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Abad-Fau A, Sevilla E, Martín-Burriel I, Moreno B, Bolea R. Update on Commonly Used Molecular Typing Methods for Clostridioides difficile. Microorganisms 2023; 11:1752. [PMID: 37512924 PMCID: PMC10384772 DOI: 10.3390/microorganisms11071752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023] Open
Abstract
This review aims to provide a comprehensive overview of the significant Clostridioides difficile molecular typing techniques currently employed in research and medical communities. The main objectives of this review are to describe the key molecular typing methods utilized in C. difficile studies and to highlight the epidemiological characteristics of the most prevalent strains on a global scale. Geographically distinct regions exhibit distinct strain types of C. difficile, with notable concordance observed among various typing methodologies. The advantages that next-generation sequencing (NGS) offers has changed epidemiology research, enabling high-resolution genomic analyses of this pathogen. NGS platforms offer an unprecedented opportunity to explore the genetic intricacies and evolutionary trajectories of C. difficile strains. It is relevant to acknowledge that novel routes of transmission are continually being unveiled and warrant further investigation, particularly in the context of zoonotic implications and environmental contamination.
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Affiliation(s)
- Ana Abad-Fau
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Eloísa Sevilla
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Inmaculada Martín-Burriel
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | - Bernardino Moreno
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Rosa Bolea
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
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Esikova TZ, Anokhina TO, Suzina NE, Shushkova TV, Wu Y, Solyanikova IP. Characterization of a New Pseudomonas Putida Strain Ch2, a Degrader of Toxic Anthropogenic Compounds Epsilon-Caprolactam and Glyphosate. Microorganisms 2023; 11:microorganisms11030650. [PMID: 36985223 PMCID: PMC10053300 DOI: 10.3390/microorganisms11030650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
In this work, a new Ch2 strain was isolated from soils polluted by agrochemical production wastes. This strain has a unique ability to utilize toxic synthetic compounds such as epsilon-caprolactam (CAP) as a sole carbon and energy source and the herbicide glyphosate (GP) as a sole source of phosphorus. Analysis of the nucleotide sequence of the 16S rRNA gene of Ch2 revealed that the strain belongs to the species Pseudomonas putida. This strain grew in the mineral medium containing CAP in a concentration range of 0.5 to 5.0 g/L and utilized 6-aminohexanoic acid and adipic acid, which are the intermediate products of CAP catabolism. The ability of strain Ch2 to degrade CAP is determined by a conjugative megaplasmid that is 550 kb in size. When strain Ch2 is cultured in a mineral medium containing GP (500 mg/L), more intensive utilization of the herbicide occurs in the phase of active growth. In the phase of declining growth, there is an accumulation of aminomethylphosphonic acid, which indicates that the C-N bond is the first site cleaved during GP degradation (glyphosate oxidoreductase pathway). Culture growth in the presence of GP during the early step of its degradation is accompanied by unique substrate-dependent changes in the cytoplasm, including the formation of vesicles of cytoplasmic membrane consisting of specific electron-dense content. There is a debate about whether these membrane formations are analogous to metabolosomes, where the primary degradation of the herbicide can take place. The studied strain is notable for its ability to produce polyhydroxyalkanoates (PHAs) when grown in mineral medium containing GP. At the beginning of the stationary growth phase, it was shown that, the amount and size of PHA inclusions in the cells drastically increased; they filled almost the entire volume of cell cytoplasm. The obtained results show that the strain P. putida Ch2 can be successfully used for the PHAs’ production. Moreover, the ability of P. putida Ch2 to degrade CAP and GP determines the prospects of its application for the biological cleanup of CAP production wastes and in situ bioremediation of soil polluted with GP.
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Affiliation(s)
- Tatiana Z. Esikova
- Laboratory of Plasmid Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
| | - Tatiana O. Anokhina
- Laboratory of Plasmid Biology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
| | - Nataliya E. Suzina
- Laboratory of Cytology of Microorganisms, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
| | - Tatiana V. Shushkova
- Laboratory of Microbial Enzymology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
| | - Yonghong Wu
- Zigui Ecological Station for Three Gorges Dam Project, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Inna P. Solyanikova
- Laboratory of Microbial Enzymology, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Center for Biological Research of the Russian Academy of Sciences, Prosp. Nauki 5, Pushchino, 142290 Pushchino, Russia
- Regional Microbiological Center, Institute of Pharmacy, Chemistry and Biology, Belgorod National Research University, 308015 Belgorod, Russia
- Correspondence:
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Make It Less difficile: Understanding Genetic Evolution and Global Spread of Clostridioides difficile. Genes (Basel) 2022; 13:genes13122200. [PMID: 36553467 PMCID: PMC9778335 DOI: 10.3390/genes13122200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
Clostridioides difficile is an obligate anaerobic pathogen among the most common causes of healthcare-associated infections. It poses a global threat due to the clinical outcomes of infection and resistance to antibiotics recommended by international guidelines for its eradication. In particular, C. difficile infection can lead to fulminant colitis associated with shock, hypotension, megacolon, and, in severe cases, death. It is therefore of the utmost urgency to fully characterize this pathogen and better understand its spread, in order to reduce infection rates and improve therapy success. This review aims to provide a state-of-the-art overview of the genetic variation of C. difficile, with particular regard to pathogenic genes and the correlation with clinical issues of its infection. We also summarize the current typing techniques and, based on them, the global distribution of the most common ribotypes. Finally, we discuss genomic surveillance actions and new genetic engineering strategies as future perspectives to make it less difficile.
