Survivability of vancomycin resistant enterococci and fitness cost of vancomycin resistance acquisition

Multispecies coinfections and presence of antibiotics shape resistance and fitness costs in a pathogenic bacterium

Increasing antimicrobial resistance (AMR) poses a challenge for treatment of bacterial diseases. In real life, bacterial infections are typically embedded within complex multispecies communities and influenced by the environment, which can shape costs and benefits of AMR. However, knowledge of such interactions and their implications for AMR in vivo is limited. To address this knowledge gap, we investigated fitness-related traits of a pathogenic bacterium (Flavobacterium columnare) in its fish host, capturing the effects of bacterial antibiotic resistance, coinfections between bacterial strains and metazoan parasites (fluke Diplostomum pseudospathaceum) and antibiotic exposure. We quantified real-time replication and virulence of sensitive and resistant bacteria and demonstrate that both bacteria can benefit from coinfection in terms of persistence and replication, depending on the coinfecting partner and antibiotic presence. We also show that antibiotics can benefit resistant bacteria by increasing bacterial replication under coinfection with flukes. These results emphasize the importance of diverse, inter-kingdom coinfection interactions and antibiotic exposure in shaping costs and benefits of AMR, supporting their role as significant contributors to spread and long-term persistence of resistance.

The pharmacokinetic-pharmacodynamic modelling framework as a tool to predict drug resistance evolution

Pharmacokinetic-pharmacodynamic (PKPD) models, which describe how drug concentrations change over time and how that affects pathogen growth, have proven highly valuable in designing optimal drug treatments aimed at bacterial eradication. However, the fast rise of antimicrobial resistance calls for increased focus on an additional treatment optimization criterion: avoidance of resistance evolution. We demonstrate here how coupling PKPD and population genetics models can be used to determine treatment regimens that minimize the potential for antimicrobial resistance evolution. Importantly, the resulting modelling framework enables the assessment of resistance evolution in response to dynamic selection pressures, including changes in antimicrobial concentration and the emergence of adaptive phenotypes. Using antibiotics and antimicrobial peptides as an example, we discuss the empirical evidence and intuition behind individual model parameters. We further suggest several extensions of this framework that allow a more comprehensive and realistic prediction of bacterial escape from antimicrobials through various phenotypic and genetic mechanisms.

New Antimicrobial Resistance Strategies: An Adaptive Resistance Network Conferring Reduced Glycopeptide Susceptibility in VISA

Background: Vancomycin-intermediate Staphylococcus aureus (VISA) emerges typically in the healthcare-associated methicillin-resistant S. aureus and more rarely in community-acquired S. aureus (CA-MRSA). VISA is a serious concern for public health due to its association with persistent infections, the failure of vancomycin treatment, and poor clinical outcomes. Currently, the burden of VISA is somewhat high, even though vancomycin is the mainstay treatment for severe MRSA infections. The molecular mechanisms of reduced glycopeptide susceptibility in S. aureus are constantly under investigation but have still not yet been fully characterized. Methods: Our goal was to investigate the reduced glycopeptide susceptibility mechanisms emerging in a VISA CA-MRSA versus its vancomycin-susceptible (VSSA) CA-MRSA parents in a hospitalized patient undergoing glycopeptide treatment. Comparative integrated omics, Illumina MiSeq whole-genome sequencing (WGS), RNA-Seq, and bioinformatics were performed. Results: Through a comparison of VISA CA-MRSA vs. its VSSA CA-MRSA parent, mutational and transcriptomic adaptations were found in a pool of genes involved, directly or indirectly, in the biosynthesis of the glycopeptide target conferring or supporting the VISA phenotype, and its cross-resistance with daptomycin. This pool included key genes responsible for the biosynthesis of the peptidoglycan precursors, i.e., D-Ala, the D-Ala-D-Ala dipeptide termini of the pentapeptide, and its incorporation in the nascent pentapeptide, as key targets of the glycopeptide resistance. Furthermore, accessory glycopeptide-target genes involved in the pathways corroborated the key adaptations, and thus, supported the acquisition of the VISA phenotype i.e., transporters, nucleotide metabolism genes, and transcriptional regulators. Finally, transcriptional changes were also found in computationally predicted cis-acting small antisense RNA triggering genes related both to the key or accessory adaptive pathways. Conclusion: Our investigation describes an adaptive resistance pathway acquired under antimicrobial therapy conferring reduced glycopeptide susceptibility in a VISA CA-MRSA due to a comprehensive network of mutational and transcriptional adaptations in genes involved in pathways responsible for the biosynthesis of glycopeptide's target or supporters of the key resistance path.

Vancomycin Resistance in Enterococcus and Staphylococcus aureus

Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus are both common commensals and major opportunistic human pathogens. In recent decades, these bacteria have acquired broad resistance to several major classes of antibiotics, including commonly employed glycopeptides. Exemplified by resistance to vancomycin, glycopeptide resistance is mediated through intrinsic gene mutations, and/or transferrable van resistance gene cassette-carrying mobile genetic elements. Here, this review will discuss the epidemiology of vancomycin-resistant Enterococcus and S. aureus in healthcare, community, and agricultural settings, explore vancomycin resistance in the context of van and non-van mediated resistance development and provide insights into alternative therapeutic approaches aimed at treating drug-resistant Enterococcus and S. aureus infections.

