Achievement of therapeutic antibiotic exposures using Bayesian dosing software in critically unwell children and adults with sepsis

PURPOSE

Early recognition and effective treatment of sepsis improves outcomes in critically ill patients. However, antibiotic exposures are frequently suboptimal in the intensive care unit (ICU) setting. We describe the feasibility of the Bayesian dosing software Individually Designed Optimum Dosing Strategies (ID-ODS™), to reduce time to effective antibiotic exposure in children and adults with sepsis in ICU.

METHODS

A multi-centre prospective, non-randomised interventional trial in three adult ICUs and one paediatric ICU. In a pre-intervention Phase 1, we measured the time to target antibiotic exposure in participants. In Phase 2, antibiotic dosing recommendations were made using ID-ODS™, and time to target antibiotic concentrations were compared to patients in Phase 1 (a pre-post-design).

RESULTS

175 antibiotic courses (Phase 1 = 123, Phase 2 = 52) were analysed from 156 participants. Across all patients, there was no difference in the time to achieve target exposures (8.7 h vs 14.3 h in Phase 1 and Phase 2, respectively, p = 0.45). Sixty-one courses in 54 participants failed to achieve target exposures within 24 h of antibiotic commencement (n = 36 in Phase 1, n = 18 in Phase 2). In these participants, ID-ODS™ was associated with a reduction in time to target antibiotic exposure (96 vs 36.4 h in Phase 1 and Phase 2, respectively, p < 0.01). These patients were less likely to exhibit subtherapeutic antibiotic exposures at 96 h (hazard ratio (HR) 0.02, 95% confidence interval (CI) 0.01-0.05, p < 0.01). There was no difference observed in in-hospital mortality.

CONCLUSIONS

Dosing software may reduce the time to achieve target antibiotic exposures. It should be evaluated further in trials to establish its impact on clinical outcomes.

Comparing Polymerase Chain Reaction Testing of Nasopharyngeal Swab and Lower Respiratory Tract Specimens for the Diagnosis of Pneumocystis jirovecii Pneumonia

Using nasopharyngeal (NP) swab samples instead of lower respiratory tract specimens for polymerase chain reaction (PCR) to diagnose Pneumocystis jirovecii pneumonia (PJP) may be better tolerated and improve diagnostic accessibility. In this 2-year Australian retrospective cohort study of patients with clinically suspected PJP, P jirovecii PCR on NP swab samples had perfect specificity but low sensitivity (0.66).

Determining Pneumocystis jirovecii Colonisation from Infection Using PCR-Based Diagnostics in HIV-Negative Individuals

BACKGROUND

Pneumocystis jirovecii pneumonia is increasingly diagnosed with highly sensitive PCR diagnostics in immunocompromised, HIV-negative individuals. We assessed the performance of our in-house quantitative PCR with the aim to optimise interpretation.

METHODS

Retrospective audit of all positive P. jirovecii qPCRs on induced sputum or BAL fluid at a single centre from 2012 to 2023. Medical and laboratory records were analysed and people with HIV were excluded. Cases were categorised as colonisation, high-probability PCP or uncertain PCP infection against a clinical gold standard incorporating clinico-radiological data. Quantitative PCR assay targeting the 5s gene was utilised throughout the time period.

RESULTS

Of the 82 positive qPCRs, 28 were categorised as high-probability PCP infection, 30 as uncertain PCP and 24 as colonisation. There was a significant difference in qPCR values stratified by clinical category but not respiratory sample type. Current assay performance with a cutoff of 2.5 × 105 copies/mL had a sensitivity of 50% (95% CI, 30.65-69.35%) and specificity of 83.33% (95% CI, 62.62-95.26%). Youden Index calculated at 6.5 × 104 copies/mL had a sensitivity of 75% (56.64-87.32%, 95% CI) and specificity of 66.67% (46.71-82.03%, 95% CI). High and low cutoffs were explored. Significant variables associated with infection were age > 70 years old, the presence of fever, hypoxia or ground glass changes.

CONCLUSIONS

A single qPCR cutoff cannot reliably determine P. jirovecii infection from colonisation. Low and high cutoffs are useful, however, a large "possible infection" cohort will remain where interpretation of clinic-radiological factors remains essential. Standardisation of assays with prospective validation in specific immunocompromised groups will allow greater generalisability and allow large-scale prospective assay validation to be performed.

Evaluation of Illumina® COVIDSeq™ as a tool for Omicron SARS-CoV-2 characterisation

The continued emergence and transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants requires ongoing genetic surveillance to support public health responses. The expansion of reliable next generation sequence (NGS) platforms has enabled the rapid characterisation of the constant emergence of new SARS-CoV-2 variants using nasopharyngeal swab specimens. Several studies have assessed the ability of COVIDSeq to type earlier SARS-CoV-2 strains (pre-Delta) rapidly and successfully, however, there is limited data showing suitability against Omicron variants. In the present study, we evaluated the performance of the Illumina COVIDSeq Assay as a streamlined amplicon-based NGS platform for detection and typing of Omicron variants. Our results demonstrate the high performance of SARS-CoV-2 sequencing using the COVIDSeq approach, with good repeatability, reproducibility and sensitivity for samples approaching CT 31. The COVIDSeq approach was 100% concordant with samples previously characterized by sequencing methods. The quick library preparation process and high throughput kit made it ideal for reflex testing, with a total time required for sequencing and analysis of approximately two days. This study demonstrates the effectiveness and versatility of the amplicon-based NGS characterisation method for SARS-CoV-2, providing a foundation for further research and development of custom-designed amplicon panels targeting different microorganisms.

