New Zealand Guidelines for cyanobacteria in recreational fresh waters: Interim Guidelines

This document is divided into four main sections, plus 14 appendices. Section 1. Introduction provides an overview of the purpose and status of the document as well as advice on who should use it. Section 2. Framework provides a background to the overall guidelines approach, recommendations on agency roles and responsibilities, and information on the condition of use of this document. Section 3. Guidelines describes the recommended three-tier monitoring and action sequence for planktonic and benthic cyanobacteria. Section 4. Sampling provides advice on sampling planktonic and benthic cyanobacteria. The appendices give further background information and include templates for data collection and reporting, including: • background information on known cyanotoxins and their distribution in New Zealand • information on the derivation of guideline values • photographs of typical bloom events • a list of biovolumes for common New Zealand cyanobacteria • templates for field assessments • suggested media releases and warning sign templates. A glossary provides definitions for abbreviations and terms used in these guidelines

The first year counts: cancer survival among Indigenous and non-Indigenous Queenslanders, 1997–2006

Objective: To examine the differential in cancer survival between Indigenous and non-Indigenous people in Queensland in relation to time after diagnosis, remoteness and area-socioeconomic disadvantage. Design, setting and participants: Descriptive study of population-based data on all 150 059 Queensland residents of known Indigenous status aged 15 years and over who were diagnosed with a primary invasive cancer during 1997–2006. Main outcome measures: Hazard ratios for the categories of area- socioeconomic disadvantage, remoteness and Indigenous status, as well as conditional 5-year survival estimates. Results: Five-year survival was lower for Indigenous people diagnosed with cancer (50.3%; 95% CI, 47.8%–52.8%) compared with non-Indigenous people (61.9%; 95% CI, 61.7%–62.2%). There was no evidence that this differential varied by remoteness (P = 0.780) or area-socioeconomic disadvantage (P = 0.845). However, it did vary by time after diagnosis. In a time-varying survival model stratified by age, sex and cancer type, the 50% excess mortality in the first year (adjusted HR, 1.50; 95% CI, 1.38–1.63) reduced to near unity at 2 years after diagnosis (HR, 1.03; 95% CI, 0.78–1.35). Conclusions: After a wide disparity in cancer survival in the first 2 years after diagnosis, Indigenous patients with cancer who survive these 2 years have a similar outlook to non-Indigenous patients. Access to services and socioeconomic factors are unlikely to be the main causes of the early lower Indigenous survival, as patterns were similar across remoteness and area- socioeconomic disadvantage. There is an urgent need to identify the factors leading to poor outcomes early after diagnosis among Indigenous people with cancer

A review of the Cochrane COVID-19 Study Register reveals inconsistency in the choice and measurement of SARS-CoV-2 infection outcomes in prevention trials

Background: Multiple studies are evaluating how to prevent SARS-CoV-2 infection. Interventions are wide ranging and include vaccines, prophylactic drugs, public health safety measures, and behavioural interventions. Heterogeneity in the outcomes measured and reported is leading to research waste and inefficiency, slowing worldwide identification and implementation of effective methods to prevent infection. A core outcome set (COS) for studies of interventions to prevent SARS-CoV-2 infection has recently been developed, identifying infection as a critical outcome to measure. This paper examines how SARS-CoV-2 infection outcomes are measured in registered COVID-19 prevention trials and considers how this can be improved. Methods: We searched the Cochrane COVID-19 Study Register to identify and review SARS-CoV-2 infection outcomes in prevention trials, including the rationale for choice of outcome measurement. We included phase 3 and 4 trials of COVID-19 prevention interventions. Early phase trials and studies relating to the transmission, treatment or management of COVID-19 were excluded. Results: We identified 430 entries in the register, of which 199 unique prevention trials were included across eight settings and 12 intervention types. Fifteen (8%) trials did not include any SARS-CoV-2 infection outcomes. The remaining 184 (92%) studies included a total of 268 SARS-CoV-2 infection outcomes, of which 32 (17%) did not specify how infection would be measured. Testing (i.e. formal diagnostic test) as a standalone method for determining infection was used in 57 (31%) trials, whereas defining infection by symptoms alone was used in 16 (9%) trials. All other trials (n=79, 43%) included multiple infection outcomes, defined in different ways. Discussion: There is considerable variation in how SARS-CoV-2 infection is measured within and across different interventions and settings. Furthermore, few studies report the rationale for outcome selection and measurement. Better transparency and standardisation of SARS-CoV-2 infection measurement is needed for the findings from prevention trials to inform decision-making.</ns3:p

