̽��ֱ�� of Cambridge - Mark Holmes

Pork labelling schemes ‘not helpful’ in making informed buying choices, say researchers

jg533 — Thu, 11 Apr 2024 09:27:35 +0000

Researchers have evaluated different types of pig farming – including woodland, organic, free range, RSPCA assured, and Red Tractor certified, to assess each systems’ impact across four areas: land use (representing biodiversity loss), greenhouse gas emissions, antibiotics use and animal welfare. Their study concludes that none of the farm types performed consistently well across all four areas – a finding that has important implications for increasingly climate conscious consumers, as well as farmers themselves.

However, there were individual farms that did perform well in all domains, including an indoor Red Tractor farm, an outdoor bred, indoor finished RSPCA assured farm and fully outdoor woodland farm. “Outliers like these show that trade-offs are not inevitable,” said lead author Dr Harriet Bartlett, Research Associate at the ̽��ֱ�� of Oxford's Smith School of Enterprise and the Environment, who was formerly at the ̽��ֱ�� of Cambridge.

“Somewhat unexpectedly we found that a handful of farms perform far better than average across all four of our environmental and welfare measures,” added senior author Andrew Balmford, Professor of Conservation Science at the ̽��ֱ�� of Cambridge. However, none of the current label or assurance schemes predicted which farms these would be.

“ ̽��ֱ��way we classify farm types and label pork isn’t helpful for making informed decisions when it comes to buying more sustainable meat. Even more importantly, we aren’t rewarding and incentivising the best-performing farmers. Instead of focusing on farm types or practices, we need to focus on meaningful outcomes for people, the planet and the pigs – and assess, and reward farms based on these,” said Bartlett.

̽��ֱ��findings also show that common assumptions around food labelling can be misplaced. For instance, Organic farming systems, which consumers might see as climate and environmentally friendly, have on average three times the CO2 output per kg of meat of more intensive Red Tractor or RSPCA assured systems and four times the land use. However, these same systems use on average almost 90% fewer antibiotic medicines, and result in improved animal welfare compared with production from Red tractor or RSPCA assured systems.

̽��ֱ��way we classify livestock farms must be improved, Bartlett says, because livestock production is growing rapidly, especially pork production, which has quadrupled in the past 50 years and already accounts for 9% of greenhouse gas emissions from livestock. Pig farming also uses more antibiotics than any other livestock sector, and 8.5% of all arable land.

“Our findings show that mitigating the environmental impacts of livestock farming isn’t a case of saying which farm type is the best,” said Bartlett. “There is substantial scope for improvement within types, and our current means of classification is not identifying the best farms for the planet and animals overall. Instead, we need to identify farms that successfully limit their impacts across all areas of societal concern, and understand, promote and incentivise their practises.”

̽��ֱ��study reached its conclusions using data from 74 UK and 17 Brazilian breed-to-finish systems, each made up of 1-3 farms and representing the annual production of over 1.2 million pigs. It is published today in the journal Nature Food.

“To the best of our knowledge, our dataset covers by far the largest and most diverse sample of pig production systems examined in any single study,” said Bartlett.

James Wood, Professor of Equine and Farm Animal Science at the ̽��ֱ�� of Cambridge, commented: “This important study identifies a key need to clarify what different farm labels should indicate to consumers; there is a pressing need to extend this work into other farming sectors. It also clearly demonstrates the critical importance that individual farmers play in promoting best practice across all farming systems.”

Trade-offs in the externalities of pig production are not inevitable was authored by academics at the ̽��ֱ�� of Oxford, ̽��ֱ�� of Cambridge and the ̽��ֱ�� of São Paulo.

̽��ֱ��research was funded by the Biotechnology and Biological Sciences Research Council (BBSRC).

Reference: Bartlett, H.,‘Trade-offs in the externalities of pig production are not inevitable.’ Nature Food, April 2024. DOI: 10.1038/s43016-024-00921-2

Adapted from a press release by the ̽��ֱ�� of Oxford.

Farmers don’t have to choose between lowering environmental impact and improving welfare for their pigs, a new study has found: it is possible to do both. But this is not reflected in the current food labelling schemes relied on by consumers.

̽��ֱ��way we classify farm types and label pork isn’t helpful for making informed decisions when it comes to buying more sustainable meat.

