Descriptive analysis of group A Streptococcus in skin swabs and acute rheumatic fever, Auckland, New Zealand, 2010-2016.

BACKGROUND: Group A Streptococcus (GAS) can trigger an immune-mediated response resulting in acute rheumatic fever (ARF). Historically, ARF has been considered a consequence of preceding GAS pharyngitis, but increasing evidence suggests that GAS skin infections may be a driver. Data on the primary care burden of GAS skin infection are limited. This paper aims to describe and compare the prevalence and distribution of GAS detection in skin swabs and ARF rates in the Auckland population. METHODS: This cross-sectional study used all laboratory skin swab data from people who had a skin swab taken as a result of a consultation with a health professional in the Auckland region (2010-2016). Initial primary hospitalisations for ARF were identified and all data were linked using unique patient identifiers to patient's age, prioritised ethnicity, sex, and socio-economic status. FINDINGS: 377,410 skin swabs from 239,494 individuals were included. 12·8% of swabs were GAS positive, an annual incidence of 4·8 per 1,000 person-years. Maori and Pacific Peoples under 20 years of age had markedly higher GAS detection in skin swabs (RR 4·0; 95% CI 3·9-4·2: RR 6·8; 95% CI 6·6-7·0) and significantly higher ARF rates (RR 30·3; 95% CI 19·5-46·9: RR 69·7 95% CI 45·8-106·1) compared with European/Other ethnicities. INTERPRETATION: The observation that GAS detection was markedly higher in Maori and Pacific Peoples provides a potential explanation for the marked ethnic differences in ARF. These findings support a greater focus on addressing the burden of skin infection in NZ, including as ARF prevention. FUNDING: The first author received a training stipend from the New Zealand College of Public Health Medicine (NZCPHM) during her Masters of Public Health.

SARS-CoV-2 antibodies in the Southern Region of New Zealand, 2020.

During New Zealand's first outbreak in early 2020 the Southern Region had the highest per capita SARS-CoV-2 infection rate. Polymerase chain reaction (PCR) testing was initially limited by a narrow case definition and limited laboratory capacity, and cases may have been missed. Our objectives were to evaluate the Abbott SARS-CoV-2 IgG nucleocapsid assay, alongside spike-based assays, and to determine the frequency of antibodies among PCR-confirmed and probable cases, and higher risk individuals in the Southern Region of New Zealand. Pre-pandemic sera (n=300) were used to establish assay specificity and sera from PCR-confirmed SARS-CoV-2 patients (n=78) to establish sensitivity. For prevalence analysis, all samples (n=1214) were tested on the Abbott assay, and all PCR-confirmed cases (n=78), probable cases (n=9), and higher risk individuals with 'grey-zone' (n=14) or positive results (n=11) were tested on four additional SARS-CoV-2 serological assays. The median time from infection onset to serum collection for PCR-confirmed cases was 14 weeks (range 11-17 weeks). The Abbott assay demonstrated a specificity of 99.7% (95% CI 98.2-99.99%) and a sensitivity of 76.9% (95% CI 66.0-85.7%). Spike-based assays demonstrated superior sensitivity ranging 89.7-94.9%. Nine previously undiagnosed sero-positive individuals were identified, and all had epidemiological risk factors. Spike-based assays demonstrated higher sensitivity than the Abbott IgG assay, likely due to temporal differences in antibody persistence. No unexpected SARS-CoV-2 infections were found in the Southern Region of New Zealand, supporting the elimination status of the country at the time this study was conducted.

Comprehensive analysis of SARS-CoV-2 antibody dynamics in New Zealand.

