1
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Gardner TM, Grosser MR. A MRSA mystery: how PBP4 and cyclic-di-AMP join forces against β-lactam antibiotics. mBio 2024; 15:e0121024. [PMID: 39028200 DOI: 10.1128/mbio.01210-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024] Open
Abstract
The high-level resistance to next-generation β-lactams frequently found in Staphylococcus aureus isolates lacking mec, which encodes the transpeptidase PBP2a traditionally associated with methicillin-resistant Staphylococcus aureus (MRSA), has remained incompletely understood for decades. A new study by Lai et al. found that the co-occurrence of mutations in pbp4 and gdpP, which respectively cause increased PBP4-mediated cell wall crosslinking and elevated cyclic-di-AMP levels, produces synergistic β-lactam resistance rivaling that of PBP2a-producing MRSA (L.-Y. Lai, N. Satishkumar, S. Cardozo, V. Hemmadi, et al., mBio 15:e02889-23. 2024, https://doi.org/10.1128/mbio.02889-23). The combined mutations are sufficient to explain the high-level β-lactam resistance of some mec-lacking strains, but the mechanism of synergy remains elusive and an avenue for further research. Importantly, the authors establish that co-occurrence of these mutations leads to antibiotic therapy failure in a Caenorhabditis elegans infection model. These results underscore the need to consider this unique and novel β-lactam resistance mechanism during the clinical diagnosis of MRSA, rather than relying on mec as a diagnostic.
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Affiliation(s)
- Taylor M Gardner
- Department of Biology, University of North Carolina Asheville, Asheville, North Carolina, USA
| | - Melinda R Grosser
- Department of Biology, University of North Carolina Asheville, Asheville, North Carolina, USA
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2
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Gondil VS, Butman HS, Young M, Walsh DJ, Narkhede Y, Zeiler MJ, Crow AH, Carpenter ME, Mardikar A, Melander RJ, Wiest O, Dunman PM, Melander C. Development of phenyl-urea-based small molecules that target penicillin-binding protein 4. Chem Biol Drug Des 2024; 103:e14569. [PMID: 38877369 PMCID: PMC11185276 DOI: 10.1111/cbdd.14569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/08/2024] [Accepted: 05/22/2024] [Indexed: 06/16/2024]
Abstract
Staphylococcus aureus has the ability to invade cortical bone osteocyte lacuno-canalicular networks (OLCNs) and cause osteomyelitis. It was recently established that the cell wall transpeptidase, penicillin-binding protein 4 (PBP4), is crucial for this function, with pbp4 deletion strains unable to invade OLCNs and cause bone pathogenesis in a murine model of S. aureus osteomyelitis. Moreover, PBP4 has recently been found to modulate S. aureus resistance to β-lactam antibiotics. As such, small molecule inhibitors of S. aureus PBP4 may represent dual functional antimicrobial agents that limit osteomyelitis and/or reverse antibiotic resistance. A high throughput screen recently revealed that the phenyl-urea 1 targets PBP4. Herein, we describe a structure-activity relationship (SAR) study on 1. Leveraging in silico docking and modeling, a set of analogs was synthesized and assessed for PBP4 inhibitory activities. Results revealed a preliminary SAR and identified lead compounds with enhanced binding to PBP4, more potent antibiotic resistance reversal, and diminished PBP4 cell wall transpeptidase activity in comparison to 1.
