. We mapped how population growth rate and resistance change over time as a function of both the antibiotic concentration and the parent strain's genetic background. We compared the wild-type strain to a strain overexpressing AcrAB-TolC pumps and a strain lacking functional pumps. In all cases, resistance emerged when cultures were treated with chloramphenicol concentrations near the MIC of their respective parent strain. The genetic background of the parent strain also influenced resistance acquisition. The wild-type strain evolved resistance within 24 h through mutations in the acrAB operon and its associated regulators. Meanwhile, the strain overexpressing AcrAB-TolC evolved resistance more slowly than the wild-type strain; this strain achieved resistance in part through point mutations in acrB and the acrAB promoter. Surprisingly, the strain without functional AcrAB-TolC efflux pumps still gained resistance, which it achieved through upregulation of redundant efflux pumps. Overall, our results suggest that treatment conditions just above the MIC pose the largest risk for the evolution of resistance and that AcrAB-TolC efflux pumps impact the pathway by which chloramphenicol resistance is achieved.IMPORTANCE Combatting the rise of antibiotic resistance is a significant challenge. Efflux pumps are an important contributor to drug resistance; they exist across many cell types and can export numerous classes of antibiotics. Cells can regulate pump expression to maintain low intracellular drug concentrations. Here, we explored how resistance emerged depending on the antibiotic concentration, as well as the presence of efflux pumps and their regulators. We found that treatments near antibiotic concentrations that inhibit the parent strain's growth were most likely to promote resistance. While wild-type, pump overexpression, and pump knockout strains were all able to evolve resistance, they differed in the absolute level of resistance evolved, the speed at which they achieved resistance, and the genetic pathways involved. These results indicate that specific treatment regimens may be especially problematic for the evolution of resistance and that the strain background can influence how resistance is achieved.

Urinary antibiotic exposure across pregnancy from Chinese pregnant women and health risk assessment: Repeated measures analysis

Multiple antibiotics are widely used in clinic practice and livestock husbandry, but exposure data based on repeated measurements are scarce among pregnant women. Here, we biomonitored 41 antibiotics and their two metabolites in urine samples from 3235 pregnant women over three trimesters. Spearman's correlation coefficient, intraclass correlation coefficient (ICC), percentile analysis and linear mixed models were employed to evaluate the correlations, variability, co-exposure patterns and predictors of antibiotics, respectively. Pregnant urinary creatinine-adjusted concentrations of antibiotics were used to estimate daily exposure dose and assessed health risks. The target antibiotics were detected in more than 90% of urine samples, primarily as preferred as veterinary antibiotics (PVAs), and the 95th percentile urinary concentrations of each individual antibiotics were range from below the limits of detection to 5.74 ng/mL. We observed considerable within-subject variation (ICC: 0.05-0.63) of urinary antibiotics concentrations during pregnancy. More than half pregnant women were co-exposed to two or more antibiotics of different usage classes, while both co-exposure to high percentiles of three usage antibiotics at one trimester or exposure to single usage antibiotics at high-dose through three trimesters were infrequent in the study population, and most pregnant women were continuously exposed to low-dose PVAs across pregnancy. A total of 4.5% samples were showed hazard index values exceeding 1 during entire pregnancy. Urinary levels of antibiotics associated with residence, maternal age and education, pre-pregnancy BMI, household income and gestational week, especially vary by sampling seasons. Taken together, most pregnant women were frequently exposure to low-dose PVAs across pregnancy and some were in a health risk associated with the disturbance of gut microbiota. Multiple measurements of urinary antibiotic concentrations are essential to more accurate charactering the exposure levels during pregnancy. Several predictors of urinary antibiotics should be taken into consideration in future researches.

Resistance to Antibiotics of Uropathogen Bacteria Isolated From Urine and Blood in Pediatric Cancer Patients: A Single Center, 12-year Study

Resistant pathogens have become a major healthcare problem in children with cancer, causing different kinds of infections such as the bloodstream ones, most common, and most frequently described and the urinary tract ones, of which less data are available. We analyzed and compared the proportions, and the trends of resistance in pathogens isolated from blood and urines in children with cancer followed in IRCCS Istituto Giannina Gaslini, Genova, Italy, from January 2007 to December 2018. Overall, 345 strains detected in urines and 282 in bloodstream infections were analyzed. Enterobacteriales were the most frequently isolated pathogens. During the study period in urines, there was a significant increase of resistance to ceftazidime, ciprofloxacin, piperacillin/tazobactam, and trimethoprim-sulfamethoxazole, but pathogens from blood were significantly more frequently resistant to amikacin, piperacillin/tazobactam, and combination therapy piperacillin/tazobactam+amikacin, even if with a decreasing trend during the study period. These data confirm the importance of surveillance of isolated microorganism and antibiotic resistance in cancer children.

On the possible ecological roles of antimicrobials

The Introduction of antibiotics into the clinical use in the middle of the 20th century had a profound impact on modern medicine and human wellbeing. The contribution of these wonder molecules to public health and science is hard to overestimate. Much research has informed our understanding of antibiotic mechanisms of action and resistance at inhibitory concentrations in the lab and in the clinic. Antibiotics, however, are not a human invention as most of them are either natural products produced by soil microorganisms or semisynthetic derivatives of natural products. Because we use antibiotics to inhibit the bacterial growth, it is generally assumed that growth inhibition is also their primary ecological function in the environment. Nevertheless, multiple studies point to diverse nonlethal effects that are exhibited at lower levels of antibiotics. Here we review accumulating evidence of antibiosis and of alternative functions of antibiotics exhibited at subinhibitory concentrations. We also speculate on how these effects might alter phenotypes, fitness, and community composition of microbes in the context of the environment and suggest directions for future research.

