Publications by authors named "David Whiley"

186 Publications

High rate of asymptomatic colonisation with antimicrobial-resistant E. coli in Australian returned travellers.

J Travel Med 2021 Sep 7. Epub 2021 Sep 7.

Research School of Population Health, Australian National University, Canberra, Australia.

Global movement of people plays a key role in the spread of antimicrobial resistant (AMR) organisms. We found that 58% of Australian travellers returning from Asia were asymptomatic carriers of AMR E. coli, including resistance to critically important antibiotics. Future studies are needed to identify interventions for travellers to reduce their risk of AMR acquisition.
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http://dx.doi.org/10.1093/jtm/taab141DOI Listing
September 2021

Point-of-care testing and treatment of sexually transmitted and genital infections during pregnancy in Papua New Guinea (WANTAIM trial): protocol for an economic evaluation alongside a cluster-randomised trial.

BMJ Open 2021 08 12;11(8):e046308. Epub 2021 Aug 12.

The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.

Introduction: Left untreated, sexually transmitted and genital infections (henceforth STIs) in pregnancy can lead to serious adverse outcomes for mother and child. Papua New Guinea (PNG) has among the highest prevalence of curable STIs including syphilis, chlamydia, gonorrhoea, trichomoniasis and bacterial vaginosis, and high neonatal mortality rates. Diagnosis and treatment of these STIs in PNG rely on syndromic management. Advances in STI diagnostics through point-of-care (PoC) testing using GeneXpert technology hold promise for resource-constrained countries such as PNG. This paper describes the planned economic evaluation of a cluster-randomised cross-over trial comparing antenatal PoC testing and immediate treatment of curable STIs with standard antenatal care in two provinces in PNG.

Methods And Analysis: Cost-effectiveness of the PoC intervention compared with standard antenatal care will be assessed prospectively over the trial period (2017-2021) from societal and provider perspectives. Incremental cost-effectiveness ratios will be calculated for the primary health outcome, a composite measure of the proportion of either preterm birth and/or low birth weight; for life years saved; for disability-adjusted life years averted; and for non-health benefits (financial risk protection and improved health equity). Scenario analyses will be conducted to identify scale-up options, and budget impact analysis will be undertaken to understand short-term financial impacts of intervention adoption on the national budget. Deterministic and probabilistic sensitivity analysis will be conducted to account for uncertainty in key model inputs.

Ethics And Dissemination: This study has ethical approval from the Institutional Review Board of the PNG Institute of Medical Research; the Medical Research Advisory Committee of the PNG National Department of Health; the Human Research Ethics Committee of the University of New South Wales; and the Research Ethics Committee of the London School of Hygiene and Tropical Medicine. Findings will be disseminated through national stakeholder meetings, conferences, peer-reviewed publications and policy briefs.

Trial Registration Number: ISRCTN37134032.
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http://dx.doi.org/10.1136/bmjopen-2020-046308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8362726PMC
August 2021

Optimising Treatment Outcomes for Children and Adults Through Rapid Genome Sequencing of Sepsis Pathogens. A Study Protocol for a Prospective, Multi-Centre Trial (DIRECT).

Front Cell Infect Microbiol 2021 23;11:667680. Epub 2021 Jun 23.

UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.

Background: Sepsis contributes significantly to morbidity and mortality globally. In Australia, 20,000 develop sepsis every year, resulting in 5,000 deaths, and more than AUD$846 million in expenditure. Prompt, appropriate antibiotic therapy is effective in improving outcomes in sepsis. Conventional culture-based methods to identify appropriate therapy have limited yield and take days to complete. Recently, nanopore technology has enabled rapid sequencing with real-time analysis of pathogen DNA. We set out to demonstrate the feasibility and diagnostic accuracy of pathogen sequencing direct from clinical samples, and estimate the impact of this approach on time to effective therapy when integrated with personalised software-guided antimicrobial dosing in children and adults on ICU with sepsis.

Methods: The DIRECT study is a pilot prospective, non-randomized multicentre trial of an integrated diagnostic and therapeutic algorithm combining rapid direct pathogen sequencing and software-guided, personalised antibiotic dosing in children and adults with sepsis on ICU.

Participants And Interventions: DIRECT will collect microbiological and pharmacokinetic samples from approximately 200 children and adults with sepsis admitted to one of four ICUs in Brisbane. In Phase 1, we will evaluate Oxford Nanopore Technologies MinION sequencing direct from blood in 50 blood culture-proven sepsis patients recruited from consecutive patients with suspected sepsis. In Phase 2, a further 50 consecutive patients with suspected sepsis will be recruited in whom MinION sequencing will be combined with Bayesian software-guided (ID-ODS) personalised antimicrobial dosing.

Outcome Measures: The primary outcome is time to effective antimicrobial therapy, defined as trough drug concentrations above the MIC of the pathogen. Secondary outcomes are diagnostic accuracy of MinION sequencing from whole blood, time to pathogen identification and susceptibility testing using sequencing direct from whole blood and from positive blood culture broth.

Discussion: Rapid pathogen sequencing coupled with antimicrobial dosing software has great potential to overcome the limitations of conventional diagnostics which often result in prolonged inappropriate antimicrobial therapy. Reduced time to optimal antimicrobial therapy may reduce sepsis mortality and ICU length of stay. This pilot study will yield key feasibility data to inform further, urgently needed sepsis studies. Phase 2 of the trial protocol is registered with the ANZCTR (ACTRN12620001122943).

Trial Registration: Registered with the Australia New Zealand Clinical Trials Registry Number ACTRN12620001122943.
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http://dx.doi.org/10.3389/fcimb.2021.667680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8261237PMC
July 2021

Exploring the implications for coincidental treatment of infection in -positive patients.

