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Wang T, Xu Y, Ling W, Mosa A, Liu S, Lin Z, Wang H, Hu X. Dissemination of antibiotic resistance genes is regulated by iron oxides: Insight into the influence on bacterial transformation. ENVIRONMENT INTERNATIONAL 2024; 185:108499. [PMID: 38368718 DOI: 10.1016/j.envint.2024.108499] [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: 10/24/2023] [Revised: 12/27/2023] [Accepted: 02/11/2024] [Indexed: 02/20/2024]
Abstract
The transportation of antibiotic resistance genes (ARGs) in manure-soil-plant continuums poses risks to human health. Horizontal gene transfer, particularly for bacterial transformation, is an important way for ARG dissemination. As crucial components in soils, iron oxides impacted the fates of various abiotic and biotic contaminants due to their active properties. However, whether they can influence the transformation of ARGs is unknown, which waits to be figured out to boost the assessment and control of ARG spread risks. In this study, we have investigated the effects of goethite, hematite, and magnetite (0-250 mg/L, with sizes < 100 nm and > 100 nm) on the transfer of ampicillin resistance genes to Escherichia coli cells. At lower iron oxide concentrations, the transformation of ARGs was first facilitated (transformation frequency reached up to 3.38-fold higher), but the facilitating effects gradually weakened and eventually disappeared as concentrations further increased. Particle size and iron oxide type were not the universal determinants controlling the transformation. At lower concentrations, iron oxides interacted with proteins and phospholipids in E. coli envelope structures, and induced the overgeneration of intracellular reactive oxygen species. Consequently, they led to pore formation and permeability enhancement on the cell membrane, thus promoting the transformation. The facilitation was also associated with the carrier-like effect of iron oxides for antibiotic resistance plasmids. At higher concentrations, the weakened facilitations were attributed to the aggregation of iron oxides. In this study, we highlight the crucial roles of the concentrations (contents) of iron oxides on the dissemination of ARGs in soils; this study may serve as a reference for ARG pollution control in future agricultural production.
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Affiliation(s)
- Tingting Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yanxing Xu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ahmed Mosa
- Soils Department, Faculty of Agriculture, Mansoura University, 35516 Mansoura, Egypt
| | - Si Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhipeng Lin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Hefei Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China.
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Saima S, Ferdous J, Sultana R, Rashid RB, Almeida S, Begum A, Jensen PKM. Detecting Enteric Pathogens in Low-Risk Drinking Water in Dhaka, Bangladesh: An Assessment of the WHO Water Safety Categories. Trop Med Infect Dis 2023; 8:321. [PMID: 37368739 DOI: 10.3390/tropicalmed8060321] [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: 02/13/2023] [Revised: 05/24/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The microbiological quality of water is usually assessed by fecal coliform bacteria, and the presence of E. coli as an indicator of fecal contamination is widely recommended by international guidelines. This study aimed to assess the prevalence of diarrheagenic pathogens, in both public and personal domain water sources and examine the reliance on the WHO drinking water risk assessment guidelines. This study was conducted in a low-income urban community in Dhaka, Bangladesh between September 2014 and October 2015. Polymerase chain reaction (PCR) was used to detect the marker and virulence genes of Escherichia coli, Vibrio cholerae, Salmonella species, and Campylobacter species, and the culture method was employed for the quantitative assessment of E. coli. According to the WHO guidelines, 48% of the public domain source water and 21% of the personal domain point-of-drinking water were classified in the low-risk group, i.e., 0 CFU of E. coli/100 mL. However, when using PCR, we detected pathogens in 39% (14/36) of the point-of-drinking water samples and 65% (74/114) of the public domain water source samples classified in the low-risk group. Our study showed that relying solely on E. coli detection as a measure of water quality may overlook the presence of other pathogens in the drinking water. In addition to the culture-based method, the detection of virulence genes by PCR should also be considered to add more scrutiny to the detection of diverse types of pathogens.
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Affiliation(s)
- Sabera Saima
- Department of Microbiology, University of Dhaka, 1000 Dhaka, Bangladesh
| | - Jannatul Ferdous
- Department of Microbiology, University of Dhaka, 1000 Dhaka, Bangladesh
- Copenhagen Center for Disaster Research, Section for Global Health, Department of Public Health, University of Copenhagen, 1014 Copenhagen, Denmark
- Department of Life Sciences, School of Environment and Life Sciences, Independent University, 1229 Dhaka, Bangladesh
| | - Rebeca Sultana
- Copenhagen Center for Disaster Research, Section for Global Health, Department of Public Health, University of Copenhagen, 1014 Copenhagen, Denmark
- icddr,b, 1212 Dhaka, Bangladesh
- Institute of Health Economics, University of Dhaka, 1000 Dhaka, Bangladesh
| | - Ridwan Bin Rashid
- Department of Microbiology, University of Dhaka, 1000 Dhaka, Bangladesh
| | - Sara Almeida
- Copenhagen Center for Disaster Research, Section for Global Health, Department of Public Health, University of Copenhagen, 1014 Copenhagen, Denmark
| | - Anowara Begum
- Department of Microbiology, University of Dhaka, 1000 Dhaka, Bangladesh
| | - Peter Kjær Mackie Jensen
- Copenhagen Center for Disaster Research, Section for Global Health, Department of Public Health, University of Copenhagen, 1014 Copenhagen, Denmark
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Geurtsen J, de Been M, Weerdenburg E, Zomer A, McNally A, Poolman J. Genomics and pathotypes of the many faces of Escherichia coli. FEMS Microbiol Rev 2022; 46:6617594. [PMID: 35749579 PMCID: PMC9629502 DOI: 10.1093/femsre/fuac031] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli's infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.
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Affiliation(s)
- Jeroen Geurtsen
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | - Mark de Been
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | | | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 Utrecht, the Netherlands
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | - Jan Poolman
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
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Kasagaki S, Hashimoto M, Maeda S. Subminimal inhibitory concentrations of ampicillin and mechanical stimuli cooperatively promote cell-to-cell plasmid transformation in Escherichia coli. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100130. [PMID: 35909620 PMCID: PMC9325862 DOI: 10.1016/j.crmicr.2022.100130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Low concentrations of ampicillin promote horizontal plasmid transfer in E. coli. Mechanical stimuli also promote horizontal plasmid transfer in E. coli. Those two kinds of stimuli cooperatively promote plasmid transfer. This plasmid transfer occurs via the cell-to-cell transformation mechanism. This transformation occurs between biofilm cells under flexible conditions.
