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.

Benefits of budesonide/glycopyrronium/formoterol fumarate dihydrate on lung function and exacerbations of COPD: a post-hoc analysis of the KRONOS study by blood eosinophil level and exacerbation history.

BACKGROUND: Japanese guidelines recommend triple inhaled corticosteroid (ICS)/long-acting muscarinic antagonist (LAMA)/long-acting ß2-agonist (LABA) therapy in patients with chronic obstructive pulmonary disease (COPD) and no concurrent asthma diagnosis who experience frequent exacerbations and have blood eosinophil (EOS) count ≥ 300 cells/mm3, and in patients with COPD and asthma with continuing/worsening symptoms despite receiving dual ICS/LABA therapy. These post-hoc analyses of the KRONOS study in patients with COPD and without an asthma diagnosis, examine the effects of fixed-dose triple therapy with budesonide/glycopyrronium/formoterol fumarate dihydrate (BGF) versus dual therapies on lung function and exacerbations based on blood EOS count - focusing on blood EOS count 100 to < 300 cells/mm3 - as a function of exacerbation history and COPD severity. METHODS: In KRONOS, patients were randomized to receive treatments that included BGF 320/14.4/10 µg, glycopyrronium/formoterol fumarate dihydrate (GFF) 14.4/10 µg, or budesonide/formoterol fumarate dihydrate (BFF) 320/10 µg via metered dose inhaler (two inhalations twice-daily for 24 weeks). These post-hoc analyses assessed changes from baseline in morning pre-dose trough forced expiratory volume in 1 s (FEV1) over 12-24 weeks and moderate or severe COPD exacerbations rates over 24 weeks. The KRONOS study was not prospectively powered for these subgroup analyses. RESULTS: Among patients with blood EOS count 100 to < 300 cells/mm3, least squares mean treatment differences for lung function improvement favored BGF over BFF in patients without an exacerbation history in the past year and in patients with moderate and severe COPD, with observed differences ranging from 62 ml to 73 ml across populations. In this same blood EOS population, moderate or severe exacerbation rates were reduced for BGF relative to GFF by 56% in patients without an exacerbation history in the past year, by 47% in patients with moderate COPD, and by 50% in patients with severe COPD. CONCLUSIONS: These post-hoc analyses of patients with moderate-to-very severe COPD from the KRONOS study seem to indicate clinicians may want to consider a step-up to triple therapy in patients with persistent/worsening symptoms with blood EOS count > 100 cells/mm3, even if disease severity is moderate and there is no recent history of exacerbations. TRIAL REGISTRATION: ClinicalTrials.gov registry number NCT02497001 (registration date, 13 July 2015).

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.

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.

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 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.

Transmission Dynamics of Shiga Toxin-Producing Escherichia coli in New Zealand Cattle from Farm to Slaughter.

Cattle are asymptomatic carriers of Shiga toxin-producing Escherichiacoli (STEC) strains that can cause serious illness or death in humans. In New Zealand, contact with cattle feces and living near cattle populations are known risk factors for human STEC infection. Contamination of fresh meat with STEC strains also leads to the potential for rejection of consignments by importing countries. We used a combination of PCR/matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) and whole-genome sequencing (WGS) to evaluate the presence and transmission of STEC on farms and in processing plants to better understand the potential pathways for human exposure and thus mitigate risk. Animal and environmental samples (n = 2,580) were collected from six farms and three meat processing plants in New Zealand during multiple sampling sessions in spring of 2015 and 2016. PCR/MALDI-TOF analysis revealed that 6.2% were positive for "Top 7" STEC. Top 7 STEC strains were identified in all sample sources (n = 17) tested. A marked increase in Top 7 STEC prevalence was observed between calf hides on farm (6.3% prevalence) and calf hides at processing plants (25.1% prevalence). Whole-genome sequencing was performed on Top 7 STEC bacterial isolates (n = 40). Analysis of STEC O26 (n = 25 isolates) revealed relatively low genetic diversity on individual farms, consistent with the presence of a resident strain disseminated within the farm environment. Public health efforts should focus on minimizing human contact with fecal material on farms and during handling, transport, and slaughter of calves. Meat processing plants should focus on minimizing cross-contamination between the hides of calves in a cohort during transport, lairage, and slaughter.IMPORTANCE Cattle are asymptomatic carriers of Shiga toxin-producing E. coli (STEC) strains, which can cause serious illness or death in humans. Contact with cattle feces and living near cattle are known risk factors for human STEC infection. This study evaluated STEC carriage in young calves and the farm environment with an in-depth evaluation of six farms and three meat processing plants over 2 years. An advanced molecular detection method and whole-genome sequencing were used to provide a detailed evaluation of the transmission of STEC both within and between farms. The study revealed widespread STEC contamination within the farm environment, but no evidence of recent spread between farms. Contamination of young dairy calf hides increased following transport and holding at meat processing plants. The elimination of STEC in farm environments may be very difficult given the multiple transmission routes; interventions should be targeted at decreasing fecal contamination of calf hides during transport, lairage, and processing.

