Breakthrough Test Enables Targeted Antibiotic Therapy for Various Enterobacter Species

Some of their representatives demonstrate high resistance to commonly-used antibiotics, as a result of which the reserve antibiotic colistin is used as the last resort therapy option. In order to avoid unnecessary reliance on colistin and reduce the risk of resistance, bacteria are tested for sensitivity or resistance to colistin before commencing treatment. However, commonly used tests for Enterobacter are unreliable. Scientists have resolved this problem by developing a simple, sensitive and robust test for the genus Enterobacter, which now enables targeted antibiotic therapy for the different Enterobacter species.

The microbiological tests currently used for colistin resistance and other antibiotic resistances do not enable accurate conclusions about the spread of resistance in various Enterobacter species. This can be partly attributed to the imprecise taxonomic classification of clinical Enterobacter isolates as well as high error rate in determining resistance. In a comprehensive study with broad participation within the German Center for Infection Research (DZIF, Brunswick, Germany), a team of scientists has now achieved a breakthrough and clarified the relationships between the numerous Enterobacter species as well as optimized resistance testing.

For their study, the researchers analyzed Enterobacter isolates collected at German university hospitals over a period of three years. Using genome-based taxonomic studies, they found Enterobacter xiangfangensis was the most frequently occurring species in German hospitals: An analysis of a data pool of more than 3246 isolates worldwide - representing a collection from over 20 years – found that this species accounted for 68.7% of all Enterobacter detected. The determination of antibiotic resistance profiles using phenotypic assays recommended by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) provided mixed results in terms of colistin resistance.

“It turned out that many isolates were either not or barely resistant in these tests, even though the bacteria carried all the genes necessary for the expression of colistin resistance,” explained Dr. Swapnil Doijad, the study's first author. The result raised questions for which the researchers obtained an initial answer by further investigating the isolates in which resistance was not clearly detectable using mass spectrometry.

“Depending on the particular Enterobacter species, we detected low levels of modified lipid A, the anchor structure of lipopolysaccharides (LPS) - a crucial component of the bacterial membrane and required for colistin resistance - even from bacteria grown in colistin-free medium,” commented Dr. Nicolas Gisch, the study’s co-first author. “These modifications of lipid A appear to be dependent on the bacterial species and are inherent, meaning their expression is embedded in a more complex regulation and not alone triggered by colistin."

“The result suggests that there is species-dependent variation in the heteroresistance seen in Enterobacter: In routine test systems, the bacteria are sometimes resistant, sometimes not,” explained Dr. Can Imirzalioglu, the study’s co-author.

Using more sophisticated methods, the researchers were able to elucidate the phenomenon of heteroresistance in the genus Enterobacter. "Our analyses revealed that these bacteria have a sensor on their surface that responds to the pH value, i.e., the acidity in the environment, and regulates accordingly, either up or down, the genes required for the expression of colistin resistance," explained Prof. Trinad Chakraborty, senior author of the study.

Genetic variations and interactions in this sensing pathway for environmental pH led to species-dependent differences regarding the extent of colistin resistance in the various Enterobacter species in conventional test systems. On the basis of their findings, the researchers have developed a simple new assay that eliminates heteroresistance effects and enables unambiguous and reliable determination of the true levels of colistin resistance for any isolate. The assay can prevent therapeutic failures when recommending the antibiotic, thereby paving the way for a targeted and economical treatment of Enterobacter species with the reserve antibiotic across the world.

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