Effect of Exposure to Chlorhexidine Residues at "During Use" Concentrations on Antimicrobial Susceptibility Profile, Efflux, Conjugative Plasmid Transfer, and Metabolism of Escherichia coli

There is no standardized protocol to predict the concentration levels of microbicides that are left on surfaces as a result of the use of these products, and there is no standardized method to predict the potential risk that such levels pose to emerging antibacterial resistance. The ability to distinguish between selection and adaption processes for antimicrobial resistance in bacteria and the impact of different concentrations of microbicide exposure have not been fully investigated to date. This study considers the effect of exposure to a low concentration of chlorhexidine digluconate (CHX) on selected phenotypes of Escherichia coli and relates the findings to the risk of emerging antimicrobial resistance. A concentration of 0.006 mg/ml CHX is a realistic "during use" exposure concentration measured on surfaces. At this concentration, it was possible for CHX-susceptible bacteria to survive, adapt through metabolic alterations, exhibit a transient decrease in antimicrobial susceptibility, and express stable clinical cross-resistance to front-line antibiotics. Efflux activity was present naturally in tested isolates, and it increased in the presence of 0.00005 mg/ml CHX but ceased with 0.002 mg/ml CHX. Phenotypic microarray assays highlighted a difference in metabolic regulation at 0.00005 mg/ml and 0.002 mg/ml CHX; more changes occurred after growth with the latter concentration. Metabolic phenotype changes were observed for substrates involved with the metabolism of some amino acids, cofactors, and secondary metabolites. It was possible for one isolate to continue transferring ampicillin resistance in the presence of 0.00005 mg/ml CHX, whilst 0.002 mg/ml CHX prevented conjugative transfer. In conclusion, E. coli phenotype responses to CHX exposure are concentration dependent, with realistic residual CHX concentrations resulting in stable clinical cross-resistance to antibiotics.

Novel rapid room temperature synthesis of conjugated microporous polymer for metal-free photocatalytic degradation of fluoroquinolones

The existence of Fluoroquinolones (FQs), non-biodegradable pharmacophores, in the natural environment possesses a serious threat. We herein report a novel, rapid, room-temperature synthesis of semiconducting conjugated microporous polymer (CMP) for the decontamination of four second-generation FQs, Norfloxacin, Enrofloxacin, Ciprofloxacin, and Ofloxacin. The CMP demonstrated impressive gas uptake and FQ adsorption ability. Decreased HOMO-LUMO bandgap resulted in enhanced exciton pair generation on visible-light-illumination. Additionally, a high degree of photocurrent response and suitable redox potentials of the material conjointly endorsed its almost quantitative FQ-degradation efficiency. Ofloxacin showed the best removal efficiency with 0.061 and 0.207 min^-1 adsorption and degradation rate constants, respectively, one of the highest values reported. The CMP exhibited equipotent activity for other FQs as well. On increasing the concentration of the FQs or decreasing the incident photo-intensity, quantitative removal efficiencies are observed. Changing the pH of the medium from acidic to alkaline did not impart any change in catalytic activity as well. The reactive species involved viz. O₂^-, ¹O₂, etc. and their roles in the degradation process were determined through control and trapping experiments. A plausible in-depth mechanistic pathway was assessed from the FQ degradation intermediates, and the reactive catalytic species substantiating step-by-step break down of the antibiotic backbone.

High levels of antibiotic resistance genes and opportunistic pathogenic bacteria indicators in urban wild bird feces

This study analyzed fresh feces from three common bird species that live in urban environments and interact with human communities. Antibiotic resistance genes (ARGs) encoding resistance to three major classes of antibiotics (i.e., tetracyclines, β-lactams, and sulfonamides) and the mobile genetic element integrase gene (intI1) were abundant (up to 10⁹, 10⁸, 10⁹, and 10¹⁰ copies/g dry feces for tetW, bla_TEM, sul1, and intI1, respectively), with relative concentrations surprisingly comparable to that in poultry and livestock that are occasionally fed antibiotics. Biomarkers for opportunistic pathogens were also abundant (up to 10⁷ copies/g dry feces) and the dominant isolates (i.e., Enterococcus spp. and Pseudomonas aeruginosa) harbored both ARGs and virulence genes. ARGs in bird feces followed first-order attenuation with half-lives ranging from 1.3 to 11.1 days in impacted soil. Although residual antibiotics were detected in the feces, no significant correlation was observed between fecal antibiotic concentrations and ARG relative abundance. Thus, other unaccounted factors likely contributed selective pressure for ARG maintenance. These findings highlight the contribution of wild urban bird feces to the maintenance and dissemination of ARGs, and the associated health risks.

Understanding the risk of emerging bacterial resistance to over the counter antibiotics in topical sore throat medicines

AIMS

The aims of this study were to explore the development of bacterial resistance and cross-resistance in four common human pathogens following realistic exposure to antibiotics found in over-the-counter (OTC) sore throat medicines: gramicidin, neomycin, bacitracin and tyrothricin.

METHODS AND RESULTS

Bacterial exposure to in-use (concentration in the product before use) and diluted concentration (i.e. during use) of antibiotic where conducted in broth for 24 h or until growth was visible. The changes in bacterial susceptibility profile before and after exposure was determined using standardized ISO microdilution broth. Antibiotic testing was performed according to EUCAST guidelines. We demonstrated that test bacteria were able to survive exposure to the in-use concentrations of some antibiotics used in OTC medicines. Exposure to during use concentrations of bacitracin resulted in stable increase in minimal inhibitory concentration (MIC) (>8-fold) in Staphylococcus aureus and Acinetobacter baumannii. Exposure to tyrothricin resulted in a stable increase in MIC (2·4-fold) in Klebsiella pneumoniae, and exposure to neomycin resulted in a stable increase MIC (5000-fold higher than the baseline) in Streptococcus pyogenes. Clinical cross-resistance to other antibiotics (ciprofloxacin, fusidic acid, gentamicin, cefpodoxime, amoxicillin/clavulanic acid and cefotaxime) was also demonstrated following exposure to bacitracin or tyrothricin. Bacitracin exposure lead to a stable bacterial resistance after 10 passages.

CONCLUSIONS

Our results indicate that OTC antibiotic medicines have the potential to drive resistance and cross-resistance in vitro.

SIGNIFICANCE AND IMPACT OF THE STUDY

Tackling antibiotic resistance is a high worldwide priority. It is widely accepted that the overuse and misuse of antibiotics increase the risk of the development and spread of antibiotic resistance within communities. A number of OTC sore throat products, widely available across the world for topical use in respiratory indications, contain locally delivered antibiotics. Our findings showed that these antibiotics in OTC medicines present a risk for emerging cross-resistance in a number of bacterial respiratory pathogens.

Bacteriological and molecular study of Salmonella species associated with central nervous system manifestation in chicken flocks

BACKGROUND AND AIM

Salmonella species often cause systemic health problems in poultry flocks, sometimes including nervous systems manifestations. This impact of Salmonella has rarely been studied. This study aimed to define an alternative pathogenic pathway for Salmonella spp. invasion of brain tissue in chicken flocks. Brain infection produces neurological manifestations; Salmonella strains isolated from brain tissue showed the presences of two virulence genes. Confirmation of the pathway of isolates from intestinal mucosa through the blood-brain barrier was attained using experimental infections in specific pathogen-free (SPF)-day-old chicks through two routes of inoculation.

