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Crosby T, Stadler LB. Plasmid Backbone Impacts Conjugation Rate, Transconjugant Fitness, and Community Assembly of Genetically Bioaugmented Soil Microbes for PAH Bioremediation. ACS ENVIRONMENTAL AU 2025; 5:241-252. [PMID: 40125281 PMCID: PMC11926752 DOI: 10.1021/acsenvironau.4c00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Revised: 01/09/2025] [Accepted: 01/13/2025] [Indexed: 03/25/2025]
Abstract
Many polycyclic aromatic hydrocarbons (PAHs) in the environment resulting from crude oil spills and the incomplete combustion of organic matter are highly toxic, mutagenic, or carcinogenic to microorganisms and humans. Bioremediation of PAHs using microorganisms that encode biodegradative genes is a promising approach for environmental PAH cleanup. However, the viability of exogenous microorganisms is often limited due to competition with the native microbial community. Instead of relying on the survival of one or a few species of bacteria, genetic bioaugmentation harnesses conjugative plasmids that spread functional genes to native microbes. In this study, two plasmid backbones that differ in copy number regulation, replication, and mobilization genes were engineered to contain a PAH dioxygenase gene (bphC) and conjugated to soil bacteria including Bacillus subtilis, Pseudomonas putida, and Acinetobacter sp., as well as a synthetic community assembled from these bacteria. Fitness effects of the plasmids in transconjugants significantly impacted the rates of conjugative transfer and biotransformation rates of a model PAH (2,3-dihydroxybiphenyl). A synergistic effect was observed in which synthetic communities bioaugmented with bphC had significantly higher PAH degradation rates than bacteria grown in monocultures. Finally, conjugation rates were significantly associated with the relative abundances of bacteria in synthetic communities, underscoring how fitness impacts of plasmids can shape the microbial community structure and function.
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Affiliation(s)
- Tessa
M. Crosby
- Department of Civil and Environmental
Engineering, Rice University, Houston, Texas 77006, United States
| | - Lauren B. Stadler
- Department of Civil and Environmental
Engineering, Rice University, Houston, Texas 77006, United States
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2
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Young MG, Straub TJ, Worby CJ, Metsky HC, Gnirke A, Bronson RA, van Dijk LR, Desjardins CA, Matranga C, Qu J, Villicana JB, Azimzadeh P, Kau A, Dodson KW, Schreiber HL, Manson AL, Hultgren SJ, Earl AM. Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582780. [PMID: 38463963 PMCID: PMC10925322 DOI: 10.1101/2024.02.29.582780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Low-abundance members of microbial communities are difficult to study in their native habitats. This includes Escherichia coli, a minor, but common inhabitant of the gastrointestinal tract and opportunistic pathogen, including of the urinary tract, where it is the primary pathogen. While multi-omic analyses have detailed critical interactions between uropathogenic Escherichia coli (UPEC) and the bladder that mediate UTI outcome, comparatively little is known about UPEC in its pre-infection reservoir, partly due to its low abundance there (<1% relative abundance). To accurately and sensitively explore the genomes and transcriptomes of diverse E. coli in gastrointestinal communities, we developed E. coli PanSelect which uses a set of probes designed to specifically recognize and capture E. coli's broad pangenome from sequencing libraries. We demonstrated the ability of E. coli PanSelect to enrich, by orders of magnitude, sequencing data from diverse E. coli using a mock community and a set of human stool samples collected as part of a cohort study investigating drivers of recurrent urinary tract infections (rUTI). Comparisons of genomes and transcriptomes between E. coli residing in the gastrointestinal tracts of women with and without a history of rUTI suggest that rUTI gut E. coli are responding to increased levels of oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease. E. coli PanSelect is well suited for investigations of native in vivo biology of E. coli in other environments where it is at low relative abundance, and the framework described here has broad applicability to other highly diverse, low abundance organisms.
