Rafi Ahmad

• Branders, Sverre; Grabherr, Manfred G. & Ahmad, Rafi (2024). Real-time Taxonomic Characterization of Long-read Mixed-species Sequencing Samples in Sorted Motif Distance Space: Voyager. bioRxiv. ISSN 2692-8205. doi: 10.1101/2024.04.13.589333.
• Ali, Jawad; Johansen, Wenche & Ahmad, Rafi (2024). Short turnaround time of seven to nine hours from sample collection until informed decision for sepsis treatment using nanopore sequencing. Scientific Reports. ISSN 2045-2322. 14(1). doi: 10.1038/s41598-024-55635-z. Vis sammendrag

  Bloodstream infections (BSIs) and sepsis are major health problems, annually claiming millions of lives. Traditional blood culture techniques, employed to identify sepsis-causing pathogens and assess antibiotic susceptibility, usually take 2–4 days. Early and accurate antibiotic prescription is vital in sepsis to mitigate mortality and antibiotic resistance. This study aimed to reduce the wait time for sepsis diagnosis by employing shorter blood culture incubation times for BD BACTEC™ bottles using standard laboratory incubators, followed by real-time nanopore sequencing and data analysis. The method was tested on nine blood samples spiked with clinical isolates from the six most prevalent sepsis-causing pathogens. The results showed that pathogen identification was possible at as low as 102–104 CFU/mL, achieved after just 2 h of incubation and within 40 min of nanopore sequencing. Moreover, all the antimicrobial resistance genes were identified at 103–107 CFU/mL, achieved after incubation for 5 h and only 10 min to 3 h of sequencing. Therefore, the total turnaround time from sample collection to the information required for an informed decision on the right antibiotic treatment was between 7 and 9 h. These results hold significant promise for better clinical management of sepsis compared with current culture-based methods.

• Bellankimath, Anurag Basavaraj; Chapagain, Crystal; Branders, Sverre; Ali, Jawad; Wilson, Robert Charles & Johansen, Truls E. Bjerklund [Vis alle 7 forfattere av denne artikkelen] (2024). Detection of pathogens and antimicrobial resistant genes from urine within 5 hours using Nanopore sequencing. bioRxiv. ISSN 2692-8205. doi: 10.1101/2024.03.04.582689.
• Das, Sathi; Saxena, Kanchan; Tinguely, Jean-Claude; Pal, Arijit; Wickramasinghe, Nima L. & Khezri, Abdolrahman [Vis alle 13 forfattere av denne artikkelen] (2023). SERS Nanowire Chip and Machine Learning-Enabled Classification of Wild-Type and Antibiotic-Resistant Bacteria at Species and Strain Levels. ACS Applied Materials & Interfaces. ISSN 1944-8244. 15(20), s. 24047–24058. doi: 10.1021/acsami.3c00612.
• Das, Sathi; Saxena, Kanchan; Khezri, Abdolrahman; Dubey, Vishesh Kumar; Ahmad, Azeem & Tinguely, Jean-Claude [Vis alle 9 forfattere av denne artikkelen] (2023). Rapid identification of antimicrobial drug resistance strains of E-coli using SERS nanowire chip. Proceedings of SPIE, the International Society for Optical Engineering. ISSN 0277-786X. 12396. doi: 10.1117/12.2650578. Fulltekst i vitenarkiv
• Ahmad, Azeem; Hettiarachchi, Ramith; Khezri, Abdolrahman; Ahluwalia, Balpreet Singh; Wadduwage, Dushan & Ahmad, Rafi (2023). Highly sensitive quantitative phase microscopy and deep learning aided with whole genome sequencing for rapid detection of infection and antimicrobial resistance. Frontiers in Microbiology. ISSN 1664-302X. 14. doi: 10.3389/fmicb.2023.1154620. Fulltekst i vitenarkiv
• Avershina, Ekaterina; Khezri, Abdolrahman & Ahmad, Rafi (2023). Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics—Current State and Whole Genome Sequencing Implementation Perspectives. Antibiotics. ISSN 2079-6382. 12(4). doi: 10.3390/antibiotics12040781. Fulltekst i vitenarkiv
• Ali, Jawad; Joshi, Mukund; Ahmadi, Asal; Strætkvern, Knut Olav & Ahmad, Rafi (2023). Increased growth temperature and vitamin B12 supplementation reduces the lag time for rapid pathogen identification in BHI agar and blood cultures. F1000 Research. ISSN 2046-1402. 12(131). doi: 10.12688/f1000research.129668.2. Fulltekst i vitenarkiv Vis sammendrag

  Background: The rapid diagnostics of pathogens is essential to prescribe appropriate and early antibiotic therapy. The current methods for pathogen detection require the bacteria to grow in a culture medium, which is time-consuming. This increases the mortality rate and the global burden of antimicrobial resistance. Culture-free detection methods are still under development and are not used in the clinical routine. Therefore decreasing the culture time for accurate detection of infection and resistance is vital for diagnosis. Methods: In this study, we wanted to investigate easy-to-implement factors (in a minimal laboratory set-up), including inoculum size, incubation temperature, and additional supplementation (e.g., vitamin B12 and trace metals), that can significantly reduce the lag time (tlag). These factors were arranged in simple two-level factorial designs using Gram-positive (Escherichia coli and Pseudomonas aeruginosa) and Gram-negative (Staphylococcus aureus and Bacillus subtilis) bacteria, including clinical isolates with known antimicrobial resistance profiles. Blood samples spiked with a clinical isolate of E. coli CCUG17620 were also tested to see the effect of elevated incubation temperature on bacterial growth in blood cultures. Results: We observed that increased incubation temperature (42°C) along with vitamin B12 supplementation significantly reduced the tlag (10 – 115 minutes or 4% - 49%) in pure clinical isolates and blood samples spiked with E. coli CCUG17620. In the case of the blood sample, PCR results also detected bacterial DNA after only 3h of incubation and at three times the CFU/mL. Conclusions: Enrichment of bacterial culture media with growth supplements such as vitamin B12 and increased incubation temperature can be a cheap and rapid method for the early detection of pathogens. This is a proof-of-concept study restricted to a few bacterial strains and growth conditions. In the future, the effect of other growth conditions and difficult-to-culture bacteria should be explored to shorten the lag phase.

