Provision of smoking cessation support for patients following a diagnosis of cancer in Ireland

There is growing evidence that smoking cessation (SC) improves outcomes following diagnosis of cancer. Notwithstanding adverse outcomes, a significant number of those diagnosed with cancer continue to smoke. Our objective was to document the SC services provided for patients with cancer by specialist adult cancer hospitals across Ireland, a country with a stated tobacco endgame goal. A cross-sectional survey based on recent national clinical guidelines was used to determine SC care delivery across eight adult cancer specialist hospitals, and one specialist radiotherapy centre. Qualtrics was used. The response rate was 88.9% with data reported from seven cancer hospitals and one specialist radiotherapy centre, all indicating they had some SC related provision (100%). Stop smoking medications were provided to cancer inpatients in two hospitals, at outpatients and attending day ward services in one hospital. Smokers with cancer were referred automatically to the SC service in two hospitals at diagnosis. While stop smoking medications were available 24 h a day in five hospitals, most did not stock all three (Nicotine Replacement Therapy, Bupropion, Varenicline). One hospital advised they had data on uptake of SC services for smokers with cancer but were unable to provide detail. There is considerable variation in SC information and services provided to cancer patients across adult cancer specialist centres in Ireland, reflecting the suboptimal practice of smoking cessation for patients with cancer found in the limited international audits. Such audits are essential to demonstrate service gaps and provide a baseline for service improvement.

Smoking cessation for cancer patients through the lens of cancer specialists: challenges & solutions

Background

The benefits of smoking cessation (SC) for cancer patients are widely recognised. However, there has been a limited emphasis on SC in this context and it continues to be a challenge for cancer patients. As part of a larger feasibility study aiming to develop a structured SC pathway for cancer patients in Ireland, this qualitative study explored the SC practices, experiences and opinions of oncology healthcare professionals (HCPs).

Methods

Semi-structured interviews were conducted with 18 HCPs from lung, breast, cervical, head and neck and general oncology, across 4 specialist adult cancer hospitals in Ireland. Interview transcripts were analysed using thematic analysis.

Results

Four key themes emerged:

(1) Frequently ask and advise but infrequently assist: most HCPs ask about smoking and many advise about available supports, but few refer patients to SC services. Where offered, referrals were to hospital SC services and/or nicotine replacement therapy was prescribed; no HCP prescribed varenicline or bupropion. Barriers included lack of time, ill-defined referral pathways and lack of knowledge.

(2) Increased willingness but differing ability to quit: most patients were interested in quitting post diagnosis and had varying support needs, linked to cancer stage, social circumstances and stress levels.

(3) Need for an integrated or parallel service: all HCPs suggested that a structured and defined referral pathway will facilitate SC.

(4) Motivational counselling and pharmacotherapy combination: many HCPs suggested face to face as the best mode of intervention initially, with regular follow ups and ongoing support virtually, started pre-treatment, with an empathetic and empowering approach with provision of both motivational counselling and SC pharmacotherapy.

Conclusions

Smoking post cancer diagnosis has serious implications for cancer treatment and prognosis but is frequently overlooked. These findings will inform the design of a SC pathway for cancer patients.

Key messages

• Despite increased willingness to quit, there is inadequate and inconsistent SC support provision for cancer patients.

• Tailored SC support should be an integral part of comprehensive cancer care.

Tomographic reconstruction of a spatially-extended source from the perimeter of a restricted-access zone using a SCoTSS compton gamma imager

It is a standard procedure in many countries that response to a nuclear or radiological accident or incident would involve mobile aerial- or ground-based survey with highly sensitive gamma-ray detectors to map the distribution of radioactivity. There may however arise situations in which ground- or air-based detectors are not able to access an area to survey for radioactive materials, therefore technologies and techniques that can estimate the position and activity of radioactive materials from a distance are under development. Tomographic reconstruction methods, well-known in medical physics, permit the reconstruction of an N-dimensional map or image, from a number of N-1-dimensional cross-sectional images, or back-projections. We are investigating a tomographic reconstruction method to reconstruct the radioactivity distribution within a restricted-access zone using measurements from a Compton gamma imager placed at several locations around the perimeter of the zone. In this work an extended source of La-140 with an activity of 35 GBq was deposited within a 500 m by 500 m zone that was surveyed from the perimeter at six locations using a Silicon photomultiplier-based Compton Telescope for Safety and Security (SCoTSS) gamma imager. The reconstructed Compton images from multiple viewpoints were then projected back into the zone to reconstruct the distribution of La-140 within it. This tomographic method reconstructed high intensity along the known location of the La-140 source, suggesting that the method is able to localize the radioactive material. A simple fit to measured counts using a point-source approximation of the source distribution yielded a strength estimate of (7 ± 2) GBq at time of deposition, a reasonable result given the presence of soil and snow attenuation. Our method provides an expedient estimate of the distribution of radioactivity using tomographic techniques. It may be used to inform decisions made on the scene in urgent situations where the distribution of radioactivity must be reconstructed from a distance.

