The biological cost of mutational antibiotic resistance: any practical conclusions?

Interactions within higher-order antibiotic combinations do not influence the rate of adaptation in bacteria

The prevalence and strength of antibiotic resistance has led to an ongoing battle between the development of new treatments and the evolution of resistance. Combining multiple drugs simultaneously is a potential solution for combating antibiotic resistance. However, this approach introduces new factors that must be considered, including the influence of drug interactions on the rate of resistance evolution. When antibiotics are used in combination, their effects can be additive, synergistic, or antagonistic. In this study, we investigated the effect of higher-order interactions involving 3 drugs on resistance evolution in Staphylococcus epidermidis. Previous studies have shown that synergistic interactions can increase the adaptation rate. However, the effects of higher-order interactions on rates of adaptation are unclear. We investigated the adaptation of Staphylococcus epidermidis to single-, 2-, and 3-drug environments to assess how interactions within drug combinations influence the rate of adaptation. We analyzed both the overall interaction and emergent interaction, the latter being a unique interaction that occurs in 3-drug combinations due to the presence of all three drugs, rather than simply strong pairwise interactions. Our results show that neither the overall interactions nor the emergent interactions affect adaptation rates.

Correlation between rrs gene mutations and amikacin resistance in Mycobacterium abscessus: implications for fitness cost and clinical prevalence

OBJECTIVES

Amikacin is crucial for treating Mycobacterium abscessus (Mab) infections, with resistance primarily attributed to rrs gene mutations. The correlation between specific mutations and amikacin susceptibility, along with the associated fitness cost, requires further investigation.

METHODS

We isolated spontaneous amikacin-resistant mutants in vitro and identified their mutation sites in the rrs gene via Sanger sequencing, which were then compared with existing reports. Using CRISPR/Cas12a-assisted recombineering, we engineered Mab strains with specific rrs mutations. The growth rate and fitness costs in vitro were evaluated, in conjunction with drug susceptibility testing to determine the relationship between rrs mutations and amikacin resistance.

RESULTS

The mutation frequency of Mab for amikacin resistance ranged from 4.68 × 10⁻⁷ to 9.38 × 10⁻⁹. Three rrs mutation sites (A1375G, C1376T, G1458T) were identified, with A1375G being the most prevalent. Two additional sites, T1373A and T1465A, have been reported previously but not detected in this study. The five gene-edited strains demonstrated resistance to amikacin and cross-resistance to other aminoglycosides, and all exhibited slower in vitro growth rates than the wild-type Mab. Competitive experiments revealed that T1373A and T1465A have high fitness costs, while C1376T and G1458T have weak fitness costs and A1375G shows no fitness costs.

CONCLUSIONS

Our findings confirm that rrs mutations confer high-level amikacin resistance, with the limited mutation spectrum in clinical isolates possibly linked to higher spontaneous mutation frequency and lower fitness costs.

Phage treatment of multidrug-resistant bacterial infections in humans, animals, and plants: The current status and future prospects

Phages, including the viruses that lyse bacterial pathogens, offer unique therapeutic advantages, including their capacity to lyse antibiotic-resistant bacteria and disrupt biofilms without harming the host microbiota. The lack of new effective antibiotics and the growing limitations of existing antibiotics have refocused attention on phage therapy as an option in complex clinical cases such as burn wounds, cystic fibrosis, and pneumonia. This review describes clinical cases and preclinical studies in which phage therapy has been effective in both human and veterinary medicine, and in an agricultural context. In addition, critical challenges, such as the narrow host range of bacteriophages, the possibility of bacterial resistance, and regulatory constraints on the widespread use of phage therapy, are addressed. Future directions include optimizing phage therapy through strategies ranging from phage cocktails to broadening phage host range through genetic modification, and using phages as vaccines or biocontrol agents. In the future, if phage can be efficiently delivered, maintained in a stable state, and phage-antibiotic synergy can be achieved, phage therapy will offer much needed treatment options. However, the successful implementation of phage therapy within the current standards of practice will also require the considerable development of regulatory infrastructure and greater public acceptance. In closing, this review highlights the promise of phage therapy as a critical backup or substitute for antibiotics. It proposes a new role as a significant adjunct to, or even replacement for, antibiotics in treating multidrug-resistant bacterial infections.

Fitness Burden for the Stepwise Acquisition of First- and Second-Line Antimicrobial Reduced-Susceptibility in High-Risk ESKAPE MRSA Superbugs

Background: The fitness costs (FCs) of antimicrobial resistance (AMR) are crucial issues in antimicrobial resistance (AMR) onset, spread, and, consequently, public health. In Staphylococcus aureus, AMR can induce significant FCs due to slow growth, low competitiveness, and virulence. Here, we investigated the genomics and FCs emerging for progressively acquiring daptomycin (DAP) and glycopeptide (GLY) reduced susceptibility in MRSA. Methods: Genomics was carried out using Illumina-MiSeq Whole-genome sequencing and bioinformatics. The biological FCs of isogenic MRSA strain pairs progressively acquiring DAP and GLY-reduced susceptibility, under DAP/GLY mono or combined therapy, were performed by in-vitro independent and competitive mixed growth, phenotypic in-vitro virulence analysis, and in-vivo G. mellonella larvae killing. Results: Genomics evidenced four different extremely resistant high-risk clones, i.e., ST-5 N315 HA-MRSA, ST-398 LA-MRSA, ST-22 USA-100 HA-EMRSA-15, and ST-1 MW2 CA-MRSA. In-vitro fitness assays revealed slow growth, lower competitiveness, and reduced virulence, predominantly in Galleria mellonella killing ability, in DAP-S hGISA, DAP-R GSSA, DAP-R hGISA, and DAP-R GISA strains. Conclusions: The occurrence of glycopeptide and daptomycin reduced susceptibility conferred increasing FCs, paid as a gradual reduction in virulence, competitiveness, and slow growth performance.

Transcriptomic analysis of benznidazole-resistant Trypanosoma cruzi clone reveals nitroreductase I-independent resistance mechanisms

The enzyme nitroreductase I (NTRI) has been implicated as the primary gene responsible for resistance to benznidazole (Bz) and nifurtimox in Trypanosoma cruzi. However, Bz-resistant T. cruzi field isolates carrying the wild-type NTR-I enzyme suggest that additional mechanisms independent of this enzyme may contribute to the resistance phenotype. To investigate these alternative mechanisms, in this paper, we pressured a Trypanosoma cruzi clone with a high Bz concentration over several generations to select Bz-resistant clones. Surprisingly, we found a highly drug-resistant clone carrying a wild-type NTRI. However, the knockout of this gene using CRISPR-Cas9 in the sensitive clone showed that NTRI indeed induces resistance to Bz and supports the idea that the resistant one exhibits mechanisms other than NTRI. To explore these new mechanisms, we performed an RNA-seq analysis, which revealed genes involved in metabolic pathways related to oxidative stress, energy metabolism, membrane transporters, DNA repair, and protein synthesis. Our results support the idea that resistance to benznidazole is a multigenic trait. A Deeper understanding of these genes is essential for developing new drugs to treat Chagas disease.

Colistin Resistance Mechanism and Management Strategies of Colistin-Resistant Acinetobacter baumannii Infections

The emergence of antibiotic-resistant Acinetobacter baumannii (A. baumannii) is a pressing threat in clinical settings. Colistin is currently a widely used treatment for multidrug-resistant A. baumannii, serving as the last line of defense. However, reports of colistin-resistant strains of A. baumannii have emerged, underscoring the urgent need to develop alternative medications to combat these serious pathogens. To resist colistin, A. baumannii has developed several mechanisms. These include the loss of outer membrane lipopolysaccharides (LPSs) due to mutation of LPS biosynthetic genes, modification of lipid A (a constituent of LPSs) structure through the addition of phosphoethanolamine (PEtN) moieties to the lipid A component by overexpression of chromosomal pmrCAB operon genes and eptA gene, or acquisition of plasmid-encoded mcr genes through horizontal gene transfer. Other resistance mechanisms involve alterations of outer membrane permeability through porins, the expulsion of colistin by efflux pumps, and heteroresistance. In response to the rising threat of colistin-resistant A. baumannii, researchers have developed various treatment strategies, including antibiotic combination therapy, adjuvants to potentiate antibiotic activity, repurposing existing drugs, antimicrobial peptides, nanotechnology, photodynamic therapy, CRISPR/Cas, and phage therapy. While many of these strategies have shown promise in vitro and in vivo, further clinical trials are necessary to ensure their efficacy and widen their clinical applications. Ongoing research is essential for identifying the most effective therapeutic strategies to manage colistin-resistant A. baumannii. This review explores the genetic mechanisms underlying colistin resistance and assesses potential treatment options for this challenging pathogen.

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.

