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van Hal SJ, Jensen SO, Tong SYC, Bentley S, Holden MT. Unravelling the complex interplay between antibiotic consumption and adaptive changes in methicillin-resistant Staphylococcus aureus. J Antimicrob Chemother 2024; 79:891-896. [PMID: 38412336 DOI: 10.1093/jac/dkae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/29/2024] [Indexed: 02/29/2024] Open
Abstract
OBJECTIVES This study aims to elucidate the genomic dynamics driving the emergence of antimicrobial resistance (AMR), with a specific focus on the interplay between AMR and antimicrobial usage. METHODS We conducted a comprehensive analysis using a ST239 methicillin-resistant Staphylococcus aureus (MRSA) dataset over a continuous 12-year period from a single hospital. Genomic analyses were performed tracking the changes in MRSA populations, particularly the emergence of reduced vancomycin susceptibility, and assessing the impact of glycopeptide use on these emergence events. RESULTS Our findings reveal a significant correlation between hospital glycopeptide usage and the selection of MRSA strains with reduced vancomycin susceptibility. Genomic analyses provided insights into the molecular mechanisms driving resistance emergence, including the slowing of the molecular clock rate in response to heightened antimicrobial consumption. CONCLUSIONS In conclusion, this study the highlights the complex dynamics between AMR and antimicrobial use at the hospital level. The observed correlation between antimicrobial consumption and the development of less susceptible MRSA strains underscores the importance of antimicrobial stewardship programmes and the establishment of optimal consumption thresholds for mitigating AMR effectively.
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Affiliation(s)
- Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
- Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
| | - Slade O Jensen
- Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Stephen Y C Tong
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Stephen Bentley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Matthew T Holden
- School of Medicine, University of St Andrews, St Andrews, Fife KY16 9TF, UK
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Malone M, Nygren E, Hamberg T, Radzieta M, Jensen SO. In vitro and in vivo evaluation of the antimicrobial effectiveness of non-medicated hydrophobic wound dressings. Int Wound J 2024; 21:e14416. [PMID: 37770025 PMCID: PMC10824701 DOI: 10.1111/iwj.14416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/03/2023] Open
Abstract
There is an increasing use of non-medicated wound dressing with claims of irreversible bacterial binding. Most of the data are from in vitro models which lack clinical relevance. This study employed a range of in vitro experiments to address this gap and we complemented our experimental designs with in vivo observations using dressings obtained from patients with diabetes-related foot ulcers. A hydrophobic wound dressing was compared with a control silicone dressing in vitro. Test dressings were placed on top of a Pseudomonas aeruginosa challenge suspension with increasing concentrations of suspension inoculum in addition to supplementation with phosphate buffered saline (PBS) or increased protein content (IPC). Next, we used the challenge suspensions obtained at the end of the first experiment, where bacterial loads from the suspensions were enumerated following test dressing exposure. Further, the time-dependent bacterial attachment was investigated over 1 and 24 h. Lastly, test dressings were exposed to a challenge suspension with IPC, with or without the addition of the bacteriostatic agent Deferiprone to assess the impacts of limiting bacterial growth in the experimental design. Lastly, two different wound dressings with claims of bacterial binding were obtained from patients with chronic diabetes-related foot ulcers after 72 h of application and observed using scanning electron microscope (SEM). Bacteria were enumerated from each dressing after a 1-h exposure time. There was no statistical difference in bacterial attachment between both test dressings when using different suspension inoculum concentrations or test mediums. Bacterial attachment to the two test dressings was significantly lower (p < 0.0001) when IPC was used instead of PBS. In the challenge suspension with PBS, only the hydrophobic dressing achieved a statistically significant reduction in bacterial loads (0.5 ± 0.05 log colony forming units; p = 0.001). In the presence of IPC, there was no significant reduction in bacterial loads for either test dressing. When bacterial growth was arrested, attachment to the test dressings did not increase over time, suggesting that the number of bacteria on the test dressings increases over time due to bacterial growth. SEM identified widespread adsorption of host fouling across the test dressings which occurred prior to microbial binding. Therein, microbial attachment occurred predominantly to host fouling and not directly to the dressings. Bacterial binding is not unique to dialkylcarbamoyl chloride (DACC) dressings and under clinically relevant in vitro conditions and in vivo observations, we demonstrate (in addition to previously published work) that the bacterial binding capabilities are not effective at reducing the number of bacteria in laboratory models or human wounds.
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Affiliation(s)
- Matthew Malone
- Research and DevelopmentMolnlycke Healthcare ABGothenburgSweden
- South West Sydney Limb Preservation and Wound ResearchSouth West Sydney Local Health DistrictSydneyNew South WalesAustralia
- Infectious Diseases and Microbiology, School of MedicineWestern Sydney UniversitySydneyNew South WalesAustralia
| | - Erik Nygren
- Research and DevelopmentMolnlycke Healthcare ABGothenburgSweden
| | - Tina Hamberg
- Research and DevelopmentMolnlycke Healthcare ABGothenburgSweden
| | - Michael Radzieta
- South West Sydney Limb Preservation and Wound ResearchSouth West Sydney Local Health DistrictSydneyNew South WalesAustralia
- Infectious Diseases and Microbiology, School of MedicineWestern Sydney UniversitySydneyNew South WalesAustralia
| | - Slade O. Jensen
- South West Sydney Limb Preservation and Wound ResearchSouth West Sydney Local Health DistrictSydneyNew South WalesAustralia
- Infectious Diseases and Microbiology, School of MedicineWestern Sydney UniversitySydneyNew South WalesAustralia
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Flora A, Jepsen R, Kozera EK, Woods JA, Cains GD, Radzieta M, Jensen SO, Malone M, Frew JW. Mast cells are upregulated in hidradenitis suppurativa tissue, associated with epithelialized tunnels and normalized by spleen tyrosine kinase antagonism. Exp Dermatol 2024; 33:e14894. [PMID: 37522746 DOI: 10.1111/exd.14894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/26/2023] [Accepted: 07/16/2023] [Indexed: 08/01/2023]
Abstract
Mast cells have traditionally been associated with allergic inflammatory responses; however, they play important roles in cutaneous innate immunity and wound healing. The Hidradenitis Suppurativa tissue transcriptome is associated with alterations in innate immunity and wound healing-associated pathways; however, the role of mast cells in the disease is unexplored. We demonstrate that mast cell-associated gene expression (using whole tissue RNAseq) is upregulated, and in-silico cellular deconvolution identifies activated mast cells upregulated and resting mast cells downregulated in lesional tissue. Tryptase/Chymase positive mast cells (identified using IHC) localize adjacent to epithelialized tunnels, fibrotic regions of the dermis and at perivascular sites associated with Neutrophil Extracellular Trap formation and TNF-alpha production. Treatment with Spleen Tyrosine Kinase antagonist (Fostamatinib) reduces the expression of mast cell-associated gene transcripts, associated biochemical pathways and the number of tryptase/chymase positive mast cells in lesional hidradenitis suppurativa tissue. This data indicates that although mast cells are not the most abundant cell type in Hidradenitis Suppurativa tissue, the dysregulation of mast cells is paralleled with B cell/plasma cell inflammation, inflammatory epithelialized tunnels and epithelial budding. This provides an explanation as to the mixed inflammatory activation signature seen in HS, the correlation with dysregulated wound healing and potential pathways involved in the development of epithelialized tunnels.
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Affiliation(s)
- A Flora
- Laboratory of Translational Cutaneous Medicine, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
- University of New South Wales, Sydney, New South Wales, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - R Jepsen
- Holdsworth House Medical Practice, Sydney, New South Wales, Australia
| | - E K Kozera
- University of New South Wales, Sydney, New South Wales, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - J A Woods
- University of New South Wales, Sydney, New South Wales, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - G D Cains
- University of New South Wales, Sydney, New South Wales, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - M Radzieta
- South West Sydney Limb Preservation and Wound Research, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
- School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - S O Jensen
- School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - M Malone
- South West Sydney Limb Preservation and Wound Research, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
- School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - J W Frew
- Laboratory of Translational Cutaneous Medicine, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
- University of New South Wales, Sydney, New South Wales, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, New South Wales, Australia
- Holdsworth House Medical Practice, Sydney, New South Wales, Australia
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4
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Flora A, Jepsen R, Kozera EK, Woods JA, Cains GD, Radzieta M, Jensen SO, Malone M, Frew JW. Human dermal fibroblast subpopulations and epithelial mesenchymal transition signals in hidradenitis suppurativa tunnels are normalized by spleen tyrosine kinase antagonism in vivo. PLoS One 2023; 18:e0282763. [PMID: 37922232 PMCID: PMC10624284 DOI: 10.1371/journal.pone.0282763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/19/2023] [Indexed: 11/05/2023] Open
Abstract
Hidradenitis Suppurativa is a chronic inflammatory disease of which the pathogenesis is incompletely understood. Dermal fibroblasts have been previously identified as a major source of inflammatory cytokines, however information pertaining to the characteristics of subpopulations of fibroblasts in HS remains unexplored. Using in silico-deconvolution of whole-tissue RNAseq, Nanostring gene expression panels and confirmatory immunohistochemistry we identified fibroblast subpopulations in HS tissue and their relationship to disease severity and lesion morphology. Gene signatures of SFRP2+ fibroblast subsets were increased in lesional tissue, with gene signatures of SFRP1+ fibroblast subsets decreased. SFRP2+ and CXCL12+ fibroblast numbers, measured by IHC, were increased in HS tissue, with greater numbers associated with epithelialized tunnels and Hurley Stage 3 disease. Pro-inflammatory CXCL12+ fibroblasts were also increased, with reductions in SFRP1+ fibroblasts compared to healthy controls. Evidence of Epithelial Mesenchymal Transition was seen via altered gene expression of SNAI2 and altered protein expression of ZEB1, TWIST1, Snail/Slug, E-Cadherin and N-Cadherin in HS lesional tissue. The greatest dysregulation of EMT associated proteins was seen in biopsies containing epithelialized tunnels. The use of the oral Spleen tyrosine Kinase inhibitor Fostamatinib significantly reduced expression of genes associated with chronic inflammation, fibroblast proliferation and migration suggesting a potential role for targeting fibroblast activity in HS.
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Affiliation(s)
- Akshay Flora
- Laboratory of Translational Cutaneous Medicine, Ingham Institute for Applied Medical Research, Sydney, Australia
- University of New South Wales, Sydney, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, Australia
| | | | - Emily K. Kozera
- University of New South Wales, Sydney, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, Australia
| | - Jane A. Woods
- University of New South Wales, Sydney, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, Australia
| | - Geoffrey D. Cains
- University of New South Wales, Sydney, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, Australia
| | - Michael Radzieta
- South West Sydney Limb Preservation and Wound Research, Ingham Institute for Applied Medical Research, Liverpool, Australia
- School of Medicine, Western Sydney University, Sydney, Australia
| | - Slade O. Jensen
- School of Medicine, Western Sydney University, Sydney, Australia
| | - Matthew Malone
- South West Sydney Limb Preservation and Wound Research, Ingham Institute for Applied Medical Research, Liverpool, Australia
- School of Medicine, Western Sydney University, Sydney, Australia
| | - John W. Frew
- Laboratory of Translational Cutaneous Medicine, Ingham Institute for Applied Medical Research, Sydney, Australia
- University of New South Wales, Sydney, Australia
- Department of Dermatology, Liverpool Hospital, Sydney, Australia
- Holdsworth House Medical Practice, Sydney, Australia
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Zhou X, Kumar P, Bhuyan DJ, Jensen SO, Roberts TL, Münch GW. Neuroinflammation in Alzheimer's Disease: A Potential Role of Nose-Picking in Pathogen Entry via the Olfactory System? Biomolecules 2023; 13:1568. [PMID: 38002250 PMCID: PMC10669446 DOI: 10.3390/biom13111568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder characterized by progressive cognitive decline and memory impairment. Many possible factors might contribute to the development of AD, including amyloid peptide and tau deposition, but more recent evidence suggests that neuroinflammation may also play an-at least partial-role in its pathogenesis. In recent years, emerging research has explored the possible involvement of external, invading pathogens in starting or accelerating the neuroinflammatory processes in AD. In this narrative review, we advance the hypothesis that neuroinflammation in AD might be partially caused by viral, bacterial, and fungal pathogens entering the brain through the nose and the olfactory system. The olfactory system represents a plausible route for pathogen entry, given its direct anatomical connection to the brain and its involvement in the early stages of AD. We discuss the potential mechanisms through which pathogens may exploit the olfactory pathway to initiate neuroinflammation, one of them being accidental exposure of the olfactory mucosa to hands contaminated with soil and feces when picking one's nose.
