Mechanisms and clinical relevance of bacterial heteroresistance

Emergence and spread of ST5 methicillin-resistant Staphylococcus aureus with accessory gene regulator dysfunction: genomic insights and antibiotic resistance

The globally disseminated Staphylococcus aureus ST5 clone poses a major public health threat due to its multidrug resistance and virulence. Here, we identified an agr-dysfunctional (agrA-I238K) ST5 MRSA clone that has spread across East and Southeast Asia, with recent increases in China since its emergence in the 1970s. Comparative genomic analyses identified distinct single-nucleotide polymorphisms and mobile genetic elements linked to enhanced resistance and virulence. This clone exhibits resistance to seven antimicrobial classes, including third-generation tetracyclines and fusidic acid, and shares phenotypic and genetic similarities with the vancomycin-intermediate S. aureus Mu50 strain, including reduced susceptibility to vancomycin, teicoplanin, and daptomycin. The agrA-I238K mutation attenuates hemolytic activity, increases biofilm formation, and reduces daptomycin susceptibility, suggesting a key role in the clone's success. Our results demonstrate the important role of agrA-I238K mutation in the widespread distribution of agr-dysfunctional MRSA and highlight the importance of genomic surveillance in tracking the spread of agr-dysfunctional ST5 MRSA.

Overview of heteroresistance to multiple antibiotics in clinical Klebsiella pneumoniae isolates and combination therapeutic strategies

Objectives

To assess the prevalence of heteroresistance in 201 clinical isolates of Klebsiella pneumoniae to 16 clinically significant antibiotics. Furthermore, to investigate the interaction effects of combination antibiotic therapies for heteroresistant isolates.

Methods

Isolates were pre-screened for growth of resistant subpopulations at resistant breakpoint concentrations for each isolate/antibiotic combination. Any strain containing colony growth at the resistant breakpoint was selected as a candidate heteroresistant strain, and population analysis profiling (PAP) tested for confirmation of HR phenotype. Dual PAP and time-kill assay were conducted to assess the efficacy of antibiotic combinations in suppressing resistant subpopulations.

Results

Ninety-seven percent of isolates were shown to be heteroresistant to at least one antibiotic. Heteroresistance to at least two antibiotics was exhibited by 72.1% of strains. The prevalence of heteroresistance varied across antibiotics, with proportions ranging from 1.5% for imipenem to 85.1% for polymyxin B. The case of Kp486 was heteroresistant to amikacin, ceftazidime/avibactam, tigecycline and polymyxin B. The resistant subpopulations displayed distinct PAP curves and differences in growth and killing kinetics, indicating independent mechanisms for heteroresistance to each of the four antibiotics. Dual PAP experiments showed enhanced killing effects for combinations of antibiotics. In time-kill experiments, pairwise combinations of four drugs achieved a reduction of 3 to 6 logs within 6 h, preventing regrowth of resistant subpopulations. However, combinations with ampicillin did not enhance the activity of tigecycline, polymyxin B or ceftazidime/avibactam.

Conclusions

Heteroresistance in clinical K. pneumoniae is common and can complicate treatment outcomes. The effects of combination antibiotic therapy depend on the heteroresistance of bacteria to both drugs.

Evaluating the predictive power of combined gene expression dynamics from single cells on antibiotic survival

Heteroresistance and persistence are examples of mechanisms that can allow otherwise drug-susceptible bacteria to survive and resume growth after antibiotic exposure. These temporary forms of antibiotic tolerance can be caused by the upregulation of stress response genes or a decrease in cell growth rate. However, it is not clear how the expression of multiple genes contributes to tolerance phenotypes. Using fluorescent reporters for stress-related genes, we conducted real-time measurements of expression prior to, during, and after antibiotic exposure. We first identified relationships between growth rate and reporter levels based on auto- and cross-correlation analysis, revealing consistent patterns where changes in growth rate were anticorrelated with fluorescence following a delay. We then used pairs of stress gene reporters and time-lapse fluorescence microscopy to measure the growth rate and reporter levels in cells that survived or died following antibiotic exposure. Using these data, we asked whether combined information about reporter expression and growth rate could improve our ability to predict whether a cell would survive or die following antibiotic exposure. We developed a Bayesian inference model to predict how the combination of dual reporter expression levels and growth rate impacts ciprofloxacin survival in Escherichia coli. We found clear evidence of the impact of growth rate and gadX promoter activity on survival. Unexpectedly, our results also revealed examples where additional information from multiple genes decreased prediction accuracy, highlighting an important and underappreciated effect that can occur when integrating data from multiple simultaneous measurements.IMPORTANCETransient increases in bacterial antibiotic tolerance can result in treatment failure despite an infection initially presenting as susceptible, presenting a significant challenge in antibiotic therapy. This phenomenon can also provide a window of opportunity for bacteria to acquire permanent genetic resistance mutations. Although understanding the underlying mechanisms of these antibiotic tolerance phenotypes is crucial for developing effective approaches to treatment, current approaches for studying these transient phenotypes have limitations. Here, we use fluorescent reporters to monitor the expression of genes involved in stress response over time, aiming to link expression with antibiotic survival outcomes. Our results reveal a counterintuitive finding: monitoring multiple gene reporters does not necessarily improve our ability to predict antibiotic survival outcomes compared to single gene reporters. This result emphasizes the need for a deeper mechanistic understanding of the relationship between stress response gene expression and antibiotic tolerance.

Lineage-dependent variations in single-cell antibiotic susceptibility reveal the selective inheritance of phenotypic resistance in bacteria

Genetically identical bacterial cells often exhibit heterogeneous responses to antibiotics - some survive, others die. Here, we show that this heterogeneity propagates across generations to give rise to phenotypic resistance. Using real-time single-cell tracking, we exposed Escherichia coli to the β-lactam cefsulodin at its clinical breakpoint concentration and analyzed cell fate within genealogical trees statistically. Cell survival was strongly correlated among family members, driving the selective enrichment of robust lineages within an otherwise susceptible population. Our genealogical population model identified heritable phenotypic resistance as a key factor underlying this enrichment, which was validated experimentally. Comparing enrichment dynamics between the wild-type and a tolC knock-out strain, deficient in multidrug efflux, uncovered nuanced changes that increased the intergenerational memory of phenotypic resistance. Our findings provide evidence for heritable phenotypic resistance and demonstrate how its propagation through cell-to-cell heterogeneity enables the survival of minority cells within isogenic populations.

Antibiotic-recalcitrant Salmonella during infection

Antibiotic-recalcitrant infections, defined as the prolonged carriage of pathogenic bacteria even in the presence of antibiotics, are often caused by bacteria that are genetically susceptible to the drug. These recalcitrant bacteria fail to proliferate in the presence of antibiotics but remain viable such that they may recolonize their niche following antibiotic withdrawal. Significant progress has been made in our understanding of antibiotic-recalcitrant Salmonella, which are thought to be the source of infection relapse. In recent years, it has been shown that recalcitrant bacteria manipulate host immune defences and could directly contribute to the spread of antimicrobial resistance. In this Review, we provide an overview of what is currently known about the antibiotic recalcitrance of Salmonella during infection and highlight knowledge gaps requiring additional research in the future.

Colistin antibacterial activity, clinical effectiveness, and mechanisms of intrinsic and acquired resistance

Following a period of disuse owing to the emergence of multidrug-resistant Gram-negative bacteria, colistin has regained global attention as an antibiotic of last resort. The resurgence in its utilization has led to a concurrent increase in acquired resistance, presenting a significant challenge in clinical treatment. Predominantly, resistance mechanisms involve alterations in the lipid A component of the lipopolysaccharide (LPS) structure. These alterations are facilitated by the addition of cationic phosphoethanolamine (pEtN) or 4-amino-L-arabinose, often driven by the upregulation of two-component regulatory systems such as PmrAB and PhoPQ. Structural components of bacteria, such as capsules and efflux pumps, can also play an important role in the resistance mechanism. In addition to these biochemical modifications, structural components of bacteria like capsules and efflux pumps also play crucial roles in mediating resistance. Another significant mechanism is the acquisition of the plasmid-mediated mobilized colistin resistance (mcr) gene, which poses a global health threat due to its ability to transfer between different bacterial genera. Contemporary strategies to combat colistin resistance include the development and use of novel drugs and inhibitors. To devise effective interventions, it is imperative to first elucidate the precise mechanisms of colistin resistance and determine the roles of various contributing factors.

A high-throughput anaerobic method for viability assays

Viability testing for anaerobes is a time-consuming and expensive process, posing challenges for research and public health settings. Here, we present a rapid, economical, and reliable method for testing anaerobe viability using the Geometric Viability Assay (GVA) with Clostridium perfringens as our model, a bacterium known for causing toxin-related systemic and enteric diseases. This method is efficient and cost-effective, requiring one pipette tip per sample, and is compatible with the economical anaerobic jar system. The results align with traditional plate-based assays in terms of colony-forming unit (CFU) measurements. Anaerobic GVA has low technical bias and a dynamic range extending over 5 orders of magnitude. In addition, our method determined the bactericidal activity of antibiotics in a dose-dependent manner, when an antibiotic sensitivity testing (AST) was performed with a panel of four antibiotics (ampicillin, gentamicin, meropenem, and tetracycline). Furthermore, the minimum concentrations for complete bactericidal activity (MBC) of four clinical isolates were determined and the MBC concentration for tetracycline was up to 8× higher than the concentration for complete growth inhibition (MIC). Additional tests involving Clostridium bifermentans and Clostridium sporogenes demonstrated the generality of our method for other anaerobic species. Beyond viability testing, the GVA measured spore concentrations of various Clostridium perfringens isolates, showing consistency with classical plating methods. Our study confirms that the anaerobic GVA is a valuable tool for rapid, accurate viability screening in anaerobic settings and is compatible with routine assays, such as AST and spore screening. This method enhances the scalability and utility of anaerobic viability-based assays.