Adjuvants restore colistin sensitivity in mouse models of highly colistin-resistant isolates, limiting bacterial proliferation and dissemination

Antimicrobial resistance (AMR) has led to a marked reduction in the effectiveness of many antibiotics, representing a substantial and escalating concern for global health. Particularly alarming is resistance in Gram-negative bacteria due to the scarcity of therapeutic options for treating infections caused by these pathogens. This challenge is further compounded by the rising incidence of resistance to colistin, an antibiotic traditionally considered a last resort for the treatment of multi-drug resistant (MDR) Gram-negative bacterial infections. In this study, we demonstrate that adjuvants restore colistin sensitivity in vivo. We previously reported that the salicylanilide kinase inhibitor IMD-0354, which was originally developed to inhibit the human kinase IKKβ in the NFκB pathway, is a potent colistin adjuvant. Subsequent analog synthesis using an amide isostere approach led to the creation of a series of novel benzimidazole compounds with enhanced colistin adjuvant activity. Herein, we demonstrate that both IMD-0354 and a lead benzimidazole effectively restore colistin susceptibility in mouse models of highly colistin-resistant Klebsiella pneumoniae and Acinetobacter baumannii-induced peritonitis. These novel adjuvants show low toxicity in vivo, significantly reduce bacterial load, and prevent dissemination that could otherwise result in systemic infection.

Environmental risks in swine biogas slurry-irrigated soils: A comprehensive analysis of antibiotic residues, resistome, and bacterial pathogens

Simple anaerobic digestion is insufficient to completely remove residual parent antibiotics and antibiotic resistance genes (ARGs) from animal manure. ARG prevalence in swine biogas slurry-irrigated soils threatens human health. However, comprehensive analysis of antibiotic residues, high-resolution resistance gene profiles, and pathogenic microbiomes in biogas slurry-irrigated soils is very limited. Here, we comprehensively determined the antibiotics, resistome, and potential pathogens distribution in these soils, using high-performance liquid chromatography-tandem mass spectrometry, high-throughput quantitative PCR, and 16S rRNA gene sequencing. The results revealed a significant enrichment of tetracyclines and fluoroquinolones antibiotics and ARGs in soils with prolonged biogas slurry irrigation, with a total of 12 antibiotics, 175 unique ARGs, and 9 mobile genetic elements (MGEs) detected. Quantification of veterinary antibiotic residues (especially chlortetracycline) showed significant correlations with multiple ARGs. The abundance of ARGs and MGEs was highest in the biogas slurry-irrigated soils, denoting a tight link between the application of biogas slurry and the spread of antibiotic resistance. The presence of 50 potential pathogenic bacterial genera, including 13 with multidrug resistance, was identified. Variation partitioning, combined with hierarchical partitioning analysis, indicated that Firmicutes, MGEs, and tetracyclines were the key drivers shaping the ARG profiles in biogas slurry-irrigated soils. The findings offer insights into the mechanisms of antibiotic residue and ARGs spread from the agricultural practice of biogas slurry irrigation, underscoring the necessity of sustainable soil management to mitigate the spread of antibiotic resistance.

Impact of multidrug resistance on the virulence and fitness of Pseudomonas aeruginosa: a microbiological and clinical perspective

Pseudomonas aeruginosa is one of the most common nosocomial pathogens and part of the top emergent species associated with antimicrobial resistance that has become one of the greatest threat to public health in the twenty-first century. This bacterium is provided with a wide set of virulence factors that contribute to pathogenesis in acute and chronic infections. This review aims to summarize the impact of multidrug resistance on the virulence and fitness of P. aeruginosa. Although it is generally assumed that acquisition of resistant determinants is associated with a fitness cost, several studies support that resistance mutations may not be associated with a decrease in virulence and/or that certain compensatory mutations may allow multidrug resistance strains to recover their initial fitness. We discuss the interplay between resistance profiles and virulence from a microbiological perspective but also the clinical consequences in outcomes and the economic impact.

Variation in the response to antibiotics and life-history across the major Pseudomonas aeruginosa clone type (mPact) panel

Pseudomonas aeruginosa is a ubiquitous, opportunistic human pathogen. Since it often expresses multidrug resistance, new treatment options are urgently required. Such new treatments are usually assessed with one of the canonical laboratory strains, PAO1 or PA14. However, these two strains are unlikely representative of the strains infecting patients, because they have adapted to laboratory conditions and do not capture the enormous genomic diversity of the species. Here, we characterized the major P. aeruginosa clone type (mPact) panel. This panel consists of 20 strains, which reflect the species' genomic diversity, cover all major clone types, and have both patient and environmental origins. We found significant strain variation in distinct responses toward antibiotics and general growth characteristics. Only few of the measured traits are related, suggesting independent trait optimization across strains. High resistance levels were only identified for clinical mPact isolates and could be linked to known antimicrobial resistance (AMR) genes. One strain, H01, produced highly unstable AMR combined with reduced growth under drug-free conditions, indicating an evolutionary cost to resistance. The expression of microcolonies was common among strains, especially for strain H15, which also showed reduced growth, possibly indicating another type of evolutionary trade-off. By linking isolation source, growth, and virulence to life history traits, we further identified specific adaptive strategies for individual mPact strains toward either host processes or degradation pathways. Overall, the mPact panel provides a reasonably sized set of distinct strains, enabling in-depth analysis of new treatment designs or evolutionary dynamics in consideration of the species' genomic diversity.

IMPORTANCE

New treatment strategies are urgently needed for high-risk pathogens such as the opportunistic and often multidrug-resistant pathogen Pseudomonas aeruginosa. Here, we characterize the major P. aeruginosa clone type (mPact) panel. It consists of 20 strains with different origins that cover the major clone types of the species as well as its genomic diversity. This mPact panel shows significant variation in (i) resistance against distinct antibiotics, including several last resort antibiotics; (ii) related traits associated with the response to antibiotics; and (iii) general growth characteristics. We further developed a novel approach that integrates information on resistance, growth, virulence, and life-history characteristics, allowing us to demonstrate the presence of distinct adaptive strategies of the strains that focus either on host interaction or resource processing. In conclusion, the mPact panel provides a manageable number of representative strains for this important pathogen for further in-depth analyses of treatment options and evolutionary dynamics.

Microbiota and metabolic adaptation shape Staphylococcus aureus virulence and antimicrobial resistance during intestinal colonization

Depletion of microbiota increases susceptibility to gastrointestinal colonization and subsequent infection by opportunistic pathogens such as methicillin-resistant Staphylococcus aureus (MRSA). How the absence of gut microbiota impacts the evolution of MRSA is unknown. The present report used germ-free mice to investigate the evolutionary dynamics of MRSA in the absence of gut microbiota. Through genomic analyses and competition assays, we found that MRSA adapts to the microbiota-free gut through sequential genetic mutations and structural changes that enhance fitness. Initially, these adaptations increase carbohydrate transport; subsequently, evolutionary pathways largely diverge to enhance either arginine metabolism or cell wall biosynthesis. Increased fitness in arginine pathway mutants depended on arginine catabolic genes, especially nos and arcC, which promote microaerobic respiration and ATP generation, respectively. Thus, arginine adaptation likely improves redox balance and energy production in the oxygen-limited gut environment. Findings were supported by human gut metagenomic analyses, which suggest the influence of arginine metabolism on colonization. Surprisingly, these adaptive genetic changes often reduced MRSA's antimicrobial resistance and virulence. Furthermore, resistance mutation, typically associated with decreased virulence, also reduced colonization fitness, indicating evolutionary trade-offs among these traits. The presence of normal microbiota inhibited these adaptations, preserving MRSA's wild-type characteristics that effectively balance virulence, resistance, and colonization fitness. The results highlight the protective role of gut microbiota in preserving a balance of key MRSA traits for long-term ecological success in commensal populations, underscoring the potential consequences on MRSA's survival and fitness during and after host hospitalization and antimicrobial treatment.

Community coalescence and plant host filtering determine the spread of tetracycline resistance genes from pig manure into the microbiome continuum of the soil-plant system

The spread of livestock manure-borne antibiotic resistance genes (ARGs) into agroecosystems through manure application poses a potential threat to human health. However, there is still a knowledge gap concerning ARG dissemination in coalescing manure, soil and plant microbiomes. Here, we examined the fate of tetracycline resistance genes (TRGs) originating from pig manure microbiomes and spread in the soil-A thaliana system and explored the effects of microbial functions on TRGs spread at different interfaces. Our results indicate that the TRGs abundances in all microbiome continuum of the soil-A. thaliana system were significantly increased with the application of a living manure microbiome, although the addition of manure with both an active and inactive microbiome caused a shift in the microbial community composition. This was attributed to the increasing relative abundances of tetA, tetL, tetM, tetO, tetW and tolC in the system. The application of living manure with DOX residues resulted in the highest relative abundance of total TRGs (3.30×10-3 copies/16S rRNA gene copies) in the rhizosphere soil samples. Community coalescence of the manure and soil microbiomes increased the abundance of Firmicutes in the soil and root microbiome, which directly explains the increase in TRG abundance observed in these interfaces. In contrast, the leaf microbiome differed markedly from that of the remaining samples, indicating strong plant host filtering effects on Firmicutes and TRGs from pig manure. The random forest machine learning model revealed microbial functions and their significant positive correlation with TRG abundance in the microbiome continuum of the system. Our findings revealed that community coalescence is the main driver of TRG spread from manure to the soil and root microbiomes. Plant host filtering effects play a crucial role in allowing certain microbial groups to occupy ecological niches in the leaves, thereby limiting the establishment of manure-borne TRGs in aboveground plant tissues.