A Process Chemistry Benchmark for sp2-sp3 Cross Couplings.

As sp2-sp3 disconnections gain acceptance in the medicinal chemist's toolbox, an increasing number of potential drug candidates containing this motif are moving into the pharmaceutical development pipeline. This raises a new set of questions and challenges around the novel, direct methodologies available for forging these bonds. These questions gain further importance in the context of process chemistry, where the focus is the development of scalable processes that enable the large-scale delivery of clinical supplies. In this paper, we describe our efforts to apply a wide variety of standard, photo-, and electrochemical sp2-sp3 cross-coupling methods to a pharmaceutically relevant intermediate and optimize each through a combination of high throughput and mechanistically guided experimentation. With data regarding the performance, benefits, and limitations of these novel methods, we evaluate them against a more traditional two-step palladium-catalyzed process. This work reveals trends and similarities between these sp2-sp3 bond-forming methods and suggests a path forward for further refinements.

Shifts in the Molecular Epidemiology of Campylobacter jejuni Infections in a Sentinel Region of New Zealand following Implementation of Food Safety Interventions by the Poultry Industry.

In 2006, New Zealand had the highest notification rate of campylobacteriosis in the world, and poultry was considered the leading source of campylobacteriosis. Implementation of food safety interventions by the poultry industry led to a decrease in the campylobacteriosis notification rate. The aim is to examine the impact of targeted food safety interventions implemented by the New Zealand poultry industry on the source attribution of Campylobacter jejuni infections in a sentinel region. Campylobacter jejuni isolates collected from the Manawatu region of New Zealand between 2005 and 2007 ("before intervention") and 2008 and 2015 ("after intervention") from human clinical cases, chicken meat, ruminant feces, environmental water, and wild bird sources were subtyped by multilocus sequence typing. Viable counts of Campylobacter spp. from carcasses were analyzed using a zero-inflated Poisson regression model. In the period before intervention, sequence type 474 (ST-474) was the most common sequence type (ST) recovered from human cases, accounting for 28.2% of the isolates. After intervention, the proportion of human cases positive for ST-474 reduced to 9.3%. Modeling indicated that chicken meat, primarily from one supplier, was the main source of C. jejuni infection in the Manawatu region before intervention. However, after intervention poultry collectively had a similar attribution to ruminants, but more human cases were attributed to ruminants than any single chicken supplier. Viable counts on carcasses were lower in all poultry suppliers after intervention. This study provides evidence of changes in the source attribution of campylobacteriosis following targeted food safety interventions in one sector of the food supply chain.IMPORTANCE This study provides a unique insight into the effects of food safety interventions implemented in one sector of the food industry on the transmission routes of a major foodborne agent. Following the implementation of food safety interventions by the poultry industry, shifts in the molecular epidemiology of Campylobacter jejuni infections in a sentinel region of New Zealand were observed. Targeted interventions to reduce disease incidence are effective but require continued surveillance and analysis to indicate where further interventions may be beneficial.