Autochthonous faecal viral transfer (FVT) impacts the murine microbiome after antibiotic perturbation

BACKGROUND

It has become increasingly accepted that establishing and maintaining a complex and diverse gut microbiota is fundamental to human health. There are growing efforts to identify means of modulating and influencing the microbiota, especially in individuals who have experienced a disruption in their native microbiota. Faecal microbiota transplantation (FMT) is one method that restores diversity to the microbiota of an individual by introducing microbes from a healthy donor. FMT introduces the total microbial load into the recipient, including the bacteria, archaea, yeasts, protists and viruses. In this study, we investigated whether an autochthonous faecal viral transfer (FVT), in the form of a sterile faecal filtrate, could impact the recovery of a bacteriome disrupted by antibiotic treatment.

RESULTS

Following antibiotic disruption of the bacteriome, test mice received an FVT harvested prior to antibiotic treatment, while control mice received a heat- and nuclease-treated FVT. In both groups of mice, the perturbed microbiome reverted over time to one more similar to the pre-treatment one. However, the bacteriomes of mice that received an FVT, in which bacteriophages predominate, separated from those of the control mice as determined by principal co-ordinate analysis (PCoA). Moreover, analysis of the differentially abundant taxa indicated a closer resemblance to the pre-treatment bacteriome in the test mice that had received an FVT. Similarly, metagenomic sequencing of the virome confirmed that faecal bacteriophages of FVT and control mice differed over time in both abundance and diversity, with the phages constituting the FVT persisting in mice that received them.

CONCLUSIONS

An autochthonous virome transfer reshaped the bacteriomes of mice post-antibiotic treatment such that they more closely resembled the pre-antibiotic microbiota profile compared to mice that received non-viable phages. Thus, FVT may have a role in addressing antibiotic-associated microbiota alterations and potentially prevent the establishment of post-antibiotic infection. Given that bacteriophages are biologically inert in the absence of their host bacteria, they could form a safe and effective alternative to whole microbiota transplants that could be delivered during/following perturbation of the gut flora.

Randomized Trial of 2 Self-Titrated Oral Appliances for Airway Management

The effectiveness and predictability of 2 different oral appliance (OA) designs to reduce the respiratory event index (REI) in moderate and severe obstructive sleep apnea (OSA) patients requires elucidation. The primary aim of the trial was to determine if 2 widely used midline-traction and bilateral-thrust OA designs differ in effectiveness to reduce the REI within a single test population categorized by OSA severity. Moderate and severe adult OSA patients, who were previously prescribed continuous positive airway pressure therapy (CPAP) but were dissatisfied with it (n = 56), were studied by home-polygraphy in a randomized crossover trial using either midline-traction with restricted mouth opening (MR) or bilateral thrust with opening permitted (BP) design OAs. OAs were used nightly for 4 wk (T2) followed by a 1-wk washout period, then 4 wk (T4) using the alternate OA. REI and oxygen saturation (SaO₂) were primary outcomes, while predictability and efficacy comparison of the 2 OAs were secondary outcomes. Thirty-six participants had used MR and BP OAs during both 4-wk study legs. Twenty (55.6%) MR OA-using participants, 25 (69.4%) BP OA-using participants, and 16 (44.4%) participants using both OAs had significant REI reductions. Overall baseline (T0) median REI (interquartile range) of 33.7 (20.7-54.9) was reduced to 18.0 (8.5-19.4) at T2 and to 12.5 (8.2-15.9) at T4 (P < 0.001). Comparison of the 2 sequence groups' (MR-BP and BP-MR) REI showed the median differences between T0 and T2 and T4 were highly significant (P < 0.001). Regression analysis predicted about half of all users will have REIs between 8 and 16 after 2 mo. Baseline overjet measures >2.9 mm predicted greater OA advancement at T4. Mean and minimum SaO₂ did not change significantly from T0 to T2 or T4. MR and BP OA designs similarly attenuated REI in moderate and severe OSA individuals who completed the 8-wk study protocol with greater REI reduction in those with severe OSA (ClinicalTrials.gov NCT03219034).