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Genomic Investigation into the Virulome, Pathogenicity, Stress Response Factors, Clonal Lineages, and Phylogenetic Relationship of Escherichia coli Strains Isolated from Meat Sources in Ghana. Genes (Basel) 2020; 11:genes11121504. [PMID: 33327465 PMCID: PMC7764966 DOI: 10.3390/genes11121504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Escherichia coli are among the most common foodborne pathogens associated with infections reported from meat sources. This study investigated the virulome, pathogenicity, stress response factors, clonal lineages, and the phylogenomic relationship of E. coli isolated from different meat sources in Ghana using whole-genome sequencing. Isolates were screened from five meat sources (beef, chevon, guinea fowl, local chicken, and mutton) and five areas (Aboabo, Central market, Nyorni, Victory cinema, and Tishegu) based in the Tamale Metropolis, Ghana. Following microbial identification, the E. coli strains were subjected to whole-genome sequencing. Comparative visualisation analyses showed different DNA synteny of the strains. The isolates consisted of diverse sequence types (STs) with the most common being ST155 (n = 3/14). Based Upon Related Sequence Types (eBURST) analyses of the study sequence types identified four similar clones, five single-locus variants, and two satellite clones (more distantly) with global curated E. coli STs. All the isolates possessed at least one restriction-modification (R-M) and CRISPR defence system. Further analysis revealed conserved stress response mechanisms (detoxification, osmotic, oxidative, and periplasmic stress) in the strains. Estimation of pathogenicity predicted a higher average probability score (Pscore ≈ 0.937), supporting their pathogenic potential to humans. Diverse virulence genes that were clonal-specific were identified. Phylogenomic tree analyses coupled with metadata insights depicted the high genetic diversity of the E. coli isolates with no correlation with their meat sources and areas. The findings of this bioinformatic analyses further our understanding of E. coli in meat sources and are broadly relevant to the design of contamination control strategies in meat retail settings in Ghana.
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Molecular Characterization and Diagnosis of Nosocomial Clostridium difficile Infection in Hospitalized Patients. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2020. [DOI: 10.5812/archcid.97330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Pu T, Mei Z, Zhang W, Liang WJ, Zhou X, Liang J, Deng Z, Wang Z. An in vitro DNA phosphorothioate modification reaction. Mol Microbiol 2019; 113:452-463. [PMID: 31749226 DOI: 10.1111/mmi.14430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/10/2019] [Accepted: 11/17/2019] [Indexed: 12/25/2022]
Abstract
Phosphorothioation (PT) involves the replacement of a nonbridging phosphate oxygen on the DNA backbone with sulfur. In bacteria, the procedure is both sequence- and stereo-specific. We reconstituted the PT reaction using purified DndCDE from Salmonella enterica and IscS from Escherichia coli. We determined that the in vitro process of PT was oxygen sensitive. Only one strand on a double-stranded (ds) DNA substrate was modified in the reaction. The modification was dominant between G and A in the GAAC/GTTC conserved sequence. The modification between G and T required the presence of PT between G and A on the opposite strand. Cysteine, S-adenosyl methionine (SAM) and the formation of an iron-sulfur cluster in DndCDE (DndCDE-FeS) were essential for the process. Results from SAM cleavage reactions support the supposition that PT is a radical SAM reaction. Adenosine triphosphate (ATP) promoted the reaction but was not essential. The data and conclusions presented suggest that the PT reaction in bacteria involves three steps. The first step is the binding of DndCDE-FeS to DNA and searching for the modification sequence, possibly with the help of ATP. Cysteine locks DndCDE-FeS to the modification site with an appropriate protein conformation. SAM triggers the radical SAM reaction to complete the oxygen-sulfur swapping.
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Affiliation(s)
- Tianning Pu
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhiling Mei
- Shanghai Thinkgene Biotech CO., LTD, Shanghai, People's Republic of China
| | - Wei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Wei-Jun Liang
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, UK
| | - Xiufen Zhou
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jingdan Liang
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Martin JSH, Eyre DW, Fawley WN, Griffiths D, Davies K, Mawer DPC, Peto TEA, Crook DW, Walker AS, Wilcox MH. Patient and Strain Characteristics Associated With Clostridium difficile Transmission and Adverse Outcomes. Clin Infect Dis 2019; 67:1379-1387. [PMID: 29659753 PMCID: PMC6186849 DOI: 10.1093/cid/ciy302] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/23/2018] [Indexed: 01/05/2023] Open
Abstract
Background No study has used whole-genome sequencing (WGS) to investigate risk factors for Clostridium difficile (CD) transmission between cases, or assessed the impact of recent acquisition on patient outcome. Methods This 20 month retrospective cohort study included consecutive cytotoxin-positive diarrheal samples, which underwent culture, ribotyping, and WGS (Illumina). Sequenced isolates were compared using single nucleotide variants (SNVs). Independent predictors of acquisition from another case, onward transmission, 120-day recurrence, and 30-day mortality were identified using logistic regression with backwards elimination. Results Of 660 CD cases, 640 (97%) were sequenced, of which 567 (89%) shared a ribotype with a prior case, but only 227 (35%) were ≤2 SNVs from a prior case, supporting recent acquisition. Plausible (<2 SNVs) recent ward-based acquisition from a symptomatic case was more frequent in certain ribotypes; 64% (67/105) for ribotype-027 cases, compared with 11% (6/57) for ribotype-078. Independent risk factors (adjusted P < .05) for CD acquisition included older age, longer inpatient duration, and ribotype; these factors, and male sex, increased onward transmission. Patients with a plausible donor had a greater risk of recurrence (adjusted P = .001) and trended towards greater 30-day mortality (adjusted P = .06). Ribotype had no additional mortality or recurrence impact after adjusting for acquisition (P > .1). Conclusions Greater transmission of certain lineages suggests CD may have different reservoirs and modes of transmission. Acquiring CD from a recent case is associated with poorer clinical outcomes. Clinical characteristics associated with increased healthcare-associated CD transmission could be used to target preventative interventions.
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Affiliation(s)
| | - David W Eyre
- Nuffield Department of Medicine, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom
| | - Warren N Fawley
- Public Health England-Leeds Regional Laboratory, United Kingdom
| | - David Griffiths
- Nuffield Department of Medicine, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom
| | - Kerrie Davies
- Leeds Teaching Hospitals & University of Leeds, United Kingdom
| | | | - Timothy E A Peto
- Nuffield Department of Medicine, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Medicine, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom.,Public Health England, Colindale, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Medicine, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom
| | - Mark H Wilcox
- Leeds Teaching Hospitals & University of Leeds, United Kingdom
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Phosphorothioated DNA Is Shielded from Oxidative Damage. Appl Environ Microbiol 2019; 85:AEM.00104-19. [PMID: 30737351 DOI: 10.1128/aem.00104-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 02/05/2019] [Indexed: 11/20/2022] Open
Abstract
DNA is the carrier of genetic information. DNA modifications play a central role in essential physiological processes. Phosphorothioation (PT) modification involves the replacement of an oxygen atom on the DNA backbone with a sulfur atom. PT modification can cause genomic instability in Salmonella enterica under hypochlorous acid stress. This modification restores hydrogen peroxide (H2O2) resistance in the catalase-deficient Escherichia coli Hpx- strain. Here, we report biochemical characterization results for a purified PT modification protein complex (DndCDE) from S. enterica We observed multiplex oligomeric states of DndCDE by using native PAGE. This protein complex bound avidly to PT-modified DNA. DndCDE with an intact iron-sulfur cluster (DndCDE-FeS) possessed H2O2 decomposition activity, with a V max of 10.58 ± 0.90 mM min-1 and a half-saturation constant, K 0.5S, of 31.03 mM. The Hill coefficient was 2.419 ± 0.59 for this activity. The protein's activity toward H2O2 was observed to be dependent on the intact DndCDE and on the formation of an iron-sulfur (Fe-S) cluster on the DndC subunit. In addition to cysteine residues that mediate the formation of this Fe-S cluster, other cysteine residues play a catalytic role. Finally, catalase activity was also detected in DndCDE from Pseudomonas fluorescens Pf0-1. The data and conclusions presented suggest that DndCDE-FeS is a short-lived catalase. Our experiments also indicate that the complex binds to PT sites, shielding PT DNA from H2O2 damage. This catalase shield might be able to extend from PT sites to the entire bacterial genome.IMPORTANCE DNA phosphorothioation has been reported in many bacteria. These PT-hosting bacteria live in very different environments, such as the human body, soil, or hot springs. The physiological function of DNA PT modification is still elusive. A remarkable property of PT modification is that purified genomic PT DNA is susceptible to oxidative cleavage. Among the oxidants, hypochlorous acid and H2O2 are of physiological relevance for human pathogens since they are generated during the human inflammation response to bacterial infection. However, expression of PT genes in the catalase-deficient E. coli Hpx- strain restores H2O2 resistance. Here, we seek to solve this obvious paradox. We demonstrate that DndCDE-FeS is a short-lived catalase that binds tightly to PT DNA. It is thus possible that by docking to PT sites the catalase activity protects the bacterial genome against H2O2 damage.
