Research

Our research is approaching interactions between organisms from an evolutionary biology perspective, which we use to understand pathogens (and their non-pathogenic relatives) as well as beneficial or neutral symbioses (in particular mosquito-microbe interactions). We use computational and molecular biology tools to disentangle these interactions and how they evolved.

At the moment, these are some of the main focus areas in the team:

The evolution of high-risk lineages in Gram-negative bacterial pathogens, and the reciprocal interaction of antimicrobial resistance spread and bacterial population dynamics.

The impact acquired vs. chromosomal resistance mechanisms on different opportunistic bacterial pathogen species.

The evolution of bacterial cell surface proteomes and carbohydrate structures for more efficient vaccine design.

Mosquito-microbiome interactions and their impact on vector-borne virus and parasite transmission.

Wolbachia as a vector control tool.

Insect-specific viruses for vector control.

2024

Longitudinal analysis within one hospital in sub-Saharan Africa over 20 years reveals repeated replacements of dominant clones of Klebsiella pneumoniae and stresses the importance to include temporal patterns for vaccine design considerations

Eva Heinz, Oliver Pearse, Allan Zuza, Sithembile Bilima, Chisomo Msefula, Patrick Musicha, Patriciah Siyabu, Edith Tewesa, Fabrice E. Graf, Rebecca Lester, Samantha Lissauer, Jennifer Cornick, Joseph M. Lewis, Kondwani Kawaza, Nicholas R. Thomson, Nicholas A. Feasey

Genome Medicine · 06 May 2024

Optimised methods for the targeted surveillance of extended-spectrum beta-lactamase producing Escherichia coli in human stool

Sarah Gallichan, Sally Forrest, Esther Picton-Barlow, Claudia McKeown, Maria Moore, Eva Heinz, Nicholas A Feasey, Joseph M Lewis, Fabrice E Graf

Cold Spring Harbor Laboratory · 03 Apr 2024

Antimicrobial Resistance E. coli

A high-resolution genomic and phenotypic analysis of resistance evolution of an Escherichia coli strain from a critical care patient treated with piperacillin/tazobactam.

Alice J Fraser, Robert Ball, Daire Cantillon, Laura Brettell, Fabrice E Graf, Joseph M. Lewis, Jon J. van Aartsen, Christopher M. Parry, Eva Heinz, Thomas Edwards

Cold Spring Harbor Laboratory · 16 Jan 2024

Antimicrobial Resistance E. coli

Aedes aegypti gut transcriptomes respond differently to microbiome transplants from field‐caught or laboratory‐reared mosquitoes

Shivanand Hegde, Laura E. Brettell, Shannon Quek, Kayvan Etebari, Miguel A. Saldaña, Sassan Asgari, Kerri L. Coon, Eva Heinz, Grant L. Hughes

Environmental Microbiology · 08 Jan 2024

Aedes Microbiome Resource

Authorship reflexivity statements: additional considerations

Melissa Taylor, Eva Heinz, Mtisunge Gondwe, Refiloe Masekela, Ben Morton, Rose Oronje, Andre Vercueil, Seye Abimbola, Angela Obasi

BMJ Global Health · 01 Jan 2024

Research Integrity Parachute Research Review/Editorial

2023

Mechanisms of transcriptional regulation inAnopheles gambiaerevealed by allele specific expression

Naomi A. Dyer, Eric R. Lucas, Sanjay C. Nagi, Daniel P. McDermott, Jon H. Brenas, Alistair Miles, Chris S. Clarkson, Henry D. Mawejje, Craig S. Wilding, Marc S. Halfon, Hasiba Asma, Eva Heinz, Martin J. Donnelly

Cold Spring Harbor Laboratory · 22 Nov 2023

Anopheles Insecticide Resistance

Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates — MosAIC (Mosquito-Associated Isolate Collection)

Aidan Foo, Laura E. Brettell, Holly L. Nichols, 2022 UW-Madison Capstone in Microbiology Students, Miguel Medina Munoz, Jessica Lysne, Vishaal Dhokiya, Ananya F. Hoque, Doug E. Brackney, Eric P. Caragata, Michael Hutchinson, Marcelo Jacobs-Lorena, David J. Lampe, Edwige Martin, Claire Valiente Moro, Michael Povelones, Sarah M. Short, Blaire Steven, Jiannong Xu, Timothy D. Paustian, Michelle R. Rondon, Grant L. Hughes, Kerri L. Coon, Eva Heinz

bioRxiv · 04 Oct 2023

Aedes Anopheles Culex Microbiome Resource

The RNA virome of human and animal parasitic nematodes

Shannon Quek, Amber Hadermann, Yang Wu, Lander De Coninck, Shrilakshmi Hegde, Jordan Boucher, Jessica Cresswell, Ella Foreman, Andrew Steven, E. LaCourse, Stephen Ward, Samuel Wanji, Grant Hughes, Edward Patterson, Simon Wagstaff, Joseph Turner, Eva Heinz, Jelle Matthijnssens, Robert Colebunders, Mark Taylor

