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Torrillo PA, Lieberman TD. Reversions mask the contribution of adaptive evolution in microbiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557751. [PMID: 37745437 PMCID: PMC10515931 DOI: 10.1101/2023.09.14.557751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
When examining bacterial genomes for evidence of past selection, the results obtained depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhibit stronger evidence of purifying selection as assessed byd N / d S , the normalized ratio of nonsynonymous to synonymous mutations. Here, we show that the classical interpretation of this scale-dependence, weak purifying selection, leads to problematic mutation accumulation when applied to available gut microbiome data. We propose an alternative, adaptive reversion model with exactly opposite implications for dynamical intuition and applications ofd N / d S . Reversions that occur and sweep within-host populations are nearly guaranteed in microbiomes due to large population sizes, short generation times, and variable environments. Using analytical and simulation approaches, we show that adaptive reversion can explain thed N / d S decay given only dozens of locally-fluctuating selective pressures, which is realistic in the context of Bacteroides genomes. The success of the adaptive reversion model argues for interpreting low values ofd N / d S obtained from long-time scales with caution, as they may emerge even when adaptive sweeps are frequent. Our work thus inverts the interpretation of an old observation in bacterial evolution, illustrates the potential of mutational reversions to shape genomic landscapes over time, and highlights the importance of studying bacterial genomic evolution on short time scales.
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Affiliation(s)
- Paul A. Torrillo
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tami D. Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
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2
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Liu Y, Chu K, Hua Z, Li Q, Lu Y, Ye F, Dong Y, Li X. Dynamics of antibiotic resistance genes in the sediments of a water-diversion lake and its human exposure risk behaviour. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172563. [PMID: 38641096 DOI: 10.1016/j.scitotenv.2024.172563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
The dynamics and exposure risk behaviours of antibiotic resistance genes (ARGs) in the sediments of water-diversion lakes remain poorly understood. In this study, spatiotemporal investigations of ARG profiles in sediments targeting non-water (NWDP) and water diversion periods (WDP) were conducted in Luoma Lake, a typical water-diversion lake, and an innovative dynamics-based risk assessment framework was constructed to evaluate ARG exposure risks to local residents. ARGs in sediments were significantly more abundant in the WDP than in the NWDP, but there was no significant variation in their spatial distribution in either period. Moreover, the pattern of ARG dissemination in sediments was unchanged between the WDP and NWDP, with horizontal gene transfer (HGT) and vertical gene transfer (VGT) contributing to ARG dissemination in both periods. However, water diversion altered the pattern in lake water, with HGT and VGT in the NWDP but only HGT in the WDP, which were critical pathways for the dissemination of ARGs. The significantly lower ARG sediment-water partition coefficient in the WDP indicated that water diversion could shift the fate of ARGs and facilitate their aqueous partitioning. Risk assessment showed that all age groups faced a higher human exposure risk of ARGs (HERA) in the WDP than in the NWDP, with the 45-59 age group having the highest risk. Furthermore, HERA increased overall with the bacterial carrying capacity in the local environment and peaked when the carrying capacity reached three (NWDP) or four (WDP) orders of magnitude higher than the observed bacterial population. HGT and VGT promoted, whereas ODF covering gene mutation and loss mainly reduced HERA in the lake. As the carrying capacity increased, the relative contribution of ODF to HERA remained relatively stable, whereas the dominant mechanism of HERA development shifted from HGT to VGT.
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Affiliation(s)
- Yuanyuan Liu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Kejian Chu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China.
| | - Zulin Hua
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Qiming Li
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Ying Lu
- Institute for Smart City of Chongqing University in Liyang, Liyang 213300, PR China
| | - Fuzhu Ye
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Yueyang Dong
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Xiaoqing Li
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
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3
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Villalba de la Peña M, Kronholm I. Antimicrobial resistance in the wild: Insights from epigenetics. Evol Appl 2024; 17:e13707. [PMID: 38817397 PMCID: PMC11134192 DOI: 10.1111/eva.13707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 03/04/2024] [Accepted: 04/26/2024] [Indexed: 06/01/2024] Open
Abstract
Spreading of bacterial and fungal strains that are resistant to antimicrobials poses a serious threat to the well-being of humans, animals, and plants. Antimicrobial resistance has been mainly investigated in clinical settings. However, throughout their evolutionary history microorganisms in the wild have encountered antimicrobial substances, forcing them to evolve strategies to combat antimicrobial action. It is well known that many of these strategies are based on genetic mechanisms, but these do not fully explain important aspects of the antimicrobial response such as the rapid development of resistance, reversible phenotypes, and hetero-resistance. Consequently, attention has turned toward epigenetic pathways that may offer additional insights into antimicrobial mechanisms. The aim of this review is to explore the epigenetic mechanisms that confer antimicrobial resistance, focusing on those that might be relevant for resistance in the wild. First, we examine the presence of antimicrobials in natural settings. Then we describe the documented epigenetic mechanisms in bacteria and fungi associated with antimicrobial resistance and discuss innovative epigenetic editing techniques to establish causality in this context. Finally, we discuss the relevance of these epigenetic mechanisms on the evolutionary dynamics of antimicrobial resistance in the wild, emphasizing the critical role of priming in the adaptation process. We underscore the necessity of incorporating non-genetic mechanisms into our understanding of antimicrobial resistance evolution. These mechanisms offer invaluable insights into the dynamics of antimicrobial adaptation within natural ecosystems.
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Affiliation(s)
| | - Ilkka Kronholm
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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4
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Nashwan AJ, Shah HH, Hussain T, Rauf SA, Ahmed SK. Environmental Drivers of Antimicrobial Resistance in Low and Middle-Income Countries: The Impacts of a Changing World. ENVIRONMENTAL HEALTH INSIGHTS 2024; 18:11786302241246420. [PMID: 38605979 PMCID: PMC11008345 DOI: 10.1177/11786302241246420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024]
Abstract
This letter highlights the impact of environmental drivers on antimicrobial resistance (AMR) in low and middle-income countries (LMICs) and highlights the need for a comprehensive approach to address this global health threat. Key factors, such as agricultural practices, wastewater treatment, and pollution, contribute to the development and spread of resistant pathogens. Utilizing the One Health approach, the paper emphasizes the importance of promoting responsible antimicrobial use, strengthening public health systems, investing in innovative research, and raising public awareness. By understanding and addressing these environmental drivers, we can work toward safeguarding global health and ensuring a sustainable future.
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Affiliation(s)
| | | | - Tooba Hussain
- Dow University of Health Sciences, Karachi, Pakistan
| | | | - Sirwan Khalid Ahmed
- College of Nursing, University of Raparin, Rania, Sulaymaniyah, Kurdistan Region, Iraq
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5
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Pal A, Andersson DI. Bacteria can compensate the fitness costs of amplified resistance genes via a bypass mechanism. Nat Commun 2024; 15:2333. [PMID: 38485998 PMCID: PMC10940297 DOI: 10.1038/s41467-024-46571-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 03/01/2024] [Indexed: 03/18/2024] Open
Abstract
Antibiotic heteroresistance is a phenotype in which a susceptible bacterial population includes a small subpopulation of cells that are more resistant than the main population. Such resistance can arise by tandem amplification of DNA regions containing resistance genes that in single copy are not sufficient to confer resistance. However, tandem amplifications often carry fitness costs, manifested as reduced growth rates. Here, we investigated if and how these fitness costs can be genetically ameliorated. We evolved four clinical isolates of three bacterial species that show heteroresistance to tobramycin, gentamicin and tetracyclines at increasing antibiotic concentrations above the minimal inhibitory concentration (MIC) of the main susceptible population. This led to a rapid enrichment of resistant cells with up to an 80-fold increase in the resistance gene copy number, an increased MIC, and severely reduced growth rates. When further evolved in the presence of antibiotic, these strains acquired compensatory resistance mutations and showed a reduction in copy number while maintaining high-level resistance. A deterministic model indicated that the loss of amplified units was driven mainly by their fitness costs and that the compensatory mutations did not affect the loss rate of the gene amplifications. Our findings suggest that heteroresistance mediated by copy number changes can facilitate and precede the evolution towards stable resistance.
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Affiliation(s)
- Ankita Pal
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23, Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23, Uppsala, Sweden.
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6
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Dao TH, Echlin H, McKnight A, Marr ES, Junker J, Jia Q, Hayden R, van Opijnen T, Isberg RR, Cooper VS, Rosch JW. Streptococcus pneumoniae favors tolerance via metabolic adaptation over resistance to circumvent fluoroquinolones. mBio 2024; 15:e0282823. [PMID: 38193698 PMCID: PMC10865975 DOI: 10.1128/mbio.02828-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Streptococcus pneumoniae is a major human pathogen of global health concern and the rapid emergence of antibiotic resistance poses a serious public health problem worldwide. Fluoroquinolone resistance in S. pneumoniae is an intriguing case because the prevalence of fluoroquinolone resistance does not correlate with increasing usage and has remained rare. Our data indicate that deleterious fitness costs in the mammalian host constrain the emergence of fluoroquinolone resistance both by de novo mutation and recombination. S. pneumoniae was able to circumvent such deleterious fitness costs via the development of antibiotic tolerance through metabolic adaptation that reduced the production of reactive oxygen species, resulting in a fitness benefit during infection of mice treated with fluoroquinolones. These data suggest that the emergence of fluoroquinolone resistance is tightly constrained in S. pneumoniae by fitness tradeoffs and that mutational pathways involving metabolic networks to enable tolerance phenotypes are an important contributor to the evasion of antibiotic-mediated killing.IMPORTANCEThe increasing prevalence of antibiotic resistant bacteria is a major global health concern. While many species have the potential to develop antibiotic resistance, understanding the barriers to resistance emergence in the clinic remains poorly understood. A prime example of this is fluroquinolone resistance in Streptococcus pneumoniae, whereby, despite continued utilization, resistance to this class of antibiotic remains rare. In this study, we found that the predominant pathways for developing resistance to this antibiotic class severely compromised the infectious capacity of the pneumococcus, providing a key impediment for the emergence of resistance. Using in vivo models of experimental evolution, we found that S. pneumoniae responds to repeated fluoroquinolone exposure by modulating key metabolic pathways involved in the generation of redox molecules, which leads to antibiotic treatment failure in the absence of appreciable shifts in resistance levels. These data underscore the complex pathways available to pathogens to evade antibiotic mediating killing via antibiotic tolerance.
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Affiliation(s)
- Tina H. Dao
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Haley Echlin
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Abigail McKnight
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Enolia S. Marr
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Julia Junker
- Nationales Referenzzentrum für Streptokokken Abteilung Medizinische Mikrobiologie, Universitätsklinikum RWTH Aachen, Aachen, Germany
| | - Qidong Jia
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Randall Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Tim van Opijnen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ralph R. Isberg
- Deptartment of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Vaughn S. Cooper
- Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jason W. Rosch
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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7
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Nguyen ANT, Gorrell R, Kwok T, Connallon T, McDonald MJ. Horizontal gene transfer facilitates the molecular reverse-evolution of antibiotic sensitivity in experimental populations of H. pylori. Nat Ecol Evol 2024; 8:315-324. [PMID: 38177692 DOI: 10.1038/s41559-023-02269-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 11/09/2023] [Indexed: 01/06/2024]
Abstract
Reversing the evolution of traits harmful to humans, such as antimicrobial resistance, is a key ambition of applied evolutionary biology. A major impediment to reverse evolution is the relatively low spontaneous mutation rates that revert evolved genotypes back to their ancestral state. However, the repeated re-introduction of ancestral alleles by horizontal gene transfer (HGT) could make reverse evolution likely. Here we evolve populations of an antibiotic-resistant strain of Helicobacter pylori in growth conditions without antibiotics while introducing an ancestral antibiotic-sensitive allele by HGT. We evaluate reverse evolution using DNA sequencing and find that HGT facilitates the molecular reverse evolution of the antibiotic resistance allele, and that selection for high rates of HGT drives the evolution of increased HGT rates in low-HGT treatment populations. Finally, we use a theoretical model and carry out simulations to infer how the fitness costs of antibiotic resistance, rates of HGT and effects of genetic drift interact to determine the probability and predictability of reverse evolution.
