1
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Liu Y, Blanco-Toral C, Larrouy-Maumus G. The role of cyclic nucleotides in bacterial antimicrobial resistance and tolerance. Trends Microbiol 2024:S0966-842X(24)00218-X. [PMID: 39242230 DOI: 10.1016/j.tim.2024.08.006] [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: 06/08/2024] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 09/09/2024]
Abstract
Nucleotide signalling molecules - mainly cyclic 3',5'-adenosine phosphate (cAMP), bis-(3',5')-cyclic diguanosine monophosphate (c-di-GMP), and bis-(3',5')-cyclic diadenosine monophosphate (c-di-AMP) - contribute to the regulation of cellular pathways. Numerous recent works have focused on the involvement of these cyclic nucleotide phosphates (cNPs) in bacterial resistance and tolerance to antimicrobial treatment. Indeed, the rise of antimicrobial resistance (AMR) is a rising global threat to human health, while the rise of antimicrobial tolerance underlies the development of AMR and long-term infections, placing an additional burden on this problem. Here, we summarise the current understanding of cNP signalling in bacterial physiology with a focus on our understanding of how cNP signalling affects AMR and antimicrobial tolerance in different bacterial species. We also discuss additional cNP-related drug targets in bacterial pathogens that may have therapeutic potential.
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Affiliation(s)
- Yi Liu
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Claudia Blanco-Toral
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Gerald Larrouy-Maumus
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK.
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2
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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 PMCID: PMC11323572 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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3
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Di Gregorio S, Weltman G, Fabbri C, Fernández S, Zárate S, Smayevsky J, Power P, Campos J, Llarrull LI, Mollerach M. Genetic and Phenotypic Changes Related to the Development of mec-Independent Oxacillin Non-Susceptibility in ST8 Staphylococcus aureus Recovered after Antibiotic Therapy in a Patient with Bacteremia. Antibiotics (Basel) 2024; 13:554. [PMID: 38927220 PMCID: PMC11200602 DOI: 10.3390/antibiotics13060554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/30/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
The mec-independent oxacillin non-susceptible S. aureus (MIONSA) strains represent a great clinical challenge, as they are not easily detected and can lead to treatment failure. However, the responsible molecular mechanisms are still very little understood. Here, we studied four clinical ST8-MSSA-t024 isolates recovered during the course of antibiotic treatment from a patient suffering successive episodes of bacteremia. The first isolates (SAMS1, SAMS2, and SAMS3) were susceptible to cefoxitin and oxacillin. The last one (SA2) was susceptible to cefoxitin, resistant to oxacillin, lacked mec genes, and had reduced susceptibility to teicoplanin. SA2 showed higher β-lactamase activity than SAMS1. However, β-lactamase hyperproduction could not be linked to oxacillin resistance as it was not inhibited by clavulanic acid, and no genetic changes that could account for its hyperproduction were found. Importantly, we hereby report the in vivo acquisition and coexistence of different adaptive mutations in genes associated with peptidoglycan synthesis (pbp2, rodA, stp1, yjbH, and yvqF/vraT), which is possibly related with the development of oxacillin resistance and reduced susceptibility to teicoplanin in SA2. Using three-dimensional models and PBP binding assays, we demonstrated the high contribution of the SA2 PBP2 Ala450Asp mutation to the observed oxacillin resistance phenotype. Our results should be considered as a warning for physicians and microbiologists in the region, as MIONSA detection and treatment represent an important clinical challenge.
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Affiliation(s)
- Sabrina Di Gregorio
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
| | - Gabriela Weltman
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
| | - Carolina Fabbri
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, Rosario 2000, Argentina
| | - Silvina Fernández
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
| | - Soledad Zárate
- Laboratorio de Bacteriología, Micología y Parasitología, Centro de Educación Médica e Investigaciones Clínicas “Norberto Quirno” (CEMIC), Ciudad Autónoma de Buenos Aires 1431, Argentina
| | - Jorgelina Smayevsky
- Laboratorio de Bacteriología, Micología y Parasitología, Centro de Educación Médica e Investigaciones Clínicas “Norberto Quirno” (CEMIC), Ciudad Autónoma de Buenos Aires 1431, Argentina
| | - Pablo Power
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
| | - Josefina Campos
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires 1282, Argentina
| | - Leticia Irene Llarrull
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 27 de Febrero 210 bis, Rosario 2000, Argentina
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, Rosario 2000, Argentina
| | - Marta Mollerach
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autómoma de Buenos Aires 1113, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires 1113, Argentina
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4
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Brissac T, Guyonnet C, Sadouni A, Hernández-Montoya A, Jacquemet E, Legendre R, Sismeiro O, Trieu-Cuot P, Lanotte P, Tazi A, Firon A. Coordinated regulation of osmotic imbalance by c-di-AMP shapes ß-lactam tolerance in Group B Streptococcus. MICROLIFE 2024; 5:uqae014. [PMID: 38993744 PMCID: PMC11238645 DOI: 10.1093/femsml/uqae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 07/13/2024]
Abstract
Streptococcus agalactiae is among the few pathogens that have not developed resistance to ß-lactam antibiotics despite decades of clinical use. The molecular basis of this long-lasting susceptibility has not been investigated, and it is not known whether specific mechanisms constrain the emergence of resistance. In this study, we first report ß-lactam tolerance due to the inactivation of the c-di-AMP phosphodiesterase GdpP. Mechanistically, tolerance depends on antagonistic regulation by the repressor BusR, which is activated by c-di-AMP and negatively regulates ß-lactam susceptibility through the BusAB osmolyte transporter and the AmaP/Asp23/GlsB cell envelope stress complex. The BusR transcriptional response is synergistic with the simultaneous allosteric inhibition of potassium and osmolyte transporters by c-di-AMP, which individually contribute to low-level ß-lactam tolerance. Genome-wide transposon mutagenesis confirms the role of GdpP and highlights functional interactions between a lysozyme-like hydrolase, the KhpAB RNA chaperone and the protein S immunomodulator in the response of GBS to ß-lactam. Overall, we demonstrate that c-di-AMP acts as a turgor pressure rheostat, coordinating an integrated response at the transcriptional and post-translational levels to cell wall weakening caused by ß-lactam activity, and reveal additional mechanisms that could foster resistance.
