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Kruis T, Menzel P, Schwarzer R, Wiesener S, Schoenrath F, Klefisch F, Stegemann M, Pfäfflin F. Outbreak of Pandoraea commovens Infections among Non-Cystic Fibrosis Intensive Care Patients, Germany, 2019-2021. Emerg Infect Dis 2023; 29:2229-2237. [PMID: 37877517 PMCID: PMC10617358 DOI: 10.3201/eid2911.230493] [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] [Indexed: 10/26/2023] Open
Abstract
Pandoraea spp. are gram-negative, nonfermenting rods mainly known to infect patients with cystic fibrosis (CF). Outbreaks have been reported from several CF centers. We report a Pandoraea spp. outbreak comprising 24 non-CF patients at a large university hospital and a neighboring heart center in Germany during July 2019-December 2021. Common features in the patients were critical illness, invasive ventilation, antimicrobial pretreatment, and preceding surgery. Complicated and relapsing clinical courses were observed in cases with intraabdominal infections but not those with lower respiratory tract infections. Genomic analysis of 15 isolates identified Pandoraea commovens as the genetically most similar species and confirmed the clonality of the outbreak strain, designated P. commovens strain LB-19-202-79. The strain exhibited resistance to most antimicrobial drugs except ampicillin/sulbactam, imipenem, and trimethoprim/sulfamethoxazole. Our findings suggest Pandoraea spp. can spread among non-CF patients and underscore that clinicians and microbiologists should be vigilant in detecting and assessing unusual pathogens.
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Patil NR, Tripathi M, Charaya K, Angrup A, Ahuja C, Mohindra S. Skull base osteomyelitis by Pandoraea apista: An unusual pathogen at unusual location - A case report. Surg Neurol Int 2021; 12:447. [PMID: 34621562 PMCID: PMC8492433 DOI: 10.25259/sni_472_2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/12/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Pandoraea apista is predominantly recovered from the respiratory tract of patients with cystic fibrosis (CF). Authors report first case of central nervous system infection by P. apista in the form of skull base osteomyelitis. Case Description: A 67-year-old male presented with complaints of earache and hearing deficit for few months. The radiology was suggestive of skull base osteomyelitis and polypoidal soft tissue extending from the middle cranial fossa to the infratemporal fossa. The sample from the targeted area revealed P. apista on matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. With adequate antibiotic therapy, there was clinicoradiologic improvement. P. apista is an infection exclusively seen in pulmonary infection in patients with CF. We identified its intracranial involvement in a patient for the 1st time in the literature. The serendipitous diagnosis needs evaluation on specific PCR and matrix-assisted laser desorption spectrometry. The treatment with antibiotics provides a definite cure. Conclusion: We report a rare opportunistic infection with central nervous system involvement which can be cured by accurate diagnosis and appropriate antibiotic treatment.
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Affiliation(s)
- Ninad Ramesh Patil
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manjul Tripathi
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Kshitij Charaya
- Department of Otorhinolaryngology, Indus Hospital, Sahibzada Ajit Singh Nagar, Punjab, India
| | - Archana Angrup
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Chirag Ahuja
- Department of Neuroradiodiagnosis, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sandeep Mohindra
- Department of Neurosurgery, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Gatt YE, Margalit H. Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens. Mol Biol Evol 2021; 38:1101-1121. [PMID: 33118035 PMCID: PMC7947768 DOI: 10.1093/molbev/msaa278] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Within-host adaptation is a hallmark of chronic bacterial infections, involving substantial genomic changes. Recent large-scale genomic data from prolonged infections allow the examination of adaptive strategies employed by different pathogens and open the door to investigate whether they converge toward similar strategies. Here, we compiled extensive data of whole-genome sequences of bacterial isolates belonging to miscellaneous species sampled at sequential time points during clinical infections. Analysis of these data revealed that different species share some common adaptive strategies, achieved by mutating various genes. Although the same genes were often mutated in several strains within a species, different genes related to the same pathway, structure, or function were changed in other species utilizing the same adaptive strategy (e.g., mutating flagellar genes). Strategies exploited by various bacterial species were often predicted to be driven by the host immune system, a powerful selective pressure that is not species specific. Remarkably, we find adaptive strategies identified previously within single species to be ubiquitous. Two striking examples are shifts from siderophore-based to heme-based iron scavenging (previously shown for Pseudomonas aeruginosa) and changes in glycerol-phosphate metabolism (previously shown to decrease sensitivity to antibiotics in Mycobacterium tuberculosis). Virulence factors were often adaptively affected in different species, indicating shifts from acute to chronic virulence and virulence attenuation during infection. Our study presents a global view on common within-host adaptive strategies employed by different bacterial species and provides a rich resource for further studying these processes.