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Affiliation(s)
- An N T Nguyen
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca Gorrell
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Terry Kwok
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Biomedical Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Tim Connallon
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia.
| | - Michael J McDonald
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia.
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
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8
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Yi J, Kim J, Ahn J. Dynamic responses of Salmonella Typhimurium to re-exposure to sublethal ciprofloxacin. FEMS Microbiol Lett 2024; 371:fnae050. [PMID: 39012705 DOI: 10.1093/femsle/fnae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 06/15/2024] [Accepted: 06/26/2024] [Indexed: 07/18/2024] Open
Abstract
This study was designed to evaluate the history-dependent behaviors of Salmonella Typhimurium re-exposed to sublethal levels of ciprofloxacin. The S. Typhimurium cells were pre-exposed to 0 (CON), 1/16 (LOW), 1/8 (MED), and 1/4 (HIGH) minimum inhibitory concentrations (MICs) of ciprofloxacin, followed by re-exposure to the same concentrations. The bacterial growth, postantibiotic effect (PAE), relative fitness, and swimming motility of treatments were evaluated in the absence of ciprofloxacin. The lag phase duration (LPD) was estimate to assess bacterial recovery under ciprofloxacin exposure. A disk diffusion assay was used to determine the cross-resistance and collateral sensitivity of CON, LOW, MED, and HIGH treatments to ciprofloxacin (CIP), ceftriaxone (CEF), erythromycin (ERY), gentamicin (GEN), and polymyxin B (POL). The S. Typhimurium cells pre-exposed to ciprofloxacin were susceptible in antibiotic-free media, showing delayed growth. The highest PAE (>1 h) and bacterial fluctuation (CV = 5%) were observed at the High treatment compared to the CON. The HIGH treatment had the lowest relative fitness levels (0.87) and swimming motility (55 mm). The LPD was significantly decreased at the LOW treatment (1.8 h) when re-exposed to 1/16 × MIC of ciprofloxacin. The LOW, MED, and HIGH treatments showed the cross-resistance to POL and the collateral sensitivity to CEF, ERY, and GEN. The pre-exposure to ciprofloxacin could induce phenotypic diversity, corresponding to the history-dependent behaviors. These results provide important insights for the dynamic nature of bacterial populations when re-exposed to sublethal concentrations of antibiotics.
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Affiliation(s)
- Jiseok Yi
- Department of Biomedical Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Junhwan Kim
- Department of Biomedical Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
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9
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MacGillivray KA, Ng SL, Wiesenfeld S, Guest RL, Jubery T, Silhavy TJ, Ratcliff WC, Hammer BK. Trade-offs constrain adaptive pathways to the type VI secretion system survival. iScience 2023; 26:108332. [PMID: 38025790 PMCID: PMC10679819 DOI: 10.1016/j.isci.2023.108332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 08/25/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
The Type VI Secretion System (T6SS) is a nano-harpoon used by many bacteria to inject toxins into neighboring cells. While much is understood about mechanisms of T6SS-mediated toxicity, less is known about the ways that competitors can defend themselves against this attack, especially in the absence of their own T6SS. Here we subjected eight replicate populations of Escherichia coli to T6SS attack by Vibrio cholerae. Over ∼500 generations of competition, isolates of the E. coli populations evolved to survive T6SS attack an average of 27-fold better, through two convergently evolved pathways: apaH was mutated in six of the eight replicate populations, while the other two populations each had mutations in both yejM and yjeP. However, the mutations we identified are pleiotropic, reducing cellular growth rates, and increasing susceptibility to antibiotics and elevated pH. These trade-offs help us understand how the T6SS shapes the evolution of bacterial interactions.
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Affiliation(s)
- Kathryn A. MacGillivray
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Siu Lung Ng
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Sophia Wiesenfeld
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Randi L. Guest
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Tahrima Jubery
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Thomas J. Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - William C. Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Brian K. Hammer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
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10
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Srinivasan A, Sajeevan A, Rajaramon S, David H, Solomon AP. Solving polymicrobial puzzles: evolutionary dynamics and future directions. Front Cell Infect Microbiol 2023; 13:1295063. [PMID: 38145044 PMCID: PMC10748482 DOI: 10.3389/fcimb.2023.1295063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/03/2023] [Indexed: 12/26/2023] Open
Abstract
Polymicrobial infections include various microorganisms, often necessitating different treatment methods than a monomicrobial infection. Scientists have been puzzled by the complex interactions within these communities for generations. The presence of specific microorganisms warrants a chronic infection and impacts crucial factors such as virulence and antibiotic susceptibility. Game theory is valuable for scenarios involving multiple decision-makers, but its relevance to polymicrobial infections is limited. Eco-evolutionary dynamics introduce causation for multiple proteomic interactions like metabolic syntropy and niche segregation. The review culminates both these giants to form evolutionary dynamics (ED). There is a significant amount of literature on inter-bacterial interactions that remain unsynchronised. Such raw data can only be moulded by analysing the ED involved. The review culminates the inter-bacterial interactions in multiple clinically relevant polymicrobial infections like chronic wounds, CAUTI, otitis media and dental carries. The data is further moulded with ED to analyse the niche colonisation of two notoriously competitive bacteria: S.aureus and P.aeruginosa. The review attempts to develop a future trajectory for polymicrobial research by following recent innovative strategies incorporating ED to curb polymicrobial infections.
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Affiliation(s)
| | | | | | | | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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11
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Yi J, Ahn J. Heterogeneous Phenotypic Responses of Antibiotic-Resistant Salmonella Typhimurium to Food Preservative-Related Stresses. Antibiotics (Basel) 2023; 12:1702. [PMID: 38136736 PMCID: PMC10740406 DOI: 10.3390/antibiotics12121702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
This study was designed to evaluate the response of antibiotic-resistant Salmonella Typhimurium to food preservative-related stresses, such as lactic acid and sodium chloride (NaCl). S. Typhimurium cells were exposed to 1 µg/mL of ciprofloxacin (CIP), 0.2% lactic acid (LA), 6% NaCl, CIP followed by LA (CIP-LA), and CIP followed by NaCl (CIP-NaCl). The untreated S. Typhimurium cells were the control (CON). All treatments were as follows: CON, CIP, LA, NaCl, CIP-LA, and CIP-NaCl. The phenotypic heterogeneity was evaluated by measuring the antimicrobial susceptibility, bacterial fluctuation, cell injury, persistence, and cross-resistance. The CIP, CIP-LA, and CIP-NaCl groups were highly resistant to ciprofloxacin, showing MIC values of 0.70, 0.59, and 0.54 µg/mL, respectively, compared to the CON group (0.014 µg/mL). The susceptibility to lactic acid was not changed after exposure to NaCl, while that to NaCl was decreased after exposure to NaCl. The Eagle phenomenon was observed in the CIP, CIP-LA, and CIP-NaCl groups, showing Eagle effect concentrations (EECs) of more than 8 µg/mL. No changes in the MBCs of lactic acid and NaCl were observed in the CIP, LA, and CIP-LA groups, and the EECs of lactic acid and NaCl were not detected in all treatments. The bacterial fluctuation rates of the CIP-LA and CIP-NaCl groups were considerably increased to 33% and 41%, respectively, corresponding to the injured cell proportions of 82% and 89%. CIP-NaCl induced persister cells as high as 2 log cfu/mL. The LA and NaCl treatments decreased the fitness cost. The CIP-NaCl treatment showed positive cross-resistance to erythromycin (ERY) and tetracycline (TET), while the LA and NaCl treatments were collaterally susceptible to chloramphenicol (CHL), ciprofloxacin (CIP), piperacillin (PIP), and TET. The results provide new insight into the fate of antibiotic-resistant S. Typhimurium during food processing and preservation.
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Affiliation(s)
- Jiseok Yi
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea;
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea;
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea
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12
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Savageau MA. Phenotype Design Space Provides a Mechanistic Framework Relating Molecular Parameters to Phenotype Diversity Available for Selection. J Mol Evol 2023; 91:687-710. [PMID: 37620617 PMCID: PMC10598110 DOI: 10.1007/s00239-023-10127-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
Two long-standing challenges in theoretical population genetics and evolution are predicting the distribution of phenotype diversity generated by mutation and available for selection, and determining the interaction of mutation, selection and drift to characterize evolutionary equilibria and dynamics. More fundamental for enabling such predictions is the current inability to causally link genotype to phenotype. There are three major mechanistic mappings required for such a linking - genetic sequence to kinetic parameters of the molecular processes, kinetic parameters to biochemical system phenotypes, and biochemical phenotypes to organismal phenotypes. This article introduces a theoretical framework, the Phenotype Design Space (PDS) framework, for addressing these challenges by focusing on the mapping of kinetic parameters to biochemical system phenotypes. It provides a quantitative theory whose key features include (1) a mathematically rigorous definition of phenotype based on biochemical kinetics, (2) enumeration of the full phenotypic repertoire, and (3) functional characterization of each phenotype independent of its context-dependent selection or fitness contributions. This framework is built on Design Space methods that relate system phenotypes to genetically determined parameters and environmentally determined variables. It also has the potential to automate prediction of phenotype-specific mutation rate constants and equilibrium distributions of phenotype diversity in microbial populations undergoing steady-state exponential growth, which provides an ideal reference to which more realistic cases can be compared. Although the framework is quite general and flexible, the details will undoubtedly differ for different functions, organisms and contexts. Here a hypothetical case study involving a small molecular system, a primordial circadian clock, is used to introduce this framework and to illustrate its use in a particular case. The framework is built on fundamental biochemical kinetics. Thus, the foundation is based on linear algebra and reasonable physical assumptions, which provide numerous opportunities for experimental testing and further elaboration to deal with complex multicellular organisms that are currently beyond its scope. The discussion provides a comparison of results from the PDS framework with those from other approaches in theoretical population genetics.
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Affiliation(s)
- Michael A Savageau
- Department of Microbiology & Molecular Genetics, University of California, 228 Briggs, Davis, CA, 95616, USA.
- Department of Biomedical Engineering, University of California, One Shields Avenue, Davis, CA, 95616, USA.
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13
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Lobinska G, Pilpel Y, Ram Y. Phenotype switching of the mutation rate facilitates adaptive evolution. Genetics 2023; 225:iyad111. [PMID: 37293818 PMCID: PMC10471227 DOI: 10.1093/genetics/iyad111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 02/05/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
The mutation rate plays an important role in adaptive evolution. It can be modified by mutator and anti-mutator alleles. Recent empirical evidence hints that the mutation rate may vary among genetically identical individuals: evidence from bacteria suggests that the mutation rate can be affected by expression noise of a DNA repair protein and potentially also by translation errors in various proteins. Importantly, this non-genetic variation may be heritable via a transgenerational epigenetic mode of inheritance, giving rise to a mutator phenotype that is independent from mutator alleles. Here, we investigate mathematically how the rate of adaptive evolution is affected by the rate of mutation rate phenotype switching. We model an asexual population with two mutation rate phenotypes, non-mutator and mutator. An offspring may switch from its parental phenotype to the other phenotype. We find that switching rates that correspond to so-far empirically described non-genetic systems of inheritance of the mutation rate lead to higher rates of adaptation on both artificial and natural fitness landscapes. These switching rates can maintain within the same individuals both a mutator phenotype and intermediary mutations, a combination that facilitates adaptation. Moreover, non-genetic inheritance increases the proportion of mutators in the population, which in turn increases the probability of hitchhiking of the mutator phenotype with adaptive mutations. This in turns facilitates the acquisition of additional adaptive mutations. Our results rationalize recently observed noise in the expression of proteins that affect the mutation rate and suggest that non-genetic inheritance of this phenotype may facilitate evolutionary adaptive processes.