Harriet Bartlett

Charity Burggraaf/ Getty

Two pigs on a farm

̽��ֱ��text in this work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 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 – 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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New animal welfare scoring system could enable better-informed food and farming choices

jg533 — Wed, 22 Mar 2023 00:01:30 +0000

This means that animal welfare can now, for the first time, be properly considered alongside other impacts of farming to help identify which farming systems are best.

This is vital for improving animal welfare in livestock production, at a time when demand for meat is rising globally and the way animals are farmed is changing - with concerns about the welfare of intensive and indoor systems.

Animal welfare assessments could also enable consumers to be better informed when choosing what to eat.

Britain has various labelling schemes for meat products to assure consumers that certain standards have been met. ̽��ֱ��team used their new system to test how the different labels compare in terms of animal welfare.

Farms producing ‘woodland’ labelled pork products scored best for pig welfare, followed by ‘organic’, then free-range, RSPCA assured, Red Tractor, and finally those with no certification.

“We have shown that it’s possible to reliably assess animal welfare on farms. This means decisions about which types of farm are better or worse for animal welfare can be based on proper calculations, rather than assumptions – as is currently the case,” said Dr Harriet Bartlett, first author of the study, who carried out this work while a researcher at the ̽��ֱ�� of Cambridge’s Department of Veterinary Medicine. She is now a Research Associate in Sustainable Food Solutions at the ̽��ֱ�� of Oxford.

Bartlett added: “Now animal welfare can be included in overall assessments of farm sustainability alongside other measures like carbon emissions and biodiversity impacts, so we can make better informed decisions about how we choose to farm and what we choose to eat.”

Coming up with an overall measurement of animal welfare has previously been difficult because of disagreement on which factors are most important. For example, is a health problem more important than a behaviour problem? What level of welfare is good enough?

̽��ֱ��new system assesses the quality of an animal’s life through a wide-ranging set of welfare measurements, reflecting a range of concerns about welfare. ̽��ֱ��results can be integrated into a single score to enable comparison across farms.

This will enable exploration of trade-offs between animal welfare and other issues of concern to consumers, such as the impact of farming on the environment.

̽��ֱ��results are published today in the journal Proceedings of the Royal Society B.

Assessment of the pigs looked at everything from health problems like coughing, sneezing, and lameness, to the way they interacted: biting each other’s ears or tails, or engaging with their environment, for example.

Various scoring methods were tested - giving more or less weight to the different aspects of animal welfare - on 74 pig farming systems in the UK. ̽��ֱ��team were surprised to find that each method gave broadly the same overall result in terms of which farms, and types of farms, performed best and worst.

“Despite ongoing debate about how to measure animal welfare, we found we can identify which types of farms we might want to encourage and which we shouldn’t with reasonable consistency,” said Professor Andrew Balmford in the ̽��ֱ�� of Cambridge’s Department of Zoology, who was involved in the study.

̽��ֱ��new welfare measurements combine quality of life with length of life, and scores can be produced ‘per unit’ of production. ̽��ֱ��welfare scores can also allow several farms to be grouped together – for example when animals are kept on different farms at different growth stages.

“This work opens up possibilities for greater rolling out of welfare assessment scores in food labelling, including in other species as well as pigs. Until now, the methods available have made this impractical,” said Professor James Wood at the ̽��ֱ�� of Cambridge’s Department of Veterinary Medicine, who was involved in the study.

̽��ֱ��technique of ‘Life Cycle Assessment’ is widely used to quantify environmental impacts, such as greenhouse gas emissions and land use, across all stages of farm animal production. But until now there hasn’t been a way of measuring animal welfare that enables valid comparisons across different farming systems, so Life Cycle Assessments do not include it and as a result, welfare concerns have sometimes been overlooked.

Food production accounts for over a quarter of all global greenhouse gas emissions. Making farming systems more sustainable, in the face of growing global demand for meat, is a major challenge for farmers and the government.

‘Woodland’ labelled pork is from farms that provide at least partial tree cover for the pigs, and ‘Organic’ provides outdoor access for the animals. ̽��ֱ��‘RSPCA assured’ label is welfare focused, while ‘Free range’ is not a formal assurance, but typically refers to fully outdoor farming systems. Most UK pig farms produce ‘Red Tractor’ labelled pork, which has lower production costs – translating to a lower price for consumers.

This research was funded by the BBSRC, the Royal Society, MRC, and ̽��ֱ��Alborada Trust.

Reference

Bartlett, H. et al: ‘Advancing the quantitative characterisation of farm animal welfare.’ Proc Roy Soc B. March 2023. DOI 10.1098/rspb.2023.0120

Cambridge ̽��ֱ�� scientists have come up with a system of measuring animal welfare that enables reliable comparison across different types of pig farming.