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Affiliation(s)
- Xian Zhou
- NICM Health Research Institute, Western Sydney University, Westmead, NSW 2145, Australia; (X.Z.); (D.J.B.)
| | - Paayal Kumar
- Pharmacology Unit, School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia;
| | - Deep J. Bhuyan
- NICM Health Research Institute, Western Sydney University, Westmead, NSW 2145, Australia; (X.Z.); (D.J.B.)
| | - Slade O. Jensen
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (S.O.J.); (T.L.R.)
- Microbiology and Infectious Diseases Unit, School of Medicine, Western Sydney University, Liverpool, NSW 2170, Australia
| | - Tara L. Roberts
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia; (S.O.J.); (T.L.R.)
- Oncology Unit, School of Medicine, Western Sydney University, Liverpool, NSW 2170, Australia
| | - Gerald W. Münch
- NICM Health Research Institute, Western Sydney University, Westmead, NSW 2145, Australia; (X.Z.); (D.J.B.)
- Pharmacology Unit, School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia;
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Ax T, Ganse B, Fries FN, Szentmáry N, de Paiva CS, March de Ribot F, Jensen SO, Seitz B, Millar TJ. Dry eye disease in astronauts: a narrative review. Front Physiol 2023; 14:1281327. [PMID: 37929210 PMCID: PMC10620524 DOI: 10.3389/fphys.2023.1281327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
Long-duration spaceflight can have adverse effects on human health. One of the most common ocular conditions experienced by astronauts is dry eye disease (DED). Symptoms of DED include feelings of eye irritation, eye strain, foreign body sensation and blurred vision. Over 30% of International Space Station expedition crew members reported irritation and foreign body sensation. We reviewed the current literature on the prevalence and mechanisms of DED in astronauts and its potential implications for long-duration spaceflight, including the influence of environmental factors, such as microgravity and fluid shift on tear film physiology in space. DED has negative effects on astronaut performance, which is why there is a need for further research into the pathophysiology and countermeasures. As an in-flight countermeasure, neurostimulation seems to be among the most promising options.
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Affiliation(s)
- Timon Ax
- Department of Ophthalmology, Saarland University Medical Center, Homburg/Saar, Germany
- School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Bergita Ganse
- Werner Siemens-Endowed Chair for Innovative Implant Development (Fracture Healing), Departments and Institutes of Surgery, Saarland University, Homburg/Saar, Germany
- Department of Trauma, Hand and Reconstructive Surgery, Departments and Institutes of Surgery, Saarland University, Homburg/Saar, Germany
| | - Fabian N. Fries
- Department of Ophthalmology, Saarland University Medical Center, Homburg/Saar, Germany
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg/Saar, Germany
| | - Nóra Szentmáry
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg/Saar, Germany
| | - Cintia S. de Paiva
- Ocular Surface Center, Department of Ophthalmology, Baylor College of Medicine, Cullen Eye Institute, Houston, TX, United States
| | | | - Slade O. Jensen
- School of Medicine, Western Sydney University, Sydney, NSW, Australia
- Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, NSW, Australia
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center, Homburg/Saar, Germany
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Sarosh A, Kwong SM, Jensen SO, Northern F, Walton WG, Eakes TC, Redinbo MR, Firth N, McLaughlin KJ. pSK41/pGO1-family conjugative plasmids of Staphylococcus aureus encode a cryptic repressor of replication. Plasmid 2023; 128:102708. [PMID: 37967733 DOI: 10.1016/j.plasmid.2023.102708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023]
Abstract
The majority of large multiresistance plasmids of Staphylococcus aureus utilise a RepA_N-type replication initiation protein, the expression of which is regulated by a small antisense RNA (RNAI) that overlaps the rep mRNA leader. The pSK41/pGO1-family of conjugative plasmids additionally possess a small (86 codon) divergently transcribed ORF (orf86) located upstream of the rep locus. The product of pSK41 orf86 was predicted to have a helix-turn-helix motif suggestive of a likely function in transcriptional repression. In this study, we investigated the effect of Orf86 on transcription of thirteen pSK41 backbone promoters. We found that Orf86 only repressed transcription from the rep promoter, and hence now redesignate the product as Cop. Over-expression of Cop in trans reduced the copy number of pSK41 mini-replicons, both in the presence and absence of rnaI. in vitro protein-DNA binding experiments with purified 6 × His-Cop demonstrated specific DNA binding, adjacent to, and partially overlapping the -35 hexamer of the rep promoter. The crystal structure of Cop revealed a dimeric structure similar to other known transcriptional regulators. Cop mRNA was found to result from "read-through" transcription from the strong RNAI promoter that escapes the rnaI terminator. Thus, PrnaI is responsible for transcription of two distinct negative regulators of plasmid copy number; the antisense RNAI that primarily represses Rep translation, and Cop protein that can repress rep transcription. Deletion of cop in a native plasmid did not appear to impact copy number, indicating a cryptic auxiliary role.
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Affiliation(s)
- Alvina Sarosh
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales 2751, Australia; Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Liverpool, New South Wales 2170, Australia
| | - Faith Northern
- Chemistry Department, Vassar College, Poughkeepsie, NY 12604, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Thomas C Eakes
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biochemistry, Microbiology and Genomics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia.
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Malone M, Radzieta M, Schwarzer S, Walker A, Bradley J, Jensen SO. In vivo observations of biofilm adhering to a dialkylcarbamoyl chloride-coated mesh dressing when applied to diabetes-related foot ulcers: A proof of concept study. Int Wound J 2022. [PMID: 36567138 DOI: 10.1111/iwj.14054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/27/2022] [Accepted: 12/04/2022] [Indexed: 12/27/2022] Open
Abstract
In this proof-of-concept study of twenty participants, we sought to determine if a DACC (Dialkylcarbamoyl chloride)-coated mesh dressing demonstrates an ability to adhere biofilm when placed on Diabetes Related Foot Ulcers (DRFUs) with chronic infection. The study also sought to determine if removal of the DACC-coated mesh dressings contributes to reducing the total number of bacteria in DRFUs, by exploring the total microbial loads, microbial community composition, and diversity. Standard of care was provided in addition to the application of DACC or DACC hydrogel every three days for a total of two weeks. Wound swabs, tissue curettage, and soiled dressings were collected pre and post-treatment. Tissue specimens obtained pre-treatment were analysed with scanning electron microscopy (SEM) and peptide nucleic acid fluorescent in situ hybridisation (PNA-FISH) with confocal laser scanning microscopy and confirmed the presence of biofilm in all DRFUs. SEM confirmed the presence of biofilms readily adhered to soiled DACC-coated mesh dressings pre- and post-treatment in all participants. Real-time quantitative polymerase chain reaction (qPCR) demonstrated the mean total microbial load of DRFUs in 20 participants did not change after two weeks of therapy (pre-treatment = 4.31 Log10 16 S copies (±0.8) versus end of treatment = 4.32 Log10 16 S copies (±0.9), P = .96, 95% CI -0.56 to 0.5). 16 S sequencing has shown the microbial composition of DACC dressings and wound swabs pre- and post-treatment remained similar (DACC; R = -.047, P = .98, Swab; R = -.04, P = .86), indicating the microbial communities originate from the ulcer. Biofilms adhere to DACC-coated mesh dressings; however, this may not reduce the total microbial load present within DRFU tissue. Wound dressings for use in hard-to-heal wounds should be used as an adjunct to a good standard of care which includes debridement and wound bed preparation.
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Affiliation(s)
- Matthew Malone
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, New South Wales, Australia.,High Risk Foot Service, Liverpool Hospital, South West Sydney LHD, Sydney, New South Wales, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - Michael Radzieta
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, New South Wales, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - Saskia Schwarzer
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, New South Wales, Australia.,High Risk Foot Service, Liverpool Hospital, South West Sydney LHD, Sydney, New South Wales, Australia
| | - Amy Walker
- High Risk Foot Service, Monash Health, Clayton, Victoria, Australia
| | - Justin Bradley
- High Risk Foot Service, Monash Health, Clayton, Victoria, Australia
| | - Slade O Jensen
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, New South Wales, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
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Domazetovska A, Jensen SO, Gray M, Radzieta M, Maley M. Culture-Free Phylogenetic Analysis of Legionella pneumophila Using Targeted CRISPR/Cas9 Next-Generation Sequencing. Microbiol Spectr 2022; 10:e0035922. [PMID: 35862996 PMCID: PMC9430934 DOI: 10.1128/spectrum.00359-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/19/2022] [Indexed: 11/20/2022] Open
Abstract
Currently available methods for the laboratory investigation of Legionella pneumophila outbreaks require organism culture. The ability to sequence L. pneumophila directly from clinical samples would significantly reduce delays. Here, we develop a method for targeted next-generation sequencing (NGS) of selected L. pneumophila genes utilizing a CRISPR/Cas9-based target enrichment system. We determine the method's utility by typing cultured L. pneumophila isolates and subsequently apply the method directly to patient samples. We sequenced 10 L. pneumophila isolates by 2 methods, (i) whole-genome sequencing (WGS) and (ii) targeted (CRISPR/Cas9-based) finding low-abundance sequences by hybridization (FLASH)-NGS, sequencing 57 selected genes. The targeted NGS of 57 genes was more efficient than WGS, and phylogenetic analysis of the 57 genes yielded the same classification of the L. pneumophila isolates as that based on analysis of whole-genome data. Furthermore, targeted NGS of L. pneumophila performed directly on patient respiratory samples correctly classified the patients according to their corresponding cultured isolates. This provides proof of concept that targeted NGS can be used to sequence L. pneumophila directly from patient samples. Studies on a larger number of patient samples will further validate this method. Nonetheless, CRISPR/Cas9 targeted NGS methods have the potential to be widely applicable to microbial-outbreak investigations in the future, particularly in the context of difficult and slow-growing organisms. IMPORTANCE The bacterium Legionella pneumophila is responsible for outbreaks of serious and life-threatening pneumonia called Legionnaires' disease. There is a need for new molecular methods that allow investigation of Legionella outbreaks directly from patient samples, without the need for prior microbiological culture, which causes delays. Our study aims to address this problem. We have utilized a CRISPR/Cas9-based targeted next-generation sequencing (NGS) method that can be applied directly on human specimens. Furthermore, we show that analysis of the sequences of a small number of targeted genes offers the same classification of L. pneumophila as that based on data derived from the whole genome. Given the rising interest globally in sequencing pathogens directly from human samples, CRISPR/Cas9 targeted NGS methods have the potential to be widely applicable to microbial-outbreak investigations in the future, particularly in the context of difficult and slow-growing organisms.
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Affiliation(s)
- Ana Domazetovska
- Department of Microbiology and Infectious Diseases, Liverpool Hospital, Liverpool, New South Wales, Australia
- NSW Health Pathology, Microbiology, Liverpool Hospital, Liverpool, New South Wales, Australia
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia
| | - Slade O. Jensen
- Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, Australia
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia
| | - Matthew Gray
- NSW Health Pathology, Microbiology, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Michael Radzieta
- Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, Australia
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia
| | - Michael Maley
- Department of Microbiology and Infectious Diseases, Liverpool Hospital, Liverpool, New South Wales, Australia
- NSW Health Pathology, Microbiology, Liverpool Hospital, Liverpool, New South Wales, Australia
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Radzieta M, Malone M, Ahmad M, Dickson HG, Schwarzer S, Jensen SO, Lavery LA. Metatranscriptome sequencing identifies Escherichia are major contributors to pathogenic functions and biofilm formation in diabetes related foot osteomyelitis. Front Microbiol 2022; 13:956332. [PMID: 35979499 PMCID: PMC9376677 DOI: 10.3389/fmicb.2022.956332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/11/2022] [Indexed: 11/26/2022] Open
Abstract
Osteomyelitis in the feet of persons with diabetes is clinically challenging and is associated with high rates of amputation. In this study RNA-sequencing was employed to explore microbial metatranscriptomes with a view to understand the relative activity and functions of the pathogen/s responsible for diabetes foot osteomyelitis (DFO). We obtained 25 intraoperative bone specimens from persons with confirmed DFO, observing that Escherichia spp. (7%), Streptomyces spp. (7%), Staphylococcus spp. (6%), Klebsiella spp. (5%) and Proteus spp. (5%) are the most active taxa on average. Data was then subset to examine functions associated with pathogenesis (virulence and toxins), biofilm formation and antimicrobial/multi-drug resistance. Analysis revealed Escherichia spp. are the most active taxa relative to pathogenic functions with K06218 (mRNA interferase relE), K03699 (membrane damaging toxin tlyC) and K03980 (putative peptidoglycan lipid II flippase murJ), K01114 (membrane damaging toxin plc) and K19168 (toxin cptA) being the most prevalent pathogenic associated transcripts. The most abundant transcripts associated with biofilm pathways included components of the biofilm EPS matrix including glycogen synthesis, cellulose synthesis, colonic acid synthesis and flagella synthesis. We further observed enrichment of a key enzyme involved in the biosynthesis of L-rhamnose (K01710 -dTDP-glucose 4,6-dehydratase rfbB, rmlB, rffG) which was present in all but four patients with DFO.