Balancing the Virulence and Antimicrobial Resistance in VISA DAP-R CA-MRSA Superbug

Background: Methicillin-resistant Staphylococcus aureus (MRSA) with intermediate resistance to Vancomycin (VISA) is reported worldwide. These strains frequently emerge among hospital-associated (HA)-MRSA and rarely within community-acquired (CA)-MRSA. Here, the genomic and transcriptomic adaptations distinguishing VISA daptomycin resistant (DAP-R) CA-MRSA, which emerged in a hospitalized patient under glycopeptide treatment, were explored. Methods: Whole-genome sequencing, RNA-Seq and bioinformatics were carried out. Results: Our CA-MRSA clustered in the USA400 lineage showing additional antimicrobial resistance (AMR) versus DAP and glycopeptides. Resistomics revealed adaptations related to glycopeptide, daptomycin and rifampin resistance (mprF nsSNPS and overexpression of glycopeptide and daptomycin-resistance related genes). Similar changes were detected in virulence traits (agrA HI-nsSNPs and toxin gene underexpression), in which a decrease was observed despite the abundance of virulence-related genes. Our results predicted a balance in adaptations, decreasing the virulence and biological costs to support the co-occurrence of extensive AMR in a hypervirulent genomic background. Conclusion: Our data show that VISA DAP-R CA-MRSA shifts the potential hypervirulent behavior of CA-MRSA towards the acquisition and maintenance of extensive AMR, by a decrease in virulence and biological costs mediated by a “compensatory modulatory mutation” silencing the Agr quorum-sensing cascade.

Antibiotic Resistance Carriage Causes a Lower Survivability Due to Stress Associated with High-Pressure Treatment among Strains from Starter Cultures

Simple Summary

High-pressure processing is one of the most promising novel food preservation methods that is increasingly used in the food industry. It is applied in various food products such as dairy, meat, juices, and jams to improve safety and shelf-life by the inactivation of microorganisms and preserving of quality attributes. It is reported that the level of antibiotic resistance may influence the ability of strains to survive stress conditions. In this study, it was investigated if carrying antibiotic resistance genes affects the survival of lactic acid bacteria (Lactococcus and the former Lactobacillus) strains during high-pressure treatment. It was demonstrated that carrying antibiotic resistance genes strains showed a lower survival in response to pressure than strains carrying up to one resistance gene. The same observations were made for both genera. Appropriately selected parameters of high-pressure treatment may help in the elimination of antibiotic-resistant strains.

Abstract

High-pressure processing is one of the most promising novel food preservation methods that is increasingly used in the food industry. Its biggest advantage is that it is a nonthermal method that ensures the microbiological safety of the product while maintaining other features, including nutritional value. If products made with starter cultures are subjected to high-pressure treatment, the process parameters should be selected so as not to eliminate all microorganisms in the product. The aim of the study was to investigate if carrying antibiotic resistance genes affects the survival of lactic acid bacteria (Lactococcus and the former Lactobacillus) strains during high-pressure treatment. Survival was assessed using the plate count method. It was shown that the strains carrying antibiotic resistance genes showed a lower survival to high pressure. This might be explained by the phenomenon of fitness cost, consisting in a reduced adaptation of antibiotic-resistant strains related to metabolic expenditure. The obtained results indicate the need for further research in this field and the need to select food processing parameters depending on the strains intentionally included in the food.

Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters

Antibiotic-resistance genes (ARGs) regulated by invertible promoters can mitigate the fitness cost of maintaining ARGs in the absence of antibiotics and could potentially prolong the persistence of ARGs in bacterial populations. However, the origin, prevalence, and distribution of these ARGs regulated by invertible promoters remains poorly understood. Here, we sought to assess the threat posed by ARGs regulated by invertible promoters by systematically searching for ARGs regulated by invertible promoters in the human gut microbiome and examining their origin, prevalence, and distribution. Through metagenomic assembly of 2227 human gut metagenomes and genomic analysis of the Unified Human Gastrointestinal Genome (UHGG) collection, we identified ARGs regulated by invertible promoters and categorized them into three classes based on the invertase-regulating phase variation. In the human gut microbiome, ARGs regulated by invertible promoters are exclusively found in Bacteroidales species. Through genomic analysis, we observed that ARGs regulated by invertible promoters have convergently originated from ARG insertions into glycan-synthesis loci that were regulated by invertible promoters at least three times. Moreover, all three classes of invertible promoters regulating ARGs are located within integrative conjugative elements (ICEs). Therefore, horizontal transfer via ICEs could explain the wide taxonomic distribution of ARGs regulated by invertible promoters. Overall, these findings reveal that glycan-synthesis loci regulated by invertible promoters in Bacteroidales species are an important hotspot for the emergence of clinically-relevant ARGs regulated by invertible promoters.

