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Hillyer T, Benin BM, Sun C, Aguirre N, Willard B, Sham YY, Shin WS. A novel strategy to characterize the pattern of β-lactam antibiotic-induced drug resistance in Acinetobacter baumannii. Sci Rep 2023; 13:9177. [PMID: 37280269 DOI: 10.1038/s41598-023-36475-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/04/2023] [Indexed: 06/08/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAb) is an urgent public health threat, according to the CDC. This pathogen has few treatment options and causes severe nosocomial infections with > 50% fatality rate. Although previous studies have examined the proteome of CRAb, there have been no focused analyses of dynamic changes to β-lactamase expression that may occur due to drug exposure. Here, we present our initial proteomic study of variation in β-lactamase expression that occurs in CRAb with different β-lactam antibiotics. Briefly, drug resistance to Ab (ATCC 19606) was induced by the administration of various classes of β-lactam antibiotics, and the cell-free supernatant was isolated, concentrated, separated by SDS-PAGE, digested with trypsin, and identified by label-free LC-MS-based quantitative proteomics. Thirteen proteins were identified and evaluated using a 1789 sequence database of Ab β-lactamases from UniProt, the majority of which were Class C β-lactamases (≥ 80%). Importantly, different antibiotics, even those of the same class (e.g. penicillin and amoxicillin), induced non-equivalent responses comprising various isoforms of Class C and D serine-β-lactamases, resulting in unique resistomes. These results open the door to a new approach of analyzing and studying the problem of multi-drug resistance in bacteria that rely strongly on β-lactamase expression.
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Affiliation(s)
- Trae Hillyer
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Bogdan M Benin
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Chuanqi Sun
- Department of Neurology, University of California, Los Angeles, CA, USA
| | - Noah Aguirre
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Belinda Willard
- Proteomics and Metabolomics Core, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yuk Yin Sham
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Woo Shik Shin
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, USA.
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2
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Hillyer T, Benin BM, Sun C, Aguirre N, Willard B, Sham YY, Shin WS. A novel strategy to characterize the pattern of β-lactam antibiotic-induced drug resistance in Acinetobacter baumannii. RESEARCH SQUARE 2023. [PMID: 36711967 PMCID: PMC9882603 DOI: 10.21203/rs.3.rs-2359505/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAb) is an urgent public health threat, according to the CDC. This pathogen has few treatment options and causes severe nosocomial infections with > 50% fatality rate. Although previous studies have examined the proteome of CRAb, there have been no focused analyses of dynamic changes to β-lactamase expression that may occur due to drug exposure. Here, we present our initial proteomic study of variation in β-lactamase expression that occurs in CRAb with different β-lactam antibiotics. Briefly, drug resistance to Ab (ATCC 19606) was induced by the administration of various classes of β-lactam antibiotics, and the cell-free supernatant was isolated, concentrated, separated by SDS-PAGE, digested with trypsin, and identified by label-free LC-MS-based quantitative proteomics. Peptides were identified and evaluated using a 1789 sequence database of Ab β-lactamases from UniProt. Importantly, we observed that different antibiotics, even those of the same class ( e.g. penicillin and amoxicillin), induce non-equivalent responses comprising various Class C and D serine-β-lactamases, resulting in unique resistomes. These results open the door to a new approach of analyzing and studying the problem of multi-drug resistance in bacteria that rely strongly on β-lactamase expression.
