A cost-utility study of elective haemorrhoidectomies in Canada

AIM

The aim was to estimate the 10-year cost-utility of haemorrhoidectomy surgery with preference-based measures of health using Canadian health utility measures and costs.

METHODS

Patients undergoing elective haemorrhoidectomies by general and colorectal surgeons in British Columbia, Vancouver, between September 2015 and November 2022, completed preoperatively and postoperatively the EuroQol five-dimension five-level health-related quality of life questionnaire (EQ-5D-5L). Quality-adjusted life years (QALYs) attributable to surgery were calculated by discounting preoperative and postoperative health utility values derived from the EQ-5D-5L. Costs were measured from a health system perspective which incorporated costs of hospital stay and specialists' fees. Results are presented in 2021 Canadian dollars.

RESULTS

Of 94 (47%) patients who completed both the preoperative and postoperative questionnaires, the mean gain in QALYs 10 years after surgery was 1.0609, assuming a 3.5% annual discounting rate. The average cost of the surgery was $3166. The average cost per QALY was $2985 when benefits of the surgery were assumed to accrue for 10 years. The cost per QALY was higher for women ($3821) compared with men ($2485). Participants over the age of 70 had the highest cost per QALY ($8079/QALY).

CONCLUSIONS

Haemorrhoidectomies have been associated with significant gains in health status and are inexpensive relative to the associated gains in quality of life based on patients' perspectives of their improvement in health and well-being.

Patient-reported outcome measures for children and adolescents having dental bleaching in the UK

PURPOSE

Dental bleaching in paediatric patients can be used to address discolouration of teeth due to trauma, endodontic treatment, or enamel and dentine defects. Despite being a minimally invasive and successful treatment, the use of bleaching products in children and young people remains controversial. This evaluation was designed to provide insight into the child's perspective on dental bleaching and the influence that this treatment has upon their life.

METHOD

A dental bleaching patient reported outcome measure (PROM) was developed and piloted in 2019. Data were collected from 3 UK units (January-March 2020). Children attending these units for bleaching reviews were invited to complete the PROM.

RESULTS

Twenty seven PROM questionnaires were completed including 19 courses of external bleaching and 8 courses of internal/external bleaching. The average age was 14 years old (9-17 years). The common indications for bleaching were Amelogenesis Imperfecta, dental trauma and Molar Incisor Hypomineralisation. Patients reported improvements in their appearance (89%) and self-confidence (81%). Sensitivity was the most common side effect, reported in 63% of cases.

CONCLUSION

This PROM supports the use of dental bleaching in children and young people when treating dental disease that causes discolouration. Bleaching not only improved the appearance of teeth, but also patients' self-confidence. Sensitivity is a common side effect and clinicians should discuss this common risk and its management with patients and their families.

Use of local anesthesia for inguinal hernia repair has decreased over time in the VA system

PURPOSE

In 2003, randomized trials demonstrated potentially improved outcomes when local instead of general anesthesia is used for inguinal hernia repair. Our study aimed to evaluate how the use of local anesthesia for this procedure changed over time following the publication of the trials' level 1 evidence.

METHODS

We used the 1998-2018 Veterans Affairs Surgical Quality Improvement Program database to identify adults who underwent open, unilateral inguinal hernia repair under local or general anesthesia. Our primary outcome was the percentage of cases performed under local anesthesia. We used a time-series design to examine the trend and rate of change of the use of local anesthesia.

RESULTS

We included 97,437 veterans, of which 22,333 (22.9%) had hernia surgery under local anesthesia. The median age of veterans receiving local anesthesia remained stable at 64-67 years over time. The use of local anesthesia decreased steadily, from 38.2% at the beginning year to 15.1% in the final year (P < 0.0001). The publication of results from randomized trials (in 2003) did not appear to increase the overall use or change the rate of decline in the use of local anesthesia. Overall, we found that the use of local anesthesia decreased by about 1.5% per year.

CONCLUSION

The utilization of local anesthesia for inguinal hernia repair in the VA has steadily declined over the last 20 + years, despite data showing equivalence or superiority to general anesthesia. Future studies should explore barriers to the use of local anesthesia for hernia repair.

Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria

Antibiotic resistance (AR) is a threat to modern medicine, and plasmids are driving the global spread of AR by horizontal gene transfer across microbiomes and environments. Determining the mobile resistome responsible for this spread of AR among environments is essential in our efforts to attenuate the current crisis. Biosolids are a wastewater treatment plant (WWTP) byproduct used globally as fertilizer in agriculture. Here, we investigated the mobile resistome of biosolids that are used as fertilizer. This was done by capturing resistance plasmids that can transfer to human pathogens and commensal bacteria. We used a higher-throughput version of the exogenous plasmid isolation approach by mixing several ESKAPE pathogens and a commensal Escherichia coli with biosolids and screening for newly acquired resistance to about 10 antibiotics in these strains. Six unique resistance plasmids transferred to Salmonella typhimurium, Klebsiella aerogenes, and E. coli. All the plasmids were self-transferable and carried 3-6 antibiotic resistance genes (ARG) conferring resistance to 2-4 antibiotic classes. These plasmids-borne resistance genes were further embedded in genetic elements promoting intracellular recombination (i.e., transposons or class 1 integrons). The plasmids belonged to the broad-host-range plasmid (BHR) groups IncP-1 or PromA. Several of them were persistent in their new hosts when grown in the absence of antibiotics, suggesting that the newly acquired drug resistance traits would be sustained over time. This study highlights the role of BHRs in the spread of ARG between environmental bacteria and human pathogens and commensals, where they may persist. The work further emphasizes biosolids as potential vehicles of highly mobile plasmid-borne antibiotic resistance genes.

Health and quality of life among a cohort of patients having lateral internal sphincterotomy for anal fissures

AIM

The aim of this study is to report changes in health-related quality of life attributable to lateral internal sphincterotomy for treatment of anal fissure. There is very little evidence on whether the overall health-related quality of life of patients is detrimentally affected by the condition, or which aspects of self-perceived health status improve after lateral internal sphincterotomy. This study will articulate which aspects of health tend to improve and guide postoperative expectations appropriately. Knowledge gained from this study may also identify gaps in an individual patient's episode of care.

METHOD

Patients were prospectively identified when they consented to surgical treatment of their anal fissure and were contacted by phone to participate. Participants completed a number of patient-reported outcomes preoperatively and 6 months postoperatively. Faecal incontinence-related quality of life, pain and depression were measured at both time points. The severity of faecal incontinence was measured at both times.

RESULTS

Participants reported high levels of pain preoperatively. Postoperatively, improvement in pain exceeded the threshold of clinical relevance (P < 0.01). Thirty-five per cent of participants reported significant effects of faecal incontinence preoperatively, while 26% did so postoperatively. Participants with multiple comorbidities were more likely to report faecal incontinence postoperatively than preoperatively.

CONCLUSION

This study reports that lateral internal sphincterotomy improved pain symptoms without adverse effects on continence. Not all domains of health-related quality of life were similarly positively affected by anal fissure repair.

Surgical site infection in elective colonic and rectal resections: effect of oral antibiotics and mechanical bowel preparation compared with mechanical bowel preparation only

AIM

Surgical site infections are disproportionately common after colorectal surgery and may be largely preventable. The objective of this retrospective cohort study was to determine the effect of oral antibiotics and mechanical bowel preparation on surgical site infections.