Horizontal gene transfer (HGT) is a bacterial evolution tool for improved survival. Although several environmental stimuli induce or promote HGT, the diversity and complexity of the environmental factors have not been sufficiently elucidated. In this study, we showed that the biofilm culture of Escherichia coli at the air–solid interface in the presence of a subminimal inhibitory concentration (sub-MIC) of ampicillin (∼0.5–4 µg/mL) and subsequent mechanical stimulation (rolling small glass balls, ø = 5–8 mm) cooperatively promoted horizontal plasmid transfer without the usual competence-inducing conditions. Either of the two treatments promoted plasmid transfer at a lower frequency than when the treatments were combined. The effect of several parameters on the two treatments was tested and then optimized, achieving a high frequency of plasmid transfer (up to 10−6 per cell) under optimal conditions. Plasmid transfer was DNase-sensitive for both treatments, demonstrating its mechanism of transformation. Plasmid transfer occurred using various E. coli strains, plasmids, ball materials, shaking conditions, and even the mechanical stimulation of brushing the biofilm with a toothbrush, indicating the conditional flexibility of this phenomenon. This is the first demonstration of the promoting effect of the combination of a sub-MIC antibiotic and mechanical stimulation on horizontal plasmid transfer between E. coli cells via transformation. Regarding environmental bacterial physiology, the aggregations or biofilms of bacterial cells may encounter both sub-MIC antibiotics and mechanical stimuli in some specific environments, therefore, this type of HGT could also occur naturally.
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Washington MA, Taitt CR, Blythe J, Hering K, Barnhill J. Escherichia coli as a Potential Reservoir of Antimicrobial Resistance Genes on the Island of O'ahu. HAWAI'I JOURNAL OF HEALTH & SOCIAL WELFARE 2021; 80:9-14. [PMID: 33490961 PMCID: PMC7811132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The problem of antimicrobial-resistant bacteria has not been adequately explored in the tropical island environment. To date, there has not been a systematic investigation into the prevalence and distribution of antimicrobial resistance determinants in the Hawaiian Islands. Urinary isolates are the most common bacterial pathogens encountered in the clinical laboratory. Therefore, the antimicrobial resistance determinant profiles of these organisms can serve as a sentinel of the overall antimicrobial resistance situation in a localized patient population. In this study, 82 clinical isolates of Escherichia coli derived from 82 distinct patients were collected at a large medical center on the island of O'ahu. Each isolate was evaluated for the presence of antimicrobial resistance genes using a microarray-based approach. A total of 36 antimicrobial resistance genes covering 10 classes of antimicrobial compounds were identified. Most isolates were found to harbor between 3 and 5 antimicrobial resistance genes. Only a few isolates were found to harbor more than 12 genes. Significantly, a high rate of phenotypic resistance to one of the first-line treatments for uncomplicated urinary tract infection (sulfamethoxazole) was identified. This phenotype was correlated to the presence of sulfonamides and trimethoprim resistance determinants. Since E. coli is one of the most encountered pathogens in the hospital environment, the presence of clinically relevant resistance determinants in isolates of this organism from a clinical setting on O'ahu is a significant finding that warrants further investigation.
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Affiliation(s)
- Michael A. Washington
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY (MAW, KH, JB)
| | | | - Jauchia Blythe
- Department of Clinical Investigation, Tripler Army Medical Center, Honolulu, HI (JB)
| | - Kalei Hering
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY (MAW, KH, JB)
| | - Jason Barnhill
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY (MAW, KH, JB)
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Riva F, Riva V, Eckert EM, Colinas N, Di Cesare A, Borin S, Mapelli F, Crotti E. An Environmental Escherichia coli Strain Is Naturally Competent to Acquire Exogenous DNA. Front Microbiol 2020; 11:574301. [PMID: 33013812 PMCID: PMC7494812 DOI: 10.3389/fmicb.2020.574301] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022] Open
Abstract
The diffusion of antibiotic resistance determinants in different environments, e.g., soil and water, has become a public concern for global health and food safety and many efforts are currently devoted to clarify this complex ecological and evolutionary issue. Horizontal gene transfer (HGT) has an important role in the spread of antibiotic resistance genes (ARGs). However, among the different HGT mechanisms, the capacity of environmental bacteria to acquire naked exogenous DNA by natural competence is still poorly investigated. This study aimed to characterize the ability of the environmental Escherichia coli strain ED1, isolated from the crustacean Daphnia sp., to acquire exogenous DNA by natural competence. Transformation experiments were carried out varying different parameters, i.e., cell growth phase, amount of exogenous DNA and exposition to artificial lake water (ALW) and treated wastewater to mimic environmental-like conditions that may be encountered in the agri-food system. Results were compared with those showed by the laboratory E. coli strain DH5α. Our experimental data, supported by genomic sequencing, showed that, when exposed to pure water, ED1 strain was able to acquire exogenous DNA with frequencies (10–8–10–9) statistically higher than the ones observed for DH5α strain (10–10). Interestingly, higher values were retrieved for ED1 than DH5α strains exposed to ALW (10–7 vs. 10–9, respectively) or treated wastewater (10–8 vs. 10–10, respectively). We tested, therefore, ED1 strain ability to colonize the rhizosphere of lettuce, a model plant representative of raw-consumed vegetables of high economic importance in the ready-to-eat food industry. Results showed that ED1 strain was able to efficiently colonize lettuce rhizosphere, revealing a stable colonization for 14 days-long period. In conclusion, ED1 strain ability to acquire exogenous DNA in environmental-like conditions by natural competence, combined with its ability to efficiently and stably colonize plant rhizosphere, poses the attention to food and human safety showing a possible route of diffusion of antibiotic resistance in the agri-food system, sustaining the “One Health” warnings related to the antibiotic spread.
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Affiliation(s)
- Francesco Riva
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Valentina Riva
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Ester M Eckert
- Molecular Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Noemi Colinas
- Molecular Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy.,Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, Spain
| | - Andrea Di Cesare
- Molecular Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Elena Crotti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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7
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Natural Transformation in Escherichia coli. Methods Mol Biol 2019. [PMID: 31584163 DOI: 10.1007/978-1-4939-9877-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Escherichia coli is well known for its ability to undergo artificial transformation. This bacterium is not generally recognized as naturally transformable. However, several past studies have demonstrated that laboratory and natural strains of E. coli can express modest natural competence under feasible environmental conditions. Here we describe a protocol outlining natural transformation in E. coli in environmental media such as natural freshwater.
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Hasegawa H, Suzuki E, Maeda S. Horizontal Plasmid Transfer by Transformation in Escherichia coli: Environmental Factors and Possible Mechanisms. Front Microbiol 2018; 9:2365. [PMID: 30337917 PMCID: PMC6180151 DOI: 10.3389/fmicb.2018.02365] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/14/2018] [Indexed: 12/16/2022] Open
Abstract
Transformation is one mode of horizontal gene transfer (HGT) in bacteria, wherein extracellular naked DNA is taken up by cells that have developed genetic competence. Sensitivity to DNase, which degrades naked DNA, is the key to distinguishing transformation from the DNase-resistant HGT mechanisms. In general, Escherichia coli is not believed to be naturally transformable; it develops high competence only under artificial conditions, including exposure to high Ca2+ concentrations. However, E. coli can reportedly express modest competence under certain conditions that are feasible in natural environments outside laboratory. In addition, recent data suggest that environmental factors influence multiple routes of transformation. In this mini review, we (1) summarize our studies on transformation-based HGT using E. coli experimental systems and (2) discuss the possible occurrence of transformation via multiple mechanisms in the environment and its possible impact on the spread of antibiotic resistance genes.