Harriet Bartlett

Pigs on a farm

̽��ֱ��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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MRSA arose in hedgehogs long before antibiotic use

jg533 — Tue, 04 Jan 2022 11:07:30 +0000

Staphylococcus aureus first developed resistance to the antibiotic methicillin around 200 years ago, according to a large international collaboration including the ̽��ֱ�� of Cambridge, the Wellcome Sanger Institute, Denmark’s Serum Statens Institut and the Royal Botanic Gardens, Kew, which has traced the genetic history of the bacteria.

They were investigating the surprising discovery - from hedgehog surveys from Denmark and Sweden - that up to 60% of hedgehogs carry a type of MRSA called mecC-MRSA. ̽��ֱ��new study also found high levels of MRSA in swabs taken from hedgehogs across their range in Europe and New Zealand.

̽��ֱ��study is published today in the journal Nature.

̽��ֱ��researchers believe that antibiotic resistance evolved in Staphylococcus aureus as an adaptation to having to exist side-by-side on the skin of hedgehogs with the fungus Trichophyton erinacei, which produces its own antibiotics.

̽��ֱ��resulting methicillin-resistant Staphylococcus aureus is better known as the superbug MRSA. ̽��ֱ��discovery of this centuries-old antibiotic resistance predates antibiotic use in medical and agricultural settings.

“Using sequencing technology we have traced the genes that give mecC-MRSA its antibiotic resistance all the way back to their first appearance, and found they were around in the nineteenth century,” said Dr Ewan Harrison, a researcher at the Wellcome Sanger Institute and ̽��ֱ�� of Cambridge and a senior author of the study.

He added: “Our study suggests that it wasn’t the use of penicillin that drove the initial emergence of MRSA, it was a natural biological process. We think MRSA evolved in a battle for survival on the skin of hedgehogs, and subsequently spread to livestock and humans through direct contact.”

Antibiotic resistance in bugs causing human infections was previously thought to be a modern phenomenon, driven by the clinical use of antibiotics. Misuse of antibiotics is now accelerating the process, and antibiotic resistance is rising to dangerously high levels in all parts of the world.

Since almost all the antibiotics we use today arose in nature, the researchers say it is likely that resistance to them already exists in nature too. Overuse of any antibiotic in humans or livestock will favour resistant strains of the bug, so it is only a matter of time before the antibiotic starts to lose its effectiveness.

“This study is a stark warning that when we use antibiotics, we have to use them with care. There’s a very big wildlife ‘reservoir’ where antibiotic-resistant bacteria can survive – and from there it’s a short step for them to be picked up by livestock, and then to infect humans,” said Professor Mark Holmes, a researcher in the ̽��ֱ�� of Cambridge’s Department of Veterinary Medicine and a senior author of the report.

In 2011, previous work led by Professor Holmes first identified mecC -MRSA in human and dairy cow populations. At the time it was assumed the strain had arisen in the cows because of the large amount of antibiotics they are routinely given.

MRSA was first identified in patients in 1960, and around 1 in 200 of all MRSA infections are caused by mecC-MRSA. Due to its resistance to antibiotics, MRSA is much harder to treat than other bacterial infections. ̽��ֱ��World Health Organization now considers MRSA one of the world’s greatest threats to human health. It is also a major challenge in livestock farming.

̽��ֱ��findings are not a reason to fear hedgehogs, say the researchers: humans rarely get infections with mecC-MRSA, even though it has been present in hedgehogs for more than 200 years.

”It isn’t just hedgehogs that harbour antibiotic-resistant bacteria - all wildlife carries many different types of bacteria, as well as parasites, fungi and viruses,” said Holmes.

He added: “Wild animals, livestock and humans are all interconnected: we all share one ecosystem. It isn’t possible to understand the evolution of antibiotic resistance unless you look at the whole system.”

This research was funded by the Medical Research Council.

Reference
Larsen, J et al: ‘Emergence of methicillin resistance predates the clinical use of antibiotics.’ Nature, January 2022, DOI: 10.1038/s41586-021-04265-w

Scientists have found evidence that a type of the antibiotic-resistant superbug MRSA arose in nature long before the use of antibiotics in humans and livestock, which has traditionally been blamed for its emergence.

