strategic indo-swedish cooperative ... " proposal form strategic indo-swedish cooperative...
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Proposal Form
STRATEGIC INDO-SWEDISH COOPERATIVE PROGRAMME ON “HEALTH AND DISEASE PREVENTION”
A. PROJECT 1. Title of Project: Novel approaches to investigate the genomics and expression of differential virulence and emergence of multi-drug resistance in species of Klebsiella 2. Specific research field: Field: Infectious diseases Sub field: Anti-microbial resistance 3. Project Duration: 01/04/2017 ～ 31 /03 /2020 (3 years) 4. Summary of Project (i) Key Words: Enterobacteriaceae, Klebsiella spp., genomics, transcriptomics, proteomics, qPCR array, anti- microbial resistance, virulence factors (ii) Objectives:
1) Whole-genome analysis of clinical isolates of species of Klebsiella causing urinary tract infections (UTI),
bacteremia and pneumonia;
2) Evaluation of multi-drug resistance and virulence factors using RNA-Seq;
3) Analysis of expression of anti-microbial resistance and virulence factors in Klebsiella spp. from
laboratory grown pathogenic isolates using qPCR array;
4) Analysis of multi-drug resistance and virulence factors, using Mass Spectrometry (MS)-based
proteomics;
5) Evaluate new drugs (from Wockhardt Ltd) for their effect on modulating the expression of virulence
factors and drug resistance genes
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Vadodara, Jan 15, 2017
Curriculum vitae
Devarshi Gajjar
Associate Professor
Department of Microbiology and Biotechnology Centre
Faculty of Science
M. S. University of Baroda
Vadodara-390 002
Phone no: 0265-2794396; email: [email protected]
Date of Birth: 4th August 1977 Gender: Female
EDUCATION
1999- 2003 Sardar Patel University, Department of Biosciences, Vallabh Vidyanagar, India
Ph.D. Microbiology
1997-1999 M. S. University of Baroda, Department of Microbiology and Biotechnology Centre, Vadodara,
India
M.Sc. Microbiology
1994-1997 B P Baria Science College, South Gujarat University, Surat, Gujarat, India
B.Sc. Microbiology
PROFESSIONAL EXPERIENCE
JUNE 2013 – TILL DATE ASSOCIATE PROFESSOR,
Department of Microbiology and Biotechnology Centre
Faculty of Science
The M. S. University of Baroda, Vadodara
2004-MAY 2013 Scientist,
Iladevi Cataract and IOL Research Centre, Ahmedabad.
GRANTS
ONGOING: GSBTM project: “Studies on virulence factors of Fusarium and Aspergillus spp.”-
2013 to 2016
ONGOING : ICMR project: “Molecular mechanisms of Antibiotic Resistance in Pseudomonas
spp. causing ocular infections” 2016 to 2019
COMPLETED : ICMR project: ‘Studies on virulence factors and antifungal susceptibility of
Fusarium spp. isolated from fungal keratitis’ [IRIS No. 2010-02120]- June 2011 to 2014
Recipient of Women’s Scientist Fellowship (WOS-A) from Department of Science and Technology,
Government of India; for the period of 2009 to 2012(No.SR/WOS-A/LS-120/2008)
Recipient of Research Associate Fellowship from Indian Council of Medical Research; for the period of
April 2004 to 2006 (Ref 3/1/2(12) Oph./2004-NCD-II) (IRIS ID No.2004 04780)
INTERNATIONAL CONFEENCES
Presented oral papers at :
1. 18th Congress of the International Society for Human and Animal Mycology, Berlin, Germany (11-
15 June 2012) 2. The Anual Meeting of Association for Research in Vision and Ophthalmology (ARVO), Fort Lauderdale,
USA- (1-5 May 2010)
3. The ASIA-ARVO meeting on Research in vision and Ophthalmology, Suntech, Singapore- (2-5 March
2007)
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Presented Posters at :
1. ASIA-ARVO meeting on Research in vision and Ophthalmology, New Delhi, India- (28th-31st October
2013) 2. ASIA-ARVO meeting on Research in vision and Ophthalmology, Suntech, Singapore- (2-5 March
2007)
Invited talk on “The lens and Dolichol” at Institute of Biochemistry and Biophysics, Polish Academy of
Sciences, Warsaw-POLAND September 2007
NEWS ARTICLES:
Abhay R. Vasavada, Mamidipudi R. Praveen, Devarshi U. Gajjar,Deepak Pandita,
Cover story on “The stromal hydration of clear corneal incisions: Is the benefit real or imaginary?” Cataract and
refractive surgery today June 2007
Dr. Devarshi Gajjar and Sukrati Gagrani
Article in Gujarati on Side Effects of antibiotics, safe use and disposal of antibiotics, Sandesh, 17th July -2016
Vadodara
AWARDS:
1. Awarded Second prize for poster entitled "Quantification and characterization of proteases from
Fusarium species isolated from keratitis patients” ASIA-ARVO meeting on Research in vision and
Ophthalmology, New Delhi, India- (28th-31st October 2013)
2. Awarded best poster presentation for the poster entitled “Antioxidative enzyme activities in the lens
epithelium of patients with senile cataracts” At 16th Annual Meeting of Indian Eye Research Group,
Hyderabad, India-2007
3. 1st Prize awarded to Miss Swati Madhu for oral paper presentation on :
Madhu SN and Gajjar D Quantification of total naphthoquinone in pathogenic Fusarium spp. presented at
Science excellence 2015 - 26th september under M.Phil-PhD catagory organized by Department of Botany,
Gujarat University, Ahmedabad .
PUBLICATIONS (Recent Five):
1. Kayastha F, Johar K, Gajjar D, Arora A, Madhu H, Ganatra D, Vasavada A. Andrographolide
suppresses epithelial mesenchymal transition by inhibition of MAPK signalling pathway in
lens epithelial cells. J Biosci. 2015 Jun;40(2):313-24.
2. Ganatra DA, Rajkumar S, Patel AR, Gajjar DU, Johar K, Arora AI, Kayastha FB, Vasavada
AR. Association of histone acetylation at the ACTA2 promoter region with epithelial
mesenchymal transition of lens epithelial cells. Eye (Lond). 2015 Jun;29(6):828-38.
3. Pal AK, Gajjar DU, Vasavada AR. DOPA and DHN pathway orchestrate melanin synthesis in
Aspergillus species. Med Mycol. 2014 Jan;52(1):10-8.
4. Vasavada V, Vasavada AR, Vasavada VA, Srivastava S, Gajjar DU, Mehta S. Incision integrity and
postoperative outcomes after microcoaxial phacoemulsification performed using 2 incision-dependent
systems. J Cataract Refract Surg. 2013 Apr;39(4):563-71.
5. Gajjar DU, Pal AK, Ghodadra BK, Vasavada AR. Microscopic evaluation, molecular identification,
antifungal susceptibility, and clinical outcomes in fusarium, Aspergillus and, dematiaceous keratitis.
Biomed Res Int. 2013;2013:605308.
6. Ganatra DA, Johar KS, Parmar TJ, Patel AR, Rajkumar S, Arora AI, Kayastha FB, Pal AK, Gajjar
DU, Vasavada AR. Estrogen mediated protection of cytoskeleton against oxidative stress. Indian J Med
Res. 2013 Jan;137(1):117-24.
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(iii) Approach: Klebsiella spp. are one of the top five pathogens world wide and their multidrug resistance has posed a serious health care issue, but little is known about their differential pathogenesis and emergence of drug resistance. Hence, continuous efforts are being made to understand their differential pathogenesis and emergence of drug resistance. In our present research proposal, an integrated genomics, trancriptomics and proteomics approach will be employed to understand various aspects of their pathogenesis. There has been a continuous and tremendous increase in drug resistance in Klebsiella spp. within India, although the molecular details of this phenomenon remain largely unknown. There is only one report of a whole genome sequence analysis for a clinical isolate and no studies on expression analyses, including transcriptomic or proteomic analyses have been carried out. Members of Klebsiella genus isolated from urinary tract infections (UTIs), bacteremia and pneumonia will be included. We propose whole-genome sequencing for comparison of isolates [n=100 (from India); n=50 (from Sweden)]) in order to understand the comparative amountof genomic diversity and repertoire of various genes/plasmids associated with drug resistance, virulence and transmission. This will give an idea of probable spread of these isolates and their clonal propagation. We will also conduct RNA-Seq from the cultures representing UTI, bacteremia and pneumonia in these isolates from both countries. This will decipher a comparative transcriptome analysis of the pathogens, thus revealing novel therapeutic or diagnostic targets. This trancriptomics data will be used for designing a real-time qPCR array,targeting candidate genes (for virulence) so as to further analyze them in a larger number of isolates (n=100). The data will be compared with responses to therapy and genes responsible for highly virulent clones would be identified. The data can be used for selecting prospective drug targets as well. In the final stage, new drugs (provided by Wockhardt) will be tested at various concentrations. They will also be evaluated for their efficiencies in modulating the expression of virulence genes and antimicrobial resistance genes. Distribution of work: 1. Collections of isolates will be done both in India and Sweden. Library construction will be done in India for Indian isolates and in Sweden for isolates from there. 2. Whole genome sequencing and RNA-seq will be done at Sweden. The initial bioinformatic analysis will also be done in Sweden during which the necessary expertise will be built in Indian laboratories through this collaborative work. Interpretation of the bioinformatics results and analysis of their implications will be carried out jointly through e-communication and exchange. 3. Analysis of multi-drug resistance and virulence factors, using Mass Spectrometry (MS)-based proteomics will be done in Sweden. 4. The real time qPCR arrays for quantification of candidate genes in large number of isolates will be done in India. 5. Finally, testing of drugs will be done in India. (iv)Expected outcome: This study will provide detailed genomic insights into the multi-drug resistant members of the Klebsiella spp. in India and will identify genomic loci associated with highly virulent phenotype and emergence of drug resistance.