METHOD

A retrospective study of a consecutive series of elective colonic and rectal resections following an Enhanced Recovery After Surgery pathway, which also included mechanical bowel preparation, from 1 September 2014 to 30 September 2017. The addition of oral antibiotics (neomycin and metronidazole) to the mechanical bowel preparation procedure was assessed. Development of surgical site infections within 30 days was the main outcome measured. The secondary outcome was assessment of possible surgical site infection predictors.

RESULTS

Seven-hundred thirty-two patients were included: 313 (43%) preintervention (mechanical bowel preparation only); and 419 (57%) postintervention (mechanical bowel preparation plus oral antibiotics). Surgical site infection rates preintervention and. postintervention were: overall, 20.8% vs 10.5%, P < 0.001; superficial, 10.9% vs 4.3%, P < 0.001; and organ space, 9.9% vs 6.2%, P = 0.03. Subgroup analysis of colonic resections revealed a significant reduction in overall (17.1% vs 6.8%), superficial (10.7% vs 4.3%) and organ space (6.4% vs. 2.6%) infections. Rectal resections had significant reduction in overall (26.2% vs 15.3%) and superficial (11.1% vs 4.4%) infection rates but not in organ space infections (15.1% vs 10.9%). Multivariate regression analysis revealed open vs minimally invasive surgery (P < 0.001) and omission of oral antibiotics (P = 0.004) as independent predictors of surgical site infections.

CONCLUSION

Administration of oral antibiotics resulted in significant reduction of superficial and organ space infections after colonic resection; after rectal resection, significant reduction only of superficial infections was found.

Transanal Endoscopic Microsurgery (TEM) for rectal GI stromal tumor

BACKGROUND

Transanal endoscopic microsurgery (TEM) is effective in treating adenomas and select early rectal cancers. Our objective is to evaluate TEM in treating early rectal GISTs.

METHODS

Patients were identified in a prospective database with pathology confirmed rectal GIST prior to TEM over 10 years. Demographic, pathologic, operative and follow-up data was analysed and presented with descriptive statistics.

RESULTS

7 cases of rectal GIST were treated with TEM with a follow-up time of 31 months (0-71). Median tumor distance from the anal verge was 4 cm (2.5-6) and median tumor size was 3 cm (2-5.7). Negative margins were achieved in 4/7 patients. Those with positive margins were treated with repeat TEM or imatinib. 1 patient had local recurrence successfully treated by TEM.

CONCLUSIONS

Overall, TEM is safe for locally excising GISTs. As rectal GISTs are rare, a multicenter registry may better elucidate outcomes with this treatment.

Vision using multiple distinct rod opsins in deep-sea fishes

Vertebrate vision is accomplished through light-sensitive photopigments consisting of an opsin protein bound to a chromophore. In dim light, vertebrates generally rely on a single rod opsin [rhodopsin 1 (RH1)] for obtaining visual information. By inspecting 101 fish genomes, we found that three deep-sea teleost lineages have independently expanded their RH1 gene repertoires. Among these, the silver spinyfin (Diretmus argenteus) stands out as having the highest number of visual opsins in vertebrates (two cone opsins and 38 rod opsins). Spinyfins express up to 14 RH1s (including the most blueshifted rod photopigments known), which cover the range of the residual daylight as well as the bioluminescence spectrum present in the deep sea. Our findings present molecular and functional evidence for the recurrent evolution of multiple rod opsin-based vision in vertebrates.

Simultaneous measurement of p53:Mdm2 and p53:Mdm4 protein-protein interactions in whole cells using fluorescence labelled foci

In this report we describe the development of a Fluorescent Protein-Protein Interaction-visualization (FLUOPPI) to enable the simultaneous measurement of both Mdm2:p53 and Mdm4:p53 interactions in order to assess the relative efficiencies of mimetic molecules of the p53 peptide helix against both PPIs. Mdm2 and Mdm4 overexpression frequently leads to the inactivation of non-mutated p53 in human cancers, via inhibition of its transcriptional activity, enhancing its degradation by the proteasome or by preventing its nuclear import. Development of inhibitors to disrupt the binding of one or both of these protein interactions have been the subject of intensive pharmaceutical development for anti-cancer therapies. Using the bimodal FLUOPPI system we have characterised compounds that were either monospecific for Mdm2 or bispecific for both Mdm2 and Mdm4. We have also demonstrated that the FLUOPPI assay can reliably differentiate between specific and non-specific disruption of these protein complexes via accurate assessment and normalization to the cell population under measurement. We envision that this methodology will increase the efficiency of identifying compounds that are either specific against a single PPI from a closely related family of interactions or compounds that interact across multiple related PPI pairs, depending on which is more desirable.

Can less be more? Organ preservation strategies in the management of rectal cancer

Background

Total mesorectal excision (tme) is the current standard of care for the treatment of rectal cancer. However, that surgery is associated with significant morbidity and mortality. Clinicians and patients are seeking alternatives to radical resection. Currently, prevalent organ-sparing strategies under investigation include local excision and nonoperative management (nom).

Methods

We reviewed the current evidence in the literature to create an overview of the use of transanal endoscopic surgery and watch-and-wait strategies in the modern management of rectal cancer.

Results

Compared with radical resection, transanal endoscopic surgery in patients with early rectal cancer (cT1) having favourable histopathologic features is associated with an increased risk of local recurrence, but no difference in 5-year survival. In patients with T2 or early T3 cancer, strategies that use neoadjuvant or adjuvant therapy as adjuncts to local excision are under evaluation. Nonoperative management is a new option for patients who experience a complete clinical response after neoadjuvant chemoradiotherapy (ncrt). The selection criteria that will appropriately identify patients for whom nom will succeed are not established.

Conclusions

Local excision is appropriate for early rectal cancer with favourable histopathologic features. Although organ-preserving strategies are promising, the quality of the evidence to date is insufficient to replace the current standard care in most patients. Patients should be offered nom in the safe setting of a clinical trial or registry. Rigorous follow-up, including endoscopy and imaging at frequent intervals is recommended when radical resection is forgone.

Comparative genomics of Bifidobacterium species isolated from marmosets and humans

The genus Bifidobacterium is purported to have beneficial consequences for human health and is a major component of many gastrointestinal probiotics. Although species of Bifidobacterium are generally at low relative frequency in the adult human gastrointestinal tract, they can constitute high proportions of the gastrointestinal communities of adult marmosets. To identify genes that might be important for the maintenance of Bifidobacterium in adult marmosets, ten strains of Bifidobacterium were isolated from the feces of seven adult marmosets, and their genomes were sequenced. There were six B. reuteri strains, two B. callitrichos strains, one B. myosotis sp. nov. and one B. tissieri sp. nov. among our isolates. Phylogenetic analysis showed that three of the four species we isolated were most closely related to B. bifidum, B. breve and B. longum, which are species found in high abundance in human infants. There were 1357 genes that were shared by at least one strain of B. reuteri, B. callitrichos, B. breve, and B. longum, and 987 genes that were found in all strains of the four species. There were 106 genes found in B. reuteri and B. callitrichos but not in human bifidobacteria, and several of these genes were involved in nutrient uptake. These pathways for nutrient uptake appeared to be specific to Bifidobacterium from New World monkeys. Additionally, the distribution of Bifidobacterium in fecal samples from captive adult marmosets constituted as much as 80% of the gut microbiome, although this was variable between individuals and colonies. We suggest that nutrient transporters may be important for the maintenance of Bifidobacterium during adulthood in marmosets.

