Development of a multiplex droplet digital PCR assay for simultaneous detection and quantification of Escherichia coli, E. marmotae, and E. ruysiae in water samples.

Escherichia coli are widely used by water quality managers as Fecal Indicator Bacteria, but current quantification methods do not differentiate them from benign, environmental Escherichia species such as E. marmotae (formerly named cryptic clade V) or E. ruysiae (cryptic clades III and IV). Reliable and specific techniques for their identification are required to avoid confounding microbial water quality assessments. To address this, a multiplex droplet digital PCR (ddPCR) assay targeting lipB (E. coli and E. ruysiae) and bglC (E. marmotae) was designed. The ddPCR performance was assessed using in silico analysis; genomic DNA from 40 local, international, and reference strains of target and non-target coliforms; and spiked water samples in a range relevant to water quality managers (1 to 1000 cells/100 mL). Results were compared to an analogous quantitative PCR (qPCR) and the Colilert method. Both PCR assays showed excellent sensitivity with a limit of detection of 0.05 pg/µL and 0.005 pg/µl for ddPCR and qPCR respectively, and of quantification of 0.5 pg/µL of genomic DNA. The ddPCR allowed differentiation and quantification of three Escherichia species per run by amplitude multiplexing and showed a high concordance with concentrations measured by Colilert once proportional bias was accounted for. In silico specificity testing underlined the possibility to further detect and distinguish Escherichia cryptic clade VI. Finally, the applicability of the ddPCR was successfully tested on environmental water samples where E. marmotae and E. ruysiae potentially confound E. coli counts based on the Most Probable Number method, highlighting the utility of this novel ddPCR as an efficient and rapid discriminatory test to improve water quality assessments.

High-resolution genomic analysis to investigate the impact of the invasive brushtail possum (Trichosurus vulpecula) and other wildlife on microbial water quality assessments.

Escherichia coli are routine indicators of fecal contamination in water quality assessments. Contrary to livestock and human activities, brushtail possums (Trichosurus vulpecula), common invasive marsupials in Aotearoa/New Zealand, have not been thoroughly studied as a source of fecal contamination in freshwater. To investigate their potential role, Escherichia spp. isolates (n = 420) were recovered from possum gut contents and feces and were compared to those from water, soil, sediment, and periphyton samples, and from birds and other introduced mammals collected within the Makirikiri Reserve, Dannevirke. Isolates were characterized using E. coli-specific real-time PCR targeting the uidA gene, Sanger sequencing of a partial gnd PCR product to generate a gnd sequence type (gST), and for 101 isolates, whole genome sequencing. Escherichia populations from 106 animal and environmental sample enrichments were analyzed using gnd metabarcoding. The alpha diversity of Escherichia gSTs was significantly lower in possums and animals compared with aquatic environmental samples, and some gSTs were shared between sample types, e.g., gST535 (in 85% of samples) and gST258 (71%). Forty percent of isolates gnd-typed and 75% of reads obtained by metabarcoding had gSTs shared between possums, other animals, and the environment. Core-genome single nucleotide polymorphism (SNP) analysis showed limited variation between several animal and environmental isolates (<10 SNPs). Our data show at an unprecedented scale that Escherichia clones are shared between possums, other wildlife, water, and the wider environment. These findings support the potential role of possums as contributors to fecal contamination in Aotearoa/New Zealand freshwater. Our study deepens the current knowledge of Escherichia populations in under-sampled wildlife. It presents a successful application of high-resolution genomic methods for fecal source tracking, thereby broadening the analytical toolbox available to water quality managers. Phylogenetic analysis of isolates and profiling of Escherichia populations provided useful information on the source(s) of fecal contamination and suggest that comprehensive invasive species management strategies may assist in restoring not only ecosystem health but also water health where microbial water quality is compromised.

Temporal Risk of Nonfatal Cardiovascular Events After Chronic Obstructive Pulmonary Disease Exacerbation: A Population-based Study.