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Real-time qPCR arrays for rapid detection of drug-resistant variants/genes will be extremely helpful in choosing the most-effective antibiotics for therapy of patients with infectious disease and will help implement the anti-microbial stewardship programme. 5. Personal Data of Principal Investigators INDIA
Name of PI Dr. Devarshi U Gajjar
Title/Designation Associate Professor
Department Department of Microbiology and Biotechnology Centre
Organization Faculty of Science, The Maharaja Sayajirao University of Baroda
Address Sayajiganj
Office phone# 0265
Cell phone# 919898933299
Fax#
e-mail [email protected], [email protected]
Date of Birth 4th August 1977
SWEDEN
Name of PI Dr. Edward Moore
Title/Designation Professor of Bacteriology
Department Department of Infectious Diseases
Organization Sahlgrenska Academy of the University of Gothenburg
Address Guldhedsgatan 10A, 41346 Gothenburg
Office phone# +46-31-342-4696
Cell phone# +46-70-259-8355
Fax# +46-31-
e-mail [email protected] ; [email protected]
Date of Birth 3rdJanuary 1954
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6. Project Partners Partners in Indian Team: Name Organization, Division Title Degree Specialty (Leader) Dr. Devarshi Gajjar Associate Professor Ph.D Microbiology (Partners) Dr. Pushpendra Singh UGC – FRP
Assistant Professor and Ramlingaswami Fellow
Ph.D Microbiology, Genomics
Director, Drug Discovery Programme, Wockhardt Ltd
Ph.D Drug Discovery
Advisors Dr. Geeti Maheshwari Consultant Medical Microbiologist Toprani labs, Vadodara
MD. Medical Microbiology
Microbial Diagnosis
Dr. Jyoti Patankar Consultant Medical Microbiologist Sterling Hospitals, Vadodara
MD, Medical Microbiology
Microbial Diagnosis
Dr. Suresh Desai Pathologist, Metropolis Labs, Surat
MD, Pathologist Diagnosis
Partners in Swedish Team
Name Organization, Division
Title Degree Specialty
(Leader) Dr. Edward Moore Professor PhD Microbiology, Biochemistry
(Partners) Dr. Roger Karlsson
Asst. Professor PhD Chemistry
Dr. Erik Kristiansson
Assoc. Professor PhD Bioinformatics, Biostatistics
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B. TECHNICAL INFORMATION 1. Objectives of Project (Up to 200 words)
I. Whole-genome analysis of clinical isolates of Klebsiella spp. causing urinary tract infections
(UTI), bacteremia and pneumonia;
II. Evaluation of multi-drug resistance and virulence factors, using RNA-Seq;
III. Analysis of expression of anti-microbial resistance and virulence factors in Klebsiella spp. from
laboratory grown pathogenic isolates using qPCR array;
IV. Analysis of multi-drug resistance and virulence factors, using Mass Spectrometry (MS)-based
proteomics;
V. Evaluate new drugs (from Wockhardt Ltd) for their effect on modulating the expression of
virulence factors and drug resistance genes
2. Justification for collaboration, including background to the proposed project, each partner’s expertise and specific contribution to the project, and the added value of the proposed collaboration (up to 400 words): The bacterial family, Enterobacteriaceae, including the genus Klebsiella, are common human pathogens associated with infectious diseases in hospital and community settings; urinary tract infections (UTIs), bacteremia and pneumonia are the most common,with Klebsiella spp. ranking 2nd after E.coli in UTIs and bacteraemia (Mendelson et al.,2005), and among the top 5 pathogens causing infection in patients in neonatal intensive care units, and the 2nd most frequent cause of Gram-negative neonatal bacteremia (Qureshi et al, 2015). Klebsiella spp. are commonly resistant to multiple anti-microbials and are acknowledged to be a major source of antimicrobial resistance genes that spreads to other Gram-negative pathogens (Karkey et al., 2014). Multi-drug resistance is one of the most serious concerns to be addressed with respect to Klebsiella infections. On the other hand, various attributes possessed by Klebsiella spp. group them into virulent and even hyper-virulent strains. Klebsiella possess many virulence factors, such as exopolysaccharides, capsule, lipopolysaccharides, fimbrae, siderophores, etc. (Podschun et al.,1998). There are currently no studies from India on isolates of Klebsiella spp. to assess the presence or expression of such virulence factors. Furthermore, there are no data comparing isolates from hospital settings with isolates from community infections. Clinical samples from patients will be collected in India and Sweden. The proposed study has multipleparts; (I) Whole-genome sequencing will be carried out, using available/commercial sequencing facilities. (II) For transcriptome analysis also, the experimental work will be conducted in both the Institutes. (III) For the proteomics analyses, the work will be carried out in Sweden. (IV) The bioinformatics analyses will be carried out by the Bioinformatician partner -Kristiansson (Sweden), whose laboratory has developed the pipelines for processing the genomics, transcriptomics and proteomics data from NGS platforms. Finally, the real-time PCR array for expression analysis (antibiotic resistance and virulence) in a reasonable number of samples (n=100) will be done in India. These data
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will be used for developing a point of care assay for patients, guiding the judicious use of antibiotics. Such a detailed genomics, transcriptomics and proteomics study is not possible without technical expertise. Our team possesses diverse and necessary skill sets for the experimental work proposed in this project and have conducted these studies previously (Truman R*, Singh P* et al NEJM 2011, Schuenemann V*, Singh P*, et al Science 2013; Singh P et al PNAS 2015; Lancet Infectious Diseases, under review, * joint first author). The Indian partners have significant experience in microbiological characterization and antibiotic susceptibility testing of various clinical isolates which have been collected over a period of several months from community- and hospital-acquired infections. The Swedish partners have excellent skills in carrying out expression studies for several pathogens and have developed bioinformatics workflow. Upon finishing comparative accounts of genomic, trancriptomic and proteomic features of various Klebsiellaspp, the validation of trancriptome expression in a larger set of samples would be achievable using the expertise, resources and clinical isolates in the laboratory of Indian collaborators. Since prevalence of highly resistant strains is more prominent in India, it is logical to conduct the validation study in India, so that results can be generated on a representative number of clinical isolates in lesser time. Some of these candidate genes will also be evaluated in additional clinical isolates from Sweden as well, so that the efficacy of the candidate diagnostic tests/therapeutic targets can be validated, using the collection of isolates representing wider geographical origins and thus would be more robust.
3. Descriptions of the Cooperative research project – maximum 6 pages
Background :
The introduction of antibiotics for treatment of infectious disease represents one of the most important advances in medicine and healthcare. However, due to excessive consumption of antibiotics, anti-microbial resistance (AMR) in bacteria has expanded world-wide and is increasing at accelerating rates. The global range of resistance in bacteria, particularly in human pathogens, presents major challenges for treatment and preventing the spread of infection. A review commissioned by the UK government has estimated the near-future global toll of AMR at tens of millions of deaths and indirect costs of at least $100 trillion in sacrificed gross national products per year (O’Neill, 2016). The World Health Organization (WHO) has predicted the advent of infectious diseases for which no antibiotic treatment will be available (WHO, 2014). The WHO identified Escherichia coli and Klebsiella pneumonia among the bacterial agents of ‘greatest global concern for AMR’ world-wide, associated with hospital- and community-acquired infections. These are among the most relevant AMR infectious, pathogenic bacteria in Sweden, as well. With this outlook in the persistent escalation of AMR, combined with continuing decline in new antibiotic discovery, increasing awareness and understanding of AMR must be realized. The development of innovative, reliable, rapid and cost-effective analytical techniques for comprehensive diagnostics and characterizations of AMR in infectious bacteria is essential, to prevent rising mortality and reduce the costs associated with AMR infections.
With increasing capacities of ‘Next-Generation Sequencing (NGS)’ technologies (Dunne et al., 2012), whole-genome sequence (WGS) analyses of AMR bacteria provide the potential for new insights into resistance mechanisms (Kristiansson et al., 2011). However, while WGS determinations and genomics analyses are effective in elucidating the total metabolic potential of microorganisms, DNA-based analyses, alone, are not able to provide information on the expression of AMR factors that produce resistant phenotypes of bacterial strains.
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The developments in NGS and increasing WGS data becoming available in public databases have seen the parallel advances in transcriptomics and proteomics analyses of microorganisms. Recent developments in mass spectrometry (MS) instrumentation and ‘soft’ (i.e., relatively non-destructive) ionization techniques have enabled efficient analyses of bacterial cellular proteins and direct determination of the expression of genome-encoded proteins.
This proposed project will apply novel methods and protocols of genomics, transcriptomics and proteomics for comprehensive analyses of the expressed ‘resistome’ responsible for AMR in infectious bacteria.
The members of the genus Klebsiella, are common human pathogens that lead to a wide range of diseases in both hospital and community settings. Of all the reported infections by Klebsiella, UTIs, bacteremia and pneumonia are the most common. Three species in the genus Klebsiella are associated with illness in humans: K. pneumoniae, K.oxytoca, and K.granulomatis. K. pneumoniae is mostly associated with lung and bacteremia infections while K. oxytoca is mainly associated with UTIs. Klebsiella spp. ranks 2nd after E.coli in UTIs and bacteremia (Mendelson et al.,2005). K. oxytoca is among the top 4 pathogens that cause infection in patients in neonatal intensive care units and is the second most frequent cause of Gram-negative neonatal bacteremia (Qureshi et al., 2015). However, very few studies from India have identified the Klebsiella isolates. Most studies only report the drug sensitivity testing and some report the presence of few resistance genes using PCR. Since, multi-drug resistance is one of the most serious concerns in Klebsiella infections in India there is a need to undertake a detailed study to address the problem.