A multi-centre randomized controlled trial of open vs closed management of the rectal defect after transanal endoscopic microsurgery

AIM

Transanal endoscopic microsurgery (TEM) is a technically challenging strategy that allows expanded indications for local excision of rectal lesions. Transluminal suturing is difficult, so open management of the resultant defect is appealing. Expert opinion suggests there is more pain when the defect is left open. The aim of this study was to determine if closure of the defect created during full thickness excision of rectal lesions with TEM leads to less postoperative pain compared to leaving the defect open.

METHOD

At the time of surgery, patients undergoing a full thickness TEM were randomized to sutured (TEM-S) or open (TEM-O) management of the rectal defect. At five Canadian academic colorectal surgery centres, experienced TEM surgeons enrolled patients ≥ 18 years treated by full thickness TEM. The primary outcome was postoperative pain measured by the visual analogue scale. Secondary outcomes included postoperative pain medication use and 30-day postoperative complications, including bleeding, infection and hospital readmission.

RESULTS

Between March 2012 and October 2013, 50 patients were enrolled and randomized to sutured (TEM-S, n = 28) or open (TEM-O, n = 22) management of the rectal defect. There was no difference between the two study groups in postoperative pain on postoperative day 1 (2.8 vs 2.6, P = 0.76), day 3 (2.8 vs 2.1, P = 0.23) and day 7 (2.8 vs 1.7, P = 0.10).

CONCLUSION

In this multicentre randomized controlled trial, there was no difference in postoperative pain between sutured or open defect management in patients having a full thickness excision with TEM.

Prediction model and web-based risk calculator for postoperative ileus after loop ileostomy closure

Background

Postoperative ileus (POI) is a significant complication after loop ileostomy closure given both its frequency and impact on the patient. The purpose of this study was to develop and externally validate a prediction model for POI after loop ileostomy closure.

Methods

The model was developed and validated according to the TRIPOD checklist for prediction model development and validation. The development cohort included consecutive patients who underwent loop ileostomy closure in two teaching hospitals in Montreal, Canada. Candidate variables considered for inclusion in the model were chosen a priori based on subject knowledge. The final prediction model, which modelled the 30-day cumulative incidence of POI using logistic regression, was selected using the highest area under the receiver operating characteristic curve (AUC) criterion. Model calibration was assessed using the Hosmer–Lemeshow goodness-of-fit test. The model was then validated externally in an independent cohort of similar patients from the University of British Columbia.

Results

The development cohort included 531 patients, in whom the incidence of POI was 16·8 per cent. The final model included five variables: age, ASA fitness grade, underlying pathology/treatment, interval between ileostomy creation and closure, and duration of surgery for ileostomy closure (AUC 0·68, 95 per cent c.i. 0·61 to 0·74). The model demonstrated good calibration (P = 0·142). The validation cohort consisted of 216 patients, and the incidence of POI was 15·7 per cent. On external validation, the model maintained good discrimination (AUC 0·72, 0·63 to 0·81) and calibration (P = 0·538).

Conclusion

A prediction model was developed for POI after loop ileostomy closure and included five variables. The model maintained good performance on external validation.

Avoided emissions and conservation of scrub mangroves: potential for a Blue Carbon project in the Gulf of California, Mexico

Mangroves are considered ideal ecosystems for Blue Carbon projects. However, because of their short stature, some mangroves ('scrub' mangroves, less than 2 m) do not fulfil the current definition of 'forests', which makes them ineligible for emission reduction programmes such as REDD+. Short stature mangroves can be the dominant form of mangroves in arid and nutrient-poor landscapes, and emissions from their deforestation and degradation could be substantial. Here, we describe a Blue Carbon project in the Gulf of California, Mexico, to illustrate that projects that avoid emissions from deforestation and degradation could provide financial resources to protect mangroves that cannot be included in other emission reduction programmes. The goal of the project is to protect 16 058 ha of mangroves through conservation concessions from the Mexican Federal Government. The cumulative avoided emissions of the project are 2.84 million Mg CO₂ over 100 years, valued at $US 426 000 per year (US$15 per Mg CO₂ in the California market). The funds could be used for community-based projects that will improve mangrove management, such as surveillance, eradication of invasive species, rehabilitation after tropical storms and environmental education. The strong institutional support, secure financial status, community engagement and clear project boundaries provide favourable conditions to implement this Blue Carbon project. Financial resources from Blue Carbon projects, even in mangroves of short stature, can provide substantial resources to enhance community resilience and mangrove protection.

Transanal endoscopic microsurgery as day surgery - a single-centre experience with 500 patients

AIM

Transanal endoscopic microsurgery (TEM) is the current treatment of choice for rectal adenomas and early rectal cancer. Postoperative admission to hospital is common but possibly unnecessary. Our objective was to analyse predictors and outcomes of TEM patients having same day discharge (TEM-D) compared with those who were admitted to hospital (TEM-A).

METHOD

At St Paul's Hospital (SPH), demographic, surgical, pathological and follow-up data have been collected prospectively since TEM was started in 2007. Trends in admission and readmission rates were analysed using the Cochran-Armitage trend test, and predictors of admission were analysed using univariate and multivariate logistic regressions.

RESULTS

Between 2007 and 2016, 500 patients were treated by TEM at SPH. The overall admission rate was 29% (145/500), but this decreased to 19% in the last 3 years of the study (P < 0.001). The readmission rate was 5.2% (n = 26/500) and did not change significantly over the study period (P = 0.30). Reasons for admission included the following: surgeon discretion/monitoring (35%), urinary retention (26%), haemorrhage (10%), breach of peritoneal cavity (7%), infection (7%) and other (15%). The most common reasons for readmission were haemorrhage (54%, n = 14), pain (19%, n = 5) and infection (12%, n = 3). Factors associated with admission were as follows: tumour height (OR 1.09, 1.02-1.17), prolonged operative time (OR 1.25, 1.14-1.37), unsutured surgical defect (OR 1.99, 1.22-3.25) and surgeon experience (OR 4.62, 2.75-7.77).

CONCLUSION

Outpatient TEM is safe and carries a low risk of readmission. In centres with an outpatient TEM strategy, predictors of hospital admission include proximal tumours, prolonged surgical time and open management of the surgical defect.

Salvage TME following TEM: a possible indication for TaTME

BACKGROUND

Salvage surgery after transanal endoscopic microsurgery (TEM) has shown mixed results. Transanal total mesorectal excision (TaTME) might be advantageous in this population. The aim of this study was to assess the short-term oncologic and operative outcomes of salvage surgery after TEM, comparing TaTME to conventional salavge TME (sTME).

METHODS

Consecutive patients treated with salvage surgery after TEM were identified. Patients who underwent TaTME were compared to those who had conventional sTME. The primary outcome was the ability to perform an appropriate oncologic procedure defined by a composite outcome (negative distal margins, negative radial margins and complete or near complete mesorectum specimen).

