Illustration of interconnected pathways showing the transmission of antibiotic resistance.

Decoding Superbugs: How Whole Genome Sequencing Can Help Us Win the Fight

Beau Callahan in Health & Wellness July 2025 • 4 min read.

"A Swiss study explores how advanced genetic analysis can pinpoint the sources of antibiotic-resistant bacteria, paving the way for better infection control strategies."

The rise of antibiotic-resistant bacteria, often dubbed “superbugs,” is one of the most pressing threats to global health. Once easily treatable infections are becoming increasingly difficult, and sometimes impossible, to cure. Extended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae are a particularly concerning group of these superbugs, capable of resisting many common antibiotics.

Initially associated with hospital-acquired infections, ESBL-producing bacteria are now increasingly found in community settings. This shift suggests that these superbugs are no longer just a hospital problem but are spreading through various pathways, including food, water, and international travel. Understanding how these bacteria transmit is crucial to developing effective prevention and control strategies.

A groundbreaking study conducted in Switzerland is using whole genome sequencing (WGS) to track the transmission of ESBL-producing Enterobacteriaceae. This advanced technique allows researchers to analyze the complete genetic makeup of bacteria, identifying the sources and pathways of transmission with unprecedented accuracy. By mapping the spread of these superbugs, the study aims to inform targeted interventions that can help curb the growing threat of antibiotic resistance.

What Makes ESBL-Producing Bacteria So Dangerous?

Illustration of interconnected pathways showing the transmission of antibiotic resistance.

ESBL-producing Enterobacteriaceae are a family of bacteria that have developed resistance to many beta-lactam antibiotics, which are among the most widely used drugs for treating bacterial infections. This resistance is due to enzymes called extended-spectrum beta-lactamases (ESBLs), which the bacteria produce to break down these antibiotics, rendering them ineffective.

The danger of ESBL-producing bacteria lies in their ability to cause infections that are difficult to treat. Common infections, such as urinary tract infections, bloodstream infections, and pneumonia, can become life-threatening when caused by these resistant bacteria. This often leads to longer hospital stays, increased healthcare costs, and higher mortality rates.

Widespread Resistance: ESBLs make bacteria resistant to multiple antibiotics.
Difficult Treatment: Infections are harder and more expensive to treat.
Increased Mortality: Untreatable infections can lead to higher death rates.

Adding to the complexity, ESBL genes are often found on plasmids, which are mobile genetic elements that can be easily transferred between bacteria. This horizontal gene transfer allows resistance to spread rapidly, even between different species of bacteria. Understanding the movement of these plasmids is key to controlling the epidemic.

Looking Ahead: How Can We Fight Back?

The Swiss study highlights the importance of a multi-faceted approach to combating antibiotic resistance. By using whole genome sequencing to track the transmission of ESBL-producing bacteria, researchers can identify key sources and pathways of spread. This knowledge can then be used to inform targeted interventions, such as improved infection control practices in hospitals, enhanced surveillance of food and water sources, and promotion of responsible antibiotic use.

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This article is based on research published under:

DOI-LINK: 10.1136/bmjopen-2018-021823, Alternate LINK

Title: Transmission Of Esbl-Producing Enterobacteriaceae And Their Mobile Genetic Elements—Identification Of Sources By Whole Genome Sequencing: Study Protocol For An Observational Study In Switzerland

Subject: General Medicine

Journal: BMJ Open

Publisher: BMJ

Authors: Tanja Stadler, Dominik Meinel, Lisandra Aguilar-Bultet, Jana S Huisman, Ruth Schindler, Adrian Egli, Helena M B Seth-Smith, Lucas Eichenberger, Peter Brodmann, Philipp Hübner, Claudia Bagutti, Sarah Tschudin-Sutter

Published: 2018-02-01

Everything You Need To Know

What are Extended-Spectrum Beta-Lactamases (ESBLs), and why are ESBL-producing Enterobacteriaceae considered 'superbugs'?

Extended-spectrum beta-lactamases (ESBLs) are enzymes produced by certain bacteria, particularly Enterobacteriaceae, that render many beta-lactam antibiotics ineffective. These antibiotics are commonly used to treat bacterial infections. ESBL-producing Enterobacteriaceae are called 'superbugs' because their resistance to multiple antibiotics makes infections difficult to treat, leading to longer hospital stays, increased healthcare costs, and higher mortality rates. The danger of ESBL-producing bacteria also lies in their ability to cause common infections such as urinary tract infections and pneumonia, which can become life-threatening.

How does whole genome sequencing (WGS) aid in tracking and controlling the spread of ESBL-producing Enterobacteriaceae?

Whole genome sequencing (WGS) is an advanced technique that analyzes the complete genetic makeup of bacteria. By using WGS on ESBL-producing Enterobacteriaceae, researchers can pinpoint the sources and pathways of transmission with high accuracy. This allows for the identification of key sources and spread pathways. With this knowledge, targeted interventions, such as improved infection control in hospitals and enhanced food and water surveillance, can be implemented. Essentially, WGS provides a detailed map of the superbug's spread, enabling more effective control strategies.

Why is the increasing presence of ESBL-producing bacteria in community settings a major concern?

The increasing presence of ESBL-producing bacteria in community settings is concerning because it indicates that these superbugs are no longer confined to hospitals. This shift implies that ESBL-producing Enterobacteriaceae are spreading through various pathways like food, water, and international travel. As a result, the risk of infection from these antibiotic-resistant bacteria extends beyond healthcare facilities, making it more difficult to control their spread and protect the general population. The movement of ESBL genes on plasmids between bacteria is a factor. Understanding all transmission routes is crucial for developing effective prevention strategies.

What role do plasmids play in the spread of antibiotic resistance among bacteria, particularly ESBL-producing Enterobacteriaceae?

Plasmids are mobile genetic elements that can be easily transferred between bacteria through a process called horizontal gene transfer. ESBL genes are often located on these plasmids, which allows resistance to spread rapidly, even between different species of bacteria. This horizontal gene transfer contributes significantly to the widespread antibiotic resistance observed in ESBL-producing Enterobacteriaceae, making infections harder to treat and control. Understanding the movement of these plasmids is key to controlling the epidemic, as it highlights how quickly resistance can spread within and between bacterial populations.

Besides tracking transmission, what other strategies are essential in combating the rise of antibiotic-resistant bacteria like ESBL-producing Enterobacteriaceae?

Combating antibiotic-resistant bacteria requires a multi-faceted approach. While tracking the transmission of ESBL-producing Enterobacteriaceae using whole genome sequencing is important, other essential strategies include improved infection control practices in hospitals to prevent the spread within healthcare settings, enhanced surveillance of food and water sources to identify and eliminate potential sources of contamination, and the promotion of responsible antibiotic use to reduce the selective pressure that drives the development of resistance. Addressing these factors collectively is necessary to curb the growing threat of antibiotic resistance effectively.