Pharmacodynamic modelling of in vitro activity of tetracycline against a representative, naturally occurring population of porcine Escherichia coli

Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses

Antibiotic resistance poses mounting risks to human health, as current antibiotics are losing efficacy against increasingly resistant pathogenic bacteria. Of particular concern is the emergence of multidrug-resistant strains, which has been rapid among Gram-negative bacteria such as Escherichia coli. A large body of work has established that antibiotic resistance mechanisms depend on phenotypic heterogeneity, which may be mediated by stochastic expression of antibiotic resistance genes. The link between such molecular-level expression and the population levels that result is complex and multi-scale. Therefore, to better understand antibiotic resistance, what is needed are new mechanistic models that reflect single-cell phenotypic dynamics together with population-level heterogeneity, as an integrated whole. In this work, we sought to bridge single-cell and population-scale modeling by building upon our previous experience in "whole-cell" modeling, an approach which integrates mathematical and mechanistic descriptions of biological processes to recapitulate the experimentally observed behaviors of entire cells. To extend whole-cell modeling to the "whole-colony" scale, we embedded multiple instances of a whole-cell E. coli model within a model of a dynamic spatial environment, allowing us to run large, parallelized simulations on the cloud that contained all the molecular detail of the previous whole-cell model and many interactive effects of a colony growing in a shared environment. The resulting simulations were used to explore the response of E. coli to two antibiotics with different mechanisms of action, tetracycline and ampicillin, enabling us to identify sub-generationally-expressed genes, such as the beta-lactamase ampC, which contributed greatly to dramatic cellular differences in steady-state periplasmic ampicillin and was a significant factor in determining cell survival.

Effect of Different Tolerable Levels of Constitutive mcr-1 Expression on Escherichia coli

To study the effect of different tolerable levels of constitutive mcr-1 expression on Escherichia coli, and to provide direct evidence for moderate resistance mediated by mcr-1, construction of E. coli strains carrying mcr-1 on the chromosome with promoters of different strengths was conducted using λ-red recombination. Our results demonstrated that over-high expression of mcr-1 cannot be tolerated, and seven constructs with more than 200-fold mcr-1 transcriptional expression differences were obtained. The colistin MICs of the seven strains increased with the increase of MCR-1 levels, and the highest MIC was 8 μg/mL. Lower expression of mcr-1 didn't demonstrate many effects on bacteria, while higher tolerable expression of mcr-1 tended to show fitness costs in growth rate, competitive ability, and cell structures, but no obvious change of virulence was observed in mice. Bacteria demonstrated colistin MICs of 4-8 μg/mL at mcr-1 expression levels similar to clinical isolates, which were the mcr-1 expression levels with relatively lower fitness costs. IMPORTANCE The effects of relatively lower tolerable levels of mcr-1 were not evaluated thoroughly, and direct evidence for moderate resistance mediated by mcr-1 was lacking. In the present study, we made constructs carrying mcr-1 on the E. coli K12 chromosome under the control of serial constitutive promoters of different strengths and studied the effects of different tolerable levels of mcr-1 expression in vitro and in vivo. The results demonstrated that generally, except QH0007 (the construct with the highest mcr-1 expression that showed some extent of cell death), the fitness costs of tolerable mcr-1 expression on bacteria were not apparent or low. Bacteria demonstrated colistin MICs of 4-8 μg/mL at mcr-1 expression levels similar to clinical isolates, which corresponded to the lower levels of mcr-1 expression that can lead to colistin resistance, indicating the cleverness of bacteria to balance the benefit and cost of MCR-1-mediated colistin resistance.