Consensus guidelines for interventional cardiology services delivery during covid-19 pandemic in Australia and new Zealand

The global coronavirus disease (COVID-19) pandemic poses an unprecedented stress on healthcare systems internationally. These Health system-wide demands call for efficient utilisation of resources at this time in a fair, consistent, ethical and efficient manner would improve our ability to treat patients. Excellent co-operation between hospital units (especially intensive care unit [ICU], emergency department [ED] and cardiology) is critical in ensuring optimal patient outcomes. The purpose of this document is to provide practical guidelines for the effective use of interventional cardiology services in Australia and New Zealand. The document will be updated regularly as new evidence and knowledge is gained with time. Goals Considerations.

Exploratory analysis of covariation of microbiota-derived vitamin K and cognition in older adults

BACKGROUND

Vitamin K has multiple important physiological roles, including blood coagulation and beneficial effects on myelin integrity in the brain. Some intestinal microbes possess the genes to produce vitamin K in the form of menaquinone (MK). MK appears in higher concentration in tissues, such as the brain, particularly MK4, than the dietary form of phylloquinone (PK). Lower PK concentrations have been reported in patients with Alzheimer disease while higher serum PK concentrations have been positively associated with verbal episodic memory. Despite knowledge of the importance of vitamin K for various health parameters, few studies have measured MK concentration and biosynthesis by gut commensals.

OBJECTIVE

The aim of the current study was to investigate the relation between genes involved in gut-microbiota derived MK, concentrations of MK isoforms, and cognitive function.

METHODS

Shotgun metagenomic sequencing of the gut microbiome of 74 elderly individuals with different cognitive ability levels was performed. From this, gene counts for microbial MK biosynthesis were determined. Associations between clusters of individuals, grouped based on a similar presence and prevalence of MK biosynthesis genes, and cognitive ability were investigated. Fecal MK concentrations were quantified by HPLC to investigate correlations with subject clusters.

RESULTS

Separation of subject groups defined by banded quantification of the genetic potential of their microbiome to biosynthesize MK was associated with significant differences in cognitive ability [assessed using the Mini-Mental State Examination (MMSE)]. Three MK isoforms were found to be positively associated with MMSE, along with the identification of key components of the MK pathway that drive this association. Although the causality and direction of these associations remain unknown, these findings justify further studies.

CONCLUSIONS

This study provides evidence that although total concentrations of MK did not covary with cognition, certain MK isoforms synthesized by the gut microbiome, particularly the longer chains, are positively associated with cognition.

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.

Viromes of one year old infants reveal the impact of birth mode on microbiome diversity

Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome/phageome during this developmental period. We performed a metagenomic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD) or caesarean section (CS) influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity. We demonstrate that CrAssphage is acquired early in life, both in this cohort and two others, although no difference in birth mode is detected. A previous study has shown that bacterial OTU’s (operational taxonomic units) identified in the same infants could not discriminate between birth mode at 12 months of age. Therefore, our results indicate that vertical transmission of viral communities from mother to child may play a role in shaping the early life microbiome, and that birth mode should be considered when studying the early life gut virome.

Reproducible protocols for metagenomic analysis of human faecal phageomes

BACKGROUND

Recent studies have demonstrated that the human gut is populated by complex, highly individual and stable communities of viruses, the majority of which are bacteriophages. While disease-specific alterations in the gut phageome have been observed in IBD, AIDS and acute malnutrition, the human gut phageome remains poorly characterised. One important obstacle in metagenomic studies of the human gut phageome is a high level of discrepancy between results obtained by different research groups. This is often due to the use of different protocols for enriching virus-like particles, nucleic acid purification and sequencing. The goal of the present study is to develop a relatively simple, reproducible and cost-efficient protocol for the extraction of viral nucleic acids from human faecal samples, suitable for high-throughput studies. We also analyse the effect of certain potential confounding factors, such as storage conditions, repeated freeze-thaw cycles, and operator bias on the resultant phageome profile. Additionally, spiking of faecal samples with an exogenous phage standard was employed to quantitatively analyse phageomes following metagenomic sequencing. Comparative analysis of phageome profiles to bacteriome profiles was also performed following 16S rRNA amplicon sequencing.

RESULTS

Faecal phageome profiles exhibit an overall greater individual specificity when compared to bacteriome profiles. The phageome and bacteriome both exhibited moderate change when stored at + 4 °C or room temperature. Phageome profiles were less impacted by multiple freeze-thaw cycles than bacteriome profiles, but there was a greater chance for operator effect in phageome processing. The successful spiking of faecal samples with exogenous bacteriophage demonstrated large variations in the total viral load between individual samples.

