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Antimicrobial resistance (AMR) plays an important role in the pathogenesis and spread of Clostridioides difficile infection (CDI), the leading healthcare-related gastrointestinal infection in the world. An association between AMR and CDI outbreaks is well documented, however, data is limited to a few 'epidemic' strains in specific geographical regions. Here, through detailed analysis of 10,330 publicly-available C. difficile genomes from strains isolated worldwide (spanning 270 multilocus sequence types (STs) across all known evolutionary clades), this study provides the first species-wide snapshot of AMR genomic epidemiology in C. difficile. Of the 10,330 C. difficile genomes, 4,532 (43.9%) in 89 STs across clades 1 - 5 carried at least one genotypic AMR determinants, with 901 genomes (8.7%) carrying AMR determinants for three or more antimicrobial classes (multidrug-resistant, MDR). No AMR genotype was identified in any strains belonging to the cryptic clades. C. difficile from Australia/New Zealand had the lowest AMR prevalence compared to strains from Asia, Europe and North America (p<0.0001). Based on the phylogenetic clade, AMR prevalence was higher in clades 2 (84.3%), 4 (81.5%) and 5 (64.8%) compared to other clades (collectively 26.9%) (p<0.0001). MDR prevalence was highest in clade 4 (61.6%) which was over three times higher than in clade 2, the clade with the second-highest MDR prevalence (18.3%). There was a strong association between specific AMR determinants and three major epidemic C. difficile STs: ST1 (clade 2) with fluoroquinolone resistance (mainly T82I substitution in GyrA) (p<0.0001), ST11 (clade 5) with tetracycline resistance (various tet-family genes) (p<0.0001) and ST37 (clade 4) with macrolide-lincosamide-streptogramin B (MLSB) resistance (mainly ermB) (p<0.0001) and MDR (p<0.0001). A novel and previously overlooked tetM-positive transposon termed Tn6944 was identified, predominantly among clade 2 strains. This study provides a comprehensive review of AMR in the global C. difficile population which may help in the early detection of drug-resistant C. difficile strains, and prevention of spread world-wide.
Korakrit Imwattana; César Rodríguez; Thomas V. Riley; Daniel R. Knight. A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile. 2021, 1 .
AMA StyleKorakrit Imwattana, César Rodríguez, Thomas V. Riley, Daniel R. Knight. A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile. . 2021; ():1.
Chicago/Turabian StyleKorakrit Imwattana; César Rodríguez; Thomas V. Riley; Daniel R. Knight. 2021. "A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile." , no. : 1.
Clostridioides difficile infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across C. difficile underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 C. difficile genomes spanning the eight currently defined phylogenetic clades. Through whole-genome average nucleotide identity, and pangenomic and Bayesian analyses, we identified major taxonomic incoherence with clear species boundaries for each of the recently described cryptic clades CI–III. The emergence of these three novel genomospecies predates clades C1–5 by millions of years, rewriting the global population structure of C. difficile specifically and taxonomy of the Peptostreptococcaceae in general. These genomospecies all show unique and highly divergent toxin gene architecture, advancing our understanding of the evolution of C. difficile and close relatives. Beyond the taxonomic ramifications, this work may impact the diagnosis of CDI.
Daniel R Knight; Korakrit Imwattana; Brian Kullin; Enzo Guerrero-Araya; Daniel Paredes-Sabja; Xavier Didelot; Kate E Dingle; David W Eyre; César Rodríguez; Thomas V Riley. Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy. eLife 2021, 10, 1 .
AMA StyleDaniel R Knight, Korakrit Imwattana, Brian Kullin, Enzo Guerrero-Araya, Daniel Paredes-Sabja, Xavier Didelot, Kate E Dingle, David W Eyre, César Rodríguez, Thomas V Riley. Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy. eLife. 2021; 10 ():1.
Chicago/Turabian StyleDaniel R Knight; Korakrit Imwattana; Brian Kullin; Enzo Guerrero-Araya; Daniel Paredes-Sabja; Xavier Didelot; Kate E Dingle; David W Eyre; César Rodríguez; Thomas V Riley. 2021. "Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy." eLife 10, no. : 1.
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.
Adriana Badilla-Lobo; César Rodríguez. Microbiological features, epidemiology, and clinical presentation of Clostridioides difficile strains from MLST Clade 2: A narrative review. Anaerobe 2021, 69, 102355 .
AMA StyleAdriana Badilla-Lobo, César Rodríguez. Microbiological features, epidemiology, and clinical presentation of Clostridioides difficile strains from MLST Clade 2: A narrative review. Anaerobe. 2021; 69 ():102355.
Chicago/Turabian StyleAdriana Badilla-Lobo; César Rodríguez. 2021. "Microbiological features, epidemiology, and clinical presentation of Clostridioides difficile strains from MLST Clade 2: A narrative review." Anaerobe 69, no. : 102355.