Modelling the antimicrobial pharmacodynamics for bacterial strains with versus without acquired resistance to fluoroquinolones or cephalosporins

OBJECTIVES

Antimicrobial resistance threatens therapeutic options for human and animal bacterial diseases worldwide. Current antimicrobial treatment regimens were designed against bacterial strains that were fully susceptible to them. To expand the useable lifetime of existing antimicrobial drug classes by modifying treatment regimens, data are needed on the antimicrobial pharmacodynamics (PD) against strains with reduced susceptibility. In this study, we generated and mathematically modelled the PD of the fluoroquinolone ciprofloxacin and the cephalosporin ceftriaxone against non-typhoidal Salmonella enterica subsp. enterica strains with varying levels of acquired resistance.

METHODS

We included Salmonella strains across categories of reduced susceptibility to fluoroquinolones or cephalosporins reported to date, including isolates from human infections, food-animal products sold in retail, and food-animal production. We generated PD data for each drug and strain via time-kill assay. Mathematical models were compared in their fit to represent the PD. The best-fit model's parameter values across the strain susceptibility categories were compared.

RESULTS

The inhibitory baseline sigmoid I_max (or E_max) model was best fit for the PD of each antimicrobial against a majority of the strains. There were statistically significant differences in the PD parameter values across the strain susceptibility categories for each antimicrobial.

CONCLUSION

The results demonstrate predictable multiparameter changes in the PD of these first-line antimicrobials depending on the Salmonella strain's susceptibility phenotype and specific genes conferring reduced susceptibility. The generated PD parameter estimates could be used to optimise treatment regimens against infections by strains with reduced susceptibility.

Comparison on the Growth Heterogeneity of Vibrio parahaemolyticus Coupled with Strain Source and Genotype Analyses in Different Oligotrophic Conditions

ABSTRACT

Vibrio parahaemolyticus is an important foodborne pathogen in aquatic products that can survive long term in an oligotrophic environment and maintain pathogenicity. In this study, the growth curves of 38 strains of V. parahaemolyticus (pathogenic and environmental strains) under different oligotrophic conditions (tryptone soy broth [TSB] and TSB medium diluted 2, 4, and 6 times) were simulated and their growth heterogeneities were compared. The growth kinetic parameters (maximum specific growth rate and lag time) were calculated by the modified Gompertz model. The results showed that oligotrophic conditions affected the growth variability of strains, and the coefficient of variation of all strains reached the maximum in the 4-fold dilution of TSB. Under different oligotrophic conditions, the lag time of the pathogenic strains was shorter than that of the environmental strains, whereas the maximum specific growth rate of the environmental strains was greater. This indicated that pathogenic strains were more adaptable to the nutrient-deficient environment. The analysis of different genotypes revealed that the strains with genotype tlh+/tdh+/trh- showed greater growth variability in oligotrophic environments. These results provided theoretical support for the accuracy of the risk assessment of aquatic products.

HIGHLIGHTS

Pathogenic Escherichia coli Possess Elevated Growth Rates under Exposure to Sub-Inhibitory Concentrations of Azithromycin

Antimicrobial resistance (AMR) has been identified by the World Health Organization (WHO) as one of the ten major threats to global health. Advances in technology, including whole-genome sequencing, have provided new insights into the origin and mechanisms of AMR. However, our understanding of the short-term impact of antimicrobial pressure and resistance on the physiology of bacterial populations is limited. We aimed to investigate morphological and physiological responses of clinical isolates of E. coli under short-term exposure to key antimicrobials. We performed whole-genome sequencing on twenty-seven E. coli isolates isolated from children with sepsis to evaluate their AMR gene content. We assessed their antimicrobial susceptibility profile and measured their growth dynamics and morphological characteristics under exposure to varying concentrations of ciprofloxacin, ceftriaxone, tetracycline, gentamicin, and azithromycin. AMR was common, with all organisms resistant to at least one antimicrobial; a total of 81.5% were multi-drug-resistant (MDR). We observed an association between resistance profile and morphological characteristics of the E. coli over a three-hour exposure to antimicrobials. Growth dynamics experiments demonstrated that resistance to tetracycline promoted the growth of E. coli under antimicrobial-free conditions, while resistance to the other antimicrobials incurred a fitness cost. Notably, antimicrobial exposure heterogeneously suppressed bacterial growth, but sub-MIC concentrations of azithromycin increased the maximum growth rate of the clinical isolates. Our results outline complex interactions between organism and antimicrobials and raise clinical concerns regarding exposure of sub-MIC concentrations of specific antimicrobials.