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Affiliation(s)
- Terry Brissac
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Cécile Guyonnet
- Université Paris Cité, Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique UMR8104, Team Bacteria and Perinatality, 75015, Paris, France
- Department of Bacteriology, French National Reference Center for Streptococci, Assistance Publique-Hôpitaux de Paris Hôpitaux Universitaires Paris Centre, Hôpital Cochin, 75005, Paris, France
- Fédération Hospitalo-Universitaire Fighting Prematurity, 75005, Paris, France
| | - Aymane Sadouni
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Ariadna Hernández-Montoya
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Elise Jacquemet
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015 Paris, France
| | - Rachel Legendre
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015 Paris, France
| | - Odile Sismeiro
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Patrick Trieu-Cuot
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Philippe Lanotte
- Université de Tours, INRAE, UMR 1282 ISP, 3700, Tours, France
- CHRU de Tours, Service de Bactériologie-Virologie, 37044, Tours, France
| | - Asmaa Tazi
- Université Paris Cité, Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique UMR8104, Team Bacteria and Perinatality, 75015, Paris, France
- Department of Bacteriology, French National Reference Center for Streptococci, Assistance Publique-Hôpitaux de Paris Hôpitaux Universitaires Paris Centre, Hôpital Cochin, 75005, Paris, France
- Fédération Hospitalo-Universitaire Fighting Prematurity, 75005, Paris, France
| | - Arnaud Firon
- Department of Microbiology, Biology of Gram-positive Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
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5
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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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6
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Nielsen TK, Petersen IB, Xu L, Barbuti MD, Mebus V, Justh A, Alqarzaee AA, Jacques N, Oury C, Thomas V, Kjos M, Henriksen C, Frees D. The Spx stress regulator confers high-level β-lactam resistance and decreases susceptibility to last-line antibiotics in methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 2024:e0033524. [PMID: 38690894 DOI: 10.1128/aac.00335-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/05/2024] [Indexed: 05/03/2024] Open
Abstract
Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a leading cause of mortality worldwide. MRSA has acquired resistance to next-generation β-lactam antibiotics through the horizontal acquisition of the mecA resistance gene. Development of high resistance is, however, often associated with additional mutations in a set of chromosomal core genes, known as potentiators, which, through poorly described mechanisms, enhance resistance. The yjbH gene was recently identified as a hot spot for adaptive mutations during severe infections. Here, we show that inactivation of yjbH increased β-lactam MICs up to 16-fold and transformed MRSA cells with low levels of resistance to being homogenously highly resistant to β-lactams. The yjbH gene encodes an adaptor protein that targets the transcriptional stress regulator Spx for degradation by the ClpXP protease. Using CRISPR interference (CRISPRi) to knock down spx transcription, we unambiguously linked hyper-resistance to the accumulation of Spx. Spx was previously proposed to be essential; however, our data suggest that Spx is dispensable for growth at 37°C but becomes essential in the presence of antibiotics with various targets. On the other hand, high Spx levels bypassed the role of PBP4 in β-lactam resistance and broadly decreased MRSA susceptibility to compounds targeting the cell wall or the cell membrane, including vancomycin, daptomycin, and nisin. Strikingly, Spx potentiated resistance independently of its redox-sensing switch. Collectively, our study identifies a general stress pathway that, in addition to promoting the development of high-level, broad-spectrum β-lactam resistance, also decreases MRSA susceptibility to critical antibiotics of last resort.
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Affiliation(s)
- Tobias Krogh Nielsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Birkjær Petersen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lijuan Xu
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria Disen Barbuti
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Viktor Mebus
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anni Justh
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Abdulelah Ahmed Alqarzaee
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Nicolas Jacques
- Laboratory of Cardiology, GIGA Institute, University of Liège Hospital, Liège, Belgium
| | - Cécile Oury
- Laboratory of Cardiology, GIGA Institute, University of Liège Hospital, Liège, Belgium
| | - Vinai Thomas
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Camilla Henriksen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dorte Frees
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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7
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Zhang K, Potter RF, Marino J, Muenks CE, Lammers MG, Dien Bard J, Dingle TC, Humphries R, Westblade LF, Burnham CAD, Dantas G. Comparative genomics reveals the correlations of stress response genes and bacteriophages in developing antibiotic resistance of Staphylococcus saprophyticus. mSystems 2023; 8:e0069723. [PMID: 38051037 PMCID: PMC10734486 DOI: 10.1128/msystems.00697-23] [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: 07/07/2023] [Accepted: 10/23/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Staphylococcus saprophyticus is the second most common bacteria associated with urinary tract infections (UTIs) in women. The antimicrobial treatment regimen for uncomplicated UTI is normally nitrofurantoin, trimethoprim-sulfamethoxazole (TMP-SMX), or a fluoroquinolone without routine susceptibility testing of S. saprophyticus recovered from urine specimens. However, TMP-SMX-resistant S. saprophyticus has been detected recently in UTI patients, as well as in our cohort. Herein, we investigated the understudied resistance patterns of this pathogenic species by linking genomic antibiotic resistance gene (ARG) content to susceptibility phenotypes. We describe ARG associations with known and novel SCCmec configurations as well as phage elements in S. saprophyticus, which may serve as intervention or diagnostic targets to limit resistance transmission. Our analyses yielded a comprehensive database of phenotypic data associated with the ARG sequence in clinical S. saprophyticus isolates, which will be crucial for resistance surveillance and prediction to enable precise diagnosis and effective treatment of S. saprophyticus UTIs.
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Affiliation(s)
- Kailun Zhang
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Robert F. Potter
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Jamie Marino
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, USA
| | - Carol E. Muenks
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Matthew G. Lammers
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Tanis C. Dingle
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Romney Humphries
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Gautam Dantas
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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8
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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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9
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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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10
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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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11
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Ba X, Raisen CL, Restif O, Cavaco LM, Vingsbo Lundberg C, Lee JYH, Howden BP, Bartels MD, Strommenger B, Harrison EM, Larsen AR, Holmes MA, Larsen J. Cryptic susceptibility to penicillin/β-lactamase inhibitor combinations in emerging multidrug-resistant, hospital-adapted Staphylococcus epidermidis lineages. Nat Commun 2023; 14:6479. [PMID: 37838722 PMCID: PMC10576800 DOI: 10.1038/s41467-023-42245-y] [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: 04/04/2023] [Accepted: 10/04/2023] [Indexed: 10/16/2023] Open
Abstract
Global spread of multidrug-resistant, hospital-adapted Staphylococcus epidermidis lineages underscores the need for new therapeutic strategies. Here we show that many S. epidermidis isolates belonging to these lineages display cryptic susceptibility to penicillin/β-lactamase inhibitor combinations under in vitro conditions, despite carrying the methicillin resistance gene mecA. Using a mouse thigh model of S. epidermidis infection, we demonstrate that single-dose treatment with amoxicillin/clavulanic acid significantly reduces methicillin-resistant S. epidermidis loads without leading to detectable resistance development. On the other hand, we also show that methicillin-resistant S. epidermidis is capable of developing increased resistance to amoxicillin/clavulanic acid during long-term in vitro exposure to these drugs. These findings suggest that penicillin/β-lactamase inhibitor combinations could be a promising therapeutic candidate for treatment of a high proportion of methicillin-resistant S. epidermidis infections, although the in vivo risk of resistance development needs to be further addressed before they can be incorporated into clinical trials.
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Affiliation(s)
- Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Claire L Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Lina Maria Cavaco
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Jean Y H Lee
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mette D Bartels
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Birgit Strommenger
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jesper Larsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark.