JAC Antimicrob Resist 2021 Mar 16;3(1):dlab033. Epub 2021 Mar 16.

The University of Queensland Centre for Clinical Research (UQ-CCR), Queensland, Australia.

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http://dx.doi.org/10.1093/jacamr/dlab033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8210116PMC
March 2021

MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.

BMC Genomics 2021 Jun 25;22(1):474. Epub 2021 Jun 25.

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.

Background: Oxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers due to the accessibility and affordability of its devices. However, easy and automated construction of high-quality bacterial genomes using nanopore reads remains challenging. Here we aimed to create a reproducible end-to-end bacterial genome assembly pipeline using ONT in combination with Illumina sequencing.

Results: We evaluated the performance of several popular tools used during genome reconstruction, including base-calling, filtering, assembly, and polishing. We also assessed overall genome accuracy using ONT both natively and with Illumina. All steps were validated using the high-quality complete reference genome for the Escherichia coli sequence type (ST)131 strain EC958. Software chosen at each stage were incorporated into our final pipeline, MicroPIPE. Further validation of MicroPIPE was carried out using 11 additional ST131 E. coli isolates, which demonstrated that complete circularised chromosomes and plasmids could be achieved without manual intervention. Twelve publicly available Gram-negative and Gram-positive bacterial genomes (with available raw ONT data and matched complete genomes) were also assembled using MicroPIPE. We found that revised basecalling and updated assembly of the majority of these genomes resulted in improved accuracy compared to the current publicly available complete genomes.

Conclusions: MicroPIPE is built in modules using Singularity container images and the bioinformatics workflow manager Nextflow, allowing changes and adjustments to be made in response to future tool development. Overall, MicroPIPE provides an easy-access, end-to-end solution for attaining high-quality bacterial genomes. MicroPIPE is available at https://github.com/BeatsonLab-MicrobialGenomics/micropipe .
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http://dx.doi.org/10.1186/s12864-021-07767-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8235852PMC
June 2021

Rapid detection of NDM and VIM carbapenemase encoding genes by recombinase polymerase amplification and lateral flow-based detection.

Eur J Clin Microbiol Infect Dis 2021 May 11. Epub 2021 May 11.

UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia.

Carbapenemase-producing organisms (CPOs) pose a serious clinical threat and rapid detection tools are essential to aid in patient management. We developed rapid and simple molecular tests to detect bla and bla carbapenemase genes using recombinase polymerase amplification (RPA) combined with a lateral flow detection. The tests could provide results in approximately 15 min when using DNA extracts, with limits of detection of 9.2 copies/μl for the bla assay and 7.5 copies/μl for bla assay, and successfully detected all isolates harbouring the carbapenemase encoding genes in a panel of 57 isolates. These RPA tests may be suitable for use in low-resource settings to tailor rapid implementation of infection control precautions and antibiotic stewardship.
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http://dx.doi.org/10.1007/s10096-021-04267-6DOI Listing
May 2021

Rapid macrolide and amikacin resistance testing for in people with cystic fibrosis.

J Med Microbiol 2021 Apr;70(4)

The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia.

complex (MABSC) is an environmental organism and opportunistic pathogen. MABSC pulmonary infections in people with cystic fibrosis are of growing clinical concern. Resistance data guide the use of macrolides and amikacin in MABSC pulmonary disease treatment. MABSC can acquire resistance against macrolides or amikacin via 23S or 16S rRNA gene mutations, respectively. Current culture-based methods for MABSC detection and antibiotic resistance characterization are typically prolonged, limiting their utility to directly inform treatment or clinical trials. Culture-independent molecular methods may help address this limitation. To develop real-time PCR assays for characterization of key 23S or 16S rRNA gene mutations associated with constitutive resistance in MABSC. We designed two real-time PCR assays to detect the key 23S and 16S rRNA gene mutations. The highly conserved nature of rRNA genes was a major design challenge. To reduce potential cross-reactivity, primers included non-template bases and targeted single-nucleotide polymorphisms unique to MABSC. We applied these assays, as well as a previously developed real-time PCR assay for MABSC detection, to 968 respiratory samples from people with cystic fibrosis. The results from the molecular methods were compared to those for gold standard culture methods and 23S and 16S rRNA gene sequencing.The real-time PCR MABSC detection assay provided a sensitivity of 83.8 % and a specificity of 97.8 % compared to culture. The results from the real-time PCR resistance detection assays were mostly concordant (>77.4 %) with cultured isolate sequencing. The real-time PCR resistance detection assays identified several samples harbouring both resistant and susceptible MABSC, while culture-dependent methods only identified susceptible MABSC in these samples. Using the molecular methods described here, results for health care providers or researchers could be available days or weeks earlier than is currently possible via culture-based antibiotic susceptibility testing.
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http://dx.doi.org/10.1099/jmm.0.001349DOI Listing
April 2021

High coverage of diverse invasive meningococcal serogroup B strains by the 4-component vaccine 4CMenB in Australia, 2007-2011: Concordant predictions between MATS and genetic MATS.

Hum Vaccin Immunother 2021 Sep 13;17(9):3230-3238. Epub 2021 Apr 13.

Queensland Paediatric Infectious Disease Laboratory, Children's Health Queensland Hospitals and Health Service, Queensland Children's Hospital, Brisbane, Australia.