Highly Elastic and Water Stable Zein Microfibers as a Potential Drug Delivery System for Wound Healing

The development of biomaterials for wound healing applications requires providing a number of properties, such as antimicrobial action, facilitation of cell proliferation, biocompatibility and biodegradability. The aim of the present study was to investigate morphological and mechanical properties of zein-based microfibers, ultimately aimed at creating an environment suitable for wound healing. This was achieved through co-axial electrospinning of core-shell microfibers, with zein protein in the core and polyethylene oxide (PEO) in the shell. Small amounts of PEO or stearic acid were additionally incorporated into the fiber core to modify the morphology and mechanical properties of zein fibers. The presence of PEO in the core was found to be essential for the formation of tubular fibers, whereas PEO in the shell enhanced the stability of the microfibers in water and ensured high elasticity of the microfiber mats. Tetracycline hydrochloride was present in an amorphous form within the fibers, and displayed a burst release as a result of pore-formation in the fibers. The developed systems exhibited antimicrobial activity against Staphylococcus aureus and Escherichia coli, and showed no cytotoxic effect on fibroblasts. Biocompatibility, antimicrobial activity and favorable morphological and mechanical properties make the developed zein-based microfibers a potential biomaterial for wound healing purposes.

Monte Carlo Simulations Suggest Current Chlortetracycline Drug-Residue Based Withdrawal Periods Would Not Control Antimicrobial Resistance Dissemination from Feedlot to Slaughterhouse

Antimicrobial use in beef cattle can increase antimicrobial resistance prevalence in their enteric bacteria, including potential pathogens such as Escherichia coli. These bacteria can contaminate animal products at slaughterhouses and cause food-borne illness, which can be difficult to treat if it is due to antimicrobial resistant bacteria. One potential intervention to reduce the dissemination of resistant bacteria from feedlot to consumer is to impose a withdrawal period after antimicrobial use, similar to the current withdrawal period designed to prevent drug residues in edible animal meat. We investigated tetracycline resistance in generic E. coli in the bovine large intestine during and after antimicrobial treatment by building a mathematical model of oral chlortetracycline pharmacokinetics-pharmacodynamics and E. coli population dynamics. We tracked three E. coli subpopulations (susceptible, intermediate, and resistant) during and after treatment with each of three United States chlortetracycline indications (liver abscess reduction, disease control, disease treatment). We compared the proportion of resistant E. coli before antimicrobial use to that at several time points after treatment and found a greater proportion of resistant enteric E. coli after the current withdrawal periods than prior to treatment. In order for the proportion of resistant E. coli in the median beef steer to return to the pre-treatment level, withdrawal periods of 15 days after liver abscess reduction dosing (70 mg daily), 31 days after disease control dosing (350 mg daily), and 36 days after disease treatment dosing (22 mg/kg bodyweight for 5 days) are required in this model. These antimicrobial resistance withdrawal periods would be substantially longer than the current U.S. withdrawals of 0–2 days or Canadian withdrawals of 5–10 days. One published field study found similar time periods necessary to reduce the proportion of resistant E. coli following chlortetracycline disease treatment to those suggested by this model, but additional carefully designed field studies are necessary to confirm the model results. This model is limited to biological processes within the cattle and does not include resistance selection in the feedlot environment or co-selection of chlortetracycline resistance following other antimicrobial use.

