Plasmid-mediated colistin-resistance genes: mcr

The emergence of highly resistant and hypervirulent Escherichia coli ST405 clone in a tertiary hospital over 8 years

The emergence of carbapenem-resistant Escherichia coli (CREC) poses crucial challenges in clinical management, requiring continuous monitoring to inform control and treatment strategies. This study aimed to investigate the genomic and epidemiological characteristics of CREC isolates obtained from a tertiary hospital in China between 2015 and 2022. Next-generation sequencing was used for genomic profiling, and clinical data from patients were integrated into the analysis. ST405 (21.2%), ST167 (20.3%) and ST410 (15.9%) were the most prevalent of the 30 distinct sequence types (STs) identified among the 113 unique CREC isolates. Infections caused by the ST405 CREC clone and severe underlying diseases were associated with higher in-hospital mortality rates, particularly in patients aged ≥65 years. Furthermore, the ST405 clone exhibited a greater number of virulence and resistance genes than non-ST405 CREC clones. The virulence gene eaeX and resistance genes mph(E) and msr(E) were exclusively found in ST405 clones, while other virulence genes (agn43, ipad and malX) and resistance genes (armA, catB3 and arr-3) were more prevalent in this clones. Additionally, ST405 showed higher minimum inhibitory concentrations for both meropenem and imipenem and showed superior growth under the meropenem challenge. Galleria mellonella virulence assays revealed that the ST405 CREC clone was more virulent than other predominant CREC STs. Our findings underscore the clinical threat posed by the ST405 CREC clone, which exhibits both enhanced virulence and extensive drug resistance. These results highlight the urgent need for stringent surveillance and targeted interventions to curb its further dissemination and prevent potential outbreaks.

Emergence of a clinical carbapenem-resistant Escherichia coli co-harboring blandm-5 and mcr-1.1 on the same plasmid

OBJECTIVES

Escherichia coli is a major pathogen, and the emergence of carbapenem-resistant E. coli (CREC) significantly restricts clinical treatment options. Polymyxins are considered the last-line treatment for CREC infections; however, the occurrence of polymyxin-resistant CREC, particularly following reports of plasmid-mediated colistin resistance (mcr), poses an increasing challenge.

METHODS

In this study, we identified a polymyxin-resistant CREC strain isolated from the rectal swab of a patient hospitalized in a hematology ward. Antimicrobial susceptibility testings, S1-PFGE, Southern blot analysis, Conjugation Experiment, whole genome sequencing (WGS) and bioinformatic analysis were used to characterize the strain.

RESULTS

The strain showed resistance to all tested antimicrobial agents except tigecycline. By bioinformatic analysis, the strain was found to carry one copy of the mcr-1.1 gene and two copies of blaNDM-5 genes. One blaNDM-5 and the mcr-1.1 gene were co-located on a plasmid (pCDE2901_MCR-NDM), while the second blaNDM-5 gene resided on another plasmid (pCDE2901_NDM). The blaNDM-5 gene in pCDE2901_MCR-NDM was likely mobilized from pCDE2901_NDM via a transposon. The plasmid pCDE2901_NDM could successfully transferred from the donor strain CDE2901 to the recipient strain EC600, while the plasmid pCDE2901_MCR-NDM was unable to undergo horizontal transfer despite harboring mobile-associated genes.

CONCLUSIONS

Given the critical role of polymyxins in treating CREC infections, the co-transfer of polymyxin and carbapenem resistance may severely undermine the efficacy of clinical therapies. Strengthened surveillance and monitoring are imperative to curtail the spread of extensively drug-resistant (XDR) pathogens.

Mobile genetic elements in Klebsiella pneumoniae

Klebsiella pneumoniae is a clinically important pathogenic bacteria that poses a serious threat to human health. In particular, the emergence of hypervirulent and multidrug-resistant K. pneumoniae has posed great challenges in clinical anti-infective therapy. In the K. pneumoniae genome, mobile genetic elements (MGEs), such as plasmids, prophages, transposons, and insertion sequences, enhance bacterial viability and adaptation by mediating the horizontal transfer of virulence genes, antibiotic resistance genes, and other adaptive genes. This paper reviews the types and characteristics of the main MGEs in K. pneumoniae, focusing on their effects on bacterial virulence and antibiotic resistance, with the aim of providing clues for developing infection control measures and new antibacterial drugs.

Epidemiological and genomic insights of mcr-1-positive colistin-resistant Klebsiella pneumoniae species complex strains from wastewater treatment plants in Shanghai

The emergence of mcr-1-positive Klebsiella pneumoniae species complex (MP-KpSC) poses a significant threat to public health due to its resistance to last-resort antibiotics like colistin. This study aimed to investigate the prevalence, genomic characteristics, and transmission features of MP-KpSC in wastewater treatment plants (WWTPs) in Shanghai, China. A total of 13 (0.36 %) MP-KpSC isolates were identified, including 12 K. pneumoniae and 1 K. quasipneumoniae subsp. similipneumoniae (Kqps). Nine multidrug-resistant (MDR) MP-KpSC and 3 extensively drug-resistant (XDR) MP-KpSC strains were identified. Twenty-two resistance determinants were present in over 30 % of the strains, with the most prevalent being mcr-1 (100 %), floR (84.62 %), mphA (69.23 %), and tet(A) (69.23 %). MP-KpSC exhibited 11 sequence types, 4 plasmid types, 6 mcr-1-flanked regions, 4 clonal groups, and diverse serotypes. In 53.85 % of strains, transposons were identified within the mcr-1-flanked regions. One strain contained both mcr-8.2 and mcr-1 gene. Notably, the mcr-1 gene was identified for the first time in Kqps and was located on the conjugative IncP1 plasmid, with ISApl1 elements upstream of it. Worryingly, two carbapenem- and colistin-resistant XDR MP-KpSC stains, and three possible hypervirulence (hv) were found in MDR MP-KpSC strains. Moreover, multiple virulence genes and mcr-1, on the same contig with IS679 insert element. The evolutionary trajectories of these strains among WWTPs-human-animals were unveiled in Shanghai. The study reveals that WWTPs serve as critical environmental reservoirs for MP-KpSC, highlighting the potential transmission risks posed by XDR and hv strains to both humans and aquatic ecosystems. These findings advocate for the implementation of active surveillance targeting WWTPs to curb the spread of MP-KpSC.

Matrine Restores Colistin Efficacy Against mcr-1-Carrying Escherichia coli

The emergence of mcr-1-mediated colistin resistance has become a critical global health concern, highlighting the urgent need for innovative approaches to restore colistin's therapeutic potential. In this study, we evaluated the antibacterial activity of four matrine-type alkaloids-namely, matrine, oxymatrine, sophocarpine, and sophoramine-against mcr-1-positive Escherichia coli. While these alkaloids showed limited efficacy when used alone, the combination of matrine with colistin exhibited remarkable synergistic effects, as demonstrated by checkerboard assays and time-kill curve analyses. The matrine-colistin combination caused minimal erythrocyte damage while effectively attenuating resistance development in vitro. This synergy was further corroborated in a murine infection model, where the combination significantly reduced bacterial loads in target tissues. Mechanistic studies revealed that the matrine-colistin combination enhances antimicrobial activity by disrupting bacterial membrane integrity, increasing intracellular colistin accumulation, and triggering reactive oxygen species-mediated oxidative damage. Collectively, these findings highlight the potential of matrine as a promising adjuvant to overcome colistin resistance, providing a novel therapeutic approach to address the challenge of infections cause by multidrug-resistant Gram-negative bacteria.

Drivers of the emergence and dissemination of high-risk resistance genes in cattle farm

Extended spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacterales (CPE) are recognized by WHO as critical concerns. The high cephalosporin resistance rate in a cattle farm in 2018 prompted us to conduct long-term (2019-2023) and extensive monitoring to explore risk factors for the import and transmission of ESBLs and CPE in this farm. Among 1288 samples from cattle, the environment, milk, and biological vectors, 48.8 % carried blaCTX-M-positive Enterobacterales with blaCTX-M-55 being dominant (76.4 %), and blaNDM-5-positive strains emerged in 2022 with a 1.9 % detection rate. blaCTX-M-55 and blaNDM-5 were likely introduced through various routes, especially wild birds, and have persisted due to overuse of cephalosporins in the farm. The spread of these genes was driven by the horizontal transmission of IncHI2 and IncX3 plasmids and clonal dissemination of certain clones. Cross-regional and cross-border transmission of blaCTX-M-55- and/or blaNDM-5-bearing bacteria and plasmids possibly occurred via wild birds, animal trade, and other means. Our findings suggest that the import, persistence, and dissemination of these genes within and beyond this farm, were fueled by suboptimal biosecurity practices and inadequate antibiotic stewardship, highlighting the urgency for integrated public and ecosystem health policies to prevent the spread of resistance genes as part of a holistic One Health strategy. ENVIRONMENTAL IMPLICATION: The high prevalence and long-term persistence of extended-spectrum β-lactamases and the emergence of carbapenemases in cattle and the environment signify a critical risk of transmitting high-risk resistance genes, posing a significant threat to human health. Consequently, bacteria carrying these genes in animal farms should be regarded as "hazardous materials". Import, persistence, and dissemination of these genes within and beyond this farm were exacerbated by suboptimal biosecurity practices and inadequate antibiotic stewardship, highlighting the urgency for integrated public and ecosystem health policies to mitigate the environmental risks associated with gene transmission as part of a comprehensive One Health strategy.

