Refinement of acoustic-tagging protocol for twaite shad Alosa fallax (Lacépède), a species sensitive to handling and sedation

Telemetry investigations to gather essential information about fish migrations are reliant on the behaviour, condition and survival of the animals being unaltered by the tagging procedure. Twaite shad (Alosa fallax Lacépède; 'shad’) is a threatened clupeid fish for which there is a considerable knowledge gap on their anadromous movements. They are also reported to be sensitive to handling and anaesthesia, resulting in practical difficulties in tag implantation; previous investigations externally attached tags without sedation. The aim of this study was to incrementally refine the acoustic-tagging protocol for shad via application of a previously un-tried anaesthetic (i.e. tricaine methanesulphonate (MS-222)) and by surgical implantation of the tag in the peritoneal cavity. All captured shad (n = 25) survived handling, anaesthesia and tagging, and were detected moving upstream after release. Surgically implantation (n = 5) was significantly faster than externally mounting the tag (n = 20) and time to recover was similar. Total upstream movement, total movement, residence time in receiver array and speed of upstream movement were statistically similar for externally and internally tagged fish. Post-spawning, a large proportion (68%) of tagged fish returned to the estuary, downstream of the receiver array. Internal tagging under anaesthesia is recommended for studying anadromous movements of shad, given welfare benefits during surgery and once at liberty, thus increasing the likelihood of tagged fish performing natural behaviours. Further, implantation of tags programmed to last many years enables multiple spawning migrations by the same individuals to be studied, which would lead to substantial advances in ecological knowledge and potentially reduce the number of fish tagged

Exploiting genomics for antimicrobial resistance surveillance at One Health interfaces.

The intersection of human, animal, and ecosystem health at One Health interfaces is recognised as being of key importance in the evolution and spread of antimicrobial resistance (AMR) and represents an important, and yet rarely realised opportunity to undertake vital AMR surveillance. A working group of international experts in pathogen genomics, AMR, and One Health convened to take part in a workshop series and online consultation focused on the opportunities and challenges facing genomic AMR surveillance in a range of settings. Here we outline the working group's discussion of the potential utility, advantages of, and barriers to, the implementation of genomic AMR surveillance at One Health interfaces and propose a series of recommendations for addressing these challenges. Embedding AMR surveillance at One Health interfaces will require the development of clear beneficial use cases, especially in low-income and middle-income countries. Evidence of directionality, risks to human and animal health, and potential trade implications were also identified by the working group as key issues. Addressing these challenges will be vital to enable genomic surveillance technology to reach its full potential for assessing the risk of transmission of AMR between the environment, animals, and humans at One Health interfaces.

Genomics for antimicrobial resistance surveillance to support infection prevention and control in health-care facilities

Integration of genomic technologies into routine antimicrobial resistance (AMR) surveillance in health-care facilities has the potential to generate rapid, actionable information for patient management and inform infection prevention and control measures in near real time. However, substantial challenges limit the implementation of genomics for AMR surveillance in clinical settings. Through a workshop series and online consultation, international experts from across the AMR and pathogen genomics fields convened to review the evidence base underpinning the use of genomics for AMR surveillance in a range of settings. Here, we summarise the identified challenges and potential benefits of genomic AMR surveillance in health-care settings, and outline the recommendations of the working group to realise this potential. These recommendations include the definition of viable and cost-effective use cases for genomic AMR surveillance, strengthening training competencies (particularly in bioinformatics), and building capacity at local, national, and regional levels using hub and spoke models

Genomics for public health and international surveillance of antimicrobial resistance.

Historically, epidemiological investigation and surveillance for bacterial antimicrobial resistance (AMR) has relied on low-resolution isolate-based phenotypic analyses undertaken at local and national reference laboratories. Genomic sequencing has the potential to provide a far more high-resolution picture of AMR evolution and transmission, and is already beginning to revolutionise how public health surveillance networks monitor and tackle bacterial AMR. However, the routine integration of genomics in surveillance pipelines still has considerable barriers to overcome. In 2022, a workshop series and online consultation brought together international experts in AMR and pathogen genomics to assess the status of genomic applications for AMR surveillance in a range of settings. Here we focus on discussions around the use of genomics for public health and international AMR surveillance, noting the potential advantages of, and barriers to, implementation, and proposing recommendations from the working group to help to drive the adoption of genomics in public health AMR surveillance. These recommendations include the need to build capacity for genome sequencing and analysis, harmonising and standardising surveillance systems, developing equitable data sharing and governance frameworks, and strengthening interactions and relationships among stakeholders at multiple levels

Working in the Public Interest Law Conference

The two-day conference included a variety of panel discussions and roundtables on such topics as: civil liberties; race and the criminal justice system; decriminalizing mental illness; funding public defender systems; the media\u27s role in the law; immigration; lesbian, gay, bisexual and transgendered youth in state sponsored institutions; environmental justice; and women\u27s reproductive rights