Fitness cost of vancomycin-resistant Enterococcus faecium plasmids associated with hospital infection outbreaks

BACKGROUND

Vancomycin resistance is mostly associated with Enterococcus faecium due to Tn1546-vanA located on narrow- and broad-host plasmids of various families. This study's aim was to analyse the effects of acquiring Tn1546-carrying plasmids with proven epidemicity in different bacterial host backgrounds.

METHODS

Widespread Tn1546-carrying plasmids of different families RepA_N (n = 5), Inc18 (n = 4) and/or pHTβ (n = 1), and prototype plasmids RepA_N (pRUM) and Inc18 (pRE25, pIP501) were analysed. Plasmid transferability and fitness cost were assessed using E. faecium (GE1, 64/3) and Enterococcus faecalis (JH2-2/FA202/UV202) recipient strains. Growth curves (Bioscreen C) and Relative Growth Rates were obtained in the presence/absence of vancomycin. Plasmid stability was analysed (300 generations). WGS (Illumina-MiSeq) of non-evolved and evolved strains (GE1/64/3 transconjugants, n = 49) was performed. SNP calling (Breseq software) of non-evolved strains was used for comparison.

RESULTS

All plasmids were successfully transferred to different E. faecium clonal backgrounds. Most Tn1546-carrying plasmids and Inc18 and RepA_N prototypes reduced host fitness (-2% to 18%) while the cost of Tn1546 expression varied according to the Tn1546-variant and the recipient strain (9%-49%). Stability of Tn1546-carrying plasmids was documented in all cases, often with loss of phenotypic resistance and/or partial plasmid deletions. SNPs and/or indels associated with essential bacterial functions were observed on the chromosome of evolved strains, some of them linked to increased fitness.

CONCLUSIONS

The stability of E. faecium Tn1546-carrying plasmids in the absence of selective pressure and the high intra-species conjugation rates might explain the persistence of vancomycin resistance in E. faecium populations despite the significant burden they might impose on bacterial host strains.

Fitness cost and compensation mechanism of sulfonamide resistance genes (sul1, sul2, and sul3) in Escherichia coli

The fitness cost of antibiotic resistance is a crucial factor to determine the evolutionary and transmission success of resistant bacteria. Exploring the fitness cost and compensation mechanism of antibiotic resistance genes (ARGs) in bacteria may effectively reduce the transmission of drug-resistant genes in the environment. Engineered bacteria with the same genetic background that carry sulfonamide resistance gene were generated to explore the fitness cost of sulfonamide resistance gene in Escherichia coli. There were significant differences in the protein expression of the two-component system pathway (fliZ, fliA, fliC and lrhA), folate biosynthesis pathway (sul1, sul2 and sul3), ABC transporter system (ugpC, rbsA and gsiA), and outer membrane pore protein OmpD through the comparative analysis of differential proteins compared to sensitive bacteria. Thus, we could speculate the possible fitness compensation mechanism. Finally, quantitative Real-time PCR (qRT-PCR) was used to verify the functions of some differential proteins at the transcriptional level. The fitness cost and compensatory evolution of antibiotic resistance are an essential part of bacterial evolution.

Spinning and Fully Integrated Microdevice for Rapid Screening of Vancomycin-Resistant Enterococcus

This study introduces a spinning and fully integrated paper-based microdevice that can perform multiple functions, including DNA extraction, amplification, and colorimetric detection, for monitoring two major vancomycin-resistant Enterococci (VREs), which carry the vanA and vanB genes. The spinning microdevice is composed of a stationary part and a spinning part. The square-shaped stationary part has two zones: the lysis and reaction zones. The spinning part, which has a spin wheel-like shape, was inserted perpendicularly into the stationary part so that its two semicircles remained on the upper and lower parts. Sodium hydroxide-treated glass microfiber filter discs, inserted in the upper semicircle, were soaked in the lysis chambers by folding them toward the lysis zone to capture DNA in the lysis chambers. The captured DNA was transferred to the reaction chambers by folding the discs toward the reaction chambers. Water was added to the sodium hydroxide-treated glass microfiber filter discs to elute purified DNA into the reaction chambers. The upper semicircle was then unfolded, and the reaction chambers were sealed for subsequent loop-mediated isothermal amplification (LAMP) for 45 min. After the reaction, the spinning part was spun in the lysis zone direction to bring the lower semicircle, inserted with phenolphthalein-treated glass microfiber filter discs, toward the upper part of the stationary part. By folding it toward the reaction chambers, the lower semicircle came into contact with them and the phenolphthalein-treated glass microfiber filter discs were soaked in the reaction chambers and expressed color after 30 s. Based on the pH change during the LAMP reaction, the phenolphthalein-treated discs remained pink in the absence of target DNA, while those in contact with the positive samples turned colorless. A sensitive detection with a VRE limit of detection of 10² CFU/mL for tap water spiked with VRE carrying the vanA gene was achieved using this microdevice. Both VREs, carrying vanA and vanB genes, were successfully identified from tap water and contaminated equipment surfaces within 75 min. The introduced microdevice demonstrated a rapid, accurate, and sensitive performance for the environmental assessment of VRE contamination in resource-limited regions.

The Antimicrobial Resistance Crisis: An Inadvertent, Unfortunate but Nevertheless Informative Experiment in Evolutionary Biology

The global rise of antimicrobial resistance (AMR) phenotypes is an exemplar for rapid evolutionary response. Resistance arises as a consequence of humanity’s widespread and largely indiscriminate use of antimicrobial compounds. However, some features of this crisis remain perplexing. The remarkably widespread and rapid rise of diverse, novel and effective resistance phenotypes is in stark contrast to the apparent paucity of antimicrobial producers in the global microbiota. From the viewpoint of evolutionary theory, it should be possible to use selection coefficients to examine these phenomena. In this work we introduce an elaboration on the selection coefficient s termed selective efficiency, considering the genetic, metabolic, ecological and evolutionary impacts that accompany selective phenotypes. We then demonstrate the utility of the selective efficiency concept using AMR and antimicrobial production phenotypes as ‘worked examples’ of the concept. In accomplishing this objective, we also put forward cogent hypotheses to explain currently puzzling aspects of the AMR crisis. Finally, we extend the selective efficiency concept into a consideration of the ongoing management of the AMR crisis.

Prevalence of vancomycin-resistant enterococcus in Africa in one health approach: a systematic review and meta-analysis

Vancomycin-resistant enterococci are a global challenge currently as reported by the World Health Organization. It is also important to recognize that combating antimicrobial resistance needs to recognize the interconnections between people, animals, plants and their shared environment in creating public health, the so-called One Health approach. Although the presence of VRE has been described in many regions of the world, there is a lack of comprehensive data indicating their prevalence of in Africa. Therefore, this study aimed to aggregate the result of studies describing VRE reported across multiple regions in Africa. A literature search was conducted on PubMed, Google scholar, and Hinari with the term “Vancomycin resistance enterococcus in Africa” on August 1–3, 2019. All available articles were downloaded to “Endnote version 7.1” then to Microsoft Word 2013. Articles determined to meet our criteria for the review was extracted to Microsoft Excel 2013. Those articles that reported the prevalence of vancomycin resistance Enterococcus obtained from all sample types and published from 2010 to 2019 in the English language were included for the review. A meta-analysis was conducted with OpenMetaAnalyst version R.3.1.0 software. The effect size was determined using a binary random effect model and statically significant considered when p < 0.05. Heterogeneity determined with the inconsistency index. A leave one out analysis used to perform the sensitivity analysis. There were 151 articles identified from the database searches; of this, 36 articles included after extensive review with two independent authors. Out of 4073 samples collected, 1488 isolates identified with an overall pooled prevalence of VRE 26.8% (95% CI; 10.7–43.0%) in Africa with a one-health perspective. The analysis showed that considerable heterogeneity among the studies (I² = 99.97%; p < 0.001). Subgroup analysis in-country, African region, laboratory method, year of publication, and sample source showed that a high prevalence was identified from South Africa (74.8%), South African regions (74.8%), PCR (959.2%), 2010–2015 years (30.3%) and environmental (52.2%), respectively. This meta-analysis indicates that there was a high-pooled prevalence of vancomycin-resistant enterococci in African. A lot should be done to prevent and control the transmission of vancomycin resistance enterococci to a human being from the environment in the continent.

Vancomycin resistance plasmids affect persistence of Enterococcus faecium in water

Vancomycin resistant enterococci (VRE) cause 20,000 infections annually in the United States, most of which are nosocomial. Recent findings of VRE in sewage-contaminated surface waters demonstrate an alternate route of human exposure, and a possible setting for horizontal gene exchange facilitated by plasmids and other mobile genetic elements. Maintenance of antibiotic resistance genes and proteins may, however, present a fitness cost in the absence of selective pressure, particularly in habitats such as environmental waters that are not optimal for gut-associated bacteria. Nutrient levels, which are transiently elevated following sewage spills, may also affect survival. We tested the hypotheses that nutrients and/or plasmids conferring vancomycin resistance affect Enterococcus faecium survival in river water by measuring decay of strains that differed only by their plasmid, under natural and augmented nutrient conditions. In natural river water, decay rate (log₁₀ reduction) correlated directly with plasmid size; however, plasmid presence and size had no effect on decay rate when nutrients levels were augmented. Under natural nutrient levels, the vancomycin-resistant strain with the largest plasmid (200 kb) decayed significantly more rapidly than the plasmid-less, susceptible parent strain, in contrast to similar decay rates among strains under augmented nutrient conditions. This work is among the first to show that plasmids conferring antibiotic resistance affect fitness of Enterococcus species in secondary habitats such as surface water. The nutrient-dependent nature of the fitness cost suggests that conveyance of VRE to environmental waters in nutrient-rich sewage may prolong survival of these pathogens, providing greater opportunity for host infection and/or horizontal gene transfer.