Genome-based epidemiology and antimicrobial resistance of Neisseria gonorrhoeae in Spain: A prospective multicentre study

BACKGROUND

Whole-genome sequencing (WGS) of Neisseria gonorrhoeae isolates combined with epidemiological and phenotypic data provides better understanding of population dynamics.

AIM

The objective of this study was to investigate the molecular epidemiology of N. gonorrhoeae isolates from three centres in Spain and determine associations of antimicrobial resistance.

METHODS

Genetic characterization was performed in 170 N. gonorrhoeae isolates. WGS was carried out with the HiSeq platform (Illumina). Genome assemblies were submitted to the PubMLST Neisseria database website to determine NG-MAST, MLST and NG-STAR. Antimicrobial resistance genes and point mutations were identified with PubMLST. Phylogenomic comparison was based on whole-genome single nucleotide polymorphism analysis.

RESULTS

Twenty-six MLST, 49 NG-MAST and 41 NG-STAR sequence types were detected, the most prevalent being MLST-ST9363 (27.1%), NG-MAST ST569 (12.4%) and NG-STAR ST193 (14.7%). Phylogenetic analysis identified 13 clusters comprising 69% of the isolates, with two of note: one involved cefixime-resistant isolates from Barcelona presenting a mosaic penA X and belonging to MLST-ST7363 and the other involved azithromycin-resistant isolates from Mallorca that possessed the C2611T mutation in the four 23S rRNA alleles belonging to MLST-ST1901.

CONCLUSION

The population of N. gonorrhoeae is quite heterogeneous in Spain. Our results agree with previous data published in Europe, albeit with some differences in distribution between regions. This study describes the circulation of two gonococcal populations with a specific resistance profile and sequence type in a specific geographic area. WGS is an effective tool for epidemiological surveillance of gonococcal infection and detection of resistance genes.

The changing epidemiology of Neisseria gonorrhoeae genogroups and antimicrobial resistance in Queensland, Australia, 2010-15: a case series analysis of unique Neisseria gonorrhoeae isolates

BACKGROUND

Neisseria gonorrhoeae (NG) can lead to serious reproductive and sexual health outcomes, and the annual number of NG notifications in Australia increased steadily from 10329 in 2010 to 29549 by 2020. Australian populations most affected are urban men who have sex with men and First Nations peoples living in remote areas, and a resurgence in urban heterosexuals has been observed since 2012.

METHODS

A case series analysis of Queensland NG isolates (2010-15) exploring temporal trends and antimicrobial resistance by demographic and geographic distribution and genotype was performed. Proportions describe age, sex, strain, genogroup (NG multi-antigen sequence typing), region, swab site, antimicrobial sensitivity and isolate rates per 100000 population. Dominant genogroups were identified.

RESULTS

Among 3953 isolates, the median age was 25years (IQR 20-34years) and most (n =2871/3915, 73%) were men. Brisbane city (68.8) and Far North Queensland (54.1) excluding Cairns showed the highest rates. Forty-six genogroups were documented, seven (G2992, G6876, G1415, G4186, G5, G1407 and G6937) comprised half of all isolates. The predominant male genogroup was G2992 (16%), and G6876 (20%) for females; G5 was predominantly male from 2010 to 2011, but equal in both sexes from 2012 to 2015.

CONCLUSION

Considerable temporal, geographical and demographical diversity was observed in Queensland NG isolates, which has public health implications. Certain genogroups are more transient than others, and evidence suggests bridging from male-dominant networks to heterosexual networks. Molecular surveillance can enhance tracking the epidemiology and movement of NG in Australia, highlighting the necessity of genotyping to expose potentially prevalent strains circulating in undetected or underrepresented networks by current screening methods.

Mycoplasma hominis and Ureaplasma urealyticum infections in the immediate post-lung transplant period: A case series and literature review

Mycoplasma hominis and Ureaplasma species infections in the post-transplant setting are believed to be donor-derived and can be associated with poor outcomes. Difficulty in culturing and identifying these organisms is a significant barrier to diagnosis and early intervention. Tetracyclines, macrolides and fluoroquinolones are the mainstay treatments to cure these infections; however, there are increasing reports of antibiotic resistance. In this case series, we report our single-centre experience with M. hominis and U. urealyticum infection after lung transplantation (9 recipients, all men, mean age 56 years). Delayed diagnosis was common. Young donor age (mean age 23 yrs) and high-risk donor social history (67%) were repeatedly noted in these cases, and all infections were associated with significant morbidity (anastomosis and sternal wound infection, empyema, mediastinitis, pericarditis). Two patients died; with one directly related to Ureaplasma urealyticum infection. In conclusion post lung transplant M. hominis, and U. urealyticum infections are challenging and carry high morbidity. More prospective studies are required to assess the true prevalence, full spectrum of complications and utility of molecular diagnostics to aid early diagnosis and identify antibiotic susceptibility of Mycoplasma and Ureaplasma infections in the post-lung transplant setting.

Limited evidence of patient-to-patient transmission of Staphylococcus aureus strains between children with cystic fibrosis, Queensland, Australia

OBJECTIVES

Here we used whole genome sequencing (WGS) to understand strain diversity and potential for patient-to-patient transmission of Staphylococcus aureus among children with cystic fibrosis (CF) in Queensland, Australia.

METHODS

S. aureus isolates (n = 401) collected between January 2018 and April 2019 from 184 patients with CF (n = 318 isolates) and 76 patients without CF (n = 83 isolates) were subjected to WGS and subsequent multilocus sequence typing (MLST), and a phylogeny was constructed from core genome single nucleotide polymorphism (SNP) analysis. The subsequent data was compared with available patient information.

