Early identification of a ward-based outbreak of Clostridioides difficile using prospective multilocus sequence type-based Oxford Nanopore genomic surveillance.

OBJECTIVE: To describe an outbreak of sequence type (ST)2 Clostridioides difficile infection (CDI) detected by a recently implemented multilocus sequence type (MLST)-based prospective genomic surveillance system using Oxford Nanopore Technologies (ONT) sequencing. SETTING: Hemato-oncology ward of a public tertiary referral centre. METHODS: From February 2022, we began prospectively sequencing all C. difficile isolated from inpatients at our institution on the ONT MinION device, with the output being an MLST. Bed-movement data are used to construct real-time ST-specific incidence charts based on ward exposures over the preceding three months. RESULTS: Between February and October 2022, 76 of 118 (64.4%) CDI cases were successfully sequenced. There was wide ST variation across cases and the hospital, with only four different STs being seen in >4 patients. A clear predominance of ST2 CDI cases emerged among patients with exposure to our hemato-oncology ward between May and October 2022, which totalled ten patients. There was no detectable rise in overall CDI incidence for the ward or hospital due to the outbreak. Following a change in cleaning product to an accelerated hydrogen peroxide wipe and several other interventions, no further outbreak-associated ST2 cases were detected. A retrospective phylogenetic analysis using original sequence data showed clustering of the suspected outbreak cases, with the exception of two cases that were retrospectively excluded from the outbreak. CONCLUSIONS: Prospective genomic surveillance of C. difficile using ONT sequencing permitted the identification of an outbreak of ST2 CDI that would have otherwise gone undetected.

Incorporating patient, nursing and environmental factors into antimicrobial stewardship: effects of simplifying treatment from cefuroxime to ceftriaxone.

AIM: Our antimicrobial guidelines (AGs) were changed in 2021 to recommend once-daily ceftriaxone in place of three-times-daily cefuroxime as preferred cephalosporin. This analysis sought to assess the effects of this on incidence of Clostridioides difficile infection (CDI), third-generation cephalosporin-resistant Enterobacterales (3GCR-E) and resource utilisation. METHOD: Before and after analysis of 30-day CDI and 3GCR-E incidence following receipt of cefuroxime/ceftriaxone pre- and post-AG change. Total nursing time and waste production relating to cefuroxime/ceftriaxone delivery were calculated pre- and post-change. RESULTS: CDI incidence was 0.6% pre- and 1.0% post-change (adjusted odds ratio [aOR] 1.44, p=0.07) and 3GCR-E incidence 3.5% and 3.1% (aOR 0.90, p=0.33). Mean per-quarter estimated nursing administration time decreased from 2,065 to 1,163 hours (902 nurse-hour reduction) and antibiotic-related waste generation from 1,131kg to 748kg (383kg reduction). Overall days of therapy per-quarter of cefuroxime/ceftriaxone were unchanged between periods. CONCLUSION: This simplification of our AG from a three-times-daily to a once-daily antibiotic resulted in considerable savings for our hospital (roughly 1.7 full-time equivalent nurses and over a tonne of waste yearly), with no significant increases in CDI or 3GCR-E. The impact of dosing schedules on non-antibiotic-spectrum factors, such as nursing time and resource usage, is worthy of consideration when designing AGs.

An exception-reporting approach for wound swab culture: effect on post-report antibiotic initiation.

A prior analysis suggested that wound swab culture (WSC) results were driving unnecessary antibiotic use in patients who were not already receiving treatment. As a quality-improvement initiative, our laboratory introduced an "exception-reporting" protocol on 1 March 2023, whereby typical wound pathogens susceptible to recommended empiric therapy (flucloxacillin/cefalexin) were not reported, and a comment was provided, stating no significant resistant organisms had been detected. Full results were available to clinicians on request. Cultures falling outside protocol criteria were reported in the standard fashion. This analysis sought to assess the effect of exception-reporting on post-report antibiotic initiation (PRAI). All community WSC results were matched to antibiotic dispensing records from October 2021 to December 2023. Sampling without treatment pre-report was termed "test and wait" (TaW). Following TaW, PRAI was identified if antibiotics were started within 5 days post-report. There were 1,819 and 764 WSCs received in the pre-change and post-change periods, respectively, where an initial TaW approach had been taken and an organism eligible for exception-reporting had been isolated. In the post-change period, 407 (53.3%) met the criteria and were exception-reported. PRAI occurred in 901 (49.5%) pre-change samples, compared to 102 (25.1%, P < 0.01) with exception-reporting. There was no detectable increase in hospitalization or repeat WSC collection in the 30 days following exception-reporting. Exception-reporting was associated with a markedly reduced proportion of patients being initiated on antibiotics following WSC where an organism had been isolated. The naming of organisms in reports appears to drive unnecessary antibiotic prescribing in many patients. These results require confirmation in other jurisdictions. IMPORTANCE: Wound swab culture is a high-volume test performed in clinical microbiology laboratories. In this analysis, we have shown that an alternative approach to reporting positive wound swab cultures has resulted in a large reduction in post-report antibiotic initiation, suggesting that the current standard method of reporting generates considerable unnecessary antibiotic use. If these findings are replicated elsewhere, wider adoption of this reporting would represent an opportunity for many clinical microbiology laboratories to have a significant impact on community antimicrobial stewardship.

