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1.
Nat Commun ; 15(1): 2610, 2024 Mar 23.
Article in English | MEDLINE | ID: mdl-38521779

ABSTRACT

The rise of antibiotic resistance is a critical public health concern, requiring an understanding of mechanisms that enable bacteria to tolerate antimicrobial agents. Bacteria use diverse strategies, including the amplification of drug-resistance genes. In this paper, we showed that multicopy plasmids, often carrying antibiotic resistance genes in clinical bacteria, can rapidly amplify genes, leading to plasmid-mediated phenotypic noise and transient antibiotic resistance. By combining stochastic simulations of a computational model with high-throughput single-cell measurements of blaTEM-1 expression in Escherichia coli MG1655, we showed that plasmid copy number variability stably maintains populations composed of cells with both low and high plasmid copy numbers. This diversity in plasmid copy number enhances the probability of bacterial survival in the presence of antibiotics, while also rapidly reducing the burden of carrying multiple plasmids in drug-free environments. Our results further support the tenet that multicopy plasmids not only act as vehicles for the horizontal transfer of genetic information between cells but also as drivers of bacterial adaptation, enabling rapid modulation of gene copy numbers. Understanding the role of multicopy plasmids in antibiotic resistance is critical, and our study provides insights into how bacteria can transiently survive lethal concentrations of antibiotics.


Subject(s)
Anti-Bacterial Agents , Escherichia coli , Plasmids/genetics , Anti-Bacterial Agents/pharmacology , Drug Resistance, Microbial/genetics , Escherichia coli/genetics , Gene Dosage , Drug Resistance, Bacterial/genetics
2.
Proc Natl Acad Sci U S A ; 120(51): e2314135120, 2023 Dec 19.
Article in English | MEDLINE | ID: mdl-38096417

ABSTRACT

Conjugative plasmids play a key role in the dissemination of antimicrobial resistance (AMR) genes across bacterial pathogens. AMR plasmids are widespread in clinical settings, but their distribution is not random, and certain associations between plasmids and bacterial clones are particularly successful. For example, the globally spread carbapenem resistance plasmid pOXA-48 can use a wide range of enterobacterial species as hosts, but it is usually associated with a small number of specific Klebsiella pneumoniae clones. These successful associations represent an important threat for hospitalized patients. However, knowledge remains limited about the factors determining AMR plasmid distribution in clinically relevant bacteria. Here, we combined in vitro and in vivo experimental approaches to analyze pOXA-48-associated AMR levels and conjugation dynamics in a collection of wild-type enterobacterial strains isolated from hospitalized patients. Our results revealed significant variability in these traits across different bacterial hosts, with Klebsiella spp. strains showing higher pOXA-48-mediated AMR and conjugation frequencies than Escherichia coli strains. Using experimentally determined parameters, we developed a simple mathematical model to interrogate the contribution of AMR levels and conjugation permissiveness to plasmid distribution in bacterial communities. The simulations revealed that a small subset of clones, combining high AMR levels and conjugation permissiveness, play a critical role in stabilizing the plasmid in different polyclonal microbial communities. These results help to explain the preferential association of plasmid pOXA-48 with K. pneumoniae clones in clinical settings. More generally, our study reveals that species- and strain-specific variability in plasmid-associated phenotypes shape AMR evolution in clinically relevant bacterial communities.


Subject(s)
Anti-Bacterial Agents , Permissiveness , Humans , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Drug Resistance, Bacterial/genetics , Plasmids/genetics , Klebsiella pneumoniae/genetics , Klebsiella/genetics , Escherichia coli/genetics , Bacteria/genetics
3.
Adv Healthc Mater ; 12(30): e2301548, 2023 12.
Article in English | MEDLINE | ID: mdl-37315950