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Affiliation(s)
- Yair E Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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Greninger AL, Addetia A, Tao Y, Adler A, Qin X. Inactivation of genes in oxidative respiration and iron acquisition pathways in pediatric clinical isolates of Small colony variant Enterobacteriaceae. Sci Rep 2021; 11:7457. [PMID: 33811225 PMCID: PMC8018945 DOI: 10.1038/s41598-021-86764-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 03/11/2021] [Indexed: 02/01/2023] Open
Abstract
Isolation of bacterial small colony variants (SCVs) from clinical specimens is not uncommon and can fundamentally change the outcome of the associated infections. Bacterial SCVs often emerge with their normal colony phenotype (NCV) co-isolates in the same sample. The basis of SCV emergence in vivo is not well understood in Gram-negative bacteria. In this study, we interrogated the causal genetic lesions of SCV growth in three pairs of NCV and SCV co-isolates of Escherichia coli, Citrobacter freundii, and Enterobacter hormaechei. We confirmed SCV emergence was attributed to limited genomic mutations: 4 single nucleotide variants in the E. coli SCV, 5 in C. freundii, and 8 in E. hormaechei. In addition, a 10.2 kb chromosomal segment containing 11 genes was deleted in the E. hormaechei SCV isolate. Each SCV had at least one coding change in a gene associated with bacterial oxidative respiration and another involved in iron capture. Chemical and genetic rescue confirmed defects in heme biosynthesis for E. coli and C. freundii and lipoic acid biosynthesis in E. hormaachei were responsible for the SCV phenotype. Prototrophic growth in all 3 SCV Enterobacteriaceae species was unaffected under anaerobic culture conditions in vitro, illustrating how SCVs may persist in vivo.
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Affiliation(s)
- Alexander L. Greninger
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA USA ,grid.240741.40000 0000 9026 4165Seattle Children’s Hospital, Seattle, WA USA
| | - Amin Addetia
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA USA ,grid.240741.40000 0000 9026 4165Seattle Children’s Hospital, Seattle, WA USA
| | - Yue Tao
- grid.16821.3c0000 0004 0368 8293Shanghai Children’s Medical Center, Translational Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127 China
| | - Amanda Adler
- grid.240741.40000 0000 9026 4165Seattle Children’s Hospital, Seattle, WA USA
| | - Xuan Qin
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA USA ,grid.240741.40000 0000 9026 4165Seattle Children’s Hospital, Seattle, WA USA
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Peeters C, De Canck E, Cnockaert M, De Brandt E, Snauwaert C, Verheyde B, Depoorter E, Spilker T, LiPuma JJ, Vandamme P. Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism. Front Microbiol 2019; 10:2556. [PMID: 31781066 PMCID: PMC6851202 DOI: 10.3389/fmicb.2019.02556] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 10/23/2019] [Indexed: 01/31/2023] Open
Abstract
Comparative analysis of partial gyrB, recA, and gltB gene sequences of 84 Pandoraea reference strains and field isolates revealed several clusters that included no taxonomic reference strains. The gyrB, recA, and gltB phylogenetic trees were used to select 27 strains for whole-genome sequence analysis and for a comparative genomics study that also included 41 publicly available Pandoraea genome sequences. The phylogenomic analyses included a Genome BLAST Distance Phylogeny approach to calculate pairwise digital DNA–DNA hybridization values and their confidence intervals, average nucleotide identity analyses using the OrthoANIu algorithm, and a whole-genome phylogeny reconstruction based on 107 single-copy core genes using bcgTree. These analyses, along with subsequent chemotaxonomic and traditional phenotypic analyses, revealed the presence of 17 novel Pandoraea species among the strains analyzed, and allowed the identification of several unclassified Pandoraea strains reported in the literature. The genus Pandoraea has an open pan genome that includes many orthogroups in the ‘Xenobiotics biodegradation and metabolism’ KEGG pathway, which likely explains the enrichment of these species in polluted soils and participation in the biodegradation of complex organic substances. We propose to formally classify the 17 novel Pandoraea species as P. anapnoica sp. nov. (type strain LMG 31117T = CCUG 73385T), P. anhela sp. nov. (type strain LMG 31108T = CCUG 73386T), P. aquatica sp. nov. (type strain LMG 31011T = CCUG 73384T), P. bronchicola sp. nov. (type strain LMG 20603T = ATCC