̽��ֱ�� of Cambridge - Kate Baker

COVID-19 showed the importance of genomic surveillance – we need it to help fight antimicrobial resistance

cjb250 — Tue, 14 Nov 2023 23:30:16 +0000

AMR already causes substantial sickness and death worldwide, responsible for approximately 1.27 million deaths in 2019. Some estimates suggest that by 2050, it could kill as many as 10 million people each year.

Professor Sharon Peacock at the ̽��ֱ�� of Cambridge – the driving force behind the UK’s pioneering COVID-19 Genomics UK Consortium – said: “Over the past century, antibiotics have transformed our ability to treat infection and illness and reduce mortality. But bacteria are becoming increasingly resistant, and with a limited pipeline of new antibiotics, we risk effectively returning to the pre-antibiotic era where we can no longer treat infections.

“When the world was hit by the COVID-19 pandemic, we showed how powerful a tool genomic surveillance could be in helping us fight back. This work grew out of its increasing application to real-world problems such as detecting outbreaks in hospitals and in the community – including food borne outbreaks. We now need to take what we learned from the pandemic including its bold and largescale use and reapply it to the complex problem of AMR.”

̽��ֱ��genome, which is ‘written’ in DNA or RNA, consists of a string of nucleotides. Each time a copy of the genome is made, errors can arise – for example, one of the A, C, G and T nucleotides of DNA might get swapped. These changes allow scientists to create lineages – family trees – showing how the genome has evolved and spread. In the case of SARS-CoV-2, they allowed scientists to identify sources of infection, spot so-called ‘variants of concern’ and see whether public health measures such as lockdown, travel restrictions and vaccination were working.

̽��ֱ��potential to improve surveillance of AMR pathogens may be even higher than for SARS-CoV-2 as the genome data can detect and track outbreaks, provide a prediction for effective antibiotic treatment, reveal the mechanism for resistance including mutations and the acquisition of new DNA, and help understand the movement of resistance mechanisms between bacteria.

Although surveillance of AMR bacteria is already used in some settings, the growing evidence of its potential has largely not translated into routine use. Writing today in ̽��ֱ��Lancet Microbe, a working group has set out how genomic surveillance could be applied to the problem of AMR more widely, including the barriers that need to be overcome, presenting a series of recommendations including building capacity, training of existing and new workforces, standardising the way that surveillance is done to detect AMR, and agreeing equitable data sharing and governance.

̽��ֱ��group, which is funded by Wellcome, was initiated by Professor Peacock in conjunction with Wellcome SEDRIC (Surveillance and Epidemiology of Drug Resistance Infection Consortium) and delivered by a team of nearly 100 experts co-led by Professor Kate Baker and Dr Elita Jauneikaite. Five papers will be published in the same edition of the journal, highlighting the breadth of review and analysis undertaken by the team.

̽��ֱ��series covers multiple areas for the application of genomic AMR surveillance including in hospital settings to help identify outbreaks and inform infection prevention and control and informing clinical decision-making at a patient level. They also highlight applications at a public health level to detect emerging threats and to design and assess suitable interventions like vaccination. It even has the potential to track AMR pathogens moving between humans, animals, and the environment. ̽��ֱ��team also considered future innovations in genomic surveillance of AMR, looking at how the next phase of genomic technologies and analysis methods might further transform the surveillance landscape.

A number of barriers will first need to be overcome, however. These include a lack of resources and political will, and the need for more training, particularly around bioinformatics (the analysis of genome data). There are also practical barriers, including in many countries a weak epidemiological surveillance and microbiology infrastructure, poor supply chains and pricing structures, and issues around effective cooperation and data sharing.

Professor Kate Baker, ̽��ֱ�� of Cambridge, said: “We are on the cusp of realising the full potential for genomics in tackling AMR, but there is still a lot of work that needs to be done. We need the scientific, public health and political communities to work together to make this happen. AMR is an urgent problem. It is not something that will happen in years to come – it is happening now.”

