51
|
Hallinen KM, Karslake J, Wood KB. Delayed antibiotic exposure induces population collapse in enterococcal communities with drug-resistant subpopulations. eLife 2020; 9:e52813. [PMID: 32207406 PMCID: PMC7159880 DOI: 10.7554/elife.52813] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 03/16/2020] [Indexed: 12/18/2022] Open
Abstract
The molecular underpinnings of antibiotic resistance are increasingly understood, but less is known about how these molecular events influence microbial dynamics on the population scale. Here, we show that the dynamics of E. faecalis communities exposed to antibiotics can be surprisingly rich, revealing scenarios where increasing population size or delaying drug exposure can promote population collapse. Specifically, we demonstrate how density-dependent feedback loops couple population growth and antibiotic efficacy when communities include drug-resistant subpopulations, leading to a wide range of behavior, including population survival, collapse, or one of two qualitatively distinct bistable behaviors where survival is favored in either small or large populations. These dynamics reflect competing density-dependent effects of different subpopulations, with growth of drug-sensitive cells increasing but growth of drug-resistant cells decreasing effective drug inhibition. Finally, we demonstrate how populations receiving immediate drug influx may sometimes thrive, while identical populations exposed to delayed drug influx collapse.
Collapse
Affiliation(s)
- Kelsey M Hallinen
- Department of Biophysics, University of MichiganAnn ArborUnited States
| | - Jason Karslake
- Department of Biophysics, University of MichiganAnn ArborUnited States
| | - Kevin B Wood
- Department of Biophysics, University of MichiganAnn ArborUnited States
- Department of Physics, University of MichiganAnn ArborUnited States
| |
Collapse
|
52
|
Ciccarese D, Zuidema A, Merlo V, Johnson DR. Interaction-dependent effects of surface structure on microbial spatial self-organization. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190246. [PMID: 32200742 DOI: 10.1098/rstb.2019.0246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Surface-attached microbial communities consist of different cell types that, at least to some degree, organize themselves non-randomly across space (referred to as spatial self-organization). While spatial self-organization can have important effects on the functioning, ecology and evolution of communities, the underlying determinants of spatial self-organization remain unclear. Here, we hypothesize that the presence of physical objects across a surface can have important effects on spatial self-organization. Using pairs of isogenic strains of Pseudomonas stutzeri, we performed range expansion experiments in the absence or presence of physical objects and quantified the effects on spatial self-organization. We demonstrate that physical objects create local deformities along the expansion frontier, and these deformities increase in magnitude during range expansion. The deformities affect the densities of interspecific boundaries and diversity along the expansion frontier, and thus affect spatial self-organization, but the effects are interaction-dependent. For competitive interactions that promote sectorized patterns of spatial self-organization, physical objects increase the density of interspecific boundaries and diversity. By contrast, for cross-feeding interactions that promote dendritic patterns, they decrease the density of interspecific boundaries and diversity. These qualitatively different outcomes are probably caused by fundamental differences in the orientations of the interspecific boundaries. Thus, in order to predict the effects of physical objects on spatial self-organization, information is needed regarding the interactions present within a community and the general geometric shapes of spatial self-organization that emerge from those interactions. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
Collapse
Affiliation(s)
- Davide Ciccarese
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Anita Zuidema
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Valeria Merlo
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| |
Collapse
|
53
|
Wu F, Tan C. Dead bacterial absorption of antimicrobial peptides underlies collective tolerance. J R Soc Interface 2020; 16:20180701. [PMID: 30958185 DOI: 10.1098/rsif.2018.0701] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The collective tolerance towards antimicrobial peptides (APs) is thought to occur primarily through mechanisms associated with live bacterial cells. In contrast to the focus on live cells, we discover that the LL37 antimicrobial peptide kills a subpopulation of Escherichia coli, forming dead cells that absorb the remaining LL37 from the environment. Combining mathematical modelling with population and single-cell experiments, we show that bacteria absorb LL37 at a timing that coincides with the permeabilization of their cytoplasmic membranes. Furthermore, we show that one bacterial strain can absorb LL37 and protect another strain from killing by LL37. Finally, we demonstrate that the absorption of LL37 by dead bacteria can be reduced using a peptide adjuvant. In contrast to the known collective tolerance mechanisms, we show that the absorption of APs by dead bacteria is a dynamic process that leads to emergent population behaviour.
Collapse
Affiliation(s)
- Fan Wu
- Department of Biomedical Engineering, University of California Davis , Davis, CA 95616 , USA
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis , Davis, CA 95616 , USA
| |
Collapse
|
54
|
Galera-Laporta L, Garcia-Ojalvo J. Antithetic population response to antibiotics in a polybacterial community. SCIENCE ADVANCES 2020; 6:eaaz5108. [PMID: 32181369 PMCID: PMC7060062 DOI: 10.1126/sciadv.aaz5108] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/05/2019] [Indexed: 05/31/2023]
Abstract
Much is known about the effects of antibiotics on isolated bacterial species, but their influence on polybacterial communities is less understood. Here, we study the joint response of a mixed community of nonresistant Bacillus subtilis and Escherichia coli bacteria to moderate concentrations of the β-lactam antibiotic ampicillin. We show that when the two organisms coexist, their population response to the antibiotic is opposite to that in isolation: Whereas in monoculture B. subtilis is tolerant and E. coli is sensitive to ampicillin, in coculture it is E. coli who can proliferate in the presence of the antibiotic, while B. subtilis cannot. This antithetic behavior is predicted by a mathematical model constrained only by the responses of the two species in isolation. Our results thus show that the collective response of mixed bacterial ecosystems to antibiotics can run counter to what single-species potency studies tell us about their efficacy.
Collapse
|
55
|
Dynamic motility selection drives population segregation in a bacterial swarm. Proc Natl Acad Sci U S A 2020; 117:4693-4700. [PMID: 32060120 DOI: 10.1073/pnas.1917789117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Population expansion in space, or range expansion, is widespread in nature and in clinical settings. Space competition among heterogeneous subpopulations during range expansion is essential to population ecology, and it may involve the interplay of multiple factors, primarily growth and motility of individuals. Structured microbial communities provide model systems to study space competition during range expansion. Here we use bacterial swarms to investigate how single-cell motility contributes to space competition among heterogeneous bacterial populations during range expansion. Our results revealed that motility heterogeneity can promote the spatial segregation of subpopulations via a dynamic motility selection process. The dynamic motility selection is enabled by speed-dependent persistence time bias of single-cell motion, which presumably arises from physical interaction between cells in a densely packed swarm. We further showed that the dynamic motility selection may contribute to collective drug tolerance of swarming colonies by segregating subpopulations with transient drug tolerance to the colony edge. Our results illustrate that motility heterogeneity, or "motility fitness," can play a greater role than growth rate fitness in determining the short-term spatial structure of expanding populations.
Collapse
|
56
|
Foreman R, Wollman R. Mammalian gene expression variability is explained by underlying cell state. Mol Syst Biol 2020; 16:e9146. [PMID: 32043799 PMCID: PMC7011657 DOI: 10.15252/msb.20199146] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 12/04/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
Gene expression variability in mammalian systems plays an important role in physiological and pathophysiological conditions. This variability can come from differential regulation related to cell state (extrinsic) and allele-specific transcriptional bursting (intrinsic). Yet, the relative contribution of these two distinct sources is unknown. Here, we exploit the qualitative difference in the patterns of covariance between these two sources to quantify their relative contributions to expression variance in mammalian cells. Using multiplexed error robust RNA fluorescent in situ hybridization (MERFISH), we measured the multivariate gene expression distribution of 150 genes related to Ca2+ signaling coupled with the dynamic Ca2+ response of live cells to ATP. We show that after controlling for cellular phenotypic states such as size, cell cycle stage, and Ca2+ response to ATP, the remaining variability is effectively at the Poisson limit for most genes. These findings demonstrate that the majority of expression variability results from cell state differences and that the contribution of transcriptional bursting is relatively minimal.
Collapse
Affiliation(s)
- Robert Foreman
- Institute for Quantitative and Computational BiosciencesUniversity of California, Los AngelesLos AngelesCAUSA
- Program in Bioinformatics and Systems BiologyUniversity of California, San DiegoSan DiegoCAUSA
| | - Roy Wollman
- Institute for Quantitative and Computational BiosciencesUniversity of California, Los AngelesLos AngelesCAUSA
- Program in Bioinformatics and Systems BiologyUniversity of California, San DiegoSan DiegoCAUSA
- Department of Integrative Biology and PhysiologyDepartment of Chemistry and BiochemistryUniversity of California, Los AngelesLos AngelesCAUSA
| |
Collapse
|
57
|
Carvalho G, Forestier C, Mathias JD. Antibiotic resilience: a necessary concept to complement antibiotic resistance? Proc Biol Sci 2019; 286:20192408. [PMID: 31795866 DOI: 10.1098/rspb.2019.2408] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Resilience is the capacity of systems to recover their initial state or functions after a disturbance. The concepts of resilience and resistance are complementary in ecology and both represent different aspects of the stability of ecosystems. However, antibiotic resilience is not used in clinical bacteriology whereas antibiotic resistance is a recognized major problem. To join the fields of ecology and clinical bacteriology, we first review the resilience concept from ecology, socio-ecological systems and microbiology where it is widely developed. We then review resilience-related concepts in microbiology, including bacterial tolerance and persistence, phenotypic heterogeneity and collective tolerance and resistance. We discuss how antibiotic resilience could be defined and argue that the use of this concept largely relies on its experimental measure and its clinical relevance. We review indicators in microbiology which could be used to reflect antibiotic resilience and used as valuable indicators to anticipate the capacity of bacteria to recover from antibiotic treatments.