IMPORTANCE

The routine assessment for the viability of anaerobes is based on bacterial plating, but so far, it has been limited in throughput by the long preparation steps and the tedious anaerobic culturing. Thus, comparatively little is known about the susceptibility pattern, and the sporulation of anaerobes because of the absence of the proper method. Here, we show GVA can quantify the anaerobic Clostridiums colonies accurately by utilizing an anaerobic jar to measure viable cells and spores in high throughput with minimal volumes of reagents and at a comparable time to the traditional viability testing practice. Furthermore, this method enabled high-throughput detection of the bactericidal activity of the antibiotics against anaerobes and allowed for the quantification of hetero-tolerant/resistant subpopulation, which was previously unattainable. Our approach is rapid and easy to use, making it ideal for various applications where high-throughput capabilities can drive innovation, including drug-microbe interactions, host-microbe interactions, and microbe-microbe interactions.

Prevalence, misclassification, and clinical consequences of the heteroresistant phenotype in Escherichia coli bloodstream infections in patients in Uppsala, Sweden: a retrospective cohort study

BACKGROUND

Antibiotic heteroresistance is a common bacterial phenotype characterised by the presence of small resistant subpopulations within a susceptible population. During antibiotic exposure, these resistant subpopulations can be enriched and potentially lead to treatment failure. In this study, we examined the prevalence, misclassification, and clinical effect of heteroresistance in Escherichia coli bloodstream infections for the clinically important antibiotics cefotaxime, gentamicin, and piperacillin-tazobactam.

METHODS

We conducted a retrospective cohort analysis of patients (n=255) admitted to in-patient care and treated for E coli bloodstream infections within the Uppsala region in Sweden between Jan 1, 2014, and Dec 31, 2015. Patient inclusion criteria were admission to hospital on suspicion of infection, starting systemic antibiotics at the time of admission, positive blood cultures for the growth of E coli upon admission, and residency in the Uppsala health-care region at the time of admission. Exclusion criteria were growth of an additional pathogen than E coli in blood cultures taken at admission or previous inclusion of the patients in the study for another bloodstream infection. Antibiotic susceptibility of preserved blood culture isolates of E coli was assessed for cefotaxime, gentamicin, and piperacillin-tazobactam by disk diffusion and breakpoint crossing heteroresistance (BCHR) was identified using population analysis profiling. The clinical outcome parameters were obtained from patient records. The primary outcome variable was length of hospital stay due to the E coli bloodstream infection, defined as the time between admission and discharge from inpatient care as noted on the physician's notes. Secondary outcomes were time to fever resolution, admission to intermediary care unit or intensive care unit during time in hospital, switching or adding another intravenous antibiotic treatment, re-admission to hospital within 30 days of original admission, recurrent E coli infection within 30 days of admission to hospital, and all-cause mortality within 90 days of admission.

FINDINGS

A total of 255 participants with a corresponding E coli isolate (out of 500 screened for eligibility) met the inclusion criteria, with 135 female patients and 120 male patients. One (<1%) of 255 strains was BCHR for cefotaxime, 109 (43%) of 255 strains were BCHR for gentamicin, and 22 (9%) of 255 strains were BCHR for piperacillin-tazobactam. Clinical susceptibility testing misclassified 120 (96%) of 125 heteroresistant bacterial strains as susceptible. The BCHR phenotypes had no correlation to length of hospital stay due to the E coli bloodstream infection. However, patients with piperacillin-tazobactam BCHR strains who received piperacillin-tazobactam had 3·1 times higher odds for admittance to the intermediate care unit (95% CI 1·1-9·6, p=0·041) than the remainder of the cohort, excluding those treated with gentamicin. Similarly, those infected with gentamicin BCHR who received gentamicin showed higher odds for admittance to the intensive care unit (5·6 [1·1-42·0, p=0·043]) and mortality (7·1 [1·2-49·2, p=0·030]) than patients treated with gentamicin who were infected with non-gentamicin BCHR E coli.

INTERPRETATION

In a cohort of patients with E coli bloodstream infections, heteroresistance is common and frequently misidentified in routine clinical testing. Several negative effects on patient outcomes are associated with heteroresistant strains.

FUNDING

Wallenberg Foundation, Swedish Research Council, and US National Institutes Of Health.

De novo evolution of antibiotic resistance to Oct-TriA1

The rise of antimicrobial resistance as a global health concern has led to a strong interest in compounds able to inhibit the growth of bacteria without detectable levels of resistance evolution. A number of these compounds have been reported in recent years, including the tridecaptins, a small family of lipopeptides typified by the synthetic analogue octyl-tridecaptin A1. Hypothesizing that prior reports of negligible resistance evolution have been due in part to limitations in the laboratory evolution systems used, we have attempted to select for resistant mutants using a soft agar gradient evolution (SAGE) system developed by our lab. Following optimization of the media conditions by incorporation of the anti-synaeresis agent xanthan gum into the agar matrix, we successfully evolved high-level resistance to both octyl-tridecaptin A1 as well as the challenging lipopeptide antibiotic polymyxin B. Decreased tridecaptin susceptibility was linked to mutations in outer membrane proteins ompC, lptD and mlaA, with the effect of these genes confirmed through a mix of allelic replacement and knockout studies. Overall, this work demonstrates the robust evolutionary potential of bacteria, even in the face of challenging antimicrobial agents.

Single-Bacterium Diagnosis via Terahertz Near-Field Dielectric Nanoimaging

Single-bacterium diagnostic methods with unprecedented precision and rapid turnaround times are promising tools for facilitating the transition from empirical treatment to personalized anti-infection treatment. Terahertz (THz) radiation, a cutting-edge technology for identifying pathogens, enables the label-free and non-destructive detection of intermolecular vibrational modes and bacterial dielectric properties. However, this individual dielectric property-based detection and the mismatched spatial resolution are limited for the single-bacterium identification of various species of pathogens. Here, we demonstrate a single-bacterium THz dielectric nanoimaging (STDN) strategy by customized THz scattering-type scanning near-field optical microscopy. The THz nanoimages of bacteria are explained and confirmed by theoretical modeling and near-field measurement. By synchronously tracking the bacterial intrinsic dielectric property and extrinsic morphology, the strategy achieved 99.3% and 91.6% accuracy in species identification and antibiotic susceptibility testing with the trained classifier within 2 hours. This proof-of-concept STDN strategy may propel precise bacterial infection management and help to counteract antibiotic resistance.

IS26 carrying blaKPC-2 mediates carbapenem resistance heterogeneity in extensively drug-resistant Klebsiella pneumoniae isolated from clinical sites

BACKGROUND

Due to the widespread and irrational use of antibiotics, the emergence and prevalence of carbapenem-resistant Klebsiella pneumoniae (K. pneumoniae) have become a major challenge in controlling bacterial infections in hospitals. The blaKPC-2 gene located on mobile genetic elements has further complicated the control of resistant bacteria transmission.

RESULTS

In this study, K. pneumoniae strains were isolated from blood cultures of patients. Using the Kirby-Bauer disk diffusion method, we found carbapenem resistance heterogeneity. The resistant subpopulation KPTA-R1 and the sensitive subpopulation KPTA-S1 were purified. Whole-genome sequencing revealed that the blaKPC-2 gene in KPTA-R1 was located on an IncFII plasmid (pKPC-R), within a composite transposon (PCTs) formed by two direct repeats of IS26 elements. The structure was identified as IS26-RecA-ISKpn27-blaKPC-2-ISKpn6-IS26. However, in KPTA-S1, a similar plasmid, pAR-S, lacked this segment. Sequence comparison analysis indicates that the deletion of this blaKPC-2 encoding sequence in this IncFII plasmid is associated with transposition activity mediated by IS26. Multi-sequence comparison of the plasmids showed that the IS26 transposon facilitated the sequence polymorphism of these plasmids.

CONCLUSION

This study reveals the key role of IS26-mediated transposition activity, through homologous recombination, in the emergence of carbapenem resistance heterogeneity in clinical K. pneumoniae strains carrying blaKPC-2. IS26 is able to promote the evolution of resistance in the IncFII plasmid, and through copy-in cointegration or targeted conservative cointegration may result in the acquisition or loss of antibiotic resistance, which may affect clinical care and pose a public health risk.

A duplex one-step recombinase aided PCR assay for the rapid and sensitive detection of the isoniazid resistance genes katG and inhA in Mycobacterium tuberculosis

Objectives

Drug resistance in tuberculosis seriously affects the eradication of tuberculosis, and isoniazid resistance is the second most commonly observed drug resistance in patients with tuberculosis. Timely and accurate detection of isoniazid resistance is critical to the treatment of tuberculosis.

