Characteristics of Clostridium difficile infection in a high complexity hospital and report of the circulation of the NAP1/027 hypervirulent strain in Colombia

Gualtero, Sandra; Abril, Lina Alejandra; Camelo, Nathalia; Sanchez, Susi Daniela; Dávila, Fabián A.; Arias, Gerson; Silva, Edwin; Bustos, Ingrid Gissel; Josa-Montero, Diego; Torres, Isabel Cristina; Zambrano, Luis Carlos; Pareja, María José

doi:10.7705/biomedica.v37i4.3244

Cited by 12 publications

(6 citation statements)

References 28 publications

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“…Practice guidelines indicated the two biggest risk factors of CDI were exposure to antibiotics and the organism [40]; Gualtero et al’s research [41] demonstrated chronic kidney disease was the most common comorbidities associated with CDI. In concurrence with these studies, the multivariate regression model indicated that prior use of antimicrobial agents ( p = 0.001, OR = 5.035) and kidney disease ( p = 0.015, OR = 8.329) were closely related to CDI.…”

Section: Discussionmentioning

confidence: 99%

Epidemiology of Clostridium difficile infection in hospitalized adults and the first isolation of C. difficile PCR ribotype 027 in central China

Zhou

et al. 2019

BMC Infect Dis

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Background Clostridium difficile infection (CDI) is an emerging healthcare problem in the world. The purpose of this study was to perform a systematic epidemiological research of CDI in Tongji hospital, the central of China. Methods Stool samples from hospitalized adults suspected of CDI were enrolled. The diagnosis of CDI were based on the combination of clinical symptoms and laboratory results. Clinical features of CDI and non-CDI patients were compared by appropriate statistical tests to determine the risk factors of CDI. Multilocus sequence typing (MLST) was employed for molecular epidemiological analysis. Susceptibility testing and relevant antimicrobial agent resistance genes were performed as well. Results From June 2016 to September 2017, 839 hospitalized adults were enrolled. Among them, 107 (12.8%, 107/839) patients were C. difficile culture positive, and 73 (8.7%, 73/839) were infected with toxigenic C. difficile (TCD), with tcdA + tcdB+ strains accounting for 90.4% (66/73) and tcdA-tcdB+ for 9.6% (7/73). Meanwhile, two TCD strains were binary toxin positive and one of them was finally identified as CD027. Severe symptoms were observed in these two cases. Multivariate analysis indicated antibiotic exposure ( p = 0.001, OR = 5.035) and kidney disease ( p = 0.015, OR = 8.329) significantly increased the risk of CDI. Phylogenetic tree analysis demonstrated 21 different STs, including one new ST (ST467); and the most dominant type was ST54 (35.6%, 26/73). Multidrug-resistant (MDR) TCD were 53.4% (39/73); resistance to ciprofloxacin, erythromycin, and clindamycin were > 50%. Other antibiotics showed relative efficiency and all strains were susceptible to metronidazole and vancomycin. All moxifloxacin-resistant isolates carried a mutation in GyrA (Thr82 → Ile), with one both having mutation in GyrB (Ser366 → Ala). Conclusions Knowledge of epidemiological information for CDI is limited in China. Our finding indicated tcdA + tcdB+ C. difficile strains were the dominant for CDI in our hospital. Significant risk factors for CDI in our setting appeared to be antibiotic exposure and kidney disease. Metronidazole and vancomycin were still effective for CDI. Although no outbreak was observed, the first isolation of CD027 in center China implied the potential spread of this hypervirulent clone. Further studies are needed to enhance our understanding of the epidemiology of CDI in China. Electronic supplementary material The online version of this article (10.1186/s12879-019-3841-6) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Epidemiology of Clostridium difficile infection in hospitalized adults and the first isolation of C. difficile PCR ribotype 027 in central China

Zhou

et al. 2019

BMC Infect Dis

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“…The reads obtained from WGS were de novo assembled using Unicycler v0.4.8, an assembly pipeline for bacterial genomes defined as a SPAdes-optimiser (Spades v3.13.1) which generates the best possible assembly [ 25 ], using default parameters. The quality of the genome assembly was evaluated using the GenomeQC_Filter_v1-5 script [ 26 ], which considers as parameters the maximum number of contigs per genome (fixed to 400) and a maximum size of each genome (considering 8 Mbp) and then extracts the small subunit 16S rRNA gene sequences (16S rRNA).…”

