Severe underquantification of HIV-1 group O isolates by major commercial PCR-based assays

HIV-1 diversity poses major challenges to viral load assays because genetic polymorphisms can impede nucleic acid detection. In addition to the on-going viral diversification within the HIV-1 group M pandemic, HIV-1 genetic diversity is further increased by non-group M infections, such as HIV-1 groups O (HIV-1-O), N and P. We here conducted a systematic evaluation of commercially available PCR assays to detect HIV-1-O isolates. We collected 25 primary HIV-1-O isolates covering all genetic clusters within HIV-1-O. Subsequently, this panel of isolates was tested on eight commercially available quantitative and five qualitative HIV-1 PCR-based assays in serial dilutions. Sequence analyses were performed for severe cases of underquantification or lack of detection. We observed differences between the assays in quantification that depended on the HIV-1-O isolate's subgroup. All three tested HIV-1-O subgroup IV isolates were underquantified by the Roche CAP/CTM >800-fold compared to the Abbott RealTime assay. In contrast, the latter assay underquantified several subgroup I isolates >200-fold. Notably, the Xpert HIV-1 Viral Load test from Cepheid failed to detect two of the HIV-1-O isolates, whereas the Roche Cobas 8800 assay readily detected all isolates. Comparative sequence analyses identified polymorphisms in the HIV-1-O long-terminal repeat and integrase genes that likely underlie inadequate nucleic acid amplification. Potential viral load underquantification should be considered in therapeutic monitoring of HIV-1-O-infected patients. Pre-clinical assessments of HIV-1 diagnostic assays could be harmonized by establishing improved and internationally standardized panels of HIV-1 isolates that cover the dynamic diversity of circulating HIV-1 strains.

Prophylactic salpingectomy for prevention of ovarian cancer at the time of elective laparoscopic cholecystectomy

Background

Most serous ovarian cancers are now understood to originate in the fallopian tubes. Removing the tubes (salpingectomy) likely reduces the risk of developing high‐grade serous ovarian cancer. Numerous gynaecological societies now recommend prophylactic (or opportunistic) salpingectomy at the time of gynaecological surgery in appropriate women, and this is widely done. Salpingectomy at the time of non‐gynaecological surgery has not been explored and may present an opportunity for primary prevention of ovarian cancer.

Methods

This study investigated whether prophylactic salpingectomy with the intention of reducing the risk of developing ovarian cancer would be accepted and could be accomplished at the time of elective laparoscopic cholecystectomy. Women aged at least 45 years scheduled for elective laparoscopic cholecystectomy were recruited. They were counselled and offered prophylactic bilateral salpingectomy at the time of cholecystectomy. Outcome measures were rate of accomplishment of salpingectomy, time and procedural steps needed for salpingectomy, and complications.

Results

A total of 105 patients were included in the study. The rate of acceptance of salpingectomy was approximately 60 per cent. Salpingectomy was performed in 98 of 105 laparoscopic cholecystectomies (93·3 per cent) and not accomplished because of poor visibility or adhesions in seven (6·7 per cent). Median additional operating time was 13 (range 4–45) min. There were no complications attributable to salpingectomy. One patient presented with ovarian cancer 28 months after prophylactic salpingectomy; histological re‐evaluation of the tubes showed a previously undetected, focal serous tubal intraepithelial carcinoma.

Conclusion

Prophylactic salpingectomy can be done during elective laparoscopic cholecystectomy.

P6529Safety of emergency pretreatment regimen for contrast allergy before percutaneous coronary intervention for ST-elevation myocardial infarction

Background

Primary percutaneous coronary intervention (PPCI) is the best treatment for ST-elevation myocardial infarction (STEMI). However, patients with prior contrast reactions may not receive PCI due to concern over a recurrent contrast reaction.

Purpose

To determine the clinical efficacy of emergency pretreatment regimens for contrast allergy in STEMI patients undergoing PPCI.