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Affiliation(s)
- Gabriela Lobinska
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Ram
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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14
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Arunkumar R, Zhou SO, Day JP, Bakare S, Pitton S, Zhang Y, Hsing CY, O’Boyle S, Pascual-Gil J, Clark B, Chandler RJ, Leitão AB, Jiggins FM. Natural selection has driven the recurrent loss of an immunity gene that protects Drosophila against a major natural parasite. Proc Natl Acad Sci U S A 2023; 120:e2211019120. [PMID: 37552757 PMCID: PMC10438844 DOI: 10.1073/pnas.2211019120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 06/26/2023] [Indexed: 08/10/2023] Open
Abstract
Polymorphisms in immunity genes can have large effects on susceptibility to infection. To understand the origins of this variation, we have investigated the genetic basis of resistance to the parasitoid wasp Leptopilina boulardi in Drosophila melanogaster. We found that increased expression of the gene lectin-24A after infection by parasitic wasps was associated with a faster cellular immune response and greatly increased rates of killing the parasite. lectin-24A encodes a protein that is strongly up-regulated in the fat body after infection and localizes to the surface of the parasite egg. In certain susceptible lines, a deletion upstream of the lectin-24A has largely abolished expression. Other mutations predicted to abolish the function of this gene have arisen recurrently in this gene, with multiple loss-of-expression alleles and premature stop codons segregating in natural populations. The frequency of these alleles varies greatly geographically, and in some southern African populations, natural selection has driven them near to fixation. We conclude that natural selection has favored the repeated loss of an important component of the immune system, suggesting that in some populations, a pleiotropic cost to lectin-24A expression outweighs the benefits of resistance.
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Affiliation(s)
- Ramesh Arunkumar
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Shuyu Olivia Zhou
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Jonathan P. Day
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Sherifat Bakare
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Department of Biochemical Sciences, School of Biosciences, University of Surrey, 388 Stag Hill, Guildford,GU2 7XH, United Kingdom
| | - Simone Pitton
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Biosciences Department, Università degli Studi di Milano, Via Celoria 26, Milano, MI20133, Italy
| | - Yexin Zhang
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Chi-Yun Hsing
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Sinead O’Boyle
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- School of Biomolecular and Biomedical Science, University College Dublin, DublinD04 V1W8, Ireland
| | - Juan Pascual-Gil
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Facultad de Ciencias, Universidad Autónoma de Madrid, C. Francisco Tomás y Valiente 7, 28049Madrid, Spain
| | - Belinda Clark
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Rachael J. Chandler
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
- Department of Biochemical Sciences, School of Biosciences, University of Surrey, 388 Stag Hill, Guildford,GU2 7XH, United Kingdom
| | - Alexandre B. Leitão
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
| | - Francis M. Jiggins
- Department of Genetics, School of Biological Sciences, University of Cambridge, Downing Street, CambridgeCB2 3EH, United Kingdom
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15
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Diaz Caballero J, Wheatley RM, Kapel N, López-Causapé C, Van der Schalk T, Quinn A, Shaw LP, Ogunlana L, Recanatini C, Xavier BB, Timbermont L, Kluytmans J, Ruzin A, Esser M, Malhotra-Kumar S, Oliver A, MacLean RC. Mixed strain pathogen populations accelerate the evolution of antibiotic resistance in patients. Nat Commun 2023; 14:4083. [PMID: 37438338 DOI: 10.1038/s41467-023-39416-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 06/12/2023] [Indexed: 07/14/2023] Open
Abstract
Antibiotic resistance poses a global health threat, but the within-host drivers of resistance remain poorly understood. Pathogen populations are often assumed to be clonal within hosts, and resistance is thought to emerge due to selection for de novo variants. Here we show that mixed strain populations are common in the opportunistic pathogen P. aeruginosa. Crucially, resistance evolves rapidly in patients colonized by multiple strains through selection for pre-existing resistant strains. In contrast, resistance evolves sporadically in patients colonized by single strains due to selection for novel resistance mutations. However, strong trade-offs between resistance and growth rate occur in mixed strain populations, suggesting that within-host diversity can also drive the loss of resistance in the absence of antibiotic treatment. In summary, we show that the within-host diversity of pathogen populations plays a key role in shaping the emergence of resistance in response to treatment.
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Affiliation(s)
| | - Rachel M Wheatley
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Natalia Kapel
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Carla López-Causapé
- Servicio de Microbiología, Hospital Universitari Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Thomas Van der Schalk
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Angus Quinn
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Liam P Shaw
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Lois Ogunlana
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Claudia Recanatini
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Leen Timbermont
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Jan Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Alexey Ruzin
- Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Mark Esser
- Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Antonio Oliver
- Servicio de Microbiología, Hospital Universitari Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - R Craig MacLean
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK.
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16
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Vanacker M, Lenuzza N, Rasigade JP. The fitness cost of horizontally transferred and mutational antimicrobial resistance in Escherichia coli. Front Microbiol 2023; 14:1186920. [PMID: 37455716 PMCID: PMC10348881 DOI: 10.3389/fmicb.2023.1186920] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacteria implies a tradeoff between the benefit of resistance under antimicrobial selection pressure and the incurred fitness cost in the absence of antimicrobials. The fitness cost of a resistance determinant is expected to depend on its genetic support, such as a chromosomal mutation or a plasmid acquisition, and on its impact on cell metabolism, such as an alteration in an essential metabolic pathway or the production of a new enzyme. To provide a global picture of the factors that influence AMR fitness cost, we conducted a systematic review and meta-analysis focused on a single species, Escherichia coli. By combining results from 46 high-quality studies in a multilevel meta-analysis framework, we find that the fitness cost of AMR is smaller when provided by horizontally transferable genes such as those encoding beta-lactamases, compared to mutations in core genes such as those involved in fluoroquinolone and rifampicin resistance. We observe that the accumulation of acquired AMR genes imposes a much smaller burden on the host cell than the accumulation of AMR mutations, and we provide quantitative estimates of the additional cost of a new gene or mutation. These findings highlight that gene acquisition is more efficient than the accumulation of mutations to evolve multidrug resistance, which can contribute to the observed dominance of horizontally transferred genes in the current AMR epidemic.
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Affiliation(s)
- Marie Vanacker
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Natacha Lenuzza
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Jean-Philippe Rasigade
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
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17
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Higgins C, Huber L. Rhodococcus equi: challenges to treat infections and to mitigate antimicrobial resistance. J Equine Vet Sci 2023:104845. [PMID: 37295760 DOI: 10.1016/j.jevs.2023.104845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
Rhodococcus equi, a gram-positive facultative intracellular pathogen and a soil saprophyte, is one of the most common causes of pneumonia in young foals. It poses a threat to the economy in endemic horse-breeding farms and to animal welfare annually. Many farms use thoracic ultrasonographic screening and antimicrobial treatment of subclinically affected foals as a preventive measure against severe R. equi infections. The wide use antimicrobials to treat subclinically affected foals has contributed to the emergence of multidrug resistant (MDR)-R. equi in both clinical isolates from sick foals and in the environment of horse-breeding farms. Alternatives to treat foals infected with MDR-R. equi are scarce and the impact of the emergence of MDR-R. equi in the environment of farms is still unknown. The aim of this review is to discuss the emergence of MDR-R. equi in the United States and the challenges faced to guide antimicrobial use practices. Reduction of antimicrobial use at horse-breeding farms is essential for the preservation of antimicrobial efficacy and, ultimately, human, animal, and environmental health.
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Affiliation(s)
- Courtney Higgins
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, 1130 Wire Road, Auburn, Alabama, USA 36832.
| | - Laura Huber
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, 1130 Wire Road, Auburn, Alabama, USA 36832.
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18
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Evolutionary rescue of resistant mutants is governed by a balance between radial expansion and selection in compact populations. Nat Commun 2022; 13:7916. [PMID: 36564390 PMCID: PMC9789051 DOI: 10.1038/s41467-022-35484-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Mutation-mediated treatment resistance is one of the primary challenges for modern antibiotic and anti-cancer therapy. Yet, many resistance mutations have a substantial fitness cost and are subject to purifying selection. How emerging resistant lineages may escape purifying selection via subsequent compensatory mutations is still unclear due to the difficulty of tracking such evolutionary rescue dynamics in space and time. Here, we introduce a system of fluorescence-coupled synthetic mutations to show that the probability of evolutionary rescue, and the resulting long-term persistence of drug resistant mutant lineages, is dramatically increased in dense microbial populations. By tracking the entire evolutionary trajectory of thousands of resistant lineages in expanding yeast colonies we uncover an underlying quasi-stable equilibrium between the opposing forces of radial expansion and natural selection, a phenomenon we term inflation-selection balance. Tailored computational models and agent-based simulations corroborate the fundamental nature of the observed effects and demonstrate the potential impact on drug resistance evolution in cancer. The described phenomena should be considered when predicting multi-step evolutionary dynamics in any mechanically compact cellular population, including pathogenic microbial biofilms and solid tumors. The insights gained will be especially valuable for the quantitative understanding of response to treatment, including emerging evolution-based therapy strategies.
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19
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Wang L, Yu Y, Tao Y, Zhao M, Zhang L, Xue J, Zhao Y, Zhan P, Sun Y. The Quinone-Derived Small Molecule M5N32 Is an Effective Anti-Helicobacter pylori Agent Both In Vivo and In Vitro. J Infect Dis 2022; 226:S493-S502. [PMID: 36478249 DOI: 10.1093/infdis/jiac401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Helicobacter pylori has become increasingly resistant to all commonly used clinical antibiotics. Therefore, new anti-H. pylori drugs need to be identified. Recently, quinones were found to inhibit growth of H. pylori with quinone-derived small-molecule compounds identified as having antitumor effects. METHODS The minimum inhibitory concentrations of the compounds against H. pylori were measured by agar plate dilution method. The inhibition of biofilm formation by the compounds was assessed by SYTO9-PI double staining. The reactive oxygen species induced by the compounds were detected by DCFH-DA stain. The clearance effects of the compounds for H. pylori in mouse were evaluated by counting colony-forming units and hematoxylin and eosin staining. RESULTS Our results revealed strong inhibition of M5N32 in vitro against H. pylori in both the planktonic and biofilm-forming states. Resistance to M5N32 was not developed in successive generations of the bacteria. In vivo, the combination of M5N32 and omeprazole showed enhanced effects in comparison to the standard triple therapy. M5N32 was nontoxic to normal tissues. CONCLUSIONS M5N32 is effective in the treatment of H. pylori infections, providing potential development of anti-H. pylori medicines in the treatment of H. pylori infections.
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Affiliation(s)
- Liyuan Wang
- Department of Microbiology, Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunology of Shandong Province, School of Basic Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yanbo Yu
- Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Yucen Tao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Mingzhong Zhao
- Department of Microbiology, Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunology of Shandong Province, School of Basic Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Lu Zhang
- Department of Microbiology, Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunology of Shandong Province, School of Basic Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Junyuan Xue
- Department of Microbiology, Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunology of Shandong Province, School of Basic Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yican Zhao
- Department of Microbiology, Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunology of Shandong Province, School of Basic Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yundong Sun
- Department of Microbiology, Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunology of Shandong Province, School of Basic Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
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20
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Madden DE, McCarthy KL, Bell SC, Olagoke O, Baird T, Neill J, Ramsay KA, Kidd TJ, Stewart AG, Subedi S, Choong K, Fraser TA, Sarovich DS, Price EP. Rapid fluoroquinolone resistance detection in Pseudomonas aeruginosa using mismatch amplification mutation assay-based real-time PCR. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background. Antimicrobial resistance (AMR) is an ever-increasing global health concern. One crucial facet in tackling the AMR epidemic is earlier and more accurate AMR diagnosis, particularly in the dangerous and highly multi-drug-resistant ESKAPE pathogen,
Pseudomonas aeruginosa
.
Objectives. We aimed to develop two SYBR Green-based mismatch amplification mutation assays (SYBR-MAMAs) targeting GyrA T83I (gyrA248) and GyrA D87N, D87Y and D87H (gyrA259). Together, these variants cause the majority of fluoroquinolone (FQ) AMR in
P. aeruginosa
.
Methods. Following assay validation, the gyrA248 and gyrA259 SYBR-MAMAs were tested on 84 Australian clinical
P. aeruginosa
isolates, 46 of which demonstrated intermediate/full ciprofloxacin resistance according to antimicrobial susceptibility testing.
Results. Our two SYBR-MAMAs correctly predicted an AMR phenotype in the majority (83%) of isolates with intermediate/full FQ resistance. All FQ-sensitive strains were predicted to have a sensitive phenotype. Whole-genome sequencing confirmed 100 % concordance with SYBR-MAMA genotypes.
