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Dabernig-Heinz J, Lohde M, Hölzer M, Cabal A, Conzemius R, Brandt C, Kohl M, Halbedel S, Hyden P, Fischer MA, Pietzka A, Daza B, Idelevich EA, Stöger A, Becker K, Fuchs S, Ruppitsch W, Steinmetz I, Kohler C, Wagner GE. A multicenter study on accuracy and reproducibility of nanopore sequencing-based genotyping of bacterial pathogens. J Clin Microbiol 2024; 62:e0062824. [PMID: 39158309 PMCID: PMC11389150 DOI: 10.1128/jcm.00628-24] [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] [Received: 04/26/2024] [Accepted: 07/25/2024] [Indexed: 08/20/2024] Open
Abstract
Nanopore sequencing has shown the potential to democratize genomic pathogen surveillance due to its ease of use and low entry cost. However, recent genotyping studies showed discrepant results compared to gold-standard short-read sequencing. Furthermore, although essential for widespread application, the reproducibility of nanopore-only genotyping remains largely unresolved. In our multicenter performance study involving five laboratories, four public health-relevant bacterial species were sequenced with the latest R10.4.1 flow cells and V14 chemistry. Core genome MLST analysis of over 500 data sets revealed highly strain-specific typing errors in all species in each laboratory. Investigation of the methylation-related errors revealed consistent DNA motifs at error-prone sites across participants at read level. Depending on the frequency of incorrect target reads, this either leads to correct or incorrect typing, whereby only minimal frequency deviations can randomly determine the final result. PCR preamplification, recent basecalling model updates and an optimized polishing strategy notably diminished the non-reproducible typing. Our study highlights the potential for new errors to appear with each newly sequenced strain and lays the foundation for computational approaches to reduce such typing errors. In conclusion, our multicenter study shows the necessity for a new validation concept for nanopore sequencing-based, standardized bacterial typing, where single nucleotide accuracy is critical.
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Affiliation(s)
- Johanna Dabernig-Heinz
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Mara Lohde
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Martin Hölzer
- Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany
| | - Adriana Cabal
- Austrian Agency for Health and Food Safety, Vienna, Austria
| | | | - Christian Brandt
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Matthias Kohl
- Medical and Life Sciences Faculty, Furtwangen University, Villingen-Schwenningen, Germany
| | - Sven Halbedel
- Nosocomial Pathogens and Antibiotic Resistances (FG13), Robert Koch Institute, Wernigerode, Germany
- Institute for Medical Microbiology and Hospital Hygiene, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Patrick Hyden
- Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Martin A. Fischer
- Enteropathogenic bacteria and Legionella (FG11), Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Ariane Pietzka
- Austrian Agency for Health and Food Safety, Graz, Austria
| | - Beatriz Daza
- Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Evgeny A. Idelevich
- Friedrich Loeffler Institute for Medical Microbiology, F.-Sauerbruch-Str., Greifswald, Germany
| | - Anna Stöger
- Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Karsten Becker
- Friedrich Loeffler Institute for Medical Microbiology, F.-Sauerbruch-Str., Greifswald, Germany
| | - Stephan Fuchs
- Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany
| | | | - Ivo Steinmetz
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christian Kohler
- Friedrich Loeffler Institute for Medical Microbiology, F.-Sauerbruch-Str., Greifswald, Germany
| | - Gabriel E. Wagner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
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Yamazaki Y, Ito T, Tamai M, Nakagawa S, Nakamura Y. The role of Staphylococcus aureus quorum sensing in cutaneous and systemic infections. Inflamm Regen 2024; 44:9. [PMID: 38429810 PMCID: PMC10905890 DOI: 10.1186/s41232-024-00323-8] [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: 12/18/2023] [Accepted: 02/15/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Staphylococcus aureus is a leading cause of human bacterial infections worldwide. It is the most common causative agent of skin and soft tissue infections, and can also cause various other infections, including pneumonia, osteomyelitis, as well as life-threatening infections, such as sepsis and infective endocarditis. The pathogen can also asymptomatically colonize human skin, nasal cavity, and the intestine. S. aureus colonizes approximately 20-30% of human nostrils, being an opportunistic pathogen for subsequent infection. Its strong ability to silently spread via human contact makes it difficult to eradicate S. aureus. A major concern with S. aureus is its capacity to develop antibiotic resistance and adapt to diverse environmental conditions. The variability in the accessory gene regulator (Agr) region of the genome contributes to a spectrum of phenotypes within the bacterial population, enhancing the likelihood of survival in different environments. Agr functions as a central quorum sensing (QS) system in S. aureus, allowing bacteria to adjust gene expression in response to population density. Depending on Agr expression, S. aureus secretes various toxins, contributing to virulence in infectious diseases. Paradoxically, expressing Agr may be disadvantageous in certain situations, such as in hospitals, causing S. aureus to generate Agr mutants responsible for infections in healthcare settings. MAIN BODY This review aims to demonstrate the molecular mechanisms governing the diverse phenotypes of S. aureus, ranging from a harmless colonizer to an organism capable of infecting various human organs. Emphasis will be placed on QS and its role in orchestrating S. aureus behavior across different contexts. SHORT CONCLUSION The pathophysiology of S. aureus infection is substantially influenced by phenotypic changes resulting from factors beyond Agr. Future studies are expected to give the comprehensive understanding of S. aureus overall profile in various settings.
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Affiliation(s)
- Yuriko Yamazaki
- Cutaneous Allergy and Host Defense, Immunology Frontier Research Center, Osaka, University, Osaka, 565-0871, Japan
- Department of Dermatology, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Tomoka Ito
- Department of Dermatology, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Masakazu Tamai
- Department of Dermatology, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Seitaro Nakagawa
- Department of Dermatology, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Yuumi Nakamura
- Cutaneous Allergy and Host Defense, Immunology Frontier Research Center, Osaka, University, Osaka, 565-0871, Japan.
- Department of Dermatology, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan.
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Campbell MJ, Beenken KE, Ramirez AM, Smeltzer MS. The major role of sarA in limiting Staphylococcus aureus extracellular protease production in vitro is correlated with decreased virulence in diverse clinical isolates in osteomyelitis. Virulence 2023; 14:2175496. [PMID: 36748843 PMCID: PMC9928472 DOI: 10.1080/21505594.2023.2175496] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
We previously demonstrated that MgrA, SarA, SarR, SarS, SarZ, and Rot bind at least three of the four promoters associated with genes encoding primary extracellular proteases in Staphylococcus aureus (Aur, ScpA, SspA/SspB, SplA-F). We also showed that mutation of sarA results in a greater increase in protease production, and decrease in biofilm formation, than mutation of the loci encoding any of these other proteins. However, these conclusions were based on in vitro studies. Thus, the goal of the experiments reported here was to determine the relative impact of the regulatory loci encoding these proteins in vivo. To this end, we compared the virulence of mgrA, sarA, sarR, sarS, sarZ, and rot mutants in a murine osteomyelitis model. Mutants were generated in the methicillin-resistant USA300 strain LAC and the methicillin-sensitive USA200 strain UAMS-1, which was isolated directly from the bone of an osteomyelitis patient during surgical debridement. Mutation of mgrA and rot limited virulence to a statistically significant extent in UAMS-1, but not in LAC, while the sarA mutant exhibited reduced virulence in both strains. The reduced virulence of the sarA mutant was correlated with reduced cytotoxicity for osteoblasts and osteoclasts, reduced biofilm formation, and reduced sensitivity to the antimicrobial peptide indolicidin, all of which were directly attributable to increased protease production in both LAC and UAMS-1. These results illustrate the importance of considering diverse clinical isolates when evaluating the impact of regulatory mutations on virulence and demonstrate the significance of SarA in limiting protease production in vivo in S. aureus.
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Affiliation(s)
- Mara J. Campbell
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Karen E. Beenken
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Aura M. Ramirez
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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Pivard M, Caldelari I, Brun V, Croisier D, Jaquinod M, Anzala N, Gilquin B, Teixeira C, Benito Y, Couzon F, Romby P, Moreau K, Vandenesch F. Complex Regulation of Gamma-Hemolysin Expression Impacts Staphylococcus aureus Virulence. Microbiol Spectr 2023; 11:e0107323. [PMID: 37347186 PMCID: PMC10434192 DOI: 10.1128/spectrum.01073-23] [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: 03/15/2023] [Accepted: 05/25/2023] [Indexed: 06/23/2023] Open
Abstract
Staphylococcus aureus gamma-hemolysin CB (HlgCB) is a core-genome-encoded pore-forming toxin that targets the C5a receptor, similar to the phage-encoded Panton-Valentine leucocidin (PVL). Absolute quantification by mass spectrometry of HlgCB in 39 community-acquired pneumonia (CAP) isolates showed considerable variations in the HlgC and HlgB yields between isolates. Moreover, although HlgC and HlgB are encoded on a single operon, their levels were dissociated in 10% of the clinical strains studied. To decipher the molecular basis for the variation in hlgCB expression and protein production among strains, different regulation levels were analyzed in representative clinical isolates and reference strains. Both the HlgCB level and the HlgC/HlgB ratio were found to depend on hlgC promoter activity and mRNA processing and translation. Strikingly, only one single nucleotide polymorphism (SNP) in the 5' untranslated region (UTR) of hlgCB mRNA strongly impaired hlgC translation in the USA300 strain, leading to a strong decrease in the level of HlgC but not in HlgB. Finally, we found that high levels of HlgCB synthesis led to mortality in a rabbit model of pneumonia, correlated with the implication of the role of HlgCB in severe S. aureus CAP. Taken together, this work illustrates the complexity of virulence factor expression in clinical strains and demonstrates a butterfly effect where subtle genomic variations have a major impact on phenotype and virulence. IMPORTANCE S. aureus virulence in pneumonia results in its ability to produce several virulence factors, including the leucocidin PVL. Here, we demonstrate that HlgCB, another leucocidin, which targets the same receptors as PVL, highly contributes to S. aureus virulence in pvl-negative strains. In addition, considerable variations in HlgCB quantities are observed among clinical isolates from patients with CAP. Biomolecular analyses have revealed that a few SNPs in the promoter sequences and only one SNP in the 5' UTR of hlgCB mRNA induce the differential expression of hlgCB, drastically impacting hlgC mRNA translation. This work illustrates the subtlety of regulatory mechanisms in bacteria, especially the sometimes major effects on phenotypes of single nucleotide variation in noncoding regions.
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Affiliation(s)
- Mariane Pivard
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Isabelle Caldelari
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Virginie Brun
- Université Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, Grenoble, France
- Université Grenoble Alpes, CEA, LETI, Clinatec, Grenoble, France
| | | | - Michel Jaquinod
- Université Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, Grenoble, France
| | | | - Benoît Gilquin
- Université Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, Grenoble, France
- Université Grenoble Alpes, CEA, LETI, Clinatec, Grenoble, France
| | - Chloé Teixeira
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Yvonne Benito
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
| | - Florence Couzon
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Pascale Romby
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg, France
| | - Karen Moreau
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - François Vandenesch
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
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Ribeiro M, Sousa M, Borges V, Gomes JP, Duarte S, Isidro J, Vieira L, Torres C, Santos H, Capelo JL, Poeta P, Igrejas G. Bioinformatics study of expression from genomes of epidemiologically related MRSA CC398 isolates from human and wild animal samples. J Proteomics 2022; 268:104714. [PMID: 36058542 DOI: 10.1016/j.jprot.2022.104714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/28/2022] [Indexed: 10/14/2022]
Abstract
One of the most important livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) genetic lineages is the clonal complex (CC) 398, which can cause typical S. aureus-associated infections in people. In this work, whole-genome sequencing, RNA-sequencing, and gel-based comparative proteomics were applied to study the genetic characteristics of three MRSA CC398 isolates recovered from humans (strains C5621 and C9017), and from an animal (strain OR418). Of the three strains, C9017 presented the broadest resistance genotype, including resistance to fluroquinolone, clindamycin, tiamulin, macrolide and aminoglycoside antimicrobial classes. The scn, sak, and chp genes of the immune evasion cluster system were solely detected in OR418. Pangenome analysis showed a total of 288 strain-specific genes, most of which are hypothetical or phage-related proteins. OR418 had the most pronounced genetic differences. RNAIII (δ-hemolysin) gene was clearly the most expressed gene in OR418 and C5621, but it was not detected in C9017. Significant differences in the proteome profiles were found between strains. For example, the immunoglobulin-binding protein Sbi was more abundant in OR418. Considering that Sbi is a multifunctional immune evasion factor in S. aureus, the results point to OR418 strain having high zoonotic potential. Overall, multiomics biomarker signatures can assume an important role to advance precision medicine in the years to come. SIGNIFICANCE: MRSA is one of the most representative drug-resistant pathogens and its dissemination is increasing due to MRSA capability of establishing new reservoirs. LA-MRSA is considered an emerging problem worldwide and CC398 is one of the most important genetic lineages. In this study, three MRSA CC398 isolates recovered from humans and from a wild animal were analyzed through whole-genome sequencing, RNA-sequencing, and gel-based comparative proteomics in order to gather systems-wide omics data and better understand the genetic characteristics of this lineage to identify distinctive markers and genomic features of relevance to public health. The scn, sak, and chp genes of the immune evasion cluster system were solely detected in OR418. Pangenome analysis showed a total of 288 strain-specific genes, most of which are hypothetical or phage-related proteins. OR418 had the most pronounced genetic differences. RNAIII (δ-hemolysin) gene was clearly the most expressed gene in OR418 and C5621, but it was not detected in C9017. Significant differences in the proteome profiles were found between strains.