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Affiliation(s)
| | | | - Sumio Maeda
- Graduate School of Humanities and Sciences, Nara Women’s University, Nara, Japan
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Basu S, Mukherjee M. Incidence and risk of co-transmission of plasmid-mediated quinolone resistance and extended-spectrum β-lactamase genes in fluoroquinolone-resistant uropathogenic Escherichia coli: a first study from Kolkata, India. J Glob Antimicrob Resist 2018; 14:217-223. [DOI: 10.1016/j.jgar.2018.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 02/15/2018] [Accepted: 03/24/2018] [Indexed: 10/17/2022] Open
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Evaluation of resistance gene transfer from heat-treated Escherichia coli. Int J Food Microbiol 2018; 270:39-43. [PMID: 29477666 DOI: 10.1016/j.ijfoodmicro.2018.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 02/08/2018] [Accepted: 02/16/2018] [Indexed: 02/06/2023]
Abstract
Antimicrobial-resistant Escherichia coli may be present in various foods. The aim of this study was to evaluate the impact of heat treatment, simulating food preparation, on the possibility of antimicrobial resistance genes being transferred from E. coli cells. The study was performed on antimicrobial-resistant E. coli cells in suspension in a sterile saline solution. The stability of resistance genes and the possibility of their transfer by transformation or conjugation were analyzed. Results showed that antimicrobial-resistant E. coli cells managing to survive after a few minutes at 60 °C retained their antimicrobial resistance. No plasmid could be transferred by conjugation from antimicrobial-resistant E. coli cells heated to 60 °C for ten or more minutes. Twelve electroporation experiments were performed using a bacterial suspension heated to 70 °C for 30 min. Genes coding for resistance to extended-spectrum cephalosporins, tetracycline or sulfonamides were transferred to an E. coli DH5α recipient on two occasions. In conclusion we showed that heat-treated E. coli may occasionally transfer resistance genes.
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Fink R, Moran E. Biosafety for Large-Scale Containment Level 1 Operations Using Recombinant DNA Technology: No Emerging Hazards. APPLIED BIOSAFETY 2016. [DOI: 10.1177/153567600501000104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Richard Fink
- Wyeth BioPharma, Andover, Massachussetts and 2Wyeth Medica Ireland, Clondalkin, Dublin, Repulic of Ireland
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Werbowy O, Kaczorowski T. Plasmid pEC156, a Naturally Occurring Escherichia coli Genetic Element That Carries Genes of the EcoVIII Restriction-Modification System, Is Mobilizable among Enterobacteria. PLoS One 2016; 11:e0148355. [PMID: 26848973 PMCID: PMC4743918 DOI: 10.1371/journal.pone.0148355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/19/2016] [Indexed: 11/30/2022] Open
Abstract
Type II restriction-modification systems are ubiquitous in prokaryotes. Some of them are present in naturally occurring plasmids, which may facilitate the spread of these systems in bacterial populations by horizontal gene transfer. However, little is known about the routes of their dissemination. As a model to study this, we have chosen an Escherichia coli natural plasmid pEC156 that carries the EcoVIII restriction modification system. The presence of this system as well as the cis-acting cer site involved in resolution of plasmid multimers determines the stable maintenance of pEC156 not only in Escherichia coli but also in other enterobacteria. We have shown that due to the presence of oriT-type F and oriT-type R64 loci it is possible to mobilize pEC156 by conjugative plasmids (F and R64, respectively). The highest mobilization frequency was observed when pEC156-derivatives were transferred between Escherichia coli strains, Enterobacter cloacae and Citrobacter freundii representing coliform bacteria. We found that a pEC156-derivative with a functional EcoVIII restriction-modification system was mobilized in enterobacteria at a frequency lower than a plasmid lacking this system. In addition, we found that bacteria that possess the EcoVIII restriction-modification system can efficiently release plasmid content to the environment. We have shown that E. coli cells can be naturally transformed with pEC156-derivatives, however, with low efficiency. The transformation protocol employed neither involved chemical agents (e.g. CaCl2) nor temperature shift which could induce plasmid DNA uptake.
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Affiliation(s)
- Olesia Werbowy
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, Gdansk, Poland
| | - Tadeusz Kaczorowski
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, Gdansk, Poland
- * E-mail:
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Positive Effect of Carbon Sources on Natural Transformation in Escherichia coli: Role of Low-Level Cyclic AMP (cAMP)-cAMP Receptor Protein in the Derepression of rpoS. J Bacteriol 2015; 197:3317-28. [PMID: 26260461 DOI: 10.1128/jb.00291-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/05/2015] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED Natural plasmid transformation of Escherichia coli is a complex process that occurs strictly on agar plates and requires the global stress response factor σ(S). Here, we showed that additional carbon sources could significantly enhance the transformability of E. coli. Inactivation of phosphotransferase system genes (ptsH, ptsG, and crr) caused an increase in the transformation frequency, and the addition of cyclic AMP (cAMP) neutralized the promotional effect of carbon sources. This implies a negative role of cAMP in natural transformation. Further study showed that crp and cyaA mutations conferred a higher transformation frequency, suggesting that the cAMP-cAMP receptor protein (CRP) complex has an inhibitory effect on transformation. Moreover, we observed that rpoS is negatively regulated by cAMP-CRP in early log phase and that both crp and cyaA mutants show no transformation superiority when rpoS is knocked out. Therefore, it can be concluded that both the crp and cyaA mutations derepress rpoS expression in early log phase, whereby they aid in the promotion of natural transformation ability. We also showed that the accumulation of RpoS during early log phase can account for the enhanced transformation aroused by additional carbon sources. Our results thus demonstrated that the presence of additional carbon sources promotes competence development and natural transformation by reducing cAMP-CRP and, thus, derepressing rpoS expression during log phase. This finding could contribute to a better understanding of the relationship between nutrition state and competence, as well as the mechanism of natural plasmid transformation in E. coli. IMPORTANCE Escherichia coli, which is not usually considered to be naturally transformable, was found to spontaneously take up plasmid DNA on agar plates. Researching the mechanism of natural transformation is important for understanding the role of transformation in evolution, as well as in the transfer of pathogenicity and antibiotic resistance genes. In this work, we found that carbon sources significantly improve transformation by decreasing cAMP. Then, the low level of cAMP-CRP derepresses the general stress response regulator RpoS via a biphasic regulatory pattern, thereby contributing to transformation. Thus, we demonstrate the mechanism by which carbon sources affect natural transformation, which is important for revealing information about the interplay between nutrition state and competence development in E. coli.
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Matsuda A, Kurono N, Kawano C, Shirota K, Hirabayashi A, Horino M, Etchuya R, Sobue R, Sasaki Y, Miyaue S, Sekoguchi A, Sugiura C, Shibata Y, Ito M, Ando T, Maeda S. Genome-wide screen for Escherichia coli genes involved in repressing cell-to-cell transfer of non-conjugative plasmids. Biochem Biophys Res Commun 2012; 428:445-50. [PMID: 23131563 DOI: 10.1016/j.bbrc.2012.10.098] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 10/24/2012] [Indexed: 10/27/2022]
Abstract
Acquiring new genetic traits by lateral gene transfer is a bacterial strategy for environment adaptation. We previously showed that Escherichia coli could laterally transmit non-conjugative plasmids in co-cultures containing strains with and without the plasmid. In this study, using the Keio collection, a comprehensive library of E. coli knock-out mutants for non-essential genes, we screened for genes responsible for repressing cell-to-cell plasmid transfer in recipient cells. By stepwise screening, we identified 55 'transfer-up' mutants that exhibited approximately 2- to 30-fold increased activities. We confirmed plasmid acquisition by these 'up' mutants and revealed that there were no significant changes in antibiotic resistance in the original Keio strains. The presumed functions of these gene products covered a wide range of activities, including metabolism and synthesis, transport, transcription or translation and others. Two competence-gene homologues (ybaV and yhiR) were identified from among these genes. The presumed localizations of these 55 gene products were estimated to be 34 cytoplasmic proteins, 20 in or around the cell surface and 1 unknown location. Our results suggest that these 55 genes may be involved in repressing plasmid uptake during cell-to-cell plasmid transfer.