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Mwangi S, Timmons J, Fitz-coy S, Parveen S. Characterization of Clostridium perfringens recovered from broiler chicken affected by necrotic enteritis. Poult Sci 2019; 98:128-135. [DOI: 10.3382/ps/pey332] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/06/2018] [Indexed: 11/20/2022] Open
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Perez JBDS, Fernando C, Nosach RV, Huang Y, Harding JCS, Hill JE. In vitro attenuation of a virulent swine isolate of Brachyspira hampsonii. Pathog Dis 2018; 76:4563581. [PMID: 29069340 DOI: 10.1093/femspd/ftx116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/19/2017] [Indexed: 11/13/2022] Open
Abstract
Brachyspira hampsonii causes dysentery-like disease in infected pigs. Serial passage of a virulent swine isolate (P13) one-hundred times in laboratory culture medium was conducted to produce an attenuated strain, and to identify genomic determinants of virulence through comparison of genome sequences of the original and passaged strains. The resulting strain, P113, did not differ from P13 in terms of diagnostic biochemical characteristics but had an enhanced growth rate in culture, indicating laboratory adaptation. Whole genome sequencing of P113 revealed several single-nucleotide changes including a T to C transition that results in an R to G amino acid change in a putative mannose-1-phosphate guanylytransferase that is implicated in production of lipo-oligosaccharide. P113 was partially attenuated in a mouse model of infection, indicated by significantly fewer observations of abnormal feces in mice infected with P113 relative to P13. No differences were detected in bacterial shedding in feces, demonstrating that the ability of the organism to colonize mice was not affected. Passage through a mouse did not further alter the virulence of P113. Results of this study provide insight into genomic determinants of virulence in B. hampsonii and a live attenuated vaccine candidate.
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Affiliation(s)
- Jason Byron D S Perez
- Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon S7N 5B4, SK, Canada
| | - Champika Fernando
- Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon S7N 5B4, SK, Canada
| | - Roman V Nosach
- Department of Large Animal Clinical Sciences, University of Saskatchewan, 52 Campus Drive, Saskatoon S7N 5B4, Canada
| | - Yanyun Huang
- Prairie Diagnostic Services Inc., 52 Campus Drive, Saskatoon S7N5B4, Canada
| | - John C S Harding
- Department of Large Animal Clinical Sciences, University of Saskatchewan, 52 Campus Drive, Saskatoon S7N 5B4, Canada
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon S7N 5B4, SK, Canada
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DNA Backbone Sulfur-Modification Expands Microbial Growth Range under Multiple Stresses by its anti-oxidation function. Sci Rep 2017; 7:3516. [PMID: 28615635 PMCID: PMC5471199 DOI: 10.1038/s41598-017-02445-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 04/11/2017] [Indexed: 11/26/2022] Open
Abstract
DNA phosphorothioate (PT) modification is a sulfur modification on the backbone of DNA introduced by the proteins DndA-E. It has been detected within many bacteria isolates and metagenomic datasets, including human pathogens, and is considered to be widely distributed in nature. However, little is known about the physiological function of this modification, and thus its evolutionary significance and application potential remains largely a mystery. In this study, we focused on the advantages of DNA PT modification to bacterial cells coping with environmental stresses. We show that the mesophile Escherichia coli and the extremophile Shewanella piezotolerans both expanded their growth ranges following exposure to extreme temperature, salinity, pH, pressure, UV, X-ray and heavy metals as a result of DNA phophorothioation. The phophorothioated DNA reacted to both H2O2 and hydroxyl radicals in vivo, and protected genomic DNA as well as sensitive enzymes from intracellular oxidative damage. We further demonstrate that this process has evolved separate from its associated role in DNA restriction and modification. These findings provide a physiological role for a covalent modification widespread in nature and suggest possible applications in biotechnology and biomedicine.
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Agafonova NV, Doronina NV, Kaparullina EN, Fedorov DN, Gafarov AB, Sazonova OI, Sokolov SL, Trotsenko YA. A novel Delftia plant symbiont capable of autotrophic methylotrophy. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717010039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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First report of Clostridium difficile NAP1/027 in a Mexican hospital. PLoS One 2015; 10:e0122627. [PMID: 25915544 PMCID: PMC4411131 DOI: 10.1371/journal.pone.0122627] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/23/2015] [Indexed: 12/18/2022] Open
Abstract
Background and Objective Clostridium difficile NAP1/ribotype 027 is associated with severe disease and high mortality rates. Our aim was to determine the prevalence of NAP1/ribotype 027 among C. difficile isolates in a tertiary care hospital, and review the main clinical data. Methods We included 106 stool samples from 106 patients. Samples were tested for A&B toxins and were cultured on CCFA agar. The genes tcdA, tcdB, tcdC, cdtA, and cdtB were amplified using PCR in clinical isolates. The tcdA 3’-end deletion analysis, PCR-ribotyping, and pulsed-field gel electrophoresis (PFGE) were also performed. Stool samples that were positive for culture were tested by the GeneXpert C. difficile assay. Clinical data were collected. Results Thirty-six patients tested positive for A&B toxins; and 22 patients had positive culture for C. difficile, 14 of which tested positive for the A&B toxins and all 22 patients tested positive by the GeneXpert C. difficile assay. Risk factors included an average hospital stay of 16.1 days prior to toxin detection, average antibiotic use for 16.2 days, and a median of 3 antibiotics used. The 30-day crude mortality rate was 8.4%. Six of the 22 patients died, and 3 of those deaths were directly attributed to C. difficile infection. The majority of isolates, 90.9% (20/22), carried genes tcdB, tcdA, cdtA, and cdtB; and these strains carried the corresponding downregulator gene tcdC, with an 18-bp deletion. PFGE was performed on 17 isolates, and one main pattern was observed. Analysis of the ribotyping data showed similar results. Conclusion The above findings represent the clonal spread of C. difficile in our institution, which mainly includes the NAP1/027 strain. This is the first report of C. difficile ribotype NAP1/027 in Mexico.
