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Isolation of Novel Afipia septicemium and Identification of Previously Unknown Bacteria Bradyrhizobium sp. OHSU_III from Blood of Patients with Poorly Defined Illnesses

Cultures previously set up for isolation of mycoplasmal agents from blood of patients with poorly-defined illnesses, although not yielding positive results, were cryopreserved because of suspicion of having low numbers of unknown microbes living in an inactive state in the broth. We re-initiated a s...

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Autores principales: Lo, Shyh-Ching, Hung, Guo-Chiuan, Li, Bingjie, Lei, Haiyan, Li, Tianwei, Nagamine, Kenjiro, Zhang, Jing, Tsai, Shien, Bryant, Richard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3796525/
https://www.ncbi.nlm.nih.gov/pubmed/24155888
http://dx.doi.org/10.1371/journal.pone.0076142
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author Lo, Shyh-Ching
Hung, Guo-Chiuan
Li, Bingjie
Lei, Haiyan
Li, Tianwei
Nagamine, Kenjiro
Zhang, Jing
Tsai, Shien
Bryant, Richard
author_facet Lo, Shyh-Ching
Hung, Guo-Chiuan
Li, Bingjie
Lei, Haiyan
Li, Tianwei
Nagamine, Kenjiro
Zhang, Jing
Tsai, Shien
Bryant, Richard
author_sort Lo, Shyh-Ching
collection PubMed
description Cultures previously set up for isolation of mycoplasmal agents from blood of patients with poorly-defined illnesses, although not yielding positive results, were cryopreserved because of suspicion of having low numbers of unknown microbes living in an inactive state in the broth. We re-initiated a set of 3 cultures for analysis of the "uncultivable" or poorly-grown microbes using NGS technology. Broth of cultures from 3 blood samples, submitted from OHSU between 2000 and 2004, were inoculated into culture flasks containing fresh modified SP4 medium and kept at room temperature (RT), 30°C and 35°C. The cultures showing evidence of microbial growth were expanded and subjected to DNA analysis by genomic sequencing using Illumina MiSeq. Two of the 3 re-initiated blood cultures kept at RT after 7–8 weeks showed evidence of microbial growth that gradually reached into a cell density with detectable turbidity. The microbes in the broth when streaked on SP4 agar plates produced microscopic colonies in ∼ 2 weeks. Genomic studies revealed that the microbes isolated from the 2 blood cultures were a novel Afipia species, tentatively named Afipia septicemium. Microbes in the 3(rd) culture (OHSU_III) kept at RT had a limited level of growth and could not reach a plateau with high cell density. Genomic sequencing identified the microbe in the culture as a previously unknown species of Bradyrhizobium bacteria. This study reports on the isolation of novel Afipia and Bradyrhizobium species. Isolation of Bradyrhizobium species bacteria has never been reported in humans. The study also reveals a previously unrecognized nature of hematogenous infections by the 2 unique groups of Bradyrhizobiaceae. Our studies show that improvement of culture system plus effective use of NGS technology can facilitate findings of infections by unusual microbes in patients having poorly-defined, sometimes mysterious illnesses.
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spelling pubmed-37965252013-10-23 Isolation of Novel Afipia septicemium and Identification of Previously Unknown Bacteria Bradyrhizobium sp. OHSU_III from Blood of Patients with Poorly Defined Illnesses Lo, Shyh-Ching Hung, Guo-Chiuan Li, Bingjie Lei, Haiyan Li, Tianwei Nagamine, Kenjiro Zhang, Jing Tsai, Shien Bryant, Richard PLoS One Research Article Cultures previously set up for isolation of mycoplasmal agents from blood of patients with poorly-defined illnesses, although not yielding positive results, were cryopreserved because of suspicion of having low numbers of unknown microbes living in an inactive state in the broth. We re-initiated a set of 3 cultures for analysis of the "uncultivable" or poorly-grown microbes using NGS technology. Broth of cultures from 3 blood samples, submitted from OHSU between 2000 and 2004, were inoculated into culture flasks containing fresh modified SP4 medium and kept at room temperature (RT), 30°C and 35°C. The cultures showing evidence of microbial growth were expanded and subjected to DNA analysis by genomic sequencing using Illumina MiSeq. Two of the 3 re-initiated blood cultures kept at RT after 7–8 weeks showed evidence of microbial growth that gradually reached into a cell density with detectable turbidity. The microbes in the broth when streaked on SP4 agar plates produced microscopic colonies in ∼ 2 weeks. Genomic studies revealed that the microbes isolated from the 2 blood cultures were a novel Afipia species, tentatively named Afipia septicemium. Microbes in the 3(rd) culture (OHSU_III) kept at RT had a limited level of growth and could not reach a plateau with high cell density. Genomic sequencing identified the microbe in the culture as a previously unknown species of Bradyrhizobium bacteria. This study reports on the isolation of novel Afipia and Bradyrhizobium species. Isolation of Bradyrhizobium species bacteria has never been reported in humans. The study also reveals a previously unrecognized nature of hematogenous infections by the 2 unique groups of Bradyrhizobiaceae. Our studies show that improvement of culture system plus effective use of NGS technology can facilitate findings of infections by unusual microbes in patients having poorly-defined, sometimes mysterious illnesses. Public Library of Science 2013-10-14 /pmc/articles/PMC3796525/ /pubmed/24155888 http://dx.doi.org/10.1371/journal.pone.0076142 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
spellingShingle Research Article
Lo, Shyh-Ching
Hung, Guo-Chiuan
Li, Bingjie
Lei, Haiyan
Li, Tianwei
Nagamine, Kenjiro
Zhang, Jing
Tsai, Shien
Bryant, Richard
Isolation of Novel Afipia septicemium and Identification of Previously Unknown Bacteria Bradyrhizobium sp. OHSU_III from Blood of Patients with Poorly Defined Illnesses
title Isolation of Novel Afipia septicemium and Identification of Previously Unknown Bacteria Bradyrhizobium sp. OHSU_III from Blood of Patients with Poorly Defined Illnesses
title_full Isolation of Novel Afipia septicemium and Identification of Previously Unknown Bacteria Bradyrhizobium sp. OHSU_III from Blood of Patients with Poorly Defined Illnesses
title_fullStr Isolation of Novel Afipia septicemium and Identification of Previously Unknown Bacteria Bradyrhizobium sp. OHSU_III from Blood of Patients with Poorly Defined Illnesses
title_full_unstemmed Isolation of Novel Afipia septicemium and Identification of Previously Unknown Bacteria Bradyrhizobium sp. OHSU_III from Blood of Patients with Poorly Defined Illnesses
title_short Isolation of Novel Afipia septicemium and Identification of Previously Unknown Bacteria Bradyrhizobium sp. OHSU_III from Blood of Patients with Poorly Defined Illnesses
title_sort isolation of novel afipia septicemium and identification of previously unknown bacteria bradyrhizobium sp. ohsu_iii from blood of patients with poorly defined illnesses
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3796525/
https://www.ncbi.nlm.nih.gov/pubmed/24155888
http://dx.doi.org/10.1371/journal.pone.0076142
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