Collapse
Affiliation(s)
- Gabriel Carvalho
- Université Clermont Auvergne, Irstea, UR LISC, Centre de Clermont-Ferrand, 9 Avenue Blaise Pascal CS 20085, F-63178, Aubière, France
| | | | - Jean-Denis Mathias
- Université Clermont Auvergne, Irstea, UR LISC, Centre de Clermont-Ferrand, 9 Avenue Blaise Pascal CS 20085, F-63178, Aubière, France
| |
Collapse
|
58
|
PQS Produced by the Pseudomonas aeruginosa Stress Response Repels Swarms Away from Bacteriophage and Antibiotics. J Bacteriol 2019; 201:JB.00383-19. [PMID: 31451543 DOI: 10.1128/jb.00383-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/21/2019] [Indexed: 11/20/2022] Open
Abstract
We investigate the effect of bacteriophage infection and antibiotic treatment on the coordination of swarming, a collective form of flagellum- and pilus-mediated motility in bacteria. We show that phage infection of the opportunistic bacterial pathogen Pseudomonas aeruginosa abolishes swarming motility in the infected subpopulation and induces the release of the Pseudomonas quinolone signaling molecule PQS, which repulses uninfected subpopulations from approaching the infected area. These mechanisms have the overall effect of limiting the infection to a subpopulation, which promotes the survival of the overall population. Antibiotic treatment of P. aeruginosa elicits the same response, abolishing swarming motility and repulsing approaching swarms away from the antibiotic-treated area through a PQS-dependent mechanism. Swarms are entirely repelled from the zone of antibiotic-treated P. aeruginosa, consistent with a form of antibiotic evasion, and are not repelled by antibiotics alone. PQS has multiple functions, including serving as a quorum-sensing molecule, activating an oxidative stress response, and regulating the release of virulence and host-modifying factors. We show that PQS serves additionally as a stress warning signal that causes the greater population to physically avoid cell stress. The stress response at the collective level observed here in P. aeruginosa is consistent with a mechanism that promotes the survival of bacterial populations.IMPORTANCE We uncover a phage- and antibiotic-induced stress response in the clinically important opportunistic pathogen Pseudomonas aeruginosa Phage-infected P. aeruginosa subpopulations are isolated from uninfected subpopulations by the production of a stress-induced signal. Activation of the stress response by antibiotics causes P. aeruginosa to physically be repelled from the area containing antibiotics altogether, consistent with a mechanism of antibiotic evasion. The stress response observed here could increase P. aeruginosa resilience against antibiotic treatment and phage therapy in health care settings, as well as provide a simple evolutionary strategy to avoid areas containing stress.
Collapse
|
59
|
Wood K. Microbial Ecology: Complex Bacterial Communities Reduce Selection for Antibiotic Resistance. Curr Biol 2019; 29:R1143-R1145. [PMID: 31689403 DOI: 10.1016/j.cub.2019.09.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Competition between antibiotic-resistant and -susceptible bacteria is well studied in single-species communities, but less is known about selection for resistance in more complex ecologies. A new experiment shows natural microbial communities can hinder selection by increasing the fitness costs of resistance or by offering protection to drug-sensitive strains.
Collapse
Affiliation(s)
- Kevin Wood
- Department of Biophysics and Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
60
|
Maltas J, Wood KB. Pervasive and diverse collateral sensitivity profiles inform optimal strategies to limit antibiotic resistance. PLoS Biol 2019; 17:e3000515. [PMID: 31652256 PMCID: PMC6834293 DOI: 10.1371/journal.pbio.3000515] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 11/06/2019] [Accepted: 10/07/2019] [Indexed: 11/19/2022] Open
Abstract
Evolved resistance to one antibiotic may be associated with "collateral" sensitivity to other drugs. Here, we provide an extensive quantitative characterization of collateral effects in Enterococcus faecalis, a gram-positive opportunistic pathogen. By combining parallel experimental evolution with high-throughput dose-response measurements, we measure phenotypic profiles of collateral sensitivity and resistance for a total of 900 mutant-drug combinations. We find that collateral effects are pervasive but difficult to predict because independent populations selected by the same drug can exhibit qualitatively different profiles of collateral sensitivity as well as markedly different fitness costs. Using whole-genome sequencing of evolved populations, we identified mutations in a number of known resistance determinants, including mutations in several genes previously linked with collateral sensitivity in other species. Although phenotypic drug sensitivity profiles show significant diversity, they cluster into statistically similar groups characterized by selecting drugs with similar mechanisms. To exploit the statistical structure in these resistance profiles, we develop a simple mathematical model based on a stochastic control process and use it to design optimal drug policies that assign a unique drug to every possible resistance profile. Stochastic simulations reveal that these optimal drug policies outperform intuitive cycling protocols by maintaining long-term sensitivity at the expense of short-term periods of high resistance. The approach reveals a new conceptual strategy for mitigating resistance by balancing short-term inhibition of pathogen growth with infrequent use of drugs intended to steer pathogen populations to a more vulnerable future state. Experiments in laboratory populations confirm that model-inspired sequences of four drugs reduce growth and slow adaptation relative to naive protocols involving the drugs alone, in pairwise cycles, or in a four-drug uniform cycle.
Collapse
Affiliation(s)
- Jeff Maltas
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kevin B. Wood
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Physics, University of Michigan, Ann Arbor, Michigan, United States of America
| |
Collapse
|
61
|
Wen Q, Liu XJ, Zhu WC, Li L, Li MY, Peng XX, Li H. Characterization of balofloxacin-stressed proteomics and identification of balofloxacin-binding proteins pre-peptidase and integration host factor in Edwardsiella tarda. J Proteomics 2019; 205:103413. [DOI: 10.1016/j.jprot.2019.103413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/23/2019] [Accepted: 06/06/2019] [Indexed: 12/13/2022]
|
62
|
Ilhan J, Kupczok A, Woehle C, Wein T, Hülter NF, Rosenstiel P, Landan G, Mizrahi I, Dagan T. Segregational Drift and the Interplay between Plasmid Copy Number and Evolvability. Mol Biol Evol 2019; 36:472-486. [PMID: 30517696 PMCID: PMC6389322 DOI: 10.1093/molbev/msy225] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The ubiquity of plasmids in all prokaryotic phyla and habitats and their ability to transfer between cells marks them as prominent constituents of prokaryotic genomes. Many plasmids are found in their host cell in multiple copies. This leads to an increased mutational supply of plasmid-encoded genes and genetically heterogeneous plasmid genomes. Nonetheless, the segregation of plasmid copies into daughter cells during cell division is considered to occur in the absence of selection on the plasmid alleles. We investigate the implications of random genetic drift of multicopy plasmids during cell division-termed here "segregational drift"-to plasmid evolution. Performing experimental evolution of low- and high-copy non-mobile plasmids in Escherichia coli, we find that the evolutionary rate of multicopy plasmids does not reflect the increased mutational supply expected according to their copy number. In addition, simulated evolution of multicopy plasmid alleles demonstrates that segregational drift leads to increased loss frequency and extended fixation time of plasmid mutations in comparison to haploid chromosomes. Furthermore, an examination of the experimentally evolved hosts reveals a significant impact of the plasmid type on the host chromosome evolution. Our study demonstrates that segregational drift of multicopy plasmids interferes with the retention and fixation of novel plasmid variants. Depending on the selection pressure on newly emerging variants, plasmid genomes may evolve slower than haploid chromosomes, regardless of their higher mutational supply. We suggest that plasmid copy number is an important determinant of plasmid evolvability due to the manifestation of segregational drift.
Collapse
Affiliation(s)
- Judith Ilhan
- Institute of Microbiology, Kiel University, Kiel, Germany
| | - Anne Kupczok
- Institute of Microbiology, Kiel University, Kiel, Germany
| | | | - Tanita Wein
- Institute of Microbiology, Kiel University, Kiel, Germany
| | - Nils F Hülter
- Institute of Microbiology, Kiel University, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Giddy Landan
- Institute of Microbiology, Kiel University, Kiel, Germany
| | - Itzhak Mizrahi
- The Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tal Dagan
- Institute of Microbiology, Kiel University, Kiel, Germany
| |
Collapse
|
63
|
Prats-Ejarque G, Li J, Ait-Ichou F, Lorente H, Boix E. Testing a Human Antimicrobial RNase Chimera Against Bacterial Resistance. Front Microbiol 2019; 10:1357. [PMID: 31275278 PMCID: PMC6594349 DOI: 10.3389/fmicb.2019.01357] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/31/2019] [Indexed: 12/11/2022] Open
Abstract
The emergence of bacterial resistance to the most commonly used antibiotics encourages the design of novel antimicrobial drugs. Antimicrobial proteins and peptides (AMPs) are the key players in host innate immunity. They exert a rapid and multifaceted action that reduces the development of bacterial adaptation mechanisms. Human antimicrobial RNases belonging to the vertebrate specific RNase A superfamily participate in the maintenance of tissue and body fluid sterility. Among the eight human canonical RNases, RNase 3 stands out as the most cationic and effective bactericidal protein against Gram-negative species. Its enhanced ability to disrupt the bacterial cell wall has evolved in detriment of its catalytic activity. Based on structure-functional studies we have designed an RNase 3/1 hybrid construct that combines the high catalytic activity of RNase 1 with RNase 3 bactericidal properties. Next, we have explored the ability of this hybrid RNase to target the development of bacterial resistance on an Acinetobacter baumannii cell culture. Synergy assays were performed in combination with colistin, a standard antimicrobial peptide used as an antibiotic to treat severe infections. Positive synergism was observed between colistin and the RNase 3/1 hybrid protein. Subsequently, using an in vitro experimental evolution assay, by exposure of a bacterial culture to colistin at incremental doses, we demonstrated the ability of the RNase 3/1 construct to reduce the emergence of bacterial antimicrobial resistance. The results advance the potential applicability of RNase-based drugs as antibiotic adjuvants.
