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We report here the complete genome sequence of Mycobacterium tuberculosis strain Colonial S-type 1 (CS1), which has been responsible for ongoing outbreaks of tuberculosis in New Zealand over the past 30 years. CS1 appears to be highly transmissible, with greater rates of progression to active disease, compared to other circulating M. tuberculosis strains; therefore, comparison of its genomic content is of interest.

The primary aim of this study was to identify the source of healthcare-associated Staphylococcus aureus bacteraemia (HA-SAB) in acute district health board (DHB) hospitals to inform future national quality improvement activities.De-identified HA-SAB event source information was submitted to the Commission from all DHBs for the period 1 January 2017 to 30 June 2021. Data was categorised and analysed to identify trends and significant sources of infection.There were 1,867 HA-SAB events. Of the events where S. aureus susceptibility results were reported, 159 (10%) isolates were methicillin-resistant S. aureus. The principal sources of HA-SAB were medical devices (65%), surgical site infection (10%), and organ site (8%). Ninety-five percent of medical devices were for vascular access, primarily central venous catheters (50%) and peripheral intravenous catheters (45%).This study has identified intravascular devices as significant sources of HA-SAB. Ongoing surveillance for HA-SAB source is required to identify the major risk factors and to support quality improvement activities targeting infection prevention measures and best practice related to intravascular and other medical devices.

Summary The objective of this study was to review the antifungal susceptibility of clinical mould isolates performed by the New Zealand Mycology Reference Laboratory. Isolates were either local or referred for testing from other New Zealand laboratories. All isolates were tested by the broth colorimetric microdilution method, Sensititre YeastOne (SYO). Epidemiological cut-off values (ECVs) derived from either the Clinical and Laboratory Standards Institute (CLSI) method or SYO were used to determine the proportion of non-wild type (non-WT) isolates, i.e., those with an increased likelihood to harbour acquired mechanisms of resistance. A total of 614 isolates were tested. Most isolates (55%) were from the respiratory tract followed by musculoskeletal tissue (17%), eye (10%) and abdomen (5%). The azoles had similar activity except for voriconazole which was less active against the Mucorales. The echinocandins had good activity against Aspergillus spp., other hyaline moulds and dematiaceous isolates but were inactive against Fusarium spp., Lomentospora prolificans and the Mucorales. Amphotericin B had best activity against the Mucorales. The two least susceptible groups were Fusarium spp. and L. prolificans isolates. Three Aspergillus isolates were non-WT for amphotericin B, and four non-WT for azoles. Non-WT were not encountered for caspofungin. Non-Aspergillus isolates in New Zealand have susceptibility patterns similar to those reported elsewhere. In contrast to a growing number of other countries, azole resistance was rare in A. fumigatus sensu stricto. Non-WT isolates were uncommon. The results provide a baseline for monitoring emerging antifungal resistance in New Zealand and support current Australasian treatment guidelines for invasive fungal infections.

To describe risk factors for surgical site infection (SSI) caused by aerobic Gram-negative organisms after hip and knee arthroplasty.Publicly funded hip and knee arthroplasties (performed between 1 July 2013 and 31 December 2017) that developed SSIs were compared to those that did not. SSIs were grouped by causative organism: Gram-negative (Pseudomonas spp. or enteric Gram-negative bacilli) or staphylococcal (pure or mixed growth of Staphylococcus spp.). Independent risk factors in each group were identified.24,842 (54%) hip and 20,993 (46%) knee arthroplasties were performed. There were 497 (1.1%) SSIs. Staphylococci were responsible for 233 SSIs (47%) and Gram-negatives were responsible for 73 (15%). Age, sex, body mass index ≥35kg/m2, smoking status, socioeconomic deprivation, American Society of Anesthesiologists classification, revision surgery and prophylactic antibiotic dose were all independent predictors of all-cause SSI. On subgroup analysis, socioeconomic deprivation and Pasifika ethnicity were independent risk factors for Gram-negative SSI, but not staphylococcal SSI.In this study, socioeconomic deprivation and ethnicity were independent and novel risk factors for Gram-negative SSI following arthroplasty. Some of the SSI risk factors can be modified before arthroplasty (e.g., appropriate timing of prophylactic antibiotics, smoking cessation, weight loss). Non-modifiable risk factors can help identify high-risk procedures where additional pre- and post-operative interventions may be warranted.

Antimicrobial resistance of Neisseria gonorrhoeae (NG) is of global public health concern. The aim of this study was to explore demographic and behavioural factors associated with antimicrobial susceptibility of NG to ceftriaxone and azithromycin. Gonococcal isolates (n = 391) from clients attending the Auckland Sexual Health Service, New Zealand, from July 2014 – June 2015 (n = 206), and July 2017 – June 2018 (n = 185), were tested for susceptibility to ceftriaxone and azithromycin. Laboratory data were linked with behavioural and demographic data. Geometric mean azithromycin MICs increased across the two time periods (0.239 mg/L in 2014/15 to 0.347 mg/L in 2017/18, p