Transmission rates of veterinary and clinically important antibiotic resistant Escherichia coli: A meta- ANALYSIS

The transmission rate per hour between hosts is a key parameter for simulating transmission dynamics of antibiotic-resistant bacteria, and might differ for antibiotic resistance genes, animal species, and antibiotic usage. We conducted a Bayesian meta-analysis of resistant Escherichia coli (E. coli) transmission in broilers and piglets to obtain insight in factors determining the transmission rate, infectious period, and reproduction ratio. We included blaCTX-M-1, blaCTX-M-2, blaOXA-162, catA1, mcr-1, and fluoroquinolone resistant E. coli. The Maximum a Posteriori (MAP) transmission rate in broilers without antibiotic treatment ranged from 0.4∙10-3 to 2.5∙10-3 depending on type of broiler (SPF vs conventional) and inoculation strains. For piglets, the MAP in groups without antibiotic treatment were between 0.7∙10-3 and 0.8∙10-3, increasing to 0.9∙10-3 in the group with antibiotic treatment. In groups without antibiotic treatment, the transmission rate of resistant E. coli in broilers was almost twice the transmission rate in piglets. Amoxicillin increased the transmission rate of E. coli carrying blaCTX-M-2 by three-fold. The MAP infectious period of resistant E. coli in piglets with and without antibiotics is between 971 and 1065 hours (40 - 43 days). The MAP infectious period of resistant E. coli in broiler without antibiotics is between 475 and 2306 hours (20 - 96 days). The MAP infectious period of resistant E. coli in broiler with antibiotics is between 2702 and 3462 hours (113 - 144 days) which means a lifelong colonization. The MAP basic reproduction ratio in piglets of infection with resistant E. coli when using antibiotics is 27.70, which is higher than MAP in piglets without antibiotics between 15.65 and 18.19. The MAP basic reproduction ratio in broilers ranges between 3.46 and 92.38. We consider three possible explanations for our finding that in the absence of antibiotics the transmission rate is higher among broilers than among piglets: i) due to the gut microbiome of animals, ii) fitness costs of bacteria, and iii) differences in experimental set-up between the studies. Regarding infectious period and reproduction ratio, the effect of the resistance gene, antibiotic treatment, and animal species are inconclusive due to limited data.

Correlation between antimicrobial resistance, biofilm formation, and virulence determinants in uropathogenic Escherichia coli from Egyptian hospital

BACKGROUND

Uropathogenic Escherichia coli (UPEC) is the main etiological agent behind community-acquired and hospital-acquired urinary tract infections (UTIs), which are among the most prevalent human infections. The management of UPEC infections is becoming increasingly difficult owing to multi-drug resistance, biofilm formation, and the possession of an extensive virulence arsenal. This study aims to characterize UPEC isolates in Tanta, Egypt, with regard to their antimicrobial resistance, phylogenetic profile, biofilm formation, and virulence, as well as the potential associations among these factors.

METHODS

One hundred UPEC isolates were obtained from UTI patients in Tanta, Egypt. Antimicrobial susceptibility was assessed using the Kirby-Bauer method. Extended-spectrum β-lactamases (ESBLs) production was screened using the double disk synergy test and confirmed with PCR. Biofilm formation was evaluated using the microtiter-plate assay and microscopy-based techniques. The phylogenetic groups of the isolates were determined. The hemolytic activity, motility, siderophore production, and serum resistance of the isolates were also evaluated. The clonal relatedness of the isolates was assessed using ERIC-PCR.

RESULTS

Isolates displayed elevated resistance to cephalosporins (90-43%), sulfamethoxazole-trimethoprim (63%), and ciprofloxacin (53%). Ninety percent of the isolates were multidrug-resistant (MDR)/ extensively drug-resistant (XDR) and 67% produced ESBLs. Notably, there was an inverse correlation between biofilm formation and antimicrobial resistance, and 31%, 29%, 32%, and 8% of the isolates were strong, moderate, weak, and non-biofilm producers, respectively. Beta-hemolysis, motility, siderophore production, and serum resistance were detected in 64%, 84%, 65%, and 11% of the isolates, respectively. Siderophore production was correlated to resistance to multiple antibiotics, while hemolysis was more prevalent in susceptible isolates and associated with stronger biofilms. Phylogroups B2 and D predominated, with lower resistance and stronger biofilms in group B2. ERIC-PCR revealed considerable diversity among the isolates.

CONCLUSION

This research highlights the dissemination of resistance in UPEC in Tanta, Egypt. The evident correlation between biofilm and resistance suggests a resistance cost on bacterial cells; and that isolates with lower resistance may rely on biofilms to enhance their survival. This emphasizes the importance of considering biofilm formation ability during the treatment of UPEC infections to avoid therapeutic failure and/or infection recurrence.

The Effect of the Stringent Response and Oxidative Stress Response on Fitness Costs of De Novo Acquisition of Antibiotic Resistance

Resistance evolution during exposure to non-lethal levels of antibiotics is influenced by various stress responses of bacteria which are known to affect growth rate. Here, we aim to disentangle how the interplay between resistance development and associated fitness costs is affected by stress responses. We performed de novo resistance evolution of wild-type strains and single-gene knockout strains in stress response pathways using four different antibiotics. Throughout resistance development, the increase in minimum inhibitory concentration (MIC) is accompanied by a gradual decrease in growth rate, most pronounced in amoxicillin or kanamycin. By measuring biomass yield on glucose and whole-genome sequences at intermediate and final time points, we identified two patterns of how the stress responses affect the correlation between MIC and growth rate. First, single-gene knockout E. coli strains associated with reactive oxygen species (ROS) acquire resistance faster, and mutations related to antibiotic permeability and pumping out occur earlier. This increases the metabolic burden of resistant bacteria. Second, the ΔrelA knockout strain, which has reduced (p)ppGpp synthesis, is restricted in its stringent response, leading to diminished growth rates. The ROS-related mutagenesis and the stringent response increase metabolic burdens during resistance development, causing lower growth rates and higher fitness costs.

Sub-inhibitory antibiotic treatment selects for enhanced metabolic efficiency

Bacterial growth and metabolic rates are often closely related. However, under antibiotic selection, a paradox in this relationship arises: antibiotic efficacy decreases when bacteria are metabolically dormant, yet antibiotics select for resistant cells that grow fastest during treatment. That is, antibiotic selection counterintuitively favors bacteria with fast growth but slow metabolism. Despite this apparent contradiction, antibiotic resistant cells have historically been characterized primarily in the context of growth, whereas the extent of analogous changes in metabolism is comparatively unknown. Here, we observed that previously evolved antibiotic-resistant strains exhibited a unique relationship between growth and metabolism whereby nutrient utilization became more efficient, regardless of the growth rate. To better understand this unexpected phenomenon, we used a simplified model to simulate bacterial populations adapting to sub-inhibitory antibiotic selection through successive bottlenecking events. Simulations predicted that sub-inhibitory bactericidal antibiotic concentrations could select for enhanced metabolic efficiency, defined based on nutrient utilization: drug-adapted cells are able to achieve the same biomass while utilizing less substrate, even in the absence of treatment. Moreover, simulations predicted that restoring metabolic efficiency would re-sensitize resistant bacteria exhibiting metabolic-dependent resistance; we confirmed this result using adaptive laboratory evolutions of Escherichia coli under carbenicillin treatment. Overall, these results indicate that metabolic efficiency is under direct selective pressure during antibiotic treatment and that differences in evolutionary context may determine both the efficacy of different antibiotics and corresponding re-sensitization approaches.IMPORTANCEThe sustained emergence of antibiotic-resistant pathogens combined with the stalled drug discovery pipelines highlights the critical need to better understand the underlying evolution mechanisms of antibiotic resistance. To this end, bacterial growth and metabolic rates are often closely related, and resistant cells have historically been characterized exclusively in the context of growth. However, under antibiotic selection, antibiotics counterintuitively favor cells with fast growth, and slow metabolism. Through an integrated approach of mathematical modeling and experiments, this study thereby addresses the significant knowledge gap of whether antibiotic selection drives changes in metabolism that complement, and/or act independently, of antibiotic resistance phenotypes.

In vitro susceptibility of nontuberculous mycobacteria in China

OBJECTIVES

This study aimed to measure the prevalence of resistance to antimicrobial agents, and explore the risk factors associated with drug resistance by using nontuberculous Mycobacteria (NTM) isolates from China.

METHODS

A total of 335 NTM isolates were included in our analysis. Broth dilution method was used to determine in vitro drug susceptibility of NTM isolates.