Methods

A duplex one-step recombinase-aided PCR (DO-RAP) assay was developed for the rapid and sensitive detection of the katG Ser315Thr and inhA-15 (C-T) mutations in Mycobacterium tuberculosis, which are the most common isoniazid-resistant mutations. Quantitative recombinant plasmids were used to evaluate the sensitivity of DO-RAP, and 91 Mycobacterium tuberculosis strains with different genotypes, as well as 5 common respiratory tract bacteria, were used to evaluate the specificity of DO-RAP. A total of 78 sputum specimens were simultaneously detected using DO-RAP, quantitative PCR (qPCR) and sanger sequencing of nested PCR products. Sanger sequencing results were used as the standard to verify the clinical performance of DO-RAP.

Results

The reaction time of DO-RAP was less than 1 h. The sensitivity of DO-RAP was 2 copies/reaction, which was 10 times higher than qPCR. The sensitivity of DO-RAP for detecting heterogenous resistance was 5%. There was no cross-reactivity between the isoniazid wild-type gene, drug-resistant mutant genes, and other common respiratory tract bacteria. Compared with Sanger sequencing, the sensitivity, specificity, PPV and NPV of DO-RAP were all 100%. There were 7 specimens with gray zone or negative qPCR results but positive DO-RAP test results.

Conclusion

The DO-RAP can be adopted in ordinary qPCR equipment for the rapid, highly sensitive and specific detection of the isoniazid resistance genes of Mycobacterium tuberculosis.

Proteostasis modulates gene dosage evolution in antibiotic-resistant bacteria

Evolution of gene expression frequently drives antibiotic resistance in bacteria. We had previously (Patel and Matange, eLife, 2021) shown that, in Escherichia coli, mutations at the mgrB locus were beneficial under trimethoprim exposure and led to overexpression of dihydrofolate reductase (DHFR), encoded by the folA gene. Here, we show that DHFR levels are further enhanced by spontaneous duplication of a genomic segment encompassing folA and spanning hundreds of kilobases. This duplication was rare in wild-type E. coli. However, its frequency was elevated in a lon-knockout strain, altering the mutational landscape early during trimethoprim adaptation. We then exploit this system to investigate the relationship between trimethoprim pressure and folA copy number. During long-term evolution, folA duplications were frequently reversed. Reversal was slower under antibiotic pressure, first requiring the acquisition of point mutations in DHFR or its promoter. Unexpectedly, despite resistance-conferring point mutations, some populations under high trimethoprim pressure maintained folA duplication to compensate for low abundance DHFR mutants. We find that evolution of gene dosage depends on expression demand, which is generated by antibiotic and exacerbated by proteolysis of drug-resistant mutants of DHFR. We propose a novel role for proteostasis as a determinant of copy number evolution in antibiotic-resistant bacteria.

Mechanisms of mepA Overexpression and Membrane Potential Reduction Leading to Ciprofloxacin Heteroresistance in a Staphylococcus aureus Isolate

Heteroresistance has seriously affected the evaluation of antibiotic efficacy against pathogenic bacteria, causing misjudgment of antibiotics' sensitivity in clinical therapy, leading to treatment failure, and posing a serious threat to current medical health. However, the mechanism of Staphylococcus aureus heteroresistance to ciprofloxacin remains unclear. In this study, heteroresistance to ciprofloxacin in S. aureus strain 529 was confirmed by antimicrobial susceptibility testing and population analysis profiling (PAP), with the resistance of subclonal 529_HR based on MIC being 8-fold that of the original bacteria. A 7-day serial MIC evaluation and growth curves demonstrate that their phenotype was stable, with 529_HR growing more slowly than 529, but reaching a plateau in a similar proportion. WGS analysis showed that there were 11 nonsynonymous mutations and one deletion gene between the two bacteria, but none of these SNPs were directly associated with ciprofloxacin resistance. Transcriptome data analysis showed that the expression of membrane potential related genes (qoxA, qoxB, qoxC, qoxD, mprF) was downregulated, and the expression of multidrug resistance efflux pump gene mepA was upregulated. The combination of ciprofloxacin and limonene restored the 529_HR MIC from 1 mg/L to 0.125 mg/L. Measurement of the membrane potential found that 529_HR had a lower potential, which may enable it to withstand the ciprofloxacin-induced decrease in membrane potential. In summary, we demonstrated that upregulation of mepA gene expression and a reduction in membrane potential are the main heteroresistance mechanisms of S. aureus to ciprofloxacin. Additionally, limonene may be a potentially effective agent to inhibit ciprofloxacin heteroresistance phenotypes.

Clinical characteristics, molecular epidemiology and mechanisms of colistin heteroresistance in Enterobacter cloacae complex

Introduction

Colistin has emerged as the last resort for treating multidrug-resistant Enterobacter cloacae complex (ECC) infections. The primary purposes of this study were to demonstrate the presence of colistin heteroresistance in ECC and to further investigate their clinical characteristics, molecular epidemiology and mechanisms.

Methods

Population analysis profiles (PAP) were performed to confirm the heteroresistance phenotype. Average nucleotide identity (ANI) was determined to classify ECC species. Phylogenetic analysis based on core genome single nucleotide polymorphisms (cg-SNPs), multilocus sequence typing (MLST) and core genome MLST (cg-MLST). Risk factors and clinical outcomes of infections were analyzed through a retrospective case-control study. Potential mechanisms of colistin heteroresistance were evaluated using polymerase chain reaction (PCR), efflux pump inhibition assays and reverse transcription quantitative PCR (RT-qPCR).

Results

A high proportion (24.4%) of the non-resistant strains were colistin-heteroresistant isolates. Among the several ECC species, Enterobacter kobei had the largest percentage (29.4%) of colistin-heteroresistant isolates, followed by Enterobacter hormaechei (20.5%) and Enterobacter bugandensis (20.0%). Notably, only one strain (0.8%; 1/132) of Enterobacter hormaechei was fully resistant to colistin. Different ECC species showed varying heteroresistance levels: Enterobacter roggenkampii, Enterobacter kobei, Enterobacter asburiae and Enterobacter bugandensis displayed high heteroresistance levels  (MIC ≥ 128 mg/L). 75% of all ST116 and ST56 strains were heteroresistant to colistin. The infection of ST116 and ST56 strains as well as exposure to cephalosporin antibiotics were independent risk factors for colistin-heteroresistant ECC infections. Mechanistic analysis revealed that heteroresistance strongly correlated with the overexpression of arnA, regulated by the PhoPQ two-component system (TCS). Notably, mgrB had minimal impact. AcrAB-TolC efflux pump genes showed unsynchronized expression; High acrB expression was strongly associated with colistin heteroresistance, while acrA and tolC were not.

Discussion

Colistin heteroresistance showed species-dependent variations in levels and prevalence rates. The colistin-heteroresistant mechanisms were complex, involving coordinated regulation of multiple genes. These results highlighted the need for tailored antimicrobial stewardship. In addition, the development of direct, reliable and rapid clinical methods for detecting heteroresistance is essential for improving infection management and prevention.

Rational design of peptides to overcome drug resistance by metabolic regulation

Chemotherapy is widely used clinically, however, its efficacy is often compromised by the development of drug resistance, which arises from prolonged administration of drugs or other stimuli. One of the driven causes of drug resistance in tumors or bacterial infections is metabolic reprogramming, which alters mitochondrial metabolism, disrupts metabolic pathways and causes ion imbalance. Bioactive peptide materials, due to their biocompatibility, diverse bioactivities, customizable sequences, and ease of modification, have shown promise in overcoming drug resistance. This review provides an in-depth analysis of metabolic reprogramming and associated microenvironmental changes that contribute to drug resistance in common tumors and bacterial infections, suggesting potential therapeutic targets. Additionally, we explore peptide-based materials for regulating metabolism and their potential synergic effect with other therapies, highlighting the mechanisms by which these peptides reverse drug resistance. Finally, we discuss future perspectives and the clinical challenges in peptide-based treatments, aiming to offer insights for overcoming drug-resistant diseases.

Quantitative analysis of relationship between mutation rate and speed of adaptation under antibiotic exposure in Escherichia coli

Mutations are the ultimate source of biological evolution that creates genetic variation in populations. Mutations can create new advantageous traits but can also potentially interfere with pre-existing organismal functions. Therefore, organisms may have evolved mutation rates to appropriate levels to maintain or improve their fitness. In this study, we aimed to experimentally quantify the relationship between the mutation rate and evolution of antibiotic resistance. We conducted an evolution experiment using 12 Escherichia coli mutator strains with increased mutation rates and five antibiotics. Our results demonstrated that the rate of adaptation generally increased with higher mutation rates, except in a single mutator strain with the highest mutation rate, which exhibited a significant decline in evolutionary speed. To further elucidate these findings, we developed a simple population dynamics model that successfully recapitulated the observed dependence of adaptation speed on mutation rate. These findings provide important insights into the evolution of mutation rate accompanied by the evolution.

The implications of mutations in multiple genes associated with ethambutol resistance among multidrug-resistant tuberculosis isolates from China

OBJECTIVES

To assess the mutation effects of ethambutol (EMB) resistance-associated genes, including embCAB operon, ubiA, embR, and aftA, on the EMB resistance levels among multidrug-resistant tuberculosis (MDR-TB) isolates from China.