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12
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Kobras CM, Monteith W, Somerville S, Delaney JM, Khan I, Brimble C, Corrigan RM, Sheppard SK, Fenton AK. Loss of Pde1 function acts as an evolutionary gateway to penicillin resistance in Streptococcus pneumoniae. Proc Natl Acad Sci U S A 2023; 120:e2308029120. [PMID: 37796984 PMCID: PMC10576035 DOI: 10.1073/pnas.2308029120] [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: 05/14/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023] Open
Abstract
Streptococcus pneumoniae is a major human pathogen and rising resistance to β-lactam antibiotics, such as penicillin, is a significant threat to global public health. Mutations occurring in the penicillin-binding proteins (PBPs) can confer high-level penicillin resistance but other poorly understood genetic factors are also important. Here, we combined strictly controlled laboratory experiments and population analyses to identify a new penicillin resistance pathway that is independent of PBP modification. Initial laboratory selection experiments identified high-frequency pde1 mutations conferring S. pneumoniae penicillin resistance. The importance of variation at the pde1 locus was confirmed in natural and clinical populations in an analysis of >7,200 S. pneumoniae genomes. The pde1 mutations identified by these approaches reduce the hydrolytic activity of the Pde1 enzyme in bacterial cells and thereby elevate levels of cyclic-di-adenosine monophosphate and penicillin resistance. Our results reveal rapid de novo loss of function mutations in pde1 as an evolutionary gateway conferring low-level penicillin resistance. This relatively simple genomic change allows cells to persist in populations on an adaptive evolutionary pathway to acquire further genetic changes and high-level penicillin resistance.
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Affiliation(s)
- Carolin M. Kobras
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - William Monteith
- Department of Biology, Ineos Oxford Institute for Antimicrobial Research, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Sophie Somerville
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - James M. Delaney
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Imran Khan
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Camilla Brimble
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Rebecca M. Corrigan
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Samuel K. Sheppard
- Department of Biology, Ineos Oxford Institute for Antimicrobial Research, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Andrew K. Fenton
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
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13
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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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14
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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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15
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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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16
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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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17
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Sawhney SS, Ransom EM, Wallace MA, Reich PJ, Dantas G, Burnham CAD. 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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 11/30/2021] [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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Affiliation(s)
- Sanjam S. Sawhney
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Eric M. Ransom
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Patrick J. Reich
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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18
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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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Sommer A, Fuchs S, Layer F, Schaudinn C, Weber RE, Richard H, Erdmann MB, Laue M, Schuster CF, Werner G, Strommenger B. Mutations in the gdpP gene are a clinically relevant mechanism for β-lactam resistance in meticillin-resistant Staphylococcus aureus lacking mec determinants. Microb Genom 2021; 7. [PMID: 34486969 PMCID: PMC8715439 DOI: 10.1099/mgen.0.000623] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In Staphylococcus aureus, resistance to β-lactamase stable β-lactam antibiotics is mediated by the penicillinbinding protein 2a, encoded by mecA or by its homologues mecB or mecC. However, a substantial number of meticillin-resistant isolates lack known mec genes and, thus, are called meticillin resistant lacking mec (MRLM). This study aims to identify the genetic mechanisms underlying the MRLM phenotype. A total of 141 MRLM isolates and 142 meticillin-susceptible controls were included in this study. Oxacillin and cefoxitin minimum inhibitory concentrations were determined by broth microdilution and the presence of mec genes was excluded by PCR. Comparative genomics and a genome-wide association study (GWAS) approach were applied to identify genetic polymorphisms associated with the MRLM phenotype. The potential impact of such mutations on the expression of PBP4, as well as on cell morphology and biofilm formation, was investigated. GWAS revealed that mutations in gdpP were significantly associated with the MRLM phenotype. GdpP is a phosphodiesterase enzyme involved in the degradation of the second messenger cyclic-di-AMP in S. aureus. A total of 131 MRLM isolates carried truncations, insertions or deletions as well as amino acid substitutions, mainly located in the functional DHH-domain of GdpP. We experimentally verified the contribution of these gdpP mutations to the MRLM phenotype by heterologous complementation experiments. The mutations in gdpP had no effect on transcription levels of pbp4; however, cell sizes of MRLM strains were reduced. The impact on biofilm formation was highly strain dependent. We report mutations in gdpP as a clinically relevant mechanism for β-lactam resistance in MRLM isolates. This observation is of particular clinical relevance, since MRLM are easily misclassified as MSSA (meticillin-susceptible S. aureus), which may lead to unnoticed spread of β-lactam-resistant isolates and subsequent treatment failure.
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Affiliation(s)
- Anna Sommer
- Department of Infectious Diseases, Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Stephan Fuchs
- Methodology and Research Infrastructure, Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Franziska Layer
- Department of Infectious Diseases, Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Christoph Schaudinn
- Centre for Biological Threats and Special Pathogens, Advanced Light and Electron Microscopy, Robert Koch Institute, Berlin, Germany
| | - Robert E Weber
- Department of Infectious Diseases, Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Hugues Richard
- Methodology and Research Infrastructure, Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Mareike B Erdmann
- Department of Infectious Diseases, Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Michael Laue
- Centre for Biological Threats and Special Pathogens, Advanced Light and Electron Microscopy, Robert Koch Institute, Berlin, Germany
| | - Christopher F Schuster
- Department of Infectious Diseases, Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Guido Werner
- Department of Infectious Diseases, Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Birgit Strommenger
- Department of Infectious Diseases, Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
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Morroni G, Fioriti S, Salari F, Brenciani A, Brescini L, Mingoia M, Giovanetti E, Pocognoli A, Giacometti A, Molinelli E, Offidani A, Simonetti O, Cirioni O. Characterization and Clonal Diffusion of Ceftaroline Non-Susceptible MRSA in Two Hospitals in Central Italy. Antibiotics (Basel) 2021; 10:antibiotics10081026. [PMID: 34439075 PMCID: PMC8388857 DOI: 10.3390/antibiotics10081026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/13/2021] [Accepted: 08/21/2021] [Indexed: 11/16/2022] Open
Abstract
Background: Ceftaroline represents a novel fifth-generation cephalosporin to treat infections caused by methicillin-resistant Staphylococcus aureus (MRSA). Methods: Ceftaroline susceptibility of 239 MRSA isolates was assessed by disk diffusion and a MIC test strip following both EUCAST and CLSI guidelines. Non-susceptible isolates were epidemiologically characterized by pulsed-field gel electrophoresis, spa typing, and multilocus sequence typing, and further investigated by PCR and whole genome sequencing to detect penicillin-binding protein (PBP) mutations as well as antibiotic resistance and virulence genes. Results: Fourteen isolates out of two hundred and thirty-nine (5.8%) were non-susceptible to ceftaroline (MIC > 1 mg/L), with differences between the EUCAST and CLSI interpretations. The characterized isolates belonged to seven different pulsotypes and three different clones (ST228/CC5-t041-SCCmecI, ST22/CC22-t18014-SCCmecIV, and ST22/CC22-t022-SCCmecIV), confirming a clonal diffusion of ceftaroline non-susceptible strains. Mutations in PBPs involved PBP2a for ST228-t041-SCCmecI strains and all the other PBPs for ST22-t18014-SCCmecIV and ST22-t022-SCCmecIV clones. All isolates harbored antibiotic resistance and virulence genes with a clonal distribution. Conclusion: Our study demonstrated that ceftaroline non-susceptibile isolates belonged not only to ST228 strains (the most widespread clone in Italy) but also to ST22, confirming the increasing role of these clones in hospital infections.
