Advances in land surface modelling

Land surface models have an increasing scope. Initially designed to capture the feedbacks between the land and the atmosphere as part of weather and climate prediction, they are now used as a critical tool in the urgent need to inform policy about land-use and water-use management in a world that is changing physically and economically. This paper outlines the way that models have evolved through this change of purpose and what might the future hold. It highlights the importance of distinguishing between advances in the science within the modelling components, with the advances of how to represent their interaction. This latter aspect of modelling is often overlooked but will increasingly manifest as an issue as the complexity of the system, the time and space scales of the system being modelled increase. These increases are due to technology, data availability and the urgency and range of the problems being studied

Global Surveillance of Emerging Influenza Virus Genotypes by Mass Spectrometry

Effective influenza surveillance requires new methods capable of rapid and inexpensive genomic analysis of evolving viral species for pandemic preparedness, to understand the evolution of circulating viral species, and for vaccine strain selection. We have developed one such approach based on previously described broad-range reverse transcription PCR/electrospray ionization mass spectrometry (RT-PCR/ESI-MS) technology.Analysis of base compositions of RT-PCR amplicons from influenza core gene segments (PB1, PB2, PA, M, NS, NP) are used to provide sub-species identification and infer influenza virus H and N subtypes. Using this approach, we detected and correctly identified 92 mammalian and avian influenza isolates, representing 30 different H and N types, including 29 avian H5N1 isolates. Further, direct analysis of 656 human clinical respiratory specimens collected over a seven-year period (1999-2006) showed correct identification of the viral species and subtypes with >97% sensitivity and specificity. Base composition derived clusters inferred from this analysis showed 100% concordance to previously established clades. Ongoing surveillance of samples from the recent influenza virus seasons (2005-2006) showed evidence for emergence and establishment of new genotypes of circulating H3N2 strains worldwide. Mixed viral quasispecies were found in approximately 1% of these recent samples providing a view into viral evolution.Thus, rapid RT-PCR/ESI-MS analysis can be used to simultaneously identify all species of influenza viruses with clade-level resolution, identify mixed viral populations and monitor global spread and emergence of novel viral genotypes. This high-throughput method promises to become an integral component of influenza surveillance

Direct demonstration of bacterial biofilms on prosthetic mesh after ventral herniorrhaphy

Background: Prosthetic mesh is employed routinely in the treatment of ventral and parastomal hernias, but its use can lead to major complications, including infection, extrusion, and fistula. Bacterial biofilms have been posited to play a role in mesh-related infection, but although bacteria have been noted to form biofilms on mesh surfaces in vitro, they have never been visualized directly in biofilms on mesh recovered from patients experiencing infectious complications.Methods: Five patients who developed complications after ventral hernia repair with prosthetic mesh were operated on again. Explanted mesh was examined for biofilm with confocal laser scanning microscopy (CLSM) and fluorescence in situ hybridization (FISH). In two cases, a novel molecular assay (the Ibis T5000) was used to characterize the biofilm-forming bacteria.Results: The CLSM examination demonstrated adherent biofilms on mesh surfaces in all five patients. Biofilms also were noted on investing fibrous tissue. The FISH study was able to discriminate between bacterial species in polymicrobial biofilms. In two patients the Ibis T5000 detected more species of constituent biofilm bacteria than did standard culture. Removal of the mesh and reconstruction with autologous tissues or biologic materials resolved the presenting complaints in all cases.Conclusion: Bacterial biofilms should be considered an important contributor to the pathology and complications associated with prosthetic mesh implanted in the abdominal wall. If biofilms are present, complete removal of the mesh and repair of the resulting defect without alloplastic materials is an effective intervention<br/

Demonstration of bacillus cereus in orthopaedic-implant-related infection with use of a multi-primer polymerase chain reaction-mass spectrometric assay: report of two cases

The recent advent of a novel coupled PCR-mass spectrometric technology, the Ibis T5000(Abbott Laboratories, Chicago, Illinois) offers multiple potential advantages for molecular detection of periprosthetic joint infection or other implant-related infections. The Ibis assay simultaneously tests for &gt;3,000 species, including virtually all known pathogens, in a multiplex fashion, eliminating the need for an a priori choice regarding the likely infecting organism. For known pathogens, the Ibis is capable of yielding information down to the species level and can simultaneously assay for antibiotic resistance markers. It is semiquantitative and provides for a rapid turnaround, with clinically useful results available in as little as six hours. Although the Ibis T5000 is not yet approved by the Food and Drug Administration (FDA) for use in clinical diagnostics, we have used it to investigate clinical samples from multiple sources

Characterization of a mixed MRSA/MRSE biofilm in an explanted total ankle arthroplasty

Bacterial biofilms have been observed in many prosthesis-related infections, and this mode-of-growth renders the infection both difficult to treat, and especially difficult to detect and diagnose by standard culture methods. We (1) tested a novel coupled PCR-mass spectroscopic assay (the Ibis T5000) on an ankle arthroplasty that was culture negative on pre-operative aspiration, and then (2) confirmed that the Ibis assay had in fact detected viable multi-species biofilm by further micrographic and molecular examinations, including confocal microscopy using Live/Dead stain, bacterial fluorescent in situ hybridization (FISH), and reverse-transciptase-PCR (RT-PCR) assay for bacterial messenger RNA. The Ibis technology detected Staphylococcus aureus, Staphylococcus epidermidis, and the methicillin resistance gene mecA in soft tissues associated with the explanted hardware. Viable S. aureus were confirmed using RT-PCR, and viable cocci in biofilm configuration were detected microscopically on both tissue and hardware. Species-specific bacterial FISH confirmed a poly-microbial biofilm containing S. aureus. A novel culture method recovered S. aureus and S. epidermidis (both methicillin-resistant) from the tibial metal component. These observations suggest that molecular methods, particularly the new Ibis methodology, may be a useful adjunct to routine cultures in the detection of biofilm bacteria in prosthetic joint infectio

Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections

Abstract Background Necrotizing soft tissue infections (NSTIs) are a group of infections affecting all soft tissues. NSTI involves necrosis of the afflicted tissue and is potentially life threatening due to major and rapid destruction of tissue, which often leads to septic shock and organ failure. The gold standard for identification of pathogens is culture; however molecular methods for identification of microorganisms may provide a more rapid result and may be able to identify additional microorganisms that are not detected by culture. Methods In this study, tissue samples (n = 20) obtained after debridement of 10 patients with NSTI were analyzed by standard culture, fluorescence in situ hybridization (FISH) and multiple molecular methods. The molecular methods included analysis of microbial diversity by 1) direct 16S and D2LSU rRNA gene Microseq 2) construction of near full-length 16S rRNA gene clone libraries with subsequent Sanger sequencing for most samples, 3) the Ibis T5000 biosensor and 4) 454-based pyrosequencing. Furthermore, quantitative PCR (qPCR) was used to verify and determine the relative abundance of Streptococcus pyogenes in samples. Results For 70 % of the surgical samples it was possible to identify microorganisms by culture. Some samples did not result in growth (presumably due to administration of antimicrobial therapy prior to sampling). The molecular methods identified microorganisms in 90 % of the samples, and frequently detected additional microorganisms when compared to culture. Although the molecular methods generally gave concordant results, our results indicate that Microseq may misidentify or overlook microorganisms that can be detected by other molecular methods. Half of the patients were found to be infected with S. pyogenes, but several atypical findings were also made including infection by a) Acinetobacter baumannii, b) Streptococcus pneumoniae, and c) fungi, mycoplasma and Fusobacterium necrophorum. Conclusion The study emphasizes that many pathogens can be involved in NSTIs, and that no specific “NSTI causing” combination of species exists. This means that clinicians should be prepared to diagnose and treat any combination of microbial pathogens. Some of the tested molecular methods offer a faster turnaround time combined with a high specificity, which makes supplemental use of such methods attractive for identification of microorganisms, especially for fulminant life-threatening infections such as NSTI

Occurrence, Distribution, and Origins of Streptococcus pneumoniae Serotype 6C, a Recently Recognized Serotype▿

The prevalence of Streptococcus pneumoniae serotype 6C, a recently recognized serotype that cross-reacts serologically with serotype 6A, was investigated. Isolates of serotype 6A in various collections were recovered, and serotype 6C was differentiated from 6A by multiplex PCR of DNA extracts by using appropriate primers. Antimicrobial susceptibility was performed by Clinical and Laboratory Standards Institute broth microdilution, and selected isolates were typed by pulsed-field gel electrophoresis, repetitive sequence-based PCR typing, and rapid multilocus sequence typing (MLST) by electrospray ionization mass spectrometry of PCR products. A total of 60 serotype 6C isolates were found: 30 of 122 Cleveland isolates collected from 1979 to 2007, 19 of 39 pediatric isolates collected nationwide in 2005 and 2006, and 11 pediatric isolates from Massachusetts collected in 2006 and 2007. Only four isolates were recovered prior to introduction of the conjugate pneumococcal vaccine in 2000; the earliest isolate was recovered in 1989. The sources of the isolates included blood (n = 5), the lower respiratory tract (n = 27), the sinus (n = 5), the ear (n = 2), and the nasopharynx (n = 18); isolates were recovered from 49 children and 11 adults. Pediatric isolates were found in all six major U.S. geographic regions. Antimicrobial susceptibility showed that 22 isolates were nonsusceptible to penicillin, macrolides, and trimethoprim-sulfamethoxazole, 8 had other resistance patterns, and 30 were fully susceptible. The three typing methods used showed similar clusters of up to eight isolates per cluster. MLST showed five clusters related to serotype 6A, two clusters related to serotype 6B, one cluster related to serotype 3, and one cluster related to serotype 34. This study documents the occurrence, nationwide distribution, diversity, likely origins, and increasing incidence after 2001 of this recently recognized serotype. Serotype 6C warrants consideration for addition to future conjugate pneumococcal vaccines

Identification of Pathogenic Vibrio Species by Multilocus PCR-Electrospray Ionization Mass Spectrometry and Its Application to Aquatic Environments of the Former Soviet Republic of Georgia▿ †

The Ibis T5000 is a novel diagnostic platform that couples PCR and mass spectrometry. In this study, we developed an assay that can identify all known pathogenic Vibrio species and field-tested it using natural water samples from both freshwater lakes and the Georgian coastal zone of the Black Sea. Of the 278 total water samples screened, 9 different Vibrio species were detected, 114 (41%) samples were positive for V. cholerae, and 5 (0.8%) samples were positive for the cholera toxin A gene (ctxA). All ctxA-positive samples were from two freshwater lakes, and no ctxA-positive samples from any of the Black Sea sites were detected