A proof of concept for a deep learning system that can aid embryologists in predicting blastocyst survival after thaw

The ability to understand whether embryos survive the thaw process is crucial to transferring competent embryos that can lead to pregnancy. The objective of this study was to develop a proof of concept deep learning model capable of assisting embryologist assessment of survival of thawed blastocysts prior to embryo transfer. A deep learning model was developed using 652 labeled time-lapse videos of freeze-thaw blastocysts. The model was evaluated against and along embryologists on a test set of 99 freeze-thaw blastocysts, using images obtained at 0.5 h increments from 0 to 3 h post-thaw. The model achieved AUCs of 0.869 (95% CI 0.789, 0.934) and 0.807 (95% CI 0.717, 0.886) and the embryologists achieved average AUCs of 0.829 (95% CI 0.747, 0.896) and 0.850 (95% CI 0.773, 0.908) at 2 h and 3 h, respectively. Combining embryologist predictions with model predictions resulted in a significant increase in AUC of 0.051 (95% CI 0.021, 0.083) at 2 h, and an equivalent increase in AUC of 0.010 (95% CI -0.018, 0.037) at 3 h. This study suggests that a deep learning model can predict in vitro blastocyst survival after thaw in aneuploid embryos. After correlation with clinical outcomes of transferred embryos, this model may help embryologists ascertain which embryos may have failed to survive the thaw process and increase the likelihood of pregnancy by preventing the transfer of non-viable embryos.

High-resolution genotyping of Lymphogranuloma Venereum (LGV) strains of Chlamydia trachomatis in London using multi-locus VNTR analysis-ompA genotyping (MLVA-ompA)

Background

Lymphogranuloma venereum (LGV) is caused by Chlamydia trachomatis strains with ompA genotypes L1 to L3. An LGV epidemic associated with the L2b genotype has emerged in the past few decades amongst men who have sex with men (MSM). C. trachomatis genotypes can be discriminated by outer membrane protein A gene (ompA) sequencing, however this method has limited resolution. This study employed a high-resolution genotyping method, namely, multi-locus tandem repeat (VNTR) analysis with ompA sequencing (MLVA-ompA), to assess the distribution of LGV MLVA-ompA genotypes amongst individuals attending genitourinary medicine (GUM) clinics in London.

Methods

Clinical specimens were collected from individuals attending eight London-based GUM clinics. Specimens that tested positive for C. trachomatis by commercial nucleic acid amplification test (NAAT) were confirmed as LGV by pmpH real-time PCR. LGV-positive DNA extracts were subsequently genotyped using MLVA-ompA.

Results

Two hundred and thirty DNA extracts were confirmed as LGV, and 162 (70%) yielded complete MLVA-ompA genotypes. Six LGV MLVA-ompA genotypes were identified: 1.9.2b-L2, 1.9.3b-L2b, 1.9.2b-L2b, 1.9.2b-L2b/D, 1.4a.2b-L2b, and 5.9.2b-L1. The following LGV ompA genotypes were identified (in descending order of abundance): L2, L2b, L2b/D, and L1. Eight ompA sequences with the hybrid L2b/D profile were detected. The hybrid sequence was identical to the ompA of a recombinant L2b/D strain detected in Portugal in 2017.

Conclusions

The L2 ompA genotype was found to predominate in the London study population. The study detected an unusual hybrid L2b/D ompA profile that was previously reported in Portugal. We recommend further monitoring and surveillance of LGV strains within the UK population.

The Nature and Extent of Plasmid Variation in Chlamydia trachomatis

Chlamydia trachomatis is an obligate intracellular pathogen of humans, causing both the sexually transmitted infection, chlamydia, and the most common cause of infectious blindness, trachoma. The majority of sequenced C. trachomatis clinical isolates carry a 7.5-Kb plasmid, and it is becoming increasingly evident that this is a key determinant of pathogenicity. The discovery of the Swedish New Variant and the more recent Finnish variant highlight the importance of understanding the natural extent of variation in the plasmid. In this study we analysed 524 plasmid sequences from publicly available whole-genome sequence data. Single nucleotide polymorphisms (SNP) in each of the eight coding sequences (CDS) were identified and analysed. There were 224 base positions out of a total 7550 bp that carried a SNP, which equates to a SNP rate of 2.97%, nearly three times what was previously calculated. After normalising for CDS size, CDS8 had the highest SNP rate at 3.97% (i.e., number of SNPs per total number of nucleotides), whilst CDS6 had the lowest at 1.94%. CDS5 had the highest total number of SNPs across the 524 sequences analysed (2267 SNPs), whereas CDS6 had the least SNPs with only 85 SNPs. Calculation of the genetic distances identified CDS6 as the least variable gene at the nucleotide level (d = 0.001), and CDS5 as the most variable (d = 0.007); however, at the amino acid level CDS2 was the least variable (d = 0.001), whilst CDS5 remained the most variable (d = 0.013). This study describes the largest in-depth analysis of the C. trachomatis plasmid to date, through the analysis of plasmid sequence data mined from whole genome sequences spanning 50 years and from a worldwide distribution, providing insights into the nature and extent of existing variation within the plasmid as well as guidance for the design of future diagnostic assays. This is crucial at a time when single-target diagnostic assays are failing to detect natural mutants, putting those infected at risk of a serious long-term and life-changing illness.

Development and Assessment of a Diagnostic DNA Oligonucleotide Microarray for Detection and Typing of Meningitis-Associated Bacterial Species

Meningitis is commonly caused by infection with a variety of bacterial or viral pathogens. Acute bacterial meningitis (ABM) can cause severe disease, which can progress rapidly to a critical life-threatening condition. Rapid diagnosis of ABM is critical, as this is most commonly associated with severe sequelae with associated high mortality and morbidity rates compared to viral meningitis, which is less severe and self-limiting. We have designed a microarray for detection and diagnosis of ABM. This has been validated using randomly amplified DNA targets (RADT), comparing buffers with or without formamide, in glass slide format or on the Alere ArrayTube^TM (Alere Technologies GmbH) microarray platform. Pathogen-specific signals were observed using purified bacterial nucleic acids and to a lesser extent using patient cerebral spinal fluid (CSF) samples, with some technical issues observed using RADT and glass slides. Repurposing the array onto the Alere ArrayTube^TM platform and using a targeted amplification system increased specific and reduced nonspecific hybridization signals using both pathogen nucleic and patient CSF DNA targets, better revealing pathogen-specific signals although sensitivity was still reduced in the latter. This diagnostic microarray is useful as a laboratory diagnostic tool for species and strain designation for ABM, rather than for primary diagnosis.

