Characterisation of Neisseria gonorrhoeae strain differences in patients with multisite infection.

BACKGROUND: Neisseria gonorrhoeae, the aetiological agent of gonorrhoea, is an increasing global health priority due to high levels of antimicrobial resistance (AMR). It is estimated that up to 42% of patients are infected at multiple anatomical sites simultaneously. Previous studies identified that 7%-40% of those with multisite infection have different strains infecting different sites, with potentially different antimicrobial susceptibility profiles. This study aims to estimate the proportion of patients with multisite infection through differential antimicrobial susceptibility testing (AST) profiles and sequence-based molecular methods. METHODS: This was a cross-sectional study of multisite gonococcal isolates provided by three National Health Service laboratories. Minimum inhibitory concentrations (MICs) for cefixime, ceftriaxone, azithromycin, ciprofloxacin, tetracycline and spectinomycin were determined. Possible multistrain infections were defined as isolates with a significant difference in MIC to at least one antimicrobial. Whole genome sequencing (WGS) was performed to determine multistrain infection through N. gonorrhoeae multiantigen sequence typing (NG-MAST), N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR), multilocus sequencing typing (MLST) and single nucleotide polymorphism (SNP) phylogeny, and to compare AST profiles with identified AMR genes. RESULTS: Ninety-one isolates were collected from 41 patients with multisite infections. Of these 41 patients, 6 (14.6%) had N. gonorrhoeae isolates with discordant MICs. WGS-based typing confirmed that four out of six patients were infected with different gonococcal strains. The relatedness of isolates with the same MLST across multiple patients was differentiated using SNP-based analysis, and this included the identification of a potential transmission event. WGS-based AMR prediction for all antimicrobials tested correlated well with the phenotypic data. CONCLUSION: This study demonstrates that potentially a significant proportion of patients with multisite infections are infected with multiple gonococcal strains, with differing AST profiles, at different anatomical sites. This has implications for patient sampling, susceptibility testing protocols, AMR surveillance and potentially appropriate antibiotic therapy.

Strongyloidiasis in Auckland: A ten-year retrospective study of diagnosis, treatment and outcomes of a predominantly Polynesian and Fijian migrant cohort.

BACKGROUND: Strongyloides stercoralis is not endemic in Aotearoa New Zealand (AoNZ). However, approximately one third of Auckland residents are born in endemic countries. This study aimed to describe the epidemiology and management of strongyloidiasis in Auckland, with a focus on migrants from Pacific Island Countries and Territories. METHODS: This study retrospectively reviewed clinical, laboratory and pharmacy records data for all people diagnosed with strongyloidiasis in the Auckland region between July 2012 and June 2022. People with negative Strongyloides serology were included to estimate seropositivity rate by country of birth. FINDINGS: Over ten years, 691 people were diagnosed with strongyloidiasis. Most diagnoses were made by serology alone (622, 90%). The median age was 63 years (range 15-92), 500 (72%) were male, and the majority were born in Polynesia (350, 51%), Fiji (130, 19%) or were of Pasifika ethnicity (an additional 7%). Twelve participants (1.7%) had severe strongyloidiasis at diagnosis. The total proportion treated with ivermectin was only 70% (484/691), with no differences between immunocompromised and immunocompetent participants, nor by ethnicity. The outcome of treatment (based on a combination of serology and/or eosinophilia and/or stool microscopy) could only be determined in 50% of the treated cohort. One participant failed treatment with ivermectin, experiencing recurrent strongyloidiasis, and another participant died in association with severe strongyloidiasis. The rate of 'positive' Strongyloides serology was highest among participants born in Samoa (48%), Fiji (39%), and Southeast Asian countries (34%). INTERPRETATION: Strongyloidiasis was common and under-treated in Auckland during the study period. Clinicians should have a low threshold for considering strongyloidiasis in migrants from endemic countries, including Polynesia and Fiji.

Epidemiology of carbapenem resistant Acinetobacter baumannii in New Zealand.

