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Article ; Online: Evaluating preanalytical sample storage parameters for nucleic acid-based detection of

Fernando, Janath A / Krysiak, Marcelina / Prestedge, Jacqueline / Azzato, Francesca / Williamson, Deborah A / Pasricha, Shivani

Sexually transmitted infections

2024 Volume 100, Issue 1, Page(s) 48–51

Abstract: Objectives: To ensure accurate diagnosis of infectious diseases, preanalytical factors should be considered when assessing specimen quality and subsequent test result. Accordingly, we aimed to systematically assess the effect of storage time, ... ...

Abstract	Objectives: To ensure accurate diagnosis of infectious diseases, preanalytical factors should be considered when assessing specimen quality and subsequent test result. Accordingly, we aimed to systematically assess the effect of storage time, temperature and buffer on the analytical sensitivity of detecting the sexually transmitted pathogen, Methods: Cultured Results: In total, 2756 samples were processed, with Conclusions: Increased prevalence of sample self-collection for sexually transmitted infections (STIs) warrants an evaluation of preanalytical sample storage variables on diagnostic testing performance. Here, across a range of time points, temperatures and storage buffers,
MeSH term(s)	Humans ; Neisseria gonorrhoeae/genetics ; Nucleic Acid Amplification Techniques/methods ; Chlamydia trachomatis/genetics ; Sensitivity and Specificity ; Chlamydia Infections/diagnosis ; Gonorrhea/diagnosis ; Sexually Transmitted Diseases ; Nucleic Acids
Chemical Substances	Nucleic Acids
Language	English
Publishing date	2024-01-17
Publishing country	England
Document type	Journal Article
ZDB-ID	1420303-0
ISSN	1472-3263 ; 1368-4973
ISSN (online)	1472-3263
ISSN	1368-4973
DOI	10.1136/sextrans-2023-055859
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Article ; Online: Emergence and clonal expansion of a qacA-harbouring sequence type 45 lineage of methicillin-resistant Staphylococcus aureus.

Nong, Yi / Steinig, Eike / Pollock, Georgina L / Taiaroa, George / Carter, Glen P / Monk, Ian R / Pang, Stanley / Daley, Denise A / Coombs, Geoffrey W / Forde, Brian M / Harris, Patrick N A / Sherry, Norelle L / Howden, Benjamin P / Pasricha, Shivani / Baines, Sarah L / Williamson, Deborah A

Communications biology

2024 Volume 7, Issue 1, Page(s) 349

Abstract: The past decade has seen an increase in the prevalence of sequence type (ST) 45 methicillin-resistant Staphylococcus aureus (MRSA), yet the underlying drivers for its emergence and spread remain unclear. To better understand the worldwide dissemination ... ...

Abstract	The past decade has seen an increase in the prevalence of sequence type (ST) 45 methicillin-resistant Staphylococcus aureus (MRSA), yet the underlying drivers for its emergence and spread remain unclear. To better understand the worldwide dissemination of ST45 S. aureus, we performed phylogenetic analyses of Australian isolates, supplemented with a global population of ST45 S. aureus genomes. Our analyses revealed a distinct lineage of multidrug-resistant ST45 MRSA harbouring qacA, predominantly found in Australia and Singapore. Bayesian inference predicted that the acquisition of qacA occurred in the late 1990s. qacA was integrated into a structurally variable region of the chromosome containing Tn552 (carrying blaZ) and Tn4001 (carrying aac(6')-aph(2")) transposable elements. Using mutagenesis and in vitro assays, we provide phenotypic evidence that qacA confers tolerance to chlorhexidine. These findings collectively suggest both antimicrobial resistance and the carriage of qacA may play a role in the successful establishment of ST45 MRSA.
MeSH term(s)	Humans ; Methicillin-Resistant Staphylococcus aureus/genetics ; Staphylococcus aureus/genetics ; Bayes Theorem ; Phylogeny ; Staphylococcal Infections/epidemiology ; Membrane Transport Proteins/genetics ; Bacterial Proteins/genetics ; Australia
Chemical Substances	Membrane Transport Proteins ; Bacterial Proteins
Language	English
Publishing date	2024-03-21
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-024-06012-z
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Article ; Online: Structural and Functional Characterization of

Voth, Kevin / Pasricha, Shivani / Chung, Ivy Yeuk Wah / Wibawa, Rachelia R / Zainudin, Engku Nuraishah Huda E / Hartland, Elizabeth L / Cygler, Miroslaw

Biomolecules

2021 Volume 11, Issue 12

Abstract: Legionella ... ...