Duration of intravenous antibiotic therapy for children with acute osteomyelitis or septic arthritis: a feasibility study

BACKGROUND

There is little current consensus regarding the route or duration of antibiotic treatment for acute osteomyelitis (OM) and septic arthritis (SA) in children.

OBJECTIVE

To assess the overall feasibility and inform the design of a future randomised controlled trial (RCT) to reduce the duration of intravenous (i.v.) antibiotic use in paediatric OM and SA.

DESIGN

(1) A prospective service evaluation (cohort study) to determine the current disease spectrum and UK clinical practice in paediatric OM/SA; (2) a prospective cohort substudy to assess the use of targeted polymerase chain reaction (PCR) in diagnosing paediatric OM/SA; (3) a qualitative study to explore families' views and experiences of OM/SA; and (4) the development of a core outcome set via a systematic review of literature, Delphi clinician survey and stakeholder consensus meeting.

SETTING

Forty-four UK secondary and tertiary UK centres (service evaluation).

PARTICIPANTS

Children with OM/SA.

INTERVENTIONS

PCR diagnostics were compared with culture as standard of care. Semistructured interviews were used in the qualitative study.

RESULTS

Data were obtained on 313 cases of OM/SA, of which 218 (61.2%) were defined as simple disease and 95 (26.7%) were defined as complex disease. The epidemiology of paediatric OM/SA in this study was consistent with existing European data. Children who met oral switch criteria less than 7 days from starting i.v. antibiotics were less likely to experience treatment failure (9.6%) than children who met oral switch criteria after 7 days of i.v. therapy (16.1% when switch was between 1 and 2 weeks; 18.2% when switch was > 2 weeks). In 24 out of 32 simple cases (75%) and 8 out of 12 complex cases (67%) in which the targeted PCR was used, a pathogen was detected. The qualitative study demonstrated the importance to parents and children of consideration of short- and long-term outcomes meaningful to families themselves. The consensus meeting agreed on the following outcomes: rehospitalisation or recurrence of symptoms while on oral antibiotics, recurrence of infection, disability at follow-up, symptom free at 1 year, limb shortening or deformity, chronic OM or arthritis, amputation or fasciotomy, death, need for paediatric intensive care, and line infection. Oral switch criteria were identified, including resolution of fever for ≥ 48 hours, tolerating oral food and medicines, and pain improvement.

LIMITATIONS

Data were collected in a 6-month period, which might not have been representative, and follow-up data for long-term complications are limited.

CONCLUSIONS

A future RCT would need to recruit from all tertiary and most secondary UK hospitals. Clinicians have implemented early oral switch for selected patients with simple disease without formal clinical trial evidence of safety. However, the current criteria by which decisions to make the oral switch are made are not clearly established or evidence based.

FUTURE WORK

A RCT in simple OM and SA comparing shorter- or longer-course i.v. therapy is feasible in children randomised after oral switch criteria are met after 7 days of i.v. therapy, excluding children meeting oral switch criteria in the first week of i.v. therapy. This study design meets clinician preferences and addresses parental concerns not to randomise prior to oral switch criteria being met.

FUNDING

The National Institute for Health Research Health Technology Assessment programme.

The Chlamydia muridarum plasmid revisited : new insights into growth kinetics

Background: Research in chlamydial genetics is challenging because of its obligate intracellular developmental cycle. In vivo systems exist that allow studies of different aspects of basic biology of chlamydiae, the murine Chlamydia muridarum model is one of great importance and thus an essential research tool. C. muridarum carries a plasmid that has a role in virulence.  Our aim was to compare and contrast the C. muridarum plasmid-free phenotype with that of a chromosomally isogenic plasmid-bearing strain, through the inclusion phase of the developmental cycle.

Methods: We measured infectivity for plasmid bearing and plasmid-cured C. muridarum by inclusion forming assays in McCoy cells and in parallel bacterial chromosome replication by quantitative PCR, throughout the developmental cycle. In addition to these studies, we have carefully monitored chlamydial inclusion formation by confocal microscopy and transmission electron microscopy. A new E.coli/chlamydial shuttle vector (pNigg::GFP) was constructed using standard cloning technology and used to transform C. muridarum for further phenotypic studies.

Results: We have advanced the definition of the chlamydial phenotype away from the simple static observation of mature inclusions and redefined the C. muridarum plasmid-based phenotype on growth profile and inclusion morphology. Our observations on the growth properties of plasmid-cured C. muridarum challenge the established interpretations, especially with regard to inclusion growth kinetics. Introduction of the shuttle plasmid pNigg::GFP into plasmid-cured C. muridarum restored the wild-type plasmid-bearing phenotype and confirmed that loss of the plasmid was the sole cause for the changes in growth and chromosomal replication.

Conclusions: Accurate growth curves and sampling at multiple time points throughout the developmental cycle is necessary to define plasmid phenotypes.  There are subtle but important (previously unnoticed) differences in the overall growth profile of plasmid-bearing and plasmid-free C. muridarum.  We have proven that the differences described are solely due to the plasmid pNigg.

GW170817: Observation of Gravitational Waves from a Binary Neutron Star Inspiral

On August 17, 2017 at 12∶41:04 UTC the Advanced LIGO and Advanced Virgo gravitational-wave detectors made their first observation of a binary neutron star inspiral. The signal, GW170817, was detected with a combined signal-to-noise ratio of 32.4 and a false-alarm-rate estimate of less than one per 8.0×10^{4}  years. We infer the component masses of the binary to be between 0.86 and 2.26  M_{⊙}, in agreement with masses of known neutron stars. Restricting the component spins to the range inferred in binary neutron stars, we find the component masses to be in the range 1.17-1.60  M_{⊙}, with the total mass of the system 2.74_{-0.01}^{+0.04}M_{⊙}. The source was localized within a sky region of 28  deg^{2} (90% probability) and had a luminosity distance of 40_{-14}^{+8}  Mpc, the closest and most precisely localized gravitational-wave signal yet. The association with the γ-ray burst GRB 170817A, detected by Fermi-GBM 1.7 s after the coalescence, corroborates the hypothesis of a neutron star merger and provides the first direct evidence of a link between these mergers and short γ-ray bursts. Subsequent identification of transient counterparts across the electromagnetic spectrum in the same location further supports the interpretation of this event as a neutron star merger. This unprecedented joint gravitational and electromagnetic observation provides insight into astrophysics, dense matter, gravitation, and cosmology.