RESULTS

During the study period, 41 patients had salvage surgery after TEM. Of those, 11 patients had TaTME while 30 patients had sTME. All patients in the TaTME group met the composite outcome of appropriate oncologic procedure compared to 76.7% for the conventional sTME group (p = 0.19). TaTME was associated with significantly higher rates of sphincter preservation (100 vs. 50%, p = 0.01), higher rates of laparoscopic surgery (100 vs. 23.3%, p < 0.001) and lower rates of conversion to open surgery (9.1 vs. 57%, p < 0.001). No difference was found in postoperative morbidity (36.3 vs. 36.7%, p = 0.77).

CONCLUSIONS

The present study demonstrates that for patients requiring salvage surgery after TEM, TaTME is associated with significantly higher rates of sphincter-sparing surgery when compared to conventional transabdominal TME while producing adequate short-term oncologic outcomes. Salvage surgery after TEM might be a clear indication for TaTME rather than conventional surgery.

Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations

Vision is the dominant sensory modality in many organisms for foraging, predator avoidance, and social behaviors including mate selection. Vertebrate visual perception is initiated when light strikes rod and cone photoreceptors within the neural retina of the eye. Sensitivity to individual colors, i.e., peak spectral sensitivities (λmax) of visual pigments, are a function of the type of chromophore and the amino acid sequence of the associated opsin protein in the photoreceptors. Large differences in peak spectral sensitivities can result from minor differences in amino acid sequence of cone opsins. To determine how minor sequence differences could result in large spectral shifts we selected a spectrally-diverse group of 14 teleost Rh2 cone opsins for which sequences and λmax are experimentally known. Classical molecular dynamics simulations were carried out after embedding chromophore-associated homology structures within explicit bilayers and water. These simulations revealed structural features of visual pigments, particularly within the chromophore, that contributed to diverged spectral sensitivities. Statistical tests performed on all the observed structural parameters associated with the chromophore revealed that a two-term, first-order regression model was sufficient to accurately predict λmax over a range of 452-528 nm. The approach was accurate, efficient and simple in that site-by-site molecular modifications or complex quantum mechanics models were not required to predict λmax. These studies identify structural features associated with the chromophore that may explain diverged spectral sensitivities, and provide a platform for future, functionally predictive opsin modeling.

Coordination of radiologic and clinical care reduces the wait time to breast cancer diagnosis

BACKGROUND

In 2009, a Rapid Access Breast Clinic (rabc) was opened at our urban hospital. Compared with the traditional system (ts), the navigated care through the clinic was associated with a significantly shorter time to surgical consultation. Since 2009, many radiology facilities have introduced facilitated-care pathways for patients with breast pathology. Our objective was to determine if that change in diagnostic imaging pathways had eliminated the advantage in time to care previously shown for the rabc.

METHODS

All patients seen in the rabc and the office-based ts in November-December 2012 were included in the analysis. A retrospective chart review tabulated demographic, surgeon, pathology, and radiologic data, including time intervals to care for all patients. The results were compared with data from 2009.

RESULTS

In 2012, time from presentation to surgical consultation was less for the rabc group than for the ts group (36 days vs. 73 days, p < 0.001) for both malignant (31 days vs. 55 days, p = 0.008) and benign diagnoses (43 days vs. 79 days, p < 0.001). Comparing the 2012 results with results from 2009, a decline in mean wait time was observed for the ts group (86 days vs. 73 days, p = 0.02). Compared with patients having investigations in the ts, rabc patients with cancer were more likely to undergo surgery within 60 days of presentation (33% vs. 15%, p = 0.04).

CONCLUSIONS

The coordination of radiology and clinical care reduces wait times for diagnosis and surgery in breast cancer. To achieve recommended targets, we recommend implementation of more systematic coordination of care for a breast cancer diagnosis and of navigation to surgeons for patients needing surgical care.

Characterization of Four Multidrug Resistance Plasmids Captured from the Sediments of an Urban Coastal Wetland

Self-transmissible and mobilizable plasmids contribute to the emergence and spread of multidrug-resistant bacteria by enabling the horizontal transfer of acquired antibiotic resistance. The objective of this study was to capture and characterize self-transmissible and mobilizable resistance plasmids from a coastal wetland impacted by urban stormwater runoff and human wastewater during the rainy season. Four plasmids were captured, two self-transmissible and two mobilizable, using both mating and enrichment approaches. Plasmid genomes, sequenced with either Illumina or PacBio platforms, revealed representatives of incompatibility groups IncP-6, IncR, IncN3, and IncF. The plasmids ranged in size from 36 to 144 kb and encoded known resistance genes for most of the major classes of antibiotics used to treat Gram-negative infections (tetracyclines, sulfonamides, β-lactams, fluoroquinolones, aminoglycosides, and amphenicols). The mobilizable IncP-6 plasmid pLNU-11 was discovered in a strain of Citrobacter freundii enriched from the wetland sediments with tetracycline and nalidixic acid, and encodes a novel AmpC-like β-lactamase (bla_WDC-1), which shares less than 62% amino acid sequence identity with the PDC class of β-lactamases found in Pseudomonas aeruginosa. Although the IncR plasmid pTRE-1611 was captured by mating wetland bacteria with P. putida KT2440 as recipient, it was found to be mobilizable rather than self-transmissible. Two self-transmissible multidrug-resistance plasmids were also captured: the small (48 kb) IncN3 plasmid pTRE-131 was captured by mating wetland bacteria with Escherichia coli HY842 where it is seemed to be maintained at nearly 240 copies per cell, while the large (144 kb) IncF plasmid pTRE-2011, which was isolated from a cefotaxime-resistant environmental strain of E. coli ST744, exists at just a single copy per cell. Furthermore, pTRE-2011 bears the globally epidemic bla_CTX-M-55 extended-spectrum β-lactamase downstream of ISEcp1. Our results indicate that urban coastal wetlands are reservoirs of diverse self-transmissible and mobilizable plasmids of relevance to human health.

Annotation of plasmid genes

Good annotation of plasmid genomes is essential to maximise the value of the rapidly increasing volume of plasmid sequences. This short review highlights some of the current issues and suggests some ways forward. Where a well-studied related plasmid system exists we recommend that new annotation adheres to the convention already established for that system, so long as it is based on sound principles and solid experimental evidence, even if some of the new genes are more similar to homologues in different systems. Where a well-established model does not exist we provide generic gene names that reflect likely biochemical activity rather than overall purpose particularly, for example, where genes clearly belong to a type IV secretion system but it is not known whether they function in conjugative transfer or virulence. We also recommend that annotators use a whole system naming approach to avoid ending up with an illogical mixture of names from other systems based on the highest scoring match from a BLAST search. In addition, where function has not been experimentally established we recommend using just the locus tag, rather than a function-related gene name, while recording possible functions as notes rather than in a provisional name.

Human Cytomegalovirus nuclear egress and secondary envelopment are negatively affected in the absence of cellular p53

Human Cytomegalovirus (HCMV) infection is compromised in cells lacking p53, a transcription factor that mediates cellular stress responses. In this study we have investigated compromised functional virion production in cells with p53 knocked out (p53KOs). Infectious center assays found most p53KOs released functional virions. Analysis of electron micrographs revealed modestly decreased capsid production in infected p53KOs compared to wt. Substantially fewer p53KOs displayed HCMV-induced infoldings of the inner nuclear membrane (IINMs). In p53KOs, fewer capsids were found in IINMs and in the cytoplasm. The deficit in virus-induced membrane remodeling within the nucleus of p53KOs was mirrored in the cytoplasm, with a disproportionately smaller number of capsids re-enveloped. Reintroduction of p53 substantially recovered these deficits. Overall, the absence of p53 contributed to inhibition of the formation and function of IINMs and re-envelopment of the reduced number of capsids able to reach the cytoplasm.