ABSTRACT

Blockage of blood supply while administering chemotherapy to tumors, using trans-arterial chemoembolization (TACE), is the most common treatment for intermediate and advanced-stage unresectable Hepatocellular carcinoma (HCC). However, HCC is characterized by a poor prognosis and high recurrence rates (≈30%), partly due to a hypoxic pro-angiogenic and pro-cancerous microenvironment. This study investigates how modifying tissue stress while improving drug exposure in target organs may maximize the therapeutic outcomes. Porous degradable polymeric microspheres (MS) are designed to obtain a gradual occlusion of the hepatic artery that nourishes the liver, while enabling efficient drug perfusion to the tumor site. The fabricated porous MS are introduced intrahepatically and designed to release a combination therapy of Doxorubicin (DOX) and Tirapazamine (TPZ), which is a hypoxia-activated prodrug. Liver cancer cell lines that are treated with the combination therapy under hypoxia reveal a synergic anti-proliferation effect. An orthotopic liver cancer model, based on N1-S1 hepatoma in rats, is used for the efficacy, biodistribution, and safety studies. Porous DOX-TPZ MS are very effective in suppressing tumor growth in rats, and induction tissue necrosis is associated with high intratumor drug concentrations. Porous particles without drugs show some advantages over nonporous particles, suggesting that morphology may affect the treatment outcomes.


Subject(s)
Carcinoma, Hepatocellular , Chemoembolization, Therapeutic , Liver Neoplasms , Rats , Animals , Liver Neoplasms/drug therapy , Carcinoma, Hepatocellular/drug therapy , Microspheres , Tissue Distribution , Porosity , Doxorubicin/pharmacology , Doxorubicin/therapeutic use , Tirapazamine/pharmacology , Tirapazamine/therapeutic use , Hypoxia/drug therapy , Tumor Microenvironment
4.
Am Nat ; 201(5): 659-679, 2023 05.
Article in English | MEDLINE | ID: mdl-37130231

ABSTRACT

AbstractHost-parasite coevolution is expected to drive the evolution of genetic diversity because the traits used in arms races-namely, host range and parasite resistance-are hypothesized to trade off with traits used in resource competition. We therefore tested data for several trade-offs among 93 isolates of bacteriophage λ and 51 Escherichia coli genotypes that coevolved during a laboratory experiment. Surprisingly, we found multiple trade-ups (positive trait correlations) but little evidence of several canonical trade-offs. For example, some bacterial genotypes evaded a trade-off between phage resistance and absolute fitness, instead evolving simultaneous improvements in both traits. This was surprising because our experimental design was predicted to expose resistance-fitness trade-offs by culturing E. coli in a medium where the phage receptor, LamB, is also used for nutrient acquisition. On reflection, LamB mediates not one but many trade-offs, allowing for more complex trait interactions than just pairwise trade-offs. Here, we report that mathematical reasoning and laboratory data highlight how trade-ups should exist whenever an evolutionary system exhibits multiple interacting trade-offs. Does this mean that coevolution should not promote genetic diversity? No, quite the contrary. We deduce that whenever positive trait correlations are observed in multidimensional traits, other traits may trade off and so provide the right circumstances for diversity maintenance. Overall, this study reveals that there are predictive limits when data account only for pairwise trait correlations, and it argues that a wider range of circumstances than previously anticipated can promote genetic and species diversity.


Subject(s)
Bacteriophages , Escherichia coli , Escherichia coli/genetics , Mutation , Phenotype , Host Specificity , Bacteriophages/genetics , Biological Evolution
5.
Ecol Evol ; 12(12): e9469, 2022 Dec.
Article in English | MEDLINE | ID: mdl-36479025