GW170814: A Three-Detector Observation of Gravitational Waves from a Binary Black Hole Coalescence

On August 14, 2017 at 10∶30:43 UTC, the Advanced Virgo detector and the two Advanced LIGO detectors coherently observed a transient gravitational-wave signal produced by the coalescence of two stellar mass black holes, with a false-alarm rate of ≲1 in 27 000 years. The signal was observed with a three-detector network matched-filter signal-to-noise ratio of 18. The inferred masses of the initial black holes are 30.5_{-3.0}^{+5.7}M_{⊙} and 25.3_{-4.2}^{+2.8}M_{⊙} (at the 90% credible level). The luminosity distance of the source is 540_{-210}^{+130}  Mpc, corresponding to a redshift of z=0.11_{-0.04}^{+0.03}. A network of three detectors improves the sky localization of the source, reducing the area of the 90% credible region from 1160   deg^{2} using only the two LIGO detectors to 60  deg^{2} using all three detectors. For the first time, we can test the nature of gravitational-wave polarizations from the antenna response of the LIGO-Virgo network, thus enabling a new class of phenomenological tests of gravity.

Detailed molecular epidemiology of Chlamydia trachomatis in the population of Southampton attending the genitourinary medicine clinic in 2012-13 reveals the presence of long established genotypes and transitory sexual networks

Chlamydia trachomatis is the most common sexually transmitted infection (STI) in England. Our objective was to perform a detailed survey of the molecular epidemiology of C. trachomatis in the population of Southampton UK attending the genitourinary medicine clinic (GUM) to seek evidence of sexual network activity. Our hypothesis was that certain genotypes can be associated with specific demographic determinants. 380 positive samples were collected from 375 C. trachomatis positive GUM attendees out of the 3118 who consented to be part of the survey. 302 of the positive samples were fully genotyped. All six of the predominant genotypes possessed ompA locus type E. One ward of Southampton known to contain a large proportion of students had a different profile of genotypes compared to other areas of the city. Some genotypes appeared embedded in the city population whilst others appeared transient. Predominant circulating genotypes remain stable within a city population whereas others are sporadic. Sexual networks could be inferred but not conclusively identified using the data from this survey.

Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion

Chlamydia trachomatis is the world's most prevalent bacterial sexually transmitted infection and leading infectious cause of blindness, yet it is one of the least understood human pathogens, in part due to the difficulties of in vitro culturing and the lack of available tools for genetic manipulation. Genome sequencing has reinvigorated this field, shedding light on the contemporary history of this pathogen. Here, we analyze 563 full genomes, 455 of which are novel, to show that the history of the species comprises two phases, and conclude that the currently circulating lineages are the result of evolution in different genomic ecotypes. Temporal analysis indicates these lineages have recently expanded in the space of thousands of years, rather than the millions of years as previously thought, a finding that dramatically changes our understanding of this pathogen's history. Finally, at a time when almost every pathogen is becoming increasingly resistant to antimicrobials, we show that there is no evidence of circulating genomic resistance in C. trachomatis.

Development and evaluation of an enzyme-linked immunosorbent assay for the detection of antibodies to a common urogenital derivative of Chlamydia trachomatis plasmid-encoded PGP3

BACKGROUND

Urogenital infection with Chlamydia trachomatis is the most commonly diagnosed sexually transmitted infection in the developed world. Accurate measurement and therefore understanding the seroprevalence of urogenital C. trachomatis infections requires a rigorously optimised and validated ELISA. Previous ELISAs based on the C. trachomatis plasmid-encoded protein, PGP3, have been described but lack standardisation and critical controls or use a less common PGP3 as the capture antigen.

METHODOLOGY/PRINCIPAL FINDINGS

A sensitive and specific indirect ELISA was developed based on recombinant PGP3 derived from a urogenital strain of C. trachomatis, serovar E (pSW2), using a rigorous validation protocol. Serum samples were collected from 166 genitourinary medicine (GUM) clinic patients diagnosed as positive or negative for urogenital C. trachomatis infection by nucleic acid amplification testing (NAATs). Overall sensitivity and specificity compared to NAATs was 68.18% and 98.0%, respectively. Sensitivities for female and male samples were 71.93% and 64.15%, respectively. Comparison of samples from these patients diagnosed positive for C. trachomatis by NAAT and patients diagnosed negative by NAAT revealed statistical significance (p≤0.0001).

CONCLUSIONS

We have developed and validated a sensitive and specific ELISA to detect anti-PGP3 antibodies as an indicator of past and current infection to C. trachomatis using PGP3 from a common urogenital strain. It is anticipated that this assay will be used for seroepidemiological analysis of urogenital C. trachomatis in populations.

Highly diverse MLVA-ompA genotypes of rectal Chlamydia trachomatis among men who have sex with men in Brighton, UK and evidence for an HIV-related sexual network

OBJECTIVES

In this prospective study, we aimed to determine the distribution of genotypes by multilocus variable number tandem repeat (VNTR) analysis plus analysis of the ompA gene (MLVA-ompA) of rectal Chlamydia trachomatis among men who have sex with men (MSM) attending Brighton Genitourinary Medicine (GUM) Clinic and to examine any correlations with clinical variables, including HIV status, and to isolate rectal C. trachomatis cultures maximising the possibility of obtaining complete genotyping data.

METHODS

Samples were assigned genotypes by PCR and sequencing of the markers of the MLVA-ompA genotyping system. Rectal C. trachomatis was isolated in cell culture using McCoy cells. Data regarding demographics, HIV status, rectal symptoms and history of sexually transmitted infections, including C. trachomatis, were collected.

