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Wang N, Li S, Shi M, Ni N, Zhang X, Guo X, Lin H, Luo Y. Trajectory of antibiotic resistome response to antibiotics gradients: A comparative study from pharmaceutical and associated wastewater treatment plants to receiving river. WATER RESEARCH 2024; 266:122444. [PMID: 39298897 DOI: 10.1016/j.watres.2024.122444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 09/09/2024] [Accepted: 09/12/2024] [Indexed: 09/22/2024]
Abstract
Pharmaceutical wastewater often contains significant levels of antibiotic residues, which continuously induce and promote antibiotic resistance during the sewage treatment process. However, the specific impact of antibiotics on the emergence of antibiotic resistance genes (ARGs), microbiomes, and mobile genetic elements (MGEs), as well as the dose-response relationship remain unclear. Herein, through metagenomic sequencing and analysis, we investigated the fate, transmission, and associated risk of ARGs over a ten-year period of exposure to a gradient of sulfonamide antibiotics at a pharmaceutical wastewater treatment plant (PWWTP), an associated wastewater treatment plant (WWTP), and the receiving river. Through abundance comparison and principal co-ordinates analysis (PCoA), our results revealed distinct ARG, microbiome, and MGE profiles across different antibiotic concentrations. Notably, there was a decreasing trend in the abundance of ARGs and MGEs as the antibiotic concentrations were attenuated (p < 0.05). Further partial least squares path modeling analysis, Procrustes analysis and network analysis indicated that variation in MGEs and microbiomes were the driving forces behind the distribution of ARGs. Based on these findings, we proposed an antibiotic-microbiome-MGE-ARG dissemination paradigm, in which integrons as key drivers were closely associated with prevalent ARGs such as sul1, sul2, and aadA. With a focus on human pathogenic bacteria and the associated health risks of ARGs, we conducted pathogen source analysis and calculated the antibiotic resistome risk index (ARRI). Our findings highlighted potential risks associated with the transition from PWWTP to WWTP, raising concerns regarding risk amplification due to the mixed treatment of antibiotic-laden industrial wastewater and domestic sewage. Overall, the results of our study provide valuable information for optimizing wastewater treatment practices to better manage antibiotic resistance.
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Affiliation(s)
- Na Wang
- Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Nanjing Institute of Environmental Science, Ministry of Ecology and Environment of the People's Republic of China, Nanjing 210042, China
| | - Shuchang Li
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact, Hebei Engineering Research Center of Sewage Treatment and Resource Utilization, Hebei University of Engineering, Handan 056038, China
| | - Mali Shi
- Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Nanjing Institute of Environmental Science, Ministry of Ecology and Environment of the People's Republic of China, Nanjing 210042, China
| | - Ni Ni
- Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Nanjing Institute of Environmental Science, Ministry of Ecology and Environment of the People's Republic of China, Nanjing 210042, China
| | - Xiaohui Zhang
- Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Nanjing Institute of Environmental Science, Ministry of Ecology and Environment of the People's Republic of China, Nanjing 210042, China
| | - Xinyan Guo
- Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Nanjing Institute of Environmental Science, Ministry of Ecology and Environment of the People's Republic of China, Nanjing 210042, China.
| | - Huai Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Yi Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
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Lansch-Justen L, El Karoui M, Alexander HK. Estimating mutation rates under heterogeneous stress responses. PLoS Comput Biol 2024; 20:e1012146. [PMID: 38805543 PMCID: PMC11161091 DOI: 10.1371/journal.pcbi.1012146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 06/07/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024] Open
Abstract
Exposure to environmental stressors, including certain antibiotics, induces stress responses in bacteria. Some of these responses increase mutagenesis and thus potentially accelerate resistance evolution. Many studies report increased mutation rates under stress, often using the standard experimental approach of fluctuation assays. However, single-cell studies have revealed that many stress responses are heterogeneously expressed in bacterial populations, which existing estimation methods have not yet addressed. We develop a population dynamic model that considers heterogeneous stress responses (subpopulations of cells with the response off or on) that impact both mutation rate and cell division rate, inspired by the DNA-damage response in Escherichia coli (SOS response). We derive the mutant count distribution arising in fluctuation assays under this model and then implement maximum likelihood estimation of the mutation-rate increase specifically associated with the expression of the stress response. Using simulated mutant count data, we show that our inference method allows for accurate and precise estimation of the mutation-rate increase, provided that this increase is sufficiently large and the induction of the response also reduces the division rate. Moreover, we find that in many cases, either heterogeneity in stress responses or mutant fitness costs could explain similar patterns in fluctuation assay data, suggesting that separate experiments would be required to identify the true underlying process. In cases where stress responses and mutation rates are heterogeneous, current methods still correctly infer the effective increase in population mean mutation rate, but we provide a novel method to infer distinct stress-induced mutation rates, which could be important for parameterising evolutionary models.
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Affiliation(s)
- Lucy Lansch-Justen
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Meriem El Karoui
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Centre for Engineering Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Bacterial Systems Biology and Anti Microbial Resistance, Laboratoire de Biologie et Pharmacologie Appliquée, École Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
| | - Helen K. Alexander
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Centre for Engineering Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
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Pell ME, Blankenship HM, Gaddy JA, Davies HD, Manning SD. Intrapartum antibiotic prophylaxis selects for mutators in group B streptococci among persistently colonized patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587590. [PMID: 38617326 PMCID: PMC11014637 DOI: 10.1101/2024.04.01.587590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Through vaginal colonization, GBS causes severe pregnancy outcomes including neonatal sepsis and meningitis. Although intrapartum antibiotic prophylaxis (IAP) has reduced early-onset disease rates, persistent GBS colonization has been observed in patients following prophylaxis. To determine whether IAP selects for genomic signatures that enhance GBS survival and persistence in the vaginal tract, whole-genome sequencing was performed on 97 isolates from 58 patients before (prenatal) and after (postpartum) IAP/childbirth. Core-gene mutation analysis identified 7,025 mutations between the paired isolates. Three postpartum isolates accounted for 98% of mutations and were classified as "mutators" because of point mutations within DNA repair systems. In vitro assays revealed stronger biofilms in two mutators. These findings suggest that antibiotics select for mutations that promote survival in vivo, which increases the likelihood of transmission to neonates. They also demonstrate how mutators can provide a reservoir of beneficial mutations that enhance fitness and genetic diversity in the GBS population.
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Affiliation(s)
- Macy E Pell
- Michigan State University, Department of Microbiology, Genetics, and Immunology (MGI), E. Lansing, MI
| | - Heather M Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories, Division of Infectious Diseases, Lansing, MI
| | - Jennifer A Gaddy
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
- Tennessee Valley Healthcare Systems, Department of Veterans Affairs, Nashville, TN
| | | | - Shannon D Manning
- Michigan State University, Department of Microbiology, Genetics, and Immunology (MGI), E. Lansing, MI
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Li M, Liu Y, Gong Y, Yan X, Wang L, Zheng W, Ai H, Zhao Y. Recent advances in nanoantibiotics against multidrug-resistant bacteria. NANOSCALE ADVANCES 2023; 5:6278-6317. [PMID: 38024316 PMCID: PMC10662204 DOI: 10.1039/d3na00530e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023]
Abstract
Multidrug-resistant (MDR) bacteria-caused infections have been a major threat to human health. The abuse of conventional antibiotics accelerates the generation of MDR bacteria and makes the situation worse. The emergence of nanomaterials holds great promise for solving this tricky problem due to their multiple antibacterial mechanisms, tunable antibacterial spectra, and low probabilities of inducing drug resistance. In this review, we summarize the mechanism of the generation of drug resistance, and introduce the recently developed nanomaterials for dealing with MDR bacteria via various antibacterial mechanisms. Considering that biosafety and mass production are the major bottlenecks hurdling the commercialization of nanoantibiotics, we introduce the related development in these two aspects. We discuss urgent challenges in this field and future perspectives to promote the development and translation of nanoantibiotics as alternatives against MDR pathogens to traditional antibiotics-based approaches.
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Affiliation(s)
- Mulan Li
- Cancer Research Center, Jiangxi University of Chinese Medicine No. 1688 Meiling Avenue, Xinjian District Nanchang Jiangxi 330004 P. R. China
| | - Ying Liu
- Key Laboratory of Follicular Development and Reproductive Health in Liaoning Province, Third Affiliated Hospital of Jinzhou Medical University No. 2, Section 5, Heping Road Jin Zhou Liaoning 121000 P. R. China
| | - Youhuan Gong
- Cancer Research Center, Jiangxi University of Chinese Medicine No. 1688 Meiling Avenue, Xinjian District Nanchang Jiangxi 330004 P. R. China
| | - Xiaojie Yan
- Cancer Research Center, Jiangxi University of Chinese Medicine No. 1688 Meiling Avenue, Xinjian District Nanchang Jiangxi 330004 P. R. China
| | - Le Wang
- Cancer Research Center, Jiangxi University of Chinese Medicine No. 1688 Meiling Avenue, Xinjian District Nanchang Jiangxi 330004 P. R. China
| | - Wenfu Zheng
- CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology No. 11 Zhongguancun Beiyitiao, Haidian District Beijing 100190 P. R. China
- The University of Chinese Academy of Sciences 19A Yuquan Road, Shijingshan District Beijing 100049 P. R. China
- Cannano Tefei Technology, Co. LTD Room 1013, Building D, No. 136 Kaiyuan Avenue, Huangpu District Guangzhou Guangdong Province 510535 P. R. China
| | - Hao Ai
- Key Laboratory of Follicular Development and Reproductive Health in Liaoning Province, Third Affiliated Hospital of Jinzhou Medical University No. 2, Section 5, Heping Road Jin Zhou Liaoning 121000 P. R. China
| | - Yuliang Zhao
- CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology No. 11 Zhongguancun Beiyitiao, Haidian District Beijing 100190 P. R. China
- The University of Chinese Academy of Sciences 19A Yuquan Road, Shijingshan District Beijing 100049 P. R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences 19B Yuquan Road, Shijingshan District Beijing 100049 P. R. China
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Gifford DR, Berríos-Caro E, Joerres C, Suñé M, Forsyth JH, Bhattacharyya A, Galla T, Knight CG. Mutators can drive the evolution of multi-resistance to antibiotics. PLoS Genet 2023; 19:e1010791. [PMID: 37311005 DOI: 10.1371/journal.pgen.1010791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/18/2023] [Indexed: 06/15/2023] Open
Abstract
Antibiotic combination therapies are an approach used to counter the evolution of resistance; their purported benefit is they can stop the successive emergence of independent resistance mutations in the same genome. Here, we show that bacterial populations with 'mutators', organisms with defects in DNA repair, readily evolve resistance to combination antibiotic treatment when there is a delay in reaching inhibitory concentrations of antibiotic-under conditions where purely wild-type populations cannot. In populations of Escherichia coli subjected to combination treatment, we detected a diverse array of acquired mutations, including multiple alleles in the canonical targets of resistance for the two drugs, as well as mutations in multi-drug efflux pumps and genes involved in DNA replication and repair. Unexpectedly, mutators not only allowed multi-resistance to evolve under combination treatment where it was favoured, but also under single-drug treatments. Using simulations, we show that the increase in mutation rate of the two canonical resistance targets is sufficient to permit multi-resistance evolution in both single-drug and combination treatments. Under both conditions, the mutator allele swept to fixation through hitch-hiking with single-drug resistance, enabling subsequent resistance mutations to emerge. Ultimately, our results suggest that mutators may hinder the utility of combination therapy when mutators are present. Additionally, by raising the rates of genetic mutation, selection for multi-resistance may have the unwanted side-effect of increasing the potential to evolve resistance to future antibiotic treatments.