Rationale: Cardiovascular events after chronic obstructive pulmonary disease (COPD) exacerbations are recognized. Studies to date have been post hoc analyses of trials, did not differentiate exacerbation severity, included death in the cardiovascular outcome, or had insufficient power to explore individual outcomes temporally.Objectives: We explore temporal relationships between moderate and severe exacerbations and incident, nonfatal hospitalized cardiovascular events in a primary care-derived COPD cohort.Methods: We included people with COPD in England from 2014 to 2020, from the Clinical Practice Research Datalink Aurum primary care database. The index date was the date of first COPD exacerbation or, for those without exacerbations, date upon eligibility. We determined composite and individual cardiovascular events (acute coronary syndrome, arrhythmia, heart failure, ischemic stroke, and pulmonary hypertension) from linked hospital data. Adjusted Cox regression models were used to estimate average and time-stratified adjusted hazard ratios (aHRs).Measurements and Main Results: Among 213,466 patients, 146,448 (68.6%) had any exacerbation; 119,124 (55.8%) had moderate exacerbations, and 27,324 (12.8%) had severe exacerbations. A total of 40,773 cardiovascular events were recorded. There was an immediate period of cardiovascular relative rate after any exacerbation (1-14 d; aHR, 3.19 [95% confidence interval (CI), 2.71-3.76]), followed by progressively declining yet maintained effects, elevated after one year (aHR, 1.84 [95% CI, 1.78-1.91]). Hazard ratios were highest 1-14 days after severe exacerbations (aHR, 14.5 [95% CI, 12.2-17.3]) but highest 14-30 days after moderate exacerbations (aHR, 1.94 [95% CI, 1.63-2.31]). Cardiovascular outcomes with the greatest two-week effects after a severe exacerbation were arrhythmia (aHR, 12.7 [95% CI, 10.3-15.7]) and heart failure (aHR, 8.31 [95% CI, 6.79-10.2]).Conclusions: Cardiovascular events after moderate COPD exacerbations occur slightly later than after severe exacerbations; heightened relative rates remain beyond one year irrespective of severity. The period immediately after an exacerbation presents a critical opportunity for clinical intervention and treatment optimization to prevent future cardiovascular events.

Modeled small airways lung deposition of two fixed-dose triple therapy combinations assessed with in silico functional respiratory imaging.

BACKGROUND: Small airways disease plays a key role in the pathogenesis of chronic obstructive pulmonary disease (COPD) and is a major cause of obstruction; therefore, it is a critical pharmacotherapy target. This study evaluated lung deposition of two inhaled corticosteroid (ICS)/long-acting ß2-agonist/long-acting muscarinic antagonist single-inhaler triple therapies using in silico functional respiratory imaging (FRI). Deposition was assessed using real-world inhalation profiles simulating everyday use where optimal inhalation may be compromised. METHODS: Three-dimensional airway models were produced from 20 patients with moderate-to-very severe COPD. Total, central, and regional small airways deposition as a percentage of delivered dose of budesonide/glycopyrronium/formoterol fumarate dihydrate (BGF) 160/7.2/5 µg per actuation and fluticasone furoate/umeclidinium/vilanterol (FF/UM/VI) 100/62.5/25 µg were evaluated using in silico FRI based on in vitro aerodynamic particle size distributions of each device. Simulations were performed using multiple inhalation profiles of varying durations and flow rates representing patterns suited for a pressurized metered-dose inhaler or dry-powder inhaler (four for BGF, two for FF/UM/VI, with one common profile). For the common profile, deposition for BGF versus FF/UM/VI was compared post-hoc using paired t-tests. RESULTS: Across inhalation profiles, mean total lung deposition was consistently higher with BGF (47.0-54.1%) versus FF/UM/VI (20.8-22.7%) and for each treatment component, with greater deposition for BGF also seen in the central large airways. Mean regional small airways deposition was also greater across inhalation profiles with BGF (16.9-23.6%) versus FF/UM/VI (6.8-8.7%) and for each treatment component. For the common profile, total, central, and regional small airways deposition were significantly greater for BGF versus FF/UM/VI (nominal p < 0.001), overall and for treatment components; notably, regional small airways deposition of the ICS components was approximately five-fold greater with budesonide versus fluticasone furoate (16.1% vs. 3.3%). CONCLUSIONS: BGF was associated with greater total, central, and small airways deposition for all components versus FF/UM/VI. Importantly, using an identical inhalation profile, there was an approximately five-fold difference in small airways deposition for the ICS components, with only a small percentage of the ICS from FF/UM/VI reaching the small airways. Further research is needed to understand if the enhanced delivery of BGF translates to clinical benefits.

Mortality risk reduction with budesonide/glycopyrrolate/formoterol fumarate versus fluticasone furoate/umeclidinium/vilanterol in COPD: a matching-adjusted indirect comparison based on ETHOS and IMPACT.

