1
|
Montelongo Hernandez C, Putonti C, Wolfe AJ. Urinary Plasmids Reduce Permissivity to Coliphage Infection. Microbiol Spectr 2023; 11:e0130923. [PMID: 37409956 PMCID: PMC10433841 DOI: 10.1128/spectrum.01309-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
The microbial community of the urinary tract (urinary microbiota or urobiota) has been associated with human health. Bacteriophages (phages) and plasmids present in the urinary tract, like in other niches, may shape urinary bacterial dynamics. While urinary Escherichia coli strains associated with urinary tract infection (UTI) and their phages have been catalogued for the urobiome, bacterium-plasmid-phage interactions have yet to be explored. In this study, we characterized urinary E. coli plasmids and their ability to decrease permissivity to E. coli phage (coliphage) infection. Putative F plasmids were predicted in 47 of 67 urinary E. coli isolates, and most of these plasmids carried genes that encode toxin-antitoxin (TA) modules, antibiotic resistance, and/or virulence. Urinary E. coli plasmids, from urinary microbiota strains UMB0928 and UMB1284, were conjugated into E. coli K-12 strains. These transconjugants included genes for antibiotic resistance and virulence, and they decreased permissivity to coliphage infection by the laboratory phage P1vir and the urinary phages Greed and Lust. Plasmids in one transconjugant were maintained in E. coli K-12 for up to 10 days in the absence of antibiotic resistance selection; this included the maintenance of the antibiotic resistance phenotype and decreased permissivity to phage. Finally, we discuss how F plasmids present in urinary E. coli strains could play a role in coliphage dynamics and the maintenance of antibiotic resistance in urinary E. coli. IMPORTANCE The urinary tract contains a resident microbial community called the urinary microbiota or urobiota. Evidence exists that it is associated with human health. Bacteriophages (phages) and plasmids present in the urinary tract, like in other niches, may shape urinary bacterial dynamics. Bacterium-plasmid-phage interactions have been studied primarily in laboratory settings and are yet to be thoroughly tested in complex communities. This is especially true of the urinary tract, where the bacterial genetic determinants of phage infection are not well understood. In this study, we characterized urinary E. coli plasmids and their ability to decrease permissivity to E. coli phage (coliphage) infection. Urinary E. coli plasmids, encoding antibiotic resistance and transferred by conjugation into naive laboratory E. coli K-12 strains, decreased permissivity to coliphage infection. We propose a model by which urinary plasmids present in urinary E. coli strains could help to decrease phage infection susceptibility and maintain the antibiotic resistance of urinary E. coli. This has consequences for phage therapy, which could inadvertently select for plasmids that encode antibiotic resistance.
Collapse
Affiliation(s)
- Cesar Montelongo Hernandez
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| |
Collapse
|
2
|
Sundaramoorthy NS, Shankaran P, Gopalan V, Nagarajan S. New tools to mitigate drug resistance in Enterobacteriaceae - Escherichia coli and Klebsiella pneumoniae. Crit Rev Microbiol 2022:1-20. [PMID: 35649163 DOI: 10.1080/1040841x.2022.2080525] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Treatment to common bacterial infections are becoming ineffective of late, owing to the emergence and dissemination of antibiotic resistance globally. Escherichia coli and Klebsiella pneumoniae are the most notorious microorganisms and are among the critical priority pathogens listed by WHO in 2017. These pathogens are the predominant cause of sepsis, urinary tract infections (UTIs), pneumonia, meningitis and pyogenic liver abscess. Concern arises due to the resistance of bacteria to most of the beta lactam antibiotics like penicillin, cephalosporin, monobactams and carbapenems, even to the last resort antibiotics like colistin. Preventing influx by modulation of porins, extruding the antibiotics by overexpression of efflux pumps, mutations of drug targets/receptors, biofilm formation, altering the drug molecules and rendering them ineffective are few resistance mechanisms that are adapted by Enterobacteriaeceae upon exposure to antibiotics. The situation is exacerbated due to the process of horizontal gene transfer (HGT), wherein the genes encoding resistance mechanisms are transferred to the neighbouring bacteria through plasmids/phages/uptake of free DNA. Carbapenemases, other beta lactamases and mcr genes coding for colistin resistance are widely disseminated leading to limited/no therapeutic options against those infections. Development of new antibiotics can be viewed as a possible solution but it involves major investment, time and labour despite which, the bacteria can easily adapt to the new antibiotic and evolve resistance in a relatively short time. Targeting the resistance mechanisms can be one feasible alternative to tackle these multidrug resistant (MDR) pathogens. Removal of plasmid (plasmid curing) causing resistance, use of bacteriophages and bacteriotherapy can be other potential approaches to combat infections caused by MDR E. coli and K. pneumoniae. The present review discusses the efficacies of these therapies in mitigating these infections, which can be potentially used as an adjuvant therapy along with existing antibiotics.