Collapse
Affiliation(s)
| | | | | | | | - Ester Boix
- Faculty of Biosciences, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Barcelona, Spain
| |
Collapse
|
64
|
Escudeiro P, Pothier J, Dionisio F, Nogueira T. Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes. mSphere 2019; 4:e00135-19. [PMID: 31043514 PMCID: PMC6495336 DOI: 10.1128/msphere.00135-19] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/11/2019] [Indexed: 01/12/2023] Open
Abstract
Human beings have used large amounts of antibiotics, not only in medical contexts but also, for example, as growth factors in agriculture and livestock, resulting in the contamination of the environment. Even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are affected as well. Therefore, both pathogenic and nonpathogenic bacteria have gradually become resistant to antibiotics. We tested whether there is still cooccurrence of resistance and virulence determinants. We performed a comparative study of environmental and human gut metagenomes from different individuals and from distinct human populations across the world. We found a great diversity of antibiotic resistance determinants (AR diversity [ARd]) and virulence factors (VF diversity [VFd]) in metagenomes. Importantly there is a correlation between ARd and VFd, even after correcting for protein family richness. In the human gut, there are less ARd and VFd than in more diversified environments, and yet correlations between the ARd and VFd are stronger. They can vary from very high in Malawi, where antibiotic consumption is unattended, to nonexistent in the uncontacted Amerindian population. We conclude that there is cooccurrence of resistance and virulence determinants in human gut microbiomes, suggesting a possible coselective mechanism.IMPORTANCE Every year, thousands of tons of antibiotics are used, not only in human and animal health but also as growth promoters in livestock. Consequently, during the last 75 years, antibiotic-resistant bacterial strains have been selected in human and environmental microbial communities. This implies that, even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are also affected. Here, we performed a comparative study of environmental and human gut microbial communities issuing from different individuals and from distinct human populations across the world. We found that antibiotic resistance and pathogenicity are correlated and speculate that, by selecting for resistant bacteria, we may be selecting for more virulent strains as a side effect of antimicrobial therapy.
Collapse
Affiliation(s)
- Pedro Escudeiro
- cE3c-Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Joël Pothier
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Francisco Dionisio
- cE3c-Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa Nogueira
- cE3c-Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
65
|
Burcham ZM, Schmidt CJ, Pechal JL, Brooks CP, Rosch JW, Benbow ME, Jordan HR. Detection of critical antibiotic resistance genes through routine microbiome surveillance. PLoS One 2019; 14:e0213280. [PMID: 30870464 PMCID: PMC6417727 DOI: 10.1371/journal.pone.0213280] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/18/2019] [Indexed: 12/29/2022] Open
Abstract
Population-based public health data on antibiotic resistance gene carriage is poorly surveyed. Research of the human microbiome as an antibiotic resistance reservoir has primarily focused on gut associated microbial communities, but data have shown more widespread microbial colonization across organs than originally believed, with organs previously considered as sterile being colonized. Our study demonstrates the utility of postmortem microbiome sampling during routine autopsy as a method to survey antibiotic resistance carriage in a general population. Postmortem microbial sampling detected pathogens of public health concern including genes for multidrug efflux pumps, carbapenem, methicillin, vancomycin, and polymixin resistances. Results suggest that postmortem assessments of host-associated microbial communities are useful in acquiring community specific data while reducing selective-participant biases.
Collapse
Affiliation(s)
- Zachary M. Burcham
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States of America
| | - Carl J. Schmidt
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
| | - Jennifer L. Pechal
- Department of Entomology, Michigan State University, East Lansing, MI, United States of America
| | - Christopher P. Brooks
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States of America
| | - Jason W. Rosch
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - M. Eric Benbow
- Department of Entomology, Michigan State University, East Lansing, MI, United States of America
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, United States of America
| | - Heather R. Jordan
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States of America
- * E-mail:
| |
Collapse
|
66
|
George J, Halami PM. Presence of extracellular DNA & protein in biofilm formation by gentamicin-resistant Lactobacillus plantarum. Indian J Med Res 2019; 149:257-262. [PMID: 31219091 PMCID: PMC6563752 DOI: 10.4103/ijmr.ijmr_2022_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Indexed: 01/09/2023] Open
Abstract
Background & objectives Bacterial biofilms a multi-layered defence, comprise extracellular DNA (eDNA) and proteins, protect bacteria from harmful environment and nutrient limitation and utilize the mutual benefits within a community. Bacterial biofilms also defend bacteria from harsh environments such as antibiotic treatment. This leads to poor antibiotic penetration, slow growth, adaptive stress responses, and formation of persister cells. This study was done to determine the relation of antibiotic resistance deciphered by the biofilms in Lactobacillus plantarum, a lactic acid bacteria (LAB) with probiotic significance. Methods The gentamicin-resistant L. plantarum isolates were allowed to form biofilms and subjected to DNase I and proteinase K treatment. The optical density (OD) values were recorded for the biofilm assay and the cell count for the number of viable cells was taken for the control and the test samples. Percentage reduction was calculated based on the difference between the initial and final OD for both the parameters. Results The biofilm assay revealed that the native L. plantarum isolates which were phenotypically susceptible, possessed the ability to form biofilms. The OD values were significantly decreased in comparison to the biofilm-forming control culture when these were treated with DNase I and proteinase K. Interpretation & conclusions The study revealed that the biofilms formed by L. plantarum comprised of eDNA and proteins which was evidenced by the reduction in OD values and percentage in comparison to the control upon DNase I and proteinase K treatment. This indicates that the eDNA and biofilm matrix proteins are vital constituents of biofilms and may carry significant risk when coupled with antibiotic resistance.
Collapse
Affiliation(s)
- Jaimee George
- Department of Microbiology & Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru, India
| | - Prakash Motiram Halami
- Department of Microbiology & Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru, India
| |
Collapse
|
67
|
Meredith HR, Andreani V, Ma HR, Lopatkin AJ, Lee AJ, Anderson DJ, Batt G, You L. Applying ecological resistance and resilience to dissect bacterial antibiotic responses. SCIENCE ADVANCES 2018; 4:eaau1873. [PMID: 30525104 PMCID: PMC6281428 DOI: 10.1126/sciadv.aau1873] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/07/2018] [Indexed: 05/14/2023]
Abstract
An essential property of microbial communities is the ability to survive a disturbance. Survival can be achieved through resistance, the ability to absorb effects of a disturbance without a notable change, or resilience, the ability to recover after being perturbed by a disturbance. These concepts have long been applied to the analysis of ecological systems, although their interpretations are often subject to debate. Here, we show that this framework readily lends itself to the dissection of the bacterial response to antibiotic treatment, where both terms can be unambiguously defined. The ability to tolerate the antibiotic treatment in the short term corresponds to resistance, which primarily depends on traits associated with individual cells. In contrast, the ability to recover after being perturbed by an antibiotic corresponds to resilience, which primarily depends on traits associated with the population. This framework effectively reveals the phenotypic signatures of bacterial pathogens expressing extended-spectrum β-lactamases (ESBLs) when treated by a β-lactam antibiotic. Our analysis has implications for optimizing treatment of these pathogens using a combination of a β-lactam and a β-lactamase (Bla) inhibitor. In particular, our results underscore the need to dynamically optimize combination treatments based on the quantitative features of the bacterial response to the antibiotic or the Bla inhibitor.
Collapse
Affiliation(s)
| | - Virgile Andreani
- Inria Saclay–Île-de-France, Palaiseau, France
- Institut Pasteur, Paris, France
| | - Helena R. Ma
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Anna J. Lee
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Deverick J. Anderson
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Duke University School of Medicine, Durham, NC, USA
| | - Gregory Batt
- Inria Saclay–Île-de-France, Palaiseau, France
- Institut Pasteur, Paris, France
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| |
Collapse
|
68
|
Nogueira T, David PHC, Pothier J. Antibiotics as both friends and foes of the human gut microbiome: The microbial community approach. Drug Dev Res 2018; 80:86-97. [PMID: 30370682 DOI: 10.1002/ddr.21466] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/14/2018] [Accepted: 08/15/2018] [Indexed: 12/28/2022]
Abstract
The exposure of the human gut to antibiotics can have a great impact on human health. Antibiotics pertain to the preservation of human health and are useful tools for fighting bacterial infections. They can be used for curing infections and can play a critical role in immunocompromised or chronic patients, or in fighting childhood severe malnutrition. Yet, the genomic and phylogenetic diversity of the human gut changes under antibiotic exposure. Antibiotics can also have severe side effects on human gut health, due to the spreading of potential antibiotic resistance genetic traits and to their correlation with virulence of some bacterial pathogens. They can shape, and even disrupt, the composition and functioning diversity of the human gut microbiome. Traditionally bacterial antibiotic resistances have been evaluated at clone or population level. However, the understanding of these two apparently disparate perspectives as both friends and foes may come from the study of microbiomes as a whole and from the evaluation of both positive and negative effects of antibiotics on microbial community dynamics and diversity. In this review we present some metagenomic tools and databases that enable the studying of antibiotic resistance in human gut metagenomes, promoting the development of personalized medicine strategies, new antimicrobial therapy protocols and patient follow-up.