Whole genome sequencing of Klebsiella isolates from hospital-acquired infections has been reported from Netherlands (Zhao et al., 2016), China (Gao et al., 2012), Korea (Lee et al., 2014), Malaysia (Al-Marzooq et al., 2015), Italy (Donati et al., 2014) and Australia (Espedido et al., 2013). Only one Klebsiella isolate has been sequenced from India (Rafiq et al., 2016). The purpose of most of the above studies were to track the source of the outbreak and also trace the spread of the pathogen. However, it can be hypothesised that the major pool / source of drug resistant isolates come from the community infections, which are clonally propagating and eventually reaching the hospital settings. Hence, it would be appropriate to analyze these isolates from community infections and compare them with isolates from nosocomial infections. Inspite of a number of measures implemented to control the spread of AMR, the resistance has increased ever the period of last decade. This could be attributed to different factors including: uncontrolled consumption of anti-microbial agents through self-medication, inappropriate antibiotic prescription, the substandard quality of some drugs. Hence, this study would also be a part of the continuous monitoring/surveillance of Klebsiella isolates.
There are currently no studies from India for Klebsiella isolates studying the presence or expression of such virulence factors. Also there is no data comparing the isolates from hospital settings with the isolates from community infections. Recently, two studies on transcriptome analysis and RNA SEQ were reported.
Impact:
Whole genome analysis will be done for the first time from Indian isolates. Transcriptome data will enable us to identify certain virulence factors in hyper-virulent strains. Real time PCR array for
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expression of drug resistance genes when done over a period of time and from patients already taking drugs will help us in streamlining /restricting the use of certain drug that are more prone to develop resistance. MS-based proteomics protocols have been successfully developed and used to identify and match discriminative peptides for analysing bacteria, including Escherichia coli, as well as Helicobacter pylori, Streptococcus pneumonia, Haemophilus influenza, Moraxella catarrhalis and other species. These studies focused on confirming the MS-proteotyping methodology for applications of bacterial characterizations. Analyses have demonstrated ability to detect the expression of antibiotic resistance genes, i.e., β-lactamases, in bacteria that are known to be resistant and also a subsequent increase in expression of such genes when they have been exposed to antibiotic stress. These data have demonstrated the potential in using the MS-based proteomics methodologies for diagnostics of AMR in pathogenic bacteria.
The scope of identifying new drugs in their ability to restrict spread of resistance genes/modulate expression to virulence genes/ resistance genes to combat infection is high because of the Industry partnership (Wockhardt Ltd) in the project.
Implementation:
The work plan will be implemented at both places India and Sweden
The protocols for MS-based proteomics analyses of bacteria have been developed and optimized within the framework of an on-going European Union (EU)-funded project, TAILORED-Treatment (www.tailored-treatment.eu/). However, the EU project has focused on developing methodologies for the diagnostics and treatment of respiratory infections. In this project, the methods developed within the EU project will be extended to the optimization of the protocols for the analysis of antimicrobial resistance and virulence factors, with a focus on applications to the analysis of Klebsiella spp. from UTI, bacteremia and pneumonia.
Actor constellations:
1. Dr. Devarshi Gajjar: Project Leader at MSU Baroda, India.
Would be responsible for the following duties
a) Implementation of project at MSU, Baroda. b) Recruitment of Project staff. c) Monitoring sample collection and collaborating with various laboratories for sample collection.
At present the lab has Klebsiella spp. isolates from three laboratories namely, Metropolis Labs, Toprani Labs and Sterling Hospitals.
2. Dr. Pushpendra Singh: Project Partner at MSU Baroda, India.
a) Responsible for library construction for whole-genome sequencing and RNA SEQ in India
3. Director, Drug Discovery Programme, Wockhardt Ltd.
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a) Responsible for selection of new drugs in pipeline at Wockhardt for their further testing for clinical isolates
4. Dr. Edward Moore: Principal Investigator at University of Gothenburg would be responsible for the following duties
a) Implementation of project in Sweden, preparation and submission of reports; b) Recruitment of personnel; c) Monitoring sample collection and collaborating with Sahlgrenska University Hospital for sample
and strain collections; d) Overseeing whole-genome sequence analyses.
5. Dr. Roger Karlsson: Project Partner at Nanoxis Consulting AB
a) Responsible for MS-based proteomics analyses of bacterial isolates and AMR and virulence factors.
6. Dr. Erik Kristiansson: Project Partner at Chalmers Technological College
a) Responsible for bioinformatics analyses of WGS, RNA-sequencing and proteomics data.
Work plan (schedule, milestones and deliverables) Settings: Sample collection will be done during the entire span of the project (2017 to 2020). During the first year of collection, samples will be collected from infections (UTIs, bacteremia and pneumonia) and grouped into virulent and hyper-virulent strains (on the basis of Exopolysaccharide production). Microbial drug testing will be done, using E-test according to CLSI guidelines. On an average, we receive 3-4 isolates /week. Methodology for Objective 1: Whole Genome sequencing (WGS) of pathogens: Total DNA (gDNA and plasmid) extraction from clinical isolates will be extracted using standard DNA extraction methods (Qiagen) following the manufacturer’s protocols. After quality and quantity determination of the isolated genomic DNA from previous step, we will prepare dual indexed libraries using a Lib prep reagents (for example Illumina Nextera library preparation kit with 96 indexes for multiplexing of samples). We will be sequencing 10 samples per flow cell of a Miseq Illumina platform with read length of 250 or 300 bp using v3 kits (or a multiplex level of 50 isolates on a HiSeq platform with read length of 100 bp using single end sequencing using NGS platform using available/commercial sequencing platform. In India, the samples/ libraries for sequencing will be prepared at Dr. Gajjar and Dr. Singh’ labs. Bio-informatic analysis of WGS data for SNP identification: Raw data in Fastq format along with the quality control files will be received through HTML link at both the institutes. This data will be processed thorough a common work flow with uniform criteria of quality filter and cut-offs for variant (SNP/Indel) identification. These pipelines will be customized using the existing expertise of the Swedish collaborators. First we will remove raw reads of low quality from sequencing data. High quality (Q>30) reads will be aligned to the available reference genome of the Klebsiellaspp member using Burrows-Wheeler Aligner (Li et al 2010) and variants will be recorded by GATK tools. We will then compare the identified variants with the existing databases of SNPs from the respective reference genome. After discarding the phylogenetically related and synonymous SNPs, we
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will focus our subsequent analysis on non-synonymous SNPs. In addition, the presence/absence of the plasmids and any additional genes/efflux pumps related to drug resistance will be also investigated. Phylogenetic analysis of pathogens for study of microevolution and molecular epidemiology: The enormous amount of information generated from WGS will provide detailed insights into the genome biology of a pathogen and also provides better resolution for studying the pathogen transmission. The genome scale phylogenetic comparison of these strains will allow any transmission hotspots also and will detect the predominant genotypes circulating in a given geographical area, for example in Gujarat state ( or more specifically in the Vadodara city from where these isolates have been collected). This will also allow identification of certain SNPs which are common in great majority of MDR isolates and hence could serve as a tool for easier and quicker prediction of resistance by employing a simple PCR/qPCR or LPA (Line probe assay), particularly in the suspected cases of community or nosocomial infection. This could be extremely useful for development of a point-of-care test, specially customized for the mutations in the prevalent isolates, for example those more common in Indian patients. Methodology for Objective 2 : RNA-Seq based transcriptomics For RNA-Seq based comparative transcriptomics RNA-Seq in this project aims at comparing the expression levels of genes in less virulent (associated with UTI) vs hyper-virulent (causing pneumonia) strains of various species of Klebsiella. The additional comparison is between the drug susceptible vs multidrug resistant isolates. For the second part, we will also take into the consideration whether this is primarily accountable due to presence/absence of various plasmids or due to genomic variants in the bacterial chromosome. RNA extraction and quality determination: Total RNA from pure cultures will be extracted using Qiagen RNeasy kits and will be quantitated using Qubit fluorometer/Nanodrop followed by quality assessment on Bioanalyzer/Fragment Analyzer instrument to determine the RIN (RNA Integrity Number). Stranded Library prep and quantitation: Multiplexed Lib preparation will be carried out using Illumina kits (For example, TruSeq stranded Lib prep kit), avoiding the predominant rRNA using Ribozero kits following the manufacturer’s instruction. Sequencing: Paired-end multiplexed sequencing will be carried out using 100 bp read length on a HiSeq platform (or using 150 bp read lengthon a MiSeq platform). Bioinformatic analysis and pathway identification: The resultant reads upon RNA-Seq will be mapped onto reference genomes using the programs TopHat and Cufflink (http://tophat.cbcb.umd.edu) (Trapnell et al 2009) or ‘Spliced Transcripts Alignment to a Reference’ (STAR) (Dobin et al 2010). The aligned reads will be assembled into transcripts using Cufflinks (Trapnell et al 2010; 2012). Reads with no match, that may represent horizontally transferred elements, will be assembled de novo using Trinity. The relative abundance of the transcripts will then be determined using CuffDiff, which takes the aligned reads from two or more conditions and reports differentially expressed gene. Differentially abundant genes will be statistically assessed using a DESeq2, which implements robust models especially developed for RNA-seq data. The expression data will be further analyzed for Pathway identification, using Ingenuity Pathway Analysis (IPA) or DAVID to identify dysregulated pathways in less virulent vs hyper-virulent strains. Identified pathways will then be selected for further characterizing them as the potential novel therapeutic target, for example using docking or in-silico prediction of binding sites of known drug compounds. Methodology for Objective 3: qPCR array for candidate genes for antimicrobial resistance and virulence
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Real time PCR primers will be designed for selected genes and qRT-PCR will be performed from 100 isolates to measure gene expression for the selected genes. Methodology for Objective 4: MS-based proteomics analyses of anti-microbial resistance and virulence Bacterial strains will be grown with and without antibiotic stress and lysed by bead-beating, and frozen at -20 °C until analyses. Bacterial lysates are injected into the LPI Hexalane FlowCell (Nanoxis Consulting AB, www.nanoxisconsulting.com; Patent Application No. WO2006068619). Bacterial proteins in cell lysates are immobilized to the Flow Cell membrane. Peptides are generated by trypsin digestions of bound bacterial proteins. The tryptic peptides are analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS). The LC-MS/MS output is converted for identification of peptides, using an in-house informatics pipe-line. The reference database used for peptide identification is a customized database consisting of 56,967,781 non-redundant proteins from the NCBI Genbank NR (43) and 6,320,906 peptide sequences from the reference genomes archived within the Human Microbiome Project (44). The resulting database contains a total of 59,349,300 distinct protein sequences. The MS-proteomics methods have been developed, in which significant parts of the proteome of an organism are analyzed in single runs. MS-based proteomic analyses of bacteria enables elucidation by generating a “snapshot” of a significant part of the entire proteome of an organism in relation to the genome. Analyses of high numbers of bacterial peptides, typically more than 1,000 generated from enzymatic digestion of cellular proteins, affords the possibility of attaining high levels of resolution in identifying expressed protein biomarkers (Karlsson et al, 2010; Karlsson et al., 2012). With such analytical means, it is feasible to detect and identify discriminative peptides for anti-microbial resistance and virulence (Karlsson et al., 2016; Gonzales-Siles et al., 2017). These strategies and protocols have been used successfully to detect distinct AMR factors associated with ESBL in E. coli strains. Methodology for Objective 5: Testing of new drugs The transcriptomics and proteomics data will be shared with the industrial partner and selection of drugs will be done jointly between all the three partners. Efficacy of drugs will be tested using CSLI guidelines. The effect of drugs on the expression of virulence factors and drug resistance genes will also be done. Time schedule and milestones :
Task Month 1-6
Month 6-12
Month 12-18
Month 18-30
Month 30-36
Recruitment of staff, Acquiring instruments, chemicals, etc. Collection of isolates (INDIA AND SWEDEN)
Whole genome sequencing of all isolates (INDIA AND SWEDEN)
Transcriptomic analysis using RNA seq (SWEDEN)
Proteomics using mass spectrometric analysis (SWEDEN)
qRTPCR array for quantification of virulence factors and multidrug resistance genes (INDIA)
Testing of drugs (INDIA) Compilation of data and report submission
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Deliverables: A comparative study on genomics, transcriptomics and proteomics will result into an integrated data on the pathogenesis and AMR in Klebsiella spp. Form-‐5 4. Plan for the execution of the Cooperative Project - with clear description of research activities on both sides as well as of the elements of cooperation and exchange, 3 pages maximum Work Plan in INDIA
Collection of samples and Drug sensitivity testing DNA extraction Whole genome sequencing: Lib Prep and Quantitation qRT-PCR array for virulence factors and drug resistance genes: Selection of candidate genes and Primer designing
Testing of drugs: Based on qPCR data and in consultation with the Scientists at Wockhardt Likewise, at Sweden: Work Plan in SWEDEN Collection of samples RNA-Seq and Proteomics Bioinformatics Data analysis The milestones of these steps and experimental details are described in the Work Plan.
