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Pagan E, Merino N, Berdejo D, Campillo R, Gayan E, García-Gonzalo D, Pagan R. Adaptive evolution of Salmonella Typhimurium LT2 exposed to carvacrol lacks a uniform pattern. Appl Microbiol Biotechnol 2024; 108:38. [PMID: 38175235 PMCID: PMC10766787 DOI: 10.1007/s00253-023-12840-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 10/05/2023] [Accepted: 10/17/2023] [Indexed: 01/05/2024]
Abstract
Emergence of genetic variants with increased resistance/tolerance to natural antimicrobials, such as essential oils, has been previously evidenced; however, it is unknown whether mutagenesis follows a general or a specific pattern. For this purpose, we carried out four adaptive laboratory evolutions (ALE) in parallel of Salmonella enterica Typhimurium with carvacrol. After 10 evolution steps, we selected and characterized one colony from each lineage (SeCarA, SeCarB, SeCarC, and SeCarD). Phenotypic characterization of the four evolved strains revealed enhanced survival to lethal treatments; two of them (SeCarA and SeCarB) showed an increase of minimum inhibitory concentration of carvacrol and a better growth fitness in the presence of carvacrol compared to wild-type strain. Whole genome sequencing revealed 10 mutations, of which four (rrsH, sseG, wbaV, and flhA) were present in more than one strain, whereas six (nirC, fliH, lon, rob, upstream yfhP, and upstream argR) were unique to individual strains. Single-mutation genetic constructs in SeWT confirmed lon and rob as responsible for the increased resistance to carvacrol as well as to antibiotics (ampicillin, ciprofloxacin, chloramphenicol, nalidixic acid, rifampicin, tetracycline, and trimethoprim). wbaV played an important role in increased tolerance against carvacrol and chloramphenicol, and flhA in cross-tolerance to heat treatments. As a conclusion, no common phenotypical or genotypical pattern was observed in the isolated resistant variants of Salmonella Typhimurium emerged under carvacrol stress. Furthermore, the demonstration of cross-resistance against heat and antibiotics exhibited by resistant variants raises concerns regarding food safety. KEY POINTS: • Stable resistant variants of Salmonella Typhimurium emerged under carvacrol stress • No common pattern of mutagenesis after cyclic exposures to carvacrol was observed • Resistant variants to carvacrol showed cross-resistance to heat and to antibiotics.
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Affiliation(s)
- Elisa Pagan
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza-CITA, Zaragoza, Spain
| | - Natalia Merino
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza-CITA, Zaragoza, Spain
| | - Daniel Berdejo
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza-CITA, Zaragoza, Spain
| | - Raul Campillo
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza-CITA, Zaragoza, Spain
| | - Elisa Gayan
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza-CITA, Zaragoza, Spain
| | - Diego García-Gonzalo
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza-CITA, Zaragoza, Spain
| | - Rafael Pagan
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Instituto Agroalimentario de Aragón-IA2, Universidad de Zaragoza-CITA, Zaragoza, Spain.
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2
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Morrison JJ, Madden EK, Banas DA, DiBiasio EC, Hansen M, Krogfelt KA, Rowley DC, Cohen PS, Camberg JL. Metabolic flux regulates growth transitions and antibiotic tolerance in uropathogenic Escherichia coli. J Bacteriol 2024; 206:e0016224. [PMID: 38814092 DOI: 10.1128/jb.00162-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 05/06/2024] [Indexed: 05/31/2024] Open
Abstract
Reducing growth and limiting metabolism are strategies that allow bacteria to survive exposure to environmental stress and antibiotics. During infection, uropathogenic Escherichia coli (UPEC) may enter a quiescent state that enables them to reemerge after the completion of successful antibiotic treatment. Many clinical isolates, including the well-characterized UPEC strain CFT073, also enter a metabolite-dependent, quiescent state in vitro that is reversible with cues, including peptidoglycan-derived peptides and amino acids. Here, we show that quiescent UPEC is antibiotic tolerant and demonstrate that metabolic flux in the tricarboxylic acid (TCA) cycle regulates the UPEC quiescent state via succinyl-CoA. We also demonstrate that the transcriptional regulator complex integration host factor and the FtsZ-interacting protein ZapE, which is important for E. coli division during stress, are essential for UPEC to enter the quiescent state. Notably, in addition to engaging FtsZ and late-stage cell division proteins, ZapE also interacts directly with TCA cycle enzymes in bacterial two-hybrid assays. We report direct interactions between the succinate dehydrogenase complex subunit SdhC, the late-stage cell division protein FtsN, and ZapE. These interactions may enable communication between oxidative metabolism and the cell division machinery in UPEC. Moreover, these interactions are conserved in an E. coli K-12 strain. This work suggests that there is coordination among the two fundamental and essential pathways that regulate overall growth, quiescence, and antibiotic susceptibility. IMPORTANCE Uropathogenic Escherichia coli (UPEC) are the leading cause of urinary tract infections (UTIs). Upon invasion into bladder epithelial cells, UPEC establish quiescent intracellular reservoirs that may lead to antibiotic tolerance and recurrent UTIs. Here, we demonstrate using an in vitro system that quiescent UPEC cells are tolerant to ampicillin and have decreased metabolism characterized by succinyl-CoA limitation. We identify the global regulator integration host factor complex and the cell division protein ZapE as critical modifiers of quiescence and antibiotic tolerance. Finally, we show that ZapE interacts with components of both the cell division machinery and the tricarboxylic acid cycle, and this interaction is conserved in non-pathogenic E. coli, establishing a novel link between cell division and metabolism.
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Affiliation(s)
- Josiah J Morrison
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Ellen K Madden
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Daniel A Banas
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Eric C DiBiasio
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Mads Hansen
- Department of Natural Science and Environment, Centre for Mathematical Modeling - Human Health and Disease, University of Roskilde, Roskilde, Denmark
| | - Karen A Krogfelt
- Department of Natural Science and Environment, Centre for Mathematical Modeling - Human Health and Disease, University of Roskilde, Roskilde, Denmark
| | - David C Rowley
- Department of Biomedical and Pharmaceutical Sciences, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Paul S Cohen
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Jodi L Camberg
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
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3
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Amábile-Cuevas CF, Lund-Zaina S. Non-Canonical Aspects of Antibiotics and Antibiotic Resistance. Antibiotics (Basel) 2024; 13:565. [PMID: 38927231 PMCID: PMC11200725 DOI: 10.3390/antibiotics13060565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.
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Affiliation(s)
| | - Sofia Lund-Zaina
- Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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4
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Zhu W, Xiao L, Hong S, Wang W, Li W, Luo H, Zhang X, Zhang X, Xue Y, Wang D, Niu J, Drlica K, Zhao X. Exogenous Glucose Interferes with Antimicrobial-Mediated ROS Accumulation and Bacterial Death. ACS Infect Dis 2024; 10:1896-1903. [PMID: 38735064 DOI: 10.1021/acsinfecdis.4c00167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Glucose is widely used in the reconstitution of intravenous medications, which often include antimicrobials. How glucose affects antimicrobial activity has not been comprehensively studied. The present work reports that glucose added to bacteria growing in a rich medium suppresses the bactericidal but not the bacteriostatic activity of several antimicrobial classes, thereby revealing a phenomenon called glucose-mediated antimicrobial tolerance. Glucose, at concentrations corresponding to blood-sugar levels of humans, increased survival of Escherichia coli treated with quinolones, aminoglycosides, and cephalosporins with little effect on minimal inhibitory concentration. Glucose suppressed a ROS surge stimulated by ciprofloxacin. Genes involved in phosphorylated fructose metabolism contributed to glucose-mediated tolerance, since a pfkA deficiency, which blocks the formation of fructose-1,6-bisphosphate, eliminated protection by glucose. Disrupting the pentose phosphate pathway or the TCA cycle failed to alter glucose-mediated tolerance, consistent with an upstream involvement of phosphorylated fructose. Exogenous sodium pyruvate or sodium citrate reversed glucose-mediated antimicrobial tolerance. Both metabolites bypass the effects of fructose-1,6-bisphosphate, a compound known to scavenge hydroxyl radical and chelate iron, activities that suppress ROS accumulation. Treatment with these two compounds constitutes a novel way to mitigate the glucose-mediated antimicrobial tolerance that may exist during intravenous antimicrobial therapy, especially for diabetes patients.
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Affiliation(s)
- Weiwei Zhu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang-An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, 4221-117 South Xiang-An Road, Xiang-An District, Xiamen, Fujian Province 361102, China
| | - Lisheng Xiao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang-An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, 4221-117 South Xiang-An Road, Xiang-An District, Xiamen, Fujian Province 361102, China
| | - Shouqiang Hong
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang-An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, 4221-117 South Xiang-An Road, Xiang-An District, Xiamen, Fujian Province 361102, China
| | - Weijie Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang-An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, 4221-117 South Xiang-An Road, Xiang-An District, Xiamen, Fujian Province 361102, China
| | - Weiwei Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang-An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, 4221-117 South Xiang-An Road, Xiang-An District, Xiamen, Fujian Province 361102, China
| | - Huan Luo
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang-An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, 4221-117 South Xiang-An Road, Xiang-An District, Xiamen, Fujian Province 361102, China
| | - Xinyang Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang-An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, 4221-117 South Xiang-An Road, Xiang-An District, Xiamen, Fujian Province 361102, China
| | - Xue Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang-An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, 4221-117 South Xiang-An Road, Xiang-An District, Xiamen, Fujian Province 361102, China
| | - Yunxin Xue
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang-An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, 4221-117 South Xiang-An Road, Xiang-An District, Xiamen, Fujian Province 361102, China
| | - Dai Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang-An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, 4221-117 South Xiang-An Road, Xiang-An District, Xiamen, Fujian Province 361102, China
| | - Jianjun Niu
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, 209 South Hubin Road, Siming District, Xiamen, Fujian Province 361004, China
| | - Karl Drlica
- Public Health Research Institute and Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, United States of America
| | - Xilin Zhao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang-An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, 4221-117 South Xiang-An Road, Xiang-An District, Xiamen, Fujian Province 361102, China
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5
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Zhang M, Song H, Yang S, Zhang Y, Tian Y, Wang Y, Liu D. Deciphering the Antibacterial Mechanisms of 5-Fluorouracil in Escherichia coli through Biochemical and Transcriptomic Analyses. Antibiotics (Basel) 2024; 13:528. [PMID: 38927194 PMCID: PMC11200800 DOI: 10.3390/antibiotics13060528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
The emergence of carbapenem-resistant Gram-negative pathogens presents a clinical challenge in infection treatment, prompting the repurposing of existing drugs as an essential strategy to address this crisis. Although the anticancer drug 5-fluorouracil (5-FU) has been recognized for its antibacterial properties, its mechanisms are not fully understood. Here, we found that the minimal inhibitory concentration (MIC) of 5-FU against Escherichia coli was 32-64 µg/mL, including strains carrying blaNDM-5, which confers resistance to carbapenems. We further elucidated the antibacterial mechanism of 5-FU against E. coli by using genetic and biochemical analyses. We revealed that the mutation of uracil phosphoribosyltransferase-encoding gene upp increased the MIC of 5-FU against E. coli by 32-fold, indicating the role of the upp gene in 5-FU resistance. Additionally, transcriptomic analysis of E. coli treated with 5-FU at 8 µg/mL and 32 µg/mL identified 602 and 1082 differentially expressed genes involved in carbon and nucleic acid metabolism, DNA replication, and repair pathways. The biochemical assays showed that 5-FU induced bacterial DNA damage, significantly increased intracellular ATP levels and the NAD+/NADH ratio, and promoted reactive oxygen species (ROS) production. These findings suggested that 5-FU may exert antibacterial effects on E. coli through multiple pathways, laying the groundwork for its further development as a therapeutic candidate against carbapenem-resistant bacterial infections.
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Affiliation(s)
- Muchen Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (M.Z.); (S.Y.); (Y.Z.); (Y.T.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Huangwei Song
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China;
| | - Siyuan Yang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (M.Z.); (S.Y.); (Y.Z.); (Y.T.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yan Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (M.Z.); (S.Y.); (Y.Z.); (Y.T.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yunrui Tian
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (M.Z.); (S.Y.); (Y.Z.); (Y.T.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yang Wang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (M.Z.); (S.Y.); (Y.Z.); (Y.T.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Dejun Liu
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (M.Z.); (S.Y.); (Y.Z.); (Y.T.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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6
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Kohram M, Sanderson AE, Loui A, Thompson PV, Vashistha H, Shomar A, Oltvai ZN, Salman H. Nonlethal deleterious mutation-induced stress accelerates bacterial aging. Proc Natl Acad Sci U S A 2024; 121:e2316271121. [PMID: 38709929 PMCID: PMC11098108 DOI: 10.1073/pnas.2316271121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/29/2024] [Indexed: 05/08/2024] Open
Abstract
Random mutagenesis, including when it leads to loss of gene function, is a key mechanism enabling microorganisms' long-term adaptation to new environments. However, loss-of-function mutations are often deleterious, triggering, in turn, cellular stress and complex homeostatic stress responses, called "allostasis," to promote cell survival. Here, we characterize the differential impacts of 65 nonlethal, deleterious single-gene deletions on Escherichia coli growth in three different growth environments. Further assessments of select mutants, namely, those bearing single adenosine triphosphate (ATP) synthase subunit deletions, reveal that mutants display reorganized transcriptome profiles that reflect both the environment and the specific gene deletion. We also find that ATP synthase α-subunit deleted (ΔatpA) cells exhibit elevated metabolic rates while having slower growth compared to wild-type (wt) E. coli cells. At the single-cell level, compared to wt cells, individual ΔatpA cells display near normal proliferation profiles but enter a postreplicative state earlier and exhibit a distinct senescence phenotype. These results highlight the complex interplay between genomic diversity, adaptation, and stress response and uncover an "aging cost" to individual bacterial cells for maintaining population-level resilience to environmental and genetic stress; they also suggest potential bacteriostatic antibiotic targets and -as select human genetic diseases display highly similar phenotypes, - a bacterial origin of some human diseases.