Cutting-edge tools for unveiling the dynamics of plasmid-host interactions

The plasmid-mediated transfer of antibiotic resistance genes (ARGs) in complex microbiomes presents a significant global health challenge. This review examines recent technological advancements that have enabled us to move beyond the limitations of culture-dependent detection of conjugation and have enhanced our ability to track and understand the movement of ARGs in real-world scenarios. We critically assess the applications of single-cell sequencing, fluorescence-based techniques and advanced high-throughput chromatin conformation capture (Hi-C) approaches in elucidating plasmid-host interactions at unprecedented resolution. We also evaluate emerging techniques such as CRISPR-based phage engineering and discuss their potential for developing targeted strategies to curb ARG dissemination. Emerging data derived from these technologies have challenged our previous paradigms on plasmid-host compatibility and an awareness of an emerging uncharted realm for ARGs.

In vitro synergistic effects of mefloquine combined with other antimicrobial agents on carbapenem-resistant Enterobacterales

PURPOSE

Human health is seriously threatened by carbapenem-resistant Enterobacterales (CRE) due to the lack of effective treatment. The purpose of this study is to examine the efficacy of mefloquine (MEF) together with multiple drugs against 96 clinical CRE isolates including 94 Klebsiella pneumoniae carbapenemase (KPC)-producers or Metallo-β-lactamases (MBLs)-producers and 2 colistin antibiotic resistance enzyme MCR-1-producers.

METHODS

Using the broth microdilution method, MICs of MEF in combination with multiple antimicrobial agents, including colistin (COL), imipenem, aztreonam-avibactam (ATM-AVI), ceftazidime-avibactam (CAZ-AVI) for 96 CRE isolates were determined. Time-kill assays were implemented for 3 colistin-resistant (COL-R) isolates to analyze in vitro synergistic impacts of COL combined with MEF.

RESULTS

MEF alone showed little antibacterial activity with MICs greater than 128 µg/mL for all the 96 clinical CRE isolates. The addition of MEF (32 µg/mL) increased the sensitivity of almost all strains (98.9%, 95/96) to COL, reducing the MICs range of COL from ≤ 0.0625->8 µg/mL to ≤ 0.004-0.5 µg/mL. In particular, we observed that COL-MEF combination therapy had a significant effect on COL-R isolates, reducing their MICs from resistance to susceptibility. Moreover, the MIC50 and MIC90 of imipenem were both reduced by 2-fold in almost all strains with the addition of MEF (32 µg/mL), and in single MBL-producers, the MIC50 (from 16 to 4 µg/mL) and MIC90 (from 128 to 32 µg/mL) were both reduced by 4-fold. In addition, the MIC50 and MIC90 values of 96 CRE isolates of CAZ-AVI and ATM-AVI did not decrease significantly after combined with MEF (32 µg/mL). For the time-kill assays of 3 COL-R isolates, COL or MEF alone had almost no killing effect, however, when MEF was combined with COL, the isolates were completely killed within 4 h, and NDM-5-producing Klebsiella pneumoniae did not regenerate within 24 h.

CONCLUSIONS

According to our study, COL-MEF may offer a potential alternative for treating CRE infections, especially COL-R Gram-negative bacterial infections.

Emergence of an XDR Klebsiella pneumoniae ST5491 strain co-harboring NDM-5, MCR-1.1, tmexCD1-toprJ1, and a novel plasmid carrying CTX-M-15

Objective

The rapid emergence of antimicrobial resistance (AMR) in Klebsiella pneumoniae poses a significant global health threat. The study aimed to analyze and describe the genomic architecture and resistance mechanisms of an extensively drug-resistant (XDR) K. pneumoniae isolate, KP09, by focusing on plasmids that harbor multiple resistance genes, including tmexCD1-toprJ1, blaCTX-M-15 , blaNDM-5 , and mcr-1.1.

Methods

The KP09 strain, isolated from a clinical sample, was subjected to antimicrobial susceptibility testing and conjugation experiments. Whole-genome sequencing with both long- and short-read methods facilitated hybrid assembly for complete genome reconstruction. Bioinformatics analyses identified resistance genes, plasmid structures, and sequence types (STs), whereas comparative genomic analysis elucidated the context and dissemination mechanisms of resistance determinants.

Results

KP09 exhibited broad-spectrum resistance to carbapenems, colistin, eravacycline, and tigecycline, and only remained susceptible to cefiderocol. The conjugation experiments successfully produced four transconjugants, each carrying specific plasmids: JKP09-1 harbored the tmexCD1-toprJ1 gene, JKP09-2 harbored tmexCD1-toprJ1 and mcr-1.1 genes, JKP09-3 harbored the mcr-1.1 gene, and JKP09-4 harbored blaNDM-5 and mcr-1.1 genes. Genomic analysis revealed a novel IncFIA/IncFII/IncQ1 hybrid plasmid carrying bla CTX-M-15, along with a large conjugative plasmid encoding the tmexCD1-toprJ1 efflux pump. The bla NDM-5 and mcr-1.1 genes were located in separate IncX-type plasmids, suggesting independent dissemination pathways. Furthermore, KP09 was identified as a new sequence type, ST5491, closely related to the endemic ST15 clone. The comparative analysis highlighted the role of mobile genetic elements, such as IS26 and ISEcp1, in facilitating the spread of resistance genes.

Conclusion

This study provides critical information on the genetic mechanisms that drive AMR in K. pneumoniae, including the identification of a novel bla CTX-M-15 encoding IncFIA/IncFII/IncQ1 hybrid plasmid and the emergence of the ST5491 strain. Understanding the genetic basis of resistance is essential to inform public health interventions and mitigate the impact of AMR.

Development of nanovehicles for co-delivery of colistin and ArnT inhibitors

Antimicrobial resistance (AMR) represents a critical global health challenge, with increasing prevalence among high-priority pathogens such as Pseudomonas aeruginosa. Colistin, a last-resort antibiotic, faces limitations in efficacy due to toxicity and bacterial resistance, primarily driven by lipid A modifications that impair colistin binding. In P. aeruginosa, resistance to colistin is mainly due to activation of the arn operon whose last enzyme is ArnT. This study explores a liposomal nanocarrier approach to co-deliver colistin with an ArnT inhibitor, isostevic acid (ISA), aiming to restore colistin's efficacy against resistant P. aeruginosa strain. We designed liposomes incorporating colistin in the aqueous core and ISA within the lipid bilayer, optimizing formulations to achieve stable, high-efficiency encapsulation by varying the cholesterol/egg phosphatidylcholine ratios. These co-loaded liposomes demonstrated enhanced antimicrobial activity, significantly lowering the minimum inhibitory concentration (MIC) of colistin against resistant strain. The dual-drug liposomes also achieved bactericidal effects at lower colistin concentrations compared to the free drug, attributed to the synergistic action of ISA as an adjuvant that locks colistin resistance mechanisms. The results suggest that liposome-mediated co-delivery of colistin and ISA offers a promising strategy to counteract colistin-resistant infections. This approach could improve the clinical management of multidrug-resistant P. aeruginosa and highlights the potential for liposomal systems to modulate drug release and target bacterial resistance mechanisms.

Synergistic activity of menadione in combination with colistin against colistin-susceptible and colistin-resistant Gram-negative bacteria

OBJECTIVE

Antibiotic resistance poses a formidable challenge, especially with the emergence of multidrug-resistant Gram-negative bacteria. Colistin serves as a last-resort antibiotic to combat multidrug-resistance, but it is limited by its nephrotoxicity and rising resistance. This study introduces menadione, a synthetic form of vitamin K, as a potential adjuvant to enhance colistin's efficacy against both susceptible and resistant strains of Gram-negative bacteria.

METHODS

Through checkerboard dilution assays, we demonstrate that menadione significantly lowers the MICs of colistin, with fractional inhibitory concentration indices ranging from 0.031 to 0.375. Furthermore, synergistic effects were confirmed via time-kill kinetics, indicating effective bacterial growth inhibition. The study also explores the mechanism underlying this synergy, revealing that menadione in combination with colistin disrupts the bacterial outer membrane, reduces the proton motive force and adenosine triphosphate content, and amplify the production of reactive oxygen species, contributing to bacterial cell death.

RESULTS

Menadione was shown to prevent the evolution of colistin resistance.

CONCLUSIONS

This research highlights the potential of using menadione as a colistin adjuvant to combat antibiotic-resistant Gram-negative bacteria, providing a promising approach to extend the utility of existing antibiotics in clinical settings.

Inhibitory effects of benzyl isothiocyanate on widespread mcr-1-harbouring IncX4 plasmid transfer

The global dissemination of mobile colistin resistance (mcr) genes represents a significant public health threat due to colistin's critical role in treating multidrug-resistant (MDR) bacterial infections. We identified high rates of carbapenem resistance in Escherichia coli (27.82%) and Klebsiella pneumoniae (57.98%) and colistin resistance in E. coli (7.52%) and K. pneumoniae (19.68%) among MDR clinical isolates in Thailand. We reported sequences of self-transferable IncX4 plasmids (~ 34 kb) that facilitated the spread of the mcr-1.1 gene among six diverse MDR strains, often co-transferring blaCTX-M-55. Additionally, E. coli ST101 was found to co-transfer mcr-1.1, mcr-3.5, blaCTX-M-55, and tet(X4) via three plasmids (~ 34-kb IncX4, ~ 84-kb IncFII, ~ 278-kb IncHI2), resulting in increases in MICs for colistin, ceftriaxone, and tigecycline. Core SNP analysis revealed that closely related IncX4 plasmids harbouring mcr-1 (< 35 SNP differences) were reported from at least 12 countries. We first demonstrated the inhibitory effects of benzyl isothiocyanate (BITC) on the conjugation of mcr-1-bearing IncX4 plasmids to 1.57 ± 1.00% to 48.86 ± 12.31% relative to control (100%), targeting VirB4 and VirB11 proteins, reducing ATPase activity by over 30%. This study highlights the widespread mcr-1-harbouring IncX4 plasmids and proposes BITC as a potential inhibitor to control the dissemination of colistin resistance.