RESULTS

WGS revealed that patients with CF were essentially colonised by the same genotypes as those seen in patients without CF. Sequence types (ST) for our patients with CF were predominantly ST5 (20.1%), ST30 (7.3%), ST15 (6.3%) and ST8 (5.3%). Two Australian clones, ST93 and ST239, typically seen in skin infections and health-care settings, respectively, were notably absent from our patients with CF. Based on a SNP distance threshold of 14 SNPs, 20 cluster types involving 50/260 patients were evident; of these, 6 clusters contained only patients found to be siblings or otherwise living in the same household. Epidemiological relationships could not be determined for a remaining 14 cluster types involving 38 patients, comprising 2-7 (median 2) patients each. Multiple S. aureus genotypes were observed in 19/73 CF patients who provided more than one sample.

CONCLUSION

These results show that WGS is a useful tool for surveillance of S. aureus strains in children with CF and that the strains in our CF cohort were largely consistent with those circulating in patients without CF. Overall, this confirms previous findings and indicates that S. aureus acquisition in children with CF is similar to that of other patient groups, with limited evidence of potential patient-to-patient transmission within this patient group.

Near-infrared spectroscopy as a feasible method for the differentiation of Neisseria gonorrhoeae from Neisseria commensals and antimicrobial resistant from susceptible gonococcal strains

Rapid and cost-effective diagnosis of Neisseria gonorrhoeae (NG) are important measures for the control and management of gonococcal infection. Current diagnostic tools such as nucleic acid amplification tests and bacterial culture are not feasible in many resource-poor settings, and so syndromic patient management is commonplace. Alternative cost-effective diagnostic tools are therefore needed. Here, we sought to explore the utility and feasibility of Near Infrared Spectroscopy (NIRS) to (1) identify and differentiate NG from Neisseria commensals and (2) to differentiate fully susceptible NG from resistant NG. NIRS correctly classified NG from Neisseria commensals (R²= 0.89; SECV 0.164) and to a lesser capacity, susceptible NG from resistant (R² = 0.60; SECV 0.32). To the best our knowledge, this is the first proof of concept study in the field. Further evaluations are now warranted to enhance capacity and accuracy of this diagnostic approach.

SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern

The continuous transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has required that diagnostic capabilities be constantly monitored and updated as new variants emerge and prior variants disappear. Although whole genome sequencing provides full characterisation of SARS-CoV-2 directly from patient samples, this has limited throughput and requires sufficient resources. To enhance screening for circulating variants, we designed a rapid in-house RT-PCR assay to target a spike mutation (D950N) in Delta variants, which is not detected in the remaining variants of concern (VOCs). Assay sensitivity for detecting Delta variants was 93% and specificity was 100% using a sequenced sample bank of several lineages. As the D950N mutation is prevalent in >95% of the global Delta variant sequences deposited in GISAID, this assay has the potential to provide rapid results to determine if the samples are presumptively Delta variants and can support clinicians in timely clinical decision-making for effective treatments and surveillance.

Combination therapy for Mycoplasma genitalium, and new insights into the utility of parC mutant detection to improve cure

BACKGROUND

Mycoplasma genitalium (MG) infection is challenging to cure due to rising antimicrobial resistance and limited treatment options.

METHODS

This was a prospective evaluation of the efficacy and tolerability of resistance-guided combination antimicrobial therapy for MG-treatment at Melbourne Sexual Health Centre (August 2019-December 2020). All patients received 7-days doxycycline prior to combination therapy based on the macrolide-resistant profile. Macrolide-susceptible infections received combination doxycycline+azithromycin (1g day-1, 500mg days-2-4) and macrolide-resistant infections combination doxycycline+moxifloxacin (400mg daily 7-days). Adherence and adverse effects were recorded at test-of-cure, recommended 14-28-days after antimicrobial completion. Sequencing was performed to determine the prevalence of single nucleotide polymorphisms (SNPs) in the parC gene and their association with moxifloxacin-treatment outcomes in macrolide-resistant infections.

RESULTS

Of 100 patients with macrolide-susceptible MG treated with doxycycline+azithromycin, 93 were cured (93.0%; 95%CI:86.1%-97.1%). Of 247 patients with macrolide-resistant MG receiving doxycycline+moxifloxacin, 210 were cured (85.0%; 95%CI:80.0%-89.2%). parC sequencing was available for 164 (66%) macrolide-resistant infections; 29% had SNPs at parC S83 or D87 (23% S83I). The absence of SNPs at parC S83/D87 was associated with 98.3% cure (95%CI:93.9-99.8%) following doxycycline+moxifloxacin. The presence of the parC S83I-SNP was associated with failure in 62.5% (95%CI:45.8-77.3%). Side-effects were common (40-46%) and predominantly mild and gastrointestinal.

CONCLUSION

Combination doxycycline+azithromycin achieved high cure for macrolide-susceptible infections. However, in the context of a high prevalence of the parC S83I mutation (23%) in macrolide-resistant infections, doxycycline+moxifloxacin cured only 85%Infections that were wildtype for S83/D87 experienced high cure following doxycycline+moxifloxacin, supporting the use of a parC-resistance/susceptibility testing strategy in clinical care.

The impact of COVID-19 epidemic phase and changes in mean viral loads: implications for SARS-CoV-2 testing strategies

The sensitivity of SARS-CoV-2 diagnostic tests is inherently linked to viral load. We explored whether average viral loads changed at a population level in Queensland, Australia during the early phase of the pandemic. RT-PCR threshold cycle (C_T) values, a crude marker for viral load, were compared for samples collected in February/March-2020 to those collected in April/May-2020, noting that the major public health interventions began in late-March 2020. Positive detections peaked mid-March, which coincided with the highest detection numbers and lowest C_T values. However, this changed from April where the later C_T samples (C_T > 30) predominated. Overall, in February/March 29% (267/922) of samples had C_T values >30 cycles compared to 88% (559/636) in April/May. Our study shows that SARS-CoV-2 viral loads in patients may vary at a population level over time. This needs considering when assessing suitability of diagnostic methods, particularly when methods in question are known to have reduced sensitivity.