AIM The optimisation of diagnosis and management of paediatric Clostridioides (formerly Clostridium) difficile (C. difficile) infection (CDI) has importance on multiple levels, from individual patient to population disease management and infection control. This study aimed to evaluate current practice at a paediatric tertiary hospital against Australasian Society for Infectious Diseases 2016 guidelines. METHODS Prospective audit was undertaken. All positive C. difficile tests (by two step immunoassay then polymerase chain reaction) over 6 month period were reviewed for appropriateness of testing, including review of clinical characteristics and treatment of appropriately requested positive tests (CDI cases). Consecutive test requests for C. difficile over 2 month period were reviewed for appropriateness of testing. RESULTS Of 70 consecutive test requests, 64 met laboratory criteria for processing. Of these, 31 (48%) out of 64 were asymptomatic or had clinically insignificant or laxative-associated diarrhoea. Overall, 44 (63%) out of 70 were deemed inappropriate requests. Of 45 positive tests, 17 (38%) were appropriately requested. Amongst inappropriate requests, 13 (46%) out of 28 were treated; those aged >2 years were significantly more likely to be treated (P

Purpose While many guidelines recommend higher doses of cefazolin for patients with higher body weights, there are scant outcome data showing the benefit of higher doses. Surgical site infection (SSI) rates by dose of cefazolin used for surgical prophylaxis after hip or knee arthroplasty were analyzed. Methods Analysis of patient data entered into New Zealand’s national, prospective, surveillance and quality improvement SSI Improvement Programme database for the period July 2013 through December 2017 was conducted. The US Centers for Disease Control and Prevention’s National Healthcare Safety Network SSI definitions were used, and patients were followed for 90 days after surgery. Underdosing was defined as use of 1 g of cefazolin in patients weighing 80 kg or more or a cefazolin dose of Results There were 38,288 procedures where cefazolin was used for prophylaxis; patient body weight was known for all these procedures. Of the 1,840 patients who received 1 g of cefazolin, 676 (37%) weighed 80 kg or more. Of the 2,011 patients weighing 120 kg or more, 1,464 (73%) were underdosed. After multivariable analysis, male gender, higher total surgical risk scores, performance of revision and hip arthroplasties, and cefazolin underdosing were associated with higher SSI rates. For the 2,106 underdosed patients, the odds ratio for SSI was 2.19 (95% confidence interval, 1.61-2.99; P < 0.0001). The number of higher-weight patients needed to treat to prevent 1 SSI was 83, with an estimated cost of Conclusion Patients undergoing hip or knee arthroplasty and with weights of ≥80 kg and those with weights of ≥120 kg should receive cefazolin doses of 2 g and ≥3 g, respectively, for SSI prophylaxis. The question of whether a dose of ≥4 g is needed in patients weighing 120 kg or more or who are above a given body mass index threshold (eg, >35 kg/m2 or >40 kg/m2) remains unanswered.

Summary Background Legionnaires' disease is under-diagnosed because of inconsistent use of diagnostic tests and uncertainty about whom to test. We assessed the increase in case detection following large-scale introduction of routine PCR testing of respiratory specimens in New Zealand. Methods LegiNZ was a national surveillance study done over 1-year in which active case-finding was used to maximise the identification of cases of Legionnaires' disease in hospitals. Respiratory specimens from patients of any age with pneumonia, who could provide an eligible lower respiratory specimen, admitted to one of 20 participating hospitals, covering a catchment area of 96% of New Zealand's population, were routinely tested for legionella by PCR. Additional cases of Legionnaires' disease in hospital were identified through mandatory notification. Findings Between May 21, 2015, and May 20, 2016, 5622 eligible specimens from 4862 patients were tested by PCR. From these, 197 cases of Legionnaires' disease were detected. An additional 41 cases were identified from notification data, giving 238 cases requiring hospitalisation. The overall incidence of Legionnaires' disease cases in hospital in the study area was 5·4 per 100 000 people per year, and Legionella longbeachae was the predominant cause, found in 150 (63%) of 238 cases. Interpretation The rate of notified disease during the study period was three-times the average over the preceding 3 years. Active case-finding through systematic PCR testing better clarified the regional epidemiology of Legionnaires' disease and uncovered an otherwise hidden burden of disease. These data inform local Legionnaires' disease testing strategies, allow targeted antibiotic therapy, and help identify outbreaks and effective prevention strategies. The same approach might have similar benefits if applied elsewhere in the world. Funding Health Research Council of New Zealand.

Background Clostridioides difficile Infection (CDI) is a form of antibiotic associated infectious diarrhoea resulting in significant morbidity and mortality. Community acquired disease in low risk individuals is increasingly recognised. There are limited New Zealand data published. Aim To determine the incidence and location of onset of CDI cases in the Manawatu region, and further describe the demographics, risk factors and prevalent C. difficile ribotypes of the population. Methods We performed an incidence case-control study of CDI in the Manawatu region between September 2018 and September 2019. Cases were matched to controls with a negative test for C. difficile. Demographic and comorbidity data, location of onset, drug exposure, disease recurrence and 30-day mortality were collected. Ribotype analysis was performed on C. difficile isolates. Results 32 specimens tested toxin positive over twelve months, yielding an incidence of 18.3 cases per 100,000 person-years. 25% of cases had community onset disease. Cases were more likely to have had amoxicillin/clavulanate or ceftriaxone prescribed. Elevated blood white cell count and lower HbA1c were significantly associated with CDI. The dominant ribotype was 014/020, 2 cases were RT 023. Conclusion Our data are similar to previous national data. RT 023 has not been previously reported in New Zealand and has been associated with severe colitis. We demonstrated a significant proportion of community acquired cases and the true incidence may be higher. Vigilance for community onset disease is required. This data may allow observation of temporal changes in incidence and infection patterns of CDI in New Zealand. This article is protected by copyright. All rights reserved.

