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1.
Open Forum Infect Dis ; 9(9): ofac472, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-36196300

RESUMO

Mycoplasma orale is a rare cause of invasive infection in immunodeficient hosts. Phosphatidylinositol 3-kinase, regulatory subunit 1 (PI3KR1) mutations predispose patients to sinopulmonary infections, alongside bronchiectasis autoimmunity and lymphoproliferation. We report 2 cases of PI3KR1 deficiency with invasive M orale and effective treatment options.

2.
Mol Genet Genomics ; 297(1): 213-225, 2022 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-34988605

RESUMO

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.


Assuntos
Erwinia/classificação , Pantoea/classificação , DNA Bacteriano/análise , DNA Bacteriano/genética , Enterobacteriaceae/classificação , Enterobacteriaceae/genética , Erwinia/genética , Tipagem de Sequências Multilocus , Pantoea/genética , Filogenia , RNA Ribossômico 16S/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
3.
Int J Syst Evol Microbiol ; 70(12): 6524-6530, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33125313

RESUMO

The diverse members of the Enterobacterales are agriculturally and medically relevant species that have continued to undergo taxonomic revision. To assess the current taxonomy of 64 genera of the Enterobacterales, we carried out a phylogenetic analysis using 32 single-copy core proteins. The resulting phylogeny was robust, and shows that eight genera - Biostraticola, Enterobacillus, Gibbsiella, Limnobaculum, Izhakiella, 'Nissabacter', Rosenbergiella and Samsonia - are currently assigned to incorrect families. Taxonomic reassignment of these genera was also supported by average amino acid identity comparisons. We propose taxonomic revision of these genera to reflect their phylogenetic position within the Enterobacterales.


Assuntos
Enterobacteriaceae/classificação , Filogenia , Técnicas de Tipagem Bacteriana , DNA Bacteriano/genética , Análise de Sequência de DNA
4.
Phage (New Rochelle) ; 1(1): 45-56, 2020 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-36147614

RESUMO

Background: Pantoea is a genus within the Enterobacterales whose members encompass free-living and host-associated lifestyles. Despite our growing understanding of the role of mobile genetic elements in the biology, ecology, and evolution of this bacterial group, few Pantoea bacteriophages have been identified and characterized. Materials and Methods: A bacteriophage that could infect Pantoea agglomerans was isolated from barnyard soil. We used electron microscopy and complete genome sequencing to identify the viral family, and evaluated its host range across 10 different Pantoea species groups using both bacterial lawn and phage lawn assays. The latter assays were carried out using a scalable microplate assay to increase throughput and enable spectrophotometric quantitation. We also performed a phylogenetic analysis to determine the closest relatives of our phage. Results: Phage vB_PagP-SK1 belongs to the genus Teseptimavirus of the Podoviridae family in the order Caudovirales. The 39,938 bp genome has a modular structure with early, middle, and late genes, along with the characteristic direct terminal repeats of 172 bp. Genome composition and synteny were similar to that of the Erwinia amylovora phage, vB_EamP-L1, with the exception of a few loci that are most similar to genes of phage infecting other members of the Enterobacteriaceae. A total of 94 Pantoea strains were surveyed and vB_PagP-SK1 was found to infect 15 Pantoea strains across three species, predominantly P. agglomerans, along with one Erwinia billingiae strain. Conclusions: vB_PagP-SK1 belongs to the Teseptimavirus genus and has a host range that spans multiple species groups, and is most closely related to the E. amylovora phage, vB_EamP-L1. The presence of xenologous genes in its genome indicates that the genome is a mosaic of multiple Teseptimavirus phages that infect members of the Enterobacteriaceae.

5.
PLoS One ; 14(11): e0224731, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31682625

RESUMO

The Enterobacterial genus Pantoea contains both free-living and host-associating species, with considerable debate as to whether documented reports of human infections by members of this species group are accurate. MALDI-TOF-based identification methods are commonly used in clinical laboratories as a rapid means of identification, but its reliability for identification of Pantoea species is unclear. In this study, we carried out cpn60-based molecular typing of 54 clinical isolates that had been identified as Pantoea using MALDI-TOF and other clinical typing methods. We found that 24% had been misidentified, and were actually strains of Citrobacter, Enterobacter, Kosakonia, Klebsiella, Pseudocitrobacter, members of the newly described Erwinia gerundensis, and even several unclassified members of the Enterobacteriaceae. The 40 clinical strains that were confirmed to be Pantoea were identified as Pantoea agglomerans, Pantoea allii, Pantoea dispersa, Pantoea eucalypti, and Pantoea septica as well as the proposed species group, Pantoea latae. Some species groups considered largely environmental or plant-associated, such as P. allii and P. eucalypti were also among clinical specimens. Our results indicate that MALDI-TOF-based identification methods may misidentify strains of the Enterobacteriaceae as Pantoea.


Assuntos
Técnicas de Tipagem Bacteriana/métodos , Infecções por Enterobacteriaceae/microbiologia , Pantoea/classificação , Erros de Diagnóstico , Infecções por Enterobacteriaceae/diagnóstico , Humanos , Pantoea/genética , Pantoea/isolamento & purificação , Filogenia , Plantas/microbiologia , Reprodutibilidade dos Testes , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
6.
Mol Genet Genomics ; 293(6): 1453-1467, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30027301

RESUMO

For many pathogenic members of the Enterobacterales, siderophores play an important role in virulence, yet the siderophores of the host-associating members of the genus Pantoea remain unexplored. We conducted a genome-wide survey of environmental and host-associating strains of Pantoea to identify known and candidate siderophore biosynthetic clusters. Our analysis identified three clusters homologous to those of enterobactin, desferrioxamine, and aerobactin that were prevalent among Pantoea species. Using both phylogenetic and comparative genomic approaches, we demonstrate that the enterobactin-like cluster was present in the common ancestor of all Pantoea, with evidence for three independent losses of the cluster in P. eucalypti, P. eucrina, and the P. ananatis-P. stewartii lineage. The desferrioxamine biosynthetic cluster, previously described and characterized in Pantoea, was horizontally acquired from its close relative Erwinia, with phylogenetic evidence that these transfer events were ancient and occurred between ancestral lineages. The aerobactin cluster was identified in three host-associating species groups, P. septica, P. ananatis, and P. stewartii, with strong evidence for horizontal acquisition from human-pathogenic members of the Enterobacterales. Our work identifies and describes the key siderophore clusters in Pantoea, shows three distinct evolutionary processes driving their diversification, and provides a foundation for exploring the roles that these siderophores may play in human opportunistic infections.


Assuntos
Infecções por Enterobacteriaceae/genética , Interação Gene-Ambiente , Interações Hospedeiro-Patógeno/genética , Pantoea/genética , Sideróforos/biossíntese , Sideróforos/genética , Animais , Vias Biossintéticas/genética , Desferroxamina/metabolismo , Infecções por Enterobacteriaceae/microbiologia , Evolução Molecular , Transferência Genética Horizontal , Especificidade de Hospedeiro/genética , Humanos , Família Multigênica , Filogenia , Virulência
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