Collapse
Affiliation(s)
- Niranjana Sri Sundaramoorthy
- Center for Research on Infectious Diseases, School of Chemical and Biotechnology, SASTRA deemed University, Thanjavur, Tamil Nadu, India
| | - Prakash Shankaran
- Center for Research on Infectious Diseases, School of Chemical and Biotechnology, SASTRA deemed University, Thanjavur, Tamil Nadu, India
| | - Vidhya Gopalan
- Department of Virology, Kings Institute of Preventative Medicine, Guindy, Chennai, Tamil Nadu, India
| | - Saisubramanian Nagarajan
- Center for Research on Infectious Diseases, School of Chemical and Biotechnology, SASTRA deemed University, Thanjavur, Tamil Nadu, India
| |
Collapse
|
3
|
Heiden SE, Sydow K, Schaefer S, Klempien I, Balau V, Bauer P, Hübner NO, Schaufler K. Nearly Identical Plasmids Encoding VIM-1 and Mercury Resistance in Enterobacteriaceae from North-Eastern Germany. Microorganisms 2021; 9:microorganisms9071345. [PMID: 34206177 PMCID: PMC8305640 DOI: 10.3390/microorganisms9071345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/11/2022] Open
Abstract
The emergence of carbapenemase-producing Enterobacteriaceae limits therapeutic options and presents a major public health problem. Resistances to carbapenems are mostly conveyed by metallo-beta-lactamases (MBL) including VIM, which are often encoded on resistance plasmids. We characterized four VIM-positive isolates that were obtained as part of a routine diagnostic screening from two laboratories in north-eastern Germany between June and August 2020. Whole-genome sequencing was performed to address (a) phylogenetic properties, (b) plasmid content, and (c) resistance gene carriage. In addition, we performed phenotypic antibiotic and mercury resistance analyses. The genomic analysis revealed three different bacterial species including C. freundii, E. coli and K. oxytoca with four different sequence types. All isolates were geno- and phenotypically multidrug-resistant (MDR) and the phenotypic profile was explained by the underlying resistance gene content. Three isolates of four carried nearly identical VIM-1-resistance plasmids, which in addition encoded a mercury resistance operon and showed some similarity to two publicly available plasmid sequences from sources other than the two laboratories above. Our results highlight the circulation of a nearly identical IncN-type VIM-1-resistance plasmid in different Enterobacteriaceae in north-eastern Germany.
Collapse
Affiliation(s)
- Stefan E. Heiden
- Pharmaceutical Microbiology, University of Greifswald, 17489 Greifswald, Germany; (S.E.H.); (K.S.)
| | - Katharina Sydow
- Pharmaceutical Microbiology, University of Greifswald, 17489 Greifswald, Germany; (S.E.H.); (K.S.)
| | - Stephan Schaefer
- MVZ Laboratory Limbach Vorpommern-Rügen, 18435 Stralsund, Germany;
| | - Ingo Klempien
- Klinische Hygiene und Infektiologie, Helios Hanseklinikum, 18435 Stralsund, Germany;
| | - Veronika Balau
- IMD Laboratory Greifswald, Institute of Medical Diagnostics, 17493 Greifswald, Germany;
| | | | - Nils-Olaf Hübner
- Central Unit for Infection Prevention and Control, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Katharina Schaufler
- Pharmaceutical Microbiology, University of Greifswald, 17489 Greifswald, Germany; (S.E.H.); (K.S.)
- Correspondence: ; Tel.: +49-38344204869
| |
Collapse
|
4
|
Heiden SE, Hübner NO, Bohnert JA, Heidecke CD, Kramer A, Balau V, Gierer W, Schaefer S, Eckmanns T, Gatermann S, Eger E, Guenther S, Becker K, Schaufler K. A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition. Genome Med 2020; 12:113. [PMID: 33298160 PMCID: PMC7724794 DOI: 10.1186/s13073-020-00814-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Antibiotic-resistant Klebsiella pneumoniae are a major cause of hospital- and community-acquired infections, including sepsis, liver abscess, and pneumonia, driven mainly by the emergence of successful high-risk clonal lineages. The K. pneumoniae sequence type (ST) 307 lineage has appeared in several different parts of the world after first being described in Europe in 2008. From June to October 2019, we recorded an outbreak of an extensively drug-resistant ST307 lineage in four medical facilities in north-eastern Germany. METHODS Here, we investigated these isolates and those from subsequent cases in the same facilities. We performed whole-genome sequencing to study phylogenetics, microevolution, and plasmid transmission, as well as phenotypic experiments including growth curves, hypermucoviscosity, siderophore secretion, biofilm formation, desiccation resilience, serum survival, and heavy metal resistance for an in-depth characterization of this outbreak clone. RESULTS Phylogenetics suggest a homogenous phylogram with several sub-clades containing either isolates from only one patient or isolates originating from different patients, suggesting inter-patient transmission. We identified three large resistance plasmids, carrying either NDM-1, CTX-M-15, or OXA-48, which K. pneumoniae ST307 likely donated to other K. pneumoniae isolates of different STs and even other bacterial species (e.g., Enterobacter cloacae) within the clinical settings. Several chromosomally and plasmid-encoded, hypervirulence-associated virulence factors (e.g., yersiniabactin, metabolite transporter, aerobactin, and heavy metal resistance genes) were identified in addition. While growth, biofilm formation, desiccation resilience, serum survival, and heavy metal resistance were comparable to several control strains, results from siderophore secretion and hypermucoviscosity experiments revealed superiority of the ST307 clone, similar to an archetypical, hypervirulent K. pneumoniae strain (hvKP1). CONCLUSIONS The combination of extensive drug resistance and virulence, partly conferred through a "mosaic" plasmid carrying both antibiotic resistance and hypervirulence-associated features, demonstrates serious public health implications.
Collapse
Affiliation(s)
- Stefan E Heiden
- Institute of Pharmacy, Pharmaceutical Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany
| | - Nils-Olaf Hübner
- Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Jürgen A Bohnert
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Claus-Dieter Heidecke
- Department of General, Visceral, Thoracic and Vascular Surgery, University Medicine Greifswald, Greifswald, Germany
| | - Axel Kramer
- Institute for Hygiene and Environmental Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Veronika Balau
- IMD Laboratory Greifswald, Institute of Medical Diagnostics, Greifswald, Germany
| | | | | | - Tim Eckmanns
- Department for Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Sören Gatermann
- National Reference Centre for Multidrug-Resistant Gram-Negative Bacteria, Ruhr University Bochum, Bochum, Germany
| | - Elias Eger
- Institute of Pharmacy, Pharmaceutical Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany
| | - Sebastian Guenther
- Institute of Pharmacy, Pharmaceutical Biology, University of Greifswald, Greifswald, Germany
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Katharina Schaufler
- Institute of Pharmacy, Pharmaceutical Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany.
| |
Collapse
|
5
|
Schierack P, Heiden SE, Khan MM, Nikolaus L, Kolenda R, Stubbe M, Lkhagvasuren D, Rödiger S, Guenther S, Schaufler K. Genomic and Phenotypic Analysis of an ESBL-Producing E. coli ST1159 Clonal Lineage From Wild Birds in Mongolia. Front Microbiol 2020; 11:1699. [PMID: 32793163 PMCID: PMC7385280 DOI: 10.3389/fmicb.2020.01699] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/29/2020] [Indexed: 12/05/2022] Open
Abstract
Background In addition to the broad dissemination of pathogenic extended-spectrum beta-lactamase (ESBL)-producing Escherichia (E.) coli in human and veterinary medicine and the community, their occurrence in wildlife and the environment is a growing concern. Wild birds in particular often carry clinically relevant ESBL-producing E. coli. Objectives We analyzed ESBL-producing and non-ESBL-producing E. coli obtained from wild birds in Mongolia to identify phylogenetic and functional characteristics that would explain the predominance of a particular E. coli clonal lineage in this area. Methods We investigated ESBL-producing E. coli using whole-genome sequencing and phylogenetics to describe the population structure, resistance and virulence features and performed phenotypic experiments like biofilm formation and adhesion to epithelial cells. We compared the phenotypic characteristics to non-ESBL-producing E. coli from the same background (Mongolian wild birds) and genomic results to publicly available genomes. Results and Conclusion We found ESBL-producing E. coli sequence type (ST) 1159 among wild birds in Mongolia. This clonal lineage carried virulence features typical for extra-intestinal pathogenic or enterotoxigenic E. coli. Comparative functional experiments suggested no burden of resistance in the ST1159 isolates, which is despite their carriage of ESBL-plasmids. Wild birds will likely disseminate these antibiotic-resistant pathogens further during migration.
Collapse
Affiliation(s)
- Peter Schierack
- Multiparametric Diagnostics, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany
| | - Stefan E Heiden
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Muhammad Moman Khan
- Multiparametric Diagnostics, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany
| | - Lena Nikolaus
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Rafal Kolenda
- Multiparametric Diagnostics, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany
| | - Michael Stubbe
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Davaa Lkhagvasuren
- Department of Biology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Stefan Rödiger
- Multiparametric Diagnostics, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Senftenberg, Germany
| | | | | |
Collapse
|
6
|
ESBL-plasmid carriage in E. coli enhances in vitro bacterial competition fitness and serum resistance in some strains of pandemic sequence types without overall fitness cost. Gut Pathog 2018; 10:24. [PMID: 29983750 PMCID: PMC6003029 DOI: 10.1186/s13099-018-0243-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/13/2018] [Indexed: 12/26/2022] Open
Abstract
Background Extended spectrum beta lactamase (ESBL)-producing extraintestinal pathogenic Escherichia coli infections are of global interest because of their clinical and economic impact. The ESBL resistance genes disseminate through plasmids, and are found in successful global lineages such as ST131 and ST648. The carriage of plasmids has been suggested to result in a fitness burden, but recently it was shown that ESBL-plasmids enhanced virulence in pandemic ST131 and ST648 lineages without affecting their fitness. Herein, we investigated the influence of ESBL-plasmids on bacterial competition and serum resistance, both of which are essential characteristics of ExPEC during infections. Methods Triplets of ESBL-plasmid-carrying wildtype (WT), plasmid-cured variant (PCV) and transformant (T) of five ExPEC strains of ST131 and ST648 were used for bacterial competition experiments with colicin-producing commensal E. coli, competitive adhesion experiments and serum survival. In addition, resilience after SDS, acid, osmotic challenges and RNA sequence data were analyzed. Results In all five strains tested, ESBL-plasmid carriage did not negatively influence E. coli fitness in direct bacterial competition with commensal E. coli in vitro. That is, WTs did not show any disadvantages when compared to their isogenic plasmid-free PCV. For one strain we even found the opposite as PCV17433 was out-competed by a commensal strain, which suggests an even protective role of the ESBL-plasmid carried by the WT17433. Similarly, in the serum-resistance experiments, the PCVs of two strains (PCV17433 and PCV17887) were more sensitive to serum, unlike WTs and Ts. The observed inter-strain differences could be explained by the different genetic content of plasmids carried in those strains. Conclusions Overall, we found no compelling evidence for an increased burden resulting from the carriage of ESBL-plasmids in the absence of antimicrobial selection pressure in the strains of pandemic ST131 and ST648; rather, the possession of certain ESBL-plasmids was beneficial for some strains in regarding competition fitness and serum survival. Electronic supplementary material The online version of this article (10.1186/s13099-018-0243-z) contains supplementary material, which is available to authorized users.