• Ahmadi, Asal; Khezri, Abdolrahman; Nørstebø, Håvard & Ahmad, Rafi (2023). A culture-, amplification-independent, and rapid method for identification of pathogens and antibiotic resistance profile in bovine mastitis milk. Frontiers in Microbiology. ISSN 1664-302X. 13. doi: 10.3389/fmicb.2022.1104701. Fulltekst i vitenarkiv
• Hanrahan, Niall; Lister, Adam; Highmore, Callum; Rajith, Leena; Avershina, Ekaterina & Ali, Jawad [Vis alle 9 forfattere av denne artikkelen] (2022). Enhanced Raman techniques for infection diagnostics. Proceedings of SPIE, the International Society for Optical Engineering. ISSN 0277-786X. 12203, s. 6–17. doi: 10.1117/12.2635324. Fulltekst i vitenarkiv
• Khan, Yusuf; Hammarström, Daniel; Ellefsen, Stian & Ahmad, Rafi (2022). Normalization of gene expression data revisited: the three viewpoints of the transcriptome in human skeletal muscle undergoing load-induced hypertrophy and why they matter. BMC Bioinformatics. ISSN 1471-2105. 23(1). doi: 10.1186/s12859-022-04791-y. Fulltekst i vitenarkiv Vis sammendrag

  Background The biological relevance and accuracy of gene expression data depend on the adequacy of data normalization. This is both due to its role in resolving and accounting for technical variation and errors, and its defining role in shaping the viewpoint of biological interpretations. Still, the choice of the normalization method is often not explicitly motivated although this choice may be particularly decisive for conclusions in studies involving pronounced cellular plasticity. In this study, we highlight the consequences of using three fundamentally different modes of normalization for interpreting RNA-seq data from human skeletal muscle undergoing exercise-training-induced growth. Briefly, 25 participants conducted 12 weeks of high-load resistance training. Muscle biopsy specimens were sampled from m. vastus lateralis before, after two weeks of training (week 2) and after the intervention (week 12), and were subsequently analyzed using RNA-seq. Transcript counts were modeled as (1) per-library-size, (2) per-total-RNA, and (3) per-sample-size (per-mg-tissue). Result Initially, the three modes of transcript modeling led to the identification of three unique sets of stable genes, which displayed differential expression profiles. Specifically, genes showing stable expression across samples in the per-library-size dataset displayed training-associated increases in per-total-RNA and per-sample-size datasets. These gene sets were then used for normalization of the entire dataset, providing transcript abundance estimates corresponding to each of the three biological viewpoints (i.e., per-library-size, per-total-RNA, and per-sample-size). The different normalization modes led to different conclusions, measured as training-associated changes in transcript expression. Briefly, for 27% and 20% of the transcripts, training was associated with changes in expression in per-total-RNA and per-sample-size scenarios, but not in the per-library-size scenario. At week 2, this led to opposite conclusions for 4% of the transcripts between per-library-size and per-sample-size datasets (↑ vs. ↓, respectively). Conclusion Scientists should be explicit with their choice of normalization strategies and should interpret the results of gene expression analyses with caution. This is particularly important for data sets involving a limited number of genes or involving growing or differentiating cellular models, where the risk of biased conclusions is pronounced.

• Avershina, Ekaterina; Frye, Stephan Alfons; ali, jawad; Taxt, Arne Michael & Ahmad, Rafi (2022). Ultrafast and Cost-Effective Pathogen Identification and Resistance Gene Detection in a Clinical Setting Using Nanopore Flongle Sequencing. Frontiers in Microbiology. ISSN 1664-302X. 13. doi: 10.3389/fmicb.2022.822402. Vis sammendrag

  Rapid bacterial identification and antimicrobial resistance gene (ARG) detection are crucial for fast optimization of antibiotic treatment, especially for septic patients where each hour of delayed antibiotic prescription might have lethal consequences. This work investigates whether the Oxford Nanopore Technology’s (ONT) Flongle sequencing platform is suitable for real-time sequencing directly from blood cultures to identify bacteria and detect resistance-encoding genes. For the analysis, we used pure bacterial cultures of four clinical isolates of Escherichia coli and Klebsiella pneumoniae and two blood samples spiked with either E. coli or K. pneumoniae that had been cultured overnight. We sequenced both the whole genome and plasmids isolated from these bacteria using two different sequencing kits. Generally, Flongle data allow rapid bacterial ID and resistome detection based on the first 1,000–3,000 generated sequences (10 min to 3 h from the sequencing start), albeit ARG variant identification did not always correspond to ONT MinION and Illumina sequencing-based data. Flongle data are sufficient for 99.9% genome coverage within at most 20,000 (clinical isolates) or 50,000 (positive blood cultures) sequences generated. The SQK-LSK110 Ligation kit resulted in higher genome coverage and more accurate bacterial identification than the SQK-RBK004 Rapid Barcode kit.