OBJECTIVES: Circulating antibodies are important markers of previous infection and immunity. Questions remain with respect to the durability and functionality of SARS-CoV-2 antibodies. This study explored antibody responses in recovered COVID-19 patients in a setting where the probability of re-exposure is effectively nil, owing to New Zealand's successful elimination strategy. METHODS: A triplex bead-based assay that detects antibody isotype (IgG, IgM and IgA) and subclass (IgG1, IgG2, IgG3 and IgG4) responses against Nucleocapsid (N) protein, the receptor binding domain (RBD) and Spike (S) protein of SARS-CoV-2 was developed. After establishing baseline levels with pre-pandemic control sera (n = 113), samples from PCR-confirmed COVID-19 patients with mild-moderate disease (n = 189) collected up to 8 months post-infection were examined. The relationship between antigen-specific antibodies and neutralising antibodies (NAbs) was explored with a surrogate neutralisation assay that quantifies inhibition of the RBD/hACE-2 interaction. RESULTS: While most individuals had broad isotype and subclass responses to each antigen shortly after infection, only RBD and S protein IgG, as well as NAbs, were relatively stable over the study period, with 99%, 96% and 90% of samples, respectively, having responses over baseline 4-8 months post-infection. Anti-RBD antibodies were strongly correlated with NAbs at all time points (Pearson's r ≥ 0.87), and feasibility of using finger prick sampling to accurately measure anti-RBD IgG was demonstrated. CONCLUSION: Antibodies to SARS-CoV-2 persist for up to 8 months following mild-to-moderate infection. This robust response can be attributed to the initial exposure without immune boosting given the lack of community transmission in our setting.

Appropriateness of trimethoprim as empiric treatment for cystitis in 15-55 year-old women: an audit.

AIM: To assess whether trimethoprim remains an appropriate empiric treatment for uncomplicated cystitis in women 15-55 years old. METHODS: General practitioners in Auckland, Nelson-Marlborough, Otago and Southland were invited to participate in this audit of current practice. Participating general practitioners were asked to submit urine to the laboratory for microscopy and culture from any woman aged 15-55 years presenting with uncomplicated cystitis. Urine samples submitted as part of the audit were identified by a "copy to" code. Data on laboratory results were extracted from the laboratory information system. RESULTS: Data were collected from June 2016 to August 2018. Four hundred and eighty-one samples were submitted, of which 340 (70.7%) met the inclusion criteria of the audit. A urinary pathogen was identified in 181 (53.2%) specimens, of which 148 (81.8%) were E. coli, 13 (7.2%) other coliforms and 20 (11.0%) Staphylococcus saprophyticus. Of the E. coli isolates, 109 of 148 (73.6%, 95% CI 66.6-80.7) were susceptible to trimethoprim, 144 of 144 (100%, 95% CI 100-100) to nitrofurantoin and 143 of 148 (96.6%, 95% CI 93.7-99.5) to cefalexin. Of the urinary pathogens, 139 of 185 (75.1%, 95% CI 68.9-81.4) were susceptible to trimethoprim, 164 of 177 tested (92.7%, 95% CI 88.8-96.5) to nitrofurantoin and 166 of 178 tested (93.3%, 95% CI 89.6-96.9) to cefalexin. Overall, a uropathogen resistant to trimethoprim was detected in 13.5%, to nitrofurantoin in 3.8%, and to cefalexin in 3.5% of samples tested. CONCLUSION: Similar rates of resistance to trimethoprim were seen in women 15-55 years old presenting with cystitis compared with unselected samples submitted from the general community. Given the high rates of resistance, trimethoprim is no longer appropriate as an empiric treatment option for cystitis in this group. Nitrofurantoin or cefalexin are appropriate alternative empiric treatment options. Given the current recommendation that a urine sample should not be submitted to the laboratory from women with uncomplicated cystitis, ongoing audits will be required to ensure that empiric treatment recommendations remain appropriate.

Development and Evaluation of a New Triplex Immunoassay That Detects Group A Streptococcus Antibodies for the Diagnosis of Rheumatic Fever.