Collapse
|
7
|
Jiang X, Liu X, Law COK, Wang Y, Lo WU, Weng X, Chan TF, Ho PL, Lau TCK. The CTX-M-14 plasmid pHK01 encodes novel small RNAs and influences host growth and motility. FEMS Microbiol Ecol 2017; 93:3940222. [DOI: 10.1093/femsec/fix090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/07/2017] [Indexed: 01/24/2023] Open
Affiliation(s)
- Xinlei Jiang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Xuan Liu
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Carmen O. K. Law
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Ya Wang
- Department of Microbiology, University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region
| | - Wai U Lo
- Department of Microbiology, University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region
| | - Xing Weng
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Ting Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - P. L. Ho
- Department of Microbiology, University of Hong Kong, Hong Kong, Hong Kong Special Administrative Region
| | - Terrence C. K. Lau
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| |
Collapse
|
8
|
Kamruzzaman M, Shoma S, Thomas CM, Partridge SR, Iredell JR. Plasmid interference for curing antibiotic resistance plasmids in vivo. PLoS One 2017; 12:e0172913. [PMID: 28245276 PMCID: PMC5330492 DOI: 10.1371/journal.pone.0172913] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/10/2017] [Indexed: 11/21/2022] Open
Abstract
Antibiotic resistance increases the likelihood of death from infection by common pathogens such as Escherichia coli and Klebsiella pneumoniae in developed and developing countries alike. Most important modern antibiotic resistance genes spread between such species on self-transmissible (conjugative) plasmids. These plasmids are traditionally grouped on the basis of replicon incompatibility (Inc), which prevents coexistence of related plasmids in the same cell. These plasmids also use post-segregational killing (‘addiction’) systems, which poison any bacterial cells that lose the addictive plasmid, to guarantee their own survival. This study demonstrates that plasmid incompatibilities and addiction systems can be exploited to achieve the safe and complete eradication of antibiotic resistance from bacteria in vitro and in the mouse gut. Conjugative ‘interference plasmids’ were constructed by specifically deleting toxin and antibiotic resistance genes from target plasmids. These interference plasmids efficiently cured the corresponding antibiotic resistant target plasmid from different Enterobacteriaceae in vitro and restored antibiotic susceptibility in vivo to all bacterial populations into which plasmid-mediated resistance had spread. This approach might allow eradication of emergent or established populations of resistance plasmids in individuals at risk of severe sepsis, enabling subsequent use of less toxic and/or more effective antibiotics than would otherwise be possible, if sepsis develops. The generalisability of this approach and its potential applications in bioremediation of animal and environmental microbiomes should now be systematically explored.
Collapse
Affiliation(s)
- Muhammad Kamruzzaman
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
| | - Shereen Shoma
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
| | - Christopher M. Thomas
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Sally R. Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
- Westmead Hospital, Westmead, New South Wales, Australia
| | - Jonathan R. Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
- Westmead Hospital, Westmead, New South Wales, Australia
- * E-mail:
| |
Collapse
|
9
|
Description of the First Escherichia coli Clinical Isolate Harboring the Colistin Resistance Gene mcr-1 from the Indian Subcontinent. Antimicrob Agents Chemother 2016; 61:AAC.01945-16. [PMID: 27795381 DOI: 10.1128/aac.01945-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
10
|
Shubin M, Schaufler K, Tedin K, Vehkala M, Corander J. Identifying Multiple Potential Metabolic Cycles in Time-Series from Biolog Experiments. PLoS One 2016; 11:e0162276. [PMID: 27676629 PMCID: PMC5038949 DOI: 10.1371/journal.pone.0162276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 08/20/2016] [Indexed: 11/26/2022] Open
Abstract
Biolog Phenotype Microarray (PM) is a technology allowing simultaneous screening of the metabolic behaviour of bacteria under a large number of different conditions. Bacteria may often undergo several cycles of metabolic activity during a Biolog experiment. We introduce a novel algorithm to identify these metabolic cycles in PM experimental data, thus increasing the potential of PM technology in microbiology. Our method is based on a statistical decomposition of the time-series measurements into a set of growth models. We show that the method is robust to measurement noise and captures accurately the biologically relevant signals from the data. Our implementation is made freely available as a part of an R package for PM data analysis and can be found at www.helsinki.fi/bsg/software/Biolog_Decomposition.