CONCLUSIONS

The faecal phageome sequencing protocol developed in this study provides a valuable additional view of the human gut microbiota that is complementary to 16S amplicon sequencing and/or metagenomic sequencing of total faecal DNA. The protocol was optimised for several confounding factors that are encountered while processing faecal samples, to reduce discrepancies observed within and between research groups studying the human gut phageome. Rapid storage, limited freeze-thaw cycling and spiking of faecal samples with an exogenous phage standard are recommended for optimum results.

Amino acid profile and metabolic syndrome in a male Mediterranean population: A cross-sectional study

BACKGROUND AND AIMS

The metabolic syndrome (MetS) refers to a cluster of clinically relevant factors that increases the risk of cardiovascular diseases and all-cause mortality. Circulating levels of several amino acids and metabolites related to one-carbon metabolism have been associated with cardiometabolic risk factors and MetS. We aimed to identify the amino acid profile that is significantly associated with MetS among an all male Mediterranean population.

METHODS AND RESULTS

One hundred middle-aged men (54.6 ± 8.9 years) participated in a cross-sectional study carried out during 2011-2012. The International Diabetes Federation (IDF) criteria were used to define MetS. Fasting plasma levels of 20 common amino acids and 15 metabolites related to amino acid and one-carbon metabolism were measured using gas chromatography (GC-MS/MS) and liquid chromatography tandem mass spectrometry (LC-MS/MS). Principal components analysis was applied. Fifty-six participants fulfilled the IDF criteria for defining MetS. Five factors were extracted from the 35 measured metabolites. The branched-chain amino acids/aromatic amino acids (BCAA/AAA) related pattern and the glutamine/glycine/serine/asparagine (Gln/Gly/Ser/Asn) related pattern were significantly associated with MetS (odds ratio, 95% confidence interval; 6.41, 2.43-16.91, and 0.47, 0.23-0.96, respectively) after adjustment for age, current smoking status, physical activity level and medical treatment for hypertension, dyslipidaemia, type 2 diabetes mellitus. Further adjustment for liver function markers (i.e. glutamic oxaloacetic transaminase, glutamic pyruvic transaminase, and γ-glutamyltransferase), and plasma adiponectin levels did not significantly affect the associations.

CONCLUSION

The BCAA/AAA pattern was positively associated, while the Gln/Gly/Ser/Asn pattern was inversely associated with established cardiometabolic risk factors and MetS. Plasma adiponectin levels or markers of liver function did not significantly affect these associations.

Protein and chemotherapy profiling of extracellular vesicles harvested from therapeutic induced senescent triple negative breast cancer cells

Triple negative breast cancer (TNBC) is an aggressive subtype with relatively poor clinical outcomes and limited treatment options. Chemotherapy, while killing cancer cells, can result in the generation of highly chemoresistant therapeutic induced senescent (TIS) cells that potentially form stem cell niches resulting in metastases. Intriguingly, senescent cells release significantly more extracellular vesicles (EVs) than non-senescent cells. Our aim was to profile EVs harvested from TIS TNBC cells compared with control cells to identify a potential mechanism by which TIS TNBC cells maintain survival in the face of chemotherapy. TIS was induced and confirmed in Cal51 TNBC cells using the chemotherapeutic paclitaxel (PTX) (Taxol). Mass spectrometry (MS) analysis of EVs harvested from TIS compared with control Cal51 cells was performed using Ingenuity Pathway Analysis and InnateDB programs. We demonstrate that TIS Cal51 cells treated with 75 nM PTX for 7 days became senescent (senescence-associated β-galactosidase (SA-β-Gal) positive, Ki67-negative, increased p21 and p16, G2/M cell cycle arrest) and released significantly more EVs (P=0.0002) and exosomes (P=0.0007) than non-senescent control cells. Moreover, TIS cells displayed an increased expression of the multidrug resistance protein 1/p-glycoprotein. MS analysis demonstrated that EVs derived from senescent Cal51 cells contained 142 proteins with a significant increased fold change compared with control EVs. Key proteins included ATPases, annexins, tubulins, integrins, Rabs and insoluble senescence-associated secretory phenotype (SASP) factors. A fluorescent analogue of PTX (Flutax-2) allowed appreciation of the removal of chemotherapy in EVs from senescent cells. Treatment of TIS cells with the exosome biogenesis inhibitor GW4869 resulted in reduced SA-β-Gal staining (P=0.04). In summary, this study demonstrates that TIS cells release significantly more EVs compared with control cells, containing chemotherapy and key proteins involved in cell proliferation, ATP depletion, apoptosis and the SASP. These findings may partially explain why cancer senescent cells remain viable despite chemotherapeutic challenge.

