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Jayasinghe H, Lee SJ, Adam H, Karlowsky J, Zhanel GG, Walkty A. Pantoea septica bacteremia in a 3-month-old infant with RAG2 severe combined immune deficiency: A case report. Diagn Microbiol Infect Dis 2024; 110:116499. [PMID: 39173567 DOI: 10.1016/j.diagmicrobio.2024.116499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/23/2024] [Accepted: 08/16/2024] [Indexed: 08/24/2024]
Abstract
We present the case of a 3-month-old immunocompromised infant who developed a vascular catheter-related bloodstream infection caused by Pantoea septica. Susceptibility testing results for this isolate and 10 additional clinical strains are provided to help define the susceptibility profile of this infrequently recovered organism.
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Affiliation(s)
- Himath Jayasinghe
- Department of Internal Medicine, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Santina J Lee
- Department of Pediatrics and Child Health, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Heather Adam
- Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada; Shared Health, Winnipeg, Manitoba, Canada
| | - James Karlowsky
- Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada; Shared Health, Winnipeg, Manitoba, Canada
| | - George G Zhanel
- Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew Walkty
- Department of Internal Medicine, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada; Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada; Shared Health, Winnipeg, Manitoba, Canada.
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Legese MH, Mihret A, Asrat D, Pulmones R, Hasan B, Aseffa A, Roberts AP, Swedberg G. Whole genome analysis of Pantoea species identified from sepsis patients in selected Ethiopian referral hospitals: emerging pathogens. BMC Microbiol 2024; 24:407. [PMID: 39395976 PMCID: PMC11470727 DOI: 10.1186/s12866-024-03561-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 09/30/2024] [Indexed: 10/14/2024] Open
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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Affiliation(s)
- Melese Hailu Legese
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
- Department of Medical Biochemistry and Microbiology, Biomedical Centre, Uppsala University, Uppsala, Sweden.
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Adane Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, 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
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Kelly SA, O'Connell NH, Thompson TP, Dillon L, Wu J, Creevey C, Powell J, Gilmore BF, Dunne CP. A novel characterized multi-drug-resistant Pseudocitrobacter sp. isolated from a patient colonized while admitted to a tertiary teaching hospital. J Hosp Infect 2024; 145:193-202. [PMID: 38215945 DOI: 10.1016/j.jhin.2023.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/14/2024]
Abstract
BACKGROUND Reports of nosocomial infections typically describe recognised microorganisms. Here, a novel bacterial species was isolated, based on rectal swab screening for carbapenemases post-admission, then phenotypically and genetically characterized. METHODS Sensititre, Vitek and API kits, MALDI and Illumina MiSeq were employed before profiles and phylogeny were compared with other related species. FINDINGS Determined to be a possible Enterobacterales, the isolate was found to have 99.7% 16s rRNA identity to Pseudocitrobacter corydidari; an Asian cockroach-associated species. Given the highly conserved/low variability of 16S rRNA genes in Enterobacterales, average nucleotide identity (ANI) analysis compared the new isolate's genome with those of 18 Enterobacteriaceae species, including confirmed species of Pseudocitrobacter and unnamed Pseudocitrobacter species in the SILVA database. Of these, Pseudocitrobactercorydidari had the highest ANI at 0.9562. The published genome of the only known isolate of P.corydidari does not include Antimicrobial Resistance Genes (ARGs), with exception of potential drug efflux transporters. In contrast, our clinical isolate bears recognised antimicrobial resistance genes, including Klebsiella pneumoniae carbapenemase. The associated genome suggests resistance to carbapenems, β-lactams, sulfonamides, fluoroquinolones, macrolides, aminoglycosides and cephalosporins. Phenotypic antimicrobial resistance was confirmed. CONCLUSION Evident variations in ARG profiles, human colonization and origin in a clinically relevant niche that is geographically, physically and chemically disparate lend credibility for divergent evolution or, less likely, parallel evolution with P. corydidari. Genome data for this new species have been submitted to GENBANK using the proposed nomenclature Pseudocitrobacter limerickensis. The patient was colonized, rather than infected, and did not require antimicrobial treatment.
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Affiliation(s)
- S A Kelly
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - N H O'Connell
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland; School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity, University of Limerick, Limerick, Ireland
| | - T P Thompson
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - L Dillon
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - J Wu
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - C Creevey
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - J Powell
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland; School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity, University of Limerick, Limerick, Ireland
| | - B F Gilmore
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - C P Dunne
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity, University of Limerick, Limerick, Ireland.
