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

BMC Microbiology volume 24, Article number: 407 (2024) Cite this article

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 blaCTX−M−15, blaTEM−1D, blaSCO−1, and aac(3)-lla. The novel Pantoea spp. isolate harboured blaCTX−M−9 and blaTEM−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.

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Introduction

Enterobacterales are major aetiologies [1] of sepsis, a life-threatening disorder resulting from a dysregulated immune response to an infection [2]. The Genus Pantoea is characterized as flagellated, nonencapsulated, and non-spore-forming Enterobacterales [3]. Naturally, it inhabits plants, soil, and water [4] and comprises of several species including P. agglomerans, P. dispersa, and P. septica [3, 5, 6]. Pantoea spp. are considered plant pathogens [5] but can cause human infections [7].

Human infections due to Pantoea spp. have been reported worldwide [8,9,10] with P. agglomerans and P. dispersa as the most common [3, 11]. They can infect various organs and are associated with sepsis, cutaneous infection, acute dacryocystitis, cholangitis, hepatocellular carcinoma, and obstructive pulmonary disease [4, 8,9,10, 12,13,14,15,16,17].

In addition, P. agglomerans and P. dispersa are recognized as emerging sepsis pathogens and reports are increasing [7, 16, 18,19,20]. Pantoea spp. associated sepsis is believed to be due to the contamination of indwelling catheters, intravenous fluids, nutrition supplements, blood products, and their delivery mechanisms [17, 20,21,22,23]. Generally, Pantoea spp. isolated from human samples are susceptible to most antibiotic classes [23,24,25], however, the emergence of multidrug-resistant Pantoea spp. has been reported [3, 26].

In routine clinical laboratory tests, identification of Pantoea spp. using the traditional biochemical methods is difficult due to similarities with other Enterobacterales in colony morphology and biochemical reactions [3, 27, 28]. In contrast, the use of advanced bacterial identification systems like MALDI-TOF [29], 16S rRNA, and whole genome sequencing (WGS) enables accurate typing of emerging strains [3, 30, 31].

Globally, there is a scarcity of data related to the magnitude, antimicrobial resistance (AMR) genes, and molecular features of Pantoea spp. isolates that cause sepsis. Moreover, in sub-Saharan countries, including Ethiopia, the identification of these emerging pathogens using conventional methods is challenging. This study aimed for whole genome analysis of Pantoea species identified from sepsis patients in selected Ethiopian referral hospitals.

Materials and methods

At four teaching/referral hospitals located in central, southern, and northern Ethiopia, a multi-center prospective cross-sectional study was conducted among patients with sepsis between October 2019 and September 2020 (Fig. 1). These hospitals were Tikur Anbessa Specialized Hospital (TASH) and Yekatit 12 Specialized Hospital Medical College (Y12HMC) in central Ethiopia, Hawassa University Comprehensive Specialized Hospital (HUCSH) and Dessie Referral Hospital (DRH) in southern and northern Ethiopia, respectively. Among those who sought medical service in these hospitals, patients suspected of sepsis were included. The attending physician’s clinical diagnosis was used to identify eligible patients. All age groups were included, but patients who received antibiotic treatment within the preceding ten days were excluded. The sociodemographic and clinical data of eligible patients were gathered. Data on antibiotics administered for the management of sepsis and patient outcomes were gathered retrospectively. A total of 1416 clinically diagnosed cases of sepsis from different wards were enrolled in this study.

Fig. 1
figure 1

The four Ethiopian referral hospitals selected for this study and where Enterobacterales were isolated

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Blood sample collection and transportation

Professional nurses experienced in sample collection for blood culture, and microbiologists at the bacteriology laboratory were recruited as data collectors. Upon patient identification, 1 ml, 2 ml, 3–5, and 5–10 ml of blood was collected from children who were < 1, 2–5, 6–11, and 12–17 years old respectively, and 10 ml from adults as shown in the previous publication [32]. For children and adults, a 1:5 and 1:10 blood-to-broth dilution was made respectively. A single blood culture bottle was processed for each patient due to manpower and laboratory setting shortages.

