New Approach to Finding Antibiotic Alternatives Using Bacterial Data

Researchers have devised an approach for identifying novel antimicrobial drugs with clinical potential using bacterial databases, offering insights into finding alternatives to existing antibiotics.

The discovery, published as a Reviewed Preprint in eLife, provides a significant new technique for finding novel lysins (enzymes created by phages during infection) with antimicrobial efficacy, according to the authors.

They explain the strength of evidence for the therapeutic potential of two lysins identified during the study: PHAb10 and PHAb11. They state that the discoveries will be of broad interest to microbiologists, who will want to investigate further.

Antibiotic resistance, in which disease-causing microbes adapt to survive treatments that originally killed them, is a global public health problem. The misuse of antimicrobial agents in people, livestock and industrial agriculture is primarily responsible for the spread and building of resistance.

Lysins, which are derived from phages – viruses that infect and replicate within bacteria – have antimicrobial effects and are considered to be a promising alternative to antibiotics, due to their low risk of resistance and the unique way in which they work. However, the discovery of lysins to treat infections is hampered by a limited amount of published phage genome data.”

Li Zhang, Lead Author and PhD Candidate, National Key Laboratory, Agricultural Microbiology, Huazhong Agricultural University

Recent research on lysins has connected their antimicrobial effects to internal peptides, short chains of up to 50 amino acids with an antimicrobial peptide-like structure.

This prompted Zhang and colleagues to investigate if they might uncover novel lysins with antimicrobial activity by scanning databases of bacterial proteomes, which are the whole collection of proteins produced by the genome in bacteria rather than the genomes themselves.

The researchers employed P307, a well-documented antimicrobial peptide, as a template to search for novel antimicrobial lysins in the proteome database of the bacteria Acinetobacter baumannii.

The National Center for Biotechnology Information has made this database available. The study discovered five novel lysins with antibacterial properties: PHAb7-11. In particular, PHAb10 and PHAb11 showed the most potential in the team’s preliminary tests.

To test the antibacterial activity of the five lysins, the researchers chemically synthesized their gene-coding sequences and expressed them in Escherichia coli (E. coli) cells. They next evaluated their effectiveness against three types of bacteria: A. baumannii, P. aeruginosa, and E. coli. This indicated that the lysins had strong antibacterial action even at low doses.

The next step was to determine the antibacterial activity of PHAb10 and PHAb11 under various circumstances. Previous research has demonstrated that lysins behave differently against bacteria in the exponential and stationary life cycles.

In the stationary phase, bacterial reproduction and growth slow when resources become scarce, but in the exponential phase, bacteria expand fast when resources are abundant, and circumstances are favorable.

The scientists discovered that PHAb10 and PHAb11 had strong antibacterial action against six distinct bacterial cultures, both stationary and exponential. Importantly, these lysins worked independently of whether the bacterial cultures were resistant to standard antibiotics.

The scientists observed that PHAb10 and PHAb11 preserved considerable antibacterial activity following heat treatment at 100℃ for one hour, but PHAb7, PHAb8, and PHAb9 lost their action under similar conditions. To further understand the thermostability of PHAb10, the researchers employed X-ray crystallography to examine its crystal structure.

They observed that PHAb10 underwent a folding-refolding process during heat treatment, in which dimeric units in its structure paired off under heat stress to promote stability and returned to dimeric units when cooled.

Seven pairs of intermolecular interactions facilitate this switching and is analogous to the opening and closing of a zipper. Finally, the scientists tested PHAb10 against two mouse models of bacterial infection and discovered that it eliminated the disease safely and efficiently, demonstrating therapeutic promise.

eLife’s reviewers emphasized the need for more tests to strengthen the team's findings, such as a live/dead assay, which utilizes fluorescent dyes to distinguish between live and dead bacterial cells. This would offer further information on how successfully the lysins destroy bacteria.

Our work demonstrates that daily updated big data, such as bacterial genomes and proteomes, could be a crucial tool in the fight against antibiotic resistance. We used our screening strategy to successfully identify new antimicrobial lysins with therapeutic promise. PHAb10 and PHAb11 are highly thermostable lysins, with a broad spectrum of antimicrobial action. If future studies validate our findings, these lysins could be explored further as potential therapeutic treatments.”

Hang Yang, Study Senior Author and Professor, Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences