1
|
Yu D, Andersson-Li M, Maes S, Andersson-Li L, Neumann NF, Odlare M, Jonsson A. Development of a logic regression-based approach for the discovery of host- and niche-informative biomarkers in Escherichia coli and their application for microbial source tracking. Appl Environ Microbiol 2024; 90:e0022724. [PMID: 38940567 PMCID: PMC11267920 DOI: 10.1128/aem.00227-24] [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: 02/07/2024] [Accepted: 06/07/2024] [Indexed: 06/29/2024] Open
Abstract
Microbial source tracking leverages a wide range of approaches designed to trace the origins of fecal contamination in aquatic environments. Although source tracking methods are typically employed within the laboratory setting, computational techniques can be leveraged to advance microbial source tracking methodology. Herein, we present a logic regression-based supervised learning approach for the discovery of source-informative genetic markers within intergenic regions across the Escherichia coli genome that can be used for source tracking. With just single intergenic loci, logic regression was able to identify highly source-specific (i.e., exceeding 97.00%) biomarkers for a wide range of host and niche sources, with sensitivities reaching as high as 30.00%-50.00% for certain source categories, including pig, sheep, mouse, and wastewater, depending on the specific intergenic locus analyzed. Restricting the source range to reflect the most prominent zoonotic sources of E. coli transmission (i.e., bovine, chicken, human, and pig) allowed for the generation of informative biomarkers for all host categories, with specificities of at least 90.00% and sensitivities between 12.50% and 70.00%, using the sequence data from key intergenic regions, including emrKY-evgAS, ibsB-(mdtABCD-baeSR), ompC-rcsDB, and yedS-yedR, that appear to be involved in antibiotic resistance. Remarkably, we were able to use this approach to classify 48 out of 113 river water E. coli isolates collected in Northwestern Sweden as either beaver, human, or reindeer in origin with a high degree of consensus-thus highlighting the potential of logic regression modeling as a novel approach for augmenting current source tracking efforts.IMPORTANCEThe presence of microbial contaminants, particularly from fecal sources, within water poses a serious risk to public health. The health and economic burden of waterborne pathogens can be substantial-as such, the ability to detect and identify the sources of fecal contamination in environmental waters is crucial for the control of waterborne diseases. This can be accomplished through microbial source tracking, which involves the use of various laboratory techniques to trace the origins of microbial pollution in the environment. Building on current source tracking methodology, we describe a novel workflow that uses logic regression, a supervised machine learning method, to discover genetic markers in Escherichia coli, a common fecal indicator bacterium, that can be used for source tracking efforts. Importantly, our research provides an example of how the rise in prominence of machine learning algorithms can be applied to improve upon current microbial source tracking methodology.
Collapse
Affiliation(s)
- Daniel Yu
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | | | - Sharon Maes
- Department of Natural Sciences, Design and Sustainable Development, Mid Sweden University, Östersund, Sweden
| | - Lili Andersson-Li
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Norman F. Neumann
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Monica Odlare
- Department of Natural Sciences, Design and Sustainable Development, Mid Sweden University, Östersund, Sweden
| | - Anders Jonsson
- Department of Natural Sciences, Design and Sustainable Development, Mid Sweden University, Östersund, Sweden
| |
Collapse
|
2
|
Chubiz LM. The Mar, Sox, and Rob Systems. EcoSal Plus 2023; 11:eesp00102022. [PMID: 37220096 PMCID: PMC10729928 DOI: 10.1128/ecosalplus.esp-0010-2022] [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: 09/14/2022] [Accepted: 03/03/2023] [Indexed: 01/28/2024]
Abstract
Environments inhabited by Enterobacteriaceae are diverse and often stressful. This is particularly true for Escherichia coli and Salmonella during host association in the gastrointestinal systems of animals. There, E. coli and Salmonella must survive exposure to various antimicrobial compounds produced or ingested by their host. A myriad of changes to cellular physiology and metabolism are required to achieve this feat. A central regulatory network responsible for sensing and responding to intracellular chemical stressors like antibiotics are the Mar, Sox, and Rob systems found throughout the Enterobacteriaceae. Each of these distinct regulatory networks controls expression of an overlapping set of downstream genes whose collective effects result in increased resistance to a wide array of antimicrobial compounds. This collection of genes is known as the mar-sox-rob regulon. This review will provide an overview of the mar-sox-rob regulon and molecular architecture of the Mar, Sox, and Rob systems.