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Affiliation(s)
- Danna R Gifford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, United Kingdom
| | - Ernesto Berríos-Caro
- Department of Physics and Astronomy, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, United Kingdom
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Christine Joerres
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Marc Suñé
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Jessica H Forsyth
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Anish Bhattacharyya
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Tobias Galla
- Department of Physics and Astronomy, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, United Kingdom
- Instituto de Física Interdisciplinar y Sistemas Complejos, IFISC (CSIC-UIB), Campus Universitat Illes Balears, Palma de Mallorca, Spain
| | - Christopher G Knight
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, United Kingdom
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Wang D, Ning Q, Deng Z, Zhang M, You J. Role of environmental stresses in elevating resistance mutations in bacteria: Phenomena and mechanisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119603. [PMID: 35691443 DOI: 10.1016/j.envpol.2022.119603] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/28/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Mutations are an important origin of antibiotic resistance in bacteria. While there is increasing evidence showing promoted resistance mutations by environmental stresses, no retrospective research has yet been conducted on this phenomenon and its mechanisms. Herein, we summarized the phenomena of stress-elevated resistance mutations in bacteria, generalized the regulatory mechanisms and discussed the environmental and human health implications. It is shown that both chemical pollutants, such as antibiotics and other pharmaceuticals, biocides, metals, nanoparticles and disinfection byproducts, and non-chemical stressors, such as ultraviolet radiation, electrical stimulation and starvation, are capable of elevating resistance mutations in bacteria. Notably, resistance mutations are more likely to occur under sublethal or subinhibitory levels of these stresses, suggesting a considerable environmental concern. Further, mechanisms for stress-induced mutations are summarized in several points, namely oxidative stress, SOS response, DNA replication and repair systems, RpoS regulon and biofilm formation, all of which are readily provoked by common environmental stresses. Given bacteria in the environment are confronted with a variety of unfavorable conditions, we propose that the stress-elevated resistance mutations are a universal phenomenon in the environment and represent a nonnegligible risk factor for ecosystems and human health. The present review identifies a need for taking into account the pollutants' ability to elevate resistance mutations when assessing their environmental and human health risks and highlights the necessity of including resistance mutations as a target to prevent antibiotic resistance evolution.
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Affiliation(s)
- Dali Wang
- Guangdong Provincial Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China
| | - Qing Ning
- Guangdong Provincial Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China
| | | | - Meng Zhang
- Shenzhen Dapeng New District Center for Disease Control and Prevention, Shenzhen, 518000, China
| | - Jing You
- Guangdong Provincial Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 511443, China.
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7
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Byun KH, Ha Han S, Woo Choi M, Hong Park S, Ha SD. Effect of sublethal concentrations of bactericidal antibiotics on mutation frequency and stress response of Listeria monocytogenes. Food Res Int 2022; 151:110903. [PMID: 34980420 DOI: 10.1016/j.foodres.2021.110903] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 11/04/2022]
Abstract
The purpose of this study was to investigate sublethal concentrations (SLC) of bactericidal antibiotics (ampicillin, gentamicin, kanamycin, and vancomycin) on the mutation frequency and stress response of antibiotic-induced-mutated (AIM) Listeria monocytogenes. Three L. monocytogenes strains (reference, clinical, and food isolate strains) were used in this study. SLC of bactericidal antibiotics significantly increased the mutation frequency in L. monocytogenes. It was found that AIM L. monocytogenes had a superior biofilm-forming ability than nontreated L. monocytogenes. This result correlated with the amounts of EPS produced (polysaccharide and protein) in the early stage of biofilm formation. AIM L. monocytogenes showed strong viability under food-associated stress (thermal, osmotic, and acidic) compared to nontreated L. monocytogenes. In addition, expression levels of motility (flaA) and virulence genes (hlyA, actA, and prfA) of AIM L. monocytogenes were significantly downregulated in the reference strain but significantly upregulated or similar to the expression levels in the clinical and food isolate strains compared to nontreated L. monocytogenes. Based on our results, SLC of bactericidal antibiotics increased the mutation frequency in L. monocytogenes, facilitated the adaptation of the bacterium to food-associated stress, and led to an increase in its pathogenicity.
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Affiliation(s)
- Kye-Hwan Byun
- Department of Food Science and Technology, Advanced Food Safety Research Group, Brain Korea 21 Plus, Chung-Ang University, Nae-ri, Daeduk-myun, Ansung, Kyunggido 17546, Republic of Korea
| | - Sang Ha Han
- Department of Food Science and Technology, Advanced Food Safety Research Group, Brain Korea 21 Plus, Chung-Ang University, Nae-ri, Daeduk-myun, Ansung, Kyunggido 17546, Republic of Korea
| | - Min Woo Choi
- Department of Food Science and Technology, Advanced Food Safety Research Group, Brain Korea 21 Plus, Chung-Ang University, Nae-ri, Daeduk-myun, Ansung, Kyunggido 17546, Republic of Korea
| | - Si Hong Park
- Food Science and Technology, Oregon State University, Corvallis, OR, USA
| | - Sang-Do Ha
- Department of Food Science and Technology, Advanced Food Safety Research Group, Brain Korea 21 Plus, Chung-Ang University, Nae-ri, Daeduk-myun, Ansung, Kyunggido 17546, Republic of Korea.
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Vidal JE, Wier MN, A. Angulo-Zamudio U, McDevitt E, Jop Vidal AG, Alibayov B, Scasny A, Wong SM, Akerley BJ, McDaniel LS. Prophylactic Inhibition of Colonization by Streptococcus pneumoniae with the Secondary Bile Acid Metabolite Deoxycholic Acid. Infect Immun 2021; 89:e0046321. [PMID: 34543118 PMCID: PMC8594607 DOI: 10.1128/iai.00463-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/07/2021] [Indexed: 12/26/2022] Open
Abstract
Streptococcus pneumoniae colonizes the nasopharynx of children and the elderly but also kills millions worldwide yearly. The secondary bile acid metabolite deoxycholic acid (DoC) affects the viability of human pathogens but also plays multiple roles in host physiology. We assessed in vitro the antimicrobial activity of DoC and investigated its potential to eradicate S. pneumoniae colonization using a model of human nasopharyngeal colonization and an in vivo mouse model of colonization. At a physiological concentration, DoC (0.5 mg/ml; 1.27 mM) killed all tested S. pneumoniae strains (n = 48) 2 h postinoculation. The model of nasopharyngeal colonization showed that DoC eradicated colonization by S. pneumoniae strains as soon as 10 min postexposure. The mechanism of action did not involve activation of autolysis, since the autolysis-defective double mutants ΔlytAΔlytC and ΔspxBΔlctO were as susceptible to DoC as was the wild type (WT). Oral streptococcal species (n = 20), however, were not susceptible to DoC (0.5 mg/ml). Unlike trimethoprim, whose spontaneous resistance frequency (srF) for TIGR4 or EF3030 was ≥1 × 10-9, no spontaneous resistance was observed with DoC (srF, ≥1 × 10-12). Finally, the efficacy of DoC to eradicate S. pneumoniae colonization was assessed in vivo using a topical route via intranasal (i.n.) administration and as a prophylactic treatment. Mice challenged with S. pneumoniae EF3030 carried a median of 4.05 × 105 CFU/ml 4 days postinoculation compared to 6.67 × 104 CFU/ml for mice treated with DoC. Mice in the prophylactic group had an ∼99% reduction of the pneumococcal density (median, 2.61 × 103 CFU/ml). Thus, DoC, an endogenous human bile salt, has therapeutic potential against S. pneumoniae.
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Affiliation(s)
- Jorge E. Vidal
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Meagan N. Wier
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | | | - Erin McDevitt
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Ana G. Jop Vidal
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Babek Alibayov
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Anna Scasny
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Sandy M. Wong
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Brian J. Akerley
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Larry S. McDaniel
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
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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 13: Diaminopyrimidines: trimethoprim. EFSA J 2021; 19:e06865. [PMID: 34729093 PMCID: PMC8546793 DOI: 10.2903/j.efsa.2021.6865] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The specific concentrations of trimethoprim 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 bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. The FARSC for trimethoprim was estimated. Uncertainties and data gaps associated to the levels reported were addressed. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. No suitable data for the assessment were available. It was recommended to perform further studies to supply more diverse and complete data related to the requirements for calculation of the FARSC for trimethoprim.
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10
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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 10: Quinolones: flumequine and oxolinic acid. EFSA J 2021; 19:e06862. [PMID: 34729090 PMCID: PMC8546796 DOI: 10.2903/j.efsa.2021.6862] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The specific concentrations of flumequine and oxolinic acid 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 bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data are available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. No suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these antimicrobials.
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Inactivation of UmuC Protein Significantly Reduces Resistance to Ciprofloxacin and SOS Mutagenesis in Escherichia coli Mutants Harboring Intact umuD Gene. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.111828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Ciprofloxacin induces SOS response and mutagenesis by activation of UmuD’2C (DNA polymerase V) and DinB (DNA polymerase IV) in Escherichia coli, leading to antibiotic resistance during therapy. Inactivation of DNA polymerase V can result in the inhibition of mutagenesis in E. coli. Objectives: The aim of this research was to investigate the effect of UmuC inactivation on resistance to ciprofloxacin and SOS mutagenesis in E. coli mutants. Methods: Ciprofloxacin-resistant mutants were produced in a umuC- genetic background in the presence of increasing concentrations of ciprofloxacin. The minimum inhibitory concentration of umuC-mutants was measured by broth dilution method. Alterations in the rifampin resistance-determing region of rpoB gene were assessed by PCR amplification and DNA sequencing. The expression of SOS genes was measured by quantitative real-time PCR assay. Results: Results showed that despite the induction of SOS response (overexpression of recA, dinB, and umuD genes) following exposure to ciprofloxacin in E. coli umuC mutants, resistance to ciprofloxacin and SOS mutagenesis significantly decreased. However, rifampicin-resistant clones emerged in this genetic background. One of these clones showed mutations in the rifampicin resistance-determining region of rpoB (cluster II). The low mutation frequency of E. coli might be associated with the presence and overexpression of umuD gene, which could somehow limit the activity of DinB, the location and type of mutations in the β subunit of RNA polymerase. Conclusions: In conclusion, for increasing the efficiency of ciprofloxacin against Gram-negative bacteria, use of an inhibitor of umuC, along with ciprofloxacin, would be helpful.
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12
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Ching C, Orubu ESF, Sutradhar I, Wirtz VJ, Boucher HW, Zaman MH. Bacterial antibiotic resistance development and mutagenesis following exposure to subinhibitory concentrations of fluoroquinolones in vitro: a systematic review of the literature. JAC Antimicrob Resist 2020; 2:dlaa068. [PMID: 34223024 PMCID: PMC8210091 DOI: 10.1093/jacamr/dlaa068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/15/2020] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND Understanding social and scientific drivers of antibiotic resistance is critical to help preserve antibiotic efficacy. These drivers include exposure to subinhibitory antibiotic concentrations in the environment and clinic. OBJECTIVES To summarize and quantify the relationship between subinhibitory fluoroquinolone exposure and antibiotic resistance and mutagenesis to better understand resistance patterns and mechanisms. METHODS Following PRISMA guidelines, PubMed, Web of Science and Embase were searched for primary in vitro experimental studies on subinhibitory fluoroquinolone exposure and bacterial antibiotic resistance and mutagenesis, from earliest available dates through to 2018 without language limitation. A specifically developed non-weighted tool was used to assess risk of bias. RESULTS Evidence from 62 eligible studies showed that subinhibitory fluoroquinolone exposure results in increased resistance to the selecting fluoroquinolone. Most increases in MIC were low (median minimum of 3.7-fold and median maximum of 32-fold) and may not be considered clinically relevant. Mechanistically, resistance is partly explained by target mutations but also changes in drug efflux. Collaterally, resistance to other fluoroquinolones and unrelated antibiotic classes also develops. The mean ± SD quality score for all studies was 2.6 ± 1.8 with a range of 0 (highest score) to 7 (lowest score). CONCLUSIONS Low and moderate levels of resistance and efflux changes can create an opportunity for higher-level resistance or MDR. Future studies, to elucidate the genetic regulation of specific resistance mechanisms, and increased policies, including surveillance of low-level resistance changes or genomic surveillance of efflux pump genes and regulators, could serve as a predictor of MDR development.