Two Gram-positive, anaerobic bacteria, designated 27733 and 27737, were isolated from a soft tissue infection from a human patient. They were preliminarily identified asClostridium perfringensthrough a series of phenotypic tests, including Gram-staining, determination of lipase and hemolytic activities, MALDI-ToF profiling, and a commercial biochemical identification system. In line with these results, genomes obtained for both isolates were ~3.56 Mbp in size, showed a DNA G+C content of ~28.4%, and containedC. perfringensribosomal markers (i.e. 16S rRNA gene identity >99.0% toC. perfringensATCC13124T). A closer examination of these sequences; however, revealed low average Nucleotide Identity (~87%) and digital DNA-DNA Hybridization (~35%) values between isolates 27733/27737 andC. perfringensATCC13124T, as well as substantial differences in gene content to multipleC. perfringensstrains, indicating that they represent a novel species within the genusClostridium.Congruently, Bayesian dating analyses placed the divergence of this new species andC. perfringensfrom its common ancestor hundreds of thousands of years ago. Isolates 27733/27737 are not genomically identical (34-197 SNPs apart) and carry genes forC. perfringens-liketoxins (<94% nucleotide sequence identity), includingplc(alpha toxin),pfoA(perfringolysin O, theta-toxin),nagHIJKL(hyalorudinase, mu-toxin),nanHIJ(exo-alpha sialidase), andcloSI(alpha-clostripain). They do not have known antibiotic resistance genes but were catalogued as resistant to clindamycin through phenotypic tests. On the basis of the presented evidence, and due to its resemblance and potential confusion withC. perfringens,we herein propose the speciesC. perfringenosumsp. nov. and strain 27733 as its type strain.
César Rodríguez; Raymond Kiu; Carlos Quesada-Gómez; Cindy Sandí; Lindsay J Hall. Clostridium perfringenosumsp. nov., a closely related species toClostridium perfringensand its virulence factors, isolated from a human soft tissue infection. 2020, 1 .
AMA StyleCésar Rodríguez, Raymond Kiu, Carlos Quesada-Gómez, Cindy Sandí, Lindsay J Hall. Clostridium perfringenosumsp. nov., a closely related species toClostridium perfringensand its virulence factors, isolated from a human soft tissue infection. . 2020; ():1.
Chicago/Turabian StyleCésar Rodríguez; Raymond Kiu; Carlos Quesada-Gómez; Cindy Sandí; Lindsay J Hall. 2020. "Clostridium perfringenosumsp. nov., a closely related species toClostridium perfringensand its virulence factors, isolated from a human soft tissue infection." , no. : 1.
Clostridioides difficile infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across C. difficile underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 C. difficile genomes spanning the eight currently defined phylogenetic clades. Through whole-genome average nucleotide identity, pangenomic and Bayesian analyses, we identified major taxonomic incoherence with clear species boundaries for each of the recently described cryptic clades CI-III. The emergence of these three novel genomospecies predates clades C1-5 by millions of years, rewriting the global population structure of C. difficile specifically and taxonomy of the Peptostreptococcaceae in general. These genomospecies all show unique and highly divergent toxin gene architecture, advancing our understanding of the evolution of C. difficile and close relatives. Beyond the taxonomic ramifications, this work impacts the diagnosis of CDI worldwide.
Daniel R. Knight; Korakrit Imwattana; Brian Kullin; Enzo Guerrero-Araya; Daniel Paredes-Sabja; Xavier Didelot; Kate E. Dingle; David W. Eyre; César Rodríguez; Thomas V. Riley. The Clostridioides difficile species problem: global phylogenomic analysis uncovers three ancient, toxigenic, genomospecies. 2020, 1 .
AMA StyleDaniel R. Knight, Korakrit Imwattana, Brian Kullin, Enzo Guerrero-Araya, Daniel Paredes-Sabja, Xavier Didelot, Kate E. Dingle, David W. Eyre, César Rodríguez, Thomas V. Riley. The Clostridioides difficile species problem: global phylogenomic analysis uncovers three ancient, toxigenic, genomospecies. . 2020; ():1.
Chicago/Turabian StyleDaniel R. Knight; Korakrit Imwattana; Brian Kullin; Enzo Guerrero-Araya; Daniel Paredes-Sabja; Xavier Didelot; Kate E. Dingle; David W. Eyre; César Rodríguez; Thomas V. Riley. 2020. "The Clostridioides difficile species problem: global phylogenomic analysis uncovers three ancient, toxigenic, genomospecies." , no. : 1.
The major toxins of Clostridioides difficile (TcdA, TcdB, CDT) are chromosomally encoded in nearly all known strains. Following up on previous findings, we identified 5 examples of a family of putative conjugative plasmids with tcdB and cdtAB in clinical C. difficile isolates from multilocus sequence typing clades C-I, 2, and 4.
Gabriel Ramírez-Vargas; César Rodríguez. Putative Conjugative Plasmids with tcdB and cdtAB Genes in Clostridioides difficile. Emerging Infectious Diseases 2020, 26, 2287 -2290.
AMA StyleGabriel Ramírez-Vargas, César Rodríguez. Putative Conjugative Plasmids with tcdB and cdtAB Genes in Clostridioides difficile. Emerging Infectious Diseases. 2020; 26 (9):2287-2290.
Chicago/Turabian StyleGabriel Ramírez-Vargas; César Rodríguez. 2020. "Putative Conjugative Plasmids with tcdB and cdtAB Genes in Clostridioides difficile." Emerging Infectious Diseases 26, no. 9: 2287-2290.
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.
Enzo Guerrero-Araya; Claudio Meneses; Eduardo Castro-Nallar; Ana M. Guzmán D.; Manuel Álvarez-Lobos; Carlos Quesada-Gómez; Daniel Paredes-Sabja; César Rodríguez. Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico. Microbial Genomics 2020, 6, e000355 .