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Affiliation(s)
- Miguel Ribeiro
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal
| | - Margarida Sousa
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - Sílvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisbon, Portugal; Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Carmen Torres
- Biochemistry and Molecular Biology Unit, Faculty of Science and Technology, University of La Rioja, 26006 Logroño, Spain
| | - Hugo Santos
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal; Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - José Luís Capelo
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Patrícia Poeta
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal; Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real 5000-801, Portugal; CECAV-Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal.
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Kim JM, Chung SH, Kim I, Kim JS. Comparison of peaks in the matrix-assisted laser desorption ionization time-of-flight mass spectrometry spectra of Staphylococcus aureus grown on various blood agar plates. J Microbiol Methods 2022; 196:106471. [PMID: 35460710 DOI: 10.1016/j.mimet.2022.106471] [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: 11/02/2021] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 12/27/2022]
Abstract
Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is routinely used for bacterial identification in clinical laboratories. Bacterial protein expression may differ according to their growth conditions, especially the culture medium composition. We aimed to study the peak variations of Staphylococcus aureus grown on various blood agar plates (BAP), especially phenol-soluble modulin-mec (PSM-mec) peak (m/z 2409) associated with mecA gene conferring methicillin resistance. Methicillin-resistant S. aureus (MRSA) ATCC 43300 and eight clinical MRSA isolates were cultured on various commercial BAPs including tryptic soy agar-based BAPs, Columbia agar-based BAP and in-house BAPs with the addition of yeast extract. Analysis of the MALDI-TOF peaks of S. aureus, cultured on various BAPs, revealed the peak intensities of low-molecular weight proteins to vary depending on the composition of BAPs, especially the presence or absence of yeast extract. Especially, the PSM-mec and delta-toxin peaks showed low intensity for S. aureus ATCC 43300 and clinical isolates. No significant differences were found in the number of peaks, but some peaks had lower intensity, corresponding to the medium containing yeast extract, in low-mass region (<m/z 4000). BAPs based on tryptic soy agar rather than Columbia agar seems to be appropriate for the detection of PSM-mec, a methicillin resistance marker of S. aureus and delta-toxin, an agr function indicator.
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Affiliation(s)
- Jung-Min Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Sung Hee Chung
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Inhee Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea.
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7
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Sherwin G, Breen J. Streptococcus uberis
‐associated mastitis in dairy herds: dealing with outbreaks and improving control. IN PRACTICE 2022. [DOI: 10.1002/inpr.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Rom JS, Beenken KE, Ramirez AM, Walker CM, Echols EJ, Smeltzer MS. Limiting protease production plays a key role in the pathogenesis of the divergent clinical isolates of Staphylococcus aureus LAC and UAMS-1. Virulence 2021; 12:584-600. [PMID: 33538230 PMCID: PMC7872036 DOI: 10.1080/21505594.2021.1879550] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/17/2020] [Accepted: 01/10/2021] [Indexed: 01/13/2023] Open
Abstract
Using the USA300, methicillin-resistant Staphylococcus aureus strain LAC, we previously examined the impact of regulatory mutations implicated in biofilm formation on protease production and virulence in a murine sepsis model. Here we examined the impact of these mutations in the USA200, methicillin-sensitive strain UAMS-1. Mutation of agr, mgrA, rot, sarA and sigB attenuated the virulence of UAMS-1. A common characteristic of codY, rot, sigB, and sarA mutants was increased protease production, with mutation of rot having the least impact followed by mutation of codY, sigB and sarA, respectively. Protein A was undetectable in conditioned medium from all four mutants, while extracellular nuclease was only present in the proteolytically cleaved NucA form. The abundance of high molecular weight proteins was reduced in all four mutants. Biofilm formation was reduced in codY, sarA and sigB mutants, but not in the rot mutant. Eliminating protease production partially reversed these phenotypes and enhanced biofilm formation. This was also true in LAC codY, rot, sarA and sigB mutants. Eliminating protease production enhanced the virulence of LAC and UAMS-1 sarA, sigB and rot mutants in a murine sepsis model but did not significantly impact the virulence of the codY mutant in either strain. Nevertheless, these results demonstrate that repressing protease production plays an important role in defining critical phenotypes in diverse clinical isolates of S. aureus and that Rot, SigB and SarA play critical roles in this regard.
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Affiliation(s)
- Joseph S. Rom
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Karen E. Beenken
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Aura M. Ramirez
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Christopher M. Walker
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Ethan J. Echols
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Mark S. Smeltzer
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Department of Orthopaedic Surgery, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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9
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Lee YW, Bae S, Yang E, Chung H, Kim E, Jung J, Kim MJ, Chong YP, Kim SH, Choi SH, Lee SO, Kim YS. Clinical and Microbiological Characteristics of Hospital-Acquired Methicillin-Resistant Staphylococcus aureus Bacteremia Caused by a Community-Associated PVL-Negative Strain. Open Forum Infect Dis 2021; 8:ofab424. [PMID: 34676275 PMCID: PMC8527597 DOI: 10.1093/ofid/ofab424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Background ST72-SCCmecIV, a community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strain in Korea, originated in the community and has been spreading in health care settings. Herein, we describe the clinical and microbiological characteristics of patients with hospital-acquired MRSA bacteremia (MRSAB) caused by community-associated strains. Methods We analyzed hospital-acquired MRSAB cases caused by ST72-SCCmecIV using a prospective cohort of patients with SAB in a tertiary hospital in Korea from July 2008 to December 2018. We compared the clinical and microbiological characteristics of ST72-SCCmecIV with ST5-SCCmecII, a representative hospital-associated genotype strain. Results Of the 1782 S. aureus bacteremia (SAB) cases, 628 (35.2%) were hospital-acquired MRSAB. Of the 628 isolates, 431 (68.6%) were ST5-SCCmecII and 152 (24.2%) were ST72-SCCmecIV. Patients with ST72-SCCmecIV were younger than those with ST5-SCCmecII and less likely to have a history of recent surgery, antibiotic treatment, nasal MRSA colonization, and central venous catheter placement. Compared with ST5-SCCmecII, ST72-SCCmecIV isolates were more likely to have vancomycin MICs ≤1.0 mg/L (P < .001). Osteoarticular infection as the site of infection (7.2% [11/152] vs 1.4% [6/431]) was more common in patients with ST72-SCCmecIV. There were no significant differences in the rate of recurrence (≤90 days), persistent bacteremia (≥7 days), or 30- and 90-day mortality rates between the 2 groups. Conclusions Osteoarticular infections were more prevalent in ST72-SCCmecIV MRSAB. Mortality rates between the ST72-SCCmecIV and ST5-SCCmecII groups were not significantly different.
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Affiliation(s)
- Yun Woo Lee
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seongman Bae
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Eunmi Yang
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Hyemin Chung
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Eunsil Kim
- Center for Antimicrobial Resistance and Microbial Genetics, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jiwon Jung
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Min Jae Kim
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yong Pil Chong
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sung-Han Kim
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sang-Ho Choi
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sang-Oh Lee
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yang Soo Kim
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.,Center for Antimicrobial Resistance and Microbial Genetics, University of Ulsan College of Medicine, Seoul, Republic of Korea
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10
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Rumpf C, Lange J, Schwartbeck B, Kahl BC. Staphylococcus aureus and Cystic Fibrosis-A Close Relationship. What Can We Learn from Sequencing Studies? Pathogens 2021; 10:1177. [PMID: 34578208 PMCID: PMC8466686 DOI: 10.3390/pathogens10091177] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023] Open
Abstract
Staphylococcus aureus is next to Pseudomonas aeruginosa the most isolated pathogen from the airways of cystic fibrosis (CF) patients, who are often infected by a dominant S. aureus clone for extended periods. To be able to persist, the pathogen has to adapt to the hostile niche of the airways to counteract host defence, antibiotic therapy and the competition with coinfecting pathogens. S. aureus is equipped with many virulence factors including adhesins, toxins that are localized on the chromosome, on plasmids or are phage-related. S. aureus is especially versatile and adaptation and evolution of the pathogen occurs by the acquisition of new genes by horizontal gene transfer (HGT), changes in nucleotides (single nucleotide variations, SNVs) that can cause a selective advantage for the bacteria and become fixed in subpopulations. Methicillin-resistant S. aureus are a special threat to CF patients due to the more severe lung disease occurring in infected patients. Today, with decreasing costs for sequencing, more and more studies using S. aureus isolates cultured from CF patients are being published, which use whole genome sequencing (WGS), multilocus sequence typing (MLST) or spa-sequence typing (spa-typing) to follow the population dynamics of S. aureus, elucidate the underlying mechanisms of phenotypic variants, newly acquired resistance or adaptation to the host response in this particular niche. In the first part of this review, an introduction to the genetic make-up and the pathogenesis of S. aureus with respect to CF is provided. The second part presents an overview of recent studies and their findings using genotypic methods such as single or multilocus sequencing and whole genome sequencing, which identify factors contributing to the adaptation of S. aureus and its evolution in the airways of individuals with CF.
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Affiliation(s)
| | | | | | - Barbara C. Kahl
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (C.R.); (J.L.); (B.S.)
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11
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Su M, Davis MH, Peterson J, Solis-Lemus C, Satola SW, Read TD. Effect of genetic background on the evolution of Vancomycin-Intermediate Staphylococcus aureus (VISA). PeerJ 2021; 9:e11764. [PMID: 34306830 PMCID: PMC8284308 DOI: 10.7717/peerj.11764] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/22/2021] [Indexed: 11/20/2022] Open
Abstract
Vancomycin-intermediate Staphylococcus aureus (VISA) typically arises through accumulation of chromosomal mutations that alter cell-wall thickness and global regulatory pathways. Genome-based prediction of VISA requires understanding whether strain background influences patterns of mutation that lead to resistance. We used an iterative method to experimentally evolve three important methicillin-resistant S. aureus (MRSA) strain backgrounds-(CC1, CC5 and CC8 (USA300)) to generate a library of 120 laboratory selected VISA isolates. At the endpoint, isolates had vancomycin MICs ranging from 4 to 10 μg/mL. We detected mutations in more than 150 genes, but only six genes (already known to be associated with VISA from prior studies) were mutated in all three background strains (walK, prs, rpoB, rpoC, vraS, yvqF). We found evidence of interactions between loci (e.g., vraS and yvqF mutants were significantly negatively correlated) and rpoB, rpoC, vraS and yvqF were more frequently mutated in one of the backgrounds. Increasing vancomycin resistance was correlated with lower maximal growth rates (a proxy for fitness) regardless of background. However, CC5 VISA isolates had higher MICs with fewer rounds of selection and had lower fitness costs than the CC8 VISA isolates. Using multivariable regression, we found that genes differed in their contribution to overall MIC depending on the background. Overall, these results demonstrated that VISA evolved through mutations in a similar set of loci in all backgrounds, but the effect of mutation in common genes differed with regard to fitness and contribution to resistance in different strains.