RESULTS

1809 MSM attending the clinic between October 2011 and January 2013 took part in the study, 112 (6.2%) of whom had rectal samples that tested positive for C. trachomatis. 85/112 (75.9%) C. trachomatis-positive rectal samples were assigned 66 different genotypes. Two distinct genotype subclusters were identified: subcluster 1 consisted of more HIV-negative men than subcluster 2 (p=0.025), and the MLVA-ompA genotypes in these subclusters reflected this. Isolates were successfully cultured from 37 of the 112 specimens, from which 27 otherwise unobtainable (from direct PCR) MLVA-ompA genotypes were gained.

CONCLUSIONS

The most prevalent genotypes were G, E and D representing some overlap with the heterosexual distribution in UK. Subcluster 1 consisted of more 'heterosexual genotypes' and significantly more HIV-negative men than subcluster 2, associated with 'MSM genotypes'. There was a higher diversity of C. trachomatis strains among MSM in Brighton than observed in other cities.

Rapid detection of diagnostic targets using isothermal amplification and HyBeacon probes--a homogenous system for sequence-specific detection

Isothermal amplification is a rapid, simple alternative to PCR, with amplification commonly detected using fluorescently labelled oligonucleotide probes, intercalating dyes or increased turbidity as a result of magnesium pyrophosphate generation. SNP identification is possible but requires either allele-specific primers or multiple dye-labelled probes, but further downstream processing is often required for allelic identification. Here we demonstrate that modification of common isothermal amplification methods by the addition of HyBeacon probes permits homogeneous sequence detection and discrimination by melting or annealing curve analysis. Furthermore, we demonstrate that isothermal amplification and sequence discrimination is possible directly from a crude sample such as an expressed buccal swab.

Ascitic microbiota composition is correlated with clinical severity in cirrhosis with portal hypertension

Identification of pathogenic bacteria in ascites correlates with poor clinical outcomes. Ascites samples are commonly reported culture-negative, even where frank infection is indicated. Culture-independent methods have previously reported bacterial DNA in ascites, however, whether this represents viable bacterial populations has not been determined. We report the first application of 16S rRNA gene pyrosequencing and quantitative PCR in conjunction with propidium monoazide sample treatment to characterise the viable bacterial composition of ascites. Twenty five cirrhotic patients undergoing paracentesis provided ascites. Samples were treated with propidium monoazide to exclude non-viable bacterial DNA. Total bacterial load was quantified by 16S rRNA Q-PCR with species identity and relative abundance determined by 16S rRNA gene pyrosequencing. Correlation of molecular microbiology data with clinical measures and diagnostic microbiology was performed. Viable bacterial signal was obtained in 84% of ascites samples, both by Q-PCR and pyrosequencing. Approximately 190,000 ribosomal pyrosequences were obtained, representing 236 species, including both gut and non gut-associated species. Substantial variation in the species detected was observed between patients. Statistically significant relationships were identified between the bacterial community similarity and clinical measures, including ascitic polymorphonuclear leukocyte count and Child-Pugh class. Viable bacteria are present in the ascites of a majority of patients with cirrhosis including those with no clinical signs of infection. Microbiota composition significantly correlates with clinical measures. Entry of bacteria into ascites is unlikely to be limited to translocation from the gut, raising fundamental questions about the processes that underlie the development of spontaneous bacterial peritonitis.

Staphylococcus aureus small-colony variants are independently associated with worse lung disease in children with cystic fibrosis

BACKGROUND

Cystic fibrosis (CF) lung disease is associated with diverse bacteria chronically infecting the airways. Slow-growing, antibiotic-resistant mutants of Staphylococcus aureus known as small-colony variants (SCVs) have been isolated from respiratory secretions from European adults and children with CF lung disease using specific but infrequently used culture techniques. Staphylococcus aureus SCVs can be selected either by exposure to specific antibiotics or by growth with another CF pathogen, Pseudomonas aeruginosa. We sought to determine the prevalence, clinical significance, and likely mechanisms of selection of S. aureus SCVs among a US cohort of children with CF.

METHODS

We performed a 2-year study of 100 children with CF using culture techniques sensitive for S. aureus SCVs, and evaluated associations with clinical characteristics using multivariable regression models.

RESULTS

Staphylococcus aureus SCV infection was detected among 24% of participants and was significantly associated with a greater drop in lung function during the study (P = .007, adjusted for age and lung function at enrollment). This association persisted after adjusting for infection with other known CF pathogens, including P. aeruginosa and methicillin-resistant S. aureus. Evidence indicated that S. aureus SCVs were likely selected in vivo by treatment with the antibiotic trimethoprim-sulfamethoxazole and possibly by coinfection with P. aeruginosa.

CONCLUSIONS

Infection with SCV S. aureus was independently associated with worse CF respiratory outcomes in this pediatric cohort. As many clinical microbiology laboratories do not specifically detect S. aureus SCVs, validation and extension of these findings would require widespread changes in the usual laboratory and clinical approaches to these bacteria.

Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture

The use of whole-genome sequencing as a tool for the study of infectious bacteria is of growing clinical interest. Chlamydia trachomatis is responsible for sexually transmitted infections and the blinding disease trachoma, which affect hundreds of millions of people worldwide. Recombination is widespread within the genome of C. trachomatis, thus whole-genome sequencing is necessary to understand the evolution, diversity, and epidemiology of this pathogen. Culture of C. trachomatis has, until now, been a prerequisite to obtain DNA for whole-genome sequencing; however, as C. trachomatis is an obligate intracellular pathogen, this procedure is technically demanding and time consuming. Discarded clinical samples represent a large resource for sequencing the genomes of pathogens, yet clinical swabs frequently contain very low levels of C. trachomatis DNA and large amounts of contaminating microbial and human DNA. To determine whether it is possible to obtain whole-genome sequences from bacteria without the need for culture, we have devised an approach that combines immunomagnetic separation (IMS) for targeted bacterial enrichment with multiple displacement amplification (MDA) for whole-genome amplification. Using IMS-MDA in conjunction with high-throughput multiplexed Illumina sequencing, we have produced the first whole bacterial genome sequences direct from clinical samples. We also show that this method can be used to generate genome data from nonviable archived samples. This method will prove a useful tool in answering questions relating to the biology of many difficult-to-culture or fastidious bacteria of clinical concern.