Meningococcal serogroup B (MenB) accounts for an important proportion of invasive meningococcal disease (IMD). The 4-component vaccine against MenB (4CMenB) is composed of factor H binding protein (fHbp), neisserial heparin-binding antigen (NHBA), adhesin A (NadA), and outer membrane vesicles of the New Zealand strain with Porin 1.4. A meningococcal antigen typing system (MATS) and a fully genomic approach, genetic MATS (gMATS), were developed to predict coverage of MenB strains by 4CMenB. We characterized 520 MenB invasive disease isolates collected over a 5-year period (January 2007-December 2011) from all Australian states/territories by multilocus sequence typing and estimated strain coverage by 4CMenB. The clonal complexes most frequently identified were ST-41/44 CC/Lineage 3 (39.4%) and ST-32 CC/ET-5 CC (23.7%). The overall MATS predicted coverage was 74.6% (95% coverage interval: 61.1%-85.6%). The overall gMATS prediction was 81.0% (lower-upper limit: 75.0-86.9%), showing 91.5% accuracy compared with MATS. Overall, 23.7% and 13.1% (MATS) and 26.0% and 14.0% (gMATS) of isolates were covered by at least 2 and 3 vaccine antigens, respectively, with fHbp and NHBA contributing the most to coverage. When stratified by year of isolate collection, state/territory and age group, MATS and gMATS strain coverage predictions were consistent across all strata. The high coverage predicted by MATS and gMATS indicates that 4CMenB vaccination may have an impact on the burden of MenB-caused IMD in Australia. gMATS can be used in the future to monitor variations in 4CMenB strain coverage over time and geographical areas even for non-culture confirmed IMD cases.
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http://dx.doi.org/10.1080/21645515.2021.1904758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8381844PMC
September 2021

Analytical validation of a real-time hydrolysis probe PCR assay for quantifying Plasmodium falciparum parasites in experimentally infected human adults.

Malar J 2021 Apr 10;20(1):181. Epub 2021 Apr 10.

QIMR Berghofer Medical Research Institute, Brisbane, Australia.

Background: Volunteer infection studies have become a standard model for evaluating drug efficacy against Plasmodium infections. Molecular techniques such as qPCR are used in these studies due to their ability to provide robust and accurate estimates of parasitaemia at increased sensitivity compared to microscopy. The validity and reliability of assays need to be ensured when used to evaluate the efficacy of candidate drugs in clinical trials.

Methods: A previously described 18S rRNA gene qPCR assay for quantifying Plasmodium falciparum in blood samples was evaluated. Assay performance characteristics including analytical sensitivity, reportable range, precision, accuracy and specificity were assessed using experimental data and data compiled from phase 1 volunteer infection studies conducted between 2013 and 2019. Guidelines for validation of laboratory-developed molecular assays were followed.

Results: The reportable range was 1.50 to 6.50 log parasites/mL with a limit of detection of 2.045 log parasites/mL of whole blood based on a parasite diluted standard series over this range. The assay was highly reproducible with minimal intra-assay (SD = 0.456 quantification cycle (C) units [0.137 log parasites/mL] over 21 replicates) and inter-assay (SD = 0.604 C units [0.182 log parasites/mL] over 786 qPCR runs) variability. Through an external quality assurance program, the QIMR assay was shown to generate accurate results (quantitative bias + 0.019 log parasites/mL against nominal values). Specificity was 100% after assessing 164 parasite-free human blood samples.

Conclusions: The 18S rRNA gene qPCR assay is specific and highly reproducible and can provide reliable and accurate parasite quantification. The assay is considered fit for use in evaluating drug efficacy in malaria clinical trials.
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http://dx.doi.org/10.1186/s12936-021-03717-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8035755PMC
April 2021

Emergence and impact of oprD mutations in Pseudomonas aeruginosa strains in cystic fibrosis.

J Cyst Fibros 2021 Mar 25. Epub 2021 Mar 25.

QIMR Berghofer Medical Research Institute, Brisbane, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia; Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia. Electronic address:

Background: Antimicrobial resistance in cystic fibrosis (CF) Pseudomonas aeruginosa airway infection is complex and often attributed to chromosomal mutations. How these mutations emerge in specific strains or whether particular gene mutations are clinically informative is unclear. This study focused on oprD, which encodes an outer membrane porin associated with carbapenem resistance when it is downregulated or inactivated.

Aim: Determine how mutations in oprD emerge in two prevalent Australian shared CF strains of P. aeruginosa and their clinical relevance.

Methods: The two most common shared CF strains in Queensland were investigated using whole genome sequencing and their oprD sequences and antimicrobial resistance phenotypes were established. P. aeruginosa mutants with the most common oprD variants were constructed and characterised. Clinical variables were compared between people with or without evidence of infection with strains harbouring these variants.

Results: Frequently found nonsense mutations arising from a 1-base pair substitution in oprD evolved independently in three sub-lineages, and are likely major contributors to the reduced carbapenem susceptibility observed in the clinical isolates. Lower baseline FEV %predicted was identified as a risk factor for infection with a sub-lineage (odds ratio=0.97; 95% confidence interval 0.96-0.99; p<0.001). However, acquiring these sub-lineage strains did not confer an accelerated decline in FEV nor increase the risk of death/lung transplantation.

Conclusions: Sub-lineages harbouring specific mutations in oprD have emerged and persisted in the shared strain populations. Infection with the sub-lineages was more likely in people with lower lung function, but this was not predictive of a worse clinical trajectory.
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http://dx.doi.org/10.1016/j.jcf.2021.03.007DOI Listing
March 2021

Antiseptic mouthwash for gonorrhoea prevention (OMEGA): a randomised, double-blind, parallel-group, multicentre trial.

Lancet Infect Dis 2021 05 4;21(5):647-656. Epub 2021 Mar 4.

Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia; Central Clinical School, Monash University, Melbourne, VIC, Australia; China-Australia Joint Research Centre for Infectious Diseases, School of Public Health, Xi'an Jiaotong University, Xi'an, China.

Background: To address the increasing incidence of gonorrhoea and antimicrobial resistance, we compared the efficacy of Listerine and Biotène mouthwashes for preventing gonorrhoea among men who have sex with men (MSM).