A long and abundant non-coding RNA in Lactobacillus salivarius

Lactobacillus salivarius, found in the intestinal microbiota of humans and animals, is studied as an example of the sub-dominant intestinal commensals that may impart benefits upon their host. Strains typically harbour at least one megaplasmid that encodes functions contributing to contingency metabolism and environmental adaptation. RNA sequencing (RNA-seq)transcriptomic analysis of L. salivarius strain UCC118 identified the presence of a novel unusually abundant long non-coding RNA (lncRNA) encoded by the megaplasmid, and which represented more than 75 % of the total RNA-seq reads after depletion of rRNA species. The expression level of this 520 nt lncRNA in L. salivarius UCC118 exceeded that of the 16S rRNA, it accumulated during growth, was very stable over time and was also expressed during intestinal transit in a mouse. This lncRNA sequence is specific to the L. salivarius species; however, among 45 L. salivarius genomes analysed, not all (only 34) harboured the sequence for the lncRNA. This lncRNA was produced in 27 tested L. salivarius strains, but at strain-specific expression levels. High-level lncRNA expression correlated with high megaplasmid copy number. Transcriptome analysis of a deletion mutant lacking this lncRNA identified altered expression levels of genes in a number of pathways, but a definitive function of this new lncRNA was not identified. This lncRNA presents distinctive and unique properties, and suggests potential basic and applied scientific developments of this phenomenon.

Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera

Lactobacilli are a diverse group of species that occupy diverse nutrient-rich niches associated with humans, animals, plants and food. They are used widely in biotechnology and food preservation, and are being explored as therapeutics. Exploiting lactobacilli has been complicated by metabolic diversity, unclear species identity and uncertain relationships between them and other commercially important lactic acid bacteria. The capacity for biotransformations catalysed by lactobacilli is an untapped biotechnology resource. Here we report the genome sequences of 213 Lactobacillus strains and associated genera, and their encoded genetic catalogue for modifying carbohydrates and proteins. In addition, we describe broad and diverse presence of novel CRISPR-Cas immune systems in lactobacilli that may be exploited for genome editing. We rationalize the phylogenomic distribution of host interaction factors and bacteriocins that affect their natural and industrial environments, and mechanisms to withstand stress during technological processes. We present a robust phylogenomic framework of existing species and for classifying new species.

Lactobacillus is a lactic acid bacteria and has a wide range of application from use in probiotic food production to biotherapeutics. Here, the authors sequence and compare the genomes of 213 different Lactobacillus strains and related genera, and provide new insight into phylogenomic organization and adaptive immunity elements in this bacteria family.

The role of China in the global spread of the current cholera pandemic

Epidemics and pandemics of cholera, a severe diarrheal disease, have occurred since the early 19th century and waves of epidemic disease continue today. Cholera epidemics are caused by individual, genetically monomorphic lineages of Vibrio cholerae: the ongoing seventh pandemic, which has spread globally since 1961, is associated with lineage L2 of biotype El Tor. Previous genomic studies of the epidemiology of the seventh pandemic identified three successive sub-lineages within L2, designated waves 1 to 3, which spread globally from the Bay of Bengal on multiple occasions. However, these studies did not include samples from China, which also experienced multiple epidemics of cholera in recent decades. We sequenced the genomes of 71 strains isolated in China between 1961 and 2010, as well as eight from other sources, and compared them with 181 published genomes. The results indicated that outbreaks in China between 1960 and 1990 were associated with wave 1 whereas later outbreaks were associated with wave 2. However, the previously defined waves overlapped temporally, and are an inadequate representation of the shape of the global genealogy. We therefore suggest replacing them by a series of tightly delineated clades. Between 1960 and 1990 multiple such clades were imported into China, underwent further microevolution there and then spread to other countries. China was thus both a sink and source during the pandemic spread of V. cholerae, and needs to be included in reconstructions of the global patterns of spread of cholera.

Cholera is a life-threatening, diarrheal disease caused by the bacterium Vibrio cholerae. After a long interregnum of decades without epidemics, the seventh cholera pandemic spread globally since 1961, causing considerable morbidity and mortality. Our analysis of published and newly sequenced genomes provides details on genetic groupings within V. cholerae, so-called clades, that have developed during the recent pandemic spread of these bacteria, and, in some cases, persisted to modern times. We reconstructed some of the pathways taken by the current pandemic since its origins in Indonesia, and show that both South Asia and East Asia are important pathogenic reservoirs and sources of international transmissions.