Collapse
Affiliation(s)
- Teresa Nogueira
- cE3c - Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro H C David
- cE3c - Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Joël Pothier
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, Muséum National d'Histoire naturelle, CNRS, EPHE, CP, Paris, France
| |
Collapse
|
69
|
Velic A, Mathew A, Hines P, Yarlagadda PKDV. Control of bacterial attachment by fracture topography. J Mech Behav Biomed Mater 2018; 91:416-424. [PMID: 30424978 DOI: 10.1016/j.jmbbm.2018.10.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 10/09/2018] [Accepted: 10/09/2018] [Indexed: 01/11/2023]
Abstract
In the biomedical arena, bacterial fouling is a precursor to complications such as implant infection and nosocomial infection. These complications are further compounded by biochemical mechanisms of resistance that threaten the action of traditional antibacterial strategies. Accordingly, antibacterial property by physical, not biochemical, mechanisms of action is becoming increasingly popular and promising. The present work falls in line with this paradigm shift. Here, microtextured Ti-6Al-4V surfaces were manufactured by destructive tension at three different cross-head speeds, probed with scanning electron microscopy (SEM) and multifocus optical microscopy, and treated with Staphylococcus aureus to study bacterial attachment. The fractographic study revealed the presence of dual-mode fracture, typical of Ti-6Al-4V, comprising regions of both ductile, microvoid coalescence and brittle, cleavage faceting. Based on load-extension curves, quantitative roughness data, and qualitative SEM visualisation, it was evident that cross-head speed modulated fracture behaviour such that increased speed produced more brittle fracture whilst lower speeds produced more ductile fracture. The topography associated with ductile fracture was found to possess notable antibiofouling property due to geometric constrains imposed by the coalesced microvoids. Accordingly, fracture at low cross-head speeds (1 mm/min and 10 mm/min) yielded significant reduction in bacterial attachment, whilst fracture at high cross-head speeds (100 mm/min) did not. The greatest reduction (~72%) was achieved at a cross-head speed of 1 mm/min. These findings suggest that antibiofouling property can be elicited by fracture and further 'tuned' by fracture speed. Discovery of this novel, albeit simple, avenue for topography-mediated antibacterial property calls for further research into alternate techniques for the manufacture of 'physical antibacterial surfaces'.
Collapse
Affiliation(s)
- Amar Velic
- School of Chemistry, Physics and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane, Australia
| | - Asha Mathew
- School of Chemistry, Physics and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane, Australia
| | - Peter Hines
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, Australia
| | - Prasad K D V Yarlagadda
- School of Chemistry, Physics and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane, Australia.
| |
Collapse
|
70
|
Estrela S, Brown SP. Community interactions and spatial structure shape selection on antibiotic resistant lineages. PLoS Comput Biol 2018; 14:e1006179. [PMID: 29927925 PMCID: PMC6013025 DOI: 10.1371/journal.pcbi.1006179] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 05/06/2018] [Indexed: 01/21/2023] Open
Abstract
Polymicrobial interactions play an important role in shaping the outcome of antibiotic treatment, yet how multispecies communities respond to antibiotic assault is still little understood. Here we use an individual-based simulation model of microbial biofilms to investigate how competitive and mutualistic interactions between an antibiotic-resistant and a susceptible strain (or species) influence the two-lineage community response to antibiotic exposure. Our model predicts that while increasing competition and antibiotics leads to increasing competitive release of the antibiotic-resistant strain, hitting a mutualistic community of cross-feeding species with antibiotics leads to a mutualistic suppression effect where both susceptible and resistant species are harmed. We next show that the impact of antibiotics is further governed by emergent spatial feedbacks within communities. Mutualistic cross-feeding communities can rescue susceptible members by subsidizing their growth inside the biofilm despite lack of access to the nutrient-rich and high-antibiotic growing front. Moreover, we show that antibiotic detoxification by resistant cells can protect nearby susceptible cells, but such cross-protection is more effective in mutualistic communities because mutualism drives mixing of resistant and susceptible cells. In contrast, competition leads to segregation, which ultimately prevents susceptible cells to profit from detoxification. Understanding how the interplay between microbial metabolic interactions and community spatial structuring shapes the outcome of antibiotic treatment can be key to effectively leverage the power of antibiotics and promote microbiome health. Pathogens -microorganisms that make us sick- often live within dynamic and complex multispecies communities, where they may not only compete for limiting resources but also exchange beneficial resources or services with other resident species. While antibiotics are commonly used to get rid of such harmful microbes, the community-wide effects of antibiotic treatment and its consequences for antibiotic resistance are still not well understood. How do competitive or mutually beneficial interactions between antibiotic resistant and susceptible species influence community resistance to antibiotics? Here we investigate this question using a computational model. We find that antibiotic exposure favours the resistant lineage when resistant and susceptible strains are competitors but harms both types when they are mutualists. With antibiotic-detoxifying resistant cells, cross-protection of susceptible cells is more effective in mutualistic communities because mutualism drives mixing of susceptible and resistant cells. In contrast, competition leads to their segregation, precluding susceptible cells to profit from their competitor’s local detoxification. Our findings highlight that knowing not only what species are present but also how they interact with each other and arrange themselves in space is central to understanding antibiotic resistance and to informing the development of strategies that promote microbiome health.
Collapse
Affiliation(s)
- Sylvie Estrela
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
- * E-mail:
| | - Sam P. Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| |
Collapse
|
71
|
Diener VN, Gay A, Soyka MB, Attin T, Schmidlin PR, Sahrmann P. What is the influence of tonsillectomy on the level of periodontal pathogens on the tongue dorsum and in periodontal pockets. BMC Oral Health 2018; 18:62. [PMID: 29625605 PMCID: PMC5889595 DOI: 10.1186/s12903-018-0521-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/20/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND For periodontal treatment, the full mouth disinfection approach suggests disinfection of oral soft tissues, such as tongue and tonsils concomitant to scaling and root planning since patients might benefit from treatment of these oral niches either. Periodontopathogenes in tonsillar tissue support this hypothesis. This prospective controlled clinical study investigated the change in the oral flora of patients who underwent tonsillectomy. Pockets were tested for eleven bacterial species before and six weeks after the surgical intervention. METHODS Fifty generally healthy adults were included in this study. The test group consisted of 25 patients with tonsillectomy. The control group included 25 patients with otorhinolarynologic surgery without involvement of the oral cavity. Clinical parameters such as probing pocket depth, bleeding-on-probing index and plaque index were registered the evening before surgery. Also bacterial samples from the gingival sulcus and dorsum linguae were taken, and an additional sample from the removed tonsils in the test group. Six weeks after the intervention microbial samples of pockets and tongue were taken again. Data were tested for significant differences using Wilcoxon rank and Whitney-u-test. RESULTS No relevant intra- or intergroup differences were found for the change of the eleven investigated species. CONCLUSION Based on the results of the present study, tonsillectomy does not seem to have an immediate relevant effect on the bacterial flora of tongue or periodontium. This study design was approved by the ethical committee of Zurich (KEK-ZH-Nr.2013-0419). TRIAL REGISTRATION The trial was retrospectively registered in the German Clinical Trials Register ( DRK00014077 ) on February 20, 2018.
Collapse
Affiliation(s)
- V N Diener
- Clinic for Preventive Dentistry, Periodontology and Cariologiy, Center of Dental Medicine, University of Zurich, Zurich, Switzerland.
| | - A Gay
- Department of Otolaryngology, Head and Neck Surgery, University Hospital of Zurich, Zurich, Switzerland
| | - M B Soyka
- Department of Otolaryngology, Head and Neck Surgery, University Hospital of Zurich, Zurich, Switzerland
| | - T Attin
- Clinic for Preventive Dentistry, Periodontology and Cariologiy, Center of Dental Medicine, University of Zurich, Zurich, Switzerland
| | - P R Schmidlin
- Clinic for Preventive Dentistry, Periodontology and Cariologiy, Center of Dental Medicine, University of Zurich, Zurich, Switzerland
| | - P Sahrmann
- Clinic for Preventive Dentistry, Periodontology and Cariologiy, Center of Dental Medicine, University of Zurich, Zurich, Switzerland
| |
Collapse
|
72
|
Carvalho G, Balestrino D, Forestier C, Mathias JD. How do environment-dependent switching rates between susceptible and persister cells affect the dynamics of biofilms faced with antibiotics? NPJ Biofilms Microbiomes 2018; 4:6. [PMID: 29560270 PMCID: PMC5854711 DOI: 10.1038/s41522-018-0049-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 02/06/2018] [Accepted: 02/09/2018] [Indexed: 01/24/2023] Open
Abstract
Persisters form sub-populations of stress-tolerant cells that play a major role in the capacity of biofilms to survive and recover from disturbances such as antibiotic treatments. The mechanisms of persistence are diverse and influenced by environmental conditions, and persister populations are more heterogeneous than formerly suspected. We used computational modeling to assess the impact of three switching strategies between susceptible and persister cells on the capacity of bacterial biofilms to grow, survive and recover from antibiotic treatments. The strategies tested were: (1) constant switches, (2) substrate-dependent switches and (3) antibiotic-dependent switches. We implemented these strategies in an individual-based biofilm model and simulated antibiotic shocks on virtual biofilms. Because of limited available data on switching rates in the literature, nine parameter sets were assessed for each strategy. Substrate and antibiotic-dependent switches allowed high switching rates without affecting the growth of the biofilms. Compared to substrate-dependent switches, constant and antibiotic-dependent switches were associated with higher proportions of persisters in the top of the biofilms, close to the substrate source, which probably confers a competitive advantage within multi-species biofilms. The constant and substrate-dependent strategies need a compromise between limiting the wake-up and death of persisters during treatments and leaving the persister state fast enough to recover quickly after antibiotic-removal. Overall, the simulations gave new insights into the relationships between the dynamics of persister populations in biofilms and their dynamics of growth, survival and recovery when faced with disturbances.