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Affiliation(s)
- Michelle Su
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Michelle H Davis
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Jessica Peterson
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Claudia Solis-Lemus
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sarah W Satola
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA.,Department of Dermatology, School of Medicine, Emory University, Atlanta, Georgia, USA
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12
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Genotypic and Phenotypic Characterization of Staphylococcus aureus Isolates from the Respiratory Tract in Mechanically-Ventilated Patients. Toxins (Basel) 2021; 13:toxins13020122. [PMID: 33562023 PMCID: PMC7915691 DOI: 10.3390/toxins13020122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/03/2021] [Accepted: 02/03/2021] [Indexed: 12/17/2022] Open
Abstract
Staphylococcus aureus is a commensal and frequent colonizer of the upper respiratory tract. When mechanical ventilation disrupts natural defenses, S. aureus is frequently isolated from the lower airways, but distinguishing between colonization and infection is difficult. The objectives of this study were (1) to investigate the bacterial genome sequence in consecutive isolates in order to identify changes related to the pathological adaptation to the lower respiratory tract and (2) to explore the relationship between specific phenotypic and genotypic features with the patient’s study group, persistence of the clinical isolate and clinical outcome. A set of 94 clinical isolates were selected and corresponded to 34 patients that were classified as having pneumonia (10), tracheobronchitis (11) and bronchial colonization (13). Clinical strains were phenotypically characterized by conventional identification and susceptibility testing methods. Isolates underwent whole genome sequencing using Illumina HiSeq4000. Genotypic characterization was performed with an in-house pipeline (BacterialTyper). Genomic variation arising within-host was determined by comparing mapped sequences and de novo assemblies. Virulence factors important in staphylococcal colonization and infection were characterized using previously established functional assays. (1) Toxin production was assessed using a THP-1 cytotoxicity assay, which reports on the gross cytotoxicity of individual isolates. In addition, we investigated the expression of the major virulence factor, alpha-toxin (Hla) by Western blot. (2) Adhesion to the important extracellular matrix molecule, fibronectin, was determined using a standardized microtitre plate assay. Finally, invasion experiments using THP-1 and A539 cell lines and selected clinical strains were also performed. Repeated isolation of S. aureus from endotracheal aspirate usually reflects persistence of the same strain. Within-host variation is detectable in this setting, but it shows no evidence of pathological adaptation related to virulence, resistance or niche adaptations. Cytotoxicity was variable among isolates with 14 strains showing no cytotoxicity, with these latter presenting an unaltered Fn binding capacity. No changes on cytotoxicity were reported when comparing study groups. Fn binding capacity was reported for almost all strains, with the exception of two strains that presented the lowest values. Strains isolated from patients with pneumonia presented a lower capacity of adhesion in comparison to those isolated during tracheobronchitis (p = 0.002). Hla was detected in 71 strains (75.5%), with most of the producer strains in pneumonia and bronchial colonization group (p = 0.06). In our cohort, Hla expression (presence or absence) in sequential isolates was usually preserved (70%) although in seven cases the expression varied over time. No relationship was found between low cytotoxicity and intracellular persistence in invasion experiments. In our study population, persistent S. aureus isolation from airways in ventilated patients does not reflect pathological adaptation. There is an important diversity of sequence types. Cytotoxicity is variable among strains, but no association with study groups was found, whereas isolates from patients with pneumonia had lower adhesion capability. Favorable clinical outcome correlated with increased bacterial adhesion in vitro. Most of the strains isolated from the lower airways were Hla producers and no correlation with an adverse outcome was reported. The identification of microbial factors that contribute to virulence is relevant to optimize patient management during lower respiratory tract infections.
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13
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Ramirez AM, Beenken KE, Byrum SD, Tackett AJ, Shaw LN, Gimza BD, Smeltzer MS. SarA plays a predominant role in controlling the production of extracellular proteases in the diverse clinical isolates of Staphylococcus aureus LAC and UAMS-1. Virulence 2020; 11:1738-1762. [PMID: 33258416 PMCID: PMC7738309 DOI: 10.1080/21505594.2020.1855923] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
Using DNA affinity chromatography we demonstrate that the S. aureus regulatory proteins MgrA, Rot, SarA, and SarS bind DNA baits derived from the promoter regions associated with the genes encoding aureolysin, ScpAB, SspABC, and SplA-F. Three of four baits also bound SarR and SarZ, the exception in both cases being the ScpAB-associated bait. Using the USA300, methicillin-resistant strain LAC and the USA200, methicillin-sensitive strain UAMS-1, we generated mutations in the genes encoding each of these proteins alone and in combination with sarA and examined the impact on protease production, the accumulation of high molecular weight proteins, and biofilm formation. These studies confirmed that multiple regulatory loci are involved in limiting protease production to a degree that impacts all of these phenotypes, but also demonstrate that sarA plays a predominant role in this regard. Using sarA mutants unable to produce individual proteases alone and in combination with each other, we also demonstrate that the increased production of aureolysin and ScpA is particularly important in defining the biofilm-deficient phenotype of LAC and UAMS-1 sarA mutants, while aureolysin alone plays a key role in defining the reduced accumulation of alpha toxin and overall cytotoxicity as assessed using both osteoblasts and osteoclasts.
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Affiliation(s)
- Aura M. Ramirez
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Karen E. Beenken
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stephanie D. Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, and Arkansas Children’s Research Institute, Little Rock, AR, USA
| | - Alan J. Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, and Arkansas Children’s Research Institute, Little Rock, AR, USA
| | - Lindsey N. Shaw
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL
| | - Brittney D. Gimza
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL
| | - Mark S. Smeltzer
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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14
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Ranganathan N, Johnson R, Edwards AM. The general stress response of Staphylococcus aureus promotes tolerance of antibiotics and survival in whole human blood. MICROBIOLOGY (READING, ENGLAND) 2020; 166:1088-1094. [PMID: 33095698 PMCID: PMC7723259 DOI: 10.1099/mic.0.000983] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/06/2020] [Indexed: 12/29/2022]
Abstract
Staphylococcus aureus is a frequent cause of invasive human infections such as bacteraemia and infective endocarditis. These infections frequently relapse or become chronic, suggesting that the pathogen has mechanisms to tolerate the twin threats of therapeutic antibiotics and host immunity. The general stress response of S. aureus is regulated by the alternative sigma factor B (σB) and provides protection from multiple stresses including oxidative, acidic and heat. σB also contributes to virulence, intracellular persistence and chronic infection. However, the protective effect of σB on bacterial survival during exposure to antibiotics or host immune defences is poorly characterized. We found that σB promotes the survival of S. aureus exposed to the antibiotics gentamicin, ciprofloxacin, vancomycin and daptomycin, but not oxacillin or clindamycin. We also found that σB promoted staphylococcal survival in whole human blood, most likely via its contribution to oxidative stress resistance. Therefore, we conclude that the general stress response of S. aureus may contribute to the development of chronic infection by conferring tolerance to both antibiotics and host immune defences.
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Affiliation(s)
- Nisha Ranganathan
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Rd, London, SW7 2AZ, UK
- Present address: Charing Cross Hospital, Fulham, Palace Road, W6 8RF, UK
| | - Rebecca Johnson
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Rd, London, SW7 2AZ, UK
- Present address: Horizon Discovery, Waterbeach, Cambridge, CB25 9TL, UK
| | - Andrew M. Edwards
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Rd, London, SW7 2AZ, UK
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15
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Silence as a way of niche adaptation: mecC-MRSA with variations in the accessory gene regulator (agr) functionality express kaleidoscopic phenotypes. Sci Rep 2020; 10:14787. [PMID: 32901059 PMCID: PMC7479134 DOI: 10.1038/s41598-020-71640-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 08/19/2020] [Indexed: 11/09/2022] Open
Abstract
Functionality of the accessory gene regulator (agr) quorum sensing system is an important factor promoting either acute or chronic infections by the notorious opportunistic human and veterinary pathogen Staphylococcus aureus. Spontaneous alterations of the agr system are known to frequently occur in human healthcare-associated S. aureus lineages. However, data on agr integrity and function are sparse regarding other major clonal lineages. Here we report on the agr system functionality and activity level in mecC-carrying methicillin resistant S. aureus (MRSA) of various animal origins (n = 33) obtained in Europe as well as in closely related human isolates (n = 12). Whole genome analysis assigned all isolates to four clonal complexes (CC) with distinct agr types (CC599 agr I, CC49 agr II, CC130 agr III and CC1943 agr IV). Agr functionality was assessed by a combination of phenotypic assays and proteome analysis. In each CC, isolates with varying agr activity levels were detected, including the presence of completely non-functional variants. Genomic comparison of the agr I-IV encoding regions associated these phenotypic differences with variations in the agrA and agrC genes. The genomic changes were detected independently in divergent lineages, suggesting that agr variation might foster viability and adaptation of emerging MRSA lineages to distinct ecological niches.
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16
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Chung HY, Kim YT, Kwon JG, Im HH, Ko D, Lee JH, Choi SH. Molecular interaction between methicillin-resistant Staphylococcus aureus (MRSA) and chicken breast reveals enhancement of pathogenesis and toxicity for food-borne outbreak. Food Microbiol 2020; 93:103602. [PMID: 32912577 DOI: 10.1016/j.fm.2020.103602] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 06/27/2020] [Accepted: 07/21/2020] [Indexed: 12/24/2022]
Abstract
To study pathogenesis and toxicity of Staphylococcus aureus in foods, FORC_062 was isolated from a human blood sample and complete genome sequence has a type II SCCmec gene cluster and a type II toxin-antitoxin system, indicating an MRSA strain. Its mobile gene elements has many pathogenic genes involved in host infection, biofilm formation, and various enterotoxin and hemolysin genes. Clinical MRSA is often found in animal foods and ingestion of MRSA-contaminated foods causes human infection. Therefore, it is very important to understand the role of contaminated foods. To elucidate the interaction between clinical MRSA FORC_062 and raw chicken breast, transcriptome analysis was conducted, showing that gene expressions of amino acid biosynthesis and metabolism were specifically down-regulated, suggesting that the strain may import and utilize amino acids from the chicken breast, but not able to synthesize them. However, toxin gene expressions were up-regulated, suggesting that human infection of S. aureus via contaminated food may be more fatal. In addition, the contaminated foods enhance multiple-antibiotic resistance activities and virulence factors in this clinical MRSA. Consequently, MRSA-contaminated food may play a role as a nutritional reservoir as well as in enhancing factor for pathogenesis and toxicity of clinical MRSA for severe food-borne outbreaks.
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Affiliation(s)
- Han Young Chung
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, And Center for Food Safety and Toxicology, Seoul National University, Seoul, 08826, South Korea; Food-borne Pathogen Omics Research Center (FORC), Seoul National University, Seoul, 08826, South Korea
| | - You-Tae Kim
- Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea; Food-borne Pathogen Omics Research Center (FORC), Seoul National University, Seoul, 08826, South Korea
| | - Joon-Gi Kwon
- Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea; Food-borne Pathogen Omics Research Center (FORC), Seoul National University, Seoul, 08826, South Korea
| | - Han Hyeok Im
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, And Center for Food Safety and Toxicology, Seoul National University, Seoul, 08826, South Korea; Food-borne Pathogen Omics Research Center (FORC), Seoul National University, Seoul, 08826, South Korea
| | - Duhyun Ko
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, And Center for Food Safety and Toxicology, Seoul National University, Seoul, 08826, South Korea; Food-borne Pathogen Omics Research Center (FORC), Seoul National University, Seoul, 08826, South Korea
| | - Ju-Hoon Lee
- Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, South Korea; Food-borne Pathogen Omics Research Center (FORC), Seoul National University, Seoul, 08826, South Korea.
| | - Sang Ho Choi
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, And Center for Food Safety and Toxicology, Seoul National University, Seoul, 08826, South Korea; Food-borne Pathogen Omics Research Center (FORC), Seoul National University, Seoul, 08826, South Korea.