• Khezri, Abdolrahman; Avershina, Ekaterina & Ahmad, Rafi (2021). Hybrid Assembly Provides Improved Resolution of Plasmids, Antimicrobial Resistance Genes, and Virulence Factors in Escherichia coli and Klebsiella pneumoniae Clinical Isolates. Microorganisms. ISSN 2076-2607. 9(12), s. 1–18. doi: 10.3390/microorganisms9122560. Fulltekst i vitenarkiv Vis sammendrag

  Emerging new sequencing technologies have provided researchers with a unique opportunity to study factors related to microbial pathogenicity, such as antimicrobial resistance (AMR) genes and virulence factors. However, the use of whole-genome sequence (WGS) data requires good knowledge of the bioinformatics involved, as well as the necessary techniques. In this study, a total of nine Escherichia coli and Klebsiella pneumoniae isolates from Norwegian clinical samples were sequenced using both MinION and Illumina platforms. Three out of nine samples were sequenced directly from blood culture, and one sample was sequenced from a mixed-blood culture. For genome assembly, several long-read, (Canu, Flye, Unicycler, and Miniasm), short-read (ABySS, Unicycler and SPAdes) and hybrid assemblers (Unicycler, hybridSPAdes, and MaSurCa) were tested. Assembled genomes from the best-performing assemblers (according to quality checks using QUAST and BUSCO) were subjected to downstream analyses. Flye and Unicycler assemblers performed best for the assembly of long and short reads, respectively. For hybrid assembly, Unicycler was the top-performing assembler and produced more circularized and complete genome assemblies. Hybrid assembled genomes performed substantially better in downstream analyses to predict putative plasmids, AMR genes and β-lactamase gene variants, compared to MinION and Illumina assemblies. Thus, hybrid assembly has the potential to reveal factors related to microbial pathogenicity in clinical and mixed samples.

• Mølmen, Knut Sindre; Hammarström, Jens Konrad Daniel; Falch, Gunnar Slettaløkken; Grundtvig, Morten; Koll, Lise & Hanestadhaugen, Marita [Vis alle 14 forfattere av denne artikkelen] (2021). Chronic obstructive pulmonary disease does not impair responses to resistance training. Journal of Translational Medicine. ISSN 1479-5876. 19. doi: 10.1186/s12967-021-02969-1. Fulltekst i vitenarkiv Vis sammendrag

  Background: Subjects with chronic obstructive pulmonary disease (COPD) are prone to accelerated decay of muscle strength and mass with advancing age. This is believed to be driven by disease-inherent systemic pathophysiologies, which are also assumed to drive muscle cells into a state of anabolic resistance, leading to impaired abilities to adapt to resistance exercise training. Currently, this phenomenon remains largely unstudied. In this study, we aimed to investigate the assumed negative effects of COPD for health- and muscle-related responsiveness to resistance training using a healthy control-based translational approach. Methods: Subjects with COPD (n = 20, GOLD II-III, FEV1predicted 57 ± 11%, age 69 ± 5) and healthy controls (Healthy, n = 58, FEV1predicted 112 ± 16%, age 67 ± 4) conducted identical whole-body resistance training interventions for 13 weeks, consisting of two weekly supervised training sessions. Leg exercises were performed unilaterally, with one leg conducting high-load training (10RM) and the contralateral leg conducting low-load training (30RM). Measurements included muscle strength (nvariables = 7), endurance performance (nvariables = 6), muscle mass (nvariables = 3), muscle quality, muscle biology (m. vastus lateralis; muscle fiber characteristics, RNA content including transcriptome) and health variables (body composition, blood). For core outcome domains, weighted combined factors were calculated from the range of singular assessments. Results: COPD displayed well-known pathophysiologies at baseline, including elevated levels of systemic low-grade inflammation ([c-reactive protein]serum), reduced muscle mass and functionality, and muscle biological aberrancies. Despite this, resistance training led to improved lower-limb muscle strength (15 ± 8%), muscle mass (7 ± 5%), muscle quality (8 ± 8%) and lower-limb/whole-body endurance performance (26 ± 12%/8 ± 9%) in COPD, resembling or exceeding responses in Healthy, measured in both relative and numeric change terms. Within the COPD cluster, lower FEV1predicted was associated with larger numeric and relative increases in muscle mass and superior relative improvements in maximal muscle strength. This was accompanied by similar changes in hallmarks of muscle biology such as rRNA-content↑, muscle fiber cross-sectional area↑, type IIX proportions↓, and changes in mRNA transcriptomics. Neither of the core outcome domains were differentially affected by resistance training load. Conclusions: COPD showed hitherto largely unrecognized responsiveness to resistance training, rejecting the notion of disease-related impairments and rather advocating such training as a potent measure to relieve pathophysiologies. Trial registration: ClinicalTrials.gov ID: NCT02598830. Registered November 6th 2015, https://clinicaltrials.gov/ct2/show/NCT02598830. Keywords: Anabolic resistance; COPD; Pathophysiology; Skeletal muscle; Strength training; Training load.

• Mølmen, Knut Sindre; Hammarström, Jens Konrad Daniel; Pedersen, Karianne; Lie, Anne Cecilie Lian; Steile, Ragnvald B. & Nygård, Håvard [Vis alle 18 forfattere av denne artikkelen] (2021). Vitamin D3 supplementation does not enhance the effects of resistance training in older adults . Journal of Cachexia, Sarcopenia and Muscle. ISSN 2190-5991. 12(3), s. 599–628. doi: 10.1002/jcsm.12688. Fulltekst i vitenarkiv Vis sammendrag