Abstract	Legionella pneumophila
MeSH term(s)	Adenosine Diphosphate Ribose/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Crystallography, X-Ray ; HEK293 Cells ; HeLa Cells ; Humans ; Legionella pneumophila/enzymology ; Legionella pneumophila/growth & development ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Folding ; THP-1 Cells ; Type IV Secretion Systems/chemistry ; Type IV Secretion Systems/metabolism ; Ubiquitin-Conjugating Enzymes/metabolism ; Ubiquitination
Chemical Substances	Bacterial Proteins ; Type IV Secretion Systems ; Adenosine Diphosphate Ribose (20762-30-5) ; UBE2Q1 protein, human (EC 2.3.2.23) ; Ubiquitin-Conjugating Enzymes (EC 2.3.2.23)
Language	English
Publishing date	2021-11-30
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom11121802
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Article ; Online: The Impact of Mouthwash on the Oropharyngeal Microbiota of Men Who Have Sex with Men: a Substudy of the OMEGA Trial.

Plummer, Erica L / Maddaford, Kate / Murray, Gerald L / Fairley, Christopher K / Pasricha, Shivani / Mu, Andre / Bradshaw, Catriona S / Williamson, Deborah A / Chow, Eric P F

Microbiology spectrum

2022 Volume 10, Issue 1, Page(s) e0175721

Abstract: Mouthwash is a commonly used product and has been proposed as an alternative intervention to prevent gonorrhea transmission. However, the long-term effects of mouthwash on the oral microbiota are largely unknown. We investigated the impact of 12 weeks of ...

Abstract	Mouthwash is a commonly used product and has been proposed as an alternative intervention to prevent gonorrhea transmission. However, the long-term effects of mouthwash on the oral microbiota are largely unknown. We investigated the impact of 12 weeks of daily mouthwash use on the oropharyngeal microbiota in a subset of men who have sex with men who participated in a randomized trial comparing the efficacy of two alcohol-free mouthwashes for the prevention of gonorrhea. We characterized the oropharyngeal microbiota using 16S rRNA gene sequencing of tonsillar fossae samples collected before and after 12 weeks of daily use of Listerine mouthwash or Biotène dry mouth oral rinse. Permutational multivariate analysis of variance (PERMANOVA) was used to assess differences in oropharyngeal microbiota composition following mouthwash use. Differential abundance testing was performed using ALDEx2, with false-discovery rate correction. A total of 306 samples from 153 men were analyzed (Listerine,
MeSH term(s)	Adult ; Double-Blind Method ; Drug Combinations ; Glucose Oxidase/pharmacology ; Gonorrhea ; Homosexuality, Male ; Humans ; Lactoperoxidase/pharmacology ; Male ; Microbiota/drug effects ; Microbiota/genetics ; Mouthwashes/pharmacology ; Muramidase/pharmacology ; Oropharynx/microbiology ; RNA, Ribosomal, 16S ; Salicylates ; Sexual and Gender Minorities ; Terpenes ; Young Adult
Chemical Substances	Biotene ; Drug Combinations ; Mouthwashes ; RNA, Ribosomal, 16S ; Salicylates ; Terpenes ; Listerine (51273-66-6) ; Glucose Oxidase (EC 1.1.3.4) ; Lactoperoxidase (EC 1.11.1.-) ; Muramidase (EC 3.2.1.17)
Language	English
Publishing date	2022-01-12
Publishing country	United States
Document type	Journal Article ; Multicenter Study ; Randomized Controlled Trial ; Research Support, Non-U.S. Gov't
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.01757-21
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Article ; Online: Inhibitory Activity of Antibacterial Mouthwashes and Antiseptic Substances against Neisseria gonorrhoeae.

