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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: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] [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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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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Summer M, Ali S, Tahir HM, Abaidullah R, Fiaz U, Mumtaz S, Fiaz H, Hassan A, Mughal TA, Farooq MA. Mode of Action of Biogenic Silver, Zinc, Copper, Titanium and Cobalt Nanoparticles Against Antibiotics Resistant Pathogens. J Inorg Organomet Polym Mater 2024; 34:1417-1451. [DOI: 10.1007/s10904-023-02935-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/02/2023] [Indexed: 08/04/2024]
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Heidarian S, Guliaev A, Nicoloff H, Hjort K, Andersson DI. High prevalence of heteroresistance in Staphylococcus aureus is caused by a multitude of mutations in core genes. PLoS Biol 2024; 22:e3002457. [PMID: 38175839 PMCID: PMC10766187 DOI: 10.1371/journal.pbio.3002457] [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: 09/11/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Heteroresistance (HR) is an enigmatic phenotype where, in a main population of susceptible cells, small subpopulations of resistant cells exist. This is a cause for concern, as this small subpopulation is difficult to detect by standard antibiotic susceptibility tests, and upon antibiotic exposure the resistant subpopulation may increase in frequency and potentially lead to treatment complications or failure. Here, we determined the prevalence and mechanisms of HR for 40 clinical Staphylococcus aureus isolates, against 6 clinically important antibiotics: daptomycin, gentamicin, linezolid, oxacillin, teicoplanin, and vancomycin. High frequencies of HR were observed for gentamicin (69.2%), oxacillin (27%), daptomycin (25.6%), and teicoplanin (15.4%) while none of the isolates showed HR toward linezolid or vancomycin. Point mutations in various chromosomal core genes, including those involved in membrane and peptidoglycan/teichoic acid biosynthesis and transport, tRNA charging, menaquinone and chorismite biosynthesis and cyclic-di-AMP biosynthesis, were the mechanisms responsible for generating the resistant subpopulations. This finding is in contrast to gram-negative bacteria, where increased copy number of bona fide resistance genes via tandem gene amplification is the most prevalent mechanism. This difference can be explained by the observation that S. aureus has a low content of resistance genes and absence of the repeat sequences that allow tandem gene amplification of these genes as compared to gram-negative species.
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Affiliation(s)
- Sheida Heidarian
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Andrei Guliaev
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Hervé Nicoloff
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Karin Hjort
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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Dengler Haunreiter V, Tarnutzer A, Bär J, von Matt M, Hertegonne S, Andreoni F, Vulin C, Künzi L, Menzi C, Kiefer P, Christen P, Vorholt JA, Zinkernagel AS. C-di-AMP levels modulate Staphylococcus aureus cell wall thickness, response to oxidative stress, and antibiotic resistance and tolerance. Microbiol Spectr 2023; 11:e0278823. [PMID: 37948390 PMCID: PMC10715141 DOI: 10.1128/spectrum.02788-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE Antibiotic resistance and tolerance are substantial healthcare-related problems, hampering effective treatment of bacterial infections. Mutations in the phosphodiesterase GdpP, which degrades cyclic di-3', 5'-adenosine monophosphate (c-di-AMP), have recently been associated with resistance to beta-lactam antibiotics in clinical Staphylococcus aureus isolates. In this study, we show that high c-di-AMP levels decreased the cell size and increased the cell wall thickness in S. aureus mutant strains. As a consequence, an increase in resistance to cell wall targeting antibiotics, such as oxacillin and fosfomycin as well as in tolerance to ceftaroline, a cephalosporine used to treat methicillin-resistant S. aureus infections, was observed. These findings underline the importance of investigating the role of c-di-AMP in the development of tolerance and resistance to antibiotics in order to optimize treatment in the clinical setting.
