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International Journal of Infectious... Jan 2021For decades, the term "anti-anaerobic" has been commonly used to refer to antibiotics exhibiting activity against anaerobic bacteria, also designated as anaerobes. This... (Review)
Review
For decades, the term "anti-anaerobic" has been commonly used to refer to antibiotics exhibiting activity against anaerobic bacteria, also designated as anaerobes. This term is used in various situations ranging from infections associated with well-identified pathogens like Clostridioides difficile, or Fusobacterium necrophorum in Lemierre's syndrome, that require specific antibiotic treatments to polymicrobial infections generally resulting from the decreased permeability of anatomical barriers (e.g., intestinal translocation and stercoral peritonitis) or infectious secondary localizations (e.g., brain abscess and infectious pleurisy). In these cases, the causal bacteria generally remain unidentified and the antimicrobial treatment is empirical. However, major progress in the knowledge of human bacterial microbiotas in the last 10 years has shown how diverse are the species involved in these communities. Here, we sought to reappraise the concept of anti-anaerobic spectrum in the light of recent advances in the microbiota field. We first highlight that the term anaerobic itself does not represent the tremendous diversity of the bacteria it spans, and then we stress that the antibiotic susceptibility profiles for most anaerobic bacteria remain unaddressed. Furthermore, we provide examples challenging the relevance of the "anti-anaerobic" spectrum from a clinical and ecological perspective.
Topics: Anaerobiosis; Animals; Anti-Bacterial Agents; Bacteria, Anaerobic; Humans; Microbiota; Terminology as Topic
PubMed: 33127500
DOI: 10.1016/j.ijid.2020.10.052 -
Microbiology (Reading, England) Jan 2002The design and evaluation of a set of universal primers and probe for the amplification of 16S rDNA from the Domain Bacteria to estimate total bacterial load by...
The design and evaluation of a set of universal primers and probe for the amplification of 16S rDNA from the Domain Bacteria to estimate total bacterial load by real-time PCR is reported. Broad specificity of the universal detection system was confirmed by testing DNA isolated from 34 bacterial species encompassing most of the groups of bacteria outlined in Bergey's Manual of Determinative Bacteriology. However, the nature of the chromosomal DNA used as a standard was critical. A DNA standard representing those bacteria most likely to predominate in a given habitat was important for a more accurate determination of total bacterial load due to variations in 16S rDNA copy number and the effect of generation time of the bacteria on this number, since rapid growth could result in multiple replication forks and hence, in effect, more than one copy of portions of the chromosome. The validity of applying these caveats to estimating bacterial load was confirmed by enumerating the number of bacteria in an artificial sample mixed in vitro and in clinical carious dentine samples. Taking these parameters into account, the number of anaerobic bacteria estimated by the universal probe and primers set in carious dentine was 40-fold greater than the total bacterial load detected by culture methods, demonstrating the utility of real-time PCR in the analysis of this environment.
Topics: Bacteria, Aerobic; Bacteria, Anaerobic; Bacterial Infections; Colony Count, Microbial; Culture Media; DNA Probes; DNA, Bacterial; DNA, Ribosomal; Dental Caries; Dentin; Gene Dosage; Humans; Polymerase Chain Reaction; RNA, Ribosomal, 16S; Taq Polymerase
PubMed: 11782518
DOI: 10.1099/00221287-148-1-257 -
Environment International Mar 2019The technology of integrating nanoscale zero-valent iron (nZVI) and functional anaerobic bacteria has broad prospects for groundwater remediation. This review focuses on... (Review)
Review
The technology of integrating nanoscale zero-valent iron (nZVI) and functional anaerobic bacteria has broad prospects for groundwater remediation. This review focuses on the interactions between nZVI and three kinds of functional anaerobic bacteria: organohalide-respiring bacteria (OHRB), sulfate reducing bacteria (SRB) and iron reducing bacteria (IRB), which are commonly used in the anaerobic bioremediation. The coupling effects of nZVI and the functional bacteria on the contaminant removal in the integrated system are summarized. Generally, nZVI could create a suitable living condition for the growth and activity of anaerobic bacteria. OHRB and SRB could synergistically degrade organic halides and remove heavy metals with nZVI, and IRB could reactive the passivated nZVI by reducing the iron (hydr)oxides on the surface of nZVI. Moreover, the roles of these anaerobic bacteria in contaminant removal coupling with nZVI and the degradation mechanisms are illustrated. In addition, this review also discusses the main factors influencing the removal efficiency of contaminants in the integrated treatment system, including nZVI species and dosage, inorganic ions, organic matters, pH, type of pollutants, temperature, and carbon/energy sources, etc. Among these factors, the nZVI species and dosage play a fundamental role due to the potential cytotoxicity of nZVI, which might exert a negative impact on the performance of this integrated system. Lastly, the future research needs are proposed to better understand this integrated technology and effectively apply it in groundwater remediation.