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Affiliation(s)
- Ayako Matsuda
- Graduate School of Humanities and Sciences, Nara Women's University, Kitauoya-nishimachi, Nara 630-8506, Japan
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15
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Shanthi J, Pazhanimurugan R, Gopikrishnan V, Balagurunathan R. Mechanism of drug resistance, characterization of plasmid-borne determinants and transformation study in P. aeruginosa from burn and ICU units-its susceptibility pattern. Burns 2012; 39:643-9. [PMID: 22980776 DOI: 10.1016/j.burns.2012.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 08/09/2012] [Accepted: 08/14/2012] [Indexed: 11/28/2022]
Abstract
The transfer of drug resistance between hospital pathogens has led to alarming increase of multidrug resistant strains imposing therapeutic challenges. These resistant isolates harbor various mechanisms to counteract the drugs administered and have been reported to deliver these factors to sensitive strains in hostile environment. The present study aimed to screen for multidrug resistant Pseudomonas aeruginosa strains for the production of extended-spectrum β-lactamases, metallo-β-lactamases, AmpC β-lactamase, drug efflux phenotypes and co-transfer the resistance for cephalosporin and other non-beta lactam antibiotics in CaCl2 treated drug sensitive E. coli strains. From the 87 samples processed about 23 isolates of P. aeruginosa were ESBL and MBL positive, 5 (20%) were found to be AmpC β-lactamase producers, efflux mechanism was observed in 8 isolates, 15 isolates had MIC of 16 μg/ml. A putative efflux mechanism was observed in 8 out of 23 isolates that showed decrease in the MIC of meropenem with reserpine. The plasmid profile was characterized for all the common isolates obtained from burn and ICU units. About 69.66% of E. coli recombinants scored positive for both beta lactam and non-beta lactam antibiotics is due to co transfer of resistant plasmid obtained from P. aeruginosa.
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Affiliation(s)
- J Shanthi
- Bharathiar University, Coimbatore 641046, Tamil Nadu, India
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16
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Domingues S, Harms K, Fricke WF, Johnsen PJ, da Silva GJ, Nielsen KM. Natural transformation facilitates transfer of transposons, integrons and gene cassettes between bacterial species. PLoS Pathog 2012; 8:e1002837. [PMID: 22876180 PMCID: PMC3410848 DOI: 10.1371/journal.ppat.1002837] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 06/19/2012] [Indexed: 12/24/2022] Open
Abstract
We have investigated to what extent natural transformation acting on free DNA substrates can facilitate transfer of mobile elements including transposons, integrons and/or gene cassettes between bacterial species. Naturally transformable cells of Acinetobacter baylyi were exposed to DNA from integron-carrying strains of the genera Acinetobacter, Citrobacter, Enterobacter, Escherichia, Pseudomonas, and Salmonella to determine the nature and frequency of transfer. Exposure to the various DNA sources resulted in acquisition of antibiotic resistance traits as well as entire integrons and transposons, over a 24 h exposure period. DNA incorporation was not solely dependent on integrase functions or the genetic relatedness between species. DNA sequence analyses revealed that several mechanisms facilitated stable integration in the recipient genome depending on the nature of the donor DNA; homologous or heterologous recombination and various types of transposition (Tn21-like and IS26-like). Both donor strains and transformed isolates were extensively characterized by antimicrobial susceptibility testing, integron- and cassette-specific PCRs, DNA sequencing, pulsed field gel electrophoreses (PFGE), Southern blot hybridizations, and by re-transformation assays. Two transformant strains were also genome-sequenced. Our data demonstrate that natural transformation facilitates interspecies transfer of genetic elements, suggesting that the transient presence of DNA in the cytoplasm may be sufficient for genomic integration to occur. Our study provides a plausible explanation for why sequence-conserved transposons, IS elements and integrons can be found disseminated among bacterial species. Moreover, natural transformation of integron harboring populations of competent bacteria revealed that interspecies exchange of gene cassettes can be highly efficient, and independent on genetic relatedness between donor and recipient. In conclusion, natural transformation provides a much broader capacity for horizontal acquisitions of genetic elements and hence, resistance traits from divergent species than previously assumed. Genetic elements, such as transposons and integrons, frequently carry antimicrobial resistance determinants and can be found widely disseminated among pathogenic bacteria. Their distribution pattern suggests dissemination through horizontal gene transfer. The role of natural transformation in horizontal transfer of genetic elements other than those that are self-replicative (plasmids) has remained largely unexplored. We have tested if natural transformation can facilitate transfer of transposons and class 1 integrons between bacterial species. We here provide experimental evidence showing that natural transformation can be a general mechanism for dissemination of genetic elements that by themselves do not encode interspecies transfer functions (e.g. transposons, insertion sequences). We demonstrate that antibiotic resistance determinants present in such genetic elements can spread by natural transformation between species of clinical interest. We show by quantitative data that interspecies exchange of resistance gene cassettes is highly efficient among integron-containing strains and species. Our study also provides a plausible explanation for how sequence-conserved integrons can become distributed among bacterial species.
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Affiliation(s)
- Sara Domingues
- Centre of Pharmaceutical Studies, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Klaus Harms
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - W. Florian Fricke
- Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Pål J. Johnsen
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Gabriela J. da Silva
- Centre of Pharmaceutical Studies, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Kaare Magne Nielsen
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
- Genøk-Centre for Biosafety, Tromsø, Norway
- * E-mail:
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17
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Abstract
Escherichia coli has homologues of the competence genes other species use for DNA uptake and processing, but natural competence and transformation have never been detected. Although we previously showed that these genes are induced by the competence regulator Sxy as in other gamma-proteobacteria, no conditions are known that naturally induce sxy expression. We have now tested whether the competence gene homologues encode a functional DNA uptake machinery and whether DNA uptake leads to recombination, by investigating the effects of plasmid-borne sxy expression on natural competence in a wide variety of E. coli strains. High- and low-level sxy expression alone did not induce transformation in any of the strains tested, despite varying the transforming DNA, its concentration, and the incubation conditions used. Direct measurements of uptake of radiolabelled DNA were below the limit of detection, however transformants were readily detected when recombination functions were provided by the lambda Red recombinase. This is the first demonstration that E. coli sxy expression can induce natural DNA uptake and that E. coli's competence genes do encode a functional uptake machinery. However, the amount of transformation cells undergo is limited both by low levels of DNA uptake and by inefficient DNA processing/recombination.