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Affiliation(s)
- Vijay S. Gondil
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Hailey S. Butman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, United States
| | - Mikaeel Young
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Danica J. Walsh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, United States
| | - Yogesh Narkhede
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, United States
| | - Michael J. Zeiler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, United States
| | - Andrew H. Crow
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, United States
| | - Morgan E. Carpenter
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, United States
| | - Aashay Mardikar
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Roberta J. Melander
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, United States
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, United States
| | - Paul M. Dunman
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Christian Melander
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, United States
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3
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Lai LY, Satishkumar N, Cardozo S, Hemmadi V, Marques LB, Huang L, Filipe SR, Pinho MG, Chambers HF, Chatterjee SS. Altered PBP4 and GdpP functions synergistically mediate MRSA-like high-level, broad-spectrum β-lactam resistance in Staphylococcus aureus. mBio 2024; 15:e0288923. [PMID: 38530033 PMCID: PMC11077961 DOI: 10.1128/mbio.02889-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/04/2024] [Indexed: 03/27/2024] Open
Abstract
Infections caused by Staphylococcus aureus are a leading cause of mortality worldwide. S. aureus infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are particularly difficult to treat due to their resistance to next-generation β-lactams (NGBs) such as methicillin, nafcillin, and oxacillin. Resistance to NGBs, which is alternatively known as broad-spectrum β-lactam resistance, is classically mediated by PBP2a, a penicillin-binding protein encoded by mecA (or mecC) in MRSA. Thus, presence of mec genes among S. aureus spp. serves as the predictor of resistance to NGBs and facilitates determination of the proper therapeutic strategy for a staphylococcal infection. Although far less appreciated, mecA-deficient S. aureus strains can also exhibit NGB resistance. These strains, which are collectively termed as methicillin-resistant lacking mec (MRLM), are currently being identified in increasing numbers among natural resistant isolates of S. aureus. The mechanism/s through which MRLMs produce resistance to NGBs remains unknown. In this study, we demonstrate that mutations that alter PBP4 and GdpP functions, which are often present among MRLMs, can synergistically mediate resistance to NGBs. Furthermore, our results unravel that this novel mechanism potentially enables MRLMs to produce resistance toward NGBs at levels comparable to those of MRSAs. Our study provides a fresh new perspective about alternative mechanisms of NGB resistance, challenging our current overall understanding of high-level, broad-spectrum β-lactam resistance in S. aureus. It thus suggests reconsideration of the current approach toward diagnosis and treatment of β-lactam-resistant S. aureus infections. IMPORTANCE In Staphylococcus aureus, high-level, broad-spectrum resistance to β-lactams such as methicillin, also referred to as methicillin resistance, is largely attributed to mecA. This study demonstrates that S. aureus strains that lack mecA but contain mutations that functionally alter PBP4 and GdpP can also mediate high-level, broad-spectrum resistance to β-lactams. Resistance brought about by the synergistic action of functionally altered PBP4 and GdpP was phenotypically comparable to that displayed by mecA, as seen by increased bacterial survival in the presence of β-lactams. An analysis of mutations detected in naturally isolated strains of S. aureus revealed that a significant proportion of them had similar pbp4 and GGDEF domain protein containing phosphodiesterase (gdpP) mutations, making this study clinically significant. This study not only identifies important players of non-classical mechanisms of β-lactam resistance but also indicates reconsideration of current clinical diagnosis and treatment protocols of S. aureus infections.
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Affiliation(s)
- Li-Yin Lai
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, Baltimore, Maryland, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA
| | - Nidhi Satishkumar
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, Baltimore, Maryland, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA
| | - Sasha Cardozo
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, Baltimore, Maryland, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA
| | - Vijay Hemmadi
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, Baltimore, Maryland, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA
| | - Leonor B. Marques
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Liusheng Huang
- Department of Clinical Pharmacy, Drug Research Unit, University of California, San Francisco, California, USA
| | - Sergio R. Filipe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Mariana G. Pinho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Henry F. Chambers
- Division of Infectious Diseases, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Som S. Chatterjee
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, Baltimore, Maryland, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA
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4
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Lai LY, Satishkumar N, Cardozo S, Hemmadi V, Marques LB, Huang L, Filipe SR, Pinho MG, Chambers HF, Chatterjee SS. Altered PBP4 and GdpP functions synergistically mediate MRSA-like high-level, broad-spectrum β-lactam resistance in Staphylococcus aureus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564222. [PMID: 37961375 PMCID: PMC10634853 DOI: 10.1101/2023.10.26.564222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Infections caused by Staphylococcus aureus are a leading cause of mortality worldwide. S. aureus infections caused by Methicillin-Resistant Staphylococcus aureus (MRSA) are particularly difficult to treat due to their resistance to Next Generation β-lactams (NGB) such as Methicillin, Nafcillin, Oxacillin etc. Resistance to NGBs, which is alternatively known as broad-spectrum β-lactam resistance is classically mediated by PBP2a, a Penicillin-Binding Protein encoded by mecA (or mecC) in MRSA. Thus, presence of mec genes among S. aureus serves as the predictor of resistance to NGBs and facilitates determination of the proper therapeutic strategy for a staphylococcal infection. Although far less appreciated, mecA deficient S. aureus strains can also exhibit NGB resistance. These strains, which are collectively termed as Methicillin-Resistant Lacking mec (MRLM) are currently being identified in increasing numbers among natural resistant isolates of S. aureus. The mechanism/s through which MRLMs produce resistance to NGBs remains unknown. In this study, we demonstrate that mutations that alter PBP4 and GdpP functions, which are often present among MRLMs can synergistically mediate resistance to NGBs. Furthermore, our results unravel that this novel mechanism potentially enables MRLMs to produce resistance towards NGBs at levels comparable to that of MRSAs. Our study, provides a fresh new perspective about alternative mechanisms of NGBs resistance, challenging our current overall understanding of high-level, broad-spectrum β-lactam resistance in S. aureus. It thus suggests reconsideration of the current approach towards diagnosis and treatment of β-lactam resistant S. aureus infections.