  Background: Lifestyle therapy with resistance training is a potent measure to counteract age-related loss in muscle strength and mass. Unfortunately, many individuals fail to respond in the expected manner. This phenomenon is particularly common among older adults and those with chronic diseases (e.g. chronic obstructive pulmonary disease, COPD) and may involve endocrine variables such as vitamin D. At present, the effects of vitamin D supplementation on responses to resistance training remain largely unexplored. Methods: Ninety-five male and female participants (healthy, n = 71; COPD, n = 24; age 68 ± 5 years) were randomly assigned to receive either vitamin D3 or placebo supplementation for 28 weeks in a double-blinded manner (latitude 61°N, September-May). Seventy-eight participants completed the RCT, which was initiated by 12 weeks of supplementation-only (two weeks with 10 000 IU/day, followed by 2000 IU/day), followed by 13 weeks of combined supplementation (2000 IU/day) and supervised whole-body resistance training (twice weekly), interspersed with testing and measurements. Outcome measures included multiple assessments of muscle strength (nvariables = 7), endurance performance (n = 6), and muscle mass (n = 3, legs, primary), as well as muscle quality (legs), muscle biology (m. vastus lateralis; muscle fibre characteristics, transcriptome), and health-related variables (e.g. visceral fat mass and blood lipid profile). For main outcome domains such as muscle strength and muscle mass, weighted combined factors were calculated from the range of singular assessments. Results: Overall, 13 weeks of resistance training increased muscle strength (13% ± 8%), muscle mass (9% ± 8%), and endurance performance (one-legged, 23% ± 15%; whole-body, 8% ± 7%), assessed as weighted combined factors, and were associated with changes in health variables (e.g. visceral fat, -6% ± 21%; [LDL]serum , -4% ± 14%) and muscle tissue characteristics such as fibre type proportions (e.g. IIX, -3% points), myonuclei per fibre (30% ± 65%), total RNA/rRNA abundances (15%/6-19%), and transcriptome profiles (e.g. 312 differentially expressed genes). Vitamin D3 supplementation did not affect training-associated changes for any of the main outcome domains, despite robust increases in [25(OH)D]serum (∆49% vs. placebo). No conditional effects were observed for COPD vs. healthy or pre-RCT [25(OH)D]serum . In secondary analyses, vitamin D3 affected expression of gene sets involved in vascular functions in muscle tissue and strength gains in participants with high fat mass, which advocates further study. Conclusions: Vitamin D3 supplementation did not affect muscular responses to resistance training in older adults with or without COPD. Keywords: Cholecalciferol; Muscle plasticity; Strength training. © 2021 The Authors. Journal of Cachexia, Sarcopenia and Muscle published by John Wiley & Sons Ltd on behalf of Society on Sarcopenia, Cachexia and Wasting Disorders.

• Avershina, Ekaterina; Sharma, Priyanka; Taxt, Arne Michael; Singh, Harpreet; Frye, Stephan Alfons & Paul, Kolin [Vis alle 10 forfattere av denne artikkelen] (2021). AMR-Diag: Neural network based genotype-to-phenotype prediction of resistance towards β-lactams in Escherichia coli and Klebsiella pneumoniae. Computational and Structural Biotechnology Journal. ISSN 2001-0370. 19, s. 1896–1906. doi: 10.1016/j.csbj.2021.03.027. Fulltekst i vitenarkiv
• Modica, Maria Vittoria; Ahmad, Rafi; Ainsworth, Stuart; Anderluh, Gregor; Antunes, Agostinho & Beis, Dimitris [Vis alle 23 forfattere av denne artikkelen] (2021). The new COST Action European Venom Network (EUVEN)—synergy and future perspectives of modern venomics. GigaScience. ISSN 2047-217X. 10(3), s. 1–5. doi: 10.1093/gigascience/giab019. Fulltekst i vitenarkiv
• Khezri, Abdolrahman; Avershina, Ekaterina & Ahmad, Rafi (2020). Plasmid Identification and Plasmid-Mediated Antimicrobial Gene Detection in Norwegian Isolates. Microorganisms. ISSN 2076-2607. 9(52). doi: 10.3390/microorganisms9010052. Fulltekst i vitenarkiv Vis sammendrag

  Norway is known for being one of the countries with the lowest levels of antimicrobial resistance (AMR). AMR, through acquired genes located on transposons or conjugative plasmids, is the horizontal transmission of genes required for a given bacteria to withstand antibiotics. In this work, bioinformatic analysis of whole-genome sequences and hybrid assembled data from Escherichia coli, and Klebsiella pneumoniae isolates from Norwegian patients was performed. For detection of putative plasmids in isolates, the plasmid assembly mode in SPAdes was used, followed by annotation of resulting contigs using PlasmidFinder and two curated plasmid databases (Brooks and PLSDB). Furthermore, ResFinder and Comprehensive Antibiotic Resistance Database (CARD) were used for the identification of antibiotic resistance genes (ARGs). The IncFIB plasmid was detected as the most prevalent plasmid in both E. coli, and K. pneumoniae isolates. Furthermore, ARGs such as aph(3″)-Ib, aph(6)-Id, sul1, sul2, tet(D), and qnrS1 were identified as the most abundant plasmid-mediated ARGs in Norwegian E. coli and K. pneumoniae isolates, respectively. Using hybrid assembly, we were able to locate plasmids and predict ARGs more confidently. In conclusion, plasmid identification and ARG detection using whole-genome sequencing data are heavily dependent on the database of choice; therefore, it is best to use several tools and/or hybrid assembly for obtaining reliable identification results. View Full-Text Keywords: Escherichia coli; Klebsiella pneumoniae; antimicrobial resistance; plasmid; plasmid-mediated genes; horizontal gene transfer

• Khan, Yusuf; Hammarström, Jens Konrad Daniel; Rønnestad, Bent; Ellefsen, Stian & Ahmad, Rafi (2020). Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline. BMC Bioinformatics. ISSN 1471-2105. 21(1). doi: 10.1186/s12859-020-03866-y. Fulltekst i vitenarkiv Vis sammendrag

