Molecular antimicrobial resistance surveillance for neisseria gonorrhoeae, Northern Territory, Australia

Neisseria gonorrhoeae antimicrobial resistance (AMR) is a globally recognized health threat; new strategies are needed to enhance AMR surveillance. The Northern Territory of Australia is unique in that 2 different first-line therapies, based primarily on geographic location, are used for gonorrhea treatment. We tested 1,629 N. gonorrhoeae nucleic acid amplification test–positive clinical samples, collected from regions where ceftriaxone plus azithromycin or amoxicillin plus azithromycin are recommended first-line treatments, by using 8 N. gonorrhoeae AMR PCR assays. We compared results with those from routine culture-based surveillance data. PCR data confirmed an absence of ceftriaxone resistance and a low level of azithromycin resistance (0.2%), and that penicillin resistance was \u3c5% in amoxicillin plus azithromycin regions. Rates of ciprofloxacin resistance and penicillinase-producing N. gonorrhoeae were lower when molecular methods were used. Molecular methods to detect N. gonorrhoeae AMR can increase the evidence base for treatment guidelines, particularly in settings where culture-based surveillance is limited

Retrospective review of Treponema pallidum PCR and serology results: Are both tests necessary?

There has been a resurgence of syphilis diagnoses in Australia. We investigated whether ourpolymerase chain reaction (PCR) test provides any additional diagnostic information over syphilis serology (chemi-luminescence immunoassay (CMIA),particle agglutination (TPPA) and rapid reagin (RPR) flocculation test). A retrospective audit was conducted of allPCR requests that came through our laboratory from January 2010 to June 2017; data collected included age, gender, site of swab,PCR, syphilis serology and HSV 1 and HSV 2 PCR results. A total of 441PCR tests were performed, with on average three requests forPCR per month in 2011, which increased to 17.2 per month in 2017. There were 323 patients who had bothPCR and syphilis serology performed, with 67% of swabs taken from the genitals.PCR was positive in 61/323 (19%) patients, of which 59/61 (97%) also had positive syphilis serology result (sensitivity 68%, specificity 99%, positive predictive value 97% and negative predictive value 89%). Syphilis serology was positive in 91/323 patients (28%) of which 61 (66%) were alsoPCR positive (sensitivity 97%, specificity 88%, positive predictive value 60% and negative predictive value 99%). The Cohen's Kappa value was 0.74, indicating substantial agreement between the two tests. Our results show most patients with positivePCR results also had positive syphilis serology. Therefore,PCR adds little clinical value over serology for diagnosis of syphilis in certain clinical settings

An Economical Tandem Multiplex Real-Time PCR Technique for the Detection of a Comprehensive Range of Respiratory Pathogens

This study used real-time PCR assays to screen small sample volumes for a comprehensive range of 35 respiratory pathogens. Initial thermocycling was limited to 20 cycles to avoid competition for reagents, followed by a secondary real-time multiplex PCR. Supplementary semi-nested human metapneumovirus and picornavirus PCR assays were required to complete the acute respiratory pathogen profile. Potential pathogens were detected in 85 (70%) of pernasal aspirates collected from 121 children with acute respiratory symptoms. Multiple pathogens were detected in 29 (24%) of those samples. The tandem multiplex real-time PCR was an efficient method for the rapid detection of multiple pathogens

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

Neisseria gonorrhoeae, the causative pathogen of gonorrhoea, has shown impressive agility in developing resistance to successive classes of antimicrobials used for therapy, leading to a progressive reduction in available treatment options. Ceftriaxone is the last-line treatment option for gonorrhoea, and many countries recommend dual therapy with ceftriaxone (250–1000 mg) in combination with azithromycin (1–2 g). However, since the introduction of dual therapy, the global prevalence of azithromycin resistance has increased. Additionally, the extensively drug-resistant N gonorrhoeae FC428 clone, which is associated with ceftriaxone resistance and intermediate resistance to azithromycin, has been reported to have spread internationally, with epidemiological links to the Asia-Pacific region

A Novel Duplex Real-Time Reverse-Transcription PCR Assay for the Detection of Influenza A and the Novel Influenza A(H1N1) Strain