Topics: Bacteria, Anaerobic; Biodegradation, Environmental; Environmental Restoration and Remediation; Groundwater; Iron; Nanotechnology; Water Pollutants, Chemical; Water Purification
PubMed: 30660027
DOI: 10.1016/j.envint.2019.01.030 -
Clinical Microbiology and Infection :... Nov 2018There has been increased interest in the study of anaerobic bacteria that cause human infection during the past decade. Many new genera and species have been described... (Review)
Review
BACKGROUND
There has been increased interest in the study of anaerobic bacteria that cause human infection during the past decade. Many new genera and species have been described using 16S rRNA gene sequencing of clinical isolates obtained from different infection sites with commercially available special culture media to support the growth of anaerobes. Several systems, such as anaerobic pouches, boxes, jars and chambers provide suitable anaerobic culture conditions to isolate even strict anaerobic bacteria successfully from clinical specimens. Beside the classical, time-consuming identification methods and automated biochemical tests, the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has revolutionized identification of even unusual and slow-growing anaerobes directly from culture plates, providing the possibility of providing timely information about anaerobic infections.
AIMS
The aim of this review article is to present methods for routine laboratories, which carry out anaerobic diagnostics on different levels.
SOURCES
Relevant data from the literature mostly published during the last 7 years are encompassed and discussed.
CONTENT
The review involves topics on the anaerobes that are members of the commensal microbiota and their role causing infection, the key requirements for collection and transport of specimens, processing of specimens in the laboratory, incubation techniques, identification and antimicrobial susceptibility testing of anaerobic bacteria. Advantages, drawbacks and specific benefits of the methods are highlighted.
IMPLICATIONS
The present review aims to update and improve anaerobic microbiology in laboratories with optimal conditions as well as encourage its routine implementation in laboratories with restricted resources.
Topics: Anti-Bacterial Agents; Bacteria, Anaerobic; Bacterial Infections; Drug Resistance, Bacterial; Humans; Laboratories
PubMed: 29458156
DOI: 10.1016/j.cmi.2018.02.008 -
FEMS Microbiology Reviews Jul 2013Among the Gram-positive anaerobic bacteria associated with clinical infections, the Gram-positive anaerobic cocci (GPAC) are the most prominent and account for... (Review)
Review
Among the Gram-positive anaerobic bacteria associated with clinical infections, the Gram-positive anaerobic cocci (GPAC) are the most prominent and account for approximately 25-30% of all isolated anaerobic bacteria from clinical specimens. Still, routine culture and identification of these slowly growing anaerobes to the species level has been limited in the diagnostic laboratory, mainly due to the requirement of prolonged incubation times and time-consuming phenotypic identification. In addition, GPAC are mostly isolated from polymicrobial infections with known pathogens and therefore their relevance has often been overlooked. However, through improvements in diagnostic and in particular molecular techniques, the isolation and identification of individual genera and species of GPAC associated with specific infections have been enhanced. Furthermore, the taxonomy of GPAC has undergone considerable changes over the years, mainly due to the development of molecular identification methods. Existing species have been renamed and novel species have been added, resulting in changes of the nomenclature. As the abundance and significance of GPAC in clinical infections grow, knowledge of virulence factors and antibiotic resistance patterns of different species becomes more important. The present review describes recent advances of GPAC and what is known of the biology and pathogenic effects of Anaerococcus, Finegoldia, Parvimonas, Peptoniphilus and Peptostreptococcus, the most important GPAC genera isolated from human infections.