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17
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Su M, Lyles JT, Petit III RA, Peterson J, Hargita M, Tang H, Solis-Lemus C, Quave CL, Read TD. Genomic analysis of variability in Delta-toxin levels between Staphylococcus aureus strains. PeerJ 2020; 8:e8717. [PMID: 32231873 PMCID: PMC7100594 DOI: 10.7717/peerj.8717] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/10/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The delta-toxin (δ-toxin) of Staphylococcus aureus is the only hemolysin shown to cause mast cell degranulation and is linked to atopic dermatitis, a chronic inflammatory skin disease. We sought to characterize variation in δ-toxin production across S. aureus strains and identify genetic loci potentially associated with differences between strains. METHODS A set of 124 S. aureus strains was genome-sequenced and δ-toxin levels in stationary phase supernatants determined by high performance liquid chromatography (HPLC). SNPs and kmers were associated with differences in toxin production using four genome-wide association study (GWAS) methods. Transposon mutations in candidate genes were tested for their δ-toxin levels. We constructed XGBoost models to predict toxin production based on genetic loci discovered to be potentially associated with the phenotype. RESULTS The S. aureus strain set encompassed 40 sequence types (STs) in 23 clonal complexes (CCs). δ-toxin production ranged from barely detectable levels to >90,000 units, with a median of >8,000 units. CC30 had significantly lower levels of toxin production than average while CC45 and CC121 were higher. MSSA (methicillin sensitive) strains had higher δ-toxin production than MRSA (methicillin resistant) strains. Through multiple GWAS approaches, 45 genes were found to be potentially associated with toxicity. Machine learning models using loci discovered through GWAS as features were able to predict δ-toxin production (as a high/low binary phenotype) with a precision of .875 and specificity of .990 but recall of .333. We discovered that mutants in the carA gene, encoding the small chain of carbamoyl phosphate synthase, completely abolished toxin production and toxicity in Caenorhabditis elegans. CONCLUSIONS The amount of stationary phase production of the toxin is a strain-specific phenotype likely affected by a complex interaction of number of genes with different levels of effect. We discovered new candidate genes that potentially play a role in modulating production. We report for the first time that the product of the carA gene is necessary for δ-toxin production in USA300. This work lays a foundation for future work on understanding toxin regulation in S. aureus and prediction of phenotypes from genomic sequences.
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Affiliation(s)
- Michelle Su
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States of America
| | - James T. Lyles
- Center for the Study of Human Health, College of Arts and Sciences, Emory University, Atlanta, GA, United States of America
| | - Robert A. Petit III
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States of America
| | - Jessica Peterson
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States of America
| | - Michelle Hargita
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States of America
| | - Huaqiao Tang
- Center for the Study of Human Health, College of Arts and Sciences, Emory University, Atlanta, GA, United States of America
| | - Claudia Solis-Lemus
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, United States of America
| | - Cassandra L. Quave
- Center for the Study of Human Health, College of Arts and Sciences, Emory University, Atlanta, GA, United States of America
- Department of Dermatology, School of Medicine, Emory University, Atlanta, GA, United States of America
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, United States of America
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, United States of America
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18
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Ramirez AM, Byrum SD, Beenken KE, Washam C, Edmondson RD, Mackintosh SG, Spencer HJ, Tackett AJ, Smeltzer MS. Exploiting Correlations between Protein Abundance and the Functional Status of saeRS and sarA To Identify Virulence Factors of Potential Importance in the Pathogenesis of Staphylococcus aureus Osteomyelitis. ACS Infect Dis 2020; 6:237-249. [PMID: 31722523 PMCID: PMC7294808 DOI: 10.1021/acsinfecdis.9b00291] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We used a murine model of postsurgical osteomyelitis (OM) to evaluate the relative virulence of the Staphylococcus aureus strain LAC and five isogenic variants that differ in the functional status of saeRS and sarA relative to each other. LAC and a variant in which saeRS activity is increased (saeC) were comparably virulent to each other, while ΔsaeRS, ΔsarA, ΔsaeRS/ΔsarA, and saeC/ΔsarA mutants were all attenuated to a comparable degree. Phenotypic comparisons including a mass-based proteomics approach that allowed us to assess the number and abundance of full-length proteins suggested that mutation of saeRS attenuates virulence in our OM model owing primarily to the decreased production of S. aureus virulence factors, while mutation of sarA does so owing to protease-mediated degradation of these same virulence factors. This was confirmed by demonstrating that eliminating protease production restored virulence to a greater extent in a LAC sarA mutant than in the isogenic saeRS mutant. Irrespective of the mechanism involved, mutation of saeRS or sarA was shown to result in reduced accumulation of virulence factors of potential importance. Thus, using our proteomics approach we correlated the abundance of specific proteins with virulence in these six strains and identified 14 proteins that were present in a significantly increased amount (log2 ≥ 5.0) in both virulent strains by comparison to all four attenuated strains. We examined biofilm formation and virulence in our OM model using a LAC mutant unable to produce one of these 14 proteins, specifically staphylocoagulase. The results confirmed that mutation of coa limits biofilm formation and, to a lesser extent, virulence in our OM model, although in both cases the limitation was reduced by comparison to the isogenic sarA mutant.
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Affiliation(s)
- Aura M. Ramirez
- Department of Microbiology
and Immunology, College of Medicine, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 511, Little Rock, Arkansas 72205, United States
| | - Stephanie D. Byrum
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 516, Little Rock, Arkansas 72205, United States,Arkansas
Children’s Research Institute, 1 Children’s Way, Little Rock, Arkansas 72202, United States
| | - Karen E. Beenken
- Department of Microbiology
and Immunology, College of Medicine, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 511, Little Rock, Arkansas 72205, United States
| | - Charity Washam
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 516, Little Rock, Arkansas 72205, United States,Arkansas
Children’s Research Institute, 1 Children’s Way, Little Rock, Arkansas 72202, United States
| | - Rick D. Edmondson
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 516, Little Rock, Arkansas 72205, United States
| | - Samuel G. Mackintosh
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 516, Little Rock, Arkansas 72205, United States
| | - Horace J. Spencer
- Department of Biostatistics, University of Arkansas for Medical Sciences, 4301 W. Markham Street, Little Rock, Arkansas 72205, United States
| | - Alan J. Tackett
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 516, Little Rock, Arkansas 72205, United States,Arkansas
Children’s Research Institute, 1 Children’s Way, Little Rock, Arkansas 72202, United States
| | - Mark S. Smeltzer
- Department of Microbiology
and Immunology, College of Medicine, University
of Arkansas for Medical Sciences, 4301 W. Markham Street, Slot 511, Little Rock, Arkansas 72205, United States,Department
of Orthopaedic Surgery, University of Arkansas
for Medical Sciences, 4301 W. Markham Street, Slot 531, Little Rock, Arkansas 72205, United States,Phone: 501-686-7958. E-mail:
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19
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The Impacts of msaABCR on sarA-Associated Phenotypes Are Different in Divergent Clinical Isolates of Staphylococcus aureus. Infect Immun 2020; 88:IAI.00530-19. [PMID: 31740526 PMCID: PMC6977130 DOI: 10.1128/iai.00530-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/07/2019] [Indexed: 12/27/2022] Open
Abstract
The staphylococcal accessory regulator (sarA) plays an important role in Staphylococcus aureus infections, including osteomyelitis, and the msaABCR operon has been implicated as an important factor in modulating expression of sarA Thus, we investigated the contribution of msaABCR to sarA-associated phenotypes in the S. aureus clinical isolates LAC and UAMS-1. Mutation of msaABCR resulted in reduced production of SarA and a reduced capacity to form a biofilm in both strains. Biofilm formation was enhanced in a LAC msa mutant by restoring the production of SarA, but this was not true in a UAMS-1 msa mutant. Similarly, extracellular protease production was increased in a LAC msa mutant but not a UAMS-1 msa mutant. This difference was reflected in the accumulation and distribution of secreted virulence factors and in the impact of extracellular proteases on biofilm formation in a LAC msa mutant. Most importantly, it was reflected in the relative impact of mutating msa as assessed in a murine osteomyelitis model, which had a significant impact in LAC but not in UAMS-1. In contrast, mutation of sarA had a greater impact on all of these in vitro and in vivo phenotypes than mutation of msaABCR, and it did so in both LAC and UAMS-1. These results suggest that, at least in osteomyelitis, it would be therapeutically preferable to target sarA rather than msaABCR to achieve the desired clinical result, particularly in the context of divergent clinical isolates of S. aureus.
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Subramanian D, Bhasuran B, Natarajan J. Genomic analysis of RNA-Seq and sRNA-Seq data identifies potential regulatory sRNAs and their functional roles in Staphylococcus aureus. Genomics 2019; 111:1431-1446. [DOI: 10.1016/j.ygeno.2018.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 09/21/2018] [Accepted: 09/26/2018] [Indexed: 12/17/2022]
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Coagulase-Negative Staphylococci Pathogenomics. Int J Mol Sci 2019; 20:ijms20051215. [PMID: 30862021 PMCID: PMC6429511 DOI: 10.3390/ijms20051215] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/28/2019] [Accepted: 03/07/2019] [Indexed: 01/16/2023] Open
Abstract
Coagulase-negative Staphylococci (CoNS) are skin commensal bacteria. Besides their role in maintaining homeostasis, CoNS have emerged as major pathogens in nosocomial settings. Several studies have investigated the molecular basis for this emergence and identified multiple putative virulence factors with regards to Staphylococcus aureus pathogenicity. In the last decade, numerous CoNS whole-genome sequences have been released, leading to the identification of numerous putative virulence factors. Koch’s postulates and the molecular rendition of these postulates, established by Stanley Falkow in 1988, do not explain the microbial pathogenicity of CoNS. However, whole-genome sequence data has shed new light on CoNS pathogenicity. In this review, we analyzed the contribution of genomics in defining CoNS virulence, focusing on the most frequent and pathogenic CoNS species: S. epidermidis, S. haemolyticus, S. saprophyticus, S. capitis, and S. lugdunensis.
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Tuchscherr L, Pöllath C, Siegmund A, Deinhardt-Emmer S, Hoerr V, Svensson CM, Thilo Figge M, Monecke S, Löffler B. Clinical S. aureus Isolates Vary in Their Virulence to Promote Adaptation to the Host. Toxins (Basel) 2019; 11:toxins11030135. [PMID: 30823631 PMCID: PMC6468552 DOI: 10.3390/toxins11030135] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/18/2019] [Accepted: 02/21/2019] [Indexed: 12/11/2022] Open
Abstract
Staphylococcus aureus colonizes epithelial surfaces, but it can also cause severe infections. The aim of this work was to investigate whether bacterial virulence correlates with defined types of tissue infections. For this, we collected 10–12 clinical S. aureus strains each from nasal colonization, and from patients with endoprosthesis infection, hematogenous osteomyelitis, and sepsis. All strains were characterized by genotypic analysis, and by the expression of virulence factors. The host–pathogen interaction was studied through several functional assays in osteoblast cultures. Additionally, selected strains were tested in a murine sepsis/osteomyelitis model. We did not find characteristic bacterial features for the defined infection types; rather, a wide range in all strain collections regarding cytotoxicity and invasiveness was observed. Interestingly, all strains were able to persist and to form small colony variants (SCVs). However, the low-cytotoxicity strains survived in higher numbers, and were less efficiently cleared by the host than the highly cytotoxic strains. In summary, our results indicate that not only destructive, but also low-cytotoxicity strains are able to induce infections. The low-cytotoxicity strains can successfully survive, and are less efficiently cleared from the host than the highly cytotoxic strains, which represent a source for chronic infections. The understanding of this interplay/evolution between the host and the pathogen during infection, with specific attention towards low-cytotoxicity isolates, will help to optimize treatment strategies for invasive and therapy-refractory infection courses.
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Affiliation(s)
- Lorena Tuchscherr
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany.
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, 07747 Jena, Germany.
| | - Christine Pöllath
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany.
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, 07747 Jena, Germany.
| | - Anke Siegmund
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany.
| | - Stefanie Deinhardt-Emmer
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany.
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, 07747 Jena, Germany.
| | - Verena Hoerr
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany.
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, 07747 Jena, Germany.
| | - Carl-Magnus Svensson
- Applied Systems Biology, Leibniz-Institute for Natural Product Research and Infection Biology, 07745 Jena, Germany.
| | - Marc Thilo Figge
- Applied Systems Biology, Leibniz-Institute for Natural Product Research and Infection Biology, 07745 Jena, Germany.
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany.
- Institute of Medical Microbiology and Hygiene, Medical Faculty Carl Gustav Carus, 01307 Dresden, Germany.
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany.
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, 07747 Jena, Germany.