OBJECTIVE: Chronic obstructive pulmonary disease (COPD) is a leading cause of death worldwide. While two approved fixed-dose inhaled corticosteroid/long-acting muscarinic antagonist (LAMA)/long-acting ß2-agonist (LABA) triple therapies reduce all-cause mortality (ACM) versus dual LAMA/LABA therapy in patients with COPD, head-to-head studies have not compared the effects of these therapies on ACM. We compared ACM in adults with moderate-to-very severe COPD receiving budesonide/glycopyrrolate/formoterol fumarate (BGF) in ETHOS versus fluticasone furoate/umeclidinium/vilanterol (FF/UMEC/VI) in IMPACT using a matching-adjusted indirect comparison (MAIC). METHODS: A systematic literature review identified two studies (ETHOS [NCT02465567]; IMPACT [NCT02164513]) of ≥52 weeks reporting ACM as an efficacy endpoint in patients receiving triple therapy. As ETHOS and IMPACT lack a common comparator, an unanchored MAIC compared ACM between licensed doses of BGF (320/18/9.6 µg) from ETHOS and FF/UMEC/VI (100/62.5/25 µg) from IMPACT in patients with moderate-to-very severe COPD. Using on- and off-treatment data from the final retrieved datasets of the intention-to-treat populations, BGF data were adjusted according to aggregate FF/UMEC/VI data using 11 baseline covariates; a supplementary unadjusted indirect treatment comparison was also conducted. P-values for these post-hoc analyses are not adjusted for Type I error. RESULTS: ACM over 52 weeks was statistically significantly reduced by 39% for BGF versus FF/UMEC/VI in the MAIC (hazard ratio [HR] [95% CI]: 0.61 [0.38, 0.95], p = 0.030) and unadjusted analysis (HR [95% CI]: 0.61 [0.41, 0.92], p = 0.019). CONCLUSION: In this MAIC, which adjusted for population heterogeneity between ETHOS and IMPACT, ACM was significantly reduced with BGF versus FF/UMEC/VI in patients with moderate-to-very severe COPD.

Chronic obstructive pulmonary disease (known as COPD) is a leading cause of death worldwide, being responsible for over 3 million deaths in 2019. People living with COPD are more likely to die. Importantly, a sudden worsening of COPD symptoms (known as an exacerbation) is associated with a higher chance of death from heart-related and breathing-related problems. Therefore, reducing risk of death is an important treatment goal for COPD. Of the three medications approved for treating COPD that combine three drugs in a single-inhaler device, there are two­referred to generically as budesonide/glycopyrrolate/formoterol fumarate (BGF) and fluticasone furoate/umeclidinium/vilanterol (FF/UMEC/VI)­that can reduce the risk of death in people living with COPD compared with treatments that combine two drugs. However, no studies have directly compared the risk of death in people living with COPD treated with these medicines. We compared the risk of death in people living with moderate-to-very severe COPD who received either BGF during a clinical trial called ETHOS or FF/UMEC/VI during a clinical trial called IMPACT. To make this comparison, we used a method called "matching-adjusted indirect comparison", which used specific features (such as sex, breathing difficulty, and whether they were current smokers) to match patients from the two studies to ensure similar groups were examined. Our analysis showed a 39% decrease in the chance of death in patients who received BGF compared with patients who received FF/UMEC/VI. This finding may be important for doctors to improve patient health and reduce the risk of death in people living with COPD.

Leptospirosis in Aotearoa New Zealand: Protocol for a Nationwide Case-Control Study.