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Affiliation(s)
- Maryam Kohram
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
| | - Amy E. Sanderson
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
| | - Alicia Loui
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
| | | | - Harsh Vashistha
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
| | - Aseel Shomar
- Department of Chemical Engineering, Technion–Israel Institute of Technology, Haifa32000, Israel
| | - Zoltán N. Oltvai
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA15260
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA15260
- Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, NY14627
| | - Hanna Salman
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA15260
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7
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Ma X, Kaw HY, Yu J, Yang Q, Zhu L, Wang W. The intracellular concentrations of fluoroquinolones determined the antibiotic resistance response of Escherichia coli. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134057. [PMID: 38508108 DOI: 10.1016/j.jhazmat.2024.134057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 02/27/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
The extensive consumption of antibiotics has been reported to significantly promote the generation of antibiotic resistance (ABR), however, a quantitative causal relationship between antibiotic exposure and ABR response is absent. This study aimed to pinpoint the accurate regulatory concentration of fluoroquinolones (FQs) and to understand the biochemical mechanism of the mutual action between FQ exposure and FQ resistance response. Highly sensitive analytical methods were developed by using UPLC-MS/MS to determine the total residual, extracellular residual, total intracellular, intracellular residual and intracellular degraded concentration of three representative FQs, including ciprofloxacin (CIP), ofloxacin (OFL) and norfloxacin (NOR), with detection limits in the range of 0.002-0.057 μg/L, and recoveries in the range of 80-93%. The MICs of Escherichia coli (E. coli) were 7.0-31.4-fold of the respective MIC0 after 40-day FQ exposure, and significant negative associations were discovered between the intracellular (residual, degraded or the sum) FQ concentrations and FQ resistance. Transcriptional expression and whole-genome sequencing results indicated that reduced membrane permeability and enhanced multi-drug efflux pumps contributed to the decreasing intracellular concentration. These results unveiled the pivotal role of intracellular concentration in triggering FQ resistance, providing important information to understand the dose-response relationship between FQ exposure and FQ resistance response, and ascertain the target dose metric of FQs for eliminating FQ resistance crisis.
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Affiliation(s)
- Xuejing Ma
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Han Yeong Kaw
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Jing Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Qi Yang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Wei Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China.
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8
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Xia L, Li Y, Wang Y, Zhou H, Dandekar AA, Wang M, Xu F. Quorum-sensing regulation of phenazine production heightens Pseudomonas aeruginosa resistance to ciprofloxacin. Antimicrob Agents Chemother 2024; 68:e0011824. [PMID: 38526048 PMCID: PMC11064481 DOI: 10.1128/aac.00118-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 03/07/2024] [Indexed: 03/26/2024] Open
Abstract
Quorum sensing is a type of cell-cell communication that modulates various biological activities of bacteria. Previous studies indicate that quorum sensing contributes to the evolution of bacterial resistance to antibiotics, but the underlying mechanisms are not fully understood. In this study, we grew Pseudomonas aeruginosa in the presence of sub-lethal concentrations of ciprofloxacin, resulting in a large increase in ciprofloxacin minimal inhibitory concentration. We discovered that quorum sensing-mediated phenazine biosynthesis was significantly enhanced in the resistant isolates, where the quinolone circuit was the predominant contributor to this phenomenon. We found that production of pyocyanin changed carbon flux and showed that the effect can be partially inhibited by the addition of pyruvate to cultures. This study illustrates the role of quorum sensing-mediated phenotypic resistance and suggests a strategy for its prevention.
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Affiliation(s)
- Lexin Xia
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yue Li
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Yufan Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Hui Zhou
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ajai A. Dandekar
- Department of Microbiology, University of Washington, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Meizhen Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Feng Xu
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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9
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Ghosh S, Orman MA. Exploring the links between SOS response, mutagenesis, and resistance during the recovery period. Antimicrob Agents Chemother 2024; 68:e0146223. [PMID: 38534113 PMCID: PMC11064565 DOI: 10.1128/aac.01462-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/05/2024] [Indexed: 03/28/2024] Open
Abstract
Although the mechanistic connections between SOS-induced mutagenesis and antibiotic resistance are well established, our current understanding of the impact of SOS response levels, recovery durations, and transcription/translation activities on mutagenesis remains relatively limited. In this study, when bacterial cells were exposed to mutagens like ultraviolet light for defined time intervals, a compelling connection between the rate of mutagenesis and the RecA-mediated SOS response levels became evident. Our observations also indicate that mutagenesis primarily occurs during the subsequent recovery phase following the removal of the mutagenic agent. When transcription/translation was inhibited or energy molecules were depleted at the onset of treatment or during the early recovery phase, there was a noticeable decrease in SOS response activation and mutagenesis. However, targeting these processes later in the recovery phase does not have the same effect in reducing mutagenesis, suggesting that the timing of inhibiting transcription/translation or depleting energy molecules is crucial for their efficacy in reducing mutagenesis. Active transcription, translation, and energy availability within the framework of SOS response and DNA repair mechanisms appear to be conserved attributes, supported by their consistent manifestation across diverse conditions, including the use of distinct mutagens such as fluoroquinolones and various bacterial strains.
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Affiliation(s)
- Sreyashi Ghosh
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Mehmet A. Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
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10
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Shepherd MJ, Fu T, Harrington NE, Kottara A, Cagney K, Chalmers JD, Paterson S, Fothergill JL, Brockhurst MA. Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance. Nat Rev Microbiol 2024:10.1038/s41579-024-01041-1. [PMID: 38689039 DOI: 10.1038/s41579-024-01041-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 05/02/2024]
Abstract
The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.
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Affiliation(s)
- Matthew J Shepherd
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
| | - Taoran Fu
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Niamh E Harrington
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Anastasia Kottara
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Kendall Cagney
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Joanne L Fothergill
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Michael A Brockhurst
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
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11
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Recacha E, Kuropka B, Díaz-Díaz S, García-Montaner A, González-Tortuero E, Docobo-Pérez F, Rodríguez-Rojas A, Rodríguez-Martínez JM. Impact of suppression of the SOS response on protein expression in clinical isolates of Escherichia coli under antimicrobial pressure of ciprofloxacin. Front Microbiol 2024; 15:1379534. [PMID: 38659986 PMCID: PMC11039860 DOI: 10.3389/fmicb.2024.1379534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/19/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction/objective Suppression of the SOS response in combination with drugs damaging DNA has been proposed as a potential target to tackle antimicrobial resistance. The SOS response is the pathway used to repair bacterial DNA damage induced by antimicrobials such as quinolones. The extent of lexA-regulated protein expression and other associated systems under pressure of agents that damage bacterial DNA in clinical isolates remains unclear. The aim of this study was to assess the impact of this strategy consisting on suppression of the SOS response in combination with quinolones on the proteome profile of Escherichia coli clinical strains. Materials and methods Five clinical isolates of E. coli carrying different chromosomally- and/or plasmid-mediated quinolone resistance mechanisms with different phenotypes were selected, with E. coli ATCC 25922 as control strain. In addition, from each clinical isolate and control, a second strain was created, in which the SOS response was suppressed by deletion of the recA gene. Bacterial inocula from all 12 strains were then exposed to 1xMIC ciprofloxacin treatment (relative to the wild-type phenotype for each isogenic pair) for 1 h. Cell pellets were collected, and proteins were digested into peptides using trypsin. Protein identification and label-free quantification were done by liquid chromatography-mass spectrometry (LC-MS) in order to identify proteins that were differentially expressed upon deletion of recA in each strain. Data analysis and statistical analysis were performed using the MaxQuant and Perseus software. Results The proteins with the lowest expression levels were: RecA (as control), AphA, CysP, DinG, DinI, GarL, PriS, PsuG, PsuK, RpsQ, UgpB and YebG; those with the highest expression levels were: Hpf, IbpB, TufB and RpmH. Most of these expression alterations were strain-dependent and involved DNA repair processes and nucleotide, protein and carbohydrate metabolism, and transport. In isolates with suppressed SOS response, the number of underexpressed proteins was higher than overexpressed proteins. Conclusion High genomic and proteomic variability was observed among clinical isolates and was not associated with a specific resistant phenotype. This study provides an interesting approach to identify new potential targets to combat antimicrobial resistance.
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Affiliation(s)
- Esther Recacha
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Sara Díaz-Díaz
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
| | - Andrea García-Montaner
- Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
| | | | - Fernando Docobo-Pérez
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
| | - Alexandro Rodríguez-Rojas
- Division for Small Animal Internal Medicine, Department for Small Animals, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Jose Manuel Rodríguez-Martínez
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
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12
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Hernandez DM, Marzouk M, Cole M, Fortoul MC, Kethireddy SR, Contractor R, Islam H, Moulder T, Kalifa AR, Meneses EM, Mendoza MB, Thomas R, Masud S, Pubien S, Milanes P, Diaz-Tang G, Lopatkin AJ, Smith RP. Purine and pyrimidine synthesis differently affect the strength of the inoculum effect for aminoglycoside and β-lactam antibiotics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588696. [PMID: 38645041 PMCID: PMC11030397 DOI: 10.1101/2024.04.09.588696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The inoculum effect has been observed for nearly all antibiotics and bacterial species. However, explanations accounting for its occurrence and strength are lacking. We previously found that growth productivity, which captures the relationship between [ATP] and growth, can account for the strength of the inoculum effect for bactericidal antibiotics. However, the molecular pathway(s) underlying this relationship, and therefore determining the inoculum effect, remain undiscovered. We show that nucleotide synthesis can determine the relationship between [ATP] and growth, and thus the strength of inoculum effect in an antibiotic class-dependent manner. Specifically, and separate from activity through the tricarboxylic acid cycle, we find that transcriptional activity of genes involved in purine and pyrimidine synthesis can predict the strength of the inoculum effect for β-lactam and aminoglycosides antibiotics, respectively. Our work highlights the antibiotic class-specific effect of purine and pyrimidine synthesis on the severity of the inoculum effect and paves the way for intervention strategies to reduce the inoculum effect in the clinic.
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Affiliation(s)
- Daniella M. Hernandez
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Melissa Marzouk
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Madeline Cole
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Marla C. Fortoul
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Saipranavi Reddy Kethireddy
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Rehan Contractor
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Habibul Islam
- Department of Chemical Engineering, University of Rochester; Rochester, NY 14627; USA
| | - Trent Moulder
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Ariane R. Kalifa
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Estefania Marin Meneses
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Maximiliano Barbosa Mendoza
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Ruth Thomas
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Saad Masud
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Sheena Pubien
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Patricia Milanes
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Gabriela Diaz-Tang
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL, 33314
| | - Allison J. Lopatkin
- Department of Chemical Engineering, University of Rochester; Rochester, NY 14627; USA
- Department of Microbiology and Immunology, University of Rochester Medical Center; Rochester, NY 14627; USA
- Department of Biomedical Engineering, University of Rochester Medical Center; Rochester, NY 14627; USA
| | - Robert P. Smith
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
- Department of Medical Education, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, 33314
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13
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Hall RJ, Snaith AE, Thomas MJN, Brockhurst MA, McNally A. Multidrug resistance plasmids commonly reprogram the expression of metabolic genes in Escherichia coli. mSystems 2024; 9:e0119323. [PMID: 38376169 PMCID: PMC10949484 DOI: 10.1128/msystems.01193-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Multidrug-resistant Escherichia coli is a leading cause of global mortality. Transfer of plasmids carrying genes encoding beta-lactamases, carbapenamases, and colistin resistance between lineages is driving the rising rates of hard-to-treat nosocomial and community infections. Multidrug resistance (MDR) plasmid acquisition commonly causes transcriptional disruption, and while a number of studies have shown strain-specific fitness and transcriptional effects of an MDR plasmid across diverse bacterial lineages, fewer studies have compared the impacts of different MDR plasmids in a common bacterial host. As such, our ability to predict which MDR plasmids are the most likely to be maintained and spread in bacterial populations is limited. Here, we introduced eight diverse MDR plasmids encoding resistances against a range of clinically important antibiotics into E. coli K-12 MG1655 and measured their fitness costs and transcriptional impacts. The scale of the transcriptional responses varied substantially between plasmids, ranging from >650 to <20 chromosomal genes being differentially expressed. However, the scale of regulatory disruption did not correlate significantly with the magnitude of the plasmid fitness cost, which also varied between plasmids. The identities of differentially expressed genes differed between transconjugants, although the expression of certain metabolic genes and functions were convergently affected by multiple plasmids, including the downregulation of genes involved in L-methionine transport and metabolism. Our data show the complexity of the interaction between host genetic background and plasmid genetic background in determining the impact of MDR plasmid acquisition on E. coli. IMPORTANCE The increase in infections that are resistant to multiple classes of antibiotics, including those isolates that carry carbapenamases, beta-lactamases, and colistin resistance genes, is of global concern. Many of these resistances are spread by conjugative plasmids. Understanding more about how an isolate responds to an incoming plasmid that encodes antibiotic resistance will provide information that could be used to predict the emergence of MDR lineages. Here, the identification of metabolic networks as being particularly sensitive to incoming plasmids suggests the possible targets for reducing plasmid transfer.