Blood cultures and bacterial identification

All blood culture bottles were incubated aerobically at 37 °C for seven consecutive days and inspected daily for turbidity and hemolysis as signs of bacterial growth. Blood samples that showed growth either before the seventh day of incubation and blood samples that did not show signs of growth on the seventh day were sub-cultured onto blood agar (Oxoid Ltd, UK) and MacConkey agar (Oxoid Ltd, UK) at 37 °C for 24 h. In parallel, a gram stain was performed for each blood sample. All positive cultures were characterized by their colony characteristics, gram staining, and conventional biochemical tests. All bacteria were stored at -70 °C or -16 °C and brought to Sweden for further phenotypic and genomic characterization. All bacteria were stored and phenotypic and genomic analyses were done within one year of isolation.

Identification of P. dispersa, P. septica, and a novel Pantoea species

All bacteria were reidentified using MALDI-TOF, as described in the previous publication [32], at the Clinical Microbiology Department of Uppsala University Hospital and Karolinska Institute, Sweden. WGS was subsequently performed on all Pantoea isolates for confirmation, utilizing the raw sequence reads and assembled genomes.

Antimicrobial susceptibility testing

The antimicrobial susceptibility testing (AST) was performed using disk diffusion and interpreted based on the standardized table supplied by the Clinical and Laboratory Standards Institute [33] as described in the previous work [32]. Initially, the AST was performed at each study site and re-performed at Uppsala University.

DNA extraction and whole genome sequencing (WGS)

DNA was extracted from all Pantoea isolates using QIAamp DNA Mini Kit (QIAGEN, Germany) by taking 2–5 pure colonies that grew on cystine lactose electrolyte deficient agar at 37 °C for 24 h aerobically. DNA concentrations were measured with QubitTM3.0 (Thermo-Scientific, MA, USA). All DNA samples were submitted for WGS at the Science for Life Laboratory, Solna, Sweden. WGS was performed using Illumina HiSeq 2500 systems and genome assembly was done using SPAdes (version 3.9).

Bioinformatic quality control

Illumina sequencing reads were assessed for quality using FastQC v.0.11.5 [34] and trimmed for adapter sequences and quality control by Trimmomatic v.0.39 [35], with a sliding window quality cut-off value of Q20. Assembly quality was assessed using Quast v.5.0.2 [36]. All assemblies yielded less than 100 contigs and the mean total coverage ranged from 84x to 136x.

Antimicrobial resistance gene and plasmid replicon prediction

AMR gene presence was predicted using ARIBA v2.14.6 [37] by querying against the SRST2-ARGANNOT [38] database. Similarly, using ARIBA plasmid replicon typing was performed by querying against the PlasmidFinder database [39]. Gene and replicon identity was verified by extracting their respective sequences from de novo Shovill v.1.1.0 [40] assemblies annotated by Prokka v1.14.6 [41] via Artemis v.16.0.17 [42]. These sequences were then compared against their respective reference sequences from the European Nucleotide Archive using Clustal Omega [43].

Phylogenetic analysis

A core genome tree of Pantoea spp. isolates was constructed by mapping sequencing reads against the reference P. dispersa genome (ASM1989095v1) using Snippy v.4.6.0 [44]. One P. septica (SRR5329931), P. wallisii (ASM209548v1) and P. agglomerans (DRR294260) isolate were also included as outgroups. Recombinant regions were then excluded from the alignment by Gubbins v.2.3.4 [45]. ACTG-only SNPs were extracted from the recombination-free alignment using snp-sites v.2.3.3 [46]. Tree calculation was performed using IQ-TREE v.1.6.12 [47], with the general time reversible model and gamma correction using ascertainment bias correction (-m GTR + G + ASC) at 1000 bootstrap replicates.

A condensed core genome tree was similarly constructed to display the Average Nucleotide Identity between representative strains, calculated using OrthoANI v.0.93.1 [48] on the Shovill assemblies. The resultant consensus trees were annotated using the Interactive Tree of Life [49]. Genome accession numbers, sequencing and assembly quality statistics, and coding workflows are available in the Supplementary material (S1 and  S2).