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Affiliation(s)
- Gianluca Morroni
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60126 Ancona, Italy; (G.M.); (S.F.); (F.S.); (A.B.); (L.B.); (M.M.); (A.G.); (O.C.)
| | - Simona Fioriti
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60126 Ancona, Italy; (G.M.); (S.F.); (F.S.); (A.B.); (L.B.); (M.M.); (A.G.); (O.C.)
| | - Federica Salari
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60126 Ancona, Italy; (G.M.); (S.F.); (F.S.); (A.B.); (L.B.); (M.M.); (A.G.); (O.C.)
| | - Andrea Brenciani
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60126 Ancona, Italy; (G.M.); (S.F.); (F.S.); (A.B.); (L.B.); (M.M.); (A.G.); (O.C.)
| | - Lucia Brescini
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60126 Ancona, Italy; (G.M.); (S.F.); (F.S.); (A.B.); (L.B.); (M.M.); (A.G.); (O.C.)
| | - Marina Mingoia
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60126 Ancona, Italy; (G.M.); (S.F.); (F.S.); (A.B.); (L.B.); (M.M.); (A.G.); (O.C.)
| | - Eleonora Giovanetti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60126 Ancona, Italy;
| | | | - Andrea Giacometti
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60126 Ancona, Italy; (G.M.); (S.F.); (F.S.); (A.B.); (L.B.); (M.M.); (A.G.); (O.C.)
| | - Elisa Molinelli
- Dermatological Clinic, Department of Clinical and Molecular Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (E.M.); (A.O.)
| | - Annamaria Offidani
- Dermatological Clinic, Department of Clinical and Molecular Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (E.M.); (A.O.)
| | - Oriana Simonetti
- Dermatological Clinic, Department of Clinical and Molecular Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (E.M.); (A.O.)
- Correspondence: ; Tel.: +39-0715963494
| | - Oscar Cirioni
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60126 Ancona, Italy; (G.M.); (S.F.); (F.S.); (A.B.); (L.B.); (M.M.); (A.G.); (O.C.)
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Gitman MR, Alburquerque B, Chung M, van de Guchte A, Sullivan MJ, Obla A, Polanco J, Oussenko I, Smith ML, Samaroo F, Barackman D, Altman DR, Sordillo EM, van Bakel H. Modified methicillin-resistant Staphylococcus aureus detected in neonatal intensive care patients. J Antimicrob Chemother 2021; 76:2774-2777. [PMID: 34368846 PMCID: PMC8521402 DOI: 10.1093/jac/dkab266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022] Open
Abstract
Objectives As part of an active MRSA surveillance programme in our neonatal ICU, we identified nares surveillance cultures from two infants that displayed heterogeneity in methicillin resistance between isolated subclones that lacked mecA and mecC. Methods The underlying mechanism for the modified Staphylococcus aureus (MODSA) methicillin-resistance phenotype was investigated by WGS. Results Comparison of finished-quality genomes of four MODSA and four MSSA subclones demonstrated that the resistance changes were associated with unique truncating mutations in the gene encoding the cyclic diadenosine monophosphate phosphodiesterase enzyme GdpP or a non-synonymous substitution in the gene encoding PBP2. Conclusions These two cases highlight the difficulty in identifying non-mecA, non-mecC-mediated MRSA isolates in the clinical microbiology laboratory, which leads to difficulties in implementing appropriate therapy and infection control measures.
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Affiliation(s)
- Melissa R Gitman
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Bremy Alburquerque
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Marilyn Chung
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Mitchell J Sullivan
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ajay Obla
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Jose Polanco
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Irina Oussenko
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Melissa L Smith
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Flora Samaroo
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Debbie Barackman
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Deena R Altman
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Emilia Mia Sordillo
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Harm van Bakel
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
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Konstantinovski MM, Veldkamp KE, Lavrijsen APM, Bosch T, Kraakman MEM, Nooij S, Claas ECJ, Gooskens J. Hospital transmission of borderline oxacillin-resistant Staphylococcus aureus evaluated by whole-genome sequencing. J Med Microbiol 2021; 70. [PMID: 34269673 PMCID: PMC8493421 DOI: 10.1099/jmm.0.001384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction Staphylococcus aureus is a major cause of hospital infections worldwide. Awareness towards methicillin-resistant S. aureus (MRSA) infections is high but attention towards borderline oxacillin-resistant S. aureus (BORSA) is limited, possibly due to an underestimated clinical relevance, presumption of low incidence and diagnostic limitations. Gap statement BORSA surveillance has not been routinely implemented, and thus consensus with regard to a definition and infection control measures is lacking. Aim Our goals were to investigate the occurrence, molecular characteristics and clinical manifestations of BORSA infections in the hospital setting. Methodology Following an increased incidence in 2016, BORSA cases in 2014/2016 (in our institution) were more specifically evaluated. Medical records were reviewed to investigate epidemiological links, clinical characteristics and outcomes. Resistance and virulence markers were assessed by whole genome sequencing (WGS). Conventional methods: amplified fragment length polymorphism (AFLP) ; multilocus sequence typing (MLST) and multiple locus variable-number tandem repeat analysis (MLVA) were compared with core genome MLST (cgMLST) and whole-genome single nucleotide polymorphism (wgSNP) analysis to confirm genetic clusters. Results From 2009 to 2013, BORSA comprised 0.1 % of all clinical S. aureus strains. In 2016, the incidence was six-fold higher in comparison to the baseline. Whole-genome SNP and cgMLST confirmed two BORSA clusters among patients with dermatological conditions. Patients with BORSA presented with skin infections, and one case developed a severe invasive infection with a fatal outcome. Infection control measures successfully prevented further transmission in both clusters. WGS findings showed that BORSA strains carried multiple resistance and virulence genes with increased pathogenic potential. Conclusion WGS and cgMLST effectively characterized and confirmed BORSA clusters among at-risk patients with clinical manifestations ranging from mild skin infections to life-threatening bacteraemia. Clinical awareness and active monitoring are therefore warranted for the timely implementation of infection control measures to prevent BORSA transmission in high-risk patients.
