ABC Transporters Involved in Export of Cell Surface Glycoconjugates.

Microbiol Mol Biol Rev. 2010 Sep;74(3):341-62

Authors: Cuthbertson L, Kos V, Whitfield C

Summary: Complex glycoconjugates play critical roles in the biology of microorganisms. Despite the remarkable diversity in glycan structures and the bacteria that produce them, conserved themes are evident in the biosynthesis-export pathways. One of the primary pathways involves representatives of the ATP-binding cassette (ABC) transporter superfamily. These proteins are responsible for the export of a wide variety of cell surface oligo- and polysaccharides in both Gram-positive and Gram-negative bacteria. Recent investigations of the structure and function of ABC transporters involved in the export of lipopolysaccharide O antigens have revealed two fundamentally different strategies for coupling glycan polymerization to export. These mechanisms are distinguished by the presence (or absence) of characteristic nonreducing terminal modifications on the export substrates, which serve as chain termination and/or export signals, and by the presence (or absence) of a discrete substrate-binding domain in the nucleotide-binding domain polypeptide of the ABC transporter. A bioinformatic survey examining ABC exporters from known oligo- and polysaccharide biosynthesis loci identifies conserved nucleotide-binding domain protein families that correlate well with themes in the structures and assembly of glycans. The familial relationships among the ABC exporters generate hypotheses concerning the biosynthesis of structurally diverse oligo- and polysaccharides, which play important roles in the biology of bacteria with different lifestyles.

PMID: 20805402 [PubMed - in process]

Microbe hunting.

Microbiol Mol Biol Rev. 2010 Sep;74(3):363-77

Authors: Lipkin WI

Summary: Platforms for pathogen discovery have improved since the days of Koch and Pasteur; nonetheless, the challenges of proving causation are at least as daunting as they were in the late 1800s. Although we will almost certainly continue to accumulate low-hanging fruit, where simple relationships will be found between the presence of a cultivatable agent and a disease, these successes will be increasingly infrequent. The future of the field rests instead in our ability to follow footprints of infectious agents that cannot be characterized using classical microbiological techniques and to develop the laboratory and computational infrastructure required to dissect complex host-microbe interactions. I have tried to refine the criteria used by Koch and successors to prove linkage to disease. These refinements are working constructs that will continue to evolve in light of new technologies, new models, and new insights. What will endure is the excitement of the chase. Happy hunting!

PMID: 20805403 [PubMed - in process]

Genomic insights into bifidobacteria.

Microbiol Mol Biol Rev. 2010 Sep;74(3):378-416

Authors: Lee JH, O'Sullivan DJ

Summary: Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. Recently, the genome sequences of nine strains representing four species of Bifidobacterium became available. A comparative genome analysis of these genomes reveals a likely efficient capacity to adapt to their habitats, with B. longum subsp. infantis exhibiting more genomic potential to utilize human milk oligosaccharides, consistent with its habitat in the infant gut. Conversely, B. longum subsp. longum exhibits a higher genomic potential for utilization of plant-derived complex carbohydrates and polyols, consistent with its habitat in an adult gut. An intriguing observation is the loss of much of this genome potential when strains are adapted to pure culture environments, as highlighted by the genomes of B. animalis subsp. lactis strains, which exhibit the least potential for a gut habitat and are believed to have evolved from the B. animalis species during adaptation to dairy fermentation environments.

PMID: 20805404 [PubMed - in process]

Origins and evolution of antibiotic resistance.

Microbiol Mol Biol Rev. 2010 Sep;74(3):417-33

Authors: Davies J, Davies D

Summary: Antibiotics have always been considered one of the wonder discoveries of the 20th century. This is true, but the real wonder is the rise of antibiotic resistance in hospitals, communities, and the environment concomitant with their use. The extraordinary genetic capacities of microbes have benefitted from man's overuse of antibiotics to exploit every source of resistance genes and every means of horizontal gene transmission to develop multiple mechanisms of resistance for each and every antibiotic introduced into practice clinically, agriculturally, or otherwise. This review presents the salient aspects of antibiotic resistance development over the past half-century, with the oft-restated conclusion that it is time to act. To achieve complete restitution of therapeutic applications of antibiotics, there is a need for more information on the role of environmental microbiomes in the rise of antibiotic resistance. In particular, creative approaches to the discovery of novel antibiotics and their expedited and controlled introduction to therapy are obligatory.