ABSTRACT

Plasmids are extra-chromosomal genetic elements that encode a wide variety of phenotypes and can be maintained in bacterial populations through vertical and horizontal transmission, thus increasing bacterial adaptation to hostile environmental conditions like those imposed by antimicrobial substances. To circumvent the segregational instability resulting from randomly distributing plasmids between daughter cells upon division, nontransmissible plasmids tend to be carried in multiple copies per cell, with the added benefit of exhibiting increased gene dosage and resistance levels. But carrying multiple copies also results in a high metabolic burden to the bacterial host, therefore reducing the overall fitness of the population. This trade-off poses an existential question for plasmids: What is the optimal plasmid copy number? In this manuscript, we address this question by postulating and analyzing a population genetics model to evaluate the interaction between selective pressure, the number of plasmid copies carried by each cell, and the metabolic burden associated with plasmid bearing in the absence of selection for plasmid-encoded traits. Parameter values of the model were estimated experimentally using Escherichia coli K12 carrying a multicopy plasmid encoding for a fluorescent protein and bla TEM-1, a gene conferring resistance to ß-lactam antibiotics. By numerically determining the optimal plasmid copy number for constant and fluctuating selection regimes, we show that plasmid copy number is a highly optimized evolutionary trait that depends on the rate of environmental fluctuation and balances the benefit between increased stability in the absence of selection with the burden associated with carrying multiple copies of the plasmid.

6.
Mol Biol Evol ; 39(9)2022 09 01.
Article in English | MEDLINE | ID: mdl-36062982

ABSTRACT

Bacterial adaptation to stressful environments often produces evolutionary constraints whereby increases in resistance are associated with reduced fitness in a different environment. The exploitation of this resistance-cost trade-off has been proposed as the basis of rational antimicrobial treatment strategies designed to limit the evolution of drug resistance in bacterial pathogens. Recent theoretical, laboratory, and clinical studies have shown that fluctuating selection can maintain drug efficacy and even restore drug susceptibility, but can also increase the rate of adaptation and promote cross-resistance to other antibiotics. In this paper, we combine mathematical modeling, experimental evolution, and whole-genome sequencing to follow evolutionary trajectories towards ß-lactam resistance under fluctuating selective conditions. Our experimental model system consists of eight populations of Escherichia coli K12 evolving in parallel to a serial dilution protocol designed to dynamically control the strength of selection for resistance. We implemented adaptive ramps with mild and strong selection, resulting in evolved populations with similar levels of resistance, but with different evolutionary dynamics and diverging genotypic profiles. We found that mutations that emerged under strong selection are unstable in the absence of selection, in contrast to resistance mutations previously selected in the mild selection regime that were stably maintained in drug-free environments and positively selected for when antibiotics were reintroduced. Altogether, our population dynamics model and the phenotypic and genomic analysis of the evolved populations show that the rate of resistance adaptation is contingent upon the strength of selection, but also on evolutionary constraints imposed by prior drug exposures.


Subject(s)
Drug Resistance, Bacterial , Escherichia coli , Adaptation, Physiological/genetics , Anti-Bacterial Agents/pharmacology , Drug Resistance, Bacterial/genetics , Escherichia coli/genetics , Mutation
7.
Front Microbiol ; 12: 606396, 2021.
Article in English | MEDLINE | ID: mdl-34803935

ABSTRACT

With plasmid-mediated antibiotic resistance thriving and threatening to become a serious public health problem, it is paramount to increase our understanding of the forces that enable the spread and maintenance of drug resistance genes encoded in mobile genetic elements. The relevance of plasmids as vehicles for the dissemination of antibiotic resistance genes, in addition to the extensive use of plasmid-derived vectors for biotechnological and industrial purposes, has promoted the in-depth study of the molecular mechanisms controlling multiple aspects of a plasmids' life cycle. This body of experimental work has been paralleled by the development of a wealth of mathematical models aimed at understanding the interplay between transmission, replication, and segregation, as well as their consequences in the ecological and evolutionary dynamics of plasmid-bearing bacterial populations. In this review, we discuss theoretical models of plasmid dynamics that span from the molecular mechanisms of plasmid partition and copy-number control occurring at a cellular level, to their consequences in the population dynamics of complex microbial communities. We conclude by discussing future directions for this exciting research topic.