Synergistic Antibacterial Activity of Amorolfine Combined with Colistin Against Acinetobacter baumannii

Emerging resistance to colistin in Acinetobacter baumannii is concerning because of the limited therapeutic options for this important clinical pathogen. Given the shortage of new antibiotics, one strategy that has been proven to be therapeutically effective is to overcome antibiotic-resistant pathogens by combining existing antibiotics with another antibiotic or non-antibiotic. This study was designed to investigate the potential synergistic antibacterial activity of amorolfine, a morpholine antifungal drug, in combination with colistin against A. baumannii. In this work, antibiotic susceptibility testing, checkerboard assays, and time-kill curves were used to investigate the synergistic efficacy of colistin combined with amorolfine. The molecular mechanisms of combination therapy were analyzed using fluorometric assays, UV-vis spectroscopy, and molecular docking. Finally, we evaluated the in vivo efficacy of combination therapy against A. baumannii. In brief, the combination therapy showed significant synergistic activity against A. baumannii (FICI = 0.094). In addition, the combination of amorolfine improved the membrane disruption of colistin, and amorolfine exhibited the capacity of binding to DNA. Moreover, in a mouse sepsis model, this combination therapy increased survival compared to colistin monotherapy. Our findings demonstrated that amorolfine serves as a potential colistin adjuvant against Acinetobacter baumannii.

Revisiting therapeutic options against resistant klebsiella pneumoniae infection: Phage therapy is key

Multi-drug resistant and carbapenem-resistant hypervirulent Klebsiella pneumoniae strains are spreading globally at an alarming rate, emerging as one of the most serious threats to global public health. The formidable challenges posed by the current arsenal of antimicrobials highlight the urgent need for novel strategies to combat K. pneumoniae infections. This review begins with a comprehensive analysis of the global dissemination of virulence factors and critical resistance profiles in K. pneumoniae, followed by an evaluation of the accessibility of novel therapeutic approaches for treating K. pneumoniae in clinical settings. Among these, phage therapy stands out for its considerable potential in addressing life-threatening K. pneumoniae infections. We critically examine the existing preclinical and clinical evidence supporting phage therapy, identifying key limitations that impede its broader clinical adoption. Additionally, we rigorously explore the role of genetic engineering in expanding the host range of K. pneumoniae phages, and discuss the future trajectory of this technology. In light of the 'Bad Bugs, No Drugs' era, we advocate leveraging artificial intelligence and deep learning to optimize and expand the application of phage therapy, representing a crucial advancement in the fight against the escalating threat of K. pneumoniae infections.

Genomic analyses reveal presence of extensively drug-resistant Salmonella enterica serovars isolated from clinical samples in Guizhou province, China, 2019-2023

Background

The emergence of extensively drug-resistant (XDR) Salmonella in humans poses a significant public health and therapeutic challenge. However, limited data are available on XDR Salmonella isolates from Guizhou province, China. This study aimed to investigate the molecular epidemiology and resistance patterns of XDR Salmonella isolates from clinical samples in this region.

Methods

A total of 931 Salmonella isolates were screened for XDR isolates through antimicrobial susceptibility testing. These XDR isolates were subjected to whole-genome sequencing (WGS) and bioinformatic analysis to further systematically investigating the molecular epidemiology and resistance patterns of XDR Salmonella isolates.

Results

Between 2019 and 2023, 931 Salmonella isolates were collected from clinical samples in Guizhou. Of these isolates, 51 (5.5%) were identified as XDR and classified into 16 serovars. Among the serovars, 15 corresponded to a specific sequence type, except for S. Typhimurium serovars. The predominant serovars, S. 1,4,[5],12:i:-, S. Enteritidis, and S. Kentucky, were divided into ST34, ST11, and ST198, respectively. Genomic analysis showed that all XDR isolates harbored at least eight antimicrobial resistance genes (ARGs) and multidrug efflux pumps. Highly prevalent point mutations in gyrA (D87 and S83) and parC (S80I) were detected, along with eight plasmid-mediated quinolone resistance (PMQR) genes. The qnrS1 gene was the most common (43.1%), followed by oqxA, aac-(6')-lb-cr variant, qnrB4, qnrS2, qnrA1, qepA2, and oqxB. The predominant β-lactamase gene was blaTEM-1 (54.9%), and blaCTX-M-55 (35.3%) was the most prevalent extended-spectrum β-lactamase subtype. Notably, blaNDM-1 gene was identified for the first time in Salmonella from Guizhou, and one S. 1,4,[5],12:i:- isolate contained the mcr-1.1 gene. ARGs profiles varied by serovars, with S. 1,4,[5],12:i:- isolates carrying the highest number. Ten plasmid types were identified, predominantly IncHI2/IncHI2A (47.5%). Key resistance genes such as tetA, PMQR, blaCTX-M , mcr-1.1, and blaNDM-1 were located on IncHI2/IncHI2A plasmids. Notably, 75.0% of the conjugative plasmids belonged to IncHI2/IncHI2A, indicating that horizontal gene transfer through conjugation facilitates ARGs dissemination. Core genome multilocus sequence typing (cgMLST) analysis revealed significant genetic diversity, with 39 core genome sequence types (cgSTs) identified and no evidence of outbreaks.

Conclusion

The rising prevalence of XDR Salmonella in Guizhou province is concerning. Initial whole-genome sequencing (WGS) data provide critical insights for understanding and controlling XDR Salmonella infections, aiding public health officials in identifying emerging threats and trends.

Inosine monophosphate overcomes the coexisting resistance of mcr-1 and blaNDM-1 in Escherichia coli

INTRODUCTION

The rise of antibiotic-resistant bacteria, particularly those harboring mcr-1 and blaNDM-1, threatens public health by reducing the efficacy of colistin and carbapenems. Recently, the co-spread of mcr-1 and blaNDM-1 has been reported, and the emergence of dual-resistant Enterobacteriaceae severely exacerbates antimicrobial resistance.

OBJECTIVES

This study aims to investigate the impact of mcr-1 and blaNDM-1 expression on metabolism in Escherichia coli and to identify potential antimicrobial agents capable of overcoming the resistance conferred by these genes.

METHODS

We employed non-targeted metabolomics to profile the metabolic perturbations of E. coli strains harboring mcr-1 and blaNDM-1. The bactericidal effects of the differential metabolite, inosine monophosphate (IMP), were assessed both in vitro using time-killing assays and in vivo using a mouse infection model. The antimicrobial mechanism of IMP was elucidated through transcriptomic analysis and biochemical approaches.

RESULTS

Metabolic profiling revealed significant alterations in the purine pathway, with IMP demonstrating potent bactericidal activity against E. coli strains carrying both resistance genes. IMP increased membrane permeability, disrupted proton motive force, reduced ATP levels, induced oxidative damage by promoting reactive oxygen species and inhibiting bacterial antioxidant defenses, and improved the survival rate of infected mice.

CONCLUSION

Our findings suggest that IMP could be a promising candidate for combating mcr-1 and blaNDM-1-mediated resistance and provide a novel approach for discovering antimicrobial agents against colistin- and carbapenem-resistant bacteria.

Insights into biofilm-mediated mechanisms driving last-resort antibiotic resistance in clinical ESKAPE pathogens

The rise of antibiotic-resistant bacteria poses a grave threat to global health, with the ESKAPE pathogens, which comprise Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. being among the most notorious. The World Health Organization has reserved a group of last-resort antibiotics for treating multidrug-resistant bacterial infections, including those caused by ESKAPE pathogens. This situation calls for a comprehensive understanding of the resistance mechanisms as it threatens public health and hinder progress toward the Sustainable Development Goal (SDG) 3: Good Health and Well-being. The present article reviews resistance mechanisms, focusing on emerging resistance mutations in multidrug-resistant ESKAPE pathogens, particularly against last-resort antibiotics, and describes the role of biofilm formation in multidrug-resistant ESKAPE pathogens. It discusses the latest therapeutic advances, including the use of antimicrobial peptides and CRISPR-Cas systems, and the modulation of quorum sensing and iron homeostasis, which offer promising strategies for countering resistance. The integration of CRISPR-based tools and biofilm-targeted approaches provides a potential framework for managing ESKAPE infections. By highlighting the spread of current resistance mutations and biofilm-targeted approaches, the review aims to contribute significantly to advancing our understanding and strategies in combatting this pressing global health challenge.

Recent advances and challenges in metal-based antimicrobial materials: a review of strategies to combat antibiotic resistance

Despite the availability of a series of classical antibiotic drugs, bacterial infections continue to represent a significant and urgent threat to global human health. The emergence of drug-resistant bacteria and the slow pace of antibiotic development have rendered current treatment methods inadequate in meeting the clinical demands of bacterial infections. Consequently, there is an increasingly urgent and vital need for the development of safe, efficient, and alternative novel antimicrobial agents in the medical and healthcare field. Over the past five years, there has been a notable expansion in the field of nanomedicine with regard to the prevention and control of infectious diseases. The objective of this article is to provide a comprehensive review of the latest research developments in the field of metal nanomaterials for medical antimicrobial therapy. We begin by delineating the gravity of the bacterial infection crisis, subsequently undertaking a comprehensive examination of the potential mechanisms through which nanoparticles may combat bacterial infections and the specific applications of these nanomaterials in the treatment of diverse infectious diseases. In conclusion, we eagerly anticipate the future development directions of metal nanomaterials in the field of antimicrobial therapy. We believe that with continuous technological advancements and innovations, this field will make even more outstanding contributions to safeguarding human health and well-being.