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., This study shows that 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 New Zealand. The figure was created with BioRender.com.

ObjectivesCirculating 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.MethodsA triplex bead-based assay that detects antibody isotype (IgG, IgM and IgA) and subclass (IgG1, IgG2, IgG3, IgG4) responses against Nucleocapsid (N) protein, 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 eight 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.ResultsWhile 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 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.ConclusionAntibodies to SARS-CoV-2 persist for up to eight 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.

We conducted a multicentre cross sectional observational study of laboratory, public health and hospitalisation data for PCR-confirmed COVID-19 cases within the New Zealand Northern Region, between 12 February and 8 June 2020. The aim of this study was to describe population level SARS-CoV-2 upper respiratory tract (URT) viral load dynamics by stratifying positivity rates and polymerase chain reaction (PCR) cycle threshold (Ct) values of URT samples from COVID-19 cases by days since symptom onset, and to explore utility of Ct values in determining length of time post-infection and thus potential infectivity. Of 123,124 samples tested for SARS-CoV-2 by PCR, 579 samples (407 positive and 172 negative) from 368 symptomatic non-hospitalised individuals with PCR-confirmed infection were included. Sample positivity rate was 61.5% (8/13) for pre-symptomatic samples, rising to 93.2% (317/340) for samples collected during the purported symptomatic infectious period (days 0–10 post-symptom onset), and dropping to 36.3% (82/226) for post-infectious period samples (day 11 onwards). URT viral load peaked shortly after symptom onset, with median Ct values ranging 20.00–29.99 until 15 days post-symptom onset, and >30.00 after this time. Of samples with a Ct value of

Background Serological assays that detect antibodies to SARS-CoV-2 are critical for determining past infection and investigating immune responses in the COVID-19 pandemic. We established ELISA-based immunoassays using locally produced antigens when New Zealand went into a nationwide lockdown and the supply chain of diagnostic reagents was a widely held domestic concern. The relationship between serum antibody binding measured by ELISA and neutralising capacity was investigated using a surrogate viral neutralisation test (sVNT). Methods A pre-pandemic sera panel (n = 113), including respiratory infections with symptom overlap with COVID-19, was used to establish assay specificity. Sera from PCR‑confirmed SARS-CoV-2 patients (n = 21), and PCR-negative patients with respiratory symptoms suggestive of COVID-19 (n = 82) that presented to the two largest hospitals in Auckland during the lockdown period were included. A two-step IgG ELISA based on the receptor binding domain (RBD) and spike protein was adapted to determine seropositivity, and neutralising antibodies that block the RBD/hACE‑2 interaction were quantified by sVNT. Results The calculated cut-off (>0.2) in the two-step ELISA maximised specificity by classifying all pre-pandemic samples as negative. Sera from all PCR-confirmed COVID-19 patients were classified as seropositive by ELISA ≥7 days after symptom onset. There was 100% concordance between the two-step ELISA and the sVNT with all 7+ day sera from PCR‑confirmed COVID-19 patients also classified as positive with respect to neutralising antibodies. Of the symptomatic PCR-negative cohort, one individual with notable travel history was classified as positive by two-step ELISA and sVNT, demonstrating the value of serology in detecting prior infection. Conclusions These serological assays were established and assessed at a time when human activity was severely restricted in New Zealand. This was achieved by generous sharing of reagents and technical expertise by the international scientific community, and highly collaborative efforts of scientists and clinicians across the country. The assays have immediate utility in supporting clinical diagnostics, understanding transmission in high-risk cohorts and underpinning longer‑term ‘exit’ strategies based on effective vaccines and therapeutics.

In humans, there is an endogenous, near 24-h (i.e., circadian) variation in mood with the best mood occurring during the circadian day and the worst mood occurring during the circadian night. Only positive affect, and not negative affect, has been shown to contribute to this circadian rhythm. We discovered a sharp circadian peak in negative affect during the circadian night coincident with a circadian trough in positive affect. These findings may help explain the association of depression with insomnia, the increased risk of suicide with nocturnal wakefulness, and the correlation between circadian misalignment and symptom severity in Major Depressive Disorder.

We reviewed the antifungal susceptibility testing results of local yeast isolates (2001-2015) to record the impact of recently updated interpretive criteria and epidemiological cut-off values (ECVs) for yeast species.Susceptibility testing was performed using SensititreA total of 2345 isolates were tested; 62.0% were from sterile body sites or tissue. Application of new CLSI interpretative criteria for fluconazole increased the proportion of non-susceptible isolates of Candida parapsilosis, Candida tropicalis and Candida glabrata (P≤0.03 for all species). For voriconazole, the greatest increase was for C. tropicalis (P0.0001). Application of new CLSI interpretive criteria for caspofungin increased the proportion of non-susceptible isolates for C. glabrata and Pichia kudriavzevii (P0.0001 for both). The new amphotericin ECV (≤2mg/L) did not reveal any non-wild-type (non-WT) isolates in the five species covered. YeastOne itraconazole ECVs detected 2%, 5% and 6% non-WT isolates for P. kudriavzevii, C. tropicalis and C. glabrata, respectively. No itraconazole non-WT isolates of Clavispora lusitaniae were detected.Whilst most results are similar to other large surveys of fungal susceptibility, the new CLSI interpretive criteria significantly altered the proportion of non-susceptible isolates to fluconazole, voriconazole and caspofungin for several Candida spp. Application of CLSI and YeastOne-derived ECVs revealed the presence of a low proportion of non-WT isolates for many species. The results serve as a baseline to monitor the susceptibility of Candida and other yeast species in New Zealand over time.