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Affiliation(s)
- Vanina Dengler Haunreiter
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Andrea Tarnutzer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Julian Bär
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Manuela von Matt
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sanne Hertegonne
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Federica Andreoni
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Clément Vulin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lisa Künzi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Carmen Menzi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Patrick Kiefer
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Philipp Christen
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Julia A. Vorholt
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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6
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Li C, Yin L, He X, Jin Y, Zhu X, Wu R. Competition-cooperation mechanism between Escherichia coli and Staphylococcus aureus based on systems mapping. Front Microbiol 2023; 14:1192574. [PMID: 38029174 PMCID: PMC10657823 DOI: 10.3389/fmicb.2023.1192574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Interspecies interactions are a crucial driving force of species evolution. The genes of each coexisting species play a pivotal role in shaping the structure and function within the community, but how to identify them at the genome-wide level has always been challenging. Methods In this study, we embed the Lotka-Volterra ordinary differential equations in the theory of community ecology into the systems mapping model, so that this model can not only describe how the quantitative trait loci (QTL) of a species directly affects its own phenotype, but also describe the QTL of the species how to indirectly affect the phenotype of its interacting species, and how QTL from different species affects community behavior through epistatic interactions. Results By designing and implementing a co-culture experiment for 100 pairs of Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), we mapped 244 significant QTL combinations in the interaction process of the two bacteria using this model, including 69 QTLs from E. coli and 59 QTLs from S. aureus, respectively. Through gene annotation, we obtained 57 genes in E. coli, among which the genes with higher frequency were ypdC, nrfC, yphH, acrE, dcuS, rpnE, and ptsA, while we obtained 43 genes in S. aureus, among which the genes with higher frequency were ebh, SAOUHSC_00172, capF, gdpP, orfX, bsaA, and phnE1. Discussion By dividing the overall growth into independent growth and interactive growth, we could estimate how QTLs modulate interspecific competition and cooperation. Based on the quantitative genetic model, we can obtain the direct genetic effect, indirect genetic effect, and genome-genome epistatic effect related to interspecific interaction genes, and then further mine the hub genes in the QTL networks, which will be particularly useful for inferring and predicting the genetic mechanisms of community dynamics and evolution. Systems mapping can provide a tool for studying the mechanism of competition and cooperation among bacteria in co-culture, and this framework can lay the foundation for a more comprehensive and systematic study of species interactions.
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Affiliation(s)
- Caifeng Li
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lixin Yin
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaoqing He
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology, Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Yi Jin
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology, Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Xuli Zhu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology, Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology, Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
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7
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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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Giulieri SG. Case Commentary: The hidden side of oxacillin resistance in Staphylococcus aureus. Antimicrob Agents Chemother 2023; 67:e0071623. [PMID: 37655923 PMCID: PMC10583679 DOI: 10.1128/aac.00716-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Abstract
Acquisition of PBP2a (encoded by the mec gene) is the key resistance mechanism to β-lactams in Staphylococcus aureus. The mec gene can be easily detected by PCR assays; however, these tools will miss mec-independent oxacillin resistance. This phenotype is mediated by mutations in cell wall metabolism genes that can be acquired during persistent infections under prolonged antibiotic exposure. The complex case presented by Hess et al. (Antimicrob Agents Chemother 67:e00437-23, 2023, https://doi.org/10.1128/aac.00437-23) highlights the diagnostic and therapeutic challenges in the management of mec-independent oxacillin resistance.
