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Sheykhsaran E, Abbasi A, Memar MY, Ghotaslou R, Baghi HB, Mazraeh FN, Laghousi D, Sadeghi J. The role of Staphylococcus aureus in cystic fibrosis pathogenesis and clinico-microbiological interactions. Diagn Microbiol Infect Dis 2024; 109:116294. [PMID: 38678689 DOI: 10.1016/j.diagmicrobio.2024.116294] [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: 07/28/2023] [Revised: 01/05/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024]
Abstract
Cystic fibrosis (CF) is a progressive and inherited disease that affects approximately 70000 individuals all over the world annually. A mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene serves as its defining feature. Bacterial infections have a significant impact on the occurrence and development of CF. In this manuscript, we discuss the role and virulence factors of Staphylococcus aureus as an important human pathogen with the ability to induce respiratory tract infections. Recent studies have reported S. aureus as the first isolated bacteria in CF patients. Methicillin-resistant Staphylococcus aureus (MRSA) pathogens are approximately resistant to all β-lactams. CF patients are colonized by MRSA expressing various virulence factors including toxins, and Staphylococcal Cassette Chromosome mec (SCCmec) types, and have the potential for biofilm formation. Therefore, variations in clinical outcomes will be manifested. SCCmec type II has been reported in CF patients more than in other SCCmec types from different countries. The small-colony variants (SCVs) as specific morphologic subtypes of S. aureus with slow growth and unusual properties can also contribute to persistent and difficult-to-treat infections in CF patients. The pathophysiology of SCVs is complicated and not fully understood. Patients with cystic fibrosis should be aware of the intrinsic risk factors for complex S. aureus infections, including recurring infections, physiological issues, or coinfection with P. aeruginosa.
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Affiliation(s)
- Elham Sheykhsaran
- Immunology Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran; Students' Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amin Abbasi
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ghotaslou
- Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Bannazadeh Baghi
- Immunology Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran; Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fariba Naeimi Mazraeh
- Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Delara Laghousi
- Social Determinants of Health Research Center, Health Management and Safety Promotion Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Sadeghi
- Immunology Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Long DR, Holmes EA, Lo HY, Penewit K, Almazan J, Hodgson T, Berger NF, Bishop ZH, Lewis JD, Waalkes A, Wolter DJ, Salipante SJ. Clinical and in vitro models identify distinct adaptations enhancing Staphylococcus aureus pathogenesis in human macrophages. PLoS Pathog 2024; 20:e1012394. [PMID: 38991026 PMCID: PMC11265673 DOI: 10.1371/journal.ppat.1012394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 07/23/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024] Open
Abstract
Staphylococcus aureus is a facultative intracellular pathogen of human macrophages, which facilitates chronic infection. The genotypes, pathways, and mutations influencing that phenotype remain incompletely explored. Here, we used two distinct strategies to ascertain S. aureus gene mutations affecting pathogenesis in macrophages. First, we analyzed isolates collected serially from chronic cystic fibrosis (CF) respiratory infections. We found that S. aureus strains evolved greater macrophage invasion capacity during chronic human infection. Bacterial genome-wide association studies (GWAS) identified 127 candidate genes for which mutation was significantly associated with macrophage pathogenesis in vivo. In parallel, we passaged laboratory S. aureus strains in vitro to select for increased infection of human THP-1 derived macrophages, which identified 15 candidate genes by whole-genome sequencing. Functional validation of candidate genes using isogenic transposon mutant knockouts and CRISPR interference (CRISPRi) knockdowns confirmed virulence contributions from 37 of 39 tested genes (95%) implicated by in vivo studies and 7 of 10 genes (70%) ascertained from in vitro selection, with one gene in common to the two strategies. Validated genes included 17 known virulence factors (39%) and 27 newly identified by our study (61%), some encoding functions not previously associated with macrophage pathogenesis. Most genes (80%) positively impacted macrophage invasion when disrupted, consistent with the phenotype readily arising from loss-of-function mutations in vivo. This work reveals genes and mechanisms that contribute to S. aureus infection of macrophages, highlights differences in mutations underlying convergent phenotypes arising from in vivo and in vitro systems, and supports the relevance of S. aureus macrophage pathogenesis during chronic respiratory infection in CF. Additional studies will be needed to illuminate the exact mechanisms by which implicated mutations affect their phenotypes.
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Affiliation(s)
- Dustin R. Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Elizabeth A. Holmes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Hsin-Yu Lo
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Jared Almazan
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Taylor Hodgson
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Nova F. Berger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Zoe H. Bishop
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Janessa D. Lewis
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Daniel J. Wolter
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
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Lo HY, Long DR, Holmes EA, Penewit K, Hodgson T, Lewis JD, Waalkes A, Salipante SJ. Transposon sequencing identifies genes impacting Staphylococcus aureus invasion in a human macrophage model. Infect Immun 2023; 91:e0022823. [PMID: 37676013 PMCID: PMC10580828 DOI: 10.1128/iai.00228-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/13/2023] [Indexed: 09/08/2023] Open
Abstract
Staphylococcus aureus is a facultative intracellular pathogen in many host cell types, facilitating its persistence in chronic infections. The genes contributing to intracellular pathogenesis have not yet been fully enumerated. Here, we cataloged genes influencing S. aureus invasion and survival within human THP-1 derived macrophages using two laboratory strains (ATCC2913 and JE2). We developed an in vitro transposition method to produce highly saturated transposon mutant libraries in S. aureus and performed transposon insertion sequencing (Tn-Seq) to identify candidate genes with significantly altered abundance following macrophage invasion. While some significant genes were strain-specific, 108 were identified as common across both S. aureus strains, with most (n = 106) being required for optimal macrophage infection. We used CRISPR interference (CRISPRi) to functionally validate phenotypic contributions for a subset of genes. Of the 20 genes passing validation, seven had previously identified roles in S. aureus virulence, and 13 were newly implicated. Validated genes frequently evidenced strain-specific effects, yielding opposing phenotypes when knocked down in the alternative strain. Genomic analysis of de novo mutations occurring in groups (n = 237) of clonally related S. aureus isolates from the airways of chronically infected individuals with cystic fibrosis (CF) revealed significantly greater in vivo purifying selection in conditionally essential candidate genes than those not associated with macrophage invasion. This study implicates a core set of genes necessary to support macrophage invasion by S. aureus, highlights strain-specific differences in phenotypic effects of effector genes, and provides evidence for selection of candidate genes identified by Tn-Seq analyses during chronic airway infection in CF patients in vivo.