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Affiliation(s)
- Michael Radzieta
- South West Sydney Limb Preservation and Wound Research, South Western Sydney Local Health District (LHD), Sydney, NSW, Australia
- Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Matthew Malone
- South West Sydney Limb Preservation and Wound Research, South Western Sydney Local Health District (LHD), Sydney, NSW, Australia
- Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
- *Correspondence: Matthew Malone
| | - Mehtab Ahmad
- Department of Vascular Surgery, Liverpool Hospital, South Western Sydney Local Health District (LHD), Sydney, NSW, Australia
| | - Hugh G. Dickson
- South West Sydney Limb Preservation and Wound Research, South Western Sydney Local Health District (LHD), Sydney, NSW, Australia
- South Western Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Saskia Schwarzer
- South West Sydney Limb Preservation and Wound Research, South Western Sydney Local Health District (LHD), Sydney, NSW, Australia
- Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Slade O. Jensen
- South West Sydney Limb Preservation and Wound Research, South Western Sydney Local Health District (LHD), Sydney, NSW, Australia
- South Western Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Lawrence A. Lavery
- Department of Plastic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, United States
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11
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Radzieta M, Peters TJ, Dickson HG, Cowin AJ, Lavery LA, Schwarzer S, Roberts T, Jensen SO, Malone M. A metatranscriptomic approach to explore longitudinal tissue specimens from non-healing diabetes related foot ulcers. APMIS 2022; 130:383-396. [PMID: 35394091 PMCID: PMC9320801 DOI: 10.1111/apm.13226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 12/13/2022]
Abstract
Cellular mechanisms and/or microbiological interactions which contribute to chronic diabetes related foot ulcers (DRFUs) were explored using serially collected tissue specimens from chronic DRFUs and control healthy foot skin. Total RNA was isolated for next-generation sequencing. We found differentially expressed genes (DEGs) and enriched hallmark gene ontology biological processes upregulated in chronic DRFUs which primarily functioned in the host immune response including: (i) Inflammatory response; (ii) TNF signalling via NFKB; (iii) IL6 JAK-STAT3 signalling; (iv) IL2 STAT5 signalling and (v) Reactive oxygen species. A temporal analysis identified RN7SL1 signal recognition protein and IGHG4 immunoglobulin protein coding genes as being the most upregulated genes after the onset of treatment. Testing relative temporal changes between healing and non-healing DRFUs identified progressive upregulation in healed wounds of CXCR5 and MS4A1 (CD20), both canonical markers of lymphocytes (follicular B cells/follicular T helper cells and B cells, respectively). Collectively, our RNA-seq data provides insights into chronic DRFU pathogenesis.
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Affiliation(s)
- Michael Radzieta
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Sydney, NSW, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Timothy J Peters
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,University of New South Wales, Sydney, NSW, Australia
| | - Hugh G Dickson
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Sydney, NSW, Australia.,South Western Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Allison J Cowin
- Future Industries Institute, University of South Australia, Adelaide, SA, Australia
| | - Lawrence A Lavery
- Department of Plastic Surgery, University of Texas Southwestern Medical Centre, Dallas, TX, USA
| | - Saskia Schwarzer
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Sydney, NSW, Australia
| | - Tara Roberts
- Oncology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Slade O Jensen
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Sydney, NSW, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Matthew Malone
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Sydney, NSW, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
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12
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Malone M, Radzieta M, Peters TJ, Dickson HG, Schwarzer S, Jensen SO, Lavery LA. Host-microbe metatranscriptome reveals differences between acute and chronic infections in diabetes-related foot ulcers. APMIS 2021; 130:751-762. [PMID: 34888950 DOI: 10.1111/apm.13200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/07/2021] [Indexed: 12/13/2022]
Abstract
Virtually all diabetes-related foot ulcers (DRFUs) will become colonized by microorganisms that may increase the risk of developing an infection. The reasons why some ulcerations develop acute clinical infections (AI-DRFUs) whilst others develop chronic infection (CI-DRFUs) and the preceding host-microbe interactions in vivo remain largely unknown. Establishing that acute and chronic infections are distinct processes requires demonstrating that these are two different strategies employed by microbes when interacting with a host. In this study, dual-RNA seq was employed to differentiate the host-microbe metatranscriptome between DRFUs that had localized chronic infection or acute clinical infection. Comparison of the host metatranscriptome in AI-DRFUs relative to CI-DRFUs identified upregulated differentially expressed genes (DEGs) that functioned as regulators of vascular lymphatic inflammatory responses, T-cell signalling and olfactory receptors. Conversely, CI-DRFUs upregulated DEGs responsible for cellular homeostasis. Gene set enrichment analysis using Hallmark annotations revealed enrichment of immune and inflammatory profiles in CI-DRFUs relative to AI-DRFUs. Analysis of the microbial metatranscriptome identified the DEGs being enriched within AI-DRFUs relative to CI-DRFUs included several toxins, two-component systems, bacterial motility, secretion systems and genes encoding for energy metabolism. Functions relevant to DRFU pathology were further explored, including biofilm and bacterial pathogenesis. This identified that the expression of biofilm-associated genes was higher within CI-DRFUs compared to that of AI-DRFUs, with mucR being the most highly expressed gene. Collectively, these data provide insights into the host-microbe function in two clinically-distinct infective phenotypes that affect DRFUs. The data reveal that bacteria in acutely infected DRFUs prioritize motility over biofilm and demonstrate greater pathogenicity and mechanisms, which likely subvert host cellular and immune pathways to establish infection. Upregulation of genes for key vascular inflammatory mediators in acutely infected ulcers may contribute, in part, to the clinical picture of a red, hot, swollen foot, which differentiates an acutely infected ulcer from that of a chronic infection.
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Affiliation(s)
- Matthew Malone
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Sydney, NSW, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Michael Radzieta
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Sydney, NSW, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Timothy J Peters
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,University of New South Wales, Sydney, NSW, Australia
| | - Hugh G Dickson
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Sydney, NSW, Australia.,South Western Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Saskia Schwarzer
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Sydney, NSW, Australia
| | - Slade O Jensen
- Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Lawrence A Lavery
- Department of Plastic Surgery, University of Texas Southwestern Medical Centre, Dallas, TX, USA
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13
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Malone M, Radzieta M, Schwarzer S, Jensen SO, Lavery LA. Efficacy of a topical concentrated surfactant gel on microbial communities in non-healing diabetic foot ulcers with chronic biofilm infections: A proof-of-concept study. Int Wound J 2021; 18:457-466. [PMID: 33476485 PMCID: PMC8273583 DOI: 10.1111/iwj.13546] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/18/2020] [Accepted: 12/28/2020] [Indexed: 12/15/2022] Open
Abstract
This proof‐of‐concept study sought to determine the effects of standard of care (SOC) and a topically applied concentrated surfactant gel (SG) on the total microbial load, community composition, and community diversity in non‐healing diabetic foot ulcers (DFUs) with chronic biofilm infections. SOC was provided in addition to a topical concentrated SG, applied every 2 days for 6 weeks. Wound swabs were obtained from the base of ulcers at baseline (week 0), week 1, mid‐point (week 3), and end of treatment (week 6). DNA sequencing and real‐time quantitative polymerase chain reaction (qPCR) were employed to determine the total microbial load, community composition, and diversity of patient samples. Tissue specimens were obtained at baseline and scanning electron microscopy and peptide nucleic acid fluorescent in situ hybridisation with confocal laser scanning microscopy were used to confirm the presence of biofilm in all 10 DFUs with suspected chronic biofilm infections. The application of SG resulted in 7 of 10 samples achieving a reduction in mean log10 total microbial load from baseline to end of treatment (0.8 Log10 16S copies, ±0.6), and 3 of 10 samples demonstrated an increase in mean Log10 total microbial load (0.6 log10 16S copies, ±0.8) from baseline to end of treatment. Composition changes in microbial communities were driven by changes to the most dominant bacteria. Corynebacterium sp. and Streptococcus sp. frequently reduced in relative abundance in patient samples from week 0 to week 6 but did not disappear. In contrast, Staphylococcus sp., Finegoldia sp., and Fusobacterium sp., relative abundances frequently increased in patient samples from week 0 to week 6. The application of a concentrated SG resulted in varying shifts to diversity (increase or decrease) between week 0 and week 6 samples at the individual patient level. Any shifts in community diversity were independent to changes in the total microbial loads. SOC and a topical concentrated SG directly affect the microbial loads and community composition of DFUs with chronic biofilm infections.
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Affiliation(s)
- Matthew Malone
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, Australia.,High Risk Foot Service, Liverpool Hospital, South West Sydney LHD, Sydney, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, Australia
| | - Michael Radzieta
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, Australia
| | - Saskia Schwarzer
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, Australia.,High Risk Foot Service, Liverpool Hospital, South West Sydney LHD, Sydney, Australia
| | - Slade O Jensen
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia
| | - Lawrence A Lavery
- Department of Plastic Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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14
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Malone M, Radzieta M, Jensen SO, Mahon C. Wound biofilms and their role in individuals with epidermolysis bullosa. Australas J Dermatol 2020; 61:279-280. [PMID: 32201933 DOI: 10.1111/ajd.13274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew Malone
- South Western Sydney LHD, Limb Preservation and Wound Research Academic Unit, Ingham Institute of Applied Medical Research, Liverpool, Sydney, NSW, Australia.,School of Medicine, Infectious Diseases and Microbiology, Western Sydney University, Campbelltown, Sydney, NSW, Australia
| | - Michael Radzieta
- South Western Sydney LHD, Limb Preservation and Wound Research Academic Unit, Ingham Institute of Applied Medical Research, Liverpool, Sydney, NSW, Australia.,School of Medicine, Infectious Diseases and Microbiology, Western Sydney University, Campbelltown, Sydney, NSW, Australia
| | - Slade O Jensen
- South Western Sydney LHD, Limb Preservation and Wound Research Academic Unit, Ingham Institute of Applied Medical Research, Liverpool, Sydney, NSW, Australia.,School of Medicine, Infectious Diseases and Microbiology, Western Sydney University, Campbelltown, Sydney, NSW, Australia
| | - Caroline Mahon
- Department of Dermatology, Canterbury District Health Board, Christchurch Hospital, Christchurch, New Zealand
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15
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Schwarzer S, James GA, Goeres D, Bjarnsholt T, Vickery K, Percival SL, Stoodley P, Schultz G, Jensen SO, Malone M. The efficacy of topical agents used in wounds for managing chronic biofilm infections: A systematic review. J Infect 2019; 80:261-270. [PMID: 31899281 DOI: 10.1016/j.jinf.2019.12.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 12/18/2019] [Accepted: 12/24/2019] [Indexed: 12/19/2022]
Abstract
OBJECTIVES Clinicians have increasingly adopted the widespread use of topical agents to manage chronic wound infections, despite limited data on their effectiveness in vivo. This study sought to evaluate the evidence for commonly employed topical agents used in wounds for the purpose of treating chronic infections caused by biofilm. METHOD We included in vitro, animal and human in vivo studies where topical agents were tested for their efficacy against biofilms, for use in wound care. For human studies, we only included those which utilised appropriate identification techniques for visualising and confirming the presence of biofilms. RESULT A total of 640 articles were identified, with 43 included after meeting eligibility. In vitro testing accounted for 90% (n = 39) of all included studies, five studies using animal models and three human in vivo studies. Sixteen different laboratory models were utilised, with the most frequent being the minimum biofilm eradication concentration (MBEC™) / well plate assay (38%, n = 15 of 39). A total of 44 commercially available topical agents were grouped into twelve categories with the most commonly tested agents being silver, iodine and polyhexamethylene biguanide (PHMB). In vitro results on efficacy demonstrated iodine as having the highest mean log10 reductions of all agents (4.81, ±3.14). CONCLUSION There is large disparity in the translation of laboratory studies to researchers undertaking human trials relating to the effectiveness of commercially available topical agents. There is insufficient human in vivo evidence to definitively recommend any commercially available topical agent over another for the treatment of chronic wound biofilms. The heterogeneity identified between study designs (in vitro to in vivo) further limits the generalisability of results.
