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Azuma N. Manipulation and analysis of large DNA molecules by controlling their dynamics using micro and nanogaps. Biosci Biotechnol Biochem 2025; 89:508-514. [PMID: 39611351 DOI: 10.1093/bbb/zbae179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2024] [Accepted: 11/18/2024] [Indexed: 11/30/2024]
Abstract
Manipulation and analysis methods for large DNAs are critical for epidemiological, clinical, diagnostic, and fundamental research on bacteria, membrane vesicles, plants, yeast, and human cells. However, the physical properties of large DNAs often challenge their manipulation and analysis with high accuracy and speed using conventional methods such as gel electrophoresis and column-based methods. This review presents the approaches that leverage micrometer- and nanometer-sized gaps within microchannels to control the dynamics and conformations of large DNAs, thereby overcoming these challenges. By designing gap structures and migration conditions based on the relationship between gap parameters and the physical characteristics of large DNAs-such as diameter and persistence length-these methods enable swifter and more precise manipulation and analysis of large DNAs, including size separation, concentration, purification, and single-molecule analysis.
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Affiliation(s)
- Naoki Azuma
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Nagoya, Japan
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2
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Chong SW, Shen Y, Palomba S, Vigolo D. Nanofluidic Lab-On-A-Chip Systems for Biosensing in Healthcare. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2025; 21:e2407478. [PMID: 39491535 DOI: 10.1002/smll.202407478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Revised: 10/21/2024] [Indexed: 11/05/2024]
Abstract
Biosensing plays a vital role in healthcare monitoring, disease detection, and treatment planning. In recent years, nanofluidic technology has been increasingly explored to be developed into lab-on-a-chip biosensing systems. Given now the possibility of fabricating geometrically defined nanometric channels that are commensurate with the size of many biomolecules, nanofluidic-based devices are likely to become a key technology for the analysis of various clinical biomarkers, including DNA (deoxyribonucleic acid) and proteins in liquid biopsies. This review summarizes the fundamentals and technological advances of nanofluidics from the purview of single-molecule analysis, detection of low-abundance molecules, and single-cell analysis at the subcellular level. The extreme confinement and dominant surface charge effects in nanochannels provide unique advantages to nanofluidic devices for the manipulation and transport of target biomarkers. When coupled to a microfluidic network to facilitate sample introduction, integrated micro-nanofluidic biosensing devices are proving to be more sensitive and specific in molecular analysis compared to conventional assays in many cases. Based on recent progress in nanofluidics and current clinical trends, the review concludes with a discussion of near-term challenges and future directions for the development of nanofluidic-based biosensing systems toward enabling a new wave of lab-on-a-chip technology for personalized and preventive medicine.
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Affiliation(s)
- Shin Wei Chong
- School of Biomedical Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Yi Shen
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Stefano Palomba
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Physics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Daniele Vigolo
- School of Biomedical Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, 2006, Australia
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3
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Wranne MS, Karami N, Kk S, Jaén-Luchoro D, Yazdanshenas S, Lin YL, Kabbinale A, Flach CF, Westerlund F, Åhrén C. Comparison of CTX-M encoding plasmids present during the early phase of the ESBL pandemic in western Sweden. Sci Rep 2024; 14:11880. [PMID: 38789462 PMCID: PMC11126669 DOI: 10.1038/s41598-024-62663-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024] Open
Abstract
Plasmids encoding blaCTX-M genes have greatly shaped the evolution of E. coli producing extended-spectrum beta-lactamases (ESBL-E. coli) and adds to the global threat of multiresistant bacteria by promoting horizontal gene transfer (HGT). Here we screened the similarity of 47 blaCTX-M -encoding plasmids, from 45 epidemiologically unrelated and disperse ESBL-E. coli strains, isolated during the early phase (2009-2014) of the ESBL pandemic in western Sweden. Using optical DNA mapping (ODM), both similar and rare plasmids were identified. As many as 57% of the plasmids formed five ODM-plasmid groups of at least three similar plasmids per group. The most prevalent type (28%, IncIl, pMLST37) encoded blaCTX-M-15 (n = 10), blaCTX-M-3 (n = 2) or blaCTX-M-55 (n = 1). It was found in isolates of various sequence types (STs), including ST131. This could indicate ongoing local HGT as whole-genome sequencing only revealed similarities with a rarely reported, IncIl plasmid. The second most prevalent type (IncFII/FIA/FIB, F1:A2:B20) harboring blaCTX-M-27, was detected in ST131-C1-M27 isolates, and was similar to plasmids previously reported for this subclade. The results also highlight the need for local surveillance of plasmids and the importance of temporospatial epidemiological links so that detection of a prevalent plasmid is not overestimated as a potential plasmid transmission event in outbreak investigations.
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Affiliation(s)
- Moa S Wranne
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Nahid Karami
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden.
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden.
| | - Sriram Kk
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Shora Yazdanshenas
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Yii-Lih Lin
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Arpitha Kabbinale
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Christina Åhrén
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
- Swedish Strategic Program Against Antimicrobial Resistance (Strama), Region Västra Götaland, Gothenburg, Sweden
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4
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Nyblom M, Johnning A, Frykholm K, Wrande M, Müller V, Goyal G, Robertsson M, Dvirnas A, Sewunet T, KK S, Ambjörnsson T, Giske CG, Sandegren L, Kristiansson E, Westerlund F. Strain-level bacterial typing directly from patient samples using optical DNA mapping. COMMUNICATIONS MEDICINE 2023; 3:31. [PMID: 36823379 PMCID: PMC9950433 DOI: 10.1038/s43856-023-00259-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Identification of pathogens is crucial to efficiently treat and prevent bacterial infections. However, existing diagnostic techniques are slow or have a too low resolution for well-informed clinical decisions. METHODS In this study, we have developed an optical DNA mapping-based method for strain-level bacterial typing and simultaneous plasmid characterisation. For the typing, different taxonomical resolutions were examined and cultivated pure Escherichia coli and Klebsiella pneumoniae samples were used for parameter optimization. Finally, the method was applied to mixed bacterial samples and uncultured urine samples from patients with urinary tract infections. RESULTS We demonstrate that optical DNA mapping of single DNA molecules can identify Escherichia coli and Klebsiella pneumoniae at the strain level directly from patient samples. At a taxonomic resolution corresponding to E. coli sequence type 131 and K. pneumoniae clonal complex 258 forming distinct groups, the average true positive prediction rates are 94% and 89%, respectively. The single-molecule aspect of the method enables us to identify multiple E. coli strains in polymicrobial samples. Furthermore, by targeting plasmid-borne antibiotic resistance genes with Cas9 restriction, we simultaneously identify the strain or subtype and characterize the corresponding plasmids. CONCLUSION The optical DNA mapping method is accurate and directly applicable to polymicrobial and clinical samples without cultivation. Hence, it has the potential to rapidly provide comprehensive diagnostics information, thereby optimizing early antibiotic treatment and opening up for future precision medicine management.
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Affiliation(s)
- My Nyblom
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Anna Johnning
- grid.5371.00000 0001 0775 6028Department of Mathematical Sciences, Chalmers University of Technology & University of Gothenburg, Gothenburg, 412 96 Sweden ,grid.452079.dDepartment of Systems and Data Analysis, Fraunhofer-Chalmers Centre, Gothenburg, 412 88 Sweden ,Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, 405 30 Sweden
| | - Karolin Frykholm
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Marie Wrande
- grid.8993.b0000 0004 1936 9457Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 751 23 Sweden
| | - Vilhelm Müller
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Gaurav Goyal
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Miriam Robertsson
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Albertas Dvirnas
- grid.4514.40000 0001 0930 2361Department of Astronomy and Theoretical Physics, Lund University, Lund, 223 62 Sweden
| | - Tsegaye Sewunet
- grid.4714.60000 0004 1937 0626Department of Laboratory Medicine, Karolinska Institutet, Stockholm, 141 86 Sweden
| | - Sriram KK
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Tobias Ambjörnsson
- grid.4514.40000 0001 0930 2361Department of Astronomy and Theoretical Physics, Lund University, Lund, 223 62 Sweden
| | - Christian G. Giske
- grid.4714.60000 0004 1937 0626Department of Laboratory Medicine, Karolinska Institutet, Stockholm, 141 86 Sweden ,grid.24381.3c0000 0000 9241 5705Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, 171 76 Sweden
| | - Linus Sandegren
- grid.8993.b0000 0004 1936 9457Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 751 23 Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology & University of Gothenburg, Gothenburg, 412 96, Sweden. .,Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, 405 30, Sweden.
| | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96, Sweden. .,Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, 405 30, Sweden.
