Detection of expanded-spectrum β-lactamases in Gram-negative bacteria in the 21st century

Abstract

Emerging β-lactamase-producing-bacteria (ESBL, AmpC and carbapenemases) have become a serious problem in our community due to their startling spread worldwide and their ability to cause infections which are difficult to treat. Diagnosis of these β-lactamases is of clinical and epidemiological interest. Over the past 10 years, several methods have been developed aiming to rapidly detect these emerging enzymes, thus preventing their rapid spread. In this review, we describe the range of screening and detection methods (phenotypic, molecular and other) for detecting these β-lactamases but also whole genome sequencing as a tool for detecting the genes encoding these enzymes.

Keywords:

• antibiotic resistance
• Gram-negative bacteria
• molecular detection
• phenotypic detection
• whole genome sequencing
• β-lactamases

Financial & competing interests disclosure

Charbel Al-Bayssari’s thesis was supported by the AZM Research Center for Biotechnology and its Application, Lebanese University, Lebanon, by the National Council for Scientific Research, Lebanon, and by IHU Méditerranée Infection and the French CNRS. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Key issues

• Antibiotic resistance has become a major concern due to its striking increase around the world.

• Emerging β-lactamase-producing bacteria (ESBL, AmpC and carbapenemase) cause infections which are difficult to treat.

• Detection of these β-lactamases is crucial not only for implementing optimal antimicrobial treatment, but also for preventing their spread.

• Several phenotypic and molecular-based techniques have been developed over the past decade to detect these emerging β-lactamases.

• New techniques have been shown to be very economical and reliable for detecting these enzymes, such as the MALDI-TOF Ultaflex and the CarbaNP test.

• Several techniques for high-throughput sequencing have been developed recently, allowing for research into the genetic determinants of antimicrobial resistance.

• The dramatic decline in the cost of whole genome sequencing will make this technology available in standard diagnostic laboratories, particularly with the development of bioinformatic tools such as ARG-ANNOT and ResFinder, which can detect existing antibiotic resistance genes.

• Even if whole genome sequencing becomes available in routine microbiology, it should not become a substitute for the traditional method for detecting antibiotic resistance, such as antibiotic susceptibility testing, because this technology, with its developing tools, cannot detect new determinant genes.

Notes