Research Square Platform LLC · 15 Sep 2023

virome Nematodes

Recovery of metagenomic data from the Aedes aegypti microbiome using a reproducible snakemake pipeline: MINUUR

Aidan Foo, Louise Cerdeira, Grant L. Hughes, Eva Heinz

Wellcome Open Research · 26 May 2023

Aedes Microbiome Method

Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity

Joseph M. Lewis, Madalitso Mphasa, Rachel Banda, Mathew A. Beale, Jane Mallewa, Catherine Anscome, Allan Zuza, Adam P. Roberts, Eva Heinz, Nicholas R. Thomson, Nicholas A. Feasey

Microbial Genomics · 01 Jan 2023

Antimicrobial Resistance E.coli Sub-saharan Africa

2022

Vertical and Horizontal Transmission of Cell Fusing Agent Virus in Aedes aegypti

Rhiannon A. E. Logan, Shannon Quek, Joseph N. Muthoni, Anneliese von Eicken, Laura E. Brettell, Enyia R. Anderson, Marcus E. N. Villena, Shivanand Hegde, Grace T. Patterson, Eva Heinz, Grant L. Hughes, Edward I. Patterson

Applied and Environmental Microbiology · 22 Sep 2022

Insect-specific viruses Aedes

Colonization dynamics of extended-spectrum beta-lactamase-producing Enterobacterales in the gut of Malawian adults

Joseph M. Lewis, Madalitso Mphasa, Rachel Banda, Mathew A. Beale, Eva Heinz, Jane Mallewa, Christopher Jewell, Brian Faragher, Nicholas R. Thomson, Nicholas A. Feasey

Nature Microbiology · 05 Sep 2022

Antimicrobial Resistance E.coli Klebsiella Sub-saharan Africa Genome Epidemiology

LSTM press release

The genus Serratia revisited by genomics

David J. Williams, Patrick A. D. Grimont, Adrián Cazares, Francine Grimont, Elisabeth Ageron, Kerry A. Pettigrew, Daniel Cazares, Elisabeth Njamkepo, François-Xavier Weill, Eva Heinz, Matthew T. G. Holden, Nicholas R. Thomson, Sarah J. Coulthurst

Nature Communications · 03 Sep 2022

Bacterial Cell Envelope Resource

Multiple Plasmodium falciparum drug resistance polymorphisms identified in a pregnant woman with severe malaria and a concomitant spontaneous abortion in Cross River, Nigeria, West Africa

Mary Aigbiremo Oboh, Fatou Faal, Oluwagbemisola Elizabeth Adeniji, Simon Correa, Anthony Uyimulam Amawu, Ekon Ogban, Eva Heinz, Grant Hughes, Martin M. Meremikwu, Alfred Amambua-Ngwa

Malaria Journal · 03 Jun 2022

Malaria Anopheles

Wolbachia endosymbionts in two Anopheles species indicates independent acquisitions and lack of prophage elements

Shannon Quek, Louise Cerdeira, Claire L. Jeffries, Sean Tomlinson, Thomas Walker, Grant L. Hughes, Eva Heinz

Microbial Genomics · 21 Apr 2022

Wolbachia Anopheles

LSTM press release

Piperacillin/tazobactam-resistant, cephalosporin-susceptible Escherichia coli bloodstream infections are driven by multiple acquisition of resistance across diverse sequence types

Thomas Edwards, Eva Heinz, Jon van Aartsen, Alex Howard, Paul Roberts, Caroline Corless, Alice J. Fraser, Christopher T. Williams, Issra Bulgasim, Luis E. Cuevas, Christopher M. Parry, Adam P. Roberts, Emily R. Adams, Jenifer Mason, Alasdair T. M. Hubbard

Microbial Genomics · 11 Apr 2022

Antimicrobial Resistance E.coli

Equity in global health research: A proposal to adopt author reflexivity statements

Sepeedeh Saleh, Refiloe Masekela, Eva Heinz, Seye Abimbola, Ben Morton, Andre Vercueil, Lisa Reimer, Chisomo Kalinga, Maaike Seekles, Bruce Biccard, Jeremiah Chakaya, Angela Obasi, Ndekya Oriyo,