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5. Facilities related to project activity available at the institutions where the project will be carried out: In India: The Department of Microbiology, M S University of Baroda is one of the pioneering departments in country imparting post-graduate training in Microbiology and Biotechnology. The Department was established in 1964 and is one of the first five departments selected for the Biotechnology teaching programme funded by DBT since 1985. Dr. Devarshi Gajjar, PI, has an established lab with biosafety level II for handling opportunistic pathogens. Currently two projects; on pathogens- Fusarium (GSBTM funded) and Pseudomonas (ICMR funded) are being undertaken. The department has all basic facilities for carrying out the proposed work. In Sweden: The University of Gothenburg (www.gu.se) is a leading University in Sweden, serving approximately 40,000 students and 6,000 employees, comprising 8 faculties with more than 60 departments, with extensive educational and research facilities. The Faculty of Medicine, Sahlgrenska Academy, provides education and conducts research in the fields of medicine, pharmacy, odontology, and healthcare sciences in close association with the Sahlgrenska University Hospital. UG is represented by personnel within the Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy (www.salgrenska.gu.se), which is a platform connecting university and hospital joint research activities. Nanoxis Consulting AB is a commercial service provider focusing on services and contract research in proteomics, with special attention to MS-based proteomics of membrane proteins and bacteria. NC is involved in several projects related to bacterial proteomics with academic and industrial partners and has more than 10 years experience in planning, executing and generating and delivering data in proteomics-related projects. NC is located in Gothenburg, Sweden. Chalmers University of Technology was founded in 1829, offering M.Sc. Eng., M.Arch., B.Sc.Eng., Nautical, Licentiate and doctors programs, as well as continued development programs for professionals. Chalmers has approximately 11,000 students and 2,500 employees. Each year around 350 Ph.D. and Licentiate degrees are awarded as well as 1,000 M.Sc.Eng and M.Arch. degrees. Approximately 40% of Sweden's graduate engineers and architects were educated at Chalmers. UG, NC and Chalmerswill provide the facilities and equipment for state-of-the-art clinical microbiological, molecular biological and analytical chemistry analyses. UG and Sahlgrenska Academy core facilities provide infrastructure and expertise in next-generation nucleic acid sequencing, mass spectrometry, NMR, genomics and proteomics analyses. The SciLife Clinical Genomics Facility of UG maintains a supported 400-core cluster with 144 Tb storage for sequence assembly and mapping, using automated pipelines available to researchers through the Next Generation Diagnostics Platform. The facility has 2 MiSeq and one NextSeq500 with another MiSeq, one NextSeg 500 and two Ion S5 to be delivered during 2017. The UG team has access to clinical samples and resources through the Department of Clinical Microbiology of the Sahlgrenska University Hospital. Chalmers offers an infrastructure in Computational Biology focused on systems biology, systems medicine and analysis of big data as well as
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mass spectrometry (Chalmers Mass Spectrometry Infrastructure). Chalmers is a node in the Swedish National Infrastructure for Computing (SNIC), which provides computational resources on the local clusters and in the Swedish metabolomics center (SMC), which can further support metabolomics analyses. In addition, UG, NC and Chalmersareincluded within the Centre for Antibiotic Resistance Research (CARe), which is a platform connecting more than 30 principal investigators in the field of AMR, multi-resistance of Gram-negative bacteria with a focus on resistance to the so-called ‘last-resort’ antibiotics, such as carbapenemases, commonly carried in multi-resistant Klebsiella spp. 6. Information of visiting persons for technical mission (per annum). Estimation of the expected plan of visits; any further modification, according to the needs of joint project has to be communicated and approved by the participants institutions. A. India to Sweden Name Organization Duration Purpose 1st Year - 2nd Year Dr. Pushpendra
Singh MSU, Baroda 3 weeks Compilation of genomics, trancriptomics
and proteomics data, Discussion with Swedish collaborators, Designing qRT-PCR array
3rd Year Dr. Devarshi Gajjar
MSU, Baroda 3 weeks Compilation of entire data, discussion with Swedish collaborators
B. Sweden to India Name Organization Duration Purpose 1st Year Dr. Edward
Moore Sahlgrenska Academy of the University of Gothenburg, Sweden
4 weeks Overseeing whole genomics and transcriptomics work Discussion with Indian collaborators, Conduct training for Indian JRFs
2nd Year Dr. Roger Karlsson
Nanoxis Consulting AB Sweden
3 weeks Conduct proteomics training for Indian JRFs and other students at the department
3rd Year Dr. Erik Kristiansson
Chalmers Technological College, Sweden
3 weeks To conduct bioinformatics training for the Indian JRFs and other students Compilation of data and discussion with Indian collaborators
7. Expected results of Cooperation (e.g. joint publications, patents etc.) Are any of the expected results likely to have commercial value? (up to 100 words): The collaborative project will certainly result into joint publications. If we are successful in finding some novel virulence factors / drug resistance markers which contribute to the pathogenesis of these pathogens then they can be exploited for developing targets. Also, there is a chance for the development of diagnostic markers based on the expression profile of the virulence factors and drug resistance genes which may in turn aid the clinicians in prescribing the most suitable antibiotics.
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8. Personal and Professional Data (CV) of Indian and Swedish PIs must be attached. ANNEXURE I 9. Complementary resources: Cite other national or international funding resources for related scientific projects including funding agencies, funding period and grant amount. Funding received By Dr. Devarshi Gajjar: 1. ONGOING: GSBTM project: “Studies on virulence factors of Fusarium and Aspergillus spp.”-2013
to 2017; Amount: 1200000/- Rupees 2. ONGOING : ICMR project: “Molecular mechanisms of Antibiotic Resistance in Pseudomonas
spp.causing ocular infections” 2016 to 2019; Amount : 3500000/- Rupees 3. COMPLETED : ICMR project: ‘Studies on virulence factors and antifungal susceptibility of
Fusariumspp. isolated from fungal keratitis’ [IRIS No. 2010-02120]- June 2011 to 2014; Amount : 2400000/- Rupees
Funding received by Dr. Edward Moore 1. ONGOING: Principal Investigator for Joint-Programme Initiative – Anti-Microbial Resistance (JPI-AMR) and Vetenskapsrådet project: “Predicting cell-cell horizontal transmission of antibiotics resistance from genome and phenome” 20170101 to 20201231; Amount: 3.4 MSEK / 1.78 M€ total 2. ONGOING: Co-applicant for University of Gothenburg Centres for Global Societal Challenges Programme: “Centre for Antibiotic Resistance Research (CARe)” 20160401 to 20220331; Amount: 50 M SEK; J. Larsson and F. Carlsson, Coordinators 3. ONGOING: Principal Investigator for VästraGötalandsregion ALF-LUA project: “Proteomics-based diagnosis of infectious diseases and antibiotic resistance: a sensitive, rapid and cost-effective alternative” (ALFGBG-437221; 2.175 MSEK) 20150101 to 20171231; Amount: 2.175 M SEK 4. ONGOING:Principal Investigator for Swedish International Development Agency (SIDA) project: “Detection and characterization of genes associated with the synthesis of bioactive compounds in bacteria from marine sediments of the Chilean coast: searching for novel antimicrobial agents” (Project No. 348-2013-6713); 20140101 to 20171231; Amount: 750 kSEK 5. ONGOING: Principal Investigator for European Union FP7-HEALTH-2013-INNOVATION-1 project: “Development of Tailored Anti-microbial Treatment Regimens and Novel Host-Pathogen Insights for Respiratory Tract Infections and Sepsis (TAILORED-Treatment)” (Project No. HEALTH-F3-602860-2013) 20130801 to 20170731; Amount: 1.3 M€ / 5.975 M€ total
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C. FINANCIAL INFORMATION Budget or resources for the project; one for the Swedish side and one for the Indian side Indian Side: Budget (In Rupees) (DrDevarshi Gajjar and Dr Pushpendra Singh, Dept of Microbiology & Biotech Centre, MSU Baroda)