Archaea appear to dominate the microbiome of Inflatella pellicula deep sea sponges

Microbes associated with marine sponges play significant roles in host physiology. Remarkable levels of microbial diversity have been observed in sponges worldwide through both culture-dependent and culture-independent studies. Most studies have focused on the structure of the bacterial communities in sponges and have involved sponges sampled from shallow waters. Here, we used pyrosequencing of 16S rRNA genes to compare the bacterial and archaeal communities associated with two individuals of the marine sponge Inflatella pellicula from the deep-sea, sampled from a depth of 2,900 m, a depth which far exceeds any previous sequence-based report of sponge-associated microbial communities. Sponge-microbial communities were also compared to the microbial community in the surrounding seawater. Sponge-associated microbial communities were dominated by archaeal sequencing reads with a single archaeal OTU, comprising ~60% and ~72% of sequences, being observed from Inflatella pellicula. Archaeal sequencing reads were less abundant in seawater (~11% of sequences). Sponge-associated microbial communities were less diverse and less even than any other sponge-microbial community investigated to date with just 210 and 273 OTUs (97% sequence identity) identified in sponges, with 4 and 6 dominant OTUs comprising ~88% and ~89% of sequences, respectively. Members of the candidate phyla, SAR406, NC10 and ZB3 are reported here from sponges for the first time, increasing the number of bacterial phyla or candidate divisions associated with sponges to 43. A minor cohort from both sponge samples (~0.2% and ~0.3% of sequences) were not classified to phylum level. A single OTU, common to both sponge individuals, dominates these unclassified reads and shares sequence homology with a sponge associated clone which itself has no known close relative and may represent a novel taxon.

Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona

Salmonella enterica serovar Agona has caused multiple food-borne outbreaks of gastroenteritis since it was first isolated in 1952. We analyzed the genomes of 73 isolates from global sources, comparing five distinct outbreaks with sporadic infections as well as food contamination and the environment. Agona consists of three lineages with minimal mutational diversity: only 846 single nucleotide polymorphisms (SNPs) have accumulated in the non-repetitive, core genome since Agona evolved in 1932 and subsequently underwent a major population expansion in the 1960s. Homologous recombination with other serovars of S. enterica imported 42 recombinational tracts (360 kb) in 5/143 nodes within the genealogy, which resulted in 3,164 additional SNPs. In contrast to this paucity of genetic diversity, Agona is highly diverse according to pulsed-field gel electrophoresis (PFGE), which is used to assign isolates to outbreaks. PFGE diversity reflects a highly dynamic accessory genome associated with the gain or loss (indels) of 51 bacteriophages, 10 plasmids, and 6 integrative conjugational elements (ICE/IMEs), but did not correlate uniquely with outbreaks. Unlike the core genome, indels occurred repeatedly in independent nodes (homoplasies), resulting in inaccurate PFGE genealogies. The accessory genome contained only few cargo genes relevant to infection, other than antibiotic resistance. Thus, most of the genetic diversity within this recently emerged pathogen reflects changes in the accessory genome, or is due to recombination, but these changes seemed to reflect neutral processes rather than Darwinian selection. Each outbreak was caused by an independent clade, without universal, outbreak-associated genomic features, and none of the variable genes in the pan-genome seemed to be associated with an ability to cause outbreaks.

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

The widespread use of antibiotics in association with high-density clinical care has driven the emergence of drug-resistant bacteria that are adapted to thrive in hospitalized patients. Of particular concern are globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clones that cause outbreaks and epidemics associated with health care. The most rapidly spreading and tenacious health-care-associated clone in Europe currently is EMRSA-15, which was first detected in the UK in the early 1990s and subsequently spread throughout Europe and beyond. Using phylogenomic methods to analyze the genome sequences for 193 S. aureus isolates, we were able to show that the current pandemic population of EMRSA-15 descends from a health-care-associated MRSA epidemic that spread throughout England in the 1980s, which had itself previously emerged from a primarily community-associated methicillin-sensitive population. The emergence of fluoroquinolone resistance in this EMRSA-15 subclone in the English Midlands during the mid-1980s appears to have played a key role in triggering pandemic spread, and occurred shortly after the first clinical trials of this drug. Genome-based coalescence analysis estimated that the population of this subclone over the last 20 yr has grown four times faster than its progenitor. Using comparative genomic analysis we identified the molecular genetic basis of 99.8% of the antimicrobial resistance phenotypes of the isolates, highlighting the potential of pathogen genome sequencing as a diagnostic tool. We document the genetic changes associated with adaptation to the hospital environment and with increasing drug resistance over time, and how MRSA evolution likely has been influenced by country-specific drug use regimens.