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Affiliation(s)
- Rebecca J. Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Ann E. Snaith
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Matthew J. N. Thomas
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Michael A. Brockhurst
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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14
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Chen S, Qian Y, Wan D, Li Y, Zhou C. Synthesis and Synergistic Antimicrobial Efficacy of Covalent Conjugates Composed of Epsilon-Poly-l-lysine and Beta-Lactam Antibiotics. ACS APPLIED BIO MATERIALS 2024; 7:1990-1999. [PMID: 38363728 DOI: 10.1021/acsabm.4c00093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
The increasing severity of problems posed by drug-resistant pathogens has compelled researchers to explore innovative approaches for infection prevention. Among these strategies, conjugation methods stand out for their convenience and high efficacy. In this study, multiple covalent conjugates were synthesized, incorporating the natural antimicrobial peptide epsilon-poly-l-lysine (EPL) and two commonly used β-lactam antibiotics: penicillin G or ampicillin. Enhanced antimicrobial efficacy against typical Gram-negative pathogens, along with faster kill kinetics compared to combination approaches, was demonstrated by the EPL-Ampicillin covalent conjugates. Their antimicrobial mechanism was also substantiated through SEM and fluorescence tests in this work, confirming the inheritance of membrane-disrupting properties from EPL. Furthermore, the excellent biocompatibility of the raw materials was reserved in the covalent conjugates. This simplified conjugation method holds promise for the development of infection therapeutic drugs and potentially restores the sensitivity of conventional antibiotics to drug-resistant pathogens by introducing membrane-disrupting mechanisms.
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Affiliation(s)
- Sijin Chen
- School of Material Science and Engineering, Tongji University, 4800 Caoan Road, Shanghai 201804, China
| | - Yusheng Qian
- School of Material Science and Engineering, Tongji University, 4800 Caoan Road, Shanghai 201804, China
| | - Decheng Wan
- School of Material Science and Engineering, Tongji University, 4800 Caoan Road, Shanghai 201804, China
| | - Yan Li
- School of Material Science and Engineering, Tongji University, 4800 Caoan Road, Shanghai 201804, China
| | - Chuncai Zhou
- School of Material Science and Engineering, Tongji University, 4800 Caoan Road, Shanghai 201804, China
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15
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Yu J, Lu H, Zhu L. Mutation-driven resistance development in wastewater E. coli upon low-level cephalosporins: Pharmacophore contribution and novel mechanism. WATER RESEARCH 2024; 252:121235. [PMID: 38310801 DOI: 10.1016/j.watres.2024.121235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/24/2024] [Accepted: 01/28/2024] [Indexed: 02/06/2024]
Abstract
Cephalosporins have been widely applied in clinical and veterinary settings and detected at increasing concentrations in water environments. They potentially induce high-level antibiotic resistance at environmental concentrations. This study characterized how typical wastewater bacteria developed heritable antibiotic resistance under exposure to different cephalosporins, including pharmacophore-resistance correlation, resistance mechanism, and occurrence of resistance-relevant mutations in different water environments. Wastewater-isolated E. coli JX1 was exposed to eight cephalosporins individually at 25 µg/L for 60 days. Multidrug resistance developed and diverse mutations arose in selected mutants, where a single mutation in ATP phosphoribosyltransferase encoding gene (hisG) resulted in up to 128-fold increase in resistance to meropenem. Molprint2D pharma RQSAR analysis revealed that hydrogen-bond acceptors and hydrophobic groups in the R1 and R2 substituents of cephalosporins contributed positively to antibiotic resistance. Some of these pharmacophores may persist during bio- or photo-degradation in the environment. hisG mutation confers a novel resistance mechanism by inhibiting fatty acid degradation, and its variants were more abundant in water-related E. coli (especially in the effluent of wastewater treatment plants) compared with those in non-water environments. These results suggest that specific degradation of particular pharmacophores in cephalosporins could be useful for controlling resistance development, and mutations in previously unreported resistance genes (e.g., hisG) can lead to overlooked antibiotic resistance risks in water environments.
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Affiliation(s)
- Jinxian Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China
| | - Huijie Lu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China.
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16
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Rodrigues M, Sabaeifard P, Yildiz MS, Lyon A, Coughlin L, Ahmed S, Poulides N, Toprak AC, Behrendt C, Wang X, Monogue M, Kim J, Gan S, Zhan X, Filkins L, Williams NS, Hooper LV, Koh AY, Toprak E. Susceptible bacteria can survive antibiotic treatment in the mammalian gastrointestinal tract without evolving resistance. Cell Host Microbe 2024; 32:396-410.e6. [PMID: 38359828 PMCID: PMC10942764 DOI: 10.1016/j.chom.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 12/13/2023] [Accepted: 01/24/2024] [Indexed: 02/17/2024]
Abstract
Antibiotic resistance and evasion are incompletely understood and complicated by the fact that murine interval dosing models do not fully recapitulate antibiotic pharmacokinetics in humans. To better understand how gastrointestinal bacteria respond to antibiotics, we colonized germ-free mice with a pan-susceptible genetically barcoded Escherichia coli clinical isolate and administered the antibiotic cefepime via programmable subcutaneous pumps, allowing closer emulation of human parenteral antibiotic dynamics. E. coli was only recovered from intestinal tissue, where cefepime concentrations were still inhibitory. Strikingly, "some" E. coli isolates were not cefepime resistant but acquired mutations in genes involved in polysaccharide capsular synthesis increasing their invasion and survival within human intestinal cells. Deleting wbaP involved in capsular polysaccharide synthesis mimicked this phenotype, allowing increased invasion of colonocytes where cefepime concentrations were reduced. Additionally, "some" mutant strains exhibited a persister phenotype upon further cefepime exposure. This work uncovers a mechanism allowing "select" gastrointestinal bacteria to evade antibiotic treatment.
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Affiliation(s)
- Marinelle Rodrigues
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Parastoo Sabaeifard
- Department of Pediatrics, Division of Hematology/Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Muhammed Sadik Yildiz
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adam Lyon
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Laura Coughlin
- Department of Pediatrics, Division of Hematology/Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Ahmed
- Department of Pediatrics, Division of Hematology/Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nicole Poulides
- Department of Pediatrics, Division of Hematology/Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ahmet C Toprak
- Department of Pediatrics, Division of Hematology/Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cassie Behrendt
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoyu Wang
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marguerite Monogue
- Department of Pharmacy, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, Infectious Diseases and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiwoong Kim
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shuheng Gan
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaowei Zhan
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Laura Filkins
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Noelle S Williams
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lora V Hooper
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; The Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andrew Y Koh
- Department of Pediatrics, Division of Hematology/Oncology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Erdal Toprak
- Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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17
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Mofidifar S, Yadegar A, Karimi-Jafari MH. A reconstructed genome-scale metabolic model of Helicobacter pylori for predicting putative drug targets in clarithromycin and rifampicin resistance conditions. Helicobacter 2024; 29:e13074. [PMID: 38615332 DOI: 10.1111/hel.13074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND Helicobacter pylori is considered a true human pathogen for which rising drug resistance constitutes a drastic concern globally. The present study aimed to reconstruct a genome-scale metabolic model (GSMM) to decipher the metabolic capability of H. pylori strains in response to clarithromycin and rifampicin along with identification of novel drug targets. MATERIALS AND METHODS The iIT341 model of H. pylori was updated based on genome annotation data, and biochemical knowledge from literature and databases. Context-specific models were generated by integrating the transcriptomic data of clarithromycin and rifampicin resistance into the model. Flux balance analysis was employed for identifying essential genes in each strain, which were further prioritized upon being nonhomologs to humans, virulence factor analysis, druggability, and broad-spectrum analysis. Additionally, metabolic differences between sensitive and resistant strains were also investigated based on flux variability analysis and pathway enrichment analysis of transcriptomic data. RESULTS The reconstructed GSMM was named as HpM485 model. Pathway enrichment and flux variability analyses demonstrated reduced activity in the ribosomal pathway in both clarithromycin- and rifampicin-resistant strains. Also, a significant decrease was detected in the activity of metabolic pathways of clarithromycin-resistant strain. Moreover, 23 and 16 essential genes were exclusively detected in clarithromycin- and rifampicin-resistant strains, respectively. Based on prioritization analysis, cyclopropane fatty acid synthase and phosphoenolpyruvate synthase were identified as putative drug targets in clarithromycin- and rifampicin-resistant strains, respectively. CONCLUSIONS We present a robust and reliable metabolic model of H. pylori. This model can predict novel drug targets to combat drug resistance and explore the metabolic capability of H. pylori in various conditions.
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Affiliation(s)
- Sepideh Mofidifar
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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18
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Palmieri N, Hess C, Hess M. GWAS and comparative genomics reveal candidate antibiotic resistance genes in the avian pathogen Gallibacterium anatis for six widespread antibiotics. Vet Microbiol 2024; 290:109995. [PMID: 38301451 DOI: 10.1016/j.vetmic.2024.109995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 11/20/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024]
Abstract
Gallibacterium anatis is a Gram-negative bacterium found in the respiratory and genital tracts of various animals, primarily poultry. Its association with septicemia and high mortality in poultry, along with the rise in multidrug-resistant strains, has amplified concerns. Recent research uncovered significant variability in antibiotic resistance profiles among G. anatis isolates from different Austrian flocks, and even between different organs within the same bird. In response, in the present study 60 of these isolates were sequenced and a combination of comparative genomics and genome-wide association study (GWAS) analysis was applied to understand the genetic variability of G. anatis across flocks and organs and to identify genes related to antibiotic resistance. The results showed that each flock harbored one or two strains of G. anatis with only a few strains shared between flocks, demonstrating a great variability among flocks. We identified genes associated with resistance to nalidixic acid, trimethoprim, cefoxitin, tetracycline, ampicillin and sulfamethoxazole. Our findings revealed that G. anatis may develop antibiotic resistance through two mechanisms: single-nucleotide mutations and the presence of specific genes that confer resistance. Unexpectedly, some tetracycline-resistant isolates lacked all known tetracycline-associated genes, suggesting the involvement of novel mechanisms of tetracycline resistance that require additional exploration. Furthermore, our functional annotation of resistance genes highlighted the citric acid cycle pathway as a potential key modulator of antibiotic resistance in G. anatis. In summary, this study describes the first application of GWAS analysis to G. anatis and provides new insights into the acquisition of multidrug resistance in this important avian pathogen.
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Affiliation(s)
- Nicola Palmieri
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.
| | - Claudia Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Michael Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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Kharga K, Jha S, Vishwakarma T, Kumar L. Current developments and prospects of the antibiotic delivery systems. Crit Rev Microbiol 2024:1-40. [PMID: 38425122 DOI: 10.1080/1040841x.2024.2321480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
Antibiotics have remained the cornerstone for the treatment of bacterial infections ever since their discovery in the twentieth century. The uproar over antibiotic resistance among bacteria arising from genome plasticity and biofilm development has rendered current antibiotic therapies ineffective, urging the development of innovative therapeutic approaches. The development of antibiotic resistance among bacteria has further heightened the clinical failure of antibiotic therapy, which is often linked to its low bioavailability, side effects, and poor penetration and accumulation at the site of infection. In this review, we highlight the potential use of siderophores, antibodies, cell-penetrating peptides, antimicrobial peptides, bacteriophages, and nanoparticles to smuggle antibiotics across impermeable biological membranes to achieve therapeutically relevant concentrations of antibiotics and combat antimicrobial resistance (AMR). We will discuss the general mechanisms via which each delivery system functions and how it can be tailored to deliver antibiotics against the paradigm of mechanisms underlying antibiotic resistance.