We think MRSA evolved in a battle for survival on the skin of hedgehogs, and subsequently spread to livestock and humans through direct contact

Ewan Harrison

Pia B Hansen

Hedgehog

At a glance

Hedgehogs carry a fungus and a bacteria on their skin, and the two are locked in a battle for survival
̽��ֱ��fungus secretes antibiotics to kill the bacteria, but in response the bacteria has evolved antibiotic resistance – becoming Methicillin-resistant Staphylococcus aureus, or MRSA
Up to 60% of hedgehogs carry a type of MRSA called mecC-MRSA, which causes 1 in 200 of all MRSA infections in humans
Natural biological processes, not antibiotic use, drove the initial emergence of this superbug on hedgehogs around 200 years ago

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Reducing the rise of antibiotic resistance

lw355 — Mon, 22 Nov 2021 12:00:01 +0000

Rising resistance to antibiotics is a worrying prospect, but a success story happening across the farms of the UK gives hope that something can be done.

Widely-available antibiotics could be used in the treatment of ‘superbug’ MRSA

cjb250 — Mon, 24 Jun 2019 11:33:23 +0000

Since the discovery of penicillin, the introduction of antibiotics to treat infections has revolutionised medicine and healthcare, saving millions of lives. However, widespread use (and misuse) of the drugs has led some bacteria to develop resistance, making the medicines less effective. With few new antibiotics in development, antibiotic resistance is widely considered a serious threat to the future of modern medicine, raising the spectre of untreatable infections.

One of the most widely used and clinically important groups of antibiotics is the family that includes penicillin and penicillin derivatives. ̽��ֱ��first type of penicillin resistance occurred when bacteria acquired an enzyme, known as a beta-lactamase, which destroys penicillin. To overcome this, drug manufacturers developed new derivatives of penicillin, such as methicillin, which were resistant to beta-lactamase.

In the escalating arms race, one particular type of bacteria known as Methicillin-resistant Staphylococcus aureus – MRSA – has developed widespread resistance to this class of drugs. MRSA has become a serious problem in hospital- and community-acquired infections, forcing doctors to turn to alternative antibiotics, or a cocktail of different drugs which are often less effective, and raises concerns that even these drugs will in time become ineffective.

In previous research, a team of researchers in Cambridge identified an isolate of MRSA (a sample grown in culture from a patient’s infection) that showed susceptibility to penicillin in combination with clavulanic acid. Clavulanic acid is a beta-lactamase inhibitor, which prevents the beta-lactamase enzyme destroying penicillin; it is already used as a medicine to treat kidney infections during pregnancy.

In a study published today in Nature Microbiology, a team of scientists from the UK, Denmark, Germany, Portugal, and USA used genome sequencing technology to identify which genes make MRSA susceptible to this combination of drugs. They identified a number of mutations (changes in the DNA sequence) centred around a protein known as a penicillin-binding protein 2a or PBP2a.

PBP2a is crucial to MRSA strains as it enables them to keep growing in the presence of penicillin and other antibiotics derived from penicillin. Two of these mutations reduced PBP2a expression (the amount of PBP2a produced), while two other mutations increased the ability of penicillin to bind to PBP2a in the presence of clavulanic acid. Overall the effect of these mutations means that a combination of penicillin and clavulanic acid could overcome the resistance to penicillin in a proportion of MRSA strains.

̽��ֱ��team then looked at whole genome sequences of a diverse collection of MRSA strains and found that a significant number of strains – including USA300 clone, the dominant strain in the United States – contained both mutations that confer susceptibility. This means that one of the most widespread strains of MRSA-causing infections could be treatable by a combination of drugs already licensed for use.

Using this knowledge, the researchers used a combination of the two drugs to successfully treat MRSA infections in moth larvae and then mice. Their next step will be to conduct the further experimental work required for a clinical trial in humans.

Dr Mark Holmes from the Department of Veterinary Medicine at the ̽��ֱ�� of Cambridge, a senior author of the study, says: “MRSA and other antibiotic-resistant infections are a major threat to modern medicine and we urgently need to find new ways to tackle them. Developing new medicines is extremely important, but can be a lengthy and expensive process. Our works suggests that already widely-available medicines could be used to treat one of the world’s major strains of MRSA.”

First author Dr Ewan Harrison, from the Wellcome Sanger Institute and the ̽��ֱ�� of Cambridge, adds: “This study highlights the importance of genomic surveillance – collecting and sequencing representative collections of bacterial strains. By combining the DNA sequencing data generated by genomic surveillance with laboratory testing of the strains against a broad selection of antibiotics, we may find other unexpected cracks in the armour of antibiotic-resistant bacteria that might give us new treatment options.”