RESULTS

Clarithromycin (CLA) was the most potent drug for Mycobacterium intracellulare (MI). The resistance rate of 244 MI isolates to CLA was 21%, yielding a minimum inhibitory concentrations (MIC)50 and MIC90 of 8 and 64 mg/L, respectively. 51% of 244 MI isolates exhibited resistance to amikacin (AMK). For 91 Mycobacterium abscessus complex (MABC) isolates, 6 (7%) and 49 (54%) isolates were categorized as resistant to CLA at day 3 and 14, respectively. The resistance rate to CLA for Mycobacterium abscessus subspecies abscessus (MAA) was dramatically higher than that for Mycobacterium abscessus subspecies massiliense (MAM). Additionally, the percentage of patients presenting fever in the CLA-susceptible group was significantly higher than that in the CLA-resistant group.

CONCLUSIONS

Our data demonstrate that approximate one fifth of MI isolates are resistant to CLA. We have identified a higher proportion of CLA-resistant MAA isolates than MAM. The patients caused by CLA-resistant MI are at low risk for presenting with fever relative to CLA-susceptible group.

Performance and robustness analysis reveals phenotypic trade-offs in yeast

To design strains that can function efficiently in complex industrial settings, it is crucial to consider their robustness, that is, the stability of their performance when faced with perturbations. In the present study, we cultivated 24 Saccharomyces cerevisiae strains under conditions that simulated perturbations encountered during lignocellulosic bioethanol production, and assessed the performance and robustness of multiple phenotypes simultaneously. The observed negative correlations confirmed a trade-off between performance and robustness of ethanol yield, biomass yield, and cell dry weight. Conversely, the specific growth rate performance positively correlated with the robustness, presumably because of evolutionary selection for robust, fast-growing cells. The Ethanol Red strain exhibited both high performance and robustness, making it a good candidate for bioproduction in the tested perturbation space. Our results experimentally map the robustness-performance trade-offs, previously demonstrated mainly by single-phenotype and computational studies.

Modelling the effects of antibiotic usage in livestock on human salmonellosis

Antibiotic usage in livestock has been suggested as a driver of antimicrobial resistance in human and livestock populations. This has contributed to the implementation of stewardship programs to curtail usage of antibiotics in livestock. However, the consequences of antibiotic curtailment in livestock on human health are poorly understood. There is the potential for increases in the carriage of pathogens such as Salmonella spp. in livestock, and subsequent increases in human foodborne disease. We use a mathematical model fitted to four case studies, ampicillin and tetracycline usage in fattening pig and broiler poultry populations, to explore the impact of curtailing antibiotic usage in livestock on salmonellosis in humans. Increases in the daily incidence of salmonellosis and a decrease in the proportion of resistant salmonellosis were identified following curtailment of antibiotic usage in livestock. The extent of these increases in human foodborne disease ranged from negligible, to controllable through interventions to target the farm-to-fork pathway. This study provides a motivating example of one plausible scenario following curtailment of antibiotic usage in livestock and suggests that a focus on ensuring good farm-to-fork hygiene and livestock biosecurity is sufficient to mitigate the negative human health consequences of antibiotic stewardship in livestock populations.

The balance between antibiotic resistance and fitness/virulence in Pseudomonas aeruginosa: an update on basic knowledge and fundamental research

The interplay between antibiotic resistance and bacterial fitness/virulence has attracted the interest of researchers for decades because of its therapeutic implications, since it is classically assumed that resistance usually entails certain biological costs. Reviews on this topic revise the published data from a general point of view, including studies based on clinical strains or in vitro-evolved mutants in which the resistance phenotype is seen as a final outcome, i.e., a combination of mechanisms. However, a review analyzing the resistance/fitness balance from the basic research perspective, compiling studies in which the different resistance pathways and respective biological costs are individually approached, was missing. Here we cover this gap, specifically focusing on Pseudomonas aeruginosa, a pathogen that stands out because of its extraordinary capacity for resistance development and for which a considerable number of recent and particular data on the interplay with fitness/virulence have been released. The revised information, split into horizontally-acquired vs. mutation-driven resistance, suggests a great complexity and even controversy in the resistance-fitness/virulence balance in the acute infection context, with results ranging from high costs linked to certain pathways to others that are seemingly cost-free or even cases of resistance mechanisms contributing to increased pathogenic capacities. The elusive mechanistic basis for some enigmatic data, knowledge gaps, and possibilities for therapeutic exploitation are discussed. The information gathered suggests that resistance-fitness/virulence interplay may be a source of potential antipseudomonal targets and thus, this review poses the elementary first step for the future development of these strategies harnessing certain resistance-associated biological burdens.

Selection of Multi-Drug Targets against Drug-Resistant Mycobacterium tuberculosis XDR1219 Using the Hyperbolic Mapping of the Protein Interaction Network

Tuberculosis remains the leading cause of death from a single pathogen. On the other hand, antimicrobial resistance (AMR) makes it increasingly difficult to deal with this disease. We present the hyperbolic embedding of the Mycobacterium tuberculosis protein interaction network (mtbPIN) of resistant strain (MTB XDR1219) to determine the biological relevance of its latent geometry. In this hypermap, proteins with similar interacting partners occupy close positions. An analysis of the hypermap of available drug targets (DTs) and their direct and intermediate interactors was used to identify potentially useful drug combinations and drug targets. We identify rpsA and rpsL as close DTs targeted by different drugs (pyrazinamide and aminoglycosides, respectively) and propose that the combination of these drugs could have a synergistic effect. We also used the hypermap to explain the effects of drugs that affect multiple DTs, for example, forcing the bacteria to deal with multiple stresses like ethambutol, which affects the synthesis of both arabinogalactan and lipoarabinomannan. Our strategy uncovers novel potential DTs, such as dprE1 and dnaK proteins, which interact with two close DT pairs: arabinosyltransferases (embC and embB), Ser/Thr protein kinase (pknB) and RNA polymerase (rpoB), respectively. Our approach provides mechanistic explanations for existing drugs and suggests new DTs. This strategy can also be applied to the study of other resistant strains.

Age of Antibiotic Resistance in MDR/XDR Clinical Pathogen of Pseudomonas aeruginosa

Antibiotic resistance in Pseudomonas aeruginosa remains one of the most challenging phenomena of everyday medical science. The universal spread of high-risk clones of multidrug-resistant/extensively drug-resistant (MDR/XDR) clinical P. aeruginosa has become a public health threat. The P. aeruginosa bacteria exhibits remarkable genome plasticity that utilizes highly acquired and intrinsic resistance mechanisms to counter most antibiotic challenges. In addition, the adaptive antibiotic resistance of P. aeruginosa, including biofilm-mediated resistance and the formation of multidrug-tolerant persisted cells, are accountable for recalcitrance and relapse of infections. We highlighted the AMR mechanism considering the most common pathogen P. aeruginosa, its clinical impact, epidemiology, and save our souls (SOS)-mediated resistance. We further discussed the current therapeutic options against MDR/XDR P. aeruginosa infections, and described those treatment options in clinical practice. Finally, other therapeutic strategies, such as bacteriophage-based therapy and antimicrobial peptides, were described with clinical relevance.

Mutators can drive the evolution of multi-resistance to antibiotics

Antibiotic combination therapies are an approach used to counter the evolution of resistance; their purported benefit is they can stop the successive emergence of independent resistance mutations in the same genome. Here, we show that bacterial populations with 'mutators', organisms with defects in DNA repair, readily evolve resistance to combination antibiotic treatment when there is a delay in reaching inhibitory concentrations of antibiotic-under conditions where purely wild-type populations cannot. In populations of Escherichia coli subjected to combination treatment, we detected a diverse array of acquired mutations, including multiple alleles in the canonical targets of resistance for the two drugs, as well as mutations in multi-drug efflux pumps and genes involved in DNA replication and repair. Unexpectedly, mutators not only allowed multi-resistance to evolve under combination treatment where it was favoured, but also under single-drug treatments. Using simulations, we show that the increase in mutation rate of the two canonical resistance targets is sufficient to permit multi-resistance evolution in both single-drug and combination treatments. Under both conditions, the mutator allele swept to fixation through hitch-hiking with single-drug resistance, enabling subsequent resistance mutations to emerge. Ultimately, our results suggest that mutators may hinder the utility of combination therapy when mutators are present. Additionally, by raising the rates of genetic mutation, selection for multi-resistance may have the unwanted side-effect of increasing the potential to evolve resistance to future antibiotic treatments.

The menace of colistin resistance across globe: Obstacles and opportunities in curbing its spread

Colistin-resistance in bacteria is a big concern for public health, since it is a last resort antibiotic to treat infectious diseases of multidrug resistant and carbapenem resistant Gram-negative pathogens in clinical settings. The emergence of colistin resistance in aquaculture and poultry settings has escalated the risks associated with colistin resistance in environment as well. The staggering number of reports pertaining to the rise of colistin resistance in bacteria from clinical and non-clinical settings is disconcerting. The co-existence of colistin resistant genes with other antibiotic resistant genes introduces new challenges in combatting antimicrobial resistance. Some countries have banned the manufacture, sale and distribution of colistin and its formulations for food producing animals. However, to tackle the issue of antimicrobial resistance, a one health approach initiative, inclusive of human, animal, and environmental health needs to be developed. Herein, we review the recent reports in colistin resistance in bacteria of clinical and non-clinical settings, deliberating on the new findings obtained regarding the development of colistin resistance. This review also discusses the initiatives implemented globally in mitigating colistin resistance, their strength and weakness.