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Abstract
Quorum sensing is a vital property of bacteria that enables community-wide coordination of collective behaviors. A key example of such a behavior is biofilm formation, in which groups of bacteria invest in synthesizing a protective, joint extracellular matrix. Quorum sensing involves the production, release, and subsequent detection of extracellular signaling molecules called autoinducers. The architecture of quorum-sensing signal transduction pathways is highly variable among different species of bacteria, but frequently involves posttranscriptional regulation carried out by small regulatory RNA molecules. This review illustrates the diverse roles small trans-acting regulatory RNAs can play, from constituting a network's core to auxiliary roles in adjusting the rate of autoinducer synthesis, mediating cross talk among different parts of a network, or integrating different regulatory inputs to trigger appropriate changes in gene expression. The emphasis is on describing how the study of small RNA-based regulation in quorum sensing and biofilm formation has uncovered new general properties or expanded our understanding of bacterial riboregulation.
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Byrum S, Loughran AJ, Beenken KE, Orr LM, Storey AJ, Mackintosh SG, Edmondson RD, Tackett AJ, Smeltzer MS. Label-Free Proteomic Approach to Characterize Protease-Dependent and -Independent Effects of sarA Inactivation on the Staphylococcus aureus Exoproteome. J Proteome Res 2018; 17:3384-3395. [PMID: 30209945 PMCID: PMC6209314 DOI: 10.1021/acs.jproteome.8b00288] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The staphylococcal accessory regulator A ( sarA) impacts the extracellular accumulation of Staphylococcus aureus virulence factors at the level of intracellular production and extracellular protease-mediated degradation. We previously used a proteomics approach that measures protein abundance of all proteoforms to demonstrate that mutation of sarA results in increased levels of extracellular proteases and assesses the impact of this on the accumulation of S. aureus exoproteins. Our previous approach was limited as it did not take into account that large, stable proteolytic products from a given protein could result in false negatives when quantified by total proteoforms. Here, our goal was to use an expanded proteomics approach utilizing a dual quantitative method for measuring abundance at both the total proteoform and full-length exoprotein levels to alleviate these false negatives and thereby provide for characterization of protease-dependent and -independent effects of sarA mutation on the S. aureus exoproteome. Proteins present in conditioned medium from overnight, stationary phase cultures of the USA300 strain LAC, an isogenic sarA mutant, and a sarA mutant unable to produce any of the known extracellular proteases ( sarA/protease) were resolved using one-dimensional gel electrophoresis. Quantitative proteomic comparisons of sarA versus sarA/protease mutants identified proteins that were cleaved in a protease-dependent manner owing to mutation of sarA, and comparisons of sarA/protease mutant versus the LAC parent strain identified proteins in which abundance was altered in a sarA mutant in a protease-independent manner. Furthermore, the proteins uniquely identified by the full-length data analysis approach eliminated false negatives observed in the total proteoform analysis. This expanded approach provided for a more comprehensive analysis of the impact of mutating sarA on the S. aureus exoproteome.
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Affiliation(s)
- Stephanie
D. Byrum
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States,Arkansas
Children’s Research Institute, 13 Children’s Way, Little Rock, Arkansas 72202, United States
| | - Allister J. Loughran
- Department
of Microbiology and Immunology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States
| | - Karen E. Beenken
- Department
of Microbiology and Immunology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States
| | - Lisa M. Orr
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States
| | - Aaron J. Storey
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States
| | - Samuel G. Mackintosh
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States
| | - Ricky D. Edmondson
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States
| | - Alan J. Tackett
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States,Arkansas
Children’s Research Institute, 13 Children’s Way, Little Rock, Arkansas 72202, United States,E-mail:
| | - Mark S. Smeltzer
- Department
of Microbiology and Immunology, University
of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, United States,E-mail: , Phone: (501) 686-7958
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Viedma E, Pérez-Montarelo D, Villa J, Muñoz-Gallego I, Larrosa N, Fernández-Hidalgo N, Gavaldà J, Almirante B, Chaves F. Sub-inhibitory concentrations of oxacillin modify the expression of agr locus in Staphylococcus aureus clinical strains belonging to different clonal complexes. BMC Infect Dis 2018; 18:177. [PMID: 29661157 PMCID: PMC5902860 DOI: 10.1186/s12879-018-3088-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/05/2018] [Indexed: 02/08/2023] Open
Abstract
Background The ability of Staphylococcus aureus to invade tissues and cause an infectious disease is the result of a multi-factorial process supported by the huge number of virulence factors inherent to this microorganism tightly regulated by the accessory gene regulator (agr). During antimicrobial therapy bacteria may be exposed to sub-inhibitory concentrations (subMICs) of antibiotics that may trigger transcriptional changes that may have an impact on the pathogenesis of infection. The objective of this study was to investigate the effect of oxacillin sub-MICs on agr system expression as the key component in the regulation of virulence in methicillin-susceptible (MSSA) and -resistant S. aureus (MRSA) strains. Furthermore, we studied the genetic basis of the agr locus and their potential association with the expression levels. Methods We have examined the expression of RNAIII and agrA mRNA as biomarkers for agr expression in the presence and absence of oxacillin subMICs in 10 MSSA and 4 MRSA clinical strains belonging to 5 clonal complexes (CC45-agrI, CC8-agrI, CC5-agrII, CC15-agrII and CC30-agrIII) causing endovascular complications. The DNA sequences of agr locus were obtained by whole genome sequencing. Results Our results revealed that exposure to subMICs of oxacillin had an impact on agr locus expression modifying the relative levels of expression with increases in 11 strains and with decreases in 3 strains. Thereby, the exposure to subMICs of oxacillin resulted in higher levels of expression of agr in CC15 and CC45 and lower levels in CC30. We also observed the presence of mutations in agrC and agrA in 13/14 strains with similar mutation profiles among strains within individual CCs except for strains of CC5. Although, agr expression levels differed among strains within CCs, the presence of these mutations was associated with differences in agr expression levels in most cases. Conclusions Changes in agr expression induced by exposure to oxacillin subMICs should be considered because they could lead to changes in the virulence modulation and have an adverse effect on the course of infection, especially in certain clonal complexes. Electronic supplementary material The online version of this article (10.1186/s12879-018-3088-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Esther Viedma
- Department of Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain.
| | | | - Jennifer Villa
- Department of Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Irene Muñoz-Gallego
- Department of Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Nieves Larrosa
- Department of Infectious Diseases, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | | | - Joan Gavaldà
- Department of Infectious Diseases, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Benito Almirante
- Department of Infectious Diseases, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Fernando Chaves
- Department of Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
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Rom JS, Atwood DN, Beenken KE, Meeker DG, Loughran AJ, Spencer HJ, Lantz TL, Smeltzer MS. Impact of Staphylococcus aureus regulatory mutations that modulate biofilm formation in the USA300 strain LAC on virulence in a murine bacteremia model. Virulence 2017; 8:1776-1790. [PMID: 28910576 PMCID: PMC5810510 DOI: 10.1080/21505594.2017.1373926] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Staphylococcus aureus causes acute and chronic forms of infection, the latter often associated with formation of a biofilm. It has previously been demonstrated that mutation of atl, codY, rot, sarA, and sigB limits biofilm formation in the USA300 strain LAC while mutation of agr, fur, and mgrA has the opposite effect. Here we used a murine sepsis model to assess the impact of these same loci in acute infection. Mutation of agr, atl, and fur had no impact on virulence, while mutation of mgrA and rot increased virulence. In contrast, mutation of codY, sarA, and sigB significantly attenuated virulence. Mutation of sigB resulted in reduced accumulation of AgrA and SarA, while mutation of sarA resulted in reduced accumulation of AgrA, but this cannot account for the reduced virulence of sarA or sigB mutants because the isogenic agr mutant was not attenuated. Indeed, as assessed by accumulation of alpha toxin and protein A, all of the mutants we examined exhibited unique phenotypes by comparison to an agr mutant and to each other. Attenuation of the sarA, sigB and codY mutants was correlated with increased production of extracellular proteases and global changes in extracellular protein profiles. These results suggest that the inability to repress the production of extracellular proteases plays a key role in attenuating the virulence of S. aureus in acute as well as chronic, biofilm-associated infections, thus opening up the possibility that strategies aimed at the de-repression of protease production could be used to broad therapeutic advantage. They also suggest that the impact of codY, sarA, and sigB on protease production occurs via an agr-independent mechanism.
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Affiliation(s)
- Joseph S Rom
- a Department of Microbiology and Immunology , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Danielle N Atwood
- a Department of Microbiology and Immunology , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Karen E Beenken
- a Department of Microbiology and Immunology , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Daniel G Meeker
- a Department of Microbiology and Immunology , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Allister J Loughran
- a Department of Microbiology and Immunology , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Horace J Spencer
- b Department of Biostatistics , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Tamara L Lantz
- a Department of Microbiology and Immunology , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Mark S Smeltzer
- a Department of Microbiology and Immunology , University of Arkansas for Medical Sciences , Little Rock , AR , USA.,c Department of Orthopaedic Surgery , University of Arkansas for Medical Sciences , Little Rock , AR , USA.,d Department of Pathology , University of Arkansas for Medical Sciences , Little Rock , AR , USA
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Prat C, Lacoma A. Bacteria in the respiratory tract-how to treat? Or do not treat? Int J Infect Dis 2017; 51:113-122. [PMID: 27776777 DOI: 10.1016/j.ijid.2016.09.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/30/2016] [Accepted: 09/04/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Acute and chronic respiratory tract infections are a common cause of inappropriate antimicrobial prescription. Antimicrobial therapy leads to the development of resistance and the emergence of opportunistic pathogens that substitute the indigenous microbiota. METHODS This review explores the major challenges and lines of research to adequately establish the clinical role of bacteria and the indications for antimicrobial treatment, and reviews novel therapeutic approaches. RESULTS In patients with chronic pulmonary diseases and structural disturbances of the bronchial tree or the lung parenchyma, clinical and radiographic signs and symptoms are almost constantly present, including a basal inflammatory response. Bacterial adaptative changes and differential phenotypes are described, depending on the clinical role and niche occupied. The respiratory tract has areas that are potentially inaccessible to antimicrobials. Novel therapeutic approaches include new ways of administering antimicrobials that may allow intracellular delivery or delivery across biofilms, targeting the functions essential for infection, such as regulatory systems, or the virulence factors required to cause host damage and disease. Alternatives to antibiotics and antimicrobial adjuvants are under development. CONCLUSIONS Prudent treatment, novel targets, and improved drug delivery systems will contribute to reduce the emergence of antimicrobial resistance in lower respiratory tract infections.
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Affiliation(s)
- Cristina Prat
- Microbiology Department, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Ctra del Canyet s/n, 08916 Badalona, Barcelona, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
| | - Alicia Lacoma
- Microbiology Department, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, Ctra del Canyet s/n, 08916 Badalona, Barcelona, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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Phage-Derived Protein Induces Increased Platelet Activation and Is Associated with Mortality in Patients with Invasive Pneumococcal Disease. mBio 2017; 8:mBio.01984-16. [PMID: 28096486 PMCID: PMC5241397 DOI: 10.1128/mbio.01984-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
To improve our understanding about the severity of invasive pneumococcal disease (IPD), we investigated the association between the genotype of Streptococcus pneumoniae and disease outcomes for 349 bacteremic patients. A pneumococcal genome-wide association study (GWAS) demonstrated a strong correlation between 30-day mortality and the presence of the phage-derived gene pblB, encoding a platelet-binding protein whose effects on platelet activation were previously unknown. Platelets are increasingly recognized as key players of the innate immune system, and in sepsis, excessive platelet activation contributes to microvascular obstruction, tissue hypoperfusion, and finally multiorgan failure, leading to mortality. Our in vitro studies revealed that pblB expression was induced by fluoroquinolones but not by the beta-lactam antibiotic penicillin G. Subsequently, we determined pblB induction and platelet activation by incubating whole blood with the wild type or a pblB knockout mutant in the presence or absence of antibiotics commonly administered to our patient cohort. pblB-dependent enhancement of platelet activation, as measured by increased expression of the α-granule protein P-selectin, the binding of fibrinogen to the activated αIIbβ3 receptor, and the formation of platelet-monocyte complex occurred irrespective of antibiotic exposure. In conclusion, the presence of pblB on the pneumococcal chromosome potentially leads to increased mortality in patients with an invasive S. pneumoniae infection, which may be explained by enhanced platelet activation. This study highlights the clinical utility of a bacterial GWAS, followed by functional characterization, to identify bacterial factors involved in disease severity. The exact mechanisms causing mortality in invasive pneumococcal disease (IPD) patients are not completely understood. We examined 349 patients with IPD and found in a bacterial genome-wide association study (GWAS) that the presence of the phage-derived gene pblB was associated with mortality in the first 30 days after hospitalization. Although pblB has been extensively studied in Streptococcus mitis, its consequence for the interaction between platelets and Streptococcus pneumoniae is largely unknown. Platelets are important in immunity and inflammation, and excessive platelet activation contributes to microvascular obstruction and multiorgan failure, leading to mortality. We therefore developed this study to assess whether the expression of pblB might increase the risk of death for IPD patients through its effect on enhanced platelet activation. This study also shows the value of integrating extensive bacterial genomics and clinical data in predicting and understanding pathogen virulence, which in turn will help to improve prognosis and therapy.