Topics: Animals; Anti-Bacterial Agents; Bacteria, Anaerobic; Drug Resistance, Bacterial; Gram-Positive Bacterial Infections; Gram-Positive Cocci; Humans
PubMed: 23030831
DOI: 10.1111/1574-6976.12005 -
Applied Microbiology and Biotechnology Jun 2020Lignocellulose is a widely available renewable carbon source and a promising feedstock for the production of various chemicals in biorefineries. However, its... (Review)
Review
Lignocellulose is a widely available renewable carbon source and a promising feedstock for the production of various chemicals in biorefineries. However, its recalcitrant nature is a major hurdle that must be overcome to enable economic conversion processes. Deconstruction of lignocellulose is part of the global carbon cycle, and efficient microbial degradation systems have evolved that might serve as models to improve commercial conversion processes. Biofilms-matrix encased, spatially organized clusters of microbial cells and the predominating lifestyle in nature-have been recognized for their essential role in the degradation of cellulose in nature, e.g., in soils or in the digestive tracts of ruminant animals. Cellulolytic biofilms allow for a high concentration of enzymes at the boundary layer between the solid substrate and the liquid phase and the more complete capture of hydrolysis products directly at the hydrolysis site, which is energetically favorable. Furthermore, enhanced expression of genes for carbohydrate active enzymes as a response to the attachment on solid substrate has been demonstrated for cellulolytic aerobic fungi and anerobic bacteria. In natural multispecies biofilms, the vicinity of different microbial species allows the creation of efficient food webs and synergistic interactions thereby, e.g., avoiding the accumulation of inhibiting metabolites. In this review, these topics are discussed and attempts to realize the benefits of biofilms in targeted applications such as the consolidated bioprocessing of lignocellulose are highlighted. KEY POINTS: Multispecies biofilms enable efficient lignocellulose destruction in the biosphere. Cellulose degradation by anaerobic bacteria often occurs by monolayered biofilms. Fungal biofilms immobilize enzymes and substrates in an external digestion system. Surface attached cultures typically show higher expression of cellulolytic enzymes.
Topics: Aerobiosis; Anaerobiosis; Bacteria, Anaerobic; Biofilms; Cellulose; Fungi; Hydrolysis; Lignin
PubMed: 32337627
DOI: 10.1007/s00253-020-10595-y -
Folia Microbiologica May 2019Anaerobic microorganisms (anaerobes) possess a fascinating metabolic versatility. This characteristic makes anaerobes interesting candidates for physiological studies... (Review)
Review
Anaerobic microorganisms (anaerobes) possess a fascinating metabolic versatility. This characteristic makes anaerobes interesting candidates for physiological studies and utilizable as microbial cell factories. To investigate the physiological characteristics of an anaerobic microbial population, yield, productivity, specific growth rate, biomass production, substrate uptake, and product formation are regarded as essential variables. The determination of those variables in distinct cultivation systems may be achieved by using different techniques for sampling, measuring of growth, substrate uptake, and product formation kinetics. In this review, a comprehensive overview of methods is presented, and the applicability is discussed in the frame of anaerobic microbiology and biotechnology.
Topics: Anaerobiosis; Bacteria, Anaerobic; Biomass; Bioreactors; Fermentation; Industrial Microbiology; Metabolic Engineering
PubMed: 30446943
DOI: 10.1007/s12223-018-0658-4 -
Frontiers in Cellular and Infection... 2021Because of the special culture requirements of anaerobic bacteria, their low growth-rate and the difficulties to isolate them, MALDI-TOF MS has become a reliable...