AIM: Carbapenem resistant Acinetobacter baumannii have limited treatment options and a propensity to cause hospital outbreaks. In recent years an increase in their detection has been observed in New Zealand. This study aimed to describe the molecular epidemiology of these isolates. METHOD: This study utilised carbapenem resistant A. baumannii complex isolates identified across New Zealand between January 2010 to April 2018. Whole genome sequence analysis and associated demographic information was used to contextualise local isolates within the global epidemiology and establish the relationship between isolates. RESULTS: Thirty-three carbapenem resistant A. baumannii complex isolates (31 A. baumannii sensu stricto) were identified. Twenty-four (73%) were from January 2015 onwards. Twenty-four (73%) had an identifiable epidemiological link to overseas hospitalisation. Twenty-three (74%) of 31 A. baumannii sensu stricto were sequence type (ST) 2 (Pasteur scheme). Phylogenetic analysis identified three ST2 clusters. The largest cluster, of 12 isolates, was from 2015 onwards; with nine (75%) associated with recent hospitalisation in Fiji or Samoa. CONCLUSION: Increasing numbers of carbapenem resistant A. baumannii are being identified in New Zealand. Our data show that this is in large part associated with transnational spread of a single A. baumannii sensu stricto ST 2 strain between Fiji, Samoa and New Zealand.

Evaluation of ssrA-targeted real time PCR for the detection of Bartonella species in human clinical samples and reflex sequencing for species-level identification.

The genus Bartonella includes species capable of causing disease in animals and humans. Due to its fastidious nature, direct detection of Bartonella causing human infection relies largely on molecular microbiological methods. Thus, it is imperative that diagnostic assays in use have the ability to detect a range of Bartonella species associated with human disease. In this study, we compared the performance of a real time polymerase chain reaction (PCR) assay targeting the ssrA gene to conventional rpoB-targeted PCR and sequencing for detection and differentiation of Bartonella species in human clinical samples. The real time ssrA PCR performed better for non-Bartonella henselae species, detecting B. clarridgeiae and B. quintana DNA in heart valve specimens that were not detected by rpoB PCR, and improved the sensitivity of B. henselae detection in blood specimens. Our findings suggest the real time ssrA PCR assay is suitable for detection and identification of Bartonella species in human clinical specimens.

SARS-CoV-2 viral load dynamics and real-time RT-PCR cycle threshold interpretation in symptomatic non-hospitalised individuals in New Zealand: a multicentre cross sectional observational study.

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 <20.00, 96.1% were collected during the symptomatic infectious period. However, of samples with a Ct value ≥30.00 and ≥35.00, 46.9% and 18.5%, respectively, were also collected during the symptomatic infectious period. The findings of this study indicate that at or soon after symptom onset represents the optimum time to test for SARS-CoV-2 in the URT, with median Ct values suggesting the useful testing window extends until around 15 days post-symptom onset. In asymptomatic individuals or those with unknown dates of symptom onset, Ct values <20.00 imply recent onset/potential infectivity, but Ct values ≥30.00 or ≥35.00 do not exclude recent onset/potential infectivity. Individual sample Ct values should not be used as an absolute marker of length of time post-infection or to exclude infectivity where date of symptom onset is unavailable.

Age-related differences in SARS-CoV-2 testing in the Northern Region of New Zealand.

AIM: There is concern the low incidence of coronavirus disease 2019 (COVID-19) in children reflects under-testing in this population. This study sought to describe the age-distribution of SARS-CoV-2 testing in the Northern Region of New Zealand. METHODS: A retrospective single-centre review of all SARS-CoV-2 tests performed at LabPLUS, Auckland City Hospital, between 12 February and 18 April 2020. RESULTS: A total of 22,333 tests were performed, with 313 (1.40%) positive results. The age-adjusted SARS-CoV-2 testing rate was three times higher in adults than in children. The overall proportion of positive tests was lower in children (0.86%) than adults (1.45%). However, within the paediatric population the proportion of tests positive differed significantly between those <10 years old (0.08%) and those 10-14 years old (2.6%). CONCLUSION: The lower proportion of tests positive in children <10 years of age suggests they are appropriately tested relative to their rates of disease. A large high school-associated cluster makes the higher proportion of tests positive in children 10-14 years old difficult to interpret. Older children may have a higher risk of infection and increasing testing in intermediate and high school aged children may be indicated.

Population-level exposures associated with MRSA and ESBL-E. coli infection across district health boards in Aotearoa New Zealand: an ecological study.