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Affiliation(s)
| | - Karin Ellen Veldkamp
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
| | | | - Thijs Bosch
- Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, de Bilt, Netherlands
| | - Margriet E M Kraakman
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
| | - Sam Nooij
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
| | - Eric C J Claas
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
| | - Jairo Gooskens
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
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Cyclic di-AMP Oversight of Counter-Ion Osmolyte Pools Impacts Intrinsic Cefuroxime Resistance in Lactococcus lactis. mBio 2021; 12:mBio.00324-21. [PMID: 33832972 PMCID: PMC8092236 DOI: 10.1128/mbio.00324-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The bacterial second messenger cyclic di-AMP (c-di-AMP) is a global regulator of potassium homeostasis and compatible solute uptake in many Gram-positive bacteria, making it essential for osmoregulation. The role that c-di-AMP plays in β-lactam resistance, however, is unclear despite being first identified a decade ago. The broadly conserved cyclic di-AMP (c-di-AMP) is a conditionally essential bacterial second messenger. The pool of c-di-AMP is fine-tuned through diadenylate cyclase and phosphodiesterase activities, and direct binding of c-di-AMP to proteins and riboswitches allows the regulation of a broad spectrum of cellular processes. c-di-AMP has a significant impact on intrinsic β-lactam antibiotic resistance in Gram-positive bacteria; however, the reason for this is currently unclear. In this work, genetic studies revealed that suppressor mutations that decrease the activity of the potassium (K+) importer KupB or the glutamine importer GlnPQ restore cefuroxime (CEF) resistance in diadenylate cyclase (cdaA) mutants of Lactococcus lactis. Metabolite analyses showed that glutamine is imported by GlnPQ and then rapidly converted to glutamate, and GlnPQ mutations or c-di-AMP negatively affects the pools of the most abundant free amino acids (glutamate and aspartate) during growth. In a high-c-di-AMP mutant, GlnPQ activity could be increased by raising the internal K+ level through the overexpression of a c-di-AMP-insensitive KupB variant. These results demonstrate that c-di-AMP reduces GlnPQ activity and, therefore, the level of the major free anions in L. lactis through its inhibition of K+ import. Excessive ion accumulation in cdaA mutants results in greater spontaneous cell lysis under hypotonic conditions, while CEF-resistant suppressors exhibit reduced cell lysis and lower osmoresistance. This work demonstrates that the overaccumulation of major counter-ion osmolyte pools in c-di-AMP-defective mutants of L. lactis causes cefuroxime sensitivity.
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Gómez P, Ruiz-Ripa L, Fernández-Fernández R, Gharsa H, Ben Slama K, Höfle U, Zarazaga M, Holmes MA, Torres C. Genomic Analysis of Staphylococcus aureus of the Lineage CC130, Including mecC-Carrying MRSA and MSSA Isolates Recovered of Animal, Human, and Environmental Origins. Front Microbiol 2021; 12:655994. [PMID: 33841383 PMCID: PMC8027229 DOI: 10.3389/fmicb.2021.655994] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/03/2021] [Indexed: 02/02/2023] Open
Abstract
Most methicillin resistant Staphylococcus aureus (MRSA) isolates harboring mecC gene belong to clonal complex CC130. This lineage has traditionally been regarded as animal-associated as it lacks the human specific immune evasion cluster (IEC), and has been recovered from a broad range of animal hosts. Nevertheless, sporadic mecC-MRSA human infections have been reported, with evidence of zoonotic transmission in some cases. The objective of this study was to investigate the whole-genome sequences of 18 S. aureus CC130 isolates [13 methicillin-resistant (mecC-MRSA) and five methicillin-susceptible (MSSA)] from different sequences types, obtained from a variety of host species and origins (human, livestock, wild birds and mammals, and water), and from different geographic locations, in order to identify characteristic markers and genomic features. Antibiotic resistance genes found among MRSA-CC130 were those associated with the SSCmecXI element. Most MRSA-CC130 strains carried a similar virulence gene profile. Additionally, six MRSA-CC130 possessed scn-sak and one MSSA-ST130 had lukMF'. The MSSA-ST700 strains were most divergent in their resistance and virulence genes. The pan-genome analysis showed that 29 genes were present solely in MRSA-CC130 (associated with SCCmecXI) and 21 among MSSA-CC130 isolates (associated with phages). The SCCmecXI, PBP3, GdpP, and AcrB were identical at the amino acid level in all strains, but some differences were found in PBP1, PBP2, PBP4, and YjbH proteins. An examination of the host markers showed that the 3' region of the bacteriophage φ3 was nearly identical to the reference sequence. Truncated hlb gene was also found in scn-negative strains (two of them carrying sak-type gene). The dtlB gene of wild rabbit isolates included novel mutations. The vwbp gene was found in the three MSSA-ST700 strains from small ruminants and in one MSSA-ST130 from a red deer; these strains also carried a scn-type gene, different from the human and equine variants. Finally, a phylogenetic analysis showed that the three MSSA-ST700 strains and the two MSSA-ST130 strains cluster separately from the remaining MRSA-CC130 strains with the etD2 gene as marker for the main lineage. The presence of the human IEC cluster in some mecC-MRSA-CC130 strains suggests that these isolates may have had a human origin.
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Affiliation(s)
- Paula Gómez
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Laura Ruiz-Ripa
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Rosa Fernández-Fernández
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Haythem Gharsa
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Karim Ben Slama
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Ursula Höfle
- Health and Biotechnology SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, Spain
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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: 52] [Impact Index Per Article: 17.3] [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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Zuo H, Uehara Y, Lu Y, Sasaki T, Hiramatsu K. Genetic and phenotypic diversity of methicillin-resistant Staphylococcus aureus among Japanese inpatients in the early 1980s. Sci Rep 2021; 11:5447. [PMID: 33686133 PMCID: PMC7940613 DOI: 10.1038/s41598-021-84481-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/16/2021] [Indexed: 01/02/2023] Open
Abstract
To trace the linkage between Japanese healthcare-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) strains in the early 1980s and the 2000s onward, we performed molecular characterizations using mainly whole-genome sequencing. Among the 194 S. aureus strains isolated, 20 mecA-positive MRSA (10.3%), 8 mecA-negative MRSA (4.1%) and 3 mecA-positive methicillin-susceptible S. aureus (MSSA) (1.5%) strains were identified. The most frequent sequence type (ST) was ST30 (n = 11), followed by ST5 (n = 8), ST81 (n = 4), and ST247 (n = 3). Rates of staphylococcal cassette chromosome mec (SCCmec) types I, II, and IV composed 65.2%, 13.0%, and 17.4% of isolates, respectively. Notably, 73.3% of SCCmec type I strains were susceptible to imipenem unlike SCCmec type II strains (0%). ST30-SCCmec I (n = 7) and ST5-SCCmec I (n = 5) predominated, whereas only two strains exhibited imipenem-resistance and were tst-positive ST5-SCCmec II, which is the current Japanese HA-MRSA genotype. All ST30 strains shared the common ancestor strain 55/2053, which caused the global pandemic of Panton-Valentine leukocidin-positive MSSA in Europe and the United States in the 1950s. Conspicuously more heterogeneous, the population of HA-MRSA clones observed in the 1980s, including the ST30-SCCmec I clone, has shifted to the current homogeneous population of imipenem-resistant ST5-SCCmec II clones, probably due to the introduction of new antimicrobials.
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Affiliation(s)
- Hui Zuo
- Department of Microbiology, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yuki Uehara
- Department of Microbiology, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
- Department of Clinical Laboratory, St Luke's International Hospital, Tokyo, Japan.
- Department of Infectious Diseases, St Luke's International Hospital, Tokyo, Japan.
- Center for Infection Control Science Research, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | - Yujie Lu
- Center for Infection Control Science Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takashi Sasaki
- Center for Infection Control Science Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Animal Research Center, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Keiichi Hiramatsu
- Department of Microbiology, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
- Center for Infection Control Science Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Mikkelsen K, Sirisarn W, Alharbi O, Alharbi M, Liu H, Nøhr-Meldgaard K, Mayer K, Vestergaard M, Gallagher LA, Derrick JP, McBain AJ, Biboy J, Vollmer W, O'Gara JP, Grunert T, Ingmer H, Xia G. The Novel Membrane-Associated Auxiliary Factors AuxA and AuxB Modulate β-lactam Resistance in MRSA by stabilizing Lipoteichoic Acids. Int J Antimicrob Agents 2021; 57:106283. [PMID: 33503451 DOI: 10.1016/j.ijantimicag.2021.106283] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/08/2020] [Accepted: 12/19/2020] [Indexed: 01/20/2023]
Abstract
A major determinant of β-lactam resistance in methicillin-resistant Staphylococcus aureus (MRSA) is the drug insensitive transpeptidase, PBP2a, encoded by mecA. Full expression of the resistance phenotype requires auxiliary factors. Two such factors, auxiliary factor A (auxA, SAUSA300_0980) and B (auxB, SAUSA300_1003), were identified in a screen against mutants with increased susceptibility to β-lactams in the MRSA strain, JE2. auxA and auxB encode transmembrane proteins, with AuxA predicted to be a transporter. Inactivation of auxA or auxB enhanced β-lactam susceptibility in community-, hospital- and livestock-associated MRSA strains without affecting PBP2a expression, peptidoglycan cross-linking or wall teichoic acid synthesis. Both mutants displayed increased susceptibility to inhibitors of lipoteichoic acid (LTA) synthesis and alanylation pathways and released LTA even in the absence of β-lactams. The β-lactam susceptibility of the aux mutants was suppressed by mutations inactivating gdpP, which was previously found to allow growth of mutants lacking the lipoteichoic synthase enzyme, LtaS. Using the Galleria mellonella infection model, enhanced survival of larvae inoculated with either auxA or auxB mutants was observed compared with the wild-type strain following treatment with amoxicillin. These results indicate that AuxA and AuxB are central for LTA stability and potential inhibitors can be tools to re-sensitize MRSA strains to β-lactams and combat MRSA infections.
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Affiliation(s)
- Kasper Mikkelsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Denmark
| | - Wanchat Sirisarn
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, United Kingdom
| | - Ohood Alharbi
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, United Kingdom
| | - Mohanned Alharbi
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, United Kingdom
| | - Huayong Liu
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, United Kingdom
| | | | - Katharina Mayer
- Functional Microbiology, Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Martin Vestergaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Denmark
| | - Laura A Gallagher
- Department of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Jeremy P Derrick
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, United Kingdom
| | - Andrew J McBain
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, NU Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, NU Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - James P O'Gara
- Department of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Tom Grunert
- Functional Microbiology, Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Denmark.
| | - Guoqing Xia
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, United Kingdom.
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Comprehensive Genomic Investigation of Adaptive Mutations Driving the Low-Level Oxacillin Resistance Phenotype in Staphylococcus aureus. mBio 2020; 11:mBio.02882-20. [PMID: 33293382 PMCID: PMC7733948 DOI: 10.1128/mbio.02882-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Antistaphylococcal penicillins such as oxacillin are the key antibiotics in the treatment of invasive methicillin-susceptible Staphylococcus aureus (MSSA) infections; however, mec gene-independent resistance adaptation can cause treatment failure. Despite its clinical relevance, the basis of this phenomenon remains poorly understood. Here, we investigated the genomic adaptation to oxacillin at an unprecedented scale using a large collection of 503 clinical mec-negative isolates and 30 in vitro-adapted isolates from independent oxacillin exposures. By combining comparative genomics, evolutionary convergence, and genome-wide association analysis, we found 21 genetic loci associated with low-level oxacillin resistance, underscoring the polygenic nature of this phenotype. Evidence of adaptation was particularly strong for the c-di-AMP signal transduction pathways (gdpP and dacA) and in the clpXP chaperone-protease complex. The role of mutations in gdpP in conferring low-level oxacillin resistance was confirmed by allele-swapping experiments. We found that resistance to oxacillin emerges at high frequency in vitro (median, 2.9 × 10-6; interquartile range [IQR], 1.9 × 10-6 to 3.9 × 10-6), which is consistent with a recurrent minimum inhibitory concentration (MIC) increase across the global phylogeny of clinical isolates. Nevertheless, adaptation in clinical isolates appears sporadically, with no stably adapted lineages, suggesting a high fitness cost of resistance, confirmed by growth assessment of mutants in rich media. Our data provide a broader understanding of the emergence and dynamics of oxacillin resistance adaptation in S. aureus and a framework for future surveillance of this clinically important phenomenon.IMPORTANCE The majority of Staphylococcus aureus strains causing human disease are methicillin-susceptible (MSSA) and can be treated with antistaphylococcal penicillins (such as oxacillin). While acquisition of the mec gene represents the main resistance mechanism to oxacillin, S. aureus can acquire low-level resistance through adaptive mutations in other genes. In this study, we used genomic approaches to understand the basis of S. aureus adaption to oxacillin and its dynamic at the population level. By combining a genome analysis of clinical isolates from persistent MSSA infections, in vitro selection of oxacillin resistance, and genome-wide association analysis on a large collection of isolates, we identified 21 genes linked to secondary oxacillin resistance. Adaptive mutations in these genes were easy to select when S. aureus was exposed to oxacillin, but they also came at a substantial cost in terms of bacterial fitness, suggesting that this phenotype emerges preferentially in the setting of sustained antibiotic exposure.
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Konstantinovski MM, Bekker V, Kraakman MEM, Bruijning ML, van der Zwan CJ, Lopriore E, Veldkamp KE. Borderline oxacillin-resistant Staphylococcus aureus carriage among healthcare workers at neonatal intensive care unit and paediatric ward. J Hosp Infect 2020; 108:104-108. [PMID: 33245996 DOI: 10.1016/j.jhin.2020.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND During a meticillin-resistant Staphylococcus aureus contact tracing and screening investigation, two borderline oxacillin-resistant Staphylococcus aureus (BORSA)-positive screening cultures were encountered among neonatal intensive care unit (NICU) healthcare workers (HCWs). This finding led to further investigations. AIM To assess the likelihood of an outbreak with direct transmission among HCWs. METHODS An infection control team was initiated after the discovery. The team initiated additional infection control measures and evaluated new findings. All NICUs and paediatric ward HCWs were screened for BORSA carriage, and a prospective BORSA seven-week monitoring period for patients was observed. To assess the likelihood of an outbreak with direct transmission among HCWs, the BORSA isolates were analysed using augmented fragment length polymorphism and whole-genome sequencing (WGS). FINDINGS Positive HCWs were prohibited from clinical work while awaiting the results from the screening programme. In all, 127 NICU and 77 general paediatric ward HCWs were screened for BORSA carriage; five HCWs were BORSA positive. Seventy-two patients were screened during the seven-week period yielding a total of 138 cultures, ranging from one to nine cultures per patient. No spread from HCWs to patients occurred, and the BORSA screening programme was discontinued. WGS analysis with core genome multi-locus sequence typing of all five BORSA strains showed relatedness between two NICU strains. CONCLUSION During a seven-week period, no transmission from BORSA-positive HCWs to neonates was observed in either screening or clinical cultures. More vigilance and experience is needed to design adequate evidence-based interventions in the future for this vulnerable population.
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Affiliation(s)
| | - V Bekker
- Leiden University Medical Center, Leiden, The Netherlands
| | - M E M Kraakman
- Leiden University Medical Center, Leiden, The Netherlands
| | - M L Bruijning
- Leiden University Medical Center, Leiden, The Netherlands
| | | | - E Lopriore
- Leiden University Medical Center, Leiden, The Netherlands
| | - K E Veldkamp
- Leiden University Medical Center, Leiden, The Netherlands
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30
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c-di-AMP Accumulation Impairs Muropeptide Synthesis in Listeria monocytogenes. J Bacteriol 2020; 202:JB.00307-20. [PMID: 33020220 DOI: 10.1128/jb.00307-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/17/2020] [Indexed: 12/14/2022] Open
Abstract
Cyclic di-AMP (c-di-AMP) is an essential and ubiquitous second messenger among bacteria. c-di-AMP regulates many cellular pathways through direct binding to several molecular targets in bacterial cells. c-di-AMP depletion is well known to destabilize the bacterial cell wall, resulting in increased bacteriolysis and enhanced susceptibility to cell wall targeting antibiotics. Using the human pathogen Listeria monocytogenes as a model, we found that c-di-AMP accumulation also impaired cell envelope integrity. An L. monocytogenes mutant deleted for c-di-AMP phosphodiesterases (pdeA pgpH mutant) exhibited a 4-fold increase in c-di-AMP levels and several cell wall defects. For instance, the pdeA pgpH mutant was defective for the synthesis of peptidoglycan muropeptides and was susceptible to cell wall-targeting antimicrobials. Among different muropeptide precursors, we found that the pdeA pgpH strain was particularly impaired in the synthesis of d-Ala-d-Ala, which is required to complete the pentapeptide stem associated with UDP-N-acetylmuramic acid (MurNAc). This was consistent with an increased sensitivity to d-cycloserine, which inhibits the d-alanine branch of peptidoglycan synthesis. Finally, upon examining d-Ala:d-Ala ligase (Ddl), which catalyzes the conversion of d-Ala to d-Ala-d-Ala, we found that its activity was activated by K+ Based on previous reports that c-di-AMP inhibits K+ uptake, we propose that c-di-AMP accumulation impairs peptidoglycan synthesis, partially through the deprivation of cytoplasmic K+ levels, which are required for cell wall-synthetic enzymes.IMPORTANCE The bacterial second messenger c-di-AMP is produced by a large number of bacteria and conditionally essential to many species. Conversely, c-di-AMP accumulation is also toxic to bacterial physiology and pathogenesis, but its mechanisms are largely undefined. We found that in Listeria monocytogenes, elevated c-di-AMP levels diminished muropeptide synthesis and increased susceptibility to cell wall-targeting antimicrobials. Cell wall defects might be an important mechanism for attenuated virulence in bacteria with high c-di-AMP levels.
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31
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Casey D, Sleator RD. A genomic analysis of osmotolerance in Staphylococcus aureus. Gene 2020; 767:145268. [PMID: 33157201 DOI: 10.1016/j.gene.2020.145268] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/07/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022]
Abstract
A key phenotypic characteristic of the Gram-positive bacterial pathogen, Staphylococcus aureus, is its ability to grow in low aw environments. A homology transfer based approach, using the well characterised osmotic stress response systems of Bacillus subtilis and Escherichia coli, was used to identify putative osmotolerance loci in Staphylococcus aureus ST772-MRSA-V. A total of 17 distinct putative hyper and hypo-osmotic stress response systems, comprising 78 genes, were identified. The ST772-MRSA-V genome exhibits significant degeneracy in terms of the osmotic stress response; with three copies of opuD, two copies each of nhaK and mrp/mnh, and five copies of opp. Furthermore, regulation of osmotolerance in ST772-MRSA-V appears to be mediated at the transcriptional, translational, and post-translational levels.
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Affiliation(s)
- Dylan Casey
- Department of Biological Sciences, Munster Technological University, Bishopstown Campus, Cork, Ireland
| | - Roy D Sleator
- Department of Biological Sciences, Munster Technological University, Bishopstown Campus, Cork, Ireland.
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Sasaki H, Ishikawa H, Itoh T, Arano M, Hirata K, Ueshiba H. Penicillin-Binding Proteins and Associated Protein Mutations Confer Oxacillin/Cefoxitin Tolerance in Borderline Oxacillin-Resistant Staphylococcus aureus. Microb Drug Resist 2020; 27:590-595. [DOI: 10.1089/mdr.2020.0191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Hiraku Sasaki
- Department of Health Science, Faculty of Health and Sports Science, Juntendo University, Inzai, Japan
| | - Hiroki Ishikawa
- Department of Microbiology and Immunology, Showa University School of Medicine, Shinagawa-ku, Japan
| | - Taisuke Itoh
- Department of Health Science, Faculty of Health and Sports Science, Juntendo University, Inzai, Japan
| | - Makoto Arano
- Department of Health Science, Faculty of Health and Sports Science, Juntendo University, Inzai, Japan
| | - Koya Hirata
- Department of Health Science, Faculty of Health and Sports Science, Juntendo University, Inzai, Japan
| | - Hidehiro Ueshiba
- Department of Microbiology and Immunology, Tokyo Women's Medical University School of Medicine, Shinjuku-ku, Japan
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Silva ATF, da Silva JG, Aragão BB, Peixoto RM, Mota RA. Occurrence of β-lactam-resistant Staphylococcus aureus in milk from primiparous dairy cows in the northeastern region of Brazil. Trop Anim Health Prod 2020; 52:2303-2307. [PMID: 32146685 DOI: 10.1007/s11250-020-02259-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 03/02/2020] [Indexed: 11/26/2022]
Abstract
The objective of the current study was to isolate and identify Staphylococcus (S.) aureus strains resistant to beta-lactam antibiotics from primiparous cows' milk. A total of 432 milk samples were collected from all primiparous dairy cows in early lactation that originated from 9 dairy properties. All samples were cultured in Mannitol salt agar enriched with egg yolk emulsion. Determination of genotypic resistance of S. aureus was achieved by polymerase chain reaction (PCR) for amplification of the blaZ, mecA, and mecC genes. Phenotypic resistance of S. aureus strains was evaluated by minimal inhibitory concentration (MIC) technique using broth microdilutions of penicillin G and oxacillin. From all the mammary quarters examined, S. aureus strains were detected in 27 out of 432 (6.25%) milk samples (CI95%, 4.33-8.84). From all dairy properties visited, only two out of 9 were found to have S. aureus. Hence, it was possible to evaluate genotypic and phenotypic resistance in 27 samples from two dairy farms. The isolates of S. aureus had a frequency of (20/27) 74.07% to blaZ gene (CI95%, 57.5-90.6), whereas mecA and mecC genes were not observed. According to MIC results, penicillin G had a 74.07% (20/27) resistance rate (CI95%, 57.5-90.6) and oxacillin had a 14.81% (4/27) resistance rate (CI95%, 1.4-28.2). Thus, the circulation of S. aureus strains resistant to beta-lactams has been confirmed in primiparous dairy cows in the northeastern region of Brazil, indicating the need for new management strategies involving the use of beta-lactam drugs to treat mastitis, discouraging and/or limiting their use. Also, it is important to highlight the need for further studies on epidemiology and traceability of the pathogen.