Conclusions. Our GyrA SYBR-MAMAs provide a rapid and cost-effective method for same-day identification of FQ AMR in
P. aeruginosa
. An additional SYBR-MAMA targeting the GyrB S466Y/S466F variants would increase FQ AMR prediction to 91 %. Clinical implementation of our assays will permit more timely treatment alterations in cases where decreased FQ susceptibility is identified, leading to improved patient outcomes and antimicrobial stewardship.
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Affiliation(s)
- Danielle E. Madden
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Kate L. McCarthy
- University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
- Infectious Diseases Unit, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | - Scott C. Bell
- Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, Queensland, Australia
- Child Health Research Centre, The University of Queensland, South Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Olusola Olagoke
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
| | - Timothy Baird
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Respiratory Department, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Jane Neill
- Respiratory Department, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Kay A. Ramsay
- Child Health Research Centre, The University of Queensland, South Brisbane, Queensland, Australia
| | - Timothy J. Kidd
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Adam G. Stewart
- Infectious Diseases Unit, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
- University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
| | - Shradha Subedi
- Infectious Diseases Unit, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
| | - Keat Choong
- Infectious Diseases Unit, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
| | - Tamieka A. Fraser
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Derek S. Sarovich
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Erin P. Price
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
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21
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Cisneros-Mayoral S, Graña-Miraglia L, Pérez-Morales D, Peña-Miller R, Fuentes-Hernáandez A. Evolutionary history and strength of selection determine the rate of antibiotic resistance adaptation. Mol Biol Evol 2022; 39:6692293. [PMID: 36062982 PMCID: PMC9512152 DOI: 10.1093/molbev/msac185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacterial adaptation to stressful environments often produces evolutionary constraints whereby increases in resistance are associated with reduced fitness in a different environment. The exploitation of this resistance-cost trade-off has been proposed as the basis of rational antimicrobial treatment strategies designed to limit the evolution of drug resistance in bacterial pathogens. Recent theoretical, laboratory, and clinical studies have shown that fluctuating selection can maintain drug efficacy and even restore drug susceptibility, but can also increase the rate of adaptation and promote cross-resistance to other antibiotics. In this paper, we combine mathematical modeling, experimental evolution, and whole-genome sequencing to follow evolutionary trajectories towards β-lactam resistance under fluctuating selective conditions. Our experimental model system consists of eight populations of Escherichia coli K12 evolving in parallel to a serial dilution protocol designed to dynamically control the strength of selection for resistance. We implemented adaptive ramps with mild and strong selection, resulting in evolved populations with similar levels of resistance, but with different evolutionary dynamics and diverging genotypic profiles. We found that mutations that emerged under strong selection are unstable in the absence of selection, in contrast to resistance mutations previously selected in the mild selection regime that were stably maintained in drug-free environments and positively selected for when antibiotics were reintroduced. Altogether, our population dynamics model and the phenotypic and genomic analysis of the evolved populations show that the rate of resistance adaptation is contingent upon the strength of selection, but also on evolutionary constraints imposed by prior drug exposures.
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Affiliation(s)
- Sandra Cisneros-Mayoral
- Programa de Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Mexico
| | - Lucía Graña-Miraglia
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Deyanira Pérez-Morales
- Programa de Biología de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Méexico, 62210, Cuernavaca, Mexico
| | - Rafael Peña-Miller
- Programa de Biología de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Mexico
| | - Ayari Fuentes-Hernáandez
- Programa de Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Méexico, 62210, Cuernavaca, Mexico
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22
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Pennings PS, Ogbunugafor CB, Hershberg R. Reversion is most likely under high mutation supply when compensatory mutations do not fully restore fitness costs. G3 (BETHESDA, MD.) 2022; 12:jkac190. [PMID: 35920784 PMCID: PMC9434179 DOI: 10.1093/g3journal/jkac190] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 10/02/2021] [Indexed: 06/15/2023]
Abstract
The dynamics of adaptation, reversion, and compensation have been central topics in microbial evolution, and several studies have attempted to resolve the population genetics underlying how these dynamics occur. However, questions remain regarding how certain features-the evolution of mutators and whether compensatory mutations alleviate costs fully or partially-may influence the evolutionary dynamics of compensation and reversion. In this study, we attempt to explain findings from experimental evolution by utilizing computational and theoretical approaches toward a more refined understanding of how mutation rate and the fitness effects of compensatory mutations influence adaptive dynamics. We find that high mutation rates increase the probability of reversion toward the wild type when compensation is only partial. However, the existence of even a single fully compensatory mutation is associated with a dramatically decreased probability of reversion to the wild type. These findings help to explain specific results from experimental evolution, where compensation was observed in nonmutator strains, but reversion (sometimes with compensation) was observed in mutator strains, indicating that real-world compensatory mutations are often unable to fully alleviate the costs associated with adaptation. Our findings emphasize the potential role of the supply and quality of mutations in crafting the dynamics of adaptation and reversal, with implications for theoretical population genetics and for biomedical contexts like the evolution of antibiotic resistance.
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Affiliation(s)
- Pleuni S Pennings
- Corresponding author: Department of Biology, San Francisco State University, San Francisco, CA 94132, USA.
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23
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Hemez C, Clarelli F, Palmer AC, Bleis C, Abel S, Chindelevitch L, Cohen T, Abel zur Wiesch P. Mechanisms of antibiotic action shape the fitness landscapes of resistance mutations. Comput Struct Biotechnol J 2022; 20:4688-4703. [PMID: 36147681 PMCID: PMC9463365 DOI: 10.1016/j.csbj.2022.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/15/2022] Open
Abstract
Antibiotic-resistant pathogens are a major public health threat. A deeper understanding of how an antibiotic's mechanism of action influences the emergence of resistance would aid in the design of new drugs and help to preserve the effectiveness of existing ones. To this end, we developed a model that links bacterial population dynamics with antibiotic-target binding kinetics. Our approach allows us to derive mechanistic insights on drug activity from population-scale experimental data and to quantify the interplay between drug mechanism and resistance selection. We find that both bacteriostatic and bactericidal agents can be equally effective at suppressing the selection of resistant mutants, but that key determinants of resistance selection are the relationships between the number of drug-inactivated targets within a cell and the rates of cellular growth and death. We also show that heterogeneous drug-target binding within a population enables resistant bacteria to evolve fitness-improving secondary mutations even when drug doses remain above the resistant strain's minimum inhibitory concentration. Our work suggests that antibiotic doses beyond this "secondary mutation selection window" could safeguard against the emergence of high-fitness resistant strains during treatment.
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Affiliation(s)
- Colin Hemez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Graduate Program in Biophysics, Harvard University, Boston, MA 02115, USA
- Corresponding authors at: Broad Institute, 75 Ames St, Room 3035, Cambridge, MA 02412, USA (C. Hemez). Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway (P. Abel zur Wiesch).
| | - Fabrizio Clarelli
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Adam C. Palmer
- Department of Pharmacology, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christina Bleis
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sören Abel
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Division of Infection Control, Norwegian Institute of Public Health, Oslo 0318, Norway
| | - Leonid Chindelevitch
- Department of Infectious Disease Epidemiology, Imperial College, London SW7 2AZ, UK
| | - Theodore Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA
| | - Pia Abel zur Wiesch
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Division of Infection Control, Norwegian Institute of Public Health, Oslo 0318, Norway
- Corresponding authors at: Broad Institute, 75 Ames St, Room 3035, Cambridge, MA 02412, USA (C. Hemez). Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway (P. Abel zur Wiesch).
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24
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Rivera-Velez A, Huber L, Sinha S, Cohen ND. Fitness cost conferred by the novel erm(51) and rpoB mutation on environmental multidrug resistant-Rhodococcus equi. Vet Microbiol 2022; 273:109531. [PMID: 35944389 DOI: 10.1016/j.vetmic.2022.109531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022]
Abstract
Rhodococcus equi is a common cause of severe pneumonia in foals. Emergence of macrolide-resistant R. equi isolated from foals and their environment has been reported in the United States. A novel erm(51) gene was recently identified in R. equi in soil from horse farms in Kentucky. Our objective was to determine the effect of the erm(51) gene and associated rpoB mutation on the fitness of multidrug resistant-R. equi (MDR-R. equierm(51)+, rpoB+) under different nutrient conditions. Bacterial growth curves were generated for 3 MDR-R. equierm(51)+, rpoB+ isolates and 3 wild-type (WTN) R. equi isolates recovered from environmental samples of farms in central Kentucky. Growth was measured over 30.5 h in brain-heart infusion broth (BHI), minimal medium (MM), and minimal medium without iron (MM-I). All isolates had significantly (P < 0.05) higher growth in BHI compared to either MM or MM-I. MDR-R. equierm(51)+, rpoB+ exhibited significantly lower growth compared to WTN isolates in BHI (nutrient-rich condition), but not in either MM or MM-I (nutrient-restricted conditions). This study indicates that under nutrient-rich conditions fitness of MDR-R. equierm(51)+, rpoB+ is reduced relative to susceptible isolates; however, under nutrient-restricted conditions MDR-R. equierm(51)+, rpoB+ isolates grow similarly to susceptible isolates. These findings indicate that MDR-R. equierm(51)+, rpoB+ might be outcompeted by susceptible isolates in nature when practices to reduce antimicrobial pressure, such as reducing antimicrobial use in foals, are implemented. But it also raises the concern that these resistant genotypes might persist in the environment of horse-breeding farms in the face of selective pressures such as antimicrobials or nutrient restriction.
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Affiliation(s)
- Andres Rivera-Velez
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Laura Huber
- Pathobiology Department, College of Veterinary Medicine, Auburn University, 1130 wire Rd, Auburn, AL 36832, USA.
| | - Samiran Sinha
- Department of Statistics, Texas A&M University, College Station, TX 77843, USA.
| | - Noah D Cohen
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
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25
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Johannessen H, Anthonisen IL, Zecic N, Hegstad K, Ranheim TE, Skaare D. Characterization and Fitness Cost of Tn7100, a Novel Integrative and Conjugative Element Conferring Multidrug Resistance in Haemophilus influenzae. Front Microbiol 2022; 13:945411. [PMID: 35935209 PMCID: PMC9355037 DOI: 10.3389/fmicb.2022.945411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/16/2022] [Indexed: 12/15/2022] Open
Abstract
A multidrug-resistant (MDR) strain of Haemophilus influenzae, Hi-228, with phenotypic resistance toward ampicillin, cefotaxime, chloramphenicol, gentamicin, and azithromycin, was isolated in Oslo, Norway. The strain was part of a clonal outbreak (2016–2017) comprising five ST143 strains with identical resistotypes. Hi-228 carries a novel integrative and conjugative element (ICE), Tn7100, contributing to this remarkable and previously unreported MDR profile. Tn7100 contains the following resistance genes: blaTEM−1B, catA2, aac(6′)-Im, aph(2″)-Ib, mef (E), and mel. The latter four are previously unreported or rarely reported in H. influenzae. In this study, we investigated the genetic environment, mechanisms of transfer, impact on phenotypic susceptibility, and fitness cost of this ICE. We found that Tn7100 has an overall structure similar to the previously described ICE Tn6686, with blaTEM−1B and catA2 carried by Tn3 and Tn10, respectively. The major difference between Tn7100 and Tn6686 is that Tn7100 lacks tet(B) but carries the resistance gene pairs aac(6′)-Im and aph(2″)-Ib and mef (E) and mel. The gene pairs are located on the novel transposable elements Tn7470 and Tn7471, which have high sequence identities to a plasmid in Enterobacterales and an ICE in streptococcal species, respectively. Tn7100 does circularize and is transferable, however, at a low frequency. Head-to-head competition experiments showed that uptake of Tn7100 reduces bacterial fitness. Our study shows that MDR strains are capable of clonal spread and that the H. influenzae supragenome comprises an increasingly wide range of transferable resistance genes, with evidence of transfer from unrelated genera. The findings offer a glimpse into the genome dynamics of H. influenzae, highlighting the importance of rational antibiotic usage to contain antimicrobial resistance and the emergence of MDR strains in this important pathogen.