Collapse
Affiliation(s)
- Mikhail Shubin
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Katharina Schaufler
- Institute of Microbiology and Epizootics, Freie Univerität Berlin, Berlin, Germany
| | - Karsten Tedin
- Institute of Microbiology and Epizootics, Freie Univerität Berlin, Berlin, Germany
| | - Minna Vehkala
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Faculty of Medicine, University of Oslo, Oslo, Norway
| |
Collapse
|
11
|
Toxin-Antitoxin Systems in Clinical Pathogens. Toxins (Basel) 2016; 8:toxins8070227. [PMID: 27447671 PMCID: PMC4963858 DOI: 10.3390/toxins8070227] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/07/2016] [Indexed: 12/17/2022] Open
Abstract
Toxin-antitoxin (TA) systems are prevalent in bacteria and archaea. Although not essential for normal cell growth, TA systems are implicated in multiple cellular functions associated with survival under stress conditions. Clinical strains of bacteria are currently causing major human health problems as a result of their multidrug resistance, persistence and strong pathogenicity. Here, we present a review of the TA systems described to date and their biological role in human pathogens belonging to the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) and others of clinical relevance (Escherichia coli, Burkholderia spp., Streptococcus spp. and Mycobacterium tuberculosis). Better understanding of the mechanisms of action of TA systems will enable the development of new lines of treatment for infections caused by the above-mentioned pathogens.
Collapse
|
12
|
Schaufler K, Semmler T, Pickard DJ, de Toro M, de la Cruz F, Wieler LH, Ewers C, Guenther S. Carriage of Extended-Spectrum Beta-Lactamase-Plasmids Does Not Reduce Fitness but Enhances Virulence in Some Strains of Pandemic E. coli Lineages. Front Microbiol 2016; 7:336. [PMID: 27014251 PMCID: PMC4794485 DOI: 10.3389/fmicb.2016.00336] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/03/2016] [Indexed: 11/20/2022] Open
Abstract
Pathogenic ESBL-producing E. coli lineages occur frequently worldwide, not only in a human health context but in animals and the environment, also in settings with low antimicrobial pressures. This study investigated the fitness costs of ESBL-plasmids and their influence on chromosomally encoded features associated with virulence, such as those involved in the planktonic and sessile behaviors of ST131 and ST648 E. coli. ESBL-plasmid-carrying wild-type E. coli strains, their corresponding ESBL-plasmid-“cured” variants (PCV), and complementary ESBL-carrying transformants were comparatively analyzed using growth curves, Omnilog® phenotype microarray (PM) assays, macrocolony and biofilm formation, swimming motility, and RNA sequence analysis. Growth curves and PM results pointed toward similar growth and metabolic behaviors among the strains. Phenotypic differences in some strains were detected, including enhanced curli fimbriae and/or cellulose production as well as a reduced swimming capacity of some ESBL-carrying strains, as compared to their respective PCVs. RNA sequencing mostly confirmed the phenotypic results, suggesting that the chromosomally encoded csgD pathway is a key factor involved. These results contradict the hypothesis that ESBL-plasmid-carriage leads to a fitness loss in ESBL-carrying strains. Instead, the results indicate an influence of some ESBL-plasmids on chromosomally encoded features associated with virulence in some E. coli strains. In conclusion, apart from antibiotic resistance selective advantages, ESBL-plasmid-carriage may also lead to enhanced virulence or adaption to specific habitats in some strains of pandemic ESBL-producing E. coli lineages.
