Streptococcus pneumoniae

Antibiotic resistance is an ancient biological mechanism in bacteria, although its proliferation in our contemporary world has been amplified through antimicrobial therapy. Recent studies conducted on ancient environmental and human samples have uncovered numerous antibiotic-resistant bacteria and resistance genes. The resistance genes that have been reported from the analysis of ancient bacterial DNA include genes coding for several classes of antibiotics, such as glycopeptides, β-lactams, tetracyclines, and macrolides. The investigation of the resistome of ancient bacteria is a recent and emerging field of research, and technological advancements such as next-generation sequencing will further contribute to its growth. It is hoped that the knowledge gained from this research will help us to better understand the evolution of antibiotic resistance genes and will also be used in drug design as a proactive measure against antibiotic resistance.

Review of: Primer to the Immune Response, 2nd ed.; Tak Mak, Mary Saunders, and Bradley Jett; (2014). Elsevier Inc., London, UK. 702 pages.

Majority of aerobic, or facultatively aerobic, gram-positive cocci isolated from clinical specimens are distributed among the genera Staphylococcus, Streptococcus, and Enterococcus. This chapter provides tables containing organisms with similar cellular morphologies, either "streptococcal," consisting of gram-positive cocci or coccobacilli arranged primarily in pairs and/or chains, or "staphylococcal," signifying that cells appear as cocci arranged in pairs, tetrads, clusters, and irregular groups. The commonly isolated aerobic gram-positive cocci (staphylococci, streptococci, enterococci) can usually be accurately identified by determining a few basic phenotypic traits (cellular morphology, catalase reaction, and production of pyrrolidonyl arylamidase [PYR]). The chapter highlights the fact that it is increasingly difficult to identify some of the less frequently isolated organisms solely on the basis of phenotypic traits, as new genera and species of aerobic gram-positive cocci are described and characterized. Basic phenotypic tests can usually suggest a possible identity for strains of infrequently encountered aerobic gram-positive cocci, but evaluation with a larger battery of phenotypic tests or molecular identification methods is often valuable, if not indispensible, for accurate identification. Nucleic acid probe tests and amplification methods for identification of some of the commonly isolated aerobic gram-positive cocci are commercially available and designed for use in medium to large-volume clinical microbiology laboratories. The chapter concludes by emphasizing that the comparison of 16S rRNA gene sequences is the most useful method for molecular characterization of the aerobic gram-positive cocci of clinical interest, although sequence comparison of other genes may also be helpful for identification.

Traditionally, the detection and identification of bacteria were based on conventional tube-based biochemical reactions, and their results were compared to historical charts of expected biochemical reactions. Automation in microbiology first occurred in the early 1970s with the introduction of semiautomated blood culture instruments, followed by instrumented systems for identification and susceptibility testing of bacteria. This chapter reviews the systems used for the detection of bacteria and yeasts from blood and provides an overview of technologies for microorganism identification. The volume of blood obtained for culture is one of the most important variables in the detection of bloodstream infections (BSIs). The chapter describes the identification of microorganisms by nonphenotypic methods from instrument-flagged blood culture bottles, and from pure culture. The approximate turnaround time of the fluorescence in situ hybridization (FISH) procedure is 2.5 to 3 h (without batch testing), compared with >18 to 24 h for identification of bacteria and yeasts by conventional methods. The selection of DNA targets to identify bacteria and fungi relies on the concept that some genes have conserved segments flanked by variable regions. The technology is based on analyzing the protein composition of a bacterial cell, with ribosomal proteins comprising most bacterial proteins being detected. Another technique to characterize bacteria is the application of electrospray ionization-mass spectrometry to analyze products of multilocus, broad-range PCR (PCR/ESI-MS).

Commercial antimicrobial susceptibility testing (AST) systems were introduced into clinical microbiology laboratories during the 1980s and have been used in the majority of laboratories since the 1990s. Manual and semiautomated broth microdilution systems are utilized for small volumes of susceptibility testing, while larger laboratories often choose an automated broth microdilution system. The AST systems include data management software that may be interfaced with a laboratory information system (LIS) and offer various levels of expert system and epidemiological analyses. This chapter focuses primarily on commercial susceptibility testing systems currently available in the United States. It discusses advantages and disadvantages of automated systems. Reports of AST performance for detecting problematic resistance phenotypes are also discussed. Expert systems to assist in the critical review of AST results are available for all commercial susceptibility systems currently marketed in the United States. Most expert systems use a rules-based approach focusing on AST results for one drug at a time without considering results for other agents tested simultaneously. Factors to consider when selecting an AST system include cost, performance, work flow, data management capabilities, and manufacturer technical support. Future advances in the development of AST systems may increase their clinical impact with the incorporation of molecular techniques that dramatically shorten the time required for results.

