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Mojica MF, Rutter JD, Taracila M, Abriata LA, Fouts DE, Papp-Wallace KM, Walsh TJ, LiPuma JJ, Vila AJ, Bonomo RA. Population Structure, Molecular Epidemiology, and β-Lactamase Diversity among Stenotrophomonas maltophilia Isolates in the United States. mBio 2019; 10:e00405-19. [PMID: 31266860 PMCID: PMC6606795 DOI: 10.1128/mbio.00405-19] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/03/2019] [Indexed: 01/06/2023] Open
Abstract
Stenotrophomonas maltophilia is a Gram-negative, nonfermenting, environmental bacillus that is an important cause of nosocomial infections, primarily associated with the respiratory tract in the immunocompromised population. Aiming to understand the population structure, microbiological characteristics and impact of allelic variation on β-lactamase structure and function, we collected 130 clinical isolates from across the United States. Identification of 90 different sequence types (STs), of which 63 are new allelic combinations, demonstrates the high diversity of this species. The majority of the isolates (45%) belong to genomic group 6. We also report excellent activity of the ceftazidime-avibactam and aztreonam combination, especially against strains recovered from blood and respiratory infections for which the susceptibility is higher than the susceptibility to trimethoprim-sulfamethoxazole, considered the "first-line" antibiotic to treat S. maltophilia Analysis of 73 blaL1 and 116 blaL2 genes identified 35 and 43 novel variants of L1 and L2 β-lactamases, respectively. Investigation of the derived amino acid sequences showed that substitutions are mostly conservative and scattered throughout the protein, preferentially affecting positions that do not compromise enzyme function but that may have an impact on substrate and inhibitor binding. Interestingly, we detected a probable association between a specific type of L1 and L2 and genomic group 6. Taken together, our results provide an overview of the molecular epidemiology of S. maltophilia clinical strains from the United States. In particular, the discovery of new L1 and L2 variants warrants further study to fully understand the relationship between them and the β-lactam resistance phenotype in this pathogen.IMPORTANCE Multiple antibiotic resistance mechanisms, including two β-lactamases, L1, a metallo-β-lactamase, and L2, a class A cephalosporinase, make S. maltophilia naturally multidrug resistant. Thus, infections caused by S. maltophilia pose a big therapeutic challenge. Our study aims to understand the microbiological and molecular characteristics of S. maltophilia isolates recovered from human sources. A highlight of the resistance profile of this collection is the excellent activity of the ceftazidime-avibactam and aztreonam combination. We hope this result prompts controlled and observational studies to add clinical data on the utility and safety of this therapy. We also identify 35 and 43 novel variants of L1 and L2, respectively, some of which harbor novel substitutions that could potentially affect substrate and/or inhibitor binding. We believe our results provide valuable knowledge to understand the epidemiology of this species and to advance mechanism-based inhibitor design to add to the limited arsenal of antibiotics active against this pathogen.
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Affiliation(s)
- Maria F Mojica
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Joseph D Rutter
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Magdalena Taracila
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Krisztina M Papp-Wallace
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, Louis Stokes Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Thomas J Walsh
- Transplantation Oncology Infectious Diseases Program, Weill Cornell Medical Center, New York, New York, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Medical Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA
- GRECC, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
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Wrenbeck EE, Faber MS, Whitehead TA. Deep sequencing methods for protein engineering and design. Curr Opin Struct Biol 2017; 45:36-44. [PMID: 27886568 PMCID: PMC5440218 DOI: 10.1016/j.sbi.2016.11.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/01/2016] [Indexed: 11/27/2022]
Abstract
The advent of next-generation sequencing (NGS) has revolutionized protein science, and the development of complementary methods enabling NGS-driven protein engineering have followed. In general, these experiments address the functional consequences of thousands of protein variants in a massively parallel manner using genotype-phenotype linked high-throughput functional screens followed by DNA counting via deep sequencing. We highlight the use of information rich datasets to engineer protein molecular recognition. Examples include the creation of multiple dual-affinity Fabs targeting structurally dissimilar epitopes and engineering of a broad germline-targeted anti-HIV-1 immunogen. Additionally, we highlight the generation of enzyme fitness landscapes for conducting fundamental studies of protein behavior and evolution. We conclude with discussion of technological advances.
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Affiliation(s)
- Emily E Wrenbeck
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, United States
| | - Matthew S Faber
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
| | - Timothy A Whitehead
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, United States; Departments of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, United States.
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