Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission

Background: Carbapenemase-producing Enterobacteriaceae (CPE), including KPC-producing Klebsiella pneumoniae (KPC-Kpn), are an increasing threat to patient safety. Objectives: To use WGS to investigate the extent and complexity of carbapenemase gene dissemination in a controlled KPC outbreak. Materials and methods: Enterobacteriaceae with reduced ertapenem susceptibility recovered from rectal screening swabs/clinical samples, during a 3 month KPC outbreak (2013–14), were investigated for carbapenemase production, antimicrobial susceptibility, variable-number-tandem-repeat profile and WGS [short-read (Illumina), long-read (MinION)]. Short-read sequences were used for MLST and plasmid/Tn4401 fingerprinting, and long-read sequence assemblies for plasmid identification. Phylogenetic analysis used IQTree followed by ClonalFrameML, and outbreak transmission dynamics were inferred using SCOTTI. Results: Twenty patients harboured KPC-positive isolates (6 infected, 14 colonized), and 23 distinct KPC-producing Enterobacteriaceae were identified. Four distinct KPC plasmids were characterized but of 20 KPC-Kpn (from six STs), 17 isolates shared a single pKpQIL-D2 KPC plasmid. All isolates had an identical transposon (Tn4401a), except one KPC-Kpn (ST661) with a single nucleotide variant. A sporadic case of KPC-Kpn (ST491) with Tn4401a-carrying pKpQILD2 plasmid was identified 10 months before the outbreak. This plasmid was later seen in two other species and other KPC-Kpn (ST14,ST661) including clonal spread of KPC-Kpn (ST661) from a symptomatic case to nine ward contacts. Conclusions: WGS of outbreak KPC isolates demonstrated blaKPC dissemination via horizontal transposition (Tn4401a), plasmid spread (pKpQIL-D2) and clonal spread (K. pneumoniae ST661). Despite rapid outbreak control, considerable dissemination of blaKPC still occurred among K. pneumoniae and other Enterobacteriaceae, emphasizing its high transmission potential and the need for enhanced control efforts

New insights on structure and stratigraphic interpretation for assessing the hydrocarbon potentiality of the offshore Nile Delta basin, Egypt

The study area lies around the petroleum provinces of the Egyptian Offshore Nile Delta basin. The existing exploration data are sparse, and any effort made on the strati-structural interpretation is challenging for exploratory drilling campaigns, even with meager well control. Keeping in view the issues and major challenges, the authors propose new methodologies, tools and new insights into the interpretation of the existing data and information, to make the study area more attractive for investors and detailed exploration studies. The published geological work existing within the vicinity of the study area is an added value to the new insights of current interpretation and knowledge acquisition. Pliocene–Pleistocene section is the main target in the study area, since it has quality reservoirs, holding commercial hydrocarbons. Pre-salt source rocks may have charged the reservoirs in the study area. Structural complexities and heterogeneities at target levels are likely to impact the seismic wavelet property intricacies and thus the data processing qualities. Post- and pre-salt tectonics in the northern part of Sinai, the Nile Cone, and how they affect the structural framework and the seismic interpretation work in the study area are described. For the purpose of understanding the combinational trapping mechanism, stratigraphic features and the structural geology are integrated using new tools and technologies. Several strati-structural plays are interpreted in the study area that support the detailed exploration campaigns, and the existing major hydrocarbon plays associated within shelf, slope and deep-marine geological events in nearby offshore regions. Diapir salt, rotated fault blocks and growth faults within syn-sediment systems are other plays to be investigated. The study is an effort of compiled work from many published sources, putting all ideas into a positive perspective and has better understanding of new opportunities, leads and prospects for investment purposes in the Nile Delta offshore basin