Methods: The OMEGA trial was a multicentre, parallel-group, double-blind randomised controlled trial among MSM, done at three urban sexual health clinics and one general practice clinic in Australia. Men were eligible if they were diagnosed with oropharyngeal gonorrhoea by nucleic acid amplification test (NAAT) in the previous 30 days or were aged 16-24 years. They were randomly assigned to receive Listerine (intervention) or Biotène (control) via a computer-generated sequence (1:1 ratio, block size of four). Participants, clinicians, data collectors, data analysts, and outcome adjudicators were masked to the interventions after assignment. Participants were instructed to rinse and gargle with 20 mL of mouthwash for 60 s at least once daily for 12 weeks. Oropharyngeal swabs were collected by research nurses every 6 weeks, and participants provided saliva samples every 3 weeks, to be tested for Neisseria gonorrhoeae with NAAT and quantitative PCR. The primary outcome was proportion of MSM diagnosed with oropharyngeal N gonorrhoeae infection at any point over the 12-week period, defined as a positive result for either oropharyngeal swabs or saliva samples by NAAT, and the cumulative incidence of oropharyngeal gonorrhoea at the week 12 visit. A modified intention-to-treat analysis for the primary outcome was done that included men who provided at least one follow-up specimen over the 12-week study period. The trial was registered on the Australian and New Zealand Clinical Trials Registry (ACTRN12616000247471).

Findings: Between March 30, 2016, and Oct 26, 2018, 786 MSM were screened and 256 were excluded. 264 MSM were randomly assigned to the Biotène group and 266 to the Listerine group. The analysis population included 227 (86%) men in the Biotène group and 219 (82%) in the Listerine group. Oropharyngeal gonorrhoea was detected in ten (4%) of 227 of MSM in the Biotène group and in 15 (7%) of 219 in the Listerine group (adjusted risk difference 2·5%, 95% CI -1·8 to 6·8). The cumulative incidence of oropharyngeal gonorrhoea at the week 12 visit did not differ between the two mouthwash groups (adjusted risk difference 3·1%, 95% CI -1·4 to 7·7).

Interpretation: Listerine did not reduce the incidence of oropharyngeal gonorrhoea compared with Biotène. However, previous research suggests that mouthwash might reduce the infectivity of oropharyngeal gonorrhoea; therefore, further studies of mouthwash examining its inhibitory effect on N gonorrhoeae are warranted to determine if it has a potential role for the prevention of transmission.

Funding: Australian National Health and Medical Research Council.
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http://dx.doi.org/10.1016/S1473-3099(20)30704-0DOI Listing
May 2021

Reflex Detection of Ciprofloxacin Resistance in Neisseria gonorrhoeae by Use of the SpeeDx ResistancePlus GC Assay.

J Clin Microbiol 2021 04 20;59(5). Epub 2021 Apr 20.

Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia

Resistance-guided therapy (RGT) for gonorrhea may reduce unnecessary use of broad-spectrum antibiotics. When reflexed from the Aptima Combo 2 assay, the ResistancePlus GC assay demonstrated 94.8% sensitivity and 100.0% specificity for detection. Of the 379 concordant -positive samples, 86.8% were found to possess the S91F mutation, which was highly predictive for ciprofloxacin resistance and stable across 3,144 publicly available genomes. Our work supports the feasibility of implementing RGT for gonorrhea into routine molecular workflows.
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http://dx.doi.org/10.1128/JCM.00089-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8091848PMC
April 2021

Limited evidence for the role of environmental factors in the unusual peak of influenza in Brisbane during the 2018-2019 Australian summer.

Sci Total Environ 2021 Jul 19;776:145967. Epub 2021 Feb 19.

School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, QLD 4072, Australia. Electronic address:

Objective: To explore the contribution of environmental factors in the unusual pattern of influenza activity observed in Brisbane, Australia during the summer of 2018-2019.

Methods: Distributed lag nonlinear models (DLNMs) were used to estimate the effect of environmental factors on weekly influenza incidence in Brisbane. Next generation sequencing was then employed to analyze minor and majority variants in influenza strains isolated from Brisbane children during this period.

Results: There were limited marked differences in the environmental factors observed in Brisbane between the 2018-2019 summer period and the same period of the proceeding years, with the exception of significant reduction in rainfall. DLNM showed that reduced rainfall in Brisbane (at levels consistent with the 2018-2019 period) correlated with a dramatic increase in the relative risk of influenza. Sulfur dioxide (SO) levels were also increased in the 2018-2019 period, although these levels did not correlate with an increased risk of influenza. Sequencing of a limited number of pediatric influenza virus strains isolated during the 2018-2019 showed numerous mutations within the viral HA.

Conclusions: Taken together, these data suggest a limited role for key environmental factors in the influenza activity observed in Brisbane, Australia during the summer of 2018-2019. One alternative explanation may that viral factors, in addition to other factors not studied herein, contributed to the unusual influenza season. Our findings provide fundamental information that may be beneficial to a better understanding of the seasonal trends of influenza virus.
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http://dx.doi.org/10.1016/j.scitotenv.2021.145967DOI Listing
July 2021

Mycoplasma genitalium infections can comprise a mixture of both fluoroquinolone-susceptible and fluoroquinolone-resistant strains.

J Antimicrob Chemother 2021 03;76(4):887-892

The University of Queensland Centre for Clinical Research (UQ-CCR), Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.

Background: Mycoplasma genitalium was recently added to the CDC's antimicrobial resistance threats 'watch list', as it has rapidly become resistant to mainstay treatments. In Australia, treatment failure with fluoroquinolones remain commonplace, even when Sanger sequencing fails to identify evidence of resistance mutations.