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Chakraborty N, Meyerhoff J, Jett M, Hammamieh R. Genome to Phenome: A Systems Biology Approach to PTSD Using an Animal Model. Methods Mol Biol 2017; 1598:117-154. [PMID: 28508360 DOI: 10.1007/978-1-4939-6952-4_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Post-traumatic stress disorder (PTSD) is a debilitating illness that imposes significant emotional and financial burdens on military families. The understanding of PTSD etiology remains elusive; nonetheless, it is clear that PTSD is manifested by a cluster of symptoms including hyperarousal, reexperiencing of traumatic events, and avoidance of trauma reminders. With these characteristics in mind, several rodent models have been developed eliciting PTSD-like features. Animal models with social dimensions are of particular interest, since the social context plays a major role in the development and manifestation of PTSD.For civilians, a core trauma that elicits PTSD might be characterized by a singular life-threatening event such as a car accident. In contrast, among war veterans, PTSD might be triggered by repeated threats and a cumulative psychological burden that coalesced in the combat zone. In capturing this fundamental difference, the aggressor-exposed social stress (Agg-E SS) model imposes highly threatening conspecific trauma on naïve mice repeatedly and randomly.There is abundant evidence that suggests the potential role of genetic contributions to risk factors for PTSD. Specific observations include putatively heritable attributes of the disorder, the cited cases of atypical brain morphology, and the observed neuroendocrine shifts away from normative. Taken together, these features underscore the importance of multi-omics investigations to develop a comprehensive picture. More daunting will be the task of downstream analysis with integration of these heterogeneous genotypic and phenotypic data types to deliver putative clinical biomarkers. Researchers are advocating for a systems biology approach, which has demonstrated an increasingly robust potential for integrating multidisciplinary data. By applying a systems biology approach here, we have connected the tissue-specific molecular perturbations to the behaviors displayed by mice subjected to Agg-E SS. A molecular pattern that links the atypical fear plasticity to energy deficiency was thereby identified to be causally associated with many behavioral shifts and transformations.PTSD is a multifactorial illness sensitive to environmental influence. Accordingly, it is essential to employ the optimal animal model approximating the environmental condition that elicits PTSD-like symptoms. Integration of an optimal animal model with a systems biology approach can contribute to a more knowledge-driven and efficient next-generation care management system and, potentially, prevention of PTSD.
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Affiliation(s)
- Nabarun Chakraborty
- Integrative Systems Biology, Geneva Foundation, USACEHR, 568 Doughten Drive, Fredrick, MD, 21702-5010, USA
| | - James Meyerhoff
- Integrative Systems Biology, Geneva Foundation, USACEHR, 568 Doughten Drive, Fredrick, MD, 21702-5010, USA
| | - Marti Jett
- Integrative Systems Biology, US Army Center for Environmental Health Research, USACEHR, 568 Doughten Drive, Frederick, MD, 21702-5010, USA
| | - Rasha Hammamieh
- Integrative Systems Biology, US Army Center for Environmental Health Research, USACEHR, 568 Doughten Drive, Frederick, MD, 21702-5010, USA.
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Mauro T, Rouillon A, Felden B. Insights into the regulation of small RNA expression: SarA represses the expression of two sRNAs in Staphylococcus aureus. Nucleic Acids Res 2016; 44:10186-10200. [PMID: 27596601 PMCID: PMC5137438 DOI: 10.1093/nar/gkw777] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 08/09/2016] [Accepted: 08/24/2016] [Indexed: 11/14/2022] Open
Abstract
The opportunistic pathogen Staphylococcus aureus expresses transcription factors (TFs) and regulatory small RNAs (sRNAs) which are essential for bacterial adaptation and infectivity. Until recently, the study of S. aureus sRNA gene expression regulation was under investigated, but it is now an expanding field. Here we address the regulation of Srn_3610_SprC sRNA, an attenuator of S. aureus virulence. We demonstrate that SarA TF represses srn_3610_sprC transcription. DNase I footprinting and deletion analyses show that the SarA binding site on srn_3610_sprC belongs to an essential 22 bp DNA region. Comparative analysis also revealed another possible site, this time in the srn_9340 promoter. SarA specifically binds these two sRNA promoters with high affinity in vitro and also represses their transcription in vivo. Chromatin immunoprecipitation (ChIP) assays confirmed SarA attachment to both promoters. ChIP and electrophoretic mobility shift assays targeting σA RNA polymerase subunit or using bacterial RNA polymerase holoenzyme suggested that SarA and the σA bind srn_3610_sprC and srn_9340 promoters in a mutually exclusive way. Beyond the mechanistic study of SarA repression of these two sRNAs, this work also suggests that some S. aureus sRNAs belong to the same regulon and act jointly in responding to environmental changes.
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Affiliation(s)
- Tony Mauro
- Inserm U835, Biochimie Pharmaceutique, University of Rennes 1, 35000 Rennes, France
| | - Astrid Rouillon
- Inserm U835, Biochimie Pharmaceutique, University of Rennes 1, 35000 Rennes, France
| | - Brice Felden
- Inserm U835, Biochimie Pharmaceutique, University of Rennes 1, 35000 Rennes, France
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31
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Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infection Control in an Institutional Setting. J Clin Microbiol 2016; 54:2874-2881. [PMID: 27558178 DOI: 10.1128/jcm.00790-16] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/12/2016] [Indexed: 11/20/2022] Open
Abstract
The increasing prevalence of multidrug-resistant (MDR) bacteria is a serious global challenge. Here, we studied prospectively whether bacterial whole-genome sequencing (WGS) for real-time MDR surveillance is technical feasible, returns actionable results, and is cost-beneficial. WGS was applied to all MDR isolates of four species (methicillin-resistant Staphylococcus aureus [MRSA], vancomycin-resistant Enterococcus faecium, MDR Escherichia coli, and MDR Pseudomonas aeruginosa) at the University Hospital Muenster, Muenster, Germany, a tertiary care hospital with 1,450 beds, during two 6-month intervals. Turnaround times (TAT) were measured, and total costs for sequencing per isolate were calculated. After cancelling prior policies of preemptive isolation of patients harboring certain Gram-negative MDR bacteria in risk areas, the second interval was conducted. During interval I, 645 bacterial isolates were sequenced. From culture, TATs ranged from 4.4 to 5.3 days, and costs were €202.49 per isolate. During interval II, 550 bacterial isolates were sequenced. Hospital-wide transmission rates of the two most common species (MRSA and MDR E. coli) were low during interval I (5.8% and 2.3%, respectively) and interval II (4.3% and 5.0%, respectively). Cancellation of isolation of patients infected with non-pan-resistant MDR E. coli in risk wards did not increase transmission. Comparing sequencing costs with avoided costs mostly due to fewer blocked beds during interval II, we saved in excess of €200,000. Real-time microbial WGS in our institution was feasible, produced precise actionable results, helped us to monitor transmission rates that remained low following a modification in isolation procedures, and ultimately saved costs.
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Smeltzer MS. Staphylococcus aureus Pathogenesis: The Importance of Reduced Cytotoxicity. Trends Microbiol 2016; 24:681-682. [PMID: 27450110 DOI: 10.1016/j.tim.2016.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 10/21/2022]
Abstract
Toxin production clearly contributes to the pathogenesis of Staphylococcus aureus, but that does not mean it is always in the best interest of the pathogen. Indeed, the ability to limit toxin production may provide an important mechanism for persistence, dissemination, and development of invasive disease within an individual human host.
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Affiliation(s)
- Mark S Smeltzer
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, 4301W. Markham, Little Rock, AR 72205, USA.
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DNA microarray analysis of Staphylococcus aureus causing bloodstream infection: bacterial genes associated with mortality? Eur J Clin Microbiol Infect Dis 2016; 35:1285-95. [PMID: 27177754 DOI: 10.1007/s10096-016-2663-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/24/2016] [Indexed: 01/07/2023]
Abstract
Providing evidence for microbial genetic determinants' impact on outcome in Staphylococcus aureus bloodstream infections (SABSI) is challenging due to the complex and dynamic microbe-host interaction. Our recent population-based prospective study reported an association between the S. aureus clonal complex (CC) 30 genotype and mortality in SABSI patients. This follow-up investigation aimed to examine the genetic profiles of the SABSI isolates and test the hypothesis that specific genetic characteristics in S. aureus are associated with mortality. SABSI isolates (n = 305) and S. aureus CC30 isolates from asymptomatic nasal carriers (n = 38) were characterised by DNA microarray analysis and spa typing. Fisher's exact test, least absolute shrinkage and selection operator (LASSO) and elastic net regressions were performed to discern within four groups defined by patient outcome and characteristics. No specific S. aureus genetic determinants were found to be associated with mortality in SABSI patients. By applying LASSO and elastic net regressions, we found evidence suggesting that agrIII and cna were positively and setC (=selX) and seh were negatively associated with S. aureus CC30 versus non-CC30 isolates. The genes chp and sak, encoding immune evasion molecules, were found in higher frequencies in CC30 SABSI isolates compared to CC30 carrier isolates, indicating a higher virulence potential. In conclusion, no specific S. aureus genes were found to be associated with mortality by DNA microarray analysis and state-of-the-art statistical analyses. The next natural step is to test the hypothesis in larger samples with higher resolution methods, like whole genome sequencing.
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Laabei M, Massey R. Using functional genomics to decipher the complexity of microbial pathogenicity. Curr Genet 2016; 62:523-5. [PMID: 26898530 PMCID: PMC4929159 DOI: 10.1007/s00294-016-0576-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 12/22/2022]
Abstract
From the first identification of bacteria as a causative agent of disease, researchers have been developing methods and techniques to understand their pathogenic processes. For decades, this work has been limited to looking at a small number of genetically manipulatable isolates in in vitro assays or animal models of infection. Despite these limitations such work has facilitated the development of successful therapeutic strategies, most notably vaccines that target specific virulence-related features. There are however many antimicrobial resistant pathogens for which vaccination strategies have not worked, as we simply do not know enough about how they cause disease. We are however at the dawn of a new era in the study of microbial pathogenicity, where large collections of bacteria isolated directly from human infections can be sequenced and assayed to identify the bacterial features that affect disease severity in humans. Here, we describe our attempt to perform such a study focussed on the major human pathogen Staphylococcus aureus, which demonstrates the step changes such approaches can make to understanding microbial pathogenicity.
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Affiliation(s)
- Maisem Laabei
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Ruth Massey
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.
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Liu G, Weston CQ, Pham LK, Waltz S, Barnes H, King P, Sphar D, Yamamoto RT, Forsyth RA. Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB. PLoS One 2016; 11:e0146064. [PMID: 26727463 PMCID: PMC4699840 DOI: 10.1371/journal.pone.0146064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/11/2015] [Indexed: 01/05/2023] Open
Abstract
We describe continuing work to develop restriction endonucleases as tools to enrich targeted genomes of interest from diverse populations. Two approaches were developed in parallel to segregate genomic DNA based on cytosine methylation. First, the methyl-sensitive endonuclease HpaII was used to bind non-CG methylated DNA. Second, a truncated fragment of McrB was used to bind CpG methylated DNA. Enrichment levels of microbial genomes can exceed 100-fold with HpaII allowing improved genomic detection and coverage of otherwise trace microbial genomes from sputum. Additionally, we observe interesting enrichment results that correlate with the methylation states not only of bacteria, but of fungi, viruses, a protist and plants. The methods presented here offer promise for testing biological samples for pathogens and global analysis of population methylomes.