Colour Doppler ultrasound of the ocular circulation in patients with systemic lupus erythematosus identifies altered microcirculatory haemodynamics

We assessed whether quantitative analysis of Doppler flow velocity waveforms is able to identify subclinical microvascular abnormalities in SLE and whether eigenvector analysis can detect changes not detectable using the resistive index (RI). Fifty-four SLE patients with no conventional cardiovascular risk factors, major organ involvement or retinopathy were compared to 32 controls. Flow velocity waveforms were obtained from the ophthalmic artery (OA), central retinal artery (CRA) and common carotid artery (CA). The waveforms were analysed using eigenvector decomposition and compared between groups at each arterial site. The RI was also determined. The RI was comparable between groups. In the OA and CRA, there were significant differences in the lower frequency sinusoidal components ( P < 0.05 for each component). No differences were apparent in the CA between groups. Eigenvector analysis of Doppler flow waveforms, recorded in proximity of the terminal vascular bed, identified altered ocular microvascular haemodynamics in SLE. Altered waveform structure could not be identified by changes in RI, the traditional measure of downstream vascular resistance. This analytical approach to waveform analysis is more sensitive in detecting preclinical microvascular abnormalities in SLE. It may hold potential as a useful tool for assessing disease activity, response to treatment, and predicting future vascular complications.

The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods

BACKGROUND

In the past decade or more, the emphasis for reconstructing species phylogenies has moved from the analysis of a single gene to the analysis of multiple genes and even completed genomes. The simplest method of scaling up is to use familiar analysis methods on a larger scale and this is the most popular approach. However, duplications and losses of genes along with horizontal gene transfer (HGT) can lead to a situation where there is only an indirect relationship between gene and genome phylogenies. In this study we examine five widely-used approaches and their variants to see if indeed they are more-or-less saying the same thing. In particular, we focus on Conditioned Reconstruction as it is a method that is designed to work well even if HGT is present.

RESULTS

We confirm a previous suggestion that this method has a systematic bias. We show that no two methods produce the same results and most current methods of inferring genome phylogenies produce results that are significantly different to other methods.

CONCLUSION

We conclude that genome phylogenies need to be interpreted differently, depending on the method used to construct them.

Estrogen receptor α and β profiling in human breast cancer

BACKGROUND

The identification of a second estrogen receptor (ER-beta) has significant implications for therapeutic strategy in breast cancer management arising from the potential agonist effect of Tamoxifen at estrogen receptor sites and as such, antiestrogen therapy may be inappropriate in patients with a dominance of ER-beta.

METHODS

To determine the proportion of breast cancer patients who may be so at risk, we developed a novel multiplexed RT-PCR technique to establish the relative ER-alpha and ER-beta levels in 53 primary breast cancers, 11 normal breast tissues and six cell lines. We further assessed the prognostic significance of receptor status relative to the Nottingham prognostic index (NPI). The ER-alpha and ER-beta status was also determined by immunohistochemistry using previously published and 'in-house' scoring systems.

RESULTS

Using RT-PCR analysis, 46 tumours were hormone receptor positive (ER+) with 42 displaying ER-alpha predominance. Comparison with immunohistochemistry demonstrated 44/53 (ER-alpha) and 27/50 (ER-beta) concordance rates. There was no significant difference in the NPI between ER-alpha and ER-beta predominant cohorts or between ER+ and ER- cohorts.

CONCLUSION

This study identifies the existence of a subgroup of ER+ patients in whom Tamoxifen therapy may be inappropriate and has significant implications for adjuvant therapy of primary breast cancer.

Frequent loss of imprinting of PEG1/MEST in invasive breast cancer

The human PEG1 gene is a newly identified imprinted gene on 7q32. Genetic aberrations of this chromosomal region are often detected in invasive breast carcinomas. In this study, we show monoallelic PEG1 expression in normal breast tissue, indicating the presence of a functional imprint, and more importantly, we demonstrate loss of imprinting (LOI) in all of seven informative invasive breast carcinomas. In contrast to this, in one case of atypical ductal hyperplasia (ADH) found in residual breast, imprinting was maintained. This raises the possibility that aberrant imprinting of PEG1 may be involved in the progression from hyperplasia to invasive breast cancer.

Atropine penalisation versus occlusion as the primary treatment for amblyopia

AIMS/BACKGROUND

Pharmacological penalisation of non-amblyopic eyes is an infrequently used alternative to occlusion for treating amblyopia. The authors compared the efficacy of atropine penalisation and that of occlusion as a primary treatment for amblyopia.

METHODS

Thirty six newly diagnosed patients with amblyopia were allocated to two groups for treatment. Eighteen patients in each group were treated either with atropine penalisation (group A) or occlusion therapy (group P).

