̽��ֱ�� of Cambridge - drug resistance

Ability of multi-drug resistant infection to evolve within cystic fibrosis patients highlights need for rapid treatment

cjb250 — Thu, 29 Apr 2021 18:00:25 +0000

Around one in 2,500 children in the UK is born with cystic fibrosis, a hereditary condition that causes the lungs to become clogged up with thick, sticky mucus. ̽��ֱ��condition tends to decrease life expectancy among patients.

In recent years, M. abscessus, a species of multi-drug resistant bacteria, has emerged as a significant global threat to individuals with cystic fibrosis and other lung diseases. It can cause a severe pneumonia leading to accelerated inflammatory damage to the lungs, and may prevent safe lung transplantation. It is also extremely difficult to treat – fewer than one in three cases is treated successfully.

In a study published today in Science, a team led by scientists at the ̽��ֱ�� of Cambridge examined whole genome data for 1,173 clinical M. abscessus samples taken from 526 patients to study how the organism has evolved – and continues to evolve. ̽��ֱ��samples were obtained from cystic fibrosis clinics in the UK, as well as centres in Europe, the USA and Australia.

̽��ֱ��team found two key processes that play an important part in the organism’s evolution. ̽��ֱ��first is known as horizontal gene transfer – a process whereby the bacteria pick up genes or sections of DNA from other bacteria in the environment. Unlike classical evolution, which is a slow, incremental process, horizontal gene transfer can lead to big jumps in the pathogen’s evolution, potentially allowing it to become suddenly much more virulent.

̽��ֱ��second process is within-host evolution. As a consequence of the shape of the lung, multiple versions of the bacteria can evolve in parallel – and the longer the infection exists, the more opportunities they have to evolve, with the fittest variants eventually winning out. Similar phenomena have been seen in the evolution of new SARS-CoV-2 variants in immunocompromised patients.

Professor Andres Floto, joint senior author from the Centre for AI in Medicine (CCAIM) and the Department of Medicine at the ̽��ֱ�� of Cambridge and the Cambridge Centre for Lung Infection at Royal Papworth Hospital, said: “What you end up with is parallel evolution in different parts of an individual’s lung. This offers bacteria the opportunity for multiple rolls of the dice until they find the most successful mutations. ̽��ֱ��net result is a very effective way of generating adaptations to the host and increasing virulence.

“This suggests that you might need to treat the infection as soon as it is identified. At the moment, because the drugs can cause unpleasant side effects and have to be administered over a long period of time – often as long as 18 months – doctors usually wait to see if the bacteria cause illness before treating the infection. But what this does is give the bug plenty of time to evolve repeatedly, potentially making it more difficult to treat.”

Professor Floto and colleagues have previously advocated routine surveillance of cystic fibrosis patients to check for asymptomatic infection. This would involve patients submitting sputum samples three or four times a year to check for the presence of M. abscessus infection. Such surveillance is carried out routinely in many centres in the UK.

Using mathematical models, the team have been able to step backwards through the organism’s evolution in a single individual and recreate its trajectory, looking for key mutations in each organism in each part of the lung. By comparing samples from multiple patients, they were then able to identify the key set of genes that enabled this organism to change into a potentially deadly pathogen.

These adaptations can occur very quickly, but the team found that their ability to transmit between patients was constrained: paradoxically, those mutations that allowed the organism to become a more successful pathogen within the patient also reduced its ability to survive on external surfaces and in the air – the key mechanisms by which it is thought to transmit between people.

Potentially one of the most important genetic changes witnessed by the team was one that contributed towards M. abscessus becoming resistant to nitric oxide, a compound naturally produced by the human immune system. ̽��ֱ��team will shortly begin a clinical trial aimed at boosting nitric oxide in patients’ lung by using inhaled acidified nitrite, which they hope would become a novel treatment for the devastating infection.

̽��ֱ��researchers say their findings highlight the need to treat patients with Mycobacterium abscessus infection immediately, counter to current medical practice.

Examining the DNA taken from patient samples is also important in helping understand routes of transmission. Such techniques are used routinely in Cambridge hospitals to map the spread of infections such as MRSA and C. difficile – and more recently, SARS-CoV-2. Insights into the spread of M. abscessus helped inform the design of the new Royal Papworth Hospital building, opened in 2019, which has a state-of-the-art ventilation system to prevent transmission. ̽��ֱ��team recently published a study showing that this ventilation system was highly effective at reducing the amount of bacteria in the air.

Professor Julian Parkhill, joint senior author from the Department of Veterinary Medicine at the ̽��ֱ�� of Cambridge, added: “M. abscessus can be a very challenging infection to treat and can be very dangerous to people living with cystic fibrosis, but we hope insights from our research will help us reduce the risk of transmission, stop the bug evolving further, and potentially prevent the emergence of new pathogenic variants.”

̽��ֱ��team have used their research to develop insights into the evolution of M. tuberculosis – the pathogen that causes TB about 5,000 years ago. In a similar way to M. abscessus, M. tuberculosis likely started life as an environmental organism, acquired genes by horizontal transfer that made particular clones more virulent, and then evolved through multiple rounds of within-host evolution. While M. abscessus is currently stopped at this evolutionary point, M. tuberculosis evolved further to be able to jump directly from one person to another.

