INTRODUCTION
Staphylococcus infections pose a serious health threat to humans, companion animals, and livestock (
1–3).
Staphylococcus aureus is a Gram-positive bacterium that can asymptomatically colonize human skin and the anterior nares, but it is also responsible for mild to severe skin and soft tissue infections and life-threatening endocarditis, pneumonia, and sepsis. The Centers for Disease Control and Prevention estimated that in 2014 there were 72,000 invasive methicillin-resistant
S. aureus (MRSA) infections in the United States, which resulted in 9,000 deaths (
4). Although the prevalence of MRSA carriage in companion animals is low (approximately 0 to 4%) (
5,
6) and infections are rare (
7), other
Staphylococcus species are common commensals and pathogens in veterinary medicine (
8).
S. schleiferi and
S. pseudintermedius are the leading causes of canine and feline skin and ear infections (
9);
S. hyicus causes high-morbidity skin infections in pigs (
10) and osteomyelitis in birds (
11), while
S. aureus,
S. agnetis, and
S. chromogenes cause mastitis in cattle and are associated with reduced milk quality (
5,
12,
13).
The emergence of drug-resistant
Staphylococcus is a global problem (
14–21). Drugs such as erythromycin and cephalexin are commonly used to treat infections in both humans and animals, leading to concern that as resistance to shared antibiotics becomes more widespread, zoonotic transmission of either drug-resistant
Staphylococcus or horizontal transfer of resistance genes (
22) may render these treatments ineffective for both humans and animals. Despite the major animal health burden posed by a range of
Staphylococcus species, much of our knowledge of
Staphylococcus biology stems from studies on only a handful species that are important causes of human disease. To address this knowledge gap, we have used whole-genome sequencing of
S. schleiferi and comparative genomics to identify novel drug targets to treat staphylococcal infections in companion animals.
DISCUSSION
The majority of studies examining the metabolism and biology of Staphylococcus have focused on S. aureus. While S. aureus is an important pathogen in humans and animals, there are many other Staphylococcus species of great importance to veterinary medicine. Early biochemical experiments conducted primarily with S. aureus helped to establish a dogma that Staphylococcus uses the mevalonate pathway to synthesize essential isoprenoids. Our data challenge this dogma and show that isoprenoid biosynthesis differs between Staphylococcus species. Given that mammals use the same pathway, it has been assumed that targeting isoprenoid biosynthesis is not a viable strategy to treat staphylococcal bacterial infections in humans or other animals. These data point to inhibitors of the nonmevalonate pathway, such as fosmidomycin, as potential antimicrobials to treat certain Staphylococcus infections in animals, in particular in companion animals where species utilizing the nonmevalonate pathway are a major cause of skin and ear infections.
The main target of fosmidomycin is the Dxr protein, but there is evidence that it can also inhibit a downstream enzyme, IspD,
in vitro and
in vivo (
39). As is the case with any antibiotic, resistance to fosmidomycin could develop in
Staphylococcus, either by blocking entry or accumulation of the drug in the bacterium or via mutations in the Dxr binding site, both of which have been reported in other pathogens (
40–42). Despite these potential problems, the current clinical literature suggests that fosmidomycin could be a promising drug to treat infections caused by
Staphylococcus species that use the nonmevalonate pathway. Fosmidomycin is extremely well-tolerated and exhibits low toxicity in mammals (
32).
Plasmodium falciparum, the cause of malaria, also synthesizes isoprenoids via the nonmevalonate pathway, and fosmidomycin was shown to be effective in killing the parasite in culture and achieved cure rates of 85 to 100% in clinical trials when administered alone or in combination with clindamycin (
43,
44).