Survivability and fitness cost of heterogeneous vancomycin-intermediate Staphylococcus aureus

The aim of this study was to observe the survivability and fitness cost of heterogeneous vancomycin-intermediate Staphylococcus aureus(hVISA) isolates. Survivability study was performed on dry cotton swab, and fitness cost was evaluated by estimating growth kinetics and generation time constant in BACTEC automated system. Total mean maximum time of recovery on primary culture was 4.1 and 7.1 weeks (P = 0.0001) for hVISA and vancomycin-sensitive S. aureus (VSSA), respectively, in dry starved condition. No significant difference between the mean value of lag phase duration (P = 0.89) was noted between hVISA and VSSA isolate in growth kinetics. However, we observed lesser generation time of hVISA isolates compared to S. aureus ATCC 29213 (P = 0.0076). This study concluded that a significant difference in generation time between VSSA and hVISA and suggests that hVISA have fitness cost compared to VSSA. However, further studies with more cases are required.

Evolution of Cost-Free Resistance under Fluctuating Drug Selection in Pseudomonas aeruginosa

Antibiotic resistance is a global problem that greatly impacts human health. How resistance persists, even in the absence of antibiotic treatment, is thus a public health problem of utmost importance. In this study, we explored the antibiotic treatment conditions under which cost-free resistance arises, using experimental evolution of the bacterium Pseudomonas aeruginosa and the quinolone antibiotic ciprofloxacin. We found that intermittent antibiotic treatment led to the evolution of cost-free resistance and demonstrate that compensatory evolution is the mechanism responsible for cost-free resistance. Our results suggest that discontinuous administration of antibiotic may be contributing to the high levels of antibiotic resistance currently found worldwide.

Antibiotic resistance evolves rapidly in response to drug selection, but it can also persist at appreciable levels even after the removal of the antibiotic. This suggests that many resistant strains can both be resistant and have high fitness in the absence of antibiotics. To explore the conditions under which high-fitness, resistant strains evolve and the genetic changes responsible, we used a combination of experimental evolution and whole-genome sequencing to track the acquisition of ciprofloxacin resistance in the opportunistic pathogen Pseudomonas aeruginosa under conditions of constant and fluctuating antibiotic delivery patterns. We found that high-fitness, resistant strains evolved readily under fluctuating but not constant antibiotic conditions and that their evolution was underlain by a trade-off between resistance and fitness. Whole-genome sequencing of evolved isolates revealed that resistance was gained through mutations in known resistance genes and that second-site mutations generally compensated for costs associated with resistance in the fluctuating treatment, leading to the evolution of cost-free resistance. Our results suggest that current therapies involving intermittent administration of antibiotics are contributing to the maintenance of antibiotic resistance at high levels in clinical settings.

IMPORTANCE Antibiotic resistance is a global problem that greatly impacts human health. How resistance persists, even in the absence of antibiotic treatment, is thus a public health problem of utmost importance. In this study, we explored the antibiotic treatment conditions under which cost-free resistance arises, using experimental evolution of the bacterium Pseudomonas aeruginosa and the quinolone antibiotic ciprofloxacin. We found that intermittent antibiotic treatment led to the evolution of cost-free resistance and demonstrate that compensatory evolution is the mechanism responsible for cost-free resistance. Our results suggest that discontinuous administration of antibiotic may be contributing to the high levels of antibiotic resistance currently found worldwide.

Application of high resolution melting assay (HRM) to study temperature-dependent intraspecific competition in a pathogenic bacterium

Studies on species’ responses to climate change have focused largely on the direct effect of abiotic factors and in particular temperature, neglecting the effects of biotic interactions in determining the outcome of climate change projections. Many microbes rely on strong interference competition; hence the fitness of many pathogenic bacteria could be a function of both their growth properties and intraspecific competition. However, due to technical challenges in distinguishing and tracking individual strains, experimental evidence on intraspecific competition has been limited so far. Here, we developed a robust application of the high-resolution melting (HRM) assay to study head-to-head competition between mixed genotype co-cultures of a waterborne bacterial pathogen of fish, Flavobacterium columnare, at two different temperatures. We found that competition outcome in liquid cultures seemed to be well predicted by growth yield of isolated strains, but was mostly inconsistent with interference competition results measured in inhibition tests on solid agar, especially as no growth inhibition between strain pairs was detected at the higher temperature. These results suggest that, for a given temperature, the factors driving competition outcome differ between liquid and solid environments.

Molecular Detection of the Virulent ExoU Genotype of Pseudomonas aeruginosa Isolated from Infected Surgical Incisions

BACKGROUND

Pseudomonas aeruginosa is one of the major pathogens responsible for hospital-acquired infections, which harbor a wide array of virulence factors. The main aim of this study was to determine the frequency of the virulent ExoU genotype in relation to the ExoS genotype among isolated P. aeruginosa from infected surgical incisions, followed by phylogenetic analysis.