Scaling up sexually transmissible infections point-of-care testing in remote Aboriginal and Torres Strait Islander communities: healthcare workers' perceptions of the barriers and facilitators

Background

Sexually transmissible infections (STIs), such as gonorrhoea and chlamydia, are highly prevalent, particularly in remote Aboriginal and Torres Strait Islander communities in Australia. In these settings, due to distance to centralised laboratories, the return of laboratory test results can take a week or longer, and many young people do not receive treatment, or it is considerably delayed. Point-of-care testing (POCT) provides an opportunity for same day diagnosis and treatment. Molecular POC testing for STIs was available at 31 regional or remote primary health care clinic sites through the Test-Treat-And-GO (TANGO2) program. This qualitative study sought to identify barriers and facilitators to further scaling up STI POCT in remote Aboriginal communities within Australia.

Methods

A total of 15 healthcare workers (including nurses and Aboriginal health practitioners) and five managers (including clinic coordinators and practice managers) were recruited from remote health services involved in the TTANGO2 program to participate in semi-structured in-depth interviews. Health services’ clinics were purposively selected to include those with high or low STI POCT uptake. Personnel participants were selected via a hybrid approach including nomination by clinic managers and purposive sampling to include those in roles relevant to STI testing and treatment and those who had received TTANGO2 training for POCT technology. Milat’s scaling up guide informed the coding framework and analysis.

Results

Acceptability of STI POCT technology among healthcare workers and managers was predominantly influenced by self-efficacy and perceived effectiveness of POCT technology as well as perceptions of additional workload burden associated with POCT. Barriers to integration of STI POCT included retention of trained staff to conduct POCT. Patient reach (including strategies for patient engagement) was broadly considered an enabler for STI testing scale up using POCT technology.

Conclusions

Remote healthcare clinics should be supported by both program and clinic management throughout scaling up efforts to ensure broad acceptability of STI POCT as well as addressing local health systems’ issues and identifying and enhancing opportunities for patient engagement.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43058-021-00232-8.

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

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 (SO₂) 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.

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

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).

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

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

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

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 log₁₀ parasites/mL with a limit of detection of 2.045 log₁₀ 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_q) units [0.137 log₁₀ parasites/mL] over 21 replicates) and inter-assay (SD = 0.604 C_q units [0.182 log₁₀ 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 log₁₀ 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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12936-021-03717-y.

A comparison of ThinPrep against four non-volatile transport media for HPV testing at or near the point of care

The Xpert HPV Test is used at point of care for cervical screening in a number of low and middle income countries (LMIC). It is validated for use with ThinPrep-PreservCyt transport medium which has a high methanol content and is therefore classified as a dangerous good for shipping, making cost, transportation and use challenging within LMIC. We compared the performance of ThinPrep against four non-volatile commercially available media for human papillomavirus (HPV) point of care testing. Ten-fold serial dilutions were prepared using three HPV cell lines each positive for 16, 18 or 31 and with each suspended in five different media types. The media types consisted of Phosphate Buffered Saline (ThermoFisher Scientific, USA), Sigma Virocult (Medical Wire and Equipment, UK), MSwab (Copan, Italy) Xpert Transport Media (Cepheid, USA) and ThinPrep-PreservCyt (Hologic, USA). A total of 105 Xpert HPV tests were conducted in a laboratory setting, with seven 10-fold dilutions of each of the three HPV genotypes tested in all five media types. The lowest HPV 10-fold dilution detected for any media, or cell line was the fifth dilution. MSwab was the only medium to detect HPV to the fifth dilution across all three cell types. MSwab transport media may be a suitable alternative to ThinPrep for Xpert HPV point of care testing. A field based, head to head comparison of both media types using the Xpert HPV assay is warranted to confirm these laboratory based findings.

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

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 × 107 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.

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

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.

Evaluation of the ResistancePlus GC (beta) assay: a commercial diagnostic test for the direct detection of ciprofloxacin susceptibility or resistance in Neisseria gonorrhoeae

OBJECTIVES

To evaluate the performance of the ResistancePlus GC (beta) assay for the simultaneous detection of Neisseria gonorrhoeae and gyrA S91 markers of resistance (S91F) and susceptibility (WT) to ciprofloxacin, from both clinical specimens and isolates.

METHODS

Performance was assessed on several sample banks, including N. gonorrhoeae isolates (n = 822), non-gonococcal isolates (n = 110), N. gonorrhoeae-positive clinical specimens (n = 402) and N. gonorrhoeae-negative specimens (n = 290). Results were compared with previous testing data, including S91 genotyping and phenotypic resistance profiles.

RESULTS

Overall, the assay demonstrated 100% sensitivity for N. gonorrhoeae detection in clinical isolates. For gyrA S91 mutation detection in clinical isolates, the assay showed 100% sensitivity/specificity compared with the genotype, and >99%/>97% sensitivity/specificity when compared with phenotype. For positive clinical specimens, the assay demonstrated >96% sensitivity for N. gonorrhoeae detection and 100% sensitivity/specificity for gyrA S91 mutation detection. The assay demonstrated >99% specificity for N. gonorrhoeae detection against non-gonococcal isolates and 100% specificity for negative clinical specimens.