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Patakova P, Vasylkivska M, Sedlar K, Jureckova K, Bezdicek M, Lovecka P, Branska B, Kastanek P, Krofta K. Whole genome sequencing and characterization of Pantoea agglomerans DBM 3797, endophyte, isolated from fresh hop ( Humulus lupulus L.). Front Microbiol 2024; 15:1305338. [PMID: 38389535 PMCID: PMC10882544 DOI: 10.3389/fmicb.2024.1305338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Background This paper brings new information about the genome and phenotypic characteristics of Pantoea agglomerans strain DBM 3797, isolated from fresh Czech hop (Humulus lupulus) in the Saaz hop-growing region. Although P. agglomerans strains are frequently isolated from different materials, there are not usually thoroughly characterized even if they have versatile metabolism and those isolated from plants may have a considerable potential for application in agriculture as a support culture for plant growth. Methods P. agglomerans DBM 3797 was cultured under aerobic and anaerobic conditions, its metabolites were analyzed by HPLC and it was tested for plant growth promotion abilities, such as phosphate solubilization, siderophore and indol-3-acetic acid productions. In addition, genomic DNA was extracted, sequenced and de novo assembly was performed. Further, genome annotation, pan-genome analysis and selected genome analyses, such as CRISPR arrays detection, antibiotic resistance and secondary metabolite genes identification were carried out. Results and discussion The typical appearance characteristics of the strain include the formation of symplasmata in submerged liquid culture and the formation of pale yellow colonies on agar. The genetic information of the strain (in total 4.8 Mb) is divided between a chromosome and two plasmids. The strain lacks any CRISPR-Cas system but is equipped with four restriction-modification systems. The phenotypic analysis focused on growth under both aerobic and anaerobic conditions, as well as traits associated with plant growth promotion. At both levels (genomic and phenotypic), the production of siderophores, indoleacetic acid-derived growth promoters, gluconic acid, and enzyme activities related to the degradation of complex organic compounds were found. Extracellular gluconic acid production under aerobic conditions (up to 8 g/l) is probably the result of glucose oxidation by the membrane-bound pyrroloquinoline quinone-dependent enzyme glucose dehydrogenase. The strain has a number of properties potentially beneficial to the hop plant and its closest relatives include the strains also isolated from the aerial parts of plants, yet its safety profile needs to be addressed in follow-up research.
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Affiliation(s)
- Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
- Department of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Katerina Jureckova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Matej Bezdicek
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Brno, Czechia
- Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Petra Lovecka
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | | | - Karel Krofta
- Hop Research Institute, Co. Ltd., Zatec, Czechia
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Casale R, Boattini M, Bianco G, Comini S, Corcione S, Garazzino S, Silvestro E, De Rosa FG, Cavallo R, Costa C. Bloodstream Infections by Pantoea Species: Clinical and Microbiological Findings from a Retrospective Study, Italy, 2018-2023. Antibiotics (Basel) 2023; 12:1723. [PMID: 38136757 PMCID: PMC10740582 DOI: 10.3390/antibiotics12121723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
(1) Background: The widespread use of MALDI-TOF coupled to mass spectrometry has improved diagnostic accuracy by identifying uncommon bacteria. Among Enterobacterales, Pantoea species have been seen to be implicated in several human infections, but their clinical and microbiological framework is currently based on a few anecdotal reports. (2) Methods: We conducted this five-year (2018-2023) single-center study aimed at investigating the prevalence and clinical and microbiological findings of Pantoea species bloodstream infections. (3) Results: Among the 4996 bloodstream infection Gram-negative isolates collected during the study period, Pantoea species accounted for 0.4% (n = 19) of isolates from 19 different patients, 5 of them being pediatric cases. Among Pantoea species isolates, P. agglomerans was the most frequently detected (45%; n = 9) followed by P. eucrina (30%; n = 6) and P. septica (15%; n = 3). Malignancy (35.7%) in adults and malignancy (40%) and cerebrovascular disease following meconium aspiration (40%) in pediatric patients as comorbidities and shivering and/or fever following parenteral infusion (36.8%) as a symptom/sign of Pantoea species bloodstream infection onset were the most frequently observed clinical features. Among adults, primary bloodstream infection was the most frequent (50%), whereas among pediatric patients, the most commonly identified sources of infection were catheter-related (40%) and the respiratory tract (40%). Overall, Pantoea species bloodstream infection isolates displayed high susceptibility to all the antibiotics except for ampicillin (63.2%), fosfomycin (73.7%), and piperacillin/tazobactam (84.2%). Targeted antibiotic treatment was prescribed as monotherapy for adults (71.4%) and combination therapy for pediatric patients (60%). The most prescribed antibiotic regimens were piperacillin/tazobactam (21.4%) in adults and meropenem- (40%) and aminoglycoside-containing (40%) antibiotics in pediatric patients. The overall 28-day all-cause mortality rate was 5.3% (n = 1). (4) Conclusions: The prevalence and 28-day mortality rate of Pantoea species bloodstream infections were low. The prescription of targeted therapy including broad-spectrum antibiotics could indicate an underestimation of the specific involvement of the Pantoea species in the onset of the disease, warranting further studies defining their pathogenic potential.
