Abstract

Introduction

β-Lactams, due to their safety, reliable killing properties and clinical efficacy, are among the most frequently prescribed antibiotics used to treat bacterial infections. However, their utility is being threatened by the worldwide proliferation of β-lactamases (BLs) with broad hydrolytic capabilities, especially in multi-drug-resistant gram-negative bacteria. These BLs are divided into four classes based on their sequence identities¹. While a handful of BLs were known in the early 1970s, their number has ever since been growing rapidly, especially with the description in clinical isolates of novel enzymes being capable of hydrolysing carbapenems, last resort antibiotics². A representative example is the class A KPC-2 that in a few years became one of the most menacing BL currently spreading worldwide³.

Historically, the principal resource of BLs was maintained from 2001 at the Lahey Clinic (http://www.lahey.org/Studies/) by George Jacoby and Karen Bush, by assigning new enzyme numbers for a number of representative BL families. From July 2015, this resource was transferred into the Bacterial Antimicrobial Resistance Reference Gene Database (https://www.ncbi.nlm.nih.gov/bioproject/313047/) maintained at the NCBI. Other resources are the Institute Pasteur MLST Database (http://bigsdb.pasteur.fr/klebsiella/klebsiella.html), the Antibiotic Resistance Genes Database⁴, the Lactamase Engineering Database^5,6, the Metallo-β-Lactamase Engineering Database⁷, the Comprehensive Antibiotic Resistance Database⁸, the β-Lactamase Database⁹, the Comprehensive β-Lactamase Molecular Annotation Resource¹⁰. However, most of these databases are either not maintained anymore, have a very broad scope or are focused on a few BL families.

The aim of our Beta-Lactamase Database (BLDB) is to compile sequence information as well as biochemical and structural data on all the currently known BLs. This comprehensive web-based database, which is updated on a weekly basis, may provide at a glance useful insights in the structure-function relationships of BLs, allowing a better understanding of substrate specificities and key residues involved in substrate recognition and hydrolysis. Altogether, the information provided by BLDB may help to foresee the impact of future mutations on the evolution of BLs.

Implementation details

The database is hosted on a dedicated virtual server in the cloud, which allows easy adjustments and evolution of computing resources according to the needs.

The core pages are implemented in PHP on a Linux Server under the CentOS 7.2 operating system, whereas the raw data is stored as tabulated files in order to facilitate the updates.

The interactive images showing the list of BL families that are present in the BLDB are generated dynamically in SVG format from the raw data, thus ensuring an updated display at any time. The corresponding URL links are directly embedded in the SVG images.

Multiple sequence alignments are automatically generated with Clustal Omega¹¹ using the default parameters. Phylogenetic trees are processed using Phylip version 3.695 (http://evolution.genetics.washington.edu/phylip/) using Clustal Omega’s DND output files and represented as SVG images to provide the best quality and minimal file size.

The radar charts representing hydrolytic profiles are dynamically built using a modified and personalised version of the D3.js JavaScript library (https://gist.github.com/nbremer/6506614).

The BLAST interface is provided by SequenceServer¹² and the BLAST+binaries are downloaded from NCBI¹³.

Input data is downloaded from NCBI using the “Entrez Direct: E-utilities on the UNIX Command Line”¹³ and from the PDB with personalised scripts.

Structures are updated semi-automatically on a weekly basis, after each PDB update. New enzymes are added following every update of the Bacterial Antimicrobial Resistance Reference Gene Database. Constant literature survey also provides newly described BLs and synthetic mutants, as well as their hydrolytic profiles. The long-term maintenance of the BLDB is ensured by the collaboration between two academic teams with active interest and experience in the field of BL-mediated antibiotic resistance.

Database architecture

BLDB is designed around five main sections, which are strongly interconnected and gathered around the main home page (Figure 1). All pages contain (i) a header showing the overall structure of the BLDB, with links for an easy access to all sections at any moment, and (ii) a footer with acknowledgments to funding bodies that have contributed to this project and with contact details.

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Figure 1.

Global architecture of the Beta-Lactamase Database. In addition to the Home page, there are five main sections, dedicated to Enzymes (classified into the four classes A, B, C and D, and further into the three sub-classes of class B), three-dimensional Structures available in the Protein Data Bank, synthetic Mutants and hydrolytic profiles (Kinetics) described in the literature, and a graphical interface for BLAST queries.

Initial content

As of 25 April 2017, BLDB contains 2666 unique enzymes from all four classes of BLs, as well as 810 three-dimensional structures of BLs that are currently available in the Protein Data Bank (PDB)¹⁴. BLDB also contains 167 mutants and 47 hydrolytic profiles.

Conclusion

BLDB is developed and maintained by two well-established research groups that are active in the field of BL-mediated antibiotic resistance. This resource is designed to provide appropriate answers to the needs of the research and clinical communities working on antimicrobial resistance.

Supplementary Material

Funding Statement

This work was supported by the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) [grant number ANR-10-LABX-33], by the JPIAMR transnational project DesInMBL [grant number ANR-14-JAMR-0002] and by the Région Ile-de-France (DIM Malinf).

References