AMA StyleEnzo Guerrero-Araya, Claudio Meneses, Eduardo Castro-Nallar, Ana M. Guzmán D., Manuel Álvarez-Lobos, Carlos Quesada-Gómez, Daniel Paredes-Sabja, César Rodríguez. Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico. Microbial Genomics. 2020; 6 (5):e000355.
Chicago/Turabian StyleEnzo Guerrero-Araya; Claudio Meneses; Eduardo Castro-Nallar; Ana M. Guzmán D.; Manuel Álvarez-Lobos; Carlos Quesada-Gómez; Daniel Paredes-Sabja; César Rodríguez. 2020. "Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico." Microbial Genomics 6, no. 5: e000355.
Introduction. The coffee berry borer (Hypothenemus hampei Ferrari, CBB) is one of the most devastating pests on coffee plantations around the world. Although CBB is susceptible to the effect of δ–endotoxins of Bacillus thuringiensis subs. israelensis (Bti) at laboratory level, the efficacy of this control method is poor in the field, presumably due to the inactivation by digestive proteases different to those required for protoxin activation. Objective. To study whether the addition of a soybean flour extract enriched with protease inhibitors (PI), mixed with Bti crystals and spores (Bti-sc) in an artificial diet, could improve the toxicity of Bti against CBB. Materials and methods. This study was performed in San José, Costa Rica, between 2012 and 2013. A set of adult female CBB insects was exposed to a mixture containing different concentrations of a partially purified soybean meal extract with active PI and lyophilized Bti-sc, and were tested through a bioassay in artificial diet to estimate the sub-lethal concentration (LC50). The mortality results were validated by observing the dissected midgut, whose ultrastructure was analyzed by transmission electron microscopy. Results. The soybean extracts partially degraded the Bti-sc complex, it reduced its LC50 by almost four times (from 1.135 to 0.315 µg µl-1) and enhanced CBB mortality in a concentration-dependent manner. Histological analyses of the midgut confirmed this synergistic effect, since severe epithelial damage to the intestinal epithelium of CBB exposed to Bti-sc + PI was visualized compared to Bti-sc alone. Conclusions. The combination of a soybean extract enriched in PI and Bti-sc enhanced the mortality effect over CBB, which was confirmed by the midgut collapse. Soybean flour is a cost-effective supplement that could increase Bti effectiveness against CBB and delay the appearance of biological resistance.
Esteve A. Mesén-Porras; Sergio Dahdouh-Cabia; Catherine Jim´énez-Quirós; Rebeca Mora Castro; César Rodríguez; Adrián A. Pinto-Tomás. Soybean protease inhibitors increase Bacillus thuringiensis subs. israelensis toxicity against Hypothenemus hampei. Agronomía Mesoamericana 2020, 461 -478.
AMA StyleEsteve A. Mesén-Porras, Sergio Dahdouh-Cabia, Catherine Jim´énez-Quirós, Rebeca Mora Castro, César Rodríguez, Adrián A. Pinto-Tomás. Soybean protease inhibitors increase Bacillus thuringiensis subs. israelensis toxicity against Hypothenemus hampei. Agronomía Mesoamericana. 2020; ():461-478.
Chicago/Turabian StyleEsteve A. Mesén-Porras; Sergio Dahdouh-Cabia; Catherine Jim´énez-Quirós; Rebeca Mora Castro; César Rodríguez; Adrián A. Pinto-Tomás. 2020. "Soybean protease inhibitors increase Bacillus thuringiensis subs. israelensis toxicity against Hypothenemus hampei." Agronomía Mesoamericana , no. : 461-478.
C. difficile induces antibiotic-associated diarrhea due to the action of two secreted toxins, TcdA and TcdB. A considerable range of virulence among C. difficile strains has been widely reported. During a hospital outbreak, 46 isolates were collected that belonged to different genotypes. Of those, the majority corresponded to two virulent strains, the globally distributed Sequence Type 1 (ST1)_North American Pulsotype 1 (NAP1) and the endemic ST54_NAPCR1 genotypes, respectively. Whereas the virulence of the latter has been attributed to increased secretion of toxins and production of a highly cytotoxic TcdB, these characteristics do not explain the increased lethality of the former. We undertook a proteomic comparative approach of the isolates participating in the outbreak to look for proteins present in the exoproteome of the ST1_NAP1and ST54_NAPCR1 strains. We used a low virulent ST2_NAP4 strain isolated also in the outbreak as control. Dendrograms constructed using the exoproteomes of the strains were very similar to those created using genomic information, suggesting an association between secreted proteins and relative virulence of the strains. By 2D electrophoresis and mass spectrometry it was found that approximately half of the proteins are shared among strains of different genotypes. From the identified proteins, the surface-located SlpA draw our attention due to its detection in ST54_NAPCR1 exoproteomes. Biochemical analysis indicated that the processing of SlpA is different in the ST54_NAPCR1 strain and confirmed that this strain secretes more SlpA than its counterparts. Furthermore, SlpA from the ST54_NAPCR1 strain exerted an increased proinflammatory activity. Altogether, these results indicate that the exoproteome composition correlates with the C. difficile genotype and suggest that particular proteins secreted by some strains could synergize with the effects of TcdA and TcdB increasing their virulence.