This chapter focuses on nonamplified nucleic acid probes and their current uses in the clinical laboratory. DNA probes are pieces of nucleic acid that are labeled in some way and are designed to seek out and bind to stretches of DNA or RNA that have sequences that are complementary to the probe. In hybridization reactions, a double-stranded DNA molecule is denatured to single strands. Several formats for the hybridization reactions exist: solid phase; in solution (liquid phase); in situ; or by use of a Southern hybridization procedure after gel electrophoresis. In sandwich hybridization assays, one probe is attached to a solid support such as a nitrocellulose filter in single-stranded form and ‘‘captures’’ homologous nucleic acids in liquid samples; a second probe, which recognizes a contiguous area of the nucleic acid, carries the reporter molecule such as a radioisotope or biotin. The target and probe nucleic acids are free to move in solution, maximizing chances that complementary sequences will bind. Southern hybridization involves using purified DNA that is cleaved with restriction endonucleases. There are numerous methods for detecting the binding of probe to target nucleic acid. Commercially available DNA probes used for culture confirmation of bacteria, mycobacteria, and fungi are discussed in the chapter. Of the assays discussed in the chapter, probes for the detection of mycobacteria have had the greatest clinical impact. The chapter describes the utility of nonamplified probes for the diagnosis of sexually transmitted diseases, vaginal infections, and streptococcal pharyngitis.

This chapter talks about the closest relatives of Streptococcus mitis that are the commensals S. oralis, S. infantis, and, in particular, the important pathogen Streptococcus pneumoniae and the still relatively unknown Streptococcus pseudopneumoniae. The genetic diversity among S. mitis strains may have important consequences in the oral cavity. Draft genomes display an artificially high total number of genes and number of paralogs due to sequencing errors and gaps leading to gene fragmentation, as well as low-quality redundant sequences at contig ends. The verification results in the conclusion that this observation is not due to the fact that (i) all but one of the non-S. pneumoniae genomes studied are draft genomes, and (ii) gene prediction standards differ among sequencing centers. First, the closed S. mitis B6 genome displays a higher coding percentage. Second, the coding density was measured in three unpublished draft S. pneumoniae genomes obtained from three different sequencing centers, and the average coding percentage was 84.9%. The previous observation that virtually every independent isolate of S. mitis represents a distinct species according to traditional taxonomic principles is supported by our multigenome analysis. The significant sharing of core genes between S. mitis and S. pneumoniae reinforces the conclusion that S. pneumoniae is one lineage of the S. mitis complex.

The composition of oral biofilm communities, and their pathogenic potential, may depend on interspecies binding and communication interactions. Multivalent coadhesive interactions characterize the binding of Porphyromonas gingivalis to oral streptococci such as Streptococcus gordonii and drive subsequent development of heterotypic S. gordonii-P. gingivalis communities. Gene regulation by two-component systems (TCSs) is a common mechanism used by bacteria to modulate cell behavior in response to environmental changes. Following the initial binding interaction between P. gingivalis and S. gordonii, adherent P. gingivalis cells undergo a programmatic phenotypic shift in order to prepare for community living. P. gingivalis produces autoinducer 2 (AI-2) and responds both to homologous signal and to AI-2 from other organisms such as S. gordonii and Actinobacillus actinomycetemcomitans. The expression of GTF, Rgg, and exo-β;-D-fructosidase (fructanase) is downregulated in the absence of LuxS, whereas expression of tagatose 1,6-diphosphate aldolase is elevated. Contact with S. cristatus propagates a signal in P. gingivalis that causes downregulation of fimA expression. Signaling is mediated by arginine deiminase (ArcA) on the surface of Streptococcus cristatus. Biofilms tend to be polymicrobial in nature, and the subgingival plaque biofilm is an exemplar of this situation, with as many as 200 species present in any one individual.