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Affiliation(s)
- Hsin-Yu Lo
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Dustin R. Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Elizbeth A. Holmes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Taylor Hodgson
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Janessa D. Lewis
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
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Ryan H, Ballard E, Stockwell RE, Duplancic C, Thomson RM, Smith K, Bell SC. A systematic review of the clinical impact of small colony variants in patients with cystic fibrosis. BMC Pulm Med 2023; 23:323. [PMID: 37658311 PMCID: PMC10474644 DOI: 10.1186/s12890-023-02611-4] [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: 01/16/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Cystic fibrosis (CF) is a life-limiting disorder that is characterised by respiratory tract inflammation that is mediated by a range of microbial pathogens. Small colony variants (SCVs) of common respiratory pathogens are being increasingly recognised in CF. The aim of this systematic review is to investigate the prevalence of SCVs, clinical characteristics and health outcomes for patients with CF, and laboratory diagnostic features of SCVs compared to non-small colony variants (NCVs) for a range of Gram-positive and Gram-negative respiratory pathogens. METHODS A literature search was conducted (PubMed, Web of Science, Embase and Scopus) in April 2020 to identify articles of interest. Data pertaining to demographic characteristics of participants, diagnostic criteria of SCVs, SCV prevalence and impact on lung function were extracted from included studies for analysis. RESULTS Twenty-five of 673 studies were included in the systematic review. Individuals infected with SCVs of Staphylococcus aureus (S. aureus) were more likely to have had prior use of the broad-spectrum antibiotic trimethoprim sulfamethoxazole (p < 0.001), and the prevalence of SCVs in patients infected with S. aureus was estimated to be 19.3% (95% CI: 13.5% to 25.9%). Additionally, patients infected with SCVs of Gram-negative and Gram-positive pathogens were identified to have a lower forced expiratory volume in one second percentage predicted (-16.8, 95% CI: -23.2 to -10.4) than those infected by NCVs. Gram-positive SCVs were commonly described as small and non-haemolytic, grown on Mannitol salt or blood agar for 24 h at 35°C and confirmed using tube coagulase testing. CONCLUSION The findings of this systematic review demonstrate that SCVs of S. aureus have a high prevalence in the CF community, and that the occurrence of SCVs in Gram-positive and Gram-negative pathogens is linked to poorer respiratory function. Further investigation is necessary to determine the effect of infection by SCVs on the CF population.
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Affiliation(s)
- Harrigan Ryan
- Centre for Children's Health Research, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia
| | - Emma Ballard
- Statistics Unit, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Rebecca E Stockwell
- Centre for Children's Health Research, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia
- Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, QLD, Australia
| | - Christine Duplancic
- Centre for Children's Health Research, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia
| | - Rachel M Thomson
- Respiratory Research Group, Gallipoli Medical Research Foundation, Greenslopes, QLD, Australia
| | - Kimberley Smith
- Centre for Children's Health Research, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia
| | - Scott C Bell
- Centre for Children's Health Research, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia.
- Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, QLD, Australia.
- Translational Research Institute, Woolloongabba, QLD, Australia.
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Kaiser KG, Delattre V, Frost VJ, Buck GW, Phu JV, Fernandez TG, Pavel IE. Nanosilver: An Old Antibacterial Agent with Great Promise in the Fight against Antibiotic Resistance. Antibiotics (Basel) 2023; 12:1264. [PMID: 37627684 PMCID: PMC10451389 DOI: 10.3390/antibiotics12081264] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Antibiotic resistance in bacteria is a major problem worldwide that costs 55 billion USD annually for extended hospitalization, resource utilization, and additional treatment expenditures in the United States. This review examines the roles and forms of silver (e.g., bulk Ag, silver salts (AgNO3), and colloidal Ag) from antiquity to the present, and its eventual incorporation as silver nanoparticles (AgNPs) in numerous antibacterial consumer products and biomedical applications. The AgNP fabrication methods, physicochemical properties, and antibacterial mechanisms in Gram-positive and Gram-negative bacterial models are covered. The emphasis is on the problematic ESKAPE pathogens and the antibiotic-resistant pathogens of the greatest human health concern according to the World Health Organization. This review delineates the differences between each bacterial model, the role of the physicochemical properties of AgNPs in the interaction with pathogens, and the subsequent damage of AgNPs and Ag+ released by AgNPs on structural cellular components. In closing, the processes of antibiotic resistance attainment and how novel AgNP-antibiotic conjugates may synergistically reduce the growth of antibiotic-resistant pathogens are presented in light of promising examples, where antibiotic efficacy alone is decreased.
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Affiliation(s)
- Kyra G. Kaiser
- Department of Physical and Environmental Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA; (K.G.K.); (V.D.); (G.W.B.)
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - Victoire Delattre
- Department of Physical and Environmental Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA; (K.G.K.); (V.D.); (G.W.B.)
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - Victoria J. Frost
- Department of Chemistry, Physics, Geology and the Environment, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA; (V.J.F.); (J.V.P.)
- Department of Biology, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA
| | - Gregory W. Buck
- Department of Physical and Environmental Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA; (K.G.K.); (V.D.); (G.W.B.)