BACKGROUND: In Aotearoa New Zealand, 90% of patients with notified leptospirosis (a zoonotic bacterial disease) have been men working in agricultural industries. However, since 2008, the epidemiology of notified cases has been gradually changing, that is, more women are affected; there are more cases associated with occupations traditionally not considered high risk in New Zealand; infecting serovars have changed; and many patients experience symptoms long after infection. We hypothesized that there is a shift in leptospirosis transmission patterns with substantial burden on affected patients and their families. OBJECTIVE: In this paper, we aimed to describe the protocols used to conduct a nationwide case-control study to update leptospirosis risk factors and follow-up studies to assess the burden and sources of leptospirosis in New Zealand. METHODS: This study used a mixed methods approach, comprising a case-control study and 4 substudies that involved cases only. Cases were recruited nationwide, and controls were frequency matched by sex and rurality. All participants were administered a case-control questionnaire (study 1), with cases being interviewed again at least 6 months after the initial survey (study 2). A subset of cases from two high-risk populations, that is, farmers and abattoir workers, were further engaged in a semistructured interview (study 3). Some cases with regular animal exposure had their in-contact animals (livestock for blood and urine and wildlife for kidney) and environment (soil, mud, and water) sampled (study 4). Patients from selected health clinics suspected of leptospirosis also had blood and urine samples collected (study 5). In studies 4 and 5, blood samples were tested using the microscopic agglutination test to test for antibody titers against Leptospira serovars Hardjo type bovis, Ballum, Tarassovi, Pomona, and Copenhageni. Blood, urine, and environmental samples were also tested for pathogenic Leptospira DNA using polymerase chain reaction. RESULTS: Participants were recruited between July 22, 2019, and January 31, 2022, and data collection for the study has concluded. In total, 95 cases (July 25, 2019, to April 13, 2022) and 300 controls (October 19, 2019, to January 26, 2022) were interviewed for the case-control study; 91 cases participated in the follow-up interviews (July 9, 2020, to October 25, 2022); 13 cases participated in the semistructured interviews (January 26, 2021, to January 19, 2022); and 4 cases had their in-contact animals and environments sampled (October 28, 2020, and July 29, 2021). Data analysis for study 3 has concluded and 2 manuscripts have been drafted for review. Results of the other studies are being analyzed and the specific results of each study will be published as individual manuscripts.. CONCLUSIONS: The methods used in this study may provide a basis for future epidemiological studies of infectious diseases. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/47900.

Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylation.

Age structure information of animal populations is fundamental to their conservation and management. In fisheries, age is routinely obtained by counting daily or annual increments in calcified structures (e.g., otoliths) which requires lethal sampling. Recently, DNA methylation has been shown to estimate age using DNA extracted from fin tissue without the need to kill the fish. In this study we used conserved known age-associated sites from the zebrafish (Danio rerio) genome to predict the age of golden perch (Macquaria ambigua), a large-bodied native fish from eastern Australia. Individuals aged using validated otolith techniques from across the species' distribution were used to calibrate three epigenetic clocks. One clock was calibrated using daily (daily clock) and another with annual (annual clock) otolith increment counts, respectively. A third used both daily and annual increments (universal clock). We found a high correlation between the otolith and epigenetic age (Pearson correlation > 0.94) across all clocks. The median absolute error was 2.4 days in the daily clock, 184.6 days in the annual clock, and 74.5 days in the universal clock. Our study demonstrates the emerging utility of epigenetic clocks as non-lethal and high-throughput tools for obtaining age estimates to support the management of fish populations and fisheries.

Predicting observable infrared signatures of nanosilicates in the diffuse interstellar medium.

The destruction time scale of dust in the diffuse interstellar medium is estimated to be an order of magnitude shorter than its residence time. Nevertheless, dust is observed in the interstellar medium, leading to the conclusion that reformation and grain growth must take place. Direct observations of nanometre-sized silicate grains, the main constituent of interstellar dust, would provide a smoking gun for the occurrence of grain condensation in the diffuse interstellar medium. Here we employ quantum chemical calculations to obtain the mid-infrared (IR) optical properties of a library of Mg-end member silicate nanoparticles with olivine (Mg2SiO4) and pyroxene (MgSiO3) stoichiometries. We use this library as an input for a foreground-screen model to predict the spectral appearance of the absorption profile due to mixtures of bulk and nanoparticle silicates towards bright background sources. The mid-IR spectrum observed towards an O8V star or a carbon-rich Wolf-Rayet star starts to change when ∼3% of the silicate mass is in the form of nanosilicates. We predict that a 3-10% nanosilicate fraction can be detected with the James Webb Space Telescope (JWST) using the mid-IR instrument (MIRI). With our upcoming JWST observations using MIRI, we will be able to detect or place limits on the nanosilicate content in the diffuse interstellar medium, and thus potentially directly confirm interstellar dust formation.

EXAcerbations of COPD and their OutcomeS on CardioVascular diseases (EXACOS-CV) Programme: protocol of multicountry observational cohort studies.