Section: Methodsmentioning

confidence: 99%

Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery

et al. 2020

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Sellimonas intestinalis is a Gram-positive and anaerobic bacterial species previously considered as uncultivable. Although little is known about this Lachnospiraceae family member, its increased abundance has been reported in patients who have recovered from intestinal homeostasis after dysbiosis events. In this context, the aim of the present study was to take advantage of a massive in vitro culture protocol that allowed the recovery of extremely oxygen-sensitive species from faecal samples, which led to isolation of S. intestinalis . Whole genome analyses of 11 S . intestinalis genomes revealed that this species has a highly conserved genome with 99.7 % 16S rRNA gene sequence similarity, average nucleotide polymorphism results >95, and 50.1 % of its coding potential being part of the core genome. Despite this, the variable portion of its genome was informative enough to reveal the existence of three lineages (lineage-I including isolates from Chile and France, lineage-II from South Korea and Finland, and lineage-III from China and one isolate from the USA) and evidence of some recombination signals. The identification of a cluster of orthologous groups revealed a high number of genes involved in metabolism, including amino acid and carbohydrate transport as well as energy production and conversion, which matches with the metabolic profile previously reported for microbiota from healthy individuals. Additionally, virulence factors and antimicrobial resistance genes were found (mainly in lineage-III), which could favour their survival during antibiotic-induced dysbiosis. These findings provide the basis of knowledge about the potential of S. intestinalis as a bioindicator of intestinal homeostasis recovery and contribute to advancing the characterization of gut microbiota members with beneficial potential.

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“…The reads obtained from WGS were De novo assembled using Unicycler v0.4.8, an assembly pipeline for bacterial genomes defined as a SPAdes-optimiser (Spades v3.13.1) which generates the best possible assembly, 36 using parameters by default. The quality of the genome assembly was evaluated using the GenomeQC_Filter_v1-5 script, 37 which considers as parameters the maximum number of contigs per genome (fixed to 400) and a maximum size of each genome (considering 8 Mbp) and then extracts the small subunit 16S rRNA gene sequences (16S-rRNA).…”

Section: Methodsmentioning

confidence: 99%

Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery

Muñoz

Guerrero-Araya²,

Cortés-Tapia³

et al. 2020

Preprint

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Comprehensive genome analyses of Sellimonas intestinalis, a potential 19 biomarker of homeostasis gut recovery 20 Sellimonas intestinalis is a Gram positive and anaerobic bacterial species 21 previously considered as uncultivable. Although little is known about this 22 Lachnospiraceae family member, its increased abundance has been reported in 23 patients who recovered intestinal homeostasis after dysbiosis events. In this 24 context, the aim of this work was taken advantage of a culturomics protocol that 25 allowed the recovery species extremely oxygen-sensitive from faecal samples, 26 which led to the establishment of an S. intestinalis isolate. Whole genome 27 sequencing and taxonomic allocation confirmation were the base to develop 28 comparative analyses including 11 public genomes closely related. 29 Phylogeographic analysis revealed the existence of three lineages (linage-I 30 including isolates from Chile and France, linage-II from South Korea and Finland, 31 and linage-III from China and one isolate from USA). Pangenome analysis on the 32 established dataset revealed that although S. intestinalis seems to have a highly 33 conserved genome (with 50.1% of its coding potential being part of the 34 coregenome), some recombination signals were evidenced. The identification of 35 cluster of orthologous groups revealed a high number of genes involved in 36 metabolism, including amino acid and carbohydrate transport as well as energy 37 production and conversion, which matches with the metabolic profile previously 38 reported for healthy microbiota. Additionally, virulence factors and antimicrobial 39 resistance genes were found (mainly in linage-III), which could favour their 40 survival during antibiotic-induced dysbiosis. These findings provide the basis of 41 knowledge about this species with potential as a bioindicator of intestinal 42 homeostasis recovery and contribute to advance in the characterization of gut 43 microbiota members with beneficial potential.44

show abstract

Characteristics of Clostridium difficile infection in a high complexity hospital and report of the circulation of the NAP1/027 hypervirulent strain in Colombia

Cited by 12 publications

References 28 publications

Epidemiology of Clostridium difficile infection in hospitalized adults and the first isolation of C. difficile PCR ribotype 027 in central China

Epidemiology of Clostridium difficile infection in hospitalized adults and the first isolation of C. difficile PCR ribotype 027 in central China

Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery

Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery

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