  Background: Human skeletal muscle responds to weight-bearing exercise with significant inter-individual differences. Investigation of transcriptome responses could improve our understanding of this variation. However, this requires bioinformatic pipelines to be established and evaluated in study-specific contexts. Skeletal muscle subjected to mechanical stress, such as through resistance training (RT), accumulates RNA due to increased ribosomal biogenesis. When a fixed amount of total-RNA is used for RNA-seq library preparations, mRNA counts are thus assessed in different amounts of tissue, potentially invalidating subsequent conclusions. The purpose of this study was to establish a bioinformatic pipeline specific for analysis of RNA-seq data from skeletal muscles, to explore the effects of different normalization strategies and to identify genes responding to RT in a volume-dependent manner (moderate vs. low volume). To this end, we analyzed RNA-seq data derived from a twelve-week RT intervention, wherein 25 participants performed both low- and moderate-volume leg RT, allocated to the two legs in a randomized manner. Bilateral muscle biopsies were sampled from m. vastus lateralis before and after the intervention, as well as before and after the fifth training session (Week 2). Result: Bioinformatic tools were selected based on read quality, observed gene counts, methodological variation between paired observations, and correlations between mRNA abundance and protein expression of myosin heavy chain family proteins. Different normalization strategies were compared to account for global changes in RNA to tissue ratio. After accounting for the amounts of muscle tissue used in library preparation, global mRNA expression increased by 43-53%. At Week 2, this was accompanied by dose-dependent increases for 21 genes in rested-state muscle, most of which were related to the extracellular matrix. In contrast, at Week 12, no readily explainable dose-dependencies were observed. Instead, traditional normalization and non-normalized models resulted in counterintuitive reverse dose-dependency for many genes. Overall, training led to robust transcriptome changes, with the number of differentially expressed genes ranging from 603 to 5110, varying with time point and normalization strategy. Conclusion: Optimized selection of bioinformatic tools increases the biological relevance of transcriptome analyses from resistance-trained skeletal muscle. Moreover, normalization procedures need to account for global changes in rRNA and mRNA abundance. Keywords: Bioinformatics pipeline; Normalization; RNA-seq; Skeletal muscle.

• Khezri, Abdolrahman; Narud, Birgitte; Stenseth, Else-Berit; Zeremichael, Teklu Tewoldebrhan; Myromslien, Frøydis Deinboll & Wilson, Robert Charles [Vis alle 8 forfattere av denne artikkelen] (2020). Sperm DNA Hypomethylation Proximal to Reproduction Pathway Genes in Maturing Elite Norwegian Red Bulls. Frontiers in Genetics. ISSN 1664-8021. doi: 10.3389/fgene.2020.00922. Fulltekst i vitenarkiv
• Taxt, Arne Michael; Avershina, Ekaterina; Frye, Stephan Alfons; Naseer, Mohammed Umaer & Ahmad, Rafi (2020). Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing. Scientific Reports. ISSN 2045-2322. 10(1). doi: 10.1038/s41598-020-64616-x. Fulltekst i vitenarkiv Vis sammendrag

  Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1–2 days for identification of bacterial agent and an additional 2–3 days for phenotypic determination of antibiotic susceptibility pattern. With the escalating burden of antimicrobial resistance (AMR) rapid diagnostics becomes increasingly important to secure adequate antibiotic therapy. Real-time whole genome sequencing represents a genotypic diagnostic approach with the ability to rapidly identify pathogens and AMR-encoding genes. Here we have used nanopore sequencing of bacterial DNA extracted from positive blood cultures for identification of pathogens, detection of plasmids and AMR-encoding genes. To our knowledge, this is the first study to gather the above-mentioned information from nanopore sequencing and conduct a comprehensive analysis for diagnostic purposes in real-time. Identification of pathogens was possible after 10 minutes of sequencing and all predefined AMR-encoding genes and plasmids from monoculture experiments were detected within one hour using raw nanopore sequencing data. Furthermore, we demonstrate the correct identification of plasmids and blaCTX-M subtypes using de novo assembled nanopore contigs. Results from this study hold great promise for future applications in clinical microbiology and for health care surveillance purposes.

• Brown, Peter; Tan, Aik-Choon; El-Esawi, Mohamed A; Liehr, Thomas; Blanck, Oliver & Ahmad, Rafi [Vis alle 50 forfattere av denne artikkelen] (2019). Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database: The Journal of Biological Databases and Curation. ISSN 1758-0463. 2019. doi: 10.1093/database/baz085.
• Khezri, Abdolrahman; Narud, Birgitte; Stenseth, Else-Berit; Johannisson, Anders; Myromslien, Frøydis Deinboll & Gaustad, Ann Helen [Vis alle 11 forfattere av denne artikkelen] (2019). DNA methylation patterns vary in boar sperm cells with different levels of DNA fragmentation. BMC Genomics. ISSN 1471-2164. 20:897, s. 1–15. doi: 10.1186/s12864-019-6307-8. Fulltekst i vitenarkiv Vis sammendrag

  Background: Sperm DNA integrity is considered essential for successful transmission of the paternal genome, fertilization and normal embryo development. DNA fragmentation index (DFI, %) has become a key parameter in the swine artificial insemination industry to assess sperm DNA integrity. Recently, in some elite Norwegian Landrace boars (boars with excellent field fertility records), a higher level of sperm DFI has been observed. In order to obtain a better understanding of this, and to study the complexity of sperm DNA integrity, liquid preserved semen samples from elite boars with contrasting DFI levels were examined for protamine deficiency, thiol profile and disulphide bonds. Additionally, the DNA methylation profiles of the samples were determined by reduced representation bisulphite sequencing (RRBS). Results: In this study, different traits related to sperm DNA integrity were investigated (n = 18 ejaculates). Upon liquid storage, the levels of total thiols and disulphide bonds decreased significantly, while the DFI and protamine deficiency level increased significantly. The RRBS results revealed similar global patterns of low methylation from semen samples with different levels of DFI (low, medium and high). Differential methylation analyses indicated that the number of differentially methylated cytosines (DMCs) increased in the low-high compared to the low-medium and the medium-high DFI groups. Annotating the DMCs with gene and CpG features revealed clear differences between DFI groups. In addition, the number of annotated transcription starting sites (TSS) and associated pathways in the low-high comparison was greater than the other two groups. Pathway analysis showed that genes (based on the closest TSS to DMCs) corresponding to low-high DFI comparison were associated with important processes such as membrane function, metabolic cascade and antioxidant defence system. Conclusion: To our knowledge, this is the first study evaluating DNA methylation in boar sperm cells with different levels of DFI. The present study shows that sperm cells with varying levels of DNA fragmentation exhibit similar global methylation, but different site-specific DNA methylation signatures. Moreover, with increasing DNA fragmentation in spermatozoa, there is an increase in the number of potentially affected downstream genes and their respective regulatory pathways.