Streptococcal serology is a cornerstone in the diagnosis of acute rheumatic fever (ARF), a postinfectious sequela associated with group A Streptococcus infection. Current tests that measure anti-streptolysin O (ASO) and anti-DNaseB (ADB) titers require parallel processing, with their predictive value limited by the low rate of decay in antibody response. Accordingly, our objective was to develop and assess the diagnostic potential of a triplex bead-based assay, which simultaneously quantifies ASO and ADB together with titers for a third antigen, SpnA. Our previous cytometric bead assay was transferred to the clinically appropriate Luminex platform by coupling streptolysin O, DNaseB, and SpnA to spectrally unique magnetic beads. Sera from more than 350 subjects, including 97 ARF patients, were used to validate the assay and explore immunokinetics. Operating parameters demonstrate that the triplex assay produces accurate and reproducible antibody titers which, for ASO and ADB, are highly correlative with existing assay methodology. When ARF patients were stratified by time (days following hospital admission), there was no difference in ASO and ADB between <28 and 28+ day groups. However, for anti-SpnA, there was a significant decrease (P < 0.05) in the 28+ day group, indicative of faster anti-SpnA antibody decay. Anti-SpnA immunokinetics support very recent group A Streptococcus infection and may assist in diagnostic classification of ARF. Further, bead-based assays enable streptococcal serology to be performed efficiently in a high-throughput manner.

Distribution of Streptococcal Pharyngitis and Acute Rheumatic Fever, Auckland, New Zealand, 2010-2016.

Group A Streptococcus (GAS) pharyngitis is a key initiator of acute rheumatic fever (ARF). In New Zealand, ARF cases occur more frequently among persons of certain ethnic and socioeconomic groups. We compared GAS pharyngitis estimates (1,257,058 throat swab samples) with ARF incidence (792 hospitalizations) in Auckland during 2010-2016. Among children 5-14 years of age in primary healthcare clinics, GAS pharyngitis was detected in similar proportions across ethnic groups (≈19%). Relative risk for GAS pharyngitis was moderately elevated among children of Pacific Islander and Maori ethnicities compared with those of European/other ethnicities, but risk for ARF was highly elevated for children of Pacific Islander and Maori ethnicity compared with those of European/other ethnicity. That ethnic disparities are much higher among children with ARF than among those with GAS pharyngitis implies that ARF is driven by factors other than rate of GAS pharyngitis alone.

Isolate independent molecular typing improves the yield of O typing of infections due to Shiga toxin producing Escherichia coli.

Molecular screening has increased detection of Shiga-toxin producing Escherichia coli (STEC). However, it is difficult to isolate the organism for epidemiological typing. We applied a molecular method for direct detection of nine O types from 110 stx positive faeces samples and compared the results with conventional isolate based methods. Using conventional methods 55/110 (50%) samples were O typed. Using the molecular method, 72/110 (65%) were O typed, including 23/38 (61%) culture negative samples. Combining both techniques typed 88/110 (80%) of samples. Molecular typing increased detection of O128 (2-25%, p<0.001), O26 (11-16%) O45 (0-6%) and O103 (1-6%) infections. Molecular typing of STEC direct from faecal samples improved O type yield; risk of bias in epidemiological and surveillance activities may be reduced by inclusion of culture independent typing methods.

Understanding group A streptococcal pharyngitis and skin infections as causes of rheumatic fever: protocol for a prospective disease incidence study.

BACKGROUND: Group A Streptococcal (GAS) infections cause the autoimmune disease acute rheumatic fever (ARF), which can progress to chronic rheumatic heart disease (RHD). Treating pharyngitis caused by GAS with antibiotics is important in preventing ARF. However, it is difficult to distinguish these infections from GAS carriers. There is growing evidence for GAS skin infections as a cause of ARF. This study will identify the incidence of true GAS pharyngitis and serological responses to GAS skin infections. The effectiveness of antibiotics for these conditions will be explored, and modifiable risk factors. Serum antibody titres indicating the upper limits of normal (ULN for ASO/ADB antibodies) will be established alongside carriage rates in asymptomatic children. METHODS: This is a prospective disease incidence study, with an associated case-control study. The study population includes 1000 children (5-14 years) from Auckland, New Zealand, 800 of whom have visited their healthcare professional, resulting in a throat or skin swab for GAS, and 200 who are asymptomatic. The conditions of interest are GAS throat swab positive pharyngitis (n = 200); GAS carriage (n = 200); GAS negative throat swab (n = 200); GAS skin infections (n = 200); and asymptomatic controls (n = 200). All participants, except asymptomatic controls, will have acute and convalescent serological testing for ASO/ADB titres (collected < 9 days, and 2-4 weeks following symptom onset, respectively), alongside viral PCR from throat swabs. Asymptomatic controls will have ASO/ADB titres measured in one blood specimen and a throat swab for microbial culture. Caregivers of children will be interviewed using a questionnaire and any GAS isolates identified will be emm typed. The persistence of GAS antibodies will also be investigated. DISCUSSION: Findings from this study will fill critical gaps in scientific knowledge to better understand the pathophysiology of ARF, improve clinical management of GAS infections, and design more effective ARF prevention programmes. In particular it will measure the incidence of true, serologically confirmed GAS pharyngitis; assess the immune response to GAS skin infections and its role as a cause of ARF; examine the effectiveness of oral antibiotics for treating GAS pharyngitis and carriage; and identify whether risk factors for GAS infections might provide intervention points for reducing ARF.

