Whole genome analysis of Pantoea species identified from sepsis patients in selected Ethiopian referral hospitals: emerging pathogens.
Melese Hailu Legese, Adane Mihret, Daniel Asrat, Ralfh Pulmones, Badrul Hasan, Abraham Aseffa, Adam P Roberts, Göte Swedberg
Author Information
Melese Hailu Legese: Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia. melese.hailu@aau.edu.et.
Adane Mihret: Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
Daniel Asrat: Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
Ralfh Pulmones: Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
Badrul Hasan: Department of Medical Biochemistry and Microbiology, Biomedical Centre, Uppsala University, Uppsala, Sweden.
Abraham Aseffa: Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
Adam P Roberts: Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
Göte Swedberg: Department of Medical Biochemistry and Microbiology, Biomedical Centre, Uppsala University, Uppsala, Sweden.
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, bla, bla and aac(3)-lla. The novel Pantoea spp. isolate harboured bla and bla 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.