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Affiliation(s)
- Helene Johannessen
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
- *Correspondence: Helene Johannessen
| | | | - Nermin Zecic
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
| | - Kristin Hegstad
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | | | - Dagfinn Skaare
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
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26
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Annotation-free delineation of prokaryotic homology groups. PLoS Comput Biol 2022; 18:e1010216. [PMID: 35675326 PMCID: PMC9212150 DOI: 10.1371/journal.pcbi.1010216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/21/2022] [Accepted: 05/16/2022] [Indexed: 11/19/2022] Open
Abstract
Phylogenomic studies of prokaryotic taxa often assume conserved marker genes are homologous across their length. However, processes such as horizontal gene transfer or gene duplication and loss may disrupt this homology by recombining only parts of genes, causing gene fission or fusion. We show using simulation that it is necessary to delineate homology groups in a set of bacterial genomes without relying on gene annotations to define the boundaries of homologous regions. To solve this problem, we have developed a graph-based algorithm to partition a set of bacterial genomes into Maximal Homologous Groups of sequences (MHGs) where each MHG is a maximal set of maximum-length sequences which are homologous across the entire sequence alignment. We applied our algorithm to a dataset of 19 Enterobacteriaceae species and found that MHGs cover much greater proportions of genomes than markers and, relatedly, are less biased in terms of the functions of the genes they cover. We zoomed in on the correlation between each individual marker and their overlapping MHGs, and show that few phylogenetic splits supported by the markers are supported by the MHGs while many marker-supported splits are contradicted by the MHGs. A comparison of the species tree inferred from marker genes with the species tree inferred from MHGs suggests that the increased bias and lack of genome coverage by markers causes incorrect inferences as to the overall relationship between bacterial taxa. Assuming genes to be the basic evolutionary unit has been commonplace in bacterial genomics. For example, when quantifying the extent of horizontal gene transfer it is common to infer gene trees and reconcile them against a species tree to account for recombination-based processes. We have developed a new method which challenges this assumption by identifying contiguous regions of true homology without regards to gene boundaries and applied it to Enterobacteriaceae, a family of bacteria containing several important human pathogens. Our results show that genes are composed of distinct homologous regions with conflicting phylogenetic histories. We further demonstrate that failing to take account of this conflict, together with the functional biases we show exist among single-copy marker genes, significantly changes the consensus evolutionary tree of Enterobacteriaceae.
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27
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Nair S, Li X, Arya GA, McDew-White M, Ferrari M, Anderson T. Nutrient Limitation Magnifies Fitness Costs of Antimalarial Drug Resistance Mutations. Antimicrob Agents Chemother 2022; 66:e0152921. [PMID: 35465723 PMCID: PMC9112896 DOI: 10.1128/aac.01529-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Drug resistance mutations tend to disrupt key physiological processes and frequently carry fitness costs, which are a central determinant of the rate of spread of these mutations in natural populations. Head-to-head competition assays provide a standard approach to measuring fitness for malaria parasites. These assays typically use a standardized culture medium containing RPMI 1640, which has a 1.4- to 5.5-fold higher concentration of amino acids than human blood. In this rich medium, we predict that fitness costs will be underestimated because resource competition is weak. We tested this prediction using an artemisinin-sensitive parasite edited to contain kelch-C580Y or R561H mutations conferring resistance to artemisinin or synonymous control mutations. We examined the impact of these single amino acid mutations on fitness, using replicated head-to-head competition experiments conducted in media containing (i) normal RPMI, (ii) modified RPMI with reduced amino acid concentration, (iii) RPMI containing only isoleucine, or (iv) 3-fold diluted RPMI. We found a significant 1.3- to 1.4-fold increase in fitness costs measured in modified and isoleucine-only media relative to normal media, while fitness costs were 2.5-fold higher in diluted media. We conclude that fitness costs are strongly affected by media composition and will be significantly underestimated in normal RPMI. Several components differed between media, including pABA and sodium bicarbonate concentrations, so we cannot directly determine which is responsible. Elevated fitness costs in nature will limit spread of artemisinin (ART) resistance but will also promote evolution of compensatory mutations that restore fitness and can be exploited to maximize selection in laboratory experiments.
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Affiliation(s)
- Shalini Nair
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Xue Li
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Grace A. Arya
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Marina McDew-White
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Marco Ferrari
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Tim Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
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28
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Rochman ND, Faure G, Wolf YI, Freddolino PL, Zhang F, Koonin EV. Epistasis at the SARS-CoV-2 Receptor-Binding Domain Interface and the Propitiously Boring Implications for Vaccine Escape. mBio 2022; 13:e0013522. [PMID: 35289643 PMCID: PMC9040817 DOI: 10.1128/mbio.00135-22] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/08/2022] [Indexed: 12/13/2022] Open
Abstract
At the time of this writing, December 2021, potential emergence of vaccine escape variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a grave global concern. The interface between the receptor-binding domain (RBD) of SARS-CoV-2 spike (S) protein and the host receptor (ACE2) overlaps the binding site of principal neutralizing antibodies (NAb), limiting the repertoire of viable mutations. Nonetheless, variants with multiple RBD mutations have risen to dominance. Nonadditive, epistatic relationships among RBD mutations are apparent, and assessing the impact of such epistasis on the mutational landscape, particularly the risk of vaccine escape, is crucial. We employed protein structure modeling using Rosetta to compare the effects of all single mutants at the RBD-NAb and RBD-ACE2 interfaces for the wild type and Delta, Gamma, and Omicron variants. Overall, epistasis at the RBD interface appears to be limited, and the effects of most multiple mutations are additive. Epistasis at the Delta variant interface weakly stabilizes NAb interaction relative to ACE2 interaction, whereas in Gamma, epistasis more substantially destabilizes NAb interaction. Despite bearing many more RBD mutations, the epistatic landscape of Omicron closely resembles that of Gamma. Thus, although Omicron poses new risks not observed with Delta, structural constraints on the RBD appear to hamper continued evolution toward more complete vaccine escape. The modest ensemble of mutations relative to the wild type that are currently known to reduce vaccine efficacy is likely to contain the majority of all possible escape mutations for future variants, predicting the continued efficacy of the existing vaccines. IMPORTANCE Emergence of vaccine escape variants of SARS-CoV-2 is arguably the most pressing problem during the COVID-19 pandemic as vaccines are distributed worldwide. We employed a computational approach to assess the risk of antibody escape resulting from mutations in the receptor-binding domain of the spike protein of the wild-type SARS-CoV-2 virus as well as the Delta, Gamma, and Omicron variants. The efficacy of the existing vaccines against Omicron could be substantially reduced relative to the wild type, and the potential for vaccine escape is of grave concern. Our results suggest that although Omicron poses new evolutionary risks not observed for Delta, structural constraints on the RBD make continued evolution toward more complete vaccine escape from either Delta or Omicron unlikely. The modest set of escape-enhancing mutations already identified for the wild type likely include the majority of all possible mutations with this effect.
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Affiliation(s)
- Nash D. Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
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29
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Trubenová B, Roizman D, Moter A, Rolff J, Regoes RR. Population genetics, biofilm recalcitrance, and antibiotic resistance evolution. Trends Microbiol 2022; 30:841-852. [PMID: 35337697 DOI: 10.1016/j.tim.2022.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/11/2022]
Abstract
Biofilms are communities of bacteria forming high-density sessile colonies. Such a lifestyle comes associated with costs and benefits: while the growth rate of biofilms is often lower than that of their free-living counterparts, this cost is readily repaid once the colony is subjected to antibiotics. Biofilms can grow in antibiotic concentrations a thousand times higher than planktonic bacteria. While numerous mechanisms have been proposed to explain biofilm recalcitrance towards antibiotics, little is yet known about their effect on the evolution of resistance. We synthesize the current understanding of biofilm recalcitrance from a pharmacodynamic and a population genetics perspective. Using the pharmacodynamic framework, we discuss the effects of various mechanisms and show that biofilms can either promote or impede resistance evolution.
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Affiliation(s)
| | - Dan Roizman
- Institute of Biology, Evolutionary Biology, Freie Universität Berlin, Germany
| | - Annette Moter
- Charité, Universitätsmedizin Berlin Biofilmcenter, Berlin, Germany
| | - Jens Rolff
- Institute of Biology, Evolutionary Biology, Freie Universität Berlin, Germany
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30
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Hernando-Amado S, Laborda P, Valverde JR, Martínez JL. Rapid decline of ceftazidime resistance in antibiotic-free and sub-lethal environments is contingent on genetic background. Mol Biol Evol 2022; 39:6543660. [PMID: 35291010 PMCID: PMC8935207 DOI: 10.1093/molbev/msac049] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Trade-offs of antibiotic resistance evolution, such as fitness cost and collateral sensitivity (CS), could be exploited to drive evolution toward antibiotic susceptibility. Decline of resistance may occur when resistance to other drug leads to CS to the first one and when compensatory mutations, or genetic reversion of the original ones, reduce fitness cost. Here we describe the impact of antibiotic-free and sublethal environments on declining ceftazidime resistance in different Pseudomonas aeruginosa resistant mutants. We determined that decline of ceftazidime resistance occurs within 450 generations, which is caused by newly acquired mutations and not by reversion of the original ones, and that the original CS of these mutants is preserved. In addition, we observed that the frequency and degree of this decline is contingent on genetic background. Our results are relevant to implement evolution-based therapeutic approaches, as well as to redefine global policies of antibiotic use, such as drug cycling.
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Affiliation(s)
| | - Pablo Laborda
- Centro Nacional de Biotecnología. CSIC, Madrid, 28049, Spain
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31
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Bordin AI, Huber L, Sanz M, Cohen N. Rhodococcus equi Foal Pneumonia: Update on Epidemiology, Immunity, Treatment, and Prevention. Equine Vet J 2022; 54:481-494. [PMID: 35188690 DOI: 10.1111/evj.13567] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/03/2022] [Accepted: 02/17/2022] [Indexed: 11/25/2022]
Abstract
Pneumonia in foals caused by the bacterium Rhodococcus equi has a worldwide distribution and is a common cause of disease and death for foals. The purpose of this narrative review is to summarise recent developments pertaining to the epidemiology, immune responses, treatment, and prevention of rhodococcal pneumonia of foals. Screening tests have been used to implement earlier detection and treatment of foals with presumed subclinical R. equi pneumonia to reduce mortality and severity of disease. Unfortunately, this practice has been linked to the emergence of antimicrobial resistant R. equi in North America. Correlates of protective immunity for R. equi infections of foals remain elusive, but recent evidence indicates that innate immune responses are important both for mediating killing and orchestrating adaptive immune responses. A macrolide antimicrobial in combination with rifampin remains the recommended treatment for foals with R. equi pneumonia. Great need exists to identify which antimicrobial combination is most effective for treating foals with R. equi pneumonia and to limit emergence of antimicrobial-resistant strains. In the absence of an effective vaccine against R. equi, passive immunisation remains the only commercially-available method for effectively reducing the incidence of R. equi pneumonia. Because passive immunisation is expensive, labour-intensive, and carries risks for foals, great need exists to develop alternative approaches for passive and active immunisation.
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Affiliation(s)
- Angela I Bordin
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843-4475, USA
| | - Laura Huber
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, 36849, USA
| | - Macarena Sanz
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, 99164-6610, USA
| | - Noah Cohen
- Equine Infectious Disease Laboratory, Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843-4475, USA
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32
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Physiological Responses of Ribosomal Protein S12 K43 Mutants of Corynebacterium glutamicum. Curr Microbiol 2022; 79:94. [PMID: 35142919 DOI: 10.1007/s00284-022-02795-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/31/2022] [Indexed: 11/03/2022]
Abstract
Bacterial resistance to streptomycin is often acquired as a consequence of mutations in rpsL, the gene encoding ribosomal protein S12. Corynebacterium glutamicum is a non-pathogenic Gram-positive soil bacterium that has been widely used in industry. In a previous study, we screened several streptomycin-resistant rpsL K43 mutants of C. glutamicum, and surprisingly found that two of them also confer chloramphenicol and/or kanamycin resistance. In order to understand whether or not a single mutation of rpsLK43 could confer resistance to multiple antibiotics, in this study we attempted to construct saturation mutagenesis of rpsL K43 by rational genetic manipulation. Despite many efforts had been made, only nine mutants were successfully constructed. They were indeed resistant to streptomycin, but not to other antibiotics. This suggested that other mutations should be acquired, contributing to multiple antibiotics in the screened strains. The growth and enhanced green fluorescent protein (eGFP) expression of these nine mutants were then investigated. The results showed that they grew differently in CGXII minimal medium, but not in BHI medium. When cultured in the absence of streptomycin, the expression of eGFP was positively proportional to the growth, approximately, while in the presence of streptomycin, the expression of eGFP was proportional to the ability of streptomycin resistance.