̽��ֱ��research was funded by the Medical Research Council (MRC), Wellcome and the Department of Health.

Dr Jessica Boname, Head of Antimicrobial Resistance at the MRC, says: “This study demonstrates how a mechanistic understanding of resistance and access to clinical data can be used to find new ways to contain and control infections with existing resources.”

Reference
Harrison, EM et al. Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus. Nature Microbiology; 24 June 2019; DOI: 10.1038/s41564-019-0471-0

Some MRSA infections could be tackled using widely-available antibiotics, suggests new research from an international collaboration led by scientists at the ̽��ֱ�� of Cambridge and the Wellcome Sanger Institute.

MRSA and other antibiotic-resistant infections are a major threat to modern medicine and we urgently need to find new ways to tackle them

Mark Holmes

NIAID

Scanning electron micrograph of a human neutrophil ingesting MRSA (yellow)

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MRSA contamination found in supermarket sausages and minced pork

cjb250 — Thu, 18 Jun 2015 14:56:43 +0000

In February, a team of researchers funded primarily by the Medical Research Council bought and analysed a total of 103 (52 pork and 51 chicken) pre-packaged fresh meat products, labelled as being of UK farm origin, from supermarkets in five different locations across in England.

All of the meat products were frozen at -20 °C and sent to the Department of Veterinary Medicine at the ̽��ֱ�� of Cambridge for testing. After thawing, researchers disinfected the exterior packaging before removing the meat. They then tested a 10g sample of meat from each packet and screened for MRSA. Two of the pork samples – one from sausages, one from minced pork – tested positive for MRSA; the sausage sample contained two strains of the bacteria.

In collaboration with the Wellcome Trust Sanger Institute an analysis of the genetic make-up of the bacteria and confirmed the presence of antibiotic resistant genes. ̽��ֱ��analysis showed that the bacteria belonged to a type of MRSA known as LA-MRSA CC398, which has emerged over the last few years in continental Europe, particularly in pigs and poultry, but was not previously believed to be widely distributed in the UK.

In many countries, LA-MRSA CC398 represents an occupational risk for those in close contact with livestock, particularly pigs and veal calves. Humans in contact with pigs (farm workers, abattoir workers and veterinarians, etc.) have significantly higher rates of the bacteria in their nasal carriage, according to epidemiological studies, for example. Other studies have revealed an association between clinical disease resulting from LA-MRSA CC398 infection and recent contact with pigs or pig farms. As with other MRSA, this type may be responsible for serious illness following wound or surgery site infections, although many people will carry MRSA on their skin or in their noses without showing signs of disease.

̽��ֱ��researchers stress that adequate cooking (heating above 71°C) and hygienic precautions during food preparation should minimise the likelihood of transmission to humans via contaminated pork. However, they argue that the discovery of MRSA in pork identifies a potential way that the bacteria can spread from farms to the wider population.

While human contamination of carcasses or meat products in the abattoir or at the meat packing plant may occur, there is good evidence that these isolates are of animal origin – possibly through the use of antibiotics to treat or control infection in livestock.

As the tests use a highly sensitive method of detection of bacterial contamination, the numbers of MRSA bacteria present may be low. ̽��ֱ��researchers say that as the two infected samples contained processed pork (sausages and minced pork), they cannot rule out that the meat packing plants from which the MRSA from this study originated also handle imported meat. If this were the case, it is conceivable that cross-contamination might have occurred between non-UK to UK sourced meat.

Dr Mark Holmes from the Department of Veterinary Medicine at the ̽��ֱ�� of Cambridge says: “This is the first time that MRSA has been detected in retail meat products in the UK. ̽��ֱ��public should not be overly worried by this as sensible food precautions and good hygiene should prevent its spread. It’s also usually pretty harmless and only causes health problems if it infects someone in poor health or gets into a wound.

“However, this does suggest that MRSA is established in our pig farms and provides a possible route of transmission from livestock, through those in direct contact with pigs, into the wider population.”

Dr Des Walsh, Head of Infections and Immunity at the MRC, added: “Studies like this are crucial not just to reveal concerns to human health through contaminated livestock, but to show resistance to antibiotics is a problem growing far beyond just humans. To win the fight against antimicrobial resistance, we need an all hands on deck approach, and that’s why we’ve teamed up with leading experts in biological, social and others sciences in a joint initiative designed to find new solutions, fast.”