There is a growing body of literature on infection with nontuberculous mycobacteria (NTM) associated with heater chiller units in the cardiac surgery population. We report a pediatric case undergoing reoperation for early right ventricle-to-pulmonary artery conduit stenosis. A successful outcome was achieved following excision of the infected conduit and six-week antibiotic treatment. To our knowledge, there is only one other pediatric cardiac case reported in the literature. Similar to the recently reported cases of infection associated with Mycobacterium chimaera in predominately adult patients after cardiac bypass surgery, we hypothesize that water-containing devices such as the heater chiller unit and water blanket acted as a reservoir for other NTM. With increasing awareness of NTM, we analyzed the 2015-2016 culture data on our fleet of eight heater chiller units. We identified an association between persistent positive cultures and the connection of a water mattress to the heater chiller unit circuit. This led us to abandoning the use of the mattress in pediatric cardiac surgery.

Surgical site infections (SSIs) are serious adverse events hindering surgical patients' recovery. In Australia and New Zealand, SSIs are a huge burden to patients and healthcare systems. A bundled approach, including pre-theatre nasal and/or skin decolonization has been used to reduce the risk of staphylococcal infection. The aim of this review is to assess the effectiveness of the bundle in preventing SSIs for cardiac and orthopaedic surgeries. The review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. Published literature was searched in PubMed, Embase and Cochrane Library of Systematic reviews. Identified articles were selected and extracted based on a priori defined Population-Intervention-Comparator-Outcome and eligibility criteria. Data of randomized controlled trials (RCTs) and comparative observational studies were synthesized by meta-analyses. Quality appraisal tools were used to assess the evidence quality. The review included six RCTs and 19 observational studies. The bundled treatment regimens varied substantially across all studies. RCTs showed a trend of Staphylococcus aureus SSIs reduction due to the bundle (relative risk = 0.59, 95% confidence interval (CI) = 0.33, 1.06) with moderate heterogeneity. Observational studies showed statistically significant reduction in all-cause and S. aureus SSIs, with 51% (95% CI = 0.41, 0.59) and 47% (95% CI = 0.35, 0.65), respectively. No publication biases were detected. SSIs in major cardiac and orthopaedic surgeries can be effectively reduced by approximately 50% with a pre-theatre patient care bundle approach.

Introduction The prevalence of mood disorders such as depression is higher in individuals with obstructive sleep apnea (OSA). Previous studies have found no significant correlation between the apnea-hypopnea index (AHI) and measures of mood and have only included participants who met diagnostic criteria for OSA. The current analysis sought to determine whether mood correlated with AHI in individuals with any AHI values including those that did not meet diagnostic criteria for OSA. Methods 31 volunteers were studied (BMI=29.2±1.0 kg/m2, mean±SE), free from medication and without psychiatric illness or chronic medical conditions with the exception of untreated OSA, uncomplicated hypertension (BP Results The average AHI was 15.3±3.1 (range of 1.1-74.1) events per hour. The average POMS-B TMD score was 21±1.5 (range of 4-46). There was a significant correlation between the POMS-B TMD score and AHI (p=0.037, r2=0.14). This result was also seen in only those individuals with AHI scores >5 (p=0.002, r2=0.4). Conclusion In this sample, individuals with higher AHI values displayed higher TMD scores. These results differ from previous data that showed no significant correlation between AHI and TMD. This is the first analysis to demonstrate a correlation between TMD and AHI while including individuals who didn’t meet diagnostic criteria for OSA. However, the relationship between AHI and TMD was also significant in those with AHI>5. More data on these measures with larger sample sizes and a more equal representation of AHI values should be gathered to provide additional evidence for this relationship. Support: Support NIH R01-HL125893; CTSA UL1TR000128, R21HL140377

ObjectiveTo evaluate what is currently known about the risk to surgeons and other operating theatre (OT) staff of human papillomavirus (HPV) transmission and HPV-related disease following surgical smoke exposure.MethodsA systematic literature search of Embase and Ovid-MEDLINE was undertaken for primary studies relevant to the presence of HPV in surgical smoke, contamination of OT staff with HPV after performing or attending smoke-generating surgical procedures, and the presence of HPV or HPV-related disease in OT staff following occupational surgical smoke exposure. Additional articles were identified by searching the reference lists of relevant published papers.ResultsTwenty-one relevant articles were identified. These demonstrate that surgical smoke from the treatment of HPV-related lesions can contain HPV DNA, and that this can contaminate the upper airways of OT staff. Whether this corresponds to infectious virus is not known. Increased prevalence of HPV infection or HPV-related disease in OT staff following occupational exposure to surgical smoke has not been convincingly shown.ConclusionsWhile HPV transmission to OT staff from surgical smoke remains unproven, it would be safest to treat surgical smoke as potentially infectious. Necessary precautions should be taken when performing smoke-generating procedures, consisting of: (1) local exhaust ventilation, (2) general room ventilation and (3) full personal protective equipment including a fit tested particulate respirator of at least N95 grade. There is currently insufficient evidence to recommend HPV vaccination for OT staff or to state that the above precautions, when used properly, would not be effective at preventing HPV transmission from surgical smoke.