AIMS: National responses to antimicrobial resistance (AMR) require an understanding of the factors driving its development and spread. Research to date has primarily focused on determining individual-level risk factors for AMR-associated infections. However, additional insights may be gained by investigating exposures associated with AMR variation at the population level. METHODS: We used an ecological study design to describe the association between the incidence rate of methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum ß-lactamase producing Escherichia coli (ESBL-E. coli) infection and population-level variables among 18 geographically distinct populations, defined by district health boards, in Aotearoa New Zealand. Associations were described using Spearman's correlational analysis. RESULTS: Positive correlations were found between the incidence of both MRSA and ESBL-E. coli infection and household crowding and community antimicrobial use. Positive correlations were also observed between MRSA and socioeconomic deprivation; age <5 years; Maori ethnicity; and Pacific ethnicity. For ESBL-E. coli, positive correlations were also observed with Asian ethnicity; Pacific ethnicity; and overseas-born new arrivals. European ethnicity was negatively correlated with both MRSA and ESBL-E. coli infection. CONCLUSIONS: These findings provide insight into the potential contribution of population-level exposures to MRSA and ESBL-E. coli infection in New Zealand. Exposures such as household crowding, community antimicrobial use and socioeconomic deprivation, are in principle modifiable and may present potentially novel opportunities to reduce the burden of AMR.

Diagnostic Performance of Pleural Fluid Adenosine Deaminase for Tuberculous Pleural Effusion in a Low-Incidence Setting.

The challenges associated with diagnosing tuberculous pleural effusion have led to the use of pleural fluid adenosine deaminase (pfADA) as a biomarker for Mycobacterium tuberculosis infection. This study retrospectively reviewed the diagnostic performance of pfADA, the pleural fluid lactate dehydrogenase (LD)/ADA ratio, and combinations of these two parameters in 1,637 episodes of pleural effusion in the low-tuberculosis (TB)-incidence setting of Auckland, Aotearoa New Zealand, from between March 2008 and November 2014. The median pfADA in 57 TB pleural effusion episodes (58.1 U/liter) was significantly higher (P < 0.001) than in 1,580 non-TB pleural effusions (11.4 U/liter). The median LD/ADA ratio in TB pleural effusion (8.2) was significantly lower (P < 0.001) than in non-TB pleural effusions (30.5). The pfADA and pleural fluid LD/ADA ratio AUCROC values (that is, receiver operating characteristic [ROC] curve analysis with determination of the ROC area under the curve) were 0.93 and 0.94, respectively. The pfADA thresholds of ≥15 and ≥30 U/liter demonstrated sensitivities of 100% (95% confidence internal = 93.7 to 100) and 93.0% (83.3 to 97.2), specificities of 62.7% (60.3 to 65.0) and 87.3% (85.6 to 88.9), positive predictive values (PPVs) of 8.8% (6.9 to 11.2) and 20.9% (16.4 to 26.4), and negative predictive values (NPVs) of 100% (99.6 to 100) and 99.7% (99.3 to 99.9), respectively. LD/ADA ratio thresholds of <25 and <15 demonstrated sensitivities of 100% (93.5 to 100) and 89.1% (78.2 to 94.9), specificities of 61.6% (59.1 to 64.0) and 84.8% (82.9 to 86.5), PPVs of 8.5% (6.6 to 10.9) and 17.3% (13.3 to 22.0), and NPVs of 100% (99.6 to 100) and 99.5% (99.0 to 99.8), respectively. A combination of pfADA ≥ 30 U/liter and an LD/ADA ratio < 15 increased the specificity and PPV to 97.8% (96.9 to 98.4) and 57.3% (46.5 to 67.5) but decreased the sensitivity to 85.5% (73.8 to 92.4). The primary value of pfADA in a low-TB-incidence setting, such as Auckland, is in utilization of its high NPV.

Hospital-Onset MRSA Bacteremia Rates Are Significantly Correlated With Sociodemographic Factors: A Step Toward Risk Adjustment.

The correlations between census-derived sociodemographic variables and hospital-onset methicillin-resistant Staphylococcus aureus bacteremia (HO-MRSAB) rates were examined at the US state level. On multivariable analysis, only percent African American remained statistically significant. This finding highlights an important disparity and suggests that risk adjustment is needed when comparing HO-MRSAB rates among US states. Infect Control Hosp Epidemiol 2018;39:479-481.