MATERIALS AND METHODS

Isolation of Salmonella spp. from five chicken flocks that showed signs of the central nervous system (CNS) effects were isolated. Isolates were characterized by serotyping, and antimicrobial assays. In addition, virulence profiles were described using detection of virulence plasmid spvC, and Salmonella plasmid sopB. A pathogenicity study of isolates in specific pathogen-free (SPF)-day-old chicks through oral and intracerebral administration performed, and experimental infection in SPF embryonated chicken eggs through intra-yolk and intra-allantoic administration was investigated. Supporting histopathology and immunohistopathology against Salmonella antigen in brain tissue were performed for flock and experimental infections.

RESULTS

Three serotypes of Salmonella were isolated from the brains of five flocks (two Salmonella Virchow, two Salmonella Kentucky, and one Salmonella Enteritidis isolates). Phage related gene sopB and plasmid-mediated operon spvC were identified in all isolated strains. The Salmonella strains were re-isolated and identified from the brain and internal organs of post-experimental infected chicks. Infected chicks showed nervous manifestations associated with Salmonella infection. The presence of positively stained Salmonella antigen in brain tissues indicates penetration of the blood-brain barrier by the Salmonella species.

CONCLUSION

Our results indicate that some virulent systemic strains of Salmonella spp. can induce CNS manifestations in chicken hosts.

Molecular Screening of β-glucuronidase and Class 1 Integron of Escherichia coli from Ready-to-Eat Foods in Tiruchirappalli, Tamil Nadu

Ready-to-eat food products procured from different roadside shops in Tiruchirappalli, Tamil Nadu were screened for Escherichia coli. A total of 500 samples from 250 vegetable and 250 meat products were collected from different hotels, restaurants and street food vendors in Tiruchirappalli, Tamilnadu. Out of 500 ready-to-eat food samples, 162 (32.4%) E. coli strains were isolated. The ready-to-eat meat products had higher bacterial count than the vegetable food samples collected due to unhygienic handling, improper storage, inadequate temperature to maintain processed meat and improper cooking. Biochemically identified E. coli colonies were screened for housekeeping gene uidA and 139 (85.8%) E. coli isolates were confirmed to possess β-glucuronidase activity. In addition, antibiotic susceptibility assay was performed using 12 antibiotics. From 139 E. coli strains, 96 (69.1%) isolates showed multidrug resistance. Among them, 16.7% showed 100% resistance to all the antibiotics tested. Whereas, multidrug resistant E. coli isolates showed increased resistance (75.9%) to streptomycin followed by 70-50% level of resistance to ceftriaxone, ampicillin, cefixime, ciprofloxacin, tetracycline, gentamicin, doxycycline, co-trimoxazole, norfloxacin, ofloxacin and chloramphenicol. Furthermore, drug resistant E. coli isolates 56 (58.3%) were detected with the presence of intI1. The source of contamination was found to be water and human handling. Drinking water supply from corporation might have been contaminated with fecal waste source is being discharged into Cauvery river which might disseminate horizontal gene transfer.

Recombinant bacteriophage LysKB317 endolysin mitigates Lactobacillus infection of corn mash fermentations

BACKGROUND

Commercial ethanol fermentation facilities traditionally rely on antibiotics for bacterial contamination control. Here we demonstrate an alternative approach to treat contamination using a novel peptidoglycan hydrolase (LysKB317) isolated from a bacteriophage, EcoSau. This endolysin was specially selected against Lactobacillus strains that were isolated as contaminants from a fuel ethanol plant. The LysKB317 gene was recombinantly expressed in Escherichia coli as a 33 kDa purified enzyme.

RESULTS

In turbidity reduction assays, the recombinant enzyme was subjected to a panel of 32 bacterial strains and was active against 28 bacterial strains representing 1 species of Acetobacter, 8 species of Lactobacillus, 1 species of Pediococcus, 3 species of Streptococcus, and 1 species of Weissella. The activity of LysKB317 was optimal around pH 6, but it has broad activity and stability from pH 4.5-7.5 up to at least 48 h. Maximum activity was observed at 50 °C up to at least 72 h. In addition, LysKB317 was stable in 30% ethanol up to at least 72 h. In experimentally infected corn mash fermentations, 1 µM endolysin reduced bacterial load by 3-log fold change, while 0.01 µM reduced bacteria by 2-log fold change. Concentration of fermentation products (ethanol, residual glucose, lactic acid, and acetic acids) for infected cultures treated with ≥ 0.01 µM LysKB317 was similar to uncontaminated controls.

CONCLUSION

Exogenously added LysKB317 endolysin is functional in conditions typically found in fuel ethanol fermentations tanks and may be developed as an alternative to antibiotics for contamination control during fuel ethanol fermentations.

Spatial and seasonal variations of antibiotics and antibiotic resistance genes and ecological risks in the coral reef regions adjacent to two typical islands in South China Sea

Although the occurrence of antibiotics and antibiotic resistance genes (ARGs) in aquatic environmental has been widely reported, the distribution and variations of these emerging contaminants in the coral reef regions remain unclear. This study investigated the occurrence of these contaminants, and their spatial and seasonal variations in both coral reef regions and non-coral reef regions adjacent to two typical islands in the South China Sea. Eighteen antibiotics and seven ARGs were detected in the surface water with total concentrations ranging from 43.2 to 441 ng/L, and 2.11 × 10⁴ to 8.00 × 10⁶ copies/L, respectively. Erythromycin-H₂O was the most dominant antibiotic in all samples. QnrD was dominant in the dry season, whereas sul1, sul2, and floR were the most abundant in the wet season, indicating obvious seasonal variations. The distribution of ARGs was mainly influenced by changes in salinity caused by anthropogenic activities in wet season.

Antibiotic-contaminated wastewater irrigated vegetables pose resistance selection risks to the gut microbiome

Wastewater reuse in food crop irrigation has led to agroecosystem pollution concerns and human health risks. However, there is limited attention on the relationship of sub-lethal antibiotic levels in vegetables and resistance selection. Most risk assessment studies show non-significant toxicity, but overlook the link between antibiotics in crops and propagation of gut microbiome resistance selection. The review highlights the risk of antibiotics in treated water used for irrigation, uptake, and accumulation in edible vegetable parts. Moreover, it elucidates the risks to the adaptive resistance selection of the gut microbiome from sub-lethal antibiotic levels, as a result of dietary contaminated vegetables. Experiments have reported that bacterial resistance selection is possible at concentrations that are several hundred-folds lower than lethal effect levels on susceptible cells. Consequently, mutants selected at low antibiotic levels, such as those from vegetables, are fitter and more resistant compared to those selected at high concentrations. Necessary standardization, such as the development of minimum acceptable antibiotic limits allowable in food crop irrigation water, with a focus on minimum selection concentration, and not only toxicity, has been proposed. Wastewater irrigation offers environmental benefits and can contribute to food security, but it has non-addressed risks. Research gaps, future perspectives, and frameworks of mitigating the potential risks are discussed.