Dr Lucy Allen, Director of Research at the Cystic Fibrosis Trust, said: “This exciting research brings real hope of better ways to treat lung infections that are resistant to other drugs. Our co-funded Innovation Hub with the ̽��ֱ�� of Cambridge really shows the power of bringing together world-leading expertise to tackle a health priority identified by people with cystic fibrosis. We’re expecting to see further impressive results in the future coming from our joint partnership.”

̽��ֱ��study was funded by the Wellcome Trust, Cystic Fibrosis Trust, NIHR Cambridge Biomedical Research Centre and Fondation Botnar.

Reference
Bryant, JM et al. Stepwise pathogenic evolution of Mycobacterium abscessus. Science; 30 Apr 2021

Scientists have been able to track how a multi-drug resistant organism is able to evolve and spread widely among cystic fibrosis patients – showing that it can evolve rapidly within an individual during chronic infection.

We hope insights from our research will help us reduce the risk of transmission, stop the bug evolving further, and potentially prevent the emergence of new pathogenic variants

Julian Parkhill

Jon Sneddon

Patient with cystic fibrosis

̽��ֱ��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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Diphtheria risks becoming ‘major global threat’ again as it evolves resistance to antimicrobials

cjb250 — Mon, 08 Mar 2021 11:07:29 +0000

̽��ֱ��researchers, led by scientists at the ̽��ֱ�� of Cambridge, say that the impact of COVID-19 on diphtheria vaccination schedules, coupled with a rise in the number of infections, risk the disease once more becoming a major global threat.

Diphtheria is a highly contagious infection that can affect the nose and throat, and sometimes the skin. If left untreated it can prove fatal. In the UK and other high-income countries, babies are vaccinated against infection. However, in low- and middle-income countries, the disease can still cause sporadic infections or outbreaks in unvaccinated and partially-vaccinated communities.

̽��ֱ��number of diphtheria cases reported globally has being increasing gradually. In 2018, there were 16,651 reported cases, more than double the yearly average for 1996–2017 (8,105 cases).

Diphtheria is primarily caused by the bacterium Corynebacterium diphtheriae and is mainly spread by coughs and sneezes, or through close contact with someone who is infected. In most cases, the bacteria cause acute infections, driven by the diphtheria toxin – the key target of the vaccine. However, non-toxigenic C. diphtheria can also cause disease, often in the form of systemic infections.

In a study published today in Nature Communications, an international team of researchers from the UK and India used genomics to map infections, including a subset from India, where over half of the globally reported cases occurred in 2018.

By analysing the genomes of 61 bacteria isolated from patients and combining these with 441 publicly available genomes, the researchers were able to build a phylogenetic tree – a genetic ‘family tree’ – to see how the infections are related and understand how they spread. They also used this information to assess the presence of antimicrobial resistance (AMR) genes and assess toxin variation.

̽��ֱ��researchers found clusters to genetically-similar bacteria isolated from multiple continents, most commonly Asia and Europe. This indicates that C. diphtheriae has been established in the human population for at least over a century, spreading across the globe as populations migrated.

̽��ֱ��main disease-causing component of C. diphtheriae is the diphtheria toxin, which is encoded by the tox gene. It is this component that is targeted by vaccines. In total, the researchers found 18 different variants of the tox gene, of which several had the potential to change the structure of the toxin.

Professor Gordon Dougan from the Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID) said: ““ ̽��ֱ��diphtheria vaccine is designed to neutralise the toxin, so any genetic variants that change the toxin’s structure could have an impact on how effective the vaccine is. While our data doesn’t suggest the currently used vaccine will be ineffective, the fact that we are seeing an ever-increasing diversity of tox variants suggests that the vaccine, and treatments that target the toxin, need to be appraised on a regular basis.”

Diphtheria infections can usually be treated with a number of classes of antibiotic. While C. diphtheriae resistant to antibiotics have been reported, the extent of such resistance remains largely unknown.

When the team looked for genes that might confer some degree of resistance to antimicrobials, they found that the average number of AMR genes per genome was increasing each decade. Genomes of bacteria isolated from infections from the most recent decade (2010-19) showed the highest average number of AMR genes per genome, almost four times as many on average than in the next highest decade, the 1990s.

Robert Will, a PhD student at CITIID and the study’s first author, said: “ ̽��ֱ��C. diphtheriae genome is complex and incredibly diverse. It’s acquiring resistance to antibiotics that are not even clinically used in the treatment of diphtheria. There must be other factors at play, such as asymptomatic infection and exposure to a plethora of antibiotics meant for treating other diseases.”

Erythromycin and penicillin are the traditionally recommended antibiotics of choice for treating confirmed cases of early-stage diphtheria, though there are several different classes of antibiotics available to treat the infection. ̽��ֱ��team identified variants resistant to six of these classes in isolates from the 2010s, higher than in any other decades.

Dr Pankaj Bhatnagar from the World Health Organization country office for India said: “AMR has rarely been considered as a major problem in the treatment of diphtheria, but in some parts of the world, the bacterial genomes are acquiring resistance to numerous classes of antibiotics. There are likely to be a number of reasons to this, including exposure of the bacteria to antibiotics in their environment or in asymptomatic patients being treated against other infections.”