Contribution of different class 2 integron elements to fitness costs in multi-drug resistant Escherichia coli and evaluation of their adaptability in “farm-to-table” environments

Integrons play a pivotal role in the dissemination of antimicrobial resistance, because they can capture and express exogenous antimicrobial resistance genes. This study aimed to elucidate the structure and contribution of different elements of class 2 integrons to fitness costs in their host bacteria and evaluate their adaptability to the "farm-to-table" process. We mapped 27 typical class 2 integrons of Escherichia coli isolated from aquatic foods and pork products, each harboring an inactive truncated class 2 integrase gene and the gene cassette (GC) array dfrA1-sat2-aadA1 with strong Pc2A/Pc2B promoters. Notably, the fitness costs associated with class 2 integrons depended on the Pc promoter strength and quantity and content of GCs in the array. Additionally, the costs of integrases were activity-dependent, and a balance was identified between GC capture ability and integron stability, which could explain the inactive truncated integrase identified. Although typical class 2 integrons exhibited low-cost structures in E. coli, the bacteria incurred biological costs, including decreasing growth rates and biofilm formation, in farm-to-table environments, especially under low-nutrient conditions. Nevertheless, sub-inhibitory antibiotic concentrations led to the selection of class 2 integron-carrying bacteria. This study provides important insights into how integrons may travel from preharvest to consumer goods.

Interspecies interaction reduces selection for antibiotic resistance in Escherichia coli

Evolution of microbial traits depends on the interaction of a species with its environment as well as with other coinhabiting species. However, our understanding of the evolution of specific microbial traits, such as antibiotic resistance in complex environments is limited. Here, we determine the role of interspecies interactions on the dynamics of nitrofurantoin (NIT) resistance selection among Escherichia coli. We created a synthetic two-species community comprised of two variants of E. coli (NIT susceptible and resistant) and Bacillus subtilis in minimal media with glucose as the sole carbon source. We show that the presence of B. subtilis significantly slows down the selection for the resistant E. coli mutant when NIT is present and that this slowdown is not due to competition for resources. Instead, the dampening of NIT resistance enrichment is largely mediated by extracellular compounds produced by B. subtilis with the peptide YydF playing a significant role. Our results not only demonstrate the impact of interspecies interactions on the evolution of microbial traits but also show the importance of using synthetic microbial systems in unravelling relevant interactions and mechanisms affecting the evolution of antibiotic resistance. This finding implies that interspecies interactions should be considered to better understand and predict resistance evolution in the clinic as well as in nature.

Heterogeneous Distribution of Proton Motive Force in Nonheritable Antibiotic Resistance

Bacterial infections that are difficult to eradicate are often treated by sequentially exposing the bacteria to different antibiotics. Although effective, this approach can give rise to epigenetic or other phenomena that may help some cells adapt to and tolerate the antibiotics. Characteristics of such adapted cells are dormancy and low energy levels, which promote survival without lending long-term genetic resistance against antibiotics. In this work, we quantified motility in cells of Escherichia coli that adapted and survived sequential exposure to lethal doses of antibiotics. In populations that adapted to transcriptional inhibition by rifampicin, we observed that ~1 of 3 cells continued swimming for several hours in the presence of lethal concentrations of ampicillin. As motility is powered by proton motive force (PMF), our results suggested that many adapted cells retained a high PMF. Single-cell growth assays revealed that the high-PMF cells resuscitated and divided upon the removal of ampicillin, just as the low-PMF cells did, a behavior reminiscent of persister cells. Our results are consistent with the notion that cells in a clonal population may employ multiple different mechanisms to adapt to antibiotic stresses. Variable PMF is likely a feature of a bet-hedging strategy: a fraction of the adapted cell population lies dormant while the other fraction retains high PMF to be able to swim out of the deleterious environment. IMPORTANCE Bacterial cells with low PMF may survive antibiotic stress due to dormancy, which favors nonheritable resistance without genetic mutations or acquisitions. On the other hand, cells with high PMF are less tolerant, as PMF helps in the uptake of certain antibiotics. Here, we quantified flagellar motility as an indirect measure of the PMF in cells of Escherichia coli that had adapted to ampicillin. Despite the disadvantage of maintaining a high PMF in the presence of antibiotics, we observed high PMF in ~30% of the cells, as evidenced by their ability to swim rapidly for several hours. These and other results were consistent with the idea that antibiotic tolerance can arise via different mechanisms in a clonal population.

High-Throughput Mutagenesis Reveals a Role for Antimicrobial Resistance- and Virulence-Associated Mobile Genetic Elements in Staphylococcus aureus Host Adaptation

Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex 398 (CC398) is the dominant livestock-associated (LA) MRSA lineage in European livestock and an increasing cause of difficult-to-treat human disease. LA-CC398 MRSA evolved from a diverse human-associated methicillin-sensitive population, and this transition from humans to livestock was associated with three mobile genetic elements (MGEs). In this study, we apply transposon-directed insertion site sequencing (TraDIS), a high-throughput transposon mutagenesis approach, to investigate genetic signatures that contribute to LA-CC398 causing disease in humans. We identified 26 genes associated with LA-CC398 survival in human blood and 47 genes in porcine blood. We carried out phylogenetic reconstruction on 1,180 CC398 isolates to investigate the genetic context of all identified genes. We found that all genes associated with survival in human blood were part of the CC398 core genome, while 2/47 genes essential for survival in porcine blood were located on MGEs. Gene SAPIG0966 was located on the previously identified Tn916 transposon carrying a tetracycline resistance gene, which has been shown to be stably inherited within LA-CC398. Gene SAPIG1525 was carried on a phage element, which in part, matched phiSa2wa_st1, a previously identified bacteriophage carrying the Panton-Valentine leucocidin (PVL) virulence factor. Gene deletion mutants constructed in two LA-CC398 strains confirmed that the SAPIG0966 carrying Tn916 and SAPIG1525 were important for CC398 survival in porcine blood. Our study shows that MGEs that carry antimicrobial resistance and virulence genes could have a secondary function in bacterial survival in blood and may be important for host adaptation. IMPORTANCE CC398 is the dominant type of methicillin-resistant Staphylococcus aureus (MRSA) in European livestock and a growing cause of human infections. Previous studies have suggested MRSA CC398 evolved from human-associated methicillin-sensitive Staphylococcus aureus and is capable of rapidly readapting to human hosts while maintaining antibiotic resistance. Using high-throughput transposon mutagenesis, our study identified 26 and 47 genes important for MRSA CC398 survival in human and porcine blood, respectively. Two of the genes important for MRSA CC398 survival in porcine blood were located on mobile genetic elements (MGEs) carrying resistance or virulence genes. Our study shows that these MGEs carrying antimicrobial resistance and virulence genes could have a secondary function in bacterial survival in blood and may be important for blood infection and host adaptation.

Antibacterial Nanomaterials: Mechanisms, Impacts on Antimicrobial Resistance and Design Principles

Antimicrobial resistance (AMR) is one of the biggest threats to the environment and health. AMR rapidly invalidates conventional antibiotics, and antimicrobial nanomaterials have been increasingly explored as alternatives. Interestingly, several antimicrobial nanomaterials show AMR-independent antimicrobial effects without detectable new resistance and have therefore been suggested to prevent AMR evolution. In contrast, some are found to trigger the evolution of AMR. Given these seemingly conflicting findings, a timely discussion of the two faces of antimicrobial nanomaterials is urgently needed. This review systematically compares the killing mechanisms and structure-activity relationships of antibiotics and antimicrobial nanomaterials. We then focus on nano-microbe interactions to elucidate the impacts of molecular initiating events on AMR evolution. Finally, we provide an outlook on future antimicrobial nanomaterials and propose design principles for the prevention of AMR evolution.

Ecological life strategies of microbes in response to antibiotics as a driving factor in soils

Antibiotics as a selection pressure driving the evolution of soil microbial communities is not well understood. Since microbial functions govern ecosystem services, an ecological framework is required to understand and predict antibiotic-induced functional and structural changes in microbial communities. Therefore, metagenomic studies explaining the impacts of antibiotics on soil microbial communities were mined, and alterations in microbial taxa were analyzed through an ecological lens using Grimes's Competitor-Stress tolerator-Ruderal (CSR) model. We propose considering antibiotics as the primary abiotic factor mentioned in the CSR model and classifying non-susceptible microbial taxa as degraders, resistant, and resilient groups analogous to competitors, stress tolerators, and ruderal strategists, respectively. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were among the phyla harboring most members with antibiotic-resistant groups. However, some antibiotic-resistant microbes in these phyla could not only tolerate but also subsist solely on antibiotics, while others degraded antibiotics as a part of secondary metabolism. Irrespective of their taxonomic affiliation, microbes with each life strategy displayed similar phenotypic characteristics. Therefore, it is recommended to consider microbial functional traits associated with each life strategy while analyzing the ecological impacts of antibiotics. Also, potential ecological crises posed by antibiotics through changes in microbial community and ecosystem functions were visualized. Applying ecological theory to understand and predict antibiotics-induced changes in microbial communities will also provide better insight into microbial behavior in the background of emerging contaminants and help develop a robust ecological classification system of microbes.