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Affiliation(s)
- Sunita Sinha
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada.
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18
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Kurono N, Matsuda A, Etchuya R, Sobue R, Sasaki Y, Ito M, Ando T, Maeda S. Genome-wide screening of Escherichia coli genes involved in execution and promotion of cell-to-cell transfer of non-conjugative plasmids: rodZ (yfgA) is essential for plasmid acceptance in recipient cells. Biochem Biophys Res Commun 2012; 421:119-23. [PMID: 22497891 DOI: 10.1016/j.bbrc.2012.03.127] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 03/27/2012] [Indexed: 01/11/2023]
Abstract
Acquisition of new genetic traits by horizontal gene transfer is a bacterial strategy for adaptation to the environment. We previously showed that Escherichia coli can transmit non-conjugative plasmids laterally in a co-culture containing strains with and without the plasmid. In this study, using the Keio collection, a comprehensive library of E. coli knock-out mutants for non-essential genes, we screened for genes responsible for the execution and promotion of cell-to-cell plasmid transfer in recipient cells. By stepwise screening of 'transfer-down' mutants, two essential genes and six promoting genes were obtained. One of the essential genes was priA, which is involved in DNA replication. This priA mutant was also unable to be transformed by artificial transformation methods, probably due to the deficiency of the plasmid maintenance function. The other essential gene was rodZ (yfgA), a gene involved in the regulation of rod-shaped structure of E. coli cells. This rodZ mutant was transformable by all three methods of artificial transformation tested, suggesting that this gene is essential for cell-to-cell plasmid transfer but not for artificial transformation. These are the first data that suggest that rodZ plays an essential role in DNA acquisition.
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Affiliation(s)
- Naomi Kurono
- Graduate School of Humanities and Sciences, Nara Women's University, Kitauoya-nishimachi, Nara 630-8506, Japan
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19
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Sobue R, Kurono N, Etchuya R, Maeda S. Identification of a novel DNA element that promotes cell-to-cell transformation in Escherichia coli. FEBS Lett 2011; 585:2223-8. [PMID: 21621537 DOI: 10.1016/j.febslet.2011.05.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 05/16/2011] [Accepted: 05/18/2011] [Indexed: 11/18/2022]
Abstract
Recently, we discovered a novel phenomenon, "cell-to-cell transformation" by which non-conjugative plasmids are transmitted horizontally in co-cultures of Escherichia coli F(-) strains. In this study, we aimed to identify the DNA element responsible for the high cell-to-cell transformability of pHSG299. By transplanting pHSG299 DNA fragments into pHSG399, a plasmid showing low transformability, we discovered that a specific 88 bp fragment of pHSG299 significantly promoted pHSG399 transformability. Although several short motif-like repetitive sequences (6-10 bp) were present in the 88 bp sequence, no known DNA motifs were recognized, suggesting that this 88 bp sequence (cell-to-cell transformation promoting sequence, CTPS; Accession number: AB634455) is a novel DNA element.
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Affiliation(s)
- Rina Sobue
- Graduate School of Humanities and Sciences, Nara Women's University, Kitauoya-Nishimachi, Nara, Japan
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20
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Etchuuya R, Ito M, Kitano S, Shigi F, Sobue R, Maeda S. Cell-to-cell transformation in Escherichia coli: a novel type of natural transformation involving cell-derived DNA and a putative promoting pheromone. PLoS One 2011; 6:e16355. [PMID: 21283723 PMCID: PMC3024429 DOI: 10.1371/journal.pone.0016355] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 12/27/2010] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli is not assumed to be naturally transformable. However, several recent reports have shown that E. coli can express modest genetic competence in certain conditions that may arise in its environment. We have shown previously that spontaneous lateral transfer of non-conjugative plasmids occurs in a colony biofilm of mixed E. coli strains (a set of a donor strain harbouring a plasmid and a plasmid-free recipient strain). In this study, with high-frequency combinations of strains and a plasmid, we constructed the same lateral plasmid transfer system in liquid culture. Using this system, we demonstrated that this lateral plasmid transfer was DNase-sensitive, indicating that it is a kind of transformation in which DNase-accessible extracellular naked DNA is essential. However, this transformation did not occur with purified plasmid DNA and required a direct supply of plasmid from co-existing donor cells. Based on this feature, we have termed this transformation type as 'cell-to-cell transformation'. Analyses using medium conditioned with the high-frequency strain revealed that this strain released a certain factor(s) that promoted cell-to-cell transformation and arrested growth of the other strains. This factor is heat-labile and protease-sensitive, and its roughly estimated molecular mass was between ∼9 kDa and ∼30 kDa, indicating that it is a polypeptide factor. Interestingly, this factor was effective even when the conditioned medium was diluted 10(-5)-10(-6), suggesting that it acts like a pheromone with high bioactivity. Based on these results, we propose that cell-to-cell transformation is a novel natural transformation mechanism in E. coli that requires cell-derived DNA and is promoted by a peptide pheromone. This is the first evidence that suggests the existence of a peptide pheromone-regulated transformation mechanism in E. coli and in Gram-negative bacteria.
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Affiliation(s)
- Rika Etchuuya
- Faculty of Human Life and Environment, Nara Women's University, Nara, Japan
| | - Miki Ito
- Faculty of Human Life and Environment, Nara Women's University, Nara, Japan
| | - Seiko Kitano
- Faculty of Human Life and Environment, Nara Women's University, Nara, Japan
| | - Fukiko Shigi
- Faculty of Human Life and Environment, Nara Women's University, Nara, Japan
| | - Rina Sobue
- Faculty of Human Life and Environment, Nara Women's University, Nara, Japan
| | - Sumio Maeda
- Faculty of Human Life and Environment, Nara Women's University, Nara, Japan
- * E-mail:
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21
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Abstract
Escherichia coli is not considered naturally competent, yet it has homologues of the genes that most competent bacteria use for DNA uptake and processing. In Haemophilus influenzae and Vibrio cholerae, these genes are regulated by the Sxy and cyclic AMP receptor (CRP) proteins. We used microarrays to find out whether similar regulation occurs in E. coli. Expression of sxy strongly induced 63 transcriptional units, 34 of which required CRP for transcriptional activation and had promoter sites resembling the Sxy- and CRP-dependent CRP-S motif previously characterized in H. influenzae. As previously reported, sxy expression also induced the sigma-H regulon. Flagellar operons were downregulated by sxy expression, although motility remained unaffected. The CRP-S regulon included all of E. coli's known competence gene homologues, so we investigated Sxy's effect on competence-associated phenotypes. A sxy knockout reduced both "natural" plasmid transformation and competitive fitness in long-term culture. In addition, expression of plasmid-borne sxy led to production of type IV pilin, the main subunit of the DNA uptake machinery of most bacteria. Although H. influenzae Sxy only weakly activated the E. coli Sxy regulon, induction was dramatically improved when it was coexpressed with its cognate CRP, suggesting that intimate interactions between Sxy and CRP are required for transcriptional activation at CRP-S sites.
