Skip to main content

Trinity College Dublin, The University of Dublin

Trinity Menu Trinity Search



You are here Research > Research Groups > Functional Genomics of Pathogenic Bacteria

Dr. Carsten Kroger
Assistant Professor, Microbiology

Publications and Further Research Outputs

Peer-Reviewed Publications

Shaban L, Ershova AS, Hamrock FJ, Shaibah A, Sulimani MM, Amin RA, Russell JN, Ravichandran R, Schaffer K, Martins M, Cameron ADS, Kröger C, Draft Genome Sequence and Annotation of Acinetobacter soli AS15, Isolated from an Irish Hospital, Microbiology Resource Announcement, 2021 Journal Article, 2021 DOI

Owen SV, Canals R, Wenner N, Hammarlöf DL, Kröger C and Hinton JCD, A window into lysogeny: Revealing temperate phage biology with transcriptomics, Microbial Genomics, 2020 Journal Article, 2020 DOI

Canals R, Hammarlöf DL, Kröger C, Owen SV, Fong WY, Lacharme-Lora L, Zhu X, Wenner N, Carden SE, Honeycutt J, Monack DM, Kingsley RA, Brownridge P, Chaudhuri RR, Rowe WPM, Predeus AV, Hokamp K, Gordon MA, Hinton JCD., Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580., PLoS biology, 17, (1), 2019, pe3000059 Journal Article, 2019 DOI

Pulford CV, Wenner N, Redway ML, Rodwell EV, Webster HJ, Escudero R, Kröger C, Canals R, Rowe W, Lopez J, Hall N, Rowley PD, Timofte D, Harrison RA, Baker KS and Hinton JCD, The diversity, evolution and ecology of Salmonella in venomous snakes, PLoS Neglected Tropical Diseases, 2019 Journal Article, 2019 DOI

Kröger C, Schauer K, Clerkin S, Maertlbauer E and Fleming AB, Draft Genome Sequence and Annotation of Acinetobacter junii MHI21018, Isolated from Bovine Colostrum, Microbiology Resource Announcements, 2019 Journal Article, 2019 DOI

Kröger C, Rothhardt JE, Brokatzky D, Felsl A, Kary SC, Heermann R, Fuchs TM, The small RNA RssR regulates myo-inositol degradation by Salmonella enterica, Scientific Reports, 2018 Journal Article, 2018 DOI

Hammarlöf DL, Kröger C, Owen SV, Canals R, Lacharme-Lora L, Wenner N, Schager AE, Wells TJ, Henderson IR, Wigley P, Hokamp K, Feasey NA, Gordon MA, Hinton JCD., Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella., Proceedings of the National Academy of Sciences of the United States of America, 2018 Journal Article, 2018 DOI

Kröger C, MacKenzie KD, Alshabib EY, Kirzinger MWB, Suchan DM, Chao TC, Akulova V, Miranda-CasoLuengo AA, Monzon VA, Conway T, Sivasankaran SK, Hinton JCD, Hokamp K, Cameron ADS., The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978., Nucleic Acids Research, 2018 Journal Article, 2018 DOI

Cameron DS, SC Dillon, C Kröger, L Beran, CJ Dorman, Broad scale redistribution of mRNA abundance and transcriptional machinery in response to growth rate in Salmonella enterica serovar Typhimurium, Microbial Genomics, 3, 2017, p1 - 10 Journal Article, 2017 TARA - Full Text DOI URL

Miranda-CasoLuengo AA, Kary SC, Erhardt M and Kröger C, Small RNA, Big Effect: Control of Flagellin Production., Trends in Microbiology, 2017 Journal Article, 2017 DOI

Perry BJ, Fitzgerald SF, Kröger C, Cameron AD, Whole-Genome Sequence and Annotation of Salmonella enterica subsp. enterica Serovar Enteritidis Phage Type 8 Strain EN1660, Genome Announcements, 2017 Journal Article, 2017 DOI

Colgan AM, Cameron AD, Kröger C, If it transcribes, we can sequence it: mining the complexities of host-pathogen-environment interactions using RNA-seq, Current Opinion in Microbiology, 9, (36), 2017, p37 - 46 Journal Article, 2017 DOI

Kröger C, Kary SC, Schauer K, Cameron AD., Genetic Regulation of Virulence and Antibiotic Resistance in Acinetobacter baumannii, Genes (Basel), 2016 Journal Article, 2016 DOI