Methods: Suspecting that Sanger sequencing may miss low-load mixed infections, we applied three additional PCR-based approaches (allele-specific primer-based PCR, probe-based PCR and amplicon deep sequencing) to detect mutations associated with fluoroquinolone susceptibility/resistance. We focused on resistance mutations at amino acid positions 83 and 87 of parC, as these were previously shown to be common in Australia.

Results: Our results showed evidence of mixtures of fluoroquinolone-susceptible and -resistant strains in up to 27/423 samples (6.4%). These included 1 sample that was indicated to be mixed by Sanger sequencing and all three additional PCR methods, 6 samples detected by two or more of the additional PCRs but not by Sanger sequencing and finally 20 samples that were detected by only one of the additional PCR methods. A key question was whether Sanger sequencing failed to detect fluoroquinolone resistance in any samples; overall, we observed that Sanger sequencing failed to detect fluoroquinolone resistance in up to 3.8% (16/423) of samples.

Conclusions: The presence of mixed susceptibility infections may have important implications for clinical patient management and stresses the need for appropriate detection of resistance and selection of antimicrobials to ensure appropriate treatment of M. genitalium infections.
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http://dx.doi.org/10.1093/jac/dkaa542DOI Listing
March 2021

High prevalence of pulmonary tuberculosis among female sex workers, men who have sex with men, and transgender women in Papua New Guinea.

Trop Med Health 2021 Jan 13;49(1). Epub 2021 Jan 13.

Papua New Guinea Institute of Medical Research, Goroka, 441 EHP, Papua New Guinea.

Background: Papua New Guinea (PNG) has a tuberculosis (TB) case notification rate of 333 cases per 100,000 population in 2016 and is one of the 14 countries classified by the World Health Organization (WHO) as "high-burden" for TB, multi-drug-resistant TB (MDR-TB), and TB/HIV. HIV epidemic is mixed with a higher prevalence among key populations, female sex workers (FSW), men who have sex with men (MSM), and transgender women (TGW).

Methods: We conducted a cross-sectional HIV biobehavioral survey (BBS) using respondent-driven sampling method among FSW, MSM, and TGW in Port Moresby, Lae, and Mt. Hagen (2016-2017). As part of the study, participants were screened for the four symptoms suggestive of TB infection using the WHO TB screening algorithm. Sputum and venous whole blood samples were collected and tested for pulmonary TB and HIV infection, respectively. Pulmonary TB testing was performed using GeneXpert®MTB/RIF molecular point-of-care test, and HIV testing was done following the PNG national HIV testing algorithm. All data discussed are weighted unless otherwise mentioned.

Results: Among FSW, 72.6%, 52.0%, and 52.9% in Port Moresby, Lae, and Mt. Hagen, respectively, experienced at least one symptom suggestive of TB infection. Among MSM and TGW, 69% and 52.6% in Port Moresby and Lae, respectively, experienced at least one symptom suggestive of TB infection. Based on GeneXpert®MTB/RIF results, the estimated TB prevalence rate among FSW was 1200, 700, and 200 per 100,000 in Port Moresby, Lae, and Mt. Hagen, respectively. Among MSM and TGW, the estimated TB prevalence rate was 1000 and 1200 per 100,000 in Port Moresby and Lae, respectively. Co-prevalence of TB/HIV among FSW was 0.1% in Port Moresby and 0.2% in Lae. There were no co-prevalent cases among FSW in Mt. Hagen or among MSM and TGW in Port Moresby and Lae.

Conclusions: Key populations have a higher estimated rate of pulmonary TB than the national rate of pulmonary and extra-pulmonary TB combined. This showed that screening key populations for TB should be integrated into HIV programs regardless of HIV status in PNG's national TB response.
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http://dx.doi.org/10.1186/s41182-020-00293-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7805114PMC
January 2021

Evaluation of Commercially Available Viral Transport Medium (VTM) for SARS-CoV-2 Inactivation and Use in Point-of-Care (POC) Testing.

Viruses 2020 10 23;12(11). Epub 2020 Oct 23.

Kirby Institute for Infection and Immunity in Society, UNSW Medicine, UNSW Sydney, Kensington, NSW 2052, Australia.

Critical to facilitating SARS-CoV-2 point-of-care (POC) testing is assurance that viruses present in specimens are inactivated onsite prior to processing. Here, we conducted experiments to determine the virucidal activity of commercially available Viral Transport Mediums (VTMs) to inactivate SARS-CoV-2. Independent testing methods for viral inactivation testing were applied, including a previously described World Health Organization (WHO) protocol, in addition to a buffer exchange method where the virus is physically separated from the VTM post exposure. The latter method enables sensitive detection of viral viability at higher viral titre when incubated with VTM. We demonstrate that VTM formulations, Primestore Molecular Transport Medium (MTM) and COPAN eNAT™ completely inactivate high-titre SARS-CoV-2 virus (>1 × 10 copies/mL) and are compatible with POC processing. Furthermore, full viral inactivation was rapidly achieved in as little as 2 min of VTM exposure. We conclude that adding certain VTM formulations as a first step post specimen collection will render SARS-CoV-2 non-infectious for transport, or for further in-field POC molecular testing using rapid turnaround GeneXpert platforms or equivalent.
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http://dx.doi.org/10.3390/v12111208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7690900PMC
October 2020

Evaluation of the SpeeDx ResistancePlus® GC and SpeeDx GC 23S 2611 (beta) molecular assays for prediction of antimicrobial resistance/susceptibility to ciprofloxacin and azithromycin in Neisseria gonorrhoeae.

J Antimicrob Chemother 2021 01;76(1):84-90

WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Sexually Transmitted Infections, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.

Background: Accurate molecular assays for prediction of antimicrobial resistance (AMR)/susceptibility in Neisseria gonorrhoeae (Ng) can offer individualized treatment of gonorrhoea and enhanced AMR surveillance.