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22
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Bakkali M. Genome dynamics of short oligonucleotides: the example of bacterial DNA uptake enhancing sequences. PLoS One 2007; 2:e741. [PMID: 17710141 PMCID: PMC1939737 DOI: 10.1371/journal.pone.0000741] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Accepted: 06/29/2007] [Indexed: 11/19/2022] Open
Abstract
Among the many bacteria naturally competent for transformation by DNA uptake-a phenomenon with significant clinical and financial implications- Pasteurellaceae and Neisseriaceae species preferentially take up DNA containing specific short sequences. The genomic overrepresentation of these DNA uptake enhancing sequences (DUES) causes preferential uptake of conspecific DNA, but the function(s) behind this overrepresentation and its evolution are still a matter for discovery. Here I analyze DUES genome dynamics and evolution and test the validity of the results to other selectively constrained oligonucleotides. I use statistical methods and computer simulations to examine DUESs accumulation in Haemophilus influenzae and Neisseria gonorrhoeae genomes. I analyze DUESs sequence and nucleotide frequencies, as well as those of all their mismatched forms, and prove the dependence of DUESs genomic overrepresentation on their preferential uptake by quantifying and correlating both characteristics. I then argue that mutation, uptake bias, and weak selection against DUESs in less constrained parts of the genome combined are sufficient enough to cause DUESs accumulation in susceptible parts of the genome with no need for other DUES function. The distribution of overrepresentation values across sequences with different mismatch loads compared to the DUES suggests a gradual yet not linear molecular drive of DNA sequences depending on their similarity to the DUES. Other genomically overrepresented sequences, both pro- and eukaryotic, show similar distribution of frequencies suggesting that the molecular drive reported above applies to other frequent oligonucleotides. Rare oligonucleotides, however, seem to be gradually drawn to genomic underrepresentation, thus, suggesting a molecular drag. To my knowledge this work provides the first clear evidence of the gradual evolution of selectively constrained oligonucleotides, including repeated, palindromic and protein/transcription factor-binding DNAs.
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Affiliation(s)
- Mohammed Bakkali
- Institute of Genetics, Queen's Medical Center, University of Nottingham, Nottingham, United Kingdom.
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23
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Oussalah M, Caillet S, Salmiéri S, Saucier L, Lacroix M. Antimicrobial effects of alginate-based film containing essential oils for the preservation of whole beef muscle. J Food Prot 2006; 69:2364-9. [PMID: 17066914 DOI: 10.4315/0362-028x-69.10.2364] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Alginate-based edible films containing 1% (wt/vol) essential oils of Spanish oregano, Chinese cinnamon, or savory were immersed in 2% (wt/vol) or 20% (wt/vol) CaCl2 solution and then applied to beef muscle slices to control the growth of Escherichia coli O157:H7 and Salmonella Typhimurium. Whole beef muscle surfaces were inoculated with one of these strains at 10(3) CFU/cm2. During the 5 days of storage, samples of meat were obtained periodically for microbiological analysis. The availability of active compounds from essential oils present in films was evaluated by determination of total phenolic compounds for oregano- and savory-based films and of total aldehydes for cinnamon-based films during storage. After 5 days of storage, films containing oregano or cinnamon essential oils were the most effective against Salmonella Typhimurium regardless of the type of pretreatment used (2 or 20% CaCl2). During the same period, meat inoculated with E. coli O157:H7 and coated with films treated with 2% CaCl2 had significantly fewer bacteria (P < or = 0.05) when oregano-based films were used than when cinnamon- and savory-based films were used. The E. coli O157:H7 concentration was higher at the end of the storage period when films were pretreated with 20% CaCl2. Evaluation of the active compounds in films revealed that availability in oregano- and savory-based films was significantly more important (P < or = 0.05) than that in cinnamon-based films regardless of the type of pretreatment used (2 or 20% CaCl2). At the end of storage, release rates of 40, 60, and 77% were noted in oregano-, savory-, and cinnamon-based films in 2% CaCl2 and rates of 65, 62, and 90% were noted in the same films in 20% CaCl2.
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Affiliation(s)
- Mounia Oussalah
- Research Laboratory in Sciences Applied to Food, Canadian Irradiation Center, Institut Armand-Frappier, Université du Québec, 531 Blvd des Prairies, Laval, Québec, Canada H7V 1B7
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24
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Palchevskiy V, Finkel SE. Escherichia coli competence gene homologs are essential for competitive fitness and the use of DNA as a nutrient. J Bacteriol 2006; 188:3902-10. [PMID: 16707682 PMCID: PMC1482900 DOI: 10.1128/jb.01974-05] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Accepted: 03/01/2006] [Indexed: 11/20/2022] Open
Abstract
Natural genetic competence is the ability of cells to take up extracellular DNA and is an important mechanism for horizontal gene transfer. Another potential benefit of natural competence is that exogenous DNA can serve as a nutrient source for starving bacteria because the ability to "eat" DNA is necessary for competitive survival in environments containing limited nutrients. We show here that eight Escherichia coli genes, identified as homologs of com genes in Haemophilus influenzae and Neisseria gonorrhoeae, are necessary for the use of extracellular DNA as the sole source of carbon and energy. These genes also confer a competitive advantage to E. coli during long-term stationary-phase incubation. We also show that homologs of these genes are found throughout the proteobacteria, suggesting that the use of DNA as a nutrient may be a widespread phenomenon.
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Affiliation(s)
- Vyacheslav Palchevskiy
- Molecular and Computational Biology Program, Department of Biological Sciences, MCB 201B, University of Southern California, Los Angeles, CA 90089-2910, USA
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25
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Hsu MC, Tsai PY, Chen KT, Li LH, Chiang CC, Tsai JJ, Ke LY, Chen HY, Li SY. Genotyping of Chlamydia trachomatis from clinical specimens in Taiwan. J Med Microbiol 2006; 55:301-308. [PMID: 16476794 DOI: 10.1099/jmm.0.46262-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study was conducted to determine the prevalence and distribution of Chlamydia trachomatis genotypes in Taiwan. Urine and endocervical-swab samples were collected from two hospitals located in northern and southern Taiwan. The genotypes of a total of 145 samples positive for C. trachomatis were analysed by sequencing the omp1 gene and this was successful in 102 samples. Nine different C. trachomatis genotypes were identified. Genotype E was the most prevalent (22 %), followed by D and Da (19 %), F (16 %), J (15 %), K (11 %), G (11 %), H (6 %) and Ba (2 %). There was a geographical difference in the prevalence of genotype H (P < 0.018) between northern and southern Taiwan. Sequence mutation analysis by blast searching against GenBank reference sequences identified 12 genetic variants from a total of 102 omp1 gene sequences.