Comprehensive analysis of Enterobacteriaceae IncX plasmids reveals robust conjugation regulators PrfaH, H-NS, and conjugation-fitness tradeoff

Conjugative IncX plasmids are vital for spreading clinically significant antibiotic resistance genes. We identified key factors governing the conjugative process of IncX plasmids, the plasmid encoded activator PrfaH and inhibitor H-NS. Deletion of prfaH completely abolishes conjugative transfer, and the PrfaH binding site is an ops-like sequence located downstream of the prfaH promoter. We solved the crystal structure of PrfaH and identified the residues that likely mediate interactions with its target. The IncX3 plasmid-encoded H-NS inhibits conjugation by directly repressing PrfaH expression, while simultaneously enhancing host fitness. This tradeoff between plasmid conjugation and fitness is indispensable for plasmid persistence in nutrient-deprived environments. The presence of PrfaH paralogs in various antibiotic resistance plasmids suggests its fundamental role in regulating plasmid transfer. Our study not only elucidates the regulatory mechanisms behind the horizontal transfer of IncX plasmids but also highlights PrfaH as a potential target for strategies aimed at combating antimicrobial resistance.

DNA Polymerase IV dinB Favors the Adaptive Fitness of mcr-carrying Bacteria Through a Negative Feedback Regulatory Mechanism

The plasmid-borne resistance gene mcr drastically undermines the effectiveness of colistin, posing a substantial threat to public health. Although several key plasmid elements that balance mcr-1 persistence and bacterial growth are identified, the regulatory interactions between mcr-1 and host bacteria remain poorly understood. Using a genome-wide CRISPRi crRNA library, it is identified that DNA polymerase IV, dinB, is essential for controlling the fitness cost associated with mcr-1 in Escherichia coli. The absence of dinB operon enhances mcr-1-mediated colistin resistance but simultaneously compromises bacterial growth and competitiveness. Meanwhile, dinB deficiency mitigates inflammatory response in RAW267.4 cells and enhances bacterial colonization in murine tissues. Further investigation reveals that mcr-1 actively upregulates dinB expression, with the increased reactive oxygen species induced by mcr-1 being crucial for this activation.   These findings suggest that dinB modulates mcr expression and bacterial fitness via a negative feedback regulatory mechanism. Leveraging this regulatory relationship, a Toxin-Intein is engineered under the control of dinB promoter to selectively target and kill mcr-positive E. coli both in vitro and in vivo. Overall, the work uncovers a novel adaptive mechanism underlying mcr persistence and provides a precise antimicrobial strategy to combat antibiotic-resistant pathogens.

Genomic diversity of mcr-carrying plasmids and the role of type IV secretion systems in IncI2 plasmids conjugation

The rapid dissemination of colistin resistance via mcr-carrying plasmids (pMCRs) poses a significant public health challenge. This study examined the genomic diversity and conjugation mechanisms of pMCRs, with a particular focus on the role of type IV secretion systems (T4SS) in IncI2 plasmids. The 868 complete plasmid sequences revealed various replicon types of pMCRs, with IncI2 as the primary epidemic type, and the co-transfer risk of multidrug resistance genes associated with IncHI2. T4SS was identified in 89.9% of pMCRs, with the T4SS sequence exclusively carried by IncI2 being conserved and typical of the VirB/D4 type, consisting of 12 subunits. Conjugation assays confirmed the essential role of the pilus subunit VirB2 and the significant impact of VirB5P3 on conjugation. This was further validated in the in vivo intra-species competitive conjugation of Escherichia coli. Structural predictions show that a hypervariable region at the C-terminus of the pentameric VirB5 co-evolves in sequence with VirB6, and the conserved N-terminal may act as a potential drug target to inhibit the plasmid transfer channel. This study will deepen the understanding of the pMCR epidemic patterns and provide additional insights for controlling the spread of resistant plasmids.

A noncanonical intrinsic terminator in the HicAB toxin-antitoxin operon promotes the transmission of conjugative antibiotic resistance plasmids

Conjugative plasmids, major vehicles for the spread of antibiotic resistance genes, often contain multiple toxin-antitoxin (TA) systems. However, the physiological functions of TA systems remain obscure. By studying two TA families commonly found on colistin-resistant IncI2 mcr-1-bearing plasmids, we discovered that the HicAB TA, rather than the StbDE TA, acts as a crucial addiction module to increase horizontal plasmid-plasmid competition. In contrast to the canonical type II TA systems in which the TA genes are cotranscribed and/or the antitoxin gene has an additional promoter to allow for an increased antitoxin/toxin ratio, the HicAB TA system with the toxin gene preceding the antitoxin gene employs internal transcription termination to allow for a higher toxin production. This intrinsic terminator, featuring a G/C-rich hairpin with a UUU tract, lies upstream of the antitoxin gene, introducing a unique mechanism for the enhancing toxin/antitoxin ratio. Critically, the hicAB TA significantly contributes to plasmid competition and plasmid persistence in the absence of antibiotic selection, and deleting this intrinsic terminator alone diminishes this function. These findings align with the observed high occurrence of hicAB in IncI2 plasmids and the persistence of these plasmids after banning colistin as a feed additive. This study reveals how reprogramming the regulatory circuits of TA operons impacts plasmid occupancy in the microbial community and provides critical targets for combating antibiotic resistance.

Acquired Bacterial Resistance to Antibiotics and Resistance Genes: From Past to Future

The discovery, commercialization, and regular administration of antimicrobial agents have revolutionized the therapeutic paradigm, making it possible to treat previously untreatable and fatal infections. However, the excessive use of antibiotics has led to develop resistance soon after their use in clinical practice, to the point of becoming a global emergency. The mechanisms of bacterial resistance to antibiotics are manifold, including mechanisms of destruction or inactivation, target site modification, or active efflux, and represent the main examples of evolutionary adaptation for the survival of bacterial species. The acquirement of new resistance mechanisms is a consequence of the great genetic plasticity of bacteria, which triggers specific responses that result in mutational adaptation, acquisition of genetic material, or alteration of gene expression, virtually producing resistance to all currently available antibiotics. Understanding resistance processes is critical to the development of new antimicrobial agents to counteract drug-resistant microorganisms. In this review, both the mechanisms of action of antibiotic resistance (AMR) and the antibiotic resistance genes (ARGs) mainly found in clinical and environmental bacteria will be reviewed. Furthermore, the evolutionary background of multidrug-resistant bacteria will be examined, and some promising elements to control or reduce the emergence and spread of AMR will be proposed.

Emerging Mobile Colistin Resistance Gene Mcr-1 and Mcr-10 in Enterobacteriaceae Isolates From Urban Sewage in China

Purpose

This study aimed to investigate the epidemiology and dissemination of mcr-positive Enterobacteriaceae in urban sewage in Yangzhou, China.

Methods

A total of 366 sewage samples were collected from the Yangzhou Wastewater Treatment Plant in Jiangsu Province. Colistin-resistant Enterobacteriaceae was identified through PCR targeting mcr-1 to mcr-10 genes. The isolates underwent antimicrobial susceptibility testing, and whole-genome sequencing was performed to analyze their genomic features. Additionally, conjugation experiments were conducted to assess the transferability of mcr-positive plasmids.

Results

Three mcr-positive Enterobacteriaceae isolates were identified, representing an isolation rate of 0.82%. These included one mcr-1-positive Escherichia coli (ST167) and two mcr-10-positive Klebsiella pneumoniae complex strains with novel sequence types ST6801 and ST6825. The mcr-1 gene was located on an IncI2 plasmid (pYZ22WS208_3) and successfully transferred to recipient strains. In contrast, the mcr-10 gene was carried on IncF plasmids (pYZ22WS067_1 and pYZ22WS223_1) but was not transferable in this study. Phylogenetic analysis revealed that the mcr-1-positive E. coli strain clustered within Clade II, alongside strains from various countries and sources. Phylogenomic analysis of mcr-10-positive isolates showed their sporadic distribution across 13 countries, with associations to diverse hosts and environments, indicating potential for widespread transmission.

Conclusion

This study demonstrates the presence of mcr-1 and mcr-10-positive Enterobacteriaceae in wastewater, emphasizing the importance of wastewater surveillance for tracking antibiotic resistance. The horizontal transfer of mcr-1 and potential spread of mcr-10 across various hosts underscore the need for ongoing monitoring and preventive measures.

Comprehensive genomic insights into a highly pathogenic clone ST656 of mcr8.1 containing multidrug-resistant Klebsiella pneumoniae from Bangladesh

Antimicrobial resistance (AMR) is a pressing global health issue, intensified by the spread of resistant pathogens like Klebsiella pneumoniae (K. pneumoniae), which frequently causes hospital-acquired infections. This study focuses on a multidrug-resistant K. pneumoniae sequence type (ST) 656 strain, isolated from canal water in Bangladesh. Whole-genome sequencing and comparative genomic analysis revealed extensive resistance mechanisms and genetic elements underlying its adaptability. The strain exhibited resistance to colistin and multiple β-lactam antibiotics, containing key resistance genes such as mcr8.1, blaLAP-2, blaTEM-1, blaSHV-11 and blaOXA-1, alongside genes for copper, zinc, and silver resistance, indicating survival capability in metal-rich environments. Virulence factor analysis identified genes supporting adhesion, biofilm formation, and immune evasion, amplifying its pathogenic potential. Plasmid and phage analyses revealed mobile genetic elements, highlighting the role of horizontal gene transfer in AMR dissemination. The study included a pangenome analysis using a dataset of 32 publicly available K. pneumoniae sequence type (ST) 656 genomes, demonstrating evidence of an expanding pangenome for K. pneumoniae ST656. This study emphasized the role of environmental sources in AMR spread and the importance of continued surveillance, particularly in settings with intensive antibiotic usage, to mitigate the spread of high-risk, multidrug-resistant clones like K. pneumoniae ST656.

