1
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Spigaglia P, Mastrantonio P, Barbanti F. Antibiotic Resistances of Clostridioides difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:169-198. [PMID: 38175476 DOI: 10.1007/978-3-031-42108-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The rapid evolution of antibiotic resistance in Clostridioides difficile and the consequent effects on prevention and treatment of C. difficile infections (CDIs) are a matter of concern for public health. Antibiotic resistance plays an important role in driving C. difficile epidemiology. Emergence of new types is often associated with the emergence of new resistances, and most of the epidemic C. difficile clinical isolates is currently resistant to multiple antibiotics. In particular, it is to worth to note the recent identification of strains with reduced susceptibility to the first-line antibiotics for CDI treatment and/or for relapsing infections. Antibiotic resistance in C. difficile has a multifactorial nature. Acquisition of genetic elements and alterations of the antibiotic target sites, as well as other factors, such as variations in the metabolic pathways or biofilm production, contribute to the survival of this pathogen in the presence of antibiotics. Different transfer mechanisms facilitate the spread of mobile elements among C. difficile strains and between C. difficile and other species. Furthermore, data indicate that both genetic elements and alterations in the antibiotic targets can be maintained in C. difficile regardless of the burden imposed on fitness, and therefore resistances may persist in C. difficile population in absence of antibiotic selective pressure.
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Affiliation(s)
- Patrizia Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Paola Mastrantonio
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Fabrizio Barbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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2
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Larcombe S, Williams GC, Amy J, Lim SC, Riley TV, Muleta A, Barugahare AA, Powell DR, Johanesen PA, Cheng AC, Peleg AY, Lyras D. A genomic survey of Clostridioides difficile isolates from hospitalized patients in Melbourne, Australia. Microbiol Spectr 2023; 11:e0135223. [PMID: 37815385 PMCID: PMC10715045 DOI: 10.1128/spectrum.01352-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/18/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE There has been a decrease in healthcare-associated Clostridioides difficile infection in Australia, but an increase in the genetic diversity of infecting strains, and an increase in community-associated cases. Here, we studied the genetic relatedness of C. difficile isolated from patients at a major hospital in Melbourne, Australia. Diverse ribotypes were detected, including those associated with community and environmental sources. Some types of isolates were more likely to carry antimicrobial resistance determinants, and many of these were associated with mobile genetic elements. These results correlate with those of other recent investigations, supporting the observed increase in genetic diversity and prevalence of community-associated C. difficile, and consequently the importance of sources of transmission other than symptomatic patients. Thus, they reinforce the importance of surveillance for in both hospital and community settings, including asymptomatic carriage, food, animals, and other environmental sources to identify and circumvent important sources of C. difficile transmission.
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Affiliation(s)
- Sarah Larcombe
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Galain C. Williams
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Jacob Amy
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Su Chen Lim
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Thomas V. Riley
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Medical, Molecular, and Forensic Sciences, Murdoch University, Perth, Western Australia, Australia
| | - Anthony Muleta
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | | | | | - Priscilla A. Johanesen
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Allen C. Cheng
- Department of Infectious Diseases, Alfred Hospital, Melbourne, Victoria, Australia
| | - Anton Y. Peleg
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Alfred Hospital, Melbourne, Victoria, Australia
| | - Dena Lyras
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
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3
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Rao RSP, Ghate SD, Shastry RP, Kurthkoti K, Suravajhala P, Patil P, Shetty P. Prevalence and heterogeneity of antibiotic resistance genes in Orientia tsutsugamushi and other rickettsial genomes. Microb Pathog 2023; 174:105953. [PMID: 36529286 DOI: 10.1016/j.micpath.2022.105953] [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: 10/22/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/16/2022]
Abstract
Despite a million infections every year and an estimated one billion people at risk, scrub typhus is regarded as a neglected tropical disease. The causative bacterium Orientia tsutsugamushi, a member of rickettsiae, seems to be intrinsically resistant to several classes of antibiotics. The emergence of antibiotic-resistant scrub typhus is likely to become a global public health concern. Yet, it is unknown as to how common antibiotic resistance genes are in O. tsutsugamushi, and how variable these loci are among the genomes of rickettsiae. By using the comprehensive antibiotic resistance database, we explored 79 complete genomes from 24 species of rickettsiae for antibiotic resistance loci. There were 244 unique antibiotic resistance genes in rickettsiae. Both the total and unique antibiotic resistance genes in O. tsutsugamushi were significantly less compared to other members of rickettsiae. However, antibiotic resistance genes in O. tsutsugamushi genomes were more unique and highly variable. Many genes such as resistant variants of evgS, and vanS A/G were present in numerous copies. These results will have important implications in the context of antibiotic-resistant scrub typhus.
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Affiliation(s)
- R Shyama Prasad Rao
- Center for Bioinformatics, NITTE deemed to be University, Mangaluru, 575018, India.