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - Julianne V. Phu
- Department of Chemistry, Physics, Geology and the Environment, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA; (V.J.F.); (J.V.P.)
- Department of Biology, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA
| | - Timea G. Fernandez
- Department of Chemistry, Physics, Geology and the Environment, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA; (V.J.F.); (J.V.P.)
- Department of Biology, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA
| | - Ioana E. Pavel
- Department of Physical and Environmental Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA; (K.G.K.); (V.D.); (G.W.B.)
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
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Keim KC, George IK, Reynolds L, Smith AC. The Clinical Significance of Staphylococcus aureus Small Colony Variants. Lab Med 2022; 54:227-234. [PMID: 36226897 DOI: 10.1093/labmed/lmac101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Abstract
A burdensome, atypical phenotype of Staphylococcus aureus (SA) called S aureus small colony variant (SA-SCV) has been identified, which is induced as a result of a combination of environmental stressors, including polymicrobial interactions. The SA-SCVs exhibit altered phenotypes as a result of metabolic dormancy caused by electron transport deficiency, leading to increased biofilm production and alterations to antimicrobial susceptibility. The SA-SCVs typically exhibit altered colony morphology and biochemical reactions compared with wild-type SA, making them difficult to detect via routine diagnostics. The SA-SCVs have been found to contribute to chronic or recurrent infections, including skin and soft-tissue infections, foreign-body associated infection, cystic fibrosis, and sepsis. There is evidence that SA-SCVs contribute to patient morbidity and mortality as a result of diagnostic difficulties and limited treatment options. New detection methods may need to be developed that can be incorporated into routine diagnostics, which would allow for better assessment of specimens and introduce new considerations for treatment.
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Affiliation(s)
- Klara C Keim
- Department of Immunology and Microbiology, School of Medicine, Anschutz Medical Campus, University of Colorado , Aurora, CO , USA
| | - Isaiah K George
- Department of Honors Studies, Texas Tech University , Lubbock, TX , USA
| | - Landrye Reynolds
- Department of Honors Studies, Texas Tech University , Lubbock, TX , USA
| | - Allie C Smith
- Department of Honors Studies, Texas Tech University , Lubbock, TX , USA
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Zhou S, Rao Y, Li J, Huang Q, Rao X. Staphylococcus aureus small-colony variants: Formation, infection, and treatment. Microbiol Res 2022; 260:127040. [DOI: 10.1016/j.micres.2022.127040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 10/18/2022]
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Tang Q, Precit MR, Thomason MK, Blanc SF, Ahmed-Qadri F, McFarland AP, Wolter DJ, Hoffman LR, Woodward JJ. Thymidine starvation promotes c-di-AMP-dependent inflammation during pathogenic bacterial infection. Cell Host Microbe 2022; 30:961-974.e6. [PMID: 35439435 DOI: 10.1016/j.chom.2022.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/01/2022] [Accepted: 03/23/2022] [Indexed: 11/03/2022]
Abstract
Antimicrobials can impact bacterial physiology and host immunity with negative treatment outcomes. Extensive exposure to antifolate antibiotics promotes thymidine-dependent Staphylococcus aureus small colony variants (TD-SCVs), commonly associated with worse clinical outcomes. We show that antibiotic-mediated disruption of thymidine synthesis promotes elevated levels of the bacterial second messenger cyclic di-AMP (c-di-AMP), consequently inducing host STING activation and inflammation. An initial antibiotic screen in Firmicutes revealed that c-di-AMP production was largely driven by antifolate antibiotics targeting dihydrofolate reductase (DHFR), which promotes folate regeneration required for thymidine biosynthesis. Additionally, TD-SCVs exhibited excessive c-di-AMP production and STING activation in a thymidine-dependent manner. Murine lung infection with TD-SCVs revealed STING-dependent elevation of proinflammatory cytokines, causing higher airway neutrophil infiltration and activation compared with normal-colony S. aureus and hemin-dependent SCVs. Collectively, our results suggest that thymidine metabolism disruption in Firmicutes leads to elevated c-di-AMP-mediated STING-dependent inflammation, with potential impacts on antibiotic usage and infection outcomes.
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Affiliation(s)
- Qing Tang
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Mimi R Precit
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Maureen K Thomason
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Sophie F Blanc
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Fariha Ahmed-Qadri
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Adelle P McFarland
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA
| | - Daniel J Wolter
- Department of Pediatrics, University of Washington, Seattle, WA 98105, USA; Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Lucas R Hoffman
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington, Seattle, WA 98105, USA; Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Joshua J Woodward
- Department of Microbiology, University of Washington, Seattle, WA 98105, USA.
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Emergence of Thymidine-Dependent Staphylococcus aureus Small-Colony Variants in Cystic Fibrosis Patients in Southern Brazil. Microbiol Spectr 2021; 9:e0061421. [PMID: 34319160 PMCID: PMC8552798 DOI: 10.1128/spectrum.00614-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized Staphylococcus aureus small-colony variant (SCV) strains isolated from cystic fibrosis (CF) patients in southern Brazil. Smaller colonies of S. aureus were isolated from respiratory samples collected consecutively from 225 CF patients from July 2013 to November 2016. Two phenotypic methods—the auxotrophic classification and a modified method of antimicrobial susceptibility testing—were employed. PCR was conducted to detect the mecA, ermA, ermB, ermC, msrA, and msrB resistance genes. Furthermore, DNA sequencing was performed to determine the mutations in the thyA gene, and multilocus sequence typing was used to identify the genetic relatedness. S. aureus strains were isolated from 186 patients (82%); suggestive colonies of SCVs were obtained in 16 patients (8.6%). The clones CC1 (ST1, ST188, and ST2383), CC5 (ST5 and ST221), and ST398 were identified. Among SCVs, antimicrobial susceptibility testing showed that 77.7% of the isolates were resistant to multiple drugs, and all of them were susceptible to vancomycin. mecA (2), ermA (1), ermB (1), ermC (3), and msrB (18) were distributed among the isolates. Phenotypically thymidine-dependent isolates had different mutations in the thyA gene, and frameshift mutations were frequently observed. Of note, revertants showed nonconservative or conservative missense mutations. SCVs are rarely identified in routine laboratory tests. IMPORTANCE Similar findings have not yet been reported in Brazil, emphasizing the importance of monitoring small-colony variants (SCVs). Altogether, our results highlight the need to improve detection methods and review antimicrobial therapy protocols in cystic fibrosis (CF) patients.