Background Postoperative infection is a serious problem in New Zealand and internationally with considerable human and financial costs. Also, in New Zealand, certain factors that contribute to postoperative infection are more common in Māori and Pacific populations. To date, most efforts to reduce postoperative infection have focussed on surgical aspects of care and on antibiotic prophylaxis, but recent research shows that anaesthesia providers may also have an impact on infection transmission. These providers sometimes exhibit imperfect hand hygiene and frequently transfer the blood or saliva of their patients to their work environment. In addition, intravenous medications may become contaminated whilst being drawn up and administered to patients. Working with relevant practitioners and other experts, we have developed an evidence-informed bundle to improve key aseptic practices by anaesthetists with the aim of reducing postoperative infection. The key elements of the bundle are the filtering of compatible drugs, context-relevant hand hygiene practices and enhanced maintenance of clean work surfaces. Methods We will seek support for implementation of the bundle from senior anaesthesia and hospital leadership and departmental “champions”. Anaesthetic teams and recovery room staff will be educated about the bundle and its potential benefits through presentations, written material and illustrative videos. We will implement the bundle in operating rooms where hip or knee arthroplasty or cardiac surgery procedures are undertaken in a five-site, stepped wedge, cluster randomised, quality improvement design. We will compare outcomes between approximately 5000 cases before and 5000 cases after implementation of our bundle. Outcome data will be collected from existing national and hospital databases. Our primary outcome will be days alive and out of hospital to 90 days, which is expected to reflect all serious postoperative infections. Our secondary outcome will be the rate of surgical site infection. Aseptic practice will be observed in sampled cases in each cluster before and after implementation of the bundle. Discussion If effective, our bundle may offer a practical clinical intervention to reduce postoperative infection and its associated substantial human and financial costs. Trial registration Australian New Zealand Clinical Trials Registry, ACTRN12618000407291. Registered on 21 March 2018. Electronic supplementary material The online version of this article (10.1186/s13063-019-3402-8) contains supplementary material, which is available to authorized users.

The Mycobacterium tuberculosis complex lineage 4 (L4), also known as the “Euro-American” lineage, is the most widely dispersed of the seven human adapted lineages. L4 is comprised of ten sublineages including L4.4, which has a moderate global distribution and is the most common L4 sublineage in New Zealand. We have used a phylodynamics approach and a dataset of 236 global M. tuberculosis genomes to trace the origins and dispersal of L4.4 strains in New Zealand that are predominantly found in Māori and Pacific people. We identify an L4.4.1.1 sublineage clade of European origin, likely French, that is prevalent in indigenous populations in both New Zealand and Canada. Molecular dating suggests that expansion of European trade networks in the early 19th century led to dispersal of this clade to the South Pacific. We also identify historical and social factors within the region that have contributed to the local spread and expansion of these strains, including recent Pacific migrations to New Zealand and the rapid urbanization of Māori in the 20th century. Our results offer new insight into the dispersal of M. tuberculosis in the South Pacific region and provide a striking example of the role of historical European migrations in the dispersal of M. tuberculosis.Author SummaryTuberculosis kills more people worldwide than any other infectious disease and indigenous populations are disproportionately affected by the disease. Here, we have used a large global dataset of Mycobacterium tuberculosis bacterial genomes to trace the historical origins of tuberculosis strains in New Zealand that are most frequently found in Māori and Pacific people. These strains are locally known as the ‘Rangipo’ and ‘Otara’ strains (both Māori place names) and belong to the “Euro-American” lineage of M. tuberculosis. Via genome analysis, we find that these strains are closely related to M. tuberculosis strains found in indigenous populations in Canada that have a European origin. We used a molecular dating approach (a molecular clock) to infer the ages of these strains and date divergence events. The timing we infer corresponds to the introduction of these strains to Polynesia via expanding European trade networks in the South Pacific in the early 19th century and suggests that the Otara strain has migrated to New Zealand from the Pacific Islands multiple times. Our results provide insight into human social phenomena underlying the expansion and dispersal of M. tuberculosis and reassert the important role of European colonial migrations in the global dispersal of the M. tuberculosis Euro-American lineage. This work also highlights the pejorative and stigmatizing mislabelling of the New Zealand strains with indigenous Māori place names, suggesting that these strains should be renamed.