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Affiliation(s)
- Min-Chih Hsu
- Laboratory for Bacteriology and Mycology, Center for Laboratory Research and Diagnostics, Center for Disease Control, Taipei, Taiwan
| | - Pei-Yi Tsai
- Laboratory for Bacteriology and Mycology, Center for Laboratory Research and Diagnostics, Center for Disease Control, Taipei, Taiwan
| | - Kow-Tong Chen
- Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Lan-Hui Li
- Taipei City Hospital, Branch for Disease Control & Prevention, Taipei, Taiwan
| | - Chien-Chou Chiang
- Taipei City Hospital, Branch for Disease Control & Prevention, Taipei, Taiwan
| | - Jih-Jin Tsai
- Chung-Ho Memorial Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Liang-Yin Ke
- Chung-Ho Memorial Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hour-Young Chen
- Laboratory for Bacteriology and Mycology, Center for Laboratory Research and Diagnostics, Center for Disease Control, Taipei, Taiwan
| | - Shu-Ying Li
- Laboratory for Bacteriology and Mycology, Center for Laboratory Research and Diagnostics, Center for Disease Control, Taipei, Taiwan
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26
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Maruyama F, Kenzaka T, Yamaguchi N, Tani K, Nasu M. Visualization and enumeration of bacteria carrying a specific gene sequence by in situ rolling circle amplification. Appl Environ Microbiol 2006; 71:7933-40. [PMID: 16332770 PMCID: PMC1317385 DOI: 10.1128/aem.71.12.7933-7940.2005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Rolling circle amplification (RCA) generates large single-stranded and tandem repeats of target DNA as amplicons. This technique was applied to in situ nucleic acid amplification (in situ RCA) to visualize and count single Escherichia coli cells carrying a specific gene sequence. The method features (i) one short target sequence (35 to 39 bp) that allows specific detection; (ii) maintaining constant fluorescent intensity of positive cells permeabilized extensively after amplicon detection by fluorescence in situ hybridization, which facilitates the detection of target bacteria in various physiological states; and (iii) reliable enumeration of target bacteria by concentration on a gelatin-coated membrane filter. To test our approach, the presence of the following genes were visualized by in situ RCA: green fluorescent protein gene, the ampicillin resistance gene and the replication origin region on multicopy pUC19 plasmid, as well as the single-copy Shiga-like toxin gene on chromosomes inside E. coli cells. Fluorescent antibody staining after in situ RCA also simultaneously identified cells harboring target genes and determined the specificity of in situ RCA. E. coli cells in a nonculturable state from a prolonged incubation were periodically sampled and used for plasmid uptake study. The numbers of cells taking up plasmids determined by in situ RCA was up to 10(6)-fold higher than that measured by selective plating. In addition, in situ RCA allowed the detection of cells taking up plasmids even when colony-forming cells were not detected during the incubation period. By optimizing the cell permeabilization condition for in situ RCA, this method can become a valuable tool for studying free DNA uptake, especially in nonculturable bacteria.
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Affiliation(s)
- Fumito Maruyama
- Environmental Science and Microbiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka 565-0871, Japan
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27
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28
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Hong H, Chun J, Lee Y. Detection of extended-spectrum beta-lactamase-producing, multidrug-resistant environmental isolates of Escherichia coli that bind to human bladder cells. Microb Drug Resist 2004; 10:184-9. [PMID: 15256035 DOI: 10.1089/1076629041310145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Compared to the number of studies examining extended-spectrum beta-lactamase (ESBL)-producing clinical isolates, environmental ESBL-producers have not been studied extensively. To investigate environmental ESBL-producing Escherichia coli, 22 cephalothin-resistant E. coli were isolated from Han River in Seoul, Korea. These isolates were resistant to ampicillin, cephalothin, and gentamicin, and 14 isolates among these were resistant to norfloxacin. All of these isolates produce AmpC and CMY, OXA, or TEM as determined by isoelectric point focusing (IEF) gel electrophoresis and PCR. One isolate (57-214) producing AmpC and OXA was resistant to all antibiotics (ampicillin, cephalothin, norfloxacin, gentamicin, cefotaxime, ceftazidime) tested in this study. Six isolates, including isolate 57-214, could adhere to T24 human bladder cells, and these isolates were not related to each other as shown with random amplified polymorphic DNA (RAPD). Results showed that environmental ESBL-producing E. coli is able to colonize in bladder cells and directly cause antibiotic-resistant urinary tract infection.
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Affiliation(s)
- Hyungin Hong
- Department of Biology and Culture Collection of Antimicrobial Resistant Microbes, Seoul Women's University, Seoul 139-774, Korea
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29
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van den Eede G, Aarts H, Buhk HJ, Corthier G, Flint HJ, Hammes W, Jacobsen B, Midtvedt T, van der Vossen J, von Wright A, Wackernagel W, Wilcks A. The relevance of gene transfer to the safety of food and feed derived from genetically modified (GM) plants. Food Chem Toxicol 2004; 42:1127-56. [PMID: 15123384 DOI: 10.1016/j.fct.2004.02.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2003] [Accepted: 02/04/2004] [Indexed: 12/31/2022]
Abstract
In 2000, the thematic network ENTRANSFOOD was launched to assess four different topics that are all related to the testing or assessment of food containing or produced from genetically modified organisms (GMOs). Each of the topics was linked to a European Commission (EC)-funded large shared cost action (see http://www.entransfood.com). Since the exchange of genetic information through horizontal (lateral) gene transfer (HGT) might play a more important role, in quantity and quality, than hitherto imagined, a working group dealing with HGT in the context of food and feed safety was established. This working group was linked to the GMOBILITY project (GMOBILITY, 2003) and the results of the deliberations are laid down in this review paper. HGT is reviewed in relation to the potential risks of consuming food or feed derived from transgenic crops. First, the mechanisms for obtaining transgenic crops are described. Next, HGT mechanisms and its possible evolutionary role are described. The use of marker genes is presented in detail as a special case for genes that may pose a risk. Furthermore, the exposure to GMOs and in particular to genetically modified (GM) deoxyribonucleic acid (DNA) is discussed as part of the total risk assessment. The review finishes off with a number of conclusions related to GM food and feed safety. The aim of this paper is to provide a comprehensive overview to assist risk assessors as well as regulators and the general public in understanding the safety issues related to these mechanisms.
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Affiliation(s)
- G van den Eede
- European Commission Directorate General Joint Research Centre, Institute for Health and Consumer Protection, Biotechnology and GMOs Unit, Via E. Fermi 1-T.P. 331, I-21020 Ispra (VA), Italy.
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30
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Abstract
For bacteria, the primary genetic barrier against the genetic exchange of DNA that is not self-transmissible is dissimilarity in the bacterial DNA sequences concerned. Genetic exchange by homologous recombination is frequent among close bacterial relatives and recent experiments have shown that it can enable the uptake of closely linked nonhomologous foreign DNA. Artificial vectors are mosaics of mobile DNA elements from free-living bacterial isolates and so bear a residual similarity to their ubiquitous natural progenitors. This homology is tightly linked to the multitude of different DNA sequences that are inserted into synthetic vectors. Can homology between vector and bacterial DNA enable the uptake of these foreign DNA inserts? In this review we investigate pUC18 as an example of an artificial vector and consider whether its homology to broad host-range antibiotic resistance transposons and plasmid origins of replication could enable the uptake of insert DNA in the light of studies of homology-facilitated foreign DNA uptake. We also discuss the disposal of recombinant DNA, its persistence in the environment and whether homologies to pUC18 may exist in naturally competent bacteria. Most DNA that is inserted into the cloning site of artificial vectors would be of little use to a bacterium, but perhaps not all.