Identification of dfrA14 in two distinct plasmids conferring trimethoprim resistance in Actinobacillus pleuropneumoniae

OBJECTIVES: The objective of this study was to determine the distribution and genetic basis of trimethoprim resistance in Actinobacillus pleuropneumoniae isolates from pigs in England. METHODS: Clinical isolates collected between 1998 and 2011 were tested for resistance to trimethoprim and sulphonamide. The genetic basis of trimethoprim resistance was determined by shotgun WGS analysis and the subsequent isolation and sequencing of plasmids. RESULTS: A total of 16 (out of 106) A. pleuropneumoniae isolates were resistant to both trimethoprim (MIC >32 mg/L) and sulfisoxazole (MIC ≥256 mg/L), and a further 32 were resistant only to sulfisoxazole (MIC ≥256 mg/L). Genome sequence data for the trimethoprim-resistant isolates revealed the presence of the dfrA14 dihydrofolate reductase gene. The distribution of plasmid sequences in multiple contigs suggested the presence of two distinct dfrA14-containing plasmids in different isolates, which was confirmed by plasmid isolation and sequencing. Both plasmids encoded mobilization genes, the sulphonamide resistance gene sul2, as well as dfrA14 inserted into strA, a streptomycin-resistance-associated gene, although the gene order differed between the two plasmids. One of the plasmids further encoded the strB streptomycin-resistance-associated gene. CONCLUSIONS: This is the first description of mobilizable plasmids conferring trimethoprim resistance in A. pleuropneumoniae and, to our knowledge, the first report of dfrA14 in any member of the Pasteurellaceae. The identification of dfrA14 conferring trimethoprim resistance in A. pleuropneumoniae isolates will facilitate PCR screens for resistance to this important antimicrobial

Evidence of illegitimate recombination between two pasteurellaceae plasmids resulting in a novel multi-resistance replicon, pM3362MDR, in Actinobacillus pleuropneumoniae

Evidence of plasmids carrying the tetracycline resistance gene, tet(B), was found in the previously reported whole genome sequences of 14 United Kingdom, and 4 Brazilian, isolates of Actinobacillus pleuropneumoniae. Isolation and sequencing of selected plasmids, combined with comparative sequence analysis, indicated that the four Brazilian isolates all harbor plasmids that are nearly identical to pB1001, a plasmid previously found in Pasteurella multocida isolates from Spain. Of the United Kingdom isolates, 13/14 harbor plasmids that are (almost) identical to pTetHS016 from Haemophilus parasuis. The remaining United Kingdom isolate, MIDG3362, harbors a 12666 bp plasmid that shares extensive regions of similarity with pOV from P. multocida (which carries bla ROB−1 , sul2, and strAB genes), as well as with pTetHS016. The newly identified multi-resistance plasmid, pM3362MDR, appears to have arisen through illegitimate recombination of pTetHS016 into the stop codon of the truncated strB gene in a pOV-like plasmid. All of the tet(B)-carrying plasmids studied were capable of replicating in Escherichia coli, and predicted origins of replication were identified. A putative origin of transfer (oriT) sequence with similar secondary structure and a nic-site almost identical to that of RP4 was also identified in these plasmids, however, attempts to mobilize them from an RP4-encoding E. coli donor strain were not successful, indicating that specific conjugation machinery may be required

Increased risk of A(H1N1)pdm09 influenza infection in UK pig industry workers compared to a general population cohort

Background: Pigs are mixing vessels for influenza viral reassortment but the extent of influenza transmission between swine and humans is not well understood. Objectives: To assess whether occupational exposure to pigs is a risk factor for human infection with human and swine-adapted influenza viruses. Methods: UK pig industry workers were frequency-matched on age, region, sampling month, and gender with a community-based comparison group from the Flu Watch study. HI assays quantified antibodies for swine and human A(H1) and A(H3) influenza viruses (titres≥40 considered seropositive and indicative of infection). Virus-specific associations between seropositivity and occupational pig exposure were examined using multivariable regression models adjusted for vaccination. Pigs on the same farms were also tested for seropositivity. Results: 42% of pigs were seropositive to A(H1N1)pdm09. Pig industry workers showed evidence of increased odds of A(H1N1)pdm09 seropositivity compared to the comparison group, albeit with wide confidence intervals (CI), Adjusted Odds Ratio after accounting for possible cross reactivity with other swine A(H1) viruses (aOR) 25.30, 95% CI [1.44-536.34], p=0.028. Conclusion: The results indicate that A(H1N1)pdm09 virus was common in UK pigs during the pandemic and subsequent period of human A(H1N1)pdm09 circulation, and occupational exposure to pigs was a risk factor for human infection. Influenza immunization of pig industry workers may reduce transmission and the potential for virus reassortment

Increased risk of A(H1N1)pdm09 influenza infection in UK pig industry workers compared to a general population cohort.