Collapse
Affiliation(s)
- Lon M. Chubiz
- Department of Biology, University of Missouri–St. Louis, St. Louis, Missouri, USA
- Biochemistry and Biotechnology Program, University of Missouri–St. Louis, St. Louis, Missouri, USA
| |
Collapse
|
3
|
Yu Y, Shao C, Gong X, Quan H, Liu D, Chen Q, Chu Y. Antimicrobial Resistance Surveillance of Tigecycline-Resistant Strains Isolated from Herbivores in Northwest China. Microorganisms 2022; 10:microorganisms10122432. [PMID: 36557685 PMCID: PMC9784582 DOI: 10.3390/microorganisms10122432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
There is no doubt that antimicrobial resistance (AMR) is a global threat to public health and safety, regardless of whether it’s caused by people or natural transmission. This study aimed to investigate the genetic characteristics and variations of tigecycline-resistant Gram-negative isolates from herbivores in northwest China. In this study, a total of 300 samples were collected from various provinces in northwest China, and 11 strains (3.67%) of tigecycline-resistant bacteria were obtained. In addition, bacterial identification and antibiotic susceptibility testing against 14 antibiotics were performed. All isolates were multiple drug-resistant (MDR) and resistant to more than three kinds of antibiotics. Using an Illumina MiSeq platform, 11 tigecycline-resistant isolates were sequenced using whole genome sequencing (WGS). The assembled draft genomes were annotated, and then sequences were blasted against the AMR gene database and virulence factor database. Several resistance genes mediating drug resistance were detected by WGS, including fluoroquinolone resistance genes (gyrA_S83L, gyrA_D87N, S83L, parC_S80I, and gyrB_S463A), fosfomycin resistance genes (GlpT_E448K and UhpT_E350Q), beta-lactam resistance genes (FtsI_D350N and S357N), and the tigecycline resistance gene (tetR N/A). Furthermore, there were five kinds of chromosomally encoded genetic systems that confer MDR (MarR_Y137H, G103S, MarR_N/A, SoxR_N/A, SoxS_N/A, AcrR N/A, and MexZ_K127E). A comprehensive analysis of MDR strains derived from WGS was used to detect variable antimicrobial resistance genes and their precise mechanisms of resistance. In addition, we found a novel ST type of Escherichia coli (ST13667) and a newly discovered point mutation (K127E) in the MexZ gene of Pseudomonas aeruginosa. WGS plays a crucial role in AMR control, prevention strategies, as well as multifaceted intervention strategies.
Collapse
Affiliation(s)
- Yongfeng Yu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Changchun Shao
- Lanzhou Institute for Food and Drug Control, Lanzhou 730050, China
| | - Xiaowei Gong
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Heng Quan
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Donghui Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Qiwei Chen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
- Correspondence: (Q.C.); (Y.C.)
| | - Yuefeng Chu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
- Correspondence: (Q.C.); (Y.C.)
| |
Collapse
|
4
|
Hadiya S, Ibrahem RA, Abd El-Baky RM, Elsabahy M, Aly SA. Nanosized Combined Antimicrobial Drugs Decreased Emergence of Resistance in Escherichia coli: A Future Promise. Microb Drug Resist 2022; 28:972-979. [DOI: 10.1089/mdr.2022.0095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Safy Hadiya
- Assiut International Center of Nanomedicine, Al-Rajhy Liver Hospital, Assiut University, Assiut, Egypt
| | - Reham A. Ibrahem
- Department of Microbiology and Immunology, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Rehab M. Abd El-Baky
- Department of Microbiology and Immunology, Faculty of Pharmacy, Minia University, Minia, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Deraya University, Minia, Egypt
| | - Mahmoud Elsabahy
- School of Biotechnology and Science Academy, Badr University in Cairo, Badr City, Cairo, Egypt
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Sherine A. Aly
- Department of Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
| |
Collapse
|
5
|
Dewi DAR, Thomas T, Ahmad Mokhtar AM, Mat Nanyan NS, Zulfigar SB, Salikin NH. Carbapenem Resistance among Marine Bacteria-An Emerging Threat to the Global Health Sector. Microorganisms 2021; 9:microorganisms9102147. [PMID: 34683467 PMCID: PMC8537846 DOI: 10.3390/microorganisms9102147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 01/24/2023] Open
Abstract
The emergence of antibiotic resistance among pathogenic microorganisms is a major issue for global public health, as it results in acute or chronic infections, debilitating diseases, and mortality. Of particular concern is the rapid and common spread of carbapenem resistance in healthcare settings. Carbapenems are a class of critical antibiotics reserved for treatment against multidrug-resistant microorganisms, and resistance to this antibiotic may result in limited treatment against infections. In addition to in clinical facilities, carbapenem resistance has also been identified in aquatic niches, including marine environments. Various carbapenem-resistant genes (CRGs) have been detected in different marine settings, with the majority of the genes incorporated in mobile genetic elements, i.e., transposons or plasmids, which may contribute to efficient genetic transfer. This review highlights the potential of the marine environment as a reservoir for carbapenem resistance and provides a general overview of CRG transmission among marine microbes.
Collapse
Affiliation(s)
- Dewa A.P. Rasmika Dewi
- School of Medicine, International University of Health and Welfare, Narita 286-8686, Japan;
- Faculty of Medicine and Health Sciences, Udayana University, Bali 80232, Indonesia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney 2052, Australia;
| | - Ana Masara Ahmad Mokhtar
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Noreen Suliani Mat Nanyan
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Siti Balqis Zulfigar
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Nor Hawani Salikin
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
- Correspondence: ; Tel.: +60-4-653-2241
| |
Collapse
|
6
|
Deskilled and Rapid Drug-Resistant Gene Detection by Centrifugal Force-Assisted Thermal Convection PCR Device. SENSORS 2021; 21:s21041225. [PMID: 33572363 PMCID: PMC7916093 DOI: 10.3390/s21041225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/17/2022]
Abstract
Here we report the improved Cyclo olefin polymer (COP) microfluidic chip and polymerase chain reaction (PCR) amplification system for point-of-care testing (POCT) in rapid detection of Carbapenem-resistant Enterobacteriaceae (CRE). The PCR solution and thermal cycling is controlled by the relative gravitational acceleration (7G) only and is expected to pose minimal problem in operation by non-expert users. Detection is based on identifying the presence of carbapenemase encoding gene through the corresponding fluorescence signal after amplification. For preliminary tests, the device has been demonstrated to detect blaIMP-6 from patients stool samples. From the prepared samples, 96.4 fg/µL was detected with good certainty within 15 min (~106 thermocycles,) which is significantly faster than the conventional culture plate method. Moreover, the device is expected to detect other target genes in parallel as determination of the presence of blaNDM-1 and blaOXA-23 from control samples has also been demonstrated. With the rising threat of drug-resistant bacteria in global healthcare, this technology can greatly aid the health sector by enabling the appropriate use of antibiotics, accelerating the treatment of carriers, and suppressing the spread.