INTRODUCTION: In patients with chronic obstructive pulmonary disease (COPD), the risk of certain cardiovascular (CV) events is increased by threefold to fivefold in the year following acute exacerbation of COPD (AECOPD), compared with a non-exacerbation period. While the effect of severe AECOPD is well established, the relationship of moderate exacerbation or prior exacerbation to elevated risk of CV events is less clear. We will conduct cohort studies in multiple countries to further characterise the association between AECOPD and CV events. METHODS AND ANALYSIS: Retrospective longitudinal cohort studies will be conducted within routinely collected electronic healthcare records or claims databases. The study cohorts will include patients meeting inclusion criteria for COPD between 1 January 2014 and 31 December 2018. Moderate exacerbation is defined as an outpatient visit and/or medication dispensation/prescription for exacerbation; severe exacerbation is defined as hospitalisation for COPD. The primary outcomes of interest are the time to (1) first hospitalisation for a CV event (including acute coronary syndrome, heart failure, arrhythmias or cerebral ischaemia) since cohort entry or (2) death. Time-dependent Cox proportional hazards models will compare the hazard of a CV event between exposed periods following exacerbation (split into these periods: 1-7, 8-14, 15-30, 31-180 and 181-365 days) and the unexposed reference time period, adjusted on time-fixed and time-varying confounders. ETHICS AND DISSEMINATION: Studies have been approved in Canada, Japan, the Netherlands, Spain and the UK, where an institutional review board is mandated. For each study, the results will be published in peer-reviewed journals.

Extended-spectrum ß-lactamase- and AmpC ß-lactamase-producing Enterobacterales associated with urinary tract infections in the New Zealand community: a case-control study.

OBJECTIVES: To assess whether having a pet in the home is a risk factor for community-acquired urinary tract infections associated with extended-spectrum ß-lactamase (ESBL)- or AmpC ß-lactamase (ACBL)- producing Enterobacterales. METHODS: An unmatched case-control study was conducted between August 2015 and September 2017. Cases (n = 141) were people with community-acquired urinary tract infection (UTI) caused by ESBL- or ACBL-producing Enterobacterales. Controls (n = 525) were recruited from the community. A telephone questionnaire on pet ownership and other factors was administered, and associations were assessed using logistic regression. RESULTS: Pet ownership was not associated with ESBL- or ACBL-producing Enterobacterales-related human UTIs. A positive association was observed for recent antimicrobial treatment, travel to Asia in the previous year, and a doctor's visit in the last 6 months. Among isolates with an ESBL-/ACBL-producing phenotype, 126/134 (94%) were Escherichia coli, with sequence type 131 being the most common (47/126). CONCLUSIONS: Companion animals in the home were not found to be associated with ESBL- or ACBL-producing Enterobacterales-related community-acquired UTIs in New Zealand. Risk factors included overseas travel, recent antibiotic use, and doctor visits.

Kilo-Scale GMP Synthesis of Renewable Semisynthetic Vaccine-Grade Squalene.

Emulsions of the triterpene squalene ((6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene, CAS 111-02-4) have been used as adjuvants in influenza vaccines since the 1990s. Traditionally sourced from shark liver oil, the overfishing of sharks and concomitant reduction in the oceanic shark population raises sustainability issues for vaccine adjuvant grade squalene. We report a semisynthetic route to squalene meeting current pharmacopeial specifications for use in vaccines that leverages the ready availability of trans-ß-farnesene ((6E)-7,11-dimethyl-3-methylene-1,6,10-dodecatriene, CAS 18794-84-8), manufactured from sustainable sugarcane via a yeast fermentation process. The scalability of the proposed route was verified by a kilo-scale GMP synthesis. We also report data demonstrating the synthesized semi-synthetic squalene's physical stability and biological activity when used in a vaccine adjuvant formulation.

Association of COPD exacerbations and acute cardiovascular events: a systematic review and meta-analysis.