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Affiliation(s)
- Li-Yin Lai
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, USA
| | - Nidhi Satishkumar
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, USA
| | - Sasha Cardozo
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, USA
| | - Vijay Hemmadi
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, USA
| | - Leonor B. Marques
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Liusheng Huang
- Drug Research Unit, Department of Clinical Pharmacy, University of California, San Francisco, San Francisco, CA, USA
| | - Sergio R. Filipe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Mariana G. Pinho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Henry F. Chambers
- Division of Infectious Diseases, School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Som S. Chatterjee
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, USA
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5
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Satishkumar N, Lai LY, Mukkayyan N, Vogel BE, Chatterjee SS. A Nonclassical Mechanism of β-Lactam Resistance in Methicillin-Resistant Staphylococcus aureus and Its Effect on Virulence. Microbiol Spectr 2022; 10:e0228422. [PMID: 36314912 PMCID: PMC9769611 DOI: 10.1128/spectrum.02284-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a group of pathogenic bacteria that are infamously resistant to β-lactam antibiotics, a property attributed to the mecA gene. Recent studies have reported that mutations associated with the promoter region of pbp4 demonstrated high levels of β-lactam resistance, suggesting the role of PBP4 as an important non-mecA mediator of β-lactam resistance. The pbp4-promoter-associated mutations have been detected in strains with or without mecA. Our previous studies that were carried out in strains devoid of mecA described that pbp4-promoter-associated mutations lead to PBP4 overexpression and β-lactam resistance. In this study, by introducing various pbp4-promoter-associated mutations in the genome of a MRSA strain, we demonstrate that PBP4 overexpression can supplement mecA-associated resistance in S. aureus and can lead to increased β-lactam resistance. The promoter and regulatory region of pbp4 is shared with a divergently transcribed gene, abcA, which encodes a multidrug exporter. We demonstrate that the promoter mutations caused an upregulation of pbp4 and downregulation of abcA, confirming that the resistant phenotype is associated with PBP4 overexpression. PBP4 has also been associated with staphylococcal pathogenesis, however, its exact role remains unclear. Using a Caenorhabditis elegans model, we demonstrate that strains having increased PBP4 expression are less virulent than wild-type strains, suggesting that β-lactam resistance mediated via PBP4 likely comes at the cost of virulence. IMPORTANCE Our study demonstrates the ability of PBP4 to be an important mediator of β-lactam resistance in not only methicillin-susceptible Staphylococcus aureus (MSSA) background strains as previously demonstrated but also in MRSA strains. When present together, PBP2a and PBP4 overexpression can produce increased levels of β-lactam resistance, causing complications in treatment. Thus, this study suggests the importance of monitoring PBP4-associated resistance in clinical settings, as well as understanding the mechanistic basis of associated resistance, so that treatments targeting PBP4 may be developed. This study also demonstrates that S. aureus strains with increased PBP4 expression are less pathogenic, providing important hints about the role of PBP4 in S. aureus resistance and pathogenesis.