Issues beyond resistance: inadequate antibiotic therapy and bacterial hypervirulence

The administration of antibiotics while critical for treatment, can be accompanied by potentially severe complications. These include toxicities associated with the drugs themselves, the selection of resistant organisms and depletion of endogenous host microbiota. In addition, antibiotics may be associated with less well-recognized complications arising through changes in the pathogens themselves. Growing evidence suggests that organisms exposed to antibiotics can respond by altering the expression of toxins, invasins and adhesins, as well as biofilm, resistance and persistence factors. The clinical significance of these changes continues to be explored; however, it is possible that treatment with antibiotics may inadvertently precipitate a worsening of the clinical course of disease. Efforts are needed to adjust or augment antibiotic therapy to prevent the transition of pathogens to hypervirulent states. Better understanding the role of antibiotic-microbe interactions and how these can influence disease course is critical given the implications on prescription guidelines and antimicrobial stewardship policies.

The social network: Impact of host and microbial interactions on bacterial antibiotic tolerance and persistence

Antibiotics have vastly improved our quality of life since their discovery and introduction into modern medicine. Yet, widespread use and misuse have compromised the efficacy of these compounds and put our ability to cure infectious diseases in jeopardy. To defend themselves against antibiotics, bacteria have evolved an arsenal of survival strategies. In addition to acquiring mutations and genetic determinants that confer antibiotic resistance, bacteria can respond to environmental cues and adopt reversible phenotypic changes that transiently enhance their ability to survive adverse conditions, including those brought on by antibiotics. These antibiotic tolerant and persistent bacteria, which are prevalent in biofilms and can survive antimicrobial therapy without inheriting resistance, are thought to underlie treatment failure and infection relapse. At infection sites, bacteria encounter a range of signals originating from host immunity and the local microbiota that can induce transcriptomic and metabolic reprogramming. In this review, we will focus on the impact of host factors and microbial interactions on antibiotic tolerance and persistence. We will also outline current efforts in leveraging the knowledge of host-microbe and microbe-microbe interactions in designing therapies that potentiate antibiotic activity and reduce the burden caused by recurrent infections.

Repeatable ecological dynamics govern the response of experimental communities to antibiotic pulse perturbation

In an era of pervasive anthropogenic ecological disturbances, there is a pressing need to understand the factors that constitute community response and resilience. A detailed understanding of disturbance response needs to go beyond associations and incorporate features of disturbances, species traits, rapid evolution and dispersal. Multispecies microbial communities that experience antibiotic perturbation represent a key system with important medical dimensions. However, previous microbiome studies on this theme have relied on high-throughput sequencing data from uncultured species without the ability to explicitly account for the role of species traits and immigration. Here, we serially passage a 34-species defined bacterial community through different levels of pulse antibiotic disturbance, manipulating the presence or absence of species immigration. To understand the ecological community response measured using amplicon sequencing, we combine initial trait data measured for each species separately and metagenome sequencing data revealing adaptive mutations during the experiment. We found that the ecological community response was highly repeatable within the experimental treatments, which could be attributed in part to key species traits (antibiotic susceptibility and growth rate). Increasing antibiotic levels were also coupled with an increasing probability of species extinction, making species immigration critical for community resilience. Moreover, we detected signals of antibiotic-resistance evolution occurring within species at the same time scale, leaving evolutionary changes in communities despite recovery at the species compositional level. Together, these observations reveal a disturbance response that presents as classic species sorting, but is nevertheless accompanied by rapid within-species evolution.

Itaconic Acid Increases the Efficacy of Tobramycin against Pseudomonas aeruginosa Biofilms

The search for novel therapeutics against pulmonary infections, in particular Pseudomonas aeruginosa (PA) biofilm infections, has been intense to deal with the emergent rise of antimicrobial resistance. Despite the numerous achievements in drug discovery and delivery strategies, only a limited number of therapeutics reach the clinic. To allow a timely preclinical development, a formulation should be highly effective, safe, and most importantly facile to produce. Thus, a simple combination of known actives that enhances the therapeutic efficacy would be a preferential choice compared to advanced drug delivery systems. In this study, we propose a novel combination of an anti-inflammatory agent-itaconic acid (itaconate, IA)-and an approved antibiotic-tobramycin (Tob) or ciprofloxacin (Cipro). The combination of Tob and IA at a molar ratio of 1:5 increased the biofilm eradicating efficacy in the strain PA14 wild type (wt) by ~4-fold compared to Tob alone. In contrast, such effect was not observed for the combination of IA with Cipro. Subsequent studies on the influence of IA on bacterial growth, pyocyanin production, and Tob biofilm penetration indicated that complexation with IA enhanced the transport of Tob through the biofilm. We recommend the simple and effective combination of Tob:IA for further testing in advanced preclinical models of PA biofilm infections.

Exposure to Environmental Levels of Pesticides Stimulates and Diversifies Evolution in Escherichia coli toward Higher Antibiotic Resistance

Antibiotic resistance is one of the most challenging issues in public health. Antibiotics have been increasingly used not only for humans and animals but also for crop protection as pesticides. Thus, antibiotics often coexist with pesticides in some environments. To investigate the effects of the co-occurring, nonantibiotic pesticides on the development of antibiotic resistance, we conducted long-term exposure experiments using an Escherichia coli K-12 model strain. The results reveal that (1) the exposure to pesticides (in mg/L) alone led to the emergence of mutants with significantly higher resistance to streptomycin; (2) the exposure to pesticides (in μg/L) together with a subinhibitory level (in high μg/L) of ampicillin synergistically stimulated the selection of ampicillin resistance and the cross-resistance to other antibiotics (i.e., ciprofloxacin, chloramphenicol, and tetracycline). Distinct and diversified genetic mutations emerged in the resistant mutants selected from the coexposure to both pesticides and ampicillin. The genetic mutations likely caused a holistic transcriptional regulation (e.g., biofilm formation, oxidative stress defense) when grown under antibiotic stress and led to increased antibiotic resistance. Together, these findings provide important fundamental insights into the development of antibiotic resistance and the resistance mechanisms under environmentally relevant conditions where antibiotics and nonantibiotic micropollutants coexist.