CONCLUSIONS

The ResistancePlus GC (beta) assay is suitable for the detection of N. gonorrhoeae and gyrA markers associated with resistance/susceptibility to ciprofloxacin directly in clinical samples. This assay could be implemented for the individualized treatment of gonorrhoea infections as well as to enhance current antimicrobial resistance surveillance methods.

Genetic relatedness of ceftriaxone-resistant and high-level azithromycin resistant Neisseria gonorrhoeae cases, United Kingdom and Australia, February to April 2018

Between February and April 2018, three ceftriaxone-resistant and high-level azithromycin-resistant Neisseria gonorrhoeae cases were identified; one in the United Kingdom and two in Australia. Whole genome sequencing was used to show that the isolates from these cases belong to a single gonococcal clone, which we name the A2543 clone.

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

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

Molecular point-of-care testing for chlamydia and gonorrhoea in Indigenous Australians attending remote primary health services (TTANGO): a cluster-randomised, controlled, crossover trial

BACKGROUND

Timely diagnosis and treatment of sexually transmissible infections will prevent morbidity and onward transmission. We aimed to assess the efficacy of a point-of-care molecular test for Chlamydia trachomatis and Neisseria gonorrhoeae infections at the cluster level to improve infection management among Indigenous Australian communities with high prevalence of sexually transmissible infections.

METHODS

In this cluster-randomised crossover study, we recruited primary health services in Western Australia, Far North Queensland, and South Australia that provide care to Indigenous people in regional or remote locations. The services were eligible if they did 150 or more tests for C trachomatis or N gonorrhoeae infection per year among individuals aged 16-29 years, and if C trachomatis or N gonorrhoeae positivity was 10% or higher. Services were randomly assigned (1:1) by use of a random-number generator, stratified by geographical region, to either standard care conditions with routine laboratory-based sexually transmissible infection testing for 12 months followed by 12 months of intervention with molecular point-of-care testing, or the reverse sequence. The primary outcome was the proportion of people (aged 16-29 years) found to have C trachomatis or N gonorrhoeae who had a positive result at retesting 3 weeks to 3 months after treatment, and a secondary outcome was treatment within 7 days, both in those aged 16-29 years and at the cluster level. We did these analyses using data from all participants who had a positive result at testing, by point-of-care of laboratory testing (ie, the intention-to-treat population). The trial is registered with Australian and New Zealand Clinical Trials Registry (ACTRN12613000808741).

FINDINGS

Between June 1, 2013, and Feb 29, 2016, 12 health services were enrolled and randomly assigned to standard care followed by intervention (six) and the reverse sequence (six). After randomisation, one health service that was initially assigned to standard care was excluded because it no longer met the inclusion criteria. 455 individuals tested positive for C trachomatis or N gonorrhoeae infection in the intervention group, and 405 tested positive in the standard care group. In the intervention group, 12 (19%) of 63 individuals retested had a positive test result, compared with nine (13%) of 67 with positive retests in the standard care group (relative ratio [RR] 1·42, 95% CI 0·64-3·13; p=0·405), and 347 (76%) were treated within 7 days in the intervention group, compared with 191 (47%) in the standard care group (RR 1·66, 1·41-1·93; p<0·0001).

INTERPRETATION

Retesting rates were too low to draw conclusions on the effect of the intervention on repeat infections. Further research will be needed to determine whether point-of-care tests have an effect on reinfection rates, and the sustainability of using this technology. However, our findings show that time to treatment of C trachomatis or N gonorrhoeae infections in primary care clinics in remote areas in Australia with a high prevalence of sexually transmissible infections could be substantially reduced by the use of molecular point-of-care tests.

FUNDING

The National Health and Medical Research Council, Australia.

Solithromycin versus ceftriaxone plus azithromycin for the treatment of uncomplicated genital gonorrhoea (SOLITAIRE-U): a randomised phase 3 non-inferiority trial

BACKGROUND

Antibiotic-resistant gonorrhoea represents a global public health threat, and new therapies are needed. We aimed to compare the efficacy and safety of solithromycin, a fourth generation macrolide, with ceftriaxone plus azithromycin for the treatment of gonorrhoea.

METHODS

We did an open-label, multicentre, non-inferiority trial of patients aged 15 years or older with uncomplicated untreated genital gonorrhoea at two sites in Australia and one site in the USA. Patients were randomly assigned (1:1) to receive single dose oral solithromycin 1000 mg or intramuscular ceftriaxone 500 mg plus oral azithromycin 1000 mg. Neisseria gonorrhoeae cultures were obtained at baseline and test of cure (day 7 ± 2). The primary outcome was the proportion of patients with eradication of genital N gonorrhoeae based on culture at test of cure, assessed in the microbiological intention-to-treat (mITT) population, which included all randomly assigned patients who received any dose of study drug and had a positive genital culture for N gonorrhoeae at baseline. Non-inferiority of solithromycin was to be concluded if the lower limit of the 95% CI for the between-group differences was greater than -10%. Safety was analysed in all patients who received any dose of study drug. This trial is registered with ClinicalTrials.gov, number NCT02210325.

FINDINGS

Between Sept 3, 2014, and Aug 27, 2015, 262 patients were randomly assigned and 261 received treatment (130 in the solithromycin group and 131 in the ceftriaxone plus azithromycin group). In the mITT population, 99 (80%) of 123 patients in the solithromycin group and 109 (84%) of 129 patients in the ceftriaxone plus azithromycin group had N gonorrhoeae eradication at test of cure (difference -4·0%, 95% CI -13·6 to 5·5), thus solithromycin did not meet the criterion for non-inferiority at the prespecified -10% margin. The frequency of adverse events was higher in the solithromycin group than the ceftriaxone plus azithromycin group (69 [53%] of 130 patients vs 45 [34%] of 131 patients), the most common of which were diarrhoea (31 [24%] of 130 patients vs 20 [15%] of 131 patients), and nausea (27 [21%] of 130 patients vs 15 [11%] of 131 patients).