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Affiliation(s)
- Carly Ching
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Ebiowei S F Orubu
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Institute for Health System Innovation & Policy, Boston University, Boston, MA, USA
| | - Indorica Sutradhar
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Veronika J Wirtz
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Helen W Boucher
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA, USA
| | - Muhammad H Zaman
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Howard Hughes Medical Institute, Boston University, Boston, MA, USA
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13
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Goneau LW, Delport J, Langlois L, Poutanen SM, Razvi H, Reid G, Burton JP. Issues beyond resistance: inadequate antibiotic therapy and bacterial hypervirulence. FEMS MICROBES 2020; 1:xtaa004. [PMID: 37333955 PMCID: PMC10117437 DOI: 10.1093/femsmc/xtaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/15/2020] [Indexed: 10/15/2023] Open
Abstract
The administration of antibiotics while critical for treatment, can be accompanied by potentially severe complications. These include toxicities associated with the drugs themselves, the selection of resistant organisms and depletion of endogenous host microbiota. In addition, antibiotics may be associated with less well-recognized complications arising through changes in the pathogens themselves. Growing evidence suggests that organisms exposed to antibiotics can respond by altering the expression of toxins, invasins and adhesins, as well as biofilm, resistance and persistence factors. The clinical significance of these changes continues to be explored; however, it is possible that treatment with antibiotics may inadvertently precipitate a worsening of the clinical course of disease. Efforts are needed to adjust or augment antibiotic therapy to prevent the transition of pathogens to hypervirulent states. Better understanding the role of antibiotic-microbe interactions and how these can influence disease course is critical given the implications on prescription guidelines and antimicrobial stewardship policies.
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Affiliation(s)
- Lee W Goneau
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto,1 King's College Cir, Toronto, ON M5S 1A8 Ontario, Canada
| | - Johannes Delport
- Department of Pathology, London Health Sciences Center - Victoria Hospital, 800 Commissioners Rd E, London, Ontario, Canada N6A 5W9
| | - Luana Langlois
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
| | - Susan M Poutanen
- Department of Laboratory Medicine and Pathobiology, University of Toronto,1 King's College Cir, Toronto, ON M5S 1A8 Ontario, Canada
- Department of Medicine, University of Toronto, 1 King's College Cir, Toronto, ON M5S 1A8 Toronto, Ontario, Canada
- Department of Microbiology, University Health Network and Sinai Health, 190 Elizabeth St. Toronto, ON M5G 2C4, Ontario, Canada
| | - Hassan Razvi
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Division of Urology, Department of Surgery, Western University, 1151 Richmond St, London, Ontario, N6A 3K7 Canada
| | - Gregor Reid
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Division of Urology, Department of Surgery, Western University, 1151 Richmond St, London, Ontario, N6A 3K7 Canada
| | - Jeremy P Burton
- Department of Microbiology and Immunology, Western University, London, Ontario, Canada
- Lawson Health Research Institute, 268 Grosvenor St, London, Ontario, N6A 4V2 Canada
- Division of Urology, Department of Surgery, Western University, 1151 Richmond St, London, Ontario, N6A 3K7 Canada
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14
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Candida albicans Genetic Background Influences Mean and Heterogeneity of Drug Responses and Genome Stability during Evolution in Fluconazole. mSphere 2020; 5:5/3/e00480-20. [PMID: 32581072 PMCID: PMC7316494 DOI: 10.1128/msphere.00480-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Antimicrobial resistance is an evolutionary phenomenon with clinical implications. We tested how replicates from diverse strains of Candida albicans, a prevalent human fungal pathogen, evolve in the commonly prescribed antifungal drug fluconazole. Replicates on average increased in fitness in the level of drug they were evolved to, with the least fit parental strains improving the most. Very few replicates increased resistance above the drug level they were evolved in. Notably, many replicates increased in genome size and changed in drug tolerance (a drug response where a subpopulation of cells grow slowly in high levels of drug), and variability among replicates in fitness, tolerance, and genome size was higher in strains that initially were more sensitive to the drug. Genetic background influenced the average degree of adaptation and the evolved variability of many phenotypes, highlighting that different strains from the same species may respond and adapt very differently during adaptation. The importance of within-species diversity in determining the evolutionary potential of a population to evolve drug resistance or tolerance is not well understood, including in eukaryotic pathogens. To examine the influence of genetic background, we evolved replicates of 20 different clinical isolates of Candida albicans, a human fungal pathogen, in fluconazole, the commonly used antifungal drug. The isolates hailed from the major C. albicans clades and had different initial levels of drug resistance and tolerance to the drug. The majority of replicates rapidly increased in fitness in the evolutionary environment, with the degree of improvement inversely correlated with parental strain fitness in the drug. Improvement was largely restricted to up to the evolutionary level of drug: only 4% of the evolved replicates increased resistance (MIC) above the evolutionary level of drug. Prevalent changes were altered levels of drug tolerance (slow growth of a subpopulation of cells at drug concentrations above the MIC) and increased diversity of genome size. The prevalence and predominant direction of these changes differed in a strain-specific manner, but neither correlated directly with parental fitness or improvement in fitness. Rather, low parental strain fitness was correlated with high levels of heterogeneity in fitness, tolerance, and genome size among evolved replicates. Thus, parental strain background is an important determinant in mean improvement to the evolutionary environment as well as the diversity of evolved phenotypes, and the range of possible responses of a pathogen to an antimicrobial drug cannot be captured by in-depth study of a single strain background. IMPORTANCE Antimicrobial resistance is an evolutionary phenomenon with clinical implications. We tested how replicates from diverse strains of Candida albicans, a prevalent human fungal pathogen, evolve in the commonly prescribed antifungal drug fluconazole. Replicates on average increased in fitness in the level of drug they were evolved to, with the least fit parental strains improving the most. Very few replicates increased resistance above the drug level they were evolved in. Notably, many replicates increased in genome size and changed in drug tolerance (a drug response where a subpopulation of cells grow slowly in high levels of drug), and variability among replicates in fitness, tolerance, and genome size was higher in strains that initially were more sensitive to the drug. Genetic background influenced the average degree of adaptation and the evolved variability of many phenotypes, highlighting that different strains from the same species may respond and adapt very differently during adaptation.
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15
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Chen HH, Stringer A, Eguale T, Rao GG, Ozawa S. Impact of Antibiotic Resistance on Treatment of Pneumococcal Disease in Ethiopia: An Agent-Based Modeling Simulation. Am J Trop Med Hyg 2020; 101:1042-1053. [PMID: 31516111 DOI: 10.4269/ajtmh.18-0930] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Antimicrobial resistance (AMR) is a growing threat to global health. Although AMR endangers continued effectiveness of antibiotics, the impact of AMR has been poorly estimated in low-income countries. This study sought to quantify the effect of AMR on treatments for pediatric pneumococcal disease in Ethiopia. We developed the DREAMR (Dynamic Representation of the Economics of AMR) model that simulate children younger than 5 years who acquire pneumococcal disease (pneumonia, meningitis, and acute otitis media) and seek treatment from various health facilities in Ethiopia over a year. We examined the AMR levels of three antibiotics (penicillin, amoxicillin, and ceftriaxone), treatment failures, and attributable deaths. We used the cost-of-illness method to assess the resulting economic impact of AMR from a societal perspective by estimating the direct and indirect treatment costs and productivity losses. Findings showed that AMR against antibiotics that were used to treat pneumococcal disease led to 195,763 treatment failures per year, which contributed to 2,925 child deaths annually in Ethiopia. Antimicrobial resistance resulted in a first-line treatment failure rate of 29.4%. In 1 year, the proportion of nonsusceptible Streptococcus pneumoniae bacteria increased by 2.1% and 0.5% for amoxicillin and penicillin, and reduced by 0.3% for less commonly used ceftriaxone. Annual costs of AMR to treat pneumococcal disease were around US$15.8 million, including US$3.3 million for ineffective first-line treatments, US$3.7 million for second-line treatments, and US$8.9 million for long-term productivity losses. Antibiotic stewardship to reduce misuse and overuse of antibiotics is essential to maintain the effectiveness of antibiotics, and lessen the health and economic burden of AMR.
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Affiliation(s)
- Hui-Han Chen
- Division of Practice Advancement and Clinical Education, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Andrew Stringer
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Tadesse Eguale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gauri G Rao
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sachiko Ozawa
- Division of Practice Advancement and Clinical Education, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Maternal and Child Health, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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16
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Lu J, Wang Y, Jin M, Yuan Z, Bond P, Guo J. Both silver ions and silver nanoparticles facilitate the horizontal transfer of plasmid-mediated antibiotic resistance genes. WATER RESEARCH 2020; 169:115229. [PMID: 31783256 DOI: 10.1016/j.watres.2019.115229] [Citation(s) in RCA: 174] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 08/04/2019] [Accepted: 10/24/2019] [Indexed: 05/21/2023]
Abstract
Antibiotic resistance in bacteria is a growing threat to global human health. Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is recognized as the primary contributor to antibiotic resistance dissemination. Silver nanoparticles (AgNPs) are widely used in personal care products as antimicrobial agents. While heavy metals are known to induce antibiotic resistance in bacteria, it is not known whether AgNPs in the environment can stimulate the HGT of ARGs. Here, we report that both AgNPs and ionic silver Ag+, at environmentally relevant and sub-lethal concentrations, facilitate the conjugative transfer of plasmid-borne ARGs across bacterial genera (from the donor Escherichia coli K-12 LE392 to the recipient Pseudomonas putida KT2440). The underlying mechanisms of the Ag+- or AgNPs-promoted HGT were unveiled by detecting oxidative stress and cell membrane permeability, combined with genome-wide RNA sequencing and proteomic analyses. It was found that both Ag+ and AgNPs exposure induced various bacterial responses that included reactive oxygen species (ROS) generation, membrane damage and the SOS response. This study exposes the potential ecological risks of environmental levels of AgNPs and Ag+ for promoting the spread of ARGs and highlights concerns regarding the management of nanoparticles and heavy metals.
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Affiliation(s)
- Ji Lu
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Yue Wang
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Min Jin
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Philip Bond
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre (AWMC), The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
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17
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Mechesso AF, Park SC. Tylosin exposure reduces the susceptibility of Salmonella Typhimurium to florfenicol and tetracycline. BMC Vet Res 2020; 16:22. [PMID: 31992283 PMCID: PMC6986020 DOI: 10.1186/s12917-020-2246-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 01/16/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Antibiotics exposure has been implicated in the emergence of bacterial strains that are resistant to structurally related or unrelated antibiotics. Tylosin is a macrolide antibiotic that has been administered to treat respiratory pathogenic bacteria in swine. Thus, this study was undertaken to evaluate the impact of exposure to a constant (3 μg/mL) and decreasing concentrations of tylosin on the susceptibility of Salmonella enterica serovar Typhimurium to various antibiotics. RESULTS S. Typhimurium strains exposed to tylosin for 12 and 24 h in the in vitro dynamic model demonstrated at least an eight-fold increase in the minimum inhibitory concentrations (MICs) of florfenicol and tetracycline. Exposure to tylosin extended the lag-time of the growth curve and enhanced the generation of reactive oxygen species. Gene expression analysis demonstrated up-regulation of the acrAB and tolC Salmonella efflux pump genes and its global regulators (marA and soxS). Besides, the expression of ompC gene was down-regulated in tylosin exposed S. Typhimurium. CONCLUSION Exposure to decreasing concentrations of tylosin could reduce the susceptibility of S. Typhimurium to florfenicol and tetracycline.
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Affiliation(s)
- Abraham Fikru Mechesso
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Bukgu, Daegu, 41566 South Korea
| | - Seung-Chun Park
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Bukgu, Daegu, 41566 South Korea
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18
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Biasutti SA, Cox E, Jeffcott LB, Dart AJ. A review of regional limb perfusion for distal limb infections in the horse. EQUINE VET EDUC 2020. [DOI: 10.1111/eve.13243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S. A. Biasutti
- Research and Clinical Training Unit University Veterinary Teaching Hospital Camden University of Sydney New South Wales Australia
| | - E. Cox
- Research and Clinical Training Unit University Veterinary Teaching Hospital Camden University of Sydney New South Wales Australia
| | - L. B. Jeffcott
- Research and Clinical Training Unit University Veterinary Teaching Hospital Camden University of Sydney New South Wales Australia
| | - A. J. Dart
- Research and Clinical Training Unit University Veterinary Teaching Hospital Camden University of Sydney New South Wales Australia
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19
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Mullis MM, Rambo IM, Baker BJ, Reese BK. Diversity, Ecology, and Prevalence of Antimicrobials in Nature. Front Microbiol 2019; 10:2518. [PMID: 31803148 PMCID: PMC6869823 DOI: 10.3389/fmicb.2019.02518] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022] Open
Abstract
Microorganisms possess a variety of survival mechanisms, including the production of antimicrobials that function to kill and/or inhibit the growth of competing microorganisms. Studies of antimicrobial production have largely been driven by the medical community in response to the rise in antibiotic-resistant microorganisms and have involved isolated pure cultures under artificial laboratory conditions neglecting the important ecological roles of these compounds. The search for new natural products has extended to biofilms, soil, oceans, coral reefs, and shallow coastal sediments; however, the marine deep subsurface biosphere may be an untapped repository for novel antimicrobial discovery. Uniquely, prokaryotic survival in energy-limited extreme environments force microbial populations to either adapt their metabolism to outcompete or produce novel antimicrobials that inhibit competition. For example, subsurface sediments could yield novel antimicrobial genes, while at the same time answering important ecological questions about the microbial community.