Possible drugs for the treatment of bacterial infections in the future: anti-virulence drugs

Antibiotic resistance is a global threat that should be urgently resolved. Finding a new antibiotic is one way, whereas the repression of the dissemination of virulent pathogenic bacteria is another. From this point of view, this paper summarizes first the mechanisms of conjugation and transformation, two important processes of horizontal gene transfer, and then discusses the approaches for disarming virulent pathogenic bacteria, that is, virulence factor inhibitors. In contrast to antibiotics, anti-virulence drugs do not impose a high selective pressure on a bacterial population, and repress the dissemination of antibiotic resistance and virulence genes. Disarmed virulence factors make virulent pathogens avirulent bacteria or pathobionts, so that we human will be able to coexist with these disarmed bacteria peacefully.

Candida albicans Genetic Background Influences Mean and Heterogeneity of Drug Responses and Genome Stability during Evolution in Fluconazole

Antimicrobial resistance is an evolutionary phenomenon with clinical implications. We tested how replicates from diverse strains of Candida albicans, a prevalent human fungal pathogen, evolve in the commonly prescribed antifungal drug fluconazole. Replicates on average increased in fitness in the level of drug they were evolved to, with the least fit parental strains improving the most. Very few replicates increased resistance above the drug level they were evolved in. Notably, many replicates increased in genome size and changed in drug tolerance (a drug response where a subpopulation of cells grow slowly in high levels of drug), and variability among replicates in fitness, tolerance, and genome size was higher in strains that initially were more sensitive to the drug. Genetic background influenced the average degree of adaptation and the evolved variability of many phenotypes, highlighting that different strains from the same species may respond and adapt very differently during adaptation.

The importance of within-species diversity in determining the evolutionary potential of a population to evolve drug resistance or tolerance is not well understood, including in eukaryotic pathogens. To examine the influence of genetic background, we evolved replicates of 20 different clinical isolates of Candida albicans, a human fungal pathogen, in fluconazole, the commonly used antifungal drug. The isolates hailed from the major C. albicans clades and had different initial levels of drug resistance and tolerance to the drug. The majority of replicates rapidly increased in fitness in the evolutionary environment, with the degree of improvement inversely correlated with parental strain fitness in the drug. Improvement was largely restricted to up to the evolutionary level of drug: only 4% of the evolved replicates increased resistance (MIC) above the evolutionary level of drug. Prevalent changes were altered levels of drug tolerance (slow growth of a subpopulation of cells at drug concentrations above the MIC) and increased diversity of genome size. The prevalence and predominant direction of these changes differed in a strain-specific manner, but neither correlated directly with parental fitness or improvement in fitness. Rather, low parental strain fitness was correlated with high levels of heterogeneity in fitness, tolerance, and genome size among evolved replicates. Thus, parental strain background is an important determinant in mean improvement to the evolutionary environment as well as the diversity of evolved phenotypes, and the range of possible responses of a pathogen to an antimicrobial drug cannot be captured by in-depth study of a single strain background.

IMPORTANCE Antimicrobial resistance is an evolutionary phenomenon with clinical implications. We tested how replicates from diverse strains of Candida albicans, a prevalent human fungal pathogen, evolve in the commonly prescribed antifungal drug fluconazole. Replicates on average increased in fitness in the level of drug they were evolved to, with the least fit parental strains improving the most. Very few replicates increased resistance above the drug level they were evolved in. Notably, many replicates increased in genome size and changed in drug tolerance (a drug response where a subpopulation of cells grow slowly in high levels of drug), and variability among replicates in fitness, tolerance, and genome size was higher in strains that initially were more sensitive to the drug. Genetic background influenced the average degree of adaptation and the evolved variability of many phenotypes, highlighting that different strains from the same species may respond and adapt very differently during adaptation.

Strategic Moves of "Superbugs" Against Available Chemical Scaffolds: Signaling, Regulation, and Challenges

Superbugs' resistivity against available natural products has become an alarming global threat, causing a rapid deterioration in public health and claiming tens of thousands of lives yearly. Although the rapid discovery of small molecules from plant and microbial origin with enhanced bioactivity has provided us with some hope, a rapid hike in the resistivity of superbugs has proven to be the biggest therapeutic hurdle of all times. Moreover, several distinct mechanisms endowed by these notorious superbugs make them immune to these antibiotics subsequently causing our antibiotic wardrobe to be obsolete. In this unfortunate situation, though the time frame for discovering novel "hit molecules" down the line remains largely unknown, our small hope and untiring efforts injected in hunting novel chemical scaffolds with unique molecular targets using high-throughput technologies may safeguard us against these life-threatening challenges to some extent. Amid this crisis, the current comprehensive review highlights the present status of knowledge, our search for bacteria Achilles' heel, distinct molecular signaling that an opportunistic pathogen bestows to trespass the toxicity of antibiotics, and facile strategies and appealing therapeutic targets of novel drugs. Herein, we also discuss multidimensional strategies to combat antimicrobial resistance.

A nanocarrier system that potentiates the effect of miconazole within different interkingdom biofilms

Background

Novel and new therapeutic strategies capable of enhancing the efficacy of existing antimicrobials is an attractive proposition to meet the needs of society.

Objective

This study aimed to evaluate the potentiating effect of a miconazole (MCZ) nanocarrier system, incorporated with iron oxide nanoparticles (IONPs) and chitosan (CS) (IONPs-CS-MCZ). This was tested on three representative complex interkingdom oral biofilm models (caries, denture and gingivitis).

Materials and methods

The planktonic and sessile minimum inhibitory concentrations (MICs) of IONPs-CS-MCZ against different Candida albicans strains were determined, as well as against all represented bacterial species that formed within the three biofilm models. Biofilms were treated for 24 hours with the IONPs-CS nanocarrier system containing MCZ at 64 mg/L, and characterized using a range of bioassays for quantitative and qualitative assessment.

Results

MIC results generally showed that IONPs-CS-MCZ was more effective than MCZ alone. IONPs-CS-MCZ also promoted reductions in the number of CFUs, biomass and metabolic activity of the representative biofilms, as well as altering biofilm ultrastructure when compared to untreated biofilms. IONPs-CS-MCZ affected the composition and reduced the CFEs for most of the microorganisms present in the three evaluated biofilms. In particular, the proportion of streptococci in the biofilm composition were reduced in all three models, whilst Fusobacterium spp. percentage reduced in the gingivitis and caries models, respectively.

Conclusion

In conclusion, the IONPs-CS-MCZ nanocarrier was efficient against three in vitro models of pathogenic oral biofilms, showing potential to possibly interfere in the synergistic interactions among fungal and bacterial cells within polymicrobial consortia.