METHODS

A total of 66 P. aeruginosa isolates were identified by cultural and biochemical characteristics. All isolates were tested for antimicrobial susceptibility against the following antimicrobial agents: imipenem, amikacin, gentamicin, amoxycillin, cefotaxime, cefepime, and levofloxacin. Molecular detection of the ExoS and ExoU as well as two other virulence genes was done by polymerase chain reaction (PCR). Sequencing of ExoU gene and phylogenetic analysis was performed.

RESULTS

Approximately 81% of the isolated P. aeruginosa were multi-drug resistant. The ExoS genotype was more prevalent (63%) among the isolates than the ExoU genotype (18%), with 9% of the isolates possessing both toxins. LasB and AprA were detected in 63.6% and 27.2% of the isolates, respectively. An association was observed between the number of virulence genes and the presence of multi-drug resistance. All the ExoU were multi-drug resistant (MDR), whereas 71% of the ExoS were MDR. Phylogenetic analysis of ExoU gene showed a 99% similarity with four different strains.

CONCLUSION

Despite the greater frequency of the ExoS genotype, the presence of the virulent MDR ExoU genotype isolates from surgical site infections is an alarming sign requiring further intervention and investigations.

Emergence of linezolid resistance in hepatobiliary infections caused by Enterococcus faecium

Enterococcal infections are common in liver transplantation and hepatopancreaticobiliary (HPB) surgery. Linezolid is frequently used to treat not only vancomycin-resistant Enterococcus (VRE), but also vancomycin-sensitive Enterococcus (VSE) infections, and resistance can develop. This study evaluated all the Liver Unit patients who developed infections with linezolid-resistant Enterococcus (LRE) in order to elicit the association with prior linezolid usage, to explore possible risk factors for infection, and to better understand the epidemiology of these isolates in this patient group. Between 2010 and 2015, infections with LRE developed in 10 patients (8 following liver transplantation and 2 following HPB surgery) after 22-108 days of treatment. Selected pulsed-field gel electrophoresis demonstrated that 2 out of 10 patients were cocolonized with different strains and indicated that cross-transmission may have occurred. In conclusion, in this group of patients with complex hepatobiliary infections, the optimal antibiotic strategies for the treatment of Enterococcus faecium infections are not clearly defined, and there is a significant risk of emergence of resistance to linezolid in E. faecium after exposure to this agent in patients, especially in the presence of a deep source of infection on a background of hepatic artery insufficiency. Caution is needed when using prolonged courses of linezolid in this setting, and further studies are necessary to determine the optimum treatment.

Malthusian Parameters as Estimators of the Fitness of Microbes: A Cautionary Tale about the Low Side of High Throughput

The maximum exponential growth rate, the Malthusian parameter (MP), is commonly used as a measure of fitness in experimental studies of adaptive evolution and of the effects of antibiotic resistance and other genes on the fitness of planktonic microbes. Thanks to automated, multi-well optical density plate readers and computers, with little hands-on effort investigators can readily obtain hundreds of estimates of MPs in less than a day. Here we compare estimates of the relative fitness of antibiotic susceptible and resistant strains of E. coli, Pseudomonas aeruginosa and Staphylococcus aureus based on MP data obtained with automated multi-well plate readers with the results from pairwise competition experiments. This leads us to question the reliability of estimates of MP obtained with these high throughput devices and the utility of these estimates of the maximum growth rates to detect fitness differences.

The fitness costs of antibiotic resistance mutations

Antibiotic resistance is increasing in pathogenic microbial populations and is thus a major threat to public health. The fate of a resistance mutation in pathogen populations is determined in part by its fitness. Mutations that suffer little or no fitness cost are more likely to persist in the absence of antibiotic treatment. In this review, we performed a meta-analysis to investigate the fitness costs associated with single mutational events that confer resistance. Generally, these mutations were costly, although several drug classes and species of bacteria on average did not show a cost. Further investigations into the rate and fitness values of compensatory mutations that alleviate the costs of resistance will help us to better understand both the emergence and management of antibiotic resistance in clinical settings.

Optimal control of vancomycin-resistant enterococci using preventive care and treatment of infections

The rising prevalence of vancomycin-resistant enterococci (VRE) is a major health problem in intensive care units (ICU) because of its association with increased mortality and high health care costs. We present a mathematical framework for determining cost-effective strategies for prevention and treatment of VRE in the ICU. A system of five ordinary differential equations describes the movement of ICU patients in and out of five VRE-related states. Two control variables representing the prevention and treatment of VRE are incorporated into the system. The basic reproductive number is derived and calculated for different levels of the two controls. An optimal control problem is formulated to minimize VRE-related deaths and costs associated with prevention and treatment controls over a finite time period. Numerical solutions illustrate optimal single and dual allocations of the controls for various cost values. Results show that preventive care has the greatest impact in reducing the basic reproductive number, while treatment of VRE infections has the most impact on reducing VRE-related deaths.