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Affiliation(s)
- S Schwarzer
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, Australia.
| | - G A James
- Centre for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - D Goeres
- Centre for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - T Bjarnsholt
- Department of Immunology and Microbiology, Costerton Biofilm Centre, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Microbiology, Copenhagen University Hospital, Copenhagen, Denmark
| | - K Vickery
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney Australia
| | - S L Percival
- 5D Health Protection Group Ltd, Centre of Excellence in Biofilm Science (CEBS), Liverpool Bio-Innovation Hub, Liverpool UK
| | - P Stoodley
- Departments of Microbial Infection and Immunity, and Orthopaedics, Ohio State University, Columbus, OH, United States
| | - G Schultz
- Department of Obstetrics & Gynecology, Institute for Wound Research, University of Florida, Gainesville, FL, United States
| | - S O Jensen
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, Australia; Infectious Diseases and Microbiology, School of Medicine, Ingham Institute for Applied Medical Research, Western Sydney University, United States
| | - M Malone
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, Australia; Infectious Diseases and Microbiology, School of Medicine, Ingham Institute for Applied Medical Research, Western Sydney University, United States
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16
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Malone M, Schwarzer S, Radzieta M, Jeffries T, Walsh A, Dickson HG, Micali G, Jensen SO. Effect on total microbial load and community composition with two vs six-week topical Cadexomer Iodine for treating chronic biofilm infections in diabetic foot ulcers. Int Wound J 2019; 16:1477-1486. [PMID: 31487117 DOI: 10.1111/iwj.13219] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/18/2019] [Accepted: 08/21/2019] [Indexed: 12/13/2022] Open
Abstract
This study compares two vs six weeks of topical antimicrobial therapy with Cadexomer Iodine in patients with diabetic foot ulcers (DFUs) complicated by chronic biofilm infections. Patients with non-healing DFUs with suspected chronic biofilm infections were eligible for enrolment. Patients were randomised to receive either two or six weeks of treatment with topical Cadexomer Iodine. Tissue biopsies from the ulcers were obtained pre-and-post treatment and underwent DNA sequencing and real-time quantitative polymerase chain reaction (PCR) to determine the total microbial load, community composition, and diversity of bacteria. Scanning electron microscopy confirmed biofilm in all 18 ulcers with suspected chronic biofilm infections. Cadexomer Iodine resulted in 14 of 18 (78%) samples achieving a mean 0.5 log10 reduction in microbial load. Regardless of treatment duration, there was no statistical difference in the reduction of total microbial loads. No difference in the rate of wound healing in the two groups was seen at 6 weeks. Cadexomer Iodine reduces the total microbial load in DFUs with chronic biofilm infections and affects microbial community composition and diversity. All ulcers in both groups showed an initial reduction in wound size with application of Cadexomer Iodine, which might reflect its effect on biofilms.
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Affiliation(s)
- Matthew Malone
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, New South Wales, Australia.,High Risk Foot Service, Liverpool Hospital, South West Sydney LHD, Sydney, New South Wales, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - Saskia Schwarzer
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, New South Wales, Australia.,High Risk Foot Service, Liverpool Hospital, South West Sydney LHD, Sydney, New South Wales, Australia
| | - Michael Radzieta
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, New South Wales, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - Thomas Jeffries
- Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - Annie Walsh
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, New South Wales, Australia.,High Risk Foot Service, Liverpool Hospital, South West Sydney LHD, Sydney, New South Wales, Australia
| | - Hugh G Dickson
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, New South Wales, Australia
| | - Grace Micali
- Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, New South Wales, Australia
| | - Slade O Jensen
- South West Sydney Limb Preservation and Wound Research, South West Sydney Local Health District, Sydney, New South Wales, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, New South Wales, Australia
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17
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Malone M, Fritz BG, Vickery K, Schwarzer S, Sharma V, Biggs N, Radzieta M, Jeffries TT, Dickson HG, Jensen SO, Bjarnsholt T. Analysis of proximal bone margins in diabetic foot osteomyelitis by conventional culture, DNA sequencing and microscopy. APMIS 2019; 127:660-670. [PMID: 31344275 DOI: 10.1111/apm.12986] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/19/2019] [Indexed: 01/21/2023]
Abstract
Multiple approaches were employed to detect pathogens from bone margins associated with Diabetic Foot Osteomyelitis (DFO). Intra-operative bone specimens of 14 consecutive subjects with suspected DFO were collected over a six-month study period from Liverpool Hospital. Infected bone and a proximal bone margins presumed to be 'clean/non-infected' were collected. Bone material was subjected to conventional culture, DNA sequencing and microscopy. In total, eight of 14 (57%) proximal bone margins had no growth by conventional culture but were identified in all proximal bone specimens by DNA sequencing. Proximal margins had lower median total microbial counts than infected specimens, but these differences were not statistically significant. Pathogens identified by sequencing in infected specimens were identified in proximal margins and the microbiomes were similar (ANOSIM = 0.02, p = 0.59). Using a combination of SEM and/or PNA-FISH, we visualized the presence of microorganisms in infected bone specimens and their corresponding proximal margins of seven patients (50%) with DFO. We identify that bacteria can still reside in what seems to be proximal 'clean' margins. The significance and implications of clinical outcomes requires further analysis from a larger sample size that incorporates differences in surgical and post-operative approaches, correlating any outcomes back to culture-sequence findings.
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Affiliation(s)
- Matthew Malone
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Ingham Institute of Applied Medical Research, Sydney, NSW, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Liverpool Hospital, South Western Sydney LHD, Sydney, NSW, Australia
| | - Blaine G Fritz
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, Costerton Biofilm Centre, University of Copenhagen, Copenhagen, Denmark
| | - Karen Vickery
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Saskia Schwarzer
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Ingham Institute of Applied Medical Research, Sydney, NSW, Australia.,Liverpool Hospital, South Western Sydney LHD, Sydney, NSW, Australia
| | - Varun Sharma
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Ingham Institute of Applied Medical Research, Sydney, NSW, Australia.,Liverpool Hospital, South Western Sydney LHD, Sydney, NSW, Australia
| | - Nathan Biggs
- Liverpool Hospital, South Western Sydney LHD, Sydney, NSW, Australia
| | - Michael Radzieta
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Ingham Institute of Applied Medical Research, Sydney, NSW, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Thomas T Jeffries
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Ingham Institute of Applied Medical Research, Sydney, NSW, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Hugh G Dickson
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Ingham Institute of Applied Medical Research, Sydney, NSW, Australia.,Liverpool Hospital, South Western Sydney LHD, Sydney, NSW, Australia
| | - Slade O Jensen
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Ingham Institute of Applied Medical Research, Sydney, NSW, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Thomas Bjarnsholt
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, Costerton Biofilm Centre, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, København, Denmark
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18
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Baines SL, Jensen SO, Firth N, Gonçalves da Silva A, Seemann T, Carter GP, Williamson DA, Howden BP, Stinear TP. Remodeling of pSK1 Family Plasmids and Enhanced Chlorhexidine Tolerance in a Dominant Hospital Lineage of Methicillin-Resistant Staphylococcus aureus. Antimicrob Agents Chemother 2019; 63:e02356-18. [PMID: 30783008 PMCID: PMC6496109 DOI: 10.1128/aac.02356-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/08/2019] [Indexed: 12/29/2022] Open
Abstract
Staphylococcus aureus is a significant human pathogen whose evolution and adaptation have been shaped in part by mobile genetic elements (MGEs), facilitating the global spread of extensive antimicrobial resistance. However, our understanding of the evolutionary dynamics surrounding MGEs, in particular, how changes in the structure of multidrug resistance (MDR) plasmids may influence important staphylococcal phenotypes, is incomplete. Here, we undertook a population and functional genomics study of 212 methicillin-resistant S. aureus (MRSA) sequence type 239 (ST239) isolates collected over 32 years to explore the evolution of the pSK1 family of MDR plasmids, illustrating how these plasmids have coevolved with and contributed to the successful adaptation of this persistent MRSA lineage. Using complete genomes and temporal phylogenomics, we reconstructed the evolution of the pSK1 family lineage from its emergence in the late 1970s and found that multiple structural variants have arisen. Plasmid maintenance and stability were linked to IS256- and IS257-mediated chromosomal integration and disruption of the plasmid replication machinery. Overlaying genomic comparisons with phenotypic susceptibility data for gentamicin, trimethoprim, and chlorhexidine, it appeared that pSK1 has contributed to enhanced resistance in ST239 MRSA isolates through two mechanisms: (i) acquisition of plasmid-borne resistance mechanisms increasing the rates of gentamicin resistance and reduced chlorhexidine susceptibility and (ii) changes in the plasmid configuration linked with further enhancement of chlorhexidine tolerance. While the exact mechanism of enhanced tolerance remains elusive, this research has uncovered a potential evolutionary response of ST239 MRSA to biocides, one of which may contribute to the ongoing persistence and adaptation of this lineage within health care institutions.
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Affiliation(s)
- Sarah L Baines
- Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Ingham Institute for Applied Medical Research, University of Western Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Glen P Carter
- Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Deborah A Williamson
- Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Infectious Diseases Department, Austin Health, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
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Johani K, Malone M, Jensen SO, Dickson HG, Gosbell IB, Hu H, Yang Q, Schultz G, Vickery K. Evaluation of short exposure times of antimicrobial wound solutions against microbial biofilms: from in vitro to in vivo. J Antimicrob Chemother 2019; 73:494-502. [PMID: 29165561 PMCID: PMC5890786 DOI: 10.1093/jac/dkx391] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/26/2017] [Indexed: 11/17/2022] Open
Abstract
Objectives Test the performance of topical antimicrobial wound solutions against microbial biofilms using in vitro, ex vivo and in vivo model systems at clinically relevant exposure times. Methods Topical antimicrobial wound solutions were tested under three different conditions: (in vitro) 4% w/v Melaleuca oil, polyhexamethylene biguanide, chlorhexidine, povidone iodine and hypochlorous acid were tested at short duration exposure times for 15 min against 3 day mature biofilms of Staphylococcus aureus and Pseudomonas aeruginosa; (ex vivo) hypochlorous acid was tested in a porcine skin explant model with 12 cycles of 10 min exposure, over 24 h, against 3 day mature P. aeruginosa biofilms; and (in vivo) 4% w/v Melaleuca oil was applied for 15 min exposure, daily, for 7 days, in 10 patients with chronic non-healing diabetic foot ulcers complicated by biofilm. Results In vitro assessment demonstrated variable efficacy in reducing biofilms ranging from 0.5 log10 reductions to full eradication. Repeated instillation of hypochlorous acid in a porcine model achieved <1 log10 reduction (0.77 log10, P = 0.1). Application of 4% w/v Melaleuca oil in vivo resulted in no change to the total microbial load of diabetic foot ulcers complicated by biofilm (median log10 microbial load pre-treatment = 4.9 log10 versus 4.8 log10, P = 0.43). Conclusions Short durations of exposure to topical antimicrobial wound solutions commonly utilized by clinicians are ineffective against microbial biofilms, particularly when used in vivo. Wound solutions should not be used as a sole therapy and clinicians should consider multifaceted strategies that include sharp debridement as the gold standard.
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Affiliation(s)
- K Johani
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia.,Central Military Laboratories and Blood Bank, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - M Malone
- High Risk Foot Service, Liverpool Hospital, South West Sydney LHD, Sydney, Australia.,Liverpool Diabetes Collaborative Research Unit, Ingham Institute of Applied Medical Research, Sydney, Australia.,Medical Sciences Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, Australia
| | - S O Jensen
- Medical Sciences Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia
| | - H G Dickson
- Ambulatory Care Department (PIXI), Liverpool Hospital, South West Sydney LHD, Sydney, Australia
| | - I B Gosbell
- Medical Sciences Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia.,Department of Microbiology and Infectious Diseases, Sydney South West Pathology Service, New South Wales Health Pathology, Liverpool, Sydney, Australia
| | - H Hu
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - Q Yang
- Department of Obstetrics and Gynecology, Institute for Wound Research, University of Florida, Gainesville, FL, USA
| | - G Schultz
- Department of Obstetrics and Gynecology, Institute for Wound Research, University of Florida, Gainesville, FL, USA
| | - K Vickery
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
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20
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Abstract
Cronobacter sakazakii neonatal infections are often epidemiologically linked to the consumption of contaminated powdered infant formula. We describe a case resulting from consumption of contaminated expressed breast milk, as confirmed by whole-genome sequencing. This case highlights potential risks associated with storage and acquisition of expressed breast milk.