A. Non-Recurring (e.g. equipments, accessories, etc.)
(all costs are shown in INR for Indian side)
S. No. Item Year 1 Year 2 Year 3 Total 1 Tape Station or Fragment Analyzer
instrument for Lib Prep steps, Lib Profile and Quality Analysis
30,00,000 30,00,000
2 Fluorometer (Qubit) 2,00,000 2,00,000 3 Pipette Set 2,00,000 2,00,000 4 PCR machine (thermocycler) 6,00,000 6,00,000 5 Real time PCR machine 20,000,00 20,00,000 6 Biosafety Cabinet and accessories
(Electric Loop sterilizer, small centrifuge etc)
10,00,000 10,00,000
7 Refrigerated centrifuge 6,00,000 6,00,000 Sub-Total (A) 76,00,000
B. Recurring
B.1 Manpower (See guidelines at Annexure-III)
S. No. Position No.
Emolument (INR)
Year 1 Year 2 Year 3 Total
1 1 positions of JRF
30,000 per month
3,60,000 3,60,000 4,03,200 11,23,200
2 1 position of Technician
20,000 per month
2,40,000 2,40,000 2,40,000 7,20,000
Sub-Total (B.1) =18,43,200 B.2 Consumables
S. No. Item
Quantity Year 1 Year 2 Year 3 Total
1. Ampure XP DNA and Lib Clean-up Beads (60 ml)
1 1,00,000 1,00,000 1,00,000 3,00,000
2. RNA purification beads (RNase free)
1 1,00,000 1,00,000 1,00,000 3,00,000
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3 Qubit assay kits for DNA and RNA quantitation
4 1,50,000
1,50,000
1,00,000 4,00,000
4 DNA fragment analysis kit
15 1,00,000
1,00,000 1,00,000 3,00,000
5 Library Prep kit for DNA Seq (WGS)
For 150 samples & controls
3,00,000 3,00,000 2,00,000 8,00,000
6 RNA-Seq Lib Prep reagents and Ribozero kit
For 50 samples
2,00,000 2,00,000 2,00,000 6,00,000
7 qPCR Kits for Library quantitation
2 kits per year
1,50,000 1,50,000 1,00,000 4,00,000
8 Sequencing Costs for a HiSeq Platform
5 lanes of HiSeq
4,00,000 4,00,000 2,00,000 10,00,000
9 Media & reagents for Drug sensitivity testing
2,00,000 2,00,000 2,00,000 6,00,000
10 Plasticwares and consumable plates
2,00,000 2,00,000 2,00,000 6,00,000
Total 53,00,000 Sub-Total (B.2) =Total 53,00,000
Other items Year 1 Year 2 Year 3 Total B.3 Travel (for one visit to Sweden and accommodation related expenses for hosting the Swedish collaborator)
2,50,000 2,50,000 1,00,000 6,00,000
B.4 Contingency (For general needs, glassware, and minor repairs, Shipment of the Libraries, controls etc)
1,50,000 1,50,000 1,00,000 4,00,000
B.5 Overhead (If applicable)
15% (of the total recurring cost)
12,21,480
Sub-total of B (B.1+B.2+B.3+B.4+B.5) 81,43,200
Grand Total (A + B) 1,69,64,680/- Total Budget estimate for MSU (Drs D Gajjar’s Lab & Dr P Singh’s Labs): Rs 1,69,64,680
Swedish side (submitted by the Swedish Collaborators to the Swedish Grant Agency) :
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References:
§ Al-Marzooq F, Mohd Yusof MY, Tay ST. Molecular Analysis of Antibiotic Resistance Determinants and Plasmids in Malaysian Isolates of Multidrug Resistant Klebsiella pneumoniae. PLoS One. 2015 Jul 23;10
§ Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., ... & Gingeras, T. R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15-21.
§ Domenico, P., Salo J., Cross S., & Cunha A., (1994). “Polysaccharide capsule-mediated resistance to opsonophagocytosis in Klebsiella pneumoniae.” Infection and immunity, 62(10), 4495-4499.
§ Donati V, Feltrin F, Hendriksen RS, Svendsen CA, Cordaro G, García-Fernández A, Lorenzetti S, Lorenzetti R, Battisti A, Franco A. Extended-spectrum-beta-lactamases, AmpC beta-lactamases and plasmid mediated quinolone resistance in klebsiella spp. from companion animals in Italy. PLoS One. 2014 Mar 4;9(3):e90564.
§ Dunne Jr, W. M., Westblade, L. F., & Ford, B. (2012). Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. European journal of clinical microbiology & infectious diseases, 31(8), 1719-1726.
§ Espedido BA, Steen JA, Ziochos H, Grimmond SM, Cooper MA, Gosbell IB, van Hal SJ, Jensen SO. Whole genome sequence analysis of the first Australian OXA-48-producing outbreak-associated Klebsiella pneumoniae isolates: the resistome and in vivo evolution. PLoS One. 2013;8(3):e59920.
§ Gonzales-Siles, L., Karlsson, R., Kenny, D., Karlsson, A., & Sjöling, Å. (2017). Proteomic analysis of enterotoxigenic Escherichia coli (ETEC) in neutral and alkaline conditions. BMC microbiology, 17(1), 11.
§ http://emedicine.medscape.com/article/219907-overview § http://www.who.int/mediacentre/factsheets/fs194/en/ § Jim O’neill. Tackling Drug-‐Resistant Infections Globally: Final Report and Recommendations.
2016 § Kristiansson, E., Fick, J., Janzon, A., Grabic, R., Rutgersson, C., Weijdegård, B., ... & Larsson,
D. J. (2011). Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements. PloS one, 6(2), e17038.
§ Lee Y, Kim BS, Chun J, Yong JH, Lee YS, Yoo JS, Yong D, Hong SG, D'Souza R, Thomson KS, Lee K, Chong Y. Clonality and Resistome analysis of KPC-producing Klebsiella pneumoniae strain isolated in Korea using whole genome sequencing. Biomed Res Int. 2014;2014:352862
§ Li, H., & Durbin, R. (2010). Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics, 26(5), 589-595.
§ Mendelson G., Hait V., Ben-Israel J., Gronich D., Granot E., & Raz R. (2005). Prevalence and risk factors of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae in an Israeli long-term care facility. European journal of clinical microbiology and infectious diseases,24(1), 17-22.
§ P Singh, A Benjak, VS Schuenmann, P Busso, A Charlotte, A Herbig, J Krause, L Vera-Cabrera,ST Cole. Insights into the evolution and origins of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis.PNAS USA 2015, 112(14): 4459-4464.
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§ Podschun, R., & Ullmann, U. (1998). Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clinical microbiology reviews, 11(4), 589-603.
§ Podschun, R., & Ullmann, U. (1998). Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clinical microbiology reviews, 11(4), 589-603.
§ Rafiq Z, Sam N, Vaidyanathan R. Whole genome sequence of Klebsiella pneumonia U25, a hypermucoviscous, multidrug resistant, biofilm producing isolate from India. Mem Inst Oswaldo Cruz. 2016 Feb;111(2):144-6.
§ Schroll C., Barken K., Krogfelt K., & Struve C. (2010). Role of type 1 and type 3 fimbriae in Klebsiella pneumoniae biofilm formation. BMC microbiology, 10(1), 179.
§ Trapnell, C., Pachter, L., & Salzberg, S. L. (2009). TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25(9), 1105-1111.
§ Truman RW *, P Singh*, R Sharma*, P Busso, J Rougemont, A Paniz-Mondolfi,A. Kapopoulou,S Brisse, DM Scollard, TP Gillis, ST Cole. Probable zoonotic leprosy in the Southern United States New England Journal of Medicine 2011; 364(17): 1626-33.
§ VJ Schuenemann*, P Singh*, T Mendum*, B Krause-Kyora*, G Jäger*, KI Bos, A Herbig, C Economou,A Benjak, P Busso, A Nebel, JL Boldsen, A Kjellstrom, H Wu, GR Stewart, Michael Taylor, P Bauer, O. Y.-C. Lee, HHT Wu, DE Minnikin, GS Besra, K Tucker, S Roffey, SO Sow, ST Cole, K Nieselt and J Krause. Genome-wide comparison of medieval and modern Mycobacterium leprae. Science 2013; 341(6142): 179-83.
§ Yinghua Guo, Zhong Cen, Yuanqiang Zou, Xiangqun Fang, Tianzhi Li, Junfeng Wang, De Chang, Longxiang Su, Yan Liu, Yanling Chen, Ruifu Yang, Changting Liu Whole-Genome Sequence of Klebsiella pneumonia Strain LCT-KP214 J Bacteriol. 2012 Jun; 194(12): 3281.
§ Zhou K, Lokate M, Deurenberg RH, Tepper M, Arends JP, Raangs EG, Lo-Ten-Foe J, Grundmann H, Rossen JW, Friedrich AW. Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae. Sci Rep. 2016 Feb 11;6:20840.