Colgan AM, Kröger C, Diard M, Hardt WD, Puente JL, Sivasankaran SK, Hokamp K, Hinton JC, The Impact of 18 Ancestral and Horizontally-Acquired Regulatory Proteins upon the Transcriptome and sRNA Landscape of Salmonella enterica serovar Typhimurium., PLoS Genetics, 12, (8), 2016, pe1006258 Journal Article, 2016 DOI

Srikumar S, Kröger C, Hébrard M, Colgan A, Owen SV, Sivasankaran SK, Cameron AD, Hokamp K, Hinton JC, RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium, PLoS Pathogens, 2015 Journal Article, 2015 DOI

MacKenzie KD, Wang Y, Shivak DJ, Wong CS, Hoffman LJ, Lam S, Kröger C, Cameron AD, Townsend HG, Köster W, White AP, Bistable Expression of CsgD in Salmonella enterica Serovar Typhimurium Connects Virulence to Persistence, Infection and immunity, 83, (6), 2015, p2312 - 2326 Journal Article, 2015 DOI

Rothhardt JE, Kröger C, Broadley SP, Fuchs TM, The orphan regulator ReiD of Salmonella enterica is essential for myo‐inositol utilization, Molecular Microbiology, 94, (3), 2014, p700 - 712 Journal Article, 2014 DOI

Kröger C, Colgan A, Srikumar S, Händler K, Sivasankaran SK, Hammarlöf DL, Canals R, Grissom JE, Conway T, Hokamp K, Hinton JC, An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium., Cell host & microbe, 14, (6), 2013, p683-95 Journal Article, 2013 TARA - Full Text DOI

Cameron ADS, Kröger C, Quinn HJ, Scally IK, Daly AJ, Kary SC, Dorman CJ, Transmission of an oxygen availability signal at the Salmonella enterica serovar Typhimurium fis promoter, PLoS One, 8, (12), 2013, pe84382 Journal Article, 2013 TARA - Full Text DOI

Kröger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JC, The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium., Proceedings of the National Academy of Sciences of the United States of America, 109, (20), 2012, pE1277-86 Journal Article, 2012 DOI

Hébrard M, Kröger C, Srikumar S, Colgan A, Händler K, Hinton JC, sRNAs and the virulence of Salmonella enterica serovar Typhimurium, RNA biology, 9, (4), 2012, p437 - 445 Journal Article, 2012 DOI

Kröger C, Srikumar S, Ellwart J, Fuchs TM, Bistability in myo-inositol utilization by Salmonella enterica serovar Typhimurium., Journal of bacteriology, 193, (6), 2011, p1427-35 Journal Article, 2011 DOI

Hébrard M, Kröger C, Sivasankaran SK, Händler K, Hinton JC, The challenge of relating gene expression to the virulence of Salmonella enterica serovar Typhimurium., Current opinion in biotechnology, 2011 Journal Article, 2011 DOI

Kröger C, Stolz J, Fuchs TM, myo-Inositol transport by Salmonella enterica serovar Typhimurium., Microbiology (Reading, England), 156, (Pt 1), 2010, p128-38 Journal Article, 2010 DOI

Kröger C, Fuchs TM, Characterization of the myo-inositol utilization island of Salmonella enterica serovar Typhimurium., Journal of bacteriology, 191, (2), 2009, p545-54 Journal Article, 2009 DOI

Kreutzenbeck P, Kröger C, Lausberg F, Blaudeck N, Sprenger GA, Freudl R, Escherichia coli twin arginine (Tat) mutant translocases possessing relaxed signal peptide recognition specificities., The Journal of biological chemistry, 282, (11), 2007, p7903-11 Journal Article, 2007 DOI

Non-Peer-Reviewed Publications

Ershova AS, Kröger, C, Restriction-Modification Systems in Acinetobacter baumannii, European Conference on Computational Biology, 2021 Poster, 2021

Hamrock F and Kröger C, Identifying posttranscriptional regulation in A. baumannii, DAPI, Dublin, 2020 Poster, 2020

Bakheet A and Kröger C, Characterization of the role of small RNAs and their binding proteins in Acinetobacter baumannii during antibiotic resistance and environmental stress, DAPI, Dublin, 2020 Poster, 2020

Owen SV, Canals R, Wenner N, Hammarlöf DL, Kröger C and Hinton JCD, A window into lysogeny: Revealing temperate phage biology with transcriptomics, biorxiv, 2019 Journal Article, 2019 DOI

