Next-generation sequencing applications in clinical bacteriology

Motro, Yair; Moran-Gilad, Jacob

doi:10.1016/j.bdq.2017.10.002

Cited by 73 publications

(52 citation statements)

References 54 publications

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“…Unbiased NGS technology amplifies all nucleic acids present in a clinical sample, including both host and microbes without requiring primers for targeted amplification, and can potentially generate microbial sequence data offering the capability of identifying a variety of organisms-bacteria, virus, fungi, or parasite [15] . As can be seen from our study, 95.35% of the NGS sequencing data were compared to the human genome, whereas less than <1 % to the pathogen genome.…”

Section: Discussionmentioning

confidence: 99%

“…NGS pathogen detection usually obtains a variety of suspected pathogens gene sequences, and how to distinguish between pathogens and contaminating “background bacteria” becomes critical. Procedures including clinical specimen collection, sample preservation, transportation and the experimental procedures, may cause pollution and lead to contaminate the specimen mixed with so called “background” microbial gene sequence, which may affect the NGS data analysis [15,19,20] , resulting in false positive results and hinder the doctors. Similar to previous reports, we found that the most common background bacterium was Propionibacterium acnes in our study (data not shown here) [14] .…”

Section: Discussionmentioning

confidence: 99%

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Next-Generation Sequencing Could be a Promising Diagnostic Approach for Pathogen Detection: Pathogenic Analysis of Pediatric Bacterial Meningitis by Next-Generation Sequencing Technology Directly from Cerebrospinal Fluid Specimens

Guo

Liu

et al. 2018

Preprint

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BackgroundBacterial meningitis remains one of the major challenges in infectious diseases, leading to sequel in many cases. A prompt diagnosis of the causative microorganism is critical to significantly improve outcome of bacterial meningitis. Although various targeted tests for cerebrospinal fluid (CSF) samples are available, it is a big problem for the identification of etiology of bacterial meningitis.MethodsHere we describe the use of unbiased sequence analyses by next-generation sequencing (NGS) technology for the identification of infectious microorganisms from CSF samples of pediatric bacterial meningitis patients in the Department of Infectious Diseases from Beijing Children’s Hospital.ResultsIn total, we had 99 bacterial meningitis patients in our study, 55 (55.6%) of these were etiologically confirmed by clinical microbiology methods. Combined with NGS, 68 cases (68.7%) were etiologically confirmed. The main pathogens identified in this study were Streptococcus pneumoniae (n=29), group B streptococcus (n=15), Staphylococcus aureus (n=7), Escherichia coli (n=7). In addition, two cases with cytomegalovirus infection and one with Taenia saginata asiatica were confirmed by NGS.ConclusionsNGS could be a promising alternative diagnostic approach for critically ill patients suffering from bacterial meningitis in pediatric population.SummaryWe conducted the study for the identification of microorganisms by next-generation sequencing directly from CSF samples of pediatric bacterial meningitis patients. And the study showed that NGS could be a promising alternative diagnostic approach for bacterial meningitis in pediatric population.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Next-Generation Sequencing Could be a Promising Diagnostic Approach for Pathogen Detection: Pathogenic Analysis of Pediatric Bacterial Meningitis by Next-Generation Sequencing Technology Directly from Cerebrospinal Fluid Specimens

Guo

Liu

et al. 2018

Preprint

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“…차세대 유전자 분석(next-generation sequencing, NGS)의 등장은 임상미생물 검사 영역에서도 많 은 변화를 가지고 왔다 [4]. 원내 외에서 집단 발생하는 감염의 병인균 typing 및 항균제내성이나 병독성에 관련된 유전자 검출에 NGS를 이용할 수 있고, 배양이 까다로운 세균도 검출이 가능하 다 [5].…”

Section: Introductionunclassified

Application of 16S rRNA Gene-Targeted Next-Generation Sequencing for Bacterial Pathogen Detection in Continuous Ambulatory Peritoneal Dialysis Peritonitis