Guidance on the development and validation of diagnostic tests that depend on nucleic acid amplification and detection

In order to comply with national and international clinical laboratory accreditation standards (e.g. the ISO 15189, Clinical Pathology Accreditation standards) and with the joint code of practice for research, there must be a method of assessing that test methods are "fit for purpose". This document gives guidance on development and describes how a validation file is produced. A test method may be a commercial kit, an in-house assay or reagent or a set of reagents bought separately and used to prepare an in house assay. A validation file is needed for both current and new test procedures. The file may refer to data recorded in workbooks, papers and reports. Modifications to assays (including commercially available assays) necessitate either an update to the validation file or creation of a new file. This paper is intended to provide a generic framework for in-house assay development and validation of new nucleic acid amplification assays including real-time polymerase chain reaction (PCR).

Nasal self-swabbing for estimating the prevalence of Staphylococcus aureus in the community

Staphylococcus aureus remains a significant cause of morbidity and mortality and, therefore, a burden on healthcare systems. Our aim was to estimate the current rate of nasal S. aureus carriage in the general population and to determine the feasibility of nasal self-swabbing as a means of detection. Two thousand people (1200 adults and 800 children) from a single NHS general practice in Southampton, UK, were randomly selected from a general practice age sex register, stratified by age and sex, and invited to undertake nasal self-swabbing in their own home. Overall, 362 (32.5%) swabs from adults and 168 (22%) from children were returned. Responses were greater for adults and those of increased age, female gender and decreasing socio-economic deprivation. The overall estimated practice carriage rate of S. aureus directly standardized for age sex was 28% [95% confidence interval (CI) 26.1-30.2%]. Carriage of meticillin-susceptible S. aureus was 27% (95% CI 26.1-30.2%), whilst that of meticillin-resistant S. aureus was 1.9% (95% CI 0.7-3.1%). Although nasal self-swabbing rates were relatively low, they are comparable to other studies and may allow large population-based carriage studies to be undertaken at relatively low cost. Importantly, this study updates prevalence data for S. aureus carriage in the community.

Long-term cultivation-independent microbial diversity analysis demonstrates that bacterial communities infecting the adult cystic fibrosis lung show stability and resilience

BACKGROUND

Culture-independent analysis of the respiratory secretions of people with cystic fibrosis (CF) has identified many bacterial species not previously detected using culture in this context. However, little is known about their clinical significance or persistence in CF airways.

METHODS

The authors characterised the viable bacterial communities in the sputum collected from 14 patients at monthly intervals over 1 year using a molecular community profiling technique-terminal restriction fragment length polymorphism. Clinical characteristics were also collected, including lung function and medications. Ecological community measures were determined for each sample. Microbial community change over time within subjects was defined using ecological analytical tools, and these measures were compared between subjects and to clinical features.

RESULTS

Bacterial communities were stable within subjects over time but varied between subjects, despite similarities in clinical course. Antibiotic therapy temporarily perturbed these communities which generally returned to pretreatment configurations within 1 month. Species usually considered CF pathogens and those not previously regarded as such exhibited similar patterns of persistence. Less diverse sputum bacterial communities were correlated to lung disease severity and relative abundance of Pseudomonas aeruginosa.

CONCLUSION

Whilst not true in all cases, the microbial communities that chronically infect the airways of patients with CF can vary little over a year despite antibiotic perturbation. The species present tended to vary more between than within subjects, suggesting that each CF airway infection is unique, with relatively stable and resilient bacterial communities. The inverse relationship between community richness and disease severity is similar to findings reported in other mucosal infections.

Genotyping markers used for multi locus VNTR analysis with ompA (MLVA-ompA) and multi sequence typing (MST) retain stability in Chlamydia trachomatis

We aimed to evaluate the stability of the Chlamydia trachomatis multi locus VNTR analysis (MLVA-ompA) and multi sequence typing (MST) systems through multiple passages in tissue culture. Firstly, we analyzed the stability of these markers through adaptation of C. trachomatis to tissue culture and secondly, we examined the stability of a four-locus MLVA-ompA and a five-locus MST system after multiple passages in tissue culture. Marker sequences were monitored through successive chlamydial developmental cycles to evaluate the stability of the individual DNA markers through many bacterial divisions and this, in turn, informed us of the usefulness of using such typing systems for short and long-term molecular epidemiology. Southampton genitourinary medicine (GUM) clinic isolates from endocervical swabs collected from C. trachomatis positive women were passaged through tissue culture. MLVA-ompA typing was applied to primary swab samples and to the same samples after C. trachomatis had been passaged through cell culture (eight passages). Sequence data from time-zero and passage-eight isolates were aligned with reference sequences to determine the stability of the markers. The Swedish new variant (nvCT) underwent 72 passages in cell culture and the markers of the two schemes were similarly analyzed. Analysis of genetic markers of the MLVA-ompA typing system before and after the isolates were introduced to tissue culture showed no change in the dominant sequence. The nvCT that had been passaged 72 times over the duration of a year also showed no variation in the dominant sequence for both the genotyping schemes. MLVA-ompA and MST markers are stable upon adaptation of C. trachomatis to tissue culture following isolation of strains from primary endocervical swab samples. These markers remain stable throughout multiple rounds of cell-division in tissue culture, concomitant with the incubation period and appearance of symptoms normally associated with host-infection. Both genotyping schemes are, therefore, suitable for epidemiology of C. trachomatis.

Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

Chlamydia trachomatis is responsible for both trachoma and sexually transmitted infections causing substantial morbidity and economic cost globally. Despite this, our knowledge of its population and evolutionary genetics is limited. Here we present a detailed whole genome phylogeny from representative strains of both trachoma and lymphogranuloma venereum (LGV) biovars from temporally and geographically diverse sources. Our analysis demonstrates that predicting phylogenetic structure using the ompA gene, traditionally used to classify Chlamydia, is misleading because extensive recombination in this region masks true relationships. We show that in many instances ompA is a chimera that can be exchanged in part or whole, both within and between biovars. We also provide evidence for exchange of, and recombination within, the cryptic plasmid, another important diagnostic target. We have used our phylogenetic framework to show how genetic exchange has manifested itself in ocular, urogenital and LGV C. trachomatis strains, including the epidemic LGV serotype L2b.