Parametric study of EEG sensitivity to phase noise during face processing

<b>Background: </b> The present paper examines the visual processing speed of complex objects, here faces, by mapping the relationship between object physical properties and single-trial brain responses. Measuring visual processing speed is challenging because uncontrolled physical differences that co-vary with object categories might affect brain measurements, thus biasing our speed estimates. Recently, we demonstrated that early event-related potential (ERP) differences between faces and objects are preserved even when images differ only in phase information, and amplitude spectra are equated across image categories. Here, we use a parametric design to study how early ERP to faces are shaped by phase information. Subjects performed a two-alternative force choice discrimination between two faces (Experiment 1) or textures (two control experiments). All stimuli had the same amplitude spectrum and were presented at 11 phase noise levels, varying from 0% to 100% in 10% increments, using a linear phase interpolation technique. Single-trial ERP data from each subject were analysed using a multiple linear regression model. <b>Results: </b> Our results show that sensitivity to phase noise in faces emerges progressively in a short time window between the P1 and the N170 ERP visual components. The sensitivity to phase noise starts at about 120–130 ms after stimulus onset and continues for another 25–40 ms. This result was robust both within and across subjects. A control experiment using pink noise textures, which had the same second-order statistics as the faces used in Experiment 1, demonstrated that the sensitivity to phase noise observed for faces cannot be explained by the presence of global image structure alone. A second control experiment used wavelet textures that were matched to the face stimuli in terms of second- and higher-order image statistics. Results from this experiment suggest that higher-order statistics of faces are necessary but not sufficient to obtain the sensitivity to phase noise function observed in response to faces. <b>Conclusion: </b> Our results constitute the first quantitative assessment of the time course of phase information processing by the human visual brain. We interpret our results in a framework that focuses on image statistics and single-trial analyses

Ipsilateral free semitendinosus tendon graft transfer for reconstruction of chronic tears of the Achilles tendon

<p>Abstract</p> <p>Background</p> <p>Many techniques have been developed for the reconstruction of the Achilles tendon in chronic tears. In presence of a large gap (greater than 6 centimetres), tendon augmentation is required.</p> <p>Methods</p> <p>We present our method of minimally invasive semitendinosus reconstruction for the Achilles tendon using one para-midline and one midline incision.</p> <p>Results</p> <p>The first incision is a 5 cm longitudinal incision, made 2 cm proximal and just medial to the palpable end of the residual tendon. The second incision is 3 cm long and is also longitudinal but is 2 cm distal and in the midline to the distal end of the tendon rupture. The distal and proximal Achilles tendon stumps are mobilised. After trying to reduce the gap of the ruptured Achilles tendon, if the gap produced is greater than 6 cm despite maximal plantar flexion of the ankle and traction on the Achilles tendon stumps, the ipsilateral semitendinosus tendon is harvested. The semitendinosus tendon is passed through small incisions in the substance of the proximal stump of the Achilles tendon, and it is sutured to the Achilles tendon. It is then passed beneath the intact skin bridge into the distal incision, and passed from medial to lateral through a transverse tenotomy in the distal stump. With the ankle in maximal plantar flexion, the semitendinosus tendon is sutured to the Achilles tendon at each entry and exit point</p> <p>Conclusion</p> <p>This minimally invasive technique allows reconstruction of the Achilles tendon using the tendon of semitendinosus preserving skin integrity over the site most prone to wound breakdown, and can be especially used to reconstruct the Achilles tendon in the presence of large gap (greater than 6 centimetres).</p

Comparison of two methods based on cross-sectional data for correcting corpus uterine cancer incidence and probabilities

BACKGROUND: Two methods are presented for obtaining hysterectomy prevalence corrected estimates of invasive cancer incidence rates and probabilities of the corpus uterine. METHODS: The first method involves cross-sectional hysterectomy data from the Utah Hospital Discharge Data Base and mortality data applied to life-table methods. The second involves hysterectomy prevalence estimates obtained directly from the Utah Behavior Risk Factor Surveillance System (BRFSS) survey. RESULTS: Hysterectomy prevalence estimates based on the first method are lower than those obtained from the second method through age 74, but higher in the remaining ages. Correction for hysterectomy prevalence is greatest among women ages 75–79. In this age group, the uncorrected rate is 125 (per 100,000) and the corrected rate based on the life-table method is 223 using 1995–97 data, 243 using 1992–94 data, and 228 from the survey method. The uncorrected lifetime probability of developing corpus uterine cancer is 2.6%; the corrected probability from the life-table method using 1995–97 data is 4.2%, using 1992–94 data is 4.5%; and based on prevalence data from the survey method is 4.6%. CONCLUSIONS: Both methods provide reasonable hysterectomy prevalence estimates for correcting corpus uterine cancer rates and probabilities. Because of declining trends in hysterectomy in recent decades, corrected estimates from the life-table method are less pronounced than those based on the survey method. These methods may be useful for obtaining corrected uterine cancer rates and probabilities in areas of the world that do not have sufficient years of hysterectomy data to directly compute prevalence