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Affiliation(s)
- Megan M. Mullis
- Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, TX, United States
| | - Ian M. Rambo
- Department of Marine Science, University of Texas Marine Science Institute, Port Aransas, TX, United States
| | - Brett J. Baker
- Department of Marine Science, University of Texas Marine Science Institute, Port Aransas, TX, United States
| | - Brandi Kiel Reese
- Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, TX, United States
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20
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Blázquez J, Rodríguez-Beltrán J, Matic I. Antibiotic-Induced Genetic Variation: How It Arises and How It Can Be Prevented. Annu Rev Microbiol 2019; 72:209-230. [PMID: 30200850 DOI: 10.1146/annurev-micro-090817-062139] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
By targeting essential cellular processes, antibiotics provoke metabolic perturbations and induce stress responses and genetic variation in bacteria. Here we review current knowledge of the mechanisms by which these molecules generate genetic instability. They include production of reactive oxygen species, as well as induction of the stress response regulons, which lead to enhancement of mutation and recombination rates and modulation of horizontal gene transfer. All these phenomena influence the evolution and spread of antibiotic resistance. The use of strategies to stop or decrease the generation of resistant variants is also discussed.
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Affiliation(s)
- Jesús Blázquez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain; .,Unidad de Enfermedades Infecciosas, Microbiologia y Medicina Preventiva, Hospital Universitario Virgen del Rocio, 41013 Seville, Spain.,Red Española de Investigacion en Patologia Infecciosa, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Ivan Matic
- Faculté de Médecine Paris Descartes, INSERM 1001, CNRS, Université Paris-Descartes-Sorbonne Paris Cité, 75014 Paris, France;
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21
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Ram Y, Hadany L. Evolution of Stress-Induced Mutagenesis in the Presence of Horizontal Gene Transfer. Am Nat 2019; 194:73-89. [PMID: 31251650 DOI: 10.1086/703457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Stress-induced mutagenesis has been observed in multiple species of bacteria and yeast. It has been suggested that in asexual populations, a mutator allele that increases the mutation rate during stress can sweep to fixation with the beneficial mutations it generates. However, even asexual microbes can undergo horizontal gene transfer and rare recombination, which typically interfere with the spread of mutator alleles. Here we examine the effect of horizontal gene transfer on the evolutionary advantage of stress-induced mutator alleles. Our results demonstrate that stress-induced mutator alleles are favored by selection even in the presence of horizontal gene transfer and more so when the mutator alleles also increase the rate of horizontal gene transfer. We suggest that when regulated by stress, mutation and horizontal gene transfer can be complementary rather than competing adaptive strategies and that stress-induced mutagenesis has important implications for evolutionary biology, ecology, and epidemiology, even in the presence of horizontal gene transfer and rare recombination.
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Sun H, Chen R, Jiang W, Chen X, Lin Z. QSAR-based investigation on antibiotics facilitating emergence and dissemination of antibiotic resistance genes: A case study of sulfonamides against mutation and conjugative transfer in Escherichia coli. ENVIRONMENTAL RESEARCH 2019; 173:87-96. [PMID: 30903818 DOI: 10.1016/j.envres.2019.03.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
Antibiotic resistance genes (ARGs), which are emerging environmental contaminants, have posed great threats to global public health. Although extensive efforts have been undertaken to investigate ARG pollution, little attention has been paid to the structural information of antibiotics when exploring their impact on the emergence and dissemination of ARGs. In this study, setting Escherichia coli (E. coli) as the test organism, the effects of sulfonamides (SAs) on growth, mutation frequency and conjugative transfer frequency were tested, and quantitative structure-activity relationship (QSAR) was used to quantitatively analyze the promotion of SAs on these biological effects and explore their possible mechanism. The constructed QSAR models reveal that SAs may increase expression of the FtsZ protein and pili in E. coli via binding to the SdiA protein, ultimately leading to SAs facilitation of growth, mutation frequency and conjugative transfer frequency. The results indicate that SAs can produce selective pressure on E. coli to promote the emergence and dissemination of ARGs. This study provides reference data for further investigation of the emergence and dissemination of ARGs under antibiotic exposure and a new perspective for the mechanistic exploration of ARG pollution.
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Affiliation(s)
- Haoyu Sun
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; Post-doctoral Research Station, College of Civil Engineering, Tongji University, Shanghai 200092, China; Shanghai Key Lab of Chemical Assessment and Sustainability, Shanghai, China
| | - Renhui Chen
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Wei Jiang
- Shanghai Customs Inspection Center of Industrial Products & Raw Material, Shanghai 200135, China
| | - Xiang Chen
- Shanghai Customs Inspection Center of Industrial Products & Raw Material, Shanghai 200135, China
| | - Zhifen Lin
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; Shanghai Key Lab of Chemical Assessment and Sustainability, Shanghai, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China.
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Rehman A, Patrick WM, Lamont IL. Mechanisms of ciprofloxacin resistance in Pseudomonas aeruginosa: new approaches to an old problem. J Med Microbiol 2019; 68:1-10. [DOI: 10.1099/jmm.0.000873] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Attika Rehman
- 1Department of Biochemistry, University of Otago, New Zealand
| | - Wayne M. Patrick
- 1Department of Biochemistry, University of Otago, New Zealand
- 2School of Biological Sciences, Victoria University of Wellington, New Zealand
| | - Iain L. Lamont
- 1Department of Biochemistry, University of Otago, New Zealand
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Gomes IB, Simões LC, Simões M. The effects of emerging environmental contaminants on Stenotrophomonas maltophilia isolated from drinking water in planktonic and sessile states. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 643:1348-1356. [PMID: 30189551 DOI: 10.1016/j.scitotenv.2018.06.263] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/02/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
Abstract
Concerns on the presence of emerging contaminants (ECs) in water sources have increased in recent years. The lack of efficient technologies to remove ECs from residual waters contributes for their appearance in drinking water distribution systems (DWDS). Therefore, sessile microorganisms on DWDS pipes are continuously exposed to trace concentrations of ECs. However, no data exists on the role of ECs on the resident microbiota. The present work aims to understand the effects of prolonged exposure of a bacterial strain of Stenotrophomonas maltophilia, isolated from a DWDS, in both planktonic and biofilm states, to trace concentrations of selected ECs (antipyrine-ANTP; diclofenac sodium salt-DCF; ibuprofen-IBP; galaxolide-GAL; tonalide-TON; carbamazepine-CBZ; clofibric acid-CA; tylosin-TY) on its tolerance to sodium hypochlorite (NaOCl) and resistance to antibiotics. Pre-established S. maltophilia biofilms were exposed to ECs for 26 d. Subsequently, the planktonic behaviour of the biofilm cells grown in the presence of ECS was characterized in terms of susceptibility to NaOCl and to selected antibiotics (levofloxacin and trimethoprim-sulfamethoxazole). Moreover, S.maltophilia was tested on its biofilm productivity in the presence of ECs (alone and mixed). These biofilms were challenged by NaOCl in order to assess the role of ECs on biofilm susceptibility. The results did not evidence remarkable effects of ECs on planktonic S. maltophilia susceptibility to NaOCl and antibiotics. However, S. maltophilia biofilm production and susceptibility to NaOCl was affected from ECs pre-exposure, particularly by the combination of different ECs (CA + CBZ, CA + IBP, CA + CBZ + IBP). S. maltophilia biofilms became more resistant to removal by NaOCl when developed in the presence of mixtures of CA + CBZ and CA + CBZ + IBP. Also, biofilm production was significantly affected. CA was present in all the combinations that altered biofilm behaviour. The overall results propose that exposure to ECs for 26 days had not a huge impact on S. maltophilia planktonic antimicrobial susceptibility. Nevertheless, the prolonged exposure to some ECs altered biofilm production and tolerance to NaOCl, with a potential practical outcome of hindering DWDS disinfection. The simultaneous presence of different ECs in the environment may amplify biofilm resilience.
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Affiliation(s)
- Inês B Gomes
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal
| | - Lúcia C Simões
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal; CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Manuel Simões
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal.
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Meneghetti KL, do Canto Canabarro M, Otton LM, Dos Santos Hain T, Geimba MP, Corção G. Bacterial contamination of human skin allografts and antimicrobial resistance: a skin bank problem. BMC Microbiol 2018; 18:121. [PMID: 30249183 PMCID: PMC6154792 DOI: 10.1186/s12866-018-1261-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 09/17/2018] [Indexed: 01/15/2023] Open
Abstract
Background Bacterial contamination remains the major problem in skin banks, even after antimicrobial treatment, and results in high rates of tissue discarding. This study aimed to analyze bacterial contamination in 32 human skin allografts from the skin bank of Dr. Roberto Corrêa Chem from the Hospital Complex Santa Casa de Misericórdia de Porto Alegre. These samples were already discarded due to microbial contamination. The identification of the bacteria isolated from skin allografts was performed by matrix assisted laser desorption ionization–time of flight. The antimicrobial susceptibility of the isolates to six different classes of antimicrobials was determined using the disk-diffusion agar method, and the evaluation of the inhibitory potential was determined by the minimal inhibitory concentration (50/90) of antimicrobials already used in the skin bank and those that most isolates were susceptible to. Results A total of 21 (65.6%) skin samples were contaminated with Gram-positive bacteria: 1 (4.7%) with Paenibacillus sp., 12 (61.9%) with Bacillus sp., 6 (28.5%) with Staphylococcus sp., and 2 (9.5%) with Bacillus sp. and Staphylococcus sp. Several resistance profiles, including multiresistance, were found among the isolates. Most of the isolates were susceptible to at least one of the antimicrobials used in the skin bank. All isolates were susceptible to amikacin, gentamicin, and tetracycline, which demonstrated the best inhibitory activities against the isolates and were considered as potential candidates for new antimicrobial treatments. Conclusions Bacillus, Paenibacillus, and Staphylococcus were isolated from the skin allografts, thus demonstrating the predominance of Gram-positive bacteria contamination. Other factors not related to the resistance phenotype may also be involved in the persistence of bacterial isolates in the skin allografts after antibiotic treatment. Gentamicin, amikacin, and tetracycline can be considered as an option for a more effective treatment cocktail. Electronic supplementary material The online version of this article (10.1186/s12866-018-1261-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karine Lena Meneghetti
- Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Universidade Federal do Rio Grande do Sul, Sarmento Leite 500, Porto Alegre, 90050-170, Brazil
| | - Micaela do Canto Canabarro
- Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Universidade Federal do Rio Grande do Sul, Sarmento Leite 500, Porto Alegre, 90050-170, Brazil
| | - Letícia Muner Otton
- Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Universidade Federal do Rio Grande do Sul, Sarmento Leite 500, Porto Alegre, 90050-170, Brazil
| | - Thaís Dos Santos Hain
- Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Universidade Federal do Rio Grande do Sul, Sarmento Leite 500, Porto Alegre, 90050-170, Brazil
| | - Mercedes Passos Geimba
- Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Universidade Federal do Rio Grande do Sul, Sarmento Leite 500, Porto Alegre, 90050-170, Brazil
| | - Gertrudes Corção
- Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Universidade Federal do Rio Grande do Sul, Sarmento Leite 500, Porto Alegre, 90050-170, Brazil.