Most Gram-negative bacteria synthesize isoprenoids via the nonmevalonate pathway. However, across different bacterial phyla, there are examples of species that use the mevalonate pathway, including
Streptococcus,
Lactobacillus,
Myxococcus, and
Borrelia. In addition, some
Pseudomonas species, including
Pseudomonas mevalonii, are known to use hydroxymethylglutaryl-CoA reductase (the third enzyme of the mevalonate pathway) for degradative functions (
45,
46). Only
Listeria monocytogenes and a few species of
Streptomyces are known to possess both pathways, but in both organisms the nonmevalonate pathway plays the essential role in primary metabolism (
37), while the mevalonate pathway is dispensable (
47). Based on our data,
Staphylococcus constitutes a unique example of a bacterial genus whose species utilize different isoprenoid biosynthesis pathways. Our phylogenetic analysis results (
Fig. 3) are consistent with previous evolutionary studies that have suggested that the nonmevalonate pathway is the ancestral pathway in bacteria and the mevalonate pathway was acquired later through lateral gene transfer (
34); this is further supported by our finding that deep-branching taxa (such as the
S. sciuri and
S. intermedius groups) use the nonmevalonate pathway, while the more recently branched taxa (including the
S. aureus and
S. epidermidis groups) use the mevalonate pathway.
An outstanding question is why
Staphylococcus species evolved to use different pathways for isoprenoid synthesis and whether pathway usage influences host range selection. There is abundant literature on virulence factors influencing host range (
48), but less is known about the role of bacterial metabolism. Interestingly, among the
Staphylococcus species we analyzed, mevalonate pathway usage was associated with species that are found across human, nonhuman primate, and animal hosts. In contrast, nonmevalonate pathway usage was only associated with an animal host range. One possible explanation for this observation may lie in the secondary metabolites produced by these pathways and their interaction with the host immune system: 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMB-PP) is an intermediate of the nonmevalonate pathway and a potent activator of Vγ2/Vδ2 (also called Vγ9/Vδ2) T cells (
49). HMB-PP has 1,000 times greater immune stimulatory activity than IPP, the analogous intermediate produced by the mevalonate pathway (
49,
50). Vγ2Vδ2 cells make up 1 to 5% of peripheral T cells but expand to >50% and rapidly traffic to barrier surfaces in response to pathogens that produce HMB-PP (
51,
52), yet these cells are only found in humans and nonhuman primates. This could lead to a scenario in which mevalonate usage (i.e., by
S. aureus) results in a relatively weak Vγ2Vδ2 signal, thereby allowing colonization of human and nonhuman primate skin. Moreover, spread to animals would not be impeded, because these hosts completely lack the Vγ2Vδ2-bearing cells. In contrast, nonmevalonate pathway usage (i.e., by
S. schleiferi and
S. pseudintermedius) would result in production of the potent Vγ2Vδ2 ligand HMB-PP, but this would only be of consequence if the bacteria were on human or nonhuman primate hosts. Thus, one plausible hypothesis is that nonmevalonate pathway usage by
Staphylococcus may contribute to an animal host range restriction, but this remains to be tested. Interestingly,
S. schleiferi and
S. pseudintermedius were first identified in human infections and are occasionally reported to cause serious human disease, but such cases are primarily observed in infants, the elderly, immunocompromised patients, or as a consequence of medical complications (
53–57), perhaps lowering the immunological barrier to transmission.
ACKNOWLEDGMENTS
We thank Meghan Davis, Stephen Cole, Kathleen O’Shea, and Kristen Constantine for assistance with bacterial growth and helpful discussions.
A.M.M. purified genomic DNA, assembled the genome sequences, analyzed sequence and subsystems data, performed comparative genomics, performed all bacterial growth and antibiotic assays, and wrote the manuscript. C.L.C. collected S. schleiferi clinical samples. S.C.R. isolated the Staphylococcus clinical isolates, performed all phenotypic testing of the strains, and archived them in a collection held at −80°C. D.P.B. analyzed subsystems data and wrote the manuscript. A.M.M., C.L.C., D.O.M., S.C.L., and D.P.B. conceived of the study, edited the manuscript, gave approval for publication, and agreed to be accountable for the work.