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MESH Headings
- 5-Methylcytosine/analysis
- CpG Islands/genetics
- DNA Methylation
- DNA Restriction Enzymes/isolation & purification
- DNA Restriction Enzymes/metabolism
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Fungal/genetics
- DNA, Fungal/isolation & purification
- DNA, Plant/genetics
- DNA, Plant/isolation & purification
- DNA, Protozoan/genetics
- DNA, Protozoan/isolation & purification
- DNA, Viral/genetics
- DNA, Viral/isolation & purification
- Deoxyribonuclease HpaII/isolation & purification
- Deoxyribonuclease HpaII/metabolism
- Escherichia coli Proteins/isolation & purification
- Escherichia coli Proteins/metabolism
- Gene Library
- Genetics, Microbial/methods
- Genomics/methods
- Humans
- Metagenome
- Microbiota/genetics
- Sequence Analysis, DNA
- Sputum/microbiology
- Substrate Specificity
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Affiliation(s)
- Guohong Liu
- FLIR Systems, Inc., La Jolla, California, 92037, United States of America
| | - Christopher Q. Weston
- FLIR Systems, Inc., La Jolla, California, 92037, United States of America
- Singlera Genomics, Inc., La Jolla, California, 92037, United States of America
| | - Long K. Pham
- FLIR Systems, Inc., La Jolla, California, 92037, United States of America
| | - Shannon Waltz
- FLIR Systems, Inc., La Jolla, California, 92037, United States of America
- Singlera Genomics, Inc., La Jolla, California, 92037, United States of America
- San Diego State University, San Diego, California, United States of America
| | - Helen Barnes
- FLIR Systems, Inc., La Jolla, California, 92037, United States of America
| | - Paula King
- FLIR Systems, Inc., La Jolla, California, 92037, United States of America
- Singlera Genomics, Inc., La Jolla, California, 92037, United States of America
| | - Dan Sphar
- FLIR Systems, Inc., La Jolla, California, 92037, United States of America
| | - Robert T. Yamamoto
- Zova Systems, LLC, San Diego, California, 92129, United States of America
| | - R. Allyn Forsyth
- FLIR Systems, Inc., La Jolla, California, 92037, United States of America
- Singlera Genomics, Inc., La Jolla, California, 92037, United States of America
- San Diego State University, San Diego, California, United States of America
- * E-mail:
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Chong CW, Pearce DA, Convey P. Emerging spatial patterns in Antarctic prokaryotes. Front Microbiol 2015; 6:1058. [PMID: 26483777 PMCID: PMC4588704 DOI: 10.3389/fmicb.2015.01058] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 09/14/2015] [Indexed: 11/13/2022] Open
Abstract
Recent advances in knowledge of patterns of biogeography in terrestrial eukaryotic organisms have led to a fundamental paradigm shift in understanding of the controls and history of life on land in Antarctica, and its interactions over the long term with the glaciological and geological processes that have shaped the continent. However, while it has long been recognized that the terrestrial ecosystems of Antarctica are dominated by microbes and their processes, knowledge of microbial diversity and distributions has lagged far behind that of the macroscopic eukaryote organisms. Increasing human contact with and activity in the continent is leading to risks of biological contamination and change in a region whose isolation has protected it for millions of years at least; these risks may be particularly acute for microbial communities which have, as yet, received scant recognition and attention. Even a matter apparently as straightforward as Protected Area designation in Antarctica requires robust biodiversity data which, in most parts of the continent, remain almost completely unavailable. A range of important contributing factors mean that it is now timely to reconsider the state of knowledge of Antarctic terrestrial prokaryotes. Rapid advances in molecular biological approaches are increasingly demonstrating that bacterial diversity in Antarctica may be far greater than previously thought, and that there is overlap in the environmental controls affecting both Antarctic prokaryotic and eukaryotic communities. Bacterial dispersal mechanisms and colonization patterns remain largely unaddressed, although evidence for regional evolutionary differentiation is rapidly accruing and, with this, there is increasing appreciation of patterns in regional bacterial biogeography in this large part of the globe. In this review, we set out to describe the state of knowledge of Antarctic prokaryote diversity patterns, drawing analogy with those of eukaryote groups where appropriate. Based on our synthesis, it is clear that spatial patterns of Antarctic prokaryotes can be unique at local scales, while the limited evidence available to date supports the group exhibiting overall regional biogeographical patterns similar to the eukaryotes. We further consider the applicability of the concept of “functional redundancy” for the Antarctic microbial community and highlight the requirements for proper consideration of their important and distinctive roles in Antarctic terrestrial ecosystems.
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Affiliation(s)
- Chun-Wie Chong
- Department of Life Sciences, School of Pharmacy, International Medical University, Kuala Lumpur Malaysia ; National Antarctic Research Center, University of Malaya, Kuala Lumpur Malaysia
| | - David A Pearce
- National Antarctic Research Center, University of Malaya, Kuala Lumpur Malaysia ; Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne UK ; University Centre in Svalbard, Longyearbyen Norway ; British Antarctic Survey, Cambridge UK
| | - Peter Convey
- National Antarctic Research Center, University of Malaya, Kuala Lumpur Malaysia ; British Antarctic Survey, Cambridge UK
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Hamed M, Nitsche-Schmitz DP, Ruffing U, Steglich M, Dordel J, Nguyen D, Brink JH, Chhatwal GS, Herrmann M, Nübel U, Helms V, von Müller L. Whole genome sequence typing and microarray profiling of nasal and blood stream methicillin-resistant Staphylococcus aureus isolates: Clues to phylogeny and invasiveness. INFECTION GENETICS AND EVOLUTION 2015; 36:475-482. [PMID: 26297907 DOI: 10.1016/j.meegid.2015.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 08/11/2015] [Accepted: 08/18/2015] [Indexed: 11/29/2022]
Abstract
Hospital-associated methicillin-resistant Staphylococcus aureus (MRSA) infections are frequently caused by predominant clusters of closely related isolates that cannot be discriminated by conventional diagnostic typing methods. Whole genome sequencing (WGS) and DNA microarray (MA) now allow for better discrimination within a prevalent clonal complex (CC). This single center exploratory study aims to distinguish invasive (blood stream infection) and non-invasive (nasal colonization) MRSA isolates of the same CC5 into phylogenetic- and virulence-associated genotypic subgroups by WGS and MA. A cohort of twelve blood stream and fifteen nasal MRSA isolates of CC5 (spa-types t003 and t504) was selected. Isolates were propagated at the same period of time from unrelated patients treated at the University of Saarland Medical Center, Germany. Rooted phylotyping based on WGS with core-genome single nucleotide polymorphism (SNP) analysis revealed two local clusters of closely related CC5 subgroups (t504 and Clade1 t003) which were separated from other local t003 isolates and from unrelated CC5 MRSA reference isolates of German origin. Phylogenetic subtyping was not associated with invasiveness when comparing blood stream and nasal isolates. Clustering based on MA profiles was not concordant with WGS phylotyping, but MA profiles may identify subgroups of isolates with nasal and blood stream origin. Among the new putative virulence associated genes identified by WGS, the strongest association with blood stream infections was shown for ebhB mutants. Analysis of the core-genome together with the accessory genome enables subtyping of closely related MRSA isolates according to phylogeny and presumably also to the potential virulence capacity of isolates.
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Affiliation(s)
- Mohamed Hamed
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany
| | | | - Ulla Ruffing
- Institute of Medical Microbiology and Hygiene, University of Saarland Medical Center, Homburg, Germany
| | | | | | - Duy Nguyen
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany
| | - Jan-Hendrik Brink
- Institute of Medical Microbiology and Hygiene, University of Saarland Medical Center, Homburg, Germany
| | - Gursharan Singh Chhatwal
- Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Mathias Herrmann
- Institute of Medical Microbiology and Hygiene, University of Saarland Medical Center, Homburg, Germany
| | | | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany
| | - Lutz von Müller
- Institute of Medical Microbiology and Hygiene, University of Saarland Medical Center, Homburg, Germany.
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38
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Atwood DN, Loughran AJ, Courtney AP, Anthony AC, Meeker DG, Spencer HJ, Gupta RK, Lee CY, Beenken KE, Smeltzer MS. Comparative impact of diverse regulatory loci on Staphylococcus aureus biofilm formation. Microbiologyopen 2015; 4:436-51. [PMID: 25810138 PMCID: PMC4475386 DOI: 10.1002/mbo3.250] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 02/06/2015] [Indexed: 01/01/2023] Open
Abstract
The relative impact of 23 mutations on biofilm formation was evaluated in the USA300, methicillin-resistant strain LAC. Mutation of sarA, atl, codY, rsbU, and sigB limited biofilm formation in comparison to the parent strain, but the limitation imposed by mutation of sarA was greater than that imposed by mutation of any of these other genes. The reduced biofilm formation of all mutants other than the atl mutant was correlated with increased levels of extracellular proteases. Mutation of fur- and mgrA-enhanced biofilm formation but in LAC had no impact on protease activity, nuclease activity, or accumulation of the polysaccharide intercellular adhesin (PIA). The increased capacity of these mutants to form a biofilm was reversed by mutation of sarA, and this was correlated with increased protease production. Mutation of sarA, mgrA, and sigB had the same phenotypic effect in the methicillin-sensitive strain UAMS-1, but mutation of codY increased rather than decreased biofilm formation. As with the UAMS-1 mgrA mutant, this was correlated with increased production of PIA. Examination of four additional clinical isolates suggests that the differential impact of codY on biofilm formation may be a conserved characteristic of methicillin-resistant versus methicillin-sensitive strains.
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Affiliation(s)
- Danielle N Atwood
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Allister J Loughran
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Ashleah P Courtney
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Allison C Anthony
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Daniel G Meeker
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Horace J Spencer
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Ravi Kr Gupta
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Chia Y Lee
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Karen E Beenken
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Mark S Smeltzer
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas.,Department of Orthopaedic Surgery, University of Arkansas for Medical Sciences, Little Rock, Arkansas.,Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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Nitzan M, Fechter P, Peer A, Altuvia Y, Bronesky D, Vandenesch F, Romby P, Biham O, Margalit H. A defense-offense multi-layered regulatory switch in a pathogenic bacterium. Nucleic Acids Res 2015; 43:1357-69. [PMID: 25628364 PMCID: PMC4330369 DOI: 10.1093/nar/gkv001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cells adapt to environmental changes by efficiently adjusting gene expression programs. Staphylococcus aureus, an opportunistic pathogenic bacterium, switches between defensive and offensive modes in response to quorum sensing signal. We identified and studied the structural characteristics and dynamic properties of the core regulatory circuit governing this switch by deterministic and stochastic computational methods, as well as experimentally. This module, termed here Double Selector Switch (DSS), comprises the RNA regulator RNAIII and the transcription factor Rot, defining a double-layered switch involving both transcriptional and post-transcriptional regulations. It coordinates the inverse expression of two sets of target genes, immuno-modulators and exotoxins, expressed during the defensive and offensive modes, respectively. Our computational and experimental analyses show that the DSS guarantees fine-tuned coordination of the inverse expression of its two gene sets, tight regulation, and filtering of noisy signals. We also identified variants of this circuit in other bacterial systems, suggesting it is used as a molecular switch in various cellular contexts and offering its use as a template for an effective switching device in synthetic biology studies.
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Affiliation(s)
- Mor Nitzan
- Racah Institute of Physics, The Hebrew University, Jerusalem 91904, Israel Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | - Pierre Fechter
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg F-67084, France
| | - Asaf Peer
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | - Yael Altuvia
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
| | - Delphine Bronesky
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg F-67084, France
| | - François Vandenesch
- CIRI, International Center for Infectiology Research,Lyon, France Inserm, U1111, Lyon, France École Normale Supérieure de Lyon, Lyon, France Université Lyon 1, Lyon, France CNRS, UMR5308, Lyon, France
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, Strasbourg F-67084, France
| | - Ofer Biham
- Racah Institute of Physics, The Hebrew University, Jerusalem 91904, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
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40
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Kirkup BC. Bacterial Strain Diversity Within Wounds. Adv Wound Care (New Rochelle) 2015; 4:12-23. [PMID: 25566411 DOI: 10.1089/wound.2014.0560] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 06/23/2014] [Indexed: 12/17/2022] Open
Abstract
Significance: Rare bacterial taxa (taxa of low relative frequency) are numerous and ubiquitous in virtually any sample-including wound samples. In addition, even the high-frequency genera and species contain multiple strains. These strains, individually, are each only a small fraction of the total bacterial population. Against the view that wounds contain relatively few kinds of bacteria, this newly recognized diversity implies a relatively high rate of migration into the wound and the potential for diversification during infection. Understanding the biological and medical importance of these numerous taxa is an important new element of wound microbiology. Recent Advances: Only recently have these numerous strains been discovered; the technology to detect, identify, and characterize them is still in its infancy. Multiple strains of both gram-negative and gram-positive bacteria have been found in a single wound. In the few cases studied, the distribution of the bacteria suggests microhabitats and biological interactions. Critical Issues: The distribution of the strains, their phenotypic diversity, and their interactions are still largely uncharacterized. The technologies to investigate this level of genomic detail are still developing and have not been largely deployed to investigate wounds. Future Directions: As advanced metagenomics, single-cell genomics, and advanced microscopy develop, the study of wound microbiology will better address the complex interplay of numerous individually rare strains with both the host and each other.
