Genomic analysis of three Clostridioides difficile isolates from urban water sources

Numberger, Daniela; Riedel, Thomas; McEwen, Gayle; Nübel, Ulrich; Frentrup, Martinique; Schober, Isabel; Bunk, Boyke; Spröer, Cathrin; Overmann, Jörg; Grossart, Hans‐Peter; Greenwood, Alex D.

doi:10.1016/j.anaerobe.2019.01.002

Cited by 14 publications

(17 citation statements)

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“…Thus, the presence of pathogens could be greatly underestimated when using 16S rRNA data only. For instance, in a previous study we could detect and isolate C. difficile from the same samples used in the current study and even detect the C. difficile toxin genes via quantitative real-time PCR, but the 16S rRNA dataset did not provide any evidence for the presence of C. difficile 103 . Therefore, there are clearly limits to high throughput sequencing studies that involve a PCR step in terms of favouring abundant taxa.…”

Section: Discussionmentioning

confidence: 65%

Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing

Numberger

Ganzert

Zoccarato

et al. 2019

Sci Rep

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173

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Wastewater treatment is crucial to environmental hygiene in urban environments. However, wastewater treatment plants (WWTPs) collect chemicals, organic matter, and microorganisms including pathogens and multi-resistant bacteria from various sources which may be potentially released into the environment via WWTP effluent. To better understand microbial dynamics in WWTPs, we characterized and compared the bacterial community of the inflow and effluent of a WWTP in Berlin, Germany using full-length 16S rRNA gene sequences, which allowed for species level determination in many cases and generally resolved bacterial taxa. Significantly distinct bacterial communities were identified in the wastewater inflow and effluent samples. Dominant operational taxonomic units (OTUs) varied both temporally and spatially. Disease associated bacterial groups were efficiently reduced in their relative abundance from the effluent by the WWTP treatment process, except for Legionella and Leptospira species which demonstrated an increase in relative proportion from inflow to effluent. This indicates that WWTPs, while effective against enteric bacteria, may enrich and release other potentially pathogenic bacteria into the environment. The taxonomic resolution of full-length 16S rRNA genes allows for improved characterization of potential pathogenic taxa and other harmful bacteria which is required to reliably assess health risk.

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Section: Discussionmentioning

confidence: 65%

Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing

Numberger

Ganzert

Zoccarato

et al. 2019

Sci Rep

Self Cite

173

View full text Add to dashboard Cite

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“…EnteroBase is already being used by the community to identify genetically related groups of isolates (Diemert and Yan 2019;Haley et al 2019;Johnson et al 2019;Miller et al 2019;Numberger et al 2019), and HierCC has been used to mark international outbreaks of S. enterica serovar Poona (Jones et al 2019b) and E. coli O26 (Jones et al 2019a). Case Study 1 illustrates how to explore HierCC genomic relationships at multiple levels, ranging from HC2000 (superlineages) for intercontinental dispersion down to HC5-10 for detecting local transmission chains.…”

Section: Discussionmentioning

confidence: 99%

The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

Zhou

Alikhan²,

Mohamed³

et al. 2019

Genome Res.

662

801

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EnteroBase is an integrated software environment that supports the identification of global population structures within several bacterial genera that include pathogens. Here, we provide an overview of how EnteroBase works, what it can do, and its future prospects. EnteroBase has currently assembled more than 300,000 genomes from Illumina short reads from Salmonella, Escherichia, Yersinia, Clostridioides, Helicobacter, Vibrio, and Moraxella and genotyped those assemblies by core genome multilocus sequence typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads. Case Study 1 illustrates this process for local transmissions of Salmonella enterica serovar Agama between neighboring social groups of badgers and humans. EnteroBase also supports single nucleotide polymorphism (SNP) calls from both genomic assemblies and after extraction from metagenomic sequences, as illustrated by Case Study 2 which summarizes the microevolution of Yersinia pestis over the last 5000 years of pandemic plague. EnteroBase can also provide a global overview of the genomic diversity within an entire genus, as illustrated by Case Study 3, which presents a novel, global overview of the population structure of all of the species, subspecies, and clades within Escherichia.

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“…Pathogenic C. difficile strains can induce diarrhea and life-threatening pseudomembranous colitis, often requiring antibiotic treatment. These strains are mainly identified by their ability to produce the enterotoxin A (TcdA) and/or the cytotoxin B (TcdB) [59]. C. difficile-associated diarrhea (CDAD) is a very common nosocomial infection related with high morbidity and mortality, which imposes a huge financial burden to healthcare facilities [60].…”

Section: Clostridioides Difficilementioning

confidence: 99%

Molecular Methods for Pathogenic Bacteria Detection and Recent Advances in Wastewater Analysis

Zhang

et al. 2021

Water

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With increasing concerns about public health and the development of molecular techniques, new detection tools and the combination of existing approaches have increased the abilities of pathogenic bacteria monitoring by exploring new biomarkers, increasing the sensitivity and accuracy of detection, quantification, and analyzing various genes such as functional genes and antimicrobial resistance genes (ARG). Molecular methods are gradually emerging as the most popular detection approach for pathogens, in addition to the conventional culture-based plate enumeration methods. The analysis of pathogens in wastewater and the back-estimation of infections in the community, also known as wastewater-based epidemiology (WBE), is an emerging methodology and has a great potential to supplement current surveillance systems for the monitoring of infectious diseases and the early warning of outbreaks. However, as a complex matrix, wastewater largely challenges the analytical performance of molecular methods. This review synthesized the literature of typical pathogenic bacteria in wastewater, types of biomarkers, molecular methods for bacterial analysis, and their recent advances in wastewater analysis. The advantages and limitation of these molecular methods were evaluated, and their prospects in WBE were discussed to provide insight for future development.

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Genomic analysis of three Clostridioides difficile isolates from urban water sources

Cited by 14 publications

References 50 publications

Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing

Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing

The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

Molecular Methods for Pathogenic Bacteria Detection and Recent Advances in Wastewater Analysis

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