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Sturød K, Salvadori G, Junges R, Petersen FC. Antibiotics alter the window of competence for natural transformation in streptococci. Mol Oral Microbiol 2018; 33:378-387. [PMID: 29968346 DOI: 10.1111/omi.12240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/29/2018] [Indexed: 12/17/2022]
Abstract
Streptococcus pneumoniae transformation occurs within a short competence window, during which the alternative sigma factor X (SigX) is activated to orchestrate the expression of genes allowing extracellular DNA uptake and recombination. Importantly, antibiotic stress promotes transcriptional changes that may affect more than 20% of the S. pneumoniae genome, including competence genes. These can be activated or repressed, depending on the antibiotic agent. For most antibiotics, however, it remains unknown whether transcriptional effects on competence translate into altered transformability. Here we investigate the effect of antibiotic subinhibitory concentrations on sigX expression using a luciferase reporter, and correlate for the first time with transformation kinetics. Induction of sigX expression by ciprofloxacin and novobiocin correlated with increased and prolonged transformability in S. pneumoniae. The prolonged effect of ciprofloxacin on competence and transformation was also observed in the streptococcal relatives Streptococcus mitis and Streptococcus mutans. In contrast, tetracycline and erythromycin, which induced S. pneumoniae sigX expression, had either an inhibitory or a nonsignificant effect on transformation, whereas streptomycin and the β-lactam ampicillin, inhibited both sigX expression and transformation. Thus, the results show that antibiotics may vary in their effects on competence, ranging from inhibitory to stimulatory effects, and that responses affecting transcription of sigX do not always correlate with the transformation outcomes. Antibiotics that increase or decrease transformation are of particular clinical relevance, as they may alter the ability of S. pneumoniae to escape vaccines and antibiotics.
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Affiliation(s)
- K Sturød
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - G Salvadori
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - R Junges
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - F C Petersen
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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27
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Koliou MG, Andreou K, Lamnisos D, Lavranos G, Iakovides P, Economou C, Soteriades ES. Risk factors for carriage of Streptococcus pneumoniae in children. BMC Pediatr 2018; 18:144. [PMID: 29699525 PMCID: PMC5921789 DOI: 10.1186/s12887-018-1119-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/18/2018] [Indexed: 12/05/2022] Open
Abstract
Background During the past decades Streptococcus pneumoniae has developed significant resistance to many classes of antimicrobial drugs. Potential risk factors for colonization of the nasopharynx by Streptococcus pneumoniae in children and for carriage of drug resistant strains were examined. Methods Between 2007 and 2008 nasopharyngeal swabs were collected from 402 children 6 months to 5 years old visiting the public sector immunization centers and outpatient departments as well as offices of paediatricians from private practice in Nicosia district in Cyprus. Information on demographic characteristics and potential risk factors of participating children were collected using a standardized questionnaire distributed to parents. Results In multivariable analyses we found that attendance at day care center, having siblings in the family and having both parents originating from Cyprus, statistically increased the risk of pneumococcal colonization. Full immunization with PCV7 appears to be a protective factor against colonization by pneumococcus. Previous administration of antimicrobials during the last month prior to specimen collection appeared to be the most consistent risk factor for carrying a non susceptible strain of Streptococcus pneumoniae to either penicillin or erythromycin. Factors such as age, nationality, previous or current breastfeeding, passive exposure to cigarette smoke and attendance in a day care center do not appear as independent risk factors for colonization by non susceptible strains. Conclusions Prudent use of antibiotics especially for upper respiratory tract infections in children as well as increased vaccination coverage by the pneumococcal conjugate vaccines could prove effective in reducing levels of colonization by drug resistant pneumococcal strains.
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Affiliation(s)
- Maria G Koliou
- Department of Paediatrics, Archbishop Makarios III Hospital, Nicosia, Cyprus. .,School of Medicine, University of Cyprus, Nicosia, Cyprus. .,Cyprus Institute of Biomedical Sciences (CIBS), Nicosia, Cyprus.
| | | | - Demetris Lamnisos
- Department of Health Sciences, School of Sciences, European University Cyprus, Nicosia, Cyprus
| | - Giagkos Lavranos
- Department of Health Sciences, School of Sciences, European University Cyprus, Nicosia, Cyprus
| | | | | | - Elpidoforos S Soteriades
- Cyprus Institute of Biomedical Sciences (CIBS), Nicosia, Cyprus.,Harvard School of Public Health, Department of Environmental Health, Environmental and Occupational Medicine and Epidemiology (EOME), Boston, USA
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28
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Zheng Q. A cautionary note on the mutation frequency in microbial research. Mutat Res 2018; 809:51-55. [PMID: 29705518 DOI: 10.1016/j.mrfmmm.2018.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/03/2018] [Accepted: 04/17/2018] [Indexed: 11/18/2022]
Abstract
The mutation frequency, also known as the mutant frequency, is an unnormalized quantity, and its normalized counterpart is the mutation rate. Due to historical reasons, the mutation frequency has been a predominant yardstick of microbial mutability in the field of mutator identification. While the mean mutation frequency is infamously erratic, replacing it with the median mutation frequency is not an effective remedy. By encouraging investigators to substitute mutation rates for mutation frequencies in microbial research, this paper directs attention to substantial open problems such as false positive control and massive nonmutant cell death.
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Affiliation(s)
- Qi Zheng
- Department of Epidemiology and Biostatistics, Texas A&M School of Public Health, 212 Adriance Lab Road, College Station, TX 77843, United States.
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29
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Ciemniak K, Cielecka-Piontek J, Szymanowska D, Wiergowska G. Intereactions between doripenem and clavulanate — Application of minimal inhibitory concentration analysis and cytometry flow for bactericidal studies. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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30
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Campbell F, Strang C, Ferguson N, Cori A, Jombart T. When are pathogen genome sequences informative of transmission events? PLoS Pathog 2018; 14:e1006885. [PMID: 29420641 PMCID: PMC5821398 DOI: 10.1371/journal.ppat.1006885] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 02/21/2018] [Accepted: 01/18/2018] [Indexed: 01/19/2023] Open
Abstract
Recent years have seen the development of numerous methodologies for reconstructing transmission trees in infectious disease outbreaks from densely sampled whole genome sequence data. However, a fundamental and as of yet poorly addressed limitation of such approaches is the requirement for genetic diversity to arise on epidemiological timescales. Specifically, the position of infected individuals in a transmission tree can only be resolved by genetic data if mutations have accumulated between the sampled pathogen genomes. To quantify and compare the useful genetic diversity expected from genetic data in different pathogen outbreaks, we introduce here the concept of ‘transmission divergence’, defined as the number of mutations separating whole genome sequences sampled from transmission pairs. Using parameter values obtained by literature review, we simulate outbreak scenarios alongside sequence evolution using two models described in the literature to describe transmission divergence of ten major outbreak-causing pathogens. We find that while mean values vary significantly between the pathogens considered, their transmission divergence is generally very low, with many outbreaks characterised by large numbers of genetically identical transmission pairs. We describe the impact of transmission divergence on our ability to reconstruct outbreaks using two outbreak reconstruction tools, the R packages outbreaker and phybreak, and demonstrate that, in agreement with previous observations, genetic sequence data of rapidly evolving pathogens such as RNA viruses can provide valuable information on individual transmission events. Conversely, sequence data of pathogens with lower mean transmission divergence, including Streptococcus pneumoniae, Shigella sonnei and Clostridium difficile, provide little to no information about individual transmission events. Our results highlight the informational limitations of genetic sequence data in certain outbreak scenarios, and demonstrate the need to expand the toolkit of outbreak reconstruction tools to integrate other types of epidemiological data. The increasing availability of genetic sequence data has sparked an interest in using pathogen whole genome sequences to reconstruct the history of individual transmission events in an infectious disease outbreak. However, such methodologies rely on pathogen genomes mutating rapidly enough to discriminate between infected individuals, an assumption that remains to be investigated. To determine pathogen outbreaks for which genetic data is expected to be informative of transmission events, we introduce here the concept of ‘transmission divergence’, defined as the number of mutations separating pathogen genome sequences sampled from transmission pairs. We characterise transmission divergence of ten major outbreak causing pathogens using simulations and find significant variation between diseases, with viral outbreaks generally exhibiting higher transmission divergence than bacterial ones. We reconstruct these outbreaks using the R-packages outbreaker and phybreak and find that genetic sequence data, though useful for rapidly evolving pathogens, provides little to no information about outbreaks with low transmission divergence, such as Streptococcus pneumoniae and Shigella sonnei. Our results demonstrate the need to incorporate other sources of outbreak data, such as contact tracing data and spatial location data, into outbreak reconstruction tools.
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Affiliation(s)
- Finlay Campbell
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail: (FC); (TJ); (AC)
| | - Camilla Strang
- Centre for Preventive Medicine, Department of Epidemiology and Disease Surveillance, Animal Health Trust, Suffolk, United Kingdom
| | - Neil Ferguson
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Anne Cori
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail: (FC); (TJ); (AC)
| | - Thibaut Jombart
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail: (FC); (TJ); (AC)
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31
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Henrikus SS, Wood EA, McDonald JP, Cox MM, Woodgate R, Goodman MF, van Oijen AM, Robinson A. DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli. PLoS Genet 2018; 14:e1007161. [PMID: 29351274 PMCID: PMC5792023 DOI: 10.1371/journal.pgen.1007161] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 01/31/2018] [Accepted: 12/19/2017] [Indexed: 11/18/2022] Open
Abstract
In Escherichia coli, damage to the chromosomal DNA induces the SOS response, setting in motion a series of different DNA repair and damage tolerance pathways. DNA polymerase IV (pol IV) is one of three specialised DNA polymerases called into action during the SOS response to help cells tolerate certain types of DNA damage. The canonical view in the field is that pol IV primarily acts at replisomes that have stalled on the damaged DNA template. However, the results of several studies indicate that pol IV also acts on other substrates, including single-stranded DNA gaps left behind replisomes that re-initiate replication downstream of a lesion, stalled transcription complexes and recombination intermediates. In this study, we use single-molecule time-lapse microscopy to directly visualize fluorescently labelled pol IV in live cells. We treat cells with the DNA-damaging antibiotic ciprofloxacin, Methylmethane sulfonate (MMS) or ultraviolet light and measure changes in pol IV concentrations and cellular locations through time. We observe that only 5–10% of foci induced by DNA damage form close to replisomes, suggesting that pol IV predominantly carries out non-replisomal functions. The minority of foci that do form close to replisomes exhibit a broad distribution of colocalisation distances, consistent with a significant proportion of pol IV molecules carrying out postreplicative TLS in gaps behind the replisome. Interestingly, the proportion of pol IV foci that form close to replisomes drops dramatically in the period 90–180 min after treatment, despite pol IV concentrations remaining relatively constant. In an SOS-constitutive mutant that expresses high levels of pol IV, few foci are observed in the absence of damage, indicating that within cells access of pol IV to DNA is dependent on the presence of damage, as opposed to concentration-driven competition for binding sites. Translesion DNA polymerases play a critical role in DNA damage tolerance in all cells. In Escherichia coli, the translesion polymerases include DNA polymerases II, IV, and V. At stalled replication forks, DNA polymerase IV is thought to compete with, and perhaps displace the polymerizing subunits of DNA polymerase III to facilitate translesion replication. The results of the current fluorescence microscopy study challenge that view. The results indicate that DNA polymerase IV acts predominantly at sites away from the replisome. These sites may include recombination intermediates, stalled transcription complexes, and single-stranded gaps left in the wake of DNA polymerase III replisomes that re-initiate replication downstream of a lesion.