PLOS Global Public Health · 30 Mar 2022

Research Integrity Parachute Research Review/Editorial

LSTM press release

Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi

Joseph M. Lewis, Madalitso Mphasa, Rachel Banda, Mathew A. Beale, Jane Mallewa, Eva Heinz, Nicholas R. Thomson, Nicholas A. Feasey

Microbial Genomics · 18 Mar 2022

Antimicrobial Resistance Klebsiella Sub-saharan Africa Surface Polysaccharides Vaccine Targets

2021

Loss of YhcB results in dysregulation of coordinated peptidoglycan, LPS and phospholipid synthesis during Escherichia coli cell growth

Emily C. A. Goodall, Georgia L. Isom, Jessica L. Rooke, Karthik Pullela, Christopher Icke, Zihao Yang, Gabriela Boelter, Alun Jones, Isabel Warner, Rochelle Da Costa, Bing Zhang, James Rae, Wee Boon Tan, Matthias Winkle, Antoine Delhaye, Eva Heinz, Jean-Francois Collet, Adam F. Cunningham, Mark A. Blaskovich, Robert G. Parton, Jeff A. Cole, Manuel Banzhaf, Shu-Sin Chng, Waldemar Vollmer, Jack A. Bryant, Ian R. Henderson

PLOS Genetics · 23 Dec 2021

Bacterial Cell Envelope Surface Proteins

Integration of whole genome sequencing and transcriptomics reveals a complex picture of the reestablishment of insecticide resistance in the major malaria vector Anopheles coluzzii

Victoria A. Ingham, Jacob A. Tennessen, Eric R. Lucas, Sara Elg, Henrietta Carrington Yates, Jessica Carson, Wamdaogo Moussa Guelbeogo, N’Fale Sagnon, Grant L. Hughes, Eva Heinz, Daniel E. Neafsey, Hilary Ranson

PLOS Genetics · 23 Dec 2021

Insecticide Resistance Anopheles

Genomic investigation of a suspected Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa

Jennifer Cornick, Patrick Musicha, Chikondi Peno, Ezgi Seager, Pui-Ying Iroh Tam, Sithembile Bilima, Aisleen Bennett, Neil Kennedy, Nicholas Feasey, Eva Heinz, Amy K. Cain

Microbial Genomics · 18 Nov 2021

Antimicrobial Resistance Sub-saharan Africa Klebsiella Genome Epidemiology

Bacterial genomic epidemiology with mixed samples

Tommi Mäklin, Teemu Kallonen, Jarno Alanko, Ørjan Samuelsen, Kristin Hegstad, Veli Mäkinen, Jukka Corander, Eva Heinz, Antti Honkela

Microbial Genomics · 16 Nov 2021

Method Genome Epidemiology

Addressing parachute research and removing barriers for LMIC researchers in Microbial Genomics

Eva Heinz, Kathryn E. Holt, Conor J. Meehan, Samuel K. Sheppard

Microbial Genomics · 27 Oct 2021

Research Integrity Parachute Research Review/Editorial

Consensus statement on measures to promote equitable authorship in the publication of research from international partnerships

B. Morton, A. Vercueil, R. Masekela, E. Heinz, L. Reimer, S. Saleh, C. Kalinga, M. Seekles, B. Biccard, J. Chakaya, S. Abimbola, A. Obasi, N. Oriyo

Anaesthesia · 14 Oct 2021

Research Integrity Parachute Research

LSTM press release

Different evolutionary trends form the twilight zone of the bacterial pan-genome

Gal Horesh, Alyce Taylor-Brown, Stephanie McGimpsey, Florent Lassalle, Jukka Corander, Eva Heinz, Nicholas R. Thomson

Microbial Genomics · 24 Sep 2021

Method Resource E. coli

BonA from Acinetobacter baumannii Forms a Divisome-Localized Decamer That Supports Outer Envelope Function

Rhys Grinter, Faye C. Morris, Rhys A. Dunstan, Pok Man Leung, Ashleigh Kropp, Matthew Belousoff, Sachith D. Gunasinghe, Nichollas E. Scott, Simone Beckham, Anton Y. Peleg, Chris Greening, Jian Li, Eva Heinz, Trevor Lithgow

mBio · 31 Aug 2021

Bacterial Cell Envelope Surface Proteins

Spatial and Genomic Data to Characterize Endemic Typhoid Transmission

Jillian S Gauld, Franziska Olgemoeller, Eva Heinz, Rose Nkhata, Sithembile Bilima, Alexander M Wailan, Neil Kennedy, Jane Mallewa, Melita A Gordon, Jonathan M Read, Robert S Heyderman, Nicholas R Thomson, Peter J Diggle, Nicholas A Feasey

