Report of the Department of Agriculture Survey for Antimicrobial Resistance in Bacteria of Animal Origin
1. What is the Department of Agriculture survey for antimicrobial resistance in bacteria of animal origin?
This program provides a snapshot of the prevalence of resistance to important antimicrobials in key indicator bacteria found in the gut of food-producing animals in Australia. It is the first large scale survey to look at antimicrobial resistance in Australia and provides a baseline to identify future trends.
The survey results support Australia’s rigorous approach to controlling the amounts and types of antibiotics used in our food animal industries. This approach is an important factor in preventing the development and spread of resistant bacteria.
2. What are antimicrobials and antimicrobial resistance?
The terms antimicrobials, or antimicrobial agents, refer to all types of natural and synthetic drugs which may kill or slow down the growth of microorganisms such as bacteria. These include antibiotics, anti-fungals, and household disinfectants. Antimicrobial agents are widely used for the treatment and prevention of human and animal diseases.
The term antimicrobial resistance refers to a property of bacteria that enables them to grow in the presence of antimicrobial drug levels that would normally be expected to inhibit or kill susceptible bacteria. Development of resistance can eventually stop or reduce the effectiveness of antimicrobial agents intended to treat human and animal infections.
The emergence of antimicrobial resistance threatens our ability to fight human and animal diseases. It could narrow the line of defence against bacterial infections to only a few antibiotics and increase health care costs. Infections caused by antimicrobial resistant bacteria are more difficult to treat, often resulting in increased morbidity, increased time in hospital and higher mortality rates.
3. What did the surveillance program look at?
In this survey, samples of gut contents were obtained from healthy animals at 31 abattoirs in Queensland, New South Wales, Victoria and South Australia. Between 200 to 300 samples each from cattle (equal numbers of feedlot, grass-fed and dairy), pigs and poultry were collected between November 2003 and July 2004. Bacteria isolated from the samples were then tested to see if they were resistant to a range of different antibiotics. Resistance testing was performed on bacteria namely, Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Enterococcus casseliflavus, Enterococcus hirae and Campylobacter isolated from these samples.
The antimicrobials tested for include those used in food-producing animals in Australia, some that are important to human medicine, and some that are not used in Australia but have an internationally recognised public health profile. Veterinary diagnostic laboratories carried out the preliminary isolation of bacteria and specialised laboratories performed resistance testing.
4. What did the survey find?
The study findings are positive for the Australian livestock industries. The results showed that a low proportion of bacteria, isolated from the guts of the three animal species tested were resistant to antibiotics. The National Health and Medical Research Council reviewed the study’s findings and found the impact on human health is likely to be small.
The survey found resistance to “critically important” antibiotics to human medicine (such as the quinolone class of drugs and third generation cephalosporins) was non-existent or low in bacteria isolated from the gut of food-producing animals that were tested. For example:
- no resistance, or a very low prevalence of resistance to 'critically important' antimicrobials to human medicine was found with the exception of streptogramins and Enterococcus faecium
- no resistance amongst Escherichia coli to either cefotaxime or ceftiofur (both third generation cephalosporins)
- no resistance to vancomycin in enterococci
- other resistances were reassuringly uncommon or not detected, including gentamicin, quinolone resistance in Escherichia coli, and quinolone resistance in Campylobacter species.
There was no multiple-resistance found in enterococci or Campylobacter isolated from chickens.
5. How comprehensive and accurate is the survey?
The survey focused on species of food-producing animals where antimicrobials are most likely to be used in ways that would result in antimicrobial resistance (such as in-feed or in-water use, or frequent use of injectable preparations).
The bacteria for resistance testing (Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Enterococcus casseliflavus, Enterococcus hirae and Campylobacter spp) were selected in a similar manner to other national surveillance programs for antimicrobial resistance in food-producing animals. The resistance status of Campylobacter spp. from broiler chickens was assessed because Campylobacter infections in humans are commonly associated with poultry. Escherichia coli and Enterococcus spp. are common in the gut of animals and man and are known to carry antibiotic resistance genes that can transfer to human pathogens if people eat them in contaminated food.
Although drug-resistant Salmonella spp. are a prominent issue in food safety and veterinary public health, the prevalence of Salmonella spp. in most animal populations is usually too low for their resistance to be assessed in a survey of this type.
Some antimicrobials used exclusively in human medicine were included where there was the potential for resistance to arise because a related drug is used in food-producing animals or where there was a concern about resistance to a particular antimicrobial class in human medicine (e.g. third-generation cephalosporins, fluoroquinolones). Some drugs were included that were not regarded as highly important in human medicine (e.g. tetracyclines). These have been extensively used in food-producing animals and resistance is commonly found in commensal (common) and pathogenic bacteria.
This program was not designed to explore the reasons why different resistance phenotypes do or do not occur in livestock. It does provide baseline data about antimicrobial resistance trends in food-producing animals in Australia.