Carriage of Extended-Spectrum-Beta-Lactamase- and AmpC Beta-Lactamase-Producing Escherichia coli Strains from Humans and Pets in the Same Households.

Extended-spectrum-beta-lactamase (ESBL)- or AmpC beta-lactamase (ACBL)-producing Escherichia coli bacteria are the most common cause of community-acquired multidrug-resistant urinary tract infections (UTIs) in New Zealand. The carriage of antimicrobial-resistant bacteria has been found in both people and pets from the same household; thus, the home environment may be a place where antimicrobial-resistant bacteria are shared between humans and pets. In this study, we sought to determine whether members (pets and people) of the households of human index cases with a UTI caused by an ESBL- or ACBL-producing E. coli strain also carried an ESBL- or ACBL-producing Enterobacteriaceae strain and, if so, whether it was a clonal match to the index case clinical strain. Index cases with a community-acquired UTI were recruited based on antimicrobial susceptibility testing of urine isolates. Fecal samples were collected from 18 non-index case people and 36 pets across 27 households. Eleven of the 27 households screened had non-index case household members (8/18 people and 5/36 animals) positive for ESBL- and/or ACBL-producing E. coli strains. Whole-genome sequence analysis of 125 E. coli isolates (including the clinical urine isolates) from these 11 households showed that within seven households, the same strain of ESBL-/ACBL-producing E. coli was cultured from both the index case and another person (5/11 households) or pet dog (2/11 households). These results suggest that transmission within the household may contribute to the community spread of ESBL- or ACBL-producing E. coliIMPORTANCEEnterobacteriaceae that produce extended-spectrum beta-lactamases (ESBLs) and AmpC beta-lactamases (ACBLs) are important pathogens and can cause community-acquired illnesses, such as urinary tract infections (UTIs). Fecal carriage of these resistant bacteria by companion animals may pose a risk for transmission to humans. Our work evaluated the sharing of ESBL- and ACBL-producing E. coli isolates between humans and companion animals. We found that in some households, dogs carried the same strain of ESBL-producing E. coli as the household member with a UTI. This suggests that transmission events between humans and animals (or vice versa) are likely occurring within the home environment and, therefore, the community as a whole. This is significant from a health perspective, when considering measures to minimize community transmission, and highlights that in order to manage community spread, we need to consider interventions at the household level.

The hypoattenuating ocular lens on CT is not always due to cataract formation.

Hypoattenuating ocular lenses on CT have been described with cataract formation in humans, however published studies are currently lacking regarding this finding in veterinary patients. The purpose of this retrospective and prospective study was to describe the varying CT appearances of the ocular lens in vivo, and investigate the causes for CT density variations in a population of cats and dogs. A total of 102 canine and feline patients with CT of the head acquired at the authors' hospital between May 2011 and March 2019 were included. A bilateral hypoattenuating halo surrounding an isoattenuating to mildly hypoattenuating core was described in the ocular lens center of every cat in which a Philips brand proprietary image construction filter was used. A similar but more varied hypoattenuating region was noted in the lenses of 45.8% of dogs where the same filter was applied, as well as 43.8% of dogs with a second, similar filter. Ophthalmic examination of three live cats and one dog with hypoattenuating lenses demonstrated normal lens translucency, excluding the presence of cataract. The effect of different proprietary filters on lens appearance was also described in three fresh cadavers with normal lenses identified on ophthalmic, macroscopic, and microscopic examination. Etiology of the hypoattenuating areas within the ocular lens was not conclusively determined. Recognition that such a variant may be seen in the absence of cataract is important, in order to prevent misdiagnosis.

Use of Genomics to Investigate Historical Importation of Shiga Toxin-Producing Escherichia coli Serogroup O26 and Nontoxigenic Variants into New Zealand.