Carlos Quesada-Gómez; Tatiana Murillo; Grettel Arce; Adriana Badilla-Lobo; Carolina Castro-Peña; José Molina; Diana López-Ureña; Sara González-Camacho; Bruno Lomonte; Carlos Chacón-Díaz; Cesar Rodríguez; Esteban Chaves-Olarte. Proteogenomic analysis of the Clostridium difficile exoproteome reveals a correlation between phylogenetic distribution and virulence potential. Anaerobe 2020, 62, 102151 .
AMA StyleCarlos Quesada-Gómez, Tatiana Murillo, Grettel Arce, Adriana Badilla-Lobo, Carolina Castro-Peña, José Molina, Diana López-Ureña, Sara González-Camacho, Bruno Lomonte, Carlos Chacón-Díaz, Cesar Rodríguez, Esteban Chaves-Olarte. Proteogenomic analysis of the Clostridium difficile exoproteome reveals a correlation between phylogenetic distribution and virulence potential. Anaerobe. 2020; 62 ():102151.
Chicago/Turabian StyleCarlos Quesada-Gómez; Tatiana Murillo; Grettel Arce; Adriana Badilla-Lobo; Carolina Castro-Peña; José Molina; Diana López-Ureña; Sara González-Camacho; Bruno Lomonte; Carlos Chacón-Díaz; Cesar Rodríguez; Esteban Chaves-Olarte. 2020. "Proteogenomic analysis of the Clostridium difficile exoproteome reveals a correlation between phylogenetic distribution and virulence potential." Anaerobe 62, no. : 102151.
Cfr is a radical S -adenosyl- l -methionine (SAM) enzyme that confers cross-resistance to antibiotics targeting the 23S rRNA through hypermethylation of nucleotide A2503. Three cfr -like genes implicated in antibiotic resistance have been described, two of which, cfr (B) and cfr (C), have been sporadically detected in Clostridium difficile . However, the methylase activity of Cfr(C) has not been confirmed.
Vanja Stojković; María Fernanda Ulate; Fanny Hidalgo-Villeda; Emmanuel Aguilar; Camilo Monge-Cascante; Marjorie Pizarro-Guajardo; Kaitlyn Tsai; Edgardo Tzoc; Margarita Camorlinga; Daniel Paredes-Sabja; Carlos Quesada-Gómez; Danica Galonić Fujimori; César Rodríguez. cfr (B), cfr (C), and a New cfr -Like Gene, cfr (E), in Clostridium difficile Strains Recovered across Latin America. Antimicrobial Agents and Chemotherapy 2019, 64, 1 .
AMA StyleVanja Stojković, María Fernanda Ulate, Fanny Hidalgo-Villeda, Emmanuel Aguilar, Camilo Monge-Cascante, Marjorie Pizarro-Guajardo, Kaitlyn Tsai, Edgardo Tzoc, Margarita Camorlinga, Daniel Paredes-Sabja, Carlos Quesada-Gómez, Danica Galonić Fujimori, César Rodríguez. cfr (B), cfr (C), and a New cfr -Like Gene, cfr (E), in Clostridium difficile Strains Recovered across Latin America. Antimicrobial Agents and Chemotherapy. 2019; 64 (1):1.
Chicago/Turabian StyleVanja Stojković; María Fernanda Ulate; Fanny Hidalgo-Villeda; Emmanuel Aguilar; Camilo Monge-Cascante; Marjorie Pizarro-Guajardo; Kaitlyn Tsai; Edgardo Tzoc; Margarita Camorlinga; Daniel Paredes-Sabja; Carlos Quesada-Gómez; Danica Galonić Fujimori; César Rodríguez. 2019. "cfr (B), cfr (C), and a New cfr -Like Gene, cfr (E), in Clostridium difficile Strains Recovered across Latin America." Antimicrobial Agents and Chemotherapy 64, no. 1: 1.
The major toxins of Clostridium difficile (TcdA, TcdB, CDT) are encoded chromosomally in nearly all known strains. Following up on a previous report, we found five new examples of a family of putative conjugative plasmids with tcdB and cdtAB in clinical C. difficile isolates from MLST Clades C-I, 2, and 4.
Gabriel Ramirez-Vargas; Cesar Rodriguez. Putative conjugative plasmids with tcdB and cdtAB genes in clinical Clostridium difficile strains from MLST clades C-I, 2 and 4. 2019, 852418 .
AMA StyleGabriel Ramirez-Vargas, Cesar Rodriguez. Putative conjugative plasmids with tcdB and cdtAB genes in clinical Clostridium difficile strains from MLST clades C-I, 2 and 4. . 2019; ():852418.
Chicago/Turabian StyleGabriel Ramirez-Vargas; Cesar Rodriguez. 2019. "Putative conjugative plasmids with tcdB and cdtAB genes in clinical Clostridium difficile strains from MLST clades C-I, 2 and 4." , no. : 852418.
Monensin (MON) is a coccidiostat used as a growth promoter that can reach the environment through fertilization with manure from farm animals. To verify whether field-relevant concentrations of this drug negatively influence the structure and activity of tropical soil bacteria, plate counts, CO2 efflux measurements, phospholipid fatty acids (PLFA) and community-level physiological profiling (CLPP) profiles were obtained for soil microcosms exposed to 1 or 10 mg kg−1 of MON across 11 days. Although 53% (1 mg kg−1) to 40% (10 mg kg−1) of the MON concentrations added to the microcosms dissipated within 5 days, a subtle concentration-dependent decrease in the number of culturable bacteria (<1 log CFU g−1), reduced (−20 to −30%) or exacerbated (+25%) soil CO2 effluxes, a marked shift of non-bacterial fatty acids, and altered respiration of amines (1.22-fold decrease) and polymers (1.70-fold increase) were noted in some of the treatments. These results suggest that MON quickly killed some microorganisms and that the surviving populations were selected and metabolically stimulated. Consequently, MON should be monitored in agronomic and environmental systems as part of One Health efforts.