6. Why didn't the survey include sheep?
Sheep were a low priority for inclusion because in Australia sheep are largely grass-fed and anecdotally antimicrobial use is uncommon in sheep. Classes of livestock with a higher exposure to antimicrobials were included. The survey did include grass fed cattle and this provided adequate representation from grazing livestock industries.
7. Why didn’t the survey include an assessment of AMR in Campylobacter from cattle and pigs?
Chickens are an important source of Campylobacter infections in humans. Resources were therefore focused on this animal species. It is recognised however that there are many other food and environmental (non-food) sources of Campylobacter infections in humans.
8. Why is there a distinction between multi-resistance and multiple resistance?
In producing this report it became apparent that there is a lack of standard terminology for describing the number of drugs to which a bacterial isolate is resistant. In this report the terms multi and multiple were used to describe resistance. Multi-resistance is defined as isolates resistant to two or more antibiotics and multiple-resistance is defined as isolates resistant to four or more antibiotics. In any future work these and other definitions would be standardised, taking into account any definitions in use elsewhere.
9. Some multiple resistance in E. coli from pigs was detected—is this a concern?
Multiple resistance is an indicator that more drugs have been used more often. Experts are concerned that diarrhoea in young pigs caused by pathogenic E. coli attract a lot of antimicrobial use and contributed to the resistance in commensal (common) E. coli. In the future, herds affected with these multiple resistant pathogens are increasingly likely to rely on drugs of higher importance. The pig industry and researchers are involved in finding ways of minimising the use of high importance drugs, because of their potential impacts on human health down the food chain.
10. How are the confidence intervals for the proportion of resistance isolates calculated and how are they interpreted?
This report used modern statistical routines to generate the best possible confidence limits for the data collected. These are termed 'exact binomial confidence limits'. Essentially the confidence intervals are a way of accounting for variability arising from sampling. It is not possible to measure the resistance of all bacteria in the whole population. This system samples bacteria for assessment. The extent that the proportion resistant in the sample measured reflects the proportion resistant in the population is assessed with confidence intervals. In the 95 per cent confidence limits reported in this study, the true level of resistance in the population has a 95 per cent probability of being somewhere between the lower and upper confidence limit.
11. How does antimicrobial resistance develop?
Antimicrobial resistance results from the exposure of microorganisms to antimicrobial drugs. Use of antimicrobial drugs allows the small number of organisms that are resistant to that drug (through mutation or transfer of resistance genes from other bacteria) to survive the treatment and continue to grow. Some bacteria are naturally resistant to some antimicrobial drugs and different antimicrobials are needed to treat infections. Overuse or inappropriate use of antibiotics is an important contributor to antimicrobial resistance.
The antimicrobial resistance of greatest concern is that acquired by bacteria through alterations in their genetic make-up as a result of random changes (mutations) in their DNA or through movement of antimicrobial resistance genes from one bacterium to another. Continued use of an antimicrobial in the face of resistance to it, allows resistant bacteria to survive the treatment and these then become the dominant bacteria in that setting.
12. Why are antimicrobials used in food-producing animals?
Antimicrobials are prescribed and used therapeutically for the treatment of animal diseases and may be added to the feed of food-producing animals to prevent infections. Some antibiotics used for these purposes also have a stated claim for growth promotion or increased feed efficiency. Only one of the antibiotics used under these circumstances, tylosin, was identified by JETACAR as being used in human medicine. Tylosin is currently under review by the APVMA. Other antibiotics that may include claims on their label for growth promotion or increasing feed efficiency are not important in human therapy and are unlikely to be involved in antimicrobial resistance in humans.
13. What do farm animals have to do with antimicrobial resistance?
The use and overuse of antibiotics, whether in humans or animals can result in bacteria that are resistant to antibiotics. Antibiotics are used in animals to control infection and there are many regulations and codes of good practice that govern their use.
In Australia, all antibiotic products used in all animals must be registered by the Australian Pesticides and Veterinary Medicines Authority (APVMA). The APVMA’s governing legislation states that the APVMA must not register any product that is harmful to people, animals, crops or the environment. The states and territories control the use of registered products in their jurisdiction.
In addition, there are third-party independently audited industry quality assurance programs that require participating producers to follow good agricultural practices in using agricultural chemicals and veterinary drugs, including antibiotics. The National Residue Survey (NRS) monitors and reports the levels of residues of veterinary drugs (including residues of antibiotics) in meat. The NRS provides results of testing to the participating primary industries to help them monitor and prevent chemical residues in products.
14. Can antimicrobial residues in food lead to antimicrobial resistance in people?
This survey does not look at whether antimicrobial resistance can be passed to people through the food chain. However, the Joint Expert Technical Advisory Committee on Antibiotic Resistance report found that it was highly unlikely that the consumption of antibiotic residues in food would lead to the development of resistance.
This is because antibiotic residue levels in food are generally low and are likely to reduce further by cooking, other food processing and by metabolism in the human gut.
15. Where can I find information on food safety issues related to antimicrobial resistance?