Vancomycin-resistant enterococci colonization-infection model: parameter impacts and outbreak risks

Vancomycin-resistant enterococci (VRE) infections have been linked to increased mortality and costs. A new model of a VRE-infested intensive care unit (ICU) is introduced. It incorporates critical features including the difference between colonization and infection, the role of special preventive care treatment cycles, fitness cost, and antibiotic use. Five patient stages are considered: susceptible, colonized with and without special preventive care, and infected with and without treatment. Parameter ranges are determined representing different ICUs and incorporated to numerically simulate the model. Basic reproductive number of the infection is derived and the impacts of the parameters are analysed. Strategies to minimize VRE infections and outbreak risk are explored with a focus on efficient and simultaneous control of critical parameters. In particular, threshold values of the level of special preventive care and ICU compliance rate are given to achieve desired goals under various constraints.

Fitness cost of fluoroquinolone resistance in Campylobacter coli and Campylobacter jejuni

In this study, the fitness cost of fluoroquinolone resistance was evaluated in vitro, on food matrices, and in vivo, using Campylobacter coli and Campylobacter jejuni in vitro selected mutants. In vitro, the growth rate of the susceptible (wild type) and resistant (mutant) strains did not differ when cultured separately. However, by conducting sequential passages of mixed cultures, the ratio of the resistant mutant to the susceptible strain decreased for C. coli but not for C. jejuni. When the wild type and the mutant were co-inoculated on food matrices, mutants were no longer detectable 3 to 5 days after artificial contamination, but the wild-type strains remained detectable for over 13 days. In mono-inoculated animals, no difference was observed between wild-type and mutant fecal titers. When co-inoculated into chickens, the susceptible strain outcompeted the resistant mutant for C. coli and for C. jejuni. However, for C. coli, if the resistant strain was already present in animals, it could persist at high titers in the digestive tract even in the presence of the wild-type strain. Together, these findings suggest that, depending on strain and study conditions, fluoroquinolone resistance can impose a fitness cost on Campylobacter.

Impact of multidrug-resistant Pseudomonas aeruginosa infection on patient outcomes

Rates of antibiotic resistance in Pseudomonas aeruginosa are increasing worldwide. The multidrug-resistant (MDR) phenotype in P. aeruginosa could be mediated by several mechanisms including multidrug efflux systems, enzyme production, outer membrane protein (porin) loss and target mutations. Currently, no international consensus on the definition of multidrug resistance exists, making direct comparison of the literature difficult. Inappropriate empirical therapy has been associated with increased mortality in P. aeruginosa infections; delays in starting appropriate therapy may contribute to increased length of hospital stay and persistence of infection. In addition, worse clinical outcomes may be associated with MDR infections owing to limited effective antimicrobial options. This article aims to summarize the contemporary literature on patient outcomes following infections caused by drug-resistant P. aeruginosa. The impact of antimicrobial therapy on patient outcomes, mortality and morbidity; and the economic impact of MDR P. aeruginosa infections will be examined.

Inducible expression eliminates the fitness cost of vancomycin resistance in enterococci

Inducible vancomycin resistance in enterococci is due to a sophisticated mechanism that combines synthesis of cell wall peptidoglycan precursors with low affinity for glycopeptides and elimination of the normal target precursors. Although this dual mechanism, which involves seven genes organized in two operons, is predicted to have a high fitness cost, resistant enterococci have disseminated worldwide. We have evaluated the biological cost of VanB-type resistance due to acquisition of conjugative transposon Tn1549 in Enterococcus faecium and Enterococcus faecalis. Because fitness was dependent on the integration site of Tn1549, an isogenic set of E. faecalis was constructed to determine the cost of inducible or constitutive expression of resistance or of carriage of Tn1549. A luciferase gene was inserted in the integrase gene of the transposon to allow differential quantification of the strains in cocultures and in the digestive tract of gnotobiotic mice. Both in vitro and in vivo, carriage of inactivated or inducible Tn1549 had no cost for the host in the absence of induction by vancomycin. In contrast, induced or constitutively resistant strains not only had reduced fitness but were severely impaired in colonization ability and dissemination among mice. These data indicate that tight regulation of resistance expression drastically reduces the biological cost associated with vancomycin resistance in Enterococcus spp. and accounts for the widespread dissemination of these strains. Our findings are in agreement with the observation that regulation of expression is common in horizontally acquired resistance and represents an efficient evolutionary pathway for resistance determinants to become selectively neutral.

The role of antibiotics and antibiotic resistance in nature

Investigations of antibiotic resistance from an environmental prospective shed new light on a problem that was traditionally confined to a subset of clinically relevant antibiotic-resistant bacterial pathogens. It is clear that the environmental microbiota, even in apparently antibiotic-free environments, possess an enormous number and diversity of antibiotic resistance genes, some of which are very similar to the genes circulating in pathogenic microbiota. It is difficult to explain the role of antibiotics and antibiotic resistance in natural environments from an anthropocentric point of view, which is focused on clinical aspects such as the efficiency of antibiotics in clearing infections and pathogens that are resistant to antibiotic treatment. A broader overview of the role of antibiotics and antibiotic resistance in nature from the evolutionary and ecological prospective suggests that antibiotics have evolved as another way of intra- and inter-domain communication in various ecosystems. This signalling by non-clinical concentrations of antibiotics in the environment results in adaptive phenotypic and genotypic responses of microbiota and other members of the community. Understanding the complex picture of evolution and ecology of antibiotics and antibiotic resistance may help to understand the processes leading to the emergence and dissemination of antibiotic resistance and also help to control it, at least in relation to the newer antibiotics now entering clinical practice.

Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste

Antibiotics are used in animal livestock production for therapeutic treatment of disease and at subtherapeutic levels for growth promotion and improvement of feed efficiency. It is estimated that approximately 75% of antibiotics are not absorbed by animals and are excreted in waste. Antibiotic resistance selection occurs among gastrointestinal bacteria, which are also excreted in manure and stored in waste holding systems. Land application of animal waste is a common disposal method used in the United States and is a means for environmental entry of both antibiotics and genetic resistance determinants. Concerns for bacterial resistance gene selection and dissemination of resistance genes have prompted interest about the concentrations and biological activity of drug residues and break-down metabolites, and their fate and transport. Fecal bacteria can survive for weeks to months in the environment, depending on species and temperature, however, genetic elements can persist regardless of cell viability. Phylogenetic analyses indicate antibiotic resistance genes have evolved, although some genes have been maintained in bacteria before the modern antibiotic era. Quantitative measurements of drug residues and levels of resistance genes are needed, in addition to understanding the environmental mechanisms of genetic selection, gene acquisition, and the spatiotemporal dynamics of these resistance genes and their bacterial hosts. This review article discusses an accumulation of findings that address aspects of the fate, transport, and persistence of antibiotics and antibiotic resistance genes in natural environments, with emphasis on mechanisms pertaining to soil environments following land application of animal waste effluent.

Acquired vancomycin resistance in clinically relevant pathogens

Acquired resistance to vancomycin is an increasing problem in pathogenic bacteria. It is best studied and most prevalent among Enterococcus and still remains rare in other pathogenic bacteria. Different genotypes of vancomycin resistance, vanA–G, have been described. The different van gene clusters consist of up to nine genes encoding proteins of different functions; their interplay leads to an alternative cell wall precursor less susceptible to glycopeptide binding. Variants of vanA and vanB types are found worldwide, with vanA predominating; their reservoir is Enterococcus faecium. Within this species a subpopulation of hospital-adapted types exists that acquired van gene clusters and which is responsible for outbreaks of vancomycin-resistant enterococci all over the world. Acquisition of vanA by methicillin-resistant Staphylococcus aureus (MRSA) is worrisome and seven cases have been described. Nonsusceptibility to glycopeptides also occurs independently from van genes and is a growing therapeutic challenge, especially in MRSA.

Mechanism and fitness costs of PR-39 resistance in Salmonella enterica serovar Typhimurium LT2

PR-39 is a porcine antimicrobial peptide that kills bacteria with a mechanism that does not involve cell lysis. Here, we demonstrate that Salmonella enterica serovar Typhimurium can rapidly acquire mutations that reduce susceptibility to PR-39. Resistant mutants appeared at a rate of 0.4 x 10(-6) per cell per generation. These mutants were about four times more resistant than the wild type and showed a greatly reduced rate of killing. Genetic analysis revealed mutations in the putative transport protein SbmA as being responsible for the observed resistance. These sbmA mutants were as fit as the wild-type parental strain as measured by growth rates in culture medium and mice and by long-term survival in stationary phase. These results suggest that resistance to certain antimicrobial peptides can rapidly develop without an obvious fitness cost for the bacteria and that resistance development could become a threat to the efficacy of antimicrobial peptides if used in a clinical setting.

Vancomycin-resistant enterococcus in critical care areas

Colonization with VRE must be identified to prevent the spread of the disease and the progression to infection in susceptible individuals. PCR assays and culturing techniques allow nurses and other members of the health care team to identify and treat colonized and infected patients. Although currently there is no effective treatment for VRE colonization, isolation precautions are paramount to prevent increased VRE transmission. Decolonization techniques should be considered in high-risk populations. For those who have clinical evidence of VRE infection, several approved treatment regimens can be implemented. The increasing incidence of VRE with simultaneous increasing resistance patterns demands the development of new antimicrobial agents. Collaborative management of both VRE colonization and infection can reduce the sky-rocketing numbers of hospital acquired infections and mortality from VRE infections.

The biological cost of mutational antibiotic resistance: any practical conclusions?

A key parameter influencing the rate and trajectory of the evolution of antibiotic resistance is the fitness cost of resistance. Recent studies have demonstrated that antibiotic resistance, whether caused by target alteration or by other mechanisms, generally confers a reduction in fitness expressed as reduced growth, virulence or transmission. These findings imply that resistance might be reversible, provided antibiotic use is reduced. However, several processes act to stabilize resistance, including compensatory evolution where the fitness cost is ameliorated by additional mutation without loss of resistance, the rare occurrence of cost-free resistance mechanisms and genetic linkage or co-selection between the resistance markers and other selected markers. Conceivably we can use this knowledge to rationally choose and design targets and drugs where the costs of resistance are the highest, and where the likelihood of compensation is the lowest.