8.
Nat Commun ; 12(1): 2653, 2021 05 11.
Article in English | MEDLINE | ID: mdl-33976161

ABSTRACT

Plasmid persistence in bacterial populations is strongly influenced by the fitness effects associated with plasmid carriage. However, plasmid fitness effects in wild-type bacterial hosts remain largely unexplored. In this study, we determined the fitness effects of the major antibiotic resistance plasmid pOXA-48_K8 in wild-type, ecologically compatible enterobacterial isolates from the human gut microbiota. Our results show that although pOXA-48_K8 produced an overall reduction in bacterial fitness, it produced small effects in most bacterial hosts, and even beneficial effects in several isolates. Moreover, genomic results showed a link between pOXA-48_K8 fitness effects and bacterial phylogeny, helping to explain plasmid epidemiology. Incorporating our fitness results into a simple population dynamics model revealed a new set of conditions for plasmid stability in bacterial communities, with plasmid persistence increasing with bacterial diversity and becoming less dependent on conjugation. These results help to explain the high prevalence of plasmids in the greatly diverse natural microbial communities.


Subject(s)
Bacteria/genetics , Gene Transfer, Horizontal , Genes, Bacterial/genetics , Genetic Variation , Genome, Bacterial/genetics , Plasmids/genetics , Algorithms , Anti-Bacterial Agents/pharmacology , Bacteria/classification , Drug Resistance, Multiple, Bacterial/genetics , Enterobacteriaceae/classification , Enterobacteriaceae/genetics , Gastrointestinal Microbiome/genetics , Humans , Microbiota/genetics , Phylogeny , Species Specificity
10.
Environ Microbiol ; 23(5): 2448-2460, 2021 05.
Article in English | MEDLINE | ID: mdl-33626217

ABSTRACT

Sulfonolipids (SLs) are bacterial lipids that are structurally related to sphingolipids. Synthesis of this group of lipids seems to be mainly restricted to Flavobacterium, Cytophaga and other members of the phylum Bacteroidetes. These lipids have a wide range of biological activities: they can induce multicellularity in choanoflagellates, act as von Willebrand factor receptor antagonists, inhibit DNA polymerase, or function as tumour suppressing agents. In Flavobacterium johnsoniae, their presence seems to be required for efficient gliding motility. Until now, no genes/enzymes involved in SL synthesis have been identified, which has been limiting for the study of some of the biological effects these lipids have. Here, we describe the identification of the cysteate-fatty acyl transferase Fjoh_2419 required for synthesis of the SL precursor capnine in F. johnsoniae. This enzyme belongs to the α-oxoamine synthase family similar to serine palmitoyl transferases, 2-amino-3-oxobutyrate coenzyme A ligase and 8-amino-7-oxononanoate synthases. Expression of the gene fjoh_2419 in Escherichia coli caused the formation of a capnine-derived molecule. Flavobacterium johnsoniae mutants deficient in fjoh_2419 lacked SLs and were more sensitive to many antibiotics. Mutant growth was not affected in liquid medium but the cells exhibited defects in gliding motility.


Subject(s)
Cysteic Acid , Flavobacterium , Alkanesulfonic Acids , Bacterial Proteins/genetics , Flavobacterium/genetics
11.
Rev. Ciênc. Méd. Biol. (Impr.) ; 19(3): 430-440, dez 5, 2020. tab, fig
Article in English | LILACS | ID: biblio-1357939

ABSTRACT

Objective: evaluation of antibiotic resistance in Gram-negative microbiota from ready-to-eat cheese samples. Methodology: this research applied an adapted methodology to select from a food sample viable Gram-negative microbiota displaying antibiotic resistance. The selected food was a cheese that is commonly consumed without thermal processing, the Minas Frescal cheese. The evaluation was followed by a PCR screening in this resistant microbiota, for genes that provide resistance to antibiotics and also to the quaternary ammonium. Results: all cheese samples harbored a resistant microbiota. In 13.3% of the cheese samples analyzed, the resistance reached all ten different antibiotics tested and, in 80%, 8 to 10 different antibiotics. In antibiotics considered critics as the carbapenems: ertapenem presented resistant microbiota in 86.7% of the samples. In cephalosporins, the resistance reached 100% in the third generation (ceftazidime) and almost half of the samples (46.7%) in the fourth generation (cefepime). In genotypic research, seven different resistance genes were found in 69.2% of the bacterial pools, including the beta-lactamase-producing genes ctx, tem, shv, tetracycline-resistant genes, and a high rate of integrons class 1 and 2. Conclusion: the results indicate phenotypically and genotypically that the Minas Frescal cheese can harbor potential resistant microbiota. Therefore, the methodology used is a viable possibility and with a broader answer about the food microbiota role in resistance. This research corroborates the food area as an important sector to be managed to reduce the process of antibiotic resistance.


