A selected ion flow tube study of the reactions of gas-phase cations with PSCl3

A selected ion flow tube was used to investigate the positive ion chemistry of thiophosphoryl chloride, PSCl$_3$. Rate coefficients and ion product branching ratios have been determined at room temperature for reactions with nineteen cations ; H$_3$O$^+$, CF$_3^+$, CF$^+$, NO$^+$, NO$_2^+$, SF$_2^+$, SF$^+$, CF$_2^+$, O$_2^+$, H$_2$O$^+$, N$_2$O$^+$, O$^+$, CO$_2^+$, CO$^+$, N$^+$, N$_2^+$, Ar$^+$, F$^+$ and Ne$^+$ (in order of increasing recombination energy). Complementary data described in the previous paper have been obtained for this molecule via the observation of threshold photoelectron photoion coincidences. For ions whose recombination energies are in the range 10-22 eV, comparisons are made between the product ion branching rations of PSCl$_3$ from photoionisation and from ion-molecule reactions. In most instances, the data from the two experiments are well correlated, suggesting that long-range charge transfer is the dominant mechanism for these ion-molecule reactions ; the agreement is particularly good for the atomic ions Ar$^+$, F$^+$ and Ne$^+$. Some reactions (e.g. O$_2^+$ + PSCl$_3$), however, exhibit significant differences; short-range charge transfer must then be occurring following the formation of an ion-molecule complex. For ions whose recombination energies are less than 10 eV (i.e. H$_3$O$^+$, CF$_3^+$, CF$^+$ and NO$^+$), reactions can only occur via a chemical process in which bonds are broken and formed, because the recombination energy of the cation is less than the ionisation energy of PSCl$_3$

The use of high-throughput sequencing to investigate an outbreak of glycopeptide-resistant Enterococcus faecium with a novel quinupristin-dalfopristin resistance mechanism.

High-throughput sequencing (HTS) has successfully identified novel resistance genes in enterococci and determined clonal relatedness in outbreak analysis. We report the use of HTS to investigate two concurrent outbreaks of glycopeptide-resistant Enterococcus faecium (GRE) with an uncharacterised resistance mechanism to quinupristin-dalfopristin (QD).Seven QD-resistant and five QD-susceptible GRE isolates from a two-centre outbreak were studied. HTS was performed to identify genes or predicted proteins that were associated with the QD-resistant phenotype. MLST and SNP typing on HTS data was used to determine clonal relatedness.Comparative genomic analysis confirmed this GRE outbreak involved two distinct clones (ST80 and ST192). HTS confirmed the absence of known QD resistance genes, suggesting a novel mechanism was conferring resistance. Genomic analysis identified two significant genetic determinants with explanatory power for the high level of QD resistance in the ST80 QD-resistant clone: an additional 56aa leader sequence at the N-terminus of the lsaE gene and a transposon containing seven genes encoding proteins with possible drug or drug-target modification activities. However, HTS was unable to conclusively determine the QD resistance mechanism and did not reveal any genetic basis for QD resistance in the ST192 clone. This study highlights the usefulness of HTS in deciphering the degree of relatedness in two concurrent GRE outbreaks. Although HTS was able to reveal some genetic candidates for uncharacterised QD resistance, this study demonstrates the limitations of HTS as a tool for identifying putative determinants of resistance to QD

Factors associated with early resumption of condomless anal sex among men who have sex with men after rectal chlamydia treatment

Background: The resumption of sexual activity shortly after commencing treatment for sexually transmitted infections (STIs) is poorly described despite contributing to onward transmission. With azithromycin remaining an option for rectal Chlamydia trachomatis, resuming sex too early after treatment may contribute to antimicrobial resistance because of exposure of newly acquired STIs to subinhibitory concentrations. Methods: Clinical and sexual behavioral data were collected from men participating in a trial assessing treatment efficacy for rectal chlamydia. Data were collected at recruitment and weekly for 3 weeks after commencing treatment. Outcome measures were resumption of any sexual activity or condomless receptive anal sex within 1, 2, or 3 weeks after commencing treatment. Generalized linear regression was used to calculate adjusted risk ratios (aRR) to identify associated factors. Results: Almost 1 in 10 men (9.5%; 95% confidence interval [CI], 7.2–12.1) resumed condomless receptive anal sex within 1 week of commencing treatment. This was associated with current preexposure prophylaxis use (aRR, 3.4; 95% CI, 2.5–4.8]) and having 9 or more sexual partners in the last 3 months (aRR, 3.2; 95% CI, 1.6–5.0). Most men (75.0%; 95% CI, 71.3–78.5) resumed any sexual activity within 3 weeks; this was associated with a greater number of sexual partners (4–8 partners; aRR, 1.2; 95% CI, 1.1–1.5; ≥9 partners; aRR, 1.5; 95% CI, 1.3–1.7). Conclusions: Resuming condomless receptive anal sex early after treatment may facilitate onward transmission and promote antimicrobial resistance for STIs. Although azithromycin remains a treatment option, this analysis highlights the need for new health promotion messages regarding early resumption of sex and continued surveillance for antimicrobial resistance.Andrew Lau, Fabian Y.S. Kong, Christopher K. Fairley, David J. Templeton, Janaki Amin, Mark A. Boyd, Catriona Bradshaw, Marcus Y. Chen, Basil Donovan, Carole Khaw, David A. Lewis, Anna McNulty, David G. Regan, Mahesh Ratnayake, Jane S. Hocking (and on behalf of all RTS investigators