̽��ֱ��research was funded by the Medical Research Council, with additional support from the Alliance to Save our Antibiotics. ̽��ֱ��results of the study are published in the online journal Eurosurveillance.

Dr Holmes was recently awarded a further £1.58 million from the MRC to look into the effects of antibiotic use on the entire population of animal gut flora, not just the disease causing bacteria. His work, using research in pigs, will help scientists understand the evolution of antibiotic resistance and help to make better choices about how to reduce the spread of antimicrobial resistance on farms.

Reference
Hadjirin, NF et al. Detection of livestock-associated methicillin-resistant Staphylococcus aureus CC398 in retail pork, United Kingdom, February 2015. Eurosurveillance

A survey carried out earlier this year has found the first evidence of the ‘superbug’ bacteria Methicillin-Resistant Staphylococcus Aureus (MRSA) in sausages and minced pork obtained from supermarkets in the UK. However, researchers stress that this does not pose a significant immediate risk to the public.

̽��ֱ��public should not be overly worried by this as sensible food precautions and good hygiene should prevent its spread

Mark Holmes

Ross Elliott

Sausages (cropped)

̽��ֱ��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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March of the superbugs

admin — Wed, 13 Feb 2013 09:38:50 +0000

Every so often, research laboratories and hospitals testing patients for the superbug methicillin-resistant Staphylococcus aureus (MRSA) have come across an oddity: a strain that appeared to be MRSA because it was resistant to antibiotics but one that tested negative with the ‘gold standard’ molecular test. ̽��ֱ��quirky cases were so infrequent that they were usually filed away for future analysis or disregarded. Until, that is, PhD student Laura Garcia-Alvarez from Cambridge’s Department of Veterinary Medicine had the tenacity to look a little further at a bacterial strain she had spotted in cows’ milk.

MRSA first appeared in 1961 and epidemic strains of this difficult-to-treat bacterium have since spread worldwide in hospitals and the community. In the farming world, MRSA causes bovine mastitis – an infection of cows’ udders – affecting both animal welfare and milk yields.

Garcia-Alvarez was working with Dr Mark Holmes on bovine mastitis when she came across one of the ‘curious anomalies’. ̽��ֱ��strain was resistant to antibiotics but in the standard molecular test was negative for the presence of mecA – the gene responsible for methicillin resistance. She had the isolates retested and then sequenced at the Wellcome Trust Sanger Institute.

It turned out that she had discovered a new strain of MRSA. Its antibiotic resistance is carried not by mecA but by mecC, a gene that is so genetically dissimilar to mecA that it can’t be picked up by the standard molecular test used to define MRSA but only by DNA sequencing.

As Holmes and Garcia-Alvarez began to spread the information to colleagues around Europe, it soon became clear that this phenomenon was not confined to cows: others had found the unusual samples in humans. “We started to get calls from hospitals and research groups who had come across a small number of human MRSA strains that behaved differently,” said Holmes. “Within a few weeks, we had a further 50 isolates. This meant that what we were looking at was a human problem too.”

Garcia-Alvarez, who at the time was a student on the Department’s postgraduate training in infectious disease dynamics programme, described how finding the same new strain in both humans and cows was worrying, although no cause for immediate alarm: “Pasteurisation of milk will prevent any risk of infection via the food chain. In the wider UK community, less than 3% of individuals carry MRSA – typically in their noses – without becoming ill.”

“Nonetheless,” added Holmes, “MRSA presents a major challenge to the control of infectious diseases. Finding a new strain – studying its prevalence, how it confers antibiotic resistance and how it’s transmitted – can tell us enormous amounts about the origins and evolution of antibiotic resistance.”

New understanding

Since the discovery, Holmes’ team has been investigating the prevalence of the strain in human and animal populations – and the potential for passing the strain between species – in partnership with Cambridge’s Department of Medicine, the Sanger Institute and the Moredun Research Institute (Scotland), and funded by the Medical Research Council.

One of their first steps was to develop a better genetic test, one that also detected the new strain. ̽��ֱ��timing was fortuitous. Moves to help hospitals identify MRSA more quickly have resulted in the development of automated systems based on genetic testing. Because the standard genetic test does not detect the new strain, the scientists have now developed a protocol that will pick up both strains.

Moreover, their recent research has shown that additional MRSA strains have emerged that possess other mechanisms of antibiotic resistance: “We’ve found about 40 human MRSA isolates that don’t have a mecA or a mecC gene, and we are trying to establish why these are resistant to methicillin-family antibiotics. In retrospect, it was incredibly lucky that the original isolate we investigated happened to have a genetic variation in a known gene that could be picked up by whole genome sequencing.”