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5
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KK S, Wranne MS, Sewunet T, Ekedahl E, Coorens M, Tangkoskul T, Thamlikitkul V, Giske CG, Westerlund F. Identification and characterization of plasmids carrying the mobile colistin resistance gene mcr-1 using optical DNA mapping. JAC Antimicrob Resist 2023; 5:dlad004. [PMID: 36743530 PMCID: PMC9891347 DOI: 10.1093/jacamr/dlad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023] Open
Abstract
Objectives Colistin is a last-resort antibiotic, but there has been a rapid increase in colistin resistance, threatening its use in the treatment of infections with carbapenem-resistant Enterobacterales (CRE). Plasmid-mediated colistin resistance, in particular the mcr-1 gene, has been identified and WGS is the go-to method in identifying plasmids carrying mcr-1 genes. The goal of this study is to demonstrate the use of optical DNA mapping (ODM), a fast, efficient and amplification-free technique, to characterize plasmids carrying mcr-1. Methods ODM is a single-molecule technique, which we have demonstrated can be used for identifying plasmids harbouring antibiotic resistance genes. We here applied the technique to plasmids isolated from 12 clinical Enterobacterales isolates from patients at a major hospital in Thailand and verified our results using Nanopore long-read sequencing. Results We successfully identified plasmids encoding the mcr-1 gene and, for the first time, demonstrated the ability of ODM to identify resistance gene sites in small (∼30 kb) plasmids. We further identified bla CTX-M genes in different plasmids than the ones encoding mcr-1 in three of the isolates studied. Finally, we propose a cut-and-stretch assay, based on similar principles, but performed using surface-functionalized cover slips for DNA immobilization and an inexpensive microscope with basic functionalities, to identify the mcr-1 gene in a plasmid sample. Conclusions Both ODM and the cut-and-stretch assay developed could be very useful in identifying plasmids encoding antibiotic resistance in hospitals and healthcare facilities. The cut-and-stretch assay is particularly useful in low- and middle-income countries, where existing techniques are limited.
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Affiliation(s)
- Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Moa S Wranne
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Elina Ekedahl
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Maarten Coorens
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | | | | | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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6
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Sewunet T, K. K. S, Nguyen HH, Sithivong N, Hoang NTB, Sychareun V, Nengmongvang K, Larsson M, Olson L, Westerlund F, Giske CG. Fecal carriage and clonal dissemination of blaNDM-1 carrying Klebsiella pneumoniae sequence type 147 at an intensive care unit in Lao PDR. PLoS One 2022; 17:e0274419. [PMID: 36194564 PMCID: PMC9531820 DOI: 10.1371/journal.pone.0274419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/29/2022] [Indexed: 12/04/2022] Open
Abstract
OBJECTIVES Carbapenemase-producing Enterobacterales (CPE) are high priority targets of global antimicrobial surveillance. Herein, we determined the colonization rate of CPE on admission to intensive care units in Vientiane, Lao PDR in August-September 2019. METHODS Data regarding clinical conditions, infection control, and antibiotic usage were collected during admission. Rectal swab samples (n = 137) collected during admission were inoculated to selective chromogenic agars, followed by confirmatory tests for extended-spectrum beta-lactamases and carbapenemases. All CPE isolates were sequenced on Illumina (HiSeq2500), reads assembled using SPAdes 3.13, and the draft genomes used to query a database (https://www.genomicepidemiology.org) for resistome, plasmid replicons, and sequence types (ST). Optical DNA mapping (ODM) was used to characterize plasmids and to determine location of resistance genes. Minimum spanning tree was generated using the Bacterial Isolate Genome Sequence database (BIGSdb) and annotated using iTOL. RESULT From 47 Enterobacterales isolated on selective agars, K. pneumoniae (25/47) and E. coli (12/47) were the most prevalent species, followed by K aerogenes (2/47), K. variicola (1/47), and K. oxytoca (1/47). The overall prevalence of ESBLs was 51.0%; E. coli 83.3% (10/12) and Klebsiella spp. 41.3% (12/29). Twenty percent of the K. pneumoniae (5/25) isolates were carbapenem-resistant, and 4/5 contained the blaNDM-1 gene. All blaNDM-1 isolates belonged to ST147 and were indistinguishable with cgMLST. ODM showed that the blaNDM-1 gene was located on identical plasmids in all isolates. CONCLUSION The prevalence of ESBL-producing Enterobacterales was high, while carbapenemases were less common. However, the detection of clonal dissemination of blaNDM-1-producing K. pneumoniae isolates in one of the intensive care units calls for vigilance. Stringent infection prevention and antimicrobial stewardship strategies are highly important measures.
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Affiliation(s)
- Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sriram K. K.
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ha Hoang Nguyen
- Hanoi Medical University, Hanoi, Vietnam
- Training and Research Academic Collaboration (TRAC) Sweden, Vietnam
| | - Noikaseumsy Sithivong
- National Center for Laboratory and Epidemiology, Ministry of Health, Vientiane, Lao PDR
| | - Ngoc Thi Bich Hoang
- Department of Microbiology, Vietnam National Children’s Hospital, Hanoi, Vietnam
| | - Vanphanom Sychareun
- Faculty of Postgraduate Studies, University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
| | - Kokasia Nengmongvang
- Faculty of Postgraduate Studies, University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
| | - Mattias Larsson
- Training and Research Academic Collaboration (TRAC) Sweden, Vietnam
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Linus Olson
- Training and Research Academic Collaboration (TRAC) Sweden, Vietnam
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
- Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Christian G. Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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7
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A simple cut and stretch assay to detect antimicrobial resistance genes on bacterial plasmids by single-molecule fluorescence microscopy. Sci Rep 2022; 12:9301. [PMID: 35660772 PMCID: PMC9166776 DOI: 10.1038/s41598-022-13315-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
Antimicrobial resistance (AMR) is a fast-growing threat to global health. The genes conferring AMR to bacteria are often located on plasmids, circular extrachromosomal DNA molecules that can be transferred between bacterial strains and species. Therefore, effective methods to characterize bacterial plasmids and detect the presence of resistance genes can assist in managing AMR, for example, during outbreaks in hospitals. However, existing methods for plasmid analysis either provide limited information or are expensive and challenging to implement in low-resource settings. Herein, we present a simple assay based on CRISPR/Cas9 excision and DNA combing to detect antimicrobial resistance genes on bacterial plasmids. Cas9 recognizes the gene of interest and makes a double-stranded DNA cut, causing the circular plasmid to linearize. The change in plasmid configuration from circular to linear, and hence the presence of the AMR gene, is detected by stretching the plasmids on a glass surface and visualizing by fluorescence microscopy. This single-molecule imaging based assay is inexpensive, fast, and in addition to detecting the presence of AMR genes, it provides detailed information on the number and size of plasmids in the sample. We demonstrate the detection of several β-lactamase-encoding genes on plasmids isolated from clinical samples. Furthermore, we demonstrate that the assay can be performed using standard microbiology and clinical laboratory equipment, making it suitable for low-resource settings.
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8
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Kk S, Ekedahl E, Hoang NTB, Sewunet T, Berglund B, Lundberg L, Nematzadeh S, Nilsson M, Nilsson LE, Le NK, Tran DM, Hanberger H, Olson L, Larsson M, Giske CG, Westerlund F. High diversity of bla NDM-1-encoding plasmids in Klebsiella pneumoniae isolated from neonates in a Vietnamese hospital. Int J Antimicrob Agents 2022; 59:106496. [PMID: 34921976 DOI: 10.1016/j.ijantimicag.2021.106496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/08/2021] [Accepted: 12/01/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVES The carbapenemase-encoding gene blaNDM-1 has been reported in Vietnam during the last 10 years, and blaNDM-producing Enterobacteriaceae are now silently and rapidly spreading. A key factor behind dissemination of blaNDM-1 is plasmids, mobile genetic elements that commonly carry antibiotic resistance genes and spread via conjugation. The diversity of blaNDM-1-encoding plasmids from neonates at a large Vietnamese hospital was characterized in this study. METHODS 18 fecal Klebsiella pneumoniae and Klebsiella quasipneumoniae isolates collected from 16 neonates at a large pediatric hospital in Vietnam were studied using optical DNA mapping (ODM) and next-generation sequencing (NGS). Plasmids carrying the blaNDM-1 gene were identified by combining ODM with Cas9 restriction. The plasmids in the isolates were compared to investigate whether the same plasmid was present in different patients. RESULTS Although the same plasmid was found in some isolates, ODM confirmed that there were at least 10 different plasmids encoding blaNDM-1 among the 18 isolates, thus indicating wide plasmid diversity. The ODM results concur with the NGS data. Interestingly, some isolates had two distinct plasmids encoding blaNDM-1 that could be readily identified with ODM. The coexistence of different plasmids carrying the same blaNDM-1 gene in a single isolate has rarely been reported, probably because of limitations in plasmid characterization techniques. CONCLUSIONS The plasmids encoding the blaNDM-1 gene in this study cohort were diverse and may represent a similar picture in Vietnamese society. The study highlights important aspects of the usefulness of ODM for plasmid analysis.
