The highly dynamic nature of bacterial heteroresistance impairs its clinical detection

Abstract

Many bacterial species and antibiotic classes exhibit heteroresistance, a phenomenon in which a susceptible bacterial isolate harbors a resistant subpopulation that can grow in the presence of an antibiotic and cause treatment failure. The resistant phenotype is often unstable and without antibiotic selection it reverts back to susceptibility. Here we studied the dynamics by which these resistant subpopulations are enriched in the presence of antibiotic and recede back to their baseline frequency in the absence of selection. An increasing understanding of this instability will allow more effective diagnostics and treatment of infections caused by heteroresistant bacteria. We show for clinical isolates of Escherichia coli and Salmonella enterica that different antibiotics at levels below the MIC of the susceptible main population can cause rapid enrichment of resistant subpopulations with increased copy number of genes that cause resistance. Modelling and growth rate measurements of bacteria with increased gene copy number in cultures and by microscopy of single-cells in a microfluidic chip show that the fitness cost of gene amplifications and their intrinsic instability drives their rapid loss in the absence of selection. Using a common antibiotic susceptibility test, we demonstrate that this test strongly underestimates the occurrence of heteroresistance in clinical isolates.

Characteristics of Helicobacter pylori Heteroresistance in Gastric Biopsies and Its Clinical Relevance

“…In China, the primary antibiotic resistance rates of H. pylori were 37.00% for CLA and 34.21% for LEV (Zhong et al, 2021). If heteroresistance cases are considered, the resistance rate for many antibiotics would be higher (Pereira et al, 2021;Wang et al, 2021).…”

Antibiotic Heteroresistance in Klebsiella pneumoniae

“…Due to phenotypic and genetic instability, heteroresistance is difficult to detect and study [ 16 , 18 , 19 ]. Rapid molecular and biochemical methods used to identify specific antibiotic resistance, such as real-time PCR or VITEK 2, are insufficient to detect heteroresistance due to the lack of a genetic marker or low sensitivity.…”

“…Heteroresistance may lead to antibiotic treatment failure due to the misclassification of heteroresistant isolates as susceptible strains. Consequently, inappropriate therapies fail to eradicate infections and facilitate the selection of resistant mutants [ 19 , 20 , 43 , 44 ]. It has been demonstrated that different antibiotics at levels below the MIC of the susceptible clinical isolates of E. coli and Salmonella enterica can cause the enrichment of resistant subpopulations with an increased copy number of resistance genes [ 19 ].…”

“…Consequently, inappropriate therapies fail to eradicate infections and facilitate the selection of resistant mutants [ 19 , 20 , 43 , 44 ]. It has been demonstrated that different antibiotics at levels below the MIC of the susceptible clinical isolates of E. coli and Salmonella enterica can cause the enrichment of resistant subpopulations with an increased copy number of resistance genes [ 19 ]. Band et al reported that cumulative exposure of carbapenem-resistant Enterobacterales to β-lactams led to the development of heteroresistant isolates, which were gradually displaced by resistant cells [ 45 ].…”

You will know by its tail: a method for quantification of heterogeneity of bacterial populations using single cell MIC profiling

“…Heterogeneity of an infecting bacterial population is an important consideration for the identification of an effective antibiotic treatment 1,2 . Some of the most common infectious diseases can be caused by more than one co-colonizing bacterial pathogen, incl.…”