Methods

We retrospectively identified all individuals with a history of contrast allergy who presented with STEMI, were pretreated for contrast allergy, and underwent PPCI at our medical center between January 2005 to May 2018. Emergency pretreatment regimen included a combination of intravenous (IV) steroid, IV famotidine and IV diphenhydramine administered immediately before PCI. Laboratory records, inpatient notes, and discharge summaries were reviewed to confirm the severity of the original contrast allergy and identify any allergic breakthrough reaction after pretreatment with an emergency regimen. Reactions were characterized as mild, moderate, severe, or of unknown severity.

Results

During the study period 15,712 individuals underwent PCI, of which 176 patients presented with STEMI, had confirmed contrast allergy, and were pretreated before undergoing PCI. No patient with a history of contrast allergy underwent PPCI without pre-treatment. Mean age was 64 years, with 52% males, and all individuals were white. The majority had hypertension (77%), 67% had dyslipidemia, 29% had diabetes mellitus, and 20% patients had a prior history of MI. Intravenous steroids used in the emergency regimen included methylprednisone (n=100), hydrocortisone (n=70), and dexamethasone (n=6). The original allergic response to ICM was mild in 59% patients, moderate in 15%, severe in 20% and of unknown severity in 13% patients. Of the 176 patients only 10 (5.6%) developed a breakthrough reaction. Most of which were mild; none was fatal. Median length of hospital stays was three days and nine patients (10.8%) passed away within 30 days of hospital admission.

Conclusions

Patients with prior contrast allergy presenting with STEMI can safely undergo PPCI after emergency pretreatment. Breakthrough reactions are infrequent and mild.

Small bowel polyp resection using device-assisted enteroscopy in Peutz-Jeghers Syndrome: Results of a specialised tertiary care centre

INTRODUCTION

Enteroscopy resection of small bowel polyps in Peutz-Jeghers syndrome has only been described in small case series. Herein, we aimed to assess the efficacy of enteroscopy resection of small bowel polyps within a specialised tertiary care centre and the impact on intraoperative enteroscopy.

METHODS

This was an observational single-centre study. All adult Peutz-Jeghers syndrome patients followed in the Predisposition Digestive Ile-de-France network who underwent an endoscopic resection of at least one small bowel polyp ≥ 1 cm by enteroscopy between 2002-2015 were included. Small bowel polyps were detected under a dedicated screening programme by previous capsule endoscopy and/or magnetic resonance enterography, performed every 2-3 years. Complete treatment was defined as the absence of polyps ≥ 1 cm after conventional endoscopic resection. Intraoperative enteroscopy or surgical resection were indicated in incomplete treatments. The overall complete treatment rate including conventional enteroscopy and intraoperative enteroscopy was also considered.

RESULTS

Endoscopic resection of 216 small bowel polyps (median: 8.6 per patient, size: 6-60 mm) was performed by 50 enteroscopies in 25 patients (mean age: 36 years, range: 18-71, 56% male) with small bowel polyp ≥ 1 cm. Twenty-three patients (92%) underwent 42 screening capsule endoscopies and 14 (57%) had 23 magnetic resonance enterographies during a median follow-up of 60 months. Complete treatment was achieved in 76%. Intraoperative enteroscopy and surgical resection were performed in four (16%) and two (8%) patients. Intraoperative enteroscopy improved by 16% the complete treatment rate and the overall rate was 92%. The complication rate was 6%.

CONCLUSION

This long-term study confirmed the efficacy and safety of endoscopic resection of small bowel polyps in Peutz-Jeghers syndrome. Intraoperative enteroscopy can be a complementary approach in selected cases.

Low mortality and short-term morbidity in very preterm infants in Austria 2011-2016

AIM

The current study determined survival, short-term neonatal morbidity and predictors for death or adverse outcome of very preterm infants in Austria.

METHODS

This population-based cohort study included 5197 very preterm infants (53.3% boys) born between 2011 and 2016 recruited from the Austrian Preterm Outcome Registry. Main outcome measures were gestational age-related mortality and major short-term morbidities.