BAA-110T), P. capi sp. nov. (type strain LMG 20602T = ATCC BAA-109T), P. captiosa sp. nov. (type strain LMG 31118T = CCUG 73387T), P. cepalis sp. nov. (type strain LMG 31106T = CCUG 39680T), P. commovens sp. nov. (type strain LMG 31010T = CCUG 73378T), P. communis sp. nov. (type strain LMG 31110T = CCUG 73383T), P. eparura sp. nov. (type strain LMG 31012T = CCUG 73380T), P. horticolens sp. nov. (type strain LMG 31112T = CCUG 73379T), P. iniqua sp. nov. (type strain LMG 31009T = CCUG 73377T), P. morbifera sp. nov. (type strain LMG 31116T = CCUG 73389T), P. nosoerga sp. nov. (type strain LMG 31109T = CCUG 73390T), P. pneumonica sp. nov. (type strain LMG 31114T = CCUG 73388T), P. soli sp. nov. (type strain LMG 31014T = CCUG 73382T), and P. terrigena sp. nov. (type strain LMG 31013T = CCUG 73381T).
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Affiliation(s)
- Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Evelien De Canck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Evie De Brandt
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Cindy Snauwaert
- BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Bart Verheyde
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Eliza Depoorter
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Theodore Spilker
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.,BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
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Kenna DTD, Coward A, Perry C, Pike R, Schaefer U, Turton J, Green H, Jones AM, Bright-Thomas RJ, Burns P, Narayan O, Wilkinson S, Turton JF. Investigation of a Pandoraea apista cluster common to adult and paediatric cystic fibrosis patients attending two hospitals in the same city. J Med Microbiol 2019; 68:1081-1095. [DOI: 10.1099/jmm.0.001010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Dervla T. D. Kenna
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Amy Coward
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Claire Perry
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Rachel Pike
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Ulf Schaefer
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | | | - Heather Green
- Manchester Adult Cystic Fibrosis Centre, Wythenshawe Hospital, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK
| | - Andrew M. Jones
- Manchester Adult Cystic Fibrosis Centre, Wythenshawe Hospital, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK
| | - Rowland J. Bright-Thomas
- Manchester Adult Cystic Fibrosis Centre, Wythenshawe Hospital, Manchester University Hospitals NHS Foundation Trust, Southmoor Road, Wythenshawe, Manchester M23 9LT, UK
| | - Phillipa Burns
- Royal Manchester Children’s Hospital, Manchester M13 9WL, UK
| | - Omendra Narayan
- Royal Manchester Children’s Hospital, Manchester M13 9WL, UK
| | | | - Jane F. Turton
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
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7
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Leggett RM, Clark MD. A world of opportunities with nanopore sequencing. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5419-5429. [PMID: 28992056 DOI: 10.1093/jxb/erx289] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Oxford Nanopore Technologies' MinION sequencer was launched in pre-release form in 2014 and represents an exciting new sequencing paradigm. The device offers multi-kilobase reads and a streamed mode of operation that allows processing of reads as they are generated. Crucially, it is an extremely compact device that is powered from the USB port of a laptop computer, enabling it to be taken out of the lab and facilitating previously impossible in-field sequencing experiments to be undertaken. Many of the initial publications concerning the platform focused on provision of tools to access and analyse the new sequence formats and then demonstrating the assembly of microbial genomes. More recently, as throughput and accuracy have increased, it has been possible to begin work involving more complex genomes and metagenomes. With the release of the high-throughput GridION X5 and PromethION platforms, the sequencing of large genomes will become more cost efficient, and enable the leveraging of extremely long (>100 kb) reads for resolution of complex genomic structures. This review provides a brief overview of nanopore sequencing technology, describes the growing range of nanopore bioinformatics tools, and highlights some of the most influential publications that have emerged over the last 2 years. Finally, we look to the future and the potential the platform has to disrupt work in human, microbiome, and plant genomics.