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Affiliation(s)
- Roberto Casale
- Microbiology and Virology Unit, University Hospital City of Health and Science of Turin, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10124 Turin, Italy
| | - Matteo Boattini
- Microbiology and Virology Unit, University Hospital City of Health and Science of Turin, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10124 Turin, Italy
- Lisbon Academic Medical Centre, 1649-028 Lisbon, Portugal
| | - Gabriele Bianco
- Microbiology and Virology Unit, University Hospital City of Health and Science of Turin, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10124 Turin, Italy
| | - Sara Comini
- Operative Unit of Clinical Pathology, Carlo Urbani Hospital, 60035 Jesi, Italy
| | - Silvia Corcione
- Department of Medical Sciences, Infectious Diseases, University of Turin, 10124 Turin, Italy
| | - Silvia Garazzino
- Infectious Diseases Unit, Department of Pediatric and Public Health Sciences, Regina Margherita Children’s Hospital, 10126 Turin, Italy
| | - Erika Silvestro
- Infectious Diseases Unit, Department of Pediatric and Public Health Sciences, Regina Margherita Children’s Hospital, 10126 Turin, Italy
| | - Francesco Giuseppe De Rosa
- Department of Medical Sciences, Infectious Diseases, University of Turin, 10124 Turin, Italy
- Unit of Infectious Diseases, Cardinal Massaia Hospital, 14100 Asti, Italy
| | - Rossana Cavallo
- Microbiology and Virology Unit, University Hospital City of Health and Science of Turin, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10124 Turin, Italy
| | - Cristina Costa
- Microbiology and Virology Unit, University Hospital City of Health and Science of Turin, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10124 Turin, Italy
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Crosby KC, Rojas M, Sharma P, Johnson MA, Mazloom R, Kvitko BH, Smits THM, Venter SN, Coutinho TA, Heath LS, Palmer M, Vinatzer BA. Genomic delineation and description of species and within-species lineages in the genus Pantoea. Front Microbiol 2023; 14:1254999. [PMID: 38029109 PMCID: PMC10665919 DOI: 10.3389/fmicb.2023.1254999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.
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Affiliation(s)
- Katherine C. Crosby
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Mariah Rojas
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Parul Sharma
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
| | - Marcela A. Johnson
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
| | - Reza Mazloom
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Theo H. M. Smits
- Environmental Genomics and System Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Stephanus N. Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Teresa A. Coutinho
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Lenwood S. Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Boris A. Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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Ruan X, Qin X, Li M. Nosocomial bloodstream infection pathogen Pantoea dispersa: a case report and literature review. J Hosp Infect 2022; 127:77-82. [PMID: 35781019 DOI: 10.1016/j.jhin.2022.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/14/2022] [Accepted: 06/21/2022] [Indexed: 10/17/2022]
Abstract
Pantoea dispersa is a gram-negative bacterium frequently found in plants, soil, and water. The genus Pantoea is a rare pathogen in human infectious diseases. The known susceptible populations include infants and postoperative and immunocompromised patients. To date, there are no reports of nosocomial bloodstream infection due to P. dispersa following chest puncture. A 72-year-old Chinese woman suffering from chest distress was found to be blood culture positive for a gram-negative bacterium. The organism was identified as P. dispersa through VITEK 2, MALDI-TOF MS, and 16S rRNA gene sequencing. Although cefoperazone-sulbactam and imipenem were used for treatment, the patient died four days later. To the best of our knowledge, this is the first case of nosocomial bloodstream infection caused by P. dispersa in China. We hope that this article would help clinicians understand better the potential pathogenicity of this pathogen.
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Affiliation(s)
- Xuelian Ruan
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China.
| | - Xue Qin
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China.
| | - Meng Li
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China.