Collapse
|
7
|
Kalasseril SG, Krishnan R, Vattiringal RK, Paul R, Mathew P, Pillai D. Detection of New Delhi Metallo-β-lactamase 1 and Cephalosporin Resistance Genes Among Carbapenem-Resistant Enterobacteriaceae in Water Bodies Adjacent to Hospitals in India. Curr Microbiol 2020; 77:2886-2895. [PMID: 32643019 DOI: 10.1007/s00284-020-02107-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/23/2020] [Indexed: 10/23/2022]
Abstract
The prevalence of carbapenem resistance among bacterial isolates from selected water bodies receiving hospital effluents and adjoining aquaculture farms in Kerala, India, was studied. Klebsiella pneumoniae followed by Escherichia coli, Klebsiella oxytoca, Enterobacter aerogenes and Acinetobacter baumannii were the predominant isolates. Antibiotic sensitivity of these isolates was determined by Kirby-Bauer disc diffusion method. Nearly 60% of the Enterobacteriaceae isolates screened were multidrug resistant of which 16.6% were carbapenem resistant. The carbapenem-resistant Enterobacteriaceae were further screened for the presence of New Delhi metallo β-lactamase-1 and cephalosporin resistance encoding genes. All NDM-1 isolates were highly resistant to carbapenem, cephalosporin, aminoglycosides, quinolones, tetracycline, and sulphonamides. K. pneumoniae harboring blaNDM-1 gene and E. coli isolates with blaCTX-M-15 and blaSHV-11 genes were detected in hospital discharge points. In aquaculture farms too, carbapenem-resistant K. pneumoniae with blaNDM-1 gene and E. coli isolates with blaCTX-M-15 were observed, although there was no use of antibiotics in these farms. However, other carbapenemase genes such as blaTEM, blaVIM, blaIMP and blaGIM were not detected in any of these isolates. The results suggest the increased prevalence of carbapenem-resistant Enterobacteriaceae in the water bodies receiving hospital effluent and its dissemination to adjacent aquaculture farms, posing a serious threat to public health.
Collapse
Affiliation(s)
- Sneha Girijan Kalasseril
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Rahul Krishnan
- Department of Aqualife Medicine, Chonnam National University, Yeosu, Republic of Korea
| | - Rejish Kumar Vattiringal
- Department of Aquaculture, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Robin Paul
- State Laboratory for Livestock, Marine & Agri Products (SLMAP), Department of Animal Husbandary, Government of Kerala, Ernakulam, India
| | - Philip Mathew
- ReAct Asia-Pacific, Centre for Environment, Sustainability and Health, Vellore, India
| | - Devika Pillai
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India.
| |
Collapse
|
8
|
Lopez NV, Farsar CJ, Harmon DE, Ruiz C. Urban and agricultural soils in Southern California are a reservoir of carbapenem-resistant bacteria. Microbiologyopen 2020; 9:1247-1263. [PMID: 32246583 PMCID: PMC7294306 DOI: 10.1002/mbo3.1034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 01/01/2023] Open
Abstract
Carbapenems are last‐resort β‐lactam antibiotics used in healthcare facilities to treat multidrug‐resistant infections. Thus, most studies on identifying and characterizing carbapenem‐resistant bacteria (CRB) have focused on clinical settings. Relatively, little is still known about the distribution and characteristics of CRBs in the environment, and the role of soil as a potential reservoir of CRB in the United States remains unknown. Here, we have surveyed 11 soil samples from 9 different urban or agricultural locations in the Los Angeles–Southern California area to determine the prevalence and characteristics of CRB in these soils. All samples tested contained CRB with a frequency of <10 to 1.3 × 104 cfu per gram of soil, with most agricultural soil samples having a much higher relative frequency of CRB than urban soil samples. Identification and characterization of 40 CRB from these soil samples revealed that most of them were members of the genera Cupriavidus, Pseudomonas, and Stenotrophomonas. Other less prevalent genera identified among our isolated CRB, especially from agricultural soils, included the genera Enterococcus, Bradyrhizobium, Achromobacter, and Planomicrobium. Interestingly, all of these carbapenem‐resistant isolates were also intermediate or resistant to at least 1 noncarbapenem antibiotic. Further characterization of our isolated CRB revealed that 11 Stenotrophomonas, 3 Pseudomonas, 1 Enterococcus, and 1 Bradyrhizobium isolates were carbapenemase producers. Our findings show for the first time that both urban and agricultural soils in Southern California are an underappreciated reservoir of bacteria resistant to carbapenems and other antibiotics, including carbapenemase‐producing CRB.