• Stathi, Dimitrios; Yang, Yu; tewari, saurabh; Hemani, Ahmed; Paul, Kolin & Grabherr, Manfred G. [Vis alle 7 forfattere av denne artikkelen] (2019). Approximate Computing Applied to Bacterial Genome Identification using Self-Organizing Maps. Proceedings of IEEE Computer Society Annual Symposium on VLSI, ISVLSI. ISSN 2159-3469. s. 560–567. doi: 10.1109/ISVLSI.2019.00106.
• Kaur, Jasmine; Sharma, Arun; Dhama, Ajay Singh; Buttolia, Harish; Ohri, V.C. & Walia, Kamini [Vis alle 10 forfattere av denne artikkelen] (2019). Developing a hybrid antimicrobial resistance surveillance system in India: Needs & challenges. Indian Journal of Medical Research (IJMR). ISSN 0971-5916. 149(2), s. 299–302. doi: 10.4103/ijmr.IJMR_2074_17. Fulltekst i vitenarkiv
• Harstad, Håvard; Ahmad, Rafi & Bredberg, Anders (2018). Nanopore-based DNA sequencing in clinical microbiology: preliminary assessment of basic requirements. bioRxiv. ISSN 2692-8205. doi: 10.1101/382580.
• Yang, Yu; Stathis, Dimitrios; Sharma, Prashant; Paul, Kolin; Hemani, Ahmed & Grabherr, Manfred G. [Vis alle 7 forfattere av denne artikkelen] (2018). RiBoSOM: Rapid Bacterial Genome Identification Using Self-Organizing Map implemented on the Synchoros SiLago Platform , SAMOS '18 Proceedings of the 18th International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation. Pythagorion, Greece — July 15 - 19, 2018 . Association for Computing Machinery (ACM). ISSN 978-1-4503-6494-2. doi: 10.1145/3229631.3229650.
• Thode, Sunniva Katharina; Rojek, Ewelina; Kozlowski, Mikolaj; Ahmad, Rafi & Haugen, Peik (2018). Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives. PLOS ONE. ISSN 1932-6203. 13:e0191860(2), s. 1–20. doi: 10.1371/journal.pone.0191860. Fulltekst i vitenarkiv
• Ahmad, Rafi; Borowiec, Paulina; Falck-Ytter, Anne Bergljot & Strætkvern, Knut Olav (2017). Extraction, Solubility and Antimicrobial Activity of (-) Usnic Acid in Ethanol, a Pharmaceutically Relevant Solvent. Natural Product Communications. ISSN 1934-578X. 12(7), s. 1101–1104. doi: 10.1177/1934578x1701200725. Vis sammendrag

  Usnic acid (UA) is the most studied bioactive secondary metabolite from lichens. Recently, UA research has focused on its antibacterial activity. However, increased application in healthcare products of UA is hampered by low solubility in aqueous solutions. Here, we report ethanol both as an alternative extraction solvent to acetone and as a pharmaceutically relevant solvent for future formulations. Dried samples of the abundant reindeer lichen (Cladonia stellaris) were extracted in a 23 factorial design using either ethanol or acetone, varying both time and solvent-to-dry mass ratio. In both extracts, UA was the predominant compound as shown by two-dimensional thin-layer chromatography (TLC). In a disc diffusion assay, both extracts demonstrated similar antibacterial susceptibility towards Gram-positive (Bacillus subtilis and Staphylococcus aureus), while showing little to no activity against Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa). Among a range of pharmaceutically relevant solvents tested, UA was only soluble in ethanol (at concentrations up to 1-2 mg mL-1).

• Wester, Astrid Louise; Solberg, Svein Øivind; Gopinathan, Unni; Ahmad, Rafi & Graham, David W. (2015). Antimicrobial resistance in a one health and one world perspective—Mechanisms and solutions. I Caplan, Michael (Red.), Reference Module in Biomedical Sciences. Elsevier. ISSN 978-0-12-801238-3. doi: 10.1016/B978-0-323-99967-0.00148-4.
• Liang, Zhe; Demko, Viktor; Wilson, Robert Charles; Johnson, Kenneth; Ahmad, Rafi & Perroud, Pierre-Francois [Vis alle 12 forfattere av denne artikkelen] (2013). The catalytic domain CysPc of the DEK1 calpain is functionally conserved in land plants. The Plant Journal. ISSN 0960-7412. 75(5), s. 742–754. doi: 10.1111/tpj.12235.
• Hansen, Geir Åsmund; Ahmad, Rafi; Hjerde, erik; Fenton, Christopher Graham; Willassen, Nils Peder & Haugen, Peik (2012). Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida. BMC Genomics. ISSN 1471-2164. 13. doi: 10.1186/1471-2164-13-37. Fulltekst i vitenarkiv
• Ahmad, Rafi; Hansen, Geir Åsmund; Hansen, Hilde; Hjerde, Erik; Pedersen, hege lynum & Paulsen, steinar [Vis alle 10 forfattere av denne artikkelen] (2012). Prediction, microarray and northern blot analyses identify new intergenic small RNAs in aliivibrio salmonicida. Journal of Molecular Microbiology and Biotechnology. ISSN 1464-1801. 22(6), s. 352–360. doi: 10.1159/000345769.
• Oliveira, Taiana Maia De; Ahmad, Rafi & Engh, Richard Alan (2011). VX680 Binding in Aurora A: pi-pi Interactions Involving the Conserved Aromatic Amino Acid of the Flexible Glycine-Rich Loop. Journal of Physical Chemistry A. ISSN 1089-5639. 115(16), s. 3895–3904. doi: 10.1021/jp108286r.
• Saradhi, Pardha; Leiros, Hanna-Kirsti S.; Ahmad, Rafi; Spencer, James; Leiros, Ingar & Walsh, Timothy R. [Vis alle 8 forfattere av denne artikkelen] (2011). Structural and Computational Investigations of VIM-7: Insights into the Substrate Specificity of VIM Metallo-beta-Lactamases. Journal of Molecular Biology (JMB). ISSN 0022-2836. 411(1), s. 174–189. doi: 10.1016/j.jmb.2011.05.035.