Genomic Insights into Colistin and Tigecycline Resistance in ESBL-Producing Escherichia coli and Klebsiella pneumoniae Harboring blaKPC Genes in Ecuador

Introduction: Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) are resistant to third-generation cephalosporins (3GCs), carbapenems, colistin, and tigecycline, making them a major public health priority, mainly within the developing world. However, their genomic epidemiology and possible determinants of resistance remain to be elucidated. Thus, this study aimed to perform a genomic characterization of E. coli and K. pneumoniae, both of which are resistant to last-line antibiotics, isolated from humans, poultry, and a dairy farm environment within Ecuador. Methods: This study analyzed nine 3GC-resistant E. coli isolates harboring the mcr-1 gene (six from poultry farms, two from human infections, and one from dairy farm compost), together with ten isolated colistin- and carbapenem-resistant K. pneumoniae clinical samples. Results: The E. coli isolates of human origin belonged to ST609 and phylogroup A, while the poultry and compost isolates belonged to phylogroups A, B1, E, and F. Diverse STs of the K. pneumoniae isolates included ST13 (five isolates), ST258 (four isolates), and ST86 (one isolate). Within the E. coli isolates, blaCTX-M-55, blaCTX-M-65, blaCTX-M-15, and blaCTX-M-2 genes were identified. This study also identified blaCMY-2 and blaKPC-3 (the latter in a carbapenem-susceptible isolate). In E. coli, the plasmid-borne mcr-1.1 gene was identified across all E. coli isolates within an IncI2 plasmid. Tigecycline-reduced susceptibility or resistance was related to missense amino acid substitutions coded in the marA and acrA genes. Within K. pneumoiae, blaCTX-M-15 and blaCTX-M-65, on the one hand, and blaKPC-2 and blaKPC-3, on the other, were associated with 3GC and carbapenem resistance, respectively. The blaKPC-2 allele was identified in a ~10 kb Tn4401 transposon (tnpR-tnpA-istA-istB-blaKPC-2-tnpA). In K pneumoniae, sequence data and phenotypic analysis linked a nonsense amino acid substitution coded in the mgrB (K3*) gene and missense amino acid substitutions coded in the marA, acrA, arnB, eptA, pmrB, pmrJ, and phoQ genes to colistin resistance. Meanwhile, tigecycline resistance was linked to nonsense and missense amino acid substitutions coded within the ramR sequence. Additionally, this study identified several integron structures, including Int191 (5'CS-dfrA14-3'CS), which was the most prevalent integron (Int) among E. coli and K. pneumoniae isolates in this study, followed by Int0 (5'CS-3'CS) and Int18 (5'CS-dfrA1-3'CS). Conclusions: These results contribute to the genomic epidemiology of MDR E. coli and K. pneumoniae in our setting and to the worldwide epidemiology in the One Health approach.

Characterization of non-typhoidal Salmonella reveals the highly prevalent mcr-1-positive S. 1,4,[5],12:i:- within eggs are derived from chickens

Salmonella is one of the most common foodborne pathogens. Antimicrobial-resistant Salmonella isolates, especially those resistant to colistin, pose a significant threat to public health worldwide. However, data about the prevalence of mcr-positive Salmonella in animals was few and the dissemination of mcr-positive Salmonella from animals to food, especially eggs, has not been fully addressed. The role of houseflies in the Salmonella transmission has also not been clarified. Here, we analyzed the prevalence and resistance characteristics of mcr-positive Salmonella in 1707 samples of animals (commercial laying hens, broilers, waterfowls and swine), eggs and flies from 23 farms in four cities of China between July 2021 and October 2022. Pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS) analyses of Salmonella from different sources were further performed. Among animals, waterfowls had the highest isolation rate of Salmonella (18.1 %, 35/193), followed by swine (6.1 %, 23/377), laying hens (4.2 %, 21/505) and broilers (1.4 %, 7/489). Two of the 53 flies (3.8 %) carried Salmonella. The detection rate of Salmonella in eggs from farms was 26.7 %. All mcr-1-positive Salmonella isolates were S. 1,4,[5],12:i:- and were only found in hens (0.2 %) and eggs (11.1 %). PFGE and WGS analyses showed that the mcr-1-positive S. 1,4,[5],12:i:- from commercial laying hens and eggs in the same farm had no single nucleotide polymorphism (SNP) variation, indicating that the mcr-1-positive S. 1,4,[5],12:i:- in eggs were derived from hens. The phylogenomic analysis also showed that the mcr-1-positive S. 1,4,[5],12:i:- isolates from hens and eggs were closely related to previously reported mcr-1-positive Salmonella from human in China, further confirming that such mcr-1-positive Salmonella in animals could transmit to humans via the food chain. Furthermore, the blaCTX-M-1G-positive S. Kentucky isolates from broiler and flies in the same farm had a limited number of variations (5-7 SNPs), proving the clonal transmission of Salmonella between broilers and flies. The S. Kentucky isolates carrying blaCTX-M-1G from broilers were also closely related to the S. Kentucky isolates from chicken meats and humans. Our findings suggest that Salmonella including those carrying mcr-1 in animals could transmit to eggs/meats and potentially trigger human infections. The houseflies can play an important role in the Salmonella transmission within farms. Salmonella carrying mcr in animals and animal products should be monitored regularly and control measures are urgently needed to reduce the dissemination of such pathogens.

Characterization of novel mutations involved in the development of resistance to colistin in Salmonella isolates from retail pork in Shanghai, China

Salmonella is an important foodborne pathogen that poses a significant threat to food safety. This study aims to assess the prevalence, genomic features, and colistin-resistant mechanisms of Salmonella isolates collected from 118 retail pork samples from January 2021 to January 2022 in Shanghai, China. Overall, 46 (39.0 %, 46/118) Salmonella isolates were collected, which were identified as 12 serotypes by genomic analysis, including Salmonella Typhimurium (n = 17) and Salmonella London (n = 6). Antimicrobial resistance profiling revealed that the resistance rate of these isolates to colistin was 13.0 % (6/46), while 60.9 % (28/46) exhibited multidrug-resistant. It was found that there were 51 distinct antimicrobial resistance genes in these 46 isolates, which were predominantly associated with resistance to aminoglycosides, fluoroquinolones, and β-lactams. More importantly, among six colistin-resistant isolates, two isolates (Salmonella Schwarzengrund and Salmonella Indiana) were found to carry the mcr-1 gene. The mechanism of resistance in the remaining four colistin-resistant isolates was further studied, and it was found that there were nine amino acid substitutions in PmrAB. It was demonstrated by site-directed mutagenesis that novel substitutions G53W in PmrA and I83V in PmrB led to colistin resistance in Salmonella (MIC = 2 or 4 μg/mL). Analysis results by real-time quantitative PCR and mass spectrometry indicated that the mutants PmrAG53W and PmrBI83V displayed higher expression levels of the gene pmrE than in the parental strain. This upregulation resulted in an increase in the production of 4-amino-4-deoxy-l-arabinose (L-Ara4N) that modified lipid A, thereby conferring resistance to colistin. These findings demonstrated that there was a high prevalence of MDR Salmonella isolates in retail pork in Shanghai, and the substitution G53W in PmrA and I83V in PmrB were independent factors contributing to the development of resistance to colistin in Salmonella via modification of lipid A with L-Ara4N.

Deciphering antibiotic resistance genes and plasmids in pathogenic bacteria from 166 hospital effluents in Shanghai, China

Although previous studies using phenotypic or metagenomic approaches have revealed the patterns of antibiotic resistance genes (ARGs) in hospital effluents in local regions, limited information is available regarding the antibiotic resistome and plasmidome in human pathogenic bacteria in hospital effluents of megacity in China. To address this knowledge gap, we analyzed effluent samples from 166 hospitals across 13 geographical districts in Shanghai, China, using both cultivation-based approaches and metagenomics. A total of 357 strains were isolated from these samples, with the predominant species being Escherichia coli (n = 61), Aeromonas hydrophila (n = 57), Klebsiella pneumoniae (n = 48), and Aeromonas caviae (n = 42). Those identified indicator bacteria were classified into biosafety level 1 (BSL-1, 60 %) and BSL-2 (40 %). We identified 1237 ARG subtypes across 22 types, predominantly including beta-lactam, tetracycline, multidrug, polymyxin, and aminoglycoside resistance genes, using culture-enriched phenotypic metagenomics. Mobile genetic elements such as plasmids, transposons (tnpA), integrons (intI1), and insertion sequences (IS91) were abundant. We recovered 135 plasmids classified into mobilizable (n = 94) and non-mobilizable (n = 41) types. Additionally, 80 metagenome-assembled genomes (MAGs) were reconstructed from the hospital effluents for the assessment of ARG transmission risks, including genes for last-line antibiotics such as blaNDM, blaKPC, blaimiH, and mcr. This study is the first to comprehensively characterize and assess the risk of antimicrobial resistance levels and plasmidome in the hospital effluents of China's megacity, providing city-wide surveillance data and evidence to inform public health interventions.

