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Nale JY, Thanki AM, Rashid SJ, Shan J, Vinner GK, Dowah ASA, Cheng JKJ, Sicheritz-Pontén T, Clokie MRJ. Diversity, Dynamics and Therapeutic Application of Clostridioides difficile Bacteriophages. Viruses 2022; 14:v14122772. [PMID: 36560776 PMCID: PMC9784644 DOI: 10.3390/v14122772] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile causes antibiotic-induced diarrhoea and pseudomembranous colitis in humans and animals. Current conventional treatment relies solely on antibiotics, but C. difficile infection (CDI) cases remain persistently high with concomitant increased recurrence often due to the emergence of antibiotic-resistant strains. Antibiotics used in treatment also induce gut microbial imbalance; therefore, novel therapeutics with improved target specificity are being investigated. Bacteriophages (phages) kill bacteria with precision, hence are alternative therapeutics for the targeted eradication of the pathogen. Here, we review current progress in C. difficile phage research. We discuss tested strategies of isolating C. difficile phages directly, and via enrichment methods from various sample types and through antibiotic induction to mediate prophage release. We also summarise phenotypic phage data that reveal their morphological, genetic diversity, and various ways they impact their host physiology and pathogenicity during infection and lysogeny. Furthermore, we describe the therapeutic development of phages through efficacy testing in different in vitro, ex vivo and in vivo infection models. We also discuss genetic modification of phages to prevent horizontal gene transfer and improve lysis efficacy and formulation to enhance stability and delivery of the phages. The goal of this review is to provide a more in-depth understanding of C. difficile phages and theoretical and practical knowledge on pre-clinical, therapeutic evaluation of the safety and effectiveness of phage therapy for CDI.
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Affiliation(s)
- Janet Y. Nale
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, Scotland’s Rural College, Inverness IV2 5NA, UK
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Anisha M. Thanki
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Srwa J. Rashid
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Jinyu Shan
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Gurinder K. Vinner
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Ahmed S. A. Dowah
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- School of Pharmacy, University of Lincoln, Lincoln LN6 7TS, UK
| | | | - Thomas Sicheritz-Pontén
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, 1353 Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Bedong 08100, Kedah, Malaysia
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Correspondence:
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Acuña-Amador L, Quesada-Gómez C, Rodríguez C. Clostridioides difficile in Latin America: A comprehensive review of literature (1984-2021). Anaerobe 2022; 74:102547. [PMID: 35337973 DOI: 10.1016/j.anaerobe.2022.102547] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 02/06/2023]
Abstract
This narrative review summarizes literature on C. difficile and C. difficile infections (CDI) that emerged from Latin America (LA) between 1984 and 2021. The revised information includes papers in English, Spanish, or Portuguese that were retrieved from the databases Pubmed, Scopus, Web of Science, Google Scholar, Scielo, and Lilacs. Information is presented chronologically and segregated in subregions, focusing on clinical presentation, risk factors, detection and typing methods, prevalence and incidence rates, circulating strains, and, when available, phenotypic traits, such as antimicrobial susceptibility patterns. Studies dealing with cases, clinical aspects of CDI, and performance evaluations of diagnostic methods predominated. However, they showed substantial differences in case definitions, measuring units, populations, and experimental designs. Although a handful of autochthonous strains were identified, predominantly in Brazil and Costa Rica, the presentation and epidemiology of CDI in LA were highly comparable to what has been reported in other regions of the world. Few laboratories isolate and type this bacterium and even less generate whole genome sequences or perform basic science on C. difficile. Less than ten countries lead academic productivity on C. difficile or CDI-related topics, and information from various countries in Central America and the Caribbean is still lacking. The review ends with a global interpretation of the data and recommendations to further develop and consolidate this discipline in LA.
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Affiliation(s)
- Luis Acuña-Amador
- Facultad de Microbiología, Universidad de Costa Rica, Costa Rica; Laboratorio de Investigación en Bacteriología Anaerobia (LIBA), Universidad de Costa Rica, Costa Rica; Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, Costa Rica.
| | - Carlos Quesada-Gómez
- Facultad de Microbiología, Universidad de Costa Rica, Costa Rica; Laboratorio de Investigación en Bacteriología Anaerobia (LIBA), Universidad de Costa Rica, Costa Rica; Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, Costa Rica.
| | - César Rodríguez
- Facultad de Microbiología, Universidad de Costa Rica, Costa Rica; Laboratorio de Investigación en Bacteriología Anaerobia (LIBA), Universidad de Costa Rica, Costa Rica; Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, Costa Rica.
