Impact of the COVID-19 related border restrictions on influenza and other common respiratory viral infections in New Zealand.

BACKGROUND: New Zealand's (NZ) complete absence of community transmission of influenza and respiratory syncytial virus (RSV) after May 2020, likely due to COVID-19 elimination measures, provided a rare opportunity to assess the impact of border restrictions on common respiratory viral infections over the ensuing 2 years. METHODS: We collected the data from multiple surveillance systems, including hospital-based severe acute respiratory infection surveillance, SHIVERS-II, -III and -IV community cohorts for acute respiratory infection (ARI) surveillance, HealthStat sentinel general practice (GP) based influenza-like illness surveillance and SHIVERS-V sentinel GP-based ARI surveillance, SHIVERS-V traveller ARI surveillance and laboratory-based surveillance. We described the data on influenza, RSV and other respiratory viral infections in NZ before, during and after various stages of the COVID related border restrictions. RESULTS: We observed that border closure to most people, and mandatory government-managed isolation and quarantine on arrival for those allowed to enter, appeared to be effective in keeping influenza and RSV infections out of the NZ community. Border restrictions did not affect community transmission of other respiratory viruses such as rhinovirus and parainfluenza virus type-1. Partial border relaxations through quarantine-free travel with Australia and other countries were quickly followed by importation of RSV in 2021 and influenza in 2022. CONCLUSION: Our findings inform future pandemic preparedness and strategies to model and manage the impact of influenza and other respiratory viral threats.

A ruptured thoracic aortic aneurysm and the difficulties of confirming syphilis.

A 43-year-old woman died suddenly and was found at PM to have a ruptured thoracic aortic aneurysm. The endothelial surface of the aorta showed a 'tree-bark' appearance. Histology of the aneurysm wall showed a patchy, mainly perivascular, plasma cell infiltrate. Multiple spirochete-like organisms were identified on T. pallidum IHC. However, PM syphilis serology (screen including rapid plasma reagin (RPR) and T. pallidum particle agglutination (TPPA)) on femoral blood was negative. PCR testing on FFPE aortic wall tissue was negative. Further history revealed routine antenatal syphilis screening tests had been negative, no known history or risk of exposure to syphilis or other treponemes. This case raises the possibility of false negative syphilis testing. While acknowledged in RPR testing, with the modern testing regime using multiple methods, the rate of false negative results is now thought to be markedly reduced, and false positive results are a much greater problem in clinical medicine. The most common cause of false negative results is early in primary infection before an immune response has been mounted and in those patients that are immunocompromised. False negative results are also more often seen in tertiary syphilis, as in this case. Newer testing methods which include 16S rRNA sequencing have become available and early discussion with a microbiologist would be recommended. Strong macroscopic and microscopic suggestion of syphilis as the cause of the aneurysm makes it necessary to include the possibility of infection in the Post Mortem Report to Coroner as this will have implications for her sexual partners and children.

Symptom persistence and recovery among COVID-19 survivors during a limited outbreak in Canterbury, New Zealand: a prospective cohort study.

BACKGROUND: In Canterbury, near complete identification of coronavirus disease 2019 (COVID-19) cases during a limited outbreak provides unique insights into sequelae. AIMS: The current study aimed to measure symptom persistence, time to return to normal activity, generalised anxiety and health-related quality of life (HrQoL) among COVID-19 survivors compared with uninfected participants. METHODS: The authors conducted a prospective cohort study of people tested for COVID-19 by reverse transcriptase polymerase chain reaction of nasopharyngeal swabs from 1 March to 30 June 2020. They enrolled participants who tested positive and negative at a 1:2 ratio, and administered community-acquired pneumonia, 7-item generalised anxiety disorder (GAD-7) and HrQoL (RAND-36) questionnaires. RESULTS: The authors recruited 145 participants, 48 with COVID-19 and 97 without COVID-19. The mean time from COVID-19 testing to completing the health questionnaire was 306 days. The mean age of patients was 46.7 years, and 70% were women. Four (8%) COVID-19-positive and eight (8%) COVID-19-negative participants required hospitalisation. Fatigue (30/48 [63%] vs 13/97 [13%]; P < 0.001), dyspnoea (13/48 [27%] vs 6/97 [6%]; P < 0.001) and chest pain (10/48 [21%] vs 1/97 [1%]; P < 0.001) were persistent in those with COVID-19. Fewer COVID-19-positive participants returned to normal activity levels (35/48 [73%] vs 94/97 97%; P < 0.001), with longer times taken (median 21 vs 14 days; P = 0.007). The GAD-7 and RAND-36 scores of both groups were similar across all anxiety and HrQoL subscales. CONCLUSIONS: Persistent symptoms and longer recovery times were found in COVID-19 survivors, but not impaired generalised anxiety levels or HrQoL compared with COVID-19-uninfected participants.