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• Ahmad, Rafi (2024). Point of diagnosis to direct treatment: Emerging technologies?
• Ahmad, Rafi (2024). How and when is rapid point of diagnostic tools to arrive and reshape management of urosepsis?
• Ahmad, Rafi (2024). Novel technological solutions for rapid diagnostics of infection and antimicrobial resistance: A One Health approach.
• Branders, Sverre; Ahmad, Rafi & Grabherr, Manfred G. (2024). Real-time Taxonomic Characterization of Long-read Mixed-species Sequencing Samples in Distance-space.
• Chapagain, Crystal; Ali, Jawad; Branders, Sverre & Ahmad, Rafi (2023). Rapid Detection of Pathogens and Antimicrobial Resistance in Urine Using Nanopore Sequencing.
• Ahmad, Rafi (2023). Novel technological solutions for rapid diagnostics of infection and antimicrobial resistance:A One Health approach.
• Ahmad, Rafi (2023). AMR-Educate: Current Status and plans forward.
• Ahmad, Rafi (2023). A culture-amplification-independent, and rapid method for identification of pathogens and antibiotic resistance profile in bovine mastitis milk.
• Ahmad, Rafi (2023). Novel technological solutions for rapid diagnostics of infection and antimicrobial resistance.
• Ahmad, Rafi (2023). What is AMR-Educate?
• Ahmad, Rafi (2023). Transforming Research, Education, and Innovation in Antimicrobial Resistance.
• Ahmad, Rafi (2023). Novel technological solutions for rapid diagnostics of infection and antimicrobial resistance:A One Health approach.
• Ahmad, Rafi (2022). Novel technological solutions for rapid diagnostics of Infection and Antimicrobial resistance: test cases from human and animal health.
• Ahmad, Rafi (2022). Presentation of AMR-Educate project.
• Ahmad, Rafi (2021). Rapid-Diag Project Personalized Rapid Diagnostics of bacterial infection and antibiotic resistance [Engelsk].
• Ahmad, Rafi (2021). Rapid-Diag Project Personalized Rapid Diagnostics of bacterial infection and antibiotic resistance.
• Modica, Maria Vittoria; Ahmad, Rafi; Ainsworth, Stuart; Anderluh, Gregor; Antunes, Agostinho & Beis, Dimitris [Vis alle 23 forfattere av denne artikkelen] (2021). Corrigendum to: The new COST Action European Venom Network (EUVEN)-synergy and future perspectives of modern venomics. GigaScience. ISSN 2047-217X. 10(12). doi: 10.1093/gigascience/giab102.
• Ahmad, Rafi (2021). AMR-Diag: Neural network based genotype-to-phenotype prediction of resistance towards β-lactams in Escherichia coli and Klebsiella pneumoniae.
• Ahmad, Rafi (2021). AMR-Diag Project Personalized Rapid Diagnostics of bacterial infection and antibiotic resistance.
• Ahmad, Rafi (2021). Personalized Healthcare: Bioinformatics & Drug Discovery Perspective.
• Ahmad, Rafi (2020). Hva er risikoen for at du får i deg resistente bakterier i mat fra utlandet? [Internett]. NCE Heidner Biocluster.
• Ahmad, Rafi (2020). Vil redusere overforbruk av antibiotika og gi legene raskere prøvesvar. [Avis]. Hamar Arbeiderblad.
• Ahmad, Rafi; Taxt, Arne Michael; Avershina, Ekaterina; Frye, Stephan Alfons & Naseer, Mohammed Umaer (2020). Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing.
• Ahmad, Rafi; Taxt, Arne Michael; Avershina, Ekaterina; Frye, Stephan Alfons & Naseer, Mohammed Umaer (2020). Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing.
• Ahmad, Rafi (2020). Clinical application of resistome data for rapid diagnostics of bacterial infection and antimicrobial resistance.
• Khan, Yusuf; Hammarström, Jens Konrad Daniel; Ellefsen, Stian & Ahmad, Rafi (2019). RNA-seq pipeline and transcriptome response to resistance training.
• Khan, Yusuf; Hammarström, Jens Konrad Daniel; Ellefsen, Stian & Ahmad, Rafi (2019). RNA-seq pipeline and transcriptome response to resistance training.
• Ahmad, Rafi (2019). Norsk antibiotika-forskning kan være med og redde tusenvis av liv. [Internett]. nrk.no.
• Ahmad, Rafi (2019). AMR-Diag prosjekt på NRK Dagsrevyen.
• Ahmad, Rafi (2019). En Helse Antimikrobell resistens.
• Ahmad, Rafi (2019). Rapid Diagnostics for effective clinical management of bacterial infection and antimicrobial resistance.
• Ahmad, Rafi (2019). AMR-Diag - et sanntids- og kostnadseffektivt diagnostisk verktøy for påvisning av antibakteriell resistens.
• Khezri, Abdolrahman; Narud, Birgitte; Stenseth, Else-Berit; Myromslien, Frøydis Deinboll; Gaustad, Ann Helen & Wilson, Robert Charles [Vis alle 8 forfattere av denne artikkelen] (2019). DNA methylation patterns differ in boar sperm cells with high and low DNA fragmentation index.
• Ahmad, Rafi (2019). A case study: Nanopore metagenomic sequencing in clinical microbiology.
• Ahmad, Rafi (2019). Role of surveillance in diagnostics of antimicrobial resistance.
• Ahmad, Rafi (2018). AMR-Diag: A Novel Diagnostic Tool for Sequence Based Prediction of Antimicrobial Resistance.