METHODS

A total of 159 MDR-TB from China had their EMB MICs quantified, and the sequences of the four ethambutol resistance-associated regions were analyzed. A multivariate regression model was established to evaluate the effects of mutations on EMB resistance.

RESULTS

Our results showed that overall 95.6% (109/114 isolates) of EMB-resistant isolates harbored at least one mutation within the regions associated with EMB resistance. Most mutations were in embB, particularly in the embB300-500, and the embC-embA intergenic regions. Mutations in other genes were seldom seen and mainly occurred along with mutations in the embB or the embC-embA among the EMB-resistant isolates. DNA sequencing of the embB300-500 and the embC-embA was the most effective approach for detecting EMB resistance, with an accuracy of 91.2%. Nevertheless, some EMB-susceptible isolates still had a single mutation in the gene related to EMB resistance. Moreover, there was a significant correlation between EMB high-level resistance and multiple mutations.

CONCLUSION

Distinct individual mutations, as well as multiple concurrent mutations, within EMB resistance-associated genes, contributed to variable levels of EMB resistance. These results have broadened our understanding of the molecular characteristics of EMB resistance in China.

Machine learning detection of heteroresistance in Escherichia coli

BACKGROUND

Heteroresistance (HR) is a significant type of antibiotic resistance observed for several bacterial species and antibiotic classes where a susceptible main population contains small subpopulations of resistant cells. Mathematical models, animal experiments and clinical studies associate HR with treatment failure. Currently used susceptibility tests do not detect heteroresistance reliably, which can result in misclassification of heteroresistant isolates as susceptible which might lead to treatment failure. Here we examined if whole genome sequence (WGS) data and machine learning (ML) can be used to detect bacterial HR.

METHODS

We classified 467 Escherichia coli clinical isolates as HR or non-HR to the often used β-lactam/inhibitor combination piperacillin-tazobactam using pre-screening and Population Analysis Profiling tests. We sequenced the isolates, assembled the whole genomes and created a set of predictors based on current knowledge of HR mechanisms. Then we trained several machine learning models on 80% of this data set aiming to detect HR isolates. We compared performance of the best ML models on the remaining 20% of the data set with a baseline model based solely on the presence of β-lactamase genes. Furthermore, we sequenced the resistant sub-populations in order to analyse the genetic mechanisms underlying HR.

FINDINGS

The best ML model achieved 100% sensitivity and 84.6% specificity, outperforming the baseline model. The strongest predictors of HR were the total number of β-lactamase genes, β-lactamase gene variants and presence of IS elements flanking them. Genetic analysis of HR strains confirmed that HR is caused by an increased copy number of resistance genes via gene amplification or plasmid copy number increase. This aligns with the ML model's findings, reinforcing the hypothesis that this mechanism underlies HR in Gram-negative bacteria.

INTERPRETATION

We demonstrate that a combination of WGS and ML can identify HR in bacteria with perfect sensitivity and high specificity. This improved detection would allow for better-informed treatment decisions and potentially reduce the occurrence of treatment failures associated with HR.

FUNDING

Funding provided to DIA from the Swedish Research Council (2021-02091) and NIH (1U19AI158080-01).

Heteroresistance in Enterobacter cloacae complex caused by variation in transient gene amplification events

Heteroresistance (HR) in bacteria describes a subpopulational phenomenon of antibiotic resistant cells of a generally susceptible population. Here, we investigated the molecular mechanisms and phenotypic characteristics underlying HR to ceftazidime (CAZ) in a clinical Enterobacter cloacae complex strain (ECC). We identified a plasmid-borne gene duplication-amplification (GDA) event of a region harbouring an ampC gene encoding a β-lactamase blaDHA-1 as the key determinant of HR. Individual colonies exhibited variations in the copy number of the genes resulting in resistance level variation which correlated with growth onset (lag times) and growth rates in the presence of CAZ. GDA copy number heterogeneity occurred within single resistant colonies, demonstrating heterogeneity of GDA on the single-cell level. The interdependence between GDA, lag time and antibiotic treatment and the strong plasticity underlying HR underlines the high risk for misdetection of antimicrobial HR and subsequent treatment failure.

Emergence of population heterogeneity in Klebsiella pneumoniae with a blaOXA-232-harboring plasmid: carbapenem resistance, virulence, and fitness

BACKGROUND

This study aimed to investigate the population heterogeneity on carbapenem susceptibility in Klebsiella pneumoniae strains that acquired a blaOXA-232-bearing ColE-type plasmid.

METHODS

A blaOXA-232-bearing plasmid was electroporated into two carbapenem-susceptible K. pneumoniae strains. High- and low-carbapenem-resistant subpopulations were identified and isolated using patch plating. The strains were subsequently subcultured in antibiotic-free media, yielding two distinct populations: a stable, high-level carbapenem-resistant strains and a heterogeneous strains. Antibiotic susceptibility tests, time-killing assays, and population profiles were conducted, along with a competition assay was performed and the growth curve analysis. To assess virulence, we performed human serum resistance and Galleria mellonella infection assays, and measured the expression of virulence genes using qRT-PCR. Additionally, whole genome sequencing was carried out for further anaysis.

RESULTS

Introduction of pOXA-232 into carbapenem-susceptible K. pneumoniae strains resulted in two isogenic transformants with distinct resistance profiles: an unstable, high-level carbapenem-resistant (HCR), and highly virulent subpopulation; and a stable, low-level carbapenem-resistant (LCR), and low-virulence subpopulation. Whole genome and expression analyses revealed dysfunctionality of ompK36 in HCR subpopulations. Subculturing of HCR led to the re-emergence of heterogeneous populations with variations in carbapenem resistance and an additional compensatory mutation of 9,000 bp deletion in the genome. Thus, stable HCR strains featuring both mutations in ompK36 and compensatory mutations developed.

CONCLUSION

This study demonstrated that underlying heterogeneity can promote the emergence of stable, high-level antibiotic resistance, even with the introduction of a plasmid carrying a low-level antibiotic resistance gene, such as blaOXA-232. This highlights the critical need to closely monitor bacterial population dynamics.

Helicobacter pylori and gastric cancer: current insights and nanoparticle-based interventions

Background: H. pylori is recognized as one of the main causes of gastric cancer, and this type of cancer is considered as one of the leading diseases causing cancer deaths all over the world. Knowledge on the interactions between H. pylori and gastric carcinogenesis is important for designing preventive measures. Objective: the objective of this review is to summarize the available literature on H. pylori and gastric cancer, specifically regarding the molecular mechanisms, nanoparticle-based therapy and clinical developments. Methods: the databases including PubMed, Google Scholar and web of science were searched as well as papers from 2010 to 2024 were considered for review. Research literature on H. pylori, gastric cancer, nanoparticles, nanomedicine, and therapeutic interventions was summarized for current findings and possible treatments. Results: the presence of H. pylori in gastric mucosa causes chronic inflammation and several molecular alterations such as DNA alteration, epigenetic changes and activation of oncogenic signaling pathways which causes gastric carcinogenesis. Conventional antibiotic treatments have some issues because of the constantly rising levels of antibiotic resistance. Lipid based nanoformulations, polymeric and metallic nanoparticles have been delivered in treatment of H. pylori to improve drug delivery and alter immunological responses. Conclusion: nanoparticle based interventions have been widely explored as drug delivery systems by improving the treatment strategies against H. pylori induced gastric cancer. Further studies and clinical trials are required to bring these findings into a clinical setting in order to possibly alter the management of H. pylori related gastric malignancies.

Insight into the Mechanisms and Clinical Relevance of Antifungal Heteroresistance

Antifungal resistance poses a critical global health threat, particularly in immuno-compromised patients. Beyond the traditional resistance mechanisms rooted in heritable and stable mutations, a distinct phenomenon known as heteroresistance has been identified, wherein a minority of resistant fungal cells coexist within a predominantly susceptible population. Heteroresistance may be induced by pharmacological factors or non-pharmacological agents. The reversible nature of it presents significant clinical challenges, as it can lead to undetected resistance during standard susceptibility testing. As heteroresistance allows fungal pathogens to survive antifungal treatment, this adaptive strategy often leads to treatment failure and recurring infection. Though extensively studied in bacteria, limited research has explored its occurrence in fungi. This review summarizes the current findings on antifungal heteroresistance mechanisms, highlighting the clinical implications of fungal heteroresistance and the pressing need for deeper mechanism insights. We aim to bring together the latest research advances in the field of antifungal heteroresistance, summarizing in detail its known characteristics, inducing factors, molecular mechanisms, and clinical significance, and describing the similarities and differences between heteroresistance, tolerance and persistence. Further research is needed to understand this phenomenon and develop more effective antifungal therapies to combat fungal infections.

Resilience of tigecycline heteroresistance phenotype in Acinetobacter baumannii

BACKGROUND

Heteroresistance, frequently observed in diverse bacterial species, imposes clinical challenges. For this study, we investigated the stability and resilience of tigecycline heteroresistance in Acinetobacter baumannii.

METHODS

Four tigecycline-heteroresistant (HR) A. baumannii strains and resistant populations (RPs) obtained from them were subjected to laboratory evolution assays for 30 days in antibiotic-free media. The heteroresistance phenotype was determined using a population analysis. Bacterial growth curves and in vitro competitiveness were determined to investigate the fitness cost of heteroresistance. Tigecycline efficacy was evaluated using an in vitro time-killing assay. Genetic mutations were identified using whole genome sequencing, and expression of genes in the two-component systems was also evaluated.