Shiga toxin-producing Escherichia coli serogroup O26 is an important public health pathogen. Phylogenetic bacterial lineages in a country can be associated with the level and timing of international imports of live cattle, the main reservoir. We sequenced the genomes of 152 E. coli O26 isolates from New Zealand and compared them with 252 E. coli O26 genomes from 14 other countries. Gene variation among isolates from humans, animals, and food was strongly associated with country of origin and stx toxin profile but not isolation source. Time of origin estimates indicate serogroup O26 sequence type 21 was introduced at least 3 times into New Zealand from the 1920s to the 1980s, whereas nonvirulent O26 sequence type 29 strains were introduced during the early 2000s. New Zealand's remarkably fewer introductions of Shiga toxin-producing Escherichia coli O26 compared with other countries (such as Japan) might be related to patterns of trade in live cattle.

Campylobacter jejuni Strains Associated with Wild Birds and Those Causing Human Disease in Six High-Use Recreational Waterways in New Zealand.

Campylobacter jejuni, a leading cause of gastroenteritis worldwide, has been frequently isolated from recreational rivers and streams in New Zealand, yet the public health significance of this is unknown. This study uses molecular tools to improve our understanding of the epidemiology and sources of Campylobacter in recreational waterways, with a view to preventing human infection. Epidemiological and microbiological data were collected between 2005 and 2009 from six high-use recreational waterways in the Manawatu-Wanganui region of the North Island. Campylobacter spp. and C. jejuni were isolated from 33.2% and 20.4% of 509 samples, respectively. Isolation of Campylobacter was observed in both low and high river flows. After adjusting for the confounding effects of river flow, there was a significantly higher likelihood of isolating Campylobacter in the winter month of June compared to January. A high diversity of C. jejuni multilocus sequence types was seen, with the most commonly isolated being the water rail-associated ST-2381 (19/91 isolates [20.9%]), ST-1225 (8/91 isolates [8.8%]), and ST-45 (6/91 isolates [6.6%]). The ST-2381 was found in all rivers, while the most commonly isolated ST from human cases in New Zealand, the poultry-associated strain ST-474, was isolated only in one river. Although the majority of Campylobacter sequence types identified in river water were strains associated with wild birds that are rarely associated with human disease, poultry and ruminant-associated Campylobacter strains that are found in human infection were also identified and could present a public health risk.IMPORTANCE In 2016, there was a large-scale waterborne outbreak of campylobacteriosis in New Zealand, which was estimated to have affected over 5,000 people. This highlighted the need for a greater understanding of the sources of contamination of both surface and groundwater and risks associated with exposure to both drinking and recreational water. This study reports the prevalence and population structure of Campylobacter jejuni in six recreational waters of the Manawatu-Wanganui region of New Zealand and models the relationship between Campylobacter spp. and ruminant-associated Campylobacter and the parameters "sites," "months," and "river flow." Here, we demonstrate that both low and high river flows, month of the year, and recreational sites could influence the Campylobacter isolation from recreational waters. The presence of genotypes associated with human infection allowed us to describe potential risks associated with recreational waters.

Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli (STEC) on New Zealand Dairy Farms: Application of a Culture-Independent Assay and Whole-Genome Sequencing.