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33
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Bhattacharjee A, Sarma S, Sen T, Singh AK. Alterations in molecular response of Mycobacterium tuberculosis against anti-tuberculosis drugs. Mol Biol Rep 2022; 49:3987-4002. [PMID: 35066765 DOI: 10.1007/s11033-021-07095-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/16/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis, has plagued humans since the early middle-ages. More than one million deaths are recorded annually due to TB, even in present times. These deaths are primarily attributed to the constant appearance of resistant TB strains. Even with the advent of new therapeutics and diagnostics techniques, tuberculosis remains challenging to control due to resistant M. tuberculosis strains. Aided by various molecular changes, these strains adapt to stress created by anti-tuberculosis drugs. MATERIALS AND METHODS The review thus is an overview of ongoing research in the genome and transcriptome of antibiotic-resistant TB. It explores omics-based research to identify mutation and utilization of differential gene expression. CONCLUSIONS This study shows several mutations distinctive in the first- and second-line drug-resistant M. tuberculosis strains. It also explores the expressional differences of genes involved in the fundamental process of the cells and how they help in drug resistance. With the development of transcriptomics-based studies, a new insight has developed to inquire about gene expression changes in drug resistance. This information on expressional pattern changes can be utilized to design the basic platform of anti-TB treatments and therapeutic approaches. These novel insights can be instrumental in disease diagnosis and global containment of resistant TB.
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Affiliation(s)
- Abhilash Bhattacharjee
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sangita Sarma
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Tejosmita Sen
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anil Kumar Singh
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Guillén S, Marcén M, Fau E, Mañas P, Cebrián G. Relationship between growth ability, virulence, and resistance to food-processing related stresses in non-typhoidal Salmonellae. Int J Food Microbiol 2022; 361:109462. [PMID: 34749188 DOI: 10.1016/j.ijfoodmicro.2021.109462] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/01/2021] [Accepted: 10/25/2021] [Indexed: 11/29/2022]
Abstract
The ability of Salmonella to resist and adapt to harsh conditions is one of the major features that have made this microorganism such a relevant health hazard. However, the impact of these resistance responses on other aspects of Salmonella physiology, such as virulence and growth ability, is still not fully understood. The objective of this study was to determine the maximum growth rates (in three different media), virulence (adhesion and invasion of Caco-2 cells), and other phenotypic characteristics (biofilm-forming ability and antimicrobial resistance) of 23 Salmonella strains belonging to different serovars, and to compare them with their previously determined stress resistance parameters. Significant differences (p < 0.05) in growth rates, virulence, and biofilm-forming ability were found among the 23 strains studied. Nevertheless, whereas less than 3-fold change between the lowest and the highest growth rate was observed, the percentage of cells capable of invading Caco-2 cells varied more than 100-fold, that to form biofilms more than 30-fold, and the antibiotic MICs varied up to 512-fold, among the different strains. Results indicate that those strains with the highest cell adhesion ability were not always the most invasive ones and suggest that, in general terms, a higher stress resistance did not imply a reduced growth ability (rate). Similarly, no association between stress resistance and biofilm formation ability (except for acid stress) or antibiotic resistance (with minor exceptions) was found. Our data also suggest that, in Salmonella, acid stress resistance would be associated with virulence, since a positive correlation of that trait with adhesion and a negative correlation with invasion was found. This study contributes to a better understanding of the physiology of Salmonella and the relationship between bacterial stress resistance, growth ability, and virulence. It also provides new data regarding intra-specific variability of a series of phenotypic characteristics of Salmonella that are relevant from the food safety perspective.
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Affiliation(s)
- Silvia Guillén
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - María Marcén
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Ester Fau
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Pilar Mañas
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Guillermo Cebrián
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain.
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Rochman ND, Faure G, Wolf YI, Freddolino PL, Zhang F, Koonin EV. Epistasis at the SARS-CoV-2 RBD Interface and the Propitiously Boring Implications for Vaccine Escape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.30.458225. [PMID: 34494024 PMCID: PMC8423221 DOI: 10.1101/2021.08.30.458225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
At the time of this writing, December 2021, potential emergence of vaccine escape variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a grave global concern. The interface between the receptor-binding domain (RBD) of SARS-CoV-2 spike (S) protein and the host receptor (ACE2) overlap with the binding site of principal neutralizing antibodies (NAb), limiting the repertoire of viable mutations. Nonetheless, variants with multiple mutations in the RBD have rose to dominance. Non-additive, epistatic relationships among RBD mutations are apparent, and assessing the impact of such epistasis on the mutational landscape is crucial. Epistasis can substantially increase the risk of vaccine escape and cannot be completely characterized through the study of the wild type (WT) alone. We employed protein structure modeling using Rosetta to compare the effects of all single mutants at the RBD-NAb and RBD-ACE2 interfaces for the WT, Delta, Gamma, and Omicron variants. Overall, epistasis at the RBD interface appears to be limited and the effects of most multiple mutations are additive. Epistasis at the Delta variant interface weakly stabilizes NAb interaction relative to ACE2 interaction, whereas in the Gamma variant, epistasis more substantially destabilizes NAb interaction. Although a small, systematic trend towards NAb destabilization not observed for Delta or Gamma was detected for Omicron, and despite bearing significantly more RBD mutations, the epistatic landscape of the Omicron variant closely resembles that of Gamma. These results suggest that, although Omicron poses new risks not observed with Delta, structural constraints on the RBD hamper continued evolution towards more complete vaccine escape. The modest ensemble of mutations relative to the WT that are currently known to reduce vaccine efficacy is likely to comprise the majority of all possible escape mutations for future variants, predicting continued efficacy of the existing vaccines.
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Affiliation(s)
- Nash D. Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Andersson DI, Bampidis V, Bengtsson‐Palme J, Bouchard D, Ferran A, Kouba M, López Puente S, López‐Alonso M, Nielsen SS, Pechová A, Petkova M, Girault S, Broglia A, Guerra B, Innocenti ML, Liébana E, López‐Gálvez G, Manini P, Stella P, Peixe L. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 1: Methodology, general data gaps and uncertainties. EFSA J 2021; 19:e06852. [PMID: 34729081 PMCID: PMC8547316 DOI: 10.2903/j.efsa.2021.6852] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The European Commission requested EFSA to assess, in collaboration with EMA, the specific concentrations of antimicrobials resulting from cross-contamination in non-target feed for food-producing animals below which there would not be an effect on the emergence of, and/or selection for, resistance in microbial agents relevant for human and animal health, as well as the levels of the antimicrobials which could have a growth promotion/increase yield effect. The assessment was performed for 24 antimicrobial active substances, as specified in the mandate. This scientific opinion describes the methodology used, and the main associated data gaps and uncertainties. To estimate the antimicrobial levels in the non-target feed that would not result in emergence of, and/or selection for, resistance, a model was developed. This 'Feed Antimicrobial Resistance Selection Concentration' (FARSC) model is based on the minimal selective concentration (MSC), or the predicted MSC (PMSC) if MSC for the most susceptible bacterial species is unavailable, the fraction of antimicrobial dose available for exposure to microorganisms in the large intestine or rumen (considering pharmacokinetic parameters), the daily faecal output or rumen volume and the daily feed intake. Currently, lack of data prevents the establishment of PMSC and/or FARSC for several antimicrobials and animal species. To address growth promotion, data from an extensive literature search were used. Specific assessments of the different substances grouped by antimicrobial classes are addressed in separate scientific opinions. General conclusions and recommendations were made.
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37
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Bock LJ, Ferguson PM, Clarke M, Pumpitakkul V, Wand ME, Fady PE, Allison L, Fleck RA, Shepherd MJ, Mason AJ, Sutton JM. Pseudomonas aeruginosa adapts to octenidine via a combination of efflux and membrane remodelling. Commun Biol 2021; 4:1058. [PMID: 34504285 PMCID: PMC8429429 DOI: 10.1038/s42003-021-02566-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/03/2021] [Indexed: 01/24/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen capable of stably adapting to the antiseptic octenidine by an unknown mechanism. Here we characterise this adaptation, both in the laboratory and a simulated clinical setting, and identify a novel antiseptic resistance mechanism. In both settings, 2 to 4-fold increase in octenidine tolerance was associated with stable mutations and a specific 12 base pair deletion in a putative Tet-repressor family gene (smvR), associated with a constitutive increase in expression of the Major Facilitator Superfamily (MFS) efflux pump SmvA. Adaptation to higher octenidine concentrations led to additional stable mutations, most frequently in phosphatidylserine synthase pssA and occasionally in phosphatidylglycerophosphate synthase pgsA genes, resulting in octenidine tolerance 16- to 256-fold higher than parental strains. Metabolic changes were consistent with mitigation of oxidative stress and altered plasma membrane composition and order. Mutations in SmvAR and phospholipid synthases enable higher level, synergistic tolerance of octenidine.
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Affiliation(s)
- Lucy J Bock
- Technology Development Group, National Infection Service, PHE Porton, Salisbury, UK.
| | - Philip M Ferguson
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, London, UK
| | - Maria Clarke
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, London, UK
| | - Vichayanee Pumpitakkul
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, London, UK
| | - Matthew E Wand
- Technology Development Group, National Infection Service, PHE Porton, Salisbury, UK
| | - Paul-Enguerrand Fady
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, London, UK
| | - Leanne Allison
- Centre for Ultrastructural Imaging, Guy's Campus, King's College London, London, UK
| | - Roland A Fleck
- Centre for Ultrastructural Imaging, Guy's Campus, King's College London, London, UK
| | - Matthew J Shepherd
- Technology Development Group, National Infection Service, PHE Porton, Salisbury, UK
| | - A James Mason
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, London, UK
| | - J Mark Sutton
- Technology Development Group, National Infection Service, PHE Porton, Salisbury, UK.
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38
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Phillips KN, Cooper TF. The cost of evolved constitutive lac gene expression is usually, but not always, maintained during evolution of generalist populations. Ecol Evol 2021; 11:12497-12507. [PMID: 34594515 PMCID: PMC8462147 DOI: 10.1002/ece3.7994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 01/13/2023] Open
Abstract
Beneficial mutations can become costly following an environmental change. Compensatory mutations can relieve these costs, while not affecting the selected function, so that the benefits are retained if the environment shifts back to be similar to the one in which the beneficial mutation was originally selected. Compensatory mutations have been extensively studied in the context of antibiotic resistance, responses to specific genetic perturbations, and in the determination of interacting gene network components. Few studies have focused on the role of compensatory mutations during more general adaptation, especially as the result of selection in fluctuating environments where adaptations to different environment components may often involve trade-offs. We examine whether costs of a mutation in lacI, which deregulated the expression of the lac operon in evolving populations of Escherichia coli bacteria, were compensated. This mutation occurred in multiple replicate populations selected in environments that fluctuated between growth on lactose, where the mutation was beneficial, and on glucose, where it was deleterious. We found that compensation for the cost of the lacI mutation was rare, but, when it did occur, it did not negatively affect the selected benefit. Compensation was not more likely to occur in a particular evolution environment. Compensation has the potential to remove pleiotropic costs of adaptation, but its rarity indicates that the circumstances to bring about the phenomenon may be peculiar to each individual or impeded by other selected mutations.