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.

Effect of directive laboratory comments on prescribing response to positive throat swab cultures.

BACKGROUND: In patients without ethnicity risk factors for acute rheumatic fever (ARF), our local guidelines recommend limiting antibiotic use following a positive throat swab culture (TSC). If symptoms are severe, a 5-7 day course is recommended. Despite this, most local patients with a positive TSC for group A Streptococcus (GAS) or Streptococcus dysgalactiae subsp. equisimilis (SDSE) were being prescribed 10 days of antibiotics. In response, we added comments to positive TSC reports recommending shorter treatment durations in those without ARF risk factors. No other antimicrobial stewardship initiatives were implemented. OBJECTIVES: To assess the effect of these comments on antibiotic course duration after positive TSC. METHODS: All community TSC results from 1 October 2021 to 31 March 2023 (1 year pre- to 6 months post-change) were matched to antibiotic dispensing data. Patients who had been empirically dispensed an antibiotic prior to the culture report were excluded. The outcome of interest was the antibiotic duration dispensed in the 5 day period after the TSC report. RESULTS: Following introduction of the comments, median course duration reduced from 10 (IQR 5-10) to 7 days (IQR 0-10; P < 0.01) and from 7 (IQR 0-10) to 0 days (IQR 0-5; P < 0.01) following GAS- and SDSE-positive TSC, respectively, in those without ARF risk factors. The percentage of people receiving 10 days of antibiotics decreased from 63.0% to 37.0% (P < 0.01) and 41.2% to 14.6% (P < 0.01) for GAS and SDSE, respectively. CONCLUSIONS: The introduction of comments providing direct prescribing advice to requestors appears to have been highly effective at improving guideline-compliant prescribing following positive TSC report.

Post-report antibiotic initiation following community non-sterile-site microbiology results: an opportunity for labs to lead stewardship?

OBJECTIVES: Positive culture results from non-sterile sites (NSSs) are poorly predictive of clinical infection. Despite this, these results are often interpreted as an indication for antibiotics, even in patients with limited signs of infection. We sought to quantify the influence of NSS culture results on post-report antibiotic initiation (PRAI) in patients who had not been started on antibiotics pre-report. METHODS: All community wound/skin swab and sputum cultures were matched to antibiotic dispensing records from February 2017 to July 2022. Prescribing behaviour was assessed pre- and post-report. Sampling without treatment pre-report was termed 'test-and-wait' (TaW). Following TaW, PRAI was identified if antibiotics were started within 5 days post-report. RESULTS: There were 65 480 wound/skin swabs and 8126 sputum samples, with TaW occurring in 21 740 (35.1%) and 4185 (54.4%), respectively. Following a TaW approach PRAI occurred in 43.3% when an organism was reported, versus 10.8% (P < 0.01) for a 'no growth' report for wound/skin swabs. For the same comparison with sputum, PRAI occurred in 47.9% versus 10.8% (P < 0.01). On multivariate analysis reporting an organism remained strongly associated with PRAI. CONCLUSIONS: Reporting an organism in those not already on antibiotics was strongly associated with PRAI. We hypothesize that for many patients TaW suggests limited evidence of infection (i.e. insufficient to justify antibiotic treatment at time of sampling), meaning positive NSS results may be driving a considerable volume of potentially unnecessary antibiotic use. Further study on this topic is required, but strategies to reduce PRAI may offer laboratories an opportunity to meaningfully impact antimicrobial stewardship efforts.

Evolving swabbing practices for COVID-19 in a New Zealand emergency department during the early stages of an emerging pandemic.

OBJECTIVE: To review if tests for suspected COVID-19 were performed according to the Ministry of Health (MoH) case definitions, identify patterns associated with testing outside of the case definition, and discuss the potential impacts on hospital services. METHODS: This was a retrospective audit of patients presenting to the Wellington Hospital ED between 24 March 2020 and 27 April 2020 who were swabbed for COVID-19 in ED. Swabs were audited against the March 15th and April 8th MoH COVID-19 case definitions. RESULTS: Five hundred and thirty-six COVID-19 swabs for 518 patients were taken during the study period. There was poor alignment of testing with the March 15th case definition, with only 11.6% of the 164 swabs taken during this period meeting the case definition. Of the 145 swabs that did not meet the case definition, the majority (n = 119, 82.1%) met symptom criteria only. Alignment of testing with the wider April 8th case definition was much higher with 88.2% meeting criteria. Factors associated with being swabbed despite not meeting the case definitions included fever >38°, a diagnosis of cancer, subsequent hospital admission, and for the March case definition only 'contact with a traveller'. CONCLUSION: There were associations found between testing outside of criteria and specific variables potentially perceived as high-risk. Poor alignment of testing with case definitions can impact hospital services through the (mis)use of limited laboratory testing capacity and implications for resource management. Improved communication and feedback between clinicians and policymakers may improve case definition implementation in a clinical setting.