Fabio Granados-Chinchilla; María De Jesús Arias-Andrés; María Laura Fernández Montes De Oca; César Rodríguez. Effect of the veterinary ionophore monensin on the structure and activity of a tropical soil bacterial community. Journal of Environmental Science and Health, Part B 2019, 55, 127 -134.
AMA StyleFabio Granados-Chinchilla, María De Jesús Arias-Andrés, María Laura Fernández Montes De Oca, César Rodríguez. Effect of the veterinary ionophore monensin on the structure and activity of a tropical soil bacterial community. Journal of Environmental Science and Health, Part B. 2019; 55 (2):127-134.
Chicago/Turabian StyleFabio Granados-Chinchilla; María De Jesús Arias-Andrés; María Laura Fernández Montes De Oca; César Rodríguez. 2019. "Effect of the veterinary ionophore monensin on the structure and activity of a tropical soil bacterial community." Journal of Environmental Science and Health, Part B 55, no. 2: 127-134.
Clostridium difficile induces antibiotic-associated diarrhea due to the release of toxin A (TcdA) and toxin B (TcdB), the latter being its main virulence factor. The epidemic strain NAP1/027 has an increased virulence attributed to different factors. We compared cellular intoxication by TcdBNAP1 with that by the reference strain VPI 10463 (TcdBVPI). In a mouse ligated intestinal loop model, TcdBNAP1 induced higher neutrophil recruitment, cytokine release, and epithelial damage than TcdBVPI. Both toxins modified the same panel of small GTPases and exhibited similar in vitro autoprocessing kinetics. On the basis of sequence variations in the frizzled-binding domain (FBD), we reasoned that TcdBVPI and TcdBNAP1 might have different receptor specificities. To test this possibility, we used a TcdB from a NAP1 variant strain (TcdBNAP1v) unable to glucosylate RhoA but with the same receptor-binding domains as TcdBNAP1. Cells were preincubated with TcdBNAP1v to block cellular receptors, prior to intoxication with either TcdBVPI or TcdBNAP1. Preincubation with TcdBNAP1v blocked RhoA glucosylation by TcdBNAP1 but not by TcdBVPI, indicating that the toxins use different host factors for cell entry. This crucial difference might explain the increased biological activity of TcdBNAP1 in the intestine, representing a contributing factor for the increased virulence of the NAP1/027 strain.
Diana López-Ureña; Josué Orozco-Aguilar; Yendry Chaves-Madrigal; Andrea Ramírez-Mata; Amanda Villalobos-Jimenez; Stefan Ost; Carlos Quesada-Gómez; César Rodríguez; Panagiotis Papatheodorou; Esteban Chaves-Olarte. Toxin B Variants from Clostridium difficile Strains VPI 10463 and NAP1/027 Share Similar Substrate Profile and Cellular Intoxication Kinetics but Use Different Host Cell Entry Factors. Toxins 2019, 11, 348 .
AMA StyleDiana López-Ureña, Josué Orozco-Aguilar, Yendry Chaves-Madrigal, Andrea Ramírez-Mata, Amanda Villalobos-Jimenez, Stefan Ost, Carlos Quesada-Gómez, César Rodríguez, Panagiotis Papatheodorou, Esteban Chaves-Olarte. Toxin B Variants from Clostridium difficile Strains VPI 10463 and NAP1/027 Share Similar Substrate Profile and Cellular Intoxication Kinetics but Use Different Host Cell Entry Factors. Toxins. 2019; 11 (6):348.
Chicago/Turabian StyleDiana López-Ureña; Josué Orozco-Aguilar; Yendry Chaves-Madrigal; Andrea Ramírez-Mata; Amanda Villalobos-Jimenez; Stefan Ost; Carlos Quesada-Gómez; César Rodríguez; Panagiotis Papatheodorou; Esteban Chaves-Olarte. 2019. "Toxin B Variants from Clostridium difficile Strains VPI 10463 and NAP1/027 Share Similar Substrate Profile and Cellular Intoxication Kinetics but Use Different Host Cell Entry Factors." Toxins 11, no. 6: 348.
Cfr is a radical S-adenosyl-L-methionine (SAM) enzyme that confers cross-resistance to all antibiotics targeting the large ribosomal subunit through hypermethylation of nucleotide A2503 of 23S rRNA. Of the four known cfr genes known to date, cfr(B) and cfr(C) have been sporadically found in C. difficile, yet functional characterization of cfr(C) is still lacking. We identified genes for putative Cfr-like enzymes among clinical C. difficile strains from Mexico, Honduras, Costa Rica, and Chile. To confirm their identity and activity, we obtained minimum inhibitory concentrations for ribosome-targeting antibiotics, annotated whole genome sequences, and performed a functional characterization of Cfr(C). The seven representative isolates analyzed displayed different levels of resistance to PhLOPSA antibiotics in the absence of the ribosome protection factor OptrA, and mutations in genes for 23S rRNAs or the ribosomal proteins L3 and L4. cfr(B) was detected in four isolates as part of a Tn6218-like transposon or an un-described mobile genetic element. In turn, cfr(C) was found integrated into an ICE-element. One isolate harbored a putative cfr-like gene that shows only 51-58% of sequence identity to Cfr and known Cfr-like enzymes. Moreover, our in vitro assays confirmed that Cfr(C) methylates E. coli and C. difficile 23S rRNA fragments. These results indicate selection of cfr-like genes in C. difficile from Latin America, suggest that the diversity of cfr-like resistance genes is larger than anticipated, and provide the first assessment of the methylation activity of Cfr(C).