BACKGROUND: Pigs are mixing vessels for influenza viral reassortment, but the extent of influenza transmission between swine and humans is not well understood. OBJECTIVES: To assess whether occupational exposure to pigs is a risk factor for human infection with human and swine-adapted influenza viruses. METHODS: UK pig industry workers were frequency-matched on age, region, sampling month, and gender with a community-based comparison group from the Flu Watch study. HI assays quantified antibodies for swine and human A(H1) and A(H3) influenza viruses (titres ≥ 40 considered seropositive and indicative of infection). Virus-specific associations between seropositivity and occupational pig exposure were examined using multivariable regression models adjusted for vaccination. Pigs on the same farms were also tested for seropositivity. RESULTS: Forty-two percent of pigs were seropositive to A(H1N1)pdm09. Pig industry workers showed evidence of increased odds of A(H1N1)pdm09 seropositivity compared to the comparison group, albeit with wide confidence intervals (CIs), adjusted odds ratio after accounting for possible cross-reactivity with other swine A(H1) viruses (aOR) 25·3, 95% CI (1·4-536·3), P = 0·028. CONCLUSION: The results indicate that A(H1N1)pdm09 virus was common in UK pigs during the pandemic and subsequent period of human A(H1N1)pdm09 circulation, and occupational exposure to pigs was a risk factor for human infection. Influenza immunisation of pig industry workers may reduce transmission and the potential for virus reassortment.This work was supported by joint funding from the Biotechnology and Biological Sciences Research Council (BBSRC), the Medical Research Council (MRC), and the Wellcome Trust (WT) [(BBSRC/MRC/WT) BB/H014306/1; (MRC/WT) MC_U122785833; (MRC) G0800767 and G0600511]; Alborada Trust (to J.L.N.W.); the RAPIDD programme of the Science & Technology Directorate (to J.L.N.W.); US Department of Homeland Security (to J.L.N.W.); and the Fogarty International Center at the National Institutes of Health (to J.L.N.W.). DAI is supported by a fellowship from the National Institute for Health Research (NIHR) (PDF-2012-05-305) (this research is independent and the views expressed in this publication are those of the authors and not necessarily those of the Department of Health or NIHR).This is the final version of the article. It first appeared from Wiley via https://doi.org//10.1111/irv.12364/abstract

Haemophilus parasuis molecular serotyping assay

Haemophilus parasuis causes Glässer's disease and pneumonia in pigs. Indirect hemagglutination (IHA) is typically used to serotype this bacterium, distinguishing 15 serovars with some nontypeable isolates. The capsule loci of the 15 reference strains have been annotated, and significant genetic variation was identified between serovars, with the exception of serovars 5 and 12. A capsule locus and in silico serovar were identified for all but two nontypeable isolates in our collection of >200 isolates. Here, we describe the development of a multiplex PCR, based on variation within the capsule loci of the 15 serovars of H. parasuis, for rapid molecular serotyping. The multiplex PCR (mPCR) distinguished between all previously described serovars except 5 and 12, which were detected by the same pair of primers. The detection limit of the mPCR was 4.29 × 10(5) ng/μl bacterial genomic DNA, and high specificity was indicated by the absence of reactivity against closely related commensal Pasteurellaceae and other bacterial pathogens of pigs. A subset of 150 isolates from a previously sequenced H. parasuis collection was used to validate the mPCR with 100% accuracy compared to the in silico results. In addition, the two in silico-nontypeable isolates were typeable using the mPCR. A further 84 isolates were analyzed by mPCR and compared to the IHA serotyping results with 90% concordance (excluding those that were nontypeable by IHA). The mPCR was faster, more sensitive, and more specific than IHA, enabling the differentiation of 14 of the 15 serovars of H. parasuis.This work was supported by a BPEX PhD studentship and a Longer and Larger (LoLa) grant from the Biotechnology and Biological Sciences Research Council (grant numbers BB/G020744/1, BB/G019177/1, BB/G019274/1 and BB/G003203/1), the UK Department for Environment, Food and Rural Affairs and Zoetis, awarded to the Bacterial Respiratory Diseases of Pigs-1 Technology (BRaDP1T) consortium. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.This is the author accepted manuscript. The final version is available from American Society for Microbiology via http://dx.doi.org/10.1128/JCM.01991-1

