Gonorrhoea treatment failure caused by a Neisseria gonorrhoeae strain with combined ceftriaxone and high-level azithromycin resistance, England, February 2018

We describe a gonorrhoea case with combined high-level azithromycin resistance and ceftriaxone resistance. In February 2018, a heterosexual male was diagnosed with gonorrhoea in the United Kingdom following sexual intercourse with a locally resident female in Thailand and failed treatment with ceftriaxone plus doxycycline and subsequently spectinomycin. Resistance arose from two mechanisms combining for the first time in a genetic background similar to a commonly circulating strain. Urgent action is essential to prevent further spread.

DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing

PURPOSE

Speed of bloodstream infection diagnosis is vital to reduce morbidity and mortality. Whole genome sequencing (WGS) performed directly from liquid blood culture could provide single-assay species and antibiotic susceptibility prediction; however, high inhibitor and human cell/DNA concentrations limit pathogen recovery. We develop a method for the preparation of bacterial DNA for WGS-based diagnostics direct from liquid blood culture.

METHODOLOGY

We evaluate three commercial DNA extraction kits: BiOstic Bacteraemia, Amplex Hyplex and MolYsis Plus. Differential centrifugation, filtration, selective lysis and solid-phase reversible immobilization bead clean-up are tested to improve human cells/DNA and inhibitor removal. Using WGS (Illumina/MinION), we assess human DNA removal, pathogen recovery, and predict species and antibiotic susceptibility inpositive blood cultures of 44 Gram-negative and 54 Staphylococcus species.Results/Key findings. BiOstic kit extractions yield the greatest mean DNA concentration, 94-301 ng µl^-1, versus 0-2.5 ng µl^-1 using Amplex and MolYsis kits. However, we note higher levels of inhibition (260/280 ratio 0.9-2.1) and human DNA (0.0-4.4×10⁶ copies) in BiOstic extracts. Differential centrifugation (2000 g, 1 min) prior to BiOstic extraction reduces human DNA by 63-89 % with selective lysis minimizing by a further 62 %. Post-extraction bead clean-up lowers inhibition. Overall, 67 % of sequenced samples (Illumina MiSeq) contain <10 % human DNA, with >93 % concordance between WGS-based species and susceptibility predictions and clinical diagnosis. If >60 % of sequencing reads are human (7/98 samples) susceptibility prediction becomes compromised. Novel MinION-based WGS (n=9) currently gives rapid species identification but not susceptibility prediction.

CONCLUSION

Our method for DNA preparation allows WGS-based diagnosis direct from blood culture bottles, providing species and antibiotic susceptibility prediction in a single assay.

Abstract B2-21: Identification of somatic RNA splicing alterations in human cancers

Recent whole-exome sequencing studies have found that somatic mutations frequently occur in splicing factors across multiple cancer types, supporting the need to systematically and globally characterize splicing alterations across human cancers. Somatic alterations that affect RNA processing of cancer genes may be caused by multiple mechanisms, including mutations in splicing factors, mutations in cis-acting splice sites and other regulatory sequences, alterations in methylation, or alterations in chromatin structure. For a global look at somatic RNA splicing alterations, we are applying the Cancer Outlier Profile Analysis (COPA) approach on ~7,000 cancer transcriptomes from 12 tumor types in The Cancer Genome Atlas (TCGA) and investigating the underlying somatic mutations that cause these splicing alterations using matched whole-exome, whole-genome, and methylation data from these samples.

To identify and quantify alternative splicing in RNA-Seq data, including unannotated splicing events, we have further developed a computational pipeline called JuncBASE. To distinguish between cancer-specific splicing alterations and normal transcriptome variation, we are utilizing ~700 RNA-Seq libraries from healthy individuals from the Genotype-Tissue Expression (GTEx) project.

COPA analysis of outlier splicing events in lung adenocarcinomas and glioblastomas successfully identified known altered splicing events in MET and EGFR, respectively, that are caused by DNA level somatic mutations. The genomic mechanisms for novel somatic splicing events in known cancer genes such as FGFR3, as well as genes previously uncharacterized in cancer genomes, are currently being investigated.

To identify splicing events that may be novel somatic driver alterations, these events have been profiled using RNA-Seq data from the Cancer Cell Line Encyclopedia and are being used as biomarkers to identify genetic vulnerabilities in high-throughput shRNA screens. This work will have a significant impact on the identification of somatic splicing events that contribute to cancer pathogenesis.

