Adam Giess

• MSc
• University of Bergen

NDM-producing Klebsiella pneumoniae strains represent major clinical and infection control challenges, particularly in resource-limited settings with high rates of antimicrobial resistance. Determining whether transmission occurs at a gene, plasmid, or bacterial strain level and within hospital and/or the community has implications for monitoring a...

Kinases and phosphatases regulate messenger RNA synthesis through post-translational modification of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (ref. 1). In yeast, the phosphatase Cdc14 is required for mitotic exit(2,3) and for segregation of repetitive regions(4). Cdc14 is also a subunit of the silencing complex...

Patients born outside the UK have contributed to a 20% rise in the UK's tuberculosis incidence since 2000, but their effect on domestic transmission is not known. Here we use whole-genome sequencing to investigate the epidemiology of tuberculosis transmission in an unselected population over 6 years. We identified all residents with Oxfordshire pos...

[This corrects the article DOI: 10.1371/journal.pone.0147990.].

Translation initiation is often attributed as the rate-determining step of eukaryotic protein synthesis and key to gene expression control. Despite this centrality, the series of steps involved in this process is poorly understood. Here, we capture the transcriptome-wide occupancy of ribosomes across all stages of translation initiation, enabling u...

Translation initiation is often attributed as the rate determining step of eukaryotic protein synthesis and key to gene expression control. Despite this centrality the series of steps involved in this process are poorly understood. Here we capture the transcriptome-wide occupancy of ribosomes across all stages of translation initiation, enabling us...

Abstract Background Extended-spectrum cephalosporin resistance (ESC-R) in Escherichia coli and Klebsiella pneumoniae is a healthcare threat; high gastrointestinal carriage rates are reported from South-east Asia. Colonisation prevalence data in Cambodia are lacking. The aim of this study was to determine gastrointestinal colonisation prevalence of...

Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated methods depend heavily on sequence composition and often underestimate the complexity of the proteome. We developed RibosomeE Profiling Assisted (re-)AnnotaTION (REPARATION), a...

Background While methods for annotation of genes are increasingly reliable, the exact identification of translation initiation sites remains a challenging problem. Since the N-termini of proteins often contain regulatory and targeting information, developing a robust method for start site identification is crucial. Ribosome profiling reads show dis...

Extended-spectrum cephalosporin resistance (ESC-R) in Escherichia coli and Klebsiella pneumoniae is a healthcare threat; high gastrointestinal carriage rates are reported from South-east Asia. Colonisation prevalence data in Cambodia are lacking. We determined gastrointestinal colonisation prevalence of ESC-resistant E. coli (ESC-R-EC) and K. pneum...

Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated methods depend heavily on sequence context and often underestimate the complexity of the proteome. We developed REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION), a de...

While methods for annotation of genes are increasingly reliable the exact identification of the translation initiation site remains a challenging problem. Since the N-termini of proteins often contain regulatory and targeting information developing a robust method for start site identification is crucial. Ribosome profiling reads show distinct patt...

Background: The 13-valent pneumococcal vaccine (PCV13) was introduced in Cambodia in January 2015. There are limited data concerning the common serotypes causing invasive pneumococcal disease (IPD). Knowledge of the circulating pneumococcal serotypes is important to monitor epidemiological changes before and after vaccine implementation. Methods:...

Streptococcus agalactiae (group B streptococcus, GBS) causes neonatal disease and stillbirth, but its burden in sub-Saharan Africa is uncertain. We assessed maternal recto–vaginal GBS colonization (7,967 women), stillbirth and neonatal disease. Whole-genome sequencing was used to determine serotypes, sequence types and phylogeny. We found low mater...

The recent widespread emergence of carbapenem resistance in Enterobacteriaceae is a major public health concern, as carbapenems are a therapy of last resort against this family of common bacterial pathogens. Resistance genes can mobilize via various mechanisms, including conjugation and transposition; however, the importance of this mobility in sho...

Streptococcus agalactiae (Group B Streptococcus, GBS) causes neonatal disease and stillbirth, but its burden in sub-Saharan Africa is uncertain. We assessed maternal recto-vaginal GBS colonisation (7967 women), stillbirth and neonatal disease. Whole genome sequencing was used to determine serotypes, sequence types (ST), and phylogeny. We found low...

Background Spontaneous reports from patients able to report vascular sequelae in real time, and recognition that serum non transferrin bound iron may reach or exceed 10μmol/L in the blood stream after iron tablets or infusions, led us to hypothesize that conventional iron treatments may provoke acute vascular injury. This prompted us to examine whe...