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Affiliation(s)
- Amanda T F Silva
- Universidade Federal Rural de Pernambuco, Av. Manuel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52171-900, Brazil.
| | - José G da Silva
- Universidade Federal Rural de Pernambuco, Av. Manuel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52171-900, Brazil
| | - Breno B Aragão
- Universidade Federal Rural de Pernambuco, Av. Manuel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52171-900, Brazil
| | - Rodolfo M Peixoto
- Instituto Federal de Educação, Ciência e Tecnologia do Sertão Pernambucano, R. Maria Luzia de Araújo, 791, João de Deus, Petrolina, PE, 56316-686, Brazil
| | - Rinaldo A Mota
- Universidade Federal Rural de Pernambuco, Av. Manuel de Medeiros, s/n, Dois Irmãos, Recife, PE, 52171-900, Brazil
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Giulieri SG, Tong SYC, Williamson DA. Using genomics to understand meticillin- and vancomycin-resistant Staphylococcus aureus infections. Microb Genom 2020; 6:e000324. [PMID: 31913111 PMCID: PMC7067033 DOI: 10.1099/mgen.0.000324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/12/2019] [Indexed: 12/15/2022] Open
Abstract
Resistance to meticillin and vancomycin in Staphylococcus aureus significantly complicates the management of severe infections like bacteraemia, endocarditis or osteomyelitis. Here, we review the molecular mechanisms and genomic epidemiology of resistance to these agents, with a focus on how genomics has provided insights into the emergence and evolution of major meticillin-resistant S. aureus clones. We also provide insights on the use of bacterial whole-genome sequencing to inform management of S. aureus infections and for control of transmission at the hospital and in the community.
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Affiliation(s)
- Stefano G. Giulieri
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Infectious Disease Department, Austin Health, Melbourne, Australia
| | - Steven Y. C. Tong
- Victorian Infectious Disease Service, Royal Melbourne Hospital, and Doherty Department University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
- Menzies School of Health Research, Darwin, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia
- Microbiology, Royal Melbourne Hospital, Melbourne, Australia
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Gostev V, Sopova J, Kalinogorskaya O, Tsvetkova I, Lobzin Y, Klotchenko S, Sidorenko S. In Vitro Ceftaroline Resistance Selection of Methicillin-Resistant Staphylococcus aureus Involves Different Genetic Pathways. Microb Drug Resist 2019; 25:1401-1409. [PMID: 31329022 DOI: 10.1089/mdr.2019.0130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The pathways in the development of ceftaroline resistance of methicillin-resistant Staphylococcus aureus (MRSA) isolates belonging to the ST8, ST239, and ST228 were evaluated. Ceftaroline-resistant derivatives were isolated through selection during 40 passages. Ceftaroline MIC measurements and whole-genome sequencing were performed after 5, 20, and 40 passages. In two ST8 derivative isolates, ceftaroline MIC increased up to 128 mg/L. Mutations were acquired in gdpP and graS in one isolate after 20 passages and in gdpP in another after 40 passages. MIC for two ST239 derivatives increased to 128 mg/L. Substitutions in Pbp4 and polymorphisms in the upstream region of pbp4 were identified in both derivatives after 40 passages. In one isolate, additional mutation in gdpP and deletion in graR were detected. In an ST228 derivative, MIC increased to 32 mg/L with one mutation in penicillin-binding protein 2a (Y446N) detected after five passages and a second (E447K) after 20 passages. Three pathways in the development of ceftaroline resistance were identified. For ST8 and ST239 derivatives mutations were detected in gdpP and pbp4, respectively, whereas in ST228 - in mecA. Most derivatives harbored additional mutations whose potential role in the development of resistance has not been determined.
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Affiliation(s)
- Vladimir Gostev
- Department of Medical Microbiology and Molecular Epidemiology, Pediatric Research and Clinical Center for Infectious Diseases, Saint Petersburg, Russia
- Department of Medical Microbiology, North-Western State Medical University named after I.I. Mechnikov, Saint Petersburg, Russia
| | - Julia Sopova
- Laboratory of Genetic Models of Human Diseases, Saint Petersburg Branch of Vavilov Institute of General Genetics, Saint Petersburg, Russia
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Olga Kalinogorskaya
- Department of Medical Microbiology and Molecular Epidemiology, Pediatric Research and Clinical Center for Infectious Diseases, Saint Petersburg, Russia
| | - Irina Tsvetkova
- Department of Medical Microbiology and Molecular Epidemiology, Pediatric Research and Clinical Center for Infectious Diseases, Saint Petersburg, Russia
| | - Yuri Lobzin
- Department of Medical Microbiology and Molecular Epidemiology, Pediatric Research and Clinical Center for Infectious Diseases, Saint Petersburg, Russia
- Department of Medical Microbiology, North-Western State Medical University named after I.I. Mechnikov, Saint Petersburg, Russia
| | - Sergey Klotchenko
- Division of Viral Molecular Biology, Smorodintsev Research Institute of Influenza, Saint Petersburg, Russia
| | - Sergey Sidorenko
- Department of Medical Microbiology and Molecular Epidemiology, Pediatric Research and Clinical Center for Infectious Diseases, Saint Petersburg, Russia
- Department of Medical Microbiology, North-Western State Medical University named after I.I. Mechnikov, Saint Petersburg, Russia
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36
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Contribution of YjbIH to Virulence Factor Expression and Host Colonization in Staphylococcus aureus. Infect Immun 2019; 87:IAI.00155-19. [PMID: 30885928 DOI: 10.1128/iai.00155-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/10/2019] [Indexed: 12/17/2022] Open
Abstract
To persist within the host and cause disease, Staphylococcus aureus relies on its ability to precisely fine-tune virulence factor expression in response to rapidly changing environments. During an unbiased transposon mutant screen, we observed that disruption of a two-gene operon, yjbIH, resulted in decreased levels of pigmentation and aureolysin (Aur) activity relative to the wild-type strain. Further analyses revealed that YjbH, a predicted thioredoxin-like oxidoreductase, is predominantly responsible for the observed yjbIH mutant phenotypes, though a minor role exists for the putative truncated hemoglobin YjbI. These differences were due to significantly decreased expression of crtOPQMN and aur Previous studies found that YjbH targets the disulfide- and oxidative stress-responsive regulator Spx for degradation by ClpXP. The absence of yjbH or yjbI resulted in altered sensitivities to nitrosative and oxidative stress and iron deprivation. Additionally, aconitase activity was altered in the yjbH and yjbI mutant strains. Decreased levels of pigmentation and aureolysin (Aur) activity in the yjbH mutant were found to be Spx dependent. Lastly, we used a murine sepsis model to determine the effect of the yjbIH deletion on pathogenesis and found that the mutant was better able to colonize the kidneys and spleens during an acute infection than the wild-type strain. These studies identified changes in pigmentation and protease activity in response to YjbIH and are the first to have shown a role for these proteins during infection.
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