Fosfomycin Resistance in Gram-Negative Bacteria

Fosfomycin, a century-old broad-spectrum antibiotic, inhibits the essential enzyme MurA in the first step of peptidoglycan biosynthesis. Its revival against multidrug-resistant Gram-negative pathogens has been driven by its unique mechanism of action and favourable safety profile. However, clinical efficacy is increasingly compromised by both intrinsic and acquired resistance mechanisms. Intrinsic resistance largely reflects chromosomally encoded fosA genes, which produce glutathione S-transferases that inactivate fosfomycin. Acquired resistance arises through mutations in transport systems (notably GlpT and UhpT), which reduce fosfomycin uptake, or via horizontal transfer of plasmid-borne inactivating enzymes such as FosA3, FosA8 and related variants. High-risk clones, including Escherichia coli ST131 and Klebsiella pneumoniae ST11, have adopted these determinants, facilitating rapid geographic dissemination. Moreover, limitations in reliable susceptibility testing have obscured true prevalence rates, complicating therapeutic decision-making. Understanding the interplay between enzymatic inactivation, reduced permeability and clonal spread is critical to preserve fosfomycin as a valuable therapeutic option, especially for urinary tract and systemic infections caused by extensively drug-resistant organisms.

Research from Nature Portfolio

Advanced functional genomics approaches have been applied to dissect resistance pathways in situ. One study employed high-throughput CRISPR-based deep mutational scanning of three envelope-associated proteins in Escherichia coli—including MurA—to map the fitness landscape of resistance-conferring mutations. Thousands of single-amino-acid variants were evaluated in their native genomic context, revealing that MurA exhibits low mutational tolerance and thus represents a robust target with limited capacity for resistance emergence. The same platform enabled prioritisation of lead inhibitors against other envelope enzymes by ranking the ease with which resistance-conferring mutations arose. These insights underscore how genomic-scale mutation profiling can guide the next generation of antimicrobials and adjuvant strategies to forestall fosfomycin resistance.

Fosfomycin Resistance in Gram-Negative Bacteria publication trend

The graph below shows the total number of articles in fosfomycin resistance in gram-negative bacteria across all publications each year (not limited to Nature Index journals).

Technical terms

FosA enzymes: Glutathione S-transferases that catalyse conjugation of glutathione to fosfomycin, inactivating the drug.

MurA: UDP-N-acetylglucosamine enolpyruvyl transferase, the essential enzyme targeted by fosfomycin in peptidoglycan synthesis.

Deep mutational scanning: A high-throughput method to generate and assess thousands of protein variants for functional and resistance-related properties.

GlpT and UhpT transporters: Membrane proteins responsible for fosfomycin uptake; loss or mutation reduces intracellular drug levels.

Inc plasmid groups: Classification of plasmids by incompatibility type, relevant to tracking horizontal gene transfer of resistance determinants.

References

1. Deep mutational scanning of essential bacterial proteins can guide antibiotic development. Nature Communications (2023).
2. FosA8-producing E. coli ST131: clinical cases in Italy, February 2023. Eurosurveillance (2024).
3. Fosfomycin resistance mechanisms in Enterobacterales: an increasing threat. Frontiers in Cellular and Infection Microbiology (2023).
4. Mobile fosfomycin resistance genes in Enterobacteriaceae—An increasing threat. MicrobiologyOpen (2020).
5. The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates. Journal of Clinical Microbiology (2019).