Atypical mycobacterial infection in patients with cystic fibrosis: update on clinical microbiology methods

While patients with cystic fibrosis (CF) have had dramatic improvement in their survival rates, this has been accompanied by the emergence of more virulent pathogens such as Pseudomonas aeruginosa and Burkholderia cepacia complex organisms. In addition, there has been emergence of organisms of increasing clinical significance such as the nontuberculous mycobacterial (NTM). Although TB infection in patients with CF is extremely uncommon, there is growing concern with regard to atypical Mycobacterium spp, in particular Mycobacterium abscessus. Many methods of decontamination of sputum, which have been adapted from TB methodologies, are ineffective; as shown by the overgrowth of P. aeruginosa, it is essential that decontamination methods are optimized to overcome this. Establishing optimal methods of isolation and determining accurate levels of prevalence is of importance as, although NTM may be isolated relatively infrequently in CF populations, their clinical status in pulmonary disease is now beginning to emerge.

Development of a genus-specific PCR assay for the molecular detection, confirmation and identification of Fusobacterium spp

A genus-specific polymerase chain reaction (PCR)-based assay is developed for the detection and identification of clinically relevant Fusobacterium species, including F. nucleatum and F. necrophorum. Two 16S ribosomal DNA (rDNA) primers, FUSO1 (forward primer: 5'-GAG AGA GCT TTG CGT CC-3' [17-mer]) and FUSO 2 (reverse primer: 5'-TGG GCG CTG AGG TTC GAC -3' [18-mer]) are designed to target conserved regions of the 16S rDNA gene for Fusobacterium spp. Subsequent proof-of-principle studies employing this assay detected Fusobacterium spp. in the faeces of eight (10%) out of 80 patients with suspected gastrointestinal infection. This assay may be used for the genus-specific detection of Fusobacterium spp. from clinical specimens and for subsequent species identification.

Food-poisoning and commercial air travel

With the introduction of budget airlines and greater competitiveness amongst all airlines, air travel has now become an extremely popular form of travel, presenting its own unique set of risks from food poisoning. Foodborne illness associated with air travel is quite uncommon in the modern era. However, when it occurs, it may have serious implications for passengers and when crew are affected, has the potential to threaten safety. Quality, safe, in-flight catering relies on high standards of food preparation and storage; this applies at the airport kitchens (or at subcontractors' facilities), on the aircraft and in the transportation vehicles which carry the food from the ground source to the aircraft. This is especially challenging in certain countries. Several foodborne outbreaks have been recorded by the airline industry as a result of a number of different failures of these systems. These have provided an opportunity to learn from past mistakes and current practice has, therefore, reached such a standard so as to minimise risk of failures of this kind. This review examines: (i) the origin of food safety in modern commercial aviation; (ii) outbreaks which have occurred previously relating to aviation travel; (iii) the microbiological quality of food and water on board commercial aircraft; and (iv) how Hazard Analysis Critical Control Points may be employed to maintain food safety in aviation travel.

Proposed definitions of community-associated meticillin-resistant Staphylococcus aureus (CA-MRSA)

A new type of meticillin-resistant Staphylococcus aureus (MRSA) is emerging as a significant pathogen in otherwise healthy individuals in the community. This MRSA is distinct from healthcare-associated (HA)-MRSA, in terms of epidemiology, microbiology and clinical manifestations. A considerable number of reports are beginning to appear describing the organism and associated infections in the literature. However, within these reports, there is a lack of consensus as to the terminology used to describe community-associated (CA)-MRSA. This confusion is further compounded with the recent emergence of nosocomial transmission of CA-MRSA within hospitals. The aim of this article is to highlight the differences between HA-MRSA and CA-MRSA and to propose standard definitions of the various subgroups of CA-MRSA.

First restriction and genetic mapping of the genomic DNA of urease-positive thermophilic campylobacters (UPTC), and small restriction fragment sequencing

A restriction and genetic map of urease-positive thermophilic campylobacter (UPTC) CF89-12 genome DNA is constructed using a pulsed-field gel electrophoresis procedure after digestion with SalI and SmaI and Southern blot hybridisation. Each of the six gene fragments (flaA, glyA, lysS, recA, sodB and ureAB) selected are mapped in only a fragment on the restriction map. Three DNA fragments for rrn operon probes are mapped in multiple regions on the map. When two SmaI-digested neighbouring small fragments hybridised with rrn probes are cloned and sequenced, a total sequence length of 7487 bp is determined. In the sequence, part of the pnp gene (734 bp) bearing a p-independent transcriptional termination region, a cluster of five tRNA genes including the putative promoter region, a hypothetical Cj0171-like 507-bp sequence containing an internal termination codon, and a part of the rrn operon including the putative promoter region (4700 bp) are identified. The 507 bp sequence carried both putative transcriptional promoter sequences, including a ribosome binding site upstream of the ATG start codon and a characteristic G9 structure, and a possible p-independent transcriptional termination region. A hypothetical Cj0170-like 204-bp sequence containing an internal termination codon also occurred, overlapping partly with the Cj0171-like sequence. Based on nucleotide sequence alignment analysis between the UPTC rrn operon examined here and the previously reported one, two different 16S-23S ribosomal DNA (rDNA) internal spacer regions are shown to exist.

