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Phylogenetic Tree of Human MRSA Isolates Indicates a Bovine Origin

NEW YORK (GenomeWeb News) – Through a phylogenetic analysis, researchers in the UK have traced the origin of human cases of community-acquired methicillin-resistant Staphyloccosus aureus to strains circulating in cows.

As the University of Edinburgh's Ross Fitzgerald and his colleagues reported in mBio today, though, those S. aureus strains didn't develop resistance to methicillin until after they crossed into people.

"Bovine strains seemed to occupy deeper parts of the phylogenetic tree — they were closer to the root than the human strains. This led us to conclude that the strains infecting humans originated in cows and that they had evolved from bovine to human host jumps," Fitzgerald, who also is a professor at the Roslin Institute, said in a statement.

While many MRSA cases are hospital-acquired infections, the US Centers for Disease Control and Prevention has warned that community-acquired cases are on the rise. Between 1999 and 2006, the agency has reported, the number of CA-MRSA cases rose more than seven fold. These cases typically infect the skin and soft tissue.

For this study, Fitzgerald and his colleagues gathered 220 samples of a specific S. aureus strain, the CC97 clone, that had been isolated from people, cows, pigs, and goats from 18 countries spanning four continents between 1956 and 2012. The CC97 clone, the researchers noted, appears to be an emerging cause of MRSA infections in people. In Denmark, where submission of MRSA to a national laboratory for genotyping is required, the number of CC97 cases has risen from two in 2007 to 22 in 2011.

The researchers performed deep whole-genome sequencing using the Illumina platform on 43 of the CC97 isolates, including 16 MRSA isolates. The core CC97 genome, they noted, contains slightly more than 2 million base pairs and 5.425 SNPs.
The researchers also sequenced the related human-specific ST28 strain as an outgroup.

Using a Bayesian approach, the investigators developed a phylogenetic tree of the CC97 strain. Overall, they noted, the isolates are grouped on the tree by the hosts they infect, and there is wide diversity among the livestock isolates, as those lines branch deeply into the tree.

The human isolates, by contrast, form shallow branches representing two clades, called A and B. Further, most of the livestock clades are basal to the human ones, and a Markov model indicates a bovine ancestor for both of the human clades, the researchers reported.

"These data indicate that CC97 isolates circulating among human populations are the result of livestock-to-human host jumps which have occurred on at least two independent occasions," the researchers write.

To determine the timing of those jumps, the researchers came up with a mutation rate for the CC97 lineage and then traced the lines back in time. The jump from cows to people for clade A, they determined, was between 1894 and 1977, and between 1938 and 1966 for clade B.

The bacteria that made those jumps, though, were unlikely to be resistant to methicillin. Of the 17 bovine isolates the researchers tested, seven were sensitive to all antimicrobials tried, while 20 of the 23 human isolates were resistant to at least one drug. All the bovine isolates were sensitive to methicillin.

Further, the earliest human isolate, collected in Denmark in 1980, was sensitive to all antibiotics tested, though all other members of its clade were resistant to multiple antibiotic classes.

Mobile elements, the researchers added, may have helped the strains adapt to their hosts. For example, a number of the livestock isolates contain a mobile genetic element encoding with the LukM/F leukotoxin or the von Willenbrand binding protein — which are ruminant-specific — and the human isolates do not have those element.

However, 19 of the 23 human isolates had a beta-toxin converting phage containing an immune evasion cluster that none of the bovine or porcine isolates had. Further, the two human CC97 clades had variations in their distributions of such IEC elements.

"It seems like these elements, such as pathogenicity islands, phages, and plasmids, are important in order for the bacterium to adapt to different host species," Fitzgerald added. "The reverse is true as well: the bovine strains have their own mobile genetic elements."

Overall, the researchers said their study indicated that livestock could be a reservoir of pathogenic bacteria that can cross the species barrier and adapt to new hosts.

"Improved biosecurity and hygiene control measures which prevent the spread of bacterial flora between livestock and human hosts may limit opportunities for successful livestock-to-human transmission," the researchers noted. "Furthermore, regular surveillance of the microbiota in livestock and humans may facilitate the early identification of emergent clones with the capacity to transmit and cause disease among human populations."