Modern Approaches to Differentiation of Live and Dead Bacteria Using Selective Amplification of Nucleic Acids

Baymiev, An. Kh.; Baymiev, Al. Kh.; Kuluev, B. R.; Shvets, Kristina; Yamidanov, R. S.; Matniyazov, R. T.; Чемерис, Д.А.; Zubov, V.V.; Alekseev, Ya. I.; Mavzyutov, A. R.; Ivanenkov, Yan A.; Чемерис, А. В.

doi:10.1134/s0026261720010038

Cited by 23 publications

(24 citation statements)

References 116 publications

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“…The specific amplification of nucleic acids, such as in polymerase chain reaction (PCR), can be employed as a culture-independent method to investigate the microbial diversity in different environmental settings with complex mixture communities, non-cultivable viable cells (NCVC), interfering contaminants, and low levels of target DNA [103]. In first step of the PCR technique, the genetic material is isolated and purified from the target samples [104].…”

Section: Molecular Biology Methodsmentioning

confidence: 99%

“…It has very short half-life inside the cell and can be used as a marker for microbial viability and identification of NCVCs [104]. The nutritional stimulation of bacterial cells immediately produces a significant amount of rRNA precursors (pre-rRNA); these strands are easier to detect than mRNAs [103]. Therefore, they can also be used as a marker for differentiating NCVC from dead cells that have been inactivated by UV irradiation, pasteurization, serum exposure, and chlorine [105].…”

Section: Molecular Biology Methodsmentioning

confidence: 99%

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Testing the Antimicrobial Characteristics of Wood Materials: A Review of Methods

et al. 2020

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Some wood species have antimicrobial properties, making them a better choice over inert surfaces in certain circumstances. However, the organic and porous nature of wood raises questions regarding the use of this material in hygienically important places. Therefore, it is reasonable to investigate the microbial survival and the antimicrobial potential of wood via a variety of methods. Based on the available literature, this review classifies previously used methods into two broad categories: one category tests wood material by direct bacterial contact, and the other tests the action of molecules previously extracted from wood on bacteria and fungi. This article discusses the suitability of these methods to wood materials and exposes knowledge gaps that can be used to guide future research. This information is intended to help the researchers and field experts to select suitable methods for testing the hygienic safety and antimicrobial properties of wood materials.

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Section: Molecular Biology Methodsmentioning

confidence: 99%

Section: Molecular Biology Methodsmentioning

confidence: 99%

Testing the Antimicrobial Characteristics of Wood Materials: A Review of Methods

et al. 2020

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“…In case of a negative test result during the follow-up consultation, meaning the NG infection cleared spontaneously or the previous NAAT result was a false-positive, the use of antibiotic treatment would be unnecessary. Two other solutions to false-positive results could be (1) to assess the viability of bacteria in positive NAAT results by new diagnostic tests and molecular targets (ie, molecular viability testing)21–23 or (2) to lower the cycle threshold cut-off values for NAAT. Lowering the cycle threshold cut-off values for NAAT could decrease false-positive test results, as contamination or non-viable bacteria will less likely result in a positive test result.…”

Section: Discussionmentioning

confidence: 99%

Section: Original Researchmentioning

confidence: 99%

Spontaneous clearance of asymptomatic anogenital and pharyngeal Neisseria gonorrhoeae: a secondary analysis from the NABOGO trial