Collapse
Affiliation(s)
- Gabriel Carvalho
- UR LISC Laboratoire d'Ingénierie pour les Systèmes Complexes, Irstea, Aubière, France
| | - Damien Balestrino
- 2LMGE, UMR6023 CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | | | - Jean-Denis Mathias
- UR LISC Laboratoire d'Ingénierie pour les Systèmes Complexes, Irstea, Aubière, France
| |
Collapse
|
73
|
Ren Y, Wang C, Chen Z, Allan E, van der Mei HC, Busscher HJ. Emergent heterogeneous microenvironments in biofilms: substratum surface heterogeneity and bacterial adhesion force-sensing. FEMS Microbiol Rev 2018; 42:259-272. [DOI: 10.1093/femsre/fuy001] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/08/2018] [Indexed: 12/18/2022] Open
Affiliation(s)
- Yijin Ren
- Department of Orthodontics, University of Groningen and University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Can Wang
- Department of Orthodontics, University of Groningen and University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
- School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, Wuhan, China
| | - Zhi Chen
- School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, Wuhan, China
| | - Elaine Allan
- UCL Eastman Dental Institute, University College London, 256 Gray's Inn Road, London WC1X 8LD, UK
| | - Henny C van der Mei
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Henk J Busscher
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| |
Collapse
|
74
|
Interplay between Antibiotic Efficacy and Drug-Induced Lysis Underlies Enhanced Biofilm Formation at Subinhibitory Drug Concentrations. Antimicrob Agents Chemother 2017; 62:AAC.01603-17. [PMID: 29061740 PMCID: PMC5740344 DOI: 10.1128/aac.01603-17] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/13/2017] [Indexed: 12/29/2022] Open
Abstract
Subinhibitory concentrations of antibiotics have been shown to enhance biofilm formation in multiple bacterial species. While antibiotic exposure has been associated with modulated expression of many biofilm-related genes, the mechanisms of drug-induced biofilm formation remain a focus of ongoing research efforts and may vary significantly across species. In this work, we investigate antibiotic-induced biofilm formation in Enterococcus faecalis, a leading cause of nosocomial infections. We show that biofilm formation is enhanced by subinhibitory concentrations of cell wall synthesis inhibitors but not by inhibitors of protein, DNA, folic acid, or RNA synthesis. Furthermore, enhanced biofilm is associated with increased cell lysis, increases in extracellular DNA (eDNA) levels, and increases in the density of living cells in the biofilm. In addition, we observe similar enhancement of biofilm formation when cells are treated with nonantibiotic surfactants that induce cell lysis. These findings suggest that antibiotic-induced biofilm formation is governed by a trade-off between drug toxicity and the beneficial effects of cell lysis. To understand this trade-off, we developed a simple mathematical model that predicts changes in antibiotic-induced biofilm formation due to external perturbations, and we verified these predictions experimentally. Specifically, we demonstrate that perturbations that reduce eDNA (DNase treatment) or decrease the number of living cells in the planktonic phase (a second antibiotic) decrease biofilm induction, while chemical inhibitors of cell lysis increase relative biofilm induction and shift the peak to higher antibiotic concentrations. Overall, our results offer experimental evidence linking cell wall synthesis inhibitors, cell lysis, increased eDNA levels, and biofilm formation in E. faecalis while also providing a predictive quantitative model that sheds light on the interplay between cell lysis and antibiotic efficacy in developing biofilms.
Collapse
|
75
|
Hesse E, O'Brien S, Tromas N, Bayer F, Luján AM, van Veen EM, Hodgson DJ, Buckling A. Ecological selection of siderophore-producing microbial taxa in response to heavy metal contamination. Ecol Lett 2017; 21:117-127. [PMID: 29161760 PMCID: PMC5765521 DOI: 10.1111/ele.12878] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/23/2017] [Accepted: 10/16/2017] [Indexed: 11/27/2022]
Abstract
Some microbial public goods can provide both individual and community-wide benefits, and are open to exploitation by non-producing species. One such example is the production of metal-detoxifying siderophores. Here, we investigate whether conflicting selection pressures on siderophore production by heavy metals - a detoxifying effect of siderophores, and exploitation of this detoxifying effect - result in a net increase or decrease. We show that the proportion of siderophore-producing taxa increases along a natural heavy metal gradient. A causal link between metal contamination and siderophore production was subsequently demonstrated in a microcosm experiment in compost, in which we observed changes in community composition towards taxa that produce relatively more siderophores following copper contamination. We confirmed the selective benefit of siderophores by showing that taxa producing large amounts of siderophore suffered less growth inhibition in toxic copper. Our results suggest that ecological selection will favour siderophore-mediated decontamination, with important consequences for potential remediation strategies.
Collapse
Affiliation(s)
- Elze Hesse
- ESI & CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Siobhán O'Brien
- ESI & CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK.,Institut für Integrative Biologie, ETH Zürich, Universitätstrasse 16, Zürich, 8092, Switzerland
| | - Nicolas Tromas
- Département de Sciences Biologiques, Université de Montréal, 90 Vincent-d'Indy, Montréal, QC, H2V 2S9, Canada
| | - Florian Bayer
- ESI & CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Adela M Luján
- ESI & CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK.,CIQUIBIC, Departamento de Química Biológica, Facultad de Ciencias Químicas, CONICET, Universidad Nacional de Córdoba, Córdoba, X5000HUA, Argentina
| | - Eleanor M van Veen
- Camborne School of Mines, CEMPS, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Dave J Hodgson
- CEC, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Angus Buckling
- ESI & CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| |
Collapse
|
76
|
Im H, Choi SY, Son S, Mitchell RJ. Combined Application of Bacterial Predation and Violacein to Kill Polymicrobial Pathogenic Communities. Sci Rep 2017; 7:14415. [PMID: 29089523 PMCID: PMC5663959 DOI: 10.1038/s41598-017-14567-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/11/2017] [Indexed: 12/02/2022] Open
Abstract
Violacein is a bisindole antibiotic that is effective against Gram-positive bacteria while the bacterial predator, Bdellovibrio bacteriovorus HD100, predates on Gram-negative strains. In this study, we evaluated the use of both together against multidrug resistant pathogens. The two antibacterial agents did not antagonize the activity of the other. For example, treatment of Staphylococcus aureus with violacein reduced its viability by more than 2,000-fold with or without B. bacteriovorus addition. Likewise, predation of Acinetobacter baumannii reduced the viability of this pathogen by more than 13,000-fold, regardless if violacein was present or not. When used individually against mixed bacterial cultures containing both Gram-positive and Gram-negative strains, violacein and B. bacteriovorus HD100 were effective against only their respective strains. The combined application of both violacein and B. bacteriovorus HD100, however, reduced the total pathogen numbers by as much as 84,500-fold. Their combined effectiveness was also demonstrated using a 4-species culture containing S. aureus, A. baumannii, Bacillus cereus and Klebsiella pneumoniae. When used alone, violacein and bacterial predation reduced the total population by only 19% and 68%, respectively. In conjunction with each other, the pathogen viability was reduced by 2,965-fold (99.98%), illustrating the prospective use of these two antimicrobials together against mixed species populations.
Collapse
Affiliation(s)
- Hansol Im
- Division of Biological Sciences, School of Life Sciences Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Seong Yeol Choi
- Division of Biological Sciences, School of Life Sciences Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Sangmo Son
- Division of Biological Sciences, School of Life Sciences Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Robert J Mitchell
- Division of Biological Sciences, School of Life Sciences Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea.
| |
Collapse
|
77
|
Yang JH, Bening SC, Collins JJ. Antibiotic efficacy-context matters. Curr Opin Microbiol 2017; 39:73-80. [PMID: 29049930 DOI: 10.1016/j.mib.2017.09.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/09/2017] [Accepted: 09/06/2017] [Indexed: 02/01/2023]
Abstract
Antibiotic lethality is a complex physiological process, sensitive to external cues. Recent advances using systems approaches have revealed how events downstream of primary target inhibition actively participate in antibiotic death processes. In particular, altered metabolism, translational stress and DNA damage each contribute to antibiotic-induced cell death. Moreover, environmental factors such as oxygen availability, extracellular metabolites, population heterogeneity and multidrug contexts alter antibiotic efficacy by impacting bacterial metabolism and stress responses. Here we review recent studies on antibiotic efficacy and highlight insights gained on the involvement of cellular respiration, redox stress and altered metabolism in antibiotic lethality. We discuss the complexity found in natural environments and highlight knowledge gaps in antibiotic lethality that may be addressed using systems approaches.
Collapse
Affiliation(s)
- Jason H Yang
- Institute for Medical Engineering & Science, Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA
| | - Sarah C Bening
- Institute for Medical Engineering & Science, Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA
| | - James J Collins
- Institute for Medical Engineering & Science, Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering at Harvard University, 3 Blackfan Cir, Boston, MA 02115, USA.
| |
Collapse
|
78
|
de Vos MGJ, Zagorski M, McNally A, Bollenbach T. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. Proc Natl Acad Sci U S A 2017; 114:10666-10671. [PMID: 28923953 PMCID: PMC5635929 DOI: 10.1073/pnas.1713372114] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience.