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21
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Abstract
Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
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22
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McCafferty CE, Abi-Hanna D, Aghajani MJ, Micali GT, Lockart I, Vickery K, Gosbell IB, Jensen SO. The validity of adenosine triphosphate measurement in detecting endoscope contamination. J Hosp Infect 2018; 100:e142-e145. [PMID: 30092293 DOI: 10.1016/j.jhin.2018.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/01/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Endoscopic procedures are vital to gastrointestinal disease diagnosis and management, but risk infection transmission. In Australia, endoscopes undergo monthly-to-quarterly microbiological testing, to prevent patient infection. Endoscopes are used more frequently, meaning contamination may not be detected by this surveillance before infection transmission occurs. AIM To evaluate the use of adenosine triphosphate (ATP) measurement, alongside standard microbiological cultures, in detecting endoscope contamination before high-level disinfection. Using these results, we also aimed to confirm the efficacy of manual cleaning in reducing levels of ATP and cfu/mL. METHODS Seventeen in-clinical-use gastroscopes and 24 in-clinical-use colonoscopes from the Liverpool Hospital Endoscopy unit were sampled across three separate cleaning stages before high-level disinfection. Colony counts and ATP measurements were then performed on these samples. FINDINGS The correlation between the cfu/mL and RLU of samples collected from colonoscopes was 0.497 (95% confidence interval: 0.28-0.66; P < 0.0001). The correlation between cfu/mL and RLU for samples collected from gastroscopes was 0.377 (0.08-0.61; P = 0.0138). RLU and cfu/mL values were shown to fall significantly (P < 0.005) following precleaning and manual cleaning. CONCLUSION There was a significant correlation between ATP and cfu/mL measured from samples collected before high-level disinfection. Precleaning and manual cleaning were shown to reduce ATP and microbiological load significantly. ATP measurement can be performed within minutes with little training and produces results that are easy to interpret. These findings warrant further research on the utility of ATP measurement as a screening tool for detecting endoscope contamination after high-level disinfection.
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Affiliation(s)
- C E McCafferty
- Ingham Institute for Applied Medical Research, Sydney, NSW, Australia; Western Sydney University, School of Medicine, Sydney, NSW, Australia.
| | - D Abi-Hanna
- Liverpool Hospital, Department of Gastroenterology and Hepatology, Sydney, NSW, Australia; University of New South Wales, School of Medicine, Sydney, NSW, Australia
| | - M J Aghajani
- Ingham Institute for Applied Medical Research, Sydney, NSW, Australia; Western Sydney University, School of Medicine, Sydney, NSW, Australia
| | - G T Micali
- Ingham Institute for Applied Medical Research, Sydney, NSW, Australia; Western Sydney University, School of Medicine, Sydney, NSW, Australia
| | - I Lockart
- Liverpool Hospital, Department of Gastroenterology and Hepatology, Sydney, NSW, Australia
| | - K Vickery
- Macquarie University, Australian School of Advanced Medicine, Sydney, NSW, Australia
| | - I B Gosbell
- Ingham Institute for Applied Medical Research, Sydney, NSW, Australia; Western Sydney University, School of Medicine, Sydney, NSW, Australia
| | - S O Jensen
- Ingham Institute for Applied Medical Research, Sydney, NSW, Australia; Western Sydney University, School of Medicine, Sydney, NSW, Australia
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23
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van Hal SJ, Ip CLC, Ansari MA, Wilson DJ, Espedido BA, Jensen SO, Bowden R. Evolutionary dynamics of Enterococcus faecium reveals complex genomic relationships between isolates with independent emergence of vancomycin resistance. Microb Genom 2018; 2. [PMID: 27713836 PMCID: PMC5049587 DOI: 10.1099/mgen.0.000048] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Enterococcus faecium, a major cause of hospital-acquired infections, remains problematic because of its propensity to acquire resistance to vancomycin, which currently is considered first-line therapy. Here, we assess the evolution and resistance acquisition dynamics of E. faecium in a clinical context using a series of 132 bloodstream infection isolates from a single hospital. All isolates, of which 49 (37 %) were vancomycin-resistant, underwent whole-genome sequencing. E. faecium was found to be subject to high rates of recombination with little evidence of sequence importation from outside the local E. faecium population. Apart from disrupting phylogenetic reconstruction, recombination was frequent enough to invalidate MLST typing in the identification of clonal expansion and transmission events, suggesting that, where available, whole-genome sequencing should be used in tracing the epidemiology of E. faecium nosocomial infections and establishing routes of transmission. Several forms of the Tn1549-like element–vanB gene cluster, which was exclusively responsible for vancomycin resistance, appeared and spread within the hospital during the study period. Several transposon gains and losses and instances of in situ evolution were inferred and, although usually chromosomal, the resistance element was also observed on a plasmid background. There was qualitative evidence for clonal expansions of both vancomycin-resistant and vancomycin-susceptible E. faecium with evidence of hospital-specific subclonal expansion. Our data are consistent with continuing evolution of this established hospital pathogen and confirm hospital vancomycin-susceptible and vancomycin-resistant E. faecium patient transmission events, underlining the need for careful consideration before modifying current E. faecium infection control strategies.
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Affiliation(s)
- Sebastiaan J van Hal
- 2 Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia.,1 Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Camilla L C Ip
- 3 Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M Azim Ansari
- 4 Oxford Martin School, University of Oxford, 34 Broad Street, Oxford, UK
| | - Daniel J Wilson
- 5 Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bjorn A Espedido
- 2 Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia.,6 Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, NSW, Australia
| | - Slade O Jensen
- 2 Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia.,6 Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, NSW, Australia
| | - Rory Bowden
- 3 Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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24
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Singh A, Münch G, Reddell P, Radzieta M, Jensen SO, Raju R. A New Anti-inflammatory Phenolic Monosaccharide from the Australian Native Rainforest Plant Elaeocarpus Eumundi. Nat Prod Commun 2018. [DOI: 10.1177/1934578x1801300619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Chemical analysis of the ethanolic extract of the Australian rainforest plant Elaeocarpus eumundi yielded a new phenolic monosaccharide (1) and the known dihydropieceid (2). The structures of both compounds were elucidated based on the spectroscopic methods including UV, HR-ESIMS and 1D, 2D NMR data. Compounds 1 and 2 exhibited good anti-inflammatory activity in LPS and IFN-γ activated RAW 264.7 macrophage cells.
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Affiliation(s)
- Ahilya Singh
- School of Medicine, Building 30, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown NSW 2560, Australia
| | - Gerald Münch
- School of Medicine, Building 30, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown NSW 2560, Australia
| | - Paul Reddell
- Ecobiotics Limited, 7 Penda Street, Yungaburra, QLD 4884, Australia
| | - Michael Radzieta
- Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia
| | - Slade O. Jensen
- Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia
| | - Ritesh Raju
- School of Medicine, Building 30, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown NSW 2560, Australia
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25
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Johani K, Fritz BG, Bjarnsholt T, Lipsky BA, Jensen SO, Yang M, Dean A, Hu H, Vickery K, Malone M. Understanding the microbiome of diabetic foot osteomyelitis: insights from molecular and microscopic approaches. Clin Microbiol Infect 2018; 25:332-339. [PMID: 29787888 DOI: 10.1016/j.cmi.2018.04.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/30/2018] [Accepted: 04/30/2018] [Indexed: 01/13/2023]
Abstract
OBJECTIVES Rigorous visual evidence on whether or not biofilms are involved in diabetic foot osteomyelitis (DFO) is lacking. We employed a suite of molecular and microscopic approaches to investigate the microbiome, and phenotypic state of microorganisms involved in DFO. METHODS In 20 consecutive subjects with suspected DFO, we collected intraoperative bone specimens. To explore the microbial diversity present in infected bone we performed next generation DNA sequencing. We used scanning electron microscopy (SEM) and peptide nucleic acid fluorescent in situ hybridization (PNA-FISH) with confocal microscopy to visualize and confirm the presence of biofilms. RESULTS In 19 of 20 (95%) studied patients presenting with DFO, it was associated with an infected diabetic foot ulcer. By DNA sequencing of infected bone, Corynebacterium sp. was the most commonly identified microorganism, followed by Finegoldia sp., Staphylococcus sp., Streptococcus sp., Porphyromonas sp., and Anaerococcus sp. Six of 20 bone samples (30%) contained only one or two pathogens, while the remaining 14 (70%) had polymicrobial communities. Using a combination of SEM and PNA-FISH, we identified microbial aggregates in biofilms in 16 (80%) bone specimens and found that they were typically coccoid or rod-shaped aggregates. CONCLUSIONS The presence of biofilms in DFO may explain why non-surgical treatment of DFO, relying on systemic antibiotic therapy, may not resolve some chronic infections caused by biofilm-producing strains.
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Affiliation(s)
- K Johani
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - B G Fritz
- University of Copenhagen, Faculty of Health and Medical Sciences, Department of Immunology and Microbiology, Costerton Biofilm Center, Denmark
| | - T Bjarnsholt
- University of Copenhagen, Faculty of Health and Medical Sciences, Department of Immunology and Microbiology, Costerton Biofilm Center, Denmark; Department of Clinical Microbiology, Rigshospitalet, Denmark
| | - B A Lipsky
- Oxford Microbiology and Infectious Diseases, University of Oxford, Oxford, UK
| | - S O Jensen
- Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Australia
| | - M Yang
- Liverpool Hospital, South Western Sydney LHD, Sydney, Australia
| | - A Dean
- Liverpool Hospital, South Western Sydney LHD, Sydney, Australia
| | - H Hu
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - K Vickery
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - M Malone
- Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Australia; Liverpool Hospital, South Western Sydney LHD, Sydney, Australia; Liverpool Diabetes Collaborative Research Unit, Ingham Institute of Applied Medical Research, Sydney, Australia.
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26
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Malone M, Johani K, Jensen SO, Gosbell IB, Dickson HG, McLennan S, Hu H, Vickery K. Effect of cadexomer iodine on the microbial load and diversity of chronic non-healing diabetic foot ulcers complicated by biofilm in vivo. J Antimicrob Chemother 2018; 72:2093-2101. [PMID: 28402558 PMCID: PMC5890712 DOI: 10.1093/jac/dkx099] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 03/03/2017] [Indexed: 12/27/2022] Open
Abstract
Objectives: The performance of cadexomer iodine was determined against microbial populations from chronic non-healing diabetic foot ulcers (DFUs) complicated by biofilm in vivo, using molecular, microscopy and zymography methods. Methods: Chronic non-healing DFUs due to suspected biofilm involvement were eligible for enrolment. DNA sequencing and real-time quantitative PCR was used to determine the microbial load and diversity of tissue punch biopsies obtained pre- and post-treatment. Scanning electron microscopy and/or fluorescence in situ hybridization confirmed the presence or absence of biofilm. Zymography was used to determine levels of wound proteases. Results: Seventeen participants were recruited over a 6 month period. Scanning electron microscopy and or fluorescence in situ hybridization confirmed the presence of biofilm in all samples. Eleven participants exhibited log10 reductions in microbial load after treatment (range 1–2 log10) in comparison with six patients who experienced <1 log10 reduction (P = 0.04). Samples were tested for levels of wound proteases pre- and post-treatment. Reductions in the microbial load correlated to reductions in wound proteases pre- and post-treatment (P = 0.03). Conclusions: To the best of our knowledge, this study represents the first in vivo evidence, employing a range of molecular and microscopy techniques, of the ability of cadexomer iodine to reduce the microbial load of chronic non-healing DFUs complicated by biofilm. Further analyses correlating log reductions to optimal duration of therapy and improvements in clinical parameters of wound healing in a larger cohort are required.