Less invasive Achilles tendon reconstruction

<p>Abstract</p> <p>Background</p> <p>The optimal management of chronic ruptures of the Achilles tendon is surgical reconstruction. Reconstruction of the Achilles tendon using peroneus brevis has been widely reported. Classically, these procedures involve relatively long surgical wounds in a relatively hypovascular area which is susceptible to wound breakdown.</p> <p>Results</p> <p>We describe our current method of peroneus brevis reconstruction for the Achilles tendon using two para-midline incisions.</p> <p>Conclusion</p> <p>This technique allows reconstruction of the Achilles tendon using peroneus brevis preserving skin integrity over the site most prone to wound breakdown, and can be especially used to reconstruct the Achilles tendon in the presence of previous surgery.</p

X-Linked Genes and Risk of Orofacial Clefts: Evidence from Two Population-Based Studies in Scandinavia

Background: Orofacial clefts are common birth defects of complex etiology, with an excess of males among babies with cleft lip and palate, and an excess of females among those with cleft palate only. Although genes on the X chromosome have been implicated in clefting, there has been no association analysis of X-linked markers. Methodology/Principal Findings: We added new functionalities in the HAPLIN statistical software to enable association analysis of X-linked markers and an exploration of various causal scenarios relevant to orofacial clefts. Genotypes for 48 SNPs in 18 candidate genes on the X chromosome were analyzed in two population-based samples from Scandinavia (562 Norwegian and 235 Danish case-parent triads). For haplotype analysis, we used a sliding-window approach and assessed isolated cleft lip with or without cleft palate (iCL/P) separately from isolated cleft palate only (iCPO). We tested three statistical models in HAPLIN, allowing for: i) the same relative risk in males and females, ii) sex-specific relative risks, and iii) X-inactivation in females. We found weak but consistent associations with the oral-facial-digital syndrome 1 (OFD1) gene (formerly known as CXORF5) in the Danish iCL/P samples across all models, but not in the Norwegian iCL/P samples. In sex-specific analyses, the association with OFD1 was in male cases only. No analyses showed associations with iCPO in either the Norwegian or the Danish sample. Conclusions: The association of OFD1 with iCL/P is plausible given the biological relevance of this gene. However, the lack of replication in the Norwegian samples highlights the need to verify these preliminary findings in other large datasets. More generally, the novel analytic methods presented here are widely applicable to investigations of the role of X-linked genes in complex traits

The oncolytic effect in vivo of reovirus on tumour cells that have survived reovirus cell killing in vitro

The use of oncolytic viruses has received considerable attention in recent years and many viruses have proved to be effective against a variety of cancer models and a few are currently being used in clinical trials. However, the possible emergence and outcome of virus-resistant tumour cells has not been addressed. We previously reported the effective use of reovirus against lymphoid malignancies, including the Burkitt's lymphoma cell line Raji. Here we isolated in vitro persistently infected (PI) Raji cells, and cells ‘cured' of persistent reovirus infection (‘cured' cells). Both PI and cured Raji cells resisted reovirus infection and cell killing in vitro. In vivo, the PI cells were non-tumorigenic in SCID mice, but cured cells regained the parental cells' ability to form tumours. Tumour xenografts from the cured cells, however, were highly susceptible to reovirus oncolysis in vivo. This susceptibility was due to the proteolytic environment within tumours that facilitates reovirus infection and cell killing. Our results show that persistent infection by reovirus impedes tumour development and that although PI cells cleared of reovirus are tumorigenic, they are killed upon rechallenge with reovirus. Both the PI and cured states are therefore not likely to be significant barriers to reovirus oncolytic therapy