Timely implementation of antiviral treatment and other public health based responses are dependent on accurate and rapid diagnosis of the novel pandemic influenza A(H1N1) strain. In this study we developed a duplex real-time PCR (RT-PCR) (dFLU-TM) assay for the simultaneous detection of a broad range of influenza A subtypes and specific detection of the novel H1N1 2009 pandemic strain. The assay was compared to the combined results of two previously described monoplex RT-PCR assays using 183 clinical samples and 10 seasonal influenza A isolates. Overall, the results showed that the dFLU-TM RT-PCR method is suitable for detection of influenza A, including the novel H1N1 pandemic strain, in clinical samples

A real-time, quantitative PCR method using hydrolysis probes for the monitoring of Plasmodium falciparum load in experimentally infected human volunteers

Background: The accurate quantification of Plasmodium falciparum parasite numbers by PCR is an important tool for monitoring growth kinetics in subjects infected and subsequently treated with anti-malarial agents

Merkel Cell Polyomavirus DNA in Respiratory Specimens from Children and Adults

Merkel cell polyomavirus (MCPyV) DNA was detected in 7 (1.3%) of 526 respiratory tract samples from patients in Australia with upper or lower respiratory tract symptoms. Partial T antigen and major capsid protein sequences of MCPyV identified in respiratory secretions showed high homology (99%–100%) to those found in Merkel cell carcinoma

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

European collaborative group: Raquel Abad Torreblanca, Lena Rós Ásmundsdóttir, Eszter Balla, Irith De Baetselier, Beatrice Bercot, Thea Bergheim, Maria José Borrego, Susanne Buder, Robert Cassar, Michelle Cole, Alje van Dam, Claudia Eder, Steen Hoffmann, Blazenka Hunjak, Samo Jeverica, Vesa Kirjavainen, Panayiota Maikanti-Charalambous, Vivi Miriagou, Beata Młynarczyk-Bonikowska, Gatis Pakarna, Peter Pavlik, Monique Perrin, Joseph Pett, Paola Stefanelli, Kate Templeton, Magnus Unemo, Jelena Viktorova, Hana ZákouckáPortugal: Maria-José Borrego (INSA)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).This work was supported by the O¨rebro County Council Research Committee and the Foundation for Medical Research at O¨rebro University Hospital, O¨rebro, Sweden.info:eu-repo/semantics/publishedVersio

Viruses causing lower respiratory symptoms in young children: Findings from the ORChID birth cohort

© 2018 Article author(s). Introduction Viral acute respiratory infections (ARIs) cause substantial child morbidity. Sensitive molecular-based assays aid virus detection, but the clinical significance of positive tests remains uncertain as some viruses may be found in both acutely ill and healthy children. We describe disease-pathogen associations of respiratory viruses and quantify virus-specific attributable risk of ARIs in healthy children during the first 2 years of life. Methods One hundred fifty-eight term newborn babies in Brisbane, Australia, were recruited progressively into a longitudinal, community-based, birth cohort study conducted between September 2010 and October 2014. A daily tick-box diary captured predefined respiratory symptoms from birth until their second birthday. Weekly parent-collected nasal swabs were batch-tested for 17 respiratory viruses by PCR assays, allowing calculation of virus-specific attributable fractions in the exposed (AFE) to determine the proportion of virus-positive children whose ARI symptoms could be attributed to that particular virus. Results Of 8100 nasal swabs analysed, 2646 (32.7%) were virus-positive (275 virus codetections, 3.4%), with human rhinoviruses accounting for 2058/2646 (77.8%) positive swabs. Viruses were detected in 1154/1530 (75.4%) ARI episodes and in 984/4308 (22.8%) swabs from asymptomatic periods. Respiratory syncytial virus (AFE: 68% (95% CI 45% to 82%)) and human metapneumovirus (AFE: 69% (95% CI 43% to 83%)) were strongly associated with higher risk of lower respiratory symptoms. Discussion The strong association of respiratory syncytial virus and human metapneumovirus with ARIs and lower respiratory symptoms in young children managed within the community indicates successful development of vaccines against these two viruses should provide substantial health benefits