Insight into synergetic mechanisms of tetracycline and the selective serotonin reuptake inhibitor, sertraline, in a tetracycline-resistant strain of Escherichia coli

Sertraline, an antidepressive drug, has been reported to inhibit general bacterial efflux pumps. In the present study, we report for the first time a synergistic effect of sertraline and tetracycline in a TetA-encoded tetracycline-resistant strain of Escherichia coli. Synergy between sertraline and tetracycline in an E. coli strain with TetA-mediated tetracycline resistance (E. coli APEC_O2) was assessed by the MIC and checkerboard assays. The global transcriptome of E. coli APEC_O2 exposed to ½ MIC concentrations of sertraline and/or tetracycline was analyzed to elucidate the interaction mechanism between sertraline and tetracycline. The fractional inhibitory concentration index for tetracycline and sertraline in E. coli APEC_O2 was 0.5. In addition, in the presence of ½ MIC of sertraline, the sensitivity of E. coli APEC_O2 to tetracycline could be restored according to clinical standards (from 64 to 4 mg l⁻¹). RNA data suggest changes in respiration that is likely to decrease intracellular pH and thereby the proton-motive force, which provides the energy for the tetracycline efflux pump. Furthermore, sertraline and tetracycline may induce a change from oxidation to fermentation in the E.coli, which further decreases pH, resulting in cell death. This study shows that sertraline interacts with tetracycline in a synergistic and AcrAB-TolC pump-independent manner. The combinational treatment was further shown to induce many changes in the global transcriptome, including altered tetA and tetR expression. The results indicate that sertraline may be used as a helper compound with the aim to reverse tetracycline resistance encoded by tetA.

Effect of Tetracycline Dose and Treatment Mode on Selection of Resistant Coliform Bacteria in Nursery Pigs

This study describes the results of a randomized clinical trial investigating the effect of oxytetracycline treatment dose and mode of administration on the selection of antibiotic-resistant coliform bacteria in fecal samples from nursery pigs. Nursery pigs (pigs of 4 to 7 weeks of age) in five pig herds were treated with oxytetracycline for Lawsonia intracellularis-induced diarrhea. Each group was randomly allocated to one of five treatment groups: oral flock treatment with a (i) high (20 mg/kg of body weight), (ii) medium (10 mg/kg), or (iii) low (5 mg/kg) dose, (iv) oral pen-wise (small-group) treatment (10 mg/kg), and (v) individual intramuscular injection treatment (10 mg/kg). All groups were treated once a day for 5 days. In all groups, treatment caused a rise in the numbers and proportions of tetracycline-resistant coliform bacteria right after treatment, followed by a significant drop by the time that the pigs left the nursery unit. The counts and proportions of tetracycline-resistant coliforms did not vary significantly between treatment groups, except immediately after treatment, when the highest treatment dose resulted in the highest number of resistant coliforms. A control group treated with tiamulin did not show significant changes in the numbers or proportions of tetracycline-resistant coliforms. Selection for tetracycline-resistant coliforms was significantly correlated to selection for ampicillin- and sulfonamide-resistant strains but not to selection for cefotaxime-resistant strains. In conclusion, the difference in the dose of oxytetracycline and the way in which the drug was applied did not cause significantly different levels of selection of tetracycline-resistant coliform bacteria under the conditions tested.IMPORTANCE Antimicrobial resistance is a global threat to human health. Treatment of livestock with antimicrobials has a direct impact on this problem, and there is a need to improve the ways that we use antimicrobials in livestock production. We hypothesized that antibiotic resistance development following treatment of diarrhea in nursery pigs could be reduced either by lowering the dose of oxytetracycline or by replacing the commonly used practice of flock treatment with individual or small-group treatments, since this would reduce the number of pigs treated. However, the study showed no significant difference between treatment groups with respect to the number or proportion of tetracycline-resistant coliforms selected. The most important conclusion is that under practical field conditions, there will be no added value, in terms of lowering resistance development, by exchanging flock treatment for individual or small-group treatment of nursery pigs. The reason for the lack of an effect of single-animal treatment is probably that such animals share the environment with treated animals and take up resistant bacteria from the environment.