Assembly and BLAST analysis for species identification

Using the assembled genome, the Basic Local Alignment (BLAST) search for Pantoea isolates was done using the BLASTN version 2.13.0 + tool at the National Center for Biotechnology Information (NCBI).

Average nucleotide identity (ANI) determination

The novelty of a Pantoea species was assessed using Average nucleotide Identity (ANI) determination. ANI was calculated using an EZBioCloud online tool [50].

Statistical analysis

The data was analysed using SPSS version 28 for analysis. Descriptive statistics (count, mean, percentages or frequency, and standard deviation) were calculated. The frequencies of acquired AMR genes and plasmid replicons were calculated. Chi-square was used to determine associations of sociodemographics with Pantoea species positivity rate. A p-value < 0.05 was considered statistically significant.

Results

Pantoea species: identification, frequencies and whole genome sequencing

In this study, a total of 1416 patients clinically investigated for sepsis were enrolled (as described in the previous work [32], and 21 Pantoea isolates were identified. While 20 Pantoea isolates were identified at DRH from the north, only one strain was isolated at TASH from central Ethiopia (Table 1). No Pantoea species were isolated at Y12HMC from central and at HUCSH in the southern parts of the country. The majority of Pantoea isolates (n = 18) were identified at the neonatal intensive care unit (NICU) of DRH from patients of age ≤29 days (Table 1). While two Pantoea isolates were identified from adult patients at the emergency outpatient department (EOPD) of DRH, one Pantoea isolate was isolated at the medical ward of TASH (Table 1).

Initially, all Pantoea isolates were incorrectly classified as Serratia or Acinetobacter species using conventional methods. All Pantoea isolates were reclassified as P. dispersa using MALDI-TOF. Furthermore, all P. dispersa were reidentified using sequence-based core genome and ANI analysis. From the 21 putative P. dispersa isolates, one was retyped as P. septica and another as a novel Pantoea species that was different from but most closely related to P. agglomerans. The rest were classified as P. dispersa (n = 19).

Table 1 Frequency of Pantoea species in relation to patient sociodemographic characteristics
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Clinical characteristics and patient outcomes

All patients whose blood cultures were positive for Pantoea species had a fever (> 38 °C) (Table 2). The majority of these patients had elevated respiratory rate, heart rate, and high or low white blood cell count. Among 18 neonates, 16 of them were diagnosed with early-onset neonatal sepsis (EONS) and 2 with late-onset neonatal sepsis (LONS). While the majority of patients had no underlying disease, one patient had acute lymphoid leukaemia (S3). Of 20 septic patients with Pantoea species at DRH, 4 of them had been referred to the hospital from other health facilities.

Patient outcomes were gathered for 18 patients retrospectively. On the same day after blood sample collection for blood culture, patients were treated with either ampicillin and gentamicin or ampicillin and cefotaxime (S4). Of 18 patients who were diagnosed with EONS, LONS, or sepsis and whose blood culture gave positive results for Pantoea species, 12 of them showed improvement while 5 patients died (Patient ID 194, 237, 265, 277, and 291) (S4). In one case, the patient was registered as self-discharge against medical advice (S4). The status of three patients (Patient ID 142, 195, and 221) could not be determined because their clinical charts had been lost for an unknown reason.

Antimicrobial susceptibility patterns of Pantoea species

Almost all Pantoea isolates were resistant to ampicillin, aztreonam, cefotaxime, and ceftriaxone that were prescribed for patients as first-line or second-line regimens (Table 2). While one P. dispersa (Sample ID 319) was sensitive to ceftazidime, cefuroxime, and gentamicin, all other Pantoea species were resistant (Table 2). The novel Pantoea spp. isolate showed resistance against ampicillin, amoxicillin-clavulanic acid, aztreonam, cefotaxime, ceftriaxone, ceftazidime, and cefuroxime (Table 2).