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Affiliation(s)
- Sarah S. Henrikus
- School of Chemistry, University of Wollongong, Wollongong, Australia
| | - Elizabeth A. Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - John P. McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Myron F. Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, California, United States of America
| | | | - Andrew Robinson
- School of Chemistry, University of Wollongong, Wollongong, Australia
- * E-mail:
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Cairns J, Becks L, Jalasvuori M, Hiltunen T. Sublethal streptomycin concentrations and lytic bacteriophage together promote resistance evolution. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0040. [PMID: 27920385 DOI: 10.1098/rstb.2016.0040] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2016] [Indexed: 12/19/2022] Open
Abstract
Sub-minimum inhibiting concentrations (sub-MICs) of antibiotics frequently occur in natural environments owing to wide-spread antibiotic leakage by human action. Even though the concentrations are very low, these sub-MICs have recently been shown to alter bacterial populations by selecting for antibiotic resistance and increasing the rate of adaptive evolution. However, studies are lacking on how these effects reverberate into key ecological interactions, such as bacteria-phage interactions. Previously, co-selection of bacteria by phages and antibiotic concentrations exceeding MICs has been hypothesized to decrease the rate of resistance evolution because of fitness costs associated with resistance mutations. By contrast, here we show that sub-MICs of the antibiotic streptomycin (Sm) increased the rate of phage resistance evolution, as well as causing extinction of the phage. Notably, Sm and the phage in combination also enhanced the evolution of Sm resistance compared with Sm alone. These observations demonstrate the potential of sub-MICs of antibiotics to impact key ecological interactions in microbial communities with evolutionary outcomes that can radically differ from those associated with high concentrations. Our findings also contribute to the understanding of ecological and evolutionary factors essential for the management of the antibiotic resistance problem.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.
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Affiliation(s)
- Johannes Cairns
- Department of Food and Environmental Sciences/Microbiology and Biotechnology, University of Helsinki, PO Box 65, 00014 Helsinki, Finland
| | - Lutz Becks
- Department of Evolutionary Ecology/Community Dynamics Group, Max Planck Institute for Evolutionary Biology, August Thienemann Street 2, Plön 24306, Germany
| | - Matti Jalasvuori
- Department of Biological and Environmental Science/Centre of Excellence in Biological Interactions, University of Jyväskylä, PO Box 35, 40014 Jyväskylä, Finland
| | - Teppo Hiltunen
- Department of Food and Environmental Sciences/Microbiology and Biotechnology, University of Helsinki, PO Box 65, 00014 Helsinki, Finland
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de With K, Allerberger F, Amann S, Apfalter P, Brodt HR, Eckmanns T, Fellhauer M, Geiss HK, Janata O, Krause R, Lemmen S, Meyer E, Mittermayer H, Porsche U, Presterl E, Reuter S, Sinha B, Strauß R, Wechsler-Fördös A, Wenisch C, Kern WV. Strategies to enhance rational use of antibiotics in hospital: a guideline by the German Society for Infectious Diseases. Infection 2017; 44:395-439. [PMID: 27066980 PMCID: PMC4889644 DOI: 10.1007/s15010-016-0885-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Introduction In the time of increasing resistance and paucity of new drug development there is a growing need for strategies to enhance rational use of antibiotics in German and Austrian hospitals. An evidence-based guideline on recommendations for implementation of antibiotic stewardship (ABS) programmes was developed by the German Society for Infectious Diseases in association with the following societies, associations and institutions: German Society of Hospital Pharmacists, German Society for Hygiene and Microbiology, Paul Ehrlich Society for Chemotherapy, The Austrian Association of Hospital Pharmacists, Austrian Society for Infectious Diseases and Tropical Medicine, Austrian Society for Antimicrobial Chemotherapy, Robert Koch Institute. Materials and methods A structured literature research was performed in the databases EMBASE, BIOSIS, MEDLINE and The Cochrane Library from January 2006 to November 2010 with an update to April 2012 (MEDLINE and The Cochrane Library). The grading of recommendations in relation to their evidence is according to the AWMF Guidance Manual and Rules for Guideline Development. Conclusion The guideline provides the grounds for rational use of antibiotics in hospital to counteract antimicrobial resistance and to improve the quality of care of patients with infections by maximising clinical outcomes while minimising toxicity. Requirements for a successful implementation of ABS programmes as well as core and supplemental ABS strategies are outlined. The German version of the guideline was published by the German Association of the Scientific Medical Societies (AWMF) in December 2013.
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Affiliation(s)
- K de With
- Division of Infectious Diseases, University Hospital Carl Gustav Carus at the TU Dresden, Fetscherstr. 74, 01307, Dresden, Germany.
| | - F Allerberger
- Division Public Health, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - S Amann
- Hospital Pharmacy, Munich Municipal Hospital, Munich, Germany
| | - P Apfalter
- Institute for Hygiene, Microbiology and Tropical Medicine (IHMT), National Reference Centre for Nosocomial Infections and Antimicrobial Resistance, Elisabethinen Hospital Linz, Linz, Austria
| | - H-R Brodt
- Department of Infectious Disease Medical Clinic II, Goethe-University Frankfurt, Frankfurt, Germany
| | - T Eckmanns
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - M Fellhauer
- Hospital Pharmacy, Schwarzwald-Baar Hospital, Villingen-Schwenningen, Germany
| | - H K Geiss
- Department of Hospital Epidemiology and Infectiology, Sana Kliniken AG, Ismaning, Germany
| | - O Janata
- Department for Hygiene and Infection Control, Danube Hospital, Vienna, Austria
| | - R Krause
- Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Graz, Austria
| | - S Lemmen
- Division of Infection Control and Infectious Diseases, University Hospital RWTH Aachen, Aachen, Germany
| | - E Meyer
- Institute of Hygiene and Environmental Medicine, Charité, University Medicine Berlin, Berlin, Germany
| | - H Mittermayer
- Institute for Hygiene, Microbiology and Tropical Medicine (IHMT), National Reference Centre for Nosocomial Infections and Antimicrobial Resistance, Elisabethinen Hospital Linz, Linz, Austria
| | - U Porsche
- Department for Clinical Pharmacy and Drug Information, Landesapotheke, Landeskliniken Salzburg (SALK), Salzburg, Austria
| | - E Presterl
- Department of Infection Control and Hospital Epidemiology, Medical University of Vienna, Vienna, Austria
| | - S Reuter
- Clinic for General Internal Medicine, Infectious Diseases, Pneumology and Osteology, Klinikum Leverkusen, Leverkusen, Germany
| | - B Sinha
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - R Strauß
- Department of Medicine 1, Gastroenterology, Pneumology and Endocrinology, University Hospital Erlangen, Erlangen, Germany
| | - A Wechsler-Fördös
- Department of Antibiotics and Infection Control, Krankenanstalt Rudolfstiftung, Vienna, Austria
| | - C Wenisch
- Medical Department of Infection and Tropical Medicine, Kaiser Franz Josef Hospital, Vienna, Austria
| | - W V Kern
- Division of Infectious Diseases, Department of Medicine, Freiburg University Medical Center, Freiburg, Germany
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Ciprofloxacin-Mediated Mutagenesis Is Suppressed by Subinhibitory Concentrations of Amikacin in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2017; 61:AAC.02107-16. [PMID: 28031197 DOI: 10.1128/aac.02107-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/19/2016] [Indexed: 12/11/2022] Open
Abstract
Resistance to antibiotics is a global health problem. Activation of the SOS response, and the subsequent elevation in mutagenesis, contributes to the appearance of resistance mutations. Among currently used drugs, quinolones are the most potent inducers of the SOS response. In the present study, we show that amikacin inhibits ciprofloxacin-mediated SOS induction and mutagenesis in Pseudomonas aeruginosa.
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35
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Mutational Consequences of Ciprofloxacin in Escherichia coli. Antimicrob Agents Chemother 2016; 60:6165-72. [PMID: 27480851 DOI: 10.1128/aac.01415-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 07/26/2016] [Indexed: 11/20/2022] Open
Abstract
We examined the mutagenic specificity of the widely used antibiotic ciprofloxacin (CPR), which displays weak to moderate mutagenic activity in several bacteria and generates short in-frame deletions in rpoB in Staphylococcus aureus To determine the spectrum of mutations in a system where any gene knockout would result in a recovered mutant, including frameshifts and both short and long deletions, we examined CPR-induced mutations in the thymidylate synthase-encoding thyA gene. Here, any mutation resulting in loss of thymidylate synthase activity generates trimethoprim (Trm) resistance. We found that deletions and insertions in all three reading frames predominated in the spectrum. They tend to be short deletions and cluster in two regions, one being a GC-rich region with potential extensive secondary structures. We also exploited the well-characterized rpoB-Rif(r) system in Escherichia coli to determine that cells grown in the presence of sublethal doses of CPR not only induced short in-frame deletions in rpoB, but also generated base substitution mutations resulting from induction of the SOS system. Some of the specific point mutations prominent in the spectrum of a strain that overproduces the dinB-encoded Pol IV were also present after growth in CPR. However, these mutations disappeared in CPR-treated dinB mutants, whereas the deletions remained. Moreover, CPR-induced deletions also occurred in a strain lacking all three SOS-induced polymerases. We discuss the implications of these findings for the consequences of overuse of CPR and other antibiotics.
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Rasmussen BB, Grotkjær T, D'Alvise PW, Yin G, Zhang F, Bunk B, Spröer C, Bentzon-Tilia M, Gram L. Vibrio anguillarum Is Genetically and Phenotypically Unaffected by Long-Term Continuous Exposure to the Antibacterial Compound Tropodithietic Acid. Appl Environ Microbiol 2016; 82:4802-4810. [PMID: 27235441 PMCID: PMC4984299 DOI: 10.1128/aem.01047-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 05/24/2016] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED Minimizing the use of antibiotics in the food production chain is essential for limiting the development and spread of antibiotic-resistant bacteria. One alternative intervention strategy is the use of probiotic bacteria, and bacteria of the marine Roseobacter clade are capable of antagonizing fish-pathogenic vibrios in fish larvae and live feed cultures for fish larvae. The antibacterial compound tropodithietic acid (TDA), an antiporter that disrupts the proton motive force, is key in the antibacterial activity of several roseobacters. Introducing probiotics on a larger scale requires understanding of any potential side effects of long-term exposure of the pathogen to the probionts or any compounds they produce. Here we exposed the fish pathogen Vibrio anguillarum to TDA for several hundred generations in an adaptive evolution experiment. No tolerance or resistance arose during the 90 days of exposure, and whole-genome sequencing of TDA-exposed lineages and clones revealed few mutational changes, compared to lineages grown without TDA. Amino acid-changing mutations were found in two to six different genes per clone; however, no mutations appeared unique to the TDA-exposed lineages or clones. None of the virulence genes of V. anguillarum was affected, and infectivity assays using fish cell lines indicated that the TDA-exposed lineages and clones were less invasive than the wild-type strain. Thus, long-term TDA exposure does not appear to result in TDA resistance and the physiology of V. anguillarum appears unaffected, supporting the application of TDA-producing roseobacters as probiotics in aquaculture. IMPORTANCE It is important to limit the use of antibiotics in our food production, to reduce the risk of bacteria developing antibiotic resistance. We showed previously that marine bacteria of the Roseobacter clade can prevent or reduce bacterial diseases in fish larvae, acting as probiotics. Roseobacters produce the antimicrobial compound tropodithietic acid (TDA), and we were concerned regarding whether long-term exposure to this compound could induce resistance or affect the disease-causing ability of the fish pathogen. Therefore, we exposed the fish pathogen Vibrio anguillarum to increasing TDA concentrations over 3 months. We did not see the development of any resistance to TDA, and subsequent infection assays revealed that none of the TDA-exposed clones had increased virulence toward fish cells. Hence, this study supports the use of roseobacters as a non-risk-based disease control measure in aquaculture.