Transcriptional regulation of drug resistance mechanisms in Salmonella: where we stand and what we need to know

Salmonellae have evolved a wide range of molecular mechanisms to neutralize the effect of antibiotics and evade the host immune system response. These mechanisms are exquisitely controlled by global and local regulators and enable the pathogens to use its energy as per need and hence allow the pathogen to economize the consumption of energy by its cellular machinery. Several families that regulate the expression of different drug resistance genes are known; some of these are: the TetR family (which affects tetracycline resistance genes), the AraC/XylS family (regulators that can act as both transcriptional activators and repressors), two-component signal transduction systems (e.g. PhoPQ, a key regulator for virulence), mercury resistance Mer-R and multiple antibiotic resistance Mar-R regulators, LysR-type global regulators (e.g. LeuO) and histone-like protein regulators (involved in the repression of newly transferred resistance genes). This minireview focuses on the role of different regulators harbored by the Salmonella genome and characterized for mediating the drug resistance mechanisms particularly via efflux and influx systems. Understanding of such transcriptional regulation mechanisms is imperative to address drug resistance issues in Salmonella and other bacterial pathogens.

Development and selection of low-level multi-drug resistance over an extended range of sub-inhibitory ciprofloxacin concentrations in Escherichia coli

To better combat bacterial antibiotic resistance, a growing global health threat, it is imperative to understand its drivers and underlying biological mechanisms. One potential driver of antibiotic resistance is exposure to sub-inhibitory concentrations of antibiotics. This occurs in both the environment and clinic, from agricultural contamination to incorrect dosing and usage of poor-quality medicines. To better understand this driver, we tested the effect of a broad range of ciprofloxacin concentrations on antibiotic resistance development in Escherichia coli. We observed the emergence of stable, low-level multi-drug resistance that was both time and concentration dependent. Furthermore, we identified a spectrum of single mutations in strains with resistant phenotypes, both previously described and novel. Low-level class-wide resistance, which often goes undetected in the clinic, may allow for bacterial survival and establishment of a reservoir for outbreaks of high-level antibiotic resistant infections.

Parallel Evolution of Tobramycin Resistance across Species and Environments

The rise of antimicrobial resistance is a leading medical threat, motivating efforts to forecast both its evolutionary dynamics and its genetic causes. Aminoglycosides are a major class of antibiotics that disrupt translation, but resistance may occur by a number of mechanisms. Here, we show the repeated evolution of resistance to the aminoglycoside tobramycin in both P. aeruginosa and A. baumannii via mutations in fusA1, encoding elongation factor G, and ptsP, encoding the nitrogen-specific phosphotransferase system. Laboratory evolution and whole-population genome sequencing were used to identify these targets, but mutations at identical amino acid positions were also found in published genomes of diverse bacterial species and clinical isolates. We also identified other resistance mechanisms associated with growth in biofilms that likely interfere with drug binding or uptake. Characterizing the evolution of multiple species in the presence of antibiotics can identify new, repeatable causes of resistance that may be predicted and counteracted by alternative treatment.

Different species exposed to a common stress may adapt by mutations in shared pathways or in unique systems, depending on how past environments have molded their genomes. Understanding how diverse bacterial pathogens evolve in response to an antimicrobial treatment is a pressing example of this problem, where discovery of molecular parallelism could lead to clinically useful predictions. Evolution experiments with pathogens in environments containing antibiotics, combined with periodic whole-population genome sequencing, can be used to identify many contending routes to antimicrobial resistance. We separately propagated two clinically relevant Gram-negative pathogens, Pseudomonas aeruginosa and Acinetobacter baumannii, in increasing concentrations of tobramycin in two different environments each: planktonic and biofilm. Independently of the pathogen, the populations adapted to tobramycin selection by parallel evolution of mutations in fusA1, encoding elongation factor G, and ptsP, encoding phosphoenolpyruvate phosphotransferase. As neither gene is a direct target of this aminoglycoside, mutations to either are unexpected and underreported causes of resistance. Additionally, both species acquired antibiotic resistance-associated mutations that were more prevalent in the biofilm lifestyle than in the planktonic lifestyle; these mutations were in electron transport chain components in A. baumannii and lipopolysaccharide biosynthesis enzymes in P. aeruginosa populations. Using existing databases, we discovered site-specific parallelism of fusA1 mutations that extends across bacterial phyla and clinical isolates. This study suggests that strong selective pressures, such as antibiotic treatment, may result in high levels of predictability in molecular targets of evolution, despite differences between organisms’ genetic backgrounds and environments.

Isolation, characterization, and comparative genomic analysis of a phage infecting high-level aminoglycoside-resistant (HLAR) Enterococcus faecalis

Enterococcus is a genus of Gram-positive bacteria that are commensal to the gastrointestinal tracts of humans but some species have been increasingly implicated as agents of nosocomial infections. The increase in infections and the spread of antibiotic-resistant strains have contributed to renewed interest in the discovery of Enterococcus phages. The aims of this study were (1) the isolation, characterization, and genome sequencing of a phage capable of infecting an antibiotic-resistant E. faecalis strain, and (2) the comparative genomic analysis of publicly-available Enterococcus phages. For this purpose, multiple phages were isolated from wastewater treatment plant (WWTP) influent using a high-level aminoglycoside-resistant (HLAR) E. faecalis strain as the host. One phage, phiNASRA1, demonstrated a high lytic efficiency (∼97.52%). Transmission electron microscopy (TEM) and whole-genome sequencing (WGS) showed that phiNASRA1 belongs to the Siphoviridae family of double-stranded DNA viruses. The phage was approximately 250 nm in length and its complete genome (40,139 bp, 34.7% GC) contained 62 open reading frames (ORFs). Phylogenetic comparisons of phiNASRA1 and 31 publicly-available Enterococcus phages, based on the large subunit terminase and portal proteins, grouped phage by provenance, size, and GC content. In particular, both phylogenies grouped phages larger than 100 kbp into distinct clades. A phylogeny based on a pangenome analysis of the same 32 phages also grouped phages by provenance, size, and GC content although agreement between the two single-locus phylogenies was higher. Per the pangenome phylogeny, phiNASRA1 was most closely related to phage LY0322 that was similar in size, GC content, and number of ORFs (40,139 and 40,934 bp, 34.77 and 34.80%, and 60 and 64 ORFs, respectively). The pangenome analysis did illustrate the high degree of sequence diversity and genome plasticity as no coding sequence was homologous across all 32 phages, and even 'conserved' structural proteins (e.g., the large subunit terminase and portal proteins) were homologous in no more than half of the 32 phage genomes. These findings contribute to a growing body of literature devoted to understanding phage biology and diversity. We propose that this high degree of diversity limited the value of the single-locus and pangenome phylogenies. By contrast, the high degree of homology between phages larger than 100 kbp suggests that pangenome analyses of more similar phages is a viable method for assessing subclade diversity. Future work is focused on validating phiNASRA1 as a potential therapeutic agent to eradicate antibiotic-resistant E. faecalis infections in an animal model.