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10
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Molecular characterization of a carbon dioxide-dependent Escherichia coli small-colony variant isolated from blood cultures. Int J Med Microbiol 2020; 310:151431. [PMID: 32654769 DOI: 10.1016/j.ijmm.2020.151431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 04/22/2020] [Accepted: 05/23/2020] [Indexed: 11/23/2022] Open
Abstract
A carbon dioxide-dependent small-colony variant of Escherichia coli SH4888 was isolated from blood cultures of a patient with cholangitis. To date, little is known regarding the molecular mechanisms leading to formation of carbon dioxide-dependent phenotypes in clinical isolates, but abnormalities in the carbonic anhydrase are thought to cause carbon dioxide autotrophy. In this study DNA sequence analysis of the carbonic anhydrase-encoding can locus in the carbon dioxide-dependent E. coli SH4888 revealed that the isolate had a 325-bp deletion spanning from the 3'-terminal region of can to the 3'-terminal region of hpt, which encodes a hypoxanthine phosphoribosyltransferase. To confirm that the carbon dioxide-dependent SCV phenotype of E. coli SH4888 was due to the can mutation, we performed a complementation test with a plasmid carrying an intact can that restored the normal phenotype. However, E. coli SH4888 had increased virulence compared to the can-complemented E. coli SH4888 in a murine infection model. In conclusion, these data confirm that impaired carbonic anhydrase function can cause a carbon dioxide-dependent SCV phenotype in E. coli SH4888 and provides a fitness advantage in terms of infection.
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11
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Mercer DK, Torres MDT, Duay SS, Lovie E, Simpson L, von Köckritz-Blickwede M, de la Fuente-Nunez C, O'Neil DA, Angeles-Boza AM. Antimicrobial Susceptibility Testing of Antimicrobial Peptides to Better Predict Efficacy. Front Cell Infect Microbiol 2020; 10:326. [PMID: 32733816 PMCID: PMC7358464 DOI: 10.3389/fcimb.2020.00326] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/29/2020] [Indexed: 12/11/2022] Open
Abstract
During the development of antimicrobial peptides (AMP) as potential therapeutics, antimicrobial susceptibility testing (AST) stands as an essential part of the process in identification and optimisation of candidate AMP. Standard methods for AST, developed almost 60 years ago for testing conventional antibiotics, are not necessarily fit for purpose when it comes to determining the susceptibility of microorganisms to AMP. Without careful consideration of the parameters comprising AST there is a risk of failing to identify novel antimicrobials at a time when antimicrobial resistance (AMR) is leading the planet toward a post-antibiotic era. More physiologically/clinically relevant AST will allow better determination of the preclinical activity of drug candidates and allow the identification of lead compounds. An important consideration is the efficacy of AMP in biological matrices replicating sites of infection, e.g., blood/plasma/serum, lung bronchiolar lavage fluid/sputum, urine, biofilms, etc., as this will likely be more predictive of clinical efficacy. Additionally, specific AST for different target microorganisms may help to better predict efficacy of AMP in specific infections. In this manuscript, we describe what we believe are the key considerations for AST of AMP and hope that this information can better guide the preclinical development of AMP toward becoming a new generation of urgently needed antimicrobials.
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Affiliation(s)
| | - Marcelo D. T. Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Searle S. Duay
- Department of Chemistry, Institute of Materials Science, University of Connecticut, Storrs, CT, United States
| | - Emma Lovie
- NovaBiotics Ltd, Aberdeen, United Kingdom
| | | | | | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
| | | | - Alfredo M. Angeles-Boza
- Department of Chemistry, Institute of Materials Science, University of Connecticut, Storrs, CT, United States
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12
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Nagano N, Kawakami Y, Matsumoto T, Tanimoto K, Kashihara M, Nagata M, Honjyo H, Yamamoto K, Takada A, Sugiura T. Isolation of thymidine-dependent and extended-spectrum-β-lactamase-producing Escherichia coli small-colony variant from urine of a septuagenarian female patient with recurrent cystitis: A case report with genetic investigation. J Infect Chemother 2020; 26:1066-1069. [PMID: 32571646 DOI: 10.1016/j.jiac.2020.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/30/2020] [Accepted: 05/16/2020] [Indexed: 11/18/2022]
Abstract
Thymidine-dependent small-colony variant (TD-SCV) of Escherichia coli was isolated from urine of a septuagenarian female patient on hemodialysis suffering from recurrent cystitis. The patient had been treated with frequent administrations of trimethoprim sulfamethoxazole (SXT), every time her cystitis symptoms developed. In the TD-SCV isolate, the deletion was detected in the thyA gene associated with thymidylate synthase. Interestingly, the isolate was found to produce extended-spectrum β-lactamase (ESBL), and the experiment on conjugational transfer of the resistance trait was successful. By means of genetic analysis, the isolate was found to carry blaCTX-M-1 group. To the best of our knowledge, this is the first report of urinary tract infection caused by the transmissible ESBL-producing TD-SCV of E. coli. MICs of the TD-SCV were obtained only on the Mueller Hinton agar media supplemented with appropriate concentrations of thymidine, which might lead to the difficulty for proper chemotherapy in daily medicine. Furthermore, transmission of the ESBL gene via plasmid should be of concern.