Morphological appearances of HDMEC pre/post 1hr treatments. (PDF)

RNA library preparations. (PDF)

Phred quality scores for reads from RNASeq libraries. (PDF)

Processes for genes differentially expressed at 1 hour at p<0.15: Colour highlighting is used to indicate Benjamini p values<0.05 (red text and yellow highlight), and p<0.15 (red text). (PDF)

RNASeq alignments to different RNA subtypes. (PDF)

Genes differentially expressed at 6 hour at p<0.05. (PDF)

Processes for genes differentially expressed at 6 hour at p<0.15: Colour highlighting is used to indicate Benjamini p values<0.05 (red text and yellow highlight), and p<0.15 (red text). (PDF)

Preliminary iron dose response studies. (PDF)

Morphological appearances of HPMEC pre/post 6hr treatments. (PDF)

Processes for genes differentially expressed between untreated dermal and pulmonary EC. Although 537 individual genes reached p<0.15, the lowest Benjamini p-values (~0.85) are equivalent to the results obtained from a random sets of genes. (PDF)

Genes differentially expressed at 1 hour at p<0.05. (PDF)

Streptococcus agalactiae (group B streptococcus, GBS) causes neonatal disease and stillbirth, but its burden in sub-Saharan Africa is uncertain. We assessed maternal recto-vaginal GBS colonization (7,967 women), stillbirth and neonatal disease. Whole-genome sequencing was used to determine serotypes, sequence types and phylogeny. We found low mater...

The recent widespread emergence of carbapenem resistance in Enterobacteriaceae is a major public health concern, as carbapenems are a therapy of last resort in this family of common bacterial pathogens. Resistance genes can mobilize via various mechanisms including conjugation and transposition, however the importance of this mobility in short-term...

Studies of the transmission epidemiology of antimicrobial-resistant Escherichia coli, such as strains harboring extended-spectrum beta-lactamase (ESBL) genes, frequently use selective culture of rectal surveillance swabs to identify isolates for molecular epidemiological investigation. Typically, only single colonies are evaluated, which risks unde...

Studies of the transmission epidemiology of antimicrobial-resistant Escherichia coli, such as those harboring extended-spectrum beta-lactamase (ESBL) genes, frequently use selective culture of rectal surveillance swabs to identify isolates for molecular epidemiological investigation. Typically, only single colonies are evaluated, which risks undere...

The global emergence of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-Kp) multilocus sequence type ST258 is widely recognized. Less is known about the molecular and epidemiological details of non-ST258 K. pneumoniae in the setting of an endemic plasmid-mediated outbreak. We describe the interplay of blaKPC plasmids, K. pneumoniae...

There are limited data on Enterobacter cloacae outbreaks and fewer describing these in association with NDM-1. With whole-genome sequencing, we tested the hypothesis that a cluster of 16 E. cloacae bacteraemia cases in a Nepali neonatal unit represented a single clonal outbreak, using a wider set of epidemiologically unrelated clinical E. cloacae i...

Introduction and objectives Concern about the DNA quality for next-generation sequencing encourages use of dedicated preparative kits. The purpose of this study was to attempt to sequence ten stored DNA samples that had been prepared from human blood using phenol chloroform methods 12–17 years earlier, frozen at -70 C and not subjected to special t...

Introduction and objectives To improve our understanding of the dynamic interplay between non-coding and coding RNA species, we developed solution-based methods to capture the entire endothelial transcriptome. In contrast to microarrays and CHIP-based methodologies, there was no pre-specification of RNA target sequences, and the identity of the DNA...

Introduction and objectives New methods of high throughput sequencing provide unparalleled access to the human genome and transcriptome. We hypothesised that next generation DNA sequencing technologies would allow us to identify an elusive novel disease gene for a pulmonary vascular disease inherited as an autosomal dominant trait: The HHT3 interva...

P0913 Objective: We sought to develop a whole-genome sequencing (WGS) based method to identify mycobacterial species, predict drug resistance and determine relatedness between strains. To maximise potential diagnostic benefits, a fast and inexpensive method of DNA extraction from early positive Mycobacterial Growth Indicator Tube (MGIT) cultures is...

Norovirus is the commonest cause of epidemic gastroenteritis among people of all ages. Outbreaks frequently occur in hospitals and the community, costing the UK an estimated [pound sign]110 m per annum. An evolutionary explanation for periodic increases in norovirus cases, despite some host-specific post immunity is currently limited to the identif...

Hereditary haemorrhagic telangiectasia (HHT) is a disease characterised by abnormal vascular structures, and most commonly caused by mutations in ENG, ACVRL1 or SMAD4 encoding endothelial cell-expressed proteins involved in TGF-β superfamily signalling. The majority of mutations reported on the HHT mutation database are predicted to lead to stop co...