Kröger C, Acinetobacter baumannii: Microbial Pathogenicity and Diagnostics, MSc in Clinical Laboratory Science, TU Dublin, 2019 Oral Presentation, 2019

Kröger C, The Primary Transcriptome of Acinetobacter baumannii, Health Protection and Surveillance Centre Dublin, 2019 Invited Talk, 2019

Kröger C, FNR is a Regulator of Salmonella Pathogenicity Island 2, Microbes in Medicine, TCD, 2019, Microbiology Society Invited Talk, 2019

Kröger C, FNR regulates the expression of SPI-2 in Salmonella Typhimurium, University of Liverpool, 2019 Invited Talk, 2019

Kröger C, RNA-seq analysis of bacterial transcriptome architecture: Why understanding gene regulation is important, Advances in Infection Research, UCD, Dublin, 2019 Oral Presentation, 2019

Pulford CV, Wenner N, Redway ML, Rodwell EV, Webster HJ, Escudero R, Kröger C, Canals R, Rowe W, Lopez J, Hall N, Rowley PD, Timofte D, Harrison RA, Baker KS and Hinton JCD, The diversity, evolution and ecology of Salmonella in venomous snakes, bioRxiv, 2019 Journal Article, 2019 DOI

Kröger C, FNR regulates the expression of SPI-2 in Salmonella Typhimurium, Microbiological Seminar, University of Regina, Canada, 2018 Invited Talk, 2018

Canals R, Hammarlöf DL, Kröger C, Owen SV, Fong WY, Lacharme-Lora L, Zhu X, Wenner N, Carden SE, Honeycutt J, Monack DM, Kingsley RA, Brownridge P, Chaudhuri RR, Rowe WPM, Predeus AV, Hokamp K, Gordon MA, Hinton JCD, Adding function to the genome of African Salmonella ST313, bioRxiv, 2018 Journal Article, 2018 DOI

Kröger C, The importance of understanding gene regulation in bacterial pathogens, VAAM Summer School, Tutzing, Germany, 2018 Oral Presentation, 2018

Kary SC and Kröger C, FNR is a regulator of Salmonella pathogenicity island 2 in Salmonella Typhimurium, Canadian Society of Microbiology Annual Conference, Winnipeg, Canada, 2018 Oral Presentation, 2018

Kary SC and Kröger C, FNR is a Repressor of SPI-2 in Salmonella Typhimurium, DAPI, Dublin, 2018 Oral Presentation, 2018

Kary SC and Kröger C, FNR is a Regulator of SPI-2 in Salmonella Typhimurium, DAPI, Dublin, 2018 Poster, 2018

Kröger C, MacKenzie KD, Hinton JCD, Hokamp K, Cameron ADS, The Primary Transcriptome, small RNAs and Regulation of Antimicrobial Resistance in Acinetobacter baumannii, 5th Meeting of Regulating with RNA in Bacteria & Archaea, Seville, Spain, 2018, 2018 Poster, 2018

Miranda Caso Luengo AA and Kröger C, RNA-seq analysis of bacterial transcriptome architecture, Advances in Infection Research, UCD, Dublin, 2018 Oral Presentation, 2018

Kröger C, Navigating the Transcriptional Landscape of Salmonella using RNA-seq, SFB 944 Seminar, University of Osnabrück, 10th January, 2017 Invited Talk, 2017

Kröger C, MacKenzie KD, Al-Shabib EY, Kirzinger MWB, Suchan DM, Chao TC, Akulova V, Miranda-CasoLuengo AA, Monzon VA, Conway T, Sivasankaran SK, Hinton JCD, Hokamp K, Cameron ADS, The primary transcriptome, small RNAs, and regulation of antimicrobial resistance in Acinetobacter baumannii, bioRxiv, 2017, p236794- Journal Article, 2017

Kary S, S Dillon, A Colgan, S Sivasankaran, K Hokamp, CJ Dorman, J Hinton, A Cameron, C Kroger, FNR is a regulator of SPI2 in Salmonella Typhimurium , Microbiology Society Annual Conference, Edinburgh International Conference Centre, April 3, 2017, pp570 - 570 Poster, 2017

Kröger C, Pathogenesis of Acinetobacter infections, MSc in Clinical Laboratory Science, TU Dublin, 2017 Oral Presentation, 2017

Hammarlöf DL, Kröger C, Owen SV, Canals R, Lacharme-Lora L, Wenner N, Wells TJ, Henderson IJ, Wigley P, Hokamp K, Feasey NA, Gordon MA, Hinton JCD, The role of a single non-coding nucleotide in the evolution of an epidemic African clade of Salmonella, bioRxiv, 2017, p175265- Journal Article, 2017