̽��ֱ��researchers say that COVID-19 has had a negative impact on childhood vaccination schedules worldwide and comes at a time when reported case numbers are rising, with 2018 showing the highest incidence in 22 years.

Dr Ankur Mutreja from CITIID, who led the study, said: “It’s more important than ever that we understand how diphtheria is evolving and spreading. Genome sequencing gives us a powerful tool for observing this in real time, allowing public health agencies to take action before it’s too late.

“We mustn’t take our eye off the ball with diphtheria, otherwise we risk it becoming a major global threat again, potentially in a modified, better adapted, form.”

̽��ֱ��research was funded primarily by the Medical Research Council, with additional support from the NIHR Cambridge Biomedical Research Centre.

Reference
Will, RC et al. Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheria. Nat Comms; 8 Mar 2021; DOI: 10.1038/s41467-021-21870-5

Diphtheria – a relatively easily-preventable infection – is evolving to become resistant to a number of classes of antibiotics and in future could lead to vaccine escape, warn researchers from the UK and India.

We mustn’t take our eye off the ball with diphtheria, otherwise we risk it becoming a major global threat again, potentially in a modified, better adapted, form

Ankur Mutreja

DFID - UK Department for International Development

UK Emergency Medical Team paediatric nurse checks a girl for symptoms of Diphtheria in the Kutapalong refugee camp, Bangladesh

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Scientists identify warning signs over effectiveness of HIV ‘wonder drug’ in sub-Saharan Africa

cjb250 — Tue, 01 Dec 2020 10:00:00 +0000

As HIV copies itself and replicates, it can develop errors, or ‘mutations’, in its genetic code (its RNA). While a drug may initially be able to suppress or even kill the virus, certain mutations can allow the virus to develop resistance to its effects. If a mutated strain begins to spread within a population, it can mean once-effective drugs are no longer able to treat people.

HIV treatment usually consists of a cocktail of drugs that includes a type of drug known as a non-nucleoside reverse-transcriptase inhibitor (NNRTI). However, in recent years, HIV has begun to develop resistance to NNRTIs. Between 10% and 15% of patients in much of sub-Saharan Africa are infected by a strain of HIV resistant to these drugs. If a patient is infected with an NNRTI-resistant strain, they are at a two- to three-fold increased risk of the drug regimen failing.

In 2019, the World Health Organization began to recommend dolutegravir as the preferred first-line treatment for HIV in most populations. Dolutegravir was dubbed a ‘wonder drug’ because it was safe, potent and cost-effective and scientists had seen no drug resistance against it in clinical trials. However, there is little data on the success of dolutegravir against circulating strains of HIV in sub-Saharan Africa.

In a study published today in Nature Communications, an international team of researchers from South Africa, the UK and the USA examined the genetic code of HIV to determine if drug resistance mutations in 874 volunteers living with HIV affected their treatment success. ̽��ֱ��individuals were enrolled in a clinical trial for people initiating HIV treatment to compare two drug regimens: efavirenz, an NNRTI and prior first-line therapy in the region, and dolutegravir.

̽��ֱ��goal of this study was to determine whether drug resistance to efavirenz prior to starting treatment affected treatment success (suppression of the virus in the blood) over the first two years of therapy with both of these two regimens.

As expected, the presence of drug resistance substantially reduced the chances of treatment success in people taking efavirenz, successfully suppressing the virus over 96 weeks in 65% of participants, compared to 85% of non-resistant individuals. However, unexpectedly, the same pattern was true for individuals taking dolutegravir-based treatments: 66% of those with efavirenz resistance mutations remained suppressed over 96 weeks, compared to 84% of those without the mutations. These relationships held true after accounting for other factors, such as treatment adherence.

“We fully expected efavirenz to be less effective among patients HIV strains resistant to NNRTIs,” said Dr Mark Siedner, faculty member at the Africa Health Research Institute in KwaZulu-Natal, South Africa and Massachusetts General Hospital in Boston, Massachusetts. “What took us completely by surprise was that dolutegravir – a different class of drug which is generally effective in the face of drug resistance – would also be less effective in people with these resistant strains.

“We are working now to tease out if this was due to the virus or the participants – for instance, if people with resistance are less likely to take their pills regularly. Either way, if this pattern holds true, it could have far reaching impacts on our predictions of long-term treatment control for millions of people taking dolutegravir in the region.”

Professor Ravi Gupta from the Department of Medicine at the ̽��ֱ�� of Cambridge said: “This a huge concern. Dolutegravir was very much seen as a ‘wonder drug’, but our study suggests it might not be as effective in a significant number of patients who are resistant to another important class of antiretroviral drugs.”

̽��ֱ��researchers say it is not clear why efavirenz-resistant mutations should affect susceptibility of dolutegravir, though one hypothesis is that integrase inhibitors such as dolutegravir push the virus to replicate and mutate faster, in turn developing resistance to the new drug in an evolutionary arms race. Alternatively, it could be due to poor adherence to treatment regimens, even though the analysis accounted for adherence by two independent methods. Further research is needed to find out why.