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Affiliation(s)
- Sriram Kk
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Elina Ekedahl
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ngoc Thi Bich Hoang
- Department of Microbiology, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory medicine, Karolinska Institutet, Stockholm, Sweden
| | - Björn Berglund
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden
| | - Ludwig Lundberg
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden; Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Shoeib Nematzadeh
- Division of Clinical Microbiology, Department of Laboratory medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maud Nilsson
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden
| | - Lennart E Nilsson
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden
| | - Ngai Kien Le
- Department of Infection Control, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Dien Minh Tran
- Department of Surgery, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Håkan Hanberger
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden
| | - Linus Olson
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden; Department of Women and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Mattias Larsson
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory medicine, Karolinska Institutet, Stockholm, Sweden; Clinical microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden..
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9
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Torstensson E, Goyal G, Johnning A, Westerlund F, Ambjörnsson T. Combining dense and sparse labeling in optical DNA mapping. PLoS One 2021; 16:e0260489. [PMID: 34843574 PMCID: PMC8629184 DOI: 10.1371/journal.pone.0260489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
Optical DNA mapping (ODM) is based on fluorescent labeling, stretching and imaging of single DNA molecules to obtain sequence-specific fluorescence profiles, DNA barcodes. These barcodes can be mapped to theoretical counterparts obtained from DNA reference sequences, which in turn allow for DNA identification in complex samples and for detecting structural changes in individual DNA molecules. There are several types of DNA labeling schemes for ODM and for each labeling type one or several types of match scoring methods are used. By combining the information from multiple labeling schemes one can potentially improve mapping confidence; however, combining match scores from different labeling assays has not been implemented yet. In this study, we introduce two theoretical methods for dealing with analysis of DNA molecules with multiple label types. In our first method, we convert the alignment scores, given as output from the different assays, into p-values using carefully crafted null models. We then combine the p-values for different label types using standard methods to obtain a combined match score and an associated combined p-value. In the second method, we use a block bootstrap approach to check for the uniqueness of a match to a database for all barcodes matching with a combined p-value below a predefined threshold. For obtaining experimental dual-labeled DNA barcodes, we introduce a novel assay where we cut plasmid DNA molecules from bacteria with restriction enzymes and the cut sites serve as sequence-specific markers, which together with barcodes obtained using the established competitive binding labeling method, form a dual-labeled barcode. All experimental data in this study originates from this assay, but we point out that our theoretical framework can be used to combine data from all kinds of available optical DNA mapping assays. We test our multiple labeling frameworks on barcodes from two different plasmids and synthetically generated barcodes (combined competitive-binding- and nick-labeling). It is demonstrated that by simultaneously using the information from all label types, we can substantially increase the significance when we match experimental barcodes to a database consisting of theoretical barcodes for all sequenced plasmids.
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Affiliation(s)
- Erik Torstensson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Gaurav Goyal
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Anna Johnning
- Department of Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden
- Systems and Data Analysis, Fraunhofer-Chalmers Centre, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
- * E-mail:
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10
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Dvirnas A, Stewart C, Müller V, Bikkarolla SK, Frykholm K, Sandegren L, Kristiansson E, Westerlund F, Ambjörnsson T. Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach. PLoS One 2021; 16:e0259670. [PMID: 34739528 PMCID: PMC8570516 DOI: 10.1371/journal.pone.0259670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/22/2021] [Indexed: 11/19/2022] Open
Abstract
Large-scale genomic alterations play an important role in disease, gene expression, and chromosome evolution. Optical DNA mapping (ODM), commonly categorized into sparsely-labelled ODM and densely-labelled ODM, provides sequence-specific continuous intensity profiles (DNA barcodes) along single DNA molecules and is a technique well-suited for detecting such alterations. For sparsely-labelled barcodes, the possibility to detect large genomic alterations has been investigated extensively, while densely-labelled barcodes have not received as much attention. In this work, we introduce HMMSV, a hidden Markov model (HMM) based algorithm for detecting structural variations (SVs) directly in densely-labelled barcodes without access to sequence information. We evaluate our approach using simulated data-sets with 5 different types of SVs, and combinations thereof, and demonstrate that the method reaches a true positive rate greater than 80% for randomly generated barcodes with single variations of size 25 kilobases (kb). Increasing the length of the SV further leads to larger true positive rates. For a real data-set with experimental barcodes on bacterial plasmids, we successfully detect matching barcode pairs and SVs without any particular assumption of the types of SVs present. Instead, our method effectively goes through all possible combinations of SVs. Since ODM works on length scales typically not reachable with other techniques, our methodology is a promising tool for identifying arbitrary combinations of genomic alterations.
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Affiliation(s)
- Albertas Dvirnas
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Callum Stewart
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Vilhelm Müller
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Santosh Kumar Bikkarolla
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Karolin Frykholm
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
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11
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KK S, Sewunet T, Wangchinda W, Tangkoskul T, Thamlikitkul V, Giske CG, Westerlund F. Optical DNA Mapping of Plasmids Reveals Clonal Spread of Carbapenem-Resistant Klebsiella pneumoniae in a Large Thai Hospital. Antibiotics (Basel) 2021; 10:antibiotics10091029. [PMID: 34572611 PMCID: PMC8466775 DOI: 10.3390/antibiotics10091029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/26/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CR-KP) in patients admitted to hospitals pose a great challenge to treatment. The genes causing resistance to carbapenems are mostly found in plasmids, mobile genetic elements that can spread easily to other bacterial strains, thus exacerbating the problem. Here, we studied 27 CR-KP isolates collected from different types of samples from 16 patients admitted to the medical ward at Siriraj Hospital in Bangkok, Thailand, using next generation sequencing (NGS) and optical DNA mapping (ODM). The majority of the isolates belonged to sequence type (ST) 16 and are described in detail herein. Using ODM, we identified the plasmid carrying the blaNDM-1 gene in the ST16 isolates and the plasmids were very similar, highlighting the possibility of using ODM of plasmids as a surrogate marker of nosocomial spread of bacteria. We also demonstrated that ODM could identify that the blaCTX-M-15 and blaOXA-232 genes in the ST16 isolates were encoded on separate plasmids from the blaNDM-1 gene and from each other. The other three isolates belonged to ST147 and each of them had distinct plasmids encoding blaNDM-1.
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Affiliation(s)
- Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden;
| | - Tsegaye Sewunet
- Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
| | - Walaiporn Wangchinda
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (W.W.); (T.T.); (V.T.)
| | - Teerawit Tangkoskul
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (W.W.); (T.T.); (V.T.)
| | - Visanu Thamlikitkul
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (W.W.); (T.T.); (V.T.)
| | - Christian G. Giske
- Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
- Department of Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden;
- Correspondence: ; Tel.: +46-31-772-3049
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12
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Lin YL, Sewunet T, KK S, Giske CG, Westerlund F. Optical maps of plasmids as a proxy for clonal spread of MDR bacteria: a case study of an outbreak in a rural Ethiopian hospital. J Antimicrob Chemother 2021; 75:2804-2811. [PMID: 32653928 PMCID: PMC7678893 DOI: 10.1093/jac/dkaa258] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/24/2020] [Accepted: 05/14/2020] [Indexed: 01/09/2023] Open
Abstract
Objectives MDR bacteria have become a prevailing health threat worldwide. We here aimed to use optical DNA mapping (ODM) as a rapid method to trace nosocomial spread of bacterial clones and gene elements. We believe that this method has the potential to be a tool of pivotal importance for MDR control. Methods Twenty-four Escherichia coli samples of ST410 from three different wards were collected at an Ethiopian hospital and their plasmids were analysed by ODM. Plasmids were specifically digested with Cas9 targeting the antibiotic resistance genes, stained by competitive binding and confined in nanochannels for imaging. The resulting intensity profiles (barcodes) for each plasmid were compared to identify potential clonal spread of resistant bacteria. Results ODM demonstrated that a large fraction of the patients carried bacteria with a plasmid of the same origin, carrying the ESBL gene blaCTX-M-15, suggesting clonal spread. The results correlate perfectly with core genome (cg)MLST data, where bacteria with the same plasmid also had very similar cgMLST profiles. Conclusions ODM is a rapid discriminatory method for identifying plasmids and antibiotic resistance genes. Long-range deletions/insertions, which are challenging for short-read next-generation sequencing, can be easily identified and used to trace bacterial clonal spread. We propose that plasmid typing can be a useful tool to identify clonal spread of MDR bacteria. Furthermore, the simplicity of the method enables possible future application in low- and middle-income countries.