Clinical, Laboratory, and Molecular Epidemiology of an Outbreak of Aseptic Meningitis Due to a Triple-Recombinant Echovirus in Ashburton, New Zealand.

Here, we describe a small enterovirus outbreak including nine cases of aseptic meningitis in a New Zealand hospital in 2017. Most patients had a lymphocytic predominance in the CSF, their length of stay was short, and there were no paediatric cases or ICU admissions. VP1 genotyping revealed that the outbreak was caused by an echovirus E30 strain closely related to strains reported from the US, UK, Brazil, and Denmark. They all form a separate cluster within lineage "h", which leads to the proposal of establishing a new lineage tentatively named "j" for this group of echovirus E30 strains. However, whole genome sequencing and reference mapping to echovirus E30 sequences showed very poor mapping of reads to the 3' half of the genome. Further bioinformatic analysis indicated that the causative agent of this outbreak might be a mosaic triple-recombinant enterovirus composed of echovirus E6, echovirus E11, and echovirus E30 genome segments.

Impact of the COVID-19 nonpharmaceutical interventions on influenza and other respiratory viral infections in New Zealand.

Stringent nonpharmaceutical interventions (NPIs) such as lockdowns and border closures are not currently recommended for pandemic influenza control. New Zealand used these NPIs to eliminate coronavirus disease 2019 during its first wave. Using multiple surveillance systems, we observed a parallel and unprecedented reduction of influenza and other respiratory viral infections in 2020. This finding supports the use of these NPIs for controlling pandemic influenza and other severe respiratory viral threats.

Impact of the COVID-19 nonpharmaceutical interventions on influenza and other respiratory viral infections in New Zealand.

Stringent nonpharmaceutical interventions (NPIs) such as lockdowns and border closures are not currently recommended for pandemic influenza control. New Zealand used these NPIs to eliminate coronavirus disease 2019 during its first wave. Using multiple surveillance systems, we observed a parallel and unprecedented reduction of influenza and other respiratory viral infections in 2020. This finding supports the use of these NPIs for controlling pandemic influenza and other severe respiratory viral threats.

Tenth Scientific Biennial Meeting of the Australasian Virology Society-AVS10 2019.

The Australasian Virology Society (AVS) aims to promote, support and advocate for the discipline of virology in the Australasian region. The society was incorporated in 2011 after 10 years operating as the Australian Virology Group (AVG) founded in 2001, coinciding with the inaugural biennial scientific meeting. AVS conferences aim to provide a forum for the dissemination of all aspects of virology, foster collaboration, and encourage participation by students and post-doctoral researchers. The tenth Australasian Virology Society (AVS10) scientific meeting was held on 2-5 December 2019 in Queenstown, New Zealand. This report highlights the latest research presented at the meeting, which included cutting-edge virology presented by our international plenary speakers Ana Fernandez-Sesma and Benjamin tenOever, and keynote Richard Kuhn. AVS10 honoured female pioneers in Australian virology, Lorena Brown and Barbara Coulson. We report outcomes from the AVS10 career development session on "Successfully transitioning from post-doc to lab head", winners of best presentation awards, and the AVS gender equity policy, initiated in 2013. Plans for the 2021 meeting are underway which will celebrate the 20th anniversary of AVS where it all began, in Fraser Island, Queensland, Australia.

A persuasive approach to antimicrobial stewardship in Christchurch hospitals produced a sustained decrease in intravenous clarithromycin dosing and expenditure via a switch to azithromycin orally.