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Affiliation(s)
- Kusum Kharga
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Himachal Pradesh, India
| | - Shubhang Jha
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Himachal Pradesh, India
| | - Tanvi Vishwakarma
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Himachal Pradesh, India
| | - Lokender Kumar
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Himachal Pradesh, India
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20
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Padhi AK, Maurya S. Uncovering the secrets of resistance: An introduction to computational methods in infectious disease research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:173-220. [PMID: 38448135 DOI: 10.1016/bs.apcsb.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Antimicrobial resistance (AMR) is a growing global concern with significant implications for infectious disease control and therapeutics development. This chapter presents a comprehensive overview of computational methods in the study of AMR. We explore the prevalence and statistics of AMR, underscoring its alarming impact on public health. The role of AMR in infectious disease outbreaks and its impact on therapeutics development are discussed, emphasizing the need for novel strategies. Resistance mutations are pivotal in AMR, enabling pathogens to evade antimicrobial treatments. We delve into their importance and contribution to the spread of AMR. Experimental methods for quantitatively evaluating resistance mutations are described, along with their limitations. To address these challenges, computational methods provide promising solutions. We highlight the advantages of computational approaches, including rapid analysis of large datasets and prediction of resistance profiles. A comprehensive overview of computational methods for studying AMR is presented, encompassing genomics, proteomics, structural bioinformatics, network analysis, and machine learning algorithms. The strengths and limitations of each method are briefly outlined. Additionally, we introduce ResScan-design, our own computational method, which employs a protein (re)design protocol to identify potential resistance mutations and adaptation signatures in pathogens. Case studies are discussed to showcase the application of ResScan in elucidating hotspot residues, understanding underlying mechanisms, and guiding the design of effective therapies. In conclusion, we emphasize the value of computational methods in understanding and combating AMR. Integration of experimental and computational approaches can expedite the discovery of innovative antimicrobial treatments and mitigate the threat posed by AMR.
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Affiliation(s)
- Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India.
| | - Shweata Maurya
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
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21
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Ke W, Xie Y, Chen Y, Ding H, Ye L, Qiu H, Li H, Zhang L, Chen L, Tian X, Shen Z, Song Z, Fan X, Zong JF, Guo Z, Ma X, Xiao M, Liao G, Liu CH, Yin WB, Dong Z, Yang F, Jiang YY, Perlin DS, Chen Y, Fu YV, Wang L. Fungicide-tolerant persister formation during cryptococcal pulmonary infection. Cell Host Microbe 2024; 32:276-289.e7. [PMID: 38215741 DOI: 10.1016/j.chom.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/25/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024]
Abstract
Bacterial persisters, a subpopulation of genetically susceptible cells that are normally dormant and tolerant to bactericides, have been studied extensively because of their clinical importance. In comparison, much less is known about the determinants underlying fungicide-tolerant fungal persister formation in vivo. Here, we report that during mouse lung infection, Cryptococcus neoformans forms persisters that are highly tolerant to amphotericin B (AmB), the standard of care for treating cryptococcosis. By exploring stationary-phase indicator molecules and developing single-cell tracking strategies, we show that in the lung, AmB persisters are enriched in cryptococcal cells that abundantly produce stationary-phase molecules. The antioxidant ergothioneine plays a specific and key role in AmB persistence, which is conserved in phylogenetically distant fungi. Furthermore, the antidepressant sertraline (SRT) shows potent activity specifically against cryptococcal AmB persisters. Our results provide evidence for and the determinant of AmB-tolerant persister formation in pulmonary cryptococcosis, which has potential clinical significance.
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Affiliation(s)
- Weixin Ke
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuyan Xie
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingying Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Ding
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leixin Ye
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haoning Qiu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Li
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Lanyue Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiuyun Tian
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenghao Shen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zili Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
| | - Jian-Fa Zong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoyu Ma
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing 100730, China
| | - Guojian Liao
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Cui Hua Liu
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Yang
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yuan-Ying Jiang
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Yihua Chen
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu V Fu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Linqi Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Wang Y, Wu Z, Wang Z, Du H, Xiao S, Lu L, Wang Z. Analyses of the Antibiofilm Activity of o-Phenanthroline Monohydrate against Enterococcus faecalis and Staphylococcus aureus and the Mechanisms Underlying These Effects. ACS Infect Dis 2024; 10:638-649. [PMID: 38258383 DOI: 10.1021/acsinfecdis.3c00516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Enterococcus faecalis and Staphylococcus aureus exhibit robust biofilm formation capabilities, the formation of which is closely linked to pathogenicity and drug resistance, thereby resulting in host infection and treatment failure. o-Phenanthroline monohydrate (o-Phen) and its derivatives demonstrate a wide range of antibacterial and antifungal activities. In this study, we aimed to explore the antibiofilm activity of o-Phen to E. faecalis and S. aureus and provide insights into the molecular mechanisms for combating biofilm resistance. We demonstrated that o-Phen possesses significant antibacterial and antibiofilm properties against E. faecalis and S. aureus, inducing alterations in bacterial morphology, compromising cell membrane integrity, and exhibiting synergistic effects with β-lactam antibiotics at sub-MIC concentrations. The adhesion ability and automatic condensation capacity of, and synthesis of, extracellular polymers by E. faecalis cells were reduced by o-Phen, resulting in the inhibition of biofilm formation. Importantly, transcriptome analysis revealed 354 upregulated and 456 downregulated genes in o-Phen-treated E. faecalis. Differentially expressed genes were enriched in 11 metabolism-related pathways, including amino acid metabolism, pyrimidine metabolism, and glycolysis/gluconeogenesis. Moreover, the oppA, CeuA, and ZnuB genes involved in the ABC transport system, and the PBP1A penicillin-binding protein-coding genes sarA and mrcA were significantly downregulated. The multidrug efflux pump system and membrane permeability genes mdtG and hlyD, and bacterial adhesion-related genes, including adcA and fss2 were also downregulated, while mraZ and ASP23 were upregulated. Thus, o-Phen is anticipated to be an effective alternative drug for the treatment of E. faecalis and S. aureus biofilm-associated infections.
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Affiliation(s)
- Yu Wang
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Zhouhui Wu
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Zhiwen Wang
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Heng Du
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Shuang Xiao
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Lin Lu
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Zhen Wang
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
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23
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Yu J, Zhang H, Ju Z, Huang J, Lin C, Wu J, Wu Y, Sun S, Wang H, Hao G, Zhang A. Increased mutations in lipopolysaccharide biosynthetic genes cause time-dependent development of phage resistance in Salmonella. Antimicrob Agents Chemother 2024; 68:e0059423. [PMID: 38193669 PMCID: PMC10848759 DOI: 10.1128/aac.00594-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/12/2023] [Indexed: 01/10/2024] Open
Abstract
Understanding how bacteria evolve resistance to phages has implications for phage-based therapies and microbial evolution. In this study, the susceptibility of 335 Salmonella isolates to the wide host range Salmonella phage BPSELC-1 was tested. Potentially significant gene sets that could confer resistance were identified using bioinformatics approaches based on phage susceptibility phenotypes; more than 90 potential antiphage defense gene sets, including those involved in lipopolysaccharide (LPS) biosynthesis, DNA replication, secretion systems, and respiratory chain, were found. The evolutionary dynamics of Salmonella resistance to phage were assessed through laboratory evolution experiments, which showed that phage-resistant mutants rapidly developed and exhibited genetic heterogeneity. Most representative Salmonella hosts (58.1% of 62) rapidly developed phage resistance within 24 h. All phage-resistant mutant clones exhibited genetic heterogeneity and observed mutations in LPS-related genes (rfaJ and rfaK) as well as other genes such as cellular respiration, transport, and cell replication-related genes. The study also identified potential trade-offs, indicating that bacteria tend to escape fitness trade-offs through multi-site mutations, all tested mutants increased sensitivity to polymyxin B, but this does not always affect their relative fitness or biofilm-forming capacity. Furthermore, complementing the rfaJ mutant gene could partially restore the phage sensitivity of phage-resistant mutants. These results provide insight into the phage resistance mechanisms of Salmonella and the complexity of bacterial evolution resulting from phage predation, which can inform future strategies for phage-based therapies and microbial evolution.
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Affiliation(s)
- Jing Yu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Haoyu Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Zijing Ju
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jiaqi Huang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China
| | - Cong Lin
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jie Wu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yingting Wu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Shuhong Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Guijuan Hao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China
| | - Anyun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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24
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Aduru SV, Szenkiel K, Rahman A, Ahmad M, Fabozzi M, Smith RP, Lopatkin AJ. Sub-inhibitory antibiotic treatment selects for enhanced metabolic efficiency. Microbiol Spectr 2024; 12:e0324123. [PMID: 38226801 PMCID: PMC10846238 DOI: 10.1128/spectrum.03241-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024] Open
Abstract
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.
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Affiliation(s)
- Sai Varun Aduru
- Department of Chemical Engineering, University of Rochester, Rochester, New York, USA
| | | | - Anika Rahman
- Department of Biology, Barnard College, New York, New York, USA
| | - Mehrose Ahmad
- Department of Biology, Barnard College, New York, New York, USA
| | - Maya Fabozzi
- Department of Biology, Barnard College, New York, New York, USA
| | - Robert P. Smith
- Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, Florida, USA
| | - Allison J. Lopatkin
- Department of Chemical Engineering, University of Rochester, Rochester, New York, USA
- Department of Biology, Barnard College, New York, New York, USA
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, New York, USA
- Data Science Institute, Columbia University, New York, New York, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
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25
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Dekker JP. Within-Host Evolution of Bacterial Pathogens in Acute and Chronic Infection. ANNUAL REVIEW OF PATHOLOGY 2024; 19:203-226. [PMID: 37832940 DOI: 10.1146/annurev-pathmechdis-051122-111408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Bacterial pathogens undergo remarkable adaptive change in response to the selective forces they encounter during host colonization and infection. Studies performed over the past few decades have demonstrated that many general evolutionary processes can be discerned during the course of host adaptation, including genetic diversification of lineages, clonal succession events, convergent evolution, and balanced fitness trade-offs. In some cases, elevated mutation rates resulting from mismatch repair or proofreading deficiencies accelerate evolution, and active mobile genetic elements or phages may facilitate genome plasticity. The host immune response provides another critical component of the fitness landscapes guiding adaptation, and selection operating on pathogens at this level may lead to immune evasion and the establishment of chronic infection. This review summarizes recent advances in this field, with a special focus on different forms of bacterial genome plasticity in the context of infection, and considers clinical consequences of adaptive changes for the host.
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Affiliation(s)
- John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA;
- National Institutes of Health Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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26
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Maeda T, Furusawa C. Laboratory Evolution of Antimicrobial Resistance in Bacteria to Develop Rational Treatment Strategies. Antibiotics (Basel) 2024; 13:94. [PMID: 38247653 PMCID: PMC10812413 DOI: 10.3390/antibiotics13010094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024] Open
Abstract
Laboratory evolution studies, particularly with Escherichia coli, have yielded invaluable insights into the mechanisms of antimicrobial resistance (AMR). Recent investigations have illuminated that, with repetitive antibiotic exposures, bacterial populations will adapt and eventually become tolerant and resistant to the drugs. Through intensive analyses, these inquiries have unveiled instances of convergent evolution across diverse antibiotics, the pleiotropic effects of resistance mutations, and the role played by loss-of-function mutations in the evolutionary landscape. Moreover, a quantitative analysis of multidrug combinations has shed light on collateral sensitivity, revealing specific drug combinations capable of suppressing the acquisition of resistance. This review article introduces the methodologies employed in the laboratory evolution of AMR in bacteria and presents recent discoveries concerning AMR mechanisms derived from laboratory evolution. Additionally, the review outlines the application of laboratory evolution in endeavors to formulate rational treatment strategies.
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Affiliation(s)
- Tomoya Maeda
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita 565-0874, Japan;
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita 565-0874, Japan;
- Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
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27
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Wang Y, Fu H, Shi XJ, Zhao GP, Lyu LD. Genome-wide screen reveals cellular functions that counteract rifampicin lethality in Escherichia coli. Microbiol Spectr 2024; 12:e0289523. [PMID: 38054714 PMCID: PMC10782999 DOI: 10.1128/spectrum.02895-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/31/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Rifamycins are a group of antibiotics with a wide antibacterial spectrum. Although the binding target of rifamycin has been well characterized, the mechanisms underlying the discrepant killing efficacy between gram-negative and gram-positive bacteria remain poorly understood. Using a high-throughput screen combined with targeted gene knockouts in the gram-negative model organism Escherichia coli, we established that rifampicin efficacy is strongly dependent on several cellular pathways, including iron acquisition, DNA repair, aerobic respiration, and carbon metabolism. In addition, we provide evidence that these pathways modulate rifampicin efficacy in a manner distinct from redox-related killing. Our findings provide insights into the mechanism of rifamycin efficacy and may aid in the development of new antimicrobial adjuvants.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission, School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Han Fu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission, School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Jie Shi
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission, School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Guo-Ping Zhao
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission, School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission, School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Tuberculosis, Shanghai Clinical Research Center for Infectious Disease (Tuberculosis), Shanghai Pulmonary Hospital, Shanghai, China
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28
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Brenzinger S, Airoldi M, Ogunleye AJ, Jugovic K, Amstalden MK, Brochado AR. The Vibrio cholerae CBASS phage defence system modulates resistance and killing by antifolate antibiotics. Nat Microbiol 2024; 9:251-262. [PMID: 38172623 DOI: 10.1038/s41564-023-01556-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
Toxic bacterial modules such as toxin-antitoxin systems hold antimicrobial potential, though successful applications are rare. Here we show that in Vibrio cholerae the cyclic-oligonucleotide-based anti-phage signalling system (CBASS), another example of a toxic module, increases sensitivity to antifolate antibiotics up to 10×, interferes with their synergy and ultimately enables bacterial lysis by these otherwise classic bacteriostatic antibiotics. Cyclic-oligonucleotide production by the CBASS nucleotidyltransferase DncV upon antifolate treatment confirms full CBASS activation under these conditions, and suggests that antifolates release DncV allosteric inhibition by folates. Consequently, the CBASS-antifolate interaction is specific to CBASS systems with closely related nucleotidyltransferases and similar folate-binding pockets. Last, antifolate resistance genes abolish the CBASS-antifolate interaction by bypassing the effects of on-target antifolate activity, thereby creating potential for their coevolution with CBASS. Altogether, our findings illustrate how toxic modules can impact antibiotic activity and ultimately confer bactericidal activity to classical bacteriostatic antibiotics.