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Affiliation(s)
- Kelly N. Phillips
- Department of Biology and BiochemistryUniversity of HoustonHoustonTexasUSA
| | - Tim F. Cooper
- Department of Biology and BiochemistryUniversity of HoustonHoustonTexasUSA
- School of Natural and Computational SciencesMassey UniversityAucklandNew Zealand
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39
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Andrianaivoarimanana V, Wagner DM, Birdsell DN, Nikolay B, Rakotoarimanana F, Randriantseheno LN, Vogler AJ, Sahl JW, Hall CM, Somprasong N, Cauchemez S, Schweizer HP, Razafimandimby H, Rogier C, Rajerison M. Transmission of antimicrobial resistant Yersinia pestis during a pneumonic plague outbreak. Clin Infect Dis 2021; 74:695-702. [PMID: 34244722 PMCID: PMC8886911 DOI: 10.1093/cid/ciab606] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Pneumonic plague (PP), caused by Yersinia pestis, is the most feared clinical form of plague due to its rapid lethality and potential to cause outbreaks. PP outbreaks are now rare due to antimicrobial therapy. METHODS A PP outbreak in Madagascar involving transmission of a Y. pestis strain resistant to streptomycin, the current recommended first-line treatment in Madagascar, was retrospectively characterized using epidemiology, clinical diagnostics, molecular characterization, and animal studies. RESULTS The outbreak occurred in February 2013 in the Faratsiho district of Madagascar and involved 22 cases, including three untreated fatalities. The 19 other cases participated in funeral practices for the fatal cases and fully recovered after combination antimicrobial therapy: intramuscular streptomycin followed by oral co-trimoxazole. The Y. pestis strain that circulated during this outbreak is resistant to streptomycin resulting from a spontaneous point mutation in the 30S ribosomal protein S12 (rpsL) gene. This same mutation causes streptomycin resistance in two unrelated Y. pestis strains, one isolated from a fatal PP case in a different region of Madagascar in 1987 and another isolated from a fatal PP case in China in 1996, documenting this mutation has occurred independently at least three times in Y. pestis. Laboratory experiments revealed this mutation has no detectable impact on fitness or virulence, and revertants to wild-type are rare in other species containing it, suggesting Y. pestis strains containing it could persist in the environment. CONCLUSION Unique AMR strains of Y. pestis continue to arise in Madagascar and can be transmitted during PP outbreaks.
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Affiliation(s)
| | | | | | | | | | | | - Amy J Vogler
- Northern Arizona University, Flagstaff, Arizona, USA
| | - Jason W Sahl
- Northern Arizona University, Flagstaff, Arizona, USA
| | - Carina M Hall
- Northern Arizona University, Flagstaff, Arizona, USA
| | - Nawarat Somprasong
- Northern Arizona University, Flagstaff, Arizona, USA.,University of Florida, Gainesville, Florida, USA
| | | | - Herbert P Schweizer
- Northern Arizona University, Flagstaff, Arizona, USA.,University of Florida, Gainesville, Florida, USA
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40
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Pedruzzi G, Rouzine IM. An evolution-based high-fidelity method of epistasis measurement: Theory and application to influenza. PLoS Pathog 2021; 17:e1009669. [PMID: 34153082 PMCID: PMC8248644 DOI: 10.1371/journal.ppat.1009669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 07/01/2021] [Accepted: 05/25/2021] [Indexed: 12/18/2022] Open
Abstract
Linkage effects in a multi-locus population strongly influence its evolution. The models based on the traveling wave approach enable us to predict the average speed of evolution and the statistics of phylogeny. However, predicting statistically the evolution of specific sites and pairs of sites in the multi-locus context remains a mathematical challenge. In particular, the effects of epistasis, the interaction of gene regions contributing to phenotype, is difficult to predict theoretically and detect experimentally in sequence data. A large number of false-positive interactions arises from stochastic linkage effects and indirect interactions, which mask true epistatic interactions. Here we develop a proof-of-principle method to filter out false-positive interactions. We start by demonstrating that the averaging of haplotype frequencies over multiple independent populations is necessary but not sufficient for epistatic detection, because it still leaves high numbers of false-positive interactions. To compensate for the residual stochastic noise, we develop a three-way haplotype method isolating true interactions. The fidelity of the method is confirmed analytically and on simulated genetic sequences evolved with a known epistatic network. The method is then applied to a large sequence database of neurominidase protein of influenza A H1N1 obtained from various geographic locations to infer the epistatic network responsible for the difference between the pre-pandemic virus and the pandemic strain of 2009. These results present a simple and reliable technique to measure epistatic interactions of any sign from sequence data. Interactions between genomic sites create a fitness landscape. The knowledge of topology and strength of interactions is vital for predicting the escape of viruses from drugs and immune response and their passing through fitness valleys. Many efforts have been invested into measuring these interactions from DNA sequence sets. Unfortunately, reproducibility of the results remains low due partly to a very small fraction of interaction pairs and partly to stochastic linkage noise masking true interactions. Here we propose a method to separate stochastic linkage and indirect interactions from epistatic interactions and apply it to influenza virus sequence data.
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Affiliation(s)
- Gabriele Pedruzzi
- Sorbonne Université, Institute de Biologie Paris-Seine, Laboratoire de Biologie Computationelle et Quantitative LCQB, Paris, France
| | - Igor M. Rouzine
- Sorbonne Université, Institute de Biologie Paris-Seine, Laboratoire de Biologie Computationelle et Quantitative LCQB, Paris, France
- * E-mail:
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41
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Wheatley R, Diaz Caballero J, Kapel N, de Winter FHR, Jangir P, Quinn A, Del Barrio-Tofiño E, López-Causapé C, Hedge J, Torrens G, Van der Schalk T, Xavier BB, Fernández-Cuenca F, Arenzana A, Recanatini C, Timbermont L, Sifakis F, Ruzin A, Ali O, Lammens C, Goossens H, Kluytmans J, Kumar-Singh S, Oliver A, Malhotra-Kumar S, MacLean C. Rapid evolution and host immunity drive the rise and fall of carbapenem resistance during an acute Pseudomonas aeruginosa infection. Nat Commun 2021; 12:2460. [PMID: 33911082 PMCID: PMC8080559 DOI: 10.1038/s41467-021-22814-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/31/2021] [Indexed: 02/08/2023] Open
Abstract
It is well established that antibiotic treatment selects for resistance, but the dynamics of this process during infections are poorly understood. Here we map the responses of Pseudomonas aeruginosa to treatment in high definition during a lung infection of a single ICU patient. Host immunity and antibiotic therapy with meropenem suppressed P. aeruginosa, but a second wave of infection emerged due to the growth of oprD and wbpM meropenem resistant mutants that evolved in situ. Selection then led to a loss of resistance by decreasing the prevalence of low fitness oprD mutants, increasing the frequency of high fitness mutants lacking the MexAB-OprM efflux pump, and decreasing the copy number of a multidrug resistance plasmid. Ultimately, host immunity suppressed wbpM mutants with high meropenem resistance and fitness. Our study highlights how natural selection and host immunity interact to drive both the rapid rise, and fall, of resistance during infection.
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Affiliation(s)
| | | | - Natalia Kapel
- University of Oxford, Department of Zoology, Oxford, UK
| | - Fien H R de Winter
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Pramod Jangir
- University of Oxford, Department of Zoology, Oxford, UK
| | - Angus Quinn
- University of Oxford, Department of Zoology, Oxford, UK
| | | | | | - Jessica Hedge
- University of Oxford, Department of Zoology, Oxford, UK
| | - Gabriel Torrens
- Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Thomas Van der Schalk
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | | | - Angel Arenzana
- Departamento de Medicina, Universidad de Sevilla, Seville, Spain
| | - Claudia Recanatini
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Leen Timbermont
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | | | - Alexey Ruzin
- Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Omar Ali
- Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
- Viela Bio, Gaithersburg, MD, USA
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Jan Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Microvida Laboratory for Medical Microbiology and Department of Infection Control, Amphia Hospital, Breda, The Netherlands
| | - Samir Kumar-Singh
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
- Molecular Pathology Group, Faculty of Medicine-Laboratory of Cell Biology and Histology, University of Antwerp, Wilrijk, Belgium
| | - Antonio Oliver
- Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Craig MacLean
- University of Oxford, Department of Zoology, Oxford, UK.
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Huber L, Giguère S, Hart KA, Slovis NM, Greiter ME, Dailey CA, Cohen ND. Association between antimicrobial treatment of subclinical pneumonia in foals and selection of macrolide- and rifampicin-resistant Rhodococcus equi strains at horse-breeding farms in central Kentucky. J Am Vet Med Assoc 2021; 258:648-653. [PMID: 33683955 DOI: 10.2460/javma.258.6.648] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To compare soil concentrations of macrolide- and rifampicin-resistant Rhodococcus equi strains (MRRE) on horse-breeding farms that used thoracic ultrasonographic screening (TUS) to identify foals with subclinical pneumonia combined with subsequent administration of macrolides and rifampin to affected foals (TUS farms) versus soil concentrations on farms that did not (non-TUS farms), determine whether the combined use of TUS and antimicrobial treatment of subclinically affected foals was associated with soil concentration of MRRE, and assess whether there were temporal effects on soil concentrations of MRRE during the foaling season. SAMPLES 720 soil samples and 20 completed questionnaires from 20 horse-breeding farms (10 TUS farms and 10 non-TUS farms) in central Kentucky. PROCEDURES A questionnaire was used to gather information from participating farms about their 2019 foaling season. Soil samples were collected during January, March, May, and July 2019 for bacterial culture and antimicrobial susceptibility testing to identify any isolates of MRRE. Results were compared for TUS farms versus non-TUS farms. Linear mixed-effects modeling was used to evaluate for potential associations between the soil concentration of MRRE and the use of TUS. RESULTS Overall, the sum of the mean soil concentrations of MRRE was significantly higher for TUS farms (8.85 log10-transformed CFUs/g) versus non-TUS farms (7.37 log10-transformed CFUs/g). CONCLUSIONS AND CLINICAL RELEVANCE Our findings indicated that farms that use TUS to identify foals with subclinical pneumonia for antimicrobial treatment select for antimicrobial-resistant R equi strains. Because prognosis is worse for foals infected with resistant versus nonresistant strains of R equi, prudent use of antimicrobials to treat foals with subclinical pulmonary lesions attributed to R equi is recommended.
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Epidemiology and Molecular Basis of Multidrug Resistance in Rhodococcus equi. Microbiol Mol Biol Rev 2021; 85:85/2/e00011-21. [PMID: 33853933 DOI: 10.1128/mmbr.00011-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The development and spread of antimicrobial resistance are major concerns for human and animal health. The effects of the overuse of antimicrobials in domestic animals on the dissemination of resistant microbes to humans and the environment are of concern worldwide. Rhodococcus equi is an ideal model to illustrate the spread of antimicrobial resistance at the animal-human-environment interface because it is a natural soil saprophyte that is an intracellular zoonotic pathogen that produces severe bronchopneumonia in many animal species and humans. Globally, R. equi is most often recognized as causing severe pneumonia in foals that results in animal suffering and increased production costs for the many horse-breeding farms where the disease occurs. Because highly effective preventive measures for R. equi are lacking, thoracic ultrasonographic screening and antimicrobial chemotherapy of subclinically affected foals have been used for controlling this disease during the last 20 years. The resultant increase in antimicrobial use attributable to this "screen-and-treat" approach at farms where the disease is endemic has likely driven the emergence of multidrug-resistant (MDR) R. equi in foals and their environment. This review summarizes the factors that contributed to the development and spread of MDR R. equi, the molecular epidemiology of the emergence of MDR R. equi, the repercussions of MDR R. equi for veterinary and human medicine, and measures that might mitigate antimicrobial resistance at horse-breeding farms, such as alternative treatments to traditional antibiotics. Knowledge of the emergence and spread of MDR R. equi is of broad importance for understanding how antimicrobial use in domestic animals can impact the health of animals, their environment, and human beings.