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Dingle TC, MacCannell DR. Molecular Strain Typing and Characterisation of Toxigenic Clostridium difficile. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Kosheleva IA, Sazonova OI, Izmalkova TY, Boronin AM. Occurrence of the SAL+ phenotype in soil pseudomonads. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714060101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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17
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Nishihara M, Takahashi H, Sudo T, Kyoi D, Kawahara T, Ikeuchi Y, Fujita T, Kuda T, Kimura B, Yanahira S. Multilocus variable-number of tandem repeat analysis (MLVA) for Clostridium tyrobutyricum strains isolated from cheese production environment. Int J Food Microbiol 2014; 190:61-5. [PMID: 25190602 DOI: 10.1016/j.ijfoodmicro.2014.08.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 08/09/2014] [Accepted: 08/15/2014] [Indexed: 11/16/2022]
Abstract
Clostridium tyrobutyricum is a gram-positive spore-forming anaerobe that is considered as the main causative agent for late blowing in cheese due to butyric acid fermentation. In this study, multilocus variable-number of tandem repeat (VNTR) analysis (MLVA) for C. tyrobutyricum was developed to identify the source of contamination by C. tyrobutyricum spores in the cheese production environment. For each contig constructed from the results of a whole genome draft sequence of C. tyrobutyricum JCM11008(T) based on next-generation sequencing, VNTR loci that were effective for typing were searched using the Tandem Repeat Finder program. Five VNTR loci were amplified by polymerase chain reaction (PCR) to determine their number of repeats by sequencing, and MLVA was conducted. 25 strains of C. tyrobutyricum isolated from the environment, raw milk, and silage were classified into 18 MLVA types (DI=0.963). Of the C. tyrobutyricum strains isolated from raw milk, natural cheese, and blown processed cheese, strains with identical MLVA type were detected, which suggested that these strains might have shifted from natural cheese to blown processed cheese. MLVA could be an effective tool for monitoring contamination of natural cheese with C. tyrobutyricum in the processed cheese production environment because of its high discriminability, thereby allowing the analyst to trace the source of contamination.
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Affiliation(s)
- Masaharu Nishihara
- Institute of Food Hygiene, Quality Assurance Department, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe-shi, Saitama 350-1165, Japan
| | - Hajime Takahashi
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan.
| | - Tomoko Sudo
- Institute of Food Hygiene, Quality Assurance Department, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe-shi, Saitama 350-1165, Japan
| | - Daisuke Kyoi
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Toshio Kawahara
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Yoshihiro Ikeuchi
- Central Food Analysis Laboratory, Quality Assurance Department, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe-shi, Saitama 350-1165, Japan
| | - Takashi Fujita
- Institute of Food Hygiene, Quality Assurance Department, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe-shi, Saitama 350-1165, Japan
| | - Takashi Kuda
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Bon Kimura
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Shuichi Yanahira
- Institute of Food Hygiene, Quality Assurance Department, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe-shi, Saitama 350-1165, Japan
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18
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Abstract
Typing of Clostridium difficile facilitates understanding of the epidemiology of the infection. Some evaluations have shown that certain strain types (for example, ribotype 027) are more virulent than others and are associated with worse clinical outcomes. Although restriction endonuclease analysis (REA) and pulsed-field gel electrophoresis have been widely used in the past, PCR ribotyping is the current method of choice for typing of C. difficile. However, global standardization of ribotyping results is urgently needed. Whole-genome sequencing of C. difficile has the potential to provide even greater epidemiologic information than ribotyping.
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19
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Adzitey F, Huda N, Ali GRR. Molecular techniques for detecting and typing of bacteria, advantages and application to foodborne pathogens isolated from ducks. 3 Biotech 2013; 3:97-107. [PMID: 28324565 PMCID: PMC3597138 DOI: 10.1007/s13205-012-0074-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 05/23/2012] [Indexed: 01/18/2023] Open
Abstract
In recent times, several foodborne pathogens have become important and a threat to public health. Surveillance studies have provided data and a better understanding into the existence and spread of foodborne pathogens. The application of molecular techniques for detecting and typing of foodborne pathogens in surveillance studies provide reliable epidemiological data for tracing the source of human infections. A wide range of molecular techniques (including pulsed field gel electrophoresis, multilocus sequence typing, random amplified polymorphism deoxyribonucleic acid, repetitive extragenic palindromic, deoxyribonucleic acid sequencing, multiplex polymerase chain reaction and many more) have been used for detecting, speciating, typing, classifying and/or characterizing foodborne pathogens of great significance to humans. Farm animals including chickens, cattle, sheep, goats and pigs, and others (such as domestic and wild animals) have been reported to be primary reservoirs for foodborne pathogens. The consumption of contaminated poultry meats or products has been considered to be the leading source of human foodborne infections. Ducks like other farm animals are important source of foodborne pathogens and have been implicated in some human foodborne illnesses and deaths. Nonetheless, few studies have been conducted to explore the potential of ducks in causing foodborne outbreaks, diseases and its consequences. This review highlights some common molecular techniques, their advantages and those that have been applied to pathogens isolated from ducks and their related sources.