Pseudozyma aphidis endophthalmitis post-cataract operation: Case discussion and management.

PURPOSE: To present a case of fungal endophthalmitis with a novel organism and our management. OBSERVATIONS: A 46 year old male presented with delayed-onset acute endophthalmitis 6 weeks after routine phacoemulsification and intraocular lens implantation. Initial treatment with intravitreal antibiotics did not improve his condition. With repeated vitreal taps, the causative organism was eventually identified as a fungus, Pseudozyma aphidis. Treatment with oral and intravitreal voriconazole, as well as pars plana vitrectomy, led to resolution of the endophthalmitis and recovery of vision to 20/25. CONCLUSIONS AND IMPORTANCE: Fungal endophthalmitis is a rare, potentially blinding complication of cataract surgery. We report our approach to this previously unreported organism, that led to an excellent visual outcome. There are no specific guidelines for fungal endophthalmitis. The management approach has to be tailored to the clinical response and emerging laboratory data from the microbiologist. Identification of the organism will require specialist laboratory references that may not be available in all hospitals. Ophthalmologists must work closely with microbiologists in order to ensure an optimal outcome.

Faecal immunochemical tests for occult blood testing should not be used outside of bowel screening: an audit of a large general practice.

INTRODUCTION The faecal immunochemical test (FIT) detects small quantities of human haemoglobin in faeces. This test has increasingly become the screening tool of choice in bowel cancer screening programmes worldwide, including New Zealand's upcoming national screening programme. AIM This study audited the appropriate use of faecal immunochemical tests (FIT) in general practice as current recommendations discourage the use of FIT outside the National Bowel Screening Programme. METHODS Data on all FIT requested by a multiclinic general practice serving 16000 patients from May 2017 to May 2018 were extracted from clinical records. Patient characteristics, results of tests, clinical rationale for the test, number of referrals and results and the completeness of clinical evaluation were recorded. RESULTS In all, 184 patients received an FIT, with 13 (7.1%) positive and 145 (78.8%) negative tests, and 26 (14.1%) tests declined by the laboratory. Nine patients (69.2%) with a positive FIT, 12 patients (8.1%) with a negative FIT and one patient (3.8%) with a declined test were referred to gastroenterology services. Seven colorectal cancers were detected, all in patients with a positive FIT who were aged between 67 and 91 years. FIT was requested most for changes in bowel habit (53%) and blood in stool (15%); 10% of tests were ordered for reassurance and 9% did not record an indication for the test. Two general practitioners (of 17 in the practice) accounted for over half of all tests requested. CONCLUSIONS Because FIT is only a screening tool for colorectal cancer, direct referral is recommended for symptomatic patients. Although cancers were detected only in patients with positive FITs, these patients would have qualified for direct referral for definitive investigation, and a referral was made concurrently. Awaiting test results may also delay necessary referrals and a negative FIT may produce false reassurance.

Suboptimal performance of rotavirus testing in a vaccinated community population should prompt laboratories to review their rotavirus testing algorithms in response to changes in disease prevalence.