Moore, Edward: 540103-3898 20161114
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Edward R.B. Moore CURRICULUM VITAE
1. Higher education 1980, BS in Biology & Biochemistry; University of Houston, Houston, USA
1984, MS in Microbiology; University of Houston, USA
2. Degree of Doctor 1990, PhD in Microbiology; University of Houston, USA
Dissertation defense: September 20, 1990
Dissertation title: “Cytochrome Oxidase and 16S Ribosomal RNA Phylogenetic
Analyses on the Gram-Negative Aerobic Non-Symbiotic Nitrogen-Fixing Bacteria”
Dissertation supervisors: Prof. Peter Jurtshuk, Jr and Prof. George E. Fox
3. Post-doctoral position 1990-1992, Post-doctoral Research Fellow, Division of Microbiology
National Research Centre for Biotechnology (GBF), Braunschweig, DE
4. Docent appointment Not applicable
5. Specialist Certification Not applicable
6. Present positions 20050416 - current, appointed Professor of Bacteriology
Department of Infectious Diseases, Institute of Biomedicine
Sahlgrenska Academy of the University of Gothenburg
20% time for research
20041101 - current, Director/Curator, Culture Collection University of Gothenburg
(CCUG), Department of Clinical Microbiology; Sahlgrenska University Hospital
and Sahlgrenska Academy of the University of Gothenburg
7. Previous positions 2000-2005, Senior Research Officer (BBSRC Gr. 4-5): Microbial Diversity
Initiative, Macaulay Research Institute, Aberdeen, Scotland, UK 2000-2003, Research Fellow: Department of Molecular and Cell Biology,
Aberdeen University, Aberdeen, Scotland, UK
1995-2000, Senior Research Scientist (BAT 1b); GBF, Braunschweig, DE
1994-198, Research Fellow: Department of Biotechnology,
Technische Universität Braunschweig, Braunschweig, DE
1992-1995, Research Scientist (BAT 2a); GBF, Braunschweig, DE
8. Interruptions Not applicable
9. Supervision, *Dr. Daniel Jaén-Luchoro; Post-doctor, 2016-current, Sahlgrenska Hospital
Post-graduate *Dr. Hedvig Jakobsson; Post-doctor, 2015-current, Univ Gothenburg
(* primary-supervisor) *Dr. Lucia Gonzales; Post-doctor, 2014-2016, Univ Gothenburg
*Dr. Liselott Svensson ; Post-doctor, 2008-2012, Sahlgrenska Hospital
*Dr. Nahid Karami ; Post-doctor, 2007-2011, Sahlgrenska Hospital
*Dr. Fiona Porteus; Post-doctor, 2002-2005, Macaulay Institute (UK)
*Dr. Roland Weller; Post-doctor, 1998-2002, GBF (DE)
*Dr. Marc Osbourne; Post-doctor, 1997-1999, GBF (DE)
*Dr. Balbina Nogales; Post-doctor, 1996-1999, GBF (DE)
*Dr. Margit Mau; Post-doctor, 1996-1997, GBF (DE)
Moore, Edward: 540103-3898 20161114
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Supervision, Francisco Sàlva-Serra; PhD, current, Univ Bealearic Islands (ES)
Graduate-student Anna Granqvist; PhD, current, Univ Gothenburg
(* primary-supervisor) Lisa Helldal; PhD, current, Univ Gothenburg
Fei Sjöberg; PhD, Oct 2014, Univ Gothenburg
Anna Johnning; PhD, Apr 2014, Univ Gothenburg
*Christoffer Brandt; MS, Jun 2013, Univ Gothenburg
Ana Vieira; MS, Jul 2011, Catholic Univ Portugal (PT)
Carlos Rocha; MS, Jul 2010, Catholic Univ Portugal (PT)
*Hironari Izumi; Feb 2006, Aberdeen University (UK)
*Susanne Baumgarte; PhD, Jan 2002, Technische Universität Braunschweig (DE)
*Cecilia Harryson; MS, Nov 2007, Univ Gothenburg
*Anna Sjökvist; MS, Feb 2006, Univ Gothenburg
*Kathryn Allton; MSc, Biotechnology, Dec 2003, Robert Gordon Univ (UK)
*Tim Boyle; MSc, Microiology, Oct 2002, Aberdeen University (UK)
*Christa Hoch; PhD, Apr 1999, TU Braunschweig (DE)
*Dietmar Böltner; Diplom, Biologie, Jul 1999, TU Braunschweig (DE)
*Susanne Baumgarte; Diplom, Biologie, Jun 1998, TU Braunschweig (DE)
Margit Mau; PhD, Jun 1996, TU Braunschweig (DE)
Teaching experience: 2002-2004, Lecturer – ‘Topical Seminars in Environmental Microbiology’; for
Post-gradudate students, Aberdeen Univ
1995-1998, Lecturer, Laboratory Course Supervisor - ‘Molecular Microbiology’,
for Postgraduate students, Technical Univ Braunschweig
1995-1999, Laboratory Course Supervisor - ’General Microbiology‘; for
2nd-year University students, Univ Houston
Research funding (2008-2016): Principal Investigator for projects funded by Västra Götaland ALF-LUA and FoU for more than 8.0 mSEK and by
the European Commission for more than 1.3 m€. Co-Applicant on projects funded by VG ALF-LUA, VG FoU,
Vetenskapsrådet and FORMAS, the EC and on projects funded by the Health Canada Agency, the Ministry of
Education and Research of Spain and the Ministry of Education, Science and Technology (FONDECyT) of Chile.
Relevant Funded Projects from National and International Research Programs (2008-2016): 2016-2022: Co-Applicant/Principle Investigator for University of Gothenburg Centres for Global Societal
Challenges Programme: “Centre for Antibiotic Resistance Research (CARe)” (50 MSEK total), J Larsson and F
Carlsson, Univ Gothenburg, Applicants
2015-2017: Applicant/Principle Investigator for VG ALF-LUA; “Proteomics-based diagnosis of infectious
diseases and antibiotic resistance: a sensitive, rapid and cost-effective alternative” (ALFGBG-437221; 2.175 MSEK)
2014-2016: Applicant/Principle Investigator for Swedish International Development Agency (SIDA): “Detection
and characterization of genes associated with the synthesis of bioactive compounds in bacteria from marine sediments
of the Chilean coast: searching for novel antimicrobial agents” (Project No. 348-2013-6713; 750 kSEK)
2013-2017: Co-Applicant/Principle Investigator for European Union - FP7-HEALTH-2013-INNOVATION-1:
“Development of Tailored Anti-microbial Treatment Regimens and Novel Host-Pathogen Insights for Respiratory
Tract Infections and Sepsis (TAILORED-Treatment)” (Project No. HEALTH-F3-602860-2013; 1.300 M€ / 5.975 M€
total), J Hayes, Erasmus Medical Centre NL, Coordinator
2012-2015: Co-Applicant/Principle Investigator for European Science Foundation (ESF) - INFRA-2012-2.2.3:
“Microbial Resource Research Infra-structure (MIRRI)” (Project No. FP7-312251; 85 k€ / 3150 M€ total), D. Fritze,
DSMZ DE, Coordinator
2012-2014: Applicant/Principle Investigator for ALF-LUA: “Multi-drug-resistant Gram-negative infectious
bacteria: new genotypic and phenotypic developments for diagnostics and epidemiological control within the clinical
environment” (Project No. ALFGBG-210591; 2.550 MSEK)
Moore, Edward: 540103-3898 20161114
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2011-2015: Co-Applicant for Vetenskapsrådet; “Antibiotic resistance in the external environment - the role of
antibiotic pollution in the selection of resistance and subsequent gene transfer to the human microbiome” (Project
No. 2010-6338-77423-98), J Larsson, Univ Gothenburg, Applicant
2011-2012: Applicant/Principle Investigator for FOU-Västra Götaland Region: “Epidemiological analyses of
multi-drug resistant Gram-negative infectious bacteria: development and application for detection and typing”
(Project No. VGFOUREG-157801; 296 kSEK)
2009-2011: Applicant/Principle Investigator for SIDA: “Microbial Diversity and Development of Antibiotic
Resistance Associated with Industrial Wastewater Treatment” (Project No. SIDA-VR 254405107; 750 kSEK)
2009-2011: Applicant/Principle Investigator for FOU-Västra Götaland Region: “Diagnoses of antibiotic
resistance in clinically-relevant bacteria: a rapid and cost-effective method for identification and typing by using
mass spectrometry” (Project No. VGFOUREG-30781; 218 kSEK)
2008-2010: Applicant/Principle Investigator for ALF-LUA: “Extended-Spectrum β-Lactamase (ESBL) Bacteria:
Identification, Epidemiology, Genetic Analysis and Control of their Proliferation within the Clinical Environment”
(Project No. ALFGBG-11574; 1.155 MSEK)
Commissions of trust: 2008 – current: Scientific Advisory Board Member, Microbial Culture Collection (MCC) Project, Pune, India
2016: Invited Reviewer of grant application: The Research Council of Norway (RCN), NO
2014: Invited Reviewer of grant application: The Atomic Energy and Alternative Energies Commission (CEA), FR
2013: External Opponent for PhD Exam - David Sanchez, Univ de les Illes Balears (UIB), ES
2013: Invited Reviewer of grant application: The Wellcome Trust, Immunology and Infectious Disease, UK
2013: Invited Reviewer of grant application: The Iceland Research Fund (IRF), IC
2009: External Opponent for PhD Exam - Ranad Shaheen, Univ Helsinki, FI
2009: Invited Reviewer of grant application: The Flanders Research Foundation (FWO), BE
2008: External Opponent for PhD Exam - Mahesh S. Dharne, Univ Pune, IN
2007: External Opponent for PhD Exam - Irina Tsitko, Univ Helsinki, FI
2007: External Opponent for PhD Exam - Margarita Gomila, Univ de les Illes Balears (UIB), ES
2005: External Opponent for PhD Exam - Jessica Bellarby. Aberdeen Univ, UK
Ongoing international research collaborations (selected): Helmholz Zentrum fûr Infektion Forschung (HZI), Braunscwheig, DE, Prof. DH Pieper
Public Health England (PHE), London, UK, Prof. HN Shah
Universidad Técnica Federico Santa Maria (UTFSM), Valparaiso, CL, Prof. M Seeger/Dr B Cámara
Universidade Católica Portuguesa – Porto (UCP), Porto, Portugal, Prof. C.M. Manaia
Universität de les Iiles Balears (UIB), Palma de Mallorca, ES, Prof. J Lalucat /Dr. M Gomila/Dr. A Bennàsar
Universiteit Gent, Gent, BE, Prof P Vandamme / Prof. Paul DeVos
Publication record My research is focused on the development and application of genotypic, genomic and proteomic tools for
diagnostics and epidemiology of infectious diseases and antibiotic resistance, with 152 peer-reviewed articles,
16 review articles and book chapter publications, more than 100 published abstracts, proceedings and presentations
and 2 patents; ISI Web of Science h-index = 42 / 6,125 citations; Google Scholar h-index = 51 / 9,410 citations.