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Affiliation(s)
- Stefano G. Giulieri
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Australia
- Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Australia
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9
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Ye R, Tomo C, Chan N, Wolfe BE. Penicillium molds impact the transcriptome and evolution of the cheese bacterium Staphylococcus equorum. mSphere 2023; 8:e0004723. [PMID: 37219436 PMCID: PMC10449494 DOI: 10.1128/msphere.00047-23] [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: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
The observation that Penicillium molds can inhibit the growth of Staphylococcus was a catalyst for the antibiotic revolution. Considerable attention has been paid to purified Penicillium metabolites that inhibit bacteria, but little is known about how Penicillium species impact the ecology and evolution of bacteria in multispecies microbial communities. Here, we investigated how four different species of Penicillium can impact global transcription and evolution of a widespread Staphylococcus species (S. equorum) using the cheese rind model microbiome. Through RNA sequencing, we identified a core transcriptional response of S. equorum against all five tested Penicillium strains, including upregulation of thiamine biosynthesis, fatty acid degradation, and amino acid metabolism as well as downregulation of genes involved in the transport of siderophores. In a 12-week evolution experiment where we co-cultured S. equorum with the same Penicillium strains, we observed surprisingly few non-synonymous mutations across S. equorum populations evolved with the Penicillium species. A mutation in a putative DHH family phosphoesterase gene only occurred in populations evolved without Penicillium and decreased the fitness of S. equorum when co-cultured with an antagonistic Penicillium strain. Our results highlight the potential for conserved mechanisms of Staphylococcus-Penicillium interactions and demonstrate how fungal biotic environments may constrain the evolution of bacterial species.IMPORTANCEFungi and bacteria are commonly found co-occurring both in natural and synthetic microbiomes, but our understanding of fungal-bacterial interactions is limited to a handful of species. Conserved mechanisms of interactions and evolutionary consequences of fungal-bacterial interactions are largely unknown. Our RNA sequencing and experimental evolution data with Penicillium species and the bacterium S. equorum demonstrate that divergent fungal species can elicit conserved transcriptional and genomic responses in co-occurring bacteria. Penicillium molds are integral to the discovery of novel antibiotics and production of certain foods. By understanding how Penicillium species affect bacteria, our work can further efforts to design and manage Penicillium-dominated microbial communities in industry and food production.
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Affiliation(s)
- Ruby Ye
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Christopher Tomo
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Neal Chan
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Benjamin E. Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA
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10
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Taponen S, Tölli HT, Rajala-Schultz PJ. Antimicrobial susceptibility of staphylococci from bovine milk samples in routine microbiological mastitis analysis in Finland. Front Vet Sci 2023; 10:1235417. [PMID: 37662993 PMCID: PMC10470832 DOI: 10.3389/fvets.2023.1235417] [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: 06/06/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023] Open
Abstract
The most frequent reason for antimicrobial use in dairy herds is mastitis and knowledge about mastitis-causing pathogens and their antimicrobial susceptibility should guide treatment decisions. The overall objective of this study was to assess antimicrobial resistance (AMR) of staphylococci in mastitic milk samples in Finland. MALDI-ToF MS identified a total of 504 Staphylococcus isolates (260 S. aureus and 244 non-aureus staphylococci, NAS) originating from bovine mastitic milk samples. Phenotypic susceptibility against cefoxitin, ceftiofur, enrofloxacin, gentamycin, oxacillin, penicillin, and tetracycline was evaluated by disk diffusion method and the presence of blaZ, mecA, and mecC genes investigated by PCR. Nitrocefin test assessed these isolates' beta-lactamase production. The most common NAS species were S. simulans, S. epidermidis, S. chromogenes, and S. haemolyticus. In total, 26.6% of the isolates (18.5% of S. aureus and 35.2% of all NAS) carried the blaZ gene. Penicillin resistance, based on disk diffusion, was lower: 18.8% of all the isolates (9.3% of S. aureus and 28.9% of all NAS) were resistant. Based on the nitrocefin test, 21.5% of the isolates produced beta-lactamase (11.6% of S. aureus and 32.0% of all NAS). Between the Staphylococcus species, the proportion of penicillin-resistant isolates varied, being lowest in S. simulans and highest in S. epidermidis. Resistance to antimicrobials other than penicillin was rare. Of the eight NAS isolates carrying the mecA gene, six were S. epidermidis. One S. aureus isolate carried the mecC gene. Agreement beyond chance, assessed by kappa coefficient, between phenotypic and genotypic resistance tests, was moderate to substantial. Some phenotypically penicillin-susceptible staphylococci carried the blaZ gene but isolates without blaZ or mec genes rarely exhibited resistance, suggesting that the more reliable treatment choice may depend upon genotypic AMR testing. Our results support earlier findings that penicillin resistance is the only significant form of antimicrobial resistance among mastitis-causing staphylococci in Finland.