INTERPRETATION

Solithromycin as a single 1000 mg dose is not a suitable alternative to ceftriaxone plus azithromycin as first-line treatment for gonorrhoea. If insufficient duration of solithromycin exposure at the infection site in a subset of individuals was the reason for treatment failures, this might be adequately addressed with dose adjustment. However, any further trials with longer dosing need to consider the potential risk of gastrointestinal effects and liver enzyme elevations.

FUNDING

Cempra Pharmaceuticals.

A diagnostic evaluation of a molecular assay used for testing and treating anorectal chlamydia and gonorrhoea infections at the point-of-care in Papua New Guinea

OBJECTIVES

Papua New Guinea has among the highest prevalences of sexually transmissible infections (STIs) globally with no services able to accurately test for anorectal Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infections. Here we prospectively evaluated the diagnostic performance of a molecular CT/NG assay used at the point-of-care (POC) with the aim of enhancing anorectal STI screening and same-day treatment.

METHODS

Men who have sex with men, transgender women and female sex workers taking part in Papua New Guinea's first large-scale biobehavioural study were enrolled and asked to provide a self-collected anorectal swab for POC GeneXpert CT/NG testing. Same-day treatment was offered if positive. A convenience sample of 396 unique and randomly selected samples were transported to Australia for comparison using the Cobas 4800 CT/NG test (Roche Molecular Diagnostics, Pleasanton, CA, USA).

RESULTS

A total of 326 samples provided valid results by Cobas whereas 70 samples provided invalid results suggesting inhibition. The positive, negative and overall percentage agreements of GeneXpert CT/NG for the detection of C. trachomatis were 96.7% (95% CI 92.3%-98.9%), 95.5% (95% CI 91.3%-98.0%) and 96.0% (95% CI 93.3%-97.8%), and for N. gonorrhoeae were 93.0% (95% CI 86.1%-97.1%), 100.0% (95% CI 98.3%-100.0%) and 97.8% (95% CI 95.6%-99.1%), respectively.

CONCLUSIONS

The overall rate of agreement between the GeneXpert and Cobas CT/NG assays was high with 96.0% for C. trachomatis and 97.8% for N. gonorrhoeae. Results from this study data suggest that the GeneXpert CT/NG assay is suitable for testing self-collected anorectal specimens at the POC and that same-day treatment was feasible.

Illumina sequencing of clinical samples for virus detection in a public health laboratory

High-throughput sequencing (HTS) provides the opportunity, once a diagnostic result is obtained, to extract additional information from a virus-containing sample. Hence, it offers advantages over established quantitative amplification technology, such as quantitative PCR, particularly in a public health environment. At this early stage of its clinical application, there have been limited studies comparing HTS performance to that of the more established quantitative PCR technology for direct detection of viruses. In this pilot-scale study, we tested HTS with a range of viruses and sample types routinely encountered in a public health virology laboratory. In comparison with quantitative PCR, our HTS method was able to sensitively (92%) detect all viruses in any sample type with the exception of certain tissues. Moreover, sufficient nucleotide sequence information was obtained to enable genotyping of strains detected, thus providing additional useful epidemiological information. While HTS sensitivity may not yet match that of PCR, the added value through enhanced epidemiological data has considerable potential to enable real-time surveillance of circulating strains so as to facilitate rapid and appropriate response to outbreaks and virus zoonotic spillover events.

Cooperative Recognition of Internationally Disseminated Ceftriaxone-Resistant Neisseria gonorrhoeae Strain

Ceftriaxone remains a first-line treatment for patients infected by Neisseria gonorrhoeae in most settings. We investigated the possible spread of a ceftriaxone-resistant FC428 N. gonorrhoeae clone in Japan after recent isolation of similar strains in Denmark (GK124) and Canada (47707). We report 2 instances of the FC428 clone in Australia in heterosexual men traveling from Asia. Our bioinformatic analyses included core single-nucleotide variation phylogeny and in silico molecular typing; phylogenetic analysis showed close genetic relatedness among all 5 isolates. Results showed multilocus sequence type 1903; N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) 233; and harboring of mosaic penA allele encoding alterations A311V and T483S (penA-60.001), associated with ceftriaxone resistance. Our results provide further evidence of international transmission of ceftriaxone-resistant N. gonorrhoeae. We recommend increasing awareness of international spread of this drug-resistant strain, strengthening surveillance to include identifying treatment failures and contacts, and strengthening international sharing of data.

A reliable and easy to transport quality control method for chlamydia and gonorrhoea molecular point of care testing

Quality control (QC) is an essential component of point-of-care testing programs. In the context of a randomised-controlled trial (TTANGO) using GeneXpert (Xpert) Chlamydia trachomatis and Neisseria gonorrhoeae (CT/NG) point-of-care testing in remote areas of Australia, we aimed to develop and utilise a stable positive control material. Bacterial cultures of CT and NG were resuspended together to provide cycle threshold (C_t) values of approximately 25 cycles for both CT and NG when tested on the Xpert CT/NG assay. These positive control suspensions were dried in aliquots, heat inactivated, and then provided to 12 participating health services as research-only QC samples in kit form. At each service, a QC sample was resuspended and tested each month on the Xpert. QC results, including Xpert C_t values, were analysed from each site over 30 months and we calculated costs per QC sample. Overall, at 12 health services there were 89 QC samples tested (average of 8 tests per site per year). Mean C_t values for the 89 controls samples were 25.25 cycles (SD = 1.15) for CT, 24.04 cycles (SD = 1.400) for one NG target and 23.35 cycles (SD = 1.55) for the other NG target. No significant differences in C_t value for CT or NG controls were observed over a trial period of 30 months. Positive QC samples for research use in a trial of a molecular point-of-care assay were inexpensive to produce and stable when stored at 2-8°C. For routine use, additional requirements such as meeting National Association of Testing Authority (NATA) regulations and Therapeutic Goods Administration (TGA) approval will need to be achieved.