Dr Elita Jauneikaite, Imperial College London, said: “We are going to be locked in an ongoing arms race with bacterial pathogens indefinitely. Genomic surveillance offers real promise to help us fight back, providing invaluable information to limit the spread and impact of AMR.”

Professor Peacock added: “It was clear from the pandemic that sequencing was a vital tool that was needed in every country worldwide. AMR is a global problem and once again we need to make sure countries worldwide are in a position both to contribute to, and benefit from genomic surveillance data.”

Janet Midega, AMR Research Lead at Wellcome and SEDRIC Board member, said: “Genomic research and surveillance are pivotal to detect pathogens and understand the transmission and trends of drug resistance in both high- and low-income settings. In order to respond effectively to this data, we need to ensure that the tools being developed are accessible and can be utilised by public health agencies around the world.”

Reference
Baker, K, et al. Overview: Harnessing genomics for antimicrobial resistance surveillance. ̽��ֱ��Lancet Microbe; 14 Nov 2023; DOI: 10.1016/S2666-5247(23)00281-1

During the COVID-19 pandemic, genomic surveillance proved vital in helping understand the evolution and spread of the SARS-CoV-2 virus. Now, an international group of researchers is calling for its potential to be harnessed to tackle antimicrobial resistance (AMR), a major global challenge that could ultimately result in many more deaths than the coronavirus pandemic.

We are on the cusp of realising the full potential for genomics in tackling AMR, but there is still a lot of work that needs to be done

Kate Baker

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Scanning electron micrograph of methicillin-resistant Staphylococcus aureus bacteria (yellow) and a dead human white blood cell (red)

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Experts call for more mental health support for parents of children with genetic learning disabilities

cjb250 — Wed, 11 Mar 2020 00:02:58 +0000

As many as one in 20 families worldwide is thought to include a child with a learning disability, but little is known about how this affects the parents’ mental health and wellbeing. Although some parents experience depression and anxiety, it is not clear why some are at greater risk than others.

Professor Claire Hughes from the ̽��ֱ�� of Cambridge Centre for Family Research, said: “It’s important that we understand why some parents are at greater risk of mental health problems than others. If a parent experiences long-term mental health problems, this could have a knock-on effect on the whole family, affecting partner relationships, the wellbeing of their child with disability, and the experiences of siblings. That’s why interventions are often more successful when they are designed to help parents in order to help children.”

To address this question, Professor Hughes assembled an interdisciplinary team of researchers from the Universities of Cambridge and Birmingham to analyse information from 888 families taking part in the IMAGINE-ID study – a UK-wide project examining the links between genetic diagnoses, learning disabilities and mental health. Parents were asked to rate their everyday feelings and the nature and impact of their child’s difficulties, as well as to provide information about their family’s social circumstances.

One parent who participated in IMAGINE-ID said that professionals tended to focus on the child’s needs and did not consider the wider needs of families: “It’s very much about getting support for your child. At no point were we ever offered any mental health support, even though we have such a massive role to play in bringing up our children. We need support as well.”

̽��ֱ��study data shows that rates of negative symptoms such as worry, anxiety and stress were much higher in the IMAGINE-ID group of parents than in the general population of parents. Mothers in the IMAGINE-ID study – who were more likely to be the main caregiver – were particularly affected. Contrary to evidence from previous studies, social factors did not predict a parent’s risk of low mood and stress: more important were the type of genetic disorder that affected their child, their child’s physical and medical needs, and their child’s behaviour.

For the first time, the researchers were able to demonstrate that the cause of a child’s disabilities is one factor that predicts the emotional wellbeing of parents. A subgroup of genetic disorders is caused by short missing or duplicated sections of DNA (known as ‘copy number variants’). Parents within this subgroup reported that their child’s difficulties had a high level of impact on family life as well as restricting their child’s activities and friendships, and these impacts were the source of their own distress.

̽��ֱ��researchers say there could be a number of explanations for these findings, varying from the complex effects of chromosomal differences on children’s development through to the availability of support for these families. They have called for more multi-disciplinary, family-focused research to determine how genetic diagnoses are linked to parents’ mental health, so that support for families can be improved in future.