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Affiliation(s)
- Benjamin C. Kirkup
- FE Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
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Abstract
INTRODUCTION Genomic science is developing rapidly, and engagement of public health professionals will be necessary to appraise new technologies and use them effectively. SOURCES OF DATA We use established domains of public health and draw on the literature and expert knowledge to illustrate how genomic technologies give rise to new applications. AREAS OF AGREEMENT Genomic technologies are useful in rare inherited disease, including population screening programmes, in health care and for surveillance, diagnosis and treatment of infectious disease. AREAS OF CONTROVERSY It is less clear when and how genetic susceptibility testing will be used for common chronic disease prevention or protection from environmental hazards. GROWING POINTS Developments in public health practice will be necessary to ensure rapid and effective implementation of genomic science. AREAS TIMELY FOR DEVELOPING RESEARCH Public health researchers should address how to accelerate the implementation of genomics for health benefit in developed and developing countries.
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Affiliation(s)
- H Burton
- PHG Foundation, 2 Worts Causeway, Cambridge CB1 8RN, UK
| | - C Jackson
- Centre for Infectious Disease Epidemiology, Mortimer Market Centre, University College London, London WC1E 6JB, UK
| | - I Abubakar
- Centre for Infectious Disease Epidemiology, Mortimer Market Centre, University College London, London WC1E 6JB, UK Centre for Infectious Disease Surveillance and Control, Public Health England, 61 Colindale Avenue, Colindale, London NW9 5EQ, UK
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Fournier PE, Dubourg G, Raoult D. Clinical detection and characterization of bacterial pathogens in the genomics era. Genome Med 2014; 6:114. [PMID: 25593594 PMCID: PMC4295418 DOI: 10.1186/s13073-014-0114-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The availability of genome sequences obtained using next-generation sequencing (NGS) has revolutionized the field of infectious diseases. Indeed, more than 38,000 bacterial and 5,000 viral genomes have been sequenced to date, including representatives of all significant human pathogens. These tremendous amounts of data have not only enabled advances in fundamental biology, helping to understand the pathogenesis of microorganisms and their genomic evolution, but have also had implications for clinical microbiology. Here, we first review the current achievements of genomics in the development of improved diagnostic tools, including those that are now available in the clinic, such as the design of PCR assays for the detection of microbial pathogens, virulence factors or antibiotic-resistance determinants, or the design of optimized culture media for 'unculturable' pathogens. We then review the applications of genomics to the investigation of outbreaks, either through the design of genotyping assays or the direct sequencing of the causative strains. Finally, we discuss how genomics might change clinical microbiology in the future.
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Affiliation(s)
- Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut hospitalo-universitaire Méditerranée-Infection, Aix-Marseille University, Faculté de Medecine, 27 Blvd Jean Moulin, Marseille, 13385, cedex 5 France
| | - Gregory Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut hospitalo-universitaire Méditerranée-Infection, Aix-Marseille University, Faculté de Medecine, 27 Blvd Jean Moulin, Marseille, 13385, cedex 5 France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut hospitalo-universitaire Méditerranée-Infection, Aix-Marseille University, Faculté de Medecine, 27 Blvd Jean Moulin, Marseille, 13385, cedex 5 France
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Bletz S, Mellmann A, Rothgänger J, Harmsen D. Ensuring backwards compatibility: traditional genotyping efforts in the era of whole genome sequencing. Clin Microbiol Infect 2014; 21:347.e1-4. [PMID: 25658529 DOI: 10.1016/j.cmi.2014.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/10/2014] [Accepted: 10/13/2014] [Indexed: 10/24/2022]
Abstract
When using next-generation whole genome sequencing (WGS), extraction of spa types from WGS data is essential for backwards compatibility with Sanger sequencing-based spa typing of methicillin-resistant Staphylococcus aureus (MRSA). We evaluated WGS-based spa typing with a 2×250 bp protocol in a diverse collection of 423 MRSA isolates using two pipelines that executed sequence quality-trimming and de novo assembly before spa typing. The SeqSphere(+) pipeline correctly typed 419 isolates (99.1%) whereas the CLCbio pipeline succeeded in 249 isolates (58.9%). In summary, WGS combined with an optimized de novo assembly enables nearly full compatibility with Sanger sequencing-based spa typing data.
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Affiliation(s)
- S Bletz
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - A Mellmann
- Institute of Hygiene, University Hospital Münster, Münster, Germany.
| | | | - D Harmsen
- Department of Periodontology, University Hospital Münster, Münster, Germany
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Read TD, Massey RC. Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology. Genome Med 2014; 6:109. [PMID: 25593593 PMCID: PMC4295408 DOI: 10.1186/s13073-014-0109-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Genome-wide association studies (GWASs) have become an increasingly important approach for eukaryotic geneticists, facilitating the identification of hundreds of genetic polymorphisms that are responsible for inherited diseases. Despite the relative simplicity of bacterial genomes, the application of GWASs to identify polymorphisms responsible for important bacterial phenotypes has only recently been made possible through advances in genome sequencing technologies. Bacterial GWASs are now about to come of age thanks to the availability of massive datasets, and because of the potential to bridge genomics and traditional genetic approaches that is provided by improving validation strategies. A small number of pioneering GWASs in bacteria have been published in the past 2 years, examining from 75 to more than 3,000 strains. The experimental designs have been diverse, taking advantage of different processes in bacteria for generating variation. Analysis of data from bacterial GWASs can, to some extent, be performed using software developed for eukaryotic systems, but there are important differences in genome evolution that must be considered. The greatest experimental advantage of bacterial GWASs is the potential to perform downstream validation of causality and dissection of mechanism. We review the recent advances and remaining challenges in this field and propose strategies to improve the validation of bacterial GWASs.
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Affiliation(s)
- Timothy D Read
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322 USA ; Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Ruth C Massey
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY UK
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Painter KL, Krishna A, Wigneshweraraj S, Edwards AM. What role does the quorum-sensing accessory gene regulator system play during Staphylococcus aureus bacteremia? Trends Microbiol 2014; 22:676-85. [PMID: 25300477 DOI: 10.1016/j.tim.2014.09.002] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/10/2014] [Accepted: 09/12/2014] [Indexed: 11/18/2022]
Abstract
Staphylococcus aureus is a major cause of bacteremia, which frequently results in serious secondary infections such as infective endocarditis, osteomyelitis, and septic arthritis. The ability of S. aureus to cause such a wide range of infections has been ascribed to its huge armoury of different virulence factors, many of which are under the control of the quorum-sensing accessory gene regulator (Agr) system. However, a significant fraction of S. aureus bacteremia cases are caused by agr-defective isolates, calling into question the role of Agr in invasive staphylococcal infections. This review draws on recent work to define the role of Agr during bacteremia and explain why the loss of this major virulence regulator is sometimes a price worth paying for S. aureus.
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Affiliation(s)
- Kimberley L Painter
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College, Armstrong Road, London SW7 2AZ, UK
| | - Aishwarya Krishna
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College, Armstrong Road, London SW7 2AZ, UK
| | - Sivaramesh Wigneshweraraj
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College, Armstrong Road, London SW7 2AZ, UK
| | - Andrew M Edwards
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College, Armstrong Road, London SW7 2AZ, UK.
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Simon NC, Aktories K, Barbieri JT. Novel bacterial ADP-ribosylating toxins: structure and function. Nat Rev Microbiol 2014; 12:599-611. [PMID: 25023120 PMCID: PMC5846498 DOI: 10.1038/nrmicro3310] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial ADP-ribosyltransferase toxins (bARTTs) transfer ADP-ribose to eukaryotic proteins to promote bacterial pathogenesis. In this Review, we use prototype bARTTs, such as diphtheria toxin and pertussis toxin, as references for the characterization of several new bARTTs from human, insect and plant pathogens, which were recently identified by bioinformatic analyses. Several of these toxins, including cholix toxin (ChxA) from Vibrio cholerae, SpyA from Streptococcus pyogenes, HopU1 from Pseudomonas syringae and the Tcc toxins from Photorhabdus luminescens, ADP-ribosylate novel substrates and have unique organizations, which distinguish them from the reference toxins. The characterization of these toxins increases our appreciation of the range of structural and functional properties that are possessed by bARTTs and their roles in bacterial pathogenesis.
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Affiliation(s)
- Nathan C. Simon
- Medical College of Wisconsin, Microbiology and Molecular Genetics, Milwaukee, WI, USA
| | - Klaus Aktories
- Institute of Experimental and Clinical Pharmacology and Toxicology; Albert-Ludwigs-University Freiburg; Freiburg, Germany
| | - Joseph T. Barbieri
- Medical College of Wisconsin, Microbiology and Molecular Genetics, Milwaukee, WI, USA
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McAdam PR, Richardson EJ, Fitzgerald JR. High-throughput sequencing for the study of bacterial pathogen biology. Curr Opin Microbiol 2014; 19:106-113. [PMID: 25033019 PMCID: PMC4150483 DOI: 10.1016/j.mib.2014.06.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 06/02/2014] [Accepted: 06/07/2014] [Indexed: 12/23/2022]
Abstract
A revolution in sequencing technologies in recent years has led to dramatically increased throughput and reduced cost of bacterial genome sequencing. An increasing number of applications of the new technologies are providing broad insights into bacterial evolution, epidemiology, and pathogenesis. For example, the capacity to sequence large numbers of bacterial isolates is enabling high resolution phylogenetic analyses of bacterial populations leading to greatly enhanced understanding of the emergence, adaptation, and transmission of pathogenic clones. In addition, RNA-seq offers improved quantification and resolution for transcriptomic analysis, and the combination of high-throughput sequencing with transposon mutagenesis is a powerful approach for the identification of bacterial determinants required for survival in vivo. In this concise review we provide selected examples of how high throughput sequencing is being applied to understand the biology of bacterial pathogens, and discuss future technological advances likely to have a profound impact on the field.
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Affiliation(s)
- Paul R McAdam
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, United Kingdom
| | - Emily J Richardson
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, United Kingdom
| | - J Ross Fitzgerald
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, United Kingdom.
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Novel aspects of RNA regulation inStaphylococcus aureus. FEBS Lett 2014; 588:2523-9. [DOI: 10.1016/j.febslet.2014.05.037] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 05/16/2014] [Accepted: 05/19/2014] [Indexed: 11/24/2022]
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Abedon ST. Phage therapy: eco-physiological pharmacology. SCIENTIFICA 2014; 2014:581639. [PMID: 25031881 PMCID: PMC4054669 DOI: 10.1155/2014/581639] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
Bacterial virus use as antibacterial agents, in the guise of what is commonly known as phage therapy, is an inherently physiological, ecological, and also pharmacological process. Physiologically we can consider metabolic properties of phage infections of bacteria and variation in those properties as a function of preexisting bacterial states. In addition, there are patient responses to pathogenesis, patient responses to phage infections of pathogens, and also patient responses to phage virions alone. Ecologically, we can consider phage propagation, densities, distribution (within bodies), impact on body-associated microbiota (as ecological communities), and modification of the functioning of body "ecosystems" more generally. These ecological and physiological components in many ways represent different perspectives on otherwise equivalent phenomena. Comparable to drugs, one also can view phages during phage therapy in pharmacological terms. The relatively unique status of phages within the context of phage therapy as essentially replicating antimicrobials can therefore result in a confluence of perspectives, many of which can be useful towards gaining a better mechanistic appreciation of phage therapy, as I consider here. Pharmacology more generally may be viewed as a discipline that lies at an interface between organism-associated phenomena, as considered by physiology, and environmental interactions as considered by ecology.
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Affiliation(s)
- Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA
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