Welcome to the Antimicrobial Resistance Call for Papers!

– The submission deadline for this Call for Papers has been extended to July 12, 2019 –

– PLOS ONE Guest Editors –

Kathryn Holt

Alison Holmes

Alessandro Cassini

Jaap Wagenaar


– PLOS Biology Guest Editors –

Patricia Bradford

Gautam Dantas

Athanasios Typas

– Call for Papers for a PLOS Collection –

Antimicrobial resistance is an increasingly pressing public health issue, which currently imposes a high burden on health care systems globally and is projected to have a significant and worsening impact in the coming decades. In the absence of effective treatments against an increasing number of microbial infections, infectious diseases will become more difficult to treat, thereby increasing their morbidity and mortality.


Consequently, efforts to prevent, mitigate, and overcome antimicrobial resistance are of global importance. Antimicrobial resistance development and spread is a natural response to the selective pressures placed upon microorganisms as a result of antimicrobial consumption and reduced infection prevention & control, particularly in healthcare settings. Therefore, strategies to combat resistance need careful evaluation, planning and implementation.


While the largest burden of antimicrobial resistance is in the form of bacterial resistance to anti-bacterials there are also similar, growing concerns about resistance to anti-fungal, anti-viral, anti-protozoan, and anti-helminth treatments.


To highlight current research tackling antimicrobial resistance in all microorganisms, PLOS ONE, PLOS Biology, PLOS Medicine, and PLOS Neglected Tropical Diseases are launching a call for papers. Manuscripts submitted in response to this call for papers and accepted for publication will be published in a dedicated collection later this year.


This Call for Papers covers multiple areas of research, including:


  • Studies that expand our fundamental understanding on the mechanisms, evolution, and spread of resistance, utilising in vitro and in vivo basic molecular research or in silicio computational modelling approaches.

  • Epidemiology, monitoring, and surveillance of antimicrobial resistance, and approaches to guiding and prioritising action and evaluating interventions. To ensure a full picture, studies can cover human health and clinical practice, animal husbandry (including livestock, poultry, aquaculture and companion animals), environmental reservoirs, and computational modelling of epidemiology. We especially encourage submissions on the impact of antimicrobial resistance on public health systems and human morbidity/mortality, and the impact on livestock agriculture as part of food security.
  • Reports of strategies to optimise use of existing agents, new drugs, novel therapies, use of vaccines, innovation in antimicrobial stewardship, and infection prevention and control. Identifying ways of combating resistance, and to complement and enhance the world’s existing tools for dealing with microbial infections. This can include innovative technologies, novel diagnostics methods, and novel uses of data and datasets.
  • Papers reporting national and global public health impact due to interventions and policy, including assessments of the economic impact of antimicrobial resistance and strategies to combat it. We also welcome social sciences research and other interdisciplinary studies using both quantitative and qualitative methods.

To contribute your research to this Call for Papers, please submit your manuscript to one of the PLOS journals below. Please take note of the submission guidelines for each journal, which may have additional requirements, in addition to the scope above.


PLOS ONE accepts scientifically rigorous research, regardless of perceived impact. PLOS ONE’s broad scope provides a platform to publish primary research, including interdisciplinary and replication studies, as well as negative results. The journal’s publication criteria are based on high ethical standards and the rigor of the methodology and conclusions reported.


PLOS Biology features works of exceptional significance, originality, and relevance in all areas of biological science, from molecules to ecosystems, including works at the interface of other disciplines, such as chemistry, medicine, and mathematics. In addition to outstanding Research Articles, we also publish provocative Short Reports, which can be based on a more limited number of experiments, and exceptional Methods and Resources. Our audience is the international scientific community as well as educators, policy makers, patient advocacy groups, and interested members of the public around the world.


PLOS Medicine publishes articles relevant to clinicians, policymakers, and researchers across a range of settings that address the major biological, environmental, social, and political determinants of health. The editors make decisions on submissions based upon their potential to directly and substantially inform clinical practice or health policy, and their relevance to our international audience.


PLOS Neglected Tropical Diseases publishes research devoted to the pathology, epidemiology, prevention, treatment and control of the neglected tropical diseases (NTDs), as well as public policy relevant to this group of diseases.


The deadline for submissions will be the 12th July 2019.