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Affiliation(s)
- D Bensasson
- Evolutionary Genomics Department, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
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31
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Wilcks A, van Hoek AHAM, Joosten RG, Jacobsen BBL, Aarts HJM. Persistence of DNA studied in different ex vivo and in vivo rat models simulating the human gut situation. Food Chem Toxicol 2004; 42:493-502. [PMID: 14871592 DOI: 10.1016/j.fct.2003.10.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2003] [Accepted: 10/25/2003] [Indexed: 10/26/2022]
Abstract
This study aimed to evaluate the possibility of DNA sequences from genetically modified plants to persist in the gastrointestinal (GI) tract. PCR analysis and transformation assays were used to study DNA persistence and integrity in various ex vivo and in vivo systems using gnotobiotic rats. DNA studied was either plasmid DNA, naked plant DNA or plant DNA embedded in maize flour. Ex vivo experiments performed by incubating plant DNA in intestinal samples, showed that DNA is rapidly degraded in the upper part of the GI tract whereas degradation is less severe in the lower part. In contrast, plasmid DNA could be recovered throughout the GI tract when intestinal samples were taken up to 5 h after feeding rats with plasmid. Furthermore, DNA isolated from these intestinal samples was able to transform electro-competent Escherichia coli, showing that the plasmid was still biologically active. The results indicate that ingested DNA may persist in the GI tract and consequently may be present for uptake by intestinal bacteria.
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Affiliation(s)
- Andrea Wilcks
- Institute of Food Safety and Nutrition, Danish Veterinary and Food Administration, Mørkhøj Bygade 19, DK-2860 Søborg, Denmark.
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Mathers JJ, Clark SR, Hausmann D, Tillman P, Benning VR, Gordon SK. Inhibition of Resistance Plasmid Transfer in Escherichia coli by Ionophores, Chlortetracycline, Bacitracin, and Ionophore/Antimicrobial Combinations. Avian Dis 2004; 48:317-23. [PMID: 15283418 DOI: 10.1637/7105] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Medicinal feed additives bacitracin, chlortetracycline (CTC), laidlomycin, lasalocid, and salinomycin inhibited the transfer of multiresistance-conferring plasmid pBR325 (Tet(r) Amp(r) Cp(r), 6.0 kb) into selected gram-negative strains with the use of an in vitro model. High concentrations of ampicillin-sensitive competence-pretreated Escherichia coli HB 101 cells were exposed to 10% (v/v) of 1:10 dimethyl sulfoxide/agent : water containing test mixtures for 0.5 hr prior to plasmid addition and transforming conditions. Transformation was inhibited for all antimicrobials and showed a positive association wich higher concentration. Additional testing of ionophore compounds separately and in combination with bacitracin, chlortetracycline, lincomycin, roxarsone, tylosin, and virginiamycin at representative feed concentrations demonstrated 80.6% to >99.9% inhibition (P < 0.001) of resistance transfer. Bacitracin alone inhibited transformation within the range of 50-500 ppm. No increase in resistance transfer was observed when poultry-derived and reference gram-negative isolates having low or no transformation efficiency were additionally tested. The results suggest that these compounds, at relevant concentrations used in animal feed, may interfere with cell envelope-associated DNA uptake channels or other transformation competence mechanisms. Through these mechanisms, ionophores and cell membrane-interactive feed agents such as CTC and bacitracin may act to inhibit resistance transfer mechanisms within poultry and livestock.
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Affiliation(s)
- Jeremy J Mathers
- Alpharma, Inc., Animal Health Division, A400 State Street, Chicago Heights, IL 60411, USA
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Albert JM, Munakata-Marr J, Tenorio L, Siegrist RL. Statistical evaluation of bacterial source tracking data obtained by rep-PCR DNA fingerprinting of Escherichia coli. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2003; 37:4554-4560. [PMID: 14594360 DOI: 10.1021/es034211q] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Pattern recognition has been applied to environmental systems for identification of numerous pollution sources including aerosolized lead and petroleum hydrocarbons. In recent years, DNA fingerprinting has gained widespread application as a means to characterize genetic variations for such purposes as microbial source tracking. This approach, however, is strongly dependent on the statistical and image analyses applied. Several statistical analyses of rep-PCR DNA fingerprints were assessed as a means to differentiate between potential sources of fecal contamination. GelCompar II and methods based on penalized discriminant analysis (PDA) and k-nearest neighbors (KNN) classification procedures were used to differentiate between 10 source groups within a library containing DNA fingerprints of 548 Escherichia coli isolates from known human and nonhuman sources. KNN performed significantly better than PDA in a jackknife analysis, though the library was not large enough to detect significant differences between GelCompar II and the other two methods. GelCompar II and KNN both attained > or = 90% correct classification in a holdout procedure. In addition, interpoint distance analyses indicate coherency within source groups, while library randomization demonstrated that KNN does not create artificial groupings. This investigation stresses the need to understand limitations of statistical analyses used in pattern recognition of DNA fingerprints.
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Affiliation(s)
- John M Albert
- Environmental Science & Engineering Division and Department of Mathematical & Computer Sciences, Colorado School of Mines, Golden, Colorado 80401, USA
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Mammeri H, Poirel L, Mangeney N, Nordmann P. Chromosomal integration of a cephalosporinase gene from Acinetobacter baumannii into Oligella urethralis as a source of acquired resistance to beta-lactams. Antimicrob Agents Chemother 2003; 47:1536-42. [PMID: 12709319 PMCID: PMC153344 DOI: 10.1128/aac.47.5.1536-1542.2003] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clinical Oligella urethralis isolate COH-1, which was uncommonly resistant to penicillins and narrow-spectrum cephalosporins, was recovered from a 55-year-old patient with a urinary tract infection. Shotgun cloning into Escherichia coli and expression experiments gave recombinant clones expressing either an AmpC beta-lactamase-type phenotype of resistance or a carbenicillin-hydrolyzing beta-lactamase-type phenotype of resistance. The AmpC beta-lactamase identified (ABA-1), which had a pI value of 8.2, had 98% amino acid identity with a chromosomally encoded cephalosporinase of Acinetobacter baumannii. A 820-bp insertion sequence element, ISOur1, belonging to the IS6 family of insertion sequence elements, was identified immediately upstream of bla(ABA-1), providing a -35 promoter sequence and likely giving rise to a hybrid promoter region. The carbenicillin-hydrolyzing beta-lactamase identified (CARB-8), which had a pI value of 6.4, differed from CARB-5 by two amino acid substitutions. Hybridization of CeuI fragment I-restricted DNA fragments of O. urethralis COH-1 with bla(ABA-1)-, bla(CARB-8)-, and 16S rRNA-specific probes indicated the chromosomal integration of the beta-lactamase genes. PCR and hybridization experiments failed to detect bla(CARB-8)- and bla(ABA-1)-like genes in three O. urethralis reference strains, indicating that the beta-lactamase genes identified were the source of acquired resistance in O. urethralis COH-1. This is one of the few examples of the interspecies transfer and the chromosomal integration of a gene encoding a naturally occurring beta-lactamase.
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Affiliation(s)
- Hedi Mammeri
- Service de Bactériologie-Virologie, Hôpital de Bicêtre, Assistance Publique/Hôpitaux de Paris, Faculté de Médecine Paris-Sud, 94275 Le Kremlin-Bicêtre, France
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