Scientists have determined how harmless E. coli gut bacteria in chickens can pick up the genes required to evolve and cause infections in poultry and people.

Colibacillosis caused by avian pathogenic E. coli (APEC) is the most common infection in chickens reared for meat or eggs. It is fatal in up to 20 percent of cases and causes multi-million pound losses in the poultry industry. Other problems include increasing antibiotic resistance and the risk of human infections, according to the research report.

Scientists sequenced and analyzed the whole genomes of 568 E. coli bacteria found in healthy and infected chickens bred at commercial poultry farms to better understand why and how the harmless bugs can turn deadly. Findings were published in the journal Nature Communications.

They found there was no single gene responsible for the switch from harmless to pathogenic, but it could be caused by several combinations of a diverse group of genes.

From harmless to dangerous
Results indicate that all bacteria in chicken intestines have the potential to pick up the genes they need to turn into a dangerous infection, through a process called horizontal gene transfer. This enables bacteria to acquire new genetic material from other bacteria nearby.

Professor Sam Sheppard, who led the study, said it was previously thought that E. coli became pathogenic by acquiring specific genes from other bugs, often in mobile elements called plasmids.

“But our study compared the genomes of disease-causing and harmless E. coli in chickens and found that they can turn bad simply by picking up genes from their environment. Bacteria do this all the time inside the guts of chicken, but most of the time the scavenged genes are detrimental to the bacteria so it becomes an evolutionary dead end,” he reported.

Poultry isolates from the dataset clustered within six of the eight known E. coli phylogroups. A total of 211 isolates, or 39 percent, belonged to sequence type 117, which with isolates in the B2, B1 and A phylogroups, made up 93 percent of the isolates.

Sheppard, from the University of Bath, said there are 26 billion chickens worldwide.

“That increases the likelihood of bacteria picking up genes that could help the bacteria survive and turn infectious, or even jump species to infect humans. We were surprised to find that it’s not just a single strain that causes APEC, but any strain can potentially acquire the monster combination of genes needed to turn bad,” he wrote.

Strains with the potential to turn pathogenic could be identified by using whole genome sequencing and rapid PCR tests to probe for specific genes that could lead to an APEC infection. Early identification of pathogens has potential to improve livestock welfare and reduce economic losses from disease.

“We identified around 20 genes that are common in pathogenic bugs and if we can look out for these key genes in a flock of birds, that would help farmers target those carriers before they cause a problem,” said Sheppard.

STEC analysis
Meanwhile, a different study has found Shiga toxin-producing E. coli (STEC) strains harboring extraintestinal pathogenic E. coli (ExPEC)-associated virulence genes can include multiple serotypes.

Researchers characterized 53 STEC strains with ExPEC-associated virulence traits isolated from infected patients and contaminated food in Italy and the Netherlands from 2000 to 2019.

Of the 53 strains, 30 had been isolated in Italy, mostly from patients with hemolytic uremic syndrome (HUS) or severe hemorrhagic colitis. HUS is associated with severe E. coli infections. Two strains were from products of bovine origin in Italy. The remaining 23 STEC strains had been isolated from patients in the Netherlands, some of whom had diarrhea or bloody diarrhea or had been hospitalized.

STEC strains with these genes belonged to 10 different serotypes, with a high prevalence of O80:H2. Five additional serotypes were found from previous sources.