RESULTS

Overall, survival rate of all live-born infants included was 91.6% and ranged from 47.1% and 73.4% among those born at 23 and 24 weeks of gestation to 84.9% and 88.2% among infants born at 25 and 26 weeks to more than 90.0% among those with a gestational age of 27 weeks or more. The overall prevalence of chronic lung disease, necrotising enterocolitis requiring surgery, intraventricular haemorrhage Grades 3-4, and retinopathy of prematurity Grades 3-5 was 10.0%, 2.1%, 5.5%, and 3.6%, respectively. Low gestational age, low birth weight, missing or incomplete course of antenatal steroids, male sex, and multiple births were significant risk predictors for death or adverse short-term outcome.

CONCLUSION

In this national cohort study, overall survival rates were high and short-term morbidity rate was low.

Implementation of a Rooftop Farm Integrated With a Teaching Kitchen and Preventive Food Pantry in a Hospital Setting

Safety-net hospitals serving populations with disproportionately high levels of poverty, food insecurity, and chronic disease can utilize innovative strategies to improve the health and environment of their communities. Boston Medical Center in Boston, Massachusetts, constructed an on-site rooftop farm to provide fresh produce for the hospital's preventive food pantry, teaching kitchen, cafeterias, and inpatient meal services. This novel model can be replicated by other organizations aiming to alleviate food insecurity, encourage healthy eating, and promote environmental sustainability.

The impact of the COMT genotype and cognitive demands on facets of intra-subject variability

Intra-Subject Variability (ISV), a potential index of catecholaminergic regulation, is elevated in several disorders linked with altered dopamine function. ISV has typically been defined as reaction time standard deviation. However, the ex-Gaussian and spectral measures capture different aspects and may delineate different underlying sources of ISV; thus reflecting different facets of the construct. We examined the impact of factors associated with dopamine metabolism, namely, Catechol-O-Methyltransferase Val158Met (COMT) genotype and Working Memory (WM) and response-switching on ISV facets in young healthy adults. The Met allele was associated with overall increased variability. The rather exclusive sensitivity of ex-Gaussian tau to frequencies below 0.025 Hz and the quasi-periodic structure of particularly slow responses support the interpretation of tau as low frequency fluctuations of neuronal networks. Sigma, by contrast, may reflect neural noise. Regarding cognitive demands, a WM load-related increase in variability was present for all genotypes and all ISV facets. Contrastingly, ISV facets reacted differently to variations in response-switching as, across genotypes, sigma was elevated for rare target trials whereas tau was elevated for frequent standard trials, particularly for Met homozygotes. Our findings support the significant role of COMT in regulating behavioural ISV with its facetted structure and presumed underlying neural processes.

Evaluation of an ear-attached accelerometer for detecting estrus events in indoor housed dairy cows

Precision dairy farming technologies have tremendous potential to improve and support farmers in herd management decisions, particularly in reproductive management. Nowadays, estrus detection in cows is challenging and several supporting tools are available. In this study, a 3D-accelerometer integrated into an ear-tag (SMARTBOW, Smartbow GmbH, Weibern, Austria) was used for the detection of cows in estrus. Movement pattern based on accelerometer data were analyzed and processed by algorithms and machine learning, resulting in estrus alerts. For the evaluation of the system, reproductive performance data of 579 estrus events of multiparous cows were used to retrospectively evaluate the accuracy of estrus alerts generated by the accelerometer-based system and the overall performance of the system. Estrus events were classified as 'gold standard' events, if an estrus followed by AI resulted in pregnancy, and as 'recorded estrus' events, if two estrus events with an interval of 18-25 d were in the herd records, independent of whether estrus was followed by AI or pregnancy. In total, 316 'gold standard' events were matched with estrus alerts generated by the accelerometer-based system, resulting in a sensitivity of 97%. Furthermore, 263 'recorded estrus' events were compared with correct or incorrect estrus alerts by the system. Sensitivity, specificity, positive and negative predictive values, accuracy, and error rate for 'recorded estrus' events were 97%, 98%, 96%, 94%, 96%, and 2%, respectively. In summary, the SMARTBOW system is suitable for an automated detection of estrus events of multiparous cows in indoor housed dairy cows.