New Perspectives on Ebola Virus Evolution

Since the recent devastating outbreak of Ebola virus disease in western Africa, there has been significant effort to understand the evolution of the deadly virus that caused the outbreak. There has been a considerable investment in sequencing Ebola virus (EBOV) isolates, and the results paint an important picture of how the virus has spread in western Africa. EBOV evolution cannot be understood outside the context of previous outbreaks, however. We have focused this study on the evolution of the EBOV glycoprotein gene (GP) because one of its products, the spike glycoprotein (GP_1,2), is central to the host immune response and because it contains a large amount of the phylogenetic signal for this virus. We inferred the maximum likelihood phylogeny of 96 nonredundant GP gene sequences representing each of the outbreaks since 1976 up to the end of 2014. We tested for positive selection and considered the placement of adaptive amino acid substitutions along the phylogeny and within the protein structure of GP_1,2. We conclude that: 1) the common practice of rooting the phylogeny of EBOV between the first known outbreak in 1976 and the next outbreak in 1995 provides a misleading view of EBOV evolution that ignores the fact that there is a non-human EBOV host between outbreaks; 2) the N-terminus of GP₁ may be constrained from evolving in response to the host immune system by the highly expressed, secreted glycoprotein, which is encoded by the same region of the GP gene; 3) although the mucin-like domain of GP₁ is essential for EBOV in vivo, it evolves rapidly without losing its twin functions: providing O-linked glycosylation sites and a flexible surface.

Initiating a watch list for Ebola virus antibody escape mutations

The 2014 Ebola virus (EBOV) outbreak in West Africa is the largest in recorded history and resulted in over 11,000 deaths. It is essential that strategies for treatment and containment be developed to avoid future epidemics of this magnitude. With the development of vaccines and antibody-based therapies using the envelope glycoprotein (GP) of the 1976 Mayinga strain, one important strategy is to anticipate how the evolution of EBOV might compromise these efforts. In this study we have initiated a watch list of potential antibody escape mutations of EBOV by modeling interactions between GP and the antibody KZ52. The watch list was generated using molecular modeling to estimate stability changes due to mutation. Every possible mutation of GP was considered and the list was generated from those that are predicted to disrupt GP-KZ52 binding but not to disrupt the ability of GP to fold and to form trimers. The resulting watch list contains 34 mutations (one of which has already been seen in humans) at six sites in the GP2 subunit. Should mutations from the watch list appear and spread during an epidemic, it warrants attention as these mutations may reflect an evolutionary response from the virus that could reduce the effectiveness of interventions such as vaccination. However, this watch list is incomplete and emphasizes the need for more experimental structures of EBOV interacting with antibodies in order to expand the watch list to other epitopes. We hope that this work provokes experimental research on evolutionary escape in both Ebola and other viral pathogens.

High Diversity of CTX-M Extended-Spectrum β-Lactamases in Municipal Wastewater and Urban Wetlands

The CTX-M-type extended-spectrum β-lactamases (ESBLs) present a serious public health threat as they have become nearly ubiquitous among clinical gram-negative pathogens, particularly the enterobacteria. To aid in the understanding and eventual control of the spread of such resistance genes, we sought to determine the diversity of CTX-M ESBLs not among clinical isolates, but in the environment, where weaker and more diverse selective pressures may allow greater enzyme diversification. This was done by examining the CTX-M diversity in municipal wastewater and urban coastal wetlands in southern California, United States, by Sanger sequencing of polymerase chain reaction amplicons. Of the five known CTX-M phylogroups (1, 2, 8, 9, and 25), only genes from groups 1 and 2 were detected in both wastewater treatment plants (WWTPs), and group 1 genes were also detected in one of the two wetlands after a winter rain. The highest relative abundance of blaCTX-M group 1 genes was in the sludge of one WWTP (2.1 × 10(-4) blaCTX-M copies/16S rRNA gene copy). Gene libraries revealed surprisingly high nucleotide sequence diversity, with 157 new variants not found in GenBank, representing 99 novel amino acid sequences. Our results indicate that the resistomes of WWTPs and urban wetlands contain diverse blaCTX-M ESBLs, which may constitute a mobile reservoir of clinically relevant resistance genes.

Diversification of broad host range plasmids correlates with the presence of antibiotic resistance genes

The IncP-1ε subgroup is a recently identified phylogenetic clade within IncP-1 plasmids, which plays an important role in the spread of antibiotic resistance and degradation of xenobiotic pollutants. Here, four IncP-1ε plasmids were exogenously captured from a petroleum-contaminated habitat in China and compared phylogenetically and genomically with previously reported IncP-1ε and other IncP-1 plasmids. The IncP-1ε plasmids can be clearly subdivided into two subclades, designated as ε-I and ε-II, based on phylogenetic analysis of backbone proteins TraI and TrfA. This was further supported by comparison of concatenated backbone genes. Moreover, the two subclades differed in the transposon types, phenotypes and insertion locations of the accessory elements. The accessory genes on ε-I plasmids were inserted between parA and traC, and harbored ISPa17 and Tn402-like transposon modules, typically carrying antibiotic resistance genes. In contrast, the accessory elements on ε-II plasmids were typically located between trfA and oriV, and contained IS1071, which was commonly inserted within the Tn501-like transposon, typically harboring a cluster of genes encoding mercury resistance and/or catabolic pathways. Our study is one of the first to compare IncP-1 plasmid genomes from China, expands the available collection of IncP-1ε plasmids and enhances our understanding of their diversity, biogeography and evolutionary history.

Fine-scale analysis of 16S rRNA sequences reveals a high level of taxonomic diversity among vaginal Atopobium spp

Although vaginal microbial communities of some healthy women have high proportions of Atopobium vaginae, the genus Atopobium is more commonly associated with bacterial vaginosis, a syndrome associated with an increased risk of adverse pregnancy outcomes and the transmission of sexually transmitted diseases. Genetic differences within Atopobium species may explain why single species can be associated with both health and disease. We used 16S rRNA gene sequences from previously published studies to explore the taxonomic diversity of the genus Atopobium in vaginal microbial communities of healthy women. Although A. vaginae was the species most commonly found, we also observed three other Atopobium species in the vaginal microbiota, one of which, A. parvulum, was not previously known to reside in the human vagina. Furthermore, we found several potential novel species of the genus Atopobium and multiple phylogenetic clades of A. vaginae. The diversity of Atopobium found in our study, which focused only on samples from healthy women, is greater than previously recognized, suggesting that analysis of samples from women with BV would yield even more diversity. Classification of microbes only to the genus level may thus obfuscate differences that might be important to better understand health or disease.

Randomized double-blind trial comparing the cosmetic outcome of cutting diathermy versus scalpel for skin incisions

Background

Controversy exists about whether cutting diathermy for skin incisions leads to a cosmetically inferior scar. Cosmetic outcomes were compared between skin incisions created with cutting diathermy versus scalpel. Wound infection rates and postoperative incisional pain were also compared.

Methods

This was a randomized double-blind trial comparing cutting diathermy and scalpel in patients undergoing bowel resection. Scar cosmesis was assessed at 6 months after surgery by a plastic surgeon and a research associate using the Vancouver Scar Scale (VSS) and the Patient and Observer Scar Assessment Scale (POSAS). Patients also used POSAS to self-evaluate their scars. Wound infections within 30 days were recorded, and incision pain scores were measured on the first 5 days after operation.