Effectiveness of standard UV depuration at inactivating Cryptosporidium parvum recovered from spiked Pacific oysters (Crassostrea gigas)

When filter-feeding shellfish are consumed raw, because of their ability to concentrate and store waterborne pathogens, they are being increasingly associated with human gastroenteritis and have become recognized as important pathogen vectors. In the shellfish industry, UV depuration procedures are mandatory to reduce pathogen levels prior to human consumption. However, these guidelines are based around more susceptible fecal coliforms and Salmonella spp. and do not consider Cryptosporidium spp., which have significant resistance to environmental stresses. Thus, there is an urgent need to evaluate the efficiency of standard UV depuration against the survival of Cryptosporidium recovered from shellfish. Our study found that in industrial-scale shellfish depuration treatment tanks, standard UV treatment resulted in a 13-fold inactivation of recovered, viable C. parvum oocysts from spiked (1 x 10(6) oocysts liter (-1)) Pacific oysters. Depuration at half power also significantly reduced (P < 0.05; ninefold) the number of viable oocysts recovered from oysters. While UV treatment resulted in significant reductions of recovered viable oocysts, low numbers of viable oocysts were still recovered from oysters after depuration, making their consumption when raw a public health risk. Our study highlights the need for increased periodic monitoring programs for shellfish harvesting sites, improved depuration procedures, and revised microbial quality control parameters, including Cryptosporidium assessment, to minimize the risk of cryptosporidiosis.

Molecular characterization of the non-coding promoter and leader regions and full-length 16S ribosomal RNA (rRNA) gene ofTaylorella asinigenitalis

The 3,339 base pair (bp) sequences encoding a putative open reading frame (ORF), non-coding promoter and leader regions (approximately 320 bp), full-length 16S ribosomal RNA (rRNA) gene (approximate 1,540 bp) and part of the 16S-23S rDNA internal spacer region (ISR) were determined from genome DNA libraries of the Taylorella asinigenitalis (UK-1) isolate. The non-coding promoter and leader regions included antiterminators (boxB, boxA and boxC) immediately upstream of the 16S rRNA gene sequence. An approximately 680 bp region upstream of the non-coding promoter region appears to contain a putative ORF with high sequence similarity to GTP cyclohydrolase I. In addition, a typical order of intercistronic tRNA genes with the 48 nucleotide spacer of 5'-16S rDNA-tRNA(Ile)-tRNA(Ala)-23S rDNA-3' was demonstrated in a part of the 16S-23S rDNA ISR. The antiterminators of boxB and boxA were also identified in the ISR.A phylogenetic analysis based on the 16S rRNA gene sequence information clearly demonstrated that the five T. asinigenitalis isolates formed a cluster together with the three T. equigenitalis strains, more similar to Pelistega europaea than the other beta-Proteobacteria from the 13 species of 11 genera.

Gauge symmetry and non-Abelian topological sectors in a geometrically constrained model on the honeycomb lattice

We study a constrained statistical-mechanical model in two dimensions that has three useful descriptions. They are (i) the Ising model on the honeycomb lattice, constrained to have three up spins and three down spins on every hexagon, (ii) the three-color and fully packed loop model on the links of the honeycomb lattice, with loops around a single hexagon forbidden, and (iii) three Ising models on interleaved triangular lattices, with domain walls of the different Ising models not allowed to cross. Unlike the three-color model, the configuration space on the sphere or plane is connected under local moves. On higher-genus surfaces there are infinitely many dynamical sectors, labeled by a noncontractible set of nonintersecting loops. We demonstrate that at infinite temperature the transfer matrix admits an unusual structure related to a gauge symmetry for the same model on an anisotropic lattice. This enables us to diagonalize the original transfer matrix for up to 36 sites, finding an entropy per plaquette S/k{B} approximately 0.3661 ... centered and substantial evidence that the model is not critical. We also find the striking property that the eigenvalues of the transfer matrix on an anisotropic lattice are given in terms of Fibonacci numbers. We comment on the possibility of a topological phase, with infinite topological degeneracy, in an associated two-dimensional quantum model.

Lack of horizontal gene transfer of methicillin-resistance genetic determinants from PBP2a-positive, coagulase-negative staphylococci to methicillin-sensitive Staphylococcus aureus using transcutaneous electrical nerve stimulation (TENS)