BACKGROUND: The majority of patients with chronic obstructive pulmonary disease (COPD) suffer from comorbid cardiovascular (CV) disease. Accumulating evidence suggests a temporal association between COPD exacerbations and acute CV events, possibly due to lung hyperinflation, increased hypoxemia and systemic inflammation. The aims of the study were to estimate the risk of (1) acute CV events [acute myocardial infarction (AMI), CV-related death] or stroke in the months following a COPD exacerbation and (2) COPD exacerbation in the months following an acute CV event. METHODS: A systematic literature review of observational studies published since 2000 was conducted by searching literature databases (Medline and Embase). Studies were eligible if conducted in adults with COPD, exposed to either COPD exacerbation or acute CV events, with outcomes of acute CV events or COPD exacerbation reported. Studies were appraised for relevance, bias and quality. Meta-analyses, using random-effect models, were performed for each outcome of interest, thus providing a pooled relative risk (RR) and its 95% confidence interval. RESULTS: Eight studies were identified, of which seven were used for the meta-analyses examining the risk of CV events 1-3 months after an exacerbation compared with none. For stroke (six studies), RR was 1.68 (95% CI = 1.19-2.38). For AMI (six studies), RR was 2.43 (95% CI = 1.40-4.20). No studies exploring risk of exacerbation following an acute CV event were identified. CONCLUSION: This meta-analysis identified a markedly increased risk of stroke or AMI within a relatively short period of time following a COPD exacerbation. Although the underlying mechanisms are not fully elucidated, patients with COPD should be monitored for risk of CV outcomes after exacerbations. In addition, preventing exacerbations may decrease the risk of subsequent acute CV events. REGISTRATION: The study protocol was published via PROSPERO: International Prospective Register of Systematic Reviews (#CRD42020211055).

Dairy Cattle Density and Temporal Patterns of Human Campylobacteriosis and Cryptosporidiosis in New Zealand.

Public health risks associated with the intensification of dairy farming are an emerging concern. Dairy cattle are a reservoir for a number of pathogens that can cause human illness. This study examined the spatial distribution of dairy cattle density and explored temporal patterns of human campylobacteriosis and cryptosporidiosis notifications in New Zealand from 1997 to 2015. Maps of dairy cattle density were produced, and temporal patterns of disease rates were assessed for urban versus rural areas and for areas with different dairy cattle densities using descriptive temporal analyses. Campylobacteriosis and cryptosporidiosis rates displayed strong seasonal patterns, with highest rates in spring in rural areas and, for campylobacteriosis, summer in urban areas. Increases in rural cases often preceded increases in urban cases. Furthermore, disease rates in areas with higher dairy cattle densities tended to peak before areas with low densities or no dairy cattle. Infected dairy calves may be a direct or indirect source of campylobacteriosis or cryptosporidiosis infection in humans through environmental or occupational exposure routes, including contact with animals or feces, recreational contact with contaminated waterways, and consumption of untreated drinking water. These results have public health implications for populations living, working, or recreating in proximity to dairy farms.

Whole-Genome Sequencing and Virulome Analysis of Escherichia coli Isolated from New Zealand Environments of Contrasting Observed Land Use.

Generic Escherichia coli is commonly used as an indicator of fecal contamination to assess water quality and human health risk. Where measured E. coli exceedances occur, the presence of other pathogenic microorganisms, such as Shiga toxin-producing E. coli (STEC), is assumed, but confirmatory data are lacking. Putative E. coli isolates (n = 709) were isolated from water, sediment, soil, periphyton, and feces samples (n = 189) from five sites representing native forest and agricultural environments. Ten E. coli isolates (1.41%) were stx2 positive, 19 (2.7%) were eae positive, and stx1-positive isolates were absent. At the sample level, stx2-positive E. coli (5 of 189, 2.6%) and eae-positive isolates (16 of 189, 8.5%) were rare. Using real-time PCR, these STEC-associated virulence factors were determined to be more prevalent in sample enrichments (stx1, 23.9%; stx2, 31.4%; eae, 53.7%) and positively correlated with generic E. coli isolate numbers (P < 0.05) determined using culture-based methods. Whole-genome sequencing (WGS) was undertaken on a subset of 238 isolates with assemblies representing seven E. coli phylogroups (A, B1, B2, C, D, E, and F), 22 Escherichia marmotae isolates, and 1 Escherichia ruysiae isolate. Virulence factors, including those from extraintestinal pathogenic E. coli, were extremely diverse in isolates from the different locations and were more common in phylogroup B2. Analysis of the virulome from WGS data permitted the identification of gene repertoires that may be involved in environmental fitness and broadly align with phylogroup. Although recovery of STEC isolates was low, our molecular data indicate that they are likely to be widely present in environmental samples containing diverse E. coli phylogroups. IMPORTANCE This study takes a systematic sampling approach to assess the public health risk of Escherichia coli recovered from freshwater sites within forest and farmland. The New Zealand landscape is dominated by livestock farming, and previous work has demonstrated that "recreational exposure to water" is a risk factor for human infection by Shiga toxin-producing Escherichia coli (STEC). Though STEC isolates were rarely isolated from water samples, STEC-associated virulence factors were identified more commonly from water sample culture enrichments and were associated with increased generic E. coli concentrations. Whole-genome sequencing data from both E. coli and newly described Escherichia spp. demonstrated the presence of virulence factors from E. coli pathotypes, including extraintestinal pathogenic E. coli. This has significance for understanding and interpreting the potential health risk from E. coli where water quality is poor and suggests a role of virulence factors in survival and persistence of E. coli and Escherichia spp.