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Yang Y, Hu H, Zhou C, Zhang W, Yu Y, Liu Q, Lu T, Zhang Q. Characteristics and accurate identification of Pantoea dispersa with a case of spontaneous rupture of hepatocellular carcinoma in China: A case report. Medicine (Baltimore) 2022; 101:e28541. [PMID: 35029210 PMCID: PMC8758028 DOI: 10.1097/md.0000000000028541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/21/2021] [Indexed: 01/05/2023] Open
Abstract
INTRODUCTION Pantoea dispersa belongs to the genus Pantoea, which is isolated from Enterobacteriaceae. It has been reported to cause some kinds of infections, but there are few detailed studies on it, especially its characteristics and identification methods, which has caused a lot of trouble in clinical work. PATIENT CONCERNS A 51-year-old Chinese man was admitted to our hospital with a 7-hour history of progressive abdominal pain. He was previously diagnosed with liver cirrhosis secondary to chronic hepatitis B infection and hepatocellular carcinoma. An emergency hepatic artery embolization for hemostasis was performed under local anesthesia. Forty-eight hours later, the patient presented sudden onset of high fever up to 39.0 °C and chill. DIAGNOSIS Morphological and phenotypic profiles were performed for preliminary identification for P dispersa. The biochemical features were obtained by VITEK 2 Test Kit. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis and 16S ribosomal RNA sequencing were performed to accurately identify P dispersa. INTERVENTION Antibiotic therapy of intravenous ceftazidime was started empirically. The antibiotic treatment was switched to intravenous cefepime at the same time because of suspected ceftazidime treatment failure and microbiological sensitivity. OUTCOMES The patient remained afebrile, and the second blood culture results were negative. Chest X-ray was normal as well. In order to control the progression of the hepatic lesion, transarterial chemoembolization was performed under local anesthesia. After completion of 14 days of antibiotic treatment, the patient was discharged with no signs of recurrence. CONCLUSION P dispersa, a gram-negative bacterium rod, were facultative anaerobic, which displayed yellow pigmentation, round, raised, smooth on culture plates. Conventional analysis was difficult to complete its identification. With biochemical tests, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis and 16S ribosomal RNA sequencing, P dispersa can be accurately identified. It will help physicians understand the related clinical manifestations and make timely and effective treatment for patients.
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Phylogenomic analysis of the Erwiniaceae supports reclassification of Kalamiella piersonii to Pantoea piersonii comb. nov. and Erwinia gerundensis to the new genus Duffyella gen. nov. as Duffyella gerundensis comb. nov. Mol Genet Genomics 2022; 297:213-225. [PMID: 34988605 DOI: 10.1007/s00438-021-01829-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/27/2021] [Indexed: 01/20/2023]
Abstract
To better understand the taxonomy of Erwinia in the context of the Erwiniaceae family, we carried out a taxogenomic analysis of the Erwiniaceae, a family that was created following the taxonomic revision of the family, Enterobacteriaceae. There has been no systematic analysis of this family, including the agriculturally relevant genus, Erwinia. Our analyses focused on 80 strains of Erwinia along with 37 strains representing 7 other genera in the family. We identified 308 common proteins, generated a genome-level phylogeny and carried out Average Nucleotide Identity, Average Amino Acid Identity and Percentage of Conserved Protein analyses. We show that multiple strains of Erwinia cannot be assigned to established species groups and that both Erwinia gerundensis and "Erwinia mediterraneensis" are not members of Erwinia. We propose the creation of the genus Duffyella gen. nov. and the reclassification of Erwinia gerundensis to this genus as the type species, Duffyella gerundensis comb. nov. Furthermore, divergence between other species within Erwinia as measured by Average Amino Acid Identity is greater than the divergence between Erwinia and other genera, supporting the possible subdivision of the genus Erwinia into at least two genera. Our analyses also suggest that there is no basis for the establishment of the genus Kalamiella within the Erwiniaceae or the taxonomic revision of the Pantoea septica lineage. Therefore, we propose reclassifying Kalamiella piersonii as Pantoea piersonii comb. nov. Our study provides new insight into the diversity of the Erwiniaceae and provides a solid foundation for advancing taxonomic revision of this broadly relevant family.
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Sanz-García F, Gil-Gil T, Laborda P, Ochoa-Sánchez LE, Martínez JL, Hernando-Amado S. Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat. Int J Mol Sci 2021; 22:8080. [PMID: 34360847 PMCID: PMC8347278 DOI: 10.3390/ijms22158080] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/24/2022] Open
Abstract
The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.
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Affiliation(s)
| | | | | | | | - José L. Martínez
- Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain; (F.S.-G.); (T.G.-G.); (P.L.); (L.E.O.-S.); (S.H.-A.)
