The Time Is Now for Gene- and Genome-Based Bacterial Diagnostics

Ehrlich, Garth D.; Post, J. Christopher

doi:10.1001/jamainternmed.2013.7042

Cited by 14 publications

(12 citation statements)

References 10 publications

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“…The earlier labour intensive nucleic acid isolation and purification methods have now been replaced by automated platforms or are incorporated into single step cartridge-based devices 4 . Newer methods include loop-mediated amplification (LAMP), transcription mediated amplification, nucleic acid sequence-based amplification (NASBA) and strand displacement amplification (SDA).…”

Section: Conventional Microbiologymentioning

confidence: 99%

Diagnostic Microbiology: Present Status and Future Prospect

Begum

Yusuf

Uddin³

2017

Bangladesh J. Infect. Dis.

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Diagnostic Microbiology is the tool that makes it possible to identify the exact pathogens of infectious diseases and the most optimal therapy at the level of individual patients. Conventional methods require time to grow the microbes in vitro under specific conditions and not all microbes can easily be cultured. This is followed by biochemical methods for identification which further makes the process lengthy. Transport of the specimens under less than ideal conditions, prior use of antibiotics and small number of organisms are among the factors that render culture-based methods less reliable. Newer methods depend on amplification of nucleic acids followed by use of probes for identification. This mitigates the need for higher microbial load, presence of metabolically active viable organisms and shortens the time. These methods can be used to detect antibiotic resistance genes directly from the specimen and help direct targeted therapy with efficacy. Since these methods will not fulfill all the diagnostic needs, a second approach is being used to shorten the time to identification after the organism has already grown. Mass spectrometry and bioinformatics are the tools making this possible. This review gives a historical perspective on diagnostic microbiology, discusses the pitfalls of current methodology and provides an overview of newer and future methods. [Bangladesh Journal of Infectious Disease 2015;2(2):42-47]

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Section: Conventional Microbiologymentioning

confidence: 99%

Diagnostic Microbiology: Present Status and Future Prospect

Begum

Yusuf

Uddin³

2017

Bangladesh J. Infect. Dis.

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“…37 New PCR technology and sequence information on the 16S rRNA genes of hundreds of different bacterial species and strains have facilitated analysis of whole genomes of a subset of bacteria; it is now possible to undertake identification of all bacterial species in a particular infection. 38,39 In orthopaedics, this technology has been used to retrospectively identify contaminating organisms in arthroplasty cases. 40 The sequence information has revealed the presence of bacteria common to deep infection (eg, Staphylococcus aureus and coagulase-negative staphylococci) as well as Streptococcus , Enterococcus , and Acinetobacter .…”

Section: Advantages Limitations and Future Applications Of Moleculamentioning

confidence: 99%

Molecular Diagnostics

Choe

Deirmengian

Hickok

et al. 2015

Journal of the American Academy of Orthopaedic Surgeons

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Orthopaedic infections are complex conditions that require immediate diagnosis and accurate identification of the causative organisms to facilitate appropriate management. Conventional methodologies for diagnosis of these infections sometimes lack accuracy or sufficient rapidity. Current molecular diagnostics are an emerging area of bench-to-bedside research in orthopaedic infections. Examples of promising molecular diagnostics include measurement of a specific biomarker in the synovial fluid, polymerase chain reaction–based detection of bacterial genes, and metabolomic determination of responses to orthopaedic infection.

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“…When comparing these technologies to sequencing-based methods, many researchers have a critical point of view, arguing that PCR-based methods lack resolution to be able to provide a strain-specific diagnosis and to reach the level of precision enabling one to perceive the supragenome concept i.e. , the knowledge of the totality of common and individual-specific genomic material in a bacterial community [ 21 , 22 ]. Recently, various studies have further reinforced this point of view [ 23 , 24 , 25 ], as PCR-based methods have been shown to be unable to discriminate some closed strains, unlike HTS.…”

Section: High-throughput Sequencing Toward a New Medicine?mentioning

confidence: 99%

“…PCR-based methods for genotyping can be adapted to HTS [ 27 ] by decreasing the cost and increasing the throughput. MLST methods were “a first step in the right direction” [ 21 ], but these genotyping methods, unlike WGS, due to the lack of resolution, are not able to provide a strain-specific diagnosis. Providing a whole genome, HTS may rise to the challenge of the supragenome.…”

Section: High-throughput Sequencing Toward a New Medicine?mentioning

confidence: 99%

High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology

2014

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The recent progresses of high-throughput sequencing (HTS) technologies enable easy and cost-reduced access to whole genome sequencing (WGS) or re-sequencing. HTS associated with adapted, automatic and fast bioinformatics solutions for sequencing applications promises an accurate and timely identification and characterization of pathogenic agents. Many studies have demonstrated that data obtained from HTS analysis have allowed genome-based diagnosis, which has been consistent with phenotypic observations. These proofs of concept are probably the first steps toward the future of clinical microbiology. From concept to routine use, many parameters need to be considered to promote HTS as a powerful tool to help physicians and clinicians in microbiological investigations. This review highlights the milestones to be completed toward this purpose.

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The Time Is Now for Gene- and Genome-Based Bacterial Diagnostics

Cited by 14 publications

References 10 publications

Diagnostic Microbiology: Present Status and Future Prospect

Diagnostic Microbiology: Present Status and Future Prospect

Molecular Diagnostics

High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology

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