Aboveground carbon accumulation by second-growth forests after deforestation in Hawai'i.

Successional processes ultimately determine and define carbon accumulations in forested ecosystems. Although primary succession on wholly new substrate occurs across the globe, secondary succession, often following storm events or anthropogenic disturbance, is more common and is capable of globally significant accumulations of carbon (C) at a time when offsets to anthropogenic carbon dioxide (CO2 ) emissions are critically needed. In Hawai'i, prior studies have investigated ecosystem development during primary succession on lava flows, including estimates of C mass accumulation. Yet relatively little is known regarding secondary succession of Hawaii's native forests, particularly regarding C mass accumulation. Here we documented aboveground C mass accumulation by native- and nonnative-dominated second-growth forests following deforestation of mature native lowland rainforests in the Puna District of Hawai'i Island. We characterized species composition and stand structure of three distinct successional forest stand types: those dominated by the native tree, Metrosideros polymorpha ('Ohi'a), and those dominated by invasive nonnative trees, Falcataria moluccana (albizia) and Psidium cattleianum (strawberry guava). We compared M. polymorpha-dominated and F. moluccana-dominated second-growth forests to adjacent mature M. polymorpha-dominated forests as well as young M. polymorpha-dominated forests undergoing initial stages of primary succession on 36-years-old lava fields. Aboveground carbon density (ACD) values of mature primary forest stands (171 Mg/ha) were comparable to those of mature continental tropical forests. M. polymorpha-dominated second-growth stands attained nearly 50% of ACD values of mature primary forests after less than 30 years of post-disturbance succession and exhibited aboveground carbon accumulation rates of ~3 Mg C·ha-1 ·year-1 . Such rates were comparable to those of second-growth forests in continental tropics. Rates of ACD accumulation by second-growth forests dominated by nonnative F. moluccana stands were similar, or slightly greater than, those of M. polymorpha-dominated stands. However, M. polymorpha individuals were virtually absent from stands dominated by either P. cattleianum or F. moluccana. Taken together, results demonstrated that re-establishment and rapid accumulation of C mass by M. polymorpha stands during secondary succession is certainly possible, but only where populations of nonnative species have not already colonized areas during early stages of secondary succession.

Genomic adaptations of Campylobacter jejuni to long-term human colonization.

BACKGROUND: Campylobacter is a genus of bacteria that has been isolated from the gastrointestinal tract of humans and animals, and the environments they inhabit around the world. Campylobacter adapt to new environments by changes in their gene content and expression, but little is known about how they adapt to long-term human colonization. In this study, the genomes of 31 isolates from a New Zealand patient and 22 isolates from a United Kingdom patient belonging to Campylobacter jejuni sequence type 45 (ST45) were compared with 209 ST45 genomes from other sources to identify the mechanisms by which Campylobacter adapts to long-term human colonization. In addition, the New Zealand patient had their microbiota investigated using 16S rRNA metabarcoding, and their level of inflammation and immunosuppression analyzed using biochemical tests, to determine how Campylobacter adapts to a changing gastrointestinal tract. RESULTS: There was some evidence that long-term colonization led to genome degradation, but more evidence that Campylobacter adapted through the accumulation of non-synonymous single nucleotide polymorphisms (SNPs) and frameshifts in genes involved in cell motility, signal transduction and the major outer membrane protein (MOMP). The New Zealand patient also displayed considerable variation in their microbiome, inflammation and immunosuppression over five months, and the Campylobacter collected from this patient could be divided into two subpopulations, the proportion of which correlated with the amount of gastrointestinal inflammation. CONCLUSIONS: This study demonstrates how genomics, phylogenetics, 16S rRNA metabarcoding and biochemical markers can provide insight into how Campylobacter adapts to changing environments within human hosts. This study also demonstrates that long-term human colonization selects for changes in Campylobacter genes involved in cell motility, signal transduction and the MOMP; and that genetically distinct subpopulations of Campylobacter evolve to adapt to the changing gastrointestinal environment.

Risk Factors for Hospitalisation amongst Leptospirosis Patients in New Zealand.

