Clostridium bacteraemia characterised by 16S ribosomal RNA gene sequencing

Woo, Patrick C. Y.; Lau, Skp; Chan, K.T.K.; Fung, Ami M. Y.; Tang, Bone Siu-Fai; Yuen, Kwok‐Yung

doi:10.1136/jcp.2004.022830

Cited by 46 publications

(31 citation statements)

References 17 publications

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“…In this study, we focused on Clostridium perfringens to determine its copresence with C. difficile because it is a common clinically diagnosed bacterial pathogen that causes diarrhea. In addition, 16S rRNA gene sequencing is capable of identifying C. perfringens at the species level (33). Considering the difficulty of detecting low-abundance organisms using the metagenomic approach, the presence of C. perfringens was designated only when the organism was identified by both the 16S rRNA gene approach and MSS.…”

Section: Resultsmentioning

confidence: 99%

Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens

et al. 2016

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The potential to rapidly capture the entire microbial community structure and/or gene content makes metagenomic sequencing an attractive tool for pathogen identification and the detection of resistance/virulence genes in clinical settings. Here, we assessed the consistency between PCR from a diagnostic laboratory, quantitative PCR (qPCR) from a research laboratory, 16S rRNA gene sequencing, and metagenomic shotgun sequencing (MSS) for Clostridium difficile identification in diarrhea stool samples. Twenty-two C. difficile-positive diarrhea samples identified by PCR and qPCR and five C. difficile-negative diarrhea controls were studied. C. difficile was detected in 90.9% of C. difficile-positive samples using 16S rRNA gene sequencing, and C. difficile was detected in 86.3% of C. difficile-positive samples using MSS. CFU inferred from qPCR analysis were positively correlated with the relative abundance of C. difficile from 16S rRNA gene sequencing (r 2 ‫؍‬ ؊0.60) and MSS (r 2 ‫؍‬ ؊0.55). C. difficile was codetected with Clostridium perfringens, norovirus, sapovirus, parechovirus, and anellovirus in 3.7% to 27.3% of the samples. A high load of Candida spp. was found in a symptomatic control sample in which no causative agents for diarrhea were identified in routine clinical testing. Beta-lactamase and tetracycline resistance genes were the most prevalent (25.9%) antibiotic resistance genes in these samples. In summary, the proof-of-concept study demonstrated that next-generation sequencing (NGS) in pathogen detection is moderately correlated with laboratory testing and is advantageous in detecting pathogens without a priori knowledge. Sequencing technology has revolutionized infectious diseases research over the past decade. Whole-genome sequencing (WGS) of pure cultures has been widely used for pathogen characterization, evolutionary studies, transmission investigations, and outbreak detection (1, 2, 3). WGS of cultured isolates is now moving from the proof-of-concept phase to implementation. The two major applications of WGS of cultured strains in clinical diagnostic microbiology are molecular epidemiology and antibiotic resistance gene prediction (4). In contrast to the WGS sequencing of cultured isolates, metagenomics assesses a community of organisms but eliminates the isolation step. This can be done by focusing on a specific conserved gene, such as the 16S rRNA gene, or by the metagenomic shotgun sequencing (MSS) of total microbial nucleic acids within samples. For the purpose of this study, metagenomics sequencing refers to either 16S rRNA gene sequencing or MSS; 16S rRNA gene sequencing and MSS using next-generation sequencing (NGS) platforms produce large quantities of data in a relatively short time. Although 16S rRNA gene sequencing is less expensive than MSS, it suffers from potential PCR-related bias. Taxonomical classification based on partial 16S rRNA gene sequencing is generally limited to phylum to genus level specificity. Nevertheless, highly heterogeneous species within certain genera can be dist...

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Section: Resultsmentioning

confidence: 99%

Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens

et al. 2016

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“…Application of the technique has led to recognition of many previously undescribed or 'rarely encountered' anaerobic Gram-positive rods for their associations with more serious diseases than previously thought (Bosshard, Zbinden, & Altwegg, 2002;Chan, Lau, et al, 2012;Lau, McNabb, et al, 2007;Woo, Lau, Chan, et al, 2005;. We have previously used 16S rRNA gene sequencing to characterise bacteraemia caused by anaerobic, non-sporulating, Gram-positive rod and found that the former genus Eggerthella accounted for a high proportion of clinically significant bacteraemia .…”

Section: Defining Disease Associations and Epidemiologymentioning

confidence: 96%

Gene Amplification and Sequencing for Bacterial Identification

Lau

Teng

et al. 2015

Methods in Microbiology

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“…The unique colony morphology of C clostridioforme and its appearance as fusiform or boat-shaped rods that may appear as Gram-stainingvariable should aid in its identification. In susceptibility tests, the use of 10 mg vancomycin per disc would show that the organism is susceptible to vancomycin and therefore not likely to be Gram-negative; however, 16S rRNA gene sequencing may be required for accurate identification (Woo et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

Clostridium clostridioforme liver abscess complicated by portal vein thrombosis in childhood

Ogah

Sethi

Karthik

2012

Journal of Medical Microbiology

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Pyogenic liver abscesses are rare in children, and show geographical differences in their epidemiology. Mortality rates remain high at 15 %. Liver abscesses caused by anaerobic organisms are rare in a paediatric setting, even more so when complicated by portal vein thrombosis (PVT). A 6-year-old girl, previously fit and well, was admitted with fever, lethargy and weight loss of 2 weeks duration. The patient was febrile on examination and a review of the systems revealed no positive findings. An abdominal ultrasound scan showed multiple interconnecting cystic lesions consistent with liver abscesses, which was confirmed by a computed tomography scan. Aspirate of the abscess was cultured, resulting in the isolation of a non-haemolytic anaerobic organism, which was difficult to identify using conventional phenotypic identification tests. 16S rRNA typing identified the organism as Clostridium clostridioforme. The liver abscess in our patient displayed a particularly aggressive clinical course with extension of the abscess to involve the upper pole of the right kidney and the appendix, which was further complicated by PVT. The role of anaerobic organisms in liver abscesses has been underreported in the past. This case, therefore, highlights the importance of incubating biological samples in anaerobic conditions in order to adequately isolate and identify anaerobic bacteria, particularly those associated with abscesses.

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Clostridium bacteraemia characterised by 16S ribosomal RNA gene sequencing

Cited by 46 publications

References 17 publications

Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens

Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens

Gene Amplification and Sequencing for Bacterial Identification

Clostridium clostridioforme liver abscess complicated by portal vein thrombosis in childhood

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