Clinical Infectious Diseases · 31 Aug 2021

Typhi Method Genome Epidemiology Sub-saharan Africa

Virulence factors and antimicrobial resistance of uropathogenic Escherichia coli (UPEC) isolated from urinary tract infections: a systematic review and meta-analysis

Gabriel Kambale Bunduki, Eva Heinz, Vincent Samuel Phiri, Patrick Noah, Nicholas Feasey, Janelisa Musaya

BMC Infectious Diseases · 04 Aug 2021

Antimicrobial Resistance E. coli Review/Editorial

Stable high-density and maternally inherited Wolbachia infections in Anopheles moucheti and Anopheles demeilloni mosquitoes

Thomas Walker, Shannon Quek, Claire L. Jeffries, Janvier Bandibabone, Vishaal Dhokiya, Roland Bamou, Mojca Kristan, Louisa A. Messenger, Alexandra Gidley, Emily A. Hornett, Enyia R. Anderson, Cintia Cansado-Utrilla, Shivanand Hegde, Chimanuka Bantuzeko, Jennifer C. Stevenson, Neil F. Lobo, Simon C. Wagstaff, Christophe Antonio Nkondjio, Seth R. Irish, Eva Heinz, Grant L. Hughes

Current Biology · 01 Jun 2021

Anopheles Wolbachia

Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae

Robert C. Will, Thandavarayan Ramamurthy, Naresh Chand Sharma, Balaji Veeraraghavan, Lucky Sangal, Pradeep Haldar, Agila Kumari Pragasam, Karthick Vasudevan, Dhirendra Kumar, Bhabatosh Das, Eva Heinz, Vyacheslav Melnikov, Stephen Baker, Vartul Sangal, Gordon Dougan, Ankur Mutreja

Nature Communications · 08 Mar 2021

Antimicrobial Resistance Vaccine Targets

A comprehensive and high-quality collection of Escherichia coli genomes and their genes

Gal Horesh, Grace A. Blackwell, Gerry Tonkin-Hill, Jukka Corander, Eva Heinz, Nicholas R. Thomson

Microbial Genomics · 01 Feb 2021

Method E. coli Resource

2020

Structure of dual BON-domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation

Jack Alfred Bryant, Faye C Morris, Timothy J Knowles, Riyaz Maderbocus, Eva Heinz, Gabriela Boelter, Dema Alodaini, Adam Colyer, Peter J Wotherspoon, Kara A Staunton, Mark Jeeves, Douglas F Browning, Yanina R Sevastsyanovich, Timothy J Wells, Amanda E Rossiter, Vassiliy N Bavro, Pooja Sridhar, Douglas G Ward, Zhi-Soon Chong, Emily CA Goodall, Christopher Icke, Alvin CK Teo, Shu-Sin Chng, David I Roper, Trevor Lithgow, Adam F Cunningham, Manuel Banzhaf, Michael Overduin, Ian R Henderson

eLife · 14 Dec 2020

Bacterial Cell Envelope Surface Proteins

Microbial interactions in the mosquito gut determine Serratia colonization and blood-feeding propensity

Elena V. Kozlova, Shivanand Hegde, Christopher M. Roundy, George Golovko, Miguel A. Saldaña, Charles E. Hart, Enyia R. Anderson, Emily A. Hornett, Kamil Khanipov, Vsevolod L. Popov, Maria Pimenova, Yiyang Zhou, Yuriy Fovanov, Scott C. Weaver, Andrew L. Routh, Eva Heinz, Grant L. Hughes

The ISME Journal · 07 Sep 2020

Aedes Microbiome Culex

Genomic and Phenotypic Analyses of Acinetobacter baumannii Isolates From Three Tertiary Care Hospitals in Thailand

Jessica Loraine, Eva Heinz, Rosesathorn Soontarach, Grace A. Blackwell, Richard A. Stabler, Supayang P. Voravuthikunchai, Potjanee Srimanote, Pattarachai Kiratisin, Nicholas R. Thomson, Peter W. Taylor

Frontiers in Microbiology · 06 Apr 2020

Acinetobacter Antimicrobial Resistance Surface Polysaccharides Vaccine Targets Immune System

Type II and type IV toxin–antitoxin systems show different evolutionary patterns in the global Klebsiella pneumoniae population

Gal Horesh, Cinzia Fino, Alexander Harms, Matthew J Dorman, Leopold Parts, Kenn Gerdes, Eva Heinz, Nicholas R Thomson

Nucleic Acids Research · 31 Mar 2020

Klebsiella Resource

2019

Gut-associated bacteria invade the midgut epithelium of Aedes aegypti and stimulate innate immunity and suppress Zika virus infection in cells