| | - Sudeep D Ghate
- Center for Bioinformatics, NITTE deemed to be University, Mangaluru, 575018, India
| | - Rajesh P Shastry
- Division of Microbiology and Biotechnology, Yenepoya Research Center, Yenepoya deemed to be University, Mangaluru, 575018, India
| | - Krishna Kurthkoti
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana PO, 690525, Kerala, India
| | - Prakash Patil
- Central Research Laboratory, KS Hegde Medical Academy (KSHEMA), NITTE deemed to be University, Mangaluru, 575018, India
| | - Praveenkumar Shetty
- Central Research Laboratory, KS Hegde Medical Academy (KSHEMA), NITTE deemed to be University, Mangaluru, 575018, India; Department of Biochemistry, KS Hegde Medical Academy (KSHEMA), NITTE deemed to be University, Mangaluru, 575018, India
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4
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Kopf A, Bunk B, Coldewey SM, Gunzer F, Riedel T, Schröttner P. Identification and Antibiotic Profiling of Wohlfahrtiimonas chitiniclastica, an Underestimated Human Pathogen. Front Microbiol 2021; 12:712775. [PMID: 34630346 PMCID: PMC8496446 DOI: 10.3389/fmicb.2021.712775] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/27/2021] [Indexed: 12/13/2022] Open
Abstract
In the past 12 years, several case reports have clearly demonstrated that Wohlfahrtiimonas chitiniclastica is capable of causing sepsis and bacteremia in humans. However, since most clinicians are not familiar with this species, little is known about its pathogenicity and treatment options while it is as rare but underestimated human pathogen. Therefore, a larger strain collection is required so that methods can be identified that are most suitable to obtain rapid and reliable identification. Moreover, the antimicrobial resistance profile needs to be elucidated in order to explore possible treatment options. Over a period of 6 years, we therefore have collected a total of 14 W. chitiniclastica isolates in routine diagnostics, which now served as the basis for a comprehensive characterization with respect to identification and antibiotic profiling. We compared the accuracy and convenience of several identification techniques in which MALDI-TOF MS and sequencing of the 16S rRNA gene have proven to be suitable for identification of W. chitiniclastica. In addition, whole genome sequencing (WGS)-based digital DNA-DNA hybridization (dDDH) was used as a reference method for strain identification, and surprised with the detection of a novel W. chitiniclastica subspecies. A combination of in silico and in vitro analyses revealed a first insight into the antimicrobial resistance profile and the molecular basis of antimicrobial resistance. Based on our findings, trimethoprim/sulfamethoxazole, levofloxacin, and cephalosporins (e.g., ceftazidime) may be the best antibiotics to use in order to treat infections caused by W. chitiniclastica, while resistance to fosfomycin, amikacin and tobramycin is observed.
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Affiliation(s)
- Anna Kopf
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Sina M Coldewey
- Clinic for Anaesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany.,Septomics Research Center, Jena University Hospital, Jena, Germany
| | - Florian Gunzer
- Department of Hospital Infection Control, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Percy Schröttner
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Dresden, Germany
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Andolfo G, Schuster C, Gharsa HB, Ruocco M, Leclerque A. Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola. BMC Genomics 2021; 22:708. [PMID: 34598677 PMCID: PMC8487129 DOI: 10.1186/s12864-021-08027-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/20/2021] [Indexed: 12/18/2022] Open
Abstract
Background Enterobacteria of the genus Providencia are mainly known as opportunistic human pathogens but have been isolated from highly diverse natural environments. The species Providencia vermicola comprises insect pathogenic bacteria carried by entomoparasitic nematodes and is investigated as a possible insect biocontrol agent. The recent publication of several genome sequences from bacteria assigned to this species has given rise to inconsistent preliminary results. Results The genome of the nematode-derived P. vermicola type strain DSM_17385 has been assembled into a 4.2 Mb sequence comprising 5 scaffolds and 13 contigs. A total of 3969 protein-encoding genes were identified. Multilocus sequence typing with different marker sets revealed that none of the previously published presumed P. vermicola genomes represents this taxonomic species. Comparative genomic analysis has confirmed a close phylogenetic relationship of P. vermicola to the P. rettgeri species complex. P. vermicola DSM_17385 carries a type III secretion system (T3SS-1) with probable function in host cell invasion or intracellular survival. Potentially antibiotic resistance-associated genes comprising numerous efflux pumps and point-mutated house-keeping genes, have been identified across the P. vermicola genome. A single small (3.7 kb) plasmid identified, pPVER1, structurally belongs to the qnrD-type family of fluoroquinolone resistance conferring plasmids that is prominent in Providencia and Proteus bacteria, but lacks the qnrD resistance gene. Conclusions The sequence reported represents the first well-supported published genome for the taxonomic species P. vermicola to be used as reference in further comparative genomics studies on Providencia bacteria. Due to a striking difference in the type of injectisome encoded by the respective genomes, P. vermicola might operate a fundamentally different mechanism of entomopathogenicity when compared to insect-pathogenic Providencia sneebia or Providencia burhodogranariea. The complete absence of antibiotic resistance gene carrying plasmids or mobile genetic elements as those causing multi drug resistance phenomena in clinical Providencia strains, is consistent with the invertebrate pathogen P. vermicola being in its natural environment efficiently excluded from the propagation routes of multidrug resistance (MDR) carrying genetic elements operating between human pathogens. Susceptibility to MDR plasmid acquisition will likely become a major criterion in the evaluation of P. vermicola for potential applications in biological pest control. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08027-w.
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Affiliation(s)
- Giuseppe Andolfo
- Department of Agricultural Sciences, University of Naples "Federico II", Via Università 100, 80055, Portici, Italy.
| | - Christina Schuster
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
| | - Haifa Ben Gharsa
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
| | - Michelina Ruocco
- Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche (CNR), Piazzale Enrico Fermi 1, 80055, Portici, Italy
| | - Andreas Leclerque
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany. .,Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche (CNR), Piazzale Enrico Fermi 1, 80055, Portici, Italy.
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6
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O’Grady K, Knight DR, Riley TV. Antimicrobial resistance in Clostridioides difficile. Eur J Clin Microbiol Infect Dis 2021; 40:2459-2478. [DOI: 10.1007/s10096-021-04311-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/08/2021] [Indexed: 02/08/2023]
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7
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Groß U, Brzuszkiewicz E, Gunka K, Starke J, Riedel T, Bunk B, Spröer C, Wetzel D, Poehlein A, Chibani C, Bohne W, Overmann J, Zimmermann O, Daniel R, Liesegang H. Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile. BMC Genomics 2018; 19:1. [PMID: 29291715 PMCID: PMC5749029 DOI: 10.1186/s12864-017-4368-0] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/06/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Clostridioides difficile infections (CDI) have emerged over the past decade causing symptoms that
range from mild, antibiotic-associated diarrhea (AAD) to life-threatening toxic megacolon. In this study, we describe a multiple and isochronal (mixed) CDI caused by the isolates DSM 27638, DSM 27639 and DSM 27640 that already initially showed different morphotypes on solid media. RESULTS The three isolates belonging to the ribotypes (RT) 012 (DSM 27639) and 027 (DSM 27638 and DSM 27640)
were phenotypically characterized and high quality closed genome sequences were generated. The genomes were compared with seven reference strains including three strains of the RT 027, two of the RT 017, and one of the RT 078 as well as a multi-resistant RT 012 strain. The analysis of horizontal gene transfer events revealed gene acquisition incidents that sort the strains within the time line of the spread of their RTs within Germany. We could show as well that horizontal gene transfer between the members of different RTs occurred within this multiple infection. In addition, acquisition and exchange of virulence-related features including antibiotic resistance genes were observed. Analysis of the two genomes assigned to RT 027 revealed three single nucleotide polymorphisms (SNPs) and apparently a regional genome modification within the flagellar switch that regulates the fli operon. CONCLUSION Our findings show that (i) evolutionary events based on horizontal gene transfer occur within an ongoing
CDI and contribute to the adaptation of the species by the introduction of new genes into the genomes, (ii) within a multiple infection of a single patient the exchange of genetic material was responsible for a much higher genome variation than the observed SNPs.
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Affiliation(s)
- Uwe Groß
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Elzbieta Brzuszkiewicz
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Katrin Gunka
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Jessica Starke
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Daniela Wetzel
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Cynthia Chibani
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Wolfgang Bohne
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Ortrud Zimmermann
- Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany.
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8
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Antibiotic Resistances of Clostridium difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1050:137-159. [PMID: 29383668 DOI: 10.1007/978-3-319-72799-8_9] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The rapid evolution of antibiotic resistance in Clostridium difficile and the consequent effects on prevention and treatment of C. difficile infections (CDIs) are matter of concern for public health. Antibiotic resistance plays an important role in driving C. difficile epidemiology. Emergence of new types is often associated with the emergence of new resistances and most of epidemic C. difficile clinical isolates is currently resistant to multiple antibiotics. In particular, it is to worth to note the recent identification of strains with reduced susceptibility to the first-line antibiotics for CDI treatment and/or for relapsing infections. Antibiotic resistance in C. difficile has a multifactorial nature. Acquisition of genetic elements and alterations of the antibiotic target sites, as well as other factors, such as variations in the metabolic pathways and biofilm production, contribute to the survival of this pathogen in the presence of antibiotics. Different transfer mechanisms facilitate the spread of mobile elements among C. difficile strains and between C. difficile and other species. Furthermore, recent data indicate that both genetic elements and alterations in the antibiotic targets can be maintained in C. difficile regardless of the burden imposed on fitness, and therefore resistances may persist in C. difficile population in absence of antibiotic selective pressure.
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9
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Fuzi M, Szabo D, Csercsik R. Double-Serine Fluoroquinolone Resistance Mutations Advance Major International Clones and Lineages of Various Multi-Drug Resistant Bacteria. Front Microbiol 2017; 8:2261. [PMID: 29250038 PMCID: PMC5715326 DOI: 10.3389/fmicb.2017.02261] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/02/2017] [Indexed: 01/06/2023] Open
Abstract
The major international sequence types/lineages of methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae and ESBL-producing E. coli were demonstrated to have been advanced by favorable fitness balance associated with high-level resistance to fluoroquinolones. The paper shows that favorable fitness in the major STs/lineages of these pathogens was principally attained by the capacity of evolving mutations in the fluoroquinolone-binding serine residues of both the DNA gyrase and topoisomerase IV enzymes. The available information on fitness balance incurred by individual and various combinations of mutations in the enzymes is reviewed in multiple species. Moreover, strong circumstantial evidence is presented that major STs/lineages of other multi-drug resistant bacteria, primarily vancomycin-resistant Enterococcus faecium (VRE), emerged by a similar mechanism. The reason(s) why the major ST/lineage strains of various pathogens proved more adept at evolving favorable mutations than most isolates of the same species remains to be elucidated.
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Affiliation(s)
- Miklos Fuzi
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Dora Szabo
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Rita Csercsik
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
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10
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Brent J, Burkhart K, Dargan P, Hatten B, Megarbane B, Palmer R, White J. Adverse Drug Reactions in the Intensive Care Unit. CRITICAL CARE TOXICOLOGY 2017. [PMCID: PMC7153447 DOI: 10.1007/978-3-319-17900-1_33] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adverse drug reactions (ADRs) are undesirable effects of medications used in normal doses [1]. ADRs can occur during treatment in an intensive care unit (ICU) or result in ICU admissions. A meta-analysis of 4139 studies suggests the incidence of ADRs among hospitalized patients is 17% [2]. Because of underreporting and misdiagnosis, the incidence of ADRs may be much higher and has been reported to be as high as 36% [3]. Critically ill patients are at especially high risk because of medical complexity, numerous high-alert medications, complex and often challenging drug dosing and medication regimens, and opportunity for error related to the distractions of the ICU environment [4]. Table 1 summarizes the ADRs included in this chapter.
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Affiliation(s)
- Jeffrey Brent
- Department of Medicine, Division of Clinical Pharmacology and Toxicology, University of Colorado, School of Medicine, Aurora, Colorado USA
| | - Keith Burkhart
- FDA, Office of New Drugs/Immediate Office, Center for Drug Evaluation and Research, Silver Spring, Maryland USA
| | - Paul Dargan
- Clinical Toxicology, St Thomas’ Hospital, Silver Spring, Maryland USA
| | - Benjamin Hatten
- Toxicology Associates, University of Colorado, School of Medicine, Denver, Colorado USA
| | - Bruno Megarbane
- Medical Toxicological Intensive Care Unit, Lariboisiere Hospital, Paris-Diderot University, Paris, France
| | - Robert Palmer
- Toxicology Associates, University of Colorado, School of Medicine, Denver, Colorado USA
| | - Julian White
- Toxinology Department, Women’s and Children’s Hospital, North Adelaide, South Australia Australia
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11
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Fuzi M. Dissimilar Fitness Associated with Resistance to Fluoroquinolones Influences Clonal Dynamics of Various Multiresistant Bacteria. Front Microbiol 2016; 7:1017. [PMID: 27458434 PMCID: PMC4935693 DOI: 10.3389/fmicb.2016.01017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/15/2016] [Indexed: 01/24/2023] Open
Abstract
Fitness cost associated with resistance to fluoroquinolones was recently shown to vary across clones of methicillin-resistant Staphylococcus aureus and extended-spectrum β-lactamase-producing Klebsiella pneumoniae. The resulting dissimilar fitness should have influenced the clonal dynamics and thereby the rates of resistance for these pathogens. Moreover, a similar mechanism was recently proposed for the emergence of the H30 and H30R lineages of ESBL-producing E. coli and the major international clone (ribotype 027) of Clostridium difficile. Furthermore, several additional international clones of various multiresistant bacteria are suspect to have been selected by an analogous process. An ability to develop favorable mutations in the gyrase and topoisomerase IV genes seems to be a prerequisite for pathogens to retain fitness while showing high-level resistance to fluoroquinolones. Since, the consumption of other "non-fluoroquinolone" groups of antibiotics have also contributed to the rise in resistance rates a more judicious use of antibiotics in general and of fluoroquinolones in particular could ameliorate the international resistance situation.
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Affiliation(s)
- Miklos Fuzi
- Institute of Medical Microbiology, Semmelweis UniversityBudapest, Hungary
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12
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Costa CL, López-Ureña D, de Oliveira Assis T, Ribeiro RA, Silva ROS, Rupnik M, Wilcox MH, de Carvalho AF, do Carmo AO, Dias AAM, de Carvalho CBM, Chaves-Olarte E, Rodríguez C, Quesada-Gómez C, de Castro Brito GA. A MLST Clade 2 Clostridium difficile strain with a variant TcdB induces severe inflammatory and oxidative response associated with mucosal disruption. Anaerobe 2016; 40:76-84. [PMID: 27311833 DOI: 10.1016/j.anaerobe.2016.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 06/10/2016] [Accepted: 06/12/2016] [Indexed: 01/13/2023]
Abstract
The epidemiology of Clostridium difficile infections is highly dynamic as new strains continue to emerge worldwide. Here we present a detailed analysis of a new C. difficile strain (ICC-45) recovered from a cancer patient in Brazil that died from severe diarrhea. A polyphasic approach assigned a new PCR-ribotype and PFGE macrorestriction pattern to strain ICC-45, which is toxigenic (tcdA(+), tcdB(+) and ctdB(+)) and classified as ST41 from MLST Clade 2 and toxinotype IXb. Strain ICC-45 encodes for a variant TcdB that induces a distinct CPE in agreement with its toxinotype. Unlike epidemic NAP1/027 strains, which are also classified to MLST Clade 2, strain ICC-45 is susceptible to fluoroquinolones and does not overproduce toxins TcdA and TcdB. However, supernatants from strain ICC-45 and a NAP1/027 strain produced similar expression of pro-inflammatory cytokines, epithelial damage, and oxidative stress response in the mouse ileal loop model. These results highlight inflammation and oxidative stress as common features in the pathogenesis of C. difficile Clade 2 strains. Finally, this work contributes to the description of differences in virulence among various C. difficile strains.
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Affiliation(s)
- Cecília Leite Costa
- Department of Morphology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil; Laboratory of Bacteriology, Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Diana López-Ureña
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Thiago de Oliveira Assis
- Department of Morphology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil; Department of Morphology, Federal University of Paraíba, João Pessoa, PB, Brazil
| | - Ronaldo A Ribeiro
- Haroldo Juaçaba Hospital, Cancer Institute of Ceará, Fortaleza, CE, Brazil; Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
| | | | - Maja Rupnik
- University of Maribor, Faculty of Medicine and National Laboratory for Health, Environment and Food, Maribor, Slovenia
| | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, The General Infirmary, Leeds, UK
| | - Alex Fiorini de Carvalho
- Experimental Genetics and Laboratory Animal Science, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Anderson Oliveira do Carmo
- Experimental Genetics and Laboratory Animal Science, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Adriana Abalen Martins Dias
- Experimental Genetics and Laboratory Animal Science, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Cibele Barreto Mano de Carvalho
- Laboratory of Bacteriology, Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Esteban Chaves-Olarte
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - César Rodríguez
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Carlos Quesada-Gómez
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica.