Relevant Publications (2008-2016): 19) Boulund F, Karlsson R, Gonzales-Siles L, Johnning A, Karami N, Al-Bayati O, Åhrén C, Moore ERB,
Kristiansson E. 2016. TCUP: Typing and characterization of bacteria using bottom-up tandem mass spectrometry
proteomics. ProteomeXchange (in press)
18) Johnning A, Jakobsson HE, Boulund F, Salvà Serra F, Moore ERB, Åhrén C, Karami N, Kristiansson E. 2016.
Draft genome sequence of extended-spectrum β-lactamase-producing Escherichia coli, strain CCUG 62462, isolated
from a urine sample. Genome Announc. (in press)
17) Jakobsson HE, Salvá-Serra F, Thorell K, Gonzales-Siles L, Boulund F, Karlsson R, Sikora P, Engstrand L,
Kristiansson E, Moore ERB. 2016. Draft genome sequence of Moraxella catarrhalis Type Strain CCUG 353T.
Genome Announc. 4(3): e00552-16; doi: 10.1128/genomeA.00552-16
Moore, Edward: 540103-3898 20161114
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16) Salvà Serra F, Jakobsson HE, Thorell K, Gonzales-Siles L, Hallbäck ET, Jaén-Luchoro D, Boulund F, Sikora P,
Karlsson R, Svensson-Stadler L, Bennasar A, Engstrand L, Kristiansson E, Moore ERB. 2016. Draft genome
sequence of Streptococcus gordonii Type Strain CCUG 33482T. Genom Announc. 4(2): e00175-16;
doi:10.1128/genomeA.00175-16
15) Undabarrena A, Beltrametti F, Clavérías FP, González M, Moore ERB, Seeger M, Cámara B. 2016. Exploring
the diversity and antimicrobial potential of marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile.
Front Microbiol. 7: 1135; doi: 10.3389/fmicb.2016.01135
14) Karlsson R, Gonzales-Siles L, Boulund F, Svensson-Stadler L, Skovbjerg S, Karlsson A, Davidson M, Hulth S,
Kristiansson E, Moore ERB. 2015. Proteotyping: Proteomic characterisation, classification and identification of
microorganisms – a prospectus. Syst Appl Microbiol. 38(4):246-257; doi: 10.1016/j.syapm.2015.03.006
13) Kondori N, Erhard M, WQelinder-Olsson C, Groenewald M, Verkley G, Moore ERB. 2015. Analyses of black
fungi by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS): species-
level identification of clinical isolates of Exophiala dermatitidis. FEMS Microbiol Lett. 362(1): 1-6; doi:
10.1093/femsle/fnu016
12) Whitehead TR, Johnson CN, Patel NB, Cotta MA, Moore ERB, Lawson PA. 2015. Savagea faecisuis gen. nov.,
sp. nov., a tylosin- and tretracycline-resistant bacterium isolated from a swine-manure storage pit. Ant v
Leeuwenhoek. 108(1):151-161; doi: 10.1007/s10482-015-0473-8
11) Nilsson AN, Emilsson G, Nyberg LK, Noble C, Svensson-Stadler L, Fritzsche J, Moore ERB, Tegenfeldt JO,
Ambjörnsson T, Westerlund F. 2014. Competitive binding-based optical DNA mapping for fast identification of
bacteria – multi-ligand transfer matrix theory and experimental application on Escherichia coli. Nucl acids Res.
42(15):e118; doi: 10.1093/nar/gku556
10) Mihaylova S, N Genov, E Moore. 2014. Susceptibility of environmental strains of Rhizobium radiobacter to
antimicrobial agents. World Appl Sci J. 31(5):859-862; doi: 10.5829/idosi.wasj.2014.31.05.1851
09) Helldal L, Karami N, Florén K, Welinder-Olsson C, Moore ERB, Ahrén C. 2013. Shift of CTX-M genotypes has
determined the increased prevalence of extended-spectrum β-lactamase-producing Escherichia coli in south-western
Sweden. Clin Microbiol Infect. 19(2):E87-E90; doi: 10.1111/1469-0691.12086
08) Johnning A, Moore ERB, Svensson-Stadler L, Shouche Y, Larsson J, Kristiansson E. The acquired genetic
mechanisms of a multi-resistant bacterium isolated from a treatment plant receiving wastewater from antibiotic
production. Appl Env Microbiol. 79:7256-7563. doi: 10.1128/AEM.02141-13
07) Karami N; Helldal L; Welinder-Olsson C; Åhrén C; Moore ERB. 2013. Sub-Typing of Extended-Spectrum-β-
Lactamase-Producing Isolates from a Nosocomial Outbreak: Application of a 10-Loci Generic Escherichia coli Multi-
Locus Variable Number Tandem Repeat Analysis. PLoS One. 8(12):e83030; doi: 10.1371/journal.pone.0083030
06) Marathe, NP, Regina VR, Walujkar SA, Charan SS, Moore ERB, Larsson DGJ, Shouche YS. 2013. A treatment
plant receiving waste water from multiple bulk drug manufacturers is a reservoir for highly multi-drug resistant
integron-bearing bacteria. PLoS One. 8(10):e77310. doi: 10.1371/journal.pone.0077310
05) Narciso-da-Rocha C, Vaz-Moreira I, Svensson-Stadler L, Moore ERB, Manaia CM. 2013. Diversity and anti-
biotic resistance of Acinetobacter spp. in water from the source to the tap. Appl Microbiol Biotechnol. 97:329-340;
doi: 10.1007/s00253-012-4190-1
04) Karlsson, R, Davidson M, Svensson-Stadler LA, Karlsson A, Olesen K, Carlsohn E, Moore ERB. 2012. Strain
typing and identification of bacteria using mass spectrometry-based proteomics. J Proteome Res. 11(5):2710-2720;
doi: 10.1021/pr2010633
03) Hinse D, Vollmer T, Erhard M, Welker M, Moore ERB, Kleesiek K, Dreier J. 2011. Differentiation of
Streptococcus bovis/equinus-complex isolates by MALDI-TOF Mass Spectrometry in comparison to sodA
sequencing analyses. Syst Appl Microbiol. 34:52-57; doi: 10.1016/j.syapm.2010.11.010
02) Welker M, Moore ERB. 2011. Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-
flight mass spectrometry in systematic microbiology. Syst Appl Microbiol 34(1):2-11; doi:
10.1016/j.syapm.2010.11.013
01) Mihaylova, S.A., M.P. Sredkova, L.A. Svensson and E.R.B. Moore. 2008. Emergence of clinical strains of
Stenotrophomonas maltophilia resistant to trimethoprim/sulfamethoxazole in a Bulgarian university hospital. J.
Biomed. Clin. Res. 1: 18-25
Karlsson, Roger: 750428-4857 20161114
1
Curriculum Vitae
Roger Ivar Daniel Karlsson
Nanoxis Consulting AB and Senior Researcher at Sahlgrenska University Hospital, Department
of Clinical Microbiology.
1. University degree: 1998 Master of Science – Chemistry – Analytical chemistry,
University of Gothenburg
2. Ph.D.: 2003 Analytical Chemistry “Fabrication and Dynamic Control of Surfactant-
Membrane Networks with Applications in Nanofluidics and Membrane-Based Transport”,
Supervisor Owe Orwar, Defense date: 2003-11-07, University of Gothenburg
3. Relevant post-doc stays: No traditional post-doc stay. Co-founder of Biotechnology
company, Nanoxis AB. 2003-2005
4. Associate Professor: The Dean of the Faculty of Science, University of Gothenburg,
accepted the applicant as Associate Professor (Docent) in Analytical Chemistry at the
Department of Chemistry & Molecular Biology, 2011-11-01
5. Present employment: Research Consultant at Nanoxis Consulting AB 40%, Senior
Researcher at Sahlgrenska University Hospital, Department of Clinical Microbiology 60%
6. Previous employments: 2003-2005 - Nanoxis AB, Project Leader Research and Development,
Co-founder. Based on results during Ph.D.-studies. Research and development concerns lipid-
based protein immobilization (LPITM) technology focusing on membrane proteins in lipid bilayer
membranes.
Assistant Professor, 2005-December 2009. 80% research and 20% teaching. Department of
Chemistry, Analytical Chemistry, University of Gothenburg.
2005-2009 – Nanoxis AB, Project Leader Research and Development 20%.
