Whole genome analysis of <i>Pantoea </i>species identified from sepsis patients in selected Ethiopian referral hospitals: emerging pathogens

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Abstract

Background

The burden of sepsis worsens due to the continuation of emerging pathogens such as multidrug-resistant Pantoea species.

Methods

A multicenter study was conducted between October 2019 and September 2020 at four hospitals located in central, southern, and northern parts of Ethiopia. A total of 1416 sepsis patients were recruited and blood cultures were performed. At each study site, positive cultures were characterized by their colony characteristics, gram stain, and conventional biochemical tests. All Pantoea species were identified using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI TOF) and subjected to whole genome sequencing (WGS) using Illumina HiSeq 2500. The phylogeny structure of Pantoea isolates was calculated using IQ-TREE v1.6.12 from single-nucleotide polymorphisms detected by Snippy v.4.6.0 and filtered by Gubbins v.2.3.4. Average nucleotide identity was estimated by using OrthoANI v.0.93.1 on Shovill v.1.1.0 assemblies. Antimicrobial resistance genes and plasmid replicons were detected using ARIBA v.2.14.6. Phylogenetic trees were visualized using iTOLv.6.5.2.

Results

Multiple Pantoea species include: P. dispersa ( n = 19), P. septica ( n = 1), and a novel Pantoea spp. ( n = 1), were identified among sepsis patients. All P. dispersa isolates and the novel Pantoea species were isolated at Dessie Referral Hospital and displayed phylogenetic clonality, including the ubiquity of an IncM1 plasmid and identical antimicrobial resistance (AMR) gene profiles, encoding bla _CTX−M−15, bla _TEM−1D, bla _SCO−1, and aac(3) -lla. The novel Pantoea spp. isolate harboured bla _CTX−M−9 and bla _TEM−1D and carried an IncN3 plasmid replicon. The P. septica was isolated at Tikur Anbessa Specialized Hospital in Addis Ababa and carried no detectable acquired AMR genes.

Conclusion

The emerging Pantoea spp. carrying multiple AMR genes were identified from sepsis patients. Implementation of strong infection prevention strategies and building surveillance capacity with advanced bacteriology laboratories capable of identifying multidrug-resistant emerging pathogens is strongly recommended.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-024-03561-5.

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Author and article information

Contributors

Melese Hailu Legese: melese.hailu@aau.edu.et , melerose85@gmail.com

Journal

Journal ID (nlm-ta): BMC Microbiol

Journal ID (iso-abbrev): BMC Microbiol

Title: BMC Microbiology

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2180

Publication date (Electronic): 12 October 2024

Publication date PMC-release: 12 October 2024

Publication date Collection: 2024

Volume: 24

Electronic Location Identifier: 407

Affiliations

[1 ]Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, ( https://ror.org/038b8e254) Addis Ababa, Ethiopia

[2 ]Armauer Hansen Research Institute, ( https://ror.org/05mfff588) Addis Ababa, Ethiopia

[3 ]Department of Medical Biochemistry and Microbiology, Biomedical Centre, Uppsala University, ( https://ror.org/048a87296) Uppsala, Sweden

[4 ]Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, ( https://ror.org/038b8e254) Addis Ababa, Ethiopia

[5 ]Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, ( https://ror.org/03svjbs84) Liverpool, UK

Article

Publisher ID: 3561

DOI: 10.1186/s12866-024-03561-5

PMC ID: 11470727

PubMed ID: 39395976

SO-VID: 8e9dab5a-ec9e-4002-9354-ececc7e27dfa

License:

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

History

Date received : 6 November 2023

Date accepted : 30 September 2024

Funding

Funded by: FundRef http://dx.doi.org/10.13039/100004441, Styrelsen för Internationellt Utvecklingssamarbete;

Award ID: ISP 2017/43:9

Custom metadata

ScienceOpen disciplines: Microbiology & Virology

Keywords: sepsis-causing emerging pathogens,novel pantoea species,antimicrobial resistance genes,plasmids,whole genome sequencing,ethiopia

Data availability:

ScienceOpen disciplines: Microbiology & Virology

Keywords: sepsis-causing emerging pathogens, novel pantoea species, antimicrobial resistance genes, plasmids, whole genome sequencing, ethiopia

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