Role of Enzymatic Activity in the Biological Cost Associated with the Production of AmpC β-Lactamases in Pseudomonas aeruginosa

In the current scenario of growing antibiotic resistance, understanding the interplay between resistance mechanisms and biological costs is crucial for designing therapeutic strategies. In this regard, intrinsic AmpC β-lactamase hyperproduction is probably the most important resistance mechanism of Pseudomonas aeruginosa, proven to entail important biological burdens that attenuate virulence mostly under peptidoglycan recycling alterations. P. aeruginosa can acquire resistance to new β-lactam-β-lactamase inhibitor combinations (ceftazidime-avibactam and ceftolozane-tazobactam) through mutations affecting ampC and its regulatory genes, but the impact of these mutations on the associated biological cost and the role that β-lactamase activity plays per se in contributing to the above-mentioned virulence attenuation are unknown. The same questions remain unsolved for plasmid-encoded AmpC-type β-lactamases such as FOX enzymes, some of which also provide resistance to new β-lactam-β-lactamase inhibitor combinations. Here, we assessed from different perspectives the effects of changes in the active center and, thus, in the hydrolytic spectrum resistance to inhibitors of AmpC-type β-lactamases on the fitness and virulence of P. aeruginosa, using site-directed mutagenesis; the previously described AmpC variants T96I, G183D, and ΔG229-E247; and, finally, blaFOX-4 versus blaFOX-8. Our results indicate the essential role of AmpC activity per se in causing the reported full virulence attenuation (in terms of growth, motility, cytotoxicity, and Galleria mellonella larvae killing), although the biological cost of the above-mentioned AmpC-type variants was similar to that of the wild-type enzymes. This suggests that there is not an important biological burden that may limit the selection/spread of these variants, which could progressively compromise the future effectiveness of the above-mentioned drug combinations. IMPORTANCE The growing antibiotic resistance of the top nosocomial pathogen Pseudomonas aeruginosa pushes research to explore new therapeutic strategies, for which the resistance-versus-virulence balance is a promising source of targets. While resistance often entails significant biological costs, little is known about the bases of the virulence attenuations associated with a resistance mechanism as extraordinarily relevant as β-lactamase production. We demonstrate that besides potential energy and cell wall alterations, the enzymatic activity of the P. aeruginosa cephalosporinase AmpC is essential for causing the full attenuation associated with its hyperproduction by affecting different features related to pathogenesis, a fact exploitable from the antivirulence perspective. Less encouraging, we also show that the production of different chromosomal/plasmid-encoded AmpC derivatives conferring resistance to some of the newest antibiotic combinations causes no significantly increased biological burdens, which suggests a free way for the selection/spread of these types of variants, potentially compromising the future effectiveness of these antipseudomonal therapies.

The evolving biology of Mycobacterium tuberculosis drug resistance

Tuberculosis, caused by Mycobacterium tuberculosis (Mtb) is an ancient disease that has remained a leading cause of infectious death. Mtb has evolved drug resistance to every antibiotic regimen ever introduced, greatly complicating treatment, lowering rates of cure and menacing TB control in parts of the world. As technology has advanced, our understanding of antimicrobial resistance has improved, and our models of the phenomenon have evolved. In this review, we focus on recent research progress that supports an updated model for the evolution of drug resistance in Mtb. We highlight the contribution of drug tolerance on the path to resistance, and the influence of heterogeneity on tolerance. Resistance is likely to remain an issue for as long as drugs are needed to treat TB. However, with technology driving new insights and careful management of newly developed resources, antimicrobial resistance need not continue to threaten global progress against TB, as it has done for decades.

Occurrence and Biological Cost of mcr-1-Carrying Plasmids Co-harbouring Beta-Lactamase Resistance Genes in Zoonotic Pathogens from Intensive Animal Production

Colistin is classified as a high-priority critical antimicrobial by the World Health Organization (WHO). A better understanding of the biological cost imposed by mcr-plasmids is paramount to comprehending their spread and may facilitate the decision about the ban of colistin in livestock. This study aimed to assess the prevalence of mcr and ESBL genes from 98 Escherichia coli and 142 Salmonella enterica isolates from food-producing animals and the impact of the mcr-1 acquisition on bacterial fitness. Only mcr-1 was identified by multiplex PCR (mcr-1 to mcr-10) in 15.3% of E. coli. Colistin MICs ranged between 8−32 mg/L. In four isolates, blaTEM-1, blaCTX-M-1, and blaCTX-M-15 co-existed with mcr-1. The IncH12, IncHI1, IncP, IncN, and IncI plasmids were transferred by conjugation to E. coli J53 at frequencies of 10−7 to 10−2 cells/recipient. Growth kinetics assays showed that transconjugants had a significantly lower growth rate than the recipient (p < 0.05), and transconjugants’ average growth rate was higher in the absence than in the presence of colistin (1.66 versus 1.32 (p = 0.0003)). Serial transfer assay during 10 days demonstrated that plasmid retention ranged from complete loss to full retention. Overall, mcr-1-bearing plasmids impose a fitness cost, but the loss of plasmids is highly variable, suggesting that other factors beyond colistin pressure regulate the plasmid maintenance in a bacterial population, and colistin withdrawal will not completely lead to a decrease of mcr-1 levels.

Global epidemiology, genetic environment, risk factors and therapeutic prospects of mcr genes: A current and emerging update

Background

Mobile colistin resistance (mcr) genes modify Lipid A molecules of the lipopolysaccharide, changing the overall charge of the outer membrane.

Results and discussion

Ten mcr genes have been described to date within eleven Enterobacteriaceae species, with Escherichia coli, Klebsiella pneumoniae, and Salmonella species being the most predominant. They are present worldwide in 72 countries, with animal specimens currently having the highest incidence, due to the use of colistin in poultry for promoting growth and treating intestinal infections. The wide dissemination of mcr from food animals to meat, manure, the environment, and wastewater samples has increased the risk of transmission to humans via foodborne and vector-borne routes. The stability and spread of mcr genes were mediated by mobile genetic elements such as the IncHI₂ conjugative plasmid, which is associated with multiple mcr genes and other antibiotic resistance genes. The cost of acquiring mcr is reduced by compensatory adaptation mechanisms. MCR proteins are well conserved structurally and via enzymatic action. Thus, therapeutics found effective against MCR-1 should be tested against the remaining MCR proteins.

Conclusion

The dissemination of mcr genes into the clinical setting, is threatening public health by limiting therapeutics options available. Combination therapies are a promising option for managing and treating colistin-resistant Enterobacteriaceae infections whilst reducing the toxic effects of colistin.

The EnvZ/OmpR Two-Component System Regulates the Antimicrobial Activity of TAT-RasGAP317-326 and the Collateral Sensitivity to Other Antibacterial Agents

The rapid emergence of antibiotic-resistant bacteria poses a serious threat to public health worldwide. Antimicrobial peptides (AMPs) are promising antibiotic alternatives; however, little is known about bacterial mechanisms of AMP resistance and the interplay between AMP resistance and the bacterial response to other antimicrobials. In this study, we identified Escherichia coli mutants resistant to the TAT-RasGAP_317-326 antimicrobial peptide and found that resistant bacteria show collateral sensitivity to other AMPs and antibacterial agents. We determined that resistance to TAT-RasGAP_317-326 peptide arises through mutations in the histidine kinase EnvZ, a member of the EnvZ/OmpR two-component system responsible for osmoregulation in E. coli. In particular, we found that TAT-RasGAP_317-326 binding and entry is compromised in E. coli peptide-resistant mutants. We showed that peptide resistance is associated with transcriptional regulation of a number of pathways and EnvZ-mediated resistance is dependent on the OmpR response regulator but is independent of the OmpC and OmpF outer membrane porins. Our findings provide insight into the bacterial mechanisms of TAT-RasGAP_317-326 resistance and demonstrate that resistance to this AMP is associated with collateral sensitivity to other antibacterial agents. IMPORTANCE Antimicrobial peptides (AMP) are promising alternatives to classical antibiotics in the fight against antibiotic resistance. Resistance toward antimicrobial peptides can occur, but little is known about the mechanisms driving this phenomenon. Moreover, there is limited knowledge on how AMP resistance relates to the bacterial response to other antimicrobial agents. Here, we address these questions in the context of the antimicrobial peptide TAT-RasGAP_317-326. We show that resistant Escherichia coli strains can be selected and do not show resistance to other antimicrobial agents. Resistance is caused by a mutation in a regulatory pathway, which lowers binding and entry of the peptide in E. coli. Our results highlight a mechanism of resistance that is specific to TAT-RasGAP_317-326. Further research is required to characterize these mechanisms and to evaluate the potential of antimicrobial combinations to curb the development of antimicrobial resistance.