Leptospirosis is a neglected zoonotic disease that is widespread in tropical and subtropical regions such as Oceania, which includes New Zealand. The incidence rate of leptospirosis in New Zealand remains high in comparison to other high-income countries, with over half of the notified patients hospitalised, and the factors associated with hospitalisation are poorly understood. This study aimed to estimate the risk factors for hospitalisation amongst leptospirosis patients using passive surveillance data: notifications from 1 January 1999 to 31 December 2017 extracted from New Zealand's notifiable disease database. There were 771 hospitalised and 673 non-hospitalised patients. Multivariable logistic regression was used to identify risk factors. The year of notification was significantly and positively associated with hospitalisation, with adjusted (adj.) OR 1.03 (95% CI:1.01-1.05). Occupation was significantly associated with hospitalisation, with the adjusted odds of hospitalisation amongst dairy farmers notified with leptospirosis at adj. OR 1.44 (95% CI: 1.02-2.02) times the adjusted odds of hospitalisation amongst farmers that worked with other livestock. Seropositivity for Leptospira interrogans Copenhageni (adj. OR 5.96, 95% CI: 1.68-21.17) and Pomona (adj. OR 1.14, 95% CI: 0.74-1.74)) was more likely to result in hospitalisation when compared to Leptospira borgpetersenii Ballum (baseline). Seropositivity for Leptospira borgpetersenii Hardjo (adj. OR 0.71, 95% CI: 0.49-1.01) and Tarassovi (adj. OR 0.39, 95% CI: 0.23-0.66) was less likely to result in hospitalisation when compared to Ballum (baseline). All the estimates were additionally adjusted for the effect of sex, age, ethnicity, reported occupational exposure, geographical location, reported season, and deprivation status Although passive surveillance data has limitations we have been able to identify that the New Zealand dairy farming population may benefit from a targeted awareness campaign.

What is winter? Modeling spatial variation in bat host traits and hibernation and their implications for overwintering energetics.

White-nose syndrome (WNS) has decimated hibernating bat populations across eastern and central North America for over a decade. Disease severity is driven by the interaction between bat characteristics, the cold-loving fungal agent, and the hibernation environment. While we further improve hibernation energetics models, we have yet to examine how spatial heterogeneity in host traits is linked to survival in this disease system. Here, we develop predictive spatial models of body mass for the little brown myotis (Myotis lucifugus) and reassess previous definitions of the duration of hibernation of this species. Using data from published literature, public databases, local experts, and our own fieldwork, we fit a series of generalized linear models with hypothesized abiotic drivers to create distribution-wide predictions of prehibernation body fat and hibernation duration. Our results provide improved estimations of hibernation duration and identify a scaling relationship between body mass and body fat; this relationship allows for the first continuous estimates of prehibernation body mass and fat across the species' distribution. We used these results to inform a hibernation energetic model to create spatially varying fat use estimates for M. lucifugus. These results predict WNS mortality of M. lucifugus populations in western North America may be comparable to the substantial die-off observed in eastern and central populations.

Genomic and phenotypic comparison of two Salmonella Typhimurium strains responsible for consecutive salmonellosis outbreaks in New Zealand.

Salmonella enterica serovar Typhimurium DT160 was the predominant cause of notified human salmonellosis cases in New Zealand from 2000 to 2010, before it was superseded by another S. Typhimurium strain, DT56 variant (DT56v). Whole genome sequencing and phenotypic testing were used to compare 109 DT160 isolates with eight DT56v isolates from New Zealand animal and human sources. Phylogenetic analysis provided evidence that DT160 and DT56v strains were distantly related with an estimated date of common ancestor between 1769 and 1821. The strains replicated at different rates but had similar antimicrobial susceptibility profiles. Both strains were resistant to the phage expressed from the chromosome of the other strain, which may have contributed to the emergence of DT56v. DT160 contained the pSLT virulence plasmid, and the sseJ and sseK2 genes that may have contributed to the higher reported prevalence compared to DT56v. A linear pBSSB1-family plasmid was also found in one of the DT56v isolates, but there was no evidence that this plasmid affected bacterial replication or antimicrobial susceptibility. One of the DT56v isolates was also sequenced using long-read technology and found to contain an uncommon chromosome arrangement for a Typhimurium isolate. This study demonstrates how comparative genomics and phenotypic testing can help identify strain-specific elements and factors that may have influenced the emergence and supersession of bacterial strains of public health importance.