Kary SC and Kröger C, FNR is a regulator of SPI-2 in Salmonella Typhimurium, Departmental Seminar, Univerity of Regina, 2017 Oral Presentation, 2017

Kröger C, RNA-seq analysis of bacterial transcriptome architecture, Advances in Infection Research, UCD, Dublin, 2017 Oral Presentation, 2017

Kröger C, Navigating the Transcriptional Landscape in Salmonella Typhimurium, Helmholtz Centre for Infection Research, Braunschweig, Germany, 2nd September, 2016 Invited Talk, 2016

Pulford CV, Escudero R, Kröger C, Wenner N, Rowley P, Harrison R and Hinton JC, Genome-based Analyses Of Salmonella Associated With A Collection Of Venemous Snakesq, 5th ASM Conference on Salmonella, Potsdam, Germany, 2016 Poster, 2016

Canals R, Hammaröf D, Kröger C, Owen SV, Rowe WP, Hokamp K, Gordon MA and Hinton JCD, Comparative multi-condition interstrain transcriptomics identifies unexpected differences between global and african sequence types of Salmonella Typhimurium, 5th ASM Conference on Salmonella, Potsdam, Germany, 2016 Poster, 2016

Srikumar S, Kröger C, Hebrard M, Colgan A, Owen SV, Sivasankaran SK, Cameron ADS, Hokamp K and Hinton JCD, RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium, DAPI, Dublin, 2016 Oral Presentation, 2016

Kröger C, Colgan A, Srikumar S, Diard M, Hardt WD, Hokamp K, Hinton JCD, SalComRegulon Adds Regulatory Insights to the Online SalCom Salmonella Gene Expression Compendium, 5th ASM Conference on Salmonella, Potsdam, Germany, 2016 Poster, 2016

Srikumar S, Kröger C, Hebrard M, Colgan A, Owen S, Sivasankaran SK, Cameron A, Hokamp K and Hinton J, RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium, 5th ASM Conference on Salmonella, Potsdam, Germany, 2016 Poster, 2016

Kumwenda B, Kröger C, Canals R, Owen SV, Darby A, Everett D, Heyderman R, Godron MA, Msefula CL and Hinton JCD, Comparative Genomic Analysis of a sub-lineage of multi-drug resistant non-typhoidal Salmonella Typhimurium ST313 that has recently emerged in Blantyre, Malawi, 5th ASM Conference on Salmonella, Potsdam, Germany, 2016 Poster, 2016

Kröger C, Regulation of SPI2 by FNR, 2nd Small RNA retreat, Berlin, Germany, 2015 Oral Presentation, 2015

Cameron ADS, C Kroger, S Dillon, L Beran, J Hinton, CJ Dorman, Transcriptional activity is localised to specific chromosomal macro domains in Salmonella enterica, BacNet 15, Sant Feliu de Guixols, Spain, May 9-14,, 2015 Poster, 2015

Kröger C, RNA-seq reveals the choreography of transcription in Salmonella, Gene Expression Workshop, Centre for Genomic Research, Liverpool, UK, 2015 Invited Talk, 2015

Kröger C, Salmonella Typhimurium ST313 and invasive Salmonella disease , Microbiological Seminar, Institute for Microbial Systems and Society, University of Regina, Canada, 2015 Invited Talk, 2015

Kröger C, Navigating the Bacterial Transcriptome using RNA-seq, Northwest Microbiology Conference, Salford, UK, 2014 Oral Presentation, 2014

Canals R, Hammarlöf D, Kröger C, Sivasankaran S, Hokamp K, Chaudhuri R, Owen S and Hinton J, Differential gene expression of two closelyrelated Salmonella Typhimurium strains under infection-relevant conditions, Microbiology Society Annual Conference, Liverpool, UK, 2014 Poster, 2014

Kröger C, Navigating the Bacterial Transcriptome using RNA-seq , Microbiological Seminar, Max von Pettenkofer Institute, LMU Munich, Germany, 2014 Invited Talk, 2014

Kröger C, Transcriptome comparisons of gastroenteritis NTS with emerging invasive Salmonella Typhimurium strains, Wellcome Trust Centre for Global Health Research Annual Scientific Meeting, Chester, UK, 2014 Invited Talk, 2014