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Spigaglia P. Recent advances in the understanding of antibiotic resistance in Clostridium difficile infection. Ther Adv Infect Dis 2016; 3:23-42. [PMID: 26862400 DOI: 10.1177/2049936115622891] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Clostridium difficile epidemiology has changed in recent years, with the emergence of highly virulent types associated with severe infections, high rates of recurrences and mortality. Antibiotic resistance plays an important role in driving these epidemiological changes and the emergence of new types. While clindamycin resistance was driving historical endemic types, new types are associated with resistance to fluoroquinolones. Furthermore, resistance to multiple antibiotics is a common feature of the newly emergent strains and, in general, of many epidemic isolates. A reduced susceptibility to antibiotics used for C. difficile infection (CDI) treatment, in particular to metronidazole, has recently been described in several studies. Furthermore, an increased number of strains show resistance to rifamycins, used for the treatment of relapsing CDI. Several mechanisms of resistance have been identified in C. difficile, including acquisition of genetic elements and alterations of the antibiotic target sites. The C. difficile genome contains a plethora of mobile genetic elements, many of them involved in antibiotic resistance. Transfer of genetic elements among C. difficile strains or between C. difficile and other bacterial species can occur through different mechanisms that facilitate their spread. Investigations of the fitness cost in C. difficile indicate that both genetic elements and mutations in the molecular targets of antibiotics can be maintained regardless of the burden imposed on fitness, suggesting that resistances may persist in the C. difficile population also in absence of antibiotic selective pressure. The rapid evolution of antibiotic resistance and its composite nature complicate strategies in the treatment and prevention of CDI. The rapid identification of new phenotypic and genotypic traits, the implementation of effective antimicrobial stewardship and infection control programs, and the development of alternative therapies are needed to prevent and contain the spread of resistance and to ensure an efficacious therapy for CDI.
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Quesada-Gómez C, López-Ureña D, Chumbler N, Kroh HK, Castro-Peña C, Rodríguez C, Orozco-Aguilar J, González-Camacho S, Rucavado A, Guzmán-Verri C, Lawley TD, Lacy DB, Chaves-Olarte E. Analysis of TcdB Proteins within the Hypervirulent Clade 2 Reveals an Impact of RhoA Glucosylation on Clostridium difficile Proinflammatory Activities. Infect Immun 2016; 84:856-65. [PMID: 26755157 PMCID: PMC4771349 DOI: 10.1128/iai.01291-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/04/2016] [Indexed: 02/04/2023] Open
Abstract
Clostridium difficile strains within the hypervirulent clade 2 are responsible for nosocomial outbreaks worldwide. The increased pathogenic potential of these strains has been attributed to several factors but is still poorly understood. During a C. difficile outbreak, a strain from this clade was found to induce a variant cytopathic effect (CPE), different from the canonical arborizing CPE. This strain (NAP1V) belongs to the NAP1 genotype but to a ribotype different from the epidemic NAP1/RT027 strain. NAP1V and NAP1 share some properties, including the overproduction of toxins, the binary toxin, and mutations in tcdC. NAP1V is not resistant to fluoroquinolones, however. A comparative analysis of TcdB proteins from NAP1/RT027 and NAP1V strains indicated that both target Rac, Cdc42, Rap, and R-Ras but only the former glucosylates RhoA. Thus, TcdB from hypervirulent clade 2 strains possesses an extended substrate profile, and RhoA is crucial for the type of CPE induced. Sequence comparison and structural modeling revealed that TcdBNAP1 and TcdBNAP1V share the receptor-binding and autoprocessing activities but vary in the glucosyltransferase domain, consistent with the different substrate profile. Whereas the two toxins displayed identical cytotoxic potencies, TcdBNAP1 induced a stronger proinflammatory response than TcdBNAP1V as determined in ex vivo experiments and animal models. Since immune activation at the level of intestinal mucosa is a hallmark of C. difficile-induced infections, we propose that the panel of substrates targeted by TcdB is a determining factor in the pathogenesis of this pathogen and in the differential virulence potential seen among C. difficile strains.
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Affiliation(s)
- Carlos Quesada-Gómez
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Diana López-Ureña
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Nicole Chumbler
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Heather K Kroh
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Carolina Castro-Peña
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - César Rodríguez
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Josué Orozco-Aguilar
- Facultad de Farmacia, Universidad de Costa Rica, San José, Costa Rica Laboratorio de Ensayos Biológicos, Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica
| | - Sara González-Camacho
- Laboratorio de Ensayos Biológicos, Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica
| | - Alexandra Rucavado
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - D Borden Lacy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA The Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
| | - Esteban Chaves-Olarte
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
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15
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Lidan C, Linhai L, Yang L, Zhaohui S, Xiaoyan H, Yuling S. Molecular characterization and antimicrobial susceptibility of tcdA-negative Clostridium difficile isolates from Guangzhou, China. Diagn Microbiol Infect Dis 2015; 84:361-5. [PMID: 26867962 DOI: 10.1016/j.diagmicrobio.2015.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/07/2015] [Accepted: 12/21/2015] [Indexed: 11/30/2022]
Abstract
This study aimed to investigate the molecular characteristics and antimicrobial susceptibility of Clostridium difficile clinical isolates in Guangzhou, China. One hundred twenty isolates were collected from Guangzhou General Hospital at the Guangzhou Military Command in China from March 2014 to April 2015, and 9 isolates were identified as tcdA-negative/tcdB-positive (A(-)B(+)) strains. Results showed that all of the strains were confirmed to be ST37 and 0 single nucleotide variants (SNVs) were found in the PaLoc region, and >60 SNVs were identified throughout the whole genome sequence. The results show the diversity of the antibiotic and gene mutations present in these strains. All of the A(-)B(+) isolates were highly resistant to clindamycin and erythromycin; showed an average sensitivity to fluoroquinolones; and maintained a high susceptibility to metronidazole, vancomycin, and tigecycline.