Table 2 Antimicrobial susceptibility patterns of Pantoea species identified from sepsis patients in Ethiopian referral hospitals
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Genetic diversity and phylogenetic structure of Pantoea isolates

Among the Pantoea spp., P. dispersa (n = 19), P. septica (n = 1), and a novel Pantoea spp. were identified using a core genome maximum likelihood tree (Fig. 2). All P. dispersa isolates displayed clonality in the tree, suggesting a clonal outbreak in the hospital, which was further supported by ANI analysis (Fig. 3). While 17 P. dispersa were isolated in the NICU, two others were identified in EOPD of DRH (Sample ID 222 and 305). Among the 4 septic patients who had a referral history at DRH, clonally related P. dispersa were identified among 3 of them who were referred from government health institutions while the novel Pantoea species was identified from a patient sent from a private health facility.

The P. dispersa isolates were, as expected, most closely related to the P. dispersa reference genome. The two most distantly related P. dispersa were also 99.5% identical. The P. septica strain, isolated in TASH, grouped with P. septica within the conventional 95% ANI species cut-off (Fig. 3).

The novel Pantoea spp. was initially identified as P. dispersa by MALDI-TOF, but it most closely grouped with the P. agglomerans outgroup. However, it was too distantly related in the core genome tree to be considered P. agglomerans. This was confirmed by ANI analysis citing 84.52% identity; thus, its species remains unconfirmed. The isolates of Pantoea spp. were collected at different time points over the collection period with a majority within a short period of time towards the end of the collection time in April and May 2020 (see details in S4).

Fig. 2
figure 2

Maximum likelihood tree generated from the core genome of 21 Pantoea isolates identified from sepsis patients in Ethiopian referral hospitals, alongside Pantoea spp. representative outgroups

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Fig. 3
figure 3

Average Nucleotide Identity matrix against a condensed maximum likelihood core genome tree. The two most distantly related P. dispersa isolates and the P. septica and novel Pantoea spp. strains were included alongside Pantoea. spp. outgroups

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Antimicrobial resistance genes and plasmid replicons of Pantoea isolates

All P. dispersa were predicted to have identical AMR gene profiles, containing the β-lactamase genes blaCTX−M−15, blaSCO−1,blaTEM−1D, and the aminoglycoside resistance gene aac(3)-IIa (Fig. 2). However, ARIBA calculated 99.88% identity to the blaTEM−1D reference sequence and alignment against this reference revealed a 2 bp variation. In contrast, the novel Pantoea spp. was predicted to contain only blaCTX−M−9 while the P. septica isolate was devoid of acquired AMR genes (Fig. 2).

The P. dispersa isolates were predicted to ubiquitously carry the IncM1 plasmid replicon while 68.4% (n = 13/19) also possessed IncL1 (Fig. 2). The most similar plasmid with IncM1 in the GenBank was Klebsiella pneumoniae plasmid pMRY13-133KPN_2 (GenBank accession number AP018454.1). All AMR genes carried by P. dispersa were located on the same 80 kb contig as the IncM1 replicon gene was located. The novel Pantoea spp. carried neither, instead carrying IncN3 located in the same 38.7 kb contig as blaCTX−M−9. The most similar plasmid to IncN3 in GenBank was pC52_003 from Klebsiella michiganensis strain C52 (GenBank accession number CP042548.1). No plasmid replicons were detected within the P. septica isolate (Fig. 2).

Discussion

The World Health Organization has recognized sepsis as a major public health problem, especially in low and middle-income countries [51]. The burden of sepsis worsens due to emerging pathogens that are challenging for accurate identification [52] and clinical management due to increasing multidrug resistance [11]. Human infections of Pantoea spp. have been reported as uncommon [22]. However, recently it is considered an emerging human pathogen [53]. The current study showed the emergence of Pantoea spp. infection among patients investigated for sepsis in Ethiopia, and a likely local clonal outbreak of P. dispersa.

In the current study, among a total of 1416 patients clinically investigated for sepsis from four Ethiopian referral hospitals 21 cases of Pantoea were identified at two hospitals. Pantoea spp. isolates (n = 20) were identified at DRH in the north and one case at TASH in central Ethiopia. Among the 21 sepsis cases due to Pantoea spp., 18 were identified at the NICU of DRH that showed similarities with other cases of neonatal sepsis due to Pantoea spp. worldwide [16, 22, 54]. Of 18 cases of sepsis due to Pantoea spp, 5 neonates died at the NICU of DRH. Their main cause of death may not be determined exactly due to the cross-sectional nature of the study design. However, it could be associated with the sepsis caused by Pantoea strains which were resistant to first-line and second-line antibiotic regimens administered for the treatment of neonatal sepsis.