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Affiliation(s)
| | - Torben Grotkjær
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Paul W D'Alvise
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Faxing Zhang
- Beijing Genomics Institute Europe, Copenhagen, Denmark
| | - Boyke Bunk
- Leibniz Institute, DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute, DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Mikkel Bentzon-Tilia
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lone Gram
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
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Torres-Barceló C, Kojadinovic M, Moxon R, MacLean RC. The SOS response increases bacterial fitness, but not evolvability, under a sublethal dose of antibiotic. Proc Biol Sci 2016; 282:20150885. [PMID: 26446807 PMCID: PMC4614765 DOI: 10.1098/rspb.2015.0885] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Exposure to antibiotics induces the expression of mutagenic bacterial stress–response pathways, but the evolutionary benefits of these responses remain unclear. One possibility is that stress–response pathways provide a short-term advantage by protecting bacteria against the toxic effects of antibiotics. Second, it is possible that stress-induced mutagenesis provides a long-term advantage by accelerating the evolution of resistance. Here, we directly measure the contribution of the Pseudomonas aeruginosa SOS pathway to bacterial fitness and evolvability in the presence of sublethal doses of ciprofloxacin. Using short-term competition experiments, we demonstrate that the SOS pathway increases competitive fitness in the presence of ciprofloxacin. Continued exposure to ciprofloxacin results in the rapid evolution of increased fitness and antibiotic resistance, but we find no evidence that SOS-induced mutagenesis accelerates the rate of adaptation to ciprofloxacin during a 200 generation selection experiment. Intriguingly, we find that the expression of the SOS pathway decreases during adaptation to ciprofloxacin, and this helps to explain why this pathway does not increase long-term evolvability. Furthermore, we argue that the SOS pathway fails to accelerate adaptation to ciprofloxacin because the modest increase in the mutation rate associated with SOS mutagenesis is offset by a decrease in the effective strength of selection for increased resistance at a population level. Our findings suggest that the primary evolutionary benefit of the SOS response is to increase bacterial competitive ability, and that stress-induced mutagenesis is an unwanted side effect, and not a selected attribute, of this pathway.
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Affiliation(s)
- Clara Torres-Barceló
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK Institut des Sciences de l'Evolution, CNRS-Université Montpellier 2, Montpellier, France
| | | | - Richard Moxon
- University of Oxford Medical Sciences Division, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - R Craig MacLean
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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Aydin S, Ince B, Ince O. Development of antibiotic resistance genes in microbial communities during long-term operation of anaerobic reactors in the treatment of pharmaceutical wastewater. WATER RESEARCH 2015; 83:337-44. [PMID: 26188597 DOI: 10.1016/j.watres.2015.07.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 07/03/2015] [Accepted: 07/04/2015] [Indexed: 05/22/2023]
Abstract
Biological treatment processes offer the ideal conditions in which a high diversity of microorganisms can grow and develop. The wastewater produced during these processes is contaminated with antibiotics and, as such, they provide the ideal setting for the acquisition and proliferation of antibiotic resistance genes (ARGs). This research investigated the occurrence and variation in the ARGs found during the one-year operation of the anaerobic sequencing batch reactors (SBRs) used to treat pharmaceutical wastewater that contained combinations of sulfamethoxazole-tetracycline-erythromycin (STE) and sulfamethoxazole-tetracycline (ST). The existence of eighteen ARGs encoding resistance to sulfamethoxazole (sul1, sul2, sul3), erythromycin (ermA, ermF, ermB, msrA, ereA), tetracycline (tetA, tetB, tetC, tetD, tetE, tetM, tetS, tetQ, tetW, tetX) and class Ι integron gene (intΙ 1) in the STE and ST reactors was investigated by quantitative real-time PCR. Due to the limited availability of primers to detect ARGs, Illumina sequencing was also performed on the sludge and effluent of the STE and ST reactors. Although there was good reactor performance in the SBRs, which corresponds to min 80% COD removal efficiency, tetA, tetB, sul1, sul2 and ermB genes were among those ARGs detected in the effluent from STE and ST reactors. A comparison of the ARGs acquired from the STE and ST reactors revealed that the effluent from the STE reactor had a higher number of ARGs than that from the ST reactor; this could be due to the synergistic effects of erythromycin. According to the expression of genes results, microorganisms achieve tetracycline and erythromycin resistance through a combination of three mechanisms: efflux pumping protein, modification of the antibiotic target and modifying enzymes. There was also a significant association between the presence of the class 1 integron and sulfamethoxazole resistance genes.
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Affiliation(s)
- Sevcan Aydin
- Istanbul Technical University, Environmental Engineering Department, Maslak, Istanbul, Turkey.
| | - Bahar Ince
- Bogazici University, Institutes of Environmental Sciences, Bebek, Istanbul, Turkey
| | - Orhan Ince
- Istanbul Technical University, Environmental Engineering Department, Maslak, Istanbul, Turkey
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Dayie NTKD, Arhin RE, Newman MJ, Dalsgaard A, Bisgaard M, Frimodt-Møller N, Slotved HC. Multidrug-Resistant Streptococcus pneumoniae Isolates from Healthy Ghanaian Preschool Children. Microb Drug Resist 2015; 21:636-42. [PMID: 26172078 DOI: 10.1089/mdr.2014.0314] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pneumoniae is the cause of high mortality among children worldwide. Antimicrobial treatment and vaccination are used to control pneumococcal infections. In Ghana, data on antimicrobial resistance and the prevalence of multidrug-resistant pneumococcal clones are scarce; hence, the aim of this study was to determine the antibiogram of S. pneumoniae recovered from Ghanaian children younger than six years of age and to what extent resistances were due to the spread of certain sero- and multilocus sequence typing (MLST) types. The susceptibility of 115 pneumococcal isolates, recovered in a previous study, to six antimicrobials was determined by disk diffusion test. Overall, 90.4% of isolates were intermediate penicillin resistant, 99.1% were trimethoprim resistant, 73.0% were tetracycline resistant, and 33.9% were sulfamethoxazole resistant. Low resistance was recorded for erythromycin (2.6%) and cefotaxime (5.2%). Overall, 72.2% of isolates were resistant to penicillin (I or R) and at least two other antimicrobials. MLST of 20 isolates showing resistance to at least four antimicrobials revealed a high diversity documented by 16 different clones, none of which had previously been associated with multidrug resistance. The resistances found may have emerged due to nonprudent antimicrobial use practices and there is a need to monitor and promote prudent antimicrobial usage in Ghana.
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Affiliation(s)
- Nicholas T K D Dayie
- 1 Department of Medical Microbiology, University of Ghana Medical School , Accra, Ghana .,2 Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen, Denmark
| | - Reuben E Arhin
- 1 Department of Medical Microbiology, University of Ghana Medical School , Accra, Ghana
| | - Mercy J Newman
- 1 Department of Medical Microbiology, University of Ghana Medical School , Accra, Ghana
| | - Anders Dalsgaard
- 2 Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen, Denmark
| | - Magne Bisgaard
- 2 Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen, Denmark
| | - Niels Frimodt-Møller
- 3 Department of Clinical Microbiology, University Hospital , Rigshospitalet, Copenhagen, Denmark
| | - Hans-Christian Slotved
- 4 Department of Microbiology and Infection Control, Statens Serum Institut , Copenhagen, Denmark
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Abstract
Because mutations are mostly deleterious, mutation rates should be reduced by natural selection. However, mutations also provide the raw material for adaptation. Therefore, evolutionary theory suggests that the mutation rate must balance between adaptability-the ability to adapt-and adaptedness-the ability to remain adapted. We model an asexual population crossing a fitness valley and analyse the rate of complex adaptation with and without stress-induced mutagenesis (SIM)-the increase of mutation rates in response to stress or maladaptation. We show that SIM increases the rate of complex adaptation without reducing the population mean fitness, thus breaking the evolutionary trade-off between adaptability and adaptedness. Our theoretical results support the hypothesis that SIM promotes adaptation and provide quantitative predictions of the rate of complex adaptation with different mutational strategies.
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Affiliation(s)
- Yoav Ram
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Lilach Hadany
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
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Ouennane S, Leprohon P, Moineau S. Diverse virulent pneumophages infect Streptococcus mitis. PLoS One 2015; 10:e0118807. [PMID: 25692983 PMCID: PMC4334900 DOI: 10.1371/journal.pone.0118807] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/23/2015] [Indexed: 01/01/2023] Open
Abstract
Streptococcus mitis has emerged as one of the leading causes of bacterial endocarditis and is related to Streptococcus pneumoniae. Antibiotic resistance has also increased among strains of S. mitis and S. pneumoniae. Phages are being reinvestigated as alternatives to antibiotics for managing infections. In this study, the two virulent phages Cp-1 (Podoviridae) and Dp-1 (Siphoviridae), previously isolated from S. pneumoniae, were found to also infect S. mitis. Microbiological assays showed that both pneumophages could not only replicate in S. mitis but also produced more visible plaques on this host. However, the burst size and phage adsorption data were lower in S. mitis as compared to S. pneumoniae. A comparison of the genomes of each phage grown on both hosts produced identical nucleotide sequences, confirming that the same phages infect both bacterial species. We also discovered that the genomic sequence of podophage Cp-1 of the Félix d'Hérelle collection is different than the previously reported sequence and thus renamed SOCP.
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Affiliation(s)
- Siham Ouennane
- Département de Biochimie, Microbiologie et Bio-Informatique, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
| | - Philippe Leprohon
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Sylvain Moineau
- Département de Biochimie, Microbiologie et Bio-Informatique, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
- * E-mail:
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Huff MD, Weisman D, Adams J, Li S, Green J, Malone LL, Clemmons S. The frequency of tetracycline resistance genes co-detected with respiratory pathogens: a database mining study uncovering descriptive trends throughout the United States. BMC Infect Dis 2014; 14:460. [PMID: 25152108 PMCID: PMC4156627 DOI: 10.1186/1471-2334-14-460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 08/18/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Center for Disease Control and Prevention (CDC) indicates that one of the largest problems threatening healthcare includes antibiotic resistance. Tetracycline, an effective antibiotic that has been in use for many years, is becoming less successful in treating certain pathogens. To better understand the temporal patterns in the growth of antibiotic resistance, patient diagnostic test records can be analyzed. METHODS Data mining methods including frequent item set mining and association rules via the Apriori algorithm were used to analyze results from 80,241 Target Enriched Multiplex-PCR (TEM-PCR) reference laboratory tests. From the data mining results, five common respiratory pathogens and their co-detection rates with tetracycline resistance genes (TRG) were further analyzed and organized according to year, patient age, and geography. RESULTS From 2010, all five pathogens were associated with at least a 24% rise in co-detection rate for TRGs. Patients from 0-2 years old exhibited the lowest rate of TRG co-detection, while patients between 13-50 years old displayed the highest frequency of TRG co-detection. The Northeastern region of the United States recorded the highest rate of patients co-detected with a TRG and a respiratory pathogen. Along the East-west gradient, the relative frequency of co-detection between TRGs and respiratory pathogens decreased dramatically. CONCLUSIONS Significant trends were uncovered regarding the co-detection frequencies of TRGs and respiratory pathogens over time. It is valuable for the field of public health to monitor trends regarding the spread of resistant infectious disease, especially since tetracycline continues to be utilized a treatment for various microbial infections. Analyzing large datasets containing TEM-PCR results for co-detections provides valuable insights into trends of antibiotic resistance gene expression so that the effectiveness of first-line treatments can be continuously monitored.
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Affiliation(s)
- Matthew D Huff
- />Diatherix Laboratories Inc., 601 Genome Way, Suite 2100, Huntsville, Al 35806 USA
| | - David Weisman
- />Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125-3393 USA
| | - John Adams
- />Knoxville Infectious Disease Consultants, P.C., 2210 Sutherland Ave., Suite 110, Knoxville, TN 37919 USA
| | - Song Li
- />Hudson Alpha Institute of Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA
| | - Jessica Green
- />Diatherix Laboratories Inc., 601 Genome Way, Suite 2100, Huntsville, Al 35806 USA
| | - Leslie L Malone
- />Diatherix Laboratories Inc., 601 Genome Way, Suite 2100, Huntsville, Al 35806 USA
| | - Scott Clemmons
- />Diatherix Laboratories Inc., 601 Genome Way, Suite 2100, Huntsville, Al 35806 USA
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Andersson DI, Hughes D. Microbiological effects of sublethal levels of antibiotics. Nat Rev Microbiol 2014; 12:465-78. [DOI: 10.1038/nrmicro3270] [Citation(s) in RCA: 986] [Impact Index Per Article: 98.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Gutierrez A, Laureti L, Crussard S, Abida H, Rodríguez-Rojas A, Blázquez J, Baharoglu Z, Mazel D, Darfeuille F, Vogel J, Matic I. β-Lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity. Nat Commun 2013; 4:1610. [PMID: 23511474 PMCID: PMC3615471 DOI: 10.1038/ncomms2607] [Citation(s) in RCA: 252] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 02/14/2013] [Indexed: 01/08/2023] Open
Abstract
Regardless of their targets and modes of action, subinhibitory concentrations of antibiotics can have an impact on cell physiology and trigger a large variety of cellular responses in different bacterial species. Subinhibitory concentrations of β-lactam antibiotics cause reactive oxygen species production and induce PolIV-dependent mutagenesis in Escherichia coli. Here we show that subinhibitory concentrations of β-lactam antibiotics induce the RpoS regulon. RpoS-regulon induction is required for PolIV-dependent mutagenesis because it diminishes the control of DNA-replication fidelity by depleting MutS in E. coli, Vibrio cholerae and Pseudomonas aeruginosa. We also show that in E. coli, the reduction in mismatch-repair activity is mediated by SdsR, the RpoS-controlled small RNA. In summary, we show that mutagenesis induced by subinhibitory concentrations of antibiotics is a genetically controlled process. Because this mutagenesis can generate mutations conferring antibiotic resistance, it should be taken into consideration for the development of more efficient antimicrobial therapeutic strategies. Sub-lethal concentrations of antibiotics are known to promote mutagenesis of bacterial DNA. Here the authors show that β-lactam antibiotics trigger mutagenesis by upregulating the stress-response protein RpoS, which downregulates mismatch-repair activity.