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Affiliation(s)
- Chen Lidan
- Graduate School of Southern Medical University, Guangzhou, Guangdong 510515, PR China; Department of Laboratory Medicine, Guangzhou General Hospital of Guangzhou Military Command of PLA, Guangzhou, Guangdong 510010, PR China
| | - Li Linhai
- Department of Laboratory Medicine, Guangzhou General Hospital of Guangzhou Military Command of PLA, Guangzhou, Guangdong 510010, PR China
| | - Liao Yang
- Department of Laboratory Medicine, Guangzhou General Hospital of Guangzhou Military Command of PLA, Guangzhou, Guangdong 510010, PR China
| | - Sun Zhaohui
- Department of Laboratory Medicine, Guangzhou General Hospital of Guangzhou Military Command of PLA, Guangzhou, Guangdong 510010, PR China
| | - Huang Xiaoyan
- Department of Laboratory Medicine, Guangzhou General Hospital of Guangzhou Military Command of PLA, Guangzhou, Guangdong 510010, PR China
| | - Shi Yuling
- Graduate School of Southern Medical University, Guangzhou, Guangdong 510515, PR China; Department of Laboratory Medicine, Guangzhou General Hospital of Guangzhou Military Command of PLA, Guangzhou, Guangdong 510010, PR China.
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16
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Baines SD, Wilcox MH. Antimicrobial Resistance and Reduced Susceptibility in Clostridium difficile: Potential Consequences for Induction, Treatment, and Recurrence of C. difficile Infection. Antibiotics (Basel) 2015; 4:267-98. [PMID: 27025625 PMCID: PMC4790285 DOI: 10.3390/antibiotics4030267] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 07/02/2015] [Accepted: 07/03/2015] [Indexed: 12/11/2022] Open
Abstract
Clostridium difficile infection (CDI) remains a substantial burden on healthcare systems and is likely to remain so given our reliance on antimicrobial therapies to treat bacterial infections, especially in an aging population in whom multiple co-morbidities are common. Antimicrobial agents are a key component in the aetiology of CDI, both in the establishment of the infection and also in its treatment. The purpose of this review is to summarise the role of antimicrobial agents in primary and recurrent CDI; assessing why certain antimicrobial classes may predispose to the induction of CDI according to a balance between antimicrobial activity against the gut microflora and C. difficile. Considering these aspects of CDI is important in both the prevention of the infection and in the development of new antimicrobial treatments.
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Affiliation(s)
- Simon D Baines
- Department of Biological and Environmental Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.
| | - Mark H Wilcox
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9JT, UK.
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, The General Infirmary, Leeds LS1 3EX, UK.
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17
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Quesada-Gómez C, López-Ureña D, Acuña-Amador L, Villalobos-Zúñiga M, Du T, Freire R, Guzmán-Verri C, del Mar Gamboa-Coronado M, Lawley TD, Moreno E, Mulvey MR, de Castro Brito GA, Rodríguez-Cavallini E, Rodríguez C, Chaves-Olarte E. Emergence of an outbreak-associated Clostridium difficile variant with increased virulence. J Clin Microbiol 2015; 53:1216-26. [PMID: 25653402 PMCID: PMC4365207 DOI: 10.1128/jcm.03058-14] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/23/2015] [Indexed: 12/18/2022] Open
Abstract
The prevalence of Clostridium difficile infections has increased due to the emergence of epidemic variants from diverse genetic lineages. Here we describe the emergence of a novel variant during an outbreak in a Costa Rican hospital that was associated with severe clinical presentations. This C. difficile variant elicited higher white blood cell counts and caused disease in younger patients than did other strains isolated during the outbreak. Furthermore, it had a recurrence rate, a 30-day attributable disease rate, and disease severity as great as those of the epidemic strain NAP1. Pulsed-field gel electrophoresis genotyping indicated that the outbreak strains belong to a previously undescribed variant, designated NAPCR1. Whole-genome sequencing and ribotyping indicated that the NAPCR1 variant belongs to C. difficile ribotype 012 and sequence type 54, as does the reference strain 630. NAPCR1 strains are resistant to fluoroquinolones due to a mutation in gyrA, and they possess an 18-bp deletion in tcdC that is characteristic of the epidemic, evolutionarily distinct, C. difficile NAP1 variant. NAPCR1 genomes contain 10% more predicted genes than strain 630, most of which are of hypothetical function and are present on phages and other mobile genetic elements. The increased virulence of NAPCR1 was confirmed by mortality rates in the hamster model and strong inflammatory responses induced by bacteria-free supernatants in the murine ligated loop model. However, NAPCR1 strains do not synthesize toxin A and toxin B at levels comparable to those in NAP1 strains. Our results suggest that the pathogenic potential of this emerging C. difficile variant is due to the acquisition of hypothetical functions associated with laterally acquired DNA.