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Badilla-Lobo A, Rodríguez C. Microbiological features, epidemiology, and clinical presentation of Clostridioidesdifficile strains from MLST Clade 2: A narrative review. Anaerobe 2021; 69:102355. [PMID: 33711422 DOI: 10.1016/j.anaerobe.2021.102355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 02/06/2023]
Abstract
Clostridioides difficile is an emerging One Health pathogen and a common etiologic agent of diarrhea, both in healthcare settings and the community. This bacterial species is highly diverse, and its global population has been classified in eight clades by multilocus sequence typing (MLST). The C. difficile MLST Clade 2 includes the NAP1/RT027/ST01 strain, which is highly recognized due to its epidemicity and association with severe disease presentation and mortality. By contrast, the remaining 83 sequence types (STs) that compose this clade have received much less attention. In response to this shortcoming, we reviewed articles published in English between 1999 and 2020 and collected information for 27 Clade 2 STs, with an emphasis on STs 01, 67, 41 and 188/231/365. Our analysis provides evidence of large phenotypic differences that preclude support of the rather widespread notion that ST01 and Clade 2 strains are "hypervirulent". Moreover, it revealed a profound lack of (meta)data for nearly 70% of the Clade 2 STs that have been identified in surveillance efforts. Targeted studies aiming to relate wet-lab and bioinformatics results to patient and clinical parameters should be performed to gain a more in-depth insight into the biology of this intriguing group of C. difficile isolates.
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Affiliation(s)
- Adriana Badilla-Lobo
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, and Master's Program in Microbiology, Parasitology, Clinical Chemistry and Immunology, Universidad de Costa Rica, Costa Rica
| | - César Rodríguez
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, and Master's Program in Microbiology, Parasitology, Clinical Chemistry and Immunology, Universidad de Costa Rica, Costa Rica.
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Kulecka M, Waker E, Ambrozkiewicz F, Paziewska A, Skubisz K, Cybula P, Targoński Ł, Mikula M, Walewski J, Ostrowski J. Higher genome variability within metabolism genes associates with recurrent Clostridium difficile infection. BMC Microbiol 2021; 21:36. [PMID: 33509087 PMCID: PMC7842062 DOI: 10.1186/s12866-021-02090-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/08/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Clostridium difficile (C. difficile) is a major source of healthcare-associated infection with a high risk of recurrence, attributable to many factors such as usage of antibiotics, older age and immunocompromised status of the patients. C. difficile has also a highly diverse genome, which may contribute to its high virulence. Herein we examined whether the genome conservation, measured as non-synonymous to synonymous mutations ratio (dN/dS) in core genes, presence of single genes, plasmids and prophages increased the risk of reinfection in a subset of 134 C. difficile isolates from our previous study in a singly hemato-oncology ward. METHODS C. difficile isolates were subjected to whole-genome sequencing (WGS) on Ion Torrent PGM sequencer. Genomes were assembled with MIRA5 and annotated with prokka and VRprofile. Logistic regression was used to asses the relationship between single gene presence and the odds of infection recurrence. DN/dS ratios were computed with codeml. Functional annotation was conducted with eggNOG-Mapper. RESULTS We have found that the presence of certain genes, associated with carbon metabolism and oxidative phosphorylation, increased the odds of infection recurrence. More core genes were under positive selective pressure in recurrent disease isolates - they were mostly associated with the metabolism of aminoacids. Finally, prophage elements were more prevalent in single infection isolates and plasmids did not influence the odds of recurrence. CONCLUSIONS Our findings suggest higher genetic plasticity in isolates causing recurrent infection, associated mainly with metabolism. On the other hand, the presence of prophages seems to reduce the isolates' virulence.
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Affiliation(s)
- Maria Kulecka
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Edyta Waker
- Department of Clinical Microbiology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Karolina Skubisz
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Patrycja Cybula
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Łukasz Targoński
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland.
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland.