AIMS: To assess a persuasive multimodel approach to decreasing unnecessary intravenous (IV) clarithromycin use for community-acquired pneumonia (CAP) in Canterbury District Health Board (CDHB) hospitals. METHODS: In December 2013, CDHB guidelines for empiric treatment of CAP changed to prioritise oral azithromycin over IV clarithromycin. The multimodel approach we used to implement this change included obtaining stakeholder agreement, improved guidelines access, education and pharmacist support. The impact of the intervention was evaluated by comparing macrolide usage and expenditure for the four years pre- and post-intervention. RESULTS: Mean annual clarithromycin IV use decreased by 72% from 6.4 to 1.8 defined daily doses (DDDs) per 1,000 occupied bed days (OBDs) post-intervention, while oral azithromycin increased by 833% (4.2 to 39.2 DDDs per 1,000 OBDs). Concurrently, oral clarithromycin use decreased by 91% (32.9 to 2.9 DDDs per 1,000 OBDs), and roxithromycin by 71% (17.0 to 5.0 DDDs per 1,000 OBDs). Mean annual total macrolide use decreased by 21% (68.2 to 53.9 DDDs per 1,000 OBDs), while expenditure decreased by 69% mainly through avoided IV administration. CONCLUSIONS: A persuasive multimodel approach to support adoption of CAP guidelines produced a sustained decrease in IV clarithromycin use, which may have clinical benefits such as reduced occurrence of catheter-related complications.

Biphasic Outbreak of Invasive Group A Streptococcus Disease in Eldercare Facility, New Zealand.

A 3-month outbreak of invasive group A Streptococcus disease at an eldercare facility, in which 5 persons died, was biphasic. Although targeted chemoprophylaxis contained the initial outbreak, a second phase of the outbreak occurred after infection control processes ended. To retrospectively investigate the genomic epidemiology of the biphasic outbreak, we used whole-genome sequencing and multiple bioinformatics approaches. Analysis of isolates from the outbreak and isolates prospectively collected during the outbreak response indicated a single S. pyogenes emm81 clone among residents and staff members. Outbreak isolates differed from nonoutbreak emm81 isolates by harboring an integrative conjugative genomic element that contained the macrolide resistance determinant erm(TR). This study shows how retrospective high-resolution genomic investigations identified rapid spread of a closed-facilty clonal outbreak that was controlled, but not readily cleared, by infection control management procedures.

Assessing the impact of a 'bundle of care' approach to Staphylococcus aureus bacteraemia in a tertiary hospital.

BACKGROUND: Staphylococcus aureus bacteraemia is associated with significant morbidity and mortality. There is evidence that standardised care bundle implementation may improve the rates of appropriate investigations and improve overall management. A S. aureus bacteraemia care bundle was introduced at Christchurch Hospital, New Zealand in early 2014. We assessed the impact of the intervention on the management and outcome of S. aureus bacteraemia. METHODS: A cohort study of cases of S. aureus bacteraemia was conducted following standardised care bundle introduction. Prospective enrolment of post-intervention patients occurred from 1st January 2014 to 30th June 2015, with retrospective review of pre-intervention cases from 1st January 2009 to 31st December 2013. RESULTS: In the pre-intervention period 447 patients had at least one episode of S. aureus bacteraemia compared to 151 patients in the post-intervention period. The two groups were similar by gender, ethnicity, and age. Significant increases in Infectious Diseases consultation rate (86.6% vs 94.8%; p=0.009), echocardiography (76.3% vs 96.3%; p<0.001), urine culture (74.0% vs 91.9%; p<0.001), follow up blood cultures (44.2% vs 83.0%; p<0.001), and at least 2 weeks of parenteral therapy (83.5% vs 92.9%; p=0.014) were observed after introduction of the bundle. There were no significant differences in rates 30-day mortality (18.6% vs. 20.5%; p=0.596), but there was a reduction in episodes of relapsed infection in the post-intervention cohort (7.4% vs 1.3%; p=0.004). CONCLUSION: An integrated care bundle for the management of S. aureus bacteraemia resulted in increased use of quality of care indicators and infectious diseases review and improved patient outcome.

Soft Tissue Infection with Diaporthe phaseolorum in Heart Transplant Recipient with End-Stage Renal Failure.

Diaporthe phaseolorum is a fungal plant parasite that has rarely been described as causing invasive human disease. We report a case of human soft tissue infection with Diaporthe phaseolorum in a heart transplant patient with end-stage renal failure in New Zealand.

Monitoring Viral Genetic Variation as a Tool To Improve Molecular Diagnostics for Mumps Virus.

Here, we report how the analysis of viral genetic variation using next-generation sequencing (NGS) can be used as a tool to improve mumps virus diagnostics. Analysis of NGS data from recently circulating mumps virus isolates allowed optimization of the current mumps virus real-time reverse transcription-PCR (RT-PCR) by primer and probe modifications due to nucleotide variations. The modified assay showed a higher efficiency and sensitivity than the previously used CDC protocol for the detection of currently circulating mumps virus strains and could therefore offer better support for outbreak control. The NGS sequence data were also used to make predictions of changes in the hemagglutinin-neuraminidase protein structure that could explain possible immune escape mechanisms.