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Affiliation(s)
- Nidhi Satishkumar
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA
| | - Li-Yin Lai
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA
| | - Nagaraja Mukkayyan
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA
| | - Bruce E. Vogel
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Som S. Chatterjee
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA
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6
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Ivanovic I, Boss R, Romanò A, Guédon E, Le-Loir Y, Luini M, Graber H. Penicillin resistance in bovine Staphylococcus aureus: Genomic evaluation of the discrepancy between phenotypic and molecular test methods. J Dairy Sci 2022; 106:462-475. [DOI: 10.3168/jds.2022-22158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022]
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7
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Giulieri SG, Guérillot R, Duchene S, Hachani A, Daniel D, Seemann T, Davis JS, Tong SYC, Young BC, Wilson DJ, Stinear TP, Howden BP. Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections. eLife 2022; 11:77195. [PMID: 35699423 PMCID: PMC9270034 DOI: 10.7554/elife.77195] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
During severe infections, Staphylococcus aureus moves from its colonising sites to blood and tissues and is exposed to new selective pressures, thus, potentially driving adaptive evolution. Previous studies have shown the key role of the agr locus in S. aureus pathoadaptation; however, a more comprehensive characterisation of genetic signatures of bacterial adaptation may enable prediction of clinical outcomes and reveal new targets for treatment and prevention of these infections. Here, we measured adaptation using within-host evolution analysis of 2590 S. aureus genomes from 396 independent episodes of infection. By capturing a comprehensive repertoire of single nucleotide and structural genome variations, we found evidence of a distinctive evolutionary pattern within the infecting populations compared to colonising bacteria. These invasive strains had up to 20-fold enrichments for genome degradation signatures and displayed significantly convergent mutations in a distinctive set of genes, linked to antibiotic response and pathogenesis. In addition to agr-mediated adaptation, we identified non-canonical, genome-wide significant loci including sucA-sucB and stp1. The prevalence of adaptive changes increased with infection extent, emphasising the clinical significance of these signatures. These findings provide a high-resolution picture of the molecular changes when S. aureus transitions from colonisation to severe infection and may inform correlation of infection outcomes with adaptation signatures. The bacterium Staphylococcus aureus lives harmlessly on our skin and noses. However, occasionally, it gets into our blood and internal organs, such as our bones and joints, where it causes severe, long-lasting infections that are difficult to treat. Over time, S. aureus acquire characteristics that help them to adapt to different locations, such as transitioning from the nose to the blood, and avoid being killed by antibiotics. Previous studies have identified changes, or ‘mutations’, in genes that are likely to play an important role in this evolutionary process. One of these genes, called accessory gene regulator (or agr for short), has been shown to control the mechanisms S. aureus use to infect cells and disseminate in the body. However, it is unclear if there are changes in other genes that also help S. aureus adapt to life inside the human body. To help resolve this mystery, Giulieri et al. collected 2,500 samples of S. aureus from almost 400 people. This included bacteria harmlessly living on the skin or in the nose, as well as strains that caused an infection. Gene sequencing revealed a small number of genes, referred to as ‘adaptive genes’, that often acquire mutations during infection. Of these, agr was the most commonly altered. However, mutations in less well-known genes were also identified: some of these genes are related to resistance to antibiotics, while others are involved in chemical processes that help the bacteria to process nutrients. Most mutations were caused by random errors being introduced in to the bacteria’s genetic code which stopped genes from working. However, in some cases, genes were turned off by small fragments of DNA moving around and inserting themselves into different parts of the genome. This study highlights a group of genes that help S. aureus to thrive inside the body and cause severe and prolonged infections. If these results can be confirmed, it may help to guide which antibiotics are used to treat different infections. Furthermore, understanding which genes are important for infection could lead to new strategies for eliminating this dangerous bacterium.
