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Sequencing-based Tracking Finds Animal-to-Human MRSA Transmission on Danish Farm

NEW YORK (GenomeWeb News) – A research team using whole-genome sequencing to track a form of methicillin-resistant Staphylococcus aureus found in livestock and humans has uncovered genetic evidence confirming animal-to-human transmission of the bug during at least one farm outbreak in Denmark.

"Our findings demonstrate that the MRSA strains we studied are capable of transmission between animals and humans," first author Ewan Harrison, a veterinary medicine researcher at the University of Cambridge, said in a statement, "which highlights the role of livestock as a potential reservoir of antibiotic-resistant bacteria."

As they reported online today in EMBO Molecular Medicine, Harrison and colleagues from the UK and Denmark assessed isolates from MRSA outbreaks on two farms located less than 30 miles from one another. Both outbreaks involved bugs carrying a divergent homologue of a penicillin-binding protein-coding gene called mecC, which has been found with increasing frequency in Denmark during the past decade. More commonly, MRSA isolates carry mecA.

Despite their geographical proximity to one another and sequence type similarities between outbreak isolates, results from new genomic and phylogenetic analyses indicated that each of the outbreaks could be traced back to MRSA with distinguishing variants. In one instance, genetic diversity patterns strongly supported animal-to-human transmission of MRSA. On the other farm, the direction of transmission could not be definitively determined.

"By looking at the single differences in nucleotides or SNPs in the DNA sequences of each isolate, it became obvious that two different strains of bacteria were responsible for the two disease outbreaks," University of Cambridge researcher Mark Holmes, the study's senior author, said in a statement.

"In one case," Holmes continued, "the results also clearly showed that the most likely direction of transmission was from animal to human."

The mecC-carrying version of MRSA is a source of concern for those trying to diagnose and track drug-resistant S. aureus cases, the researchers said, in part because it may be missed by existing diagnostic tests, such as those aimed at picking up the better-characterized mecA gene.

Apparent similarities between the mecC-MRSA detected in cattle and humans hints that MRSA strains can move between the two hosts — a possibility supported by studies of a MRSA from a multi-locus sequence type called ST398. ST398, which has been found in livestock and sometimes in humans, appears to have descended from a drug-susceptible S. aureus strain once found in humans.

In an effort to better understand the epidemiology and transmission patterns for mecC-MRSA involved in the two Danish farm outbreaks, researchers used Illumina's HiSeq 2000 to perform whole-genome sequencing on isolates from each.

Isolates from the first farm came from an infected cow and an infected 53-year-old woman, both carrying mecC-MRSA. At the second farm, the isolates came from a 69-year-old woman with a mecC-MRSA infection and from three of the 10 sheep living on that farm.

At first glance, the mecC-MRSA isolates from both farms were quite similar, the team noted, sharing MLST, antibiotic resistance, and other bacterial typing or repeat patterns. But when researchers used a set of informative, core genome SNPs to classify isolates phylogenetically, they saw clear relationships amongst isolates from a given outbreak, but fewer ties between isolates from each of the farms.

"Phylogenetic analysis revealed two distinct farm-specific clusters comprising isolates from the human case and their own livestock," study authors noted, "whereas human and animal isolates from the same farm only differed by a small number of SNPs."

This within-farm clustering was consistent with MRSA swapping between animals and humans, they said, as were other variant patterns.

On the sheep farm, the analysis revealed genetic variability between the sheep isolates that pointed to ongoing MRSA circulation in the animals over time. That data also supported the notion that the woman on the sheep farm was infected with mecC-MRSA that came from the livestock.

On the other farm, investigators had access to genetic data for isolates from just one cow and one patient, which allowed them to see close genetic ties between the two isolates, but not to determine the direction of transmission.

More broadly, the new data gave researchers the opportunity to compare the host ranges and genomic features of mecC-MRSA isolates with those of MRSA strains described in the past. For instance, they found that mecC-MRSA isolates from both Danish farms were missing certain virulence factors that are present in the ST398 sequence type or in other, community-associated forms of MRSA.

"This study demonstrates that mecC-MRSA ST130 isolates are capable of transmission between animals and humans," the team wrote, "and underscores the potential of whole-genome sequencing in epidemiological investigations and source tracking of bacterial infections."