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Affiliation(s)
- Mark G Young
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Timothy J Straub
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Colin J Worby
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Hayden C Metsky
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Andreas Gnirke
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Ryan A Bronson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Lucas R van Dijk
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands
| | | | - Christian Matranga
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - James Qu
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Jesús Bazan Villicana
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Philippe Azimzadeh
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew Kau
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Karen W Dodson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Henry L Schreiber
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Abigail L Manson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Ashlee M Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
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Dominski BH, Raitz MDF, Provenzi MA, Silveira ACDO, Sincero TCM, Ferreira FA. Characterization of Methicillin-resistant Staphylococcus aureus (MRSA) isolated in Santa Catarina (SC), Brazil. Diagn Microbiol Infect Dis 2024; 109:116244. [PMID: 38452557 DOI: 10.1016/j.diagmicrobio.2024.116244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 02/05/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
The study investigated the characteristics of Methicillin-resistant Staphylococcus aureus (MRSA) isolated in Santa Catarina. Findings revealed prevalent SCCmecII and IV, multiresistance, Leucocidin ED genes, and one ST105 isolate. The results indicated that the in-state MRSA isolates showed the same characteristics as the out-of-state isolates among the investigated features.
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Affiliation(s)
- Bruno Hech Dominski
- Laboratório de Genética Molecular Bacteriana (GeMBac), Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Campus Universitário Reitor João David Ferreira Lima, Trindade, Florianópolis, SC 88040-960, Brazil
| | - Maria de Fátima Raitz
- Laboratório de Genética Molecular Bacteriana (GeMBac), Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Campus Universitário Reitor João David Ferreira Lima, Trindade, Florianópolis, SC 88040-960, Brazil
| | - Marcel Afonso Provenzi
- Laboratório de Genética Molecular Bacteriana (GeMBac), Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Campus Universitário Reitor João David Ferreira Lima, Trindade, Florianópolis, SC 88040-960, Brazil
| | - Alessandro Conrado de Oliveira Silveira
- Departamento de Ciências Farmacêuticas, Fundação Universidade Regional de Blumenau (FURB). Rua Antônio da Veiga, 140. Itoupava Seca, Blumenau, SC 89030-903, Brazil
| | - Thais Cristine Marques Sincero
- Laboratório de Microbiologia Molecular Aplicada (MIMA); Departamento de Análises Clínicas, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina (UFSC), Campus Universitário Reitor João David Ferreira Lima, Trindade, Florianópolis, SC 88040-960, Brazil
| | - Fabienne Antunes Ferreira
- Laboratório de Genética Molecular Bacteriana (GeMBac), Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Campus Universitário Reitor João David Ferreira Lima, Trindade, Florianópolis, SC 88040-960, Brazil.
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Furtado KL, Plott L, Markovetz M, Powers D, Wang H, Hill DB, Papin J, Allbritton NL, Tamayo R. Clostridioides difficile-mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578425. [PMID: 38352512 PMCID: PMC10862863 DOI: 10.1101/2024.02.01.578425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
In a healthy colon, the stratified mucus layer serves as a crucial innate immune barrier to protect the epithelium from microbes. Mucins are complex glycoproteins that serve as a nutrient source for resident microflora and can be exploited by pathogens. We aimed to understand how the intestinal pathogen, Clostridioides diffiicile, independently uses or manipulates mucus to its benefit, without contributions from members of the microbiota. Using a 2-D primary human intestinal epithelial cell model to generate physiologic mucus, we assessed C. difficile-mucus interactions through growth assays, RNA-Seq, biophysical characterization of mucus, and contextualized metabolic modeling. We found that host-derived mucus promotes C. difficile growth both in vitro and in an infection model. RNA-Seq revealed significant upregulation of genes related to central metabolism in response to mucus, including genes involved in sugar uptake, the Wood-Ljungdahl pathway, and the glycine cleavage system. In addition, we identified differential expression of genes related to sensing and transcriptional control. Analysis of mutants with deletions in highly upregulated genes reflected the complexity of C. difficile-mucus interactions, with potential interplay between sensing and growth. Mucus also stimulated biofilm formation in vitro, which may in turn alter viscoelastic properties of mucus. Context-specific metabolic modeling confirmed differential metabolism and predicted importance of enzymes related to serine and glycine catabolism with mucus. Subsequent growth experiments supported these findings, indicating mucus is an important source of serine. Our results better define responses of C. difficile to human gastrointestinal mucus and highlight a flexibility in metabolism that may influence pathogenesis.
