Article: Human commensals producing a novel antibiotic impair pathogen colonization
In a recent study by Zipperer et al., scientists discovered a new antibiotic called lugdunin that is derived from Staphylococcus lugdunensis. The peculiar and exciting part of this discovery is that Staphylococcus lugdunensis is found in human noses and would be one of the first examples of human commensal bacteria producing antibiotics (Zipperer et al. 2016). The pressure for new antibiotics is higher than ever because of the presence of antibiotic resistant bacteria such as MRSA. The scary part of MRSA is its ability to resist many different antibiotics with mechanisms to resist penicillin, methicillin, vancomycin and many more (Lowy, 2003). In an interview with Dr. Margaret Chan, (director general of the UN’s World Health Organization) she was quoted saying “Antimicrobial resistance poses a fundamental threat to human health, development and security” (NBCnews). With many health officials worrying about the prevalence and possible spread of antibiotic resistant infections, humanity needs new antibiotics that bacteria can not resist. In this study the scientists isolate, sequence and determine the effectiveness of a new novel antibiotic called lugdunin.
In the beginning of this study the scientists tested a variety of bacteria to see if any had antimicrobial activity against Staphylococcus aureus. In their testing only one bacteria, Staphylococcus lugdunensis (strain IVK28), had noticeable antimicrobial activity. To test this the group plated S. lugduensis on an agar plate surrounded by S. aureus. In this plating there was a noticeable area around the S. lugduensis colony where no S. aureus bacteria survived. To see what caused this antimicrobial activity, the scientists performed a transposon mutagenesis on the S. lugduensis and found its antimicrobial function no longer existed once mutagenesis occurred (M1 mutated strain). Analysis of the transposon insertion site found an unknown gene that coded for a non-ribosomal peptide synthetase. This gene encoded an operon that controlled the activity of multiple antibiotic biosynthesis related genes. The operon of interest named lug controlled the expression of four genes named lug A, B, C, D. To further test whether this gene lead to the antimicrobial effects of S. lugduensis the group removed the lug D domain and found that once again its microbial effects went away.
Each of these four genes code for enzymes that contain adenylation, peptidyl carrier protein, condensation, epimerization or reductase protein domains. This type of protein domain combination within enzymes is very similar to the one we studied called DEBS which used multiple domains to make a different polypeptide sequence. To study this new novel antibiotic of interest, the group used reverse-phase high performance liquid chromatography (HPLC) on IVK28 wild-type and M1 mutant cells to isolate the antimicrobial molecule of interest (lugdunin). They then used ultraviolet/mass spectroscopy to determine the composition of lugdunin. The composition of lugdunin differed between the IVK28 and M1 forms of the enzyme (this further proved that lugdunin was the antimicrobial agent that kills S. aureus). The mass spectroscopy revealed an ionized mass of 783.45858 which did not match the mass of any other known antibiotic, which meant they had discovered a new, novel antibiotic. One problem with this method though was that the bacteria did not produce enough lugdunin to study its physical characteristics and biological properties.
To solve this Zipperer et al. removed the lug R operon repressor of the lug operon and replaced it with a xylAB promoter upstream to the lug operon. The xylAB promoter was used in tandem with a gene that coded for a xylose-sensitive repressor (XylR) of the xylAB promoter. In the presence of xylose, the repressor comes off the xylAB promoter and leads to the activation of the lug operon. This allowed the scientists to produce a viable amount of lugdunin to be further studied. First the group put the lugdunin products into through NMR, electrospray ionization high-resolution mass spectrometry and Marfey’s analysis. The electrospray ionization helps to determine the sequence of atoms in the molecule by measuring small bits of the molecule with mass spectroscopy. In tandem with this, Markey’s analysis and NMR were performed which help to show the 3-D structure of the molecule.
Proposed molecular structure of lugdunin (provided by Zipperer et al. 2016)
The one interesting part of this molecule’s structure is the presence of a thiazolidine group, which according to Zipperer et al. is not usually present in macrocyclic molecules. To make sure the group isolated the correct antimicrobial molecule of interest, the proposed lugdunin was tested on bacteria and was able to effectively kill them proving they isolated the correct molecule.
The scientists also discussed a few unique characteristics of the protein domains that make up the enzymes produced from genes lug A, B, C and D. In the second adenylation site of lug A, it has a specificity that is usually seen in binding threonine but in this case, it binds to tryptophan. This leads to the potential for a new form of specificity in adenylation protein domains. The other surprising finding came in gene lug C where one adenylation site activates three valines in a row. This use of an adenylation domain has only been discovered recently and not used in many other macromolecule mechanisms. These unique findings lead to the possibility that this mechanism is not derived from any known mechanisms.
The next focus of this study was to see the effectiveness of this drug against multiple pathogens. These bacteria included vancomycin resistant Enterococcus faecalis, MRSA and Streptococcus pneumoniae with an MIC ranging from 1.5 to 12 ug/ml. MIC stands for minimum inhibitory concentration and it is defined as the minimum concentration of the drug that can effectively prevent growth of targeted bacteria in human hosts. The MIC range mentioned before is very promising because it has a low concentration needed to start killing bacteria. The one very promising finding from this study showed that MRSA strains could be fully killed at levels 10x its MIC (1.5 ug/ml) without harming human host neutrophils or erythrocytes. The other benefit of this new antibiotic is that no where within the study did the scientists see evidence of resistance appearing even after 30 days of continuous exposure. This means bacteria targeted by lugdunin will have a very hard time developing resistance to this drug even after long term exposure. The exact mechanism of action for lugdunin was undetermined, but bacterial cells exposed to lugdunin stopped producing DNA, RNA, protein and cell-wall substrates. This most likely means it targets an enzyme or substrate within a prominent metabolic pathway.
To further test the effectiveness of the drug in live hosts, mice skin was injured using adhesive tape to take off multiple layers of skin. These wounds were then infected with S. aureus and mice were treated with lugdunin 24, 30 or 42 hours after the infection. In almost all cases except two (these two cases were most likely due to mice licking off the lugdunin), the S. aureus infection had a significant decrease in bacteria and was almost fully gone.
The last major portion of this study tested whether S. lugduensis could out compete S. aureus and if those findings reflected similarly in humans. IVK28 wild-type S. lugduensis and mutant Δlug D (missing the lug D gene and therefore cannot produce lugdunin) were grown on agar plates with S. aureus. All forms of IVK28 wild-type were able to out grow S. aureus even when inoculum had 10 times more S. aureus than S. lugduensis. On the other hand, the mutant Δlug D form was not able to outgrow S. aureus no matter what concentration it competed against. To test whether these findings happened in humans too the group acquired 187 nasal swabs from hospitalized patients colonized by S. lugdunensis, S. aureus or both. Using a chi-squared test the group found that when both S. lugdunensis and S. aureus existed in the same nasal passage, S. aureus levels were 5.9 times lower than people with just S. aureus in their nasal passages.
This article has many ground-breaking implications for future work. It has presented a new novel antibiotic that is extremely hard for bacteria to develop antibiotics to. It is one of the first antibiotics discovered that originate from bacteria that are commensal with humans. It is the first time that humanity has seen a multicyclic antibiotic that contains a thiazolidine group. Lastly, its second adenylation domain from lug A has shown a unique specificity for tryptophan. Overall, this study paves the way for new research in many different areas of study.
This connects to what we learned in class very recently. A couple days ago we discussed the mechanisms by which penicillin and vancomycin work and how certain forms of S. aureus resist them. In class we discussed the need for newer and better ways to fight certain bacterial infections and this article presents a perfect example of a new way to fight these infections.