Professor Gupta added: “What this shows is that we urgently need to prioritise point of care tests to identify people with drug resistance HIV, particularly against efavirenz, and to more closely and accurately monitor treatment adherence. ̽��ֱ��development of such tests is at an advanced stage, but there a lack of investment from funders and philanthropic donors. We urgently need agencies and individuals to step forward and help support these programmes.

“In addition, we need to provide widespread access to viral load monitoring so that we can find those who are struggling, get them on more appropriate regimens, and limit the emergence of resistance when patients are failing therapy.”

̽��ֱ��study was carried out by researchers at: the Africa Health Research Institute, ̽��ֱ�� of KwaZulu-Natal, ̽��ֱ�� of Witwatersrand, KwaZulu-Natal Research Innovation and Sequencing Platform, and the Centre for the AIDS Programme of Research in South Africa (CAPRISA), in South Africa; the ̽��ֱ�� of Cambridge, ̽��ֱ�� of Liverpool, and Imperial College London in the UK; and Massachusetts General Hospital and Harvard Medical School, USA.

̽��ֱ��research was supported by USAID, Unitaid, the South African Medical Research Council (SAMRC), with investigational drug donated by ViiV Healthcare and Gilead Sciences, and by Wellcome and the National Institutes of Health.

Reference
Siedner, MJ et al. Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase. Nat Comms; 1 Dec 2020; DOI: 10.1038/s41467-020-19801-x

Dolutegravir, the current first-line treatment for HIV, may not be as effective as hoped in sub-Saharan Africa, suggests new research published on World AIDS Day. ̽��ֱ��study finds that this so-called ‘wonder drug’ may be less effective in patients resistant to older drugs.

Dolutegravir was very much seen as a ‘wonder drug’, but our study suggests it might not be as effective in a significant number of patients who are resistant to another important class of antiretroviral drugs

Ravi Gupta

Jon Rawlinson

Know your HIV status sign in Africa

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Drug-resistant hospital bacteria persist even after deep cleaning, genomic study reveals

cjb250 — Mon, 26 Oct 2020 16:00:20 +0000

Enterococcus faecium is a bacterium commonly found in the gastrointestinal tract, where it usually resides without causing the host problems. However, in immunocompromised patients, it can lead to potentially life-threatening infection.

Over the last three decades, strains have emerged that are resistant to frontline antibiotics including ampicillin and vancomycin, limiting treatment options – and particularly worrying, these strains are often those found in hospital-acquired E. faecium infections.

A team of scientists at the ̽��ֱ�� of Cambridge and the London School of Hygiene and Tropical Medicine has pioneered an approach combining epidemiological and genomic information to chart the spread of bacteria within healthcare settings. This has helped hospitals identify sources of infection and inform infection control measures.

In a study published today in Nature Microbiology, the team has applied this technique to the spread of drug-resistant E. faecium in a hospital setting.

Dr Theodore Gouliouris from the Department of Medicine at the ̽��ֱ�� of Cambridge, and joint first author on the study, said: “We’ve known for over two decades that patients in hospital can catch and spread drug-resistant E. faecium. Preventing its spread requires us to understand where the bacteria lives – its ‘reservoirs’ – and how it is transmitted.

“Most studies to date have relied on culturing the bacteria from samples. But as we’ve shown, whole genome sequencing – looking at the DNA of the bacteria – combined with detailed patient and environmental sampling can be a powerful tool to help us chart its spread and inform ways to prevent further outbreaks.”

̽��ֱ��team followed 149 haematology patients admitted to Addenbrooke’s Hospital, Cambridge ̽��ֱ�� Hospitals NHS Foundation Trust, over a six-month period. They took stool samples from the patients and swabs from the hospital environment and cultured them for E. faecium.

Genomic analysis of the bacteria was much more effective at identifying hospital-acquired E. faecium: out of 101 patients who could be followed up, genomic analysis identified that two thirds of patients acquired E. faecium, compared to less than half using culture methods alone.

Just under half (48%) of the swabs taken from the hospital environment were positive for vancomycin-resistant E. faecium. This included 36% of medical devices, 76% of non-touch areas such as air vents, 41% of bed spaces and 68% of communal bathrooms tested.

̽��ֱ��researchers showed that even deep cleaning could not eradicate the bacteria. ̽��ֱ��hospital undertook deep cleaning on one ward over a three-day period during the study, when patients were moved elsewhere; however, when the team sampled locations prior to patients returning to the ward, they found that 9% of samples still tested positive for the bacteria. Within three days of patients returning to the ward, around half of the sampled sites tested positive.

Three-quarters (74%) of the patients (111/149) were carriers of the A1 clade – a multi-drug resistant strain of E. faecium commonly seen in hospitals that is resistant to the antibiotic ampicillin and which frequently acquires resistance to vancomycin. Of these 111 patients, 67 had strong epidemiological and genomic links with at least one other patient and/or their direct environment.

“ ̽��ֱ��fact that these cases were all linked to another patient or their environment suggests strongly that they had picked up the multi-drug resistant bacteria while in the hospital,” said Dr Francesc Coll from the London School of Hygiene and Tropical Medicine, joint first author.