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Affiliation(s)
| | - K Johani
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - S O Jensen
- Molecular Medicine Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia
| | - I B Gosbell
- Molecular Medicine Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia
| | - H G Dickson
- Liverpool Diabetes Collaborative Research Unit, Ingham Institute of Applied Medical Research, Sydney, Australia.,Ambulatory Care Department (PIXI), Liverpool Hospital, South West Sydney LHD, Sydney, Australia
| | - S McLennan
- The University of Sydney, Charles Perkins Centre, NSW, Australia
| | - H Hu
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - K Vickery
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
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27
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Menon V, Davis R, Shackel N, Espedido BA, Beukers AG, Jensen SO, van Hal SJ. Failure of daptomycin β-Lactam combination therapy to prevent resistance emergence in Enterococcus faecium. Diagn Microbiol Infect Dis 2017; 90:120-122. [PMID: 29195768 DOI: 10.1016/j.diagmicrobio.2017.10.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/18/2017] [Accepted: 10/24/2017] [Indexed: 11/16/2022]
Abstract
Daptomycin β-Lactam combination therapy offers "protection" against daptomycin non-susceptibility (DNS) development in Enterococcus faecium. We report failure of this strategy and the importance of source control. Mutations were detected in the LiaF and cls genes in DNS isolates. A single DNS isolate contained an unrecognized mutation, which requires confirmation.
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Affiliation(s)
- Vidthiya Menon
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Rebecca Davis
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Nick Shackel
- University of NSW, Gastroenterology and Liver Disease Group Ingham Institute, Department of Gastroenterology, Liverpool Hospital
| | - Bjorn A Espedido
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Western Sydney University, Sydney, NSW, Australia
| | - Alicia G Beukers
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia.
| | - Slade O Jensen
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Western Sydney University, Sydney, NSW, Australia
| | - Sebastiaan J van Hal
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
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28
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Abstract
The currently widespread and increasing prevalence of resistant bacterial pathogens is a significant medical problem. In clinical strains of staphylococci, the genetic determinants that confer resistance to antimicrobial agents are often located on mobile elements, such as plasmids. Many of these resistance plasmids are capable of horizontal transmission to other bacteria in their surroundings, allowing extraordinarily rapid adaptation of bacterial populations. Once the resistance plasmids have been spread, they are often perpetually maintained in the new host, even in the absence of selective pressure. Plasmid persistence is accomplished by plasmid-encoded genetic systems that ensure efficient replication and segregational stability during cell division. Staphylococcal plasmids utilize proteins of evolutionarily diverse families to initiate replication from the plasmid origin of replication. Several distinctive plasmid copy number control mechanisms have been studied in detail and these appear conserved within plasmid classes. The initiators utilize various strategies and serve a multifunctional role in (i) recognition and processing of the cognate replication origin to an initiation active form and (ii) recruitment of host-encoded replication proteins that facilitate replisome assembly. Understanding the detailed molecular mechanisms that underpin plasmid replication may lead to novel approaches that could be used to reverse or slow the development of resistance.
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Affiliation(s)
- Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Joshua P Ramsay
- School of Biomedical Sciences, Curtin University, Perth, WA, Australia
| | - Slade O Jensen
- Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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29
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Almatroudi A, Tahir S, Hu H, Chowdhury D, Gosbell IB, Jensen SO, Whiteley GS, Deva AK, Glasbey T, Vickery K. Staphylococcus aureus dry-surface biofilms are more resistant to heat treatment than traditional hydrated biofilms. J Hosp Infect 2017; 98:161-167. [PMID: 28919336 DOI: 10.1016/j.jhin.2017.09.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 09/11/2017] [Indexed: 01/07/2023]
Abstract
BACKGROUND The importance of biofilms to clinical practice is being increasingly realized. Biofilm tolerance to antibiotics is well described but limited work has been conducted on the efficacy of heat disinfection and sterilization against biofilms. AIM To test the susceptibility of planktonic, hydrated biofilm and dry-surface biofilm forms of Staphylococcus aureus, to dry-heat and wet-heat treatments. METHODS S. aureus was grown as both hydrated biofilm and dry-surface biofilm in the CDC biofilm generator. Biofilm was subjected to a range of temperatures in a hot-air oven (dry heat), water bath or autoclave (wet heat). FINDINGS Dry-surface biofilms remained culture positive even when treated with the harshest dry-heat condition of 100°C for 60min. Following autoclaving samples were culture negative but 62-74% of bacteria in dry-surface biofilms remained alive as demonstrated by live/dead staining and confocal microscopy. Dry-surface biofilms subjected to autoclaving at 121°C for up to 30min recovered and released planktonic cells. Recovery did not occur following autoclaving for longer or at 134°C, at least during the time-period tested. Hydrated biofilm recovered following dry-heat treatment up to 100°C for 10min but failed to recover following autoclaving despite the presence of 43-60% live cells as demonstrated by live/dead staining. CONCLUSION S. aureus dry-surface biofilms are less susceptible to killing by dry heat and steam autoclaving than hydrated biofilms, which are less susceptible to heat treatment than planktonic suspensions.
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Affiliation(s)
- A Almatroudi
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia; Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Qassim, Saudi Arabia
| | - S Tahir
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia
| | - H Hu
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia
| | - D Chowdhury
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia
| | - I B Gosbell
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia; Medical Sciences Research Group, School of Medicine, Western Sydney University, New South Wales, Australia; Department of Microbiology & Infectious Diseases, Sydney South West Pathology Service, Liverpool, New South Wales Health Pathology, New South Wales, Australia
| | - S O Jensen
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia; Medical Sciences Research Group, School of Medicine, Western Sydney University, New South Wales, Australia
| | - G S Whiteley
- Medical Sciences Research Group, School of Medicine, Western Sydney University, New South Wales, Australia; Whiteley Corporation, North Sydney, New South Wales, Australia
| | - A K Deva
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia
| | - T Glasbey
- Whiteley Corporation, North Sydney, New South Wales, Australia
| | - K Vickery
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia.
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30
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van Hal SJ, Espedido BA, Coombs GW, Howden BP, Korman TM, Nimmo GR, Gosbell IB, Jensen SO. Polyclonal emergence of vanA vancomycin-resistant Enterococcus faecium in Australia. J Antimicrob Chemother 2017; 72:998-1001. [PMID: 28031272 DOI: 10.1093/jac/dkw539] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
Objectives To investigate the genetic context associated with the emergence of vanA VRE in Australia. Methods The whole genomes of 18 randomly selected vanA -positive Enterococcus faecium patient isolates, collected between 2011 and 2013 from hospitals in four Australian capitals, were sequenced and analysed. Results In silico typing and transposon/plasmid assembly revealed that the sequenced isolates represented (in most cases) different hospital-adapted STs and were associated with a variety of different Tn 1546 variants and plasmid backbone structures. Conclusions The recent emergence of vanA VRE in Australia was polyclonal and not associated with the dissemination of a single 'dominant' ST or vanA -encoding plasmid. Interestingly, the factors contributing to this epidemiological change are not known and future studies may need to consider investigation of potential community sources.
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Affiliation(s)
- Sebastiaan J van Hal
- School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Björn A Espedido
- School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
| | - Geoffrey W Coombs
- School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia.,PathWest Laboratory Medicine, Fiona Stanley Hospital, Perth, WA, Australia
| | - Benjamin P Howden
- Austin Health, Melbourne, Vic., Australia.,Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Vic., Australia
| | | | | | - Iain B Gosbell
- School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia.,Sydney South Western Pathology Service, NSW Pathology, Sydney, NSW, Australia
| | - Slade O Jensen
- School of Medicine, Western Sydney University, Sydney, NSW, Australia.,Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
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Malone M, Johani K, Jensen SO, Gosbell IB, Dickson HG, Hu H, Vickery K. Next Generation DNA Sequencing of Tissues from Infected Diabetic Foot Ulcers. EBioMedicine 2017; 21:142-149. [PMID: 28669650 PMCID: PMC5514496 DOI: 10.1016/j.ebiom.2017.06.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/14/2017] [Accepted: 06/26/2017] [Indexed: 12/17/2022] Open
Abstract
We used next generation DNA sequencing to profile the microbiome of infected Diabetic Foot Ulcers (DFUs). The microbiota was correlated to clinical parameters and treatment outcomes to determine if directed antimicrobial therapy based on conventional microbiological cultures are relevant based on genomic analysis. Patients≥18years presenting with a new Diabetic Foot Infection (DFI) who had not received topical or oral antimicrobials in the two weeks prior to presentation, were eligible for enrolment. Tissue punch biopsies were obtained from infected DFUs for analysis. Demographics, clinical and laboratory data were collected and correlated against microbiota data. Thirty-nine patients with infected DFUs were recruited over twelve-months. Shorter duration DFUs (<six weeks) all had one dominant bacterial species (n=5 of 5, 100%, p<0.001), Staphylococcus aureus in three cases and Streptococcus agalactiae in two. Longer duration DFUs (≥six weeks) were diversely polymicrobial (p<0.01) with an average of 63 (range 19-125) bacterial species. Severe DFIs had complex microbiomes and were distinctly dissimilar to less severe infections (p=0.02), characterised by the presence of low frequency microorganisms. Nineteen patients (49%) during the study period experienced antimicrobial treatment failure, but no overall differences existed in the microbiome of patients who failed therapy and those who experienced treatment success (p=0.2). Our results confirm that short DFUs have a simpler microbiome consisting of pyogenic cocci but chronic DFUs have a highly polymicrobial microbiome. The duration of a DFU may be useful as a guide to directing antimicrobial therapy.
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Affiliation(s)
- M Malone
- High Risk Foot Service, Liverpool Hospital, South West Sydney LHD, Sydney, Australia; Liverpool Diabetes Collaborative Research Unit, Ingham Institute of Applied Medical Research, Sydney, Australia; Molecular Medicine Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, Australia.
| | - K Johani
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - S O Jensen
- Molecular Medicine Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, Australia; Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia
| | - I B Gosbell
- Molecular Medicine Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, Australia; Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia; Department of Microbiology and Infectious Diseases, Sydney South West Pathology Service, New South Wales Health Pathology, Liverpool, Sydney, Australia
| | - H G Dickson
- Liverpool Diabetes Collaborative Research Unit, Ingham Institute of Applied Medical Research, Sydney, Australia; Ambulatory Care Department (PIXI), Liverpool Hospital, South West Sydney LHD, Sydney, Australia
| | - H Hu
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - K Vickery
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
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Malone M, Gosbell IB, Dickson HG, Vickery K, Espedido BA, Jensen SO. Can molecular DNA-based techniques unravel the truth about diabetic foot infections? Diabetes Metab Res Rev 2017; 33. [PMID: 27291330 DOI: 10.1002/dmrr.2834] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 01/15/2023]
Abstract
Diabetes foot infections are a common condition and a major causal pathway to lower extremity amputation. Identification of causative pathogens is vital in directing antimicrobial therapy. Historically, clinicians have relied upon culture-dependent techniques that are now acknowledged as both being selective for microorganisms that thrive under the physiological and nutritional constraints of the microbiology laboratory and that grossly underestimate the microbial diversity of a sample. The amplification and sequence analysis of the 16S rRNA gene has revealed a diversity of microorganisms in diabetes foot infections, extending the view of the diabetic foot microbiome. The interpretation of these findings and their relevance to clinical care remains largely unexplored. The advent of molecular methods that are culture-independent and employ massively parallel DNA sequencing technology represents a potential 'game changer'. Metagenomics and its shotgun approach to surveying all DNA within a sample (whole genome sequencing) affords the possibility to characterize not only the microbial diversity within a diabetes foot infection (i.e. 'which microorganisms are present') but the biological functions of the community such as virulence and pathogenicity (i.e. 'what are the microorganisms capable of doing'), moving the focus from single species as pathogens to groups of species. This review will examine the new molecular techniques for exploration of the microbiome of infected and uninfected diabetic foot ulcers, exploring the potential of these new technologies and postulating how they could translate to improved clinical care. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- M Malone
- High Risk Foot Service, Liverpool Hospital, South Western Sydney LHD, Sydney, Australia
- LIVE DIAB CRU, Ingham Institute of Applied Medical Research, Sydney, Australia
- Molecular Medicine Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, Australia
| | - I B Gosbell
- Molecular Medicine Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, Australia
- Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia
| | - H G Dickson
- LIVE DIAB CRU, Ingham Institute of Applied Medical Research, Sydney, Australia
- Ambulatory Care Department, Liverpool Hospital, South Western Sydney LHD, Sydney, Australia
| | - K Vickery
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - B A Espedido
- Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia
- Department of Pathology, School of Medicine, Western Sydney University, Sydney, Australia
| | - S O Jensen
- Molecular Medicine Research Group, Microbiology & Infectious Diseases, School of Medicine, Western Sydney University, Sydney, Australia
- Antimicrobial Resistance and Mobile Elements Group, Ingham Institute of Applied Medical Research, Sydney, Australia
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Whiteley GS, Knight JL, Derry CW, Jensen SO, Vickery K, Gosbell IB. Response to Russotto et al. Am J Infect Control 2016; 44:733-4. [PMID: 27020083 DOI: 10.1016/j.ajic.2016.01.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 01/20/2016] [Indexed: 11/17/2022]
Affiliation(s)
- Greg S Whiteley
- School of Science and Health, University of Western Sydney, Richmond, NSW, Australia; Whiteley Corporation Pty Ltd, North Sydney, NSW, Australia.