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3
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Ribeiro M, Sousa M, Borges V, Gomes JP, Duarte S, Isidro J, Vieira L, Torres C, Santos H, Capelo JL, Poeta P, Igrejas G. Bioinformatics study of expression from genomes of epidemiologically related MRSA CC398 isolates from human and wild animal samples. J Proteomics 2022; 268:104714. [PMID: 36058542 DOI: 10.1016/j.jprot.2022.104714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/28/2022] [Indexed: 10/14/2022]
Abstract
One of the most important livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) genetic lineages is the clonal complex (CC) 398, which can cause typical S. aureus-associated infections in people. In this work, whole-genome sequencing, RNA-sequencing, and gel-based comparative proteomics were applied to study the genetic characteristics of three MRSA CC398 isolates recovered from humans (strains C5621 and C9017), and from an animal (strain OR418). Of the three strains, C9017 presented the broadest resistance genotype, including resistance to fluroquinolone, clindamycin, tiamulin, macrolide and aminoglycoside antimicrobial classes. The scn, sak, and chp genes of the immune evasion cluster system were solely detected in OR418. Pangenome analysis showed a total of 288 strain-specific genes, most of which are hypothetical or phage-related proteins. OR418 had the most pronounced genetic differences. RNAIII (δ-hemolysin) gene was clearly the most expressed gene in OR418 and C5621, but it was not detected in C9017. Significant differences in the proteome profiles were found between strains. For example, the immunoglobulin-binding protein Sbi was more abundant in OR418. Considering that Sbi is a multifunctional immune evasion factor in S. aureus, the results point to OR418 strain having high zoonotic potential. Overall, multiomics biomarker signatures can assume an important role to advance precision medicine in the years to come. SIGNIFICANCE: MRSA is one of the most representative drug-resistant pathogens and its dissemination is increasing due to MRSA capability of establishing new reservoirs. LA-MRSA is considered an emerging problem worldwide and CC398 is one of the most important genetic lineages. In this study, three MRSA CC398 isolates recovered from humans and from a wild animal were analyzed through whole-genome sequencing, RNA-sequencing, and gel-based comparative proteomics in order to gather systems-wide omics data and better understand the genetic characteristics of this lineage to identify distinctive markers and genomic features of relevance to public health. The scn, sak, and chp genes of the immune evasion cluster system were solely detected in OR418. Pangenome analysis showed a total of 288 strain-specific genes, most of which are hypothetical or phage-related proteins. OR418 had the most pronounced genetic differences. RNAIII (δ-hemolysin) gene was clearly the most expressed gene in OR418 and C5621, but it was not detected in C9017. Significant differences in the proteome profiles were found between strains.
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Affiliation(s)
- Miguel Ribeiro
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal
| | - Margarida Sousa
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - Sílvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisbon, Portugal; Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Carmen Torres
- Biochemistry and Molecular Biology Unit, Faculty of Science and Technology, University of La Rioja, 26006 Logroño, Spain
| | - Hugo Santos
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal; Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - José Luís Capelo
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Patrícia Poeta
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal; Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real 5000-801, Portugal; CECAV-Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal.
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Lopatkin AJ, Bening SC, Manson AL, Stokes JM, Kohanski MA, Badran AH, Earl AM, Cheney NJ, Yang JH, Collins JJ. Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Science 2021; 371:371/6531/eaba0862. [PMID: 33602825 DOI: 10.1126/science.aba0862] [Citation(s) in RCA: 157] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 09/16/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022]
Abstract
Although metabolism plays an active role in antibiotic lethality, antibiotic resistance is generally associated with drug target modification, enzymatic inactivation, and/or transport rather than metabolic processes. Evolution experiments of Escherichia coli rely on growth-dependent selection, which may provide a limited view of the antibiotic resistance landscape. We sequenced and analyzed E. coli adapted to representative antibiotics at increasingly heightened metabolic states. This revealed various underappreciated noncanonical genes, such as those related to central carbon and energy metabolism, which are implicated in antibiotic resistance. These metabolic alterations lead to lower basal respiration, which prevents antibiotic-mediated induction of tricarboxylic acid cycle activity, thus avoiding metabolic toxicity and minimizing drug lethality. Several of the identified metabolism-specific mutations are overrepresented in the genomes of >3500 clinical E. coli pathogens, indicating clinical relevance.