Collapse
Affiliation(s)
- Nicolas V. Lopez
- Department of BiologyCalifornia State University NorthridgeNorthridgeCAUSA
| | - Cameron J. Farsar
- Department of BiologyCalifornia State University NorthridgeNorthridgeCAUSA
| | - Dana E. Harmon
- Department of BiologyCalifornia State University NorthridgeNorthridgeCAUSA
| | - Cristian Ruiz
- Department of BiologyCalifornia State University NorthridgeNorthridgeCAUSA
| |
Collapse
|
9
|
Harmon DE, Miranda OA, McCarley A, Eshaghian M, Carlson N, Ruiz C. Prevalence and characterization of carbapenem-resistant bacteria in water bodies in the Los Angeles-Southern California area. Microbiologyopen 2019; 8:e00692. [PMID: 29987921 PMCID: PMC6460273 DOI: 10.1002/mbo3.692] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 01/15/2023] Open
Abstract
Carbapenems are β-lactam antibiotics used in healthcare settings as last resort drugs to treat infections caused by antibiotic-resistant bacteria. Carbapenem-resistant bacteria are increasingly being isolated from healthcare facilities; however, little is known about their distribution or prevalence in the environment, especially in the United States, where their distribution in water environments from the West Coast has not been studied before. The aim of this study was to determine the prevalence of carbapenem-resistant bacteria and carbapenemase genes in water bodies from the Los Angeles area (California, USA). All samples that were analyzed contained carbapenem-resistant bacteria with a frequency of between 0.1 and 324 carbapenem-resistant cfu per 100 mls of water. We identified 76 carbapenem-resistant or -intermediate isolates, most of which were also resistant to noncarbapenem antibiotics, as different strains of Enterobacter asburiae, Aeromonas veronii, Cupriavidus gilardii, Pseudomonas, and Stenotrophomonas species. Of them, 52 isolates were carbapenemase-producers. Furthermore, PCR and sequence analysis to identify the carbapenemase gene of these carbapenemase-producing isolates revealed that all Enterobacter asburiae isolates had a blaIMI-2 gene 100% identical to the reference sequence, and all Stenotrophomonas maltophlia isolates had a blaL1 gene 83%-99% identical to the reference blaL1 . Our findings indicate that water environments in Southern California are an important reservoir of bacteria-resistant to carbapenems and other antibiotics, including bacteria carrying intrinsic and acquired carbapenemase genes.
Collapse
Affiliation(s)
- Dana E. Harmon
- Department of BiologyCalifornia State University NorthridgeNorthridgeCalifornia
| | - Osvaldo A. Miranda
- Department of BiologyCalifornia State University NorthridgeNorthridgeCalifornia
| | - Ashley McCarley
- Department of BiologyCalifornia State University NorthridgeNorthridgeCalifornia
| | - Michelle Eshaghian
- Department of BiologyCalifornia State University NorthridgeNorthridgeCalifornia
| | - Natasha Carlson
- Department of BiologyCalifornia State University NorthridgeNorthridgeCalifornia
| | - Cristian Ruiz
- Department of BiologyCalifornia State University NorthridgeNorthridgeCalifornia
| |
Collapse
|
10
|
Abstract
INTRODUCTION Aspirin (acetylsalicylic acid, ASA) is often co-administered during the treatment of infections. Salicylic acid (SAL), the active metabolite of ASA, has significant effects on bacteria that might improve or (more likely) compromise the effectiveness of antibiotics. Areas covered: In this review, we summarize the interactions between SAL and antibiotics, and describe the underlying mechanisms involved. Expert opinion: In an era of rapidly increasing antibiotic resistance and lack of new antibiotic development, it is important to explore ways to optimize the effectiveness of antimicrobial treatment. This includes a better understanding of the interactions between commonly co-administered drugs. SAL might compromise the effectiveness of antibiotic treatment by inducing phenotypic resistance in bacteria. It can induce phenotypic resistance by up- or downregulating outer membrane proteins or efflux pumps, by upregulating antibiotic targets and by inducing enzymes with degrading activity. Moreover, SAL can increase the frequency of mutations leading to antibiotic resistance.
Collapse
Affiliation(s)
- Petra Zimmermann
- a Department of Paediatrics , The University of Melbourne , Parkville , Australia.,b Infectious Diseases & Microbiology Research Group , Murdoch Children's Research Institute , Parkville , Australia.,c Infectious Diseases Unit , The Royal Children's Hospital Melbourne , Parkville , Australia.,d Infectious Diseases Unit , University of Basel Children's Hospital , Basel , Switzerland
| | - Nigel Curtis
- a Department of Paediatrics , The University of Melbourne , Parkville , Australia.,b Infectious Diseases & Microbiology Research Group , Murdoch Children's Research Institute , Parkville , Australia.,c Infectious Diseases Unit , The Royal Children's Hospital Melbourne , Parkville , Australia
| |
Collapse
|
11
|
Luo Y, Luo R, Ding H, Ren X, Luo H, Zhang Y, Ye L, Cui S. Characterization of Carbapenem-Resistant Escherichia coli Isolates Through the Whole-Genome Sequencing Analysis. Microb Drug Resist 2018; 24:175-180. [PMID: 28686503 DOI: 10.1089/mdr.2017.0079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Yanping Luo
- Department of Microbiology, The General Hospital of PLA, Beijing, China
| | - Rong Luo
- Department of Microbiology, National Institutes for Food and Drug Control, The State Food and Drug Administration, Beijing, China
| | - Hong Ding
- Department of Microbiology, National Institutes for Food and Drug Control, The State Food and Drug Administration, Beijing, China
| | - Xiu Ren
- Department of Microbiology, National Institutes for Food and Drug Control, The State Food and Drug Administration, Beijing, China
| | - Haipeng Luo
- Department of Microbiology, National Institutes for Food and Drug Control, The State Food and Drug Administration, Beijing, China
| | - Ying Zhang
- Department of Microbiology, The General Hospital of PLA, Beijing, China
| | - Liyan Ye
- Department of Microbiology, The General Hospital of PLA, Beijing, China
| | - Shenghui Cui
- Department of Microbiology, National Institutes for Food and Drug Control, The State Food and Drug Administration, Beijing, China
| |
Collapse
|
12
|