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Affiliation(s)
- Stefano G Giulieri
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia
| | - Romain Guérillot
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Diane Daniel
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit, University of Melbourne, Melbourne, Australia
| | - Joshua S Davis
- Department of Infectious Diseases, John Hunter Hospital, Newcastle, Australia
| | - Steven Y C Tong
- Victorian Infectious Diseases Service, University of Melbourne, Melbourne, Australia
| | | | | | - Timothy P Stinear
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
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8
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Ftsh Sensitizes Methicillin-Resistant Staphylococcus aureus to β-Lactam Antibiotics by Degrading YpfP, a Lipoteichoic Acid Synthesis Enzyme. Antibiotics (Basel) 2021; 10:antibiotics10101198. [PMID: 34680778 PMCID: PMC8532640 DOI: 10.3390/antibiotics10101198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/17/2021] [Accepted: 09/27/2021] [Indexed: 12/20/2022] Open
Abstract
In the Gram-positive pathogen Staphylococcus aureus, FtsH, a membrane-bound metalloprotease, plays a critical role in bacterial virulence and stress resistance. This protease is also known to sensitize methicillin-resistant Staphylococcus aureus (MRSA) to β-lactam antibiotics; however, the molecular mechanism is not known. Here, by the analysis of FtsH substrate mutants, we found that FtsH sensitizes MRSA specifically to β-lactams by degrading YpfP, the enzyme synthesizing the anchor molecule for lipoteichoic acid (LTA). Both the overexpression of FtsH and the disruption of ypfP-sensitized MRSA to β-lactams were observed. The knockout mutation in ftsH and ypfP increased the thickness of the cell wall. The β-lactam sensitization coincided with the production of aberrantly large LTA molecules. The combination of three mutations in the rpoC, vraB, and SAUSA300_2133 genes blocked the β-lactam-sensitizing effect of FtsH. Murine infection with the ypfP mutant could be treated by oxacillin, a β-lactam antibiotic ineffective against MRSA; however, the effective concentration of oxacillin differed depending on the S. aureus strain. Our study demonstrated that the β-lactam sensitizing effect of FtsH is due to its digestion of YpfP. It also suggests that the larger LTA molecules are responsible for the β-lactam sensitization phenotype, and YpfP is a viable target for developing novel anti-MRSA drugs.
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9
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Satishkumar N, Alexander JAN, Poon R, Buggeln E, Argudín MA, Strynadka NCJ, Chatterjee SS. PBP4-mediated β-lactam resistance among clinical strains of Staphylococcus aureus. J Antimicrob Chemother 2021; 76:2268-2272. [PMID: 34151961 DOI: 10.1093/jac/dkab201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/24/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND PBP4, a low-molecular-weight PBP in Staphylococcus aureus, is not considered to be a classical mediator of β-lactam resistance. Previous studies carried out by our group with laboratory strains of S. aureus demonstrated the ability of PBP4 to produce β-lactam resistance through mutations associated with the pbp4 promoter and/or gene. Recent studies of β-lactam-resistant clinical isolates of S. aureus have reported similar mutations associated with pbp4. OBJECTIVES To determine if pbp4-associated mutations reported among clinical strains of S. aureus mediate β-lactam resistance. METHODS The pbp4 promoters and genes bearing mutations from clinical isolates were cloned into a heterologous host. Reporter, growth and Bocillin assays were performed to assess their role in β-lactam resistance. X-ray crystallography was used to obtain acyl-enzyme intermediate structures of the WT and mutant PBP4 with nafcillin and cefoxitin. RESULTS Of the five strains that contained pbp4 promoter mutations, three strains exhibited enhanced expression of PBP4. The R200L mutation in pbp4 resulted in increased survival in the presence of the β-lactams nafcillin and cefoxitin. Further, introduction of either a promoter or a gene mutation into the genome of a WT host increased the ability of the strains to resist the action of β-lactams. The four high-resolution X-ray structures presented demonstrate the binding pose of the β-lactams tested and provide hints for further drug development. CONCLUSIONS Mutations associated with the pbp4 promoter and pbp4 gene altered protein activity and mediated β-lactam resistance among the clinically isolated strains that were studied.