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Affiliation(s)
- Yii-Lih Lin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- School of Laboratory Sciences, Department of Microbiology, Jimma University, Jimma, Ethiopia
| | - Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Corresponding author. E-mail:
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13
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Karami N, KK S, Yazdanshenas S, Lin YL, Jaén-Luchoro D, Ekedahl E, Parameshwaran S, Lindblom A, Åhrén C, Westerlund F. Identity of blaCTX-M Carrying Plasmids in Sequential ESBL- E. coli Isolates from Patients with Recurrent Urinary Tract Infections. Microorganisms 2021; 9:microorganisms9061138. [PMID: 34070515 PMCID: PMC8226486 DOI: 10.3390/microorganisms9061138] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/10/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022] Open
Abstract
Plasmid-mediated multidrug resistance in E. coli is becoming increasingly prevalent. Considering this global threat to human health, it is important to understand how plasmid-mediated resistance spreads. From a cohort of 123 patients with recurrent urinary tract infections (RUTI) due to extended spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBL E. coli), only five events with a change of ESBL E. coli strain between RUTI episodes were identified. Their blaCTX-M encoding plasmids were compared within each pair of isolates using optical DNA mapping (ODM) and PCR-based replicon typing. Despite similar blaCTX-M genes and replicon types, ODM detected only one case with identical plasmids in the sequential ESBL E. coli strains, indicating that plasmid transfer could have occurred. For comparison, plasmids from seven patients with the same ESBL E. coli strain reoccurring in both episodes were analyzed. These plasmids (encoding blaCTX-M-3, blaCTX-M-14, and blaCTX-M-15) were unaltered for up to six months between recurrent infections. Thus, transmission of blaCTX-M plasmids appears to be a rare event during the course of RUTI. Despite the limited number (n = 23) of plasmids investigated, similar blaCTX-M-15 plasmids in unrelated isolates from different patients were detected, suggesting that some successful plasmids could be associated with specific strains, or are more easily transmitted.
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Affiliation(s)
- Nahid Karami
- Institute of Biomedicine, Department of Infectious Diseases and Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10 A, 413 46 Gothenburg, Sweden; (S.Y.); (D.J.-L.); (A.L.); (C.Å.)
- Västra Götaland Region, Sahlgrenska University Hospital, Department of Clinical Microbiology, Guldhedsgatan 10A, 413 46 Gothenburg, Sweden
- Correspondence: (N.K.); (F.W.); Tel.: +46-31-342-6173 (N.K.); +46-31-772-3049 (F.W.)
| | - Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.); (E.E.); (S.P.)
| | - Shora Yazdanshenas
- Institute of Biomedicine, Department of Infectious Diseases and Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10 A, 413 46 Gothenburg, Sweden; (S.Y.); (D.J.-L.); (A.L.); (C.Å.)
- Västra Götaland Region, Sahlgrenska University Hospital, Department of Clinical Microbiology, Guldhedsgatan 10A, 413 46 Gothenburg, Sweden
| | - Yii-Lih Lin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.); (E.E.); (S.P.)
| | - Daniel Jaén-Luchoro
- Institute of Biomedicine, Department of Infectious Diseases and Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10 A, 413 46 Gothenburg, Sweden; (S.Y.); (D.J.-L.); (A.L.); (C.Å.)
| | - Elina Ekedahl
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.); (E.E.); (S.P.)
| | - Sanjana Parameshwaran
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.); (E.E.); (S.P.)
| | - Anna Lindblom
- Institute of Biomedicine, Department of Infectious Diseases and Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10 A, 413 46 Gothenburg, Sweden; (S.Y.); (D.J.-L.); (A.L.); (C.Å.)
- Västra Götaland Region, Sahlgrenska University Hospital, Department of Clinical Microbiology, Guldhedsgatan 10A, 413 46 Gothenburg, Sweden
| | - Christina Åhrén
- Institute of Biomedicine, Department of Infectious Diseases and Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10 A, 413 46 Gothenburg, Sweden; (S.Y.); (D.J.-L.); (A.L.); (C.Å.)
- Swedish Strategic Program against Antimicrobial Resistance (Strama), Västra Götaland Region, Regionens Hus, 405 44 Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.); (E.E.); (S.P.)
- Correspondence: (N.K.); (F.W.); Tel.: +46-31-342-6173 (N.K.); +46-31-772-3049 (F.W.)
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14
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Jeffet J, Margalit S, Michaeli Y, Ebenstein Y. Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale. Essays Biochem 2021; 65:51-66. [PMID: 33739394 PMCID: PMC8056043 DOI: 10.1042/ebc20200021] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method's basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method's resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.
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Affiliation(s)
- Jonathan Jeffet
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sapir Margalit
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
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15
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Ferreira C, Bikkarolla SK, Frykholm K, Pohjanen S, Brito M, Lameiras C, Nunes OC, Westerlund F, Manaia CM. Polyphasic characterization of carbapenem-resistant Klebsiella pneumoniae clinical isolates suggests vertical transmission of the blaKPC-3 gene. PLoS One 2021; 16:e0247058. [PMID: 33635888 PMCID: PMC7909683 DOI: 10.1371/journal.pone.0247058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/30/2021] [Indexed: 11/18/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae are a major global threat in healthcare facilities. The propagation of carbapenem resistance determinants can occur through vertical transmission, with genetic elements being transmitted by the host bacterium, or by horizontal transmission, with the same genetic elements being transferred among distinct bacterial hosts. This work aimed to track carbapenem resistance transmission by K. pneumoniae in a healthcare facility. The study involved a polyphasic approach based on conjugation assays, resistance phenotype and genotype analyses, whole genome sequencing, and plasmid characterization by pulsed field gel electrophoresis and optical DNA mapping. Out of 40 K. pneumoniae clinical isolates recovered over two years, five were carbapenem- and multidrug-resistant and belonged to multilocus sequence type ST147. These isolates harboured the carbapenemase encoding blaKPC-3 gene, integrated in conjugative plasmids of 140 kbp or 55 kbp, belonging to replicon types incFIA/incFIIK or incN/incFIIK, respectively. The two distinct plasmids encoding the blaKPC-3 gene were associated with distinct genetic lineages, as confirmed by optical DNA mapping and whole genome sequence analyses. These results suggested vertical (bacterial strain-based) transmission of the carbapenem-resistance genetic elements. Determination of the mode of transmission of antibiotic resistance in healthcare facilities, only possible based on polyphasic approaches as described here, is essential to control resistance propagation.
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Affiliation(s)
- Catarina Ferreira
- CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Santosh K. Bikkarolla
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Karolin Frykholm
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Saga Pohjanen
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | | | - Olga C. Nunes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- * E-mail: (CMM); (FW)
| | - Célia M. Manaia
- CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
- * E-mail: (CMM); (FW)
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16
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Real-time compaction of nanoconfined DNA by an intrinsically disordered macromolecular counterion. Biochem Biophys Res Commun 2020; 533:175-180. [PMID: 32951838 DOI: 10.1016/j.bbrc.2020.06.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/10/2020] [Indexed: 12/31/2022]
Abstract
We demonstrate how a recently developed nanofluidic device can be used to study protein-induced compaction of genome-length DNA freely suspended in solution. The protein we use in this study is the hepatitis C virus core protein (HCVcp), which is a positively charged, intrinsically disordered protein. Using nanofluidic devices in combination with fluorescence microscopy, we observe that protein-induced compaction preferentially begins at the ends of linear DNA. This observation would be difficult to make with many other single-molecule techniques, which generally require the DNA ends to be anchored to a substrate. We also demonstrate that this protein-induced compaction is reversible and can be dynamically modulated by exposing the confined DNA molecules to solutions containing either HCVcp (to promote compaction) or Proteinase K (to disassemble the compact nucleo-protein complex). Although the natural binding partner for HCVcp is genomic viral RNA, the general biophysical principles governing protein-induced compaction of DNA are likely relevant for a broad range of nucleic acid-binding proteins and their targets.
