Experts from the University of Nottingham, United Kingdom, have developed ground-breaking software, which combines DNA sequencing and machine learning to help them find where, and to what extent, antibiotic-resistant bacteria are being transmitted between humans, animals, and the environment.

The study, which is published in PLOS Computational Biology, was led by Dr. Tania Dottorini from the School of Veterinary Medicine and Science at the University.

Anthropogenic environments (spaces created by humans), such as areas of intensive livestock farming, are seen as ideal breeding grounds for antimicrobial-resistant bacteria and antimicrobial-resistant genes, which are capable of infecting humans and carrying resistance to drugs used in human medicine. This can have huge implications for how certain illnesses and infections can be treated effectively.

source of meat in the country, and is the largest user of antibiotics for food production in the world.

In this new study, a team of experts looked at a large-scale commercial poultry farm in China and collected 154 samples from animals, carcasses, workers, and their households and environments. From the samples, they isolated a specific bacteria called Escherichia coli (E. coli). These bacteria can live quite harmlessly in a person’s gut, but can also be pathogenic, and the genome carries resistance genes against certain drugs, which can result in illnesses including severe stomach cramps, diarrhea, and vomiting.

Researchers used a computational approach that integrates machine learning, whole-genome sequencing, gene sharing networks, and mobile genetic elements, to characterize the different types of pathogens found on the farm. They found that antimicrobial genes (genes conferring resistance to the antibiotics) were present in both pathogenic and non-pathogenic bacteria.

The new approach, using machine learning, enabled the team to uncover an entire network of genes associated with antimicrobial resistance, shared across animals, farmworkers, and the environment around them. Notably, this network included genes known to cause antibiotic resistance as well as yet unknown genes associated with antibiotic resistance.

Dr. Dottorini said: “We cannot say at this stage where the bacteria originated from, we can only say we found it and it has been shared between animals and humans. As we already know there has been sharing, this is worrying, because people can acquire resistance to drugs in two different ways - from direct contact with an animal, or indirectly by eating contaminated meat. This could be a particular problem in poultry farming, as it is the most widely used meat in the world.

“The computational tools that we have developed will enable us to analyze large complex data from different sources, at the same time as identifying where hotspots for certain bacteria may be. They are fast, they are precise and they can be applied in large environments – for instance – multiple farms at the same time.

“There are many antimicrobial-resistant genes we already know about, but how do we go beyond these and unravel new targets to design new drugs?

Our approach, using machine learning, opens up new possibilities for the development of fast, affordable, and effective computational methods that can provide new insights into the epidemiology of antimicrobial resistance in livestock farming.”Dr. Tania Dottorini from the School of Veterinary Medicine and Science at the University.

The forecasts could help fishing fleets, ocean managers, and coastal communities anticipate the effects of marine heatwaves.

Researchers have developed global forecasts that can provide up to a year's notice of marine heatwaves, and sudden and pronounced increases in ocean temperatures that can dramatically affect ocean ecosystems. 

The forecasts could help fishing fleets, ocean managers, and coastal communities anticipate the effects of marine heatwaves. One such heatwave, known as “the Blob,” emerged about 2013 in the northeast Pacific Ocean and persisted through 2016. It led to shifting fish stocks, harmful algal blooms, entanglements of endangered humpback whales, and thousands of starving sea lion pups washing up on beaches.

“We have seen marine heatwaves cause sudden and pronounced changes in ocean ecosystems around the world, and forecasts can help us anticipate what may be coming,” said lead author Michael Jacox, a research scientist at NOAA Fisheries’ Southwest Fisheries Science Center in Monterey, California, and NOAA’s Physical Sciences Laboratory in Boulder, Colorado.

Marine heatwave forecasts will be available online through NOAA’s Physical Sciences Laboratory. The researchers called the forecasts a “key advance toward improved climate adaptation and resilience for marine-dependent communities around the globe.”

The forecasts leverage global climate models to predict the likely emergence of new marine heatwaves. “This is a really exciting way to use existing modeling tools in a much-needed new application,” Jacox said.

Reducing Ecological and Economic Impacts

Impacts of marine heatwaves have been documented in ecosystems around the world, particularly in the past decade. These include:

• Fish and shellfish declines that caused global fishery losses of hundreds of millions of dollars
• Shifting distributions of marine species that increased human-wildlife conflict and disputes about fishing rights
• Extremely warm waters have caused bleaching and mass mortalities of corals

On the U.S. West Coast, marine heatwaves gained notoriety following the Blob, which rattled the California Current Ecosystem starting in 2014. That marine heatwave led to an ecological cascade in which whales’ prey was concentrated unusually close to shore, and a severe bloom of toxic algae along the coast delayed the opening of the valuable Dungeness crab fishery. Humpback whales moved closer to shore to feed in some of the same waters targeted by the crab fishery. As fishermen tried to make up for a lost time after the delay by deploying additional crab traps, whales became entangled in record numbers in the lines attached to crab traps. Recent research has also connected marine heatwaves along the West Coast to a northward shift in California market squid, which has long supported one of California’s largest commercial fisheries.

NOAA Fisheries scientists have since developed a Marine Heatwave Tracker that monitors the North Pacific Ocean for signs of marine heatwaves. The forecasts go a step further to anticipate where marine heatwaves are likely to emerge in the coming months, and how long they are expected to persist.

“Extreme events in concert with increasing global temperatures can serve as a catalyst for ecosystem change and reorganization,” said Elliott Hazen, a research ecologist at the Southwest Fisheries Science Center and researcher. “While marine heatwaves can have some unanticipated effects, knowing what’s coming allows for a more precautionary approach to lessen the impact on both fisheries and protected species. Understanding the ocean is the first step towards forecasting ecological changes and incorporating that foresight into decision-making.”

El Niño-Southern Oscillation Boosts Forecast Accuracy

The forecasts are most accurate during periods influenced by the El Niño-Southern Oscillation, a well-known climate pattern in the Pacific Ocean. El Niño (the warm phase of the oscillation) could be considered the “world’s most prominent marine heatwave,” Jacox said. It demonstrates that the heatwaves themselves are not new.

The forecasts cannot predict marine heatwaves as far in advance in regions such as the Mediterranean Sea, or off the U.S. East Coast. The atmosphere and ocean fluctuate more rapidly in these areas. The forecasts provide the greatest foresight in areas with known ocean-climate patterns such as the Indo-Pacific region north of Australia, the California Current System, and the northern Brazil Current.

The scientists noted that managers of fisheries and other marine life must weigh their reaction to predicted marine heatwaves based on the potential consequences. For example, they would need to weigh the economic costs of limiting fisheries ahead of a marine heatwave against the risk of inadvertently entangling endangered whales or sea turtles.

“We’re talking about the difference between making informed choices and reacting to changes as they impact ecosystems,” Hazen said. “That is always going to be a balance, but now it is a much more informed one.”