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Affiliation(s)
- Nidhi Satishkumar
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA.,Institute of Marine and Environmental Technology, Baltimore, MD, USA
| | - J Andrew N Alexander
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Raymond Poon
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA.,Institute of Marine and Environmental Technology, Baltimore, MD, USA
| | - Emma Buggeln
- Division of HIV/AIDS, Infectious Diseases and Global Health, Department of Medicine, University of California, San Francisco, San Francisco General Hospital, San Francisco, CA, USA
| | - Maria A Argudín
- National Reference Centre for Staphylococcus aureus, Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles, Brussels, Belgium
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Som S Chatterjee
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA.,Institute of Marine and Environmental Technology, Baltimore, MD, USA
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10
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Fisher JF, Mobashery S. β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium. Chem Rev 2021; 121:3412-3463. [PMID: 33373523 PMCID: PMC8653850 DOI: 10.1021/acs.chemrev.0c01010] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biological diversity of the unicellular bacteria-whether assessed by shape, food, metabolism, or ecological niche-surely rivals (if not exceeds) that of the multicellular eukaryotes. The relationship between bacteria whose ecological niche is the eukaryote, and the eukaryote, is often symbiosis or stasis. Some bacteria, however, seek advantage in this relationship. One of the most successful-to the disadvantage of the eukaryote-is the small (less than 1 μm diameter) and nearly spherical Staphylococcus aureus bacterium. For decades, successful clinical control of its infection has been accomplished using β-lactam antibiotics such as the penicillins and the cephalosporins. Over these same decades S. aureus has perfected resistance mechanisms against these antibiotics, which are then countered by new generations of β-lactam structure. This review addresses the current breadth of biochemical and microbiological efforts to preserve the future of the β-lactam antibiotics through a better understanding of how S. aureus protects the enzyme targets of the β-lactams, the penicillin-binding proteins. The penicillin-binding proteins are essential enzyme catalysts for the biosynthesis of the cell wall, and understanding how this cell wall is integrated into the protective cell envelope of the bacterium may identify new antibacterials and new adjuvants that preserve the efficacy of the β-lactams.
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Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
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11
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Alexander JAN, Radaeva M, King DT, Chambers HF, Cherkasov A, Chatterjee SS, Strynadka NCJ. Structural analysis of avibactam-mediated activation of the bla and mec divergons in methicillin-resistant Staphylococcus aureus. J Biol Chem 2020; 295:10870-10884. [PMID: 32518158 DOI: 10.1074/jbc.ra120.013029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/02/2020] [Indexed: 02/01/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) infections cause significant mortality and morbidity globally. MRSA resistance to β-lactam antibiotics is mediated by two divergons that control levels of a β-lactamase, PC1, and a penicillin-binding protein poorly acylated by β-lactam antibiotics, PBP2a. Expression of genes encoding these proteins is controlled by two integral membrane proteins, BlaR1 and MecR1, which both have an extracellular β-lactam-binding sensor domain. Here, we solved the X-ray crystallographic structures of the BlaR1 and MecR1 sensor domains in complex with avibactam, a diazabicyclooctane β-lactamase inhibitor at 1.6-2.0 Å resolution. Additionally, we show that S. aureus SF8300, a clinically relevant strain from the USA300 clone of MRSA, responds to avibactam by up-regulating the expression of the blaZ and pbp2a antibiotic-resistance genes, encoding PC1 and PBP2a, respectively. The BlaR1-avibactam structure of the carbamoyl-enzyme intermediate revealed that avibactam is bound to the active-site serine in two orientations ∼180° to each other. Although a physiological role of the observed alternative pose remains to be validated, our structural results hint at the presence of a secondary sulfate-binding pocket that could be exploited in the design of future inhibitors of BlaR1/MecR1 sensor domains or the structurally similar class D β-lactamases. The MecR1-avibactam structure adopted a singular avibactam orientation similar to one of the two states observed in the BlaR1-avibactam structure. Given avibactam up-regulates expression of blaZ and pbp2a antibiotic resistance genes, we suggest further consideration and research is needed to explore what effects administering β-lactam-avibactam combinations have on treating MRSA infections.