Williams, Eloise / Zhang, Bowen / Chow, Eric P F / Chea, Socheata / Phillips, Tiffany R / Maddaford, Kate / Krysiak, Marcelina / Nong, Yi / Stefanatos, Helen / Pasricha, Shivani / Fairley, Christopher K / Wiliamson, Deborah A

Antimicrobial agents and chemotherapy

2022 Volume 66, Issue 6, Page(s) e0004222

Abstract: Improved treatment and prevention strategies, such as antimicrobial mouthwashes, may be important for addressing the public health threat of antimicrobial-resistant Neisseria gonorrhoeae. Here, we describe the activity of seven common antibacterial ... ...

Abstract	Improved treatment and prevention strategies, such as antimicrobial mouthwashes, may be important for addressing the public health threat of antimicrobial-resistant Neisseria gonorrhoeae. Here, we describe the activity of seven common antibacterial mouthwashes and antiseptics against N. gonorrhoeae isolates, incorporating the use of a human saliva test matrix. Our data demonstrate that antibacterial mouthwashes and antiseptics vary in their ability to inhibit the
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents ; Anti-Infective Agents, Local/pharmacology ; Gonorrhea/drug therapy ; Gonorrhea/microbiology ; Humans ; Microbial Sensitivity Tests ; Mouthwashes/pharmacology ; Neisseria gonorrhoeae
Chemical Substances	Anti-Bacterial Agents ; Anti-Infective Agents ; Anti-Infective Agents, Local ; Mouthwashes
Language	English
Publishing date	2022-05-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	217602-6
ISSN	1098-6596 ; 0066-4804
ISSN (online)	1098-6596
ISSN	0066-4804
DOI	10.1128/aac.00042-22
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Article ; Online: Legionella pneumophila

Li, Pengfei / Vassiliadis, Dane / Ong, Sze Ying / Bennett-Wood, Vicki / Sugimoto, Chihiro / Yamagishi, Junya / Hartland, Elizabeth L / Pasricha, Shivani

Frontiers in cellular and infection microbiology

2020 Volume 10, Page(s) 428

Abstract: Legionella ... ...

Abstract	Legionella pneumophila
MeSH term(s)	Acanthamoeba castellanii ; Bacterial Proteins/genetics ; Humans ; Legionella pneumophila/genetics ; Legionnaires' Disease ; Sirtuins ; Transcriptome
Chemical Substances	Bacterial Proteins ; Sirtuins (EC 3.5.1.-)
Language	English
Publishing date	2020-08-20
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2020.00428
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Article ; Online: A comparison of cotton-tipped and nylon flocked swabs for culture of Neisseria gonorrhoeae from oropharyngeal samples.

Phillips, Tiffany R / Tabesh, Marjan / Fairley, Christopher K / Maddaford, Kate / Pasricha, Shivani / Wigan, Rebecca / De Petra, Vesna / Williamson, Deborah A / Chow, Eric P F

Diagnostic microbiology and infectious disease

2021 Volume 101, Issue 3, Page(s) 115455

Abstract: Our aim was to determine if there was a difference in culture positivity for oropharyngeal gonorrhoea when sampling using a nylon-flocked versus cotton-tipped swab. We collected FLOQSwabs and cotton-tipped swabs from individuals aged ≥ 18 years who had ... ...