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Affiliation(s)
- Kathleen L. Furtado
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Lucas Plott
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Matthew Markovetz
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Deborah Powers
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Hao Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - David B. Hill
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Physics and Astronomy, College of Arts and Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason Papin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | | | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
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Chappell TC, Maiello KG, Tierney AJ, Yanagi K, Lee JA, Lee K, Mace CR, Bennett CS, Nair NU. Rapid spectrophotometric detection for optimized production of landomycins and characterization of their therapeutic potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566088. [PMID: 37986805 PMCID: PMC10659386 DOI: 10.1101/2023.11.07.566088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Microbial derived natural products remain a major source of structurally diverse bioactive compounds and chemical scaffolds that have potential as new therapeutics to target drug resistant pathogens and cancers. In particular, genome mining has revealed the vast number of cryptic or low yield biosynthetic gene clusters in the genus Streptomyces . Here, we describe our efforts to improve yields of landomycins - angucycline family polyketides under investigation as cancer therapeutics - by a genetically modified Streptomyces cyanogenus 136. After simplifying the extraction process from S. cyanogenus cultures, we identified a wavelength at which the major landomycin products absorb in culture extracts, which we used to systematically explore culture medium compositions to improve total landomycin titers. Through correlational analysis, we simplified the culture optimization process by identifying an alternative wavelength at which culture supernatants absorb yet is representative of total landomycin titers. Using the subsequently improved sample throughput, we explored landomycin production during the culturing process to further increase landomycin yield and reduce culture time. Testing the antimicrobial activity of the isolated landomycins, we report broad inhibition of Gram-positive bacteria, inhibition of fungi by landomycinone, and broad landomycin resistance by Gram-negative bacteria that is likely mediated by exclusion of landomycins by the bacterial membrane. Finally, the anticancer activity of the isolated landomycins against A549 lung carcinoma cells agrees with previous reports on other cell lines that glycan chain length correlates with activity. Given the prevalence of natural products produced by Streptomyces , as well as the light-absorbing moieties common to bioactive natural products and their metabolic precursors, our method is relevant to improving the yields of other natural products of interest.
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Balaraman V, Indran SV, Li Y, Meekins DA, Jakkula LU, Liu H, Hays MP, Souza-Neto JA, Gaudreault NN, Hardwidge PR, Wilson WC, Weber F, Richt JA. Identification of host factors for Rift Valley Fever Phlebovirus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.559935. [PMID: 37808812 PMCID: PMC10557628 DOI: 10.1101/2023.09.28.559935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Background Rift Valley fever phlebovirus (RVFV) is a zoonotic pathogen that causes Rift Valley fever (RVF) in livestock and humans. Currently, there is no licensed human vaccine or antiviral drug to control RVF. Although multiple species of animals and humans are vulnerable to RVFV infection, host factors affecting susceptibility are not well understood. Methodology To identify the host factors or genes essential for RVFV replication, we conducted a CRISPR-Cas9 knock-out screen in human A549 cells. We then validated the putative genes using siRNA-mediated knockdowns and CRISPR-Cas9-mediated knockout studies, respectively. The role of a candidate gene in the virus replication cycle was assessed by measuring intracellular viral RNA accumulation, and the virus titers by plaque assay or TCID50 assay. Findings We identified approximately 900 genes with potential involvement in RVFV infection and replication. Further evaluation of the effect of six genes on viral replication using siRNA-mediated knockdowns found that silencing two genes (WDR7 and LRP1) significantly impaired RVFV replication. For further analysis, we focused on the WDR7 gene since the role of LRP1 in RVFV replication was previously described in detail. Knock-out A549 cell lines were generated and used to dissect the effect of WRD7 on RVFV and another bunyavirus, La Crosse encephalitis virus (LACV). We observed significant effects of WDR7 knock-out cells on both intracellular RVFV RNA levels and viral titers. At the intracellular RNA level, WRD7 affected RVFV replication at a later phase of its replication cycle (24h) when compared to LACV which was affected an earlier replication phase (12h). Conclusion In summary, we have identified WDR7 as an essential host factor for the replication of two relevant bunyaviruses, RVFV and LACV. Future studies will investigate the mechanistic role by which WDR7 facilitates Phlebovirus replication.