PMID: 20805405 [PubMed - in process]

Mobility of plasmids.

Microbiol Mol Biol Rev. 2010 Sep;74(3):434-52

Authors: Smillie C, Garcillán-Barcia MP, Francia MV, Rocha EP, de la Cruz F

Summary: Plasmids are key vectors of horizontal gene transfer and essential genetic engineering tools. They code for genes involved in many aspects of microbial biology, including detoxication, virulence, ecological interactions, and antibiotic resistance. While many studies have decorticated the mechanisms of mobility in model plasmids, the identification and characterization of plasmid mobility from genome data are unexplored. By reviewing the available data and literature, we established a computational protocol to identify and classify conjugation and mobilization genetic modules in 1,730 plasmids. This allowed the accurate classification of proteobacterial conjugative or mobilizable systems in a combination of four mating pair formation and six relaxase families. The available evidence suggests that half of the plasmids are nonmobilizable and that half of the remaining plasmids are conjugative. Some conjugative systems are much more abundant than others and preferably associated with some clades or plasmid sizes. Most very large plasmids are nonmobilizable, with evidence of ongoing domestication into secondary chromosomes. The evolution of conjugation elements shows ancient divergence between mobility systems, with relaxases and type IV coupling proteins (T4CPs) often following separate paths from type IV secretion systems. Phylogenetic patterns of mobility proteins are consistent with the phylogeny of the host prokaryotes, suggesting that plasmid mobility is in general circumscribed within large clades. Our survey suggests the existence of unsuspected new relaxases in archaea and new conjugation systems in cyanobacteria and actinobacteria. Few genes, e.g., T4CPs, relaxases, and VirB4, are at the core of plasmid conjugation, and together with accessory genes, they have evolved into specific systems adapted to specific physiological and ecological contexts.

PMID: 20805406 [PubMed - in process]

From structure to function: the ecology of host-associated microbial communities.

Microbiol Mol Biol Rev. 2010 Sep;74(3):453-76

Authors: Robinson CJ, Bohannan BJ, Young VB

Summary: In the past several years, we have witnessed an increased interest in understanding the structure and function of the indigenous microbiota that inhabits the human body. It is hoped that this will yield novel insight into the role of these complex microbial communities in human health and disease. What is less appreciated is that this recent activity owes a great deal to the pioneering efforts of microbial ecologists who have been studying communities in non-host-associated environments. Interactions between environmental microbiologists and human microbiota researchers have already contributed to advances in our understanding of the human microbiome. We review the work that has led to these recent advances and illustrate some of the possible future directions for continued collaboration between these groups of researchers. We discuss how the application of ecological theory to the human-associated microbiota can lead us past descriptions of community structure and toward an understanding of the functions of the human microbiota. Such an approach may lead to a shift in the prevention and treatment of human diseases that involves conservation or restoration of the normal community structure and function of the host-associated microbiota.

PMID: 20805407 [PubMed - in process]

Chronic shedders as reservoir for nosocomial transmission of norovirus.

J Clin Microbiol. 2010 Sep 1;

Authors: Sukhrie FH, Siebenga JJ, Beersma MF, Koopmans M

Norovirus infection in immunocompromised patients may lead to prolonged norovirus shedding. Here, we demonstrate involvement of three chronic shedders in hospital outbreaks. Combined epidemiological and molecular evidence suggests that in one case NoV transmission occurred at least 17 days after the first diagnosis.

PMID: 20810762 [PubMed - as supplied by publisher]

Spoligotype-based Comparative Population Structure of Multidrug Resistant and Isoniazid Monoresistant Mycobacterium tuberculosis Complex Clinical Isolates in Poland.