Mycoplasma genitalium Macrolide and Fluoroquinolone Resistance Detection and Clinical Implications in a Selected Cohort in New Zealand.

Mycoplasma genitalium has been associated with infections of the genitourinary tract, and prevalence is secondary to Chlamydia trachomatis The clinical observation of increasing treatment failure indicating antibiotic resistance, especially in cases of recurrent urethritis, has been confirmed by molecular testing. Mutations in the 23S rRNA gene can cause macrolide resistance, and topoisomerase/gyrase mutations can cause fluoroquinolone resistance. In this study, 115 M. genitalium DNA-positive samples were analyzed. Eighty-nine (77.4%) samples had a 23S rRNA mutation present, and 26 (22.6%) were wild type (no resistance mutation). Fluoroquinolone mutation screening was performed on 86 (74.8%) of the 115 samples, of which 20 (23.3%) samples had a mutation or mutations associated with increased resistance. This study shows the increasing antibiotic resistance in New Zealand and the need for appropriate guidelines to treat at-risk patients.

Comparison of the fast track diagnostics respiratory 21 and Seegene Allplex multiplex polymerase chain reaction assays for the detection of respiratory viruses.

BACKGROUND: Real-time multiplex PCR assays are increasingly used for respiratory virus detection, and offer automated analysis in a closed tube system, but they have the disadvantage of low-throughput due to multiplexing limitations. In this study, the established fast-track respiratory 21 assay (FTD) (fast-track diagnostics, Junglinster Luxembourg) was compared to the new Seegene Allplex assay (Seegene) (Seegene Inc. Seoul, Korea) which offers greater multiplexing as multiple targets can be detected in each fluorescence channel. The Seegene Allplex assay is quicker to perform than previous Seegene respiratory multiplex assays. MATERIALS AND METHODS: The assays were evaluated using 199 mostly upper respiratory tract samples. RESULTS: A respiratory pathogen was found in 127/199 (63.8%) of samples by the FTD assay and 123/199 (61.8%) using the Seegene assay. Kappa agreement was between 0.87 and 1 for all targets except human bocavirus and adenovirus. CONCLUSION: Although the performance of the assays were similar, the Seegene assay had the advantage of simultaneous detection of two gene targets for each of the common Influenza A subtypes, improved throughput of 30 samples per run and automated result analysis. The FTD assay could only test 17 samples per run but validation for use on several different real-time thermal cyclers made it easier to integrate into an existing laboratory system. Both assays were cost effective compared to in-house multiplex PCR respiratory virus screening.

Native Joint Septic Arthritis: Epidemiology, Clinical Features, and Microbiological Causes in a New Zealand Population.

OBJECTIVE: To determine the epidemiology, clinical features, and microbiology of adult native joint septic arthritis in Canterbury, New Zealand, over a 5-year period in individuals with and without an underlying rheumatic disorder. METHODS: Patients with native joint septic arthritis were identified retrospectively and classified by Newman's criteria. The clinical characteristics were described and comparisons made between those with and without underlying rheumatic disease. RESULTS: Two hundred forty-eight cases of native joint septic arthritis (mean age 60, range 16-97 yrs) were identified with an overall incidence rate of 12.0/100,000/year (95% CI 10.6-13.6). Yearly incidence increased with age to a maximum of 73.4/100,000 in those > 90 years of age. Septic arthritis was iatrogenic in 16.9% of cases while 27% had an underlying inflammatory arthritis including gout (14.9%), calcium pyrophosphate disease (8.5%), and rheumatoid arthritis (4%). Few patients were taking immunosuppressant therapy, with just 1 taking a biological agent. Staphylococcus aureus was the most commonly identified organism. Those with underlying inflammatory arthritis were significantly older (73.6 yrs vs 55.6 yrs; p < 0.001), more likely to be female (55.2% vs 26.0%; p < 0.001), and to have septic polyarthritis (16.4% vs 4.4%; p = 0.002). The 30-day mortality was 2%, increasing to 6% at 90 days. CONCLUSION: The incidence of septic arthritis in Canterbury, New Zealand, is higher than in previous studies. Crystal arthropathy commonly coexisted with infection although autoimmune arthritis and immunosuppression was less of a factor than anticipated.