Genotype variation and genetic relationship among Escherichia coli from nursery pigs located in different pens in the same farm

BACKGROUND

So far, little is known about the genetic diversity and relatedness among Escherichia coli (E. coli) populations in the gut of swine. Information on this is required to improve modeling studies on antimicrobial resistance aiming to fight its occurrence and development. This work evaluated the genotype variation of E. coli isolated from swine fecal samples at the single pig and pen level, as well as between pens using repetitive extragenic palindromic (REP) PCR fingerprinting and pulsed field gel electrophoresis (PFGE). The genetic diversity of strains collected from media supplemented with ampicillin or tetracycline was also investigated. Besides, the genetic relationship of strains within each pen, between pens, as well as among strains within each group isolated from media with or without antibiotic, was assessed.

RESULTS

REP-PCR patterns (N = 75) were generated for all the isolates (N = 720). Two profiles (REP_2 and REP_5) dominated, accounting for 23.7 and 23.3% of all isolates, respectively. At the pig and at the pen level, the number of different strains ranged from two to eight, and from 27 to 31, respectively, and multiple isolates from a single pen were found to be identical; however, in some of the pens, additional strains occurred at a lower frequency. E. coli isolates yielding different REP profiles were subjected to PFGE and led to 41 different genotypes which were also compared.

CONCLUSIONS

Despite the presence of dominant strains, our results suggest a high genetic diversity of E. coli strains exist at the pen level and between pens. Selection with antibiotic seems to not affect the genetic diversity. The dominant REP profiles were the same found in a previous study in Denmark, which highlights that the same predominant strains are circulating in pigs of this country and might represent the archetypal E.coli commensal in pigs.

Limitations of MIC as sole metric of pharmacodynamic response across the range of antimicrobial susceptibilities within a single bacterial species

The minimum inhibitory concentration (MIC) of an antimicrobial drug for a bacterial pathogen is used as a measure of the bacterial susceptibility to the drug. However, relationships between the antimicrobial concentration, bacterial susceptibility, and the pharmacodynamic (PD) inhibitory effect on the bacterial population are more complex. The relationships can be captured by multi-parameter models such as the E_max model. In this study, time-kill experiments were conducted with a zoonotic pathogen Pasteurella multocida and the fluoroquinolone enrofloxacin. Pasteurella multocida isolates with enrofloxacin MIC of 0.01 μg/mL, 1.5 μg/mL, and 2.0 μg/mL were used. An additive inhibitory E_max model was fitted to the data on bacterial population growth inhibition at different enrofloxacin concentrations. The values of PD parameters such as maximal growth inhibition, concentration achieving a half of the maximal inhibition, and Hill coefficient that captures steepness of the relationships between the concentration and effect, varied between the isolate with low MIC and less susceptible isolates. While enrofloxacin PD against the isolate with low MIC exhibited the expected concentration-dependent characteristics, the PD against the less susceptible isolates demonstrated time-dependent characteristics. The results demonstrate that bacterial antimicrobial susceptibility may need to be described by a combination of parameters rather than a single parameter of the MIC.

Evaluation of automated time-lapse microscopy for assessment of in vitro activity of antibiotics

This study aimed to evaluate the potential of a new time-lapse microscopy based method (oCelloScope) to efficiently assess the in vitro antibacterial effects of antibiotics. Two E. coli and one P. aeruginosa strain were exposed to ciprofloxacin, colistin, ertapenem and meropenem in 24-h experiments. Background corrected absorption (BCA) derived from the oCelloScope was used to detect bacterial growth. The data obtained with the oCelloScope were compared with those of the automated Bioscreen C method and standard time-kill experiments and a good agreement in results was observed during 6-24h of experiments. Viable counts obtained at 1, 4, 6 and 24h during oCelloScope and Bioscreen C experiments were well correlated with the corresponding BCA and optical density (OD) data. Initial antibacterial effects during the first 6h of experiments were difficult to detect with the automated methods due to their high detection limits (approximately 10⁵CFU/mL for oCelloScope and 10⁷CFU/mL for Bioscreen C), the inability to distinguish between live and dead bacteria and early morphological changes of bacteria during exposure to ciprofloxacin, ertapenem and meropenem. Regrowth was more frequently detected in time-kill experiments, possibly related to the larger working volume with an increased risk of pre-existing or emerging resistance. In comparison with Bioscreen C, the oCelloScope provided additional information on bacterial growth dynamics in the range of 10⁵ to 10⁷CFU/mL and morphological features. In conclusion, the oCelloScope would be suitable for detection of in vitro effects of antibiotics, especially when a large number of regimens need to be tested.