Meet the Editors


Kathryn Holt

Guest Editor, PLOS ONE 

Kat is a computational biologist specialising in infectious disease genomics, and a Professor at Monash University and the London School of Hygiene and Tropical Medicine. She is currently a HHMI-Gates International Research Scholar and Viertel Foundation Senior Medical Research Fellow, and Editor in Chief of the UK Microbiology Society journal Microbial Genomics.

Kat has a BA/BSc from the University of Western Australia majoring in Biochemistry, Applied Statistics and Philosophy, with Honours in Genetics (2004); a PhD in Molecular Biology from the University of Cambridge and the Wellcome Trust Sanger Institute on the genomics of typhoid fever, supervised by Gordon Dougan, Julian Parkhill and Duncan Maskell (2009); and a Masters in Epidemiology from the University of Melbourne (2011). She has also held Early Career (2010-2013) and Career Development (2014-2017) Fellowships from the NHMRC of Australia.

Kat has been awarded the Australian Academy of Science’s Gottschalk Medal for Medical Research (2017), a Georgina Sweet Award for Women in Quantitative Biomedical Science (2016), L’Oréal-UNESCO Rising Talents Fellowship (2015), the NHMRC Research Excellence Award for the Top-Ranked Career Development Fellow (2014) and L’Oréal For Women In Science Australia & NZ Fellowship (2013).



Alison Holmes

Guest Editor, PLOS ONE 

Alison Holmes is a Professor of Infectious Diseases at Imperial College and a Fellow of the Academy of Medical Sciences. She has a longstanding clinical and research career in infectious diseases and global health, with particular interests in antibiotic use, antibiotic resistance, infection prevention and management, particularly in the context of acute care. She leads a large multi-disciplinary research group and network, with strong collaborations nationally and internationally. Within the NHS, she is an Associate Medical Director, Director of Infection Prevention and Control and a senior consultant in infectious diseases. She is also the Director of the National Institute of Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and AMR, and is an NIHR Senior Investigator. She chairs or sits on numerous international scientific advisory boards, funding panels and editorial boards, and serves as an executive committee member of the International Society of Infectious Diseases.



Alessandro Cassini

Guest Editor, PLOS ONE 

Alessandro Cassini studied medicine in “la Sapienza” University in Rome. During his residency in thoracic surgery he became passionate in public health and specialised in hygiene and preventive medicine. After an MSc in Health Policy Planning and Financing from LSE & LSHTM, he worked as a consultant epidemiologist in London.


In 2009 he joined ECDC to lead the Burden of Communicable Diseases in Europe (BCoDE) project with the remit of estimating and expressing the health burden of communicable diseases and related conditions, including exploring ways to bridge the communication and technical gaps between risk assessors and managers (knowledge translation) and ultimately enhance informed and evidence-based health policy decision-making.


This methodology was subsequently applied to the estimation of the burden of healthcare-associated infections, which were shown to be a top infectious disease priority, and more recently to infections with antibiotic-resistant bacteria. The latter resulted in a study involving a multi-disciplinary approach and modelling of several data sources, as well as the collaboration with OECD to extend the analysis to the economic impact of AMR.


At ECDC, Alessandro has also been responsible for ECDC country visits to discuss AMR issues, for field work in outbreak response (e.g. Ebola), for EUCAST project management and supported the development of risk ranking methodologies.


In March 2019, Alessandro joined the Infection Prevention and Control Global Unit at WHO Headquarters.



Jaap Wagenaar

Guest Editor, PLOS ONE 

Jaap Wagenaar was trained as veterinarian and completed his PhD study at Utrecht University and the USDA-National Animal Diseases Center, Ames, IA, US. In 1996 he started his research group at the Central Veterinary Institute (now: Wageningen Bioveterinary Research)  in Lelystad, the Netherlands, on food safety and in particular on Campylobacter. From 2004-2006 he worked with WHO (Headquarters, Geneva, Switzerland, and for the Tsunami-relief operations with WHO Indonesia), the Centers for Disease Control and Prevention (Atlanta, US) and the USDA Western Regional Research Center (Albany, Ca, US).


In 2006 he was appointed as chair in Clinical Infectious Diseases at the Faculty of Veterinary Medicine, Utrecht University. His research group is focussing on Campylobacter and antimicrobial resistance.  He was coordinator of a large EU-project on antimicrobial resistance (EFFORT) (2013-2018).  He is member of the WHO-AGISAR-group (Advisory Group on Integrated Surveillance of Antimicrobial Resistance) and WHO-Global Foodborne Infections Network, a global capacity  building network. He is member of the scientific panel of the Netherlands Veterinary Medicines Institute (SDa) and involved in the major reduction of antimicrobial use in livestock. He is member of the Technical Advisory Group of the Fleming Fund. He is director of the WHO Collaborating Center for Campylobacter and of the OIE-reference laboratory for Campylobacteriosis, and is acting frequently as expert for WHO, FAO and OIE.