Antimicrobial Treatment Options for Granulomatous Mastitis Caused by Corynebacterium Species.

Corynebacterium species are increasingly recognized as important pathogens in granulomatous mastitis. Currently, there are no published treatment protocols for Corynebacterium breast infections. This study describes antimicrobial treatment options in the context of other management strategies used for granulomatous mastitis. Corynebacterium spp. isolated from breast tissue and aspirate samples stored from 2002 to 2013 were identified and determined to the species level using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), 16S RNA sequencing, and rpoB gene targets. The MICs for 12 antimicrobials were performed using Etest for each isolate. Correlations of these with antimicrobial characteristics, choice of antimicrobial, and disease outcome were evaluated. Corynebacterium spp. from breast tissue and aspirate samples were confirmed in 17 isolates from 16 patients. Based on EUCAST breakpoints, Corynebacterium kroppenstedtii isolates (n = 11) were susceptible to seven antibiotic classes but resistant to ß-lactam antibiotics. Corynebacterium tuberculostearicum isolates (n = 4) were multidrug resistant. Two nonlipophilic species were isolated, Corynebacterium glucuronolyticum and Corynebacterium freneyi, both of which have various susceptibilities to antimicrobial agents. Short-course antimicrobial therapy was common (median, 6 courses per subject; range, 1 to 9 courses). Patients with C. kroppenstedtii presented with a hot painful breast mass and underwent multiple surgical procedures (median, 4 procedures; range, 2 to 6 procedures). The management of Corynebacterium breast infections requires a multidisciplinary approach and includes culture and appropriate sensitivity testing to guide antimicrobial therapy. Established infections have a poor outcome, possibly because adequate concentrations of some drugs will be difficult to achieve in lipophilic granulomata. Lipophilic antimicrobial therapy may offer a therapeutic advantage. The role of immunotherapy has not been defined.

Importance of blood cultures to aid the diagnosis of Lemierre's syndrome.

This is a case report of Lemierre's syndrome, a septic thrombophlebitis of the internal jugular vein (IJV) usually preceded by pharyngitis and bacteraemia with an anaerobic organism. Fusobacterium necrophorum is ananaerobic Gram-negative bacillus and is the most common organism reported to cause Lemierre's syndrome which usually occurs one to three weeks post pharyngitis or oropharyngeal surgery. A 21-year-old patient presented with signs of sepsis and a history of sore throat, fever, and tender cervical lymph nodes. Blood cultures grew F. necrophorum and Computed Tomography (CT) showed a filling defect in the left retromandibular vein and thrombosis in the left internal jugular vein (IJV) consistent with Lemierre's syndrome. This is an uncommon condition which normally occurs in young individuals and diagnosis is often delayed.

The prevention of early-onset neonatal group B streptococcus infection: New Zealand Consensus Guidelines 2014.

AIMS: Group B streptococcal (GBS) disease is the leading cause of early-onset neonatal sepsis in New Zealand. Disease follows vertical transmission of GBS from the mother, which can largely be prevented by intravenous intrapartum antibiotics. A 2004 New Zealand guideline recommended using clinical risk factors to identify mothers who would qualify for intrapartum antibiotics. An expert multidisciplinary group met to reconsider these guidelines in the light of a two year survey of the incidence of early onset GBS neonatal sepsis. METHODS: Representatives from the New Zealand College of Midwives, the Fetus and Newborn Committee of the Paediatric Society of New Zealand, the Royal New Zealand College of General Practitioners, the New Zealand Committee of the Royal Australian and New Zealand College of Obstetricians and Gynaecologists, the New Zealand sub-Committee of the Australasian Society of Infectious Diseases, and the Canterbury Home Birth Association met to review the literature and the most recent New Zealand data. RESULTS: The multidisciplinary group noted that the estimated incidence of early-onset GBS sepsis had halved over a 10-year period to be 0.26 per 1,000 live births in 2009-11 and that there were missed opportunities for preventing GBS infection. Consensus was reached that adoption of a national guideline on prevention and management of early onset GBS neonatal sepsis by all practitioners and District Health Boards would have the greatest potential to further reduce the incidence. CONCLUSION: A risk-based GBS prevention strategy continues to be recommended as being the most clinically and cost effective for the New Zealand context. Universal routine antenatal GBS screening is not recommended.