Abstract PD9-01: Genomic alterations associated with loss of HR expression in metastatic breast cancer

Background: Discordance in hormone receptor (HR) status between primary (p) tumors and metastatic (m) recurrences has been widely described. Loss of estrogen and progesterone receptor expression occurs in ˜12% of asynchronous recurrences, leading to triple-negative (TN) status in the metastasis. Genomic mechanisms driving HR loss and its prognostic and therapeutic implications have not been fully elucidated.

Methods: Targeted NGS (Oncopanel, OP) at Dana-Farber Cancer Institute using multiplexed copy number variation and mutation (mut) detection across the full coding regions of 300 genes and selected intronic regions of 35 genes was prospectively performed on either archival primary or metastatic samples collected in patients (pts) with metastatic breast cancer (MBC). Receptor status at initial diagnosis and recurrence were reviewed using a 1% cutoff to define HR-positivity and excluding HER2+ cases. Fisher´s exact test was used to compare frequency of alterations. Tumor mut burden (TMB) was computed normalizing the sum of reported exon mut in each pt by the exonic-bait-set size of the panel.

Results: Between 8/2013-9/2016, 929 pts with MBC underwent OP testing. Of 517 pts diagnosed with primary HR+/HER2- breast cancer, at time of recurrence 388 remained HR+/HER2- (pHR+/mHR+), 39 switched to HR-/HER2- (pHR+/mTN, of which 23 (59%) had initial HR expression >10%), 10 switched to HER2+ and 80 had unknown metastatic receptor status. Comparison between primary samples in pHR+/mHR+ (n=245) and pHR+/mTN (n=24) showed that pHR+/mTN was significantly more likely to harbor mut in TP53, STK11 and MSH6, amplifications (amp) in CCNE1 and FGFR2, and less likely to have PIK3CA mut or CCND1 amp. Median TMB in primary pHR+/mHR+ was 6.05 mut/Mb (0-37.5) and 5.68 mut/Mb (1.2-10.9) in pHR+/mTN (p=0.45). Metastatic samples in pHR+/mTN (n=15) were enriched in ARID1A, CRTC2 and CDH1 mut compared to metastases (n=40) in pts who remained TN (pTN/mTN). Deletions in CDKN2A/2B and RB1, and mut in TP53, NOTCH2 and ERCC2 were more prevalent in recurrent tumors of pHR+/mTN than pHR+/mHR+. In metastases, TMB was higher in pHR+/mTN than pTN/mTN or pHR+/mHR+ (10.9 vs. 7.0 vs. 7.3 mut/Mb, respectively; p=0.002). Median OS from initial diagnosis was 9.4 yrs in pHR+/mTN, less than pHR+/mHR+ (15.9 yrs; p=0.009) and greater than pTN/mTN (4.3 yrs; p=0.008). Median OS from MBC diagnosis was 1.8 yrs in pHR+/mTN, less than pHR+/mHR+ (6.4 yrs; p=0.001) but not significantly different than pTN/mTN (1.5 yrs, p=0.3).

 pHR+/mHR+ (n=245)pHR+/mTN (n=24)p value NFreq (%)NFreq (%) MutTP536325.72083.3<0.00001PIK3CA9438.4000GATA33514.3000.053STK1152.0312.50.026MSH641.6312.50.017AmpFGFR20028.30.008CCNE10028.30.008CCND14418.0000.018

Conclusion: Targeted NGS shows that alterations in DNA damage and cell-cycle regulation pathways in primary HR+ tumors are associated with HR loss in the metastatic setting. Primary tumors that lose HR appear more similar to basal-like than luminal tumors, despite >10% baseline HR expression in most pts, and once metastatic, survival is comparable to pTN/mTN. Metastases with HR loss have higher TMB than those that remain HR+ or TN throughout the course of the disease. These findings, if confirmed, may influence treatment and pt selection for clinical trials.

Citation Format: Garrido-Castro AC, Hughes ME, Cherniack A, Barroso-Sousa R, Bychkovsky BL, Di Lascio S, Berger A, Mittendorf EA, Files JL, Guo H, Kumari P, Cerami E, Krop IE, Wagle N, Lindeman NI, MacConaill LE, Dillon DA, Winer EP, Lin NU. Genomic alterations associated with loss of HR expression in metastatic breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD9-01.