Rotavirus vaccine has reduced disease prevalence in many countries. Consequently, we aimed to assess the reliability of a rotavirus immunoassay in the community population of Auckland and Northland, New Zealand. Between 22 October 2015 and 31 December 2016, 2873 fecal samples were tested by enzyme immunoassay (EIA, Rotascreen II, Microgen, UK) from 2748 patients (median age 8 years, range 0-101 years). Eighty-nine (3.1%) samples were reactive; 86 samples were tested by a second method. Rotavirus was confirmed in 49/86 (57%). Positive rotavirus EIAs were more likely to be confirmed in samples from cases ≥1 year of age (positive predictive value [PPV] 61%, 95% confidence interval [CI] 50-72%, P = 0.049) and in spring/summer (PPV 67%, 95% CI 55-78%, P = 0.003). Reactive rotavirus tests required confirmatory testing regardless of demographic, vaccine, or seasonal factors; a review of rotavirus testing algorithms may be necessary in other vaccinated community populations.

International normalised ratio monitoring in the community populations of the Auckland and Northland regions of New Zealand: time in therapeutic range and frequency of testing.

BACKGROUND: Warfarin remains a commonly used anticoagulant for the treatment and prevention of thrombosis. To balance the risks and benefits of therapy, monitoring of the international normalised ratio (INR) is necessary. Patients derive most benefit from warfarin when they spend ≥65% of time in the therapeutic range (INR 2-3). We performed an analysis of INR monitoring for the Auckland and Northland regions of New Zealand in order to estimate anticoagulation control and appropriateness of testing at the population level. METHODS: INR test results and patient demographics (age and sex) were extracted from the laboratory information system of Labtests and Northland Pathology Laboratories for the period of 1 January 2016 to 27 July 2016. RESULTS: We included 126 184 INR results from 10 922 patients. The median age of patients represented was 74 years and 57% were male. The overall mean time in therapeutic range was 63%, with a mean interval between INR tests of 14 days. CONCLUSION: Our results indicate that anticoagulant control in our communities could be improved, and that inappropriately frequent INR testing should be redressed. Appropriate interventions could lead to net clinical benefits and reduce resource misallocation.

Diagnosis of Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis and Mycoplasma genitalium: an observational study of testing patterns, prevalence and co-infection rates in northern New Zealand.

Background This study sought to determine community prevalence, epidemiology and testing patterns for sexually transmissible infections (STI) in northern New Zealand. METHODS: A total of 2643 samples submitted for STI testing between 26 November 2015 and 7 December 2015 underwent analysis by Aptima Combo 2 (Hologic, San Diego, CA, USA), Trichomonas vaginalis (TV), and Mycoplasma genitalium (MG) assays. Results were analysed by patient demographics. RESULTS: Four hundred and eleven pathogens were detected from 359 patients, with Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), TV, and MG detected in 178 (6.7%), 19 (0.7%), 80 (3%) and 134 (5.1%) samples respectively. With the exception of TV, STI prevalence was highest in people <25 years of age. Infection was more common in men for NG (odds ratio (OR) 5.05, P<0.001) and CT (OR 2.72, P<0.001). Maori and Pacific ethnicity were associated with increased risk of MG (OR 1.82, P=0.006,) TV (OR 6.1, P<0.001) and CT (OR 3.31, P<0.001) infection, and TV and NG infections were more prevalent as social deprivation increased. A mismatch between testing rates and prevalence of infection was seen, with fewer tests performed for males (OR 0.2, P<0.001) than females and no difference in testing of Maori and Pacific men (3064/100000) compared with men of European background (3181/100000, OR 0.96, P=0.76), despite an increased risk of disease. CONCLUSIONS: There are disparately low testing rates for STIs in certain high-risk groups in northern New Zealand.

Audit of Trichomonas vaginalis test requesting by community referrers after a change from culture to molecular testing, including a cost analysis.

