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The genus Fusobacterium currently includes 13 species. Fusobacterium nucleatum, the most frequently encountered species in humans, is heterogeneous and currently includes 5 subspecies. A potentially new subspecies of F. nucleatum that is intrinsically quinolone-resistant and phylogenetically separate from the other 5 subspecies has been identified from dog and cat oral flora. Two subspecies have been described for Fusobacterium necrophorum, and a new species, Fusobacterium equinum, which is related to F. necrophorum, has been described from horse oral flora. Additional molecular studies have characterized Fusobacterium ulcerans as separate from the phenotypically similar Fusobacterium mortiferum and Fusobacterium varium. Fusobacterium sulci and Fusobacterium alocis have been reclassified as Eubacterium sulci and Filifactor alocis, respectively. Fusobacterium prausnitzii is phylogenetically related to the Eubacterium-like organisms and will likely be reclassified in the future. The status of the remaining species is unchanged.

Because of access to 16S rDNA sequencing, changes in the taxonomy and nomenclature of anaerobic gram-negative bacteria have occurred lately. New genera and species have been described, and existing taxa have been reclassified. The present article compiles a list of clinically relevant anaerobes and provides synonyms as well as the old nomenclature used for these bacteria. Although names and classifications of anaerobic bacteria are changing quickly, it is important to keep track of new bacterial names to work toward better description and recognition of bacterium-disease associations.

Diagnostic virology has now entered the mainstream of medical practice. Multiple methods are used for the laboratory diagnosis of viral infections, including viral culture, antigen detection, nucleic acid detection, and serology. The role of culture is diminishing as new immunologic and molecular tests are developed that provide more rapid results and are able to detect a larger number of viruses. This review provides specific recommendations for the diagnostic approach to clinically important viral infections.

Mycobacterial susceptibility testing is important for the management of patients with tuberculosis and those with disease caused by certain nontuberculous mycobacteria. To help standardize methods used in the clinical microbiology laboratory for testing susceptibility of mycobacteria, the National Committee for Clinical Laboratory Standards (NCCLS) recently updated NCCLS document M24-T (published in 1995), which is the tentative standard for antimycobacterial susceptibility testing of Mycobacterium tuberculosis. The second edition of the NCCLS tentative standard (document M24-T2) differs considerably from the initial document. It contains revised guidelines for the testing of M. tuberculosis complex and newly proposed guidelines for the testing of some nontuberculous mycobacteria, including the rapidly growing mycobacteria (Mycobacterium fortuitum group, Mycobacterium chelonae, and Mycobacterium abscessus), Mycobacterium avium complex, Mycobacterium kansasii, and Mycobacterium marinum, as well as Nocardia species and other aerobic actinomycetes. The recommendations for mycobacterial susceptibility testing that are outlined in NCCLS document M24-T2 are reviewed.

Genome sequence data provide a framework for predicting potential microbial activities; however, the proteome content of the cell dictates its response to its environment. Microbiology is witnessing a major initiative to elucidate the nature of the proteome of large numbers of species. The tool driving the proteomic revolution is matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. During the analysis process, proteins are ionized and separated on the basis of their mass-to-charge ratios, which results in a characteristic mass-spectral profile. Because of the dynamic nature of the cell and the large number of external parameters that could influence its mass-spectral profile, considerable work was needed initially to optimize sample analysis and obtain consistent and reproducible results. For many anaerobes that grow poorly or are nonreactive in most diagnostic systems, proteome analysis is likely to have a major impact on microbial diagnosis and the delineation of centers of diversity associated with infections.

The outer-membrane proteins (OMPs) of bacteria function as the dynamic interface between the bacterium and its surroundings and are involved in maintenance of cell structure, binding a variety of substances, adhesion to other cells, and regulation of transport of both nutrients and bactericidal agents. There is a vast amount of information about aerobic OMPs and their roles in immunogenicity, virulence, and antimicrobial resistance. Knowledge about OMPs in anaerobic bacteria is much sparser. Genetic data present in data banks regarding aerobic porins are not readily helpful in identifying or analyzing anaerobic porins because of the large phylogenetic distance between the aerobic and anaerobic organisms. We recently identified and sequenced the genes for both a porin protein complex and an OmpA protein in Bacteroides fragilis, and the data are summarized here. Also, recent information is presented about similar OMPs found in other gram-negative anaerobic bacteria, including Bacteroides thetaiotaomicron, Bacteroides distasonis, Porphyromonas, and Fusobacterium.

In clinical microbiology, molecular genetic techniques are increasingly being used to detect and/or differentiate uncultivable, anaerobic, or fastidious microorganisms. During the past decade, DNA probe hybridization and in vitro amplification by polymerase chain reaction have also been introduced to detect oral pathogens. The present review describes experiences with methods and commercial test systems for the detection of pathogens in periodontitis and caries.

Clinical microbiology laboratories are faced with the challenge of accurately detecting emerging antibiotic resistance among a number of bacterial pathogens. In recent years, vancomycin resistance among enterococci has become prevalent, as has penicillin resistance and multidrug resistance in pneumococci. More recently, strains of methicillin-resistant Staphylococcus aureus with reduced susceptibility to vancomycin have been encountered. In addition, molecular techniques have demonstrated that there are still problems detecting methicillin resistance in staphylococci, especially in coagulase-negative species. Among members of the family Enterobacteriaceae, mutated β-lactamase enzymes may confer difficult-to-detect resistance to later-generation penicillins and cephalosporins. Anaerobic bacteria are no longer entirely predictable in their susceptibility to agents that might be selected for empiric therapy. Therefore, clinical microbiology laboratories may not be able to rely on a single susceptibility testing method or system to detect all those emerging resistant or fastidious organisms. For reliable detection, laboratories may need to employ conventional, quantitative susceptibility testing methods or use specially developed, single concentration agar screening tests for some resistant species. Certain of these screening tests are highly specific, while others may require additional confirmatory testing for definitive results. Therefore, laboratories must retain the versatility to apply several different approaches to detect resistance in both common and infrequently encountered bacterial pathogens.

The β-lactam antibiotics are the most widely used of all the groups of antimicrobials, but β-lactam resistance is increasingly common among members of the Bacteroides fragilis group. Three major mechanisms are involved in β-lactam resistance, and they act together in certain instances. In the present study, 2 resistant mutants (238m and 1186m) of Bacteroides thetaiotaomicron, obtained from clinical isolates (238 and 1186) by selection with increasing concentrations of cefoxitin, showed decreased susceptibilities to cefoxitin and other β-lactam antibiotics. Alterations in both penicillin-binding proteins (PBPs) and outer-membrane proteins (OMPs) were observed in the mutants in comparison with their parent strains. The similar alteration in OMPs was also observed in clinical isolates. In conclusion, the β-lactam—resistant mutants of B. thetaiotaomicron with deficiency in both PBPs and OMPs can be selected for by exposure to cefoxitin, and several mechanisms are involved in the β-lactam resistance in the strains investigated.

Changes in the availability of skilled laboratory personnel, new technologies, and the financial environment will all influence the practice of diagnostic microbiology in the near and more distant future. Because of the special expertise needed for the accurate identification of anaerobic bacteria, the ability to diagnose anaerobic infections may decline as a consequence of these changes. Physicians should anticipate a difficult time in the years between the loss of expertise in traditional methods and development of reliable and accurate molecular assays.