RESULTS

Tigecycline heteroresistance was preserved even in antibiotic-free media, and tigecycline-RPs reverted to heteroresistance during serial culture without tigecycline pressure. The tigecycline-RPs showed a higher fitness cost than their respective HR strains, and the HR strains exhibited a survival advantage upon tigecycline treatment. Although the AdeABC efflux pump was overexpressed in the tigecycline-RPs, it was down-regulated in the HR strains.

CONCLUSIONS

Our data indicate that tigecycline heteroresistance is a highly resilient phenotype in A. baumannii that gives a high fitness advantage to bacteria in terms of competitiveness and response to antibiotic pressure.

Pooled Antibiotic Susceptibility Testing for Polymicrobial UTI Performs Within CLSI Validation Standards

BACKGROUND/OBJECTIVES

Urinary tract infections (UTIs) pose an increasing risk of antimicrobial resistance, and novel diagnostic tests have been developed to address the limitations of standard urine culture in these cases. It is important that these novel tests be validated for agreement and error rates against the standard antibiotic susceptibility testing (AST) methods.

METHODS

Polymicrobial (≥two non-fastidious microorganisms) consecutive clinical urine specimens submitted for UTI diagnostic testing were included in this analysis. Specimens were tested with Pooled Antibiotic Susceptibility Testing (P-AST) and with broth microdilution/disk diffusion (BMD/DD) in parallel. Performance characteristics, such as essential agreement (EA%), very major errors (VMEs), and major errors (MEs), were assessed using Clinical and Laboratory Standards Institute (CLSI) standards. Specimens with P-AST-resistant and BMD/DD consensus-sensitive results were assessed for heteroresistance. Real-world clinical sample data were used to assess associations between increasing organism counts and average "sensitive" antibiotic count per sample.

RESULTS

The essential agreement between P-AST and standard isolate AST was ≥90%, VMEs were <2.0%, and MEs were <3.0%, meeting the CLSI guidelines for AST verification and validation studies. When heteroresistance was accounted for, overall VMEs and MEs were both <1.5%. The presence of additional non-fastidious organisms dropped the number of average "sensitive" antibiotics from 9.8 with one organism to 2.5 with five or more organisms. The presence of fastidious organisms did not have any meaningful impact.

CONCLUSIONS

P-AST, a component of the Guidance® UTI assay (Pathnostics, Irvine, CA, USA), performed within CLSI standards for AST in polymicrobial UTI diagnostic urine specimens.

The Possibility of Ceftolozane/Tazobactam-Resistant Pseudomonas aeruginosa Emergence After Two Days of Antibiotic Therapy: A Case Report

Although antibiotic use is known to induce antimicrobial resistance, the duration of exposure necessary for resistance development remains uncertain. In this case, a patient was initially treated with tazobactam/piperacillin (TAZ/PIPC) for bacterial pneumonia. When the treatment proved ineffective, the regimen was switched to tazobactam/ceftolozane (TAZ/CTLZ) after confirming that the Pseudomonas aeruginosa isolated at admission was susceptible to TAZ/CTLZ. Although the patient's symptoms initially improved, pneumonia exacerbation occurred 10 days after the initiation of TAZ/CTLZ. Drug susceptibility testing in P. aeruginosa isolated on the second day of TAZ/CTLZ treatment revealed resistance to the antibiotics. Genetic analysis using the polymerase chain reaction (PCR)-based open reading frame typing method demonstrated that the P. aeruginosa strains isolated before and after TAZ/CTLZ treatment were genetically identical. This case highlights the possibility of TAZ/CTLZ-resistant P. aeruginosa emerging after only two days of antibiotic exposure.

High prevalence of polymyxin-heteroresistant carbapenem-resistant Klebsiella pneumoniae and its within-host evolution to resistance among critically ill scenarios

PURPOSE

We aimed to explore the prevalence and within-host evolution of resistance in polymyxin-heteroresistant carbapenem-resistant Klebsiella pneumoniae (PHR-CRKP) in critically ill patients.

METHODS

We performed an epidemiological analysis of consecutive patients with PHR-CRKP from clinical cases. Our study investigated the within-host resistance evolution and its clinical significance during polymyxin exposure. Furthermore, we explored the mechanisms underlying the dynamic evolution of polymyxin resistance at both subpopulation and genetic levels, involved population analysis profile test, time-killing assays, competition experiments, and sanger sequencing. Additionally, comparative genomic analysis was performed on 713 carbapenemase-producing K. pneumoniae strains.

RESULTS

We enrolled 109 consecutive patients, and PHR-CRKP was found in 69.7% of patients without previous polymyxin exposure. 38.1% of PHR-CRKP isolates exhibited polymyxin resistance and led to therapeutic failure in critically ill scenarios. An increased frequency of resistant subpopulations was detected during PHR-CRKP evolution, with rapid regrowth of resistant subpopulations under high polymyxin concentrations, and a fitness cost in an antibiotic-free environment. Mechanistic analysis revealed that diverse mgrB insertions and pmrB hypermutations contributed to the dynamic changes in polymyxin susceptibility in dominant resistant subpopulations during PHR evolution, which were validated by comparative genomic analysis. Several deleterious mutations (e.g. pmrBLeu82Arg, pmrBSer85Arg) were firstly detected during PHR-CRKP evolution. Indeed, specific sequence types of K. pneumoniae demonstrated unique deletions and deleterious mutations.

CONCLUSIONS

Our study emphasizes the high prevalence of pre-existing heteroresistance in CRKP, which can lead to polymyxin resistance and fatal outcomes. Hence, it is essential to continuously monitor and observe the treatment response to polymyxins in appropriate critically ill scenarios.

Epidemiology, mechanisms, and clinical impact of bacterial heteroresistance

Bacterial heteroresistance, a phenomenon where subpopulations within a bacterial strain exhibit significantly reduced antibiotic susceptibility compared to the main population, poses a major challenge in managing infectious diseases. It is considered an intermediate stage in the evolution of bacteria towards full resistance. Heteroresistant strains often have a minimal inhibitory concentration (MIC) that appears sensitive, making detection and differentiation in clinical settings difficult. As a result, the impact on clinical outcomes is challenging to fully understand, as it often remains "hidden". In recent years, heteroresistance has received increasing attention. However, it is still poorly understood and underappreciated. We provide an overview of the epidemiology, mechanisms, and clinical impact of heteroresistance. This review underscores the critical importance of understanding and addressing bacterial heteroresistance in the ongoing fight against antibiotic resistance and infectious diseases.

Complete genome sequence of Franconibacter pulveris SL.qac10, a putative QAC-resistant isolate from an indoor built environment

Franconibacter pulveris SL.qac10 was isolated at a school in Hong Kong from swabs of flooring frequently cleaned with a quaternary ammonium compound (QAC)-based disinfectant. Its complete genome, a single chromosome and circular plasmid totalling 4.88 Mbp (56.50% G + C), was established by hybrid assembly.

Deep Amplicon Sequencing Reveals Culture-dependent Clonal Selection of Mycobacterium tuberculosis in Clinical Samples

The commonly-used drug susceptibility testing (DST) relies on bacterial culture and faces shortcomings such as long turnaround time and clonal/subclonal selection biases. Here, we developed a targeted deep amplicon sequencing (DAS) method directly applied to clinical specimens. In this DAS panel, we examined 941 drug-resistant mutations (DRMs) associated with 20 anti-tuberculosis drugs with only 4 pg of initial DNA input, and reduced the clinical testing time from 20 days to 2 days. A prospective study was conducted using 115 clinical specimens, predominantly positive for the Xpert®  Mycobacterium tuberculosis/rifampicin (Xpert MTB/RIF) assay, to evaluate DRM detection. DAS was performed on culture-free specimens, while culture-dependent isolates were used for phenotypic DST, DAS, and whole-genome sequencing (WGS). For in silico molecular DST, our result based on DAS panel revealed the similar accuracy to three published reports based on WGS. For 82 isolates, application of DAS using the resistance-determining mutation method showed better accuracy (93.03% vs. 92.16%), sensitivity (96.10% vs. 95.02%), and specificity (91.33% vs. 90.62%) than WGS using the Mykrobe software. Compared to culture-dependent WGS, culture-free DAS provides a full picture of sequence variation at the population level, exhibiting in detail the gain-and-loss variants caused by bacterial culture. Our study performs a systematic verification of the advantages of DAS in clinical applications and comprehensively illustrates the discrepancies in Mycobacterium tuberculosis before and after culture.

The impact of phenotypic heterogeneity on fungal pathogenicity and drug resistance

Phenotypic heterogeneity in genetically clonal populations facilitates cellular adaptation to adverse environmental conditions while enabling a return to the basal physiological state. It also plays a crucial role in pathogenicity and the acquisition of drug resistance in unicellular organisms and cancer cells, yet the exact contributing factors remain elusive. In this review, we outline the current state of understanding concerning the contribution of phenotypic heterogeneity to fungal pathogenesis and antifungal drug resistance.