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Affiliation(s)
| | - Matthew D Clark
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- University of East Anglia, Norwich NR4 7TJ, UK
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8
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Dupont C, Aujoulat F, Chiron R, Condom P, Jumas-Bilak E, Marchandin H. Highly Diversified Pandoraea pulmonicola Population during Chronic Colonization in Cystic Fibrosis. Front Microbiol 2017; 8:1892. [PMID: 29056926 PMCID: PMC5635052 DOI: 10.3389/fmicb.2017.01892] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 09/15/2017] [Indexed: 01/03/2023] Open
Abstract
Several environmental bacteria are considered as opportunistic pathogens in cystic fibrosis (CF) and are able to persistently colonize the CF respiratory tract (CFRT). Beside Pseudomonas aeruginosa and Burkholderia cepacia complex, Pandoraea spp. are defined as pathogenic. During chronic colonization, adaptive evolution and diversified population have been demonstrated, notably for P. aeruginosa. However, the persistence of Pandoraea in the CFRT remains largely unexplored. We studied genomic and phenotypic traits of Pandoraea pulmonicola isolates successively recovered from the airways of a single CF patient and relate the results to qualitative and quantitative evolution of other cultivable pathogens and to patient clinical status. A total of 31 isolates recovered from 18 sputum samples over a 7-year period in a single CF patient were studied. Genome dynamics was assessed by pulsed-field gel electrophoresis, ERIC-PCR fingerprinting and 16S rRNA gene PCR-temporal temperature gel electrophoresis. Phenotypic features included antimicrobial susceptibility, motility, biofilm production, and virulence in Caenorhabditis elegans model. Variability was observed for all the characteristics studied leading to highly diversified patterns (24 patterns) for the 31 clonally related isolates. Some of these modifications, mainly genomic events were concomitantly observed with CFRT microbiota composition shifts and with severe exacerbations. The diversity of P. pulmonicola population studied, observed for isolates recovered from successive samples but also within a sample suggested that existence of a diversified population may represent a patho-adaptive strategy for host persistence in the heterogeneous and fluctuating CFRT environment.
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Affiliation(s)
- Chloé Dupont
- Equipe Pathogènes Hydriques, Santé, Environnements, UMR 5569 Hydrosciences Montpellier, U.F.R des Sciences Pharmaceutiques et Biologiques and Université Montpellier, Montpellier, France
| | - Fabien Aujoulat
- Equipe Pathogènes Hydriques, Santé, Environnements, UMR 5569 Hydrosciences Montpellier, U.F.R des Sciences Pharmaceutiques et Biologiques and Université Montpellier, Montpellier, France
| | - Raphaël Chiron
- Centre de Ressources et de Compétences pour la Mucoviscidose, Hôpital Arnaud de Villeneuve, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Pauline Condom
- Equipe Pathogènes Hydriques, Santé, Environnements, UMR 5569 Hydrosciences Montpellier, U.F.R des Sciences Pharmaceutiques et Biologiques and Université Montpellier, Montpellier, France
| | - Estelle Jumas-Bilak
- Equipe Pathogènes Hydriques, Santé, Environnements, UMR 5569 Hydrosciences Montpellier, U.F.R des Sciences Pharmaceutiques et Biologiques and Université Montpellier, Montpellier, France.,Laboratoire d'Hygiène Hospitalière, Hôpital Saint-Eloi, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Hélène Marchandin
- Equipe Pathogènes Hydriques, Santé, Environnements, UMR 5569 Hydrosciences Montpellier, U.F.R des Sciences Pharmaceutiques et Biologiques and Université Montpellier, Montpellier, France.,Service de Microbiologie, Hôpital Carémeau, Centre Hospitalier Universitaire de Nîmes, Nîmes, France.,Laboratoire de Bactériologie, Hôpital Arnaud de Villeneuve, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
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