AIMS: Trichomonas vaginalis (TV) prevalence varies among different communities and peoples. The availability of robust molecular platforms for the detection of TV has advanced diagnosis; however, molecular tests are more costly than phenotypic methodologies, and testing all urogenital samples is costly. We recently replaced culture methods with the Aptima Trichomonas vaginalis nucleic acid amplification test on specific request and as reflex testing by the laboratory, and have audited this change. METHODS: Data were collected from August 2015 (microbroth culture and microscopy) and August 2016 (Aptima TV assay) including referrer, testing volumes, results and test cost estimates. RESULTS: In August 2015, 10,299 vaginal swabs, and in August 2016, 2,189 specimens (urogenital swabs and urines), were tested. The positivity rate went from 0.9% to 5.3%, and overall more TV infections were detected in 2016. The number needed to test and cost for one positive TV result respectively was 111 and $902.55 in 2015, and 19 and $368.92 in 2016. Request volumes and positivity rates differed among referrers. CONCLUSIONS: The methodology change was associated with higher overall detection of TV, and reductions in the numbers needed to test/cost for one TV diagnosis. Our audit suggests that there is room for improvement with TV test requesting in our community.

Use of the EntericBio Gastro Panel II in a diagnostic microbiology laboratory: challenges and opportunities.

We sought to verify the performance of the EntericBio real-time Gastro Panel 2 (GP2; Serosep, Ireland) assay targeting Salmonella, Shigella, Campylobacter, verotoxin producing E. coli (VTEC), Giardia, and Cryptosporidium in a high-throughput diagnostic laboratory. Following a technical verification period where 237 faecal samples were tested in parallel, guided culture and discrepancy analysis were performed. A total of 13,223 faecal samples were screened by the GP2 assay. During technical verification, sensitivity, specificity, negative and positive predictive value of the GP2 assay compared with conventional methods were 100% (83-100%), 98% (96.7-98.2%), 100% (98.5-100%), and 82.6% (69-83%), respectively. With guided culture, specificity (99.4-100%) and positive predictive value (15-100%) varied by target. Challenges with interpretation of results, particularly for VTEC, Shigella and Salmonella, are discussed.

Treatment of gonorrhoea in Auckland, New Zealand: marked variation in prescriber adherence to treatment guidelines.

BACKGROUND: The relentless emergence and spread of strains of Neisseria gonorrhoeae that are resistant to many antimicrobial agents has led to frequent changes in treatment guidelines, with a consequent risk that prescribers may not be aware of current guidelines. AIM: To determine the proportion of patients with gonorrhoea who were treated with a regimen consistent with the New Zealand Sexual Health Society (NZSHS) guidelines. METHODS: We audited the treatment given to adult patients with laboratory-proven gonorrhoea in Auckland, New Zealand, during the first 6 months of 2015. RESULTS: Treatment compliant with the current NZSHS guidelines was administered in only 65% (458/706) episodes overall. Guideline-compliant treatment was much more likely to be prescribed for patients who presented to a sexual health clinic (89%) than for patients who presented to either a general practice or other community clinic (52%) or to a hospital (56%) (P < 0.0001). Overall, 52 of 706 (7%) episodes were not treated with any antimicrobial regimen by the service that diagnosed the patients' gonorrhoea, 13 of 62 (21%) episodes in patients who presented to a hospital, 34 of 403 (8%) episodes in patients who presented to a general practice or other community clinic and 5 of 241 (2%) episodes in patients who presented to a sexual health clinic (P < 0.0001). CONCLUSION: Low levels of compliance with treatment guidelines increase the risk that antibiotic-resistant strains of N. gonorrhoeae will spread within the Auckland region. Improved compliance with treatment guidelines, particularly in patients who present either to general practice or to hospitals, is necessary to maintain the efficacy of current treatment regimens.

Acute Rheumatic Fever After Group A Streptococcus Pyoderma and Group G Streptococcus Pharyngitis.

A case of acute rheumatic fever (ARF) in an Indigenous Maori child in New Zealand after Group A Streptococcus pyoderma and Group G Streptococcus pharyngitis is reported. The case demonstrates that ARF can develop in the absence of GAS pharyngitis and highlights a need for further research into the role of pyoderma and non-Group A Streptococci infections in ARF pathogenesis.