Collapse
Affiliation(s)
- Marjon G J de Vos
- Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Marcin Zagorski
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Alan McNally
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Tobias Bollenbach
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria;
- Institute of Theoretical Physics, University of Cologne, 50937 Cologne, Germany
| |
Collapse
|
79
|
Zhurina MV, Gannesen AV, Mart’yanov SV, Teteneva NA, Shtratnikova VY, Plakunov VK. Niclosamide as a promising antibiofilm agent. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717040154] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
80
|
Carvalho G, Guilhen C, Balestrino D, Forestier C, Mathias JD. Relating switching rates between normal and persister cells to substrate and antibiotic concentrations: a mathematical modelling approach supported by experiments. Microb Biotechnol 2017; 10:1616-1627. [PMID: 28730700 PMCID: PMC5658594 DOI: 10.1111/1751-7915.12739] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 11/29/2022] Open
Abstract
We developed and compared two mathematical models of variable phenotypic switching rates between normal and persister cells that depend on substrate concentration and antibiotic presence. They could be used to simulate the formation of persisters in environments with concentration gradients such as biofilms. Our models are extensions of a previous model of the dynamics of normal and persistent cell populations developed by Balaban et al. (2004, Science 305: 1622). We calibrated the models’ parameters with experimental killing curves obtained after ciprofloxacin treatment of samples regularly harvested from planktonic batch cultures of Klebsiella pneumoniae. Our switching models accurately reproduced the dynamics of normal and persistent populations in planktonic batch cultures and under antibiotic treatment. Results showed that the models are valid for a large range of substrate concentrations and for zero or high doses of antibiotics.
Collapse
Affiliation(s)
- Gabriel Carvalho
- UR LISC Laboratoire d'ingénierie pour les systèmes complexes, Irstea, Aubière, France
| | - Cyril Guilhen
- LMGE, UMR6023 CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Damien Balestrino
- LMGE, UMR6023 CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | | | - Jean-Denis Mathias
- UR LISC Laboratoire d'ingénierie pour les systèmes complexes, Irstea, Aubière, France
| |
Collapse
|
81
|
Yusufaly TI, Boedicker JQ. Mapping quorum sensing onto neural networks to understand collective decision making in heterogeneous microbial communities. Phys Biol 2017; 14:046002. [PMID: 28656904 DOI: 10.1088/1478-3975/aa7c1e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Microbial communities frequently communicate via quorum sensing (QS), where cells produce, secrete, and respond to a threshold level of an autoinducer (AI) molecule, thereby modulating gene expression. However, the biology of QS remains incompletely understood in heterogeneous communities, where variant bacterial strains possess distinct QS systems that produce chemically unique AIs. AI molecules bind to 'cognate' receptors, but also to 'non-cognate' receptors found in other strains, resulting in inter-strain crosstalk. Understanding these interactions is a prerequisite for deciphering the consequences of crosstalk in real ecosystems, where multiple AIs are regularly present in the same environment. As a step towards this goal, we map crosstalk in a heterogeneous community of variant QS strains onto an artificial neural network model. This formulation allows us to systematically analyze how crosstalk regulates the community's capacity for flexible decision making, as quantified by the Boltzmann entropy of all QS gene expression states of the system. In a mean-field limit of complete cross-inhibition between variant strains, the model is exactly solvable, allowing for an analytical formula for the number of variants that maximize capacity as a function of signal kinetics and activation parameters. An analysis of previous experimental results on the Staphylococcus aureus two-component Agr system indicates that the observed combination of variant numbers, gene expression rates and threshold concentrations lies near this critical regime of parameter space where capacity peaks. The results are suggestive of a potential evolutionary driving force for diversification in certain QS systems.
Collapse
Affiliation(s)
- Tahir I Yusufaly
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States of America
| | | |
Collapse
|
82
|
Vetsigian K. Diverse modes of eco-evolutionary dynamics in communities of antibiotic-producing microorganisms. Nat Ecol Evol 2017. [DOI: 10.1038/s41559-017-0189] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
83
|
Bhattacharjee A, Khan M, Kleiman M, Hochbaum AI. Effects of Growth Surface Topography on Bacterial Signaling in Coculture Biofilms. ACS APPLIED MATERIALS & INTERFACES 2017; 9:18531-18539. [PMID: 28485146 DOI: 10.1021/acsami.7b04223] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacteria form interface-associated communities called biofilms, often comprising multiple species. Biofilms can be detrimental or beneficial in medical, industrial, and technological settings, and their stability and function are determined by interspecies communication via specific chemical signaling or metabolite exchange. The deterministic control of biofilm development, behavior, and properties remains an unmet challenge, limiting our ability to inhibit the formation of detrimental biofilms in biomedical settings and promote the growth of beneficial biofilms in biotechnology applications. Here, we describe the development of growth surfaces that promote the growth of commensal Escherichia coli instead of the opportunistic pathogen Pseudomonas aeruginosa. Periodically patterned growth surfaces induced robust morphological changes in surface-associated E. coli biofilms and influenced the antibiotic susceptibilities of E. coli and P. aeruginosa biofilms. Changes in the biofilm architecture resulted in the accumulation of a metabolite, indole, which controls the competition dynamics between the two species. Our results show that the surface on which a biofilm grows has important implications for species colonization, growth, and persistence when exposed to antibiotics.
Collapse
Affiliation(s)
| | - Mughees Khan
- Wyss Institute for Biologically Inspired Engineering, Harvard University , Cambridge, Massachusetts 02138, United States
| | | | | |
Collapse
|
84
|
Ersoy SC, Heithoff DM, Barnes L, Tripp GK, House JK, Marth JD, Smith JW, Mahan MJ. Correcting a Fundamental Flaw in the Paradigm for Antimicrobial Susceptibility Testing. EBioMedicine 2017; 20:173-181. [PMID: 28579300 PMCID: PMC5478264 DOI: 10.1016/j.ebiom.2017.05.026] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/20/2017] [Accepted: 05/23/2017] [Indexed: 12/25/2022] Open
Abstract
The emergence and prevalence of antibiotic-resistant bacteria are an increasing cause of death worldwide, resulting in a global ‘call to action’ to avoid receding into an era lacking effective antibiotics. Despite the urgency, the healthcare industry still relies on a single in vitro bioassay to determine antibiotic efficacy. This assay fails to incorporate environmental factors normally present during host-pathogen interactions in vivo that significantly impact antibiotic efficacy. Here we report that standard antimicrobial susceptibility testing (AST) failed to detect antibiotics that are in fact effective in vivo; and frequently identified antibiotics that were instead ineffective as further confirmed in mouse models of infection and sepsis. Notably, AST performed in media mimicking host environments succeeded in identifying specific antibiotics that were effective in bacterial clearance and host survival, even though these same antibiotics failed in results using standard test media. Similarly, our revised media further identified antibiotics that were ineffective in vivo despite passing the AST standard for clinical use. Supplementation of AST medium with sodium bicarbonate, an abundant in vivo molecule that stimulates global changes in bacterial structure and gene expression, was found to be an important factor improving the predictive value of AST in the assignment of appropriate therapy. These findings have the potential to improve the means by which antibiotics are developed, tested, and prescribed. Standard antimicrobial susceptibility testing (AST) is fundamentally flawed because it is based largely on in vitro efficacy. AST performed under conditions that mimic natural infections improves the assignment of appropriate antibiotic therapy. In vivo altered susceptibility (IVAS) provides a new paradigm for drug discovery and therapeutic intervention.
Drug testing often excludes potent antibiotics for the treatment of bacterial infections, while frequently identifying antibiotics that are ineffective. However, drug testing under conditions that mimic natural infections succeeded in identifying effective antibiotics, even though these same antibiotics failed standard tests. This work suggests that standard drug-testing may be hindering patient treatment and slowing the process of discovery of new, effective, and safe antibiotics because it disqualifies effective compounds. These findings call for an overhaul of standardized drug testing which hasn't changed in > 50 years.
Collapse
Affiliation(s)
- Selvi C Ersoy
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Douglas M Heithoff
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; Center for Nanomedicine, University of California, Santa Barbara, CA 93106, USA
| | - Lucien Barnes
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Geneva K Tripp
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - John K House
- University of Sydney, Faculty of Veterinary Science, Camden, New South Wales, Australia
| | - Jamey D Marth
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; Center for Nanomedicine, University of California, Santa Barbara, CA 93106, USA; Sanford Burnham Prebys Medical Discovery Institute, Cancer Research Center, La Jolla, CA 92037, USA
| | - Jeffrey W Smith
- Sanford Burnham Prebys Medical Discovery Institute, Cancer Research Center, La Jolla, CA 92037, USA
| | - Michael J Mahan
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; Center for Nanomedicine, University of California, Santa Barbara, CA 93106, USA.
| |
Collapse
|
85
|
Lukačišinová M, Bollenbach T. Toward a quantitative understanding of antibiotic resistance evolution. Curr Opin Biotechnol 2017; 46:90-97. [PMID: 28292709 DOI: 10.1016/j.copbio.2017.02.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 01/27/2023]
Abstract
The rising prevalence of antibiotic resistant bacteria is an increasingly serious public health challenge. To address this problem, recent work ranging from clinical studies to theoretical modeling has provided valuable insights into the mechanisms of resistance, its emergence and spread, and ways to counteract it. A deeper understanding of the underlying dynamics of resistance evolution will require a combination of experimental and theoretical expertise from different disciplines and new technology for studying evolution in the laboratory. Here, we review recent advances in the quantitative understanding of the mechanisms and evolution of antibiotic resistance. We focus on key theoretical concepts and new technology that enables well-controlled experiments. We further highlight key challenges that can be met in the near future to ultimately develop effective strategies for combating resistance.