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17
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Abstract
The DNA of our cells is constantly exposed to various types of damaging agents. One of the most critical types of damage is when both strands of the DNA break, and thus such breaks need to be efficiently repaired. It is known that CtIP promotes nucleases in DNA break repair. Here we show that CtIP can also hold the two DNA strands together in solution when DNA is free to move, using novel methodology that allows the monitoring of thousands of single DNA molecules in nanofabricated devices. DNA bridging likely facilitates the enzymatic repair steps and identifies novel CtIP functions that are crucial for repairing broken DNA. The early steps of DNA double-strand break (DSB) repair in human cells involve the MRE11-RAD50-NBS1 (MRN) complex and its cofactor, phosphorylated CtIP. The roles of these proteins in nucleolytic DSB resection are well characterized, but their role in bridging the DNA ends for efficient and correct repair is much less explored. Here we study the binding of phosphorylated CtIP, which promotes the endonuclease activity of MRN, to single long (∼50 kb) DNA molecules using nanofluidic channels and compare it to the yeast homolog Sae2. CtIP bridges DNA in a manner that depends on the oligomeric state of the protein, and truncated mutants demonstrate that the bridging depends on CtIP regions distinct from those that stimulate the nuclease activity of MRN. Sae2 is a much smaller protein than CtIP, and its bridging is significantly less efficient. Our results demonstrate that the nuclease cofactor and structural functions of CtIP may depend on the same protein population, which may be crucial for CtIP functions in both homologous recombination and microhomology-mediated end-joining.
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18
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Müller V, Nyblom M, Johnning A, Wrande M, Dvirnas A, KK S, Giske CG, Ambjörnsson T, Sandegren L, Kristiansson E, Westerlund F. Cultivation-Free Typing of Bacteria Using Optical DNA Mapping. ACS Infect Dis 2020; 6:1076-1084. [PMID: 32294378 PMCID: PMC7304876 DOI: 10.1021/acsinfecdis.9b00464] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 01/06/2023]
Abstract
A variety of pathogenic bacteria can infect humans, and rapid species identification is crucial for the correct treatment. However, the identification process can often be time-consuming and depend on the cultivation of the bacterial pathogen(s). Here, we present a stand-alone, enzyme-free, optical DNA mapping assay capable of species identification by matching the intensity profiles of large DNA molecules to a database of fully assembled bacterial genomes (>10 000). The assay includes a new data analysis strategy as well as a general DNA extraction protocol for both Gram-negative and Gram-positive bacteria. We demonstrate that the assay is capable of identifying bacteria directly from uncultured clinical urine samples, as well as in mixtures, with the potential to be discriminative even at the subspecies level. We foresee that the assay has applications both within research laboratories and in clinical settings, where the time-consuming step of cultivation can be minimized or even completely avoided.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - My Nyblom
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Anna Johnning
- Department of Mathematical
Sciences, Chalmers University of Technology
and the University of Gothenburg, 412 96 Gothenburg, Sweden
- Systems and Data Analysis, Fraunhofer-Chalmers
Centre, Chalmers Science
Park, 412 88 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research,
CARe, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Marie Wrande
- Department of Medical
Biochemistry and Microbiology, Uppsala University, Husargatan 3, Box
582, 751 23 Uppsala, Sweden
| | - Albertas Dvirnas
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden
| | - Sriram KK
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Christian G. Giske
- Department of Laboratory Medicine, Karolinska
Institutet, Alfred Nobels
Allé 8, 141 86 Stockholm, Sweden
- Department of Clinical
Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden
| | - Linus Sandegren
- Department of Medical
Biochemistry and Microbiology, Uppsala University, Husargatan 3, Box
582, 751 23 Uppsala, Sweden
| | - Erik Kristiansson
- Department of Mathematical
Sciences, Chalmers University of Technology
and the University of Gothenburg, 412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research,
CARe, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
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19
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Bouwens A, Deen J, Vitale R, D’Huys L, Goyvaerts V, Descloux A, Borrenberghs D, Grussmayer K, Lukes T, Camacho R, Su J, Ruckebusch C, Lasser T, Van De Ville D, Hofkens J, Radenovic A, Frans Janssen KP. Identifying microbial species by single-molecule DNA optical mapping and resampling statistics. NAR Genom Bioinform 2020; 2:lqz007. [PMID: 33575560 PMCID: PMC7671359 DOI: 10.1093/nargab/lqz007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/12/2019] [Indexed: 12/13/2022] Open
Abstract
Single-molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to provide an unbiased view into the composition of complex viromes and/or microbiomes. To fully enable mapping-based metagenomics, sensitivity and specificity of DNA map analysis and identification need to be improved. Using detailed simulations and experimental data, we first demonstrate how fluorescence imaging of surface stretched, sequence specifically labeled DNA fragments can yield highly sensitive identification of targets. Second, a new analysis technique is introduced to increase specificity of the analysis, allowing even closely related species to be resolved. Third, we show how an increase in resolution improves sensitivity. Finally, we demonstrate that these methods are capable of identifying species with long genomes such as bacteria with high sensitivity.
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Affiliation(s)
- Arno Bouwens
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jochem Deen
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Raffaele Vitale
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- LASIR CNRS, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Laurens D’Huys
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Vince Goyvaerts
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Adrien Descloux
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Kristin Grussmayer
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Tomas Lukes
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Rafael Camacho
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Jia Su
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Cyril Ruckebusch
- LASIR CNRS, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Theo Lasser
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Dimitri Van De Ville
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Center for Neuroprosthetics, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Department of Radiology and Medical Informatics, Université de Genève, 1205 Genève, Switzerland
| | - Johan Hofkens
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Aleksandra Radenovic
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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20
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Müller V, Dvirnas A, Andersson J, Singh V, Kk S, Johansson P, Ebenstein Y, Ambjörnsson T, Westerlund F. Enzyme-free optical DNA mapping of the human genome using competitive binding. Nucleic Acids Res 2019; 47:e89. [PMID: 31165870 PMCID: PMC6735870 DOI: 10.1093/nar/gkz489] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/03/2019] [Accepted: 05/22/2019] [Indexed: 01/24/2023] Open
Abstract
Optical DNA mapping (ODM) allows visualization of long-range sequence information along single DNA molecules. The data can for example be used for detecting long range structural variations, for aiding DNA sequence assembly of complex genomes and for mapping epigenetic marks and DNA damage across the genome. ODM traditionally utilizes sequence specific marks based on nicking enzymes, combined with a DNA stain, YOYO-1, for detection of the DNA contour. Here we use a competitive binding approach, based on YOYO-1 and netropsin, which highlights the contour of the DNA molecules, while simultaneously creating a continuous sequence specific pattern, based on the AT/GC variation along the detected molecule. We demonstrate and validate competitive-binding-based ODM using bacterial artificial chromosomes (BACs) derived from the human genome and then turn to DNA extracted from white blood cells. We generalize our findings with in-silico simulations that show that we can map a vast majority of the human genome. Finally, we demonstrate the possibility of combining competitive binding with enzymatic labeling by mapping DNA damage sites induced by the cytotoxic drug etoposide to the human genome. Overall, we demonstrate that competitive-binding-based ODM has the potential to be used both as a standalone assay for studies of the human genome, as well as in combination with enzymatic approaches, some of which are already commercialized.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Albertas Dvirnas
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - John Andersson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Vandana Singh
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Sriram Kk
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Pegah Johansson
- Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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21
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Shin E, Kim W, Lee S, Bae J, Kim S, Ko W, Seo HS, Lim S, Lee HS, Jo K. Truncated TALE-FP as DNA Staining Dye in a High-salt Buffer. Sci Rep 2019; 9:17197. [PMID: 31748571 PMCID: PMC6868158 DOI: 10.1038/s41598-019-53722-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/05/2019] [Indexed: 01/19/2023] Open
Abstract
Large DNA molecules are a promising platform for in vitro single-molecule biochemical analysis to investigate DNA-protein interactions by fluorescence microscopy. For many studies, intercalating fluorescent dyes have been primary DNA staining reagents, but they often cause photo-induced DNA breakage as well as structural deformation. As a solution, we previously developed several fluorescent-protein DNA-binding peptides or proteins (FP-DBP) for reversibly staining DNA molecules without structural deformation or photo-induced damage. However, they cannot stain DNA in a condition similar to a physiological salt concentration that most biochemical reactions require. Given these concerns, here we developed a salt-tolerant FP-DBP: truncated transcription activator-like effector (tTALE-FP), which can stain DNA up to 100 mM NaCl. Moreover, we found an interesting phenomenon that the tTALE-FP stained DNA evenly in 1 × TE buffer but showed AT-rich specific patterns from 40 mM to 100 mM NaCl. Using an assay based on fluorescence resonance energy transfer, we demonstrated that this binding pattern is caused by a higher DNA binding affinity of tTALE-FP for AT-rich compared to GC-rich regions. Finally, we used tTALE-FP in a single molecule fluorescence assay to monitor real-time restriction enzyme digestion of single DNA molecules. Altogether, our results demonstrate that this protein can provide a useful alternative as a DNA stain over intercalators.