Advances and mechanisms of traditional Chinese medicine and its active ingredients against antibiotic-resistant Escherichia coli infections

In clinical practice, antibiotics have historically been utilized for the treatment of pathogenic bacteria. However, the gradual emergence of antibiotic resistance among bacterial strains has posed a significant challenge to this approach. In 2022, Escherichia coli, a Gram-negative bacterium renowned for its widespread pathogenicity and high virulence, emerged as the predominant pathogenic bacterium in China. The rapid emergence of antibiotic-resistant E. coli strains has rendered antibiotics insufficient to fight E. coli infections. Traditional Chinese medicine (TCM) has made remarkable contributions to the health of Chinese people for thousands of years, and its significant therapeutic effects have been proven in clinical practice. In this paper, we provide a comprehensive review of the advances and mechanisms of TCM and its active ingredients against antibiotic-resistant E. coli infections. First of all, this review introduces the classification, antibiotic resistance characteristics and mechanisms of E. coli. Then, the TCM formulas and extracts are listed along with their active ingredients against E. coli, including extraction solution, minimum inhibitory concentration (MIC), and the antibacterial mechanisms. In addition, there is growing evidence supporting the synergistic therapeutic strategy of combining TCM with antibiotics for the treatment of antibiotic-resistant E. coli infections, and we provide a summary of this evidence and its underlying mechanisms. In conclusion, we present a comprehensive review of TCM and highlight its potential and advantages in the prevention and treatment of E. coli infections. We hold the opinion that TCM will play an important role in global health, pharmaceutical development, and livestock farming in the future.

The Janus Effect: The Biochemical Logic of Antibiotic Resistance

Antibiotics are essential medicines threatened by the emergence of resistance in all relevant bacterial pathogens. The engagement of the molecular targets of antibiotics offers multiple opportunities for resistance to emerge. Successful target engagement often requires passage of the antibiotic from outside into the cell interior through one or two distinct membrane barriers. Resistance can occur by preventing the accumulation of antibiotics in sufficient quantities outside the cell, decreasing the rates of entry into the cell, and modifying the antibiotic or the target once inside the cell. These competing equilibria and rates are the lens through which the balance of antibiotic efficacy or failure can be viewed. The two faces of antibiotics, cell growth inhibition or resistance, are reminiscent of Janus, the Roman god of doorways and beginnings and endings, and offer a framework through which antibiotic discovery, use, and the emergence of resistance can be rationally viewed.

Regional antimicrobial resistance gene flow among the One Health sectors in China

BACKGROUND

Antimicrobial resistance poses a significant threat to global health, with its spread intricately linked across human, animal, and environmental sectors. Revealing the antimicrobial resistance gene (ARG) flow among the One Health sectors is essential for better control of antimicrobial resistance.

RESULTS

In this study, we investigated regional ARG transmission among humans, food, and the environment in Dengfeng, Henan Province, China by combining large-scale metagenomic sequencing with culturing of resistant bacterial isolates in 592 samples. A total of 40 ARG types and 743 ARG subtypes were identified, with a predominance of multidrug resistance genes. Compared with microbes from human fecal samples, those from food and environmental samples showed a significantly higher load of ARGs. We revealed that dietary habits and occupational exposure significantly affect ARG abundance. Pseudomonadota, particularly Enterobacteriaceae, were identified as the main ARG carriers shaping the resistome. The resistome in food samples was found more affected by mobile genetic elements (MGEs), whereas in environmental samples, it was more associated with the microbial composition. We evidenced that horizontal gene transfer (HGT) mediated by plasmids and phages, together with strain transmission, particularly those associated with the Enterobacteriaceae members, drive regional ARG flow. Lifestyle, dietary habits, and occupational exposure are all correlated with ARG dissemination and flies and food are important potential sources of ARGs to humans. The widespread mobile carbapenemase gene, OXA-347, carried by non-Enterobacteriaceae bacteria in the human gut microbiota, requires particular attention. Finally, we showed that machine learning models based on microbiome profiles were effective in predicting the presence of carbapenem-resistant strains, suggesting a valuable approach for AMR surveillance.

CONCLUSIONS

Our study provides a full picture of regional ARG transmission among the One Health sectors in a county-level city in China, which facilitates a better understanding of the complex routes of ARG transmission and highlights new points of focus for AMR surveillance and control. Video Abstract.

Prevalence and molecular characteristics of colistin-resistant isolates among carbapenem-resistant Klebsiella pneumoniae in Central South China: a multicenter study

BACKGROUND

The emergence of colistin resistance in carbapenem-resistant Klebsiella pneumoniae (CRKP) is a significant public health concern, as colistin has been the last resort for treating such infections. This study aimed to investigate the prevalence and molecular characteristics of colistin-resistant CRKP isolates in Central South China.

METHODS

CRKP isolates from twelve hospitals in Central South China were screened for colistin resistance using broth microdilution. The epidemiological characteristics, virulome, resistome, plasmid replicons and two-component systems associated with colistin resistance of colistin-resistant isolates were explored by whole-genome sequencing. The mgrB gene and the relative expression of the pmrC and pmrK genes were analyzed by polymerase chain reaction (PCR) and real-time quantitative PCR, respectively. The bacterial virulence was evaluated through a Galleria mellonella larvae infection model.

RESULTS

Of the 429 nonduplicate CRKP isolates, 26 (6.1%) were colistin-resistant and they included eight clonal clusters. Six distinct sequence type (ST)-capsule loci (KL) types were identified: ST11-KL64, ST11-KL47, ST963-KL16, ST307-KL102, ST751-KL64 and ST5254-KL47. 88.5% (23/26) of them were found to carry at least one carbapenemase gene, including blaKPC-2 (65.4%, 17/26) and blaNDM-1 (7.7%, 2/26), as well as coharbouring blaKPC-2 and blaNDM-1 (15.4%, 4/26). Diverse mutations of colistin resistance-related genes were observed, with mgrB inactivation by insertions and the T157P deleterious mutation in pmrB being detected in 57.7% and 42.3% of the colistin-resistant isolates, respectively. In addition, a novel deleterious mutation, R248P, in the crrB gene was found in two ST11 isolates. 88.5% of the 26 isolates presented an increase in pmrK transcription, and 69.2% of them had an overexpression of the pmrC gene. All the 16 ST11-KL64 isolates and one ST751-KL64 isolate (65.4%, 17/26) carried at least two hypervirulence biomarkers and showed high virulence in vivo.

CONCLUSIONS

This study highlights the presence of different colistin resistance mechanisms in isolates belonging to the same clone and identified multiple clonal transmission clusters in colistin resistant isolates, including the globally high-risk ST11 and ST307 clones, of which a significant proportion exhibited high virulence. Consequently, it is crucial to enforce measures to prevent the ongoing spread of colistin resistance.

Establishment of a rapid method for the detection of Brucella canis based on recombinase-mediated thermostable nucleic acid amplification technology

Objective

To establish a rapid detection method for canine brucellosis using recombinase-aided amplification (RAA) technology.

Methods

The outer membrane protein 25 gene fragment (Omp25) of Brucella canis was targeted. Primers and fluorescent probes were designed and synthesized, and recombinant plasmids were constructed as standards. The RAA assay was optimized by screening primers and establishing a fluorescent reaction system. Sensitivity was analyzed using plasmid standards with varying copy numbers. Specificity was tested using genomes from Brucella canis, Brucella suis, Brucella melitensis, Brucella abortus, Staphylococcus aureus, pathogenic Escherichia coli, Salmonella enteritidis, Shigella spp., Proteus mirabilis, and Listeria monocytogenes. Reproducibility was evaluated using plasmid standards from the same and different batches.

Results

The optimized RAA system used primers bOmp25-F2/bOmp25-R2 and probe bOmp25-P, with a constant reaction temperature of 39°C for 15 minutes. The detection sensitivity was 1 copy/μL. No cross-reaction was observed with other Brucella species or pathogenic bacteria, indicating high specificity. Intra-batch variability was below 1.00%, and inter-batch variability was below 2.00%. The positive detection coincidence rate of RAA was significantly higher than that of commercial real-time fluorescence quantitative PCR (100% VS 86.96%, P<0.05).

Conclusion

The RAA-based rapid detection method for Brucella canis is suitable for clinical rapid testing. It offers advantages such as quick detection, high sensitivity, strong specificity, and good reproducibility. This method provides new insights for the rapid detection of canine brucellosis and the precise diagnosis of other pet diseases, making it suitable for promotion and application.

Antimicrobial resistance: a concise update

Antimicrobial resistance (AMR) is a serious threat to global public health, with approximately 5 million deaths associated with bacterial AMR in 2019. Tackling AMR requires a multifaceted and cohesive approach that ranges from increased understanding of mechanisms and drivers at the individual and population levels, AMR surveillance, antimicrobial stewardship, improved infection prevention and control measures, and strengthened global policies and funding to development of novel antimicrobial therapeutic strategies. In this rapidly advancing field, this Review provides a concise update on AMR, encompassing epidemiology, evolution, underlying mechanisms (primarily those related to last-line or newer generation of antibiotics), infection prevention and control measures, access to antibiotics, antimicrobial stewardship, AMR surveillance, and emerging non-antibiotic therapeutic approaches. The Review also discusses the potential roles of artificial intelligence in addressing AMR, including antimicrobial susceptibility testing, AMR surveillance, antimicrobial stewardship, diagnosis, and antimicrobial drug discovery and development. This Review highlights the urgent need for addressing the global effects of AMR and for rapid advancement of relevant technology in this dynamic field.