New Zealand has a low burden of multi-drug resistant TB (MDR-TB), but with increased mobility within the population, rapid detection and treatment of MDR-TB is a priority from the public health point of view. Mycobacterium Reference Laboratory in LabPLUS, Auckland City Hospital receives referred Mycobacterium tuberculosis complex (MTBC) isolates from all over New Zealand for second-line drug susceptibility testing (DST) and 24-loci MIRU VNTR genotyping. Between 2002 and 2013, 38 multidrug resistant Mycobacterium tuberculosis (MDR-TB) isolates were recorded by culture-based DST. A retrospective study revealed that in 12 of these 38 MDR-TB isolates (28%) there was a discrepancy between the genotypic and the phenotypic results. In order to address this, whole genome sequencing (WGS) was performed on the discrepant MDR-TB isolates. Reported here are the additional information on the drug resistant markers from WGS, which shed light on the discordance between results from the culture-based DST and the molecular diagnostic tests. These results underscore the utility of WGS in a reference mycobacterium laboratory in New Zealand to supplement other molecular tests and to assist in a rapid but accurate diagnosis and appropriate management of MDR-TB.

Measurements of aldosterone for diagnosis of primary aldosteronism are usually made from blood sampled in the morning when aldosterone typically peaks. We tested the relative contributions and interacting influences of the circadian system, ongoing behaviors, and prior sleep to this morning peak in aldosterone. To determine circadian rhythmicity and separate effects of behaviors on aldosterone, 16 healthy participants completed a 5-day protocol in dim light while all behaviors ranging from sleep to exercise were standardized and scheduled evenly across the 24-h circadian period. In another experiment, to test the separate effects of prior nocturnal sleep or the inactivity that accompanies sleep on aldosterone, 10 healthy participants were studied across 2 nights: 1 with sleep and 1 with maintained wakefulness (randomized order). Plasma aldosterone was measured repeatedly in each experiment. Aldosterone had a significant endogenous rhythm ( P < 0.001), rising across the circadian night and peaking in the morning (~8 AM). Activity, including exercise, increased aldosterone, and different behaviors modulated aldosterone differently across the circadian cycle (circadian phase × behavior interaction; P < 0.001). In the second experiment, prior nocturnal sleep and prior rested wakefulness both increased plasma aldosterone ( P < 0.001) in the morning, to the same extent as the change in circadian phases between evening and morning. The morning increase in aldosterone is due to effects of the circadian system plus increased morning activities and not prior sleep or the inactivity accompanying sleep. These findings have implications for the time of and behaviors preceding measurement of aldosterone, especially under conditions of shift work and jet lag.

Adverse cardiovascular events, such as myocardial infarction and sudden cardiac death, occur more frequently in the morning. Prior studies have shown that vascular endothelial function (VEF), a marker of cardiovascular disease, is attenuated during physical inactivity and declines across the night. We sought to determine whether a morning attenuation in VEF is a result of prior sleep or the inactivity that inevitably accompanies sleep. After 1 wk of a rigorously controlled sleep-wake schedule and behaviors, 10 healthy participants completed a randomized crossover protocol in dim light and constant conditions, incorporating a night of 6 h of sleep opportunity and a night of immobility while they were supine and awake. VEF was measured in the dominant brachial artery as flow mediated dilation (FMD) before and after each 6-h trial. To avoid disturbing sleep and posture of the participants, blood was drawn using a 12-ft catheter from an adjoining laboratory room before, during, and after each 6-h trial, and plasma was analyzed for markers of oxidative stress [malondialdehyde adducts (MDA)], and endothelin-1. Contrary to expectation, both nocturnal sleep and nocturnal inactivity significantly increased FMD ( P < 0.05). There was no significant change in MDA or endothelin-1 within and between trials. Contrary to expectations based on prior studies, we found that overnight sleep or the inactivity that accompanies sleep did not result in attenuation in VEF in the morning hours in healthy people. Thus, it is plausible that the endogenous circadian system, a remaining factor not studied here, is responsible for the commonly observed decline in VEF across the night.

The New Zealand Surgical Site Infection Improvement (SSII) Programme was established in 2013 to reduce the incidence of surgical site infections (SSI) in publicly funded hip and knee arthroplasties in New Zealand hospitals.The programme pursued a three-pronged strategy: 1. Surveillance of SSI with a nationwide system 2. Promotion of consistent adherence to evidence-based practices proven to reduce SSI 3. Monitoring and publicly reporting changed practice and outcome data.Between quarter 3 2013 and quarter 4 2016 there has been a nationwide increase in compliance with all process measures: correct timing for antibiotic prophylaxis; use of the recommended antibiotic in the recommended dose and alcohol-based skin antisepsis. The SSI rate in hip and knee arthroplasties has shown a significant improvement. The nationwide median rate has fallen to 0.91% since June 2015, compared with 1.36% during the baseline period of April 2013 to March 2014 (p0.01). This equates to approximately 55 fewer infections between August 2015 and June 2017, savings of NZD$2.2 million in avoided treatment and avoided disability-adjusted life years (DALYs) of NZD$5 million.The introduction of a nationwide SSI reduction programme for hip and knee arthroplasties resulted in an increase in compliance across the country with best practice that was associated with a reduction in incidence of SSI since June 2015 from the baseline period of April 2013 to March 2014, sustained to June 2017.