Abstract	Our aim was to determine if there was a difference in culture positivity for oropharyngeal gonorrhoea when sampling using a nylon-flocked versus cotton-tipped swab. We collected FLOQSwabs and cotton-tipped swabs from individuals aged ≥ 18 years who had untreated oropharyngeal gonorrhoea detected by NAAT between November 2019-June 2020.Of 78 participants, 32 (41.0%) were culture-positive for N. gonorrhoeae from either swab. Of these 32, 29 (90.6%, 95%CI: 75.0%-98.0%) were positive on both swabs, one (3.1%, 95%CI: 0.0%-16.2%) tested positive on FLOQSwab only and two (6.2%, 95%CI: 0.1%-20.8%) tested positive on cotton-tipped swabs only. There was moderate agreement between the swabs in the amount of bacterial growth (Cohen's Kappa (k)=0.745; 95%CI: 0.622-0.868, p<0.001). Our results showed that the proportion of positive results was comparable using the FLOQSwabs versus the cotton-tipped swabs for oropharyngeal gonorrhoea culture.
MeSH term(s)	Cross-Sectional Studies ; Female ; Gonorrhea/diagnosis ; Gonorrhea/microbiology ; Humans ; Male ; Middle Aged ; Neisseria gonorrhoeae/growth & development ; Neisseria gonorrhoeae/isolation & purification ; Nylons ; Oropharynx/microbiology ; Pilot Projects ; Respiratory Tract Infections/microbiology ; Specimen Handling/instrumentation ; Specimen Handling/methods ; Specimen Handling/standards ; Textiles ; Young Adult
Chemical Substances	Nylons
Language	English
Publishing date	2021-06-18
Publishing country	United States
Document type	Comparative Study ; Journal Article
ZDB-ID	604920-5
ISSN	1879-0070 ; 0732-8893
ISSN (online)	1879-0070
ISSN	0732-8893
DOI	10.1016/j.diagmicrobio.2021.115455
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Article ; Online: Clinical relevance of topical antibiotic use in co-selecting for multidrug-resistant

Nong, Yi / Taiaroa, George / Pasricha, Shivani / Guérillot, Romain / Monk, Ian R / Baines, Sarah L / Carter, Glen P / Howden, Benjamin P / Williamson, Deborah A

Antimicrobial agents and chemotherapy

2021 Volume 95, Issue 5

Abstract: Topical antibiotic preparations, such as fusidic acid (FA) or mupirocin, are used in the prevention and treatment of superficial skin infections caused by staphylococci. Previous genomic epidemiology work has suggested an association between the ... ...

Abstract	Topical antibiotic preparations, such as fusidic acid (FA) or mupirocin, are used in the prevention and treatment of superficial skin infections caused by staphylococci. Previous genomic epidemiology work has suggested an association between the widespread use of topical antibiotics and the emergence of methicillin resistant
Language	English
Publishing date	2021-02-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	217602-6
ISSN	1098-6596 ; 0066-4804
ISSN (online)	1098-6596
ISSN	0066-4804
DOI	10.1128/AAC.02048-20
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Article ; Online: Use of emerging testing technologies and approaches for SARS-CoV-2: review of literature and global experience in an Australian context.

Graham, Maryza / Ballard, Susan A / Pasricha, Shivani / Lin, Belinda / Hoang, Tuyet / Stinear, Timothy / Druce, Julian / Catton, Mike / Sherry, Norelle / Williamson, Deborah / Howden, Benjamin P

Pathology

2021 Volume 53, Issue 6, Page(s) 689–699

Abstract: Emerging testing technologies for detection of SARS-CoV-2 include those that are rapid and can be used at point-of-care (POC), and those facilitating high throughput laboratory-based testing. Tests designed to be performed at POC (such as antigen tests ... ...

Abstract	Emerging testing technologies for detection of SARS-CoV-2 include those that are rapid and can be used at point-of-care (POC), and those facilitating high throughput laboratory-based testing. Tests designed to be performed at POC (such as antigen tests and molecular assays) have the potential to expedite isolation of infectious patients and their contacts, but most are less sensitive than standard-of-care reverse transcription polymerase chain reaction (RT-PCR). Data on clinical performance of the majority of emerging assays are limited with most evaluations performed on contrived or stored laboratory samples. Further evaluations of these assays are required, particularly when performed at POC on symptomatic and asymptomatic patients and at various time-points after symptom onset. A few studies have so far shown several of these assays have high specificity. However, large prospective evaluations are needed to confirm specificity, particularly before the assays are implemented in low prevalence settings or asymptomatic populations. High throughput laboratory-based testing includes the use of new sample types (e.g., saliva to increase acceptability) or innovative uses of existing technology (e.g., sample pooling). Information detailing population-wide testing strategies for SARS-COV-2 is largely missing from peer-reviewed literature. Logistics and supply chains are key considerations in any plan to 'scale up' testing in the Australian context. The strategic use of novel assays will help strike the balance between achieving adequate test numbers without overwhelming laboratory capacity. To protect testing of high-risk populations, the aims of testing with respect to the phase of the pandemic must be considered.
MeSH term(s)	Australia ; COVID-19/diagnosis ; COVID-19 Testing/methods ; Humans ; SARS-CoV-2
Language	English
Publishing date	2021-08-10
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	7085-3
ISSN	1465-3931 ; 0031-3025
ISSN (online)	1465-3931
ISSN	0031-3025
DOI	10.1016/j.pathol.2021.08.001
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Zs.A 723: Show issues