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Affiliation(s)
- Natsumi Nagano
- Department of Clinical Laboratory, Kansai Medical University Medical Center, Moriguchi, 570-8507, Japan
| | - Yoshiyuki Kawakami
- Division of Infection Control and Microbiological Regulation, Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, Matsumoto, 390-8621, Japan; Division of Clinical Microbiology, Department of Biomedical Laboratory Sciences, School of Health Sciences, Shinshu University School of Medicine, Matsumoto, 390-8621, Japan.
| | - Takehisa Matsumoto
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Maebashi, 371-8514, Japan
| | - Koichi Tanimoto
- Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Maebashi, 371-8511, Japan
| | - Masami Kashihara
- Department of Clinical Laboratory, Kansai Medical University Medical Center, Moriguchi, 570-8507, Japan
| | - Megumi Nagata
- Department of Clinical Laboratory, Kansai Medical University Medical Center, Moriguchi, 570-8507, Japan
| | - Hideyasu Honjyo
- Department of Clinical Laboratory, Kansai Medical University Medical Center, Moriguchi, 570-8507, Japan
| | - Konosuke Yamamoto
- Department of Clinical Laboratory, Kansai Medical University Medical Center, Moriguchi, 570-8507, Japan
| | - Atsuaki Takada
- Department of Clinical Laboratory, Kansai Medical University Medical Center, Moriguchi, 570-8507, Japan
| | - Tetsuro Sugiura
- Department of Clinical Laboratory, Kansai Medical University Medical Center, Moriguchi, 570-8507, Japan
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de Souza DC, Cogo LL, Palmeiro JK, Dalla-Costa LM, de Oliveira Tomaz AP, Riedi CA, Rosario Filho NA. Thymidine-auxotrophic Staphylococcus aureus small-colony variant bacteremia in a patient with cystic fibrosis. Pediatr Pulmonol 2020; 55:1388-1393. [PMID: 32176841 DOI: 10.1002/ppul.24730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/05/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Small-colony variants (SCVs) are a morphologic subtype of Staphylococcus aureus that may occur through several mechanisms including auxotrophism for thymidine, hemin, or menadione. Auxotrophic SCV for thymidine fail to synthesize DNA specifically because of mutations in the thymidylate synthase gene. We isolated S. aureus thymidine-dependent SCVs (TD-SCV) from blood and respiratory samples of a pediatric patient with cystic fibrosis and pulmonary exacerbation. METHODS Nutritional dependence of SCVs on hemin, menadione, and thymidine was evaluated. Antimicrobial susceptibility testing was performed through broth microdilution. Polymerase chain reaction was carried out for mecA, ermA, ermB, ermC, msrA, and msrB resistance genes. DNA sequencing was used to determine mutations in thyA and the multilocus sequence typing to identify genetic relatedness. RESULTS Methicillin-sensitive S. aureus with normal and TD-SCV phenotypes were isolated from respiratory samples and a TD-SCV phenotype was isolated from blood culture. Macrolides resistance was attributed to ermC and msrB genes. All isolates belonged to ST398. The thyA gene in S. aureus is 957 nucleotides in length and encodes a protein of 318 amino acids. The TD-SCV isolates carried a -2 nt frameshift mutation (delta 667GC668) in thyA, creating a stop codon at residue 222 close to the predicted binding site for deoxyuridine monophosphate. CONCLUSIONS The pathogenesis of SCVs is complex and not fully elucidated. Factors inherent to the patient such as physiological conditions, recurrent infections, or coinfection should be considered. Although SCVs are considered less virulent, they showed the ability to invade and cause bacteremia in the patient.
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Affiliation(s)
- Dilair C de Souza
- Laboratório de Bacteriologia, Complexo Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Laura L Cogo
- Laboratório de Bacteriologia, Complexo Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Jussara K Palmeiro
- Programa de Pós-graduação em Biotecnologia e saúde da Criança e do Adolescente, Faculdades e Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil.,Departamento de Análises Clínicas, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Libera M Dalla-Costa
- Programa de Pós-graduação em Biotecnologia e saúde da Criança e do Adolescente, Faculdades e Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
| | - Ana P de Oliveira Tomaz
- Laboratório de Bacteriologia, Complexo Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil.,Programa de Pós-graduação em Biotecnologia e saúde da Criança e do Adolescente, Faculdades e Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
| | - Carlos A Riedi
- Departamento de Pediatria, Complexo Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Nelson A Rosario Filho
- Departamento de Pediatria, Complexo Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
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Wolter DJ, Onchiri FM, Emerson J, Precit MR, Lee M, McNamara S, Nay L, Blackledge M, Uluer A, Orenstein DM, Mann M, Hoover W, Gibson RL, Burns JL, Hoffman LR. Prevalence and clinical associations of Staphylococcus aureus small-colony variant respiratory infection in children with cystic fibrosis (SCVSA): a multicentre, observational study. THE LANCET RESPIRATORY MEDICINE 2019; 7:1027-1038. [PMID: 31727592 DOI: 10.1016/s2213-2600(19)30365-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/08/2019] [Accepted: 09/05/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Staphylococcus aureus is the bacterium cultured most often from respiratory secretions of people with cystic fibrosis. Both meticillin-susceptible S aureus and meticillin-resistant S aureus (MRSA) can adapt to form slow-growing, antibiotic-resistant isolates known as small-colony variants that are not routinely identified by clinical laboratories. We aimed to determine the prevalence and clinical significance of S aureus small-colony variants and their subtypes among children with cystic fibrosis. METHODS The Small Colony Variant Staphylococcus aureus (SCVSA) study was a 2-year longitudinal study of children aged 6-16 years at five US cystic fibrosis centres, using culture methods sensitive for small-colony variants. Children were eligible if they had a documented diagnosis of cystic fibrosis and a minimum of two cystic fibrosis clinic visits and two respiratory cultures in the previous 12 months at enrolment. Participants attended clinic visits quarterly, at which respiratory tract samples were taken and measures of lung function (percentage of predicted forced expiratory volume in 1 s [FEV1] and frequency of respiratory exacerbations) were recorded. We determined the prevalence of small-colony variants and their subtypes, and assessed their independent associations with lung function and respiratory exacerbations using linear mixed-effects and generalised estimating equation logistic regression models. Analyses