Objectives: We evaluated the new ResistancePlus® GC assay and the GC 23S 2611 (beta) assay (SpeeDx), for prediction of resistance/susceptibility to ciprofloxacin and azithromycin, respectively.

Methods: Nine hundred and sixty-seven whole-genome-sequenced Ng isolates from 20 European countries, 143 Ng-positive (37 with paired Ng isolates) and 167 Ng-negative clinical Aptima Combo 2 (AC2) samples, and 143 non-gonococcal Neisseria isolates and closely related species were examined with both SpeeDx assays.

Results: The sensitivity and specificity of the ResistancePlus® GC assay to detect Ng in AC2 samples were 98.6% and 100%, respectively. ResistancePlus® GC showed 100% sensitivity and specificity for GyrA S91 WT/S91F detection and 99.8% sensitivity and specificity in predicting phenotypic ciprofloxacin resistance. The sensitivity and specificity of the GC 23S 2611 (beta) assay for Ng detection in AC2 samples were 95.8% and 100%, respectively. GC 23S 2611 (beta) showed 100% sensitivity and 99.9% specificity for 23S rRNA C2611 WT/C2611T detection and 64.3% sensitivity and 99.9% specificity for predicting phenotypic azithromycin resistance. Cross-reactions with non-gonococcal Neisseria species were observed with both assays, but the analysis software solved most cross-reactions.

Conclusions: The new SpeeDx ResistancePlus® GC assay performed well in the detection of Ng and AMR determinants, especially in urogenital samples. The GC 23S 2611 (beta) assay performed relatively well, but its sensitivity, especially for predicting phenotypic azithromycin resistance, was suboptimal and further optimizations are required, including detection of additional macrolide resistance determinant(s).
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http://dx.doi.org/10.1093/jac/dkaa381DOI Listing
January 2021

Contamination of SARS-CoV-2 RT-PCR probes at the oligonucleotide manufacturer.

Pathology 2020 12 19;52(7):814-816. Epub 2020 Aug 19.

The University of Queensland Centre for Clinical Research, The University of Queensland, Brisbane, Qld, Australia; Pathology Queensland Central Laboratory, Brisbane, Qld, Australia.

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http://dx.doi.org/10.1016/j.pathol.2020.08.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7437487PMC
December 2020

Developing target product profiles for Neisseria gonorrhoeae diagnostics in the context of antimicrobial resistance: An expert consensus.

PLoS One 2020 1;15(9):e0237424. Epub 2020 Sep 1.

World Health Organization (WHO), Geneva, Switzerland.

Background: There is a need for a rapid diagnostic point of care test to detect Neisseria gonorrhoeae (NG) infection to prevent incorrect, lack or excess of treatment resulting from current syndromic management in low-resource settings. An assay to identify NG antimicrobial resistance (AMR) is also highly desirable to facilitate antibiotic stewardship. Here we describe the development of two target product profiles (TPPs): one for a test for etiological diagnosis of NG and Chlamydia trachomatis (CT) (TPP1) and one for the detection of NG AMR/susceptibility (TPP2).

Methods: Draft TPPs were initially developed based on a landscape analysis of existing diagnostics and expert input. TPPs were refined via an online Delphi survey with two rounds of input from 68 respondents. TPP characteristics on which <75% of non-industry respondents agreed were further discussed and revised by an expert working group.

Results: The need for a test to identify NG in patients with urethral or vaginal discharge was identified as a minimal requirement of TPP1, with a test that can diagnose NG in asymptomatic patients as the optimal requirement. A sensitivity of 80% was considered acceptable, either in context of syndromic management or screening high-risk populations. For TPP2, the agreed minimal requirement was for a test to be used at level 2 healthcare facilities and above, with an optimal requirement of level 1 or above. A lateral flow format was preferred for TPP1, while it was considered likely that TPP2 would require a molecular format. A total of 31 test characteristics were included in TPP1 and 27 in TPP2.

Conclusions: Following the working group revisions, TPPs were posted online for public feedback for two months, and are now finalized. The final TPPs are currently guiding the development of new diagnostics that meet the defined characteristics to reach the market within two years.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0237424PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7462286PMC
October 2020

Second- and third-generation commercial Neisseria gonorrhoeae screening assays and the ongoing issues of false-positive results and confirmatory testing.

Eur J Clin Microbiol Infect Dis 2021 Jan 7;40(1):67-75. Epub 2020 Aug 7.

Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia.

Supplementary nucleic acid amplification tests for Neisseria gonorrhoeae (NG) are widely used to circumvent specificity problems often associated with extragenital sites. This study was prompted by our observations and concerns from local sexual health physicians over increased discrepancies between Roche cobas 4800 CT/NG (c4800) and our in-house supplementary NG-PCR (NG-duplex) for oropharyngeal samples, when compared with Abbott RealTime CT/NG (m2000) performed prior. Here, we investigated these differences. Three banks of NG-positive samples were used. Bank 1 (n = 344) were screened using m2000. Banks 2 (n = 344) and 3 (n = 400) were screened using c4800. Remnant nucleic acids from all banks were tested using NG-duplex as part of routine testing. Bank 2 samples were further tested using m2000, some selectively tested using Cepheid Xpert CT/NG. Bank 3 samples were further tested using cobas CT/NG (cobas 6800 system). Confirmatory rates were significantly (p < 0.0001) higher for m2000 compared with c4800, with oropharyngeal samples the key difference. However, we also showed that our NG-duplex failed to confirm some true-positive NG samples. Using an expanded gold standard, confirmatory rates for m2000 and c4800 exceeded 90% for all anatomical sites with the exception of c4800 for oropharyngeal specimens at 78%. The observed discrepancies were due to a combination of c4800 producing false-positive results for oropharyngeal samples as well as sensitivity issues related to the NG-duplex assay. The data highlight the ongoing need for NG supplemental nucleic acid testing for oropharyngeal samples but also emphasise the need for careful selection of supplementary methods.
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http://dx.doi.org/10.1007/s10096-020-04004-5DOI Listing
January 2021

Young Aboriginal people's sexual health risk reduction strategies: a qualitative study in remote Australia.