Effectiveness of a cough management algorithm at the transitional phase from acute to chronic cough in Australian children aged <15 years: protocol for a randomised controlled trial

INTRODUCTION

Acute respiratory infections (ARIs) are leading causes of hospitalisation in Australian children and, if recurrent, are associated with increased risk of chronic pulmonary disorders later in life. Chronic (>4 weeks) cough in children following ARI is associated with decreased quality-of-life scores and increased health and societal economic costs. We will determine whether a validated evidence-based cough algorithm, initiated when chronic cough is first diagnosed after presentation with ARI, improves clinical outcomes in children compared with usual care.

METHODS AND ANALYSIS

A multicentre, parallel group, open-label, randomised controlled trial, nested within a prospective cohort study in Southeast Queensland, Australia, is underway. 750 children aged <15 years will be enrolled and followed weekly for 8 weeks after presenting with an ARI with cough. 214 children from this cohort with persistent cough at day 28 will be randomised to either early initiation of a cough management algorithm or usual care (107 per group). Randomisation is stratified by reason for presentation, site and total cough duration at day 28 (<6 and ≥6 weeks). Demographic details, risk factors, clinical histories, examination findings, cost-of-illness data, an anterior nasal swab and parent and child exhaled carbon monoxide levels (when age appropriate) are collected at enrolment. Weekly contacts will collect cough status and cost-of-illness data. Additional nasal swabs are collected at days 28 and 56. The primary outcome is time-to-cough resolution. Secondary outcomes include direct and indirect costs of illness and the predictors of chronic cough postpresentation.

ETHICS AND DISSEMINATION

The Children's Health Queensland (HREC/15/QRCH/15) and the Queensland University of Technology University (1500000132) Research Ethics Committees have approved the study. The study will inform best-practice management of cough in children.

TRIAL REGISTRATION NUMBER

ACTRN12615000132549.

A novel point-of-care testing strategy for sexually transmitted infections among pregnant women in high-burden settings: results of a feasibility study in Papua New Guinea

Background

Sexually transmitted and genital infections in pregnancy are associated with an increased risk of adverse maternal and neonatal health outcomes. High prevalences of sexually transmitted infections have been identified among antenatal attenders in Papua New Guinea. Papua New Guinea has amongst the highest neonatal mortality rates worldwide, with preterm birth and low birth weight major contributors to neonatal mortality. The overall aim of our study was to determine if a novel point-of-care testing and treatment strategy for the sexually transmitted and genital infections Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Trichomonas vaginalis (TV) and Bacterial vaginosis (BV) in pregnancy is feasible in the high-burden, low-income setting of Papua New Guinea.

Methods

Women attending their first antenatal clinic visit were invited to participate. CT/NG and TV were tested using the GeneXpert platform (Cepheid, USA), and BV tested using BVBlue (Gryphus Diagnostics, USA). Participants received same-day test results and antibiotic treatment as indicated. Routine antenatal care including HIV and syphilis screening were provided.

Results

Point-of-care testing was provided to 125/222 (56 %) of women attending routine antenatal care during the three-month study period. Among the 125 women enrolled, the prevalence of CT was 20.0 %; NG, 11.2 %; TV, 37.6 %; and BV, 17.6 %. Over half (67/125, 53.6 %) of women had one or more of these infections. Most women were asymptomatic (71.6 %; 47/67). Women aged 24 years and under were more likely to have one or more STI compared with older women (odds ratio 2.38; 95 % CI: 1.09, 5.21). Most women with an STI received treatment on the same day (83.6 %; 56/67). HIV prevalence was 1.6 % and active syphilis 4.0 %.

Conclusion

Point-of-care STI testing and treatment using a combination of novel, newly-available assays was feasible during routine antenatal care in this setting. This strategy has not previously been evaluated in any setting and offers the potential to transform STI management in pregnancy and to prevent their associated adverse health outcomes.

A preliminary evaluation of a new GeneXpert (Gx) molecular point-of-care test for the detection of Trichomonas vaginalis

OBJECTIVES

Global concerns regarding the prevalence, asymptomatic nature and burden of disease associated with Trichomonas vaginalis (TV) continue. The lack of a portable molecular point-of-care assay to detect this infectious disease has meant that many remote or low-resource settings still need to rely on delayed results from central laboratories and/or syndromic management as treatment strategies. We evaluated the new GeneXpert (Gx) TV nucleic acid amplification test (NAAT) compared with an in-house laboratory NAAT to determine whether it would be suitable for use at the point of care.

METHODS

In a state-based laboratory and using their in-house NAAT, we selected the first 60 urine samples that were positive and the first 60 that were negative (n=120) in the study period for Gx TV testing in order to reduce collection delays and avoid the freezing of samples.

RESULTS

Positive percentage agreement between the Gx TV and NAAT was 95.0% (95% CI 86.1% to 99.0%), negative percentage agreement was 100.0% (95% CI 93.5% to 100.0%) and overall percentage agreement was 97.4% (95% CI 92.5% to 99.5%). Three discordant results were detected with each being close to the cycle threshold of detection using the in-house NAAT assay.

CONCLUSIONS

Findings suggest the Gx TV assay is easy to use and has suitable overall agreement for sexually transmissible infection (STI) testing at the point of care. It may be used in combination with the Gx CT/NG assay to test for all three STIs simultaneously using this portable and modular-based NAAT platform.