The yeast Candida albicans is an important opportunistic human pathogen. For C. albicans strain typing or drug susceptibility testing, a single colony recovered from a patient sample is normally used. This is insufficient when multiple strains are present at the site sampled. How often this is the case is unclear. Previous studies, confined to oral, vaginal and vulvar samples, have yielded conflicting results and have assessed too small a number of colonies per sample to reliably detect the presence of multiple strains. We developed a next-generation sequencing (NGS) modification of the highly discriminatory C. albicans MLST (multilocus sequence typing) method, 100+1 NGS-MLST, for detection and typing of multiple strains in clinical samples. In 100+1 NGS-MLST, DNA is extracted from a pool of colonies from a patient sample and also from one of the colonies. MLST amplicons from both DNA preparations are analyzed by high-throughput sequencing. Using base call frequencies, our bespoke DALMATIONS software determines the MLST type of the single colony. If base call frequency differences between pool and single colony indicate the presence of an additional strain, the differences are used to computationally infer the second MLST type without the need for MLST of additional individual colonies. In mixes of previously typed pairs of strains, 100+1 NGS-MLST reliably detected a second strain. Inferred MLST types of second strains were always more similar to their real MLST types than to those of any of 59 other isolates (22 of 31 inferred types were identical to the real type). Using 100+1 NGS-MLST we found that 7/60 human samples, including three superficial candidiasis samples, contained two unrelated strains. In addition, at least one sample contained two highly similar variants of the same strain. The probability of samples containing unrelated strains appears to differ considerably between body sites. Our findings indicate the need for wider surveys to determine if, for some types of samples, routine testing for the presence of multiple strains is warranted. 100+1 NGS-MLST is effective for this purpose.

This study aims to determine the indications for antibiotic use in patients discharged following major surgery at Auckland City Hospital (ACH); to determine if the indications were appropriate and to identify opportunities where antimicrobial stewardship interventions would be beneficial.This was a retrospective study of adult patients who were dispensed an antibiotic within the first two days of discharge after major surgery at ACH between 1 January 2013 and 31 December 2013. The indication for antibiotic use was determined and subsequently classified as either 'appropriate', 'not assessable' or 'inappropriate'.Among the 378 patients analysed, an indication for antibiotic use was not documented in 52 patients (13.8%). Antibiotics were prescribed for an established infection in 172 patients (45.5%), as empiric therapy in 100 patients (26.4%), and as prolonged surgical antimicrobial prophylaxis in 41 patients (10.8%). Overall, nearly half of the antibiotic courses dispensed (48.7%) were either 'inappropriate' or the indication was 'not assessable'.This study demonstrates that a significant proportion of antibiotics prescribed in patients discharged following surgery are inappropriate and there is need for enhanced antimicrobial stewardship in this area.

Purpose of Review This phenomenological study explored the lived experience of six adults with developmental coordination disorder (DCD) and its potential impact on functional mobility. Utilising the International Classification of Functioning (World Health Organisation, 2001), the data derived from interviews were analysed to consider how persistent motor impairments impact on activity engagement and participation. Recent Findings Much of the research evidence pertaining to DCD focuses on children. However, there is increasing acknowledgment that for some, the motor impairments synonymous with DCD continue into adulthood. Summary The findings from this study suggest that for this group of participants, functional mobility can be compromised, restricting activity and participation. At a body structure/function level, participants identified additional impairments that moved beyond mobility, suggesting that the secondary consequences of fatigue and anxiety were disabling. However, personal factors were seen to mitigate some difficulties encountered to allow participants to remain actively engaged in a range of adult roles.

Background Vancomycin-resistant Enterococcus faecium (VRE) is a leading cause of hospital-acquired infections. New, presumably better-adapted strains of VRE appear unpredictably; it is uncertain how they spread despite improved infection control. We aimed to investigate the relatedness of a novel sequence type (ST) of vanB E. faecium - ST796 - very near its time of origin from hospitals in three Australian states and New Zealand. Methods Following near-simultaneous outbreaks of ST796 in multiple institutions, we gathered then tested colonization and bloodstream infection isolates’ antimicrobial resistance (AMR) phenotypes, and phylogenomic relationships using whole genome sequencing (WGS). Patient meta-data was explored to trace the spread of ST796. Results A novel clone of vanB E. faecium (ST796) was first detected at one Australian hospital in late 2011, then in two New Zealand hospitals linked by inter-hospital transfers from separate Melbourne hospitals. ST796 also appeared in hospitals in South Australia and New South Wales and was responsible for at least one major colonization outbreak in a Neonatal Intensive Care Unit without identifiable links between centers. No exceptional AMR was detected in the isolates. While WGS analysis showed very limited diversity at the core genome, consistent with recent emergence of the clone, clustering by institution was observed. Conclusions Evolution of new E. faecium clones, followed by recognized or unrecognized movement of colonized individuals then rapid intra-institutional cross-transmission best explain the multi-center, multistate and international outbreak we observed. Electronic supplementary material The online version of this article (10.1186/s13756-018-0335-z) contains supplementary material, which is available to authorized users.