• Ahmad, Rafi (2018). AMR-Diag: A Novel Diagnostic Tool for Sequence-Based Prediction of Antimicrobial Resistance.
• Ahmad, Rafi (2018). AMR-Diag: A Novel Diagnostic Tool for Sequence Based Prediction of Antimicrobial Resistance. .
• Ahmad, Rafi (2018). AMR-Diag - et sanntids- og kostnadseffektivt diagnostisk verktøy for påvisning av antibakteriell resistens.
• Dukic, Aleksandra; Guillaume, Pidoux; Ahmad, Rafi & Tasken, Kjetil (2017). Targeting the Connexin43-Ezrin interaction.
• Dukic, Aleksandra; Ahmad, Rafi & Tasken, Kjetil (2017). Targeting the Connexin43-Ezrin interaction.
• Ahmad, Rafi (2017). AMR-Diag: A Novel Diagnostic Tool for Sequence Based Prediction of Antimicrobial Resistance.
• Slettli, Victoria Konovalenko; Svarva, Frøydis; Danielsen, Anette & Ahmad, Rafi (2017). The use of Liberating structures in the teaching practice of the lecturers at Inland Norway University of Applied Sciences.
• Ahmad, Rafi (2017). Utvikling av nye antibiotika og diagnostikk.
• Ahmad, Rafi (2016). Bioinformatics: application and potential.
• Ahmad, Rafi (2016). Human Genetics and Next Generation Sequencing.
• Ahmad, Rafi (2016). Bioinformatics projects at Hedmark University of Applied Sciences.
• Ahmad, Rafi (2016). Bioinformatics projects at Hedmark University of Applied Sciences.
• Ahmad, Rafi (2016). Bioinformatics: Application and Potential.
• Ahmad, Rafi (2011). Computer-aided discovery of Endonuclease I inhibitors and their potential commercial applications.
• Ahmad, Rafi (2011). Insight into Computer-aided drug design: A Kinase Case Study.
• Drabløs, Finn; Petersen, Kjell; Johansen, Jostein; Nygård, Ståle; Ahmad, Rafi & Smalås, Arne [Vis alle 8 forfattere av denne artikkelen] (2010). The FUGE Bioinformatics platform: a central platform in the FUGE2 period.
• Drabløs, Finn; Petersen, Kjell; Johansen, Jostein; Nygård, Ståle; Ahmad, Rafi & Smalås, Arne [Vis alle 8 forfattere av denne artikkelen] (2010). The FUGE Bioinformatics platform: a central platform in the FUGE2 period. MITAT. Minimally invasive therapy & allied technologies. ISSN 1364-5706. 19, s. 70–71. doi: 10.3109/13645706.2010.500867.
• Joshi, Mukund; Ahmad, Rafi & Strætkvern, Knut Olav (2021). Testing of different conditions to accelerate culturing and potentially reduce the time of detection of pathogens and antimicrobial resistance. HINN.
• Bouras, Hélène Clémentine; Larsen, Frank & Ahmad, Rafi (2020). Rapid diagnostics and better clinical management of bacterial infections: Antibiotic susceptibility testing of clinical isolates and exploration of the different techniques for bacterial enrichment in spiked whole blood. Høgskolen i Hedmark.
• Kauser, Ambreen; Ekaterina, Avershina & Ahmad, Rafi (2020). Resistome Identification of Whole Genome Sequencing Data of Norwegian Isolates. Høgskolen i Hedmark.
• Shakya, Sanjeev; Taxt, Arne Michael & Ahmad, Rafi (2019). Multiplex PCR and Loop Mediated Isothermal Amplification for Detection of Antimicrobial Resistance Genes in Gram-negative Bacteria. Høgskolen i Hedmark.
• Mandal, Roshan Kumar; Larsen, Frank & Ahmad, Rafi (2019). Feasibility of using sequence-based method (AMR-Diag) for detection of antimicrobial resistance - Animals. Høgskolen i Hedmark.
• Ray, Mithlesh Kumar; Kommisrud, Elisabeth & Ahmad, Rafi (2018). Bioinformatics analysis of epigenetic data from bull and boar semen samples. Høgskolen i Hedmark.
• Wirsiy, Elizabeth Musah; Larsen, Frank & Ahmad, Rafi (2018). Feasibility of using a sequence-based method (AMR-Diag) for detection of antibiotic resistance in Humans. Høgskolen i Hedmark.
• Krivenjeva, Valentina; Wilson, Robert Charles & Ahmad, Rafi (2018). Bioinformatic Analysis of RNA-seq Data from Cultivated Strawberry (Fragaria x ananassa) and Experimental Validation of New Transcripts Related to Cold Tolerance. Høgskolen i Hedmark.
• Ahmad, Rafi; Rojek, Ewelina & Naseer, Mohammed Umaer (2018). Molecular typing, antimicrobial resistance profiling and phylogeny of Campylobacter based on whole genome sequencing. Høgskolen i Hedmark.
• Kragulj, Lana; Solberg, Trygve Roger & Ahmad, Rafi (2017). Investigating Cattle as a Potential Model to Study Human Diseases - Including Genome-Wide Association Studies and Comparative Genomics Between the Species. Høgskolen i Hedmark.
• Koirala, Narayan Prasad; Naseer, Mohammed Umaer & Ahmad, Rafi (2017). Comparing different whole genome sequence based phylogenetic approaches for the description of enterohemorrhagic Escherichia coli O103 in Norway from 2006-2016. Høgskolen i Hedmark.
• Bhandari, Prabin; Wilson, Robert Charles & Ahmad, Rafi (2016). Bioinformatic Analysis of RNA-Seq Data from Cultivated Strawberry (Fragaria x ananassa) and Identification of Transcripts Related to Cold Tolerance. Høgskolen i Hedmark.

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