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Affiliation(s)
- Frederick Adzitey
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia
- Animal Science Department, University for Development Studies, Box TL 1882, Tamale, Ghana
| | - Nurul Huda
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia
| | - Gulam Rusul Rahmat Ali
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia.
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20
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Pires-dos-Santos T, Bisgaard M, Christensen H. Genetic diversity and virulence profiles of Escherichia coli causing salpingitis and peritonitis in broiler breeders. Vet Microbiol 2013. [DOI: 10.1016/j.vetmic.2012.11.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Garde S, Gaya P, Arias R, Nuñez M. Enhanced PFGE protocol to study the genomic diversity of Clostridium spp. isolated from Manchego cheeses with late blowing defect. Food Control 2012. [DOI: 10.1016/j.foodcont.2012.05.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Paul NC, Bärgman SC, Moodley A, Nielsen SS, Guardabassi L. Staphylococcus pseudintermedius colonization patterns and strain diversity in healthy dogs: a cross-sectional and longitudinal study. Vet Microbiol 2012; 160:420-7. [PMID: 22770516 DOI: 10.1016/j.vetmic.2012.06.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 06/08/2012] [Accepted: 06/11/2012] [Indexed: 11/20/2022]
Abstract
This is the first large-scale study of Staphylococcus pseudintermedius colonization and diversity in healthy dogs where samples were collected over a long time and strains were identified by PCR according to the current taxonomy of the S. intermedius group and typed by a highly discriminatory method such as pulsed field gel electrophoresis (PFGE). A cross-sectional study of nasal, oral, perineal and inguinal carriage in 119 healthy dogs was followed by a longitudinal study where oral and perineal carriage was examined in 16 dogs for 10 times over a period of 1 year. Altogether we collected 762 samples and 285 S. pseudintermedius isolates, 182 of which were typed by PFGE to determine spatial and temporal strain diversity within individual carriers. In the cross-sectional study, S. pseudintermedius was isolated from at least one body site in 82 (69%) of the 119 dogs. The most frequent carriage sites were the perineum (66%) and the mouth (65%) followed by the nose (27%) and the groin (23%). PFGE analysis showed high heterogeneity among the isolates originating from different body sites of the same dog. Fifteen of the 16 dogs sampled longitudinally carried S. pseudintermedius in at least one sampling time, including six dogs that were negative in the cross-sectional study. Our results indicate that S. pseudintermedius carriage in dogs is more frequent and heterogeneous than S. aureus carriage in humans. This observation might reflect the hygienic standards and social behavior of the canine host, which facilitates transmission of this bacterium in the dog population.
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Affiliation(s)
- Narayan Chandra Paul
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark.
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Kim H, Lee Y, Moon HW, Lim CS, Lee K, Chong Y. Emergence of Clostridium difficile ribotype 027 in Korea. Korean J Lab Med 2011; 31:191-6. [PMID: 21779194 PMCID: PMC3129351 DOI: 10.3343/kjlm.2011.31.3.191] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 04/18/2011] [Accepted: 04/19/2011] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Clostridium difficile infection (CDI) has markedly risen and is associated with hypervirulent ribotype 027 outbreaks in North America and Europe since 2003. The aims of this study were to determine the prevalence of ribotype 027 among C. difficile isolates in Korea, to characterize the ribotype 027 isolates, and to determine the clinical severity of CDI in patients infected with these isolates. METHODS A total of 1,251 isolates of C. difficile recovered from stool specimens of suspected CDI patients at two tertiary-care hospitals and one commercial laboratory between 2002 and 2009. Genes for toxin A (tcdA), toxin B (tcdB), and binary toxin (cdtA and cdtB) were detected by PCR. Mutation in the tcdC gene was detected by sequencing after PCR amplification. For molecular genotyping, we performed PCR-ribotyping, pulsed-field gel electrophoresis (PFGE), and multilocus variable-number tandem-repeat analysis (MLVA). Minimum inhibitory concentrations of moxifloxacin were determined using Etest strips (AB bioMérieux, Sweden). RESULTS We identified 7 isolates as ribotype 027. These isolates had the same tcdC mutation as the epidemic strain, and 6 of them were resistant to moxifloxacin. The isolates were categorized into 3 different PFGE types and 7 different MLVA types. All the 7 cases had occurred sporadically. CONCLUSIONS C. difficile ribotype 027 is uncommon, but it has emerged in Korea. The spread of this ribotype should be closely monitored in order to avoid an outbreak of CDI in Korea.