RESULTS

There was a statistically significant improvement in visual acuity in both groups treated. In group A improvement of the geometric mean visual acuity of the amblyopic eye was from 6/50 to 6/11 (p < 0.001). In group P improvement of the geometric mean visual acuity was from 6/60 to 6/19 (p < 0.001). In group A non-compliance with treatment was only 6% (2/18). Non-compliance in group P was 45% (8/18) at some stages of the treatment. Neither group produced an incidence of occlusion amblyopia.

CONCLUSIONS

In this study atropine penalisation has been shown to be as effective as occlusion therapy in the treatment of amblyopia. Patient acceptance of atropine penalisation was superior to that for occlusion therapy as was shown by the compliance rate. Atropine treatment was also advantageous in that compliance could be readily checked by inspection.

Prognostic significance of microvessel density in lymph node negative breast carcinoma

We evaluated the prognostic value of tumor angiogenesis in node negative breast cancer (NNBC). Paraffin-embedded tissues from 87 patients with NNBC were immunostained for factor VIII-related antigen, using one tissue block representative of the invasive edge of the tumor. Sections were scanned at low power to identify "hotspots" of angiogenesis. Microvessel (MV) counts were performed at x200 magnification, using a grid eyepiece graticule. Within each hot spot, three fields (area of field = 0.22 mm2) were counted and averaged. The highest average for a hot spot and the highest single field value was recorded for each case. Patients were stratified into low and high MV groups and their survival compared. There were no differences in disease-free or overall survival between the two groups whether the highest average or the highest single value was used. Microvessel counts did not correlate with other prognostic features, ie, grade, size, estrogen receptor status, c-erb B-2 or accumulated P53 status. Because of the difficulty in assessing angiogenesis that is heterogenous throughout tumors, MV counting may not be suitable for clinical use as a prognostic factor in NNBC. This problem could be addressed in a prospective study involving more extensive tumor sampling.

Argyrophylic nucleolar organiser regions (AgNOR's) as a prognostic indicator in breast carcinoma

Silver staining nucleolar organiser regions (AgNOR's) were determined in archival histological specimens of breast carcinoma. Representative samples from forty-eight female patients were counted manually for AgNOR's--median 3.85 (range 1.1-10.2 AgNOR's per cell). Taking the median value of 3.85 as a cutoff, the patients were divided into two groups: A = Those with AgNOR counts > 3.85; B = Patients with AgNOR counts < or = 3.85. The 5 year survival was 21% in group A and 85% in group B (p < 0.001). There was no significant correlation between AgNOR's and tumour size, lymph node status, tumour grade, menopausal status and oestrogen receptors. We conclude that nucleolar organiser regions may be useful as a prognostic indicator in breast carcinoma especially in patients in whom other prognostic information is unavailable.

Non-M CK--a practical measure of creatine kinase isoenzymes in cancer patients

The individual creatinine kinase (CK) isoenzymes CK-BB and CK-Macro II have previously been investigated as potential tumour markers. We believe there is a need for a system to measure those CK forms not usually present in serum. We have studied a CK-MB immunoinhibition kit which measures all residual CK activity following inactivation of M-subunit activity. In 162 patients with cancer we found no difference in grading (+ or -) between detailed isoenzyme studies and the simple non-M assay. In 33 samples with elevated non-M CK, detailed analysis showed BB alone (45%), Macro II alone (9%), or both (36%). Raised activities were mainly found in patients with small cell lung cancer (SCLC) (17/40; 43%) and GI Tumours (6/11; 55%). In patients with SCLC, elevated activities were associated with disseminated disease. Preliminary evidence indicates that Non-M CK may also be a simple means of monitoring initial treatment response.

c-erbB-2 oncoprotein expression in primary human tumors

Using a specific antiserum (21N) to the c-erbB-2 oncoprotein, a total of 405 primary malignant human tumors arising in the breast (n = 191), lung (n = 110), colon/rectum (n = 23), bladder (n = 48), prostate (n = 23), and skin (n = 10) were stained immunohistochemically to detect those tumors that over-expressed this putative transmembrane receptor. Malignant cells showed intense positivity for this oncoprotein in 17% of the breast carcinomas, 4% of the colorectal tumors, 2% of the bladder tumors, and 1% of the nonsmall cell lung carcinomas. No positive staining was evident in the prostate, skin, or small cell lung carcinomas. This study shows that over-expression of the c-erbB-2 oncoprotein is common in breast cancer but relatively rare in the other malignancies studied. In addition, this oncoprotein can be identified readily in routine paraffin-embedded tissue.