Results

A total of 66 patients were randomized to cutting diathermy (31) or scalpel (35). At 6 months, there was no significant difference between the diathermy and scalpel groups in mean(s.d.) VSS scores (4·9(2·6) versus 5·0(1·9); P = 0·837), mean POSAS total scores (19·2(8·0) versus 20·0(7·4); P = 0·684) or subjective POSAS total scores (20·2(12·1) versus 21·3(10·4); P = 0·725). Neither were there significant differences in wound infection rates between the groups (5 of 30 versus 5 of 32; P = 1·000). Pain scores on day 1 after operation were significantly lower in the diathermy group (mean 1·68 versus 3·13; P = 0·018), but were not significantly different on days 2–5.

Conclusion

Cutting diathermy is a cosmetically acceptable technique for abdominal skin incisions. There is no increased risk of wound infection, and diathermy may convey benefit in terms of early postoperative wound pain. Registration number: NCT01496404 (http://www.clinicaltrials.gov).

The broad-host-range plasmid pSFA231 isolated from petroleum-contaminated sediment represents a new member of the PromA plasmid family

A self-transmissible broad-host-range (BHR) plasmid pSFA231 was isolated from petroleum-contaminated sediment in Shen-fu wastewater irrigation zone, China, using the triparental mating exogenous plasmid capture method. Based on its complete sequence the plasmid has a size of 41.5 kb and codes for 50 putative open reading frames (orfs), 29 of which represent genes involved in replication, partitioning and transfer functions of the plasmid. Phylogenetic analysis grouped pSFA231 into the newly defined PromA plasmid family, which currently includes five members. Further comparative genomic analysis shows that pSFA231 shares the common backbone regions with the other PromA plasmids, i.e., genes involved in replication, maintenance and control, and conjugative transfer. Nevertheless, phylogenetic divergence was found in specific gene products. We propose to divide the PromA group into two subgroups, PromA-α (pMRAD02, pSB102) and PromA-β (pMOL98, pIPO2T, pSFA231, pTer331), based on the splits network analysis of the RepA protein. Interestingly, a cluster of hypothetical orfs located between parA and traA of pSFA231 shows high similarity with the corresponding regions on pMOL98, pIPO2T, and pTer331, suggesting these hypothetical orfs may represent “essential” plasmid backbone genes for the PromA-β subgroup. Alternatively, they may also be accessory genes that were first acquired and then stayed as the plasmid diverged. Our study increases the available collection of complete genome sequences of BHR plasmids, and since pSFA231 is the only characterized PromA plasmid from China, our findings also enhance our understanding of the genetic diversity of this plasmid group in different parts of the world.

The bacterial microbiome in paired vaginal and vestibular samples from women with vulvar vestibulitis syndrome

Composition of the bacterial microbiome in the vagina and vestibule from 30 women with vulvar vestibulitis syndrome (VVS) and 15 healthy controls were compared by pyrosequencing 16S rRNA gene amplicons. Vaginal concentrations of interleukin (IL)-1β were determined by ELISA. Questionnaires elicited clinical and symptom data. Eighteen genera were detected in vaginal samples, and 23 genera were identified in vestibule samples, from women with VVS. The genera at both sites and the mean number of genera in subjects with VVS were largely similar to those in control subjects. However, differences were noted including higher proportions of Streptococcus and Enterococcus in women with VVS. Furthermore, Lactobacillus iners was more frequently identified in women with VVS while L. crispatus was more frequent in the control women. The dominant bacterial genera in the vagina closely paralleled the dominant genera present in the corresponding vestibular sample in both groups, leading us to postulate that vaginal secretions are an important source of bacteria present on the vestibule. Vaginal IL-1β levels were similar and varied depending on the dominant bacteria. We conclude in this pilot study that no major differences are apparent in the vagina and vestibule between women with or without VVS, except for an increased prevalence of Streptococcus and L. iners in some women with VVS.

The impact of spatial structure on viral genomic diversity generated during adaptation to thermal stress

BACKGROUND

Most clinical and natural microbial communities live and evolve in spatially structured environments. When changes in environmental conditions trigger evolutionary responses, spatial structure can impact the types of adaptive response and the extent to which they spread. In particular, localized competition in a spatial landscape can lead to the emergence of a larger number of different adaptive trajectories than would be found in well-mixed populations. Our goal was to determine how two levels of spatial structure affect genomic diversity in a population and how this diversity is manifested spatially.

METHODOLOGY/PRINCIPAL FINDINGS

We serially transferred bacteriophage populations growing at high temperatures (40°C) on agar plates for 550 generations at two levels of spatial structure. The level of spatial structure was determined by whether the physical locations of the phage subsamples were preserved or disrupted at each passage to fresh bacterial host populations. When spatial structure of the phage populations was preserved, there was significantly greater diversity on a global scale with restricted and patchy distribution. When spatial structure was disrupted with passaging to fresh hosts, beneficial mutants were spread across the entire plate. This resulted in reduced diversity, possibly due to clonal interference as the most fit mutants entered into competition on a global scale. Almost all substitutions present at the end of the adaptation in the populations with disrupted spatial structure were also present in the populations with structure preserved.

CONCLUSIONS/SIGNIFICANCE

Our results are consistent with the patchy nature of the spread of adaptive mutants in a spatial landscape. Spatial structure enhances diversity and slows fixation of beneficial mutants. This added diversity could be beneficial in fluctuating environments. We also connect observed substitutions and their effects on fitness to aspects of phage biology, and we provide evidence that some substitutions exclude each other.

EYA4 is inactivated biallelically at a high frequency in sporadic lung cancer and is associated with familial lung cancer risk

In an effort to identify novel biallelically inactivated tumor suppressor genes (TSG) in sporadic invasive and pre-invasive non-small cell lung cancer (NSCLC) genomes, we applied a comprehensive integrated multi-‘omics approach to investigate patient matched, paired NSCLC tumor and non-malignant parenchymal tissues. By surveying lung tumor genomes for genes concomitantly inactivated within individual tumors by multiple mechanisms, and by the frequency of disruption in tumors across multiple cohorts, we have identified a putative lung cancer TSG, Eyes Absent 4 (EYA4). EYA4 is frequently and concomitantly deleted, hypermethylated and underexpressed in multiple independent lung tumor data sets, in both major NSCLC subtypes, and in the earliest stages of lung cancer. We find not only that decreased EYA4 expression is associated with poor survival in sporadic lung cancers, but EYA4 SNPs are associated with increased familial cancer risk, consistent with EYA4’s proximity to the previously reported lung cancer susceptibility locus on 6q. Functionally, we find that EYA4 displays TSG-like properties with a role in modulating apoptosis and DNA repair. Cross examination of EYA4 expression across multiple tumor types suggests a cell type-specific tumorigenic role for EYA4, consistent with a tumor suppressor function in cancers of epithelial origin. This work shows a clear role for EYA4 as a putative TSG in NSCLC.