Incidence of colistin heteroresistance among carbapenem-resistant Acinetobacter baumannii clinical isolates in a tertiary care hospital in Pakistan

PURPOSE

The emergence of colistin-resistant and heteroresistant strains of carbapenem-resistant Acinetobacter baumannii (CRAB) complicates treatment and exacerbates the global health crisis of drug-resistant bacteria. This study aims to investigate the incidence and clinical implications of colistin heteroresistance in carbapenem-resistant Acinetobacter baumannii isolates from a tertiary hospital in Pakistan.

MATERIALS AND METHODS

A total of 130 CRAB isolates were collected from December 2022 to December 2023. Colistin susceptibility was assessed using broth microdilution, and heteroresistance was detected through population analysis profiling.

RESULTS

Heteroresistance (HR) was identified in 31.5% (41/130) of the isolates, while 7.7% were colistin-resistant, despite initial susceptibility indicated by broth microdilution. Clinical data revealed that HR was associated with significant 14-day clinical failure but not with 30-day all-cause mortality. Heteroresistant strains showed extensive multidrug resistance, posing a serious threat to effective treatment.

CONCLUSIONS

The study highlights the critical need for accurate detection of colistin HR to prevent treatment failure and improve patient outcomes. The prevalence of colistin HR underscores the necessity for revised diagnostic and treatment strategies in Pakistan, emphasizing the importance of recognizing and addressing this emerging threat in healthcare settings.

Pooled Antibiotic Susceptibility Testing Performs Within CLSI Standards for Validation When Measured Against Broth Microdilution and Disk Diffusion Antibiotic Susceptibility Testing of Cultured Isolates

Background/Objectives: While new methods for measuring antimicrobial susceptibility have been associated with improved patient outcomes, they should also be validated using standard protocols for error rates and other test metrics. The objective of this study was to validate a novel susceptibility assay for complicated and recurrent urinary tract infections (UTIs): pooled antibiotic susceptibility testing (P-AST). This assay was compared to broth microdilution (BMD) and disk diffusion (DD), following Clinical and Laboratory Standards Institute (CLSI) guidelines for assessment of error rates and agreement. Methods: This study analyzed consecutive fresh clinical urine specimens submitted for UTI diagnostic testing. Upon receipt, the urine samples were subjected in parallel to standard urine culture and multiplex polymerase chain reaction (M-PCR) for microbial identification and quantification. Specimens with the same monomicrobial non-fastidious bacteria detected by both M-PCR and standard urine culture (SUC) underwent standard antibiotic susceptibility testing (AST) and P-AST antibiotic susceptibility testing. Analysis was also undertaken to assess the presence of heteroresistance for specimens with P-AST-resistant and BMD/DD consensus-susceptible results. Results: The performance measures without correction for heteroresistance showed essential agreement (EA%) of ≥90%, very major errors (VMEs) of <1.5%, and major errors (MEs) of <3.0% for P-AST, all meeting the threshold guidelines established by CLSI for AST. The categorical agreement (CA%) also met acceptable criteria (>88%), as the majority of the errors were minor (mEs) with essential agreement. The very major and major error rates for P-AST decreased to <1.0% when heteroresistance was accounted for. Conclusions: The P-AST assay methodology is validated within acceptable parameters when compared to broth microdilution and disk diffusion using CLSI criteria.

Type I toxin-antitoxin systems in bacteria: from regulation to biological functions

Toxin-antitoxin systems are ubiquitous in the prokaryotic world and widely distributed among chromosomes and mobile genetic elements. Several different toxin-antitoxin system types exist, but what they all have in common is that toxin activity is prevented by the cognate antitoxin. In type I toxin-antitoxin systems, toxin production is controlled by an RNA antitoxin and by structural features inherent to the toxin messenger RNA. Most type I toxins are small membrane proteins that display a variety of cellular effects. While originally discovered as modules that stabilize plasmids, chromosomal type I toxin-antitoxin systems may also stabilize prophages, or serve important functions upon certain stress conditions and contribute to population-wide survival strategies. Here, we will describe the intricate RNA-based regulation of type I toxin-antitoxin systems and discuss their potential biological functions.

Aminoglycoside heteroresistance in Enterobacter cloacae is driven by the cell envelope stress response

Enterobacter cloacae is a Gram-negative nosocomial pathogen of the ESKAPE (Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, and Enterobacter spp.) priority group with increasing multi-drug resistance via the acquisition of resistance plasmids. However, E. cloacae can also display forms of antibiotic refractoriness, such as heteroresistance and tolerance. Here, we report that E. cloacae displays transient heteroresistance to aminoglycosides, which is accompanied with the formation of small colony variants (SCVs) with increased minimum inhibitor concentration (MIC) of gentamicin and other aminoglycosides used in the clinic, but not other antibiotic classes. To explore the underlying mechanisms, we performed RNA sequencing of heteroresistant bacteria, which revealed global gene expression changes and a signature of the CpxRA cell envelope stress response. Deletion of the cpxRA two-component system abrogated aminoglycoside heteroresistance and SCV formation, pointing to its indispensable role in these processes. The introduction of a constitutively active allele of cpxA led to high aminoglycoside MICs, consistent with cell envelope stress response driving these behaviors in E. cloacae. Cell envelope stress can be caused by environmental cues, including heavy metals. Indeed, bacterial exposure to copper increased gentamicin MIC in the wild-type but not in the ΔcpxRA mutant. Moreover, copper exposure also elevated the gentamicin MICs of clinical isolates from bloodstream infections, suggesting that CpxRA- and copper-dependent aminoglycoside resistance is broadly conserved in E. cloacae strains. Altogether, we establish that E. cloacae relies on transcriptional reprogramming via the envelope stress response pathway for transient resistance to a major class of frontline antibiotic.IMPORTANCEEnterobacter cloacae is a bacterium that belongs to the WHO high-priority group and an increasing threat worldwide due its multi-drug resistance. E. cloacae can also display heteroresistance, which has been linked to treatment failure. We report that E. cloacae shows heteroresistance to aminoglycoside antibiotics. These are important frontline microbicidal drugs used against Gram-negative bacterial infections; therefore, understanding how resistance develops among sensitive strains is important. We show that aminoglycoside resistance is driven by the activation of the cell envelope stress response and transcriptional reprogramming via the CpxRA two-component system. Furthermore, heterologous activation of envelope stress via copper, typically a heavy metal with antimicrobial actions, also increased aminoglycoside MICs of the E. cloacae type strain and clinical strains isolated from bloodstream infections. Our study suggests aminoglycoside recalcitrance in E. cloacae could be broadly conserved and cautions against the undesirable effects of copper.

Overexpression of KPC contributes to ceftazidime-avibactam heteroresistance in clinical isolates of carbapenem-resistant Klebsiella pneumoniae

Ceftazidime-avibactam (CZA) is one of the effective antibiotics used for the treatment of carbapenem-resistant Klebsiella pneumoniae (CRKP) infections, but its resistance rate has increased recently. Previous studies have focused on the mechanisms of CZA resistance, while its heteroresistance in CRKP remains poorly understood. This study aimed to investigate the characteristics and mechanisms of CZA heteroresistance in CRKP isolates. A total of 311 CRKP clinical strains were collected in China from 2020 to 2022. The MICs of CZA and other antibiotics against K. pneumoniae were determined by broth microdilution method. The occurrence of CZA heteroresistance in CRKP was evaluated with population analysis profiling (PAP) and their characteristics were detected by polymerase chain reaction (PCR). The underlying mechanism of CZA heteroresistance in CRKP strains was investigated by molecular sequencing, whole genome sequencing (WGS), quantitative real-time PCR (qRT-PCR), and in vitro functional experiments. Strategies for preventing the emergence of CZA heteroresistance and alternative treatment options for strains exhibiting CZA heteroresistance were further explored. Thirty-four (12.4%) CZA-susceptible CRKP isolates were found to exhibit heteroresistance to CZA. All heteroresistant strains belonged to KPC-2 (97.1%) or KPC-3 (2.9%). The dominant multilocus sequence typing (MLST) was ST11 (64.7%) and the prevalent capsular serotypes were KL47 (38.2%) and KL64 (32.4%). Imipenem-relebactam and meropenem-vaborbactam still exhibited excellent antimicrobial activity against the resistant subpopulations of CZA heteroresistant strains. No significant mutations were found in KPC, OmpK35/36, PBP2/3, and LamB in resistant subpopulations. The relative expression and copy number of bla KPC were significantly upregulated in 47.1% and 35.3% of the resistant subpopulations compared with their parental strains, respectively. Silencing bla KPC expression significantly decreased the CZA MIC in resistant subpopulations with high bla KPC expression and hindered the emergence of CZA heteroresistance in their parental strains. Moreover, increasing the avibactam concentration to 8 or 16 mg/L or combining CZA with 0.5 × MIC tigecycline significantly suppressed the formation of CZA heteroresistance (P<0.05). In conclusion, we identified the occurrence of CZA heteroresistance in CRKP in China, which was attributed to the overexpression of KPC. Increasing the concentration of avibactam or combining CZA with tigecycline could effectively prevent the development of CZA heteroresistance in CRKP isolates. Besides, imipenem-relebactam and meropenem-vaborbactam may serve as alternative therapeutic options when clinical isolates with CZA heteroresistance are detected.