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Affiliation(s)
- Eunji Shin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Woojung Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Jaeyoung Bae
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Sanggil Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Wooseok Ko
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Ho Seong Seo
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Korea
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Korea
| | - Hyun Soo Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea.
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea.
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22
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Kopotsa K, Osei Sekyere J, Mbelle NM. Plasmid evolution in carbapenemase-producing Enterobacteriaceae: a review. Ann N Y Acad Sci 2019; 1457:61-91. [PMID: 31469443 DOI: 10.1111/nyas.14223] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/22/2019] [Accepted: 07/26/2019] [Indexed: 12/17/2022]
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) have been listed by the WHO as high-priority pathogens owing to their high association with mortalities and morbidities. Resistance to multiple β-lactams complicates effective clinical management of CRE infections. Using plasmid typing methods, a wide distribution of plasmid replicon groups has been reported in CREs around the world, including IncF, N, X, A/C, L/M, R, P, H, I, and W. We performed a literature search for English research papers, published between 2013 and 2018, reporting on plasmid-mediated carbapenem resistance. A rise in both carbapenemase types and associated plasmid replicon groups was seen, with China, Canada, and the United States recording a higher increase than other countries. blaKPC was the most prevalent, except in Angola and the Czech Republic, where OXA-181 (n = 50, 88%) and OXA-48-like (n = 24, 44%) carbapenemases were most prevalent, respectively; blaKPC-2/3 accounted for 70% (n = 956) of all reported carbapenemases. IncF plasmids were found to be responsible for disseminating different antibiotic resistance genes worldwide, accounting for almost 40% (n = 254) of plasmid-borne carbapenemases. blaCTX-M , blaTEM , blaSHV , blaOXA-1/9 , qnr, and aac-(6')-lb were mostly detected concurrently with carbapenemases. Most reported plasmids were conjugative but not present in multiple countries or species, suggesting limited interspecies and interboundary transmission of a common plasmid. A major limitation to effective characterization of plasmid evolution was the use of PCR-based instead of whole-plasmid sequencing-based plasmid typing.
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Affiliation(s)
- Katlego Kopotsa
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa.,National Health Laboratory Service, Tshwane Division, Department of Medical Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
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23
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Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak. mBio 2019; 10:mBio.00347-19. [PMID: 31289171 PMCID: PMC6747713 DOI: 10.1128/mbio.00347-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
This study presents how a novel method, based on visualizing single plasmids using sequence-specific fluorescent labeling, could be used to analyze the genetic dynamics of an outbreak of resistant bacteria in a neonatal intensive care unit at a Swedish hospital. Plasmids are a central reason for the rapid global spread of bacterial resistance to antibiotics. In a single experimental procedure, this method replaces many traditional plasmid analysis techniques that together provide limited details and are slow to perform. The method is much faster than long-read whole-genome sequencing and offers direct genetic comparison of patient samples. We could conclude that no transfer of resistance plasmids had occurred between different bacteria during the outbreak and that secondary cases of ESBL-producing Enterobacteriaceae carriage were instead likely due to influx of new strains. We believe that the method offers potential in improving surveillance and infection control of resistant bacteria in hospitals. The global spread of antibiotic resistance among Enterobacteriaceae is largely due to multidrug resistance plasmids that can transfer between different bacterial strains and species. Horizontal gene transfer of resistance plasmids can complicate hospital outbreaks and cause problems in epidemiological tracing, since tracing is usually based on bacterial clonality. We have developed a method, based on optical DNA mapping combined with Cas9-assisted identification of resistance genes, which is used here to characterize plasmids during an extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae outbreak at a Swedish neonatal intensive care unit. The outbreak included 17 neonates initially colonized with ESBL-producing Klebsiella pneumoniae (ESBL-KP), some of which were found to carry additional ESBL-producing Escherichia coli (ESBL-EC) in follow-up samples. We demonstrate that all ESBL-KP isolates contained two plasmids with the blaCTX-M-15 gene located on the smaller one (~80 kbp). The same ESBL-KP clone was present in follow-up samples for up to 2 years in some patients, and the plasmid carrying the blaCTX-M-15 gene was stable throughout this time period. However, extensive genetic rearrangements within the second plasmid were observed in the optical DNA maps for several of the ESBL-KP isolates. Optical mapping also demonstrated that even though other bacterial clones and species carrying blaCTX-M group 1 genes were found in some neonates, no transfer of resistance plasmids had occurred. The data instead pointed toward unrelated acquisition of ESBL-producing Enterobacteriaceae (EPE). In addition to revealing important information about the specific outbreak, the method presented is a promising tool for surveillance and infection control in clinical settings.
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24
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Ferreira C, Bogas D, Bikarolla SK, Varela AR, Frykholm K, Linheiro R, Nunes OC, Westerlund F, Manaia CM. Genetic variation in the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strain. CHEMOSPHERE 2019; 220:748-759. [PMID: 30611073 DOI: 10.1016/j.chemosphere.2018.12.130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/23/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Bacteria harboring conjugative plasmids have the potential for spreading antibiotic resistance through horizontal gene transfer. It is described that the selection and dissemination of antibiotic resistance is enhanced by stressors, like metals or antibiotics, which can occur as environmental contaminants. This study aimed at unveiling the composition of the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strain (H1FC54) under different mating conditions. To meet this objective, plasmid pulsed field gel electrophoresis, optical mapping analyses and DNA sequencing were used in combination with phenotype analysis. Strain H1FC54 was observed to harbor five plasmids, three of which were conjugative and two of these, pH1FC54_330 and pH1FC54_140, contained metal and antibiotic resistance genes. Transconjugants obtained in the absence or presence of tellurite (0.5 μM or 5 μM), arsenite (0.5 μM, 5 μM or 15 μM) or ceftazidime (10 mg/L) and selected in the presence of sodium azide (100 mg/L) and tetracycline (16 mg/L) presented distinct phenotypes, associated with the acquisition of different plasmid combinations, including two co-integrate plasmids, of 310 kbp and 517 kbp. The variable composition of the conjugative plasmidome, the formation of co-integrates during conjugation, as well as the transfer of non-transferable plasmids via co-integration, and the possible association between antibiotic, arsenite and tellurite tolerance was demonstrated. These evidences bring interesting insights into the comprehension of the molecular and physiological mechanisms that underlie antibiotic resistance propagation in the environment.
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Affiliation(s)
- Catarina Ferreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal
| | - Diana Bogas
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal
| | - Santosh K Bikarolla
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE-412 96, Gothenburg, Sweden
| | - Ana Rita Varela
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal; LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Karolin Frykholm
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE-412 96, Gothenburg, Sweden
| | - Raquel Linheiro
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal
| | - Olga C Nunes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE-412 96, Gothenburg, Sweden
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal.
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25
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Krog J, Alizadehheidari M, Werner E, Bikkarolla SK, Tegenfeldt JO, Mehlig B, Lomholt MA, Westerlund F, Ambjörnsson T. Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis. J Chem Phys 2019; 149:215101. [PMID: 30525714 DOI: 10.1063/1.5051319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Nanochannels provide a means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. Here we introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force and the friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory-type argument. The estimated friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated friction constant by extracting this parameter from DNA's center-of-mass motion before and after unfolding, yielding decent agreement. We provide publically available software for performing the required image and Bayesian analysis.