Patricia Bradford

Guest Editor, PLOS Biology

Patricia is the founder of Antimicrobial Development Specialists, LLC. Previously, she has worked for AstraZeneca Pharmaceuticals, Novartis, Wyeth, and Lederle Pharmaceuticals, where she contributed to several development programs for antibiotics, including piperacillin-tazobactam, tigecycline, and ceftazidime-avibactam. She has also led biology efforts on discovery platforms for antibiotics and antivirals and have managed a diverse group of scientists working in microbiology, pharmacology, biochemistry, and bioinformatics.


Gautam Dantas

Guest Editor, PLOS Biology

Gautam Dantas, Ph.D., is a professor in the Department of Pathology & Immunology, the Department of Biomedical Engineering, the Department of Molecular Microbiology, and the Edison Family Center for Genome Sciences & Systems Biology, at Washington University in St Louis School of Medicine. He received his PhD in biochemistry from the University of Washington under the guidance of Dr. David Baker, and post-doctoral training in microbial genomics from Harvard Medical School under the guidance of Dr. George Church.

Dr. Dantas’s research interests and training lie at the interface of microbial genomics, synthetic biology, systems biology, and computational biology. His current research focuses on (1) understanding and predicting how diverse microbiomes respond to chemical and biological perturbations, (2) harnessing these insights to rationally design therapeutic strategies to curtail antibiotic resistant pathogens and remedy pathological microbiome states, and (3) engineering microbial catalysts to convert renewable biomass into value chemicals such as biofuels and pharmaceuticals.

Since 2009, he has mentored twelve postdoctoral fellows, twenty-two graduate students, six research technicians, and over 50 high-school and undergraduate interns. He is a recipient of the AAAS Newcomb Cleveland Prize, the Harvard University Certificate for Distinction in Teaching, the NIH Director’s New Innovator Award, the Kenneth Rainin Foundation Breakthrough Award, the Edward Mallinckrodt Jr. Foundation Scholar Award, the Academy of Science – St Louis Innovator Award, the Washington University Distinguished Educator Award, and American Academy of Microbiology Fellowship. More information about the Dantas Lab can be found at


Athanasios Typas

Guest Editor, PLOS Biology

Athanasios (Nassos) Typas is a trained biochemist, geneticist, and systems biologist. He leads a group at the Genome Biology Unit at EMBL, Heidelberg, Germany since 2011. His group combines systems microbiology with molecular mechanism to study bacterial cellular networks, and how bacteria interact with each other and the environment. A key focal area of the group is on drug-microbe interactions: identifying new therapeutic strategies, understanding and predicting the drug mode of action and cellular resistance potential, and dissecting the interplay of medication with the gut microbiome.

Nassos has received a number of awards (NIH K99/R00, Sofja Kovalevskaja Award- Humboldt Foundation, ERC consolidator grant) and is a member of the European Academy of Microbiology.

PLOS ONE Handling Editors

Rajesh Arora Catherine Brissette Giuseppe De Socio Rosa del Campo
Patricia Fast* Filippo Giarratana* Iddya Karunasagar D. Ashley Robinson
Zhi Ruan Yizin Shi Rita Sobral Sima Tokajian
Ivone Vaz-Moreira Stephen Walsh Digby Warner Anne Wertheimer
Kristin Mühldorfer Monica Cartelle Gestal* Miriam Garcia Chih-Horng Kuo
Andrew Singer Ron Geller Surbhi Leekha Marta Giovanetti
Daisuke Hagiwara Ulrich Nübel John Panepinto Herman Tse
Jamunarani Vadivelu* Haroon Mohammad Dafna Yahav Meghan Scobee Blackledge
Patrick Butaye Laura Folgori Alex Fiedrich Christane Forestier
  Amal Al-Bakri Shamala Devi Sekaran  

* Also acting as a Preprint Editor, searching relevant preprint servers and inviting suitable manuscripts to PLOS ONE with a guarantee of peer review.