Citation Format: Angela N. Brooks, Yawei Ge, Kevin Chau, Samuel S. Freeman, Gordon Saksena, Chandra Sekhar Pedamallu, Matthew Meyerson. Identification of somatic RNA splicing alterations in human cancers. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-21.

Transcatheter closure of persistent arterial ducts with different types of coils

BACKGROUND

Different types of coils have been designed for transcatheter closure of persistent arterial ducts. We compared the efficacy and safety of three types of coils: Gianturco coils (Cook), Cook detachable coils (Cook), and Duct Occlud devices (pfm).

METHODS

Sixty-three patients underwent coil occlusion of arterial ducts between April 1995 and July 2000. The mean age and weight were 4.8+/-3.4 years and 16.5+/-7.6 kg, respectively. The results and complications of ductal occlusion among the three types of coils were compared. Kaplan-Meier analysis was used to assess reduction in the prevalence of residual shunt with time, and multiple regression analysis was performed to identify predictors of complete occlusion.

RESULTS

Coil occlusion of persistent arterial ducts that measured 2. 2 +/- 0.8 mm was feasible in 90% (57/63) of patients. Gianturco coils were used in 29, Duct Occlud devices in 16, and Cook detachable coils in 12 patients. The prevalence of residual shunt at 24 hours, 6 months, 12 months, and 24 months was 42%, 20%, 18%, and 14%, respectively. The reduction in prevalence of residual shunt with time tended to be greater when Gianturco coils were used (P =. 067). Logistic regression identified the use of Gianturco coils to be a significant predictor of complete ductal occlusion on follow-up (P =.04). Pull-through of coils occurred in 4.8% (3/63) and coil embolization in 6.3% (4/63). There was no association between the type of coil and the risk of embolization (P = 1.00).

CONCLUSIONS

Transcatheter occlusion of small persistent arterial ducts with coils is safe and effective. There is no advantage of detachable coils (Cook detachable coils and Duct Occlud devices) over nondetachable Gianturco coils in reducing the risk of embolization. Our findings are in favor of the inexpensive, but more effective, Gianturco coils for occluding small arterial ducts of 3 mm or less.

A novel downstream positive regulatory element mediating transcription of the human high mobility group (HMG) I-C gene

The high mobility group (HMG) I proteins are small, non-histone chromosomal proteins that promote gene activation during development and within rapidly dividing cells. They do so by facilitating enhanceosome formation on inducible genes, via both protein/DNA and protein/protein interactions. The HMG I-C gene is tightly regulated, normally being expressed exclusively during embryonic development. However, HMG I-C expression is also observed frequently in a number of tumor types, and this expression has been shown to contribute to the malignant transformation process. With the aim of dissecting pathways that lead to aberrant expression of HMG I-C in tumor cells, we have analyzed HMG I-C gene regulation in the human hepatoma cell line PLC/PRF/5. One of the two HMG I-C transcripts detected in this cell line originates from a novel downstream initiation site at nucleotide -161 relative to the first methionine. Transcription from the downstream initiation site is mediated by a PRE located between nt -222 and -217. We show here that the Sp1 and Sp3 transcription factors interact with the PRE and transactivate the HMG I-C promoter in a cooperative fashion. This study provides the first characterization of this downstream HMG I-C promoter.

A novel downstream positive regulatory element mediating transcription of the human high mobility group (HMG) I-C gene

The high mobility group (HMG) I proteins are small, non-histone chromosomal proteins that promote gene activation during development and within rapidly dividing cells. They do so by facilitating enhanceosome formation on inducible genes, via both protein/DNA and protein/protein interactions. The HMG I-C gene is tightly regulated, normally being expressed exclusively during embryonic development. However, HMG I-C expression is also observed frequently in a number of tumor types, and this expression has been shown to contribute to the malignant transformation process. With the aim of dissecting pathways that lead to aberrant expression of HMG I-C in tumor cells, we have analyzed HMG I-C gene regulation in the human hepatoma cell line PLC/PRF/5. One of the two HMG I-C transcripts detected in this cell line originates from a novel downstream initiation site at nucleotide -161 relative to the first methionine. Transcription from the downstream initiation site is mediated by a PRE located between nt -222 and -217. We show here that the Sp1 and Sp3 transcription factors interact with the PRE and transactivate the HMG I-C promoter in a cooperative fashion. This study provides the first characterization of this downstream HMG I-C promoter.

Cis-element dependence and occupancy of the human invariant chain promoter in CIITA-dependent and -independent transcription

The major histocompatibility complex (MHC)-associated invariant chain (Ii) associates with the class II alpha/beta heterodimer during its biosynthesis, inhibiting association of endogenous peptides with the peptide-binding cleft. It is therefore not surprising that there are significant similarities in regulatory mechanisms controlling the expression of the structural class II MHC and Ii genes. One important similarity is that both classes of genes can be expressed via CIITA-dependent or -independent mechanisms. In this report, we have dissected CIITA-dependent and -independent transcription of the Ii gene using an isogenic B-LCL cell pair (Jijoye and clone-13) which do or do not express the class II MHC transactivator (CIITA), respectively. Experiments using mutant or deletion constructs of the Ii gene promoter indicate that while both the X-box and li-kappaB1 elements are critical for CIITA-dependent transcription in B lymphocytes, the Ii-kappaBI element is of greater importance for CIITA-independent Ii gene transcription, with the X-box playing a secondary role. Despite these clear differences in cis-element dependence of CIITA-dependent and -independent Ii transcription, there are only subtle differences in the occupancy of these elements in vivo as assessed by genomic footprinting. These differences are restricted to occupancy of the X-box and Y-box, with which the RF-X and NF-Y complexes interact in Ii-positive cells. This difference in the occupancy of the X-box and Y-box in this cell pair indicates that while protein/protein interactions between CIITA and promoter-bound factors stabilize promoter occupancy, these interactions are not absolutely required for occupancy and transcription of the invariant chain gene.

Acute sporadic non-A, non-B, non-C, non-D, non-D, non-E hepatitis

Patients presenting with clinical and laboratory features consistent with a diagnosis of acute non-A, non-B hepatitis were evaluated for evidence of hepatitis C or hepatitis E infection and for evidence of severe or prolonged disease. Antibody to hepatitis C virus (anti-HCV) was detected in 75 of 108 (69%) patients, antibody to hepatitis E virus (anti-HEV) in three patients (3%), and neither antibody in 31 (29%) patients. One patient had both anti-HCV and anti-HEV. HCV RNA was not detected in sera from any of 20 patients with seronegative (non-ABCDE) hepatitis, but in all 10 patients with anti-HCV who were tested by polymerase chain reaction (PCR). Compared with patients with acute hepatitis C, those with non-ABCDE hepatitis had a lower incidence of parenteral risk factors (6% vs. 70%; P < .001), higher peak serum bilirubin levels (45% vs. 5% with peak levels > 15 mg/dL; P < .001), more prolonged jaundice (25% vs. 0% with peak bilirubin >5 weeks after onset; P < .01), more severe prothrombin time abnormalities (26% vs. 0% with >3 second prolongation; P < .001), more severe hypoalbuminemia (39% vs. 9% with albumin <3 g/dL; P < .01), and more frequent major clinical complications (13% vs. 0% with encephalopathy; P < .01; 10% vs. 0% with death or transplant; P = .024). Patients with acute non-ABCDE hepatitis were less likely to develop chronic hepatitis than those with acute hepatitis C (23% vs. 68%; P < .05). Thus, patients with acute non-ABCDE hepatitis are epidemiologically distinct from those with acute hepatitis C and have a significantly more severe acute illness.

IgM antibody response in acute hepatitis C viral infection

IgM antibody against hepatitis C virus (IgM anti-HCV) was measured in serial samples from 15 transfusion recipients in whom posttransfusion chronic non-A, non-B hepatitis (NANBH) developed and three plasmapheresis donors during acute HCV infection using recombinant proteins derived from three immunodominant regions: core, NS-3, and NS-4 (c100). IgM anti-HCV core was detected in 13 of 15 posttransfusion patients. Nine of these patients had transient, acute-phase IgM anti-HCV core detected coincidentally or earlier than active IgG anti-HCV core response. The average duration of IgM anti-HCV core reactivity was 8.1 +/- 3.7 weeks. One patient lacking an IgM anti-HCV core response had detectable IgM anti-HCV NS-3 during the acute phase. Passive transfer of IgM anti-HCV was not observed in these posttransfusion cases, in contrast to the high frequency observed for IgG anti-HCV. Late IgM anti-HCV was detectable against core, c100, and NS-3 in three, two, and one posttransfusion patients, respectively. These data indicate that IgM anti-HCV core is a useful acute-phase marker in HCV infection.