Shivanand Hegde, Denis Voronin, Aitor Casas-Sanchez, Miguel A. Saldaña, Eva Heinz, Alvaro Acosta-Serrano, Vsevolod L. Popov, Ashok K. Chopra, Grant L. Hughes

Cold Spring Harbor Laboratory · 06 Dec 2019

Aedes Microbiome

Loss of IL-10 signaling in macrophages limits bacterial killing driven by prostaglandin E2

Subhankar Mukhopadhyay, Eva Heinz, Immacolata Porreca, Kaur Alasoo, Amy Yeung, Huei-Ting Yang, Tobias Schwerd, Jessica L. Forbester, Christine Hale, Chukwuma A. Agu, Yoon Ha Choi, Julia Rodrigues, Melania Capitani, Luke Jostins-Dean, David C. Thomas, Simon Travis, Daniel Gaffney, William C. Skarnes, Nicholas Thomson, Holm H. Uhlig, Gordon Dougan, Fiona Powrie

Journal of Experimental Medicine · 05 Dec 2019

Immune System Resource

CRISPR/Cas9-mediated gene deletion of the ompA gene in symbiotic Cedecea neteri impairs biofilm formation and reduces gut colonization of Aedes aegypti mosquitoes

Shivanand Hegde, Pornjarim Nilyanimit, Elena Kozlova, Enyia R. Anderson, Hema P. Narra, Sanjeev K. Sahni, Eva Heinz, Grant L. Hughes

PLOS Neglected Tropical Diseases · 02 Dec 2019

Aedes Microbiome

An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation

Sandra Van Puyvelde, Derek Pickard, Koen Vandelannoote, Eva Heinz, Barbara Barbé, Tessa de Block, Simon Clare, Eve L. Coomber, Katherine Harcourt, Sushmita Sridhar, Emily A. Lees, Nicole E. Wheeler, Elizabeth J. Klemm, Laura Kuijpers, Lisette Mbuyi Kalonji, Marie-France Phoba, Dadi Falay, Dauly Ngbonda, Octavie Lunguya, Jan Jacobs, Gordon Dougan, Stijn Deborggraeve

Nature Communications · 19 Sep 2019

Antimicrobial Resistance Typhimurium Genome Epidemiology Sub-saharan Africa

Isolation of five Enterobacteriaceae species harbouring blaNDM-1 and mcr-1 plasmids from a single paediatric patient

F. Martino, N. Tijet, R. Melano, A. Petroni, E. Heinz, D. De Belder, D. Faccone, M. Rapoport, E. Biondi, V. Rodrigo, M. Vazquez, F. Pasteran, N. R. Thomson, A. Corso, S. A. Gomez

PLOS ONE · 09 Sep 2019

Antimicrobial Resistance Klebsiella E. coli Enterobacter Latin America

Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center

Matthew J. Ellington, Eva Heinz, Alexander M. Wailan, Matthew J. Dorman, Marcus de Goffau, Amy K. Cain, Sonal P. Henson, Nicholas Gleadall, Christine J. Boinett, Gordon Dougan, Nicholas M. Brown, Neil Woodford, Julian Parkhill, M. Estée Török, Sharon J. Peacock, Nicholas R. Thomson

Genome Biology · 02 Sep 2019

Antimicrobial Resistance Klebsiella Enterobacter Genome Epidemiology

Investigation of the role of typhoid toxin in acute typhoid fever in a human challenge model

Malick M. Gibani, Elizabeth Jones, Amber Barton, Celina Jin, Juliette Meek, Susana Camara, Ushma Galal, Eva Heinz, Yael Rosenberg-Hasson, Gerlinde Obermoser, Claire Jones, Danielle Campbell, Charlotte Black, Helena Thomaides-Brears, Christopher Darlow, Christina Dold, Laura Silva-Reyes, Luke Blackwell, Maria Lara-Tejero, Xuyao Jiao, Gabrielle Stack, Christoph J. Blohmke, Jennifer Hill, Brian Angus, Gordon Dougan, Jorge Galán, Andrew J. Pollard

Nature Medicine · 01 Jul 2019

Typhi Surface Polysaccharides Vaccine Targets

Caribbean multi-centre study of Klebsiella pneumoniae: whole-genome sequencing, antimicrobial resistance and virulence factors

Eva Heinz, Richard Brindle, Andrina Morgan-McCalla, Keisha Peters, Nicholas R. Thomson

Microbial Genomics · 01 May 2019

Antimicrobial Resistance Klebsiella Latin America Genome Epidemiology