Host range diversification within the IncP-1 plasmid group

Broad-host-range plasmids play a critical role in the spread of antibiotic resistance and other traits. In spite of increasing information about the genomic diversity of closely related plasmids, the relationship between sequence divergence and host range remains unclear. IncP-1 plasmids are currently classified into six subgroups based on the genetic distance of backbone genes. We investigated whether plasmids from two subgroups exhibit a different host range, using two IncP-1γ plasmids, an IncP-1β plasmid and their minireplicons. Efficiencies of plasmid establishment and maintenance were compared using five species that belong to the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. The IncP-1β plasmid replicated and persisted in all five hosts in the absence of selection. Of the two IncP-1γ plasmids, both were unable to replicate in alphaproteobacterial host Sphingobium japonicum, and one established itself in Agrobacterium tumefaciens but was very unstable. In contrast, both IncP-1γ minireplicons, which produced higher levels of replication initiation protein than the wild-type plasmids, replicated in all strains, suggesting that poor establishment of the native plasmids is in part due to suboptimal replication initiation gene regulation. The findings suggest that host ranges of distinct IncP-1 plasmids only partially overlap, which may limit plasmid recombination and thus result in further genome divergence.

Comparative genomics of IncP-1ε plasmids from water environments reveals diverse and unique accessory genetic elements

The goal of this study was to determine and compare the complete genome sequences of three new broad-host-range conjugative plasmids. Plasmids pMLUA1, pMLUA3 and pMLUA4 were previously recovered from estuarine water by exogenous plasmid isolation and ranged in size from ∼55 to 59 kb. Comparative genomics showed that their backbone region was identical to the prototype pKJK5 and other IncP1-ε plasmids captured from soils. The accessory region was inserted between the tra region and parA, and presented the typical IncP-1ε ISPa17 and Tn402-like transposon modules. Nevertheless, new class 1 integrons were identified (In794, carrying aadA5 and In795, carrying qacF5-aadA5), as well as a composite transposon IS26-msr(E)-mph(E)-IS26 carrying genes that confer resistance to macrolides. A new insertion sequence, termed ISUnCu17, was also identified on pMLUA3. The architecture of the accessory regions implies the occurrence of multiple insertions and deletions. These data support the notion that IncP-1 plasmids from the ε subgroup are proficient in the capture of diverse genetic elements, including antibiotic resistance genes, and thus may contribute to the co-selection of several resistance determinants. This study constitutes the first report of completely sequenced IncP-1ε plasmids from water environments, and enhances our understanding of the geographic distribution and genetic diversity of these replicons.

Selection affects genes involved in replication during long-term evolution in experimental populations of the bacteriophage φX174

Observing organisms that evolve in response to strong selection over very short time scales allows the determination of the molecular mechanisms underlying adaptation. Although dissecting these molecular mechanisms is expensive and time-consuming, general patterns can be detected from repeated experiments, illuminating the biological processes involved in evolutionary adaptation. The bacteriophage φX174 was grown for 50 days in replicate chemostats under two culture conditions: Escherichia coli C as host growing at 37°C and Salmonella typhimurium as host growing at 43.5°C. After 50 days, greater than 20 substitutions per chemostat had risen to detectable levels. Of the 97 substitutions, four occurred in all four chemostats, five arose in both culture conditions, eight arose in only the high temperature S. typhimurium chemostats, and seven arose only in the E. coli chemostats. The remaining substitutions were detected only in a single chemostat, however, almost half of these have been seen in other similar experiments. Our findings support previous studies that host recognition and capsid stability are two biological processes that are modified during adaptation to novel hosts and high temperature. Based upon the substitutions shared across both environments, it is apparent that genome replication and packaging are also affected during adaptation to the chemostat environment, rather than to temperature or host per se. This environment is characterized by a large number of phage and very few hosts, leading to competition among phage within the host. We conclude from these results that adaptation to a high density environment selects for changes in genome replication at both protein and DNA sequence levels.

Adaptive regulatory substitutions affect multiple stages in the life cycle of the bacteriophage φX174

BACKGROUND

Previously, we showed that adaptive substitutions in one of the three promoters of the bacteriophage φX174 improved fitness at high-temperature by decreasing transcript levels three- to four-fold. To understand how such an extreme change in gene expression might lead to an almost two-fold increase in fitness at the adaptive temperature, we focused on stages in the life cycle of the phage that occur before and after the initiation of transcription. For both the ancestral strain and two single-substitution strains with down-regulated transcription, we measured seven phenotypic components of fitness (attachment, ejection, eclipse, virion assembly, latent period, lysis rate and burst size) during a single cycle of infection at each of two temperatures. The lower temperature, 37°C, is the optimal temperature at which phages are cultivated in the lab; the higher temperature, 42°C, exerts strong selection and is the condition under which these substitutions arose in evolution experiments. We augmented this study by developing an individual-based stochastic model of this same life cycle to explore potential explanations for our empirical results.

RESULTS

Of the seven fitness parameters, three showed significant differences between strains that carried an adaptive substitution and the ancestor, indicating the presence of pleiotropy in regulatory evolution. 1) Eclipse was longer in the adaptive strains at both the optimal and high-temperature environments. 2) Lysis rate was greater in the adaptive strains at the high temperature. 3) Burst size for the mutants was double that of the ancestor at the high temperature, but half that at the lower temperature. Simulation results suggest that eclipse length and latent period variance can explain differences in burst sizes and fitness between the mutant and ancestral strains.

CONCLUSIONS

Down-regulating transcription affects several steps in the phage life cycle, and all of these occur after the initiation of transcription. We attribute the apparent tradeoff between delayed progeny production and faster progeny release to improved host resource utilization at high temperature.

Intrinsically disordered regions of p53 family are highly diversified in evolution

Proteins of the p53 family are expressed in vertebrates and in some invertebrate species. The main function of these proteins is to control and regulate cell cycle in response to various cellular signals, and therefore to control the organism's development. The regulatory functions of the p53 family members originate mostly from their highly-conserved and well-structured DNA-binding domains. Many human diseases (including various types of cancer) are related to the missense mutations within this domain. The ordered DNA-binding domains of the p53 family members are surrounded by functionally important intrinsically disordered regions. In this study, substitution rates and propensities in different regions of p53 were analyzed. The analyses revealed that the ordered DNA-binding domain is conserved, whereas disordered regions are characterized by high sequence diversity. This diversity was reflected both in the number of substitutions and in the types of substitutions to which each amino acid was prone. These results support the existence of a positive correlation between protein intrinsic disorder and sequence divergence during the evolutionary process. This higher sequence divergence provides strong support for the existence of disordered regions in p53 in vivo for if they were structured, they would evolve at similar rates as the rest of the protein.

Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees

Plasmids of the incompatibility group IncP-1 can transfer and replicate in many genera of the Proteobacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental remediation. Although it is well understood that the accessory genes are transferred horizontally between plasmids, recent studies have also provided examples of recombination in the backbone genes of IncP-1 plasmids. As a consequence, phylogeny estimation based on backbone genes is expected to produce conflicting gene tree topologies. The main goal of this study was therefore to infer the evolutionary history of IncP-1 plasmids in the presence of both vertical and horizontal gene transfer. This was achieved by quantifying the incongruence among gene trees and attributing it to known causes such as 1) phylogenetic uncertainty, 2) coalescent stochasticity, and 3) horizontal inheritance. Topologies of gene trees exhibited more incongruence than could be attributed to phylogenetic uncertainty alone. Species-tree estimation using a Bayesian framework that takes coalescent stochasticity into account was well supported, but it differed slightly from the maximum-likelihood tree estimated by concatenation of backbone genes. After removal of the gene that demonstrated a signal of intergroup recombination, the concatenated tree was congruent with the species-tree estimate, which itself was robust to inclusion/exclusion of the recombinant gene. Thus, in spite of horizontal gene exchange both within and among IncP-1 subgroups, the backbone genome of these IncP-1 plasmids retains a detectable vertical evolutionary history.