Collapse
Affiliation(s)
- Katharina Schaufler
- Veterinary Faculty, Institute of Microbiology and Epizootics, Freie Universität Berlin Berlin, Germany
| | - Torsten Semmler
- Veterinary Faculty, Institute of Microbiology and Epizootics, Freie Universität BerlinBerlin, Germany; Robert Koch InstituteBerlin, Germany
| | | | - María de Toro
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria (UC-SODERCAN-CSIC), Universidad de Cantabria Santander, Spain
| | - Fernando de la Cruz
- Departamento de Biología Molecular, Instituto de Biomedicina y Biotecnología de Cantabria (UC-SODERCAN-CSIC), Universidad de Cantabria Santander, Spain
| | - Lothar H Wieler
- Veterinary Faculty, Institute of Microbiology and Epizootics, Freie Universität BerlinBerlin, Germany; Robert Koch InstituteBerlin, Germany
| | - Christa Ewers
- Veterinary Faculty, Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-Universität Giessen Giessen, Germany
| | - Sebastian Guenther
- Veterinary Faculty, Institute of Microbiology and Epizootics, Freie Universität Berlin Berlin, Germany
| |
Collapse
|
13
|
Schaufler K, Semmler T, Wieler LH, Wöhrmann M, Baddam R, Ahmed N, Müller K, Kola A, Fruth A, Ewers C, Guenther S. Clonal spread and interspecies transmission of clinically relevant ESBL-producing Escherichia coli of ST410--another successful pandemic clone? FEMS Microbiol Ecol 2015; 92:fiv155. [PMID: 26656065 DOI: 10.1093/femsec/fiv155] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2015] [Indexed: 12/23/2022] Open
Abstract
Clinically relevant extended-spectrum beta-lactamase (ESBL)-producing multi-resistant Escherichia coli have been on the rise for years. Initially restricted to mostly a clinical context, recent findings prove their prevalence in extraclinical settings independent of the original occurrence of antimicrobial resistance in the environment. To get further insights into the complex ecology of potentially clinically relevant ESBL-producing E. coli, 24 isolates from wild birds in Berlin, Germany, and 40 ESBL-producing human clinical E. coli isolates were comparatively analyzed. Isolates of ST410 occurred in both sample groups (six). In addition, three ESBL-producing E. coli isolates of ST410 from environmental dog feces and one clinical dog isolate were included. All 10 isolates were clonally analyzed showing almost identical macrorestriction patterns. They were chosen for whole-genome sequencing revealing that the whole-genome content of these 10 E. coli isolates showed a very high genetic similarity, differing by low numbers of single nucleotide polymorphisms only. This study gives initial evidence for a recent interspecies transmission of a new successful clone of ST410 E. coli between wildlife, humans, companion animals and the environment. The results underline the zoonotic potential of clinically relevant multi-resistant bacteria found in the environment as well as the mandatory nature of the 'One Health' approach.
Collapse
Affiliation(s)
- Katharina Schaufler
- Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, 14163 Berlin, Germany
| | - Torsten Semmler
- NG 1 - Microbial Genomics, Robert Koch Institute, 13302 Berlin, Germany
| | | | - Michael Wöhrmann
- Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, 14163 Berlin, Germany
| | - Ramani Baddam
- Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, 14163 Berlin, Germany Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, 500046 Hyderabad, India
| | - Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, 500046 Hyderabad, India
| | - Kerstin Müller
- Clinic of Small Animals, Veterinary Faculty, Freie Universität Berlin, 14163 Berlin, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité Universitätsklinikum, 12203 Berlin, Germany
| | - Angelika Fruth
- Department for Infectious Diseases, Division of Bacterial Infections and National Reference, Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, 38855 Wernigerode, Germany
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Veterinary Faculty, Justus-Liebig-Universität Giessen, 35392 Giessen, Germany
| | - Sebastian Guenther
- Institute of Microbiology and Epizootics, Veterinary Faculty, Freie Universität Berlin, 14163 Berlin, Germany
| |
Collapse
|
14
|
Plasmid-Mediated OqxAB Is an Important Mechanism for Nitrofurantoin Resistance in Escherichia coli. Antimicrob Agents Chemother 2015; 60:537-43. [PMID: 26552976 DOI: 10.1128/aac.02156-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/03/2015] [Indexed: 11/20/2022] Open