Further genomic analysis showed that within this multi-drug resistant strain were several subtypes (defined by how genetically-similar they were). However, it was not uncommon for a patient to be carrying more than one subtype, which – without detailed genomic analysis – could confound attempts to identify the route of transmission of an infection. Notably, despite the circulation of as many as 115 subtypes, 28% of E. faecium acquisitions were caused by just two superspreading subtypes. ̽��ֱ��authors found no evidence of resistance or tolerance to common disinfectants to explain the success of these subtypes.

Six study patients contracted an ‘invasive infection’, meaning that they had been carrying E. faecium asymptomatically in their gut, but subsequently developed a symptomatic infection. Comparing the genomes of the infecting and gut strains the authors determined that invasive E. faecium infections originated from the patients’ own gut.

“Our study builds on previous observations that drug-resistant strains of E. faecium can persist in the hospital environment despite standard cleaning – we were still surprised to find how short-lasting was the effect of deep cleaning,” added Dr Gouliouris.

“We found high levels of hospital-adapted E. faecium despite the use of cleaning products and procedures that have proven effective against the bug. It highlights how challenging it can be to tackle outbreaks in hospitals.”

Senior author Professor Sharon Peacock from the Department of Medicine at the ̽��ֱ�� of Cambridge added: “ ̽��ֱ��high rates of infection with drug-resistant E. faecium in specific vulnerable patient groups and its ability to evade cleaning measures pose an important challenge to infection control. Patient screening, adequate provision of isolation and ensuite toilet facilities, improved and more frequent cleaning procedures, and stricter health-care worker hygiene practices will all be needed to curtail this global epidemic.

“But this is also a sign of how urgently we need to tackle inappropriate use of antibiotics worldwide, which is widely recognised as posing a catastrophic threat to our health and our ability to control infections.”

̽��ֱ��research was funded by the Department of Health and Wellcome.

Reference
Gouliouris, T, Coll, F et al. Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance. Nature Microbiology; 26 Oct 2020; DOI: 10.1038/s41564-020-00806-7

Scientists have used genome sequencing to reveal the extent to which a drug-resistant gastrointestinal bacterium can spread within a hospital, highlighting the challenge hospitals face in controlling infections.

Our study builds on previous observations that drug-resistant strains of E. faecium can persist in the hospital environment despite standard cleaning – we were still surprised to find how short-lasting was the effect of deep cleaning

Theodore Gouliouris

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Antiretroviral therapy fails to treat one-third of HIV patients in Malawi hospital

Anonymous — Thu, 03 Sep 2020 11:37:55 +0000

̽��ֱ��observational study involving more than 1,300 people was led by the London School of Hygiene & Tropical Medicine (LSHTM), ̽��ֱ�� of Malawi College of Medicine and ̽��ֱ�� of Cambridge.

It found most patients admitted to hospital knew their HIV status, and that 90% were taking antiretroviral therapy. However, approximately one-third of patients established on HIV treatment had significant levels of HIV in their blood, and more than 80% of these patients had resistance to two or more of their HIV antiretroviral drugs.

Patients with multidrug resistant HIV were 70% more likely to die within two months of being admitted to hospital than those without drug resistance.

This is the first study reporting such data in hospitalised patients, as access to HIV drug resistance testing is not widely available in high-HIV-burden African settings.

Dr Ankur Gupta-Wright from LSHTM and project lead said: “There has been an unprecedented scale-up of antiretroviral therapy in high-HIV prevalence settings in sub-Saharan Africa. However, HIV remains a common cause of admission to hospital, with a high risk of death. Our results show drug resistance is an important cause.”

Distinguishing HIV drug resistance from alternative explanations for progressive illness whilst taking antiretroviral (HIV) treatment, such as patients not sticking to required dosage or stopping treatment altogether, is not usually possible. Patients who develop advanced HIV while established on ART often go undetected.

Most available data on HIV drug resistance come from outpatient clinics, where failing HIV treatment is much less common. However, hospitalised patients represent a key target group for intensified interventions, given their relatively high risks of treatment failure, advanced immunosuppression, and high short-term mortality.

This study was based on patients living with HIV who were admitted to hospital in Zomba, southern Malawi. Samples were collected at the time of hospital admission to test for the amount of HIV virus in the blood, to see if patients were responding to their HIV antiretroviral medication.

By sequencing the virus and looking for mutations, patients with high levels of HIV in their blood were tested for resistance to HIV drugs. After two months, the team compared whether patients failing ART and/or with HIV drug resistance were more likely to die.

Of 237 patients with HIV drug resistance results available, 195 (82%) had resistance to lamivudine, 128 (54%) to tenofovir, and 219 (92%) to efavirenz (all first-line drugs used to treat HIV at the time of the study).

Dr Gupta-Wright said: “These are worrying results. ART changes and saves lives, but drug resistance is threatening this progress. Timely diagnosis and management of ART failure and drug resistance in this patient population could improve individual patient outcomes and contribute to the UNAIDS 95-95-95 targets set for 2030. Rapid HIV-1 viral load tests for hospital inpatients need to be implemented, so results are available quickly and patients can be switched to alterative antiretroviral therapy.

“This could potentially save the lives of many patients living with HIV on treatment who are admitted to hospital.”

Professor Ravi Gupta, from Cambridge ̽��ֱ�� and senior author on the study said: ‘’These important findings highlight the threat posed by drug resistant HIV and call for rapid tests for drug resistant virus that could aid in determining treatments and interventions for patients in hospital.’’