et al. 2020

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Background: 16S rRNA gene-targeted next-generation sequencing (NGS) can detect microorganisms in a comprehensive reference database. To date, NGS has been successfully applied to samples such as urine, blood, and synovial fluid. However, there is no data for continuous ambulatory peritoneal dialysis (CAPD) fluid. The purpose of this study was to evaluate the clinical usefulness of microbiome analysis of CAPD fluids for the diagnosis of CAPD peritonitis. Methods:We included 21 patients with high suspicion of CAPD peritonitis. Routine CAPD fluid culture was performed using a pellet of 50 mL CAPD fluid onto the chocolate and blood agar for two days, and thioglycollate broth for one week. 16S rRNA gene-targeted NGS of pellets, stored at -70°C was performed with MiSeq (Illumina, USA). Results:Many colonized or pathogenic bacteria were detected from CAPD fluids using NGS and the microbiomes were composed of 1 to 29 genera with a cut-off 1.0. Compared to the culture results, NGS detected the same pathogens in 6 of 18 valid results (three samples failed with low read count). Additionally, using NGS, anaerobes such as Bacteroides spp. and Prevotella spp. were detected in six patients. In two of five samples in which no bacterial growth was detected, possible pathogens were detected by NGS. Conclusion:To our knowledge, this is the first report about the application of 16S rRNA genetargeted NGS for diagnosis of CAPD peritonitis. Etiology of culture-negative CAPD peritonitis can be better defined in NGS. Furthermore, it also helped the detection of anaerobic bacteria.

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“…WGS is already being used in different laboratories from different sectors including public health, food safety, and veterinary laboratories, both from the public and private sectors (Motro and Moran-Gilad, 2017;Yachison et al, 2017). However, this process is accomplished with different timelines in the different European Union (EU) Member States (MSs) and European Free Trade Association (EFTA) countries 1 .…”

Section: Introductionmentioning

confidence: 99%

Outcome of EC/EFSA questionnaire (2016) on use of Whole Genome Sequencing (WGS) for food‐ and waterborne pathogens isolated from animals, food, feed and related environmental samples in EU/EFTA countries

Fierro¹,

Thomas‐López²,

Deserio³

et al. 2018

EFS3

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Whole Genome Sequencing (WGS) is becoming increasingly used in public health and food safety laboratories. To date, there is a wide variation in the level of implementation of WGS among laboratories from different sectors in different countries, the type of analysis employed and the data interpretation. To gather information on the WGS capacity of food safety/veterinary laboratories in the European Union (EU) and associated countries (EFTA), the European Commission (DG SANTE) and the European Food Safety Authority (EFSA), supported by the EU Reference laboratories (EURLs), prepared a survey among the EU/EFTA laboratory Networks for Salmonella, Listeria monocytogenes, Escherichia coli (VTEC), Campylobacter, Coagulase Positive Staphylococci, Antimicrobial Resistance and bacteriological and viral contaminants of bivalve molluscs. Questions on the general use of WGS, pathogens tackled, analysis purposes, pipelines and tools used, place of data storage and analysis, WGS research projects, needs for support, and future interest to implement WGS were addressed. By the end of 2016, WGS was already in use in reporting laboratories from 17 out of 30 EU/EFTA countries; in particular, WGS was reported to be used in all consulted EURLs, almost half of the National Reference Laboratories (44% affirmative respondents) and only few Official Laboratories (7% affirmative respondents). The main reason for not implementing WGS was the lack of capacity (budget and expertise). WGS was mainly used for outbreak investigations, followed by surveillance, and mostly for L. monocytogenes, E. coli and Salmonella analysis. Sequencing, sequence storage and analysis were mainly done 'in house'. Several WGS pipelines/platforms/tools were in use for analysis of different microorganisms and purposes. The participating laboratories expressed a general willingness for collaboration with EURLs and European institutions. This report provides a first picture of the state of the art in relation to the use of WGS in European food safety laboratories at the end of 2016.

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Next-generation sequencing applications in clinical bacteriology

Cited by 73 publications

References 54 publications

Next-Generation Sequencing Could be a Promising Diagnostic Approach for Pathogen Detection: Pathogenic Analysis of Pediatric Bacterial Meningitis by Next-Generation Sequencing Technology Directly from Cerebrospinal Fluid Specimens

Next-Generation Sequencing Could be a Promising Diagnostic Approach for Pathogen Detection: Pathogenic Analysis of Pediatric Bacterial Meningitis by Next-Generation Sequencing Technology Directly from Cerebrospinal Fluid Specimens

Application of 16S rRNA Gene-Targeted Next-Generation Sequencing for Bacterial Pathogen Detection in Continuous Ambulatory Peritoneal Dialysis Peritonitis

Outcome of EC/EFSA questionnaire (2016) on use of Whole Genome Sequencing (WGS) for food‐ and waterborne pathogens isolated from animals, food, feed and related environmental samples in EU/EFTA countries

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