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Affiliation(s)
- J Andrew N Alexander
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Mariia Radaeva
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Dustin T King
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Henry F Chambers
- Division of Infectious Disease, Dept. of Medicine, San Francisco General Hospital, San Francisco, California, USA
| | - Artem Cherkasov
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Som S Chatterjee
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland and Institute of Marine and Environmental Technology, Baltimore, Maryland, USA ;
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada ;
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12
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Zhang L, Fu Y, Han X, Xu Q, Weng S, Yan B, Liu L, Hua X, Chen Y, Yu Y. Phenotypic Variation and Carbapenem Resistance Potential in OXA-499-Producing Acinetobacter pittii. Front Microbiol 2020; 11:1134. [PMID: 32582088 PMCID: PMC7296048 DOI: 10.3389/fmicb.2020.01134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/05/2020] [Indexed: 12/17/2022] Open
Abstract
Acinetobacter pittii is increasingly recognized as a clinically important species. Here, we identified a carbapenem-non-resistant A. pittii clinical isolate, A1254, harboring blaOXA–499, blaOXA–826, and blaADC–221. The blaOXA–499 genetic environment in A1254 was identical to that of another OXA-499-producing, but carbapenem-resistant, A. pittii isolate, YMC2010/8/T346, indicating the existence of phenotypic variation among OXA-499-producing A. pittii strains. Under imipenem-selective pressure, the A1254 isolate developed resistance to carbapenems in 60 generations. Two carbapenem-resistant mutants (CAB009 and CAB010) with mutations in the blaOXA–499 promoter region were isolated from two independently evolved populations (CAB001 and CAB004). The CAB009 mutant, with a mutation at position −14 (A to G), exhibited a four-fold higher carbapenem minimum inhibitory concentration (MIC) and a 4.53 ± 0.19 log2 fold change higher expression level of blaOXA–499 than the ancestor strain, A1254. The other mutant, CAB010, with a mutation at position −42 (G to A), showed a two-fold higher carbapenem MIC and a 1.65 ± 0.25 log2 fold change higher blaOXA–499 expression level than the ancestor strain. The blaOXA–499 gene and its promoter region were amplified from the wild-type strain and two mutant isolates and then individually cloned into the pYMAb2-Hygr vector and expressed in Acinetobacter baumannii ATCC 17978, A. pittii LMG 1035, and A. pittii A1254. All the transformed strains were resistant to carbapenem, irrespective of whether they harbored the initial or an evolved promoter sequence, and transformed strains expressing the promoter from the most resistant mutant, CAB009, showed the highest carbapenem MICs, with values of 32–64 μg/ml for imipenem and 128 μg/ml for meropenem. RNA sequencing was performed to confirm the contribution of blaOXA–499 to the development of carbapenem resistance. Although the CAB009 and CAB010 transcriptional patterns were different, blaOXA–499 was the only differentially expressed gene shared by the two mutants. Our results indicate that carbapenem-non-resistant Acinetobacter spp. strains carrying blaOXA genes have the potential to develop carbapenem resistance and need to be further investigated and monitored to prevent treatment failure due to the development of resistance.
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Affiliation(s)
- Linyue Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Ying Fu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China.,Department of Clinical Laboratory, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xinhong Han
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Qingye Xu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Shanshan Weng
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Biyong Yan
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Lilin Liu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yan Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
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13
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Fisher JF, Mobashery S. Constructing and deconstructing the bacterial cell wall. Protein Sci 2020; 29:629-646. [PMID: 31747090 PMCID: PMC7021008 DOI: 10.1002/pro.3737] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022]
Abstract
The history of modern medicine cannot be written apart from the history of the antibiotics. Antibiotics are cytotoxic secondary metabolites that are isolated from Nature. The antibacterial antibiotics disproportionately target bacterial protein structure that is distinct from eukaryotic protein structure, notably within the ribosome and within the pathways for bacterial cell-wall biosynthesis (for which there is not a eukaryotic counterpart). This review focuses on a pre-eminent class of antibiotics-the β-lactams, exemplified by the penicillins and cephalosporins-from the perspective of the evolving mechanisms for bacterial resistance. The mechanism of action of the β-lactams is bacterial cell-wall destruction. In the monoderm (single membrane, Gram-positive staining) pathogen Staphylococcus aureus the dominant resistance mechanism is expression of a β-lactam-unreactive transpeptidase enzyme that functions in cell-wall construction. In the diderm (dual membrane, Gram-negative staining) pathogen Pseudomonas aeruginosa a dominant resistance mechanism (among several) is expression of a hydrolytic enzyme that destroys the critical β-lactam ring of the antibiotic. The key sensing mechanism used by P. aeruginosa is monitoring the molecular difference between cell-wall construction and cell-wall deconstruction. In both bacteria, the resistance pathways are manifested only when the bacteria detect the presence of β-lactams. This review summarizes how the β-lactams are sensed and how the resistance mechanisms are manifested, with the expectation that preventing these processes will be critical to future chemotherapeutic control of multidrug resistant bacteria.