A novel small RNA PhaS contributes to polymyxin B-heteroresistance in carbapenem-resistant Klebsiella pneumoniae

In recent years, polymyxin has been used as a last-resort therapy for carbapenem-resistant bacterial infections. The emergence of heteroresistance (HR) to polymyxin hampers the efficacy of polymyxin treatment by amplifying resistant subpopulation. However, the mechanisms behind polymyxin HR remain unclear. Small noncoding RNAs (sRNAs) play an important role in regulating drug resistance. The purpose of this study was to investigate the effects and mechanisms of sRNA on polymyxin B (PB)-HR in carbapenem-resistant Klebsiella pneumoniae. In this study, a novel sRNA PhaS was identified by transcriptome sequencing. PhaS expression was elevated in the PB heteroresistant subpopulation. Overexpression and deletion of PhaS were constructed in three carbapenem-resistant K. pneumoniae strains. Population analysis profiling, growth curve, and time-killing curve analysis showed that PhaS enhanced PB-HR. In addition, we verified that PhaS directly targeted phoP through the green fluorescent protein reporter system. PhaS promoted the expression of phoP, thereby encouraging the expression of downstream genes pmrD and arnT. This upregulation of arnT promoted the 4-amino-4-deoxyL-arabinosaccharide (L-Ara4N) modification of lipid A in PhaS overexpressing strains, thus enhancing PB-HR. Further, within the promoter region of PhaS, specific PhoP recognition sites were identified. ONPG assays and RT-qPCR analysis confirmed that PhaS expression was positively modulated by PhoP and thus up-regulated by PB stimulation. To sum up, a novel sRNA enhancing PB-HR was identified and a positive feedback regulatory pathway of sRNA-PhoP/Q was demonstrated in the study. This helps to provide a more comprehensive and clear understanding of the underlying mechanisms behind polymyxin HR in carbapenem-resistant K. pneumoniae.

ESKAPE in China: epidemiology and characteristics of antibiotic resistance

The escalation of antibiotic resistance and the diminishing antimicrobial pipeline have emerged as significant threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria, demanding urgently effective therapies. Despite the introduction of various new antibiotics and antibiotic adjuvants, such as innovative β-lactamase inhibitors, these organisms continue to pose substantial therapeutic challenges. People's Republic of China, as a country facing a severe bacterial resistance situation, has undergone a series of changes and findings in recent years in terms of the prevalence, transmission characteristics and resistance mechanisms of antibiotic resistant bacteria. The increasing levels of population mobility have not only shaped the unique characteristics of antibiotic resistance prevalence and transmission within People's Republic of China but have also indirectly reflected global patterns of antibiotic-resistant dissemination. What's more, as a vast nation, People's Republic of China exhibits significant variations in the levels of antibiotic resistance and the prevalence characteristics of antibiotic resistant bacteria across different provinces and regions. In this review, we examine the current epidemiology and characteristics of this important group of bacterial pathogens, delving into relevant mechanisms of resistance to recently introduced antibiotics that impact their clinical utility in China.

Predicting the evolution of antibiotic resistance

Predicting the evolution of antibiotic resistance is critical for realizing precision antibiotic therapies. How exactly to achieve such predictions is a theoretical challenge. Insights from mathematical models that reflect future behavior of microbes under antibiotic stress can inform intervention protocols. However, this requires going beyond heuristic approaches by modeling ecological and evolutionary responses linked to metabolic pathways and cellular functions. Developing such models is now becoming possible due to increasing data availability from systematic experiments with microbial systems. Here, I review recent theoretical advances promising building blocks to piece together a predictive theory of antibiotic resistance evolution. I focus on the conceptual framework of eco-evolutionary response models grounded on quantitative laws of bacterial physiology. These forward-looking models can predict previously unknown behavior of bacteria upon antibiotic exposure. With current developments covering mostly the case of ribosome-targeting antibiotics, I write this Opinion piece as an invitation to generalize the principles discussed here to a broader range of drugs and context dependencies.

Evaluating the predictive power of combined gene expression dynamics from single cells on antibiotic survival

Heteroresistance can allow otherwise drug-susceptible bacteria to survive and resume growth after antibiotic exposure. This temporary form of antibiotic tolerance can be caused by the upregulation of stress response genes or a decrease in cell growth rate. However, it is not clear how expression of multiple genes contributes to the tolerance phenotype. By using fluorescent reporters for stress related genes, we conducted real time measurements of expression prior to, during, and after antibiotic exposure. We first identified relationships between growth rate and reporter levels based on auto and cross correlation analysis, revealing consistent patterns where changes in growth rate were anticorrelated with fluorescence following a delay. We then used pairs of stress gene reporters and time lapse fluorescence microcopy to measure the growth rate and reporter levels in cells that survived or died following antibiotic exposure. Using these data, we asked whether combined information about reporter expression and growth rate could improve our ability to predict whether a cell would survive or die following antibiotic exposure. We developed a Bayesian inference model to predict how the combination of dual reporter expression levels and growth rate impact ciprofloxacin survival in Escherichia coli . We found clear evidence of the impact of growth rate and the gadX promoter activity on survival. Unexpectedly, our results also revealed examples where additional information from multiple genes decreased prediction accuracy, highlighting an important and underappreciated effect that can occur when integrating data from multiple simultaneous measurements.

Emergence of carbapenem resistance in persistent Shewanella algae bacteremia: the role of pdsS G547W mutation in adaptive subpopulation dynamics

This study elucidates the in vivo genetic mechanisms contributing to the emerging resistance to carbapenem in Shewanella algae through a lens of adaptive microbial evolution. Leveraging PacBio amplification-free sequencing, we tracked the evolution of β-lactam resistance in clinical isolates from a persistent S. algae bacteremia case amidst antimicrobial therapy. Our investigation spotlighted a recurrent G547W mutation in the sensor histidine kinase (pdsS), which was associated with the overexpression of an OmpA-like protein (pdsO) within a proteobacteria-specific sortase system. Intriguingly, we observed a recurrent switch between wild-type and G547W alleles, revealing an adaptive expansion and contraction of underlying cell subpopulations in response to β-lactam exposure. Comparative transcriptome analyses further demonstrated the overexpression of genes pivotal for membrane integrity, biofilm formation, immune evasion, and β-lactamase activation in resistant samples. This underscores the pre-existence of resistant cells at minuscule frequencies even without antibiotic pressure, potentially explaining the within-host emergence of resistance during antibiotic treatments. Our findings provide pivotal insights into the dynamic genetic adaptations of S. algae under therapeutic pressures, unmasking intricate resistance mechanisms and highlighting the critical role of subpopulation dynamics in treatment outcomes.

Photodynamic inactivation and its effects on the heterogeneity of bacterial resistance

Antimicrobial resistance is a growing threat to global public health, requiring innovative approaches for its control. Photodynamic inactivation (PDI) with light-activated photosensitizers has emerged as a strategy to combat resistant bacteria, challenging the intrinsic heterogeneity of bacterial populations. This study evaluates the impact of PDI on both heterogeneity and shape of the distribution profile of resistant bacterial populations, specifically on strains of Staphylococcus aureus resistant to amoxicillin, erythromycin, and gentamicin, for exploring its potential as an adjuvant therapy in the fight against bacterial resistance. Curcumin (10 µM) was used as a photosensitizer and five cycles of PDI were applied on Staphylococcus aureus strains under 450 nm irradiation of 10 J/cm² energy density. The resistance variations amongst bacterial subpopulations were investigated by calculating the minimum inhibitory concentration (MIC) before and after PDI treatment. MIC was significantly reduced by the antibiotics tested post-PDI and a reduction in the heterogeneity of bacterial populations was recorded, suggesting PDI can effectively decrease the resistance diversity of Staphylococcus aureus. The result reinforces the potential of PDI as a valuable adjuvant therapy, offering a promising avenue for mitigating bacterial resistance and promoting more effective treatment strategies against resistant infections.

Antibiotic resistance mediated by gene amplifications

Apart from horizontal gene transfer and sequence-altering mutational events, antibiotic resistance can emerge due to the formation of tandem repeats of genomic regions. This phenomenon, also known as gene amplification, has been implicated in antibiotic resistance in both laboratory and clinical scenarios, where the evolution of resistance via amplifications can affect treatment efficacy. Antibiotic resistance mediated by gene amplifications is unstable and consequently can be difficult to detect, due to amplification loss in the absence of the selective pressure of the antibiotic. Further, due to variable copy numbers in a population, amplifications result in heteroresistance, where only a subpopulation is resistant to an antibiotic. While gene amplifications typically lead to resistance by increasing the expression of resistance determinants due to the higher copy number, the underlying mechanisms of resistance are diverse. In this review article, we describe the various pathways by which gene amplifications cause antibiotic resistance, from efflux and modification of the antibiotic, to target modification and bypass. We also discuss how gene amplifications can engender resistance by alternate mutational outcomes such as altered regulation and protein structure, in addition to just an increase in copy number and expression. Understanding how amplifications contribute to bacterial survival following antibiotic exposure is critical to counter their role in the rise of antimicrobial resistance.

Drug tolerance and persistence in bacteria, fungi and cancer cells: Role of non-genetic heterogeneity

A common feature of bacterial, fungal and cancer cell populations upon treatment is the presence of tolerant and persistent cells able to survive, and sometimes grow, even in the presence of usually inhibitory or lethal drug concentrations, driven by non-genetic differences among individual cells in a population. Here we review and compare data obtained on drug survival in bacteria, fungi and cancer cells to unravel common characteristics and cellular pathways, and to point their singularities. This comparative work also allows to cross-fertilize ideas across fields. We particularly focus on the role of gene expression variability in the emergence of cell-cell non-genetic heterogeneity because it represents a possible common basic molecular process at the origin of most persistence phenomena and could be monitored and tuned to help improve therapeutic interventions.