Abstract
Increasing consumption of nitrofurantoin (NIT) for treatment of acute uncomplicated urinary tract infections (UTI) highlights the need to monitor emerging NIT resistance mechanisms. This study investigated the molecular epidemiology of the multidrug-resistant efflux gene oqxAB and its contribution to nitrofurantoin resistance by using Escherichia coli isolates originating from patients with UTI (n = 205; collected in 2004 to 2013) and food-producing animals (n = 136; collected in 2012 to 2013) in Hong Kong. The oqxAB gene was highly prevalent among NIT-intermediate (11.5% to 45.5%) and -resistant (39.2% to 65.5%) isolates but rare (0% to 1.7%) among NIT-susceptible (NIT-S) isolates. In our isolates, the oqxAB gene was associated with IS26 and was carried by plasmids of diverse replicon types. Multilocus sequence typing revealed that the clones of oqxAB-positive E. coli were diverse. The combination of oqxAB and nfsA mutations was found to be sufficient for high-level NIT resistance. Curing of oqxAB-carrying plasmids from 20 NIT-intermediate/resistant UTI isolates markedly reduced the geometric mean MIC of NIT from 168.9 μg/ml to 34.3 μg/ml. In the plasmid-cured variants, 20% (1/5) of isolates with nfsA mutations were NIT-S, while 80% (12/15) of isolates without nfsA mutations were NIT-S (P = 0.015). The presence of plasmid-based oqxAB increased the mutation prevention concentration of NIT from 128 μg/ml to 256 μg/ml and facilitated the development of clinically important levels of nitrofurantoin resistance. In conclusion, plasmid-mediated oqxAB is an important nitrofurantoin resistance mechanism. There is a great need to monitor the dissemination of this transferable multidrug-resistant efflux pump.
Collapse
|
15
|
Wang J, Stephan R, Zurfluh K, Hächler H, Fanning S. Characterization of the genetic environment of bla ESBL genes, integrons and toxin-antitoxin systems identified on large transferrable plasmids in multi-drug resistant Escherichia coli. Front Microbiol 2015; 5:716. [PMID: 25610429 PMCID: PMC4285173 DOI: 10.3389/fmicb.2014.00716] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/01/2014] [Indexed: 01/08/2023] Open
Abstract
Objectives: Previously 14 conjugative plasmids from multi-drug resistant (MDR) Escherichia coli from healthy humans and food-producing animals in Switzerland were sequenced. The aim of this study was to extend the genetic characterization of these plasmids with a focus on blaESBL genes including blaCTX-M-1 and blaTEM, class 1 integrons and toxin-antitoxin (TA) systems contained therein. Methods: The nucleotide sequences and subsequent annotation therein of 14 conjugative plasmids were previously determined from their corresponding transconjugants. The TA loci were confirmed by RASTA-Bacteria. Results: Eight of the conjugative plasmids identified were found to encode genes expressing ESBLs. Structural heterogeneity was noted in the regions flanking both the blaCTX-M-1 and blaTEM genes. The blaCTX-M-1 genes were associated with the common insertion sequences ISEcp1 and IS26, and uniquely with an IS5 element in one case; while blaTEM genes were found to be associated with IS26 and Tn2. A new blaTEM-210 gene was identified. Seven class 1 integrons were also identified and assigned into 3 groups, denoted as In54, In369 and In501. Sixteen TA loci belonging to 4 of the TA gene families (relBE, vapBC, ccd and mazEF) were identified on 11 of these plasmids. Conclusions: Comparative sequence analysis of these plasmids provided data on the structures likely to contribute to sequence diversity associated with these accessory genes, including IS26, ISEcp1 and Tn2. All of them contribute to the dissemination of the corresponding resistance genes located on the different plasmids. There appears to be no association between β-lactam encoding genes and TA systems.
Collapse
Affiliation(s)
- Juan Wang
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin Dublin, Ireland
| | - Roger Stephan
- Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zurich Zürich, Switzerland
| | - Katrin Zurfluh
- Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zurich Zürich, Switzerland
| | - Herbert Hächler
- Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zurich Zürich, Switzerland
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin Dublin, Ireland ; School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast Belfast, UK
| |
Collapse
|