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Affiliation(s)
- Jed F. Fisher
- Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndiana
| | - Shahriar Mobashery
- Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndiana
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14
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Alexander JAN, Chatterjee SS, Hamilton SM, Eltis LD, Chambers HF, Strynadka NCJ. Structural and kinetic analyses of penicillin-binding protein 4 (PBP4)-mediated antibiotic resistance in Staphylococcus aureus. J Biol Chem 2018; 293:19854-19865. [PMID: 30366985 DOI: 10.1074/jbc.ra118.004952] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/24/2018] [Indexed: 01/08/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) causes serious community-acquired and nosocomial infections worldwide. MRSA strains are resistant to a variety of antibiotics, including the classic penicillin and cephalosporin classes of β-lactams, making them intractable to treatment. Although β-lactam resistance in MRSA has been ascribed to the acquisition and activity of penicillin-binding protein 2a (PBP2a, encoded by mecA), it has recently been observed that resistance can also be mediated by penicillin-binding protein 4 (PBP4). Previously, we have shown that broad-spectrum β-lactam resistance can arise following serial passaging of a mecA-negative COL strain of S. aureus, creating the CRB strain. This strain has two missense mutations in pbp4 and a mutation in the pbp4 promoter, both of which play an instrumental role in β-lactam resistance. To better understand PBP4's role in resistance, here we have characterized its kinetics and structure with clinically relevant β-lactam antibiotics. We present the first crystallographic PBP4 structures of apo and acyl-enzyme intermediate forms complexed with three late-generation β-lactam antibiotics: ceftobiprole, ceftaroline, and nafcillin. In parallel, we characterized the structural and kinetic effects of the PBP4 mutations present in the CRB strain. Localized within the transpeptidase active-site cleft, the two substitutions appear to have different effects depending on the drug. With ceftobiprole, the missense mutations impaired the Km value 150-fold, decreasing the proportion of inhibited PBP4. However, ceftaroline resistance appeared to be mediated by other factors, possibly including mutation of the pbp4 promoter. Our findings provide evidence that S. aureus CRB has at least two PBP4-mediated resistance mechanisms.
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Affiliation(s)
- J Andrew N Alexander
- From the Department of Biochemistry and Molecular Biology.,the Centre for Blood Research, and
| | - Som S Chatterjee
- the Division of Infectious Disease, Department of Medicine, San Francisco General Hospital, San Francisco, California 94110
| | - Stephanie M Hamilton
- the Division of Infectious Disease, Department of Medicine, San Francisco General Hospital, San Francisco, California 94110
| | - Lindsay D Eltis
- From the Department of Biochemistry and Molecular Biology.,the Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada and
| | - Henry F Chambers
- the Division of Infectious Disease, Department of Medicine, San Francisco General Hospital, San Francisco, California 94110
| | - Natalie C J Strynadka
- From the Department of Biochemistry and Molecular Biology, .,the Centre for Blood Research, and
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15
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PBP4: A New Perspective on Staphylococcus aureus β-Lactam Resistance. Microorganisms 2018; 6:microorganisms6030057. [PMID: 29932109 PMCID: PMC6164785 DOI: 10.3390/microorganisms6030057] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 12/14/2022] Open
Abstract
β-lactam antibiotics are excellent drugs for treatment of staphylococcal infections, due to their superior efficacy and safety compared to other drugs. Effectiveness of β-lactams is severely compromised due to resistance, which is widespread among clinical strains of Staphylococcus aureus. β-lactams inhibit bacterial cells by binding to penicillin binding proteins (PBPs), which perform the penultimate steps of bacterial cell wall synthesis. Among PBPs of S. aureus, PBP2a has received the most attention for the past several decades due to its preeminent role in conferring both high-level and broad-spectrum resistance to the entire class of β-lactam drugs. Studies on PBP2a have thus unraveled incredible details of its mechanism of action. We have recently identified that an uncanonical, low molecular weight PBP of S. aureus, PBP4, can also provide high-level and broad-spectrum resistance to the entire class of β-lactam drugs at a level similar to that of PBP2a. The role of PBP4 has typically been considered not so important for β-lactam resistance of S. aureus, and as a result its mode of action remains largely unknown. In this article, we review our current knowledge of PBP4 mediating β-lactam resistance in S. aureus.
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