Vanja Stojkovic; María Fernanda Ulate; Fanny Hidalgo-Villeda; Emmanuel Aguilar; Camilo Monge-Cascante; Marjorie Pizarro-Guajardo; Kaitlyn Tsai; Edgardo Tzoc; Margarita Camorlinga; Daniel Paredes-Sabja; Carlos Quesada-Gómez; Danica Galonić Fujimori; César Rodríguez; Margarita Camorlinga-Ponce. cfrB, cfrC, and a potential new cfr-like gene in Clostridium difficile strains recovered across Latin America. 2019, 1 .
AMA StyleVanja Stojkovic, María Fernanda Ulate, Fanny Hidalgo-Villeda, Emmanuel Aguilar, Camilo Monge-Cascante, Marjorie Pizarro-Guajardo, Kaitlyn Tsai, Edgardo Tzoc, Margarita Camorlinga, Daniel Paredes-Sabja, Carlos Quesada-Gómez, Danica Galonić Fujimori, César Rodríguez, Margarita Camorlinga-Ponce. cfrB, cfrC, and a potential new cfr-like gene in Clostridium difficile strains recovered across Latin America. . 2019; ():1.
Chicago/Turabian StyleVanja Stojkovic; María Fernanda Ulate; Fanny Hidalgo-Villeda; Emmanuel Aguilar; Camilo Monge-Cascante; Marjorie Pizarro-Guajardo; Kaitlyn Tsai; Edgardo Tzoc; Margarita Camorlinga; Daniel Paredes-Sabja; Carlos Quesada-Gómez; Danica Galonić Fujimori; César Rodríguez; Margarita Camorlinga-Ponce. 2019. "cfrB, cfrC, and a potential new cfr-like gene in Clostridium difficile strains recovered across Latin America." , no. : 1.
Though an overlap of Clostridium difficile PCR ribotypes (RT) in humans and animals has been noted -particularly in piglets-information regarding C. difficile isolates from swine is scarce in Latin America. A characterization of 10 C. difficile isolates obtained from this origin in Costa Rica revealed the presence of the RT078 (n = 4) and RT014/5-FLI01 (n = 6) ribotypes. Unlike two previous reports from the region, all isolates were multidrug resistant (MDR). According to a minimum spanning tree (MST) analysis, our RT078 isolates formed a clonal complex with some German RT078 isolates and the already noted overlap of RT078 strains in humans and animals. This unanticipated high level of genetic relatedness confirms the transcontinental spread and geographically unlimited clustering of RT078.
Mauricio Andino-Molina; Elías Barquero-Calvo; Christian Seyboldt; Gernot Schmoock; Heinrich Neubauer; Edgardo Tzoc; César Rodríguez; Carlos Quesada-Gómez. Multidrug-resistant Clostridium difficile ribotypes 078 and 014/5-FLI01 in piglets from Costa Rica. Anaerobe 2018, 55, 78 -82.
AMA StyleMauricio Andino-Molina, Elías Barquero-Calvo, Christian Seyboldt, Gernot Schmoock, Heinrich Neubauer, Edgardo Tzoc, César Rodríguez, Carlos Quesada-Gómez. Multidrug-resistant Clostridium difficile ribotypes 078 and 014/5-FLI01 in piglets from Costa Rica. Anaerobe. 2018; 55 ():78-82.
Chicago/Turabian StyleMauricio Andino-Molina; Elías Barquero-Calvo; Christian Seyboldt; Gernot Schmoock; Heinrich Neubauer; Edgardo Tzoc; César Rodríguez; Carlos Quesada-Gómez. 2018. "Multidrug-resistant Clostridium difficile ribotypes 078 and 014/5-FLI01 in piglets from Costa Rica." Anaerobe 55, no. : 78-82.
The population structure of Clostridium difficile currently comprises eight major genomic clades. For the highly divergent C-I clade, only two toxigenic strains have been reported, which lack the tcdA and tcdC genes and carry a complete locus for the binary toxin (CDT) next to an atypical TcdB monotoxin pathogenicity locus (PaLoc). As part of a routine surveillance of C. difficile in stool samples from diarrheic human patients, we discovered three isolates that consistently gave negative results in a PCR-based screening for tcdC. Through phenotypic assays, whole-genome sequencing, experiments in cell cultures, and infection biomodels we show that these three isolates (i) escape common laboratory diagnostic procedures, (ii) represent new ribotypes, PFGE-types, and sequence types within the Clade C-I, (iii) carry chromosomal or plasmidal TcdBs that induce classical or variant cytopathic effects (CPE), and (iv) cause different levels of cytotoxicity and hamster mortality rates. These results show that new strains of C. difficile can be detected by more refined techniques and raise questions on the origin, evolution, and distribution of the toxin loci of C. difficile and the mechanisms by which this emerging pathogen causes disease.