HCMV-infected cells maintain efficient nucleotide excision repair of the viral genome while abrogating repair of the host genome

Many viruses subvert the host cell's ability to mount and complete various DNA damage responses (DDRs) after infection. HCMV infection of permissive fibroblasts activates host DDRs at the time of viral deposition and during replication, but the DDRs remain uncompleted without arrest or apoptosis. We believe this was in part due to partitioning of the damage response and double strand break repair components. After extraction of soluble proteins, the localization of these components fell into three groups: specifically associated with the viral replication centers (RCs), diffused throughout the nucleoplasm and excluded from the RCs. Others have shown that cells are incapable of processing exogenously introduced damage after infection. We hypothesized that the inability of the cells to process damage might be due to the differential association of repair components within the RCs and, in turn, potentially preferential repair of the viral genome and compromised repair of the host genome. To test this hypothesis we used multiple strategies to examine repair of UV-induced DNA damage in mock and virus-infected fibroblasts. Comet assays indicated that repair was initiated, but was not completed in infected cells. Quantitative analysis of immunofluorescent localization of cyclobutane pyrimidine dimers (CPDs) revealed that after 24 h of repair, CPDs were significantly reduced in viral DNA, but not significantly changed in the infected host DNA. To further quantitate CPD repair, we developed a novel dual-color Southern protocol allowing visualization of host and viral DNA simultaneously. Combining this Southern methodology with a CPD-specific T4 endonuclease V alkaline agarose assay to quantitate repair of adducts, we found efficient repair of CPDs from the viral DNA but not host cellular DNA. Our data confirm that NER functions in HCMV-infected cells and almost exclusively repairs the viral genome to the detriment of the host's genome.

Human cytomegalovirus (HCMV) is a leading cause of birth defects. This may be due in part to this virus' ability to inflict specific damage to its host's DNA, combined with the disruption of an infected cell's ability to repair damage. Earlier studies found that components of the cell's repair machinery were differentially associated with the HCMV viral replication centers in the nucleus. Experiments here extend this observation to include components of the machinery involved in UV lesion repair. We hypothesized that association of components of the DNA repair machinery within the viral replication centers could favor the repair of viral DNA, but more importantly, be detrimental to the repair of cellular DNA. Infected cells were irradiated and examined for repair by three different methods. In the course of this study, we developed a new technique allowing simultaneous evaluation of both the viral and host genomes in an infected cell. These experiments found rapid, selective removal of UV lesions from the viral and not the cellular DNA within infected cells. Our results indicate the differential association of certain cellular repair proteins with this virus may have far-reaching implications in the disease pathogenesis of HCMV infection.

Differential transcription of bacteriophage φX174 genes at 37 °C and 42 °C

To investigate how high temperature affects viral transcription, the absolute amounts of mRNA for six bacteriophage φX174 genes were compared at 37°C and 42°C using Q-PCR. At 37°C, mRNA levels for all genes were consistent with previous studies, but at 42°C mRNA levels for four genes were significantly different from levels at 37°C. Transcript levels were higher for genes B and D; the promoter before gene B appears to be up-regulated at high temperature. Levels for genes F and G were reduced at high temperature, possibly due to increased efficiency of the transcription termination signal immediately upstream of gene F. These functional changes in φX174 gene regulation at high temperature have not been described previously. Studies of phage evolution at high temperatures indicate that this difference in transcript levels is subject to adaptation.

Patterns of placental development evaluated by X chromosome inactivation profiling provide a basis to evaluate the origin of epigenetic variation

BACKGROUND

Inactivation of the maternally or paternally derived X chromosome (XCI) initially occurs in a random manner in early development; however as tissues form, a ‘patchiness’ will occur in terms of which X is inactivated if cells positioned near each other are clonally descended from a common precursor. Determining the relationship between skewed XCI in different tissues and in different samples from the same tissue provides a molecular assessment of the developmental history of a particular tissue that can then be used to understand how genetic and epigenetic variation arises in development.

METHODS

XCI skewing was evaluated in and compared between amnion, chorion, trophoblast and mesenchyme using multiple sampling sites from 14 term placentae. XCI was also evaluated in chorionic villus samples obtained at multiple sites and depths from four additional term placentae. The pattern of variation was then compared with methylation variation associated with the H19/IGF2 imprinting control region (ICR); promoter regions of KISS1, PTPN6, CASP8 and APC; and LINE-1 elements.

RESULTS

Mean placental level of skewing for amnion and chorion are correlated, consistent with a common developmental origin of at least a component of these membranes from inner cell mass derivatives subsequent to XCI, while trophoblast appears to be derived independently, consistent with its origin from the trophectoderm. Villus samples taken from different depths spanning the fetal to maternal side of the placenta were highly clonally related. Comparing patterns of clonal growth identified through XCI to the distribution of epigenetic variation in other genomic regions suggests that some variation arises early in development (e.g. LINE-1 methylation), whereas other variation arises predominantly after villus tree formation (e.g. methylation at H19/IGF2 ICR).

CONCLUSIONS

The patterns of XCI skewing are consistent with a model whereby each biopsied site of chorionic villi represents one or a few individual villus trees, each of which is clonally derived from only one or a few precursor cells. Sampling of placentae to evaluate changes associated with clinical pathology should be done with consideration of the tree-to-tree differences. A limitation of this study is the small number of placentas used and therefore placental-specific differences in variation could not be assessed.

The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution

The dissemination of antibiotic resistance genes among bacteria often occurs by means of plasmids. Wastewater treatment plants (WWTP) were previously recognized as hot spots for the horizontal transfer of genetic material. One of the plasmid groups that is often associated with drug resistance is the incompatibility group IncN. The aim of this study was to gain insights into the diversity and evolutionary history of IncN plasmids by determining and comparing the complete genome sequences of the four novel multi-drug resistance plasmids pRSB201, pRSB203, pRSB205 and pRSB206 that were exogenously isolated from the final effluent of a municipal WWTP. Their sizes range between 42,875 bp and 56,488 bp and they share a common set of backbone modules that encode plasmid replication initiation, conjugative transfer, and plasmid maintenance and control. All plasmids are transferable at high rates between Escherichia coli strains, but did not show a broad host range. Different genes conferring resistances to ampicillin, streptomycin, spectinomycin, sulfonamides, tetracycline and trimethoprim were identified in accessory modules inserted in these plasmids. Comparative analysis of the four WWTP IncN plasmids and IncN plasmids deposited in the NCBI database enabled the definition of a core set of backbone genes for this group. Moreover, this approach revealed a close phylogenetic relationship between the IncN plasmids isolated from environmental and clinical samples. Phylogenetic analysis also suggests the existence of host-specific IncN plasmid subgroups. In conclusion, IncN plasmids likely contribute to the dissemination of resistance determinants between environmental bacteria and clinical strains. This is of particular importance since multi-drug resistance IncN plasmids have been previously identified in members of the Enterobacteriaceae that cause severe infections in humans.