included both univariate models (unadjusted) and multivariate models that adjusted for potential confounders, including age, sex, race, baseline microbiology, treatment with CFTR modulator, and CTFR genotype. FINDINGS Between July 1, 2014, and May 26, 2015, we enrolled 230 children. Participants were followed-up for 2 years, with a mean of 6·4 visits (SD 1·14) per participant (range 2-9 visits) and a mean interval between visits of 3·94 months (SD 1·77). Across the 2-year period, S aureus small-colony variants were detected in 64 (28%) participants. Most (103 [56%] of 185) of the small-colony variants detected in these participants were thymidine dependent. Children with small-colony variants had significantly lower mean percentage of predicted FEV1 at baseline than did children without small-colony variants (85·5 [SD 19] vs 92·4 [SD 18·6]; p=0·0145). Small-colony variants were associated with significantly lower percentage of predicted FEV1 throughout the study in regression models, both in univariate analyses (regression coefficient -7·07, 95% CI -12·20 to -1·95; p=0·0068) and in multivariate analyses adjusting for potential confounders (-5·50, -10·51 to -0·48; p=0·0316). Small colony variants of the thymidine-dependent subtype had the strongest association with lung function in multivariate regression models (regression coefficient -10·49, -17·25 to -3·73; p=0·0024). Compared with children without small-colony variants, those with small-colony variants had significantly increased odds of respiratory exacerbations in univariate analyses (odds ratio 1·73, 95% CI 1·19 to 2·52; p=0·0045). Children with thymidine-dependent small-colony variants had significantly increased odds of respiratory exacerbations (2·81, 1·69-4·67; p=0·0001), even after adjusting for age, sex, race, genotype, CFTR modulator, P aeruginosa culture status, and baseline percentage of predicted FEV1 (2·17, 1·33-3·57; p=0·0021), whereas those with non-thymidine-dependent small-colony variants did not. In multivariate models including small-colony variants and MRSA status, P aeruginosa was not independently associated with lung function (regression coefficient -4·77, 95% CI -10·36 to 0·83; p=0·10) and was associated with reduced odds of exacerbations (0·54, 0·36 to 0·81; p=0·0028). Only the small-colony variant form of MRSA was associated with reduced lung function (-8·44, -16·15 to -0·72; p=0·0318) and increased odds of exacerbations (2·15, 1·24 to 3·71; p=0·0061). INTERPRETATION Infection with small-colony variants, and particularly thymidine-dependent small-colony variants, was common in a multicentre paediatric population with cystic fibrosis and associated with reduced lung function and increased risk of respiratory exacerbations. The adoption of small-colony variant identification and subtyping methods by clinical laboratories, and the inclusion of small-colony variant prevalence data in cystic fibrosis registries, should be considered for ongoing surveillance and study. FUNDING The Cystic Fibrosis Foundation and the National Institutes of Health.
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Affiliation(s)
- Daniel J Wolter
- Department of Pediatrics and Department of Microbiology, University of Washington, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, Seattle, WA, USA
| | | | - Julia Emerson
- Department of Pediatrics and Department of Microbiology, University of Washington, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, Seattle, WA, USA
| | - Mimi R Precit
- Department of Pediatrics and Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Michael Lee
- Department of Pediatrics and Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Sharon McNamara
- Department of Pediatrics, Seattle Children's Hospital, Seattle, WA, USA
| | - Laura Nay
- Department of Pediatrics, Seattle Children's Hospital, Seattle, WA, USA
| | | | - Ahmet Uluer
- Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Brigham and Women's Hospital, Boston, MA, USA
| | - David M Orenstein
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michelle Mann
- Department of Pediatrics, Texas Children's Hospital, Houston, TX, USA
| | - Wynton Hoover
- Department of Pediatrics, University of Alabama, Tuscaloosa, AL, USA
| | - Ronald L Gibson
- Department of Pediatrics, Seattle Children's Hospital, Seattle, WA, USA
| | - Jane L Burns
- Department of Pediatrics and Department of Microbiology, University of Washington, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, Seattle, WA, USA
| | - Lucas R Hoffman
- Department of Pediatrics and Department of Microbiology, University of Washington, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, Seattle, WA, USA.
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Artificial Selection for Pathogenicity Mutations in Staphylococcus aureus Identifies Novel Factors Relevant to Chronic Infection. Infect Immun 2019; 87:IAI.00884-18. [PMID: 30642903 DOI: 10.1128/iai.00884-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 02/06/2023] Open
Abstract
Adaptation of Staphylococcus aureus to host microenvironments during chronic infection involves spontaneous mutations, yet changes underlying adaptive phenotypes remain incompletely explored. Here, we employed artificial selection and whole-genome sequencing to better characterize spontaneous chromosomal mutations that alter two pathogenicity phenotypes relevant to chronic infection in S. aureus: intracellular invasiveness and intracellular cytotoxicity. We identified 23 genes whose alteration coincided with enhanced virulence, 11 that were previously known and 12 (52%) that had no previously described role in S. aureus pathogenicity. Using precision genome editing, transposon mutants, and gene complementation, we empirically assessed the contributions of individual genes to the two virulence phenotypes. We functionally validated 14 of 21 genes tested as measurably influencing invasion and/or cytotoxicity, including 8 newly implicated by this study. We identified inactivating mutations (murA, ndhC, and a hypothetical membrane protein) and gain-of-function mutations (aroE Thr182Ile, yhcF Thr74Ile, and Asp486Glu in a hypothetical peptidase) in previously unrecognized S. aureus virulence genes that enhance pathogenesis when introduced into a clean genetic background, as well as a novel activating mutation in the known virulence regulator gene saeS (Ala106Thr). Investigation of potentially epistatic interactions identified a tufA mutation (Ala271Val) that enhances virulence only in the context of purine operon repressor gene (purR) inactivation. This project reveals a functionally diverse range of genes affected by gain- or loss-of-function mutations that contribute to S. aureus adaptive virulence phenotypes. More generally, the work establishes artificial selection as a means to determine the genetic mechanisms underlying complex bacterial phenotypes relevant to adaptation during infection.