The findings of the current study showed that Pantoea spp. are emerging as human pathogens causing sepsis. Moreover, the identification of Pantoea isolates more frequently at DRH calls for site-specific infection prevention strategies. Pantoea spp. associated neonatal sepsis in NICU may be due to contamination of parenteral nutrition, infant formula, intravenous fluid, blood products, and anaesthetic agents [22, 23, 54]. However, the source of Pantoea isolates for the current study was not identified. A follow-up investigation is necessary to explain whether the identification of Pantoea spp. isolates at DRH was a temporary outbreak or has persisted.

Using the conventional method, all Pantoea spp. isolates were misidentified as Serratia or Acinetobacter but typed accurately as Pantoea spp. using MALDI-TOF. However, after WGS determination, all were identified as P. dispersa except for two isolates: a P. septica and a novel Pantoea spp. isolate. Misidentification of Pantoea spp. using the conventional method has been reported [3, 27] and could be due to the shared colony and biochemical characteristics with other Enterobacterales. The inaccurate classification of a few Pantoea isolates as Acinetobacter species showed professional skill gaps in identifying Pantoea species. Considering the identification of Pantoea species, the implementation of advanced bacterial identification techniques in routine laboratory checks is necessary. However, the availability of resources could be the key determinant for microbiology laboratories in low-resource settings. Expansion of accurately identified species to include emerging pathogens such as Pantoea spp. would benefit healthcare systems, allowing them to tailor treatment and prevention programs.

P. dispersa isolates were phylogenetically identical and circulated both in the NICU or EOPD wards of DRH. Identification of P. dispersa among sepsis patients has been reported by other studies [3, 4, 15, 22, 55], however, this showed a possible clonal outbreak in Ethiopia. The identification of clonally related P. dispersa among patients referred from other governmental health institutions could suggest that these strains can be rapidly acquired in the hospital. The identification of a novel Pantoea isolate at DRH showed that other Pantoea spp. could emerge in clinical settings. Furthermore, since the novel Pantoea species was isolated from a patient referred from a private health facility the strain could be carried to the hospital from other sources. More importantly, the identification of P. septica in another hospital (TASH) located in a different region (Central Ethiopia) shows that, although rare, Pantoea spp. infections were not regionally locked and emerged unrelated to the P. dispersa clonal outbreak at DRH.

All P. dispersa encoded blaCTX−M−15, blaTEM−1D, blaSCO−1, and aac(3)-lla and a similar plasmid of type IncM1 that was associated with the acquired AMR genes. This study showed the emergence of P. dispersa with a plasmid-encoded ESBL gene from Ethiopia however blaCTX−M−15 carried by P. agglomerans was reported from Nigeria [11]. The novel Pantoea spp. isolate harbored blaCTX−M−9 and blaTEM−1D and carried the plasmid replicon IncN linked with blaCTX−M−9. The identification of Pantoea spp. that carried plasmid-mediated, and multiple, AMR genes calls for the implementation of robust antimicrobial stewardship and within-hospital microbiological monitoring and surveillance. The use of whole genome sequencing to determine the identity of the bacteria isolated from sepsis patients is a strength of this study and has revealed an unusual occurrence of multidrug-resistant Pantoea spp.

Limitations of the study

At study sites, the conventional microbiology methododology was unable to accurately identify Pantoea species, and the lab researchers were not alerted to sample additional Pantoea isolates and search for any sources of contamination. Though it is rare to identify gram-negative bacteria as blood culture contaminants [56], the possibility can not be ruled out. However, it could be noted that the Pantoea isolates were identified from different patients on several occasions throughout the year. Limitations of the study also include the time taken to carry out correct identification as this precluded any effort for real-time follow-up for the patients in question. More refined and robust clinical microbiology is required to accurately identify bacterial isolates within a useful timescale in terms of patient benefit.