Prevalence, transmission and genomic epidemiology of mcr-1-positive colistin-resistant Escherichia coli strains isolated from international airplane waste, local resident fecal and wastewater treatment plants

The emergence and dissemination of mcr-1-positive Escherichia coli (MCRPEC) represent a critical public health threat. Here, we conducted a prospective analysis of MCRPEC isolates from wastewater treatment plants (WWTPs), local residents' fecal (LRF), and international airplane waste (IAW) to investigate their genetic characteristics and transmission patterns circulating in human-environment domains. The MCRPEC prevalence was 2.43 % in WWTPs, 1.37 % in IAW and 0.69 % in LRF. MCRPEC showed substantial genetic diversity, encompassing 61 sequence types (primarily ST1011, ST101, and ST2705), 7 plasmid types (primarily IncI2), 8 phylogroups (primarily A and B1), 9 mcr-1-flanked lineages (primarily L5), 6 clusters (primarily C2 and C4), diverse serotypes, and 61.95 % transposon-containing strains. The mcr-1 gene co-existed with 46 antibiotic resistance genes (ARGs) and 19 virulence factor genes (VFGs). Notably, 6 IncI2 plasmids carried the blaCTX-M, IS1380, and mcr-1 genes. MCRPEC from WWTPs harbored a greater number of ARGs (56.95 ± 5.99) but fewer VFGs (15.03 ± 6.40) compared to those from human-associated sources (LRF and IAW). ST1011, ST2705, IncHI2, and L7 were prevalent in WWTP-derived MCRPEC, whereas IncX4 and L3 were more common in human-derived MCRPEC. Genetic features such as ST101, ST48, IncI2, L4, L5, C2, and C4 were simultaneously present in strains from LRF, IAW, and WWTPs. Core genetic analyses also showed genetically similar MCRPEC strains across various geographic locations. The findings underscore the extensive dissemination, strong environmental adaptation, and clonal transmission of MCRPEC across diverse reservoirs, reinforcing the urgent need for coordinated multisectoral surveillance of human and environment interfaces to effectively mitigate further transmission.

The multifaceted roles of phosphoethanolamine-modified lipopolysaccharides: from stress response and virulence to cationic antimicrobial resistance

SUMMARYLipopolysaccharides (LPS) are an integral part of the outer membrane of Gram-negative bacteria and play essential structural and functional roles in maintaining membrane integrity as well as in stress response and virulence. LPS comprises a membrane-anchored lipid A group, a sugar-based core region, and an O-antigen formed by repeating oligosaccharide units. 3-Deoxy-D-manno-octulosonic acid-lipid A (Kdo2-lipid A) is the minimum LPS component required for bacterial survival. While LPS modifications are not essential, they play multifaceted roles in stress response and host-pathogen interactions. Gram-negative bacteria encode several distinct LPS-modifying phosphoethanolamine transferases (PET) that add phosphoethanolamine (pEtN) to lipid A or the core region of LPS. The pet genes differ in their genomic locations, regulation mechanisms, and modification targets of the encoded enzyme, consistent with their various roles in different growth niches and under varied stress conditions. The discovery of mobile colistin resistance genes, which represent lipid A-modifying pet genes that are encoded on mobile elements and associated with resistance to the last-resort antibiotic colistin, has led to substantial interest in PETs and pEtN-modified LPS over the last decade. Here, we will review the current knowledge of the functional diversity of pEtN-based LPS modifications, including possible roles in niche-specific fitness advantages and resistance to host-produced antimicrobial peptides, and discuss how the genetic and structural diversities of PETs may impact their function. An improved understanding of the PET group will further enhance our comprehension of the stress response and virulence of Gram-negative bacteria and help contextualize host-pathogen interactions.

Coexistence and genomics characterization of mcr-1 and extended-spectrum-β-lactamase-producing Escherichia coli, an emerging extensively drug-resistant bacteria from sheep in China

The emergence of pathogens harboring multiple resistance genes poses a great threat to global public health. However, the coexistence of mobile resistance genes that provide resistance to both third-generation cephalosporins and colistin in sheep-origin Escherichia coli has not been previously investigated in China. This study is the first to characterize five E. coli isolates from sheep in Shaanxi province that harbor both Extended-Spectrum β-Lactamase (ESBL) and mcr-1 resistance genes. The isolates were identified and characterized by Illumina sequencing, nanopore sequencing, bioinformatic analysis, conjugation experiments, and antimicrobial susceptibility testing. Genetic analysis revealed that blaCTX-M-55 gene, mediated by the IS26, was located on the IncFIB-IncFIC plasmid, while the mcr-1 gene was located on the IncI2(Delta) plasmid. Notably, two copies of blaCTX-M-55 gene were also identified on the chromosome of one isolate (SX45), facilitated by the ISEcp1 insertion sequence. Additionally, the plasmid pSX23-2 was identified as a complex plasmid derived through homologous recombination of pMG337 from E. coli (MK878890) and pZY-1 from Citrobacter freundii (CP055248). Data mining of publicly available databases revealed that isolates carrying both blaCTX-M-55 and mcr-1 genes have been found in humans, animals, and the environment, indicating the widespread presence of these critical resistance genes across different niches. Antimicrobial susceptibility testing showed that the five isolates were resistant to a nearly all tested antibiotics, except meropenem. Conjugative transfer experiments demonstrated that the IncFIB-IncFIC and IncI2(Delta) plasmids carrying mcr-1 and blaCTX-M-55 were capable of transferring between different sequence types (STs) of sheep-origin E. coli, including ST10, ST162, and ST457. This finding suggests the potential for wide dissemination of these resistance markers among diverse E. coli strains. Overall, the characterization of these ESBL and mcr-1 co-harboring isolates enhances our understanding of the spread of these resistance genes in sheep-origin E. coli. Global surveillance of these isolates, particularly within the One Health framework, is essential to monitor and mitigate the risks posed by the dissemination of these resistance genes across various settings.

Emergence of the mobile colistin resistance gene mcr-1 in a Leclercia adecarboxylata strain isolated from wastewater in Seoul

Colistin is considered the last resort for treating infections caused by multidrug-resistant bacteria. However, the spread of the plasmid-borne colistin-resistance gene mcr-1 has become a public health threat. In this study, we identified mcr-1-harboring Leclercia adecarboxylata strain (WWCOL-134) isolated from wastewater in Seoul. The strain had a colistin MIC value of 2 µg/ml and was resistant to cefotaxime, gentamicin, tetracycline, trimethoprim and sulfamethoxazole. The mcr-1 gene, along with an array of resistance genes, was located on a 236-kb plasmid (pCOL134-1), which contained the typical IncHI2 backbone of reported mcr-1-carrying plasmids, and was transferred to an Escherichia coli strain by conjugation. To the best of our knowledge, this is the first study to report the emergence of mcr-1-harboring Leclercia sp. isolate. Our findings demonstrate the ongoing spread of colistin resistance among Enterobacterales species, emphasizing the need for surveillance of antimicrobial resistance in wastewater environments.

Bacteria carrying mobile colistin resistance genes and their control measures, an updated review

The plasmid encoded mobile colistin resistance (MCRs) enzyme poses a significant challenge to the clinical efficacy of colistin, which is frequently employed as a last resort antibiotic for treating infections caused by multidrug resistant bacteria. This transferase catalyzes the addition of positively charged phosphoethanolamine to lipid A of the outer membrane of gram-negative bacteria, thereby facilitating the acquired colistin resistance. This review aims to summarize and critically discuss recent advancements in the distribution and pathogenesis of mcr-positive bacteria, as well as the various control measures available for treating these infections. In addition, the ecology of mcr genes, colistin-resistance mechanism, co-existence with other antibiotic resistant genes, and their impact on clinical treatment are also analyzed to address the colistin resistance crisis. These insights provide a comprehensive perspective on MCRs and serve as a valuable reference for future therapeutic approaches to effectively combat mcr-positive bacterial infections.

Design, potential and limitations of conjugation-based antibacterial strategies

Over the past few decades, the global spread of antimicrobial resistance has underscored the urgent need to develop innovative non-antibiotic antibacterial strategies and to reduce antibiotic use worldwide. In response to this challenge, several methods have been developed that rely on gene transfer by conjugation to deliver toxic compounds or CRISPR systems specifically designed to kill or resensitize target bacterial strains to antibiotics. This review explores the design, potential, and limitations of these conjugation-based antibacterial strategies, focusing on the recent advances in the delivery of CRISPR systems as antibacterial effectors.

Research note: characteristics of blaNDM and mcr-1 co-producing Escherichia coli from retail chicken meat

Carbapenems and colistin are vital antimicrobials used to treat Enterobacteriaceae-caused infections. The present study aimed to characterize the coexistence mechanism of carbapenem and colistin resistance in an Escherichia coli isolated from retail chicken meat. A total of 4 E. coli isolates co-harboring carbapenem resistance gene blaNDM (2 E. coli isolates with blaNDM-5 and 2 with blaNDM-9) and colistin resistance gene mcr-1. Antimicrobial susceptibility testing exhibited that all the 4 E. coli strains had multidrug resistance profile and consistent with the resistance genes they carried. MLST showed that 3 E. coli isolates belonged to a pathogenic E. coli lineage ST354, which is closely associated with human infections and pose a serious threat to public health. Whole genome sequencing (WGS) showed that 4 mcr-1-positive plasmids with sizes of 60.4 kb to 67.4 kb all belonged to the IncI2 type. A total of 5 blaNDM-harboring plasmids ranged from 99.0 kb to 138.3 kb, among which 4 plasmids belonged to unknow type and only pCS5L-NDM belonged to IncFIA/IncFIB group of hybrid plasmids, a novel carrier for blaNDM. Comparative analysis exhibited that the mcr-1 or blaNDM-carrying plasmids of E. coli strains from chicken meat showed high identity with that from Enterobacteriaceae of human origin, which indicated the risk of mcr-1 or blaNDM dissemination from retail meat to human. The simultaneous occurrence of mcr-1 and blaNDM in E. coli emphasizes the significant of antimicrobial resistance surveillance in retail meat.

Decoding the origins, spread, and global risks of mcr-9 gene

BACKGROUND

The global spread of the plasmid-mediated mcr (mobilized colistin resistance) gene family presents a significant threat to the efficacy of colistin, a last-line defense against numerous Gram-negative pathogens. The mcr-9 is the second most prevalent variant after mcr-1.

