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Rayamajhee B, Subedi D, Peguda HK, Willcox MD, Henriquez FL, Carnt N. A Systematic Review of Intracellular Microorganisms within Acanthamoeba to Understand Potential Impact for Infection. Pathogens 2021; 10:pathogens10020225. [PMID: 33670718 PMCID: PMC7922382 DOI: 10.3390/pathogens10020225] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 12/20/2022] Open
Abstract
Acanthamoeba, an opportunistic pathogen is known to cause an infection of the cornea, central nervous system, and skin. Acanthamoeba feeds different microorganisms, including potentially pathogenic prokaryotes; some of microbes have developed ways of surviving intracellularly and this may mean that Acanthamoeba acts as incubator of important pathogens. A systematic review of the literature was performed in order to capture a comprehensive picture of the variety of microbial species identified within Acanthamoeba following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. Forty-three studies met the inclusion criteria, 26 studies (60.5%) examined environmental samples, eight (18.6%) studies examined clinical specimens, and another nine (20.9%) studies analysed both types of samples. Polymerase chain reaction (PCR) followed by gene sequencing was the most common technique used to identify the intracellular microorganisms. Important pathogenic bacteria, such as E. coli, Mycobacterium spp. and P. aeruginosa, were observed in clinical isolates of Acanthamoeba, whereas Legionella, adenovirus, mimivirus, and unidentified bacteria (Candidatus) were often identified in environmental Acanthamoeba. Increasing resistance of Acanthamoeba associated intracellular pathogens to antimicrobials is an increased risk to public health. Molecular-based future studies are needed in order to assess the microbiome residing in Acanthamoeba, as a research on the hypotheses that intracellular microbes can affect the pathogenicity of Acanthamoeba infections.
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Affiliation(s)
- Binod Rayamajhee
- School of Optometry and Vision Science, University of New South Wales (UNSW), Sydney, NSW 2052, Australia; (H.K.P.); (M.D.W.); (N.C.)
- Department of Infection and Immunology, Kathmandu Research Institute for Biological Sciences (KRIBS), Lalitpur 44700, Nepal
- Correspondence: or
| | - Dinesh Subedi
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia;
| | - Hari Kumar Peguda
- School of Optometry and Vision Science, University of New South Wales (UNSW), Sydney, NSW 2052, Australia; (H.K.P.); (M.D.W.); (N.C.)
| | - Mark Duncan Willcox
- School of Optometry and Vision Science, University of New South Wales (UNSW), Sydney, NSW 2052, Australia; (H.K.P.); (M.D.W.); (N.C.)
| | - Fiona L. Henriquez
- Institute of Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland (UWS), Paisley PA1 2BE, UK;
| | - Nicole Carnt
- School of Optometry and Vision Science, University of New South Wales (UNSW), Sydney, NSW 2052, Australia; (H.K.P.); (M.D.W.); (N.C.)
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Draft Genome Sequences of Chlamydiales Bacterium STE3 and Neochlamydia sp. Strain AcF84, Endosymbionts of Acanthamoeba spp. Microbiol Resour Announc 2020; 9:9/20/e00220-20. [PMID: 32409535 PMCID: PMC7225534 DOI: 10.1128/mra.00220-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Chlamydiales bacterium STE3 and Neochlamydia sp. strain AcF84 are obligate intracellular symbionts of Acanthamoeba spp. isolated from the biofilm of a littoral cave wall and gills from striped tiger leaf fish, respectively. We report the draft genome sequences of these two environmental chlamydiae affiliated with the family Parachlamydiaceae.
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Watanabe T, Yamazaki S, Maita C, Matushita M, Matsuo J, Okubo T, Yamaguchi H. Lateral Gene Transfer Between Protozoa-Related Giant Viruses of Family Mimiviridae and Chlamydiae. Evol Bioinform Online 2018; 14:1176934318788337. [PMID: 30038484 PMCID: PMC6050620 DOI: 10.1177/1176934318788337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/21/2018] [Indexed: 11/23/2022] Open
Abstract
Obligate intracellular chlamydiae diverged into pathogenic and environmental
chlamydiae 0.7-1.4 billion years ago. While pathogenic chlamydiae have adapted
to a wide range of vertebrates, environmental chlamydiae inhabit unicellular
amoebae, the free-living Acanthamoeba. However, how and why
this divergence occurred remains unclear. Meanwhile, giant viruses consisting of
protozoa-related and protozoa-unrelated viruses have been discovered, with the
former group being suggested to have more influenced environmental chlamydiae
during their evolution while cohabiting host amoebae. Against this background,
we attempted to visualize genes of giant viruses in chlamydial genomes by
bioinformatic analysis mainly with comparative genome and phylogenic analysis,
seeking genes present in chlamydiae that are specifically shared with
protozoa-related giant viruses. As a result, in contrast to protozoa-unrelated
giant viruses, the genes of protozoa-related giant viruses were significantly
shared in both the chlamydia genomes depending on the giant virus type. In
particular, the prevalence of Mimiviridae genes among the
protozoa-related giant virus genes in chlamydial genomes was significantly high.