Introduction The latest edition of the Diagnostic and Statistical Manual of Mental Disorders has attempted to recognise the pervasiveness of developmental coordination disorder across the lifespan. However, it falls short at describing the non-motoric symptomology such as executive functioning, social, emotional and psychiatric difficulties commonly reported in adults. Consequently, at the point of entry the self-reported functional difficulties of an adult with developmental coordination disorder may not be immediately associated with an underlying deficit within a motor domain, potentially resulting in inappropriate referrals. Method This study aimed to explore the reasons why 16 adults without a previous diagnosis of developmental coordination disorder referred themselves for a clinical assessment and consider whether their significant motor difficulties would be apparent. Results The primary self-reported concerns related to executive functioning difficulties, activities of daily living, changes in routine and social interaction and engagement. The least common self-reported concerns included gross motor skills. Conclusion Practitioners at the point of entry need to be mindful that adults with significant motor difficulties may not identify motor difficulties as their primary concern. It is, therefore, important to include screening for motor difficulties and for a future clinical landscape to comprise a referral pathway to adult neurodevelopmental clinics incorporating multidisciplinary teams.

To identify patient and surgical risk factors that are associated with periprosthetic joint infection (PJI), especially whether obesity is a risk factor following total hip arthroplasty (THA) and total knee arthroplasty (TKA).New Zealand Surgical Site Infection Improvement Programme data was analysed using deep infection within 90 days of the index procedure as the outcome. This was tested against surgical and patient factors for statistical associations in a multivariate model.A total of 10,690 primary THAs and 9,481 primary TKAs were recorded by the NZSSIIP between 2013 and 2015. Multivariate analysis showed statistically significant associations with deep infections for BMI (BMI40kg/m2 OR 5.62, 95% CI 2.25-14.0), male gender (OR 1.7, 95% CI 1.05-2.74) and age greater than 75 for THAs (age55 years OR 0.35, 95% CI 0.14-0.87). For TKAs, multivariate analysis showed statistically significant associations with deep infection for BMI (BMI40kg/m2 OR 1.94, 95% CI: 0.63-5.70) and male gender (OR 2.96, 95% CI 1.51-5.80).These findings show that obesity is one of the most important modifiable patient factors in predicting PJI following THA and TKA.

M ycoplasma genitalium has been implicated as a cause of acute and chronic nonchlamydial nongonococcal urethritis (NCNGU) and pelvic inflammatory disease (PID) ([1][1]). In New Zealand, as with many other countries, the preferred treatment for NCNGU is either azithromycin or doxycycline ([2][2]).

This report describes the introduction of an extensively antibiotic-resistant carbapenemase-producing Escherichia coli into a hospital in Auckland, New Zealand, by a patient who was a household contact of recent travellers to the Indian subcontinent. The carbapenemase was identified as New Delhi metallo-β-lactamase (NDM) and reflects probable household transmission in the context of a recent upsurge in NDM-producing Enterobacteriaceae isolation in New Zealand. The observations in this report suggest that hospital screening practices to identify carbapenemase-producing Enterobacteriaceae (CPE) colonised patients may need to be extended to include travellers to high-risk countries who were not hospitalised during their trip, and possibly also their close contacts.

Global forced displacement has climbed to unprecedented levels due largely to regional conflict. Degraded public health services leave displaced people vulnerable to multiple environmental and infectious hazards including vaccine preventable disease. While diphtheria is rarely notified in New Zealand, a 2 person outbreak of cutaneous diphtheria occurred in refugees from Afghanistan in February 2015 at the refugee resettlement centre in Auckland. Both cases had uncertain immunisation status. The index case presented with a scalp lesion during routine health screen and toxigenic Corynebacterium diphtheriae was isolated. A secondary case of cutaneous diphtheria and an asymptomatic carrier were identified from skin and throat swabs. The 2 cases and 1 carrier were placed in consented restriction until antibiotic treatment and 2 clearance swabs were available. A total of 164 contacts were identified from within the same hostel accommodation as well as staff working in the refugee centre. All high risk contacts (n=101) were swabbed (throat, nasopharynx and open skin lesions) to assess C. diphtheriae carriage status. Chemoprophylaxis was administered (1 dose of intramuscular benzathine penicillin or 10 days of oral erythromycin) and diphtheria toxoid-containing vaccine offered regardless of immunisation status. Suspected cases were restricted on daily monitoring until swab clearance. A group of 49 low risk contacts were also offered vaccination. Results suggest a significant public health effort was required for a disease rarely seen in New Zealand. In light of increased worldwide forced displacement, similar outbreaks could occur and require a rigorous public health framework for management.

We retrospectively examined medical records of 87 patients with bacteraemia caused by members of the HACEK group (Haemophilus parainfluenzae, Aggregatibacter actinomycetemcomitans, Aggregatibacter aphrophilus, Aggregatibacter paraphrophilus, Cardiobacterium spp., Eikenella corrodens and Kingella spp.) to determine whether endocarditis was present, as defined by the Duke criteria. The overall positive predictive value (PPV) of HACEK bacteraemia for endocarditis was 60 %. The PPV varied with different HACEK species from 0 % (E. corrodens) to 100 % (A. actinomycetemcomitans).

BACKGROUND New Zealand is a developed country with high incidence of bacterial infections and postinfectious sequelae including rheumatic heart disease. We sought to describe the clinical and microbiology features of children with infective endocarditis (IE) between 1994 and 2012. METHODS Retrospective review of patients

Despite New Zealand being a low-tuberculosis (TB) burden country, there are disproportionately high rates of TB in particular populations. Here, we report a rapid molecular diagnosis of the Mycobacterium tuberculosis Rangipo strain responsible for the largest recurring TB cluster in New Zealand.