Conclusion

Pantoea isolates were identified as emerging pathogens among sepsis patients in Ethiopian referral hospitals which calls for better infection prevention and control strategies. The emergence of Pantoea isolates encoding plasmid-linked AMR genes needs special emphasis and strong antimicrobial stewardship. Since Pantoea isolates were misidentified using conventional methods, the implementation of advanced bacterial identification techniques is necessary.

Data availability

The datasets generated and/or analysed during the current study are available in the National Center for Biotechnology Information repository (BioProject ID: PRJNA787062) https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA787062.

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Acknowledgements

We would like to thank Addis Ababa University, Armauer Hansen Research Institute, and Uppsala University for supporting this study. We would like to extend our gratitude to Tikur Anbessa Specialized Hospital, Yekatit 12 Hospital Medical College Hospital, Hawassa University Comprehensive Specialized Hospital, and Dessie Referral Hospital for allowing us to conduct the study. We are grateful to Amhara Public Health Institute Dessie Branch management and microbiology staff who allowed and helped us to conduct blood cultures and antimicrobial susceptibility testing in their microbiology laboratory. We are thankful to the physicians, nurses, and microbiologists from all study sites who helped us undertake this study. Lastly, our heartfelt gratitude goes to all study participants.

Funding

This work was funded by Addis Ababa University and the Addis Ababa University-AHRI collaborative project through a BSPP grant from the Swedish International Development Cooperation Agency: ISP 2017/43:9. RP is supported by the MRC via the LSTM and Lancaster University PhD Doctoral Training Program (grant no. MR/N013514/1).

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Authors and Affiliations

  1. Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia

    Melese Hailu Legese

  2. Armauer Hansen Research Institute, Addis Ababa, Ethiopia

    Melese Hailu Legese, Adane Mihret & Abraham Aseffa

  3. Department of Medical Biochemistry and Microbiology, Biomedical Centre, Uppsala University, Uppsala, Sweden

    Melese Hailu Legese, Badrul Hasan & Göte Swedberg

  4. Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia

    Melese Hailu Legese, Adane Mihret & Daniel Asrat

  5. Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK

    Ralfh Pulmones & Adam P. Roberts

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  1. Melese Hailu Legese
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  8. Göte Swedberg
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Contributions

MHL: Conceptualization, Methodology, Investigation, Software, Data curation, Formal analysis and writing—original manuscript. DA: supervision and writing—review and editing. RP: software, formal analysis and writing—review and editing. BH: methodology and writing—review and editing. AM: conceptualization, funding acquisition, resources, project administration, supervision and writing—review and editing. AA: conceptualization, methodology, supervision and writing—review and editing. AR: software, formal analysis, and writing—review and editing. GS: conceptualization, methodology, software, data curation, funding acquisition, resources, project administration, supervision, and writing—review and editing. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Melese Hailu Legese.

Ethics declarations

Ethics approval and consent to participate

The study was approved by the Department of Microbiology, Immunology and Parasitology Ethical Review Committee (DEREC/18/19/01-H) and Institutional Review Board (AAUMF 01–008) of the College of Health Sciences, Addis Ababa University. The study was also approved by the AHRI/ALERT Ethics Review Committee (protocol number: P050/18) of the Armauer Hansen Research Institute and National Ethical Review Committee (Ref No. MoSHE//RD/14.1/690/19). Written informed consent was obtained from all study participants.

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Not applicable.

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The authors declare no competing interests.

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12866_2024_3561_MOESM1_ESM.docx

Supplementary Material 1: S1 shows the coding workflow for the whole genome analysis of Pantoea species identified from sepsis patients in selected Ethiopian referral hospitals: emerging pathogens. S2 is a table that shows the Genome accession number, sequencing, and assembly quality statistics. S3 shows the clinical characteristics of patients with positive blood cultures for Pantoea isolates. S4 shows the antibiotics prescribed and clinical outcomes of patients whose blood cultures were positive for Pantoea species.

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Legese, M.H., Mihret, A., Asrat, D. et al. Whole genome analysis of Pantoea species identified from sepsis patients in selected Ethiopian referral hospitals: emerging pathogens. BMC Microbiol 24, 407 (2024). https://doi.org/10.1186/s12866-024-03561-5

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Keywords

BMC Microbiology

ISSN: 1471-2180

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