Structural Alteration of OmpR as a Source of Ertapenem Resistance in a CTX-M-15-Producing Escherichia coli O25b:H4 Sequence Type 131 Clinical Isolate. Antimicrob Agents Chemother 2017; 61:AAC.00014-17. [PMID: 28264855 DOI: 10.1128/aac.00014-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/02/2017] [Indexed: 01/06/2023] Open
Abstract
In this study, an ertapenem-nonsusceptible Escherichia coli isolate was investigated to determine the genetic basis for its carbapenem resistance phenotype. This clinical strain was recovered from a patient that received, 1 year previously, ertapenem to treat a cholangitis due to a carbapenem-susceptible extended-spectrum-β-lactamase (ESBL)-producing E. coli isolate. Whole-genome sequencing of these strains was performed using Illumina and single-molecule real-time sequencing technologies. It revealed that they belonged to the ST131 clonal group, had the predicted O25b:H4 serotype, and produced the CTX-M-15 and TEM-1 β-lactamases. One nucleotide substitution was identified between these strains. It affected the ompR gene, which codes for a regulatory protein involved in the control of OmpC/OmpF porin expression, creating a Gly-63-Val substitution. The role of OmpR alteration was confirmed by a complementation experiment that fully restored the susceptibility to ertapenem of the clinical isolate. A modeling study showed that the Gly-63-Val change displaced the histidine-kinase phosphorylation site. SDS-PAGE analysis revealed that the ertapenem-nonsusceptible E. coli strain had a decreased expression of OmpC/OmpF porins. No significant defect in the growth rate or in the resistance to Dictyostelium discoideum amoeba phagocytosis was found in the ertapenem-nonsusceptible E. coli isolate compared to its susceptible parental strain. Our report demonstrates for the first time that ertapenem resistance may emerge clinically from ESBL-producing E. coli due to mutations that modulate the OmpR activity.
Collapse
|
13
|
Tigecycline Nonsusceptibility Occurs Exclusively in Fluoroquinolone-Resistant Escherichia coli Clinical Isolates, Including the Major Multidrug-Resistant Lineages O25b:H4-ST131-H30R and O1-ST648. Antimicrob Agents Chemother 2017; 61:AAC.01654-16. [PMID: 27855067 DOI: 10.1128/aac.01654-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/08/2016] [Indexed: 11/20/2022] Open
Abstract
Tigecycline (TGC) is a last-line drug for multidrug-resistant Enterobacteriaceae We investigated the mechanism(s) underlying TGC nonsusceptibility (TGC resistant/intermediate) in Escherichia coli clinical isolates. The MIC of TGC was determined for 277 fluoroquinolone-susceptible isolates (ciprofloxacin [CIP] MIC, <0.125 mg/liter) and 194 fluoroquinolone-resistant isolates (CIP MIC, >2 mg/liter). The MIC50 and MIC90 for TGC in fluoroquinolone-resistant isolates were 2-fold higher than those in fluoroquinolone-susceptible isolates (MIC50, 0.5 mg/liter versus 0.25 mg/liter; MIC90, 1 mg/liter versus 0.5 mg/liter, respectively). Two fluoroquinolone-resistant isolates (O25b:H4-ST131-H30R and O125:H37-ST48) were TGC resistant (MICs of 4 and 16 mg/liter, respectively), and four other isolates of O25b:H4-ST131-H30R and an isolate of O1-ST648 showed an intermediate interpretation (MIC, 2 mg/liter). No TGC-resistant/intermediate strains were found among the fluoroquinolone-susceptible isolates. The TGC-resistant/intermediate isolates expressed higher levels of acrA and acrB and had lower intracellular TGC concentrations than susceptible isolates, and they possessed mutations in acrR and/or marR The MICs of acrAB-deficient mutants were markedly lower (0.25 mg/liter) than those of the parental strain. After continuous stepwise exposure to CIP in vitro, six of eight TGC-susceptible isolates had reduced TGC susceptibility. Two of them acquired TGC resistance (TGC MIC, 4 mg/liter) and exhibited expression of acrA and acrB and mutations in acrR and/or marR In conclusion, a population of fluoroquinolone-resistant E. coli isolates, including major extraintestinal pathogenic lineages O25b:H4-ST131-H30R and O1-ST648, showed reduced susceptibility to TGC due to overexpression of the efflux pump AcrAB-TolC, leading to decreased intracellular concentrations of the antibiotics that may be associated with the development of fluoroquinolone resistance.
Collapse
|
14
|
Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks. Proc Natl Acad Sci U S A 2017; 114:1135-1140. [PMID: 28096418 DOI: 10.1073/pnas.1616248114] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) are among the most severe threats to the antibiotic era. Multiple different species can exhibit resistance due to many different mechanisms, and many different mobile elements are capable of transferring resistance between lineages. We prospectively sampled CRE from hospitalized patients from three Boston-area hospitals, together with a collection of CRE from a single California hospital, to define the frequency and characteristics of outbreaks and determine whether there is evidence for transfer of strains within and between hospitals and the frequency with which resistance is transferred between lineages or species. We found eight species exhibiting resistance, with the majority of our sample being the sequence type 258 (ST258) lineage of Klebsiella pneumoniae There was very little evidence of extensive hospital outbreaks, but a great deal of variation in resistance mechanisms and the genomic backgrounds carrying these mechanisms. Local transmission was evident in clear phylogeographic structure between the samples from the two coasts. The most common resistance mechanisms were KPC (K. pneumoniae carbapenemases) beta-lactamases encoded by blaKPC2, blaKPC3, and blaKPC4, which were transferred between strains and species by seven distinct subgroups of the Tn4401 element. We also found evidence for previously unrecognized resistance mechanisms that produced resistance when transformed into a susceptible genomic background. The extensive variation, together with evidence of transmission beyond limited clonal outbreaks, points to multiple unsampled transmission chains throughout the continuum of care, including asymptomatic carriage and transmission of CRE. This finding suggests that to control this threat, we need an aggressive approach to surveillance and isolation.