Gabriel Ramírez-Vargas; Diana López-Ureña; Adriana Badilla; Josué Orozco-Aguilar; Tatiana Murillo; Priscilla Rojas; Thomas Riedel; Jörg Overmann; Gabriel Gonzalez; Esteban Chaves-Olarte; Carlos Quesada-Gómez; César Rodríguez. Novel Clade C-I Clostridium difficile strains escape diagnostic tests, differ in pathogenicity potential and carry toxins on extrachromosomal elements. Scientific Reports 2018, 8, 1 -11.
AMA StyleGabriel Ramírez-Vargas, Diana López-Ureña, Adriana Badilla, Josué Orozco-Aguilar, Tatiana Murillo, Priscilla Rojas, Thomas Riedel, Jörg Overmann, Gabriel Gonzalez, Esteban Chaves-Olarte, Carlos Quesada-Gómez, César Rodríguez. Novel Clade C-I Clostridium difficile strains escape diagnostic tests, differ in pathogenicity potential and carry toxins on extrachromosomal elements. Scientific Reports. 2018; 8 (1):1-11.
Chicago/Turabian StyleGabriel Ramírez-Vargas; Diana López-Ureña; Adriana Badilla; Josué Orozco-Aguilar; Tatiana Murillo; Priscilla Rojas; Thomas Riedel; Jörg Overmann; Gabriel Gonzalez; Esteban Chaves-Olarte; Carlos Quesada-Gómez; César Rodríguez. 2018. "Novel Clade C-I Clostridium difficile strains escape diagnostic tests, differ in pathogenicity potential and carry toxins on extrachromosomal elements." Scientific Reports 8, no. 1: 1-11.
Clostridiodes difficile strains from the NAPCR1/ST54 and NAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparing whole genome sequences of 32 NAPCR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homologous recombination (r) or nonhomologous recombination (NHR) through lateral gene transfer (LGT) have differentially shaped the microdiversification of these strains. The average number of single nucleotide polymorphisms (SNPs) in coding sequences (NAPCR1/ST54 = 24; NAP1/ST01 = 19) and SNP densities (NAPCR1/ST54 = 0.54/kb; NAP1/ST01 = 0.46/kb) in the NAPCR1/ST54 and NAP1/ST01 isolates was comparable. However, the NAP1/ST01 isolates showed 3× higher average dN/dS rates (8.35) that the NAPCR1/ST54 isolates (2.62). Regarding r, whereas 31 of the NAPCR1/ST54 isolates showed 1 recombination block (3,301-8,226 bp), the NAP1/ST01 isolates showed no bases in recombination. As to NHR, the pangenome of the NAPCR1/ST54 isolates was larger (4,802 gene clusters, 26% noncore genes) and more heterogeneous (644 ± 33 gene content changes) than that of the NAP1/ST01 isolates (3,829 gene clusters, ca. 6% noncore genes, 129 ± 37 gene content changes). Nearly 55% of the gene content changes seen among the NAPCR1/ST54 isolates (355 ± 31) were traced back to MGEs with putative genes for antimicrobial resistance and virulence factors that were only detected in single isolates or isolate clusters. Congruently, the LGT/SNP rate calculated for the NAPCR1/ST54 isolates (26.8 ± 2.8) was 4× higher than the one obtained for the NAP1/ST1 isolates (6.8 ± 2.0). We conclude that NHR-LGT has had a greater role in the microdiversification of the NAPCR1/ST54 strains, opposite to the NAP1/ST01 strains, where mutation is known to play a more prominent role.
Tatiana Murillo; Gabriel Ramírez-Vargas; Thomas Riedel; Jörg Overmann; Joakim M Andersen; Caterina Guzman-Verri; Esteban Chaves-Olarte; César Rodríguez. Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms. Genome Biology and Evolution 2018, 10, 982 -998.
AMA StyleTatiana Murillo, Gabriel Ramírez-Vargas, Thomas Riedel, Jörg Overmann, Joakim M Andersen, Caterina Guzman-Verri, Esteban Chaves-Olarte, César Rodríguez. Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms. Genome Biology and Evolution. 2018; 10 (3):982-998.
Chicago/Turabian StyleTatiana Murillo; Gabriel Ramírez-Vargas; Thomas Riedel; Jörg Overmann; Joakim M Andersen; Caterina Guzman-Verri; Esteban Chaves-Olarte; César Rodríguez. 2018. "Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms." Genome Biology and Evolution 10, no. 3: 982-998.