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Article ; Online: Rapid detection of monkeypox virus using a CRISPR-Cas12a mediated assay: a laboratory validation and evaluation study.

The Lancet. Microbe

2023 Volume 4, Issue 10, Page(s) e800–e810

Abstract: Background: The 2022 outbreak of mpox (formerly known as monkeypox) led to the spread of monkeypox virus (MPXV) in over 110 countries, demanding effective disease management and surveillance. As current diagnostics rely largely on centralised laboratory ...

Abstract	Background: The 2022 outbreak of mpox (formerly known as monkeypox) led to the spread of monkeypox virus (MPXV) in over 110 countries, demanding effective disease management and surveillance. As current diagnostics rely largely on centralised laboratory testing, our objective was to develop a simple rapid point-of-care assay to detect MPXV in clinical samples using isothermal amplification coupled with CRISPR and CRISPR-associated protein (Cas) technology. Methods: In this proof-of-concept study, we developed a portable isothermal amplification CRISPR-Cas12a-based assay for the detection of MPXV. We designed a panel of 22 primer-guide RNA sets using pangenome and gene-agnostic approaches, and subsequently shortlisted the three sets producing the strongest signals for evaluation of analytical sensitivity and specificity using a fluorescence-based readout. The set displaying 100% specificity and the lowest limit of detection (LOD) was selected for further assay validation using both a fluorescence-based and lateral-flow readout. Assay specificity was confirmed using a panel of viral and bacterial pathogens. Finally, we did a blind concordance study on genomic DNA extracted from 185 clinical samples, comparing assay results with a gold-standard quantitative PCR (qPCR) assay. We identified the optimal time to detection and analysed the performance of the assay relative to qPCR using receiver operating characteristic (ROC) curves. We also assessed the compatibility with lateral-flow strips, both visually and computationally, where strips were interpreted blinded to the fluorescence results on the basis of the presence or absence of test bands. Findings: With an optimal run duration of approximately 45 min from isothermal amplification to CRISPR-assay readout, the MPXV recombinase polymerase amplification CRISPR-Cas12a-based assay with the selected primer-guide set had an LOD of 1 copy per μL and 100% specificity against tested viral pathogens. Blinded concordance testing of 185 clinical samples resulted in 100% sensitivity (95% CI 89·3-100) and 99·3% specificity (95% CI 95·7-100) using the fluorescence readout. For optimal time to detection by fluorescence readout, we estimated the areas under the ROC curve to be 0·98 at 2 min and 0·99 at 4 min. Lateral-flow strips had 100% sensitivity (89·3-100) and 98·6% specificity (94·7-100) with both visual and computational assessment. Overall, lateral-flow results were highly concordant with fluorescence-based readouts (179 of 185 tests, 96·8% concordant), with discrepancies associated with low viral load samples. Interpretation: Our assay for the diagnosis of mpox displayed good performance characteristics compared with qPCR. Although optimisation of the assay will be required before deployment, its usability and versatility present a potential solution to MPXV detection in low-resource and remote settings, as well as a means of community-based, on-site testing. Funding: Victorian Medical Research Accelerator Fund and the Australian Government Department of Health.
Language	English
Publishing date	2023-09-15
Publishing country	England
Document type	Journal Article
ISSN	2666-5247
ISSN (online)	2666-5247
DOI	10.1016/S2666-5247(23)00148-9
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