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Affiliation(s)
- Carlos Quesada-Gómez
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Diana López-Ureña
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Luis Acuña-Amador
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | | | - Tim Du
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Rosemayre Freire
- Departamento de Morfologia, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - María del Mar Gamboa-Coronado
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | | | - Evelyn Rodríguez-Cavallini
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - César Rodríguez
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Esteban Chaves-Olarte
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
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Molecular epidemiology and antimicrobial susceptibility of Clostridium difficile isolated from a university teaching hospital in Japan. Eur J Clin Microbiol Infect Dis 2014; 34:763-72. [PMID: 25471195 DOI: 10.1007/s10096-014-2290-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/24/2014] [Indexed: 02/08/2023]
Abstract
Clostridium difficile infection control strategies require an understanding of its epidemiology. In this study, we analysed the toxin genotypes of 130 non-duplicate clinical isolates of C. difficile from a university hospital in Tokyo, Japan. Multilocus sequence typing (MLST) and eBURST analysis were performed for these isolates and nine strains previously analysed by polymerase chain reaction (PCR) ribotyping. Minimum inhibitory concentrations (MICs) were determined for six antibiotics, and the bacterial resistance mechanisms were investigated. Ninety-five toxigenic strains (73%), including seven tcdA-negative, tcdB-positive and cdtA/cdtB-negative strains (A(-)B(+)CDT(-)) and three A(+)B(+)CDT(+) strains, and 35 (27%) non-toxigenic strains, were classified into 23 and 12 sequence types, respectively. Of these, sequence type (ST)17 (21.8%) was the most predominant. MLST and eBURST analysis showed that 139 strains belonged to seven groups and singletons, and most A(+)B(+)CDT(-) strains (98%, 89/91) were classified into group 1. All isolates were susceptible to metronidazole, vancomycin and meropenem; the ceftriaxone, clindamycin and ciprofloxacin resistance rates were 49, 59 and 99%, respectively. Resistance rates to ceftriaxone and clindamycin were higher in toxigenic strains than in non-toxigenic strains (P < 0.001). All ST17 and ST81 strains were resistant to these antibiotics. The clindamycin- and fluoroquinolone-resistant strains carried erm(B) and mutations in GyrA and/or GyrB, respectively. To our knowledge, this is the first MLST-based study of the molecular epidemiology of toxigenic and non-toxigenic strains in Japan, providing evidence that non-toxigenic and toxigenic strains exhibit high genetic diversity and that toxigenic strains are more likely than non-toxigenic strains to exhibit multidrug resistance.
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19
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Clostridium difficile infection among immunocompromised patients in Rio de Janeiro, Brazil and detection of moxifloxacin resistance in a ribotype 014 strain. Anaerobe 2014; 28:85-9. [DOI: 10.1016/j.anaerobe.2014.05.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 05/21/2014] [Accepted: 05/25/2014] [Indexed: 01/05/2023]
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20
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See I, Mu Y, Cohen J, Beldavs ZG, Winston LG, Dumyati G, Holzbauer S, Dunn J, Farley MM, Lyons C, Johnston H, Phipps E, Perlmutter R, Anderson L, Gerding DN, Lessa FC. NAP1 strain type predicts outcomes from Clostridium difficile infection. Clin Infect Dis 2014; 58:1394-400. [PMID: 24604900 PMCID: PMC4697926 DOI: 10.1093/cid/ciu125] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Studies are conflicting regarding the importance of the fluoroquinolone-resistant North American pulsed-field gel electrophoresis type 1 (NAP1) strain in Clostridium difficile infection (CDI) outcome. We describe strain types causing CDI and evaluate their association with patient outcomes. METHODS CDI cases were identified from population-based surveillance. Multivariate regression models were used to evaluate the associations of strain type with severe disease (ileus, toxic megacolon, or pseudomembranous colitis within 5 days; or white blood cell count ≥15 000 cells/µL within 1 day of positive test), severe outcome (intensive care unit admission after positive test, colectomy for C. difficile infection, or death within 30 days of positive test), and death within 14 days of positive test. RESULTS Strain typing results were available for 2057 cases. Severe disease occurred in 363 (17.7%) cases, severe outcome in 100 (4.9%), and death within 14 days in 56 (2.7%). The most common strain types were NAP1 (28.4%), NAP4 (10.2%), and NAP11 (9.1%). In unadjusted analysis, NAP1 was associated with greater odds of severe disease than other strains. After controlling for patient risk factors, healthcare exposure, and antibiotic use, NAP1 was associated with severe disease (adjusted odds ratio [AOR], 1.74; 95% confidence interval [CI], 1.36-2.22), severe outcome (AOR, 1.66; 95% CI, 1.09-2.54), and death within 14 days (AOR, 2.12; 95% CI, 1.22-3.68). CONCLUSIONS NAP1 was the most prevalent strain and a predictor of severe disease, severe outcome, and death. Strategies to reduce NAP1 prevalence, such as antibiotic stewardship to reduce fluoroquinolone use, might reduce CDI morbidity.
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Affiliation(s)
- Isaac See
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA
| | - Yi Mu
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Jessica Cohen
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
- Atlanta Research and Education Foundation, Atlanta, GA
| | | | - Lisa G. Winston
- University of California San Francisco School of Medicine, San Francisco, CA
| | | | - Stacy Holzbauer
- Centers for Disease Control and Prevention Epidemiology Field Officer Assigned to Minnesota Department of Health, St. Paul, MN
| | - John Dunn
- Tennessee Department of Health, Nashville, TN
| | - Monica M. Farley
- Atlanta Veterans Medical Center, Atlanta, GA
- Emory University School of Medicine, Atlanta, GA
| | - Carol Lyons
- Connecticut Emerging Infections Program, New Haven, CT
| | - Helen Johnston
- Colorado Department of Public Health and Environment, Denver, CO
| | | | | | - Lydia Anderson
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Dale N. Gerding
- Loyola University Chicago Stritch School of Medicine, Chicago, IL
- Hines Veterans Affairs Hospital, Hines, IL
| | - Fernanda C. Lessa
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
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Characterizations of clinical isolates of clostridium difficile by toxin genotypes and by susceptibility to 12 antimicrobial agents, including fidaxomicin (OPT-80) and rifaximin: a multicenter study in Taiwan. Antimicrob Agents Chemother 2012; 56:3943-9. [PMID: 22508299 DOI: 10.1128/aac.00191-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A total of 403 nonduplicate isolates of Clostridium difficile were collected at three major teaching hospitals representing northern, central, and southern Taiwan from January 2005 to December 2010. Of these 403 isolates, 170 (42.2%) were presumed to be nontoxigenic due to the absence of genes for toxins A or B or binary toxin. The remaining 233 (57.8%) isolates carried toxin A and B genes, and 39 (16.7%) of these also had binary toxin genes. The MIC(90) of all isolates for fidaxomicin and rifaximin was 0.5 μg/ml (range, ≤ 0.015 to 0.5 μg/ml) and >128 μg/ml (range, ≤ 0.015 to >128 μg/ml), respectively. All isolates were susceptible to metronidazole (MIC(90) of 0.5 μg/ml; range, ≤ 0.03 to 4 μg/ml). Two isolates had reduced susceptibility to vancomycin (MICs, 4 μg/ml). Only 13.6% of isolates were susceptible to clindamycin (MIC of ≤ 2 μg/ml). Nonsusceptibility to moxifloxacin (n = 81, 20.1%) was accompanied by single or multiple mutations in gyrA and gyrB genes in all but eight moxifloxacin-nonsusceptible isolates. Two previously unreported gyrB mutations might independently confer resistance (MIC, 16 μg/ml), Ser416 to Ala and Glu466 to Lys. Moxifloxacin-resistant isolates were cross-resistant to ciprofloxacin and levofloxacin, but some moxifloxacin-nonsusceptible isolates remained susceptible to gemifloxacin or nemonoxacin at 0.5 μg/ml. This study found the diversity of toxigenic and nontoxigenic strains of C. difficile in the health care setting in Taiwan. All isolates tested were susceptible to metronidazole and vancomycin. Fidaxomicin exhibited potent in vitro activity against all isolates tested, while the more than 10% of Taiwanese isolates with rifaximin MICs of ≥ 128 μg/ml raises concerns.