Objetivo: avaliação da resistência a antibióticos em microbiota Gram-negativa de amostras de queijo prontas para consumo. Metodologia: esta pesquisa aplicou uma metodologia adaptada para selecionar a microbiota Gram-negativa viável apresentando resistência a antibióticos em uma amostra de alimento. O alimento selecionado foi um queijo frequentemente consumido sem processamento térmico, o queijo Minas Frescal. A avaliação foi seguida de uma triagem por PCR, nesta microbiota resistente, para genes que fornecem resistência aos antibióticos e também ao quaternário de amônio. Resultados: todas as amostras de queijo apresentaram microbiota resistente. Em 13,3% dos queijos analisados essa resistência alcançou todos os 10 diferentes antibióticos testados e em 80% entre 8 e 10 antibióticos diferentes. Em antibióticos considerados críticos como os carbapenêmicos: ertapenem apresentou microbiota resistente em 86,7% das amostras. Nas cefalosporinas, a resistência atingiu 100% na terceira geração (ceftazidima) e quase a metade das amostras (46,7%) na quarta geração (cefepime). Na pesquisa genotípica, sete diferentes genes de resistência foram encontrados em 69,2% dos pools bacterianos, incluindo o genes produtores de beta-lactamase, genes de resistência à tetraciclina, ctx, tem, shv e uma alta taxa de integron classe 1 e 2. Conclusão: os resultados indicam fenotipicamente e genotipicamente que o queijo Minas Frescal pode apresentar uma potencial microbiota resistente. Portanto, a metodologia utilizada é uma possibilidade viável e com uma resposta mais ampla sobre o papel da microbiota na resistência. Esta pesquisa corrobora a área de alimentos como um setor importante a ser gerenciado para redução no processo de resistência a antibióticos.


Subject(s)
Drug Resistance, Microbial , Carbapenems , Cephalosporins , Cheese , Food , Gram-Negative Bacteria
12.
Article in English | MEDLINE | ID: mdl-32820131

ABSTRACT

SUMMARY: Well-differentiated thyroid cancer (WDTC), including papillary, follicular, and Hurthle-cell types, is characterized by a slow course and usually remain localized to the thyroid. However, a minority of these cases develop distant metastases with the most common sites being lungs, bones, and lymph nodes. Liver metastases of WDTC are rare and are usually found along with other distant metastases sites and in a multiple or diffuse pattern of spread. The recognition of distant metastasis in WDTC has a significant impact on the treatment and prognosis. However, because of their low incidence and awareness, distant metastases are often diagnosed late. Herein, we describe a case of a 71 years old woman who during routine surveillance of a follicular variant of papillary thyroid cancer (FV-PTC), 5 years after being treated for her primary thyroid tumor, was found to have a single liver metastasis and underwent liver segmental resection. This case highlights the importance of maintaining vigilant surveillance of patients with WDTC, and illustrates the possibility of unique metastasis at unexpected sites. Further studies are needed to understand the organ tropism of some WDTC leading to distant metastases development and to better prediction of an aggressive course. LEARNING POINTS: WDTC patients with distant metastases have a poor prognosis with a 10-year survival of about 50%. The most common sites of distant metastases are lung, bone and lymph nodes. Liver metastases are rare in WDTC, are usually multiple or diffuse and are found along with other distant metastases sites. Single liver metastasis of WDTC is an unexpected pattern of spread, and very few cases are reported in the literature. Rare sites of distant metastases in WDTC can manifest many years after the primary tumor, stressing the importance of maintaining vigilant surveillance. More studies are needed to predict which WDTC tumors may develop a more aggressive course, allowing clinicians to individualize patient management.