Collapse
Affiliation(s)
| | - Tobias Bollenbach
- IST Austria, Am Campus 1, A-3400 Klosterneuburg, Austria; University of Cologne, Zülpicher Str. 47a, D-50674 Cologne, Germany.
| |
Collapse
|
86
|
Antimicrobial Dendrimeric Peptides: Structure, Activity and New Therapeutic Applications. Int J Mol Sci 2017; 18:ijms18030542. [PMID: 28273806 PMCID: PMC5372558 DOI: 10.3390/ijms18030542] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 02/15/2017] [Accepted: 02/23/2017] [Indexed: 01/09/2023] Open
Abstract
Microbial resistance to conventional antibiotics is one of the most outstanding medical and scientific challenges of our times. Despite the recognised need for new anti-infective agents, however, very few new drugs have been brought to the market and to the clinic in the last three decades. This review highlights the properties of a new class of antibiotics, namely dendrimeric peptides. These intriguing novel compounds, generally made of multiple peptidic sequences linked to an inner branched core, display an array of antibacterial, antiviral and antifungal activities, usually coupled to low haemolytic activity. In addition, several peptides synthesized in oligobranched form proved to be promising tools for the selective treatment of cancer cells.
Collapse
|
87
|
Woods EC, McBride SM. Regulation of antimicrobial resistance by extracytoplasmic function (ECF) sigma factors. Microbes Infect 2017; 19:238-248. [PMID: 28153747 DOI: 10.1016/j.micinf.2017.01.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/20/2017] [Accepted: 01/21/2017] [Indexed: 11/27/2022]
Abstract
Extracytoplasmic function (ECF) sigma factors are a subfamily of σ70 sigma factors that activate genes involved in stress-response functions. In many bacteria, ECF sigma factors regulate resistance to antimicrobial compounds. This review will summarize the ECF sigma factors that regulate antimicrobial resistance in model organisms and clinically relevant pathogens.
Collapse
Affiliation(s)
- Emily C Woods
- Department of Microbiology and Immunology, Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA.
| |
Collapse
|
88
|
Abstract
Biofilm-associated bacteria are less sensitive to antibiotics than free-living (planktonic) cells. Furthermore, with variations in the concentration of antibiotics throughout a biofilm, microbial cells are often exposed to levels below inhibitory concentrations and may develop resistance. This, as well as the irresponsible use of antibiotics, leads to the selection of pathogens that are difficult to eradicate. The Centers for Disease Control and Prevention use the terms "antibiotic" and "antimicrobial agent" interchangeably. However, a clear distinction between these two terms is required for the purpose of this assessment. Therefore, we define "antibiotics" as pharmaceutically formulated and medically administered substances and "antimicrobials" as a broad category of substances which are not regulated as drugs. This comprehensive minireview evaluates the effect of natural antimicrobials on pathogens in biofilms when used instead of, or in combination with, commonly prescribed antibiotics.
Collapse
|
89
|
Collective Resistance in Microbial Communities by Intracellular Antibiotic Deactivation. PLoS Biol 2016; 14:e2000631. [PMID: 28027306 PMCID: PMC5189934 DOI: 10.1371/journal.pbio.2000631] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/23/2016] [Indexed: 11/29/2022] Open
Abstract
The structure and composition of bacterial communities can compromise antibiotic efficacy. For example, the secretion of β-lactamase by individual bacteria provides passive resistance for all residents within a polymicrobial environment. Here, we uncover that collective resistance can also develop via intracellular antibiotic deactivation. Real-time luminescence measurements and single-cell analysis demonstrate that the opportunistic human pathogen Streptococcus pneumoniae grows in medium supplemented with chloramphenicol (Cm) when resistant bacteria expressing Cm acetyltransferase (CAT) are present. We show that CAT processes Cm intracellularly but not extracellularly. In a mouse pneumonia model, more susceptible pneumococci survive Cm treatment when coinfected with a CAT-expressing strain. Mathematical modeling predicts that stable coexistence is only possible when antibiotic resistance comes at a fitness cost. Strikingly, CAT-expressing pneumococci in mouse lungs were outcompeted by susceptible cells even during Cm treatment. Our results highlight the importance of the microbial context during infectious disease as a potential complicating factor to antibiotic therapy. Antibiotic-resistant bacterial infections are on the rise and pose a serious threat to society. The influence of genetic resistance mechanisms on antibiotic therapy is well described. However, other factors, such as epigenetic resistance or the impact of the environment on antibiotic therapy, are less well understood. Here, we describe and characterize a mechanism of noninherited antibiotic resistance that enables the survival and outgrowth of genetically susceptible bacteria during antibiotic therapy. We show that bacteria expressing the resistance factor chloramphenicol (Cm) acetyltransferase (CAT) can potently deactivate Cm in their immediate environment. The reduced Cm concentration then allows for the outgrowth of genetically susceptible bacteria in the same environment. Mathematical modeling demonstrates the presence of a parameter space in which stable coexistence between Cm-susceptible and -resistant bacteria is possible during antibiotic therapy, which we validated using single-cell analyses. Strikingly, mixed culture experiments in which mice were infected with both Cm-susceptible and -resistant pneumococci revealed that Cm-sensitive “freeloader” bacteria even outcompeted resistant bacteria during antibiotic therapy. Together, we show that the microbial context during infection is a potential complicating factor to antibiotic treatment outcomes.
Collapse
|
90
|
Affiliation(s)
- Ralf Pörtner
- Hamburg University of Technology; Institute of Bioprocess and Biosystems Engineering; Denickestr. 15 D21071 Hamburg Germany
| | - Uwe Jandt
- Hamburg University of Technology; Institute of Bioprocess and Biosystems Engineering; Denickestr. 15 D21071 Hamburg Germany
| | - An-Ping Zeng
- Hamburg University of Technology; Institute of Bioprocess and Biosystems Engineering; Denickestr. 15 D21071 Hamburg Germany
| |
Collapse
|
91
|
Huang T, Xu Y, Zeng J, Zhao DH, Li L, Liao XP, Liu YH, Sun J. Low-Concentration Ciprofloxacin Selects Plasmid-Mediated Quinolone Resistance Encoding Genes and Affects Bacterial Taxa in Soil Containing Manure. Front Microbiol 2016; 7:1730. [PMID: 27847506 PMCID: PMC5088497 DOI: 10.3389/fmicb.2016.01730] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/17/2016] [Indexed: 12/22/2022] Open
Abstract
The spread of antimicrobial resistance in environment is promoted at least in part by the inappropriate use of antibiotics in animals and humans. The present study was designed to investigate the impact of different concentrations of ciprofloxacin in soil containing manure on the development of plasmid-mediated quinolone resistance (PMQR) – encoding genes and the abundance of soil bacterial communities. For these studies, high-throughput next-generation sequencing of 16S rRNA, real-time polymerase chain reaction and standard microbiologic culture methods were utilized. We demonstrated that the dissipate rate of relative abundances of some of PMQR-encoding genes, such as qnrS, oqxA and aac(6′)-Ib-cr, were significantly lower with ciprofloxacin 0.04 and 0.4 mg/kg exposure as compared to no-ciprofloxacin control and ciprofloxacin 4 mg/kg exposure during 2 month. Also, the number of ciprofloxacin resistant bacteria was significantly greater in ciprofloxacin 0.04 and 0.4 mg/kg exposure as compared with no-ciprofloxacin control and the ciprofloxacin 4 mg/kg exposure. In addition, lower ciprofloxacin concentration provided a selective advantage for the populations of Xanthomonadales and Bacillales in orders while Agrobacterium, Bacillus, Enterococcus, and Burkholderia in genera. These findings suggest that lower concentration of ciprofloxacin resulted in a slower rate of PMQR-encoding genes dissipation and selected development of ciprofloxacin-resistant bacteria in soil amended with manure.
Collapse
Affiliation(s)
- Ting Huang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural UniversityGuangzhou, China
| | - Ying Xu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural UniversityGuangzhou, China
| | - Jie Zeng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural UniversityGuangzhou, China
| | - Dong-Hao Zhao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural UniversityGuangzhou, China
| | - Liang Li
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural UniversityGuangzhou, China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural UniversityGuangzhou, China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural UniversityGuangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural UniversityGuangzhou, China
| |
Collapse
|
92
|
Abstract
Cooperation between microbes can enable microbial communities to survive in harsh environments. Enzymatic deactivation of antibiotics, a common mechanism of antibiotic resistance in bacteria, is a cooperative behavior that can allow resistant cells to protect sensitive cells from antibiotics. Understanding how bacterial populations survive antibiotic exposure is important both clinically and ecologically, yet the implications of cooperative antibiotic deactivation on the population and evolutionary dynamics remain poorly understood, particularly in the presence of more than one antibiotic. Here, we show that two Escherichia coli strains can form an effective cross-protection mutualism, protecting each other in the presence of two antibiotics (ampicillin and chloramphenicol) so that the coculture can survive in antibiotic concentrations that inhibit growth of either strain alone. Moreover, we find that daily dilutions of the coculture lead to large oscillations in the relative abundance of the two strains, with the ratio of abundances varying by nearly four orders of magnitude over the course of the 3-day period of the oscillation. At modest antibiotic concentrations, the mutualistic behavior enables long-term survival of the oscillating populations; however, at higher antibiotic concentrations, the oscillations destabilize the population, eventually leading to collapse. The two strains form a successful cross-protection mutualism without a period of coevolution, suggesting that similar mutualisms may arise during antibiotic treatment and in natural environments such as the soil.
Collapse
|
93
|
McNally L, Brown SP. Building the microbiome in health and disease: niche construction and social conflict in bacteria. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0298. [PMID: 26150664 PMCID: PMC4528496 DOI: 10.1098/rstb.2014.0298] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Microbes collectively shape their environment in remarkable ways via the products of their metabolism. The diverse environmental impacts of macro-organisms have been collated and reviewed under the banner of ‘niche construction’. Here, we identify and review a series of broad and overlapping classes of bacterial niche construction, ranging from biofilm production to detoxification or release of toxins, enzymes, metabolites and viruses, and review their role in shaping microbiome composition, human health and disease. Some bacterial niche-constructing traits can be seen as extended phenotypes, where individuals actively tailor their environment to their benefit (and potentially to the benefit of others, generating social dilemmas). Other modifications can be viewed as non-adaptive by-products from a producer perspective, yet they may lead to remarkable within-host environmental changes. We illustrate how social evolution and niche construction perspectives offer complementary insights into the dynamics and consequences of these traits across distinct timescales. This review highlights that by understanding the coupled bacterial and biochemical dynamics in human health and disease we can better manage host health.