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Affiliation(s)
- Susanne Brenzinger
- Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martina Airoldi
- Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
| | | | - Karl Jugovic
- Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Ana Rita Brochado
- Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany.
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany.
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany.
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29
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Li S, Xiang J, Zeng Y, Peng X, Li H. Elevated proton motive force is a tetracycline resistance mechanism that leads to the sensitivity to gentamicin in Edwardsiella tarda. Microb Biotechnol 2024; 17:e14379. [PMID: 38085112 PMCID: PMC10832521 DOI: 10.1111/1751-7915.14379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 11/10/2023] [Indexed: 02/03/2024] Open
Abstract
Tetracycline is a commonly used human and veterinary antibiotic that is mostly discharged into environment and thereby tetracycline-resistant bacteria are widely isolated. To combat these resistant bacteria, further understanding for tetracycline resistance mechanisms is needed. Here, GC-MS based untargeted metabolomics with biochemistry and molecular biology techniques was used to explore tetracycline resistance mechanisms of Edwardsiella tarda. Tetracycline-resistant E. tarda (LTB4-RTET ) exhibited a globally repressed metabolism against elevated proton motive force (PMF) as the most characteristic feature. The elevated PMF contributed to the resistance, which was supported by the three results: (i) viability was decreased with increasing PMF inhibitor carbonylcyanide-3-chlorophenylhydrazone; (ii) survival is related to PMF regulated by pH; (iii) LTB4-RTET were sensitive to gentamicin, an antibiotic that is dependent upon PMF to kill bacteria. Meanwhile, gentamicin-resistant E. tarda with low PMF are sensitive to tetracycline is also demonstrated. These results together indicate that the combination of tetracycline with gentamycin will effectively kill both gentamycin and tetracycline resistant bacteria. Therefore, the present study reveals a PMF-enhanced tetracycline resistance mechanism in LTB4-RTET and provides an effective approach to combat resistant bacteria.
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Affiliation(s)
- Shao‐hua Li
- State Key Laboratory of Bio‐Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen UniversityGuangzhouChina
| | - Jiao Xiang
- State Key Laboratory of Bio‐Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen UniversityGuangzhouChina
| | - Ying‐yue Zeng
- State Key Laboratory of Bio‐Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen UniversityGuangzhouChina
| | - Xuan‐xian Peng
- State Key Laboratory of Bio‐Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen UniversityGuangzhouChina
- Laboratory for Marine Fisheries Science and Food Production ProcessesQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Guangdong Litai Pharmaceutical Co. Ltd.JieyangGuangdongChina
| | - Hui Li
- State Key Laboratory of Bio‐Control, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen UniversityGuangzhouChina
- Laboratory for Marine Fisheries Science and Food Production ProcessesQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
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30
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Yao A, Du J, Sun Q, Liu L, Song Z, He W, Liu J. Flexible Covalent Organic Network with Ordered Honeycomb Nanoarchitecture for Molecular Separations. ACS NANO 2023; 17:22916-22927. [PMID: 37962059 DOI: 10.1021/acsnano.3c08028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Membranes with precisely defined nanostructure are desirable for energy-efficient molecular separations. The emergence of membranes with honeycomb lattice or topological nanopores is of fundamental importance. The tailor-made nanostructure and morphology may have huge potential to resolve the longstanding bottlenecks in membrane science and technology. Herein, inspired by honeycomb architecture, we demonstrate an effective and scalable route based on interfacial polymerization (IP) to generate flexible and ordered covalent organic network (CON) membranes for liquid-phase molecular separations. The aperture size of a CON membrane can be reasonably designed through the strong covalent bond between molecular building blocks. The fabricated CON membrane formed by IP showed an obviously size-dependent sieving of molecules, yielding a stepwise conversion from low rejection to the expected high rejection. Moreover, the CON membrane was also found to have the sieving capability for tetracycline and ciprofloxacin, ascribed to the effect of size exclusion by an ordered single-nanoscale channel (<1 nm). This approach provides a viable strategy for creating target-sized channels from molecular-level design and demonstrates their potential for accurate molecular separations.
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Affiliation(s)
- Ayan Yao
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230052, Anhui, China
| | - Jingcheng Du
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230052, Anhui, China
| | - Qian Sun
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230052, Anhui, China
| | - Linghao Liu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230052, Anhui, China
| | - Ziye Song
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230052, Anhui, China
| | - Wen He
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230052, Anhui, China
| | - Jiangtao Liu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230052, Anhui, China
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31
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Yuan Z, Liu X, Deng S, He G, Zhang J, He Q, Chi Y, Jiang X, Xia X, Deng R. Single-Cell Genotyping of Single-Nucleotide Mutations Using In Situ Allele-Specific Loop-Mediated Isothermal Amplification. ACS Sens 2023; 8:4315-4322. [PMID: 37862679 DOI: 10.1021/acssensors.3c01679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Single-nucleotide mutations (SNMs) in the bacterial genome may cause antibiotic resistance. The visualization of SNMs can indicate antibiotic resistance phenotypes at the single-cell level but remains challenging. Herein, we proposed an in situ allele-specific isothermal amplification proceeded inside cells, allowing us to image bacterial genes with single-nucleotide resolution. The primer for loop-mediated isothermal amplification (LAMP) was designed with artificial mismatch bases to serve as an allele-specific probe, endowing LAMP to specifically amplify genes with SNMs. Due to the high amplification efficiency of LAMP, the method termed AlleLAMP can generate high gain for imaging SNMs and precisely quantify mutated quinolone-resistant Salmonella in bacterial mixture. We utilized AlleLAMP to survey the selection of antibiotic resistance under the preservative stress and found that the mutant quinolone-resistant strain owned a survival advantage over the wild-type quinolone-sensitive strain under the stress of preservatives. AlleLAMP can serve as a single-cell tool for analyzing the relationship between bacterial genotype and phenotype.
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Affiliation(s)
- Zilan Yuan
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Xinmiao Liu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Guiping He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Jiaqi Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Yuanlong Chi
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Xiue Jiang
- Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
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32
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Colilla M, Vallet-Regí M. Organically Modified Mesoporous Silica Nanoparticles against Bacterial Resistance. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2023; 35:8788-8805. [PMID: 38027542 PMCID: PMC10653088 DOI: 10.1021/acs.chemmater.3c02192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/22/2023] [Indexed: 12/01/2023]
Abstract
Bacterial antimicrobial resistance is posed to become a major hazard to global health in the 21st century. An aggravating issue is the stalled antibiotic research pipeline, which requires the development of new therapeutic strategies to combat antibiotic-resistant infections. Nanotechnology has entered into this scenario bringing up the opportunity to use nanocarriers capable of transporting and delivering antimicrobials to the target site, overcoming bacterial resistant barriers. Among them, mesoporous silica nanoparticles (MSNs) are receiving growing attention due to their unique features, including large drug loading capacity, biocompatibility, tunable pore sizes and volumes, and functionalizable silanol-rich surface. This perspective article outlines the recent research advances in the design and development of organically modified MSNs to fight bacterial infections. First, a brief introduction to the different mechanisms of bacterial resistance is presented. Then, we review the recent scientific approaches to engineer multifunctional MSNs conceived as an assembly of inorganic and organic building blocks, against bacterial resistance. These elements include specific ligands to target planktonic bacteria, intracellular bacteria, or bacterial biofilm; stimuli-responsive entities to prevent antimicrobial cargo release before arriving at the target; imaging agents for diagnosis; additional constituents for synergistic combination antimicrobial therapies; and aims to improve the therapeutic outcomes. Finally, this manuscript addresses the current challenges and future perspectives on this hot research area.
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Affiliation(s)
- Montserrat Colilla
- Departamento
de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Instituto de Investigación
Sanitaria Hospital 12 de Octubre i+12, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
- Centro
de Investigación Biomédica en Red de Bioingeniería,
Biomateriales y Nanomedicina (CIBER-BBN), Madrid 28029, Spain
| | - María Vallet-Regí
- Departamento
de Química en Ciencias Farmacéuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Instituto de Investigación
Sanitaria Hospital 12 de Octubre i+12, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
- Centro
de Investigación Biomédica en Red de Bioingeniería,
Biomateriales y Nanomedicina (CIBER-BBN), Madrid 28029, Spain
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Diebold PJ, Rhee MW, Shi Q, Trung NV, Umrani F, Ahmed S, Kulkarni V, Deshpande P, Alexander M, Thi Hoa N, Christakis NA, Iqbal NT, Ali SA, Mathad JS, Brito IL. Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. Nat Commun 2023; 14:7366. [PMID: 37963868 PMCID: PMC10645880 DOI: 10.1038/s41467-023-42998-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
The acquisition of antimicrobial resistance (AR) genes has rendered important pathogens nearly or fully unresponsive to antibiotics. It has been suggested that pathogens acquire AR traits from the gut microbiota, which collectively serve as a global reservoir for AR genes conferring resistance to all classes of antibiotics. However, only a subset of AR genes confers resistance to clinically relevant antibiotics, and, although these AR gene profiles are well-characterized for common pathogens, less is known about their taxonomic associations and transfer potential within diverse members of the gut microbiota. We examined a collection of 14,850 human metagenomes and 1666 environmental metagenomes from 33 countries, in addition to nearly 600,000 isolate genomes, to gain insight into the global prevalence and taxonomic range of clinically relevant AR genes. We find that several of the most concerning AR genes, such as those encoding the cephalosporinase CTX-M and carbapenemases KPC, IMP, NDM, and VIM, remain taxonomically restricted to Proteobacteria. Even cfiA, the most common carbapenemase gene within the human gut microbiome, remains tightly restricted to Bacteroides, despite being found on a mobilizable plasmid. We confirmed these findings in gut microbiome samples from India, Honduras, Pakistan, and Vietnam, using a high-sensitivity single-cell fusion PCR approach. Focusing on a set of genes encoding carbapenemases and cephalosporinases, thus far restricted to Bacteroides species, we find that few mutations are required for efficacy in a different phylum, raising the question of why these genes have not spread more widely. Overall, these data suggest that globally prevalent, clinically relevant AR genes have not yet established themselves across diverse commensal gut microbiota.
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Affiliation(s)
- Peter J Diebold
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Matthew W Rhee
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Qiaojuan Shi
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Nguyen Vinh Trung
- Oxford University Clinical Research Unit (OUCRU) in Ho Chi Minh City, Ho Chi Minh city, Viet Nam
| | | | | | - Vandana Kulkarni
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Prasad Deshpande
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Mallika Alexander
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit (OUCRU) in Ho Chi Minh City, Ho Chi Minh city, Viet Nam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Microbiology Department and Center for Tropical Medicine Research, Ngoc Thach University of Medicine, Ho Chi Minh city, Vietnam
| | | | | | | | | | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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Karasiński M, Wnorowska U, Durnaś B, Król G, Daniluk T, Skłodowski K, Głuszek K, Piktel E, Okła S, Bucki R. Ceragenins and Ceragenin-Based Core-Shell Nanosystems as New Antibacterial Agents against Gram-Negative Rods Causing Nosocomial Infections. Pathogens 2023; 12:1346. [PMID: 38003809 PMCID: PMC10674730 DOI: 10.3390/pathogens12111346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The growing number of infections caused by multidrug-resistant bacterial strains, limited treatment options, multi-species infections, high toxicity of the antibiotics used, and an increase in treatment costs are major challenges for modern medicine. To remedy this, scientists are looking for new antibiotics and treatment methods that will effectively eradicate bacteria while continually developing different resistance mechanisms. Ceragenins are a new group of antimicrobial agents synthesized based on molecular patterns that define the mechanism of antibacterial action of natural antibacterial peptides and steroid-polyamine conjugates such as squalamine. Since ceragenins have a broad spectrum of antimicrobial activity, with little recorded ability of bacteria to develop a resistance mechanism that can bridge their mechanism of action, there are high hopes that this group of molecules can give rise to a new family of drugs effective against bacteria resistant to currently used antibiotics. Experimental data suggests that core-shell nanosystems, in which ceragenins are presented to bacterial cells on metallic nanoparticles, may increase their antimicrobial potential and reduce their toxicity. However, studies should be conducted, among others, to assess potential long-term cytotoxicity and in vivo studies to confirm their activity and stability in animal models. Here, we summarized the current knowledge on ceragenins and ceragenin-containing nanoantibiotics as potential new tools against emerging Gram-negative rods associated with nosocomial infections.