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Affiliation(s)
- Jens Krog
- MEMPHYS-Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | | | - Erik Werner
- Department of Physics, Gothenburg University, Gothenburg, Sweden
| | - Santosh Kumar Bikkarolla
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Bernhard Mehlig
- Department of Physics, Gothenburg University, Gothenburg, Sweden
| | - Michael A Lomholt
- MEMPHYS-Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
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26
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Johnning A, Karami N, Tång Hallbäck E, Müller V, Nyberg L, Buongermino Pereira M, Stewart C, Ambjörnsson T, Westerlund F, Adlerberth I, Kristiansson E. The resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis. Microb Genom 2018; 4. [PMID: 30461373 PMCID: PMC6321870 DOI: 10.1099/mgen.0.000233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Carbapenem resistance is a rapidly growing threat to our ability to treat refractory bacterial infections. To understand how carbapenem resistance is mobilized and spread between pathogens, it is important to study the genetic context of the underlying resistance mechanisms. In this study, the resistomes of six clinical carbapenem-resistant isolates of five different species – Acinetobacter baumannii, Escherichia coli, two Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa – were characterized using whole genome sequencing. All Enterobacteriaceae isolates and the A. baumannii isolate had acquired a large number of antimicrobial resistance genes (7–18 different genes per isolate), including the following encoding carbapenemases: blaKPC-2, blaOXA-48, blaOXA-72, blaNDM-1, blaNDM-7 and blaVIM-1. In addition, a novel version of blaSHV was discovered. Four new resistance plasmids were identified and their fully assembled sequences were verified using optical DNA mapping. Most of the resistance genes were co-localized on these and other plasmids, suggesting a risk for co-selection. In contrast, five out of six carbapenemase genes were present on plasmids with no or few other resistance genes. The expected level of resistance – based on acquired resistance determinants – was concordant with measured levels in most cases. There were, however, several important discrepancies for four of the six isolates concerning multiple classes of antibiotics. In conclusion, our results further elucidate the diversity of carbapenemases, their mechanisms of horizontal transfer and possible patterns of co-selection. The study also emphasizes the difficulty of using whole genome sequencing for antimicrobial susceptibility testing of pathogens with complex genotypes.
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Affiliation(s)
- Anna Johnning
- 2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden.,1Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Nahid Karami
- 2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden.,3Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erika Tång Hallbäck
- 3Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Vilhelm Müller
- 4Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lena Nyberg
- 4Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Mariana Buongermino Pereira
- 1Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.,2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden
| | - Callum Stewart
- 5Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Tobias Ambjörnsson
- 5Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Fredrik Westerlund
- 4Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ingegerd Adlerberth
- 2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden.,3Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- 1Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.,2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden
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27
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Interspecies plasmid transfer appears rare in sequential infections with extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae. Diagn Microbiol Infect Dis 2018; 93:380-385. [PMID: 30527621 DOI: 10.1016/j.diagmicrobio.2018.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/29/2018] [Accepted: 10/24/2018] [Indexed: 02/08/2023]
Abstract
From a cohort of 1836 Swedish patients infected with ESBL-producing Enterobacteriaceae (EPE) during 2004-2014, 513 patients with recurrent EPE infection were identified. Only in 14 of the 513 patients was a change of species (ESBL-E. coli to ESBL-K. pneumoniae or vice versa) found between the index and subsequent infection. Eleven sequential urine isolates from 5 of the 14 patients were available for further analysis of possible transfer of ESBL-carrying plasmids. The plasmid content was studied using optical DNA mapping (ODM), PCR-based replicon typing, and ESBL gene sequencing. ODM allowed us to directly compare whole plasmids between isolates and found similar ESBL-carrying plasmids in 3 out of the 5 patients. The ODM results and the rarity in shift of species between ESBL-E. coli and ESBL-K. pneumoniae imply that in recurrent EPE infections interspecies plasmid transfer is uncommon.
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28
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Roosaare M, Puustusmaa M, Möls M, Vaher M, Remm M. PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads. PeerJ 2018; 6:e4588. [PMID: 29629246 PMCID: PMC5885972 DOI: 10.7717/peerj.4588] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/18/2018] [Indexed: 12/17/2022] Open
Abstract
Background Plasmids play an important role in the dissemination of antibiotic resistance, making their detection an important task. Using whole genome sequencing (WGS), it is possible to capture both bacterial and plasmid sequence data, but short read lengths make plasmid detection a complex problem. Results We developed a tool named PlasmidSeeker that enables the detection of plasmids from bacterial WGS data without read assembly. The PlasmidSeeker algorithm is based on k-mers and uses k-mer abundance to distinguish between plasmid and bacterial sequences. We tested the performance of PlasmidSeeker on a set of simulated and real bacterial WGS samples, resulting in 100% sensitivity and 99.98% specificity. Conclusion PlasmidSeeker enables quick detection of known plasmids and complements existing tools that assemble plasmids de novo. The PlasmidSeeker source code is stored on GitHub: https://github.com/bioinfo-ut/PlasmidSeeker.
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Affiliation(s)
- Märt Roosaare
- Department of Bioinformatics, IMCB, University of Tartu, Tartu, Estonia
| | - Mikk Puustusmaa
- Department of Bioinformatics, IMCB, University of Tartu, Tartu, Estonia
| | - Märt Möls
- Department of Bioinformatics, IMCB, University of Tartu, Tartu, Estonia.,Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia
| | - Mihkel Vaher
- Department of Bioinformatics, IMCB, University of Tartu, Tartu, Estonia
| | - Maido Remm
- Department of Bioinformatics, IMCB, University of Tartu, Tartu, Estonia
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29
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Lima DC, Nyberg LK, Westerlund F, Batistuzzo de Medeiros SR. Identification and DNA annotation of a plasmid isolated from Chromobacterium violaceum. Sci Rep 2018; 8:5327. [PMID: 29593241 PMCID: PMC5871888 DOI: 10.1038/s41598-018-23708-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/12/2018] [Indexed: 12/18/2022] Open
Abstract
Chromobacterium violaceum is a ß-proteobacterium found widely worldwide with important biotechnological properties and is associated to lethal sepsis in immune-depressed individuals. In this work, we report the discover, complete sequence and annotation of a plasmid detected in C. violaceum that has been unnoticed until now. We used DNA single-molecule analysis to confirm that the episome found was a circular molecule and then proceeded with NGS sequencing. After DNA annotation, we found that this extra-chromosomal DNA is probably a defective bacteriophage of approximately 44 kilobases, with 39 ORFs comprising, mostly hypothetical proteins. We also found DNA sequences that ensure proper plasmid replication and partitioning as well as a toxin addiction system. This report sheds light on the biology of this important species, helping us to understand the mechanisms by which C. violaceum endures to several harsh conditions. This discovery could also be a first step in the development of a DNA manipulation tool in this bacterium.
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Affiliation(s)
- Daniel C Lima
- Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Norte, Natal, Brazil.,Laboratório de Biologia Molecular e Genômica, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Lena K Nyberg
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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30
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Abstract
The output from whole genome sequencing is a set of contigs, i.e. short non-overlapping DNA sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult task for previously unsequenced DNA, and may not be feasible due to factors such as the lack of sufficient coverage or larger repetitive regions which generate gaps in the final sequence. Here we propose a new method for scaffolding such contigs. The proposed method uses densely labeled optical DNA barcodes from competitive binding experiments as scaffolds. On these scaffolds we position theoretical barcodes which are calculated from the contig sequences. This allows us to construct longer DNA sequences from the contig sequences. This proof-of-principle study extends previous studies which use sparsely labeled DNA barcodes for scaffolding purposes. Our method applies a probabilistic approach that allows us to discard “foreign” contigs from mixed samples with contigs from different types of DNA. We satisfy the contig non-overlap constraint by formulating the contig placement challenge as a combinatorial auction problem. Our exact algorithm for solving this problem reduces computational costs compared to previous methods in the combinatorial auction field. We demonstrate the usefulness of the proposed scaffolding method both for synthetic contigs and for contigs obtained using Illumina sequencing for a mixed sample with plasmid and chromosomal DNA.
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Abstract
Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level and both the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments and analyze the data.
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Woksepp H, Ryberg A, Berglind L, Schön T, Söderman J. Epidemiological characterization of a nosocomial outbreak of extended spectrum β-lactamase Escherichia coli ST-131 confirms the clinical value of core genome multilocus sequence typing. APMIS 2017; 125:1117-1124. [PMID: 28960453 DOI: 10.1111/apm.12753] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/23/2017] [Indexed: 01/05/2023]
Abstract
Enhanced precision of epidemiological typing in clinically suspected nosocomial outbreaks is crucial. Our aim was to investigate whether single nucleotide polymorphism (SNP) analysis and core genome (cg) multilocus sequence typing (MLST) of whole genome sequencing (WGS) data would more reliably identify a nosocomial outbreak, compared to earlier molecular typing methods. Sixteen isolates from a nosocomial outbreak of ESBL E. coli ST-131 in southeastern Sweden and three control strains were subjected to WGS. Sequences were explored by SNP analysis and cgMLST. cgMLST clearly differentiated between the outbreak isolates and the control isolates (>1400 differences). All clinically identified outbreak isolates showed close clustering (≥2 allele differences), except for two isolates (>50 allele differences). These data confirmed that the isolates with >50 differing genes did not belong to the nosocomial outbreak. The number of SNPs within the outbreak was ≤7, whereas the two discrepant isolates had >700 SNPs. Two of the ESBL E. coli ST-131 isolates did not belong to the clinically identified outbreak. Our results illustrate the power of WGS in terms of resolution, which may avoid overestimation of patients belonging to outbreaks as judged from epidemiological data and previously employed molecular methods with lower discriminatory ability.