| | - Jessica L Knight
- School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia; Antibiotic Resistance and Mobile Elements Group, Molecular Medicine Research Group, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| | - Chris W Derry
- School of Science and Health, University of Western Sydney, Richmond, NSW, Australia
| | - Slade O Jensen
- School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia; Antibiotic Resistance and Mobile Elements Group, Molecular Medicine Research Group, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| | - Karen Vickery
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Iain B Gosbell
- School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia; Antibiotic Resistance and Mobile Elements Group, Molecular Medicine Research Group, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia; Department of Microbiology and Infectious Diseases, Sydney South West Pathology Service, Liverpool, NSW, Australia
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Almatroudi A, Gosbell IB, Hu H, Jensen SO, Espedido BA, Tahir S, Glasbey TO, Legge P, Whiteley G, Deva A, Vickery K. Staphylococcus aureus dry-surface biofilms are not killed by sodium hypochlorite: implications for infection control. J Hosp Infect 2016; 93:263-70. [PMID: 27140421 DOI: 10.1016/j.jhin.2016.03.020] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 03/18/2016] [Indexed: 12/01/2022]
Abstract
BACKGROUND Dry hospital environments are contaminated with pathogenic bacteria in biofilms, which suggests that current cleaning practices and disinfectants are failing. AIM To test the efficacy of sodium hypochlorite solution against Staphylococcus aureus dry-surface biofilms. METHODS The Centers for Disease Control and Prevention Biofilm Reactor was adapted to create a dry-surface biofilm, containing 1.36 × 10(7)S. aureus/coupon, by alternating cycles of growth and dehydration over 12 days. Biofilm was detected qualitatively using live/dead stain confocal laser scanning microscopy (CLSM), and quantitatively with sonicated viable plate counts and crystal violet assay. Sodium hypochlorite (1000-20,000parts per million) was applied to the dry-surface biofilm for 10min, coupons were rinsed three times, and residual biofilm viability was determined by CLSM, plate counts and prolonged culture up to 16 days. Isolates before and after exposure underwent minimum inhibitory concentration (MIC) and minimum eradication concentration (MEC) testing, and one pair underwent whole-genome sequencing. FINDINGS Hypochlorite exposure reduced plate counts by a factor of 7 log10, and reduced biofilm biomass by a factor of 100; however, staining of residual biofilm showed that live S. aureus cells remained. On prolonged incubation, S. aureus regrew and formed biofilms. Post-exposure S. aureus isolates had MICs and MECs that were not significantly different from the parent strains. Whole-genome sequencing of one pre- and post-exposure pair found that they were virtually identical. CONCLUSIONS Hypochlorite exposure led to a 7-log kill but the organisms regrew. No resistance mutations occurred, implying that hypochlorite resistance is an intrinsic property of S. aureus biofilms. The clinical significance of this warrants further study.
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Affiliation(s)
- A Almatroudi
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia; Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Qassim, Saudi Arabia
| | - I B Gosbell
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia; Molecular Medicine Research Group, School of Medicine, Western Sydney University, New South Wales, Australia; Department of Microbiology & Infectious Diseases, Sydney South West Pathology Service - Liverpool, New South Wales Health Pathology, New South Wales, Australia
| | - H Hu
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia
| | - S O Jensen
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia; Molecular Medicine Research Group, School of Medicine, Western Sydney University, New South Wales, Australia
| | - B A Espedido
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Liverpool, New South Wales, Australia; Molecular Medicine Research Group, School of Medicine, Western Sydney University, New South Wales, Australia
| | - S Tahir
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia
| | - T O Glasbey
- Whiteley Corporation, North Sydney, New South Wales, Australia
| | - P Legge
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia
| | - G Whiteley
- Whiteley Corporation, North Sydney, New South Wales, Australia
| | - A Deva
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia
| | - K Vickery
- Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales, Australia.
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Micali GT, Espedido BA, Firth N, Jensen SO. Characterisation of a staphylococcal type IB partitioning system in gram-positive hospital pathogens. Pathology 2016. [DOI: 10.1016/j.pathol.2015.12.303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Whiteley GS, Knight JL, Derry CW, Jensen SO, Vickery K, Gosbell IB. A pilot study into locating the bad bugs in a busy intensive care unit. Am J Infect Control 2015; 43:1270-5. [PMID: 26654232 DOI: 10.1016/j.ajic.2015.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/03/2015] [Accepted: 07/07/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND The persistence of multidrug-resistant organisms (MDROs) within an intensive care unit (ICU) possibly contained within dry surface biofilms, remains a perplexing confounder and is a threat to patient safety. Identification of residential locations of MDRO within the ICU is an intervention for which new scientific approaches may assist in finding potential MDRO reservoirs. METHOD This study investigated a new approach to sampling using a more aggressive environmental swabbing technique of high-touch objects (HTOs) and surfaces, aided by 2 commercially available adenosine triphosphate (ATP) bioluminometers. RESULTS A total of 13 individual MDRO locations identified in this pilot study. The use of ATP bioluminometers was significantly associated with the identification of 12 of the 13 individual MDRO locations. The MDRO recovery and readings from the 2 ATP bioluminometers were not significantly correlated with distinct cutoffs for each ATP device, and there was no correlation between the 2 ATP devices. CONCLUSION The specific MDRO locations were not limited to the immediate patient surroundings or to any specific HTO or type of surface. The use of ATP testing helped rapidly identify the soiled locations for MDRO sampling. The greatest density of positive MDRO locations was around and within the clinical staff work station.
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Almatroudi A, Hu H, Deva A, Gosbell IB, Jacombs A, Jensen SO, Whiteley G, Glasbey T, Vickery K. A new dry-surface biofilm model: An essential tool for efficacy testing of hospital surface decontamination procedures. J Microbiol Methods 2015; 117:171-6. [DOI: 10.1016/j.mimet.2015.08.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/04/2015] [Accepted: 08/04/2015] [Indexed: 11/28/2022]
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Espedido BA, Dimitrijovski B, van Hal SJ, Jensen SO. The use of whole-genome sequencing for molecular epidemiology and antimicrobial surveillance: identifying the role of IncX3 plasmids and the spread of blaNDM-4-like genes in the Enterobacteriaceae. J Clin Pathol 2015; 68:835-8. [PMID: 26056157 DOI: 10.1136/jclinpath-2015-203044] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/20/2015] [Indexed: 11/04/2022]
Abstract
AIMS To characterise the resistome of a multi-drug resistant Klebsiella pneumoniae (Kp0003) isolated from an Australian traveller who was repatriated to a Sydney Metropolitan Hospital from Myanmar with possible prosthetic aortic valve infective endocarditis. METHODS Kp0003 was recovered from a blood culture of the patient and whole genome sequencing was performed. Read mapping and de novo assembly of reads facilitated in silico multi-locus sequence and plasmid replicon typing as well as the characterisation of antibiotic resistance genes and their genetic context. Conjugation experiments were also performed to assess the plasmid (and resistance gene) transferability and the effect on the antibiotic resistance phenotype. RESULTS Importantly, and of particular concern, the carbapenem-hydrolysing β-lactamase gene blaNDM-4 was identified on a conjugative IncX3 plasmid (pJEG027). In this respect, the blaNDM-4 genetic context is similar (at least to some extent) to what has previously been identified for blaNDM-1 and blaNDM-4-like variants. CONCLUSIONS This study highlights the potential role that IncX3 plasmids have played in the emergence and dissemination of blaNDM-4-like variants worldwide and emphasises the importance of resistance gene surveillance.
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Affiliation(s)
- Björn A Espedido
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, New South Wales, Australia Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Borce Dimitrijovski
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, New South Wales, Australia Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Sebastiaan J van Hal
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, New South Wales, Australia Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
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Espedido BA, Jensen SO, van Hal SJ. Ceftaroline fosamil salvage therapy: an option for reduced-vancomycin-susceptible MRSA bacteraemia. J Antimicrob Chemother 2015; 70:797-801. [PMID: 25406295 DOI: 10.1093/jac/dku455] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
OBJECTIVES To examine the activity of ceftaroline against reduced-vancomycin-susceptible MRSA isolates. METHODS One-hundred and three MRSA blood culture isolates (predominantly ST239-MRSA-III), with varying vancomycin phenotypes, had their ceftaroline MICs determined by broth microdilution and MIC Evaluator strip (Oxoid-Thermo Fisher). Statistical analyses were performed that examined relationships with vancomycin and daptomycin MICs. Mutations in mecA were also examined. RESULTS All 103 isolates (including 60 heteroresistant vancomycin-intermediate Staphylococcus aureus/vancomycin-intermediate S. aureus) were susceptible to ceftaroline, with one isolate displaying heteroresistance that may be related to a mecA mutation. Higher ceftaroline MICs were associated with vancomycin-susceptible S. aureus isolates. CONCLUSIONS This study highlights that ceftaroline fosamil is an option for salvage therapy based on in vitro activity.
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Affiliation(s)
- Björn A Espedido
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, NSW, Australia Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia South Western Sydney Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Slade O Jensen
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, NSW, Australia Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia South Western Sydney Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Sebastiaan J van Hal
- Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
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van Hal SJ, Steen JA, Espedido BA, Grimmond SM, Cooper MA, Holden MTG, Bentley SD, Gosbell IB, Jensen SO. In vivo evolution of antimicrobial resistance in a series of Staphylococcus aureus patient isolates: the entire picture or a cautionary tale? J Antimicrob Chemother 2013; 69:363-7. [PMID: 24047554 DOI: 10.1093/jac/dkt354] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES To obtain an expanded understanding of antibiotic resistance evolution in vivo, particularly in the context of vancomycin exposure. METHODS The whole genomes of six consecutive methicillin-resistant Staphylococcus aureus blood culture isolates (ST239-MRSA-III) from a single patient exposed to various antimicrobials (over a 77 day period) were sequenced and analysed. RESULTS Variant analysis revealed the existence of non-susceptible sub-populations derived from a common susceptible ancestor, with the predominant circulating clone(s) selected for by type and duration of antimicrobial exposure. CONCLUSIONS This study highlights the dynamic nature of bacterial evolution and that non-susceptible sub-populations can emerge from clouds of variation upon antimicrobial exposure. Diagnostically, this has direct implications for sample selection when using whole-genome sequencing as a tool to guide clinical therapy. In the context of bacteraemia, deep sequencing of bacterial DNA directly from patient blood samples would avoid culture 'bias' and identify mutations associated with circulating non-susceptible sub-populations, some of which may confer cross-resistance to alternate therapies.
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Affiliation(s)
- Sebastiaan J van Hal
- Antibiotic Resistance & Mobile Elements Group, School of Medicine, University of Western Sydney, Sydney, NSW, Australia
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Espedido BA, Steen JA, Ziochos H, Grimmond SM, Cooper MA, Gosbell IB, van Hal SJ, Jensen SO. Whole genome sequence analysis of the first Australian OXA-48-producing outbreak-associated Klebsiella pneumoniae isolates: the resistome and in vivo evolution. PLoS One 2013; 8:e59920. [PMID: 23555831 PMCID: PMC3612081 DOI: 10.1371/journal.pone.0059920] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/20/2013] [Indexed: 11/19/2022] Open
Abstract
Whole genome sequencing was used to characterize the resistome of intensive care unit (ICU) outbreak-associated carbapenem-resistant K. pneumoniae isolates. Importantly, and of particular concern, the carbapenem-hydrolyzing β-lactamase gene blaOXA-48 and the extended-spectrum β-lactamase gene blaCTX-M-14, were identified on a single broad host-range conjugative plasmid. This represents the first report of blaOXA-48 in Australia and highlights the importance of resistance gene surveillance, as such plasmids can silently spread amongst enterobacterial populations and have the potential to drastically limit treatment options. Furthermore, the in vivo evolution of these isolates was also examined after 18 months of intra-abdominal carriage in a patient that transited through the ICU during the outbreak period. Reflecting the clonality of K. pneumoniae, only 11 single nucleotide polymorphisms (SNPs) were accumulated during this time-period and many of these were associated with genes involved in tolerance/resistance to antibiotics, metals or organic solvents, and transcriptional regulation. Collectively, these SNPs are likely to be associated with changes in virulence (at least to some extent) that have refined the in vivo colonization capacity of the original outbreak isolate.