Previous research shows that approximately half of the coagulase-negative staphylococci (CNS) isolated from patients in the intensive care unit (ICU) at Belfast City Hospital were resistant to methicillin. The presence of this relatively high proportion of methicillin-resistance genetic material gives rise to speculation that these organisms may act as potential reservoirs of methicillin-resistance genetic material to methicillin-sensitive Staphylococcus aureus (MSSA). Mechanisms of horizontal gene transfer from PBP2a-positive CNS to MSSA, potentially transforming MSSA to MRSA, aided by electroporation-type activities such as transcutaneous electrical nerve stimulation (TENS), should be considered. Methicillin-resistant CNS (MR-CNS) isolates are collected over a two-month period from a variety of clinical specimen types, particularly wound swabs. The species of all isolates are confirmed, as well as their resistance to oxacillin by standard disc diffusion assays. In addition, MSSA isolates are collected over the same period and confirmed as PBP2a-negative. Electroporation experiments are designed to mimic the time/voltage combinations used commonly in the clinical application of TENS. No transformed MRSA were isolated and all viable S. aureus cells remained susceptible to oxacillin and PBP2a-negative. Experiments using MSSA pre-exposed to sublethal concentrations of oxacillin (0.25 microg/mL) showed no evidence of methicillin gene transfer and the generation of an MRSA. The study showed no evidence of horizontal transfer of methicillin resistance genetic material from MR-CNS to MSSA. These data support the belief that TENS and the associated time/voltage combinations used do not increase conjugational transposons or facilitate horizontal gene transfer from MR-CNS to MSSA.

Flagellin gene structure offlaA andflaB and adjacent gene loci in urease-positive thermophilicCampylobacter (UPTC)

Two flagellin gene (flaA and flaB) sequences and the adjacent gene loci of urease-positive thermophilic Campylobacter (UPTC)(1) were examined. The flagellin gene sequences (1.7 kb) and adjacent gene loci of the two UPTC isolates (89049 and A3), obtained from animal hosts, were very similar to those of C. lari RM2100, C. jejuni, and C. coli. However, the structure and loci of the two flagellin genes (1.46-1.47 kb) and the adjacent gene loci of a UPTC strain obtained from the natural environment (NCTC12892) clearly differed from those of C. lari RM2100 and UPTC obtained from animal hosts. The two flagellin genes of UPTC 89049 and A3 were located between topA /CLA0518 and CLA0521, whereas those of NCTC12892 were located between topA and CLA0521. The sequences involved in regulation of flagellin expression, like sigma(28), sigma(54) and transcription termination signals, were conserved in all isolates. The characteristic direct repeat sequences containing a complete repeat unit of 5'-TCTTTAAAACAAC-3' were located in the intergenic regions between flaA and flaB in UPTC89049 and A3, but not in NCTC12892. The deduced amino acid sequence alignment revealed that the two flagellin genes in NCTC12892 had a deletion of the variable region of flagellin, which was reported previously to be modified by pseudaminic acid in C. jejuni and C. coli.Consequently, these results may possibly suggest that the length of the flagellin is related to pathogenicity and colonization of Campylobacter.

Current noise in the vicinity of the 2D superconductor-insulator quantum critical point

Systems near to quantum critical points show universal scaling in response to external probes. We consider whether this scaling is reflected in their out-of-equilibrium fluctuations. We study current noise in the metallic state at the z=1 quantum critical point between a superconductor and an insulator in two dimensions. Using a Boltzmann-Langevin approach within a 1/N expansion, we show that the current noise obeys a universal scaling form S_{j}=TPhi[T/T_{eff}(E)], with T_{eff} proportional, variantsqrt[E]. This treatment recovers Johnson noise in thermal equilibrium and S_{j} proportional, variantsqrt[E] at strong electric fields. The latter differs significantly from both the shot noise in conventional metals (diffusive Fermi liquids) and the free carrier result, due to strong correlations between the critical bosonic excitations. Current-noise measurements could therefore help clarify the physics of the destruction of superconductivity in thin film superconductors.

Rapid and sensitive detection of single cryptosporidium oocysts from archived glass slides

In this study we report on the development and application of a novel method for efficiently extracting and detecting single Cryptosporidium oocysts from archived glass slides. Laser capture microscopy was used to extract low numbers of oocysts from archived glass slides. Highly sensitive real-time PCR methods were then developed to enable the rapid detection and identification of Cryptosporidium oocysts from these samples. The method was applied to fecal smears stained with a variety of standard oocyst stains and water samples. This application, with samples derived from both public health and water service laboratories, highlighted the strong potential of this method to be used as a rapid high-throughput screening tool for the routine monitoring of Cryptosporidium and other medically important pathogens from clinical, veterinary, and environmental water samples. Importantly, the application of our protocol could be used to type Cryptosporidium and other pathogens from stored archived glass slides in public health and water service laboratories, providing vital epidemiological updates and helping to identify and trace pathogens and their routes of infection and ultimately improve their control.

Topological defects and the superfluid transition of the s=1 spinor condensate in two dimensions

The s=1 spinor Bose condensate at zero temperature supports ferromagnetic and polar phases that combine magnetic and superfluid ordering. We analyze the topological defects of the polar condensate, correcting previous studies, and show that the polar condensate in two dimensions is unstable at any finite temperature; instead, there is a nematic or paired superfluid phase with algebraic order in exp(2itheta), where theta is the superfluid phase, and no magnetic order. The Kosterlitz-Thouless transition out of this phase is driven by unbinding of half-vortices (the spin-disordered version of the combined spin and phase defects found by Zhou), and the anomalous universal 8T(c)/pi stiffness jump at the transition is confirmed in numerical simulations. The anomalous stiffness jump is a clear experimental signature of this phase and the corresponding phase transition.