Innovations in Genomic AMR Surveillance

Whole genome sequencing of antimicrobial resistant (AMR) pathogens is increasingly being used for AMR surveillance, particularly in high-income countries. Innovations in genome sequencing and analysis technologies promise to revolutionise AMR surveillance and epidemiology even further. However, routine adoption of these technologies is a challenge, particularly in low- and middle-income countries. As part of a wider series of workshops and online consultations, a group of experts in AMR pathogen genomics and computational tool development conducted a situational analysis, identifying the following under-utilised innovations in genomic AMR surveillance: clinical metagenomics, environmental metagenomics, gene or plasmid tracking, and machine learning. The group recommended developing cost-effective use cases for each approach and mapping data outputs to clinical outcomes of interest to justify additional investment in capacity, training, and staff required to implement these technologies. Harmonisation and standardisation of methods, and the creation of equitable data sharing and governance frameworks, will facilitate successful implementation.NEW reports funding from Nuclear Threat Initiative, MRC, Open Philantropy and Shionogi as well as consulting fees from Nuclear Threat Initiative. VP reports funding from the Welldome Trust and NIHR. NAF reports funding from the BMGF, UKRI and NIHR. SJP is a member of the Scientific Advisory Board of Next Gen Diagnostics and was supported by Illumina to attend the ECCMID conference. EJ had partial salary cover from Wellcome Trust over the course of this work. KSB reports funding from the BBSRC and MRC and partial salary cover from Wellcome Trust and UKHSA over the course of this work. All other authors declare no conflicts of interest

Innovations in genomic antimicrobial resistance surveillance.

Whole-genome sequencing of antimicrobial-resistant pathogens is increasingly being used for antimicrobial resistance (AMR) surveillance, particularly in high-income countries. Innovations in genome sequencing and analysis technologies promise to revolutionise AMR surveillance and epidemiology; however, routine adoption of these technologies is challenging, particularly in low-income and middle-income countries. As part of a wider series of workshops and online consultations, a group of experts in AMR pathogen genomics and computational tool development conducted a situational analysis, identifying the following under-used innovations in genomic AMR surveillance: clinical metagenomics, environmental metagenomics, gene or plasmid tracking, and machine learning. The group recommended developing cost-effective use cases for each approach and mapping data outputs to clinical outcomes of interest to justify additional investment in capacity, training, and staff required to implement these technologies. Harmonisation and standardisation of methods, and the creation of equitable data sharing and governance frameworks, will facilitate successful implementation of these innovations

Exploiting genomics for AMR Surveillance at One Health interfaces

The intersection of human, animal, and ecosystem health at ‘One Health Interfaces’ is recognised as being of key importance in the evolution and spread of antimicrobial resistance (AMR) and represents an important, and yet rarely realised opportunity to undertake vital AMR surveillance. A working group of international experts in pathogen genomics, AMR, and One Health convened to take part in a workshop series and online consultation focussed on the opportunities and challenges facing genomic AMR surveillance in a range of settings. Here we outline the working group’s discussion of the potential utility, advantages of, and barriers to, the implementation of genomic AMR surveillance at One Health interfaces and propose a series of recommendations for addressing these challenges. Embedding AMR surveillance at One Health interfaces will require the development of clear beneficial use cases, especially in low- and middle-income countries. Evidence of directionality, risks to human and animal health and potential trade implications were also identified by the working group as key issues. Addressing these challenges will be vital to enable genomic surveillance technology to reach its full potential for assessing the risk of transmission of AMR between the environment, animals, and humans at One Health Interfaces.DMM reports funding from BSAC. EJ had partial salary cover from Wellcome Trust over the course of this work. SJP is a member of the Scientific Advisory Board of Next Gen Diagnostics and was supported by Illumina to attend the ECCMID conference. NAF reports funding from the BMGF, UKRI and NIHR. KSB reports funding from the BBSRC and MRC and partial salary cover from Wellcome Trust and UKHSA over the course of this work. RNZ reports funding from the MRC UK. All other authors declare no conflicts of interest

Genomics for antimicrobial resistance surveillance to support infection prevention and control in healthcare facilities

Integration of genomic technologies into routine antimicrobial resistance (AMR) surveillance in healthcare facilities has the potential to generate rapid, actionable information for patient management and inform infection prevention and control measures in near real-time. However, substantial challenges limit the implementation of genomics for AMR surveillance in clinical settings. Through a workshop series and online consultation, international experts from across the AMR and pathogen genomics fields convened to review the evidence base underpinning the use of genomics for AMR surveillance in a range of settings. Here, we summarise the challenges and potential benefits of genomic AMR surveillance in healthcare settings identified, and outline the recommendations of the working group to realise this potential. These include the definition of viable and cost-effective use cases for genomic AMR surveillance, strengthening training competencies (particularly in bioinformatics) and building capacity at local, national and regional levels using hub and spoke models.EJ had partial salary cover from Wellcome Trust over the course of this work. KSB reports funding from the BBSRC and MRC and partial salary cover from Wellcome Trust and UKHSA over the course of this work. LYH reports funding from Pfizer Inc and honoraria from BioMerieux for lecture in 2022. BE and INO report receiving funding from the UK Department of Health and Social Care: grant managed by the Fleming Fund and work performed under the auspices of the SEQAFRICA project. INO reports funding from the Bill and Melinda Gates Foundation, JPIAMR, Wellcome Trust, Grand Challenges Africa Award, UK MCR, royalties for Genetics: Genes, Genomes and Evolution (Oxford University Press), Divining Without Seeds and for Antimicrobial Resistance in Developing Countries (Springer), consulting fees from Wellcome Trust, honoraria for Harvard University seminars and Peter Wildy Lecture Award 2023. SJP is a member of the Scientific Advisory Board of Next Gen Diagnostics and was supported by Illumina to attend the ECCMID conference. NAF reports funding from the BMGF, UKRI and NIHR. All other authors declare no conflicts of interest