Intestinal metastasis from primary epidermoid anal carcinoma in a 34 year old male presented with acute bowel obstruction

Squamous cell carcinoma (SCC) of the anal canal is a rare condition comprising only 2–4% of all cancers of the colon, rectum and anus. The most common sites of metastases are liver and lung.

We report a case of 34-year-old male, who presented with diarrhoeal illness and an acutely tender protruding anal lesion initially thought to be thrombosed external hemorrhoid. Examination under anaesthesia revealed a hard and fixed mass at the level of dentate line, which was biopsied. On histopathological examination, it was confirmed as primary moderately differentiated keratinising squamous cell carcinoma. Despite initial response to concomitant chemo-radiation, 4 months later, the patient presented with large bowel obstruction. On laparotomy, a large mass involving the terminal ileum and caecum was identified. Histopathological examination revealed metastatic spread from primary anal lesion. To the best of our knowledge, this is the first reported case of a squamous cell carcinoma of anus with bowel metastasis.

Does bacterial density in cystic fibrosis sputum increase prior to pulmonary exacerbation?

BACKGROUND

Cystic Fibrosis (CF) lung disease is characterised by an inexorable decline in lung function, punctuated by periods of symptomatic worsening known as pulmonary exacerbations (referred to here as CFPE). Despite their clinical significance, the cause of CFPE remains undetermined. It has been suggested that an increase in bacterial density may be a trigger, although this has not been shown empirically.

METHODS

Here, a previously validated quantitative PCR-based approach was used to assess numbers of Pseudomonas aeruginosa and of total bacteria in respiratory secretions from patients during the period leading up to CFPE. Sputum samples collected from 12 adult CF patients were selected retrospectively to fall approximately 21, 14, 7 and 0 days prior to CFPE diagnosis. In addition, the relationships between clinical parameters (FEV(1), temperature and patient reported outcome measures) and microbiological data were investigated.

RESULTS

No significant changes either in total bacterial or P. aeruginosa numbers were identified prior to CFPE. Of all the correlations tested, only temperature showed a significant correlation with total bacterial numbers in the period leading to CFPE.

CONCLUSIONS

These findings strongly suggest that CFPE do not generally result from increased bacterial density within the airways. Instead, data presented here are consistent with alternative models of pulmonary exacerbation.

The exclusion of dead bacterial cells is essential for accurate molecular analysis of clinical samples

The DNA-based techniques used to detect bacteria in clinical samples are unable to discriminate between live bacteria, dead bacteria, and extracellular DNA. This failure to limit analysis to viable bacterial cells represents a significant problem, leading to false-positive results, as well as a failure to resolve the impact of antimicrobial therapy. The use of propidium monoazide treatment significantly reduces the contribution of dead cells and extracellular DNA to such culture-independent analyses. Here, the increased ability to resolve the impact of antibiotic therapy on Pseudomonas aeruginosa load in cystic fibrosis respiratory samples reveals statistically significant changes that would otherwise go undetected.

Characterization of community and hospital Staphylococcus aureus isolates in Southampton, UK

Staphylococcus aureus infections are a burden to healthcare systems. There remains a lack of understanding on the relative contributions of S. aureus infection in the healthcare and community settings. In this study, 59 S. aureus isolates were selected for molecular analysis. The mobile variant staphylococcal cassette chromosome mec type IV was present in both healthcare-associated meticillin-resistant S. aureus (HA-MRSA) and community-associated MRSA (CA-MRSA), as was the Panton–Valentine leukocidin gene. PFGE identified 24 distinct clonal groups whilst multi-locus sequence typing identified 26 different sequence types, including four with new combinations of alleles. This is the first time, to our knowledge, that a selection of CA and HA MSSA and MRSA strains have been subjected to molecular analysis and comparison in the UK. Definitions for CA-MRSA need further debate as the movement of strains between healthcare and community settings is confounding the use of epidemiological definitions.

One-year outcomes of radiofrequency ablation of incompetent perforator veins using the radiofrequency stylet device

Objectives

Early success treating incompetent perforator veins (IPVs) with radiofrequency ablation (RFA) and the trend to move varicose vein surgery into a walk-in walk-out service led to the design of a specific device enabling RFA of IPVs using local anaesthesia (ClosureRFS™ stylet). Our aim was to assess one-year outcomes of a clinical series of patients undergoing treatment with this device. Truncal reflux, where present, was treated initially, and RFA of IPVs was performed as a secondary procedure.

Method

Duplex ultrasound examinations were performed and the presence of IPVs documented. Results were compared with preoperative scans. IPVs were classified as closed, not closed/reopened or de novo.

Results

Of the 75 patients invited for follow-up, 53 attended at a median time of 14 months (range 11–25). Sixty-seven limbs were analysed (M:F 1:2.1, median age 62, range 25–81). Of the 124 treated IPVs, 101 were closed (82%). Clinical, aetiological, anatomical and pathological clinical score was improved in 49.3% limbs. IPV closure was reduced in patients with recurrent varicose veins compared with primary varicose veins (72.3% versus 87%, P = 0.056).

Conclusion

These results demonstrate the radiofrequency stylet device to be an effective treatment for IPVs.

Characterisation of bacteria in ascites--reporting the potential of culture-independent, molecular analysis

Spontaneous bacterial peritonitis (SBP) is a severe complication of liver disease. A significant proportion of patients have culture-negative ascites, despite having similar signs, symptoms and mortality to those with SBP. Therefore, empirical antibiotic treatment for infection is often started without knowledge of the causative organisms. Here, we investigated the potential of molecular techniques to provide rapid and accurate characterisation of the bacteria present in ascitic fluid. Ascites samples were obtained from 29 cirrhotic patients undergoing clinically indicated therapeutic paracentesis. Bacterial content was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis, quantitative polymerase chain reaction (PCR) and 16S ribosomal clone sequence analysis. Bacterial signal was detected in all samples, compared to three out of ten using standard methods. Bacterial loads ranged from 5.5 x 10(2) to 5.4 x 10(7) cfu/ml, with a mean value of 1.9 x 10(6) cfu/ml (standard deviation +/- 9.6 x 10(6) cfu/ml). In all but one instance, bacterial species identified by culture were also confirmed by molecular analyses. Preliminary data presented here suggests that culture-independent, molecular analyses could provide rapid characterisation of the bacterial content of ascites fluid, providing a basis for the investigation of SBP development and allowing early and targeted antibiotic intervention.