2010 March-June – Nanoxis AB 75% - Department of Chemistry, University of Gothenburg 10%.
2010 July-2011 Jan – Nanoxis AB 100%.
2011 Feb-June 70% Nanoxis AB 30% Department of Chemistry, University of Gothenburg.
2011 June- 2013 October Nanoxis Consulting AB 100%
7. Research supervision – Supervisor for Ingela Lanekoff, Ph.D.-student, employed 2006.
Successfully defended her thesis “Analysis of phospholipids in cellular membranes with LC
and imaging mass spectrometry” June 2011
8. Patents - Co-author and co-inventor of one patent and three pending patents
1. Chiu, D., Orwar, O., Karlsson, A., Karlsson, M., Karlsson, R. Microscopic networks of
containers and nanotubes – WO0226616
2. Karlsson, A., Karlsson, R., Pihl, J., Karlsson, M., Orwar, O., Lobovkina, T., Jesorka, A.,
Davidson, M. Device and use thereof – WO2006068619 - This patent describes the method,
technology and use of the Lipid-based Protein Immobilization technique, LPITM
3. Bauer, B., Davidson, M., Orwar, O., Karlsson, A., Karlsson, R. Plasma membrane vesicles
and methods of making and using same – WO2009130659
4. Frontal Affinity Chromatography Mass Spectrometry (FAC-MS) and the Lipid-based Protein
Immobilization technique, LPITM – WO2011040876
Karlsson, Roger: 750428-4857 20161114
2
9. Research administration- Undergraduate project examiner for ~10 Masters students.
Supervisor of ~10 undergraduate projects
10. Teaching experience
Lecturer and related undergraduate teaching organization 1999 – 2010. Analytical
chemistry (techniques such as LC, GC, CE, AAS) and bioanalytical chemistry (techniques
such as electroporation, biosensors and patch-clamp)
11. Administration and organization experience
Member of the Board of the Dept. of Chemistry, Univ. of Gothenburg, 2006-2009
Responsible for the Alumni organization at the Department of Chemistry, University of
Gothenburg, 2007-2010.
Course leader in Analytical Chemistry (basic course and advanced course), Department of
Chemistry, University of Gothenburg, 2005-2010
Course leader in Analytical Organic Chemistry, Department of Chemistry, University of
Gothenburg, 2006-2007
Course leader in Analytical Chemistry for Pharmaceutical chemistry program, Department of
Chemistry, University of Gothenburg, 2005-2006
12. Business relation
Co-founder of the companies Nanoxis AB and Nanoxis Consulting AB, Gothenburg, Sweden.
The companies are spin-off companies from the University of Gothenburg and Chalmers University
of Technology. Main investor is Vätterledens Invest AB. Co-inventor of the LPI-technology.
RELEVANT PUBLICATIONS FOR THE PROJECT
Number of citations from Google Scholar
Publications from 2009-
Karlsson, R., Karlsson, A., Bäckman, O., Johansson, B.R., Hulth, S. Identification of key proteins
involved in the anammox reaction FEMS Microbiol Lett 297:87-94 (2009). Number citations: 27
Karlsson, R. et al. Characterization of bacterial membrane proteins using a novel combination of
a lipid based protein immobilization technique with mass spectrometry. Invited to write a chapter
in the book Mass Spectrometry for Microbial Proteomics. Published by Wiley-Blackwell (John
Wiley & Sons, Inc. England). (2010). Number of citations: 2
Karlsson, R., Davidson, M., Svensson-Stadler, L., Karlsson, A., Olesen, K., Carlsohn, Moore,
E.R.B. Strain-level typing and identification of bacteria using mass spectrometry-based
proteomics. J Proteome Res 11(5), 2710-2720 (2012). Number of citations: 14
Jansson, E.T., Trkulja, C.L., Olofsson, J., Millingen, M., Wikström, J., Karlsson, A., Karlsson, R.
Davidson, M., Orwar, O. Microfluidic flow cell for sequential digestion of immobilized
proteoliposomes. Anal Chem 84(13): 5582-5588 (2012). Number of citations: 7
Karlsson, R., Karlsson, A., Bäckman, O., Johansson, B.R., Hulth, S. Subcellular localization of
an ATPase in anammox bacteria using proteomics and immunogold electron microscopy. FEMS
Microbiol Lett. 354(1):10-18 (2014). Number of citations: 4
Karlsson, R. et al. Proteotyping: Proteomic characterisation, classification and identification of
microorganisms – a prospectus. Syst Appl Microbiol 38(4):246-257 (2015). Number citations: 8
Karlsson R. et al. Proteotyping: Tandem Mass Spectrometry Shotgun Proteomic
Characterization and Typing of Pathogenic Microorganisms. In press 2016. Book Chapter in,
“The Triumph of MALDI-TOF Mass Spectrometry and New Developments in Tandem Mass
Spectrometry for Clinical Microbiology”, published by John Wiley and Sons Ltd.
Kristiansson, Erik 20161114
CURRICULUM VITAE
Name: Erik Kristiansson
Date of birth: June 16, 1978
Education
2012 Docent in mathematical statistics and bioinformatics at the Chalmers University of
Technology. Docent lecture held April 26 2012.
2007 Degree of Doctor of Philosophy in Mathematical Statistics received at Department of
Mathematical Sciences, Gothenburg University/Chalmers University of Technology.
2002 Master of Science in Electrical Engineering at Luleå University of Technology.
Current position
2015- Associate Professor, Mathematical Statistics, Department of Mathematical Sciences,
Gothenburg University/Chalmers University of Technology. The position includes 70% research and
30% teaching.
Previous positions
2011-2014 Assistant Professor with tenure track, Department of Mathematical Sciences,
Gothenburg University/Chalmers University of Technology.
2010-2011 Post-doctoral stipend funded by the Swedish Society of Medical Research
(www.ssmf.se).
2009 Post-doctoral training at the Department of Physiology and Endocrinology, University of
Gothenburg
2008 Post-doctoral training at the Department of Zoology, University of Gothenburg.
2003-2007 PhD student in Mathematical Statistics at Department of Mathematical Sciences,
Chalmers University of Technology.
Supervision of PhD students and post-docs
Johannes Dröge, post-doc (2016-), Fredrik Boulund, post-doc (2016), Anna Johnning, post-doc
(2014-), Tobias Österlund, post-doc (2014-), Anders Sjögren post-doc (2012-2015), Stefan Ebmeyer
PhD student (cosupervisor, 2016-), Mohammad Razavi PhD student (cosupervisor, 2014-), Fanny
Berglund PhD student (2014-), Mariana Pereira PhD student (2012-), Kemal Sanli PhD student
(cosupervisor, 2011-2016), Annica Wilzén PhD student (cosupervisor, 2011-), Viktor Jonsson PhD
student (2011-), Johan Bengtsson PhD student (cosupervisor, 2011-2016), Anna Larsson PhD
student (2011-), Fredrik Boulund PhD student (2011-2015), Anna Johnning PhD student
(cosupervisor, 2011-2014), Kristina Lagerstedt PhD student (cosupervisor, 2008-2009).
Seleted major grants
2016-2022 Centre for Antibiotic Resistance (CARe) at Gothenburg University, 50 MSEK in
total. Co-applicant (together with 9 other PIs).
2016-2022 Centre for Future Chemical Risk Assessment and Management Strategies - FRAM,
50 MSEK in total. Co-applicant (together with 9 other PIs).
2014-2017 VR research grant in medicine, NoCURE, personal funding 3 MSEK (together with
Joakim Larsson, GU).
2013-2017 EU 7th Framework, Tailored Treatment, funding 1.3 MEURO (together with Edward
Moore, GU). Total funding of 6 MEURO.
2013-2016 VR research grant in natural and engineering sciences, Novel methods for improved
statistical inference in quantitative metagenomics, 3.6 MSEK.
Kristiansson, Erik 20161114
2012-2016 FORMAS Strong Research Environment: NICE - Novel instruments for effect-based
assessment of chemical pollution in coastal ecosystems. Personal funding of 3 MSEK (total budget is
25 MSEK).
Selected commissions of trust
2016- Chair of steering board of Centre for Antibiotic Resistance at Gothenburg University (CARe)
2016- Steering board member of the Centre for Future Chemical Risk Assessment and Management
Strategies (FRAM)
2015- Co-director of the Chalmers Computational Biology Infrastructure (CCBI)
2014- Board member and co-founder of 1928diagnostics AB
2012- Founder and board member of the Gothenburg Bioinformatics Network
2012- Vice coordinator and steering group member of NICE (a FORMAS Strong Research
Environment)
Selected publications with relevance for this proposal
I have, between 2005 and 2016 published 81 research papers in peer-reviewed international journals.
I have 3403 citations and an h-index of 26. I have developed and co-developed more than 25 open
source bioinformatics software. Database used: Google Scholar, accessed 2016-11-11.
Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ, The structure and diversity of human,
animal and environmental resistomes, Microbiome 4 (1), 54, 2016
Österlund T, Cvijovic M, Kristiansson E, Integrative analysis of omics data, book chapter, accepted to
Biotechnology:Systems Biology, Editors Jens Nielsen and Stefan Hohmann, Wiley, 2016
Jonsson V, Österlund T, Nerman O, Kristiansson E, Variability in Metagenomic Count Data and Its
Influence on the Identification of Differentially Abundant Genes, to appear in Journal of
Computational Biology, 2016
Jonsson V, Österlund T, Nerman O, Kristiansson E, Statistical Evaluation of Methods for Identification
of Differentially Abundant Genes in Comparative Metagenomics, BMC Genomics 17(1) 2016
Boulund F, Sjögren A, Kristiansson E, Tentacle: distributed quantification of genes in metagenomes,
GigaScience 4(1) 2015
Johnning A, Moore ERB, Svensson-Stadler L, Shouche YS, Larsson DGJ, Kristiansson E. The
acquired genetic mechanisms of a multi-resistant bacterium isolated from a treatment plant receiving
wastewater from antibiotic production, Applied Environmental Microbiology 79(23) 2013
Boulund F, Johnning A, Pereira M, Larsson DGJ, Kristiansson, E. A method for identification of
quinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequence data, BMC Genomics
13:694, 2012
Kristiansson E, Fick J, Janzon A, Gabric R, Rutgersson C, Weidegård B, Söderström H, Larsson
DGJ. Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and
gene transfer elements, PLoS ONE 6(2) 2011