Prevalence and characteristics of the mcr-1 gene in retail meat samples in Zhejiang Province, China

Considering the serious threat to food safety and public health posed by pathogens with colistin resistance, colistin was banned as a growth promoter in 2017 in China. In recent years, the resistance rate of Escherichia coli isolated from animal intestines or feces to colistin has decreased. However, the prevalence and characteristics of the mcr-1 gene in retail meat have not been well explored. Herein, 106 mcr-1-negative and 16 mcr-1-positive E. coli isolates were randomly recovered from 120 retail meat samples and screened using colistin. The 106 E. coli isolates showed maximum resistance to sulfafurazole (73.58%) and tetracycline (62.26%) but susceptibility to colistin (0.00%). All 16 mcr-1-positive E. coli isolates showed resistance to colistin, were extended spectrum beta-lactamase (ESBL)-positive and exhibited complex multidrug resistance (MDR). For these 16 isolates, 17 plasmid replicons and 42 antibiotic resistance genes were identified, and at least 7 antibiotic resistance genes were found in each isolate. Acquired disinfectant resistance genes were identified in 75.00% (12/16) of the isolates. Furthermore, comparative genomic and phylogenetic analysis results indicated that these 16 mcr-1-positive E. coli isolates and the most prevalent mcr-1-harboring IncI2 plasmid in this study were closely related to other previously reported mcr-1-positive E. coli isolates and the IncI2 plasmid, respectively, showing their wide distribution. Taken together, our findings showed that retail meat products were a crucial reservoir of mcr-1 during the colistin ban period and should be continuously monitored.

Neglected resistance risks: Cooperative resistance of antibiotic resistant bacteria influenced by primary soil components

Various antibiotic resistant bacteria (ARB) can thrive in soil and resist such environmental pressures as antibiotics through cooperative resistance, thereby promoting ARB retention and antibiotic resistance genes transmission. However, there has been finite knowledge in regard to the mechanisms and potential ecological risks of cooperative resistance in soil microbiome. In this study, soil minerals and organic matters were designed to treat a mixture of two Escherichia coli strains with different antibiotic resistance (E. coli DH5α/pUC19 and E. coli XL2-Blue) to determine how soil components affected cooperative resistance, and Luria-Bertani plates containing two antibiotics were used to observe dual-drug resistant bacteria (DRB) developed via cooperative resistance. Results showed quartz, humic acid, and biochar promoted E. coli XL2-Blue with high fitness costs, whereas kaolin, montmorillonite, and soot inhibited both strains. Using fluorescence microscope and PCR, it was speculated DRB could resist the antibiotic pressure via E. coli XL2-Blue coating E. coli DH5α/pUC19. E. coli DH5α/pUC19 dominated cooperative resistance. Correlation analysis and scanning electron microscope images indicated soil components influenced cooperative resistance. Biochar promoted cooperative resistance by increasing intracellular reactive oxygen species, thereby reducing the dominant strain concentration required for DRB development. Kaolin inhibited cooperative resistance the most, followed by soot and montmorillonite.

MgrB-Dependent Colistin Resistance in Klebsiella pneumoniae Is Associated with an Increase in Host-to-Host Transmission

Due to its high transmissibility, Klebsiella pneumoniae is one of the leading causes of nosocomial infections. Here, we studied the biological cost of colistin resistance, an antibiotic of last resort, in this opportunistic pathogen using a murine model of gut colonization and transmission. Colistin resistance in K. pneumoniae is commonly the result of the inactivation of the small regulatory protein MgrB. Without a functional MgrB, the two-component system PhoPQ is constitutively active, leading to an increase in lipid A modifications and subsequent colistin resistance. Using an isogenic mgrB deletion mutant (MgrB-), we demonstrate that the mutant's colistin resistance is not associated with a fitness defect under in vitro growth conditions. However, in our murine model of K. pneumoniae gastrointestinal (GI) colonization, the MgrB- colonizes the gut poorly, allowing us to identify a fitness cost. Moreover, the MgrB- mutant has higher survival outside the host compared with the parental strain. We attribute this enhanced survivability to dysregulation of the PhoPQ two-component system and accumulation of the master stress regulator RpoS. The enhanced survival of MgrB- may be critical for its rapid host-to-host transmission observed in our model. Together, our data using multiple clinical isolates demonstrate that MgrB-dependent colistin resistance in K. pneumoniae comes with a biological cost in gut colonization. However, this cost is mitigated by enhanced survival outside the host and consequently increases its host-to-host transmission. Additionally, it underscores the importance of considering the entire life cycle of a pathogen to determine the actual biological cost associated with antibiotic resistance. IMPORTANCE The biological cost associated with colistin resistance in Klebsiella pneumoniae was examined using a murine model of K. pneumoniae gut colonization and fecal-oral transmission. A common mutation resulting in colistin resistance in K. pneumoniae is a loss-of-function mutation of the small regulatory protein MgrB that regulates the two-component system PhoPQ. Even though colistin resistance in K. pneumoniae comes with a fitness defect in gut colonization, it increases bacterial survival outside the host enabling it to transmit more effectively to a new host. The enhanced survival is dependent upon the accumulation of RpoS and dysregulation of the PhoPQ. Hence, our study expands our understanding of the underlying molecular mechanism contributing to the transmission of colistin-resistant K. pneumoniae.

A Refunding Scheme to Incentivize Narrow-Spectrum Antibiotic Development

The rapid rise of antibiotic resistance is a serious threat to global public health. The situation is exacerbated by the “antibiotics dilemma”: Developing narrow-spectrum antibiotics against resistant bacteria is most beneficial for society, but least attractive for companies, since their usage and sales volumes are more limited than for broad-spectrum drugs. After developing a general mathematical framework for the study of antibiotic resistance dynamics with an arbitrary number of antibiotics, we identify efficient treatment protocols. Then, we introduce a market-based refunding scheme that incentivizes pharmaceutical companies to develop new antibiotics against resistant bacteria and, in particular, narrow-spectrum antibiotics that target specific bacterial strains. We illustrate how such a refunding scheme can solve the antibiotics dilemma and cope with various sources of uncertainty that impede antibiotic R &D. Finally, connecting our refunding approach to the recently established Antimicrobial Resistance (AMR) Action Fund, we discuss how our proposed incentivization scheme could be financed.

Microbial Community Structure and Bacterial Lineages Associated with Sulfonamides Resistance in Anthropogenic Impacted Larut River

Anthropogenic activities often contribute to antibiotic resistance in aquatic environments. Larut River Malaysia is polluted with both organic and inorganic pollutants from domestic and industrial wastewater that are probably treated inadequately. The river is characterized by high biochemical oxygen demand, chemical oxygen demand, total suspended solids, ammonia, and heavy metals. In our previous study, sulfonamides (SAs) and sulfonamide resistance genes (sul) were detected in the Larut River. Hence, in this study, we further examined the microbial community structure, diversity of sulfonamide-resistant bacteria (SARB), and their resistance genes. The study also aimed at identifying cultivable bacteria potential carriers of sul genes in the aquatic environment. Proteobacteria (22.4–66.0%), Firmicutes (0.8–41.6%), Bacteroidetes (2.0–29.4%), and Actinobacteria (5.5–27.9%) were the most dominant phyla in both the effluents and river waters. SARB isolated consisted only 4.7% of the total genera identified, with SAR Klebsiella as the most dominant (38.0–61.3%) followed by SAR Escherichia (0–22.2%) and Acinetobacter (3.2–16.0%). The majority of the SAR Klebsiella isolated from the effluents and middle downstream were positive for sul genes. Sul genes-negative SAR Escherichia and Acinetobacter were low (<20%). Canonical-correlation analysis (CCA) showed that SAs residues and inorganic nutrients exerted significant impacts on microbial community and total sul genes. Network analysis identified 11 SARB as potential sul genes bacterial carriers. These findings indicated that anthropogenic activities exerted impacts on the microbial community structure and SAs resistance in the Larut River.

Rapid decline of ceftazidime resistance in antibiotic-free and sub-lethal environments is contingent on genetic background

Trade-offs of antibiotic resistance evolution, such as fitness cost and collateral sensitivity (CS), could be exploited to drive evolution toward antibiotic susceptibility. Decline of resistance may occur when resistance to other drug leads to CS to the first one and when compensatory mutations, or genetic reversion of the original ones, reduce fitness cost. Here we describe the impact of antibiotic-free and sublethal environments on declining ceftazidime resistance in different Pseudomonas aeruginosa resistant mutants. We determined that decline of ceftazidime resistance occurs within 450 generations, which is caused by newly acquired mutations and not by reversion of the original ones, and that the original CS of these mutants is preserved. In addition, we observed that the frequency and degree of this decline is contingent on genetic background. Our results are relevant to implement evolution-based therapeutic approaches, as well as to redefine global policies of antibiotic use, such as drug cycling.