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Ayala OD, Wakeman CA, Pence IJ, Gaddy JA, Slaughter JC, Skaar EP, Mahadevan-Jansen A. Drug-Resistant Staphylococcus aureus Strains Reveal Distinct Biochemical Features with Raman Microspectroscopy. ACS Infect Dis 2018; 4:1197-1210. [PMID: 29845863 PMCID: PMC6476553 DOI: 10.1021/acsinfecdis.8b00029] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Staphylococcus aureus ( S. aureus) is a leading cause of hospital-acquired infections, such as bacteremia, pneumonia, and endocarditis. Treatment of these infections can be challenging since strains of S. aureus, such as methicillin-resistant S. aureus (MRSA), have evolved resistance to antimicrobials. Current methods to identify infectious agents in hospital environments often rely on time-consuming, multistep culturing techniques to distinguish problematic strains (i.e., antimicrobial resistant variants) of a particular bacterial species. Therefore, a need exists for a rapid, label-free technique to identify drug-resistant bacterial strains to guide proper antibiotic treatment. Here, our findings demonstrate the ability to characterize and identify microbes at the subspecies level using Raman microspectroscopy, which probes the vibrational modes of molecules to provide a biochemical "fingerprint". This technique can distinguish between different isolates of species such as Streptococcus agalactiae and S. aureus. To determine the ability of this analytical approach to detect drug-resistant bacteria, isogenic variants of S. aureus including the comparison of strains lacking or expressing antibiotic resistance determinants were evaluated. Spectral variations observed may be associated with biochemical components such as amino acids, carotenoids, and lipids. Mutants lacking carotenoid production were distinguished from wild-type S. aureus and other strain variants. Furthermore, spectral biomarkers of S. aureus isogenic bacterial strains were identified. These results demonstrate the feasibility of Raman microspectroscopy for distinguishing between various genetically distinct forms of a single bacterial species in situ. This is important for detecting antibiotic-resistant strains of bacteria and indicates the potential for future identification of other multidrug resistant pathogens with this technique.
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Affiliation(s)
- Oscar D. Ayala
- Biophotonics Center, Vanderbilt University, 410 24th Avenue South, Nashville, Tennessee 37235, United States
- Department of Biomedical Engineering, Vanderbilt University, 5824 Stevenson Center, Nashville, Tennessee 37232, United States
| | - Catherine A. Wakeman
- Department of Biological Sciences, Texas Tech University, 2901 Main Street, Lubbock, Texas 79409, United States
| | - Isaac J. Pence
- Biophotonics Center, Vanderbilt University, 410 24th Avenue South, Nashville, Tennessee 37235, United States
- Department of Biomedical Engineering, Vanderbilt University, 5824 Stevenson Center, Nashville, Tennessee 37232, United States
| | - Jennifer A. Gaddy
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, 1161 21st Avenue South, Medical Center North, Nashville, Tennessee 37232, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, Medical Center North, Nashville, Tennessee 37232, United States
- Tennessee Valley Healthcare Systems, Department of Veterans Affairs, 1310 24th Avenue South, Nashville, Tennessee 37212, United States
| | - James C. Slaughter
- Department of Biostatistics, Vanderbilt University School of Medicine, 2525 West End Avenue, Suite 11000, Nashville, Tennessee 37203, United States
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, Medical Center North, Nashville, Tennessee 37232, United States
| | - Anita Mahadevan-Jansen
- Biophotonics Center, Vanderbilt University, 410 24th Avenue South, Nashville, Tennessee 37235, United States
- Department of Biomedical Engineering, Vanderbilt University, 5824 Stevenson Center, Nashville, Tennessee 37232, United States
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Sato T, Kawamura M, Furukawa E, Fujimura S. Screening method for trimethoprim/sulfamethoxazole-resistant small colony variants of Staphylococcus aureus. J Glob Antimicrob Resist 2018; 15:1-5. [PMID: 29857058 DOI: 10.1016/j.jgar.2018.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/08/2018] [Accepted: 05/13/2018] [Indexed: 10/16/2022] Open
Abstract
OBJECTIVES Trimethoprim/sulfamethoxazole (SXT) is used to treat Staphylococcus aureus infections. However, the effect of treatment with SXT is sometimes not sufficient and there are patients whose treatment has to be prolonged. There are few reports of isolated strains of SXT-resistant S. aureus, but it is possible that some resistant strains cannot be detected by current testing methods We have therefore developed a tool to identify these resistant strains. METHODS The mutant selection window (MSW) of SXT for 40 clinical isolates of S. aureus, including 20 methicillin-resistant S. aureus (MRSA), was determined. The optimum concentration of SXT and thymidine in agar for detecting SXT-resistant small colony variants (SCVs) of S. aureus was investigated. RESULTS The MSW50 and MSW90 of SXT, presented as a multiple of the minimum inhibitory concentration (MIC), were 16× MIC and >256× MIC, respectively. SCVs were detected within the MSW in 32 (80%) of the 40 clinical isolates studied. To maintain the morphology of SCVs, the most suitable concentrations of SXT and thymidine for screening were 4mg/L and 0.01μg/mL, respectively. All 32 SCVs were resistant to SXT (MIC >32mg/L). The sensitivity and specificity of this screening method was 100% and 88.9%, respectively. CONCLUSIONS SXT-resistant SCVs are not usually detected by routine laboratory tests performed in hospitals. However, the screening test described here can easily distinguish SXT-resistant SCVs among S. aureus isolated from specimens. This newly developed screening test could become an important tool to prevent inappropriate use of SXT.