Predictable properties of fitness landscapes induced by adaptational tradeoffs

Fitness effects of mutations depend on environmental parameters. For example, mutations that increase fitness of bacteria at high antibiotic concentration often decrease fitness in the absence of antibiotic, exemplifying a tradeoff between adaptation to environmental extremes. We develop a mathematical model for fitness landscapes generated by such tradeoffs, based on experiments that determine the antibiotic dose-response curves of Escherichia coli strains, and previous observations on antibiotic resistance mutations. Our model generates a succession of landscapes with predictable properties as antibiotic concentration is varied. The landscape is nearly smooth at low and high concentrations, but the tradeoff induces a high ruggedness at intermediate antibiotic concentrations. Despite this high ruggedness, however, all the fitness maxima in the landscapes are evolutionarily accessible from the wild type. This implies that selection for antibiotic resistance in multiple mutational steps is relatively facile despite the complexity of the underlying landscape.

Efficient detection and assessment of human exposure to trace antibiotic residues in drinking water

Human exposure to antibiotic residues in drinking water has not been well evaluated. This study is the first attempt to simultaneously and efficiently identify and quantify 92 antibiotic residues in filtered tap water (multistage filtration at the tap) (n = 36) collected from 10 areas of a large city in southern China, 10 Chinese brands of bottled/barreled water (n = 30) and six foreign brands of bottled water (n = 18) obtained from the Chinese market. The average and median concentrations of all the detected antibiotic compounds was 182 and 92 ng/L in filtered tap water, 180 and 105 ng/L in Chinese brands of bottled/barreled water, and 666 and 146 ng/L in foreign brands of bottled water, respectively. A total of 58 antibiotics were detected in the filtered tap water, and 45 and 36 antibiotics were detected in the Chinese and foreign brands of bottled water, respectively. More types of antibiotics were detected in Chinese brands of bottled water than in the other bottled waters. In addition, Chinese waters had high roxithromycin concentrations, while the foreign brands of bottled water had high concentrations of dicloxacillin. The average and median values of the estimated overall daily intake of all the detected antibiotics were 4.3 and 2.3 ng/kg/day when only filtered tap water was drunk, 4.0 and 2.5 ng/kg/day when Chinese brands of bottled water was drunk, and 16.0 and 4.9 ng/kg/day when foreign brands of bottled water was drunk. Further study is needed to develop a more comprehensive estimation of human exposure to antibiotic residues in the environment and a more in-depth understanding of the potential hazard of ingested antibiotic residues to the human microbiome.

Bacteria under antibiotic attack: Different strategies for evolutionary adaptation

Bacteria are well known for their extremely high adaptability in stressful environments. The clinical relevance of this property is clearly illustrated by the ever-decreasing efficacy of antibiotic therapies. Frequent exposures to antibiotics favor bacterial strains that have acquired mechanisms to overcome drug inhibition and lethality. Many strains, including life-threatening pathogens, exhibit increased antibiotic resistance or tolerance, which considerably complicates clinical practice. Alarmingly, recent studies show that in addition to resistance, tolerance levels of bacterial populations are extremely flexible in an evolutionary context. Here, we summarize laboratory studies providing insight in the evolution of resistance and tolerance and shed light on how the treatment conditions could affect the direction of bacterial evolution under antibiotic stress.

Precise Persuasion: Investigating Incentive Appeals for the Promotion of Antibiotic Stewardship with Message-induced Transitions

Two different lines of research-interpersonal resistance and public campaign design-lead us to consider the use of incentive appeals to motivate behavior change, with a call for greater attention to and use of positive incentives. This study tests the potential to promote antibiotic stewardship through microbiome benefits. In addition, multiple analyses were used: A causal analysis allowed us to identify what moved (e.g., which beliefs and intentions), a latent transition analysis allowed us to reveal who moved (targets, nontargets, or both), and a Markov model allowed us to estimate the stable state of these moves or, in other words, where and how the repetition of the messages would ultimately lead in terms of transitions from state to state. An experiment (N = 298), grounded in the context of antibiotic stewardship, showed that incentive appeals moved people with problematic patterns of past behavior (categorized as Persuaders, Stockers, and Dissenters) to positive patterns of behavioral intentions (categorized as Stewards). The causal analysis, latent class analysis, and equilibrium values for the separate transition matrices showed the relative benefit for a message that highlighted the health and wellness benefits of the microbiome. Implications for persuasion theory and practice are discussed.

Evaluating antimicrobial resistance in the global shrimp industry

Antimicrobial resistance (AMR) is a growing threat to global public health, and the overuse of antibiotics in animals has been identified as a major risk factor. With high levels of international trade and direct connectivity to the aquatic environment, shrimp aquaculture may play a role in global AMR dissemination. The vast majority of shrimp production occurs in low- and middle-income countries, where antibiotic quality and usage is widely unregulated, and where the integration of aquaculture with family livelihoods offers many opportunities for human, animal and environmental bacteria to come into close contact. Furthermore, in shrimp growing areas, untreated waste is often directly eliminated into local water sources. These risks are very different to many other major internationally-traded aquaculture commodities, such as salmon, which is produced in higher income countries where there are greater levels of regulation and well-established management practices. Assessing the true scale of the risk of AMR dissemination in the shrimp industry is a considerable challenge, not least because obtaining reliable data on antibiotic usage is very difficult. Combating the risks associated with AMR dissemination is also challenging due to the increasing trend towards intensification and its associated disease burden, and because many farmers currently have no alternatives to antibiotics for preventing crop failure. In this review, we critically assess the potential risks the shrimp industry poses to AMR dissemination. We also discuss some of the possible risk mitigation strategies that could be considered by the shrimp industry as it strives for a more sustainable future in production.

Antimicrobial Activity of the Quinoline Derivative HT61 against Staphylococcus aureus Biofilms

Staphylococcus aureus biofilms are a significant problem in health care settings, partly due to the presence of a nondividing, antibiotic-tolerant subpopulation. Here we evaluated treatment of S. aureus UAMS-1 biofilms with HT61, a quinoline derivative shown to be effective against nondividing Staphylococcus spp. HT61 was effective at reducing biofilm viability and was associated with increased expression of cell wall stress and division proteins, confirming its potential as a treatment for S. aureus biofilm infections.