Collapse
Affiliation(s)
- Luke McNally
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sam P Brown
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| |
Collapse
|
94
|
Gillan DC. Metal resistance systems in cultivated bacteria: are they found in complex communities? Curr Opin Biotechnol 2016; 38:123-30. [DOI: 10.1016/j.copbio.2016.01.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 12/11/2022]
|
95
|
Selective Conditions for a Multidrug Resistance Plasmid Depend on the Sociality of Antibiotic Resistance. Antimicrob Agents Chemother 2016; 60:2524-7. [PMID: 26787694 PMCID: PMC4808222 DOI: 10.1128/aac.02441-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/11/2016] [Indexed: 01/21/2023] Open
Abstract
Multidrug resistance (MDR) plasmids frequently carry antibiotic resistance genes conferring qualitatively different mechanisms of resistance. We show here that the antibiotic concentrations selecting for the RK2 plasmid inEscherichia colidepend upon the sociality of the drug resistance: the selection for selfish drug resistance (efflux pump) occurred at very low drug concentrations, just 1.3% of the MIC of the plasmid-free antibiotic-sensitive strain, whereas selection for cooperative drug resistance (modifying enzyme) occurred at drug concentrations exceeding the MIC of the plasmid-free strain.
Collapse
|
96
|
Feng Y, Hodiamont CJ, van Hest RM, Brul S, Schultsz C, ter Kuile BH. Development of Antibiotic Resistance during Simulated Treatment of Pseudomonas aeruginosa in Chemostats. PLoS One 2016; 11:e0149310. [PMID: 26872140 PMCID: PMC4752458 DOI: 10.1371/journal.pone.0149310] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/29/2016] [Indexed: 11/24/2022] Open
Abstract
During treatment of infections with antibiotics in critically ill patients in the intensive care resistance often develops. This study aims to establish whether under those conditions this resistance can develop de novo or that genetic exchange between bacteria is by necessity involved. Chemostat cultures of Pseudomonas aeruginosa were exposed to treatment regimes with ceftazidime and meropenem that simulated conditions expected in patient plasma. Development of antibiotic resistance was monitored and mutations in resistance genes were searched for by sequencing PCR products. Even at the highest concentrations that can be expected in patients, sufficient bacteria survived in clumps of filamentous cells to recover and grow out after 3 to 5 days. At the end of a 7 days simulated treatment, the minimal inhibitory concentration (MIC) had increased by a factor between 10 and 10,000 depending on the antibiotic and the treatment protocol. The fitness costs of resistance were minimal. In the resistant strains, only three mutations were observed in genes associated with beta-lactam resistance. The development of resistance often observed during patient treatment can be explained by de novo acquisition of resistance and genetic exchange of resistance genes is not by necessity involved. As far as conclusions based on an in vitro study using P. aeruginosa and only two antibiotics can be generalized, it seems that development of resistance can be minimized by treating with antibiotics in the highest concentration the patient can endure for the shortest time needed to eliminate the infection.
Collapse
Affiliation(s)
- Yanfang Feng
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Caspar J. Hodiamont
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Reinier M. van Hest
- Department of Hospital Pharmacy & Clinical Pharmacology, Academic Medical Center, Amsterdam, the Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Constance Schultsz
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
- Department of Global Health-Amsterdam Institute for Global Health and Development, Academic Medical Center, Amsterdam, The Netherlands
| | - Benno H. ter Kuile
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Office for Risk Assessment and Research Coordination Netherlands Food and Consumer Product Safety Authority, Utrecht, The Netherlands
- * E-mail: ;
| |
Collapse
|
97
|
Batoni G, Casu M, Giuliani A, Luca V, Maisetta G, Mangoni ML, Manzo G, Pintus M, Pirri G, Rinaldi AC, Scorciapino MA, Serra I, Ulrich AS, Wadhwani P. Rational modification of a dendrimeric peptide with antimicrobial activity: consequences on membrane-binding and biological properties. Amino Acids 2015; 48:887-900. [PMID: 26614437 DOI: 10.1007/s00726-015-2136-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/08/2015] [Indexed: 01/05/2023]
Abstract
Peptide-based antibiotics might help containing the rising tide of antimicrobial resistance. We developed SB056, a semi-synthetic peptide with a dimeric dendrimer scaffold, active against both Gram-negative and Gram-positive bacteria. Being the mechanism of SB056 attributed to disruption of bacterial membranes, we enhanced the amphiphilic profile of the original, empirically derived sequence [WKKIRVRLSA-NH2] by interchanging the first two residues [KWKIRVRLSA-NH2], and explored the effects of this modification on the interaction of peptide, both in linear and dimeric forms, with model membranes and on antimicrobial activity. Results obtained against Escherichia coli and Staphylococcus aureus planktonic strains, with or without salts at physiological concentrations, confirmed the added value of dendrimeric structure over the linear one, especially at physiological ionic strength, and the impact of the higher amphipathicity obtained through sequence modification on enhancing peptide performances. SB056 peptides also displayed intriguing antibiofilm properties. Staphylococcus epidermidis was the most susceptible strain in sessile form, notably to optimized linear analog lin-SB056-1 and the wild-type dendrimer den-SB056. Membrane affinity of all peptides increased with the percentage of negatively charged lipids and was less influenced by the presence of salt in the case of dendrimeric peptides. The analog lin-SB056-1 displayed the highest overall affinity, even for zwitterionic PC bilayers. Thus, in addition to electrostatics, distribution of charged/polar and hydrophobic residues along the sequence might have a significant role in driving peptide-lipid interaction. Supporting this view, dendrimeric analog den-SB056-1 retained greater membrane affinity in the presence of salt than den-SB056, despite the fact that they bear exactly the same net positive charge.
Collapse
Affiliation(s)
- Giovanna Batoni
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Mariano Casu
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria, Monserrato (CA), Italy
| | - Andrea Giuliani
- Research and Development Unit, Spider Biotech S.r.l., Colleretto Giacosa (TO), Italy
| | - Vincenzo Luca
- Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
| | - Giuseppantonio Maisetta
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Maria Luisa Mangoni
- Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
| | - Giorgia Manzo
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato (CA), Italy
| | - Manuela Pintus
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato (CA), Italy
| | - Giovanna Pirri
- Research and Development Unit, Spider Biotech S.r.l., Colleretto Giacosa (TO), Italy
| | - Andrea C Rinaldi
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato (CA), Italy.
| | - Mariano A Scorciapino
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato (CA), Italy
| | - Ilaria Serra
- Department of Biomedical Sciences, University of Cagliari, Cittadella Universitaria, Monserrato (CA), Italy
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| |
Collapse
|
98
|
Nozhevnikova AN, Botchkova EA, Plakunov VK. Multi-species biofilms in ecology, medicine, and biotechnology. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715060107] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
99
|
Bollenbach T. Antimicrobial interactions: mechanisms and implications for drug discovery and resistance evolution. Curr Opin Microbiol 2015; 27:1-9. [DOI: 10.1016/j.mib.2015.05.008] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/06/2015] [Accepted: 05/08/2015] [Indexed: 01/06/2023]
|
100
|
Zhou G, Shi QS, Huang XM, Xie XB. The Three Bacterial Lines of Defense against Antimicrobial Agents. Int J Mol Sci 2015; 16:21711-33. [PMID: 26370986 PMCID: PMC4613276 DOI: 10.3390/ijms160921711] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 08/21/2015] [Accepted: 08/31/2015] [Indexed: 01/06/2023] Open
Abstract
Antimicrobial agents target a range of extra- and/or intracellular loci from cytoplasmic wall to membrane, intracellular enzymes and genetic materials. Meanwhile, many resistance mechanisms employed by bacteria to counter antimicrobial agents have been found and reported in the past decades. Based on their spatially distinct sites of action and distribution of location, antimicrobial resistance mechanisms of bacteria were categorized into three groups, coined the three lines of bacterial defense in this review. The first line of defense is biofilms, which can be formed by most bacteria to overcome the action of antimicrobial agents. In addition, some other bacteria employ the second line of defense, the cell wall, cell membrane, and encased efflux pumps. When antimicrobial agents permeate the first two lines of defense and finally reach the cytoplasm, many bacteria will make use of the third line of defense, including alterations of intracellular materials and gene regulation to protect themselves from harm by bactericides. The presented three lines of defense theory will help us to understand the bacterial resistance mechanisms against antimicrobial agents and design efficient strategies to overcome these resistances.
Collapse
Affiliation(s)
- Gang Zhou
- Guangdong Institute of Microbiology, Guangzhou 510070, Guangdong, China.
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, Guangdong, China.
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou 510070, Guangdong, China.
| | - Qing-Shan Shi
- Guangdong Institute of Microbiology, Guangzhou 510070, Guangdong, China.
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, Guangdong, China.
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou 510070, Guangdong, China.
| | - Xiao-Mo Huang
- Guangdong Institute of Microbiology, Guangzhou 510070, Guangdong, China.
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, Guangdong, China.
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou 510070, Guangdong, China.
| | - Xiao-Bao Xie
- Guangdong Institute of Microbiology, Guangzhou 510070, Guangdong, China.
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, Guangdong, China.
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou 510070, Guangdong, China.
| |
Collapse
|