J Clin Microbiol. 2010 Sep 1;

Authors: Jagielski T, Augustynowicz-Kopec E, Zozio T, Rastogi N, Zwolska Z

Spoligotyping-based population structure of multidrug resistant (MDR) Mycobacterium tuberculosis strains isolated in Poland (n=46), representing all culture-positive MDR-TB cases was compared to that of isoniazid (INH)-monoresistant strains (n=71), isolated in 2004. The latter dataset from a previous study [Augustynowicz-Kopeć et al., J. Clin. Microbiol. 2008, 46:4041-4044] represented 87% of all INH-monoresistant strains. The clustering rates and genotypic diversity indexes for the 2 sub-populations were not significantly different (p = 0.05). The results were entered in the SITVIT2 database to assign specific shared type designations, corresponding genotypic lineages and geographical distribution, and compared to available data from neighboring countries (Germany n=704; Czech Republic n=530; Sweden n=379; Kaliningrad Russia n=90; and strains from previous studies in Poland n=317). MDR strains resulted in 27 patterns (20 unique strains within the study, and 7 clusters containing 2-6 isolates per cluster with a clustering rate of 56.5%) and belonged to following genotypic lineages: ill-defined T family (28.3%), Haarlem (17.4%), Latin American and Mediterranean (LAM, 13%), Beijing (8.7%), S family (4.35%), and the X clade (2.17%). Comparison of the genetic structure of the MDR strains with that of INH-monoresistant strains showed that a total of 9 patterns were shared by both groups; these represented 1/3rd of MDR strains and 2/3rd of INH-monoresistant strains. Interestingly, 76.1% of the MDR isolates and 71.8% of the INH-resistant isolates yielded spoligotypes that were previously reported from Poland. The observation that nearly half of the spoligotypes identified among both MDR (48.1%) and INH-monoresistant (43.3%) M. tuberculosis isolates were present among Poland's neighboring countries, suggested that a significant proportion of MDR- and INH-resistant TB cases in Poland was caused by strains actively circulating in Poland or its neighbors. Our results corroborate the leading role of the T and Haarlem genotypes in the epidemiology of drug-resistant TB in Poland. Nevertheless, the LAM and Beijing family strains that infected, correspondingly, 13% and 9% of patients with MDR-TB, were absent among the strains from patients with INH-monoresistant TB, suggesting that a proportion of MDR-TB cases in Poland is due to ongoing transmission of MDR clones exhibiting specific genotypes. Study of the population genetic relationships between MDR and INH-monoresistant strains by drawing minimum spanning trees showed that ill-defined T1 sublineage strains (1/3rd of all INH-monoresistant strains) represented by its prototype SIT53 constitute the central node of the tree, followed by strains belonging to well-defined H3, H1, and S subgroups. However, the MDR group in additon contained LAM (n=6) and Beijing (n=4) lineage isolates. With the exception of the 4 Beijing lineage strains in the latter group, and a single orphan isolate in the INH-monoresistant group, none of the remaining 112/117 isolates belonged to the Principal Genetic Group 1 (PGG1) in our study. Given the high rate of clustering, and the near absence of immigrants in the study, the persistence of MDR-TB in Poland seems to result from active transmission of MDR strains within the autochthonous population, the bulk of it being caused by evolutionary recent tubercle bacilli.

PMID: 20810763 [PubMed - as supplied by publisher]

Robust hepatitis B virus genotyping by mass spectrometry.

J Clin Microbiol. 2010 Sep 1;

Authors: Ganova-Raeva L, Ramachandran S, Honisch C, Forbi JC, Zhai X, Khudyakov Y

Genotyping of hepatitis B virus (HBV) is important for tracking HBV infections, prognosticating the development of severe liver disease and predicting outcomes of therapy. Current genotyping methods can be laborious, costly and rely on subjective data interpretation. To identify less expensive but equally reliable alternatives, we compared gold standard sequencing to a novel mass spectrometry approach. Sera from individuals with acute or chronic HBV infection (n=756), representing all genotypes, were used to PCR-amplify the HBV S gene. All amplicons were subject to base-specific cleavage and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The resulting mass peak patterns were used to identify HBV genotype by automated comparison to peak patterns simulated from reference sets of HBV sequences of known genotypes. The MALDI-TOF MS data and phylogenetic analysis of HBV sequences produced completely concordant results. Several parameters such as genetic relatedness of tested HBV variants to the reference set, chronic infections, as well as the quality of PCR products, can lower the MS score but never affected the accuracy of the genotype call. This new streamlined MS-based method provides for rapid and accurate HBV genotyping, produces automated data reports and is therefore suitable for routine use in diagnostic settings.

PMID: 20810764 [PubMed - as supplied by publisher]