Modeling the growth dynamics of multiple Escherichia coli strains in the pig intestine following intramuscular ampicillin treatment

Background

This study evaluated how dosing regimen for intramuscularly-administered ampicillin, composition of Escherichia coli strains with regard to ampicillin susceptibility, and excretion of bacteria from the intestine affected the level of resistance among Escherichia coli strains in the intestine of nursery pigs. It also examined the dynamics of the composition of bacterial strains during and after the treatment. The growth responses of strains to ampicillin concentrations were determined using in vitro growth curves. Using these results as input data, growth predictions were generated using a mathematical model to simulate the competitive growth of E. coli strains in a pig intestine under specified plasma concentration profiles of ampicillin.

Results

In vitro growth results demonstrated that the resistant strains did not carry a fitness cost for their resistance, and that the most susceptible strains were more affected by increasing concentrations of antibiotics that the rest of the strains. The modeling revealed that short treatment duration resulted in lower levels of resistance and that dosing frequency did not substantially influence the growth of resistant strains. Resistance levels were found to be sensitive to the number of competing strains, and this effect was enhanced by longer duration of treatment. High excretion of bacteria from the intestine favored resistant strains over sensitive strains, but at the same time it resulted in a faster return to pre-treatment levels after the treatment ended. When the duration of high excretion was set to be limited to the treatment time (i.e. the treatment was assumed to result in a cure of diarrhea) resistant strains required longer time to reach the previous level.

Conclusion

No fitness cost was found to be associated with ampicillin resistance in E. coli. Besides dosing factors, epidemiological factors (such as number of competing strains and bacterial excretion) influenced resistance development and need to be considered further in relation to optimal treatment strategies. The modeling approach used in the study is generic, and could be used for prediction of the effect of treatment with other drugs and other administration routes for effect on resistance development in the intestine of pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0823-3) contains supplementary material, which is available to authorized users.

Multistrain models predict sequential multidrug treatment strategies to result in less antimicrobial resistance than combination treatment

Background

Combination treatment is increasingly used to fight infections caused by bacteria resistant to two or more antimicrobials. While multiple studies have evaluated treatment strategies to minimize the emergence of resistant strains for single antimicrobial treatment, fewer studies have considered combination treatments. The current study modeled bacterial growth in the intestine of pigs after intramuscular combination treatment (i.e. using two antibiotics simultaneously) and sequential treatments (i.e. alternating between two antibiotics) in order to identify the factors that favor the sensitive fraction of the commensal flora.

Growth parameters for competing bacterial strains were estimated from the combined in vitro pharmacodynamic effect of two antimicrobials using the relationship between concentration and net bacterial growth rate. Predictions of in vivo bacterial growth were generated by a mathematical model of the competitive growth of multiple strains of Escherichia coli.

Results

Simulation studies showed that sequential use of tetracycline and ampicillin reduced the level of double resistance, when compared to the combination treatment. The effect of the cycling frequency (how frequently antibiotics are alternated in a sequential treatment) of the two drugs was dependent upon the order in which the two drugs were used.

Conclusion

Sequential treatment was more effective in preventing the growth of resistant strains when compared to the combination treatment. The cycling frequency did not play a role in suppressing the growth of resistant strains, but the specific order of the two antimicrobials did. Predictions made from the study could be used to redesign multidrug treatment strategies not only for intramuscular treatment in pigs, but also for other dosing routes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0724-5) contains supplementary material, which is available to authorized users.