METHODS

A dataset of 698 mcr-9-positive isolates from 44 countries is compiled. The historical trajectory of the mcr-9 gene is reconstructed using Bayesian analysis. The effective reproduction number is used innovatively to study the transmission dynamics of this mobile-drug-resistant gene.

FINDINGS

Our investigation traces the origins of mcr-9 back to the 1960s, revealing a subsequent expansion from Western Europe to the America and East Asia in the late 20th century. Currently, its transmissibility remains high in Western Europe. Intriguingly, mcr-9 likely emerged from human-associated Salmonella and exhibits a unique propensity for transmission within the Enterobacter. Our research provides a new perspective that this host preference may be driven by codon usage biases in plasmids. Specifically, mcr-9-carrying plasmids prefer the nucleotide C over T compared to mcr-1-carrying plasmids among synonymous codons. The same bias is seen in Enterobacter compared to Escherichia (respectively as their most dominant genus). Furthermore, we uncovered fascinating patterns of coexistence between different mcr-9 subtypes and other resistance genes. Characterized by its low colistin resistance, mcr-9 has used this seemingly benign feature to silently circumnavigate the globe, evading conventional detection methods. However, colistin-resistant Enterobacter strains with high mcr-9 expression have emerged clinically, implying a strong risk of mcr-9 evolving into a global "true-resistance-gene".

INTERPRETATION

This study explores the mcr-9 gene, emphasizing its origin, adaptability, and dissemination potential. Given the high mcr-9 expression colistin-resistant strains was observed in clinically the prevalence of mcr-9 poses a significant challenge to drug resistance prevention and control within the One Health framework.

FUNDING

This work was partially supported by the National Natural Science Foundation of China (Grant No. 32141001 and 81991533).

Characteristics of tetracycline antibiotic resistance gene enrichment and migration in soil-plant system

Tetracycline Resistance Genes (TRGs) have received widespread attention in recent years, as they are a novel environmental pollutant that can rapidly accumulate and migrate in soil plant systems through horizontal gene transfer (HGT), posing a potential threat to food safety and public health. This article systematically reviews the pollution sources, enrichment, and migration characteristics of TRGs in soil. The main sources of TRGs include livestock manure and contaminated wastewater, especially in intensive farming environments where TRGs pollution is more severe. In soil, TRGs diffuse horizontally between bacteria and migrate to plant tissues through mechanisms such as plasmid conjugation, integron mediation, and phage transduction. The migration of TRGs is not limited to the soil interior, and increasing evidence suggests that they can also enter the plant system through plant root absorption and the HGT pathway of endophytic bacteria, ultimately accumulating in plant roots, stems, leaves, fruits, and other parts. This process has a direct impact on human health, especially when TRGs are found in crops such as vegetables, which may be transmitted to the human body through the food chain. In addition, this article also deeply analyzed various factors that affect the migration of TRGs, including the residual level of tetracycline in soil, the type and concentration of microorganisms, heavy metal pollution, and the presence of new pollutants such as microplastics. These factors significantly affect the enrichment rate and migration mode of TRGs in soil. In addition, two technologies that can effectively eliminate TRGs in livestock breeding environments were introduced, providing reference for healthy agricultural production. The article concludes by summarizing the shortcomings of current research on TRGs, particularly the limited understanding of TRG migration pathways and their impact mechanisms. Future research should focus on revealing the migration mechanisms of TRGs in soil plant systems and developing effective control and governance measures to reduce the environmental transmission risks of TRGs and ensure the safety of ecosystems and human health.

Combination of aloe emodin, emodin, and rhein from Aloe with EDTA sensitizes the resistant Acinetobacter baumannii to polymyxins

Background

The continuous emergence and spread of polymyxin-resistant Acinetobacter baumannii pose a significant global health challenge, necessitating the development of novel therapeutic strategies. Aloe, with its long-standing history of medicinal use, has recently been the subject of substantial research for its efficacy against pathogenic infections.

Methods

This study investigates the potential application of anthraquinone components in aloe against polymyxin-resistant A. baumannii by liquid chromatography-mass spectrometry, in vitro activity assessment, and construction of animal infection models.

Results

The findings demonstrate that aloe emodin, emodin, rhein, and their mixtures in equal mass ratios (EAR) exhibit strain-specific antibacterial activities against polymyxin-resistant A. baumannii. Co-administration of EAR with EDTA synergistically and universally enhanced the antibacterial activity and bactericidal efficacy of polymyxins against polymyxin-resistant A. baumannii, while also reducing the frequency of polymyxin-resistant mutations in polymyxinssensitive A. baumannii. Following toxicity assessment on human hepatic and renal cell lines, the combination therapy was applied to skin wounds in mice infected with polymyxin-resistant A. baumannii. Compared to monotherapy, the combination therapy significantly accelerated wound healing and reduced bacterial burden.

Conclusions

The combination of EAR and EDTA with polymyxins offers a novel therapeutic approach for managing skin infections caused by polymyxinresistant A. baumannii.

Colistin Resistance Mediated by Mcr-3-Related Phosphoethanolamine Transferase Genes in Aeromonas Species Isolated from Aquatic Environments in Avaga and Pakro Communities in the Eastern Region of Ghana

Purpose

Colistin is classified by the World Health Organization (WHO) as a critically important and last-resort antibiotic for the treatment of infections caused by carbapenem-resistant bacteria. However, colistin resistance mediated by chromosomal mutations or plasmid-linked mobilized colistin resistance (mcr) genes has emerged.

Methods

Thirteen mcr-positive Aeromonas species isolated from water samples collected in Eastern Ghana were analyzed using whole-genome sequencing (WGS). Antimicrobial susceptibility was tested using the broth microdilution method. Resistome analysis was performed in silico using a web-based platform.

Results

The minimum inhibitory concentration (MIC) of colistin for all except three isolates was >4 µg/mL. Nine new sequence types were identified and whole-genome analysis revealed that the isolates harbored genes (mcr-3-related genes) that code for Lipid A phosphoethanolamine transferases on their chromosomes. BLAST analysis indicated that the amino acid sequences of the mcr-3-related genes detected varied from those previously reported and shared 79.04-99.86% nucleotide sequence identity with publicly available mcr-3 variants and mcr-3-related phosphoethanolamine transferases. Analysis of the genetic context of mcr-3-related genes revealed that the genetic environment surrounding mcr-3-related genes was diverse among the different species of Aeromonas but conserved among isolates of the same species. Mcr-3-related-gene-IS-mcr-3-related-gene segment was identified in three Aeromonas caviae strains.

Conclusion

The presence of mcr-3-related genes close to insertion elements is important for continuous monitoring to better understand how to control the mobilization and dissemination of antibiotic resistance genes.

Polymyxins: recent advances and challenges

Antibiotic resistance is a pressing global health challenge, and polymyxins have emerged as the last line of defense against multidrug-resistant Gram-negative (MDR-GRN) bacterial infections. Despite the longstanding utility of colistin, the complexities surrounding polymyxins in terms of resistance mechanisms and pharmacological properties warrant critical attention. This review consolidates current literature, focusing on polymyxins antibacterial mechanisms, resistance pathways, and innovative strategies to mitigate resistance. We are also investigating the pharmacokinetics of polymyxins to elucidate factors that influence their in vivo behavior. A comprehensive understanding of these aspects is pivotal for developing next-generation antimicrobials and optimizing therapeutic regimens. We underscore the urgent need for advancing research on polymyxins to ensure their continued efficacy against formidable bacterial challenges.

Flavomycin restores colistin susceptibility in multidrug-resistant Gram-negative bacteria

Polymyxin is used as a last resort antibiotics for infections caused by multi-drug resistant (MDR) Gram-negative bacteria and is often combined with other antibiotics to improve clinical effectiveness. However, the synergism of colistin and other antibiotics remains obscure. Here, we revealed a notable synergy between colistin and flavomycin, which was traditionally used as an animal growth promoter and has limited activity against Gram-negative bacteria, using checkerboard assay and time-kill curve analyses. The importance of membrane penetration induced by colistin was assessed by examining the intracellular accumulation of flavomycin and its antimicrobial impact on Escherichia coli (E. coli) strains with truncated lipopolysaccharides. Besides, a mutation in the flavomycin binding site was created to confirm its role in the observed synergy. This synergy is manifested as an augmented penetration of the E. coli outer membrane by colistin, leading to increased intracellular accumulation of flavomycin and enhanced cell killing thereafter. The observed synergy was dependent on the antimicrobial activity of flavomycin, as mutation of its binding site abolished the synergy. In vivo studies confirmed the efficacy of colistin combined with flavomycin against MDR E. coli infections. This study is the first to demonstrate the synergistic effect between colistin and flavomycin, shedding light on their respective roles in this synergism. Therefore, we propose flavomycin as an adjuvant to enhance the potency of colistin against MDR Gram-negative bacteria.

IMPORTANCE

Colistin is a critical antibiotic in combating multi-drug resistant Gram-negative bacteria, but the emergence of mobilized colistin resistance (mcr) undermines its effectiveness. Previous studies have found that colistin can synergy with various drugs; however, its exact mechanisms with hydrophobic drugs are still unrevealed. Generally, the membrane destruction of colistin is thought to be the essential trigger for its interactions with its partner drugs. Here, we use clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) for specifically mutating the binding site of one hydrophobic drug (flavomycin) and show that antimicrobial activity of flavomycin is critical for the synergy. Our results first give the evidence that the synergy is set off by colistin's membrane destruction and operated the final antimicrobial function by its partner drugs.