Pelvic vein reflux in female patients with varicose veins: comparison of incidence between a specialist private vein clinic and the vascular department of a National Health Service district general hospital

Objectives

Mounting evidence suggests that pelvic vein reflux is an important contributing factor to recurrent varicose veins. We compared the incidence in our specialist private unit (Unit A) with that of a District General Hospital (Unit B).

Methods

Results of all female patient lower limb duplex ultrasound (LLDUS) and transvaginal pelvic ultrasound (TVUS) scans performed over a one-year period were retrospectively reviewed. Patients with refluxing veins emanating from the abdomen or pelvis on LLDUS (non-saphenous reflux) routinely proceeded to TVUS in Unit A.

Results

In Unit A, non-saphenous reflux on LLDUS was present in 90–462 female patients (19.5%). In 81.1% of these, TVUS confirmed reflux in truncal pelvic veins (incidence 15.8%). In Unit B, non-saphenous reflux was present in 60–279 female patients (21.5%).

Conclusion

One in five women presenting with varicose veins have reflux of non-saphenous origin. This is the case in specialist and non-specialist units. One in six has associated pelvic vein reflux.

Five-year results of incompetent perforator vein closure using TRans-Luminal Occlusion of Perforator

Objective

To audit the five-year outcome of the TRLOP technique as indicated by the rate of IPV closure on duplex ultrasound (DUS).

Methods

Patients underwent DUS five years post-TRLOP. Experienced vascular technologists documented the presence of IPVs using a two co-ordinate system, blinded to previous results. Results were then compared with preoperative scans. IPVs were classified as: closed; not closed/reopened; or de novo. Closed IPVs were defined as the absence of any IPV at or within 5 cm of a previous IPV in the vertical and horizontal plane. Any IPVs found outside the delineated area were defined as de novo IPVs.

Results

Of 67 patients invited, 37 attended DUS (55% participation rate; men to women ratio of 14:23, age 40–84; mean 64). Preoperative clinical, aetiological, anatomical and pathological classification: C2, 36.2%; C3, 27.6%; C4, 34.5%; C6, 1.7%. From 125 IPVs analysed, 101 were closed (81%), 24 were not closed/reopened (19%) and 14 de novo IPVs were found.

Discussion

Despite these results representing our learning curve for the procedure, we found TRLOP to be an effective treatment for IPVs. The closure rates described are comparable with the published clinical series data for subfascial endoscopic perforator surgery.

MECP2 mutations in Serbian Rett syndrome patients

BACKGROUND

Rett syndrome is a severe neurodevelopmental X-linked dominant disorder affecting 1/15,000 girls worldwide. Eight years ago, the MECP2 gene was associated with the devastating clinical features observed in Rett syndrome patients.

OBJECTIVES

To investigate the spectrum and the frequency of MECP2 mutations in Serbian Rett syndrome patients.

PATIENTS AND METHODS

We screened the MECP2 coding region by conventional mutational screening (single-strand conformation polymorphism/sequencing) in 24 patients of Serbian origin and in their 41 unaffected family members. In search for gene dosage alterations in seemingly mutation-negative girls, we developed a new, specific quantitative PCR method.

RESULTS

Nineteen patients (79%) carried MECP2 mutations, five of which were novel (one nonsense mutation, one duplication and three deletions). Fourteen previously described disease-causing sequence changes and one polymorphism were also detected. Detailed case reports are given for the carriers of the novel mutations. Large MECP2 rearrangements cause Rett syndrome in a significant number of girls without 'classic' mutations in this gene. Therefore, we developed a specific quantitative PCR method, covering MECP2 exons 3 and 4, which previously has not been used for screening. No dosage alterations of the two exons were found in the four tested mutation-negative girls.

CONCLUSIONS

This is the first genetic study of Rett syndrome in Serbian patients describing the MECP2 mutational and phenotypic spectrum in this population. Detailed clinical descriptions of this ethnically homogeneous patient population add to our knowledge of genotype/phenotype correlations in this severe condition.

Evaluation of BacLite Rapid MRSA, a rapid culture based screening test for the detection of ciprofloxacin and methicillin resistant S. aureus (MRSA) from screening swabs

Background

Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial pathogen worldwide. The need for accurate and rapid screening methods to detect MRSA carriers has been clearly established. The performance of a novel assay, BacLite Rapid MRSA (Acolyte Biomedica, UK) for the rapid detection (5 h) and identification of hospital associated ciprofloxacin resistant strains of MRSA directly from nasal swab specimens was compared to that obtained by culture on Mannitol salt agar containing Oxacillin (MSAO) after 48 h incubation.

Results

A total of 1382 nasal screening swabs were tested by multiple operators. The BacLite Rapid MRSA test detected 142 out of the 157 confirmed MRSA that were detected on MSAO giving a diagnostic sensitivity of 90.4, diagnostic specificity of 95.7% and a negative predictive value of 98.7%. Of the 15 false negatives obtained by the BacLite Rapid MRSA test, seven grew small amounts (< 10 colonies of MRSA) on the MSAO culture plate and five isolates were ciprofloxacin sensitive. However there were 13 confirmed BacLite MRSA positive samples, which were negative by the direct culture method, probably due to overgrowth on the MSAO plate. There were 53 false positive results obtained by the BacLite Rapid MRSA test at 5 h and 115 cases where MRSA colonies were tentatively identified on the MSAO plate when read at 48 h, and which subsequently proved not to be MRSA.

Conclusion

The Baclite MRSA test is easy to use and provides a similar level of sensitivity to conventional culture for the detection of nasal carriage of MRSA with the advantage that the results are obtained much more rapidly.