̽��ֱ��authors acknowledge limitations of this study including the introduction of a new antiretroviral drug in Malawi last year called Dolutegravir, which may overcome some of the resistance found in this study.

̽��ֱ��study was funded by the Joint Global Health Trials Scheme of the Medical Research Council, UK Department for International Development, and Wellcome.

Reference
Gupta-Wright, A, et al. Virological failure, HIV-1 drug resistance, and early mortality in adults admitted to hospital in Malawi: an observational cohort study. Lancet HIV; 1 Sept 2020; DOI: 10.1016/S2352-3018(20)30172-7

Adapted from a press release from the London School of Hygiene & Tropical Medicine

Antiretroviral therapy (ART) failure and drug resistance are extremely common in patients living with HIV who are admitted to hospital in Malawi, according to new research published in Lancet HIV.

These important findings highlight the threat posed by drug resistant HIV and call for rapid tests for drug resistant virus that could aid in determining treatments and interventions for patients in hospital

Ravi Gupta

Andrew Moore

Get Grades Not AIDs

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Protein discovery may explain why some patients develop resistance to new class of anti-cancer drugs

cjb250 — Tue, 24 Jul 2018 23:13:28 +0000

In a study published in Nature Cell Biology, the team from the Wellcome/Cancer Research UK Gurdon Institute show that Shieldin – so-called because it shields the ends of broken DNA – regulates DNA repair and could be a useful marker for identifying which patients are likely to respond poorly to PARP inhibitors.

̽��ֱ��DNA in our cells is susceptible to damage caused by external factors such as sunlight or smoking, or internal factors including our genetics. One form of damage is when both strands of the DNA double helix break – this can lead to cell death, so cells have various repair mechanisms to fix the damage.

̽��ֱ��simplest mechanism for repairing DNA breaks is known as ‘non-homologous end-joining’ (NHEJ). This mechanism essentially ‘sticks together’ the broken DNA strands, but it is imperfect and can result in deletions of segments of DNA.

A more accurate repair mechanism is ‘homologous recombination’ (HR). This mechanism uses a copy of our DNA as a reference text to fill in any missing gaps. However, NHEJ and HR work in competition against each other: if the balance is tipped in favour of HR, then cells will use this mechanism to repair the DNA damage.

Among the proteins involved in HR is BRCA1. However, some people carry a ‘bad’ BRCA1 mutation, which makes them more susceptible to cancer. Normal cells in these people have one ‘bad’ copy of the BRCA1 gene, but still have one ‘good’ copy, meaning that they can still carry out HR – and hence are still able to carry out vital DNA repair; however, their cancer cells have lost the good copy of BRCA1 and are no longer able to carry out homologous recombination.

Professor Steve Jackson and colleagues at the Gurdon Institute previously exploited this weakness to develop PARP-inhibitor drugs, which cause a double-strand DNA break that can only be repaired by homologous recombination: so, BRCA1-negative cancer cells die, while surrounding healthy cells survive.

However, some patients taking PARP inhibitors develop resistance to the drugs – and some patients do not even respond from the outset. To understand why this should be the case, Professor Steve Jackson and colleagues used cutting-edge CRISPR-Cas 9 gene editing techniques to screen breast cancer cells with the BRCA1 mutation and identify which genes drive resistance.

They identified two genes that produce a protein complex now referred to as Shieldin. From this they were able to show that Shieldin plays an important role in NHEJ, binding at the site of the broken strands of DNA. It is this complex that appears to be the key to patients responding to PARP inhibitors.

̽��ֱ��balancing act between NHEJ and HR should mean that the cells of people with the BRCA1 mutation cannot perform homologous recombination – hence PARP inhibitors are able to kill the cells. But when Shieldin levels are depleted – which may arise from spontaneous mutations in tumour cells – the balance changes and the patient’s tumour cells regain the ability to perform homologous recombination – and hence, PARP inhibitors are no longer effective.

Professor Jackson, whose group led the research, said: “There is a balancing act within our cells – a tug of war between proteins such as BRCA1 and Shieldin. Who wins determines whether the cell carries out error-free, albeit slower DNA repair, or faster, error-prone repair.”

̽��ֱ��study’s lead author, Wellcome Clinical Fellow Dr Harveer Dev, explained: “In BRCA1 mutated cells, it appears as though the persistence of the Shieldin complex at DNA breaks renders these cells sensitive to PARP inhibitors. This explains why these drugs are normally effective in patients with BRCA1 mutations. But when Shieldin levels are low, patients can develop resistance to these drugs.”

To confirm their results, the researchers took breast cancer biopsies from patients with the BRCA1 mutation and transplanted them into mice. They found that mice that had low levels of Shieldin from the outset did not respond to the PARP inhibitors, and mice that evolved resistance to the drugs had tumours with low levels of Shieldin. They also went on to show that resistance to PARP inhibitors can lead the same cancer cells to develop vulnerabilities to alternative cancer treatments, such as radiotherapy or platinum-based chemotherapy.

Professor Jackson concluded: “As we improve our understanding of these DNA repair networks and how they interact, we should be able to better predict the responsiveness of an individual patient’s tumour to specific therapies like PARP inhibitors, and ultimately personalise cancer therapy to achieve the maximum benefit.”