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In vivo selection of moxifloxacin-resistant Clostridium difficile. Antimicrob Agents Chemother 2012; 56:2788-9. [PMID: 22371889 DOI: 10.1128/aac.06433-11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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23
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Lack of association between clinical outcome of Clostridium difficile infections, strain type, and virulence-associated phenotypes. J Clin Microbiol 2011; 49:4040-6. [PMID: 21956985 DOI: 10.1128/jcm.05053-11] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile strain NAP1/027 (North American pulsed-field gel electrophoresis [PFGE] type 1 and PCR ribotype 027 [R027]) has been associated with recent outbreaks in North America and Europe. It has been associated with more severe disease symptoms, higher mortality rates, and greater risk of relapse. This strain is thought to produce more toxins and sporulate to higher levels. However, recent studies suggest that this may not always be the case. The objective of our study was to assess, in a nonoutbreak situation, whether specific strains, such as NAP1/027, were associated with more severe disease symptoms, higher toxin production, and/or greater sporulation in vitro. We isolated and characterized C. difficile strains from 21 patients with mild to moderate, severe, or complicated symptoms of C. difficile infection (CDI). The isolates were characterized by different molecular typing methods, including PCR ribotyping, tandem repeat sequence typing (TRST), and sequencing of the tcdC gene. Fourteen isolates were of PCR ribotype 027 with deletions in tcdC, but no association with severity or clinical outcome was found. We show by immunodot blot detection of toxins with monoclonal antibodies that all R027 isolates produced more TcdA and TcdB than other strains. On the other hand, they consistently produced fewer spores than non-R027 isolates. Taken together, our data suggest that NAP1/027 isolates are not always associated with more severe disease, even though they may produce larger amounts of toxins. Our study also suggests that current assertions regarding the NAP1/027 may not apply to all isolates and that other factors may come into play.
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Solomon K, Fanning S, McDermott S, Murray S, Scott L, Martin A, Skally M, Burns K, Kuijper E, Fitzpatrick F, Fenelon L, Kyne L. PCR ribotype prevalence and molecular basis of macrolide-lincosamide-streptogramin B (MLSB) and fluoroquinolone resistance in Irish clinical Clostridium difficile isolates. J Antimicrob Chemother 2011; 66:1976-82. [DOI: 10.1093/jac/dkr275] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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25
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Fourteen-genome comparison identifies DNA markers for severe-disease-associated strains of Clostridium difficile. J Clin Microbiol 2011; 49:2230-8. [PMID: 21508155 DOI: 10.1128/jcm.00391-11] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile is a common cause of infectious diarrhea in hospitalized patients. A severe and increased incidence of C. difficile infection (CDI) is associated predominantly with the NAP1 strain; however, the existence of other severe-disease-associated (SDA) strains and the extensive genetic diversity across C. difficile complicate reliable detection and diagnosis. Comparative genome analysis of 14 sequenced genomes, including those of a subset of NAP1 isolates, allowed the assessment of genetic diversity within and between strain types to identify DNA markers that are associated with severe disease. Comparative genome analysis of 14 isolates, including five publicly available strains, revealed that C. difficile has a core genome of 3.4 Mb, comprising ∼ 3,000 genes. Analysis of the core genome identified candidate DNA markers that were subsequently evaluated using a multistrain panel of 177 isolates, representing more than 50 pulsovars and 8 toxinotypes. A subset of 117 isolates from the panel had associated patient data that allowed assessment of an association between the DNA markers and severe CDI. We identified 20 candidate DNA markers for species-wide detection and 10,683 single nucleotide polymorphisms (SNPs) associated with the predominant SDA strain (NAP1). A species-wide detection candidate marker, the sspA gene, was found to be the same across 177 sequenced isolates and lacked significant similarity to those of other species. Candidate SNPs in genes CD1269 and CD1265 were found to associate more closely with disease severity than currently used diagnostic markers, as they were also present in the toxin A-negative and B-positive (A-B+) strain types. The genetic markers identified illustrate the potential of comparative genomics for the discovery of diagnostic DNA-based targets that are species specific or associated with multiple SDA strains.
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