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Affiliation(s)
- Heejung Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
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24
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Kim SJ, Kim H, Seo Y, Yong D, Jeong SH, Chong Y, Lee K. Molecular characterization of toxin A-negative, toxin B-positive variant strains of Clostridium difficile isolated in Korea. Diagn Microbiol Infect Dis 2010; 67:198-201. [PMID: 20338708 DOI: 10.1016/j.diagmicrobio.2010.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 01/14/2010] [Accepted: 01/15/2010] [Indexed: 10/19/2022]
Abstract
A(-)B(+)Clostridium difficile strains are prevalent in Korea. We performed pulsed-field gel electrophoresis (PFGE), polymerase chain reaction ribotyping, and toxinotyping in 82 A(-)B(+) clinical isolates in Korea. PFGE showed highest discriminatory capability among the 3 methods. By PFGE, persistence of a clone was found, suggesting this clone has adapted to the hospital environment.
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Affiliation(s)
- Sue Jung Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 120-752, Korea
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25
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Sazonova OI, Izmalkova TY, Kosheleva IA, Boronin AM. Salicylate degradation by Pseudomonas putida strains not involving the “Classical” nah2 operon. Microbiology (Reading) 2008. [DOI: 10.1134/s002626170806009x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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26
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Bobulsky GS, Al-Nassir WN, Riggs MM, Sethi AK, Donskey CJ. Clostridium difficile Skin Contamination in Patients with C. difficile-Associated Disease. Clin Infect Dis 2008; 46:447-50. [DOI: 10.1086/525267] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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27
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Riggs MM, Sethi AK, Zabarsky TF, Eckstein EC, Jump RLP, Donskey CJ. Asymptomatic Carriers Are a Potential Source for Transmission of Epidemic and Nonepidemic Clostridium difficile Strains among Long-Term Care Facility Residents. Clin Infect Dis 2007; 45:992-8. [PMID: 17879913 DOI: 10.1086/521854] [Citation(s) in RCA: 395] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Accepted: 06/11/2007] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Asymptomatic fecal carriage of Clostridium difficile is common in patients staying in health care facilities, but the importance of asymptomatic carriers with regard to disease transmission is unclear. METHODS We prospectively examined the prevalence of asymptomatic carriage of epidemic North American pulsed-field gel electrophoresis type 1 and nonepidemic toxigenic C. difficile strains among long-term care patients in the context of an outbreak of C. difficile-associated disease and evaluated the frequency of skin and environmental contamination. Molecular typing was performed by pulsed-field gel electrophoresis. Logistic regression was used to assess factors associated with asymptomatic carriage, and a sensitive and specific prediction rule was developed to identify high-risk patients. RESULTS Thirty-five (51%) of 68 asymptomatic patients were carriers of toxigenic C. difficile, and 13 (37%) of these patients carried epidemic strains. Compared with noncarriers, asymptomatic carriers had higher percentages of skin (61% vs. 19%; P=.001) and environmental contamination (59% vs. 24%; P=.004). Eighty-seven percent of isolates found in skin samples and 58% of isolates found in environmental samples were identical to concurrent isolates found in stool samples. Spores on the skin of asymptomatic patients were easily transferred to investigators' hands. Previous C. difficile-associated disease (P<.001) and previous antibiotic use (P=.017) were associated with asymptomatic carriage, and the combination of these 2 variables was predictive of asymptomatic carriage (sensitivity, 77%; specificity, 58%; positive predictive value, 66%; negative predictive value, 70%). CONCLUSIONS Our findings suggest that asymptomatic carriers of epidemic and nonepidemic C. difficile strains have the potential to contribute significantly to disease transmission in long-term care facilities. Clinical factors, such as previous C. difficile-associated disease and recent antibiotic use, may be predictive of asymptomatic carriage.
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Affiliation(s)
- Michelle M Riggs
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
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28
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Bouza E, Burillo A, Muñoz P. Antimicrobial therapy of Clostridium difficile-associated diarrhea. Med Clin North Am 2006; 90:1141-63. [PMID: 17116441 DOI: 10.1016/j.mcna.2006.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Clostridium difficile-associated diarrhea (CDAD) is the most common etiologically-defined cause of hospital-acquired diarrhea. Caused by the toxins of certain strains of C difficile, CDAD represents a growing concern, with epidemic outbreaks in some hospitals where very aggressive and difficult-to-treat strains have recently been found. Incidence of CDAD varies ordinarily between 1 to 10 in every 1,000 admissions. Evidence shows that CDAD increases morbidity, length of stay, and costs. This article described the clinical manifestations of CDAD, related risk factors, considerations for confirming CDAD, antimicrobial and non-antimicrobial treatment of CDAD, and issues related to relapses. The article concludes with a discussion of recent epidemic outbreaks involving CDAD.