Identification of a New Antimicrobial Resistance Gene Provides Fresh Insights Into Pleuromutilin Resistance in Brachyspira hyodysenteriae, Aetiological Agent of Swine Dysentery

Brachyspira hyodysenteriae is the aetiological agent of swine dysentery, a globally distributed disease that causes profound economic loss, impedes the free trade and movement of animals, and has significant impact on pig health. Infection is generally treated with antibiotics of which pleuromutilins, such as tiamulin, are widely used for this purpose, but reports of resistance worldwide threaten continued effective control. In Brachyspira hyodysenteriae pleuromutilin resistance has been associated with mutations in chromosomal genes encoding ribosome-associated functions, however the dynamics of resistance acquisition are poorly understood, compromising stewardship efforts to preserve pleuromutilin effectiveness. In this study we undertook whole genome sequencing (WGS) and phenotypic susceptibility testing of 34 UK field isolates and 3 control strains to investigate pleuromutilin resistance in Brachyspira hyodysenteriae. Genome-wide association studies identified a new pleuromutilin resistance gene, tva(A) (tiamulin valnemulin antibiotic resistance), encoding a predicted ABC-F transporter. In vitro culture of isolates in the presence of inhibitory or sub-inhibitory concentrations of tiamulin showed that tva(A) confers reduced pleuromutilin susceptibility that does not lead to clinical resistance but facilitates the development of higher-level resistance via mutations in genes encoding ribosome-associated functions. Genome sequencing of antibiotic-exposed isolates identified both new and previously described mutations in chromosomal genes associated with reduced pleuromutilin susceptibility, including the 23S rRNA gene and rplC, which encodes the L3 ribosomal protein. Interesting three antibiotic-exposed isolates harboured mutations in fusA, encoding Elongation Factor G, a gene not previously associated with pleuromutilin resistance. A longitudinal molecular epidemiological examination of two episodes of swine dysentery at the same farm indicated that tva(A) contributed to development of tiamulin resistance in vivo in a manner consistent with that seen experimentally in vitro. The in vitro studies further showed that tva(A) broadened the mutant selection window and raised the mutant prevention concentration above reported in vivo antibiotic concentrations obtained when administered at certain doses. We show how the identification and characterisation of tva(A), a new marker for pleuromutilin resistance, provides evidence to inform treatment regimes and reduce the development of resistance to this class of highly important antimicrobial agents

Whole-genome sequencing of Brachyspira hyodysenteriae isolates from England and Wales reveals similarities to European isolates and mutations associated with reduced sensitivity to antimicrobials

Brachyspira hyodysenteriae is the principal cause of swine dysentery, a disease that threatens economic productivity of pigs in many countries as it can spread readily within and between farms, and only a small number of antimicrobials are authorized for treatment of pigs. In this study, we performed whole-genome sequencing (WGS) of 81 B. hyodysenteriae archived at the Animal and Plant Health Agency (APHA) from diagnostic submissions and herd monitoring in England and Wales between 2004 and 2015. The resulting genome sequences were analyzed alongside 34 genomes we previously published. Multi-locus sequence typing (MLST) showed a diverse population with 32 sequence types (STs) among the 115 APHA isolates, 25 of them identified only in England; while also confirming that the dominant European clonal complexes, CC8 and CC52, were common in the United Kingdom. A core-genome SNP tree typically clustered the isolates by ST, with isolates from some STs detected only within a specific region in England, although others were more widespread, suggesting transmission between different regions. Also, some STs were more conserved in their core genome than others, despite these isolates being from different holdings, regions and years. Minimum inhibitory concentrations to commonly used antimicrobials (Tiamulin, Valnemulin, Doxycycline, Lincomycin, Tylosin, Tylvalosin) were determined for 82 of the genome-sequenced isolates; genomic analysis revealed mutations generally correlated well with the corresponding resistance phenotype. There was a major swine dysentery intervention program in 2009–2010, and antimicrobial survival curves showed a significant reduction in sensitivity to tiamulin and valnemulin in isolates collected in and after 2010, compared to earlier isolates. This correlated with a significant increase in post-2009 isolates harboring the pleuromutilin resistance gene tva(A), which if present, may facilitate higher levels of resistance. The reduction in susceptibility of Brachyspira from diagnostic submissions to pleuromutilins, emphasizes the need for prudent treatment, control and eradication strategies