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Abstract
Pantoea is a plant pathogen infrequently reported to cause opportunistic bloodstream infections. This gram-negative bacillus is a rare cause of hospital-acquired infections in newborn infants with high mortality. Since the creation of the new genus Pantoea in 1989, the evidence base available to neonatal health care providers is limited. Most of the available literature consists of case reports and case series. This review aims to consolidate the current reported literature on Pantoea infections, focusing on newborn infants and the neonatal intensive care unit (NICU). Prematurity and the associated relative immunocompromised state are major risk factors for hospital-acquired infections due to Pantoea in newborn infants. Recent advances in molecular biology have improved our understanding of the cross-kingdom pathogenesis exhibited by Pantoea. Respiratory symptoms and association with central venous lines are the most common clinical presentation of Pantoea bacteremia in newborn infants. Early institution of appropriate antibiotic therapy against this organism could be lifesaving. Therefore, it is critical for neonatologists to understand the clinical spectrum of Pantoea infections in NICUs.
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Affiliation(s)
- Srinivasan Mani
- Pediatrics/Neonatology, State University of New York, Buffalo, USA
| | - Jayasree Nair
- Pediatrics/Neonatology, State University of New York, Buffalo, USA
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Rekha PD, Hameed A, Manzoor MAP, Suryavanshi MV, Ghate SD, Arun AB, Rao SS, Athmika, Bajire SK, Mujeeburahiman M, Young CC. First Report of Pathogenic Bacterium Kalamiella piersonii Isolated from Urine of a Kidney Stone Patient: Draft Genome and Evidence for Role in Struvite Crystallization. Pathogens 2020; 9:E711. [PMID: 32872396 PMCID: PMC7558591 DOI: 10.3390/pathogens9090711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 01/01/2023] Open
Abstract
Uropathogenic bacteria are widely distributed in the environment and urinary tract infection is implicated in kidney stone disease. Here, we report on a urease negative bacterium Kalamiella piersonii (strain YU22) isolated from the urine of a struvite stone (MgNH4PO4·6H2O) patient. The closest species, K. piersonii IIIF1SW-P2T was reported from International Space Station samples. However, there are no earlier reports on its human association. Using whole genome and experimental analysis, its involvement in urinary tract colonization and struvite crystallization was explored. The strain YU22 showed many virulence factors that are needed for host cell invasion and colonization including cell adhesion factors, swimming and swarming motilities, biofilm and siderophore among others. In vitro infection studies in HEK-293T cells demonstrated the host cell attachment and killing. It was able to utilize amino acids as sole carbon source and showed growth in synthetic and healthy urine establishing metabolic adaptation to urinary tract. Increased pH and availability of ammonium ions from amino acid breakdown promoted struvite crystallization. The results from this study support the involvement of urease negative uropathogen in the struvite lithogenesis. Further studies on other isolates of K. peirsonii are warranted to assess its health risks.
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Affiliation(s)
- Punchappady Devasya Rekha
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India; (A.H.); (M.A.P.M.); (M.V.S.); (S.D.G.); (A.B.A.); (S.S.R.); (A.); (S.K.B.)
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India; (A.H.); (M.A.P.M.); (M.V.S.); (S.D.G.); (A.B.A.); (S.S.R.); (A.); (S.K.B.)
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 40227, Taiwan;
| | - Muhammed A. P. Manzoor
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India; (A.H.); (M.A.P.M.); (M.V.S.); (S.D.G.); (A.B.A.); (S.S.R.); (A.); (S.K.B.)
| | - Mangesh V. Suryavanshi
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India; (A.H.); (M.A.P.M.); (M.V.S.); (S.D.G.); (A.B.A.); (S.S.R.); (A.); (S.K.B.)
| | - Sudeep D. Ghate
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India; (A.H.); (M.A.P.M.); (M.V.S.); (S.D.G.); (A.B.A.); (S.S.R.); (A.); (S.K.B.)
| | - A. B. Arun
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India; (A.H.); (M.A.P.M.); (M.V.S.); (S.D.G.); (A.B.A.); (S.S.R.); (A.); (S.K.B.)
| | - Sneha S. Rao
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India; (A.H.); (M.A.P.M.); (M.V.S.); (S.D.G.); (A.B.A.); (S.S.R.); (A.); (S.K.B.)
| | - Athmika
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India; (A.H.); (M.A.P.M.); (M.V.S.); (S.D.G.); (A.B.A.); (S.S.R.); (A.); (S.K.B.)
| | - Sukesh Kumar Bajire
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India; (A.H.); (M.A.P.M.); (M.V.S.); (S.D.G.); (A.B.A.); (S.S.R.); (A.); (S.K.B.)
| | - M. Mujeeburahiman
- Department of Urology, Yenepoya Medical College and Hospital, Yenepoya Deemed to be University, Mangalore 575018, India;
| | - C.-C. Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 40227, Taiwan;
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