Meanwhile, the prevalence of protozoa-related giant virus genes in pathogenic
chlamydia genomes was consistently higher than those of environmental
chlamydiae; the actual number of sequences similar to giant virus was also
significantly predominant compared with those in the environmental chlamydial
genomes. Among them, the most prevalent of giant virus was in the case of
chlamydiae with Megavirus chiliensis; total of 1338 genes of
the chlamydiae were found to be shared with the virus (444 genes specific to
environmental chlamydiae, 892 genes shared between both chlamydiae, only two
genes in the pathogenic chlamydiae). Phylogenic analysis with most prevalent
sets (Megavirus chiliensis and Protochlamydia
EI2 or Chlamydia trachomatis L2 434Bu) showed the presence of
orthologs between these with several clustered. In addition, Pearson’s single
regression analysis revealed that almost the prevalence of the genes from the
giant viruses in chlamydial genomes was negatively and specifically correlated
with the number of chlamydial open reading frames (ORFs). Thus, these results
indicated the trace of lateral gene transfer between protozoa-related giant
viruses of family Mimiviridae and chlamydiae. This is the first
demonstration of a putative linkage between chlamydiae and the giant viruses,
providing us with a hint to understand chlamydial evolution.
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Affiliation(s)
- Takanori Watanabe
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Sumire Yamazaki
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Chinatsu Maita
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Mizue Matushita
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Junji Matsuo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
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Okubo T, Matsushita M, Nakamura S, Matsuo J, Nagai H, Yamaguchi H. Acanthamoeba S13WT relies on its bacterial endosymbiont to backpack human pathogenic bacteria and resist Legionella infection on solid media. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:344-354. [PMID: 29611898 DOI: 10.1111/1758-2229.12645] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 03/22/2018] [Indexed: 06/08/2023]
Abstract
Soil-borne amoeba Acanthamoeba S13WT has an endosymbiotic relationship with an environmental Neochlamydia bacterial strain. However, regardless of extensive experiments in liquid media, the biological advantage of the symbiosis remained elusive. We therefore explored the role of the endosymbiont in predator-prey interactions on solid media. A mixed culture of the symbiotic or aposymbiotic amoebae and GFP-expressing Escherichia coli or Salmonella Enteritidis was spotted onto the centre of a LB or B-CYE agar plate preinoculated with a ring of mCherry-expressing Legionella pneumophila (Legionella 'wall'). The spread of the amoebae on the plate was assessed using a fluorescence imaging system or scanning electron microscopy. As a result, in contrast to the aposymbiotic amoebae, the symbiotic amoebae backpacked these GFP-expressing bacteria and formed flower-like fluorescence patterns in an anticlockwise direction. Other bacteria (Pseudomonas aeruginosa and Stenotrophomonas maltophilia), but not Staphylococcus aureus, were also backpacked by the symbiotic amoebae on LB agar, although lacked the movement to anticlockwise direction. Furthermore, in contrast to the aposymbiotic amoebae, the symbiotic amoebae backpacking the E. coli broke through the Legionella 'wall' on B-CYE agar plates. Thus, we concluded that Acanthamoeba S13WT required the Neochlamydia endosymbiont to backpack human pathogenic bacteria and resist Legionella infection on solid agar.
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Affiliation(s)
- Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, North-12, West-5, Kita-ku, Sapporo 060-0812, Japan
| | - Mizue Matsushita
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, North-12, West-5, Kita-ku, Sapporo 060-0812, Japan
| | - Shinji Nakamura
- Division of Biomedical Imaging Research, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Junji Matsuo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, North-12, West-5, Kita-ku, Sapporo 060-0812, Japan
| | - Hiroki Nagai
- Department of Microbiology, Gifu University School of Medicine, Yanagido 1-1, Gifu, Gifu 501-1194, Japan
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, North-12, West-5, Kita-ku, Sapporo 060-0812, Japan
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Pillonel T, Bertelli C, Greub G. Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle. Front Microbiol 2018. [PMID: 29515524 PMCID: PMC5826181 DOI: 10.3389/fmicb.2018.00079] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Chlamydiae phylum exclusively encompasses bacteria sharing a similar obligate intracellular life cycle. Existing 16S rDNA data support a high diversity within the phylum, however genomic data remain scarce owing to the difficulty in isolating strains using culture systems with eukaryotic cells. Yet, Chlamydiae genome data extracted from large scale metagenomic studies might help fill this gap. This work compares 33 cultured and 27 environmental, uncultured chlamydial genomes, in order to clarify the phylogenetic relatedness of the new chlamydial clades and to investigate the genetic diversity of the Chlamydiae phylum. The analysis of published chlamydial genomes from metagenomics bins and single cell sequencing allowed the identification of seven new deeply branching chlamydial clades sharing genetic hallmarks of parasitic Chlamydiae. Comparative genomics suggests important biological differences between those clades, including loss of many proteins involved in cell division in the genus Similichlamydia, and loss of respiratory chain and tricarboxylic acid cycle in several species. Comparative analyses of chlamydial genomes with two proteobacterial orders, the Rhizobiales and the Rickettsiales showed that genomes of different Rhizobiales families are much more similar than genomes of different Rickettsiales families. On the other hand, the chlamydial 16S rRNAs exhibit a higher sequence conservation than their Rickettsiales counterparts, while chlamydial proteins exhibit increased sequence divergence. Studying the diversity and genome plasticity of the entire Chlamydiae phylum is of major interest to better understand the emergence and evolution of this ubiquitous and ancient clade of obligate intracellular bacteria.