Publishing Process

We aim to be as transparent as possible about our publishing and peer review processes. Papers submitted to PLOS ONE and under consideration for the Antimicrobial Resistance Collection will be specially handled by hand-selected active researchers from our Editorial Board working in infectious disease research, in partnership with PLOS ONE Associate Editor Artur Arikainen. Papers submitted to PLOS Biology will be handled with our standard process, with additional input and curation from the Guest Editors. 

For more information please see the PLOS ONE Editorial and Peer Review Information page or the PLOS Biology Editor and Peer Review Information page, as relevant. 

Submission Instructions

Articles must be submitted by 12 July 2019. 

Are you ready to submit or want to learn more about how the submission process works? To make it as easy as possible for our communities, we have all of our PLOS ONE submission instructions posted online. If there are any details you can’t find, please email us at

Submission instructions for PLOS Biology are posted here and questions can be directed to

When submitting to the Collection, please specify that you are submitting to the Collection “Antimicrobial Resistance” in your cover letter. In addition, for PLOS ONE, please select the Article Type “Research Article” and enter “Antimicrobial Resistance” in the Collections field in the Additional Information section of the submission form.

Highly Cited PLOS Papers in Antimicrobial Resistance Research

Acquired Resistance of Mycobacterium tuberculosis to Bedaquiline

Authors: Koen Andries, Cristina Villellas, Nele Coeck, Kim Thys, Tom Gevers, Luc Vranckx, Nacer Lounis, Bouke C. de Jong, Anil Koul

Published: July 10, 2014

Dynamics of Soil Bacterial Communities in Response to Repeated Application of Manure Containing Sulfadiazine

Authors: Guo-Chun Ding, Viviane Radl, Brigitte Schloter-Hai, Sven Jechalke, Holger Heuer, Kornelia Smalla, Michael Schloter

Published: March 26, 2014

Adamantane-Resistant Influenza A Viruses in the World (1902–2013): Frequency and Distribution of M2 Gene Mutations

Authors: Guoying Dong, Chao Peng, Jing Luo, Chengmin Wang, Le Han, Bin Wu, Guangju Ji, Hongxuan He

Published: March 13, 2015

Resistance Determinants and Mobile Genetic Elements of an NDM-1-Encoding Klebsiella pneumoniae Strain​

Authors: Corey M. Hudson, Zachary W. Bent, Robert J. Meagher, Kelly P. Williams

Published: June 6, 2014


Differentiation of IncL and IncM Plasmids Associated with the Spread of Clinically Relevant Antimicrobial Resistance

Authors: Alessandra Carattoli , Salome N. Seiffert, Sybille Schwendener, Vincent Perreten, Andrea Endimiani

Published: May 1, 2015


Same Day Identification and Full Panel Antimicrobial Susceptibility Testing of Bacteria from Positive Blood Culture Bottles Made Possible by a Combined Lysis-Filtration Method with MALDI-TOF VITEK Mass Spectrometry and the VITEK2 System

Authors: Alexandra Machen, Tim Drake, Yun F. (Wayne) Wang

Published: February 14, 2014


Overall Decrease in the Susceptibility of Mycoplasma bovis to Antimicrobials over the Past 30 Years in France

Authors: Anne V. Gautier-Bouchardon, Séverine Ferré, Dominique Le Grand, Agnès Paoli, Emilie Gay, François Poumarat

Published: February 4, 2014


The Primary Resistance of Helicobacter pylori in Taiwan after the National Policy to Restrict Antibiotic Consumption and Its Relation to Virulence Factors—A Nationwide Study

Authors: Jyh-Ming Liou , Chi-Yang Chang , Mei-Jyh Chen, Chieh-Chang Chen, Yu-Jen Fang, Ji-Yuh Lee, Jeng-Yih Wu, Jiing-Chyuan Luo, Tai-Cherng Liou, Wen-Hsiung Chang, Cheng-Hao Tseng, Chun-Ying Wu, Tsung-Hua Yang, Chun-Chao Chang, Hsiu‐Po Wang, Bor-Shyang Sheu, Jaw-Town Lin, Ming-Jong Bair  , Ming-Shiang Wu , Taiwan Gastrointestinal Disease and Helicobacter Consortium

Published: May 5, 2015


Antimicrobial Resistance: The Major Contribution of Poor Governance and Corruption to This Growing Problem

Authors: Peter Collignon, Prema-chandra Athukorala, Sanjaya Senanayake, Fahad Khan

Published: March 18, 2015


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