Interleukin-6 Induces Gr-1+CD11b+ Myeloid Cells to Suppress CD8+ T Cell-Mediated Liver Injury in Mice

Agonist antibodies against CD137 (4-1BB) on T lymphocytes are used to increase host anti-tumor immunity, but often leading to severe liver injury in treated mice or in patients during clinical trials. Interleukin-6 (IL-6) has been reported to protect hepatocyte death, but the role of IL-6 in protecting chronic T cell-induced liver diseases is not clearly defined due to lack of relevant animal models. We aimed to define the role of IL-6 in CD8+ T cell-mediated liver injury induced by a CD137 agonistic mAb (clone 2A) in mice.We expressed IL-6 in the liver by hydrodynamic gene delivery in mice treated with 2A or control mAb and studied how IL-6 treatment affected host immunity and T cell-mediated liver injury. We found that ectopic IL-6 expression in the liver elevated intrahepatic leukocyte infiltration but prevented CD8+ T cell-mediated liver injury. In IL-6 treated mice, CD8+ T cells proliferation and IFN-γ expression were inhibited in the liver. We discovered that IL-6 increased accumulation of Gr-1+CD11b+ myeloid derived suppressor cells (MDSCs) in the liver and spleen. These MDSCs had the ability to inhibit T cells proliferation and activation. Finally, we showed that the MDSCs were sufficient and essential for IL-6-mediated protection of anti-CD137 mAb-induced liver injury.We concluded that IL-6 induced Gr-1+CD11b+ MDSCs in the liver to inhibit T cell-mediated liver injury. The findings have defined a novel mechanism of IL-6 in protecting liver from CD8+ T cell-mediated injury

'Physical activity at home (PAAH)', evaluation of a group versus home based physical activity program in community dwelling middle aged adults: rationale and study design

<p>Abstract</p> <p>Background</p> <p>It is well recognised that the adoption and longer term adherence to physical activity by adults to reduce the risk of chronic disease is a challenge. Interventions, such as group and home based physical activity programs, have been widely reported upon. However few studies have directly compared these interventions over the longer term to determine their adherence and effectiveness. Participant preference for home based or group interventions is important. Some evidence suggests that home based physical activity programs are preferred by middle aged adults and provide better long term physical activity adherence. Physiotherapists may also be useful in increasing physical activity adherence, with limited research on their impact.</p> <p>Methods</p> <p>'Physical Activity at Home' is a 2 year pragmatic randomised control trial, with a non-randomised comparison to group exercise. Middle-aged adults not interested in, or unable to attend, a group exercise program will be targeted. Sedentary community dwelling 50-65 year olds with no serious medical conditions or functional impairments will be recruited via two mail outs using the Australian federal electoral roll. The first mail out will invite participants to a 6 month community group exercise program. The second mail out will be sent to those not interested in the group exercise program inviting them to take part in a home based intervention. Eligible home based participants will be randomised into a 6 month physiotherapy-led home based physical activity program or usual care. Outcome measures will be taken at baseline, 6, 12, 18 and 24 months. The primary outcome is physical activity adherence via exercise diaries. Secondary outcomes include the Active Australia Survey, accelerometry, aerobic capacity (step test), quality of life (SF-12v2), blood pressure, waist circumference, waist-to-hip ratio and body mass index. Costs will be recorded prospectively and qualitative data will be collected.</p> <p>Discussion</p> <p>The planned 18 month follow-up post intervention will provide an indication of the effectiveness of the group and home based interventions in terms of adherence to physical activity, health benefits and cost. If the physiotherapy-led home based physical activity program is successful it could provide an alternative option for physical activity program delivery across a number of settings.</p> <p>Trial registration</p> <p>Australia and New Zealand Clinical Trials Register (ANZCTR): <a href="http://www.anzctr.org.au/ACTRN12611000890932.aspx">ACTRN12611000890932</a></p