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Affiliation(s)
- Takumi Sato
- Division of Clinical Infectious Diseases and Chemotherapy, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi Prefecture 981-8558, Japan
| | - Masato Kawamura
- Division of Clinical Infectious Diseases and Chemotherapy, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi Prefecture 981-8558, Japan
| | - Emiko Furukawa
- Division of Clinical Infectious Diseases and Chemotherapy, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi Prefecture 981-8558, Japan
| | - Shigeru Fujimura
- Division of Clinical Infectious Diseases and Chemotherapy, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi Prefecture 981-8558, Japan.
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Negishi T, Matsumoto T, Horiuchi K, Kasuga E, Natori T, Matsuoka M, Ogiwara N, Sugano M, Uehara T, Nagano N, Honda T. Characterization of clinically isolated thymidine-dependent small-colony variants of Escherichia coli producing extended-spectrum β-lactamase. J Med Microbiol 2017; 67:33-39. [PMID: 29143727 DOI: 10.1099/jmm.0.000634] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Thymidine-dependent small-colony variants (TD-SCVs) are difficult to detect or test for antimicrobial susceptibility. We investigated the characteristics of clonal TD-SCVs of Escherichia coli, both with and without blaCTX-M-3, isolated from a patient. METHODOLOGY Mutation in the thyA gene was analysed by sequencing, and morphological abnormalities in the colonies and cells of the isolates were examined. Additionally, conjugational transfer experiments were performed to prove the horizontal transferability of plasmids harbouring resistance genes. RESULTS The TD-SCVs contained a single nucleotide substitution in the thyA gene, c.62G>A, corresponding to p.Arg21His. Morphologically, their colonies were more translucent and flattened than those of the wild-type strain. In addition, cells of the TD-SCVs were swollen and elongated, sometimes with abnormal and incomplete divisions; a large amount of cell debris was also observed. Changing c.62G>A back to the wild-type sequence reversed these abnormalities. Conjugational transfer experiments showed that the TD-SCV of E. coli with blaCTX-M-3 failed to transfer blaCTX-M-3 to E. coli CSH2. However, the TD-SCV of E. coli without blaCTX-M-3 experimentally received the plasmid encoding blaSHV-18 from Klebsiella pneumoniae ATCC 700603 and transferred it to E. coli CSH2. CONCLUSION Mutation in the thyA gene causes morphological abnormalities in the colonies and cells of E. coli, as well as inducing thymidine auxotrophy. In addition, TD-SCVs horizontally transmit plasmids encoding resistance genes. It is important to detect TD-SCVs based on their characteristics because they serve as reservoirs of transferable antibiotic resistance plasmids.
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Affiliation(s)
- Tatsuya Negishi
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan.,Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Takehisa Matsumoto
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, 3-39-22 Showa-machi, Maebashi, Gunma 371-8514, Japan
| | - Kazuki Horiuchi
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Eriko Kasuga
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Tatsuya Natori
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Mina Matsuoka
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Naoko Ogiwara
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Mitsutoshi Sugano
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Takeshi Uehara
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Noriyuki Nagano
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Takayuki Honda
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
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Multicenter Evaluation of a Modified Cefoxitin Disk Diffusion Method and PBP2a Testing To Predict mecA-Mediated Oxacillin Resistance in Atypical Staphylococcus aureus. J Clin Microbiol 2016; 55:485-494. [PMID: 27903603 DOI: 10.1128/jcm.02211-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 11/22/2016] [Indexed: 11/20/2022] Open
Abstract
Phenotypic variants of Staphylococcus aureus that display small colonies, reduced pigmentation, and decreased hemolysis and/or coagulase activity are periodically isolated by the clinical laboratory. Antimicrobial susceptibility testing (AST) of these isolates is complicated, because many do not grow on routine AST media, including Mueller-Hinton agar (MHA) and cation-adjusted Mueller-Hinton broth. This multicenter study evaluated cefoxitin disk diffusion for 37 atypical S. aureus isolates (156 readings) with MHA supplemented with 5% sheep's blood (BMHA), using mecA PCR as the reference standard. The correlation of two commercial PBP2a assays with mecA PCR was also assessed. Ten isolates were negative and 27 positive for mecA No major errors for cefoxitin were observed, but 19.5% very major errors (VMEs) were observed at 24 h of incubation, and 17.2% VMEs were observed at 48 h. The proportions of VMEs ranged from 14.7 to 23.0% at 24 h, and from 13.3 to 17.6% at 48 h, across three testing laboratories. PBP2a tests were performed from growth on BMHA and blood agar plates (BAP), with and without cefoxitin disk induction. The Alere PBP2a SA culture colony test sensitivities for mecA were 90.0% with uninduced growth and 97.4% with induced growth from BMHA. On BAP, sensitivity was 96.0% with induced growth. The sensitivities of the Oxoid PBP2' latex agglutination test were 85.7% with uninduced growth and 93.9% with induced growth from BMHA and 95.9% with induced growth on BAP. On the basis of these data, we recommend that laboratories perform only mecA PCR and/or PBP2a tests when requested to perform AST on atypical isolates of S. aureus.
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