To identify how mecC confers antibiotic resistance, Holmes collaborated with Professor Alexander Tomasz at Rockefeller ̽��ֱ��, New York. They discovered that the gene is more resistant than mecA to cefoxitin (one of the newer classes of antibiotics): “Inappropriate use of antibiotics in human and veterinary medicine has favoured the selection and growth of antibiotic-resistant microorganisms,” explained Holmes. “Our finding suggests that an increased use of this drug may have driven emergence of the new strain.”

“We also now know that the new strain is found in almost every species that we’ve studied, including domestic cats and dogs, wild rats, deer, a rabbit, a common seal, sheep and a chaffinch. ̽��ֱ��bacterium may have lost factors that restricted it to certain species, or gained pan-host virulence factors that make it better able to colonise multiple species. We need to know how and why this has happened to understand the emergence of bacterial pathogens from animals and their dissemination into human populations.”

Now, their latest research has tracked transmission of the superbug, providing the first direct evidence of transmission of the new strain between livestock and humans.

̽��ֱ��researchers capitalised on a growing trend to use increasingly rapid and affordable DNA sequencing for tracking the transmission of pathogens. This technique is helping scientists to look for differences at the level of single letters in the genetic code as a means to map the direction of infection – from patient to patient, and from one animal species to another. ̽��ֱ��team investigated two cases of mecC MRSA in Danish farmers. ̽��ֱ��strains circulating in the farmers’ livestock and those isolated from the patients only differed by a small number of letters – strong evidence that the farmers had acquired their infections from their animals, in one case a sheep and in another a cow.

“ ̽��ֱ��ability to confirm animal-to-human transmission in virtual real time using this technology can’t be underestimated,” said Holmes. “High-throughput DNA sequencing is going to revolutionise clinical microbiology by enabling targeted epidemiological follow-up and infection control.”

Nearing the precipice

Mastitis is the most common infectious disease of dairy cattle, affecting the welfare of cows and, according to one estimate, costs the UK dairy industry around £170 million per year. Its control and treatment relies on the use of millions of doses of therapeutic and prophylactic antibiotics every year. “Our research on MRSA is pointing to the fact that although we are not on the precipice of having the whole system collapse through selection of bugs that are even more resistant or having husbandry systems that make it impossible to eliminate them, we are closer to the precipice than we would like to be,” said Holmes. “As it is, S. aureus is considered impossible to eliminate in dairy herds – you have to live with it once you’ve got it. “Farmers and veterinarians are in a constant battle to improve the health of dairy cows, yet farming cannot be sustained at these levels if it is generating these types of resistance. Moreover, we can’t predict how these bacterial strains will evolve – they could become more resistant, more virulent or better able to jump between species.”
Holmes views the interface between veterinary medicine and human medicine as crucial to understanding infectious diseases such as MRSA: “There is very little research on S. aureus mastitis in cows in comparison to research into it as a human pathogen, and yet now we’re beginning to see exactly the same organism being found in people and in cows. This means that we should be thinking about the epidemiology of disease control and the development of antibiotic resistance in both species. Understanding how new strains emerge will help us to understand the growing public health problem of antibiotic resistance.”

For more information, please contact Louise Walsh at the ̽��ֱ�� of Cambridge Office of External Affairs and Communications.

Scientists who recently discovered a new strain of superbug have now tracked its transmission between animals and humans.

We can’t predict how these bacterial strains will evolve – they could become more resistant, more virulent or better able to jump between species

Mark Holmes

JelleS on flickr

Cow

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New strain of MRSA discovered

gm349 — Fri, 03 Jun 2011 09:10:27 +0000

Scientists have identified a new strain of methicillin-resistant Staphylococcus aureus (MRSA) which occurs both in human and dairy cow populations.

̽��ֱ��study, led by Dr Mark Holmes at the ̽��ֱ�� of Cambridge, identified the new strain in milk from dairy cows while researching mastitis (a bacterial infection which occurs in the cows’ udders).

̽��ֱ��new strain’s genetic makeup differs greatly from previous strains, which means that the ‘gold standard’ molecular tests currently used to identify MRSA - a polymerase chain reaction technique (PCR) and slide agglutination testing - do not detect this new strain. ̽��ֱ��research findings are published today in the journal ̽��ֱ��Lancet Infectious Diseases.