Sex Health 2020 08;17(4):303-310

Kirby Institute for Infection and Immunity in Society, UNSW Sydney, Level 6, Wallace Wurth Building, UNSW Sydney, Sydney, NSW 2052, Australia; and Burnet Institute, Melbourne, Vic. 3004, Australia.

Background Surveillance data indicate that Aboriginal and Torres Strait Islander young people are more likely than their non-Indigenous counterparts to experience sexually transmissible infections (STIs) and teenage pregnancy. Despite increasing emphasis on the need for strengths-based approaches to Aboriginal sexual health, limited published data document how young Aboriginal people reduce sexual health risks encountered in their everyday lives.

Methods: In-depth interviews with 35 young Aboriginal women and men aged 16-21 years in two remote Australian settings were conducted; inductive thematic analysis examining sexual health risk reduction practices was also conducted.

Results: Participants reported individual and collective STI and pregnancy risk reduction strategies. Individual practices included accessing and carrying condoms; having a regular casual sexual partner; being in a long-term trusting relationship; using long-acting reversible contraception; having fewer sexual partners; abstaining from sex; accessing STI testing. More collective strategies included: refusing sex without a condom; accompanied health clinic visits with a trusted individual; encouraging friends to use condoms and go for STI testing; providing friends with condoms.

Conclusion: Findings broaden understanding of young Aboriginal people's sexual health risk reduction strategies in remote Aboriginal communities. Findings signal the need for multisectoral STI prevention and sexual health programs driven by young people's existing harm minimisation strategies and cultural models of collective support. Specific strategies to enhance young people's sexual health include: peer condom distribution; accompanied health service visits; peer-led health promotion; continued community-based condom distribution; enhanced access to a fuller range of available contraception in primary care settings; engaging health service-experienced young people as 'youth health workers'.
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http://dx.doi.org/10.1071/SH19204DOI Listing
August 2020

Peer-delivered point-of-care testing for Chlamydia trachomatis and Neisseria gonorrhoeae within an urban community setting: a cross-sectional analysis.

Sex Health 2020 08;17(4):359-367

School of Public Health, The University of Queensland, Herston Campus, 288 Herston Road, Herston, Qld 4006, Australia; and Corresponding author. Email:

Background The advent of fully automated nucleic acid amplification test (NAAT) technology brings new public health opportunities to provide Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) point-of-care testing (POCT) in non-traditional settings.

Methods: This pilot study evaluated the integration of the CT/NG Xpert diagnostic assay into an urban peer-led community setting providing HIV and syphilis POCT. A comprehensive protocol of testing, result notification, referral and follow up, managed by peer test facilitators, was undertaken.

Results: Over 67 weeks, there were 4523 occasions of CT/NG testing using urine, oropharyngeal and anorectal samples with 25.7% (803) of the 3123 unique participants returning for repeat testing. The prevalence of CT and NG was 9.5% and 5.4% respectively. Where CT and or NG infection was detected, 98.4% (604/614) of participants were successfully notified of detected infection and referred for treatment. Evaluation Survey responses (11.4%, 516/4523) indicated a substantial proportion of respondents (27.1%, 140/516) 'would not have tested anywhere else'. Of note, 17.8% (92/516) of participants reported no previous CT/NG test and an additional 17.8% (92/516) reported testing more than 12 months ago. A total of 95.9% (495/516) of participants 'Strongly agreed' or 'Agreed' to being satisfied with the service.

Conclusion: The project successfully demonstrated an acceptable and feasible model for a peer-delivered community-led service to provide targeted molecular CT/NG POCT. This model offers capacity to move beyond the traditional pathology and STI testing services and establish community-led models that build trust and increase testing rates for key populations of epidemiological significance.
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http://dx.doi.org/10.1071/SH19233DOI Listing
August 2020

Evaluation of the SpeeDx MG (Beta) PCR Assay for Rapid Detection of Mycoplasma genitalium Quinolone Resistance-Associated Mutations.

J Clin Microbiol 2020 09 22;58(10). Epub 2020 Sep 22.

The University of Queensland Centre for Clinical Research (UQ-CCR), Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia

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http://dx.doi.org/10.1128/JCM.01432-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7512155PMC
September 2020

, and among women with genitourinary infection and pregnancy-related complications in Tehran: A cross-sectional study.

Int J STD AIDS 2020 07 10;31(8):773-780. Epub 2020 Jun 10.

Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia.

The present study investigates the prevalence of (CT), (NG), and (TV) among women with genitourinary infection and pregnancy-related complications in Tehran. It also evaluates the demographic information, symptoms, and sequelae. Endocervical samples were obtained over a period of eight months from 360 women including 180 symptomatic patients and 180 patients with pregnancy-related complications and infertility. CT, NG, and TV were detected in 10.8%, 6.9%, and 8.3% of all patients, respectively. The prevalence of CT, NG, and TV among women in the symptomatic group was 11.1%, 7.2%, and 13.3%, respectively, and among women with pregnancy-related complications and infertility was 10.6%, 6.7%, and 3.3%, respectively. Associations between chlamydia and ectopic pregnancy (=0.001), and infertility (<0.001) were observed. Abortion (=0.008), infertility (=0.005), and ectopic pregnancy (<0.001) were associated with gonorrhea. Abnormal vaginal discharge (=0.02) and vulvar itching (=0.02) were associated with trichomoniasis. Overall, the prevalence rates of CT, NG, and TV were high in these patient groups. These high prevalences suggest that screening programs are required to reduce the burden of these sexually transmitted infections and their effects on genitourinary symptoms, pregnancy-related complications, and infertility.
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http://dx.doi.org/10.1177/0956462420922462DOI Listing
July 2020

Genotyping of Mycoplasma genitalium Suggests Acquisition of Antimicrobial Resistance in Queensland, Australia.

