Molecular methods for pathogen and microbial community detection and characterization: Current and potential application in diagnostic microbiology

Sibley, Christopher D.; Peirano, Gisele; Church, Deirdre L.

doi:10.1016/j.meegid.2012.01.011

Cited by 132 publications

(78 citation statements)

References 317 publications

(380 reference statements)

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“…The discrepancies observed between microscopy, culture, and PCR might have occurred for multiple reasons (30). Fungal contamination (30,31), loss of fungal viability (30,32), aggressive specimen processing (33), and examination of samples from two different areas (26) are some of the potential explanations. However, regardless of the reason for the lack of fungal growth or for a negative fungal PCR result, fungal elements in tissues causing pathology should be treated immediately (32).…”

Section: Discussionmentioning

confidence: 99%

Utility of PCR in Diagnosis of Invasive Fungal Infections: Real-Life Data from a Multicenter Study

et al. 2013

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Prospective studies addressing the clinical value of broad-range PCR using the internal transcribed spacer region (ITS) for diagnosis of microscopy-negative fungal infections in nonselected patient populations are lacking. We first assessed the diagnostic performance of ITS rRNA gene PCR compared with that of routine microscopic immunofluorescence examination. Second, we addressed prospectively the impact and clinical value of broad-range PCR for the diagnosis of infections using samples that tested negative by routine microscopy; the corresponding patients' data were evaluated by detailed medical record reviews. Results from 371 specimens showed a high concordance of >80% for broad-range PCR and routine conventional methods, indicating that the diagnostic performance of PCR for fungal infections is comparable to that of microscopy, which is currently considered part of the "gold standard." In this prospective study, 206 specimens with a negative result on routine microscopy were analyzed with PCR, and patients' clinical data were reviewed according to the criteria of the European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group. We found that broad-range PCR showed a sensitivity, specificity, positive predictive value, and negative predictive value of 57.1%, 97.0%, 80%, and 91.7%, respectively, for microscopy-negative fungal infections. This study defines a possible helpful role of broad-range PCR for diagnosis of microscopy-negative fungal infections in conjunction with other tests.

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Section: Discussionmentioning

confidence: 99%

Utility of PCR in Diagnosis of Invasive Fungal Infections: Real-Life Data from a Multicenter Study

et al. 2013

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“…There are a myriad of molecular methods for the study of bacteria in abscess samples, and the choice of a particular approach depends on the questions to be answered. Molecular methods for diagnostic microbiology can be used for specific detection of target species (species-specific or closed-ended analysis), identification of all or the most dominant species in a sample (broad-range or open-ended analysis), or profiling of the microbial community structure (community analysis) (72). Broad-range PCR followed by cloning and sequencing and more recently the massive parallel 454 pyrosequencing approach can be used to unravel the breadth of bacterial diversity in a site.…”

Section: Microbiology Diagnostic Methodsmentioning

confidence: 99%

Microbiology and Treatment of Acute Apical Abscesses

2013

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SUMMARY Acute apical abscess is the most common form of dental abscess and is caused by infection of the root canal of the tooth. It is usually localized intraorally, but in some cases the apical abscess may spread and result in severe complications or even mortality. The reasons why dental root canal infections can become symptomatic and evolve to severe spreading and sometimes life-threatening abscesses remain elusive. Studies using culture and advanced molecular microbiology methods for microbial identification in apical abscesses have demonstrated a multispecies community conspicuously dominated by anaerobic bacteria. Species/phylotypes commonly found in these infections belong to the genera Fusobacterium , Parvimonas , Prevotella , Porphyromonas , Dialister , Streptococcus , and Treponema . Advances in DNA sequencing technologies and computational biology have substantially enhanced the knowledge of the microbiota associated with acute apical abscesses and shed some light on the etiopathogeny of this disease. Species richness and abundance and the resulting network of interactions among community members may affect the collective pathogenicity and contribute to the development of acute infections. Disease modifiers, including transient or permanent host-related factors, may also influence the development and severity of acute abscesses. This review focuses on the current evidence about the etiology and treatment of acute apical abscesses and how the process is influenced by host-related factors and proposes future directions in research, diagnosis, and therapeutic approaches to deal with this disease.

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“…Omogoča nam dokaz DNK večine bakterijskih vrst neposredno iz kužnin in se kot tak vse bolj uveljavlja v klinični praksi.4,5 Metodo uporabljamo tudi za identifikacijo nepoznanih bakterij, osamljenih s standardnimi mikrobiološkimi postopki. 3,6 V izvirnem prispevku predstavljamo prednosti in pomanjkljivosti evbakterijskega PCR v primerjavi s kultivacijo na temelju naših enoletnih kliničnih izkušenj uporabe te metode na kužninah iz primarno sterilnih mest pri bolnikih, ki so pred odvzemom kužnin že prejemali antibiotik.…”

Section: Uvodunclassified

Evbakterijski PCR – uporabnost molekularne metode v klinični praksi

et al. 2015

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Background: Isolation and identification of bacterial pathogens enables accurate diagnosis of bacterial infection, allowing rational use of appropriate narrow-spectrum antibiotics. In some cases, the routine bacterial culture can give negative results. In those cases additional use of molecular techniques such as eubacterial (broad-range 16S rRNA) PCR may detect and identify bacterial genetic material.Methods: Between February 2012 and April 2013 42 specimens from 35 patients, already treated with antimicrobials, were taken and tested by eubacterial PCR in addition to routine microbiological culture. Results: Eubacterial PCR yielded positive result in 21/42 specimens in 18 patients (in three mixed sequences). Therefore, in 15 patients the diagnosis of bacterial infection was obtained with DNA identification and the results were interpreted in accordance to patients’ history, laboratory and image diagnostics. Only 4 specimens were culture-positive.Conclusions: Although eubacterial PCR enables the identification of any bacterial DNA in clinical specimens, there are some limitations: no information concerning antimicrobial susceptibility of the causative agents, problem of differentiating living from dead bacteria and problem to differentiate contaminants from pathogenic bacteria. The method is also expensive. In the following article recommendations for appropriate and rational use of eubacterial PCR are presented.

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Molecular methods for pathogen and microbial community detection and characterization: Current and potential application in diagnostic microbiology

Cited by 132 publications

References 317 publications

Utility of PCR in Diagnosis of Invasive Fungal Infections: Real-Life Data from a Multicenter Study

Utility of PCR in Diagnosis of Invasive Fungal Infections: Real-Life Data from a Multicenter Study

Microbiology and Treatment of Acute Apical Abscesses

Evbakterijski PCR – uporabnost molekularne metode v klinični praksi

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