Collapse
|
15
|
Molloy EM, Tietz JI, Blair PM, Mitchell DA. Biological characterization of the hygrobafilomycin antibiotic JBIR-100 and bioinformatic insights into the hygrolide family of natural products. Bioorg Med Chem 2016; 24:6276-6290. [PMID: 27234886 PMCID: PMC5108699 DOI: 10.1016/j.bmc.2016.05.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/08/2016] [Accepted: 05/13/2016] [Indexed: 01/04/2023]
Abstract
The hygrolides, a family of 16-member-ring-containing plecomacrolides produced by Actinobacteria, exhibit numerous reported bioactivities. Using HR-MS/MS, nucleophilic 1,4-addition-based labeling, NMR, and bioinformatic analysis, we identified Streptomyces varsoviensis as a novel producer of JBIR-100, a fumarate-containing hygrolide, and elucidated the previously unknown stereochemistry of the natural product. We investigated the antimicrobial activity of JBIR-100, with preliminary insight into mode of action indicating that it perturbs the membrane of Bacillus subtilis. S. varsoviensis is known to produce compounds from multiple hygrolide sub-families, namely hygrobafilomycins (JBIR-100 and hygrobafilomycin) and bafilomycins (bafilomycin C1 and D). In light of this, we identified the biosynthetic gene cluster for JBIR-100, which, to our knowledge, represents the first reported for a hygrobafilomycin. Finally, we performed a bioinformatic analysis of the hygrolide family, describing clusters from known and predicted producers. Our results indicate that potential remains for the Actinobacteria to yield novel hygrolide congeners, perhaps with differing biological activities.
Collapse
Affiliation(s)
- Evelyn M Molloy
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Jonathan I Tietz
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Patricia M Blair
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Douglas A Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| |
Collapse
|
16
|
Zhi S, Li Q, Yasui Y, Banting G, Edge TA, Topp E, McAllister TA, Neumann NF. An evaluation of logic regression-based biomarker discovery across multiple intergenic regions for predicting host specificity in Escherichia coli. Mol Phylogenet Evol 2016; 103:133-142. [DOI: 10.1016/j.ympev.2016.07.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/23/2016] [Accepted: 07/14/2016] [Indexed: 10/21/2022]
|
17
|
Potter RF, D'Souza AW, Dantas G. The rapid spread of carbapenem-resistant Enterobacteriaceae. Drug Resist Updat 2016; 29:30-46. [PMID: 27912842 DOI: 10.1016/j.drup.2016.09.002] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/23/2016] [Accepted: 09/07/2016] [Indexed: 02/07/2023]
Abstract
Carbapenems, our one-time silver bullet for multidrug resistant bacterial infections, are now threatened by widespread dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Successful expansion of Enterobacteriaceae clonal groups and frequent horizontal gene transfer of carbapenemase expressing plasmids are causing increasing carbapenem resistance. Recent advances in genetic and phenotypic detection facilitate global surveillance of CRE diversity and prevalence. In particular, whole genome sequencing enabled efficient tracking, annotation, and study of genetic elements colocalized with carbapenemase genes on chromosomes and on plasmids. Improved characterization helps detail the co-occurrence of other antibiotic resistance genes in CRE isolates and helps identify pan-drug resistance mechanisms. The novel β-lactamase inhibitor, avibactam, combined with ceftazidime or aztreonam, is a promising CRE treatment compared to current colistin or tigecycline regimens. To halt increasing CRE-associated morbidity and mortality, we must continue quality, cooperative monitoring and urgently investigate novel treatments.
Collapse
Affiliation(s)
- Robert F Potter
- Center for Genome Sciences and System Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO 63110, USA
| | - Alaric W D'Souza
- Center for Genome Sciences and System Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO 63110, USA
| | - Gautam Dantas
- Center for Genome Sciences and System Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, 660 South Euclid Ave, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in Saint Louis, 1 Brookings Drive, St. Louis, MO 63130, USA; Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110, USA.
| |
Collapse
|
18
|
Goodman KE, Simner PJ, Tamma PD, Milstone AM. Infection control implications of heterogeneous resistance mechanisms in carbapenem-resistant Enterobacteriaceae (CRE). Expert Rev Anti Infect Ther 2015; 14:95-108. [PMID: 26535959 DOI: 10.1586/14787210.2016.1106940] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Centers for Disease Control and Prevention (CDC) defines carbapenem-resistant Enterobacteriaceae (CRE) based upon a phenotypic demonstration of carbapenem resistance. However, considerable heterogeneity exists within this definitional umbrella. CRE may mechanistically differ by whether they do or do not produce carbapenemases. Moreover, patients can acquire CRE through multiple pathways: endogenously through antibiotic selective pressure on intestinal microbiota, exogenously through horizontal transmission or through a combination of these factors. Some evidence suggests that non-carbapenemase-producing CRE may be more frequently acquired by antibiotic exposure and carbapenemase-producing CRE via horizontal transmission, but definitive data are lacking. This review examines types of CRE resistance mechanisms, antibiotic exposure and horizontal transmission pathways of CRE acquisition, and the implications of these heterogeneities to the development of evidence-based CRE healthcare epidemiology policies. In our Expert Commentary & Five-Year View, we outline specific nosocomial CRE knowledge gaps and potential methodological approaches for their resolution.