Srikumar S, Kröger C, Hebrard M, Colgan A, Beckett M, Wang L, Sivasankaran SK, Breen K, Hokamp K, Zhou D and Hinton JCD, The sRNA landscape of intra-macrophage Salmonella Typhimurium, Microbiology Society Annual Conference, Liverpool, UK, 2014 Poster, 2014

Hammarlöf DL, Kröger C, Sivasankaran SK, Hokamp K, Chaudhuri RR, Gordon M and Hinton JCD, The primary transcriptome of invasive S. Typhimurium D23580 reveals new mechanisms of gene regulation, Microbiology Society Annual Conference, Liverpool, UK, 2014 Poster, 2014

Kröger C, Colgan A, Sivasankaran SK, Srikumar S, Hokamp K and Hinton JCD, Identification of bacterial promoters and small RNAs using RNA-seq, Regulating with RNA in Bacteria, Würzburg, Germany, 2013 Poster, 2013

Hebrard M, Kröger C, Sivasankaran SK, Sittka A, Papenfort K, Lucchini S, Sharma C, Vogel J and Hinton JCD, Identification of novel small non-­‐coding RNAs and the transcriptional architecture of Salmonella Typhimurium, DAPI, Dublin, 2013 Poster, 2013

Kröger C, RNA-seq-based transcriptome analysis of Salmonella Typhimurium, Young Microbiologists Symposium, John Innes Centre, Norwich, UK, 2013 Invited Talk, 2013

Kröger C, A comprehensive online resource that details expression of S. Typhimurium genes, 4th ASM Conference on Salmonella: The bacterium, the Host and the Environment, Boston, USA, 2013 Oral Presentation, 2013

Kröger C, Navigating the transcriptional landscape of Salmonella Typhimurium using RNA-seq, Medical Infection Genomics, RNA-seq workshop , University of Würzburg, 2012 Invited Talk, 2012

Kröger C, Dillon SC, Cameron ADS, Sivasankaran SK, Hokamp K, Sittka A, Leekitcharoenphon P, Ussery DW, Dorman CJ, Vogel J and Hinton JCD, Global Transcriptional Mapping and the sRNA complement of Salmonella Typhimurium, Microbiology Society Annual Conference, Dublin, 2012 Poster, 2012

Kröger C, Global Transcriptional Mapping and the sRNA complement of Salmonella Typhimurium, Small RNA retreat, Scheffau, Germany, 2012 Oral Presentation, 2012

Cameron ADS, Kröger C, Dillon SC, Handler K, Hinton J, Dorman CJ, Transcriptional activity is localized to specific chromosomal macrodomains in Salmonella enterica, Canadian Society for Microbiology meeting, University of British Columbia, Canada, June, 2012 Poster, 2012

Kröger C, Hebrard M, Sittka A, Papenfort K, Lucchini S, Sharma C, Vogel J and Hinton JC, Identification of novel small non-coding RNAs and the transcriptional architecture of Salmonella enterica serovar Typhimurium, Cold Spring Harbor Conference, Cold Spring Harbor, US, 2011 Poster, 2011

Hebrard M, Kröger C, Sivasankaran SK, Handler K, Pare S, Hokamp K, Sittka A, Chao Y, Papenfort K, Sharma C, Vogel J and Hinton JCD, The virulence of Salmonella Typhimurium is regulated by sRNA, DAPI, Dublin, 2011 Poster, 2011

Hebrard M, Kröger C, Sivasankaran SK, Sittka A, Papenfort K, Lucchini S, Sharma C, Vogel J and Hinton JCD, Identification of novel small non-coding RNAs and the transcriptional architecture of Salmonella Typhimurium, ASM Conference on Regulating with RNA in bacteria, San Juan, Puerto Rico, 2011 Poster, 2011

Kröger C, The Transcriptional Architecture of Salmonella Typhimurium SL1344, 5th IECA Conferences, Cancun, Mexico, 2011 Oral Presentation, 2011

Kröger C and Fuchs TM, myo-Inositol Metabolism of Salmonella enterica serovar Typhimurium, Metabolism Meets Virulence: International Symposium on Metabolism and Bacterial Pathogenesis, Hohenkammer, Germany, 2009 Poster, 2009

Research Expertise

Keywords

ACINETOBACTER; BACTERIA; GENE REGULATION; MICROBIOLOGY; MOLECULAR GENETICS; SALMONELLA

Recognition

Memberships

Microbiology Society 2010

American Society for Microbiology 2010

European Society of Clinical Microbiology and Infectious Diseases 2015

Society for Applied Microbiology 2019