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Affiliation(s)
- Trestan Pillonel
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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Fukumoto T, Matsuo J, Okubo T, Nakamura S, Miyamoto K, Oka K, Takahashi M, Akizawa K, Shibuya H, Shimizu C, Yamaguchi H. Acanthamoeba containing endosymbiotic chlamydia isolated from hospital environments and its potential role in inflammatory exacerbation. BMC Microbiol 2016; 16:292. [PMID: 27978822 PMCID: PMC5160005 DOI: 10.1186/s12866-016-0906-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 11/29/2016] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Environmental chlamydiae belonging to the Parachlamydiaceae are obligate intracellular bacteria that infect Acanthamoeba, a free-living amoeba, and are a risk for hospital-acquired pneumonia. However, whether amoebae harboring environmental chlamydiae actually survive in hospital environments is unknown. We therefore isolated living amoebae with symbiotic chlamydiae from hospital environments. RESULTS One hundred smear samples were collected from Hokkaido University Hospital, Sapporo, Japan; 50 in winter (February to March, 2012) and 50 in summer (August, 2012), and used for the study. Acanthamoebae were isolated from the smear samples, and endosymbiotic chlamydial traits were assessed by infectivity, cytokine induction, and draft genomic analysis. From these, 23 amoebae were enriched on agar plates spread with heat-killed Escherichia coli. Amoeba prevalence was greater in the summer-collected samples (15/30, 50%) than those of the winter season (8/30, 26.7%), possibly indicating a seasonal variation (p = 0.096). Morphological assessment of cysts revealed 21 amoebae (21/23, 91%) to be Acanthamoeba, and cultures in PYG medium were established for 11 of these amoebae. Three amoebae contained environmental chlamydiae; however, only one amoeba (Acanthamoeba T4) with an environmental chlamydia (Protochlamydia W-9) was shown the infectious ability to Acanthamoeba C3 (reference amoebae). While Protochlamydia W-9 could infect C3 amoeba, it failed to replicate in immortal human epithelial, although exposure of HEp-2 cells to living bacteria induced the proinflammatory cytokine, IL-8. Comparative genome analysis with KEGG revealed similar genomic features compared with other Protochlamydia genomes (UWE25 and R18), except for a lack of genes encoding the type IV secretion system. Interestingly, resistance genes associated with several antibiotics and toxic compounds were identified. CONCLUSION These findings are the first demonstration of the distribution in a hospital of a living Acanthamoeba carrying an endosymbiotic chlamydial pathogen.
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Affiliation(s)
- Tatsuya Fukumoto
- Hokkaido University Hospital, Nishi-5 Kita-14 Jo, Kita-ku, Sapporo, Hokkaido 060-8648 Japan
| | - Junji Matsuo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University Graduate School of Health Sciences, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido 060-0812 Japan
| | - Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University Graduate School of Health Sciences, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido 060-0812 Japan
| | - Shinji Nakamura
- Division of Biomedical Imaging Research, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421 Japan
| | - Kentaro Miyamoto
- Miyarisan Pharmaceutical Co., Ltd., 2-3-13-209, Minami, Wako-shi, Saitama 351-0104 Japan
| | - Kentaro Oka
- Miyarisan Pharmaceutical Co., Ltd., 2-3-13-209, Minami, Wako-shi, Saitama 351-0104 Japan
| | - Motomichi Takahashi
- Miyarisan Pharmaceutical Co., Ltd., 2-3-13-209, Minami, Wako-shi, Saitama 351-0104 Japan
| | - Kouji Akizawa
- Hokkaido University Hospital, Nishi-5 Kita-14 Jo, Kita-ku, Sapporo, Hokkaido 060-8648 Japan
| | - Hitoshi Shibuya
- Hokkaido University Hospital, Nishi-5 Kita-14 Jo, Kita-ku, Sapporo, Hokkaido 060-8648 Japan
| | - Chikara Shimizu
- Hokkaido University Hospital, Nishi-5 Kita-14 Jo, Kita-ku, Sapporo, Hokkaido 060-8648 Japan
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University Graduate School of Health Sciences, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido 060-0812 Japan
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