Friday, July 1, 2022

Resisting the antibiotic bug

Greater use of antibiotics in production animal systems has been attributed to the growth in antimicrobial resistance (AMR) globally. But until now little has been known about AMR in New Zealand farm systems, and whether grazing cows outdoors in a grass-fed system has any influence on its prevalence. Post-doctoral researcher Rose Collis has helped lift the level of that knowledge. She spoke to Richard Rennie.

When it came to studying just how prevalent AMR is on New Zealand dairy farms, Rose Collis took a “whole farm” approach to an issue most farmers may associate mainly with mastitis treatment and how well their cows respond to that treatment.

“We knew from some good earlier work based off sales data that NZ’s use of antibiotics is relatively low and when you look at our dairy farms here, they typically use less than more intensive indoor systems like poultry or pig production.”

Her work has proven particularly timely in light of a recent report released by the Prime Minister’s chief science advisor Professor Juliet Gerrard on this country’s AMR management strategy. 

This included a series of recommendations on both human and production animal use of antibiotics, identifying a number of holes and weaknesses in how the growing global risk was being managed here.  

The report recognised an advantage NZ has compared to some countries, with our relatively low AMR incidence, but also the risk that advantage is lost without better monitoring.

While largely focused upon human health management issues, the report also pinpointed a need for better AMR surveillance in animal systems and a need for better information sharing across all sectors on AMR prevalence.

Collis’ work involved collecting samples of effluent, faeces, soil and raw milk from two Manawatū dairy units and applying some cutting-edge sampling techniques to try and identify the type and prevalence of AMR genes and resistant bacteria on the farms.

Employing “shotgun” metagenomic sequencing enabled Collis to effectively scoop up complex samples and identify all the genetic material contained within that sample, regardless of what it was. 

“What we found was that the presence of AMR genes was low compared to overseas data. The original hypothesis that the free range, grass grazing outdoor environment does contribute to our lower AMR levels proved to be right.”

Rose Collis

As a method it provides scientists with the ability to literally take a deep dive into a population in remote or challenging environments, including ocean samples. 

“Once sampled we can sequence all the DNA contained within it and use comparative analysis from indices to look for AMR genes present.” 

This contrasts to more conventional approach of taking a culture sample and growing out bacteria to determine if they are AMR or not, although this process will also often be used alongside the shotgun sampling.

“What we found was that the presence of AMR genes was low compared to overseas data. The original hypothesis that the free range, grass grazing outdoor environment does contribute to our lower AMR levels proved to be right.”

She did find the most diverse range of those AMR genetics discovered were present in the effluent samples taken from farm effluent ponds, although still comparatively low.

“Given the study ran over 15 months, we were also able to see if there were any variations across the farming year. While there was some increase in specific antibiotic resistant bacteria over summer, the numbers were still relatively low.

“If anything, I would have been expecting a lift in AMR genes over calving-spring time.”

Her thesis also earned her an audience with the Prime Minister during a recent visit and recognition at Massey, being put on the Dean’s list of exceptional theses.

Now working with AgResearch’s Food System Integrity team, Collis is able to apply some of the skills and methods developed during her thesis to look at identifying the types of E coli that populate freshwater sources.

“This next generation sequencing provides a longer ‘read’ of the genomic DNA, and with that more information on that particular genetic material.” 

From here she hopes the technology will enable scientists to determine not only that a catchment is contaminated with E coli, but also the source, whether it be livestock, bird, or human.

Her work has confirmed that NZ’s status as one of the three lowest users of antibiotics in livestock use globally translates to less AMR in the farm environment and has proved dairy farmers have another environmental benefit worth preserving.

Collis says the sector should also receive some recognition for the efforts it has made to preserve that low AMR status and respond to calls about careful antibiotic use.

“The NZ Veterinary Association has supported the traffic light system to help vets in their antibiotic decision making, and farmers are using more alternative non-antibiotic preventatives in their dry cow therapy treatments.”

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