The clear and present danger of carbapenemase-producing Enterobacteriaceae (CPE) in New Zealand: time for a national response plan.

Antimicrobial resistance (AMR) in general poses a threat to the sustainability of modern healthcare, but a particularly urgent and serious threat is posed by a specific group of antibiotic-resistant bacteria known as carbapenemase-producing Enterobacteriaceae (CPE). CPE are resistant to nearly all antibiotics and include common pathogens such as Escherichia coli and Klebsiella pneumoniae. In New Zealand, the incidence of CPE has increased from three isolates in 2012 to 45 in 2016. The current epidemiology of CPE in New Zealand has similarities with the extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-PE) epidemic in the early 2000s (just before ESBL-PE underwent a non-linear increase in incidence). Although to date in New Zealand, nearly all CPE have been imported from overseas, this situation appears to be changing, with evidence of secondary spread in both households and healthcare facilities over the last year. In this article, we argue that CPE should be regarded as the foremost AMR threat currently facing New Zealand, and highlight the need for a comprehensive national response plan, analogous to plans for other emerging transmissible infections, such as pandemic influenza and Ebola. We also make recommendations about the components of such a plan and advocate that CPE should be recognised as a key priority in New Zealand's national AMR strategy, due to be published in May 2017.

Household transmission of NDM-producing E. coli in New Zealand.

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-ß-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.

Cytokine Kinetics in the First Week of Tuberculosis Therapy as a Tool to Confirm a Clinical Diagnosis and Guide Therapy.

BACKGROUND: Many patients treated for tuberculosis (TB) in low and middle income countries are treated based on clinical suspicion without bacteriological confirmation. This is often due to lack of rapid simple accurate diagnostics and low healthcare provider confidence in the predictive value of current tests. We previously reported in an animal TB model that levels of host markers rapidly change in response to treatment initiation. METHODS: We assessed the potential of host biomarker kinetics of TB patients during the first two weeks of therapy to identify patients responding to treatment. Adult patients clinically diagnosed with and treated for TB, 29 in Nigeria and 24 in Nepal, were analyzed. RESULTS: Changes in concentrations of non-specific host biomarkers, particularly IP-10, in response to the first week of anti-TB therapy were strongly associated with bacteriological confirmation of TB. A decrease in IP-10 level of >300pg/ml between 0 and 7 days of treatment identified 75% of both smear-positive and smear-negative culture positive patients and correctly excluded TB in all nine culture negative patients. CONCLUSIONS: Monitoring of early IP-10 responses to treatment could form the basis of a simplified assay and could help identify patients who were erroneously clinically diagnosed with TB or those infected with drug resistant strains on inappropriate treatment. We believe this approach may be particularly appropriate for difficult to diagnose patients, e.g. smear-negative HIV-positive, or those with extra-pulmonary TB, often treated without bacterial confirmation.

Testing Pooled Sputum with Xpert MTB/RIF for Diagnosis of Pulmonary Tuberculosis To Increase Affordability in Low-Income Countries.

Tuberculosis (TB) is a global public health problem, with the highest burden occurring in low-income countries. In these countries, the use of more sensitive diagnostics, such as Xpert MTB/RIF (Xpert), is still limited by costs. A cost-saving strategy to diagnose other diseases is to pool samples from various individuals and test them with single tests. The samples in positive pool samples are then retested individually to identify the patients with the disease. We assessed a pooled testing strategy to optimize the affordability of Xpert for the diagnosis of TB. Adults with presumptive TB attending hospitals or identified by canvassing of households in Abuja, Nigeria, were asked to provide sputum for individual and pooled (4 per pool) testing. The agreement of the results of testing of individual and pooled samples and costs were assessed. A total of 738 individuals submitted samples, with 115 (16%) being Mycobacterium tuberculosis positive. Valid Xpert results for individual and pooled samples were available for 718 specimens. Of these, testing of pooled samples detected 109 (96%) of 114 individual M. tuberculosis-positive samples, with the overall agreement being 99%. Xpert semiquantitative M. tuberculosis levels had a positive correlation with the smear grades, and the individual sample-positive/pooled sample-negative results were likely due to the M. tuberculosis concentration being below the detection limit. The strategy reduced cartridge costs by 31%. Savings were higher with samples from individuals recruited in the community, where the proportion of positive specimens was low. The results of testing of pooled samples had a high level of agreement with the results of testing of individual samples, and use of the pooled testing strategy reduced costs and has the potential to increase the affordability of Xpert in countries with limited resources.