J Clin Microbiol 2020 08 24;58(9). Epub 2020 Aug 24.

The University of Queensland Centre for Clinical Research, The University of Queensland, Brisbane, Australia.

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http://dx.doi.org/10.1128/JCM.00641-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7448657PMC
August 2020

Young Aboriginal people's engagement with STI testing in the Northern Territory, Australia.

BMC Public Health 2020 Apr 6;20(1):459. Epub 2020 Apr 6.

Kirby Institute for infection and immunity in society, Level 6, Wallace Wurth Building, UNSW Sydney, Sydney, NSW, 2052, Australia.

Background: Australian surveillance data document higher rates of sexually transmissible infections (STIs) among young Aboriginal people (15-29 years) in remote settings than non-Aboriginal young people. Epidemiological data indicate a substantial number of young Aboriginal people do not test for STIs. Rigorous qualitative research can enhance understanding of these findings. This paper documents socio-ecological factors influencing young Aboriginal people's engagement with clinic-based STI testing in two remote settings in the Northern Territory, Australia.

Methods: In-depth interviews with 35 young Aboriginal men and women aged 16-21 years; thematic analysis examining their perceptions and personal experiences of access to clinic-based STI testing.

Results: Findings reveal individual, social and health service level influences on willingness to undertake clinic-based STI testing. Individual level barriers included limited knowledge about asymptomatic STIs, attitudinal barriers against testing for symptomatic STIs, and lack of skills to communicate about STIs with health service staff. Social influences both promoted and inhibited STI testing. In setting 1, local social networks enabled intergenerational learning about sexual health and facilitated accompanied visits to health clinics for young women. In setting 2, however, social connectedness inhibited access to STI testing services. Being seen at clinics was perceived to lead to stigmatisation among peers and fear of reputational damage due to STI-related rumours. Modalities of health service provision both enhanced and inhibited STI testing. In setting 1, outreach strategies by male health workers provided young Aboriginal men with opportunities to learn about sexual health, initiate trusting relationships with clinic staff, and gain access to clinics. In setting 2, barriers were created by the location and visibility of the clinic, appointment procedures, waiting rooms and waiting times. Where inhibitive factors at the individual, social and health service levels exist, young Aboriginal people reported more limited access to STI testing.

Conclusions: This is the first socio-ecological analysis of factors influencing young Aboriginal people's willingness to undertake testing for STIs within clinics in Australia. Strategies to improve uptake of STI testing must tackle the overlapping social and health service factors that discourage young people from seeking sexual health support. Much can be learned from young people's lived sexual health experiences and family- and community-based health promotion practices.
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http://dx.doi.org/10.1186/s12889-020-08565-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7137447PMC
April 2020

Lessons learnt from ceftriaxone-resistant gonorrhoea in the UK and Australia.

Lancet Infect Dis 2020 03;20(3):276-278

WHO Collaborating Centre for Sexually Transmitted Infections and Antimicrobial Resistance, New South Wales Health Pathology, Department of Microbiology, The Prince of Wales Hospital, Randwick, NSW, Australia; Faculty of Medicine, School of Medical Sciences, University of New South Wales, NSW, Australia.

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http://dx.doi.org/10.1016/S1473-3099(20)30055-4DOI Listing
March 2020

Point-of-care testing and treatment of sexually transmitted infections to improve birth outcomes in high-burden, low-income settings: Study protocol for a cluster randomized crossover trial (the WANTAIM Trial, Papua New Guinea).

Wellcome Open Res 2019 22;4:53. Epub 2019 Mar 22.

Department of Microbiology, The Royal Women's Hospital Melbourne, Parkville, VIC, 3052, Australia.

, , and bacterial vaginosis have been associated with preterm birth and low birth weight, and are highly prevalent among pregnant women in many low- and middle-income settings. There is conflicting evidence on the potential benefits of screening and treating these infections in pregnancy. Newly available diagnostic technologies make it possible, for the first time, to conduct definitive field trials to fill this knowledge gap. The primary aim of this study is to evaluate whether antenatal point-of-care testing and immediate treatment of these curable sexually transmitted and genital infections (STIs) leads to reduction in preterm birth and low birth weight. : The Women and Newborn Trial of Antenatal Interventions and Management (WANTAIM) is a cluster-randomised crossover trial in Papua New Guinea to compare point-of-care STI testing and immediate treatment with standard antenatal care (which includes the WHO-endorsed STI 'syndromic' management strategy based on clinical features alone without laboratory confirmation). The unit of randomisation is a primary health care facility and its catchment communities. The primary outcome is a composite measure of two events: the proportion of women and their newborns in each trial arm, who experience either preterm birth (delivery <37 completed weeks of gestation as determined by ultrasound) and/or low birth weight (<2500 g measured within 72 hours of birth). The trial will also evaluate neonatal outcomes, as well as the cost-effectiveness, acceptability and health system requirements of this strategy, compared with standard care. WANTAIM is the first randomised trial to evaluate the effectiveness, cost-effectiveness, acceptability and health system requirements of point-of-care STI testing and treatment to improve birth outcomes in high-burden settings. If the intervention is proven to have an impact, the trial will hasten access to these technologies and could improve maternal and neonatal health in high-burden settings worldwide. ISRCTN37134032.
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http://dx.doi.org/10.12688/wellcomeopenres.15173.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6979472PMC
March 2019
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