Until recently, Clostridium difficile phages were limited to Myoviruses and Siphoviruses of medium genome length (32–57 kb). Here we report the finding of phiCD5763, a Siphovirus with a large extrachromosomal circular genome (132.5 kb, 172 ORFs) and a large capsid (205.6 ± 25.6 nm in diameter) infecting MLST Clade 1 strains of C. difficile. Two subgroups of big phage genomes similar to phiCD5763 were identified in 32 NAPCR1/RT012/ST-54 C. difficile isolates from Costa Rica and in whole genome sequences (WGS) of 41 C. difficile isolates of Clades 1, 2, 3, and 4 from Canada, USA, UK, Belgium, Iraq, and China. Through comparative genomics we discovered another putative big phage genome in a non-NAPCR1 isolate from Costa Rica, phiCD2955, which represents other big phage genomes found in 130 WGS of MLST Clade 1 and 2 isolates from Canada, USA, Hungary, France, Austria, and UK. phiCD2955 (131.6 kb, 172 ORFs) is related to a previously reported C. difficile phage genome, phiCD211/phiCDIF1296T. Detailed genome analyses of phiCD5763, phiCD2955, phiCD211/phiCDIF1296T, and seven other putative C. difficile big phage genome sequences of 131–136 kb reconstructed from publicly available WGS revealed a modular gene organization and high levels of sequence heterogeneity at several hotspots, suggesting that these genomes correspond to biological entities undergoing recombination. Compared to other C. difficile phages, these big phages have unique predicted terminase, capsid, portal, neck and tail proteins, receptor binding proteins (RBPs), recombinases, resolvases, primases, helicases, ligases, and hypothetical proteins. Moreover, their predicted gene load suggests a complex regulation of both phage and host functions. Overall, our results indicate that the prevalence of C. difficile big bacteriophages is more widespread than realized and open new avenues of research aiming to decipher how these viral elements influence the biology of this emerging pathogen.
Gabriel Ramírez-Vargas; Shan Goh; César Rodríguez. The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile. Frontiers in Microbiology 2018, 9, 26 .
AMA StyleGabriel Ramírez-Vargas, Shan Goh, César Rodríguez. The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile. Frontiers in Microbiology. 2018; 9 ():26.
Chicago/Turabian StyleGabriel Ramírez-Vargas; Shan Goh; César Rodríguez. 2018. "The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile." Frontiers in Microbiology 9, no. : 26.
Clostridium difficile is a nosocomial agent affecting immunocompromised populations under antibiotic treatment. The clinical manifestations induced by this bacterium range from mild antibiotic-associated diarrhea to potentially fatal pseudomembranous colitis. Traditionally, all the signs and symptoms produced by C. difficile have been associated to the production of two toxins, toxin A and toxin B. Both toxins belong to the family of large clostridial cytotoxins (LCTs), and their mechanism of action relies on a series of complex steps. First, these toxins recognize cell-surface located receptors allowing the entrance in membrane-surrounded compartments. The toxins are then translocated through acid sensing-dependent conformational changes and the enzymatically active domain is released into the cytosol through an autoprocessing activity. This enzymatic domain modifies through glucosylation of small guanosine triphosphatase (GTPases) from the Rho and Ras families. Consequently, the signal transduction pathways mediated by these proteins are interrupted leading to the corresponding cytoskeletal alterations and different effects which might finally result in different types of cell death. In vivo, these toxins induce toxicity on epithelial cells lining the intestinal mucosa and induce a severe inflammatory reaction characterized by the recruitment of neutrophils and secretion of several cytokines. It is precisely a combination of dead intestinal epithelial cells combined with polymorphonuclear immune cells that constitutes the characteristic pseudomembrane observed in diarrheic depositions by patients suffering complications of this infection. In this chapter, the clinical manifestations induced by C. difficile toxins, the cellular consequences of their mechanism of action and the evolution of the pathogenicity locus where they are encoded are discussed in detail.
Diana López-Ureña; Carlos Quesada-Gómez; César Rodríguez; Esteban Chaves-Olarte. Role of Clostridium difficile Toxins in Antibiotic-Associated Diarrhea and Pseudomembranous Colitis. Toxins and Drug Discovery 2018, 153 -170.
AMA StyleDiana López-Ureña, Carlos Quesada-Gómez, César Rodríguez, Esteban Chaves-Olarte. Role of Clostridium difficile Toxins in Antibiotic-Associated Diarrhea and Pseudomembranous Colitis. Toxins and Drug Discovery. 2018; ():153-170.
Chicago/Turabian StyleDiana López-Ureña; Carlos Quesada-Gómez; César Rodríguez; Esteban Chaves-Olarte. 2018. "Role of Clostridium difficile Toxins in Antibiotic-Associated Diarrhea and Pseudomembranous Colitis." Toxins and Drug Discovery , no. : 153-170.
Avian botulism outbreaks are frequently produced by type C neurotoxin secreted by Clostridium botulinum proliferating in decomposing bird carcasses and contaminated soils or water sediments. In this study, a botulism outbreak was diagnosed in broilers from a Costa Rican commercial farm through clinical signs, absence of postmortem histopathological lesions, and the confirmation of toxin in the serum of the birds. C. botulinum was furthered isolated from the intestine of these animals. This is the first report of avian botulism due to C. botulinum type C in Central America.
Evelyn Rodriguez Cavallini; Diana Lopez Urena; Tania Roman; Carlos Quesada Gomez. Avian Botulism Type C in a Commercial Poultry Farm: First Report in Central America. Journal of Bacteriology & Parasitology 2018, 09, 1 -2.
AMA StyleEvelyn Rodriguez Cavallini, Diana Lopez Urena, Tania Roman, Carlos Quesada Gomez. Avian Botulism Type C in a Commercial Poultry Farm: First Report in Central America. Journal of Bacteriology & Parasitology. 2018; 09 (03):1-2.
Chicago/Turabian StyleEvelyn Rodriguez Cavallini; Diana Lopez Urena; Tania Roman; Carlos Quesada Gomez. 2018. "Avian Botulism Type C in a Commercial Poultry Farm: First Report in Central America." Journal of Bacteriology & Parasitology 09, no. 03: 1-2.