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Guerrero-Araya E, Meneses C, Castro-Nallar E, Guzmán D. AM, Álvarez-Lobos M, Quesada-Gómez C, Paredes-Sabja D, Rodríguez C. Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico. Microb Genom 2020; 6:e000355. [PMID: 32176604 PMCID: PMC7371124 DOI: 10.1099/mgen.0.000355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/28/2020] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile B1/NAP1/RT027/ST01 has been responsible for outbreaks of antibiotic-associated diarrhoea in clinical settings worldwide and is associated with severe disease presentations and increased mortality rates. Two fluoroquinolone-resistant (FQR) lineages of the epidemic B1/NAP1/RT027/ST01 strain emerged in the USA in the early 1990s and disseminated trans continentally (FQR1 and FQR2). However, it is unclear when and from where they entered Latin America (LA) and whether isolates from LA exhibit unique genomic features when compared to B1/NAP1/RT027/ST01 isolates from other regions of the world. To answer the first issue we compared whole-genome sequences (WGS) of 25 clinical isolates typed as NAP1, RT027 or ST01 in Costa Rica (n=16), Chile (n=5), Honduras (n=3) and Mexico (n=1) to WGS of 129 global isolates from the same genotype using Bayesian phylogenomics. The second question was addressed through a detailed analysis of the number and type of mutations of the LA isolates and their mobile resistome. All but two B1/NAP1/RT027/ST01 isolates from LA belong to the FQR2 lineage (n=23, 92 %), confirming its widespread distribution. As indicated by analysis of a dataset composed of 154 WGS, the B1/NAP1/RT027/ST01 strain was introduced into the four LA countries analysed between 1998 and 2005 from North America (twice) and Europe (at least four times). These events occurred soon after the emergence of the FQR lineages and more than one decade before the first report of the detection of the B1/NAP1/RT027/ST01 in LA. A total of 552 SNPs were identified across all genomes examined (3.8-4.3 Mb) in pairwise comparisons to the R20291 reference genome. Moreover, pairwise SNP distances were among the smallest distances determined in this species so far (0 to 55). Despite this high level of genomic conservation, 39 unique SNPs (7 %) in genes that play roles in the infection process (i.e. slpA) or antibiotic resistance (i.e. rpoB, fusA) distinguished the LA isolates. In addition, isolates from Chile, Honduras and Mexico had twice as many antibiotic resistance genes (ARGs, n=4) than related isolates from other regions. Their unique set of ARGs includes a cfr-like gene and tetM, which were found as part of putative mobile genetic elements whose sequences resemble undescribed integrative and conjugative elements. These results show multiple, independent introductions of B1/NAP1/RT027/ST01 isolates from the FQR1 and FQR2 lineages from different geographical sources into LA and a rather rapid accumulation of distinct mutations and acquired ARG by the LA isolates.
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Affiliation(s)
- Enzo Guerrero-Araya
- Millennium Nucleus in the Biology of Intestinal Microbiota, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Microbiota-Host Interactions & Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Universidad Andrés Bello, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Ana M. Guzmán D.
- Department of Clinical Laboratory, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Manuel Álvarez-Lobos
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Quesada-Gómez
- Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
| | - Daniel Paredes-Sabja
- Millennium Nucleus in the Biology of Intestinal Microbiota, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Microbiota-Host Interactions & Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - César Rodríguez
- Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
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Abstract
Whole-genome sequences are now available for all the clinically important clostridia and many of the lesser or opportunistically pathogenic clostridia. The complex clade structures of C. difficile, C. perfringens, and the species that produce botulinum toxins have been delineated by whole-genome sequence analysis. The true clostridia of cluster I show relatively low levels of gross genomic rearrangements within species, in contrast to the species of cluster XI, notably C. difficile, which have been found to have very plastic genomes with significant levels of chromosomal rearrangement. Throughout the clostridial phylotypes, a large proportion of the strain diversity is driven by the acquisition and loss of mobile elements, including phages, plasmids, insertion sequences, and transposons. Genomic analysis has been used to investigate the diversity and spread of C. difficile within hospital settings, the zoonotic transfer of isolates, and the emergence, origins, and geographic spread of epidemic ribotypes. In C. perfringens the clades defined by chromosomal sequence analysis show no indications of clustering based on host species or geographical location. Whole-genome sequence analysis helps to define the different survival and pathogenesis strategies that the clostridia use. Some, such as C. botulinum, produce toxins which rapidly act to kill the host, whereas others, such as C. perfringens and C. difficile, produce less lethal toxins which can damage tissue but do not rapidly kill the host. The genomes provide a resource that can be mined to identify potential vaccine antigens and targets for other forms of therapeutic intervention.
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Tratulyte S, Miciuleviciene J, Kuisiene N. First genotypic characterization of toxigenic Clostridioides difficile in Lithuanian hospitals reveals the prevalence of the hypervirulent ribotype 027/ST1. Eur J Clin Microbiol Infect Dis 2019; 38:1953-1959. [DOI: 10.1007/s10096-019-03633-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 07/08/2019] [Indexed: 12/14/2022]
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