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Affiliation(s)
- Emilio Bouza
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Universidad Complutense, Dr. Esquerdo 46, 28007 Madrid, Spain
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29
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MacCannell DR, Louie TJ, Gregson DB, Laverdiere M, Labbe AC, Laing F, Henwick S. Molecular analysis of Clostridium difficile PCR ribotype 027 isolates from Eastern and Western Canada. J Clin Microbiol 2006; 44:2147-52. [PMID: 16757612 PMCID: PMC1489423 DOI: 10.1128/jcm.02563-05] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The prevalence and characteristics of PCR ribotype 027 strains of Clostridium difficile have come into question following recent outbreaks in Eastern Canada and elsewhere. In order to determine the distribution of this strain in other regions in Canada, we screened a bank of 1,419 isolates recovered from three different Canadian health regions between 2000 and 2004. Among isolates from a Montreal area hospital, PCR ribotype 027 strains represented 115/153 strains (75.2%) from 2003 to 2004, but ribotype 027 strains were absent in 2000 and 2001. In Calgary, by contrast, ribotype 027 rates have remained relatively stable over 4 years of surveillance, representing 51/685 (7.4%) hospital isolates and 62/373 (16.6%) strains from the community (P < 0.001). PCR ribotype 027 accounted for 8/135 (5.9%) hospital isolates in the Fraser Health Region in 2004. repetitive extragenic palindromic PCR was used to subtype a random selection of 027 isolates from each region. All 10 of the isolates from Quebec were of a single subtype, which was also dominant among isolates from Alberta (8/10 isolates) and British Columbia (6/8 isolates). Comparative sequencing of the tcdC repressor gene confirmed the documented 18-bp deletion and identified a second, single-base-pair deletion at position 117. Both deletions were conserved across all three provinces and were identified in a United Kingdom reference strain. The presence of a frameshift in the early portion of the tcdC gene implies serious functional disruption and may contribute to the hypervirulence of the 027 phenotype. PCR ribotype 027 strains appear to be widely distributed, to predate the Montreal outbreak, and to have measurable community presence in Western Canada.
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Affiliation(s)
- Duncan R MacCannell
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
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30
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Leclair D, Pagotto F, Farber JM, Cadieux B, Austin JW. Comparison of DNA fingerprinting methods for use in investigation of type E botulism outbreaks in the Canadian Arctic. J Clin Microbiol 2006; 44:1635-44. [PMID: 16672387 PMCID: PMC1479196 DOI: 10.1128/jcm.44.5.1635-1644.2006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pulsed-field gel electrophoresis (PFGE), randomly amplified polymorphic DNA (RAPD) analysis, and automated ribotyping were compared for epidemiological typing of Clostridium botulinum type E using clinical and food isolates associated with four botulism outbreaks occurring in the Canadian Arctic. All type E strains previously untypeable by PFGE, even with the use of a formaldehyde fixation step, could be typed by the addition of 50 microM thiourea to the electrophoresis running buffer. Digestion with SmaI or XhoI followed by PFGE was used to link food and clinical isolates from four different type E botulism outbreaks and differentiate them from among 39 group II strains. Strain differentiation was unsuccessful with the automated ribotyping system, producing a single characteristic EcoRI fingerprint common to all group II strains. RAPD analysis of C. botulinum group II strains was not consistently reproducible with primer OPJ-6 or OPJ-13, apparently discriminating between epidemiologically related strains. A modified PFGE protocol was judged to be the most useful method for typing epidemiologically related C. botulinum type E strains, based on its ability to type all strains reproducibly and with an adequate level of discrimination.
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Affiliation(s)
- Daniel Leclair
- Bureau of Microbial Hazards, Health Products and Food Branch, Food Directorate, Health Canada, Tunney's Pasture, PL 2204A2, Ottawa, Ontario, Canada K1A 0L2
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31
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Samore MH, Venkataraman L, DeGirolami PC, Merrigan MM, Johnson S, Gerding DN, Carmeli Y, Harbarth S. Genotypic and Phenotypic Analysis ofClostridium difficileCorrelated with Previous Antibiotic Exposure. Microb Drug Resist 2006; 12:23-8. [PMID: 16584304 DOI: 10.1089/mdr.2006.12.23] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To analyze Clostridium difficile susceptibility results and genotypes in relation to antibiotic exposures that precipitated C. difficile-associated diarrhea (CDAD), we examined 83 nosocomial C. difficile isolates recovered at a tertiary care center in Boston, Massachusetts. MICs were determined by E-test methodology using modified Brucella agar. Isolates were genotyped by pulsed-field gel electrophoresis and restriction enzyme analysis. Antibiotic susceptibilities were: ciprofloxacin (0%), clindamycin (59%), trovafloxacin (63%), ceftriaxone (73%), piperacillin/tazobactam (100%), metronidazole (100%), and vancomycin (100%). The two most common strain groups, isolated from a total of 33 patients, were much more likely to be resistant to clindamycin, erythromycin, and trovafloxacin than other strain groups [79% (26 of 33) versus 2% (1 of 50), respectively]. Clindamycin exposure was strongly associated with CDAD caused by isolates that exhibited multiple resistance to clindamycin, erythromycin, and trovafloxacin (prevalence odds ratio, 4.2; 95% confidence interval, 1.1-16.8), whereas other antimicrobials did not yield significant associations. Resistance of specific C. difficile strains to clindamycin and other antimicrobial agents may contribute to their hospital dissemination and explain, in part, the propensity of clindamycin to trigger nosocomial outbreaks.
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Affiliation(s)
- Matthew H Samore
- VA Salt Lake City Health Care System, and Division of Clinical Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA.
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32
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Affiliation(s)
- Ian R Poxton
- Medical Microbiology, University of Edinburgh Medical School, Teviot Place, Edinburgh EH8 9AG, UK
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