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Affiliation(s)
- Allison J Lopatkin
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering; Harvard University, Boston, MA, USA.,Department of Biology, Barnard College, New York, NY, USA.,Data Science Institute, Columbia University, New York, NY, USA.,Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
| | - Sarah C Bening
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan M Stokes
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering; Harvard University, Boston, MA, USA
| | - Michael A Kohanski
- Department of Otorhinolaryngology-Head and Neck Surgery, Division of Rhinology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ahmed H Badran
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicole J Cheney
- Ruy V. Lourenço Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA.,Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Jason H Yang
- Ruy V. Lourenço Center for Emerging and Re-Emerging Pathogens, Rutgers New Jersey Medical School, Newark, NJ, USA.,Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - James J Collins
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA. .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering; Harvard University, Boston, MA, USA.,Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.,Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA
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Zhang D, Hu Y, Zhu Q, Huang J, Chen Y. Proteomic interrogation of antibiotic resistance and persistence in Escherichia coli - progress and potential for medical research. Expert Rev Proteomics 2020; 17:393-409. [PMID: 32567419 DOI: 10.1080/14789450.2020.1784731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction Escherichia coli strains possess two survival strategies to endure lethal antibiotic exposure including antibiotic resistance and persistence, in which persistence can contribute to the emergence of antibiotic resistance and increasing the risk of multidrug resistance. Using high-throughput proteomics for the comprehensive understanding of mechanisms of antibiotic resistance and persistence is an effective strategy for development of target-based anti-bacterial therapies. Areas covered In this review, we summarize a comprehensive proteomic perspective of antibiotic resistance and persistence in E. coli, and overview of anti-antibiotic resistance and anti-persister molecules and strategies for the development of potential therapies. Expert opinion Proteomics allows us to globally identify the critical proteins and pathways involved in antibiotic resistance and persistence. Advancements in methodologies of proteomics and multi-omic strategies are required to overcome the limitations of proteomics and better understand mechanisms of antibiotic resistance and persistence in E. coli, and to open the possibility for identification of new targets for alternative strategies in therapeutics.
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Affiliation(s)
- Danfeng Zhang
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
| | - Yuanqing Hu
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
| | - Qiuqiang Zhu
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
| | - Jiafu Huang
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China.,Engineering Technological Center of Mushroom Industry , Zhangzhou, China
| | - Yiyun Chen
- School of Biological Science and Biotechnology, Minnan Normal University , Zhangzhou, China
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Peng B, Li H, Peng X. Proteomics approach to understand bacterial antibiotic resistance strategies. Expert Rev Proteomics 2019; 16:829-839. [PMID: 31618606 DOI: 10.1080/14789450.2019.1681978] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Introduction: The understanding of novel antibiotic resistance mechanisms is essential to develop strategies against antibiotic-resistant pathogens, which has become an urgent task due to the worldwide emergence of antibiotic resistance. Areas covered: In this review, the authors summarize the recent progress on antibiotic resistance caused by lab-evolved bacteria and clinical multidrug-resistant bacterial pathogens from the proteomics perspective. Expert opinion: Proteomics provides a new platform for a comprehensive understanding of change in protein pathways that are engaged in antibiotics resistance, which is different from a genetic view that focuses on the role of an individual gene or protein. Further work is required to understand why and how the involved pathways are integrated for surviving antibiotic-mediated killing, to use other OMICs for better comprehension of antibiotic resistance mechanisms, and to develop reprogramming proteomics, which reverts an 'antibiotic resistance proteome' to an 'antibiotic sensitive or antibiotic sensitive-like' proteome, for the control of antibiotic-resistant pathogens.
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Affiliation(s)
- Bo Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, School of Life Sciences, Sun Yat-sen University , Guangzhou , People's Republic of China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology , Qingdao , People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Zhuhai , People's Republic of China
| | - Hui Li
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, School of Life Sciences, Sun Yat-sen University , Guangzhou , People's Republic of China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology , Qingdao , People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Zhuhai , People's Republic of China
| | - Xuanxian Peng
- Center for Proteomics and Metabolomics, State Key Laboratory of Bio-Control, School of Life Sciences, Sun Yat-sen University , Guangzhou , People's Republic of China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology , Qingdao , People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Zhuhai , People's Republic of China
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