This study was funded by the Wellcome Trust and Cancer Research UK, and core funding to the Gurdon Institute from the Wellcome Trust and Cancer Research UK.

Reference
Dev H. et al. ̽��ֱ��SHLD1/2 protein complex promotes non-homologous end-joining and counters homologous recombination in BRCA1-deficient cells. Nature Cell Biology; 18 July; DOI: 10.1038/s41556-018-0140-1

A team of researchers at the ̽��ֱ�� of Cambridge has identified a protein complex that might explain why some cancer patients treated with the revolutionary new anti-cancer drugs known as PARP inhibitors develop resistance to their medication.

As we improve our understanding of these DNA repair networks and how they interact, we should be able to better predict the responsiveness of an individual patient’s tumour to specific therapies

Steve Jackson

PARP-inhibitors: A New Generation of Cancer Drugs

Shaury Nash

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Test can identify patients in intensive care at greatest risk of life-threatening infections

cjb250 — Wed, 13 Jun 2018 09:37:58 +0000

Infections in intensive care units (ICU) tend to be caused by organisms, such as multi-resistant gram-negative bacteria found in the gut, that are resistant to frontline antibiotics. Treating such infections means relying on broad spectrum antibiotics, which run the risk of breeding further drug-resistance, or antibiotics that have toxic side-effects.

Estimates of the proportion of patients in ICU who will develop a secondary infection range from one in three to one in two; around a half of these will be pneumonia. However, some people are more susceptible than others to such infections – evidence suggests that the key may lie in malfunction of the immune system.

In a study published in the journal Intensive Care Medicine, a team of researchers working across four sites in Edinburgh, Sunderland and London, has identified markers on three immune cells that correlate with an increased risk of secondary infection. ̽��ֱ��team was led by researchers at the Universities of Cambridge and Edinburgh and biotech company BD Bioscience.

“These markers help us create a ‘risk profile’ for an individual,” explains Dr Andrew Conway Morris from the Department of Medicine at the ̽��ֱ�� of Cambridge. “This tells us who is at greatest risk of developing a secondary infection.

“In the long term, this will help us target therapies at those most at risk, but it will be immediately useful in helping identify individuals to take part in clinical trials of new treatments.”

Clinical trials for interventions to prevent secondary infections have met with mixed success, in part because it has been difficult to identify and recruit those patients who are most susceptible, say the researchers. Using this new test should help fine tune the selection of clinical trial participants and improve the trials’ chances of success.

̽��ֱ��markers identified are found on the surface of key immune cells: neutrophils (frontline immune cells that attack invading pathogens), T-cells (part of our adaptive immune system that seek and destroy previously-encountered pathogens), and monocytes (a type of white blood cell).

̽��ֱ��researchers tested the correlation of the presence of these markers with susceptibility to a number of bacterial and fungal infections. An individual who tests positive for all three markers would be at two to three times greater risk of secondary infection compared with someone who tests negative for the markers.

̽��ֱ��markers do not indicate which secondary infection an individual might get, but rather that they are more susceptible in general.

“As intensive care specialists, our priority is to prevent patients developing secondary infections and, if they do, to ensure they get the best treatment,” says Professor Tim Walsh from the ̽��ֱ�� of Edinburgh, senior author on the study.

̽��ֱ��Immune Failure in Critical Therapy (INFECT) Study examined data from 138 individuals in ICUs and replicated findings from a pilot study in 2013.

A key part of enabling this study was to standardise how the research could be carried out across multiple sites, say the researchers. They used an imaging technique known as flow cytometry, which involves labelling components of the cells with fluorescent markers and then shining a laser on them such that they give off light at different wavelengths. This has previously been difficult to standardise, but the researchers successfully developed a protocol for use, ensuring they could recruit patients from the four study sites.

̽��ֱ��study was funded by Innovate UK, BD Bioscience and the National Institute of Academic Anaesthesia.

Reference
Conway Morris, A et al. Cell surface signatures of immune dysfunction risk stratify critically ill patients: INFECT Study. Intensive Care Medicine; June 2018; DOI: 10.1007/s00134-018-5247-0

Patients in intensive care units are at significant risk of potentially life-threatening secondary infections, including from antibiotic-resistant bacteria such as MRSA and C. difficile. Now, a new test could identify those at greatest risk – and speed up the development of new therapies to help at-risk patients.

In the long term, this will help us target therapies at those most at risk, but it will be immediately useful in helping identify individuals to take part in clinical trials of new treatments

Andrew Conway Morris

MilitaryHealth

Intensive Care Unit

Researcher Profile: Dr Andrew Conway Morris

Dr Andrew Conway Morris is an intensive care specialist at Addenbrooke’s Hospital, part of Cambridge ̽��ֱ�� Hospitals. It was the hospital’s location on the Cambridge Biomedical Campus that attracted him back to the city where he had been born and raised.

“I moved to Cambridge in order to take advantage of the fantastic opportunities to work with some of the world’s leading scientists, as well as develop collaborations with the growing biotech and pharmaceutical cluster centred around Addenbrooke’s Hospital,” he says.