Collapse
Affiliation(s)
- K E Goodman
- a Department of Epidemiology , The Johns Hopkins Bloomberg School of Public Health , Baltimore , MD , USA
| | - P J Simner
- b Department of Pathology, Division of Medical Microbiology , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - P D Tamma
- a Department of Epidemiology , The Johns Hopkins Bloomberg School of Public Health , Baltimore , MD , USA.,c Department of Pediatrics, Division of Pediatric Infectious Diseases , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - A M Milstone
- a Department of Epidemiology , The Johns Hopkins Bloomberg School of Public Health , Baltimore , MD , USA.,c Department of Pediatrics, Division of Pediatric Infectious Diseases , Johns Hopkins University School of Medicine , Baltimore , MD , USA.,d Department of Hospital Epidemiology and Infection Control , The Johns Hopkins Hospital , Baltimore , MD , USA
| |
Collapse
|
19
|
Identification of a novel NDM variant, NDM-13, from a multidrug-resistant Escherichia coli clinical isolate in Nepal. Antimicrob Agents Chemother 2015; 59:5847-50. [PMID: 26169399 DOI: 10.1128/aac.00332-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 07/06/2015] [Indexed: 01/19/2023] Open
Abstract
A novel New Delhi metallo-β-lactamase, NDM-13, was identified in a carbapenem-resistant Escherichia coli clinical isolate obtained from the urine of a patient in Nepal. The enzymatic activity of NDM-13 against β-lactams was similar to that of NDM-1. However, NDM-13 displayed significantly higher k cat/Km ratios for cefotaxime. The genetic environment of bla NDM-13 was determined to be tnpA-IS30-bla NDM-13-ble MBL-trpF-dsbC-cutA-groES-groL, with bla NDM-13 located within the chromosome.
Collapse
|
20
|
Munck C, Gumpert HK, Wallin AIN, Wang HH, Sommer MOA. Prediction of resistance development against drug combinations by collateral responses to component drugs. Sci Transl Med 2015; 6:262ra156. [PMID: 25391482 DOI: 10.1126/scitranslmed.3009940] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Resistance arises quickly during chemotherapeutic selection and is particularly problematic during long-term treatment regimens such as those for tuberculosis, HIV infections, or cancer. Although drug combination therapy reduces the evolution of drug resistance, drug pairs vary in their ability to do so. Thus, predictive models are needed to rationally design resistance-limiting therapeutic regimens. Using adaptive evolution, we studied the resistance response of the common pathogen Escherichia coli to 5 different single antibiotics and all 10 different antibiotic drug pairs. By analyzing the genomes of all evolved E. coli lineages, we identified the mutational events that drive the differences in drug resistance levels and found that the degree of resistance development against drug combinations can be understood in terms of collateral sensitivity and resistance that occurred during adaptation to the component drugs. Then, using engineered E. coli strains, we confirmed that drug resistance mutations that imposed collateral sensitivity were suppressed in a drug pair growth environment. These results provide a framework for rationally selecting drug combinations that limit resistance evolution.
Collapse
Affiliation(s)
- Christian Munck
- Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Heidi K Gumpert
- Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Annika I Nilsson Wallin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Harris H Wang
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Morten O A Sommer
- Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark.
| |
Collapse
|
21
|
Tanner WD, VanDerslice JA, Toor D, Benson LS, Porucznik CA, Goel RK, Atkinson RM. Development and field evaluation of a method for detecting carbapenem-resistant bacteria in drinking water. Syst Appl Microbiol 2015; 38:351-7. [DOI: 10.1016/j.syapm.2015.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/17/2015] [Accepted: 03/23/2015] [Indexed: 01/19/2023]
|
22
|
Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain. PLoS One 2014; 9:e99209. [PMID: 24905728 PMCID: PMC4048246 DOI: 10.1371/journal.pone.0099209] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/12/2014] [Indexed: 01/12/2023] Open
Abstract
Multidrug-resistant Enterobacteriaceae are emerging as a serious infectious disease challenge. These strains can accumulate many antibiotic resistance genes though horizontal transfer of genetic elements, those for β-lactamases being of particular concern. Some β-lactamases are active on a broad spectrum of β-lactams including the last-resort carbapenems. The gene for the broad-spectrum and carbapenem-active metallo-β-lactamase NDM-1 is rapidly spreading. We present the complete genome of Klebsiella pneumoniae ATCC BAA-2146, the first U.S. isolate found to encode NDM-1, and describe its repertoire of antibiotic-resistance genes and mutations, including genes for eight β-lactamases and 15 additional antibiotic-resistance enzymes. To elucidate the evolution of this rich repertoire, the mobile elements of the genome were characterized, including four plasmids with varying degrees of conservation and mosaicism and eleven chromosomal genomic islands. One island was identified by a novel phylogenomic approach, that further indicated the cps-lps polysaccharide synthesis locus, where operon translocation and fusion was noted. Unique plasmid segments and mosaic junctions were identified. Plasmid-borne blaCTX-M-15 was transposed recently to the chromosome by ISEcp1. None of the eleven full copies of IS26, the most frequent IS element in the genome, had the expected 8-bp direct repeat of the integration target sequence, suggesting that each copy underwent homologous recombination subsequent to its last transposition event. Comparative analysis likewise indicates IS26 as a frequent recombinational junction between plasmid ancestors, and also indicates a resolvase site. In one novel use of high-throughput sequencing, homologously recombinant subpopulations of the bacterial culture were detected. In a second novel use, circular transposition intermediates were detected for the novel insertion sequence ISKpn21 of the ISNCY family, suggesting that it uses the two-step transposition mechanism of IS3. Robust genome-based phylogeny showed that a unified Klebsiella cluster contains Enterobacter aerogenes and Raoultella, suggesting the latter genus should be abandoned.