Staphylococcus aureus biofilms are a significant problem in health care settings, partly due to the presence of a nondividing, antibiotic-tolerant subpopulation. Here we evaluated treatment of S. aureus UAMS-1 biofilms with HT61, a quinoline derivative shown to be effective against nondividing Staphylococcus spp. HT61 was effective at reducing biofilm viability and was associated with increased expression of cell wall stress and division proteins, confirming its potential as a treatment for S. aureus biofilm infections.

Evolutionary landscapes of Pseudomonas aeruginosa towards ribosome-targeting antibiotic resistance depend on selection strength

It is generally accepted that antibiotic-resistant mutants are selected in a range of concentrations ranging from the minimum inhibitory concentration (MIC) to the mutant preventive concentration. More recently, it has been found that antibiotic-resistant mutants can also be selected at concentrations below MIC, which expands the conditions where this selection may occur. Using experimental evolution approaches followed by whole-genome sequencing, the current study compares the evolutionary trajectories of Pseudomonas aeruginosa in the presence of tobramycin or tigecycline at lethal and sublethal concentrations. Mutants were selected at sublethal concentrations of tigecycline (1/10 and 1/50 MIC), whereas no mutants were selected in the case of tobramycin, indicating that the width of sub-MIC selective windows is antibiotic-specific. In addition, the patterns of evolution towards tigecycline resistance depend on selection strength. Sublethal concentrations of tigecycline select mutants with lower tigecycline MICs and higher MICs to other antibiotics belonging to different structural families than mutants selected under lethal concentrations. This indicates that the strength of the cross-resistance phenotype associated with tigecycline resistance is decoupled from selection strength. Accurate information on the sublethal selection window for each antibiotic of clinical value, including the phenotypes of cross-resistance of mutants selected at each antibiotic concentration, is needed to understand the role of ecosystems polluted with different antibiotic concentrations in the selection of antibiotic resistance. Integration of this information into clinical and environmental safety controls may help to tackle the problem of antibiotic resistance.

A model for the interplay between plastic tradeoffs and evolution in changing environments

Performance tradeoffs are ubiquitous in both ecological and evolutionary modeling, yet they are usually postulated and built into fitness and ecological landscapes. However, tradeoffs depend on genetic background and evolutionary history and can themselves evolve. We present a simple model capable of capturing the key feedback loop: evolutionary history shapes tradeoff strength, which, in turn, shapes evolutionary future. One consequence of this feedback is that genomes with identical fitness can have different evolutionary properties shaped by prior environmental exposure. Another is that, generically, the best adaptations to one environment may evolve in another. Our simple framework bridges the gap between the phenotypic Fisher's Geometric Model and the genotypic properties, such as modularity and evolvability, and can serve as a rich playground for investigating evolution in multiple or changing environments.

CRISPR/Cas9 recombineering-mediated deep mutational scanning of essential genes in Escherichia coli

Deep mutational scanning can provide significant insights into the function of essential genes in bacteria. Here, we developed a high-throughput method for mutating essential genes of Escherichia coli in their native genetic context. We used Cas9-mediated recombineering to introduce a library of mutations, created by error-prone PCR, within a gene fragment on the genome using a single gRNA pre-validated for high efficiency. Tracking mutation frequency through deep sequencing revealed biases in the position and the number of the introduced mutations. We overcame these biases by increasing the homology arm length and blocking mismatch repair to achieve a mutation efficiency of 85% for non-essential genes and 55% for essential genes. These experiments also improved our understanding of poorly characterized recombineering process using dsDNA donors with single nucleotide changes. Finally, we applied our technology to target rpoB, the beta subunit of RNA polymerase, to study resistance against rifampicin. In a single experiment, we validate multiple biochemical and clinical observations made in the previous decades and provide insights into resistance compensation with the study of double mutants.

TrkA undergoes a tetramer-to-dimer conversion to open TrkH which enables changes in membrane potential

TrkH is a bacterial ion channel implicated in K⁺ uptake and pH regulation. TrkH assembles with its regulatory protein, TrkA, which closes the channel when bound to ADP and opens it when bound to ATP. However, it is unknown how nucleotides control the gating of TrkH through TrkA. Here we report the structures of the TrkH-TrkA complex in the presence of ADP or ATP. TrkA forms a tetrameric ring when bound to ADP and constrains TrkH to a closed conformation. The TrkA ring splits into two TrkA dimers in the presence of ATP and releases the constraints on TrkH, resulting in an open channel conformation. Functional studies show that both the tetramer-to-dimer conversion of TrkA and the loss of constraints on TrkH are required for channel gating. In addition, deletion of TrkA in Escherichia coli depolarizes the cell, suggesting that the TrkH-TrkA complex couples changes in intracellular nucleotides to membrane potential.

Faropenem resistance causes in vitro cross-resistance to carbapenems in ESBL-producing Escherichia coli

OBJECTIVE

Faropenem is an oral penem drug with activity against Gram-positive and Gram-negative bacteria, including CTX-M-15-type extended spectrum beta-lactamase (ESBL)-producing Enterobacteriales and anaerobic bacteria. As there are structural similarities, there is concern for the development of carbapenem cross-resistance; however, there are no studies confirming this. This study examined whether in vitro development of faropenem resistance in Escherichia coli isolates would result in cross-resistance to carbapenems.

METHODS

Four well-characterized E. coli isolates from the US Centers for Disease Control and Prevention antibiotic resistance isolate bank were utilized. Three isolates (NSF1, NSF2 and NSF3) are ESBL producers (CTX-M-15) and one (NSF4) is pan-susceptible. Faropenem minimum inhibitory concentrations (MICs) were determined and resistance was induced by serial passaging in increasing concentrations of faropenem. Susceptibility to carbapenems was determined and whole-genome sequencing (WGS) was performed to identify the underlying genetic mechanism leading to carbapenem resistance.

RESULTS

Faropenem MIC increased from 1 mg/L to 64 mg/L within 10 days for NSF2 and NSF4 isolates, and from 2 mg/L to 64 mg/L within 7 days for NSF1 and NSF3 isolates. Reduced carbapenem susceptibility (ertapenem MIC ≥8 mg/L, doripenem/meropenem ≥2 mg/L and imipenem ≥1 mg/L) developed among three CTX-M-15-producing isolates that were faropenem-resistant, but not in NSF4 isolate that lacked ESBL enzyme. WGS analysis revealed non-synonymous changes in the ompC gene among three CTX-M-15-producing isolates, and a single nucleotide polymorphism (SNP) in the envZ gene in NSF4 isolate.

CONCLUSION

Induced resistance to faropenem causes cross-resistance to carbapenems among E. coli isolates containing CTX-M-15-type ESBL enzymes.