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Affiliation(s)
- Maciej Karasiński
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Mickiewicza 2C, 15-222 Bialystok, Poland; (M.K.); (U.W.); (T.D.); (K.S.)
| | - Urszula Wnorowska
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Mickiewicza 2C, 15-222 Bialystok, Poland; (M.K.); (U.W.); (T.D.); (K.S.)
| | - Bonita Durnaś
- Department of Microbiology and Immunology, Institute of Medical Science, Collegium Medicum, Jan Kochanowski University in Kielce, IX Wieków Kielc 19A, 25-317 Kielce, Poland; (B.D.); (G.K.); (K.G.)
| | - Grzegorz Król
- Department of Microbiology and Immunology, Institute of Medical Science, Collegium Medicum, Jan Kochanowski University in Kielce, IX Wieków Kielc 19A, 25-317 Kielce, Poland; (B.D.); (G.K.); (K.G.)
| | - Tamara Daniluk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Mickiewicza 2C, 15-222 Bialystok, Poland; (M.K.); (U.W.); (T.D.); (K.S.)
| | - Karol Skłodowski
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Mickiewicza 2C, 15-222 Bialystok, Poland; (M.K.); (U.W.); (T.D.); (K.S.)
| | - Katarzyna Głuszek
- Department of Microbiology and Immunology, Institute of Medical Science, Collegium Medicum, Jan Kochanowski University in Kielce, IX Wieków Kielc 19A, 25-317 Kielce, Poland; (B.D.); (G.K.); (K.G.)
| | - Ewelina Piktel
- Independent Laboratory of Nanomedicine, Medical University of Białystok, Mickiewicza 2B, 15-222 Białystok, Poland;
| | - Sławomir Okła
- Holy Cross Oncology Center of Kielce, Artwińskiego 3, 25-734 Kielce, Poland;
| | - Robert Bucki
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, Mickiewicza 2C, 15-222 Bialystok, Poland; (M.K.); (U.W.); (T.D.); (K.S.)
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35
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Yang J, Eyre DW, Lu L, Clifton DA. Interpretable machine learning-based decision support for prediction of antibiotic resistance for complicated urinary tract infections. NPJ ANTIMICROBIALS AND RESISTANCE 2023; 1:14. [PMID: 38686216 PMCID: PMC11057209 DOI: 10.1038/s44259-023-00015-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/04/2023] [Indexed: 05/02/2024]
Abstract
Urinary tract infections are one of the most common bacterial infections worldwide; however, increasing antimicrobial resistance in bacterial pathogens is making it challenging for clinicians to correctly prescribe patients appropriate antibiotics. In this study, we present four interpretable machine learning-based decision support algorithms for predicting antimicrobial resistance. Using electronic health record data from a large cohort of patients diagnosed with potentially complicated UTIs, we demonstrate high predictability of antibiotic resistance across four antibiotics - nitrofurantoin, co-trimoxazole, ciprofloxacin, and levofloxacin. We additionally demonstrate the generalizability of our methods on a separate cohort of patients with uncomplicated UTIs, demonstrating that machine learning-driven approaches can help alleviate the potential of administering non-susceptible treatments, facilitate rapid effective clinical interventions, and enable personalized treatment suggestions. Additionally, these techniques present the benefit of providing model interpretability, explaining the basis for generated predictions.
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Affiliation(s)
- Jenny Yang
- Institute of Biomedical Engineering, Department Engineering Science, University of Oxford, Oxford, UK
| | - David W. Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lei Lu
- Institute of Biomedical Engineering, Department Engineering Science, University of Oxford, Oxford, UK
| | - David A. Clifton
- Institute of Biomedical Engineering, Department Engineering Science, University of Oxford, Oxford, UK
- Oxford-Suzhou Centre for Advanced Research (OSCAR), Suzhou, China
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Yaeger LN, French S, Brown ED, Côté JP, Burrows LL. Central metabolism is a key player in E. coli biofilm stimulation by sub-MIC antibiotics. PLoS Genet 2023; 19:e1011013. [PMID: 37917668 PMCID: PMC10645362 DOI: 10.1371/journal.pgen.1011013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/14/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
Exposure of Escherichia coli to sub-inhibitory antibiotics stimulates biofilm formation through poorly characterized mechanisms. Using a high-throughput Congo Red binding assay to report on biofilm matrix production, we screened ~4000 E. coli K12 deletion mutants for deficiencies in this biofilm stimulation response. We screened using three different antibiotics to identify core components of the biofilm stimulation response. Mutants lacking acnA, nuoE, or lpdA failed to respond to sub-MIC cefixime and novobiocin, implicating central metabolism and aerobic respiration in biofilm stimulation. These genes are members of the ArcA/B regulon-controlled by a respiration-sensitive two-component system. Mutants of arcA and arcB had a 'pre-activated' phenotype, where biofilm formation was already high relative to wild type in vehicle control conditions, and failed to increase further with the addition of sub-MIC cefixime. Using a tetrazolium dye and an in vivo NADH sensor, we showed spatial co-localization of increased metabolic activity with sub-lethal concentrations of the bactericidal antibiotics cefixime and novobiocin. Supporting a role for respiratory stress, the biofilm stimulation response to cefixime and novobiocin was inhibited when nitrate was provided as an alternative electron acceptor. Deletion of a gene encoding part of the machinery for respiring nitrate abolished its ameliorating effects, and nitrate respiration increased during growth with sub-MIC cefixime. Finally, in probing the generalizability of biofilm stimulation, we found that the stimulation response to translation inhibitors, unlike other antibiotic classes, was minimally affected by nitrate supplementation, suggesting that targeting the ribosome stimulates biofilm formation in distinct ways. By characterizing the biofilm stimulation response to sub-MIC antibiotics at a systems level, we identified multiple avenues for design of therapeutics that impair bacterial stress management.
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Affiliation(s)
- Luke N. Yaeger
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Shawn French
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Eric D. Brown
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Jean Philippe Côté
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Lori L. Burrows
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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37
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Wang Y, Yang X, Zhang S, Ai J, Wang J, Chen J, Zhao L, Wang W, You H. Comparative proteomics unveils the bacteriostatic mechanisms of Ga(III) on the regulation of metabolic pathways in Pseudomonas aeruginosa. J Proteomics 2023; 289:105011. [PMID: 37776994 DOI: 10.1016/j.jprot.2023.105011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/02/2023]
Abstract
Gallium has a long history as a chemotherapeutic agent. The mechanisms of action of Ga(III)-based anti-infectives are different from conventional antibiotics, which primarily result from the chemical similarities of Ga(III) with Fe(III) and substitution of gallium into iron-dependent biological pathways. However, more aspects of the molecular mechanisms of Ga(III) against human pathogens, especially the effects on bacterial metabolic processes, remain to be understood. Herein, by using conventional quantitative proteomics, we identified the protein changes of Pseudomonas aeruginosa (P. aeruginosa) in response to Ga(NO3)3 treatment. We show that Ga(III) exhibits bacteriostatic mode of action against P. aeruginosa through affecting the expressions of a number of key enzymes in the main metabolic pathways, including glycolysis, TCA cycle, amino acid metabolism, and protein and nucleic acid biosynthesis. In addition, decreased expressions of proteins associated with pathogenesis and virulence of P. aeruginosa were also identified. Moreover, the correlations between protein expressions and metabolome changes in P. aeruginosa upon Ga(III) treatment were identified and discussed. Our findings thus expand the understanding on the antimicrobial mechanisms of Ga(III) that shed light on enhanced therapeutic strategies. BIOLOGICAL SIGNIFICANCE: Mounting evidence suggest that the efficacy and resistance of clinical antibiotics are closely related to the metabolic homeostasis in bacterial pathogens. Ga(III)-based compounds have been repurposed as antibacterial therapeutic candidates against antibiotics resistant pathogens, and represent a safe and promising treatment for clinical human infections, while more thorough understandings of how bacteria respond to Ga(III) treatment are needed. In the present study, we provide evidences at the proteome level that indicate Ga(III)-induced metabolic perturbations in P. aeruginosa. We identified and discussed the interference of Ga(III) on the expressions and activities of enzymes in the main metabolic pathways in P. aeruginosa. In view of our previous report that the antimicrobial efficacy of Ga(III) could be modulated according to Ga(III)-induced metabolome changes in P. aeruginosa, our current analyses may provide theoretical basis at the proteome level for the development of efficient gallium-based therapies by exploiting bacterial metabolic mechanisms.
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Affiliation(s)
- Yuchuan Wang
- Hebei Key Laboratory for Chronic Diseases, School of Basic Medical Sciences, China.
| | - Xue Yang
- Hebei Key Laboratory for Chronic Diseases, School of Basic Medical Sciences, China
| | - Shuo Zhang
- Hebei Key Laboratory for Chronic Diseases, School of Basic Medical Sciences, China
| | - Jiayi Ai
- Hebei Key Laboratory for Chronic Diseases, School of Basic Medical Sciences, China
| | - Junteng Wang
- School of Public Health, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Junxin Chen
- Hebei Key Laboratory for Chronic Diseases, School of Basic Medical Sciences, China
| | - Lin Zhao
- Hebei Key Laboratory for Chronic Diseases, School of Basic Medical Sciences, China
| | - Wanying Wang
- Hebei Key Laboratory for Chronic Diseases, School of Basic Medical Sciences, China
| | - Haoxin You
- Hebei Key Laboratory for Chronic Diseases, School of Basic Medical Sciences, China
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38
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Hurst MN, Beebout CJ, Hollingsworth A, Guckes KR, Purcell A, Bermudez TA, Williams D, Reasoner SA, Trent MS, Hadjifrangiskou M. The QseB response regulator imparts tolerance to positively charged antibiotics by controlling metabolism and minor changes to LPS. mSphere 2023; 8:e0005923. [PMID: 37676915 PMCID: PMC10597456 DOI: 10.1128/msphere.00059-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/02/2023] [Indexed: 09/09/2023] Open
Abstract
The modification of lipopolysaccharide (LPS) in Escherichia coli and Salmonella spp. is primarily controlled by the two-component system PmrAB. LPS modification allows bacteria to avoid killing by positively charged antibiotics like polymyxin B (PMB). We previously demonstrated that in uropathogenic E. coli (UPEC), the sensor histidine kinase PmrB also activates a non-cognate transcription factor, QseB, and this activation somehow augments PMB tolerance in UPEC. Here, we demonstrate-for the first time-that in the absence of the canonical LPS transcriptional regulator, PmrA, QseB can direct some modifications on the LPS. In agreement with this observation, transcriptional profiling analyses demonstrate regulatory overlaps between PmrA and QseB in terms of regulating LPS modification genes. However, both PmrA and QseB must be present for UPEC to mount robust tolerance to PMB. Transcriptional and metabolomic analyses also reveal that QseB transcriptionally regulates the metabolism of glutamate and 2-oxoglutarate, which are consumed and produced during the modification of lipid A. We show that deletion of qseB alters glutamate levels in the bacterial cells. The qseB deletion mutant, which is susceptible to positively charged antibiotics, is rescued by exogenous addition of 2-oxoglutarate. These findings uncover a previously unknown mechanism of metabolic control of antibiotic tolerance that may be contributing to antibiotic treatment failure in the clinic. IMPORTANCE Although antibiotic prescriptions are guided by well-established susceptibility testing methods, antibiotic treatments oftentimes fail. The presented work is significant because it uncovers a mechanism by which bacteria transiently avoid killing by antibiotics. This mechanism involves two closely related transcription factors, PmrA and QseB, which are conserved across Enterobacterales. We demonstrate that PmrA and QseB share regulatory targets in lipid A modification pathway and prove that QseB can orchestrate modifications of lipid A in Escherichia coli in the absence of PmrA. Finally, we show that QseB controls glutamate metabolism during the antibiotic response. These results suggest that rewiring of QseB-mediated metabolic genes could lead to stable antibiotic resistance in subpopulations within the host, thereby contributing to antibiotic treatment failure.