Collapse
|
23
|
Nicoloff H, Andersson DI. Lon protease inactivation, or translocation of thelongene, potentiate bacterial evolution to antibiotic resistance. Mol Microbiol 2013; 90:1233-48. [DOI: 10.1111/mmi.12429] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Hervé Nicoloff
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-751 23 Uppsala Sweden
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-751 23 Uppsala Sweden
| |
Collapse
|
24
|
McMurry LM, Levy SB. Amino acid residues involved in inactivation of the Escherichia coli multidrug resistance repressor MarR by salicylate, 2,4-dinitrophenol, and plumbagin. FEMS Microbiol Lett 2013; 349:16-24. [PMID: 24111786 DOI: 10.1111/1574-6968.12291] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/27/2013] [Accepted: 09/12/2013] [Indexed: 11/28/2022] Open
Abstract
MarR is the dedicated autorepressor of the marRAB operon found in seven genera of the Enterobacteraceae. The MarA transcriptional regulator directly activates numerous genes involved in multidrug resistance and other environmental responses. MarR is inactivated by certain phenolic ligands, such as salicylate, by an unknown mechanism. Our recent work has shown that several amino acid residues of Escherichia coli MarR affecting ligand binding are located between the dimerization and DNA-binding domains. To further characterize the ligand-binding region of MarR, we have now examined 7 point mutants generated by random mutagenesis and 11 site-directed alanine replacement mutants for inactivation by three ligands: salicylate, 2,4-dinitrophenol, and plumbagin. Inactivation of MarR was quantitated in intact cells by loss of MarR-mediated repression of a chromosomal mar-lacZ transcriptional fusion. The results showed that most of the residues important for ligand effectiveness lay in the α1 and α2 helices of MarR, between the putative DNA-binding domain and the dimerization domain of MarR, reinforcing our earlier findings. Moreover, the three ligands had different, but overlapping, sets of residues impacting their effects on MarR.
Collapse
Affiliation(s)
- Laura M McMurry
- Department of Molecular Biology and Microbiology, Center for Adaptation Genetics and Drug Resistance, Tufts University School of Medicine, Boston, MA, USA
| | | |
Collapse
|
25
|
Mutational analysis of the multiple-antibiotic resistance regulator MarR reveals a ligand binding pocket at the interface between the dimerization and DNA binding domains. J Bacteriol 2013; 195:3341-51. [PMID: 23687277 DOI: 10.1128/jb.02224-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli regulator MarR represses the multiple-antibiotic resistance operon marRAB and responds to phenolic compounds, including sodium salicylate, which inhibit its activity. Crystals obtained in the presence of a high concentration of salicylate indicated two possible salicylate sites, SAL-A and SAL-B. However, it was unclear whether these sites were physiologically significant or were simply a result of the crystallization conditions. A study carried out on MarR homologue MTH313 suggested the presence of a salicylate binding site buried at the interface between the dimerization and the DNA-binding domains. Interestingly, the authors of the study indicated a similar pocket conserved in the MarR structure. Since no mutagenesis analysis had been performed to test which amino acids were essential in salicylate binding, we examined the role of residues that could potentially interact with salicylate. We demonstrated that mutations in residues shown as interacting with salicylate at SAL-A and SAL-B in the MarR-salicylate structure had no effect on salicylate binding, indicating that these sites were not the physiological regulatory sites. However, some of these residues (P57, R86, M74, and R77) were important for DNA binding. Furthermore, mutations in residues R16, D26, and K44 significantly reduced binding to both salicylate and 2,4-dinitrophenol, while a mutation in residue H19 impaired the binding to 2,4-dinitrophenol only. These findings indicate, as for MTH313, the presence of a ligand binding pocket located between the dimerization and DNA binding domains.
Collapse
|
26
|
Duval V, Lister IM. MarA, SoxS and Rob of Escherichia coli - Global regulators of multidrug resistance, virulence and stress response. ACTA ACUST UNITED AC 2013; 2:101-124. [PMID: 24860636 DOI: 10.6000/1927-3037.2013.02.03.2] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Bacteria have a great capacity for adjusting their metabolism in response to environmental changes by linking extracellular stimuli to the regulation of genes by transcription factors. By working in a co-operative manner, transcription factors provide a rapid response to external threats, allowing the bacteria to survive. This review will focus on transcription factors MarA, SoxS and Rob in Escherichia coli, three members of the AraC family of proteins. These homologous proteins exemplify the ability to respond to multiple threats such as oxidative stress, drugs and toxic compounds, acidic pH, and host antimicrobial peptides. MarA, SoxS and Rob recognize similar DNA sequences in the promoter region of more than 40 regulatory target genes. As their regulons overlap, a finely tuned adaptive response allows E. coli to survive in the presence of different assaults in a co-ordinated manner. These regulators are well conserved amongst Enterobacteriaceae and due to their broad involvement in bacterial adaptation in the host, have recently been explored as targets to develop new anti-virulence agents. The regulators are also being examined for their roles in novel technologies such as biofuel production.
Collapse
Affiliation(s)
- Valérie Duval
- Center for Adaptation Genetics and Drug Resistance, Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111
| | - Ida M Lister
- Arietis Corporation, 650 Albany Street, Room 130, Boston, MA 02118
| |
Collapse
|