Dr Kate Baker, lead author of the research paper, based at the MRC Cognition and Brain Sciences Unit, ̽��ֱ�� of Cambridge, said: “These results suggest that we need to start looking at genetic diagnoses as useful not just for predicting a child’s needs and informing the support that they might receive, but also for predicting the broader impact that the diagnosis will have on their family.”

Francesca Wicks, former research coordinator for IMAGINE-ID and now Family Support and Information Officer for Unique, the rare chromosome and single gene disorder support charity, said: “It’s clear that not enough care and support is being offered to parents before, during and after their child’s diagnosis. ̽��ֱ��help and support offered by organisations such as Unique is incredibly valuable, but much more needs to be done within health and statutory services. Many of the families I have met have expressed feelings of anxiety and depression over the years, which is why we have produced our Carers Wellbeing guide.”

̽��ֱ��IMAGINE-ID study is funded by the UK Medical Research Council and Medical Research Foundation.

Reference
Baker, K et al. Childhood intellectual disability and parents’ mental health: integrating social, psychological and genetic influences. BJPsych; 11 March 2020; DOI: 10.1192/bjp.2020.38

Parents of children with genetic conditions that cause learning disabilities are at risk of mental health problems, suggests new research published today in the British Journal of Psychiatry. ̽��ֱ��teams behind the study have called for greater support for parents whose child receives a genetic diagnosis for their learning disability.

If a parent experiences long-term mental health problems, this could have a knock-on effect on the whole family, affecting partner relationships, the wellbeing of their child with disability, and the experiences of siblings

Claire Hughes

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Parent and child

Researcher profile: Dr Kate Baker

Image: Kate Baker (centre) with research assistant Elise Ng-Cordell (left) and post-doctoral research associate Diandra Brkic (right) on Rare Disease Day

Dr Kate Baker, a researcher at the MRC Cognition and Brain Sciences Unit, decided early on that she wanted to be a scientist as well as a doctor. At the time, she was a medical student and helping out in a brain research laboratory.

“There are just too many unanswered questions about genes, brains, and mental health, and patients deserve better answers and better treatments,” she says. “Initially I learned to study slices of post-mortem brain tissue – then I discovered that doing research with whole people is a lot more fun, even if they are more noisy and complicated.”

Kate says she has been extremely lucky to work with “fantastic” colleagues and research participants who share the same curiosities and motivations – “We want to understand brain development and improve care for children with neurodevelopmental disorders and their families. It’s a slow process but it is also very exciting and rewarding.”

Her research looks at the genetic differences that can affect children’s development by changing the way that their brain grows and functions. “ ̽��ֱ��most surprising aspect is how an extremely tiny change in one gene can have a devastating impact, whilst sometimes much larger genetic changes have only subtle effects which vary a lot from one person to another.”

Kate leads a small research team of psychologists and neuroscientists, but particularly enjoys joining forces with scientists from different research fields who use very different approaches to understand the same core problem, “working together to join the dots and build up a more complete answer”.

One such collaboration is with Professor Claire Hughes from the Centre for Family Research. Cambridge collaborations can begin in unlikely places. “Claire and I started discussing the research questions we have addressed in our new paper after a Sunday morning yoga class, not knowing we would be able to work together to actually find some answers!”

Kate hopes her research will make a difference for children and families affected by severe neurodevelopmental disorders, by changing the way we understand these conditions, and also by improving the treatments and support they can receive.

“Until now, treatments have been mainly ‘symptom-focused’, which don’t always work because the same problems, such as limited communication skills or impulsive behaviours, can come about because of many different underlying reasons. If we had a better understanding of each child’s disorder ‘under the surface’, I hope we can improve their quality of life, even for a small number of patients and families.”

As if this wasn’t enough, Kate and her family have embarked on a challenging project. “My husband, children and I have recently built our own home, on the outskirts of Cambridge. So you’re likely to find me nailing plasterboard, wheelbarrowing mud, making curtains, or (more likely) feeding all the friends and family who have come to help us with the project.”

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. Images, including our videos, are Copyright © ̽��ֱ�� of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways – as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

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