Nosocomial bacteriuria in elderly inpatients may be leading to considerable antibiotic overuse: an audit of current management practice in a secondary level care hospital in New Zealand.

BACKGROUND: Bacteriuria in the form of symptomatic urinary tract infection (UTI) and asymptomatic bacteriuria (ASB) is common in the elderly. There is no clinical benefit obtained by treating elderly individuals with ASB. However, its high prevalence leads to the overdiagnosis of UTI and unnecessary antibiotic use, which can result in adverse events, including Clostridium difficile diarrhea and reinfection with antibiotic-resistant organisms. METHODS: This was a retrospective audit that assessed the management of nosocomial bacteriuria in elderly patients admitted to the over-65 years rehabilitation unit of a secondary level care hospital in New Zealand. Identified bacteriuria episodes had the timing of sample collection relative to admission, microbial etiology, antibiotic susceptibility profile, inflammatory marker level, and treatment determined. Episodes were classified into six different clinical groups based on the presence or absence of signs and symptoms, urinary catheter status, and systemic inflammatory response. The proportion of bacteriuria episodes by clinical grouping and the level of treatment by clinical group were determined, followed by assessment of the amount of overtreatment in terms of the number of unnecessary antibiotic courses and unnecessary antibiotic treatment days. RESULTS: Significant bacteriuria was identified in 30% of patients, with 35% of urine samples collected in the immediate postadmission period. Fifty-four percent of the bacteriuria episodes were ASB or catheter-associated ASB (CA-ASB) without an inflammatory response, 24% were ASB or CA-ASB with raised inflammatory markers, and 22% were UTI or CA-UTI. The most common cause of bacteriuria was Escherichia coli, although the etiology was diverse, especially after prolonged hospitalization or in catheterized patients. A large proportion of organisms were resistant to one or more of the commonly used oral antibiotics. Treatment of ASB and CA-ASB accounted for 43% of all antibiotic courses received. Furthermore, treatment of ASB and CA-ASB combined with unnecessarily prolonged treatment days for clinically relevant infections accounted for 55% of all antibiotic treatment days received. CONCLUSION: The results suggest that inappropriate urine screening was occurring and that 43% of antibiotic courses and 55% of all antibiotic treatment days were unnecessary. Current practice is amenable to improvement by performing urine culture only when clinically indicated, focusing on clinical signs and symptoms to diagnose clinically significant UTI rather than a positive culture, and using, where possible, the ecologically least damaging antibiotic for the shortest duration required.

In sight, in mind: retailer compliance with legislation on limiting retail tobacco displays.

We investigated retailer compliance with point-of-sale display legislation, using a New Zealand region as a case study. An observational survey was conducted of nonspecialist tobacco retailers in the lower North Island of New Zealand during 2006. Compliance was assessed in relation to store type (dairies, convenience stores, supermarkets, and service stations) and by characteristics of the population of the census area unit in which the store was situated. These characteristics include the level of socioeconomic deprivation and proportions of Maori (indigenous New Zealanders), Pacific Islanders, and children aged less than 19 years. Out of the 288 stores surveyed, 185 (64%) had at least one breach of the point-of-sale regulations. The most common breaches were a failure to display a "Smoking Kills" sign, visibility of tobacco from outside the premises, and displaying tobacco less than 1 m from children's products. Compliance was significantly worse in dairies (small local general stores) and convenience stores. Stores situated in areas in the top quartile for the proportion of children were much more likely to have high levels of noncompliance (> or =3 breaches) and to display tobacco products close to children's products. This study is one of very few to systematically investigate retailer compliance with point-of-sale display regulations for tobacco products. The results suggest that the implementation of legislation to partly limit retail displays of tobacco products can be difficult. A ban on retail displays of tobacco products is likely to be a more effective and enforceable policy.