et al. 2022

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IntroductionSpontaneous clearance of asymptomatic Neisseria gonorrhoeae (NG) does occur, but data are scarce. We aimed to assess spontaneous clearance among patients with asymptomatic anal, pharyngeal, vaginal and urethral NG infections who participated in the New AntiBiotic treatment Options for uncomplicated GOnorrhoea (NABOGO) trial. In addition, we assessed the determinants associated with spontaneous clearance.MethodsThe NABOGO trial (Trial registration number: NCT03294395) was a randomised controlled, double-blind, single-centre trial assessing non-inferiority of ertapenem, gentamicin and fosfomycin to ceftriaxone for treatment of uncomplicated gonorrhoea. For asymptomatic NABOGO participants, we collected pre-enrolment and enrolment visit samples before trial medication was given. Spontaneous clearance was defined as a positive pre-enrolment nucleic acid amplification test (NAAT) result, followed by a negative NAAT at enrolment. We compared the median time between pre-enrolment and enrolment visits for patients who cleared spontaneously and for those who did not. Determinants of spontaneous clearance were assessed using logistic regression.ResultsThirty-two of 221 (14.5%) anal NG infections cleared spontaneously, 17 of 91 (18.7%) pharyngeal, 3 of 13 (23.1%) vaginal and 9 of 28 (32.1%) urethral NG infections. The median time between the pre-enrolment and enrolment visit was longer for patients who cleared their pharyngeal infection spontaneously compared with those who did not (median 8 days (IQR=7–11) vs 6 days (IQR=4–8), p=0.012); no determinants of clearance at other sites were identified. Overall, patients with more days between the pre-enrolment and enrolment visit were more likely to clear spontaneously (adjusted OR=1.06 per additional day, 95% CI 1.01 to 1.12). No association between location of NG infection and spontaneous clearance was found.ConclusionsA significant proportion of asymptomatic patients cleared their NG infections spontaneously. Given these results, treatment of all NG infections after a one-time NAAT may be excessive, and more research on the natural history of NG is needed to improve antibiotic stewardship.

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“…These methods provide information on the relative proportion of viable cells in a sample, but not which taxa are viable. New molecular based methods, such as viability PCR (vPCR), could be used to not only characterize the atmospheric microbial community but also differentiate viable from non-viable cells (Cangelosi and Meschke, 2014;Baymiev et al, 2020). Live/dead staining and vPCR are not direct measures of viability; it is assumed that cell permeability indicates compromised cell membranes and therefore non-viable cells.…”

Section: Ecological Significance Of Marine Microorganisms In the Atmospherementioning

confidence: 99%

Ocean Aerobiology

2021

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Ocean aerobiology is defined here as the study of biological particles of marine origin, including living organisms, present in the atmosphere and their role in ecological, biogeochemical, and climate processes. Hundreds of trillions of microorganisms are exchanged between ocean and atmosphere daily. Within a few days, tropospheric transport potentially disperses microorganisms over continents and between oceans. There is a need to better identify and quantify marine aerobiota, characterize the time spans and distances of marine microorganisms’ atmospheric transport, and determine whether microorganisms acclimate to atmospheric conditions and remain viable, or even grow. Exploring the atmosphere as a microbial habitat is fundamental for understanding the consequences of dispersal and will expand our knowledge of biodiversity, biogeography, and ecosystem connectivity across different marine environments. Marine organic matter is chemically transformed in the atmosphere, including remineralization back to CO2. The magnitude of these transformations is insignificant in the context of the annual marine carbon cycle, but may be a significant sink for marine recalcitrant organic matter over long (∼104 years) timescales. In addition, organic matter in sea spray aerosol plays a significant role in the Earth’s radiative budget by scattering solar radiation, and indirectly by affecting cloud properties. Marine organic matter is generally a poor source of cloud condensation nuclei (CCN), but a significant source of ice nucleating particles (INPs), affecting the formation of mixed-phase and ice clouds. This review will show that marine biogenic aerosol plays an impactful, but poorly constrained, role in marine ecosystems, biogeochemical processes, and the Earth’s climate system. Further work is needed to characterize the connectivity and feedbacks between the atmosphere and ocean ecosystems in order to integrate this complexity into Earth System models, facilitating future climate and biogeochemical predictions.

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Modern Approaches to Differentiation of Live and Dead Bacteria Using Selective Amplification of Nucleic Acids

Cited by 23 publications

References 116 publications

Testing the Antimicrobial Characteristics of Wood Materials: A Review of Methods

Testing the Antimicrobial Characteristics of Wood Materials: A Review of Methods

Spontaneous clearance of asymptomatic anogenital and pharyngeal Neisseria gonorrhoeae: a secondary analysis from the NABOGO trial

Ocean Aerobiology

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