Young people of minority ethnic origin in England and early parenthood: views from young parents and service providers

The paper explores the phenomenon of early parenthood in minority ethnic communities in England. The data were collected using focus group interviews, in-depth semi-structured interviews and a telephone survey. The sample consisted of 139 participants (41 service providers, 10 grandmothers, 88 young parents). The findings map out the complexity and diversity of experience of early parenthood amongst young people of minority ethnic origin, not least the multiple attachments many experience in relation to their social groups, religious affiliations and the traditional patterns of parenting within their immediate and extended family. Both the young parents and professionals in this study constructed early parenthood in more positive terms than is currently portrayed in the contemporary policy. The findings are analysed and discussed in relation to ethnic identity, social inclusion and exclusion. We explore participants' attempts to counter negative 'deficit' models of early parenthood with reference to perspectives on youth, parenthood and contemporary strategic policy. In conclusion, we suggest an unambiguous focus on the reduction of pregnancy is not a credible message when teenage pregnancy is a social norm for a particular ethnic or cultural group. For young parents of Muslim faith in particular, teenage parenting within marriage is not necessarily considered a 'problem' or seen as a distinctive event. Most participants did not view early parenthood as a barrier to re-establishing career and educational aspirations. A wide diversity of experience amongst young parents is evidenced in the communities studied; this needs to be reflected more comprehensively both in UK policy and in support services.

Molecular diagnostics: future probe-based strategies

Nucleic acid amplification technologies (NAATs) represent powerful tools in clinical microbiology, particularly in areas where traditional culture-based methods alone prove insufficient. A notable advantage is in reducing the time from taking samples to reporting results. This, and the specificity and sensitivity imparted by NAATs, can help to improve patient care. Both thermal and isothermal NAATs have been adapted to aid diagnosis in clinical laboratories. Current molecular diagnostic assays are generally high-tech, and are expensive to buy and perform. Easy-to-use NAATs are beginning to appear, not only facilitating acceptable throughput in clinical laboratories, but also allowing tests to move out of the laboratory, closer to the point of care. Demand for simpler, miniaturized equipment and assays, and the trend toward personalized medicine, is leading towards the development of fully integrated automation and home-use kits. The integration of diverse disciplines, such as genomics, molecular biology, microelectromechanical systems, microfluidics, microfabrication, and organic chemistry, is behind the emerging DNA microarray technology. Development of DNA microchips allows the simultaneous detection of potentially thousands of target sequences, not only favoring high throughput, but also the potential for genotyping patient subsets with respect to their response to particular drug types (pharmakogenomics). It is envisaged that the future of probe-based technologies will see the development of fully integrated assays and devices suitable for nonskilled users.

Evaluation of an isothermal signal amplification method for rapid detection of methicillin-resistant Staphylococcus aureus from patient-screening swabs

A new molecular assay (CytAMP) utilizing isothermal signal-mediated amplification of RNA was evaluated for rapid detection of methicillin (oxacillin)-resistant Staphylococcus aureus (MRSA). The assay targeted the coa (coagulase) and mecA genes, thereby simultaneously identifying S. aureus and methicillin (oxacillin) resistance. Results were obtained in approximately 3.5 h as a color signal in 96-well microtiter plates. The detection limit was between 2 x 10(5) and 10(6) CFU/assay, equivalent to 4 x 10(6) to 2 x 10(7) CFU/ml in an overnight broth. This level of growth was obtained with an initial inoculum of 10 to 50 CFU. The CytAMP assay and a mecA-femB PCR assay both detected 113 MRSA strains among 396 clinical isolates of bacteria (CytAMP sensitivity and specificity were both 100% relative to those of PCR). Conventional culture detected 109 MRSA strains, but with 19 false-positive and 23 false-negative results relative to both molecular methods. Discrepancies were also observed for 100 enrichment broths containing MRSA screening swabs, with 11 broths culture negative but PCR positive. CytAMP and PCR were more in agreement, but six broths were CytAMP negative and PCR positive. Five of these contained 10(2) to 10(5) CFU/assay (below the CytAMP detection limit of 2 x 10(5) CFU/assay), and the sixth contained 10(6) CFU/assay. Overall, culture and CytAMP had similar sensitivities and specificities relative to those of PCR, but the CytAMP assay enabled swabs to be analyzed as a batch following overnight incubation in enrichment broth, with results reported before 12 noon the next day.

Practical implementation of adaptive optics in multiphoton microscopy

A dedicated two-photon microscope incorporating adaptive-optic correction of specimen-induced aberrations is presented. Wavefront alteration of the scanning laser beam was achieved by use of a micromachined deformable mirror. Post scan head implementation produces a compact module compatible with the Bio-Rad MRC-600 scan head. Automatic aberration correction using feedback from the multiphoton fluorescence intensity allowed the adaptive optic to extend the imaging depth attainable in both artificial and biological refractive-index mismatched samples. With a 1.3-NA, x40, Nikon oil immersion objective, the imaging depth in water was extended from approximately 3.4 to 46.2 microm with a resolution defined by a FWHM axial point-spread function of 1.25 microm.

Bipseudophakia: clinicopathological correlation of a dropped lens

PURPOSE

To examine postmortem human globes containing an anterior chamber and a posterior chamber intraocular lens (IOL).

SETTING

Center for Research on Ocular Therapeutics and Biodevices, Storm Eye Institute, Charleston, South Carolina, USA.

METHODS

The globes were sectioned at the equator, and the anterior and posterior segments were macroscopically examined. Gross photographs were taken using the Miyake-Apple posterior photographic technique. Histological sections were cut and stained with hematoxylin and eosin, periodic acid-Schiff, and Masson's trichrome.

RESULTS

Histopathological findings included a large Soemmering's ring, a tear in the posterior capsule, 1 haptic of the anterior chamber IOL displaced into the iridectomy, thin and atrophic corneal epithelium, separation of Bowman's layer and stroma by fibrovascular tissue, and atrophy of the retinal ganglion cell layer and nerve fiber layer.

CONCLUSION

In cases in which secondary IOL implantation is indicated, removing the dislocated IOL appears to be a reasonable choice.