The ecology of the European badger (Meles meles) in Ireland: a review

peer-reviewedThe badger is an ecologically and economically important species. Detailed knowledge of aspects of the ecology of this animal in Ireland has only emerged through research over recent decades. Here, we review what is known about the species' Irish populations and compare these findings with populations in Britain and Europe. Like populations elsewhere, setts are preferentially constructed on south or southeast facing sloping ground in well-drained soil types. Unlike in Britain, Irish badger main setts are less complex and most commonly found in hedgerows. Badgers utilise many habitat types, but greater badger densities have been associated with landscapes with high proportions of pasture and broadleaf woodlands. Badgers in Ireland tend to have seasonally varied diets, with less dependence on earthworms than some other populations in northwest Europe. Recent research suggests that females exhibit later onset and timing of reproductive events, smaller litter sizes and lower loss of blastocysts than populations studied in Britain. Adult social groups in Ireland tend to be smaller than in Britain, though significantly larger than social groups from continental Europe. Although progress has been made in estimating the distribution and density of badger populations, national population estimates have varied widely in the Republic of Ireland. Future research should concentrate on filling gaps in our knowledge, including population models and predictive spatial modelling that will contribute to vaccine delivery, management and conservation strategies.Department of Agriculture, Fisheries and FoodTeagasc Walsh Fellowship Programm

Cohort Profile: the Born in Bradford multi-ethnic family cohort study

The Born in Bradford cohort study was established in 2007 to examine how genetic, nutritional, environmental, behavioural and social factors impact on health and development during childhood, and subsequently adult life in a deprived multi-ethnic population. Between 2007 and 2011, detailed information on socio-economic characteristics, ethnicity and family trees, lifestyle factors, environmental risk factors and physical and mental health has been collected from 12 453 women with 13 776 pregnancies (recruited at ∼28 weeks) and 3448 of their partners. Mothers were weighed and measured at recruitment, and infants have had detailed anthropometric assessment at birth and post-natally up to 2 years of age. Results of an oral glucose tolerance test and lipid profiles were obtained on the mothers during pregnancy at ∼28 weeks gestation, and pregnancy serum, plasma and urine samples have been stored. Cord blood samples have been obtained and stored and Deoxyribonucleic acid (DNA) extraction on 10 000 mother–offspring pairs is nearly completed. The study has a biobank of over 250 000 samples of maternal blood, DNA and urine, cord blood and DNA and paternal saliva. Details of how scientists can access these data are provided in this cohort profile

Emergence and global spread of epidemic healthcare-associated Clostridium difficile

Epidemic C. difficile (027/BI/NAP1) has rapidly emerged in the past decade as the leading cause of antibiotic-associated diarrhea worldwide. However, the key events in evolutionary history leading to its emergence and the subsequent patterns of global spread remain unknown. Here, we define the global population structure of C. difficile 027/BI/NAP1 using whole-genome sequencing and phylogenetic analysis. We show that two distinct epidemic lineages, FQR1 and FQR2, not one as previously thought, emerged in North America within a relatively short period after acquiring the same fluoroquinolone resistance-conferring mutation and a highly related conjugative transposon. The two epidemic lineages showed distinct patterns of global spread, and the FQR2 lineage spread more widely, leading to healthcare-associated outbreaks in the UK, continental Europe and Australia. Our analysis identifies key genetic changes linked to the rapid transcontinental dissemination of epidemic C. difficile 027/BI/NAP1 and highlights the routes by which it spreads through the global healthcare system