13.
Proc Natl Acad Sci U S A ; 117(27): 15755-15762, 2020 07 07.
Article in English | MEDLINE | ID: mdl-32571917

ABSTRACT

Mobile genetic elements (MGEs), such as plasmids, promote bacterial evolution through horizontal gene transfer (HGT). However, the rules governing the repertoire of traits encoded on MGEs remain unclear. In this study, we uncovered the central role of genetic dominance shaping genetic cargo in MGEs, using antibiotic resistance as a model system. MGEs are typically present in more than one copy per host bacterium, and as a consequence, genetic dominance favors the fixation of dominant mutations over recessive ones. In addition, genetic dominance also determines the phenotypic effects of horizontally acquired MGE-encoded genes, silencing recessive alleles if the recipient bacterium already carries a wild-type copy of the gene. The combination of these two effects governs the catalog of genes encoded on MGEs. Our results help to understand how MGEs evolve and spread, uncovering the neglected influence of genetic dominance on bacterial evolution. Moreover, our findings offer a framework to forecast the spread and evolvability of MGE-encoded genes, which encode traits of key human interest, such as virulence or antibiotic resistance.


Subject(s)
Bacteria/genetics , Evolution, Molecular , Gene Transfer, Horizontal/genetics , Interspersed Repetitive Sequences/genetics , Drug Resistance, Bacterial/genetics , Humans , Plasmids/genetics , Virulence/genetics
14.
J R Soc Interface ; 16(158): 20190363, 2019 09 27.
Article in English | MEDLINE | ID: mdl-31506045

ABSTRACT

The current crisis of antimicrobial resistance in clinically relevant pathogens has highlighted our limited understanding of the ecological and evolutionary forces that drive drug resistance adaptation. For instance, although human tissues are highly heterogeneous, most of our mechanistic understanding about antibiotic resistance evolution is based on constant and well-mixed environmental conditions. A consequence of considering spatial heterogeneity is that, even if antibiotics are prescribed at high dosages, the penetration of drug molecules through tissues inevitably produces antibiotic gradients, exposing bacterial populations to a range of selective pressures and generating a dynamic fitness landscape that changes in space and time. In this paper, we will use a combination of mathematical modelling and computer simulations to study the population dynamics of susceptible and resistant strains competing for resources in a network of micro-environments with varying degrees of connectivity. Our main result is that highly connected environments increase diffusion of drug molecules, enabling resistant phenotypes to colonize a larger number of spatial locations. We validated this theoretical result by culturing fluorescently labelled Escherichia coli in 3D-printed devices that allow us to control the rate of diffusion of antibiotics between neighbouring compartments and quantify the spatio-temporal distribution of resistant and susceptible bacterial cells.


Subject(s)
Adaptation, Physiological/drug effects , Anti-Bacterial Agents , Drug Resistance, Bacterial , Escherichia coli/growth & development , Evolution, Molecular , Models, Biological , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacokinetics , Anti-Bacterial Agents/pharmacology
15.
Horm Metab Res ; 51(1): 35-41, 2019 Jan.
Article in English | MEDLINE | ID: mdl-30497091

ABSTRACT

Metabolic syndrome is a group of disorders which include obesity, diabetes, dyslipidemias, and hypertension. This condition is rapidly increasing in an aging population. The rates of surgery in older patients is also growing and a wide range of operations including minimally invasive procedures is now available for this segment of the population. The number of patients suffering from postoperative adhesions is therefore correspondingly increasing. In addition to preventing and treating the metabolic disease itself, improved therapeutic strategies for the prevention of surgical adhesions have to be developed. Here we review the existing and novel treatment options.