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Affiliation(s)
- Björn A. Espedido
- Antibiotic Resistance and Mobile Elements Group, School of Medicine, University of Western Sydney, New South Wales, Australia
- Ingham Institute for Applied Medical Research, New South Wales, Australia
| | - Jason A. Steen
- Queensland Centre for Medical Genomics, University of Queensland, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Queensland, Australia
| | - Helen Ziochos
- Sydney South Western Pathology Service, NSW Pathology, New South Wales, Australia
| | - Sean M. Grimmond
- Queensland Centre for Medical Genomics, University of Queensland, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Queensland, Australia
| | - Matthew A. Cooper
- Institute for Molecular Bioscience, University of Queensland, Queensland, Australia
| | - Iain B. Gosbell
- Antibiotic Resistance and Mobile Elements Group, School of Medicine, University of Western Sydney, New South Wales, Australia
- Ingham Institute for Applied Medical Research, New South Wales, Australia
- Sydney South Western Pathology Service, NSW Pathology, New South Wales, Australia
| | - Sebastiaan J. van Hal
- Antibiotic Resistance and Mobile Elements Group, School of Medicine, University of Western Sydney, New South Wales, Australia
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, New South Wales, Australia
- * E-mail: (SJvH); (SOJ)
| | - Slade O. Jensen
- Antibiotic Resistance and Mobile Elements Group, School of Medicine, University of Western Sydney, New South Wales, Australia
- Ingham Institute for Applied Medical Research, New South Wales, Australia
- * E-mail: (SJvH); (SOJ)
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Liu MA, Kwong SM, Jensen SO, Brzoska AJ, Firth N. Biology of the staphylococcal conjugative multiresistance plasmid pSK41. Plasmid 2013; 70:42-51. [PMID: 23415796 DOI: 10.1016/j.plasmid.2013.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 02/01/2013] [Accepted: 02/03/2013] [Indexed: 11/27/2022]
Abstract
Plasmid pSK41 is a large, low-copy-number, conjugative plasmid from Staphylococcus aureus that is representative of a family of staphylococcal plasmids that confer multiple resistances to a wide range of antimicrobial agents. The plasmid consists of a conserved plasmid backbone containing the genes for plasmid housekeeping functions, which is punctuated by copies of IS257 that flank a Tn4001-hybrid structure and cointegrated plasmids that harbour resistance genes. This review summarises the current understanding of the biology of pSK41, focussing on the systems responsible for its replication, maintenance and transmission, and their regulation.
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Affiliation(s)
- Michael A Liu
- School of Biological Sciences, University of Sydney, NSW 2006, Australia
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Abstract
Staphylococcus aureus bacteremia (SAB) is an important infection with an incidence rate ranging from 20 to 50 cases/100,000 population per year. Between 10% and 30% of these patients will die from SAB. Comparatively, this accounts for a greater number of deaths than for AIDS, tuberculosis, and viral hepatitis combined. Multiple factors influence outcomes for SAB patients. The most consistent predictor of mortality is age, with older patients being twice as likely to die. Except for the presence of comorbidities, the impacts of other host factors, including gender, ethnicity, socioeconomic status, and immune status, are unclear. Pathogen-host interactions, especially the presence of shock and the source of SAB, are strong predictors of outcomes. Although antibiotic resistance may be associated with increased mortality, questions remain as to whether this reflects pathogen-specific factors or poorer responses to antibiotic therapy, namely, vancomycin. Optimal management relies on starting appropriate antibiotics in a timely fashion, resulting in improved outcomes for certain patient subgroups. The roles of surgery and infectious disease consultations require further study. Although the rate of mortality from SAB is declining, it remains high. Future international collaborative studies are required to tease out the relative contributions of various factors to mortality, which would enable the optimization of SAB management and patient outcomes.
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Affiliation(s)
- Sebastian J van Hal
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Service—Liverpool, South Western Sydney Local Health Network, Sydney, New South Wales, Australia.
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44
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Liew ATF, Theis T, Jensen SO, Garcia-Lara J, Foster SJ, Firth N, Lewis PJ, Harry EJ. A simple plasmid-based system that allows rapid generation of tightly controlled gene expression in Staphylococcus aureus. Microbiology (Reading) 2011; 157:666-676. [DOI: 10.1099/mic.0.045146-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have established a plasmid-based system that enables tightly controlled gene expression and the generation of GFP fusion proteins in Staphylococcus aureus simply and rapidly. This system takes advantage of an Escherichia coli–S. aureus shuttle vector that contains the replication region of the S. aureus theta-mode multiresistance plasmid pSK41, and is therefore a stable low-copy-number plasmid in the latter organism. This vector also contains a multiple cloning site downstream of the IPTG-inducible Pspac promoter for insertion of the gene of interest. Production of encoded proteins can be stringently regulated in an IPTG-dependent manner by introducing a pE194-based plasmid, pGL485, carrying a constitutively expressed lacI gene. Using GFP fusions to two essential proteins of S. aureus, FtsZ and NusA, we showed that our plasmid allowed tightly controlled gene expression and accurate localization of fusion proteins with no detrimental effect on cells at low inducer concentrations. At higher IPTG concentrations, we obtained sixfold overproduction of protein compared with wild-type levels, with FtsZ–GFP-expressing cells showing lysis and delocalized fluorescence, while NusA–GFP showed only delocalized fluorescence. These results show that our system is capable of titratable induction of gene expression for localization or overexpression studies.
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Affiliation(s)
- Andrew T. F. Liew
- The ithree Institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Torsten Theis
- The ithree Institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Slade O. Jensen
- Microbiology and Infectious Diseases, School of Medicine, University of Western Sydney, New South Wales 2751, Australia
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jorge Garcia-Lara
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Simon J. Foster
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Neville Firth
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Peter J. Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Elizabeth J. Harry
- The ithree Institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
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Jensen SO, Apisiridej S, Kwong SM, Yang YH, Skurray RA, Firth N. Analysis of the prototypical Staphylococcus aureus multiresistance plasmid pSK1. Plasmid 2010; 64:135-42. [PMID: 20547176 DOI: 10.1016/j.plasmid.2010.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 05/26/2010] [Accepted: 06/06/2010] [Indexed: 11/16/2022]
Abstract
The Staphylococcus aureus multiresistance plasmid pSK1 is the prototype of a family of structurally related plasmids that were first identified in epidemic S. aureus strains isolated in Australia during the 1980s and subsequently in Europe. Here we present the complete 28.15kb nucleotide sequence of pSK1 and discuss the genetic content and evolution of the 14kb region that is conserved throughout the pSK1 plasmid family. In addition to the previously characterized plasmid maintenance functions, this backbone region encodes 12 putative gene products, including a lipoprotein, teichoic acid translocation permease, cell wall anchored surface protein and an Fst-like toxin as part of a Type I toxin-antitoxin system. Furthermore, transcriptional profiling has revealed that plasmid carriage most likely has a minimal impact on the host, a factor that may contribute to the ability of pSK1 family plasmids to carry multiple resistance determinants.
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Affiliation(s)
- Slade O Jensen
- School of Biological Sciences, University of Sydney, New South Wales, Australia
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46
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Affiliation(s)
- Stephen M Kwong
- School of Biological Sciences, The University of Sydney, NSW 2006, Australia
| | - Slade O Jensen
- School of Biological Sciences, The University of Sydney, NSW 2006, Australia
| | - Neville Firth
- School of Biological Sciences, The University of Sydney, NSW 2006, Australia
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47
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Ni L, Jensen SO, Ky Tonthat N, Berg T, Kwong SM, Guan FHX, Brown MH, Skurray RA, Firth N, Schumacher MA. The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes. Nucleic Acids Res 2009; 37:6970-83. [PMID: 19759211 PMCID: PMC2777438 DOI: 10.1093/nar/gkp756] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Plasmids harbored by Staphylococcus aureus are a major contributor to the spread of bacterial multi-drug resistance. Plasmid conjugation and partition are critical to the dissemination and inheritance of such plasmids. Here, we demonstrate that the ArtA protein encoded by the S. aureus multi-resistance plasmid pSK41 is a global transcriptional regulator of pSK41 genes, including those involved in conjugation and segregation. ArtA shows no sequence homology to any structurally characterized DNA-binding protein. To elucidate the mechanism by which it specifically recognizes its DNA site, we obtained the structure of ArtA bound to its cognate operator, ACATGACATG. The structure reveals that ArtA is representative of a new family of ribbon–helix–helix (RHH) DNA-binding proteins that contain extended, N-terminal basic motifs. Strikingly, unlike most well-studied RHH proteins ArtA binds its cognate operators as a dimer. However, we demonstrate that it is also able to recognize an atypical operator site by binding as a dimer-of-dimers and the extended N-terminal regions of ArtA were shown to be essential for this dimer-of-dimer binding mode. Thus, these data indicate that ArtA is a master regulator of genes critical for both horizontal and vertical transmission of pSK41 and that it can recognize DNA utilizing alternate binding modes.
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Affiliation(s)
- Lisheng Ni
- Department of Biochemistry and Molecular Biology, University of Texas, MD Anderson Cancer Center, Unit 1000, Houston, TX 77030, USA
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Abstract
Strains of Staphylococcus aureus that are resistant to multiple antimicrobial compounds, including most available classes of antibiotics and some antiseptics, are a major threat to patient care owing to their stubborn intransigence to chemotherapy and disinfection. This reality has stimulated extensive efforts to understand the genetic nature of the determinants encoding antimicrobial resistance, together with the mechanisms by which these determinants evolve over time and are spread within bacterial populations. Such studies have benefited from the application of molecular genetics and in recent years, the sequencing of over a dozen complete staphylococcal genomes. It is now evident that the evolution of multiresistance is driven by the acquisition of discrete preformed antimicrobial resistance genes that are exchanged between organisms via horizontal gene transfer. Nonetheless, chromosomal mutation is the catalyst of novel resistance determinants and is likely to have an enhanced influence with the ongoing introduction of synthetic antibiotics.
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Affiliation(s)
- Slade O Jensen
- School of Biological Sciences, Macleay Building A12, University of Sydney, NSW 2006, Australia
| | - Bruce R Lyon
- School of Biological Sciences, Macleay Building A12, University of Sydney, NSW 2006, Australia
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49
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LeBard RJ, Jensen SO, Arnaiz IA, Skurray RA, Firth N. A multimer resolution system contributes to segregational stability of the prototypical staphylococcal conjugative multiresistance plasmid pSK41. FEMS Microbiol Lett 2008; 284:58-67. [DOI: 10.1111/j.1574-6968.2008.01190.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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50
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Schumacher MA, Glover TC, Brzoska AJ, Jensen SO, Dunham TD, Skurray RA, Firth N. Segrosome structure revealed by a complex of ParR with centromere DNA. Nature 2008; 450:1268-71. [PMID: 18097417 DOI: 10.1038/nature06392] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 09/18/2007] [Indexed: 11/09/2022]
Abstract
The stable inheritance of genetic material depends on accurate DNA partition. Plasmids serve as tractable model systems to study DNA segregation because they require only a DNA centromere, a centromere-binding protein and a force-generating ATPase. The centromeres of partition (par) systems typically consist of a tandem arrangement of direct repeats. The best-characterized par system contains a centromere-binding protein called ParR and an ATPase called ParM. In the first step of segregation, multiple ParR proteins interact with the centromere repeats to form a large nucleoprotein complex of unknown structure called the segrosome, which binds ParM filaments. pSK41 ParR binds a centromere consisting of multiple 20-base-pair (bp) tandem repeats to mediate both transcription autoregulation and segregation. Here we report the structure of the pSK41 segrosome revealed in the crystal structure of a ParR-DNA complex. In the crystals, the 20-mer tandem repeats stack pseudo-continuously to generate the full-length centromere with the ribbon-helix-helix (RHH) fold of ParR binding successive DNA repeats as dimer-of-dimers. Remarkably, the dimer-of-dimers assemble in a continuous protein super-helical array, wrapping the DNA about its positive convex surface to form a large segrosome with an open, solenoid-shaped structure, suggesting a mechanism for ParM capture and subsequent plasmid segregation.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry and Molecular Biology, University of Texas, M.D. Anderson Cancer Center, Unit 1000, Houston, TX 77030, USA.
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