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Call for papers - Clinical isolates data notes

Guest Editors:
Remy A. Bonnin: Paris-Saclay University, France
Brian Forde: University of Queensland, Australia
Ajaya Kumar Rout: Rani Lakshmi Bai Central Agricultural University, India

Submission Status: Open   |   Submission Deadline: 31 May 2024

The advances in sequencing techniques in the last few years, as well as the decrease of the associated costs as led to an increased usage of whole genome sequencing (WGS) of bacterial isolates in the clinical setting. WGS allows species-level classification, patient-specific new species identification, and detects polyclonal/co-infections, especially crucial against multidrug-resistant isolates. This BMC Genomic Data Collection invites Data Notes, Research Articles and Database Articles showcasing WGS of clinical bacterial isolates and relevant omics datasets.

Clinical isolates data notes

Meet the Guest Editors

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Remy A. Bonnin: Paris-Saclay University, France

Dr Bonnin is an Associate Professor, at University of Paris-Saclay Medical School. He has extensive experience in bacterial genomics, transcriptomic analyses, and investigating the acquisition of antimicrobial resistance genes via horizontal gene transfer and transposition. Additionally, he is an integral member of the French National Reference Center for carbapenem-resistance in Enterobacterales. Dr Bonnin’s research interests focus on the epidemiology of multidrug-resistant Gram-negative rods, biochemistry of beta-lactam resistance, and genetic mechanisms involved in the acquisition of resistance genes. is scholarly contributions comprise more than 145 papers published in internationally recognized peer-reviewed journals.

Brian Forde: University of Queensland, Australia

Dr Forde is an emerging authority in infectious diseases genomics and bioinformatics, currently serving as a senior research fellow and group leader of "Microbial Genomics" at the University of Queensland Centre for Clinical Research. With over a decade of postdoctoral expertise in microbial genomics, he excels in translational genomics. Notably, he headed the bioinformatics program for the Queensland Genomics Infectious Diseases (QGID) project from 2017 to 2021. His focus encompassed genomic epidemiology, proactive monitoring of critical bacterial pathogens, and translating findings into clinical applications. Beyond research, Dr Forde leads the development of custom software and analysis pipelines to assist researchers and healthcare professionals with various aspects of genomic research. His group's genomic analysis pipelines and workflows, designed for surveillance and outbreak identification, have received ISO 15189 accreditation.

Ajaya Kumar Rout: Rani Lakshmi Bai Central Agricultural University, India

Dr Rout earned a Ph.D. in Biotechnology from Fakir Mohan University, India, focusing on "Metagenomic analysis of river Ganga for microbiome and its functions." A recipient of the ICMR-Senior Research Fellow from the Division of Biomedical Informatics, Indian Council of Medical Research, he currently conducts research at Rani Lakshmi Bai Central Agricultural University, India. His expertise spans metagenomics, genomics, metatranscriptomics, structural bioinformatics, and functional genomics. With 40+ international research papers in high-impact peer-reviewed journals, his work has garnered 450+ Google Scholar citations and 10 book chapters. He serves as an Editorial Board Member for BMC Genomics, Guest Editor for Genes, Review Editor for Frontiers in Microbiology, and Reviewer for multiple international journals.

About the Collection

The advances in sequencing techniques in the last few years, as well as the decrease of the associated costs as led to an increased usage of whole genome sequencing (WGS) of bacterial isolates in the clinical setting. 

Historically, the identification of bacterial species relied on traditional microbiology techniques that provided little information on the lineage of the isolates and thus could not inform on transmission networks between patients and/or the environment or on the dynamics of infection. The value of routine genomic surveillance of bacterial isolates in providing useful information has been proven by many studies and has the potential to improve patient treatment and infection control practices.

A WGS approach can provide a species-level classification of the isolates, enable the identification of new species at the individual patient level, and can enable the detection of cases of polyclonal infection or co-infection by opportunistic pathogens. 

Another very important advantage of this approach is that it provides the resolution to accurately identify multidrug-resistant (MDR) isolates and thus treat an infection with the appropriate antibiotic as soon as possible. Quick and precise identification of MDR organisms is key in maintaining infections under control and tracing the source of such infections. Indeed, as patients’ movements can be quite complex, many MDR transmissions could remain undetected without genomic information. One of the most useful applications of WGS is that it could be used to quickly identify an MDR outbreak prospectively by identifying potential likely MDR transmissions thus allowing early infection control before the onset of that outbreak. As MDR isolates are becoming an increasing worry, a WGS approach provides a non-negligible advantage to infection control. 

Thus, bacterial WGS as a means of routine genomic surveillance of bacterial isolates in clinics has great potential to improve patient treatment and infection control practices if meaningfully integrated into clinical care.

This BMC Genomic Data Collection welcomes Data Notes reporting whole genomic sequencing of clinical bacterial isolates or any other relevant omics dataset. Research Articles and Databases will also be considered. 

Image credit: Kateryna_Kon /

  1. Chickpea (Cicer arietinum L.) production is affected by many biotic factors, among them Fusarium wilt caused by Fusarium oxysporum f. sp. ciceri and Botrytis gray mold caused by Botrytis cinerea led to severe los...

    Authors: Gurreddi Bhargavi, Meenakshi Arya, Prashant Prakash Jambhulkar, Anshuman Singh, Ajaya Kumar Rout, Bijay Kumar Behera, Sushil Kumar Chaturvedi and Ashok Kumar Singh
    Citation: BMC Genomic Data 2024 25:7

Submission Guidelines

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This Collection welcomes submission of original Research Articles, Data Notes, and Database Articles. Should you wish to submit a different article type, please read our submission guidelines to confirm that type is accepted by the journal. Articles for this Collection should be submitted via our submission system, Snapp. During the submission process you will be asked whether you are submitting to a Collection, please select "Clinical isolates data notes" from the dropdown menu.

Articles will undergo the journal’s standard peer-review process and are subject to all of the journal’s standard policies. Articles will be added to the Collection as they are published.

The Editors have no competing interests with the submissions which they handle through the peer review process. The peer review of any submissions for which the Editors have competing interests is handled by another Editorial Board Member who has no competing interests.