New Zealand has a relatively high incidence of human cases of Shiga toxin-producing Escherichia coli (STEC), with 8.9 STEC cases per 100,000 people reported in 2016. Previous research showed living near cattle and contact with cattle feces as significant risk factors for STEC infections in humans in New Zealand, but infection was not linked to food-associated factors. During the 2014 spring calving season, a random, stratified, cross-sectional study of dairy farms (n = 102) in six regions across New Zealand assessed the prevalence of the "Top 7" STEC bacteria (serogroups O157, O26, O45, O103, O111, O121, and O145) in young calves (n = 1,508), using a culture-independent diagnostic test (PCR/MALDI-TOF). Twenty percent (306/1,508) of calves on 75% (76/102) of dairy farms were positive for at least one of the "Top 7" STEC bacteria. STEC carriage by calves was associated with environmental factors, increased calf age, region, and increased number of calves in a shared calf pen. The intraclass correlation coefficient (ρ) indicated strong clustering of "Top 7" STEC-positive calves for O157, O26, and O45 serogroups within the same pens and farms, indicating that if one calf was positive, others in the same environment were likely to be positive as well. This finding was further evaluated with whole-genome sequencing, which indicated that a single E. coli O26 clonal strain could be found in calves in the same pen or farm, but different strains existed on different farms. This study provides evidence that would be useful for designing on-farm interventions to reduce direct and indirect human exposure to STEC bacteria.IMPORTANCE Cattle are asymptomatic carriers of Shiga toxin-producing E. coli (STEC) bacteria that can cause bloody diarrhea and kidney failure in humans if ingested. New Zealand has relatively high numbers of STEC cases, and contact with cattle feces and living near cattle are risk factors for human infection. This study assessed the national prevalence of STEC in young dairy cattle by randomly selecting 102 farms throughout New Zealand. The study used a molecular laboratory method that has relatively high sensitivity and specificity compared to traditional methods. "Top 7" STEC was found in 20% of calves on 75% of the farms studied, indicating widespread prevalence across the country. By examining the risk factors associated with calf carriage, potential interventions that could decrease the prevalence of "Top 7" STEC bacteria at the farm level were identified, which could benefit both public health and food safety.

Critical inhaler errors in asthma and COPD: a systematic review of impact on health outcomes.

BACKGROUND: Inhaled drug delivery is the cornerstone treatment for asthma and chronic obstructive pulmonary disease (COPD). However, use of inhaler devices can be challenging, potentially leading to critical errors in handling that can significantly reduce drug delivery to the lungs and effectiveness of treatment. METHODS: A systematic review was conducted to define 'critical' errors and their impact on health outcomes and resource use between 2004 and 2016, using key search terms for inhaler errors in asthma and COPD (Search-1) and associated health-economic and patient burden (Search-2). RESULTS: Search-1 identified 62 manuscripts, 47 abstracts, and 5 conference proceedings (n = 114 total). Search-2 identified 9 studies. We observed 299 descriptions of critical error. Age, education status, previous inhaler instruction, comorbidities and socioeconomic status were associated with worse handling error frequency. A significant association was found between inhaler errors and poor disease outcomes (exacerbations), and greater health-economic burden. CONCLUSIONS: We have shown wide variations in how critical errors are defined, and the evidence shows an important association between inhaler errors and worsened health outcomes. Given the negative impact diminished disease outcomes impose on resource use, our findings highlight the importance of achieving optimal inhaler technique, and a need for a consensus on defining critical and non-critical errors.

sourceR: Classification and source attribution of infectious agents among heterogeneous populations.

Zoonotic diseases are a major cause of morbidity, and productivity losses in both human and animal populations. Identifying the source of food-borne zoonoses (e.g. an animal reservoir or food product) is crucial for the identification and prioritisation of food safety interventions. For many zoonotic diseases it is difficult to attribute human cases to sources of infection because there is little epidemiological information on the cases. However, microbial strain typing allows zoonotic pathogens to be categorised, and the relative frequencies of the strain types among the sources and in human cases allows inference on the likely source of each infection. We introduce sourceR, an R package for quantitative source attribution, aimed at food-borne diseases. It implements a Bayesian model using strain-typed surveillance data from both human cases and source samples, capable of identifying important sources of infection. The model measures the force of infection from each source, allowing for varying survivability, pathogenicity and virulence of pathogen strains, and varying abilities of the sources to act as vehicles of infection. A Bayesian non-parametric (Dirichlet process) approach is used to cluster pathogen strain types by epidemiological behaviour, avoiding model overfitting and allowing detection of strain types associated with potentially high "virulence". sourceR is demonstrated using Campylobacter jejuni isolate data collected in New Zealand between 2005 and 2008. Chicken from a particular poultry supplier was identified as the major source of campylobacteriosis, which is qualitatively similar to results of previous studies using the same dataset. Additionally, the software identifies a cluster of 9 multilocus sequence types with abnormally high 'virulence' in humans. sourceR enables straightforward attribution of cases of zoonotic infection to putative sources of infection. As sourceR develops, we intend it to become an important and flexible resource for food-borne disease attribution studies.