Subject(s)
Metabolic Syndrome/surgery , Postoperative Complications/etiology , Tissue Adhesions/etiology , Age Factors , Animals , Humans , Metabolic Syndrome/complications , Postoperative Complications/prevention & control , Risk Factors , Tissue Adhesions/prevention & control
16.
Nat Ecol Evol ; 2(5): 873-881, 2018 05.
Article in English | MEDLINE | ID: mdl-29632354

ABSTRACT

Understanding the mechanisms governing innovation is a central element of evolutionary theory. Novel traits usually arise through mutations in existing genes, but trade-offs between new and ancestral protein functions are pervasive and constrain the evolution of innovation. Classical models posit that evolutionary innovation circumvents the constraints imposed by trade-offs through genetic amplifications, which provide functional redundancy. Bacterial multicopy plasmids provide a paradigmatic example of genetic amplification, yet their role in evolutionary innovation remains largely unexplored. Here, we reconstructed the evolution of a new trait encoded in a multicopy plasmid using TEM-1 ß-lactamase as a model system. Through a combination of theory and experimentation, we show that multicopy plasmids promote the coexistence of ancestral and novel traits for dozens of generations, allowing bacteria to escape the evolutionary constraints imposed by trade-offs. Our results suggest that multicopy plasmids are excellent platforms for evolutionary innovation, contributing to explain their extreme abundance in bacteria.


Subject(s)
Biological Evolution , Escherichia coli/genetics , Genetic Fitness , Plasmids/physiology , beta-Lactamases/metabolism , Bacteria/genetics , Escherichia coli/physiology , Models, Biological , Phenotype
17.
Mol Biol Evol ; 34(4): 802-817, 2017 04 01.
Article in English | MEDLINE | ID: mdl-28096304

ABSTRACT

Can we exploit our burgeoning understanding of molecular evolution to slow the progress of drug resistance? One role of an infection clinician is exactly that: to foresee trajectories to resistance during antibiotic treatment and to hinder that evolutionary course. But can this be done at a hospital-wide scale? Clinicians and theoreticians tried to when they proposed two conflicting behavioral strategies that are expected to curb resistance evolution in the clinic, these are known as "antibiotic cycling" and "antibiotic mixing." However, the accumulated data from clinical trials, now approaching 4 million patient days of treatment, is too variable for cycling or mixing to be deemed successful. The former implements the restriction and prioritization of different antibiotics at different times in hospitals in a manner said to "cycle" between them. In antibiotic mixing, appropriate antibiotics are allocated to patients but randomly. Mixing results in no correlation, in time or across patients, in the drugs used for treatment which is why theorists saw this as an optimal behavioral strategy. So while cycling and mixing were proposed as ways of controlling evolution, we show there is good reason why clinical datasets cannot choose between them: by re-examining the theoretical literature we show prior support for the theoretical optimality of mixing was misplaced. Our analysis is consistent with a pattern emerging in data: neither cycling or mixing is a priori better than the other at mitigating selection for antibiotic resistance in the clinic. Key words: : antibiotic cycling, antibiotic mixing, optimal control, stochastic models.


Subject(s)
Anti-Bacterial Agents/pharmacology , Dose-Response Relationship, Drug , Drug Resistance, Bacterial/drug effects , Drug Resistance, Microbial/drug effects , Biological Evolution , Evolution, Molecular , Hospitals , Humans , Models, Biological , Models, Theoretical , Treatment Outcome
18.
Mob Genet Elements ; 5(3): 1-5, 2015.
Article in English | MEDLINE | ID: mdl-26442180

ABSTRACT

In theory, plasmids can only be maintained in a population when the rate of horizontal gene transfer is larger than the combined effect of segregational loss and the decrease of fitness associated with plasmid carriage. Recent advances in genome sequencing have shown, however, that a large fraction of plasmids do not carry the genes necessary for conjugation or mobilization. So, how are so-called non-transmissible plasmids able to persist? In order to address this question, we examined a previously published evolutionary model based on the interaction between P. aeruginosa and the non-transmissible plasmid pNUK73. Both our in silico and in vitro results demonstrated that, although compensatory adaptation can decrease the rate of plasmid decay, the conditions for the maintenance of a non-transmissible plasmid are very stringent if the genes it carries are not beneficial to the bacterial host. This result suggests that apparently non-transmissible plasmids may still experience episodes of horizontal gene transfer occurring at very low frequencies, and that these scattered transmission events are sufficient to stabilize these plasmids. We conclude by discussing different genomic and microbiological approaches that could allow for the detection of these rare transmission events and thus to obtain a reliable estimate of the rate of horizontal gene transfer.