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Affiliation(s)
- Velmurugan Balaraman
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Sabarish V. Indran
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Yonghai Li
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - David A. Meekins
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Laxmi U.M.R. Jakkula
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Heidi Liu
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Micheal P. Hays
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Jayme A. Souza-Neto
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Natasha N. Gaudreault
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Philip R. Hardwidge
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - William C. Wilson
- United States Department of Agriculture, Agricultural Research Service, National Bio and Agro-Defense Facility, Foreign Arthropod-Borne Animal Diseases Research Unit, Manhattan, Kansas, United States of America
| | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
| | - Juergen A. Richt
- Center of Excellence for Emerging and Zoonotic Animal Diseases and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
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Wang Y, Gao H, Chang L, Xu J, Zhou X, Zhang C, Peng Q. Efficient Removal of Dental Plaque Biofilm from Training Typodont Teeth via Water Flosser. Bioengineering (Basel) 2023; 10:1061. [PMID: 37760162 PMCID: PMC10525826 DOI: 10.3390/bioengineering10091061] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/23/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Plaque biofilms play critical roles in the development of dental caries. Mechanical plaque control methods are considered to be most effective for plaque removal, such as brushing teeth or using flosser. Recently, water flosser has been paid much attention. Here, we tested the ability of a water flosser to remove the adhered sucrose and the dental plaque biofilms formed by Streptococcus mutans, Streptococcus sanguinis, and Actinobacillus viscosus. We found that the residual sucrose concentration was 3.54 mg/mL in the control group, 1.75 mg/mL in the syringe group (simulating the ordinary mouthwash), and 0 mg/mL in water flosser group. In addition, the residual bacterial concentration was 3.6 × 108 CFU/mL in the control group, 1.6 × 107 CFU/mL in the syringe group, and only 5.5 × 105 CFU/mL in the water flosser group. In summary, water flosser is effective for cleaning the teeth, which may have significant potential in preventing dental caries and maintaining oral health.
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Affiliation(s)
| | | | | | | | | | | | - Qiang Peng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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Räz AK, Andreoni F, Boumasmoud M, Bergada-Pijuan J, Schweizer TA, Mairpady Shambat S, Hasse B, Zinkernagel AS, Brugger SD. Limited Adaptation of Staphylococcus aureus during Transition from Colonization to Invasive Infection. Microbiol Spectr 2023; 11:e0259021. [PMID: 37341598 PMCID: PMC10433843 DOI: 10.1128/spectrum.02590-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Staphylococcus aureus carriage is a risk factor for invasive infections. Unique genetic elements favoring the transition from colonizing to invasive phenotype have not yet been identified, and phenotypic adaptation traits are understudied. We therefore assessed phenotypic and genotypic profiles of 11 S. aureus isolate pairs sampled from colonized patients simultaneously suffering from invasive S. aureus infections. Ten out of 11 isolate pairs displayed the same spa and multilocus sequence type, suggesting colonization as an origin for the invasive infection. Systematic analysis of colonizing and invasive isolate pairs showed similar adherence, hemolysis, reproductive fitness properties, antibiotic tolerance, and virulence in a Galleria mellonella infection model, as well as minimal genetic differences. Our results provide insights into the similar phenotypes associated with limited adaptation between colonizing and invasive isolates. Disruption of the physical barriers of mucosa or skin was identified in the majority of patients, further emphasizing colonization as a major risk factor for invasive disease. IMPORTANCE S. aureus is a major pathogen of humans, causing a wide range of diseases. The difficulty to develop a vaccine and antibiotic treatment failure warrant the exploration of novel treatment strategies. Asymptomatic colonization of the human nasal passages is a major risk factor for invasive disease, and decolonization procedures have been effective in preventing invasive infections. However, the transition of S. aureus from a benign colonizer of the nasal passages to a major pathogen is not well understood, and both host and bacterial properties have been discussed as being relevant for this behavioral change. We conducted a thorough investigation of patient-derived strain pairs reflecting colonizing and invasive isolates in a given patient. Although we identified limited genetic adaptation in certain strains, as well as slight differences in adherence capacity among colonizing and invasive isolates, our work suggests that barrier breaches are a key event in the disease continuum of S. aureus.