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Affiliation(s)
- Melanie N. Hurst
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Connor J. Beebout
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexis Hollingsworth
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Kirsten R. Guckes
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexandria Purcell
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Tomas A. Bermudez
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Diamond Williams
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Seth A. Reasoner
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M. Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Maria Hadjifrangiskou
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, Tennessee, USA
- Center for Personalized Microbiology, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Xiao G, Li J, Sun Z. The Combination of Antibiotic and Non-Antibiotic Compounds Improves Antibiotic Efficacy against Multidrug-Resistant Bacteria. Int J Mol Sci 2023; 24:15493. [PMID: 37895172 PMCID: PMC10607837 DOI: 10.3390/ijms242015493] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
Bacterial antibiotic resistance, especially the emergence of multidrug-resistant (MDR) strains, urgently requires the development of effective treatment strategies. It is always of interest to delve into the mechanisms of resistance to current antibiotics and target them to promote the efficacy of existing antibiotics. In recent years, non-antibiotic compounds have played an important auxiliary role in improving the efficacy of antibiotics and promoting the treatment of drug-resistant bacteria. The combination of non-antibiotic compounds with antibiotics is considered a promising strategy against MDR bacteria. In this review, we first briefly summarize the main resistance mechanisms of current antibiotics. In addition, we propose several strategies to enhance antibiotic action based on resistance mechanisms. Then, the research progress of non-antibiotic compounds that can promote antibiotic-resistant bacteria through different mechanisms in recent years is also summarized. Finally, the development prospects and challenges of these non-antibiotic compounds in combination with antibiotics are discussed.
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Affiliation(s)
| | | | - Zhiliang Sun
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (G.X.); (J.L.)
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Xiang J, Wang SW, Tao Y, Ye JZ, Liang Y, Peng XX, Yang LF, Li H. A glucose-mediated antibiotic resistance metabolic flux from glycolysis, the pyruvate cycle, and glutamate metabolism to purine metabolism. Front Microbiol 2023; 14:1267729. [PMID: 37915850 PMCID: PMC10616527 DOI: 10.3389/fmicb.2023.1267729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/18/2023] [Indexed: 11/03/2023] Open
Abstract
Introduction Bacterial metabolic environment influences antibiotic killing efficacy. Thus, a full understanding for the metabolic resistance mechanisms is especially important to combat antibiotic-resistant bacteria. Methods Isobaric tags for relative and absolute quantification-based proteomics approach was employed to compare proteomes between ceftazidime-resistant and -sensitive Edwarsiella tarda LTB4 (LTB4-RCAZ and LTB4-S, respectively). Results This analysis suggested the possibility that the ceftazidime resistance mediated by depressed glucose is implemented through an inefficient metabolic flux from glycolysis, the pyruvate cycle, glutamate metabolism to purine metabolism. The inefficient flux was demonstrated by the reduced expression of genes and the decreased activity of enzymes in the four metabolic pathways. However, supplement upstream glucose and downstream guanosine separately restored ceftazidime killing, which not only supports the conclusion that the inefficient metabolic flux is responsible for the resistance, but also provides an effective approach to reverse the resistance. In addition, the present study showed that ceftazidime is bound to pts promoter in E. tarda. Discussion Our study highlights the way in fully understanding metabolic resistance mechanisms and establishing metabolites-based metabolic reprogramming to combat antibiotic resistance.
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Affiliation(s)
- Jiao Xiang
- State Key Laboratory of Bio-Control, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shi-wen Wang
- State Key Laboratory of Bio-Control, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuan Tao
- State Key Laboratory of Bio-Control, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jing-zhou Ye
- State Key Laboratory of Bio-Control, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Liang
- Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xuan-xian Peng
- State Key Laboratory of Bio-Control, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Guangdong Litai Pharmaceutical Co., Ltd., Jieyang, China
| | - Li-fen Yang
- Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hui Li
- State Key Laboratory of Bio-Control, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Wood E, Schulenburg H, Rosenstiel P, Bergmiller T, Ankrett D, Gudelj I, Beardmore R. Ribosome-binding antibiotics increase bacterial longevity and growth efficiency. Proc Natl Acad Sci U S A 2023; 120:e2221507120. [PMID: 37751555 PMCID: PMC10556576 DOI: 10.1073/pnas.2221507120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/11/2023] [Indexed: 09/28/2023] Open
Abstract
Antibiotics, by definition, reduce bacterial growth rates in optimal culture conditions; however, the real-world environments bacteria inhabit see rapid growth punctuated by periods of low nutrient availability. How antibiotics mediate population decline during these periods is poorly understood. Bacteria cannot optimize for all environmental conditions because a growth-longevity tradeoff predicts faster growth results in faster population decline, and since bacteriostatic antibiotics slow growth, they should also mediate longevity. We quantify how antibiotics, their targets, and resistance mechanisms influence longevity using populations of Escherichia coli and, as the tradeoff predicts, populations are maintained for longer if they encounter ribosome-binding antibiotics doxycycline and erythromycin, a finding that is not observed using antibiotics with alternative cellular targets. This tradeoff also predicts resistance mechanisms that increase growth rates during antibiotic treatment could be detrimental during nutrient stresses, and indeed, we find resistance by ribosomal protection removes benefits to longevity provided by doxycycline. We therefore liken ribosomal protection to a "Trojan horse" because it provides protection from an antibiotic but, during nutrient stresses, it promotes the demise of the bacteria. Seeking mechanisms to support these observations, we show doxycycline promotes efficient metabolism and reduces the concentration of reactive oxygen species. Seeking generality, we sought another mechanism that affects longevity and we found the number of doxycycline targets, namely, the ribosomal RNA operons, mediates growth and longevity even without antibiotics. We conclude that slow growth, as observed during antibiotic treatment, can help bacteria overcome later periods of nutrient stress.
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Affiliation(s)
- Emily Wood
- Biosciences, College of Life and Environmental Sciences, University of Exeter, ExeterEX4 4QD, United Kingdom
- Engineering and Physical Sciences Research Council Hub for Quantitative Modelling in Healthcare, University of Exeter, ExeterEX4 4QJ, United Kingdom
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, Kiel24118, Germany
| | - Philip Rosenstiel
- Instituts für Klinische Molekularbiologie, Dekanat der Medizinischen Fakultät, Christian-Albrechts-Universität zu Kiel, Christian-Albrechts-Platz 4, KielD-24118, Germany
| | - Tobias Bergmiller
- Biosciences, College of Life and Environmental Sciences, University of Exeter, ExeterEX4 4QD, United Kingdom
| | - Dyan Ankrett
- Biosciences, College of Life and Environmental Sciences, University of Exeter, ExeterEX4 4QD, United Kingdom
| | - Ivana Gudelj
- Biosciences, College of Life and Environmental Sciences, University of Exeter, ExeterEX4 4QD, United Kingdom
| | - Robert Beardmore
- Biosciences, College of Life and Environmental Sciences, University of Exeter, ExeterEX4 4QD, United Kingdom
- Engineering and Physical Sciences Research Council Hub for Quantitative Modelling in Healthcare, University of Exeter, ExeterEX4 4QJ, United Kingdom
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Sanz-García F, Gil-Gil T, Laborda P, Blanco P, Ochoa-Sánchez LE, Baquero F, Martínez JL, Hernando-Amado S. Translating eco-evolutionary biology into therapy to tackle antibiotic resistance. Nat Rev Microbiol 2023; 21:671-685. [PMID: 37208461 DOI: 10.1038/s41579-023-00902-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2023] [Indexed: 05/21/2023]
Abstract
Antibiotic resistance is currently one of the most important public health problems. The golden age of antibiotic discovery ended decades ago, and new approaches are urgently needed. Therefore, preserving the efficacy of the antibiotics currently in use and developing compounds and strategies that specifically target antibiotic-resistant pathogens is critical. The identification of robust trends of antibiotic resistance evolution and of its associated trade-offs, such as collateral sensitivity or fitness costs, is invaluable for the design of rational evolution-based, ecology-based treatment approaches. In this Review, we discuss these evolutionary trade-offs and how such knowledge can aid in informing combination or alternating antibiotic therapies against bacterial infections. In addition, we discuss how targeting bacterial metabolism can enhance drug activity and impair antibiotic resistance evolution. Finally, we explore how an improved understanding of the original physiological function of antibiotic resistance determinants, which have evolved to reach clinical resistance after a process of historical contingency, may help to tackle antibiotic resistance.
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Affiliation(s)
- Fernando Sanz-García
- Departamento de Microbiología, Medicina Preventiva y Salud Pública, Universidad de Zaragoza, Zaragoza, Spain
| | - Teresa Gil-Gil
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Madrid, Spain
- Programa de Doctorado en Biociencias Moleculares, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo Laborda
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Madrid, Spain
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Clinical Microbiology, 9301, Rigshospitalet, Copenhagen, Denmark
| | - Paula Blanco
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
| | | | - Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal (IRYCIS), CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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Connor CH, Zucoloto AZ, Munnoch JT, Yu IL, Corander J, Hoskisson PA, McDonald B, McNally A. Multidrug-resistant E. coli encoding high genetic diversity in carbohydrate metabolism genes displace commensal E. coli from the intestinal tract. PLoS Biol 2023; 21:e3002329. [PMID: 37847672 PMCID: PMC10581457 DOI: 10.1371/journal.pbio.3002329] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 09/11/2023] [Indexed: 10/19/2023] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) can cause a variety of infections outside of the intestine and are a major causative agent of urinary tract infections. Treatment of these infections is increasingly frustrated by antimicrobial resistance (AMR) diminishing the number of effective therapies available to clinicians. Incidence of multidrug resistance (MDR) is not uniform across the phylogenetic spectrum of E. coli. Instead, AMR is concentrated in select lineages, such as ST131, which are MDR pandemic clones that have spread AMR globally. Using a gnotobiotic mouse model, we demonstrate that an MDR E. coli ST131 is capable of out-competing and displacing non-MDR E. coli from the gut in vivo. This is achieved in the absence of antibiotic treatment mediating a selective advantage. In mice colonised with non-MDR E. coli strains, challenge with MDR E. coli either by oral gavage or co-housing with MDR E. coli colonised mice results in displacement and dominant intestinal colonisation by MDR E. coli ST131. To investigate the genetic basis of this superior gut colonisation ability by MDR E. coli, we assayed the metabolic capabilities of our strains using a Biolog phenotypic microarray revealing altered carbon metabolism. Functional pangenomic analysis of 19,571 E. coli genomes revealed that carriage of AMR genes is associated with increased diversity in carbohydrate metabolism genes. The data presented here demonstrate that independent of antibiotic selective pressures, MDR E. coli display a competitive advantage to colonise the mammalian gut and points to a vital role of metabolism in the evolution and success of MDR lineages of E. coli via carriage and spread.
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Affiliation(s)
- Christopher H. Connor
- Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
- International Microbiome Centre, University of Calgary, Calgary, Canada
| | - Amanda Z. Zucoloto
- International Microbiome Centre, University of Calgary, Calgary, Canada
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Calvin, Phoebe, and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - John T. Munnoch
- Strathclyde Institute of Pharmaceutical and Biomedical Science, University of Strathclyde, Glasgow, United Kingdom
| | - Ian-Ling Yu
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Jukka Corander
- Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmaceutical and Biomedical Science, University of Strathclyde, Glasgow, United Kingdom
| | - Braedon McDonald
- International Microbiome Centre, University of Calgary, Calgary, Canada
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Calvin, Phoebe, and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
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Yan BB, Dong XS, Wang JP, Li XY, An L, Wang XR, Zhang LG, Meng QL, Wang C. Glutamate-pantothenate pathway promotes antibiotic resistance of Edwardsiella tarda. Front Microbiol 2023; 14:1264602. [PMID: 37779691 PMCID: PMC10533917 DOI: 10.3389/fmicb.2023.1264602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023] Open
Abstract
Although cellular metabolic states have been shown to modulate bacterial susceptibility to antibiotics, the interaction between glutamate (Glu) and chloramphenicol (CAP) resistance remains unclear because of the specificity of antibiotics and bacteria. We found that the level of Glu was upregulated in the CAP-resistant strain of Edwardsiella tarda according to a comparative metabolomics approach based on LC-MS/MS. Furthermore, we verified that exogenous metabolites related to Glu, the tricarboxylic acid (TCA) cycle, and glutathione (GSH) metabolism could promote CAP resistance in survival assays. If GSH metabolism or the TCA cycle is inhibited by L-buthionine sulfoximine or propanedioic acid, the promotion of CAP resistance by Glu in the corresponding pathway disappears. According to metabolomic analysis, exogenous Glu could change pantothenate metabolism, affecting GSH biosynthesis and the TCA cycle. These results showed that the glutamate-pantothenate pathway could promote CAP resistance by being involved in the synthesis of GSH, entering the TCA cycle by direct deamination, or indirectly affecting the metabolism of the two pathways by pantothenate. These results extend our knowledge of the effect of Glu on antibiotic resistance and suggest that the potential effect, which may aggravate antibiotic resistance, should be considered before Glu and GSH administration in the clinic.