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Affiliation(s)
- A Gutierrez
- INSERM U1001, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine Paris Descartes, Paris, France
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Rao AA, Patkari M, Reddy PJ, Srivastava R, Pendharkar N, Rapole S, Mehra S, Srivastava S. Proteomic analysis of Streptomyces coelicolor in response to Ciprofloxacin challenge. J Proteomics 2013; 97:222-34. [PMID: 23994098 DOI: 10.1016/j.jprot.2013.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 07/17/2013] [Accepted: 08/10/2013] [Indexed: 11/19/2022]
Abstract
UNLABELLED Multi-drug tolerance is an important phenotypic property that complicates treatment of infectious diseases and reshapes drug discovery. Hence a systematic study of the origins and mechanisms of resistance shown by microorganisms is imperative. Since soil-dwelling bacteria are constantly challenged with a myriad of antibiotics, they are potential reservoirs of resistance determinants that can be mobilized into pathogens over a period of time. Elucidating the resistance mechanisms in such bacteria could help future antibiotic discoveries. This research is a preliminary study conducted to determine the effects of ciprofloxacin (CIP) on the intrinsically resistant Gram-positive soil bacterium Streptomyces coelicolor. The effect was investigated by performing 2-DE on total protein extracts of cells exposed to sub-lethal concentrations of ciprofloxacin as compared to the controls. Protein identification by MALDI-TOF/TOF revealed 24 unique differentially expressed proteins, which were statistically significant. The down-regulation of proteins involved in carbohydrate metabolism indicated a shift in the cell physiology towards a state of metabolic shutdown. Furthermore, the observed decline in protein levels involved in transcription and translation machinery, along with depletion of enzymes involved in amino acid biosynthesis and protein folding could be a cellular response to DNA damage caused by CIP, thereby minimizing the effect of defective and energetically wasteful metabolic processes. This could be crucial for the initial survival of the cells before gene level changes could come into play to ensure survival under prolonged adverse conditions. These results are a first attempt towards profiling the proteome of S. coelicolor in response to antibiotic stress. This article is part of a Special Issue entitled: Trends in Microbial Proteomics. BIOLOGICAL SIGNIFICANCE Soil-dwelling bacteria could serve as a reservoir of resistance determinants for clinically important bacteria. In this work, we investigated, for the first time, the differential proteomic profile of S. coelicolor cells in response to sub-inhibitory concentrations of Ciprofloxacin using 2-DE. Results indicate a shift in the cell physiology towards a state of metabolic shutdown, possibly to counter the DNA damage by ciprofloxacin. Further, up-regulation of GAPDH, RNA pol mRNA and Translation IF2 protein indicates a reprogramming of the cell for long-term survival. This study could serve as a basis for further investigations to elucidate the general mechanism by which soil bacteria exhibit resistance to fluroquinolones. This may help in developing new drug protocols and inventing novel drugs to counter resistance to this class of antibiotics in pathogenic bacteria.
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Affiliation(s)
- Aishwarya Anand Rao
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Minal Patkari
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Panga Jaipal Reddy
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rajneesh Srivastava
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Namita Pendharkar
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Sarika Mehra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Sanjeeva Srivastava
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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Del Fiol FDS, Lopes LC, Barberato-Filho S, Motta CDCB. Evaluation of the prescription and use of antibiotics in Brazilian children. Braz J Infect Dis 2013; 17:332-7. [PMID: 23607920 PMCID: PMC9427416 DOI: 10.1016/j.bjid.2012.10.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 10/17/2012] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION Inappropriate use of antibiotics leads to increased levels of bacterial resistance making it difficult to treat upper respiratory tract infections. The appropriate use of these drugs has a fundamental role in controlling resistance and in success of treatment of childhood infections. Therefore, the aim of this study was to assess the prescription and use of antibiotics for Brazilian children. METHODS The use of antibiotics in 160 children was monitored in two Primary Health Centers by questionnaires administered to parents and caregivers that assessed the social, demographic and clinical conditions of the children. Furthermore, the antibiotic use pattern was ascertained in these children and compared to the recommendations of the Brazilian and international guidelines. RESULTS The use of these drugs had an inverse relationship with children breast-fed to six months of age, showing that breast-fed children had a tendency to use less of these drugs. There was great variability in the amoxicillin doses used for upper respiratory infections ranging from 8.2 to 91.9mg/kg/day. The doses used in most treatments were far below the doses recommended in the Brazilian and international guidelines (50% and 97%, respectively). CONCLUSION Although there are guidelines for the use of these medications, compliance is still very low, leading to under dosage and therapeutic failures. It is essential for pediatricians to be aware of and comply with the guidelines, avoid personal decisions and take measures based on strong clinical evidence. The proper use of these medications, in addition to greater therapeutic success, decreases the possibility of the appearance of resistant microorganisms.
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Rodríguez-Rojas A, Rodríguez-Beltrán J, Couce A, Blázquez J. Antibiotics and antibiotic resistance: a bitter fight against evolution. Int J Med Microbiol 2013; 303:293-7. [PMID: 23517688 DOI: 10.1016/j.ijmm.2013.02.004] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
One of the most terrible consequences of Darwinian evolution is arguably the emergence and spread of antibiotic resistance, which is becoming a serious menace to modern societies. While spontaneous mutation, recombination and horizontal gene transfer are recognized as the main causes of this notorious phenomenon; recent research has raised awareness that sub-lethal concentrations of antibiotics can also foster resistance as an undesirable side-effect. They can produce genetic changes by different ways, including a raise of free radicals within the cell, induction of error-prone DNA-polymerases mediated by SOS response, imbalanced nucleotide metabolism or affect directly DNA. In addition to certain environmental conditions, subinhibitory concentrations of antimicrobials may increase, even more, the mutagenic effect of antibiotics. Here, we review the state of knowledge on antibiotics as promoters of antibiotic resistance.
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Affiliation(s)
- Alexandro Rodríguez-Rojas
- Centro Nacional de Biotecnología CNB, Consejo Superior de Investigaciones Científicas CSIC, Darwin 3, Campus de la Universidad Autónoma, Cantoblanco-Madrid 28049, Spain
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Bacterial Responses and Genome Instability Induced by Subinhibitory Concentrations of Antibiotics. Antibiotics (Basel) 2013; 2:100-14. [PMID: 27029295 PMCID: PMC4790301 DOI: 10.3390/antibiotics2010100] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 03/04/2013] [Accepted: 03/05/2013] [Indexed: 11/17/2022] Open
Abstract
Nowadays, the emergence and spread of antibiotic resistance have become an utmost medical and economical problem. It has also become evident that subinhibitory concentrations of antibiotics, which pollute all kind of terrestrial and aquatic environments, have a non-negligible effect on the evolution of antibiotic resistance in bacterial populations. Subinhibitory concentrations of antibiotics have a strong effect on mutation rates, horizontal gene transfer and biofilm formation, which may all contribute to the emergence and spread of antibiotic resistance. Therefore, the molecular mechanisms and the evolutionary pressures shaping the bacterial responses to subinhibitory concentrations of antibiotics merit to be extensively studied. Such knowledge is valuable for the development of strategies to increase the efficacy of antibiotic treatments and to extend the lifetime of antibiotics used in therapy by slowing down the emergence of antibiotic resistance.
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Sengupta S, Chattopadhyay MK, Grossart HP. The multifaceted roles of antibiotics and antibiotic resistance in nature. Front Microbiol 2013; 4:47. [PMID: 23487476 PMCID: PMC3594987 DOI: 10.3389/fmicb.2013.00047] [Citation(s) in RCA: 293] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 02/20/2013] [Indexed: 12/14/2022] Open
Abstract
Antibiotics are chemotherapeutic agents, which have been a very powerful tool in the clinical management of bacterial diseases since the 1940s. However, benefits offered by these magic bullets have been substantially lost in subsequent days following the widespread emergence and dissemination of antibiotic-resistant strains. While it is obvious that excessive and imprudent use of antibiotics significantly contributes to the emergence of resistant strains, antibiotic resistance is also observed in natural bacteria of remote places unlikely to be impacted by human intervention. Both antibiotic biosynthetic genes and resistance-conferring genes have been known to evolve billions of years ago, long before clinical use of antibiotics. Hence it appears that antibiotics and antibiotics resistance determinants have some other roles in nature, which often elude our attention because of overemphasis on the therapeutic importance of antibiotics and the crisis imposed by the antibiotic resistance in pathogens. In the natural milieu, antibiotics are often found to be present in sub-inhibitory concentrations acting as signaling molecules supporting the process of quorum sensing and biofilm formation. They also play an important role in the production of virulence factors and influence host-parasite interactions (e.g., phagocytosis, adherence to the target cell, and so on). The evolutionary and ecological aspects of antibiotics and antibiotic resistance in the naturally occurring microbial community are little understood. Therefore, the actual role of antibiotics in nature warrants in-depth investigations. Studies on such an intriguing behavior of the microorganisms promise insight into the intricacies of the microbial physiology and are likely to provide some lead in controlling the emergence and subsequent dissemination of antibiotic resistance. This article highlights some of the recent findings on the role of antibiotics and the genes that confer resistance to antibiotics in nature.
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Baquero F, Tedim AP, Coque TM. Antibiotic resistance shaping multi-level population biology of bacteria. Front Microbiol 2013; 4:15. [PMID: 23508522 PMCID: PMC3589745 DOI: 10.3389/fmicb.2013.00015] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 01/22/2013] [Indexed: 12/21/2022] Open
Abstract
Antibiotics have natural functions, mostly involving cell-to-cell signaling networks. The anthropogenic production of antibiotics, and its release in the microbiosphere results in a disturbance of these networks, antibiotic resistance tending to preserve its integrity. The cost of such adaptation is the emergence and dissemination of antibiotic resistance genes, and of all genetic and cellular vehicles in which these genes are located. Selection of the combinations of the different evolutionary units (genes, integrons, transposons, plasmids, cells, communities and microbiomes, hosts) is highly asymmetrical. Each unit of selection is a self-interested entity, exploiting the higher hierarchical unit for its own benefit, but in doing so the higher hierarchical unit might acquire critical traits for its spread because of the exploitation of the lower hierarchical unit. This interactive trade-off shapes the population biology of antibiotic resistance, a composed-complex array of the independent "population biologies." Antibiotics modify the abundance and the interactive field of each of these units. Antibiotics increase the number and evolvability of "clinical" antibiotic resistance genes, but probably also many other genes with different primary functions but with a resistance phenotype present in the environmental resistome. Antibiotics influence the abundance, modularity, and spread of integrons, transposons, and plasmids, mostly acting on structures present before the antibiotic era. Antibiotics enrich particular bacterial lineages and clones and contribute to local clonalization processes. Antibiotics amplify particular genetic exchange communities sharing antibiotic resistance genes and platforms within microbiomes. In particular human or animal hosts, the microbiomic composition might facilitate the interactions between evolutionary units involved in antibiotic resistance. The understanding of antibiotic resistance implies expanding our knowledge on multi-level population biology of bacteria.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain
- Centros de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Ana P. Tedim
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain
- Centros de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
| | - Teresa M. Coque
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain
- Centros de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones CientíficasMadrid, Spain
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