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Affiliation(s)
- Suvi Taponen
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Saarentaus, Finland
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11
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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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12
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Mukkayyan N, Poon R, Sander PN, Lai LY, Zubair-Nizami Z, Hammond MC, Chatterjee SS. In Vivo Detection of Cyclic-di-AMP in Staphylococcus aureus. ACS OMEGA 2022; 7:32749-32753. [PMID: 36120079 PMCID: PMC9476191 DOI: 10.1021/acsomega.2c04538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Cyclic-di-AMP (CDA) is a signaling molecule that controls various cellular functions including antibiotic tolerance and osmoregulation in Staphylococcus aureus (S. aureus). In this study, we developed a novel biosensor (bsuO P6-4) for in vivo detection of CDA in S. aureus. The fluorescent biosensor is based on a natural CDA riboswitch from Bacillus subtilis connected at its P6 stem to the dye-binding aptamer Spinach. Our study showed that bsuO P6-4 could detect a wide concentration range of CDA in both laboratory and clinical strains, making it suitable for use in both basic and clinical research applications.
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Affiliation(s)
- Nagaraja Mukkayyan
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21202, United States
- Institute
of Marine and Environmental Technology, Baltimore, Maryland 21202, United States
| | - Raymond Poon
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21202, United States
- Institute
of Marine and Environmental Technology, Baltimore, Maryland 21202, United States
| | - Philipp N. Sander
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Li-Yin Lai
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21202, United States
- Institute
of Marine and Environmental Technology, Baltimore, Maryland 21202, United States
| | - Zahra Zubair-Nizami
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21202, United States
- Institute
of Marine and Environmental Technology, Baltimore, Maryland 21202, United States
| | - Ming C. Hammond
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry and Henry Eyring Center for Cell and Genome Sciences, University of Utah, Salt Lake City, Utah 84112, United States
| | - Som S. Chatterjee
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21202, United States
- Institute
of Marine and Environmental Technology, Baltimore, Maryland 21202, United States
- University
of Maryland Center for Environmental Science, Baltimore, Maryland 21202, United States
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13
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Tang Q, Precit MR, Thomason MK, Blanc SF, Ahmed-Qadri F, McFarland AP, Wolter DJ, Hoffman LR, Woodward JJ. Thymidine starvation promotes c-di-AMP-dependent inflammation during pathogenic bacterial infection. Cell Host Microbe 2022; 30:961-974.e6. [PMID: 35439435 DOI: 10.1016/j.chom.2022.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/01/2022] [Accepted: 03/23/2022] [Indexed: 11/03/2022]
Abstract
Antimicrobials can impact bacterial physiology and host immunity with negative treatment outcomes. Extensive exposure to antifolate antibiotics promotes thymidine-dependent Staphylococcus aureus small colony variants (TD-SCVs), commonly associated with worse clinical outcomes. We show that antibiotic-mediated disruption of thymidine synthesis promotes elevated levels of the bacterial second messenger cyclic di-AMP (c-di-AMP), consequently inducing host STING activation and inflammation. An initial antibiotic screen in Firmicutes revealed that c-di-AMP production was largely driven by antifolate antibiotics targeting dihydrofolate reductase (DHFR), which promotes folate regeneration required for thymidine biosynthesis. Additionally, TD-SCVs exhibited excessive c-di-AMP production and STING activation in a thymidine-dependent manner. Murine lung infection with TD-SCVs revealed STING-dependent elevation of proinflammatory cytokines, causing higher airway neutrophil infiltration and activation compared with normal-colony S. aureus and hemin-dependent SCVs. Collectively, our results suggest that thymidine metabolism disruption in Firmicutes leads to elevated c-di-AMP-mediated STING-dependent inflammation, with potential impacts on antibiotic usage and infection outcomes.
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Affiliation(s)
- Qing Tang
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Mimi R Precit
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Maureen K Thomason
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Sophie F Blanc
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Fariha Ahmed-Qadri
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Adelle P McFarland
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Daniel J Wolter
- Department of Pediatrics, University of Washington, Seattle, WA 98105, USA; Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Lucas R Hoffman
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington, Seattle, WA 98105, USA; Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Joshua J Woodward
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA.