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Affiliation(s)
- Bei-bei Yan
- Department of Neonatology, Children’s Hospital Affiliated to Shandong University, Jinan, China
- Department of Neonatology, Jinan Children’s Hospital, Jinan, China
| | - Xue-sa Dong
- Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China
| | - Jun-peng Wang
- Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China
| | - Xiao-ying Li
- Department of Neonatology, Children’s Hospital Affiliated to Shandong University, Jinan, China
- Department of Neonatology, Jinan Children’s Hospital, Jinan, China
| | - Li An
- Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China
| | - Xi-rong Wang
- Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China
| | - Long-gang Zhang
- Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China
| | - Qing-lei Meng
- Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China
| | - Chao Wang
- Department of Genetics and Breeding, Shandong Freshwater Fisheries Research Institute, Jinan, China
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Chen X, Shan T, Ren B, Zhang L, Xu HHK, Wang N, Zhou X, Li H, Cheng L. Dimethylaminododecyl Methacrylate-Incorporated Dental Materials Could Be the First Line of Defense against Helicobacter pylori. Int J Mol Sci 2023; 24:13644. [PMID: 37686449 PMCID: PMC10487857 DOI: 10.3390/ijms241713644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/01/2023] [Accepted: 09/02/2023] [Indexed: 09/10/2023] Open
Abstract
Oral cavity is an essential reservoir for H. pylori. We aimed to investigate the antibacterial effects of dimethylaminododecyl methacrylate (DMADDM) against H. pylori. Modified giomers were prepared by introducing 0%, 1.25% and 2.5% DMADDM monomers. Broth microdilution assay, spot assay, Alamer Blue assay, PMA-qPCR, crystal violet staining, scanning electron microscopy observation and live/dead bacterial staining were performed to evaluate the antibacterial and antibiofilm effects of DMADDM and modified giomers in vitro. Urease assay, qPCR, hematoxylin-eosin staining and ELISA were performed to evaluate the inflammation levels and colonization of H. pylori in vivo. In vitro experiments indicated that the minimum inhibitory concentration and minimum bactericidal concentration of DMADDM were 6.25 μg/mL and 25 μg/mL, respectively. It inhibited H. pylori in a dose- and time-dependent manner, and significantly reduced the expression of cagA, vacA, flaA and ureB. DMADDM-modified giomers inhibited the formation of H. pylori biofilm and reduced live cells within it. In vivo experiments confirmed that the pretreatment with DMADDM-modified dental resin effectively reduced the gastric colonization of oral-derived H. pylori, suppressed systemic and local gastric inflammation. DMADDM monomers and DMADDM-modified giomers possessed excellent antibacterial and antibiofilm effects on H. pylori. Pretreatment with DMADDM-modified giomers significantly inhibited the gastric infection by H. pylori.
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Affiliation(s)
- Xi Chen
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Tiantian Shan
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Biao Ren
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Lin Zhang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Hockin H. K. Xu
- Department of Advanced Oral Sciences and Therapeutics, School of Dentistry, University of Maryland, Baltimore, MD 21021, USA
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Nanxi Wang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Hong Li
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu 610041, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lei Cheng
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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Pan Z, Guo J, Zhong Y, Fan L, Su Y. Gentamicin resistance to Escherichia coli related to fatty acid metabolism based on transcriptome analysis. Can J Microbiol 2023; 69:328-338. [PMID: 37224563 DOI: 10.1139/cjm-2023-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Antibiotic overuse and misuse have promoted the emergence and spread of antibiotic-resistant bacteria. Increasing bacterial resistance to antibiotics is a major healthcare problem, necessitating elucidation of antibiotic resistance mechanisms. In this study, we explored the mechanism of gentamicin resistance by comparing the transcriptomes of antibiotic-sensitive and -resistant Escherichia coli. A total of 410 differentially expressed genes were identified, of which 233 (56.83%) were up-regulated and 177 (43.17%) were down-regulated in the resistant strain compared with the sensitive strain. Gene Ontology (GO) analysis classifies differential gene expression into three main categories: biological processes, cellular components, and molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the up-regulated genes were enriched in eight metabolic pathways, including fatty acid metabolism, which suggests that fatty acid metabolism may be involved in the development of gentamicin resistance in E. coli. This was demonstrated by measuring the acetyl-CoA carboxylase activity, plays a fundamental role in fatty acid metabolism, was increased in gentamicin-resistant E. coli. Treatment of fatty acid synthesis inhibitor, triclosan, promoted gentamicin-mediated killing efficacy to antibiotic-resistant bacteria. We also found that exogenous addition of oleic acid, which involved in fatty acid metabolism, reduced E. coli sensitivity to gentamicin. Overall, our results provide insight into the molecular mechanism of gentamicin resistance development in E. coli.
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Affiliation(s)
- Zhiyu Pan
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Juan Guo
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yilin Zhong
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Lvyuan Fan
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yubin Su
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
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Zhang L, Lin Y, Yi X, Huang W, Hu Q, Zhang Z, Wu F, Ye JW, Chen GQ. Engineering low-salt growth Halomonas Bluephagenesis for cost-effective bioproduction combined with adaptive evolution. Metab Eng 2023; 79:146-158. [PMID: 37543135 DOI: 10.1016/j.ymben.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023]
Abstract
Halophilic Halomonas bluephagenesis has been engineered to produce various added-value bio-compounds with reduced costs. However, the salt-stress regulatory mechanism remained unclear. H. bluephagenesis was randomly mutated to obtain low-salt growing mutants via atmospheric and room temperature plasma (ARTP). The resulted H. bluephagenesis TDH4A1B5 was constructed with the chromosomal integration of polyhydroxyalkanoates (PHA) synthesis operon phaCAB and deletion of phaP1 gene encoding PHA synthesis associated protein phasin, forming H. bluephagenesis TDH4A1B5P, which led to increased production of poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-co-4-hydrobutyrate) (P34HB) by over 1.4-fold. H. bluephagenesis TDH4A1B5P also enhanced production of ectoine and threonine by 50% and 77%, respectively. A total 101 genes related to salinity tolerance was identified and verified via comparative genomic analysis among four ARTP mutated H. bluephagenesis strains. Recombinant H. bluephagenesis TDH4A1B5P was further engineered for PHA production utilizing sodium acetate or gluconate as sole carbon source. Over 33% cost reduction of PHA production could be achieved using recombinant H. bluephagenesis TDH4A1B5P. This study successfully developed a low-salt tolerant chassis H. bluephagenesis TDH4A1B5P and revealed salt-stress related genes of halophilic host strains.
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Affiliation(s)
- Lizhan Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yina Lin
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xueqing Yi
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wuzhe Huang
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, Beijing, 101309, China
| | - Qitiao Hu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhongnan Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fuqing Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; MOE Key Lab of Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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48
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Shee S, Veetil RT, Mohanraj K, Das M, Malhotra N, Bandopadhyay D, Beig H, Birua S, Niphadkar S, Nagarajan SN, Sinha VK, Thakur C, Rajmani RS, Chandra N, Laxman S, Singh M, Samal A, Seshasayee AN, Singh A. Biosensor-integrated transposon mutagenesis reveals rv0158 as a coordinator of redox homeostasis in Mycobacterium tuberculosis. eLife 2023; 12:e80218. [PMID: 37642294 PMCID: PMC10501769 DOI: 10.7554/elife.80218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/25/2023] [Indexed: 08/31/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is evolutionarily equipped to resist exogenous reactive oxygen species (ROS) but shows vulnerability to an increase in endogenous ROS (eROS). Since eROS is an unavoidable consequence of aerobic metabolism, understanding how Mtb manages eROS levels is essential yet needs to be characterized. By combining the Mrx1-roGFP2 redox biosensor with transposon mutagenesis, we identified 368 genes (redoxosome) responsible for maintaining homeostatic levels of eROS in Mtb. Integrating redoxosome with a global network of transcriptional regulators revealed a hypothetical protein (Rv0158) as a critical node managing eROS in Mtb. Disruption of rv0158 (rv0158 KO) impaired growth, redox balance, respiration, and metabolism of Mtb on glucose but not on fatty acids. Importantly, rv0158 KO exhibited enhanced growth on propionate, and the Rv0158 protein directly binds to methylmalonyl-CoA, a key intermediate in propionate catabolism. Metabolite profiling, ChIP-Seq, and gene-expression analyses indicate that Rv0158 manages metabolic neutralization of propionate toxicity by regulating the methylcitrate cycle. Disruption of rv0158 enhanced the sensitivity of Mtb to oxidative stress, nitric oxide, and anti-TB drugs. Lastly, rv0158 KO showed poor survival in macrophages and persistence defect in mice. Our results suggest that Rv0158 is a metabolic integrator for carbon metabolism and redox balance in Mtb.
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Affiliation(s)
- Somnath Shee
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | | | - Karthikeyan Mohanraj
- The Institute of Mathematical Sciences, A CI of Homi Bhabha National InstituteChennaiIndia
| | - Mayashree Das
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | | | | | - Hussain Beig
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Shalini Birua
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Shreyas Niphadkar
- Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Sathya Narayanan Nagarajan
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Vikrant Kumar Sinha
- Molecular Biophysics Unit, Indian Institute of Science BangaloreBangaloreIndia
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Raju S Rajmani
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative MedicineBangaloreIndia
| | - Mahavir Singh
- Molecular Biophysics Unit, Indian Institute of Science BangaloreBangaloreIndia
| | - Areejit Samal
- The Institute of Mathematical Sciences, A CI of Homi Bhabha National InstituteChennaiIndia
| | | | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
- Centre for Infectious Disease Research, Indian Institute of Science BangaloreKarnatakaIndia
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49
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Penumutchu S, Korry BJ, Hewlett K, Belenky P. Fiber supplementation protects from antibiotic-induced gut microbiome dysbiosis by modulating gut redox potential. Nat Commun 2023; 14:5161. [PMID: 37620319 PMCID: PMC10449846 DOI: 10.1038/s41467-023-40553-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Antibiotic-induced gut dysbiosis (AID) is a frequent and serious side effect of antibiotic use and mitigating this dysbiosis is a critical therapeutic target. We propose that the host diet can modulate the chemical environment of the gut resulting in changes to the structure and function of the microbiome during antibiotic treatment. Gut dysbiosis is typically characterized by increases in aerobic respiratory bacterial metabolism, redox potential, and abundance of Proteobacteria. In this study, we explore dietary fiber supplements as potential modulators of the chemical environment in the gut to reduce this pattern of dysbiosis. Using defined-diets and whole-genome sequencing of female murine microbiomes during diet modulation and antibiotic treatment, we find that fiber prebiotics significantly reduced the impact of antibiotic treatment on microbiome composition and function. We observe reduced abundance of aerobic bacteria as well as metabolic pathways associated with oxidative metabolism. These metatranscriptomic results are corroborated by chemical measurements of eH and pH suggesting that fiber dampens the dysbiotic effects of antibiotics. This work indicates that fiber may act as a potential therapeutic for AID by modulating bacterial metabolism in the gut to prevent an increase in redox potential and protect commensal microbes during antibiotic treatment.
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Affiliation(s)
- Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912, USA
| | - Katharine Hewlett
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912, USA.
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50
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Xu Z, Wang Y, Sheng K, Rosenthal R, Liu N, Hua X, Zhang T, Chen J, Song M, Lv Y, Zhang S, Huang Y, Wang Z, Cao T, Shen Y, Jiang Y, Yu Y, Chen Y, Guo G, Yin P, Weitz DA, Wang Y. Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq. Nat Commun 2023; 14:5130. [PMID: 37612289 PMCID: PMC10447461 DOI: 10.1038/s41467-023-40137-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 07/10/2023] [Indexed: 08/25/2023] Open
Abstract
Bacteria colonize almost all parts of the human body and can differ significantly. However, the population level transcriptomics measurements can only describe the average bacteria population behaviors, ignoring the heterogeneity among bacteria. Here, we report a droplet-based high-throughput single-microbe RNA-seq assay (smRandom-seq), using random primers for in situ cDNA generation, droplets for single-microbe barcoding, and CRISPR-based rRNA depletion for mRNA enrichment. smRandom-seq showed a high species specificity (99%), a minor doublet rate (1.6%), a reduced rRNA percentage (32%), and a sensitive gene detection (a median of ~1000 genes per single E. coli). Furthermore, smRandom-seq successfully captured transcriptome changes of thousands of individual E. coli and discovered a few antibiotic resistant subpopulations displaying distinct gene expression patterns of SOS response and metabolic pathways in E. coli population upon antibiotic stress. smRandom-seq provides a high-throughput single-microbe transcriptome profiling tool that will facilitate future discoveries in microbial resistance, persistence, microbe-host interaction, and microbiome research.
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Affiliation(s)
- Ziye Xu
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Yuting Wang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Kuanwei Sheng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Raoul Rosenthal
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics, Harvard University, Cambridge, MA, USA
| | - Nan Liu
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tianyu Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Jiaye Chen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Mengdi Song
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Yuexiao Lv
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Shunji Zhang
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Yingjuan Huang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Zhaolun Wang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Ting Cao
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics, Harvard University, Cambridge, MA, USA
| | - Yifei Shen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Chen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guoji Guo
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - David A Weitz
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA.
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics, Harvard University, Cambridge, MA, USA.
| | - Yongcheng Wang
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA.
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