Colistin Resistance Mechanisms in Human Salmonella enterica Strains Isolated by the National Surveillance Enter-Net Italia (2016–2018)

Background: A collection of human-epidemiologically unrelated S. enterica strains collected over a 3-year period (2016 to 2018) in Italy by the national surveillance Enter-Net Italia was analysed. Methods: Antimicrobial susceptibility tests, including the determination of minimal inhibitory concentrations (MICs) for colistin, were performed. Colistin resistant strains were analysed by PCR to detect mobile colistin resistance (mcr) genes. In mcr-negative S. enterica serovar Enteritidis strains, chromosomal mutations potentially involved in colistin resistance were identified by a genomic approach. Results: The prevalence of colistin-resistant S. enterica strains was 7.7%, the majority (87.5%) were S. Enteritidis. mcr genes were identified only in one strain, a S. Typhimurium monophasic variant, positive for both mcr-1.1 and mcr-5.1 genes in an IncHI2 ST4 plasmid. Several chromosomal mutations were identified in the colistin-resistant mcr-negative S. Enteritidis strains in proteins involved in lipopolysaccharide and outer membrane synthesis and modification (RfbN, LolB, ZraR) and in a component of a multidrug efflux pump (MdsC). These mutated proteins were defined as possible candidates for colistin resistance in mcr-negative S. Enteritidis of our collection. Conclusions: The colistin national surveillance in Salmonella spp. in humans, implemented with genomic-based surveillance, permitted to monitor colistin resistance, determining the prevalence of mcr determinants and the study of new candidate mechanisms for colistin resistance.

Evolution of fluoroquinolone-resistant Escherichia coli in the gut after ciprofloxacin treatment

BACKGROUND

Three healthy volunteers carried similar quinolone-resistant E. coli (QREC) (pulsed field gel electrophoresis profiles) in their gut before and after 14 days ciprofloxacin treatment. Given the intensity of the selective pressure and the mutagenic properties of quinolones, we determined whether these strains had evolved at the phenotypic and/or genomic levels.

MATERIAL AND METHODS

Commensal QREC from before day-0 (D0), and a month after 14 days of ciprofloxacin (D42) were compared in 3 volunteers. Growth experiments were performed; acetate levels, mutation frequencies, quinolone MICs and antibiotic tolerance were measured at D0 and D42. Genomes were sequenced and single nucleotide polymorphisms (SNPs) between D0 and D42 were analyzed using DiscoSNP and breseq methods. Cytoplasmic proteins were extracted, HPLC performed and proteins identified using X!tandem software; abundances were measured by mass spectrometry using the Spectral Counting (SC) and eXtraction Ion Chromatograms (XIC) integration methods.

RESULTS

No difference was found in MICs, growth characteristics, acetate concentrations, mutation frequencies, tolerance profiles, phylogroups, O-and H-types, fimH alleles and sequence types between D0 and D42. No SNP variation was evidenced between D0 and D42 isolates for 2/3 subjects; 2 SNP variations were evidenced in one. At the protein level, very few significant protein abundance differences were identified between D0 and D42.

CONCLUSION

No fitness, tolerance, metabolic or genomic evolution of commensal QREC was observed overtime, despite massive exposure to ciprofloxacin in the gut. The three strains behaved as if they had been unaffected by ciprofloxacin, suggesting that gut may act as a sanctuary where bacteria would be protected from the effect of antibiotics and survive without any detrimental effect of stress.

Whole-Genome Sequencing Reveals Recent Transmission of Multidrug-Resistant Mycobacterium tuberculosis CAS1-Kili Strains in Lusaka, Zambia

Globally, tuberculosis (TB) is a major cause of death due to antimicrobial resistance. Mycobacterium tuberculosis CAS1-Kili strains that belong to lineage 3 (Central Asian Strain, CAS) were previously implicated in the spread of multidrug-resistant (MDR)-TB in Lusaka, Zambia. Thus, we investigated recent transmission of those strains by whole-genome sequencing (WGS) with Illumina MiSeq platform. Twelve MDR CAS1-Kili isolates clustered by traditional methods (MIRU-VNTR and spoligotyping) were used. A total of 92% (11/12) of isolates belonged to a cluster (≤12 SNPs) while 50% (6/12) were involved in recent transmission events, as they differed by ≤5 SNPs. All the isolates had KatG Ser315Thr (isoniazid resistance), EmbB Met306 substitutions (ethambutol resistance) and several kinds of rpoB mutations (rifampicin resistance). WGS also revealed compensatory mutations including a novel deletion in embA regulatory region (−35A > del). Several strains shared the same combinations of drug-resistance-associated mutations indicating transmission of MDR strains. Zambian strains belonged to the same clade as Tanzanian, Malawian and European strains, although most of those were pan-drug-susceptible. Hence, complimentary use of WGS to traditional epidemiological methods provides an in-depth insight on transmission and drug resistance patterns which can guide targeted control measures to stop the spread of MDR-TB.

Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance

Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.

In vivo Microevolution of Mycobacterium tuberculosis and transient emergence of atpE_Ala63Pro mutation during treatment in a pre-XDR TB patient

Bedaquiline is a novel anti-tuberculosis drug for the treatment of multidrug-resistant tuberculosis (MDR-TB) recommended by the World Health Organization (WHO) [1] and recently upgraded to the group A classification of TB drugs as one of the three key drugs, along with linezolid and fluoroquinolones, to be included in all MDR-TB treatment regimens. Based on this grouping of second-line drugs, extensively drug-resistant tuberculosis (XDR-TB) is redefined as MDR- or rifampicin-resistant-TB that is resistant to a fluoroquinolone and to either bedaquiline or linezolid or both. Moreover, bedaquiline, in combination with pretomanid and linezolid, is a part of BPaL regimen recommended for treating adult pulmonary TB patients having pre-XDR-TB or MDR-TB which is either non-responsive or intolerant to recommended standard treatment [2]. However, globally emerging resistance to bedaquiline threatens the effectiveness of novel treatment regimens for drug-resistant TB.

This letter describes microevolution of a pre-XDR MTB strain isolated from a pulmonary TB patient over an 18-month exposure to BDQ. MDR-TB therapies with BDQ require a functional background regimen to prevent emergence of additional resistance.https://bit.ly/3D05qT9

Characterization of Fitness Cost Caused by Tigecycline-Resistance Gene tet(X6) in Different Host Bacteria

The emergence and prevalence of the tet(X) gene and its variants in the environment and in clinical settings constitute a growing concern for public health worldwide. Accordingly, the tigecycline resistance gene variant tet(X6) is widely detected in Proteus spp. and Acinetobacter spp. rather than Enterobacteriaceae, while the underpinning behind this phenomenon is still unclear. To investigate the mechanisms underlying this distinct phenomenon, we assessed the fitness of the engineered plasmid pBAD-tet(X6) in different host bacteria by monitoring their growth curves, relative fitness and the ability of biofilm formation, as well as virulence in a Galleria mellonella model. MIC and qRT-PCR analysis indicated the successful expression of the tet(X6) gene in these strains in the presence of l-arabinose. Furthermore, we found that pBAD-tet(X6) displayed the lowest fitness cost in P. mirabilis compared with that in E. coli or S. Enteritidis, suggesting the fitness difference of tet(X6)-bearing plasmids in different host bacteria. Consistently, the carriage of pBAD-tet(X6) remarkably reduced the biofilm production and virulence of E. coli or S. Enteritidis. These findings not only indicate that the fitness cost difference elicited by the tet(X6) gene may be responsible for its selectivity in host bacteria but also sheds new insight into the dissemination of antibiotic resistance genes (ARGs) in clinical and environmental isolates.

Fitness cost and compensation mechanism of sulfonamide resistance genes (sul1, sul2, and sul3) in Escherichia coli

The fitness cost of antibiotic resistance is a crucial factor to determine the evolutionary and transmission success of resistant bacteria. Exploring the fitness cost and compensation mechanism of antibiotic resistance genes (ARGs) in bacteria may effectively reduce the transmission of drug-resistant genes in the environment. Engineered bacteria with the same genetic background that carry sulfonamide resistance gene were generated to explore the fitness cost of sulfonamide resistance gene in Escherichia coli. There were significant differences in the protein expression of the two-component system pathway (fliZ, fliA, fliC and lrhA), folate biosynthesis pathway (sul1, sul2 and sul3), ABC transporter system (ugpC, rbsA and gsiA), and outer membrane pore protein OmpD through the comparative analysis of differential proteins compared to sensitive bacteria. Thus, we could speculate the possible fitness compensation mechanism. Finally, quantitative Real-time PCR (qRT-PCR) was used to verify the functions of some differential proteins at the transcriptional level. The fitness cost and compensatory evolution of antibiotic resistance are an essential part of bacterial evolution.