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Affiliation(s)
- Hanna Woksepp
- Department of Clinical Microbiology, Kalmar County Hospital, Kalmar, Sweden.,Department of Medicine and Optometry, Linnaeus University, Kalmar, Sweden
| | - Anna Ryberg
- Department of Clinical Microbiology, Växjö Central Hospital, Växjö, Sweden
| | - Linda Berglind
- Division of Medical Diagnostics, Region Jönköping County, Jönköping, Sweden
| | - Thomas Schön
- Department of Clinical Microbiology, Kalmar County Hospital, Kalmar, Sweden.,Department of Medicine and Optometry, Linnaeus University, Kalmar, Sweden.,Department Infectious Diseases, Kalmar County Hospital, Kalmar, Sweden.,Department of Clinical and Experimental Medicine, Division of Medical Microbiology, Linköping University, Linköping, Sweden
| | - Jan Söderman
- Division of Medical Diagnostics, Region Jönköping County, Jönköping, Sweden
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Abstract
In optical DNA mapping technologies sequence-specific intensity variations (DNA barcodes) along stretched and stained DNA molecules are produced. These “fingerprints” of the underlying DNA sequence have a resolution of the order one kilobasepairs and the stretching of the DNA molecules are performed by surface adsorption or nano-channel setups. A post-processing challenge for nano-channel based methods, due to local and global random movement of the DNA molecule during imaging, is how to align different time frames in order to produce reproducible time-averaged DNA barcodes. The current solutions to this challenge are computationally rather slow. With high-throughput applications in mind, we here introduce a parameter-free method for filtering a single time frame noisy barcode (snap-shot optical map), measured in a fraction of a second. By using only a single time frame barcode we circumvent the need for post-processing alignment. We demonstrate that our method is successful at providing filtered barcodes which are less noisy and more similar to time averaged barcodes. The method is based on the application of a low-pass filter on a single noisy barcode using the width of the Point Spread Function of the system as a unique, and known, filtering parameter. We find that after applying our method, the Pearson correlation coefficient (a real number in the range from -1 to 1) between the single time-frame barcode and the time average of the aligned kymograph increases significantly, roughly by 0.2 on average. By comparing to a database of more than 3000 theoretical plasmid barcodes we show that the capabilities to identify plasmids is improved by filtering single time-frame barcodes compared to the unfiltered analogues. Since snap-shot experiments and computational time using our method both are less than a second, this study opens up for high throughput optical DNA mapping with improved reproducibility.
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Abstract
Optical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequence-based studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches. In addition, designing lab-on-a-chip systems based on OM is now feasible and will allow the integrated and automated microbiological analysis of biological fluids. Here, we review the basic technology of OM, detail the current state of the art of the field, and look ahead to possible future developments in OM technology for microbiological applications.
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Müller V, Westerlund F. Optical DNA mapping in nanofluidic devices: principles and applications. LAB ON A CHIP 2017; 17:579-590. [PMID: 28098301 DOI: 10.1039/c6lc01439a] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Optical DNA mapping has over the last decade emerged as a very powerful tool for obtaining long range sequence information from single DNA molecules. In optical DNA mapping, intact large single DNA molecules are labeled, stretched out, and imaged using a fluorescence microscope. This means that sequence information ranging over hundreds of kilobasepairs (kbp) can be obtained in one single image. Nanochannels offer homogeneous and efficient stretching of DNA that is crucial to maximize the information that can be obtained from optical DNA maps. In this review, we highlight progress in the field of optical DNA mapping in nanochannels. We discuss the different protocols for sequence specific labeling and divide them into two main categories, enzymatic labeling and affinity-based labeling. Examples are highlighted where optical DNA mapping is used to gain information on length scales that would be inaccessible with traditional techniques. Enzymatic labeling has been commercialized and is mainly used in human genetics and assembly of complex genomes, while the affinity-based methods have primarily been applied in bacteriology, for example for rapid analysis of plasmids encoding antibiotic resistance. Next, we highlight how the design of nanofluidic channels can been altered in order to obtain the desired information and discuss how recent advances in the field make it possible to retrieve information beyond DNA sequence. In the outlook section, we discuss future directions of optical DNA mapping, such as fully integrated devices and portable microscopes.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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Orlek A, Stoesser N, Anjum MF, Doumith M, Ellington MJ, Peto T, Crook D, Woodford N, Walker AS, Phan H, Sheppard AE. Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology. Front Microbiol 2017; 8:182. [PMID: 28232822 PMCID: PMC5299020 DOI: 10.3389/fmicb.2017.00182] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/25/2017] [Indexed: 11/20/2022] Open
Abstract
Plasmids are extra-chromosomal genetic elements ubiquitous in bacteria, and commonly transmissible between host cells. Their genomes include variable repertoires of 'accessory genes,' such as antibiotic resistance genes, as well as 'backbone' loci which are largely conserved within plasmid families, and often involved in key plasmid-specific functions (e.g., replication, stable inheritance, mobility). Classifying plasmids into different types according to their phylogenetic relatedness provides insight into the epidemiology of plasmid-mediated antibiotic resistance. Current typing schemes exploit backbone loci associated with replication (replicon typing), or plasmid mobility (MOB typing). Conventional PCR-based methods for plasmid typing remain widely used. With the emergence of whole-genome sequencing (WGS), large datasets can be analyzed using in silico plasmid typing methods. However, short reads from popular high-throughput sequencers can be challenging to assemble, so complete plasmid sequences may not be accurately reconstructed. Therefore, localizing resistance genes to specific plasmids may be difficult, limiting epidemiological insight. Long-read sequencing will become increasingly popular as costs decline, especially when resolving accurate plasmid structures is the primary goal. This review discusses the application of plasmid classification in WGS-based studies of antibiotic resistance epidemiology; novel in silico plasmid analysis tools are highlighted. Due to the diverse and plastic nature of plasmid genomes, current typing schemes do not classify all plasmids, and identifying conserved, phylogenetically concordant genes for subtyping and phylogenetics is challenging. Analyzing plasmids as nodes in a network that represents gene-sharing relationships between plasmids provides a complementary way to assess plasmid diversity, and allows inferences about horizontal gene transfer to be made.
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Affiliation(s)
- Alex Orlek
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
| | - Muna F. Anjum
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
- Department of Bacteriology, Animal and Plant Health AgencyAddlestone, UK
| | - Michel Doumith
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health EnglandLondon, UK
| | - Matthew J. Ellington
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health EnglandLondon, UK
| | - Tim Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Neil Woodford
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health EnglandLondon, UK
| | - A. Sarah Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Hang Phan
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Anna E. Sheppard
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
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Müller V, Rajer F, Frykholm K, Nyberg LK, Quaderi S, Fritzsche J, Kristiansson E, Ambjörnsson T, Sandegren L, Westerlund F. Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping. Sci Rep 2016; 6:37938. [PMID: 27905467 PMCID: PMC5131345 DOI: 10.1038/srep37938] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/01/2016] [Indexed: 12/03/2022] Open
Abstract
Bacterial plasmids are extensively involved in the rapid global spread of antibiotic resistance. We here present an assay, based on optical DNA mapping of single plasmids in nanofluidic channels, which provides detailed information about the plasmids present in a bacterial isolate. In a single experiment, we obtain the number of different plasmids in the sample, the size of each plasmid, an optical barcode that can be used to identify and trace the plasmid of interest and information about which plasmid that carries a specific resistance gene. Gene identification is done using CRISPR/Cas9 loaded with a guide-RNA (gRNA) complementary to the gene of interest that linearizes the circular plasmids at a specific location that is identified using the optical DNA maps. We demonstrate the principle on clinically relevant extended spectrum beta-lactamase (ESBL) producing isolates. We discuss how the gRNA sequence can be varied to obtain the desired information. The gRNA can either be very specific to identify a homogeneous group of genes or general to detect several groups of genes at the same time. Finally, we demonstrate an example where we use a combination of two gRNA sequences to identify carbapenemase-encoding genes in two previously not characterized clinical bacterial samples.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fredrika Rajer
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Karolin Frykholm
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lena K. Nyberg
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Saair Quaderi
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Joachim Fritzsche
- Department of Applied Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology/University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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