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Kloos J, Gama JA, Hegstad J, Samuelsen Ø, Johnsen PJ. Piggybacking on Niche Adaptation Improves the Maintenance of Multidrug-Resistance Plasmids. Mol Biol Evol 2021; 38:3188-3201. [PMID: 33760032 PMCID: PMC8321521 DOI: 10.1093/molbev/msab091] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/12/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022] Open
Abstract
The persistence of plasmids in bacterial populations represents a puzzling evolutionary problem with serious clinical implications due to their role in the ongoing antibiotic resistance crisis. Recently, major advancements have been made toward resolving this “plasmid paradox” but mainly in a nonclinical context. Here, we propose an additional explanation for the maintenance of multidrug‐resistance plasmids in clinical Escherichia coli strains. After coevolving two multidrug‐resistance plasmids encoding resistance to last resort carbapenems with an extraintestinal pathogenic E. coli strain, we observed that chromosomal media adaptive mutations in the global regulatory systems CCR (carbon catabolite repression) and ArcAB (aerobic respiration control) pleiotropically improved the maintenance of both plasmids. Mechanistically, a net downregulation of plasmid gene expression reduced the fitness cost. Our results suggest that global chromosomal transcriptional rewiring during bacterial niche adaptation may facilitate plasmid maintenance.
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Affiliation(s)
- Julia Kloos
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - João A Gama
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Joachim Hegstad
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway.,Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway.,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
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Nkhoma SC, Ahmed AOA, Zaman S, Porier D, Baker Z, Stedman TT. Dissection of haplotype-specific drug response phenotypes in multiclonal malaria isolates. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2021; 15:152-161. [PMID: 33780700 PMCID: PMC8039770 DOI: 10.1016/j.ijpddr.2021.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 10/28/2022]
Abstract
Natural infections of Plasmodium falciparum, the parasite responsible for the deadliest form of human malaria, often comprise multiple parasite lineages (haplotypes). Multiclonal parasite isolates may exhibit variable phenotypes including different drug susceptibility profiles over time due to the presence of multiple haplotypes. To test this hypothesis, three P. falciparum Cambodian isolates IPC_3445 (MRA-1236), IPC_5202 (MRA-1240) and IPC_6403 (MRA-1285) suspected to be multiclonal were cloned by limiting dilution, and the resulting clones genotyped at 24 highly polymorphic single nucleotide polymorphisms (SNPs). Isolates harbored up to three constituent haplotypes, and exhibited significant variability (p < 0.05) in susceptibility to chloroquine, mefloquine, artemisinin and piperaquine as measured by half maximal drug inhibitory concentration (IC50) assays and parasite survival assays, which measure viability following exposure to pharmacologically relevant concentrations of antimalarial drugs. The IC50 of the most abundant haplotype frequently reflected that of the uncloned parental isolate, suggesting that a single haplotype dominates the antimalarial susceptibility profile and masks the effect of minor frequency haplotypes. These results indicate that phenotypic variability in parasite isolates is often due to the presence of multiple haplotypes. Depending on intended end-use, clinical isolates should be cloned to yield single parasite lineages with well-defined phenotypes and genotypes. The availability of such standardized clonal parasite lineages through NIAID's BEI Resources program will aid research directed towards the development of diagnostics and interventions including drugs against malaria.
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Affiliation(s)
- Standwell C Nkhoma
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA.
| | - Amel O A Ahmed
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA
| | - Sharmeen Zaman
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA
| | - Danielle Porier
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA
| | - Zachary Baker
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA
| | - Timothy T Stedman
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA.
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Mahrt N, Tietze A, Künzel S, Franzenburg S, Barbosa C, Jansen G, Schulenburg H. Bottleneck size and selection level reproducibly impact evolution of antibiotic resistance. Nat Ecol Evol 2021; 5:1233-1242. [PMID: 34312522 PMCID: PMC8390372 DOI: 10.1038/s41559-021-01511-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
During antibiotic treatment, the evolution of bacterial pathogens is fundamentally affected by bottlenecks and varying selection levels imposed by the drugs. Bottlenecks-that is, reductions in bacterial population size-lead to an increased influence of random effects (genetic drift) during bacterial evolution, and varying antibiotic concentrations during treatment may favour distinct resistance variants. Both aspects influence the process of bacterial evolution during antibiotic therapy and thereby treatment outcome. Surprisingly, the joint influence of these interconnected factors on the evolution of antibiotic resistance remains largely unexplored. Here we combine evolution experiments with genomic and genetic analyses to demonstrate that bottleneck size and antibiotic-induced selection reproducibly impact the evolutionary path to resistance in pathogenic Pseudomonas aeruginosa, one of the most problematic opportunistic human pathogens. Resistance is favoured-expectedly-under high antibiotic selection and weak bottlenecks, but-unexpectedly-also under low antibiotic selection and severe bottlenecks. The latter is likely to result from a reduced probability of losing favourable variants through drift under weak selection. Moreover, the absence of high resistance under low selection and weak bottlenecks is caused by the spread of low-resistance variants with high competitive fitness under these conditions. We conclude that bottlenecks, in combination with drug-induced selection, are currently neglected key determinants of pathogen evolution and outcome of antibiotic treatment.
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Affiliation(s)
- Niels Mahrt
- grid.9764.c0000 0001 2153 9986Evolutionary Ecology and Genetics, Department of Zoology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Alexandra Tietze
- grid.9764.c0000 0001 2153 9986Evolutionary Ecology and Genetics, Department of Zoology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Sven Künzel
- grid.419520.b0000 0001 2222 4708Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - Sören Franzenburg
- grid.9764.c0000 0001 2153 9986Genetics and Bioinformatics, Department of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Camilo Barbosa
- grid.9764.c0000 0001 2153 9986Evolutionary Ecology and Genetics, Department of Zoology, Christian-Albrechts-University of Kiel, Kiel, Germany ,grid.214458.e0000000086837370Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI USA
| | - Gunther Jansen
- grid.9764.c0000 0001 2153 9986Evolutionary Ecology and Genetics, Department of Zoology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- grid.9764.c0000 0001 2153 9986Evolutionary Ecology and Genetics, Department of Zoology, Christian-Albrechts-University of Kiel, Kiel, Germany ,grid.419520.b0000 0001 2222 4708Antibiotic Resistance Group, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
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Mas A, Lagadeuc Y, Vandenkoornhuyse P. Reflections on the Predictability of Evolution: Toward a Conceptual Framework. iScience 2020; 23:101736. [PMID: 33225244 PMCID: PMC7666346 DOI: 10.1016/j.isci.2020.101736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evolution is generally considered to be unpredictable because genetic variations are known to occur randomly. However, remarkable patterns of repeated convergent evolution are observed, for instance, loss of pigments by organisms living in caves. Analogous phenotypes appear in similar environments, sometimes in response to similar constraints. Alongside randomness, a certain evolutionary determinism also exists, for instance, the selection of particular phenotypes subjected to particular environmental constraints in the “evolutionary funnel.” We pursue the idea that eco-evolutionary specialization is in some way determinist. The conceptual framework of phenotypic changes entailing specialization presented in this essay explains how evolution can be predicted. We also discuss how the predictability of evolution could be tested using the case of metabolic specialization through gene losses. We also put forward that microorganisms could be key models to test and possibly make headway evolutionary predictions and knowledge about evolution.
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Affiliation(s)
- Alix Mas
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
| | - Yvan Lagadeuc
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
| | - Philippe Vandenkoornhuyse
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, Avenue Leclerc, Rennes Cedex 35042, France
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Abstract
Many nonsporulating bacterial species can survive for years within exhausted growth media in a state termed long-term stationary phase (LTSP). We have been carrying out evolutionary experiments aimed at elucidating the dynamics of genetic adaptation under LTSP. We showed that Escherichia coli adapts to prolonged resource exhaustion through the highly convergent acquisition of mutations. In the most striking example of such convergent adaptation, we observed that across all independently evolving LTSP populations, over 90% of E. coli cells carry mutations to one of three specific sites of the RNA polymerase core enzyme (RNAPC). These LTSP adaptations reduce the ability of the cells carrying them to grow once fresh resources are again provided. Here, we examine how LTSP populations recover from costs associated with their adaptation once resources are again provided to them. We demonstrate that due to the ability of LTSP populations to maintain high levels of standing genetic variation during adaptation, costly adaptations are very rapidly purged from the population once they are provided with fresh resources. We further demonstrate that recovery from costs acquired during adaptation under LTSP occurs more rapidly than would be possible if LTSP adaptations had fixed during the time populations spent under resource exhaustion. Finally, we previously reported that under LTSP, some clones develop a mutator phenotype, greatly increasing their mutation accumulation rates. Here, we show that the mechanisms by which populations recover from costs associated with fixed adaptations may depend on mutator status.IMPORTANCE Many bacterial species can survive for decades under starvation, following the exhaustion of external growth resources. We have previously shown that bacteria genetically adapt under these conditions in a manner that reduces their ability to grow once resources again become available. Here, we study how populations that have been subject to very prolonged resource exhaustion recover from costs associated with their adaptation. We demonstrate that rapid adaptations acquired under prolonged starvation tend to be highly transient, rapidly reducing in frequency once bacteria are no longer starved. Our results shed light on the longer-term consequences of bacterial survival under prolonged starvation. More generally, these results may also be applicable to understanding longer-term consequences of rapid adaptation to additional conditions as well.
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Das SG, Direito SOL, Waclaw B, Allen RJ, Krug J. Predictable properties of fitness landscapes induced by adaptational tradeoffs. eLife 2020; 9:e55155. [PMID: 32423531 PMCID: PMC7297540 DOI: 10.7554/elife.55155] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023] Open
Abstract
Fitness effects of mutations depend on environmental parameters. For example, mutations that increase fitness of bacteria at high antibiotic concentration often decrease fitness in the absence of antibiotic, exemplifying a tradeoff between adaptation to environmental extremes. We develop a mathematical model for fitness landscapes generated by such tradeoffs, based on experiments that determine the antibiotic dose-response curves of Escherichia coli strains, and previous observations on antibiotic resistance mutations. Our model generates a succession of landscapes with predictable properties as antibiotic concentration is varied. The landscape is nearly smooth at low and high concentrations, but the tradeoff induces a high ruggedness at intermediate antibiotic concentrations. Despite this high ruggedness, however, all the fitness maxima in the landscapes are evolutionarily accessible from the wild type. This implies that selection for antibiotic resistance in multiple mutational steps is relatively facile despite the complexity of the underlying landscape.
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Affiliation(s)
- Suman G Das
- Institute for Biological Physics, University of CologneCologneGermany
| | - Susana OL Direito
- School of Physics and Astronomy, University of EdinburghEdinburghUnited Kingdom
| | - Bartlomiej Waclaw
- School of Physics and Astronomy, University of EdinburghEdinburghUnited Kingdom
| | - Rosalind J Allen
- School of Physics and Astronomy, University of EdinburghEdinburghUnited Kingdom
| | - Joachim Krug
- Institute for Biological Physics, University of CologneCologneGermany
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Marrec L, Bitbol AF. Resist or perish: Fate of a microbial population subjected to a periodic presence of antimicrobial. PLoS Comput Biol 2020; 16:e1007798. [PMID: 32275712 PMCID: PMC7176291 DOI: 10.1371/journal.pcbi.1007798] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/22/2020] [Accepted: 03/19/2020] [Indexed: 12/22/2022] Open
Abstract
The evolution of antimicrobial resistance can be strongly affected by variations of antimicrobial concentration. Here, we study the impact of periodic alternations of absence and presence of antimicrobial on resistance evolution in a microbial population, using a stochastic model that includes variations of both population composition and size, and fully incorporates stochastic population extinctions. We show that fast alternations of presence and absence of antimicrobial are inefficient to eradicate the microbial population and strongly favor the establishment of resistance, unless the antimicrobial increases enough the death rate. We further demonstrate that if the period of alternations is longer than a threshold value, the microbial population goes extinct upon the first addition of antimicrobial, if it is not rescued by resistance. We express the probability that the population is eradicated upon the first addition of antimicrobial, assuming rare mutations. Rescue by resistance can happen either if resistant mutants preexist, or if they appear after antimicrobial is added to the environment. Importantly, the latter case is fully prevented by perfect biostatic antimicrobials that completely stop division of sensitive microorganisms. By contrast, we show that the parameter regime where treatment is efficient is larger for biocidal drugs than for biostatic drugs. This sheds light on the respective merits of different antimicrobial modes of action.
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Affiliation(s)
- Loïc Marrec
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin (UMR 8237), F-75005 Paris, France
| | - Anne-Florence Bitbol
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin (UMR 8237), F-75005 Paris, France
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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