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Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit. mBio 2022; 13:e0319621. [PMID: 35038924 PMCID: PMC8764539 DOI: 10.1128/mbio.03196-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Active surveillance for methicillin-resistant Staphylococcus aureus (MRSA) is a component of our neonatal intensive care unit (NICU) infection prevention efforts. Recent atypical trends prompted review of 42 suspected MRSA isolates. Species identification was confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and methicillin resistance was reevaluated by PBP2a lateral flow assay, cefoxitin/oxacillin susceptibility testing, mecA and mecC PCR, and six commercially available MRSA detection agars. All isolates were confirmed S. aureus, but only eight were MRSA (cefoxitin resistant, PBP2a positive, mecA positive, growth on all MRSA screening agars). One MRSA isolate was cefoxitin susceptible but PBP2a and mecA positive, and the remaining 33 were cefoxitin susceptible, PBP2a negative, and mecA negative; interestingly, these isolates grew inconsistently across MRSA screening agars and had susceptibility profiles consistent with that of borderline oxacillin-resistant S. aureus (BORSA). Comparative genomic analyses found these BORSA isolates to be phylogenetically diverse and not representative of clonal expansion or shared gene content, though clones of two NICU strains were infrequently observed over 8 months. We identified 6 features-substitutions and truncations in PBP2, PBP4, and GdpP and beta-lactamase hyperproduction-that were used to generate a random forest classifier to distinguish BORSA from methicillin-susceptible S. aureus (MSSA) in our cohort. Our model demonstrated a robust ability to predict the BORSA phenotype among isolates collected across two continents (validation area under the curve [AUC], 0.902). Taking these findings together, we observed an unexpected prevalence of BORSA in our NICU, BORSA misclassification by existing MRSA screening methods, and markers that are together discriminatory for BORSA and MSSA within our cohort. This work has implications for epidemiological reporting of MRSA rates for centers using different screening methods. IMPORTANCE In this study, we found a high prevalence of Staphylococcus aureus isolates exhibiting a borderline oxacillin resistance phenotype (BORSA) in our neonatal intensive care unit (NICU) serendipitously due to the type of MRSA screening agar used by our laboratory for active surveillance cultures. Subsequent phenotypic and molecular characterization highlighted an unexpected prevalence and variability of BORSA isolates. Through whole-genome sequencing, we interrogated core and accessory genome content and generated a random forest classification model to identify mutations and truncations in the PBP2, PBP4, and GdpP proteins and beta-lactamase hyperproduction, which correlated with BORSA and MSSA phenotypes among S. aureus clinical isolates collected across two continents. In consideration of these findings, this work will help clinical microbiology laboratories and clinicians identify MRSA screening shortfalls and draw attention to the non-mecA-mediated BORSA phenotype.
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Loss of GdpP function in Staphylococcus aureus leads to β-lactam tolerance and enhanced evolution of β-lactam resistance. Antimicrob Agents Chemother 2021; 66:e0143121. [PMID: 34843389 DOI: 10.1128/aac.01431-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Infections caused by Staphylococcus aureus are a leading cause of mortality. Treating infections caused by S. aureus is difficult due to resistance against most traditional antibiotics, including β-lactams. We previously reported the presence of mutations in gdpP among S. aureus strains that were obtained by serial passaging in β-lactam drugs. Similar mutations have recently been reported in natural S. aureus isolates that are either non-susceptible or resistant to β-lactam antibiotics. gdpP codes for a phosphodiesterase that cleaves cyclic-di-AMP (CDA), a newly discovered second messenger. In this study, we sought to identify the role of gdpP in β-lactam resistance in S. aureus. Our results showed that gdpP associated mutations caused loss of phosphodiesterase function, leading to increased CDA accumulation in the bacterial cytosol. Deletion of gdpP led to an enhanced ability of the bacteria to withstand a β-lactam challenge (two to three log increase in bacterial colony forming units) by promoting tolerance without enhancing MICs of β-lactam antibiotics. Our results demonstrated that increased drug tolerance due to loss of GdpP function can provide a selective advantage in acquisition of high-level β-lactam resistance. Loss of GdpP function thus increases tolerance to β-lactams that can lead to its therapy failure and can permit β-lactam resistance to occur more readily.
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