Tutorial on kernel estimation of continuous spatial and spatiotemporal relative risk.

Kernel smoothing is a highly flexible and popular approach for estimation of probability density and intensity functions of continuous spatial data. In this role, it also forms an integral part of estimation of functionals such as the density-ratio or "relative risk" surface. Originally developed with the epidemiological motivation of examining fluctuations in disease risk based on samples of cases and controls collected over a given geographical region, such functions have also been successfully used across a diverse range of disciplines where a relative comparison of spatial density functions has been of interest. This versatility has demanded ongoing developments and improvements to the relevant methodology, including use spatially adaptive smoothers; tests of significantly elevated risk based on asymptotic theory; extension to the spatiotemporal domain; and novel computational methods for their evaluation. In this tutorial paper, we review the current methodology, including the most recent developments in estimation, computation, and inference. All techniques are implemented in the new software package sparr, publicly available for the R language, and we illustrate its use with a pair of epidemiological examples.

The Site of Bone Marrow Acquisition Affects the Myeloid to Erythroid Ratio in Apparently Healthy Dogs.

Bone marrow (BM) cytology and histopathology are complementary tools used to investigate hematological diseases. The purpose of this study was to determine if there are site-dependent differences in the diagnostic quality, myeloid to erythroid ratio (MER), and discordant findings in samples from different sites in the same dog. Eighteen apparently healthy dogs were used in the study. The sequence of sample acquisition was randomized according to a Latin square, and samples for BM cytology and histology were collected from both humeri and both ilial crests immediately after death. Board-certified clinical and anatomical pathologists read the cytology and histology, respectively. The data were analyzed using a mixed-effect model. The site of BM acquisition did not affect BM sample quality. The rate of discordant clinical findings between sites was 0.05 (95% confidence interval, 0.01-0.13). In general, by cytology, the MERs were slightly but significantly greater in samples from the ilial crests than from the humeri ( P = .01). The measured MER for histology was nearly twice that for cytology for all sites ( P < .001). In conclusion, there was a low-rate, site-dependent discordance in diagnostic findings in BM samples and differences in MER between the ilial crest and the humerus. A similar study is justified in sick dogs with hematological disease to determine the effect of sampling site on discordant findings between sites.

A Risk-Based Ecohydrological Approach to Assessing Environmental Flow Regimes.

For several decades there has been recognition that water resource development alters river flow regimes and impacts ecosystem values. Determining strategies to protect or restore flow regimes to achieve ecological outcomes is a focus of water policy and legislation in many parts of the world. However, consideration of existing environmental flow assessment approaches for application in Queensland identified deficiencies precluding their adoption. Firstly, in managing flows and using ecosystem condition as an indicator of effectiveness, many approaches ignore the fact that river ecosystems are subjected to threatening processes other than flow regime alteration. Secondly, many focus on providing flows for responses without considering how often they are necessary to sustain ecological values in the long-term. Finally, few consider requirements at spatial-scales relevant to the desired outcomes, with frequent focus on individual places rather than the regions supporting sustainability. Consequently, we developed a risk-based ecohydrological approach that identifies ecosystem values linked to desired ecological outcomes, is sensitive to flow alteration and uses indicators of broader ecosystem requirements. Monitoring and research is undertaken to quantify flow-dependencies and ecological modelling is used to quantify flow-related ecological responses over an historical flow period. The relative risk from different flow management scenarios can be evaluated at relevant spatial-scales. This overcomes the deficiencies identified above and provides a robust and useful foundation upon which to build the information needed to support water planning decisions. Application of the risk assessment approach is illustrated here by two case studies.