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Affiliation(s)
- Anna K. Räz
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Federica Andreoni
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mathilde Boumasmoud
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Judith Bergada-Pijuan
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Tiziano A. Schweizer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Barbara Hasse
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Silvio D. Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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9
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Worthan SB, McCarthy RDP, Behringer MG. Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes. J Mol Evol 2023; 91:311-324. [PMID: 36752825 PMCID: PMC10276084 DOI: 10.1007/s00239-022-10087-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/21/2022] [Indexed: 02/09/2023]
Abstract
Following the completion of an adaptive evolution experiment, fitness evaluations are routinely conducted to assess the magnitude of adaptation. In doing so, proper consideration should be given when determining the appropriate methods as trade-offs may exist between accuracy and throughput. Here, we present three instances in which small changes in the framework or execution of fitness evaluations significantly impacted the outcomes. The first case illustrates that discrepancies in fitness conclusions can arise depending on the approach to evaluating fitness, the culture vessel used, and the sampling method. The second case reveals that variations in environmental conditions can occur associated with culture vessel material. Specifically, these subtle changes can greatly affect microbial physiology leading to changes in the culture pH and distorting fitness measurements. Finally, the last case reports that heterogeneity in CFU formation time can result in inaccurate fitness conclusions. Based on each case, considerations and recommendations are presented for future adaptive evolution experiments.
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Affiliation(s)
- Sarah B Worthan
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Robert D P McCarthy
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Megan G Behringer
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA.
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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10
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Ferreira MNMR, de Paula GR, Barros RR. Distribution of virulence determinants in Streptococcus agalactiae recovered from different clinical sources. Microb Pathog 2021; 161:105255. [PMID: 34678459 DOI: 10.1016/j.micpath.2021.105255] [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: 07/15/2021] [Revised: 10/05/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022]
Abstract
Streptococcus agalactiae (group B Streptococcus, GBS) is a pathobiont, a member of human microbiota that can change from commensal to pathogen, causing a large spectrum of diseases. This study assessed virulence determinants of 32 GBS isolates recovered from different clinical sources associated with asymptomatic and symptomatic clinical outcomes that present distinct capsular types and antimicrobial resistance profiles. The ability of a unique strain to colonize and cause infection in different subjects was also evaluated. By PFGE analysis, it was observed that a given strain could be associated with both asymptomatic and symptomatic outcomes. Cell wall anchor proteins β and alpha C encoding genes (bac and bca, respectively) were detected in all capsular type Ib isolates. bca was more frequent among asymptomatic outcome-related isolates, as well as high expression of β-hemolysin/cytolysin (β-H/C). Symptomatic outcome-related isolates produced strong biofilm more frequently. All bacterial isolates recovered from urine were strong biofilm producers. In growth experiments, asymptomatic outcome-related isolates grew faster after 2 h until the end of the log phase. Taken together, these findings show virulence genotypic and phenotypic features of GBS from distinct sources, which may be helpful to understand their pathogenic potential and predict different clinical outcomes.
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Affiliation(s)
- Mariana Nunes M R Ferreira
- Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Brazil
| | - Geraldo Renato de Paula
- Departamento de Tecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Fluminense, Brazil
| | - Rosana Rocha Barros
- Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Brazil.
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