19.
PLoS Biol ; 13(4): e1002104, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25853342

ABSTRACT

We need to find ways of enhancing the potency of existing antibiotics, and, with this in mind, we begin with an unusual question: how low can antibiotic dosages be and yet bacterial clearance still be observed? Seeking to optimise the simultaneous use of two antibiotics, we use the minimal dose at which clearance is observed in an in vitro experimental model of antibiotic treatment as a criterion to distinguish the best and worst treatments of a bacterium, Escherichia coli. Our aim is to compare a combination treatment consisting of two synergistic antibiotics to so-called sequential treatments in which the choice of antibiotic to administer can change with each round of treatment. Using mathematical predictions validated by the E. coli treatment model, we show that clearance of the bacterium can be achieved using sequential treatments at antibiotic dosages so low that the equivalent two-drug combination treatments are ineffective. Seeking to treat the bacterium in testing circumstances, we purposefully study an E. coli strain that has a multidrug pump encoded in its chromosome that effluxes both antibiotics. Genomic amplifications that increase the number of pumps expressed per cell can cause the failure of high-dose combination treatments, yet, as we show, sequentially treated populations can still collapse. However, dual resistance due to the pump means that the antibiotics must be carefully deployed and not all sublethal sequential treatments succeed. A screen of 136 96-h-long sequential treatments determined five of these that could clear the bacterium at sublethal dosages in all replicate populations, even though none had done so by 24 h. These successes can be attributed to a collateral sensitivity whereby cross-resistance due to the duplicated pump proves insufficient to stop a reduction in E. coli growth rate following drug exchanges, a reduction that proves large enough for appropriately chosen drug switches to clear the bacterium.


Subject(s)
Anti-Bacterial Agents/administration & dosage , Escherichia coli/drug effects , Anti-Bacterial Agents/pharmacology , Dose-Response Relationship, Drug , Drug Administration Schedule , Drug Resistance, Multiple, Bacterial/genetics , Escherichia coli/genetics
20.
PLoS Biol ; 12(8): e1001928, 2014 Aug.
Article in English | MEDLINE | ID: mdl-25136970

ABSTRACT

Phenotypic heterogeneity can confer clonal groups of organisms with new functionality. A paradigmatic example is the bistable expression of virulence genes in Salmonella typhimurium, which leads to phenotypically virulent and phenotypically avirulent subpopulations. The two subpopulations have been shown to divide labor during S. typhimurium infections. Here, we show that heterogeneous virulence gene expression in this organism also promotes survival against exposure to antibiotics through a bet-hedging mechanism. Using microfluidic devices in combination with fluorescence time-lapse microscopy and quantitative image analysis, we analyzed the expression of virulence genes at the single cell level and related it to survival when exposed to antibiotics. We found that, across different types of antibiotics and under concentrations that are clinically relevant, the subpopulation of bacterial cells that express virulence genes shows increased survival after exposure to antibiotics. Intriguingly, there is an interplay between the two consequences of phenotypic heterogeneity. The bet-hedging effect that arises through heterogeneity in virulence gene expression can protect clonal populations against avirulent mutants that exploit and subvert the division of labor within these populations. We conclude that bet-hedging and the division of labor can arise through variation in a single trait and interact with each other. This reveals a new degree of functional complexity of phenotypic heterogeneity. In addition, our results suggest a general principle of how pathogens can evade antibiotics: Expression of virulence factors often entails metabolic costs and the resulting growth retardation could generally increase tolerance against antibiotics and thus compromise treatment.


Subject(s)
Adaptation, Physiological/genetics , Anti-Bacterial Agents/pharmacology , Gene Expression Regulation, Bacterial/drug effects , Salmonella typhimurium/genetics , Salmonella typhimurium/pathogenicity , Adaptation, Physiological/drug effects , Genes, Bacterial , Mutation/genetics , Salmonella typhimurium/drug effects , Salmonella typhimurium/physiology , Selection, Genetic/drug effects , Virulence/drug effects , Virulence/genetics
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