Effect of Blood Culture Contamination on Antibiotic Use in an Institution With Rapid Laboratory Methods and Phone-Based Clinical Follow-up of Blood Culture Results.

In a multivariate analysis of 30 574 blood culture (BC) results, BC contamination was associated with only a small increase in antibiotic length of therapy compared to no-growth BCs (difference, 0.36 days [95% confidence interval, .05-.67]; P = .02). Stewardship processes at our institution appear to be effective in reducing the impact of BC contamination.

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.

The design, validation and clinical verification of an in-house qualitative PCR to detect Yersinia enterocolitica and Yersinia pseudotuberculosis in faeces.

Yersiniosis is a zoonotic foodborne infection of public health significance. The aim of this study was to design and validate a simple, accurate and cost-effective polymerase chain reaction (PCR) to detect pathogenic Yersinia spp. in faecal samples. An intercalating dye (EvaGreen)-based real-time multiplex PCR assay was designed to detect yadA, ystB and inv by melt curve analysis, allowing undifferentiated detection of all Yersinia enterocolitica biotypes, including biotype 1A, and Yersinia pseudotuberculosis. The assay was validated using cultured bacteria and clinical samples. A total of 107 positive and 51 negative samples were tested. The sensitivity and specificity was 98% and 100%. The limit of detection was 104-105 CFU/g faeces. A total of 605 samples (9 positive) were tested in the clinical verification with an accuracy and negative predictive value of 99% [95% confidence interval (CI) 97.9-99.6%] and 99.8% (95% CI 97.9-99.6%), respectively. This is an accurate, simple and cost-effective assay for the detection of pathogenic Yersinia spp.

The burden of Legionnaires' disease in New Zealand (LegiNZ): a national surveillance study.

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.

Temporal changes in neutropenic blood culture isolates and disease associations: a single centre series of 1139 episodes.

Neutropenic infections are life-threatening and require empiric antibiotic treatment. We examined 1139 blood culture isolates from our institution over a 36-year period from neutropenic patients to examine temporal trends and disease associations. Positive associations were found between viridans streptococci and acute myeloid leukaemia, coagulase negative staphylococci and acute lymphoblastic leukaemia and Pseudomonas aeruginosa and indolent B-cell malignancies.

Lymphogranuloma venereum in men who have sex with men: evidence of local transmission in New Zealand.

Lymphogranuloma venereum (LGV) is a sexually transmitted infection caused by Chlamydia trachomatis. Five laboratory confirmed cases of LGV were detected in MSM (men who have sex with men) in the upper North Island; four in Auckland between September and December 2013 and a fifth case was detected in Waikato in June 2014. The absence of a recent travel history for four cases supports the likelihood of local transmission of this uncommon infection.

Molecular testing for viral and bacterial enteric pathogens: gold standard for viruses, but don't let culture go just yet?

Contemporary diagnostic microbiology is increasingly adopting molecular methods as front line tests for a variety of samples. This trend holds true for detection of enteric pathogens (EP), where nucleic acid amplification tests (NAAT) for viruses are well established as the gold standard, and an increasing number of commercial multi-target assays are now available for bacteria and parasites. NAAT have significant sensitivity and turnaround time advantages over traditional methods, potentially returning same-day results. Multiplex panels offer an attractive 'one-stop shop' that may provide workflow and cost advantages to laboratories processing large sample volumes. However, there are a number of issues which need consideration. Reflex culture is required for antibiotic susceptibility testing and strain typing when needed for food safety and other epidemiological investigations. Surveillance systems will need to allow for differences in disease incidence due to the enhanced sensitivity of NAAT. Laboratories should be mindful of local epidemiology when selecting which pathogens to include in multiplex panels, and be thoughtful regarding which pathogens will not be detected. Multiplex panels may not be appropriate in certain situations, such as hospital-onset diarrhoea, where Clostridium difficile testing might be all that is required, and laboratories may wish to retain the flexibility to run single tests in such situations. The clinical impact of rapid results is also likely to be relatively minor, as infective diarrhoea is a self-limiting illness in the majority of cases. Laboratories will require strategies to assist users in the interpretation of the results produced by NAAT, particularly where pathogens are detected at low levels with uncertain clinical significance. These caveats aside, faecal NAAT are increasingly being used and introduce a new era of diagnosis of gastrointestinal infection.