Because of the special culture requirements of anaerobic bacteria, their low growth-rate and the difficulties to isolate them, MALDI-TOF MS has become a reliable identification tool for these microorganisms due to the little amount of bacteria required and the accuracy of MALDI-TOF MS identifications. In this study, the performance of MALDI-TOF MS for the identification of anaerobic isolates during a 4-year period is described. Biomass from colonies grown on Brucella agar was directly smeared onto the MALDI-TOF target plate and submitted to on-plate protein extraction with 1μl of 100% formic acid. Sequencing analysis of the 16S rRNA gene was used as a reference method for the identification of isolates unreliably or not identified by MALDI-TOF MS. Overall, 95.7% of the isolates were identified to the species level using the updated V6 database vs 93.8% with previous databases lacking some anaerobic species; 68.5% of the total were reliably identified with high-confidence score values (≥2.0) and 95.0% with low-confidence values (score value ≥1.7). Besides, no differences between Gram-positive and Gram-negative isolates were detected beyond a slight decrease of correct species assignment for gram positive cocci (94.1% vs 95.7% globally). MALDI-TOF MS has demonstrated its usefulness for the identification of anaerobes, with high correlation with phenotypic and conventional methods. Over the study period, only 2.1% of the isolates could not be reliably identified and required molecular methods for a final identification. Therefore, MALDI-TOF MS provided reliable identification of anaerobic isolates, allowing clinicians to streamline the most appropriate antibiotic therapy and manage patients accordingly.
Topics: Bacteria; Bacteria, Anaerobic; Humans; RNA, Ribosomal, 16S; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 33968791
DOI: 10.3389/fcimb.2021.521014 -
Microbiology Spectrum Aug 2016Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to... (Review)
Review
Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to infection. Because obligate anaerobes are the predominant type of bacteria present in humans at skin and mucosal surfaces, immunocompromised patients are at increased risk for serious invasive infection due to anaerobes. Laboratory approaches to the diagnosis of anaerobe infections that occur due to pyogenic, polymicrobial, or toxin-producing organisms are described. The clinical interpretation and limitations of anaerobe recovery from specimens, anaerobe-identification procedures, and antibiotic-susceptibility testing are outlined. Bacteriotherapy following analysis of disruption of the host microbiome has been effective for treatment of refractory or recurrent Clostridium difficile infection, and may become feasible for other conditions in the future.
Topics: Bacteria, Anaerobic; Bacterial Infections; Bacteriological Techniques; Disease Susceptibility; Humans; Immunocompromised Host
PubMed: 27726792
DOI: 10.1128/microbiolspec.DMIH2-0015-2015 -
Acta Medica Portuguesa May 2017The wide burden of anaerobic bacteria colonizing human body comprises about 90% of its total biomass. The biotic relationship between humans and its microbiota sets... (Review)
Review
The wide burden of anaerobic bacteria colonizing human body comprises about 90% of its total biomass. The biotic relationship between humans and its microbiota sets reciprocal benefits, albeit with pathogenic potencial for the human being in particular dysbiosis situations. Infections adjacent to or originating from the skin or mucous membranes of the intestinal, genitourinary and upper respiratory tracts are often polymicrobial in nature, whereby should anaerobes be invariably included in the etiological differential diagnosis of these conditions. Gram negative bacilli such as Bacteroides fragilis group, Fusobacterium spp., Porphyromonas spp., Prevotella spp. and Gram positive cocci such as Peptostreptococcus spp. stand out for their high virulence and frequence of isolation in suppurative infections and abcesses with metastatic or contiguous relation to human microbiota. The fastidious nature of anaerobic bacteria, especially of less aerotolerant species, compels to particular techniques of sample collection, transport and cultural isolation that challenge clinicians and microbiologists for a full efficient practice. Such requirements bring on a poor identification of anaerobic bacteria in the clinical practice and undervaluation of its aetiopathogenic potential amongst common polymicrobial infections. An approach over microbial flora's composition in the different human anatomical sites is a primary goal of the present article. Clinicians are intended to recognize the variability and proportion of likely involved anaerobic microorganisms in certain infectious processes related to human microbiota, in order to optimize samples processing and the establishment of an appropriate empirical antibiotic therapy, mindful of anaerobic coverage and according to known susceptibility profiles.
Topics: Bacteria, Anaerobic; Bacterial Infections; Humans; Microbiota
PubMed: 28865506
DOI: 10.20344/amp.8098