Upper airway viruses and bacteria detection in clinical pneumonia in a population with high nasal colonisation do not relate to clinical signs

Indigenous Australian children have high (up to 90%) rates of nasopharyngeal microbial colonisation and of hospitalisation for pneumonia. In Indigenous children hospitalised with pneumonia in Central Australia, we describe the nasopharyngeal detection of viruses and bacteria and assessed whether their presence related to signs of pneumonia (tachypnoea and/or chest in-drawing) on hospital admission and during subsequent days. Nasopharyngeal swabs (NPS) and data were prospectively collected from 145 children (median age = 23.5 months, interquartile range [IQR] 8.7–50) hospitalised with pneumonia at Alice Springs Hospital, Australia, between April 2001 and July 2002. The cohort was enrolled in a randomised controlled study using zinc and/or vitamin A supplementation. NPS were taken within 24 hours of hospitalisation and kept frozen at-80°C until analysed in 2014. Polymerase chain reaction (PCR) was used to detect Moraxella catarrhalis, Haemophilus influenzae, Streptococcus pneumoniae, Staphylococcus aureus, Chlamydophila pneumoniae, Mycoplasma pneumoniae, and 16 respiratory viruses. Uni- and multi-variate analyses were used to examine the relationships. One or more organisms were present in 137 (94.5%) NPS; 133 (91.7%) detected ≥ 1 bacterium, 34 (37.2%) for ≥ 1 virus and 50 (34.5%) were positive for both viruses and bacteria. C. pneumoniae (n = 3) and M. pneumoniae (n = 2) were rare. In multi-variate analyses, age < 12 months (odds ratio [OR] 6.6 [95% confidence interval {CI} 1.7–25.4]) and fever (OR 4.1 [95% CI 1.7–10.4]) were associated with tachypnoea and chest in-drawing. However the presence of bacteria and/or virus type was not associated with tachypnoea and/or chest in-drawing on admission or during recovery. In children with high nasopharyngeal microbial colonisation rates, the utility of NPS in determining the diagnosis of clinical pneumonia or duration of tachypnoea or in-drawing is likely limited. Larger cohort and case-control studies are required to confirm our findings.

Public health implications of molecular point-of-care testing for chlamydia and gonorrhoea in remote primary care services in Australia: a qualitative study

OBJECTIVES

With accurate molecular tests now available for diagnosis of chlamydia and gonorrhoea (Chlamydia trachomatis (CT)/Neisseria gonorrhoeae (NG)) at the point-of-care (POC), we aimed to explore the public health implications (benefits and barriers) of their integration into remote primary care in Australia.

METHODS

Qualitative interviews were conducted with a purposively selected group of 18 key informants reflecting sexual health, primary care, remote Aboriginal health and laboratory expertise.

RESULTS

Participants believed that POC testing may decrease community prevalence of sexually transmitted infections (STIs), and associated morbidity by reducing the time to treatment and infectious period and expediting partner notification. Also, POC testing could improve acceptability of STI testing, increase testing coverage and result in more targeted prescribing, thereby minimising the risk of antibiotic resistance. Conversely, some felt the immediacy of diagnosis could deter certain young people from being tested. Participants also noted that POC testing may reduce the completeness of communicable disease surveillance data given the current dependence on reporting from pathology laboratories. Others expressed concern about the need to maintain and improve the flow of NG antibiotic sensitivity data, already compromised by the shift to nucleic acid-based testing. This is particularly relevant to remote areas where culture viability is problematic.

CONCLUSIONS

Results indicate a high level of support from clinicians and public health practitioners for wider access to CT/NG POC tests citing potential benefits, including earlier, more accurate treatment decisions and reductions in ongoing transmission. However, the data also highlight the need for new systems to avoid adverse impact on disease surveillance.

TRIAL REGISTRATION NUMBER

Australian and New Zealand Clinical Trials Registry: ACTRN12613000808741.

A field evaluation of a new molecular-based point-of-care test for chlamydia and gonorrhoea in remote Aboriginal health services in Australia

Background Point-of-care (POC) tests could be important public health tools in settings with treatment delays and high rates of sexually transmissible infections (STIs). Use is limited due to suboptimal performance. The performance and ease-of-use of a new molecular-based POC test for simultaneous detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) was assessed, alongside two single-organism immunochromatographic tests (ICT).

METHODS

The evaluation occurred between May 2012 and March 2013 during community STI screens in two remote Aboriginal health services. Urine was tested with the GeneXpert(®)CT/NG and if sufficient volume, also with Diaquick CT and Gonorrhoea Card. The gold standard comparison was laboratory nucleic acid amplification testing (NAAT). Operational characteristics were also assessed.

RESULTS

Among 198 samples, GeneXpert CT sensitivity and specificity was 100% [95% confidence intervals (CI): 75.9-100] and 99.5% (95% CI: 96.5-100), and NG was 100% (95% CI: 96.5-100) and 100% (95% CI: 97.5-100), respectively. Among a sample subset, Diaquick CT (n=104) sensitivity and specificity was 27.3% (95% CI: 7.3-60.7) and 66.7% (95% CI: 12.5-98.2), and Gonorrhoea Card (n=29), was 66.7% (95% CI: 12.5-98.2) and 76.9% (95% CI: 56.0-90.2), respectively. GeneXpert required 1mL of urine, four steps, 1min specimen preparation and 90min to result. ICTs required 15mL of urine, eight steps, 18min preparation and 10-15min to result.

CONCLUSION

The accuracy and operational benefits of GeneXpert CT/NG make it very suitable in these settings where delays to treatment are encountered.