Antifungal heteroresistance causes prophylaxis failure and facilitates breakthrough Candida parapsilosis infections

Breakthrough fungal infections in patients on antimicrobial prophylaxis during allogeneic hematopoietic cell transplantation (allo-HCT) represent a major and often unexplained cause of morbidity and mortality. Candida parapsilosis is a common cause of invasive candidiasis and has been classified as a high-priority fungal pathogen by the World Health Organization. In high-risk allo-HCT recipients on micafungin prophylaxis, we show that heteroresistance (the presence of a phenotypically unstable, low-frequency subpopulation of resistant cells (~1 in 10,000)) underlies breakthrough bloodstream infections by C. parapsilosis. By analyzing 219 clinical isolates from North America, Europe and Asia, we demonstrate widespread micafungin heteroresistance in C. parapsilosis. Standard antimicrobial susceptibility tests, such as broth microdilution or gradient diffusion assays, which guide drug selection for invasive infections, fail to detect micafungin heteroresistance in C. parapsilosis. To facilitate rapid detection of micafungin heteroresistance in C. parapsilosis, we constructed a predictive machine learning framework that classifies isolates as heteroresistant or susceptible using a maximum of ten genomic features. These results connect heteroresistance to unexplained antifungal prophylaxis failure in allo-HCT recipients and demonstrate a proof-of-principle diagnostic approach with the potential to guide clinical decisions and improve patient care.

Unlocking Nitrofurantoin: Understanding Molecular Mechanisms of Action and Resistance in Enterobacterales

Antimicrobial resistance (AMR) is a global health crisis that has already claimed millions of lives and is projected to affect millions more unless urgent action is taken. Effective control of AMR requires the correct choice and dosage of antibiotics, as well as robust surveillance and research. Understanding the mechanisms of antibiotic action and the emergence of resistance phenotypes along with their genotypes is essential. This knowledge, combined with insights into resistance prevalence and spread, empowers clinicians to propose alternative therapies. Nitrofurantoin, a 70-year-old antibiotic, remains effective for the treatment of uncomplicated lower UTIs. Preventing emergence and spread of nitrofurantoin-resistant superbugs would preserve the efficacy of this antibiotic which is crucial for ongoing and future AMR efforts. Nitrofurantoin resistance evolves slowly, leading to low prevalence compared to other antibiotics. However, it is often linked with extensive drug resistance, complicating treatment outcomes. Even a minor percentage of nitrofurantoin-resistant bacteria can cause significant clinical challenges due to irreversible evolution. While detailed study of these mechanisms can guide the development of strategies to combat nitrofurantoin resistance, early detection of resistant infections is critical for saving lives. The current review aimed to provide a comprehensive analysis of nitrofurantoin's mechanisms of action, resistance evolution, prevalence, and resistance prediction. Our goal is to offer valuable insights for researchers and clinicians to enhance nitrofurantoin use and address the challenges posed by AMR. Antimicrobial resistance (AMR) is a global health crisis that has already claimed millions of lives and is projected to affect millions more unless urgent action is taken. Effective control of AMR requires the correct choice and dosage of antibiotics, as well as robust surveillance and research. Understanding the mechanisms of antibiotic action and the emergence of resistance phenotypes along with their genotypes is essential. This knowledge, combined with insights into resistance prevalence and spread, empowers clinicians to propose alternative therapies. Nitrofurantoin, a 70-year-old antibiotic, remains effective for the treatment of uncomplicated lower UTIs. Preventing emergence and spread of nitrofurantoin-resistant superbugs would preserve the efficacy of this antibiotic which is crucial for ongoing and future AMR efforts. Nitrofurantoin resistance evolves slowly, leading to low prevalence compared to other antibiotics. However, it is often linked with extensive drug resistance, complicating treatment outcomes. Even a minor percentage of nitrofurantoin-resistant bacteria can cause significant clinical challenges due to irreversible evolution. While detailed study of these mechanisms can guide the development of strategies to combat nitrofurantoin resistance, early detection of resistant infections is critical for saving lives. The current review aimed to provide a comprehensive analysis of nitrofurantoin's mechanisms of action, resistance evolution, prevalence, and resistance prediction. Our goal is to offer valuable insights for researchers and clinicians to enhance nitrofurantoin use and address the challenges posed by AMR.

Phenotypic heterogeneity in bacteria: the rise of antibiotic persistence, clinical implications, and therapeutic opportunities

The rising incidence of antimicrobial resistance (AMR) and the diminishing antibiotics discovery pipeline have created an unprecedented scenario where minor infections could become untreatable. AMR phenomenon is genetically encoded, and various genetic determinants have been implicated in their emergence and spread. Nevertheless, several non-genetic phenomena are also involved in antibiotic treatment failure which requires a systematic investigation. It has been observed that in an isogenic population of bacteria, not all cells behave or respond the same way to an antibiotic, because of the inherent heterogeneity among them. This heterogeneity is not always heritable but rather phenotypic. Three distinct types of phenotypic heterogeneity, namely tolerance, persistence, and heteroresistance have been observed in bacteria having significant clinical implications influencing the treatment outcome. While tolerance is when a population can survive high doses of antibiotics without changing the minimum inhibitory concentration (MIC) of the drug, persistence occurs in a subpopulation of bacteria that can survive exposure to high antibiotic doses. In contrast, when a subpopulation shows a very high MIC in comparison to the rest of the population, the phenomenon is called heteroresistance. In this article, we have highlighted bacterial persistence with a focus on their emergence and the underlying molecular mechanisms. Moreover, we have tried to associate the genome-wide methylation status with that of the heterogeneity at a single-cell level that may explain the role of epigenetic mechanisms in the development of persistence.

Single-Cell Microfluidics: A Primer for Microbiologists

Recent advances in microfluidic technology have made it possible to image live bacterial cells with a high degree of precision and control. In particular, single-cell microfluidic designs have created new opportunities to study phenotypic variation in bacterial populations. However, the development and use of microfluidic devices require specialized resources, and these can be practical barriers to entry for microbiologists. With this review, our intentions are to help demystify the design, construction, and application of microfluidics. Our approach is to present design elements as building blocks from which a multitude of microfluidics applications can be imagined by the microbiologist.

A birth-death model to understand bacterial antimicrobial heteroresistance from time-kill curves

Antimicrobial heteroresistance refers to the presence of different subpopulations with heterogeneous antimicrobial responses within the same bacterial isolate, so they show reduced susceptibility compared with the main population. Though it is widely accepted that heteroresistance can play a crucial role in the outcome of antimicrobial treatments, predictive Antimicrobial Resistance (AMR) models accounting for bacterial heteroresistance are still scarce and need to be refined as the techniques to measure heteroresistance become standardised and consistent conclusions are drawn from data. In this work, we propose a multivariate Birth-Death (BD) model of bacterial heteroresistance and analyse its properties in detail. Stochasticity in the population dynamics is considered since heteroresistance is often characterised by low initial frequencies of the less susceptible subpopulations, those mediating AMR transmission and potentially leading to treatment failure. We also discuss the utility of the heteroresistance model for practical applications and calibration under realistic conditions, demonstrating that it is possible to infer the model parameters and heteroresistance distribution from time-kill data, i.e., by measuring total cell counts alone and without performing any heteroresistance test.

Frequency of cefiderocol heteroresistance among patients treated with cefiderocol for carbapenem-resistant Acinetobacter baumannii infections

Background

Cefiderocol exhibits potent in vitro activity against carbapenem-resistant Acinetobacter baumannii (CRAb), but this activity has not consistently translated to improved outcomes among patients. Cefiderocol heteroresistance, or the presence of a resistant subpopulation, has been proposed as one possible explanation. The objective of this study was to explore associations between heteroresistance and outcomes of patients with CRAb infections.

Methods

Baseline CRAb isolates were collected from 27 consecutive patients in the USA and Italy. Cefiderocol susceptibility was tested by broth microdilutions in triplicate. Heteroresistance was defined by population analysis profiling in duplicate. Resistance mechanisms and strain relatedness were evaluated through comparative genomic analysis.

Results

Overall, 59% of infecting CRAb isolates were identified as cefiderocol-heteroresistant; rates were higher among isolates from Italy (79%) than the USA (38%). The median Charlson Comorbidity and SOFA scores were 4 and 5, respectively; 44% of patients had pneumonia, which was the most common infection type. Rates of 28-day clinical success and survival were 30% and 73%, respectively. By broth microdilution, cefiderocol MICs ≥1 mg/L were associated with higher failure rates than MICs ≤0.5 mg/L (81% versus 55%). Rates of clinical failure were numerically higher among patients infected by cefiderocol-heteroresistant compared with susceptible CRAb (81% versus 55%). Whole-genome sequencing identified a premature stop codon in the TonB-dependent receptor gene piuA in six isolates, all of which were heteroresistant.

Conclusions

This pilot study supports the hypothesis that cefiderocol treatment failure may be associated with higher MICs and/or the presence of heteroresistance. Further studies are needed to confirm these findings.