Conway Morris undertook his undergraduate medical education in Glasgow before moving to Edinburgh to train in Anaesthesia and Intensive Care Medicine. His PhD in Edinburgh was on dysfunction of immune cells known as neutrophils in critically ill patients and looking at the development of new diagnostic tests for secondary pneumonia.

He is now a Wellcome-funded Senior Research Associate in the John Farman Intensive Care Unit at Addenbrooke’s, where he is trying to find new ways to prevent and treat infections in hospitalised and critically-ill patients.

“I carry out my work using a combination of human cell models and animal models of pneumonia and aim to develop new therapies for infection that do not rely on antibiotics,” he says. “I also have a clinical project evaluating a new molecular diagnostic test for pneumonia, which aims to deliver more rapid and accurate tests for infection.”

Outside of work, it is his children that keep him occupied. “I have two boys who occupy most of my free time - both are football-mad - and I help run a local youth football team,” he adds.

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AI 'scientist' finds that toothpaste ingredient may help fight drug-resistant malaria

cjb250 — Thu, 18 Jan 2018 10:00:15 +0000

When a mosquito infected with malaria parasites bites someone, it transfers the parasites into their bloodstream via its saliva. These parasites work their way into the liver, where they mature and reproduce. After a few days, the parasites leave the liver and hijack red blood cells, where they continue to multiply, spreading around the body and causing symptoms, including potentially life-threatening complications.

Malaria kills over half a million people each year, predominantly in Africa and south-east Asia. While a number of medicines are used to treat the disease, malaria parasites are growing increasingly resistant to these drugs, raising the spectre of untreatable malaria in the future.

Now, in a study published today in the journal Scientific Reports, a team of researchers employed the Robot Scientist ‘Eve’ in a high-throughput screen and discovered that triclosan, an ingredient found in many toothpastes, may help the fight against drug-resistance.

When used in toothpaste, triclosan prevents the build-up of plaque bacteria by inhibiting the action of an enzyme known as enoyl reductase (ENR), which is involved in the production of fatty acids.

Scientists have known for some time that triclosan also inhibits the growth in culture of the malaria parasite Plasmodium during the blood-stage, and assumed that this was because it was targeting ENR, which is found in the liver. However, subsequent work showed that improving triclosan’s ability to target ENR had no effect on parasite growth in the blood.

Working with ‘Eve’, the research team discovered that in fact, triclosan affects parasite growth by specifically inhibiting an entirely different enzyme of the malaria parasite, called DHFR. DHFR is the target of a well-established antimalarial drug, pyrimethamine; however, resistance to the drug among malaria parasites is common, particularly in Africa. ̽��ֱ��Cambridge team showed that triclosan was able to target and act on this enzyme even in pyrimethamine-resistant parasites.

“Drug-resistant malaria is becoming an increasingly significant threat in Africa and south-east Asia, and our medicine chest of effective treatments is slowly depleting,” says Professor Steve Oliver from the Cambridge Systems Biology Centre and the Department of Biochemistry at the ̽��ֱ�� of Cambridge. “ ̽��ֱ��search for new medicines is becoming increasingly urgent.”

Because triclosan inhibits both ENR and DHFR, the researchers say it may be possible to target the parasite at both the liver stage and the later blood stage.

Lead author Dr Elizabeth Bilsland, now an assistant professor at the ̽��ֱ�� of Campinas, Brazil, adds: “ ̽��ֱ��discovery by our robot ‘colleague’ Eve that triclosan is effective against malaria targets offers hope that we may be able to use it to develop a new drug. We know it is a safe compound, and its ability to target two points in the malaria parasite’s lifecycle means the parasite will find it difficult to evolve resistance.”

Robot scientist Eve was developed by a team of scientists at the Universities of Manchester, Aberystwyth, and Cambridge to automate – and hence speed up – the drug discovery process by automatically developing and testing hypotheses to explain observations, run experiments using laboratory robotics, interpret the results to amend their hypotheses, and then repeat the cycle, automating high-throughput hypothesis-led research.

Professor Ross King from the Manchester Institute of Biotechnology at the ̽��ֱ�� of Manchester, who led the development of Eve, says: “Artificial intelligence and machine learning enables us to create automated scientists that do not just take a ‘brute force’ approach, but rather take an intelligent approach to science. This could greatly speed up the drug discovery progress and potentially reap huge rewards.”

̽��ֱ��research was supported by the Biotechnology & Biological Sciences Research Council, the European Commission, the Gates Foundation and FAPESP (São Paulo Research Foundation).

Reference
Bilsland, E et al. Plasmodium dihydrofolate reductase is a second enzyme target for the antimalarial action of triclosan. Scientific Reports; 18 Jan 2018; DOI: 10.1038/s41598-018-19549-x

An ingredient commonly found in toothpaste could be employed as an anti-malarial drug against strains of malaria parasite that have grown resistant to one of the currently-used drugs. This discovery, led by researchers at the ̽��ֱ�� of Cambridge, was aided by Eve, an artificially-intelligent ‘robot scientist’.

Drug-resistant malaria is becoming an increasingly significant threat in Africa and south-east Asia, and our medicine chest of effective treatments is slowly depleting

Steve Oliver

Photo-Mix (Pixabay)

Toothpaste

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

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