Dr Laura García-Álvarez, first author of the paper, who discovered the new strain while a PhD student at the ̽��ֱ�� of Cambridge’s Veterinary School, said: “To find the same new strain in both humans and cows is certainly worrying. However, pasteurization of milk will prevent any risk of infection via the food chain. Workers on dairy farms may be at higher risk of carrying MRSA, but we do not yet know if this translates into a higher risk of infection. In the wider UK community, less than 1% of individuals carry MRSA – typically in their noses – without becoming ill.”

̽��ֱ��scientists discovered the antibiotic resistant strain while researching S. aureus, a bacterium known to cause bovine mastitis. Despite the strain being able to grow in the presence of antibiotics, when they attempted to use the standard molecular tests available – which work by identifying the presence of the gene responsible for methicillin resistance (the mecA gene) - the tests came back negative for MRSA.

When Dr Matt Holden and a research team at the Wellcome Trust Sanger Institute sequenced the entire genome (decoding all of the genes in the bacteria’s DNA) they realised that the new strain possessed unconventional DNA for MRSA. They found that the new strain does have a mecA gene but with only 60% similarity to the original mecA gene. Unfortunately, this results in molecular tests (which identify MRSA by the presence of the mecA gene) giving a false negative for this strain of MRSA.

Subsequent research revealed that the new strain was also present in humans. During the study, the new strain was found in samples from Scotland, England and Denmark (some from screening tests and others from people with MRSA disease). It has since been identified in Ireland and Germany. Additionally, by testing archived S. aureus samples, the researchers have also identified a recent upward trend in the prevalence of the antibiotic resistant bacteria.

Dr Mark Holmes said: “ ̽��ֱ��majority of MRSA testing in British hospitals is performed by seeing if the bacteria will grow in the presence of antibiotics, typically oxacillin and cefoxitin, rather than methicillin - which is now no longer manufactured. This type of testing detects both the new MRSA and conventional MRSA.

“However, it is important that any of the MRSA testing that is based on detection of the mecA gene - i.e. PCR based testing, or slide agglutination testing - be upgraded to ensure that the tests detect the new mecA gene found in the new MRSA. We have already been working with public health colleagues in the UK and Denmark to ensure that testing in these countries now detects the new MRSA.”

̽��ֱ��new research also raises questions about whether cows could be a reservoir for the new strains of MRSA.

Dr Holmes added: “Although there is circumstantial evidence that dairy cows are providing a reservoir of infection, it is still not known for certain if cows are infecting people, or people are infecting cows. This is one of the many things we will be looking into next.

“Although our research suggests that the new MRSA accounts for a small proportion of MRSA – probably less than 100 isolations per year in the UK, it does appear that the numbers are rising. ̽��ֱ��next step will be to explore how prevalent the new strain actually is and to track where it is coming from. If we are ever going to address the problem with MRSA, we need to determine its origins.”

Scientists at the Health Protection Agency (HPA) co-authored this paper, providing the analysis of the human samples of the new strain. Dr Angela Kearns, head of the HPA’s Staphylococcus Reference Laboratory said: “There are numerous strains of MRSA circulating in the UK and the rest of Europe. Even though this new strain is not picked up by the current molecular tests, they do still remain effective for the detection of over 99 per cent of MRSAs. This new strain can be picked up by another type of test, which has shown to be effective in trials in the UK and elsewhere in Europe.

“This is a very interesting find and the HPA is currently involved in further research to screen a wider population of MRSA samples to ascertain how prevalent it is. It’s important to remember MRSA is still treatable with a range of antibiotics and the risk of becoming infected with this new strain is very low.”

With funding from the Medical Research Council, the researchers will next be undertaking prevalence surveys in people and in dairy cattle in the UK to determine how much new MRSA is present in these populations. They will also be performing an epidemiological study on farms to identify any factors that may be associated with infection by the new MRSA, to look for further new MRSA strains, and to explore the potential risks of the new strain to farm workers.

Antibiotic resistant bacteria found in both humans and dairy cows.

Although our research suggests that the new MRSA accounts for a small proportion of MRSA – probably less than 100 isolations per year in the UK, it does appear that the numbers are rising. ̽��ֱ��next step will be to explore how prevalent the new strain actually is and to track where it is coming from. If we are ever going to address the problem with MRSA, we need to determine its origins.

Dr Mark Holmes, Department of Veterinary Medicine at the ̽��ֱ�� of Cambridge

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̽��ֱ�� of Cambridge - Mark Holmes

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