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Yi MH, Choi JH, Kim M, Chavarria X, Yun S, Oh S, Kang D, Yong TS, Kim JY. Microbiome of lovebug ( Plecia longiforceps) in Seoul, South Korea. Microbiol Spectr 2024; 12:e0380923. [PMID: 38809007 PMCID: PMC11218492 DOI: 10.1128/spectrum.03809-23] [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: 10/31/2023] [Accepted: 04/25/2024] [Indexed: 05/30/2024] Open
Abstract
Lovebugs appeared in large numbers across a wide area in Seoul, South Korea, in June 2023. The sudden appearance of exotic insects not only discomforts people but also fosters anxiety, as their potential for pathogen transmission would be unknown. In this study, targeted next-generation sequencing (NGS) of the 16S rRNA gene V4 region was performed using iSeq 100 to screen for bacteria in lovebugs. Forty-one lovebugs (20 females and 21 males) collected in Seoul, Korea, were identified as Plecia longiforceps based on mitochondrial cytochrome oxidase subunit 1 sequencing data using PCR. We analyzed the microbiome of the lovebugs and detected 453 species of bacteria. Among all bacteria screened based on NGS, Rickettsia was detected in all samples with an average relative abundance of 80.40%, followed by Pandoraea and Ewingella. Diversity (alpha and beta) between females and males did not differ; however, only Tumebacillus showed a higher relative abundance in females. Sequencing analysis of Rickettsia using a gltA gene-specific primer by PCR showed that it had higher sequence similarity to the Rickettsia symbiont of arthropods than to the spotted fever group rickettsiae. Eleven samples in which Pandoraea was detected by iSeq 100 were confirmed by PCR and exhibited 100% sequence identity to Pandoraea oxalativorans strain DSM 23570. Consequently, the likelihood of pathogen transmission to humans is low. The applied method may play a crucial role in swiftly identifying bacterial species in the event of future outbreaks of exotic insects that may be harmful to humans.IMPORTANCELovebugs have recently emerged in large numbers in Seoul, causing major concern regarding potential health risks. By performing the next-generation sequencing of the 16S rRNA gene V4 region, we comprehensively examined the microbiome of these insects. We identified the presence of numerous bacteria, including Rickettsia and Pandoraea. Reassuringly, subsequent tests confirmed that these detected bacteria were not pathogenic. The present study addresses health concerns related to lovebugs and shows the accuracy and efficiency of our detection technique. Such methods prove invaluable for rapidly identifying bacterial species during potential outbreaks of unfamiliar insects, thereby ensuring public safety.
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Affiliation(s)
- Myung-Hee Yi
- Department of Tropical Medicine, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, South Korea
| | - Jun Ho Choi
- Department of Tropical Medicine, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, South Korea
| | - Myungjun Kim
- Department of Tropical Medicine, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, South Korea
| | - Xavier Chavarria
- Department of Tropical Medicine, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, South Korea
| | - Sohyeon Yun
- Department of Tropical Medicine, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, South Korea
| | - Singeun Oh
- Department of Tropical Medicine, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, South Korea
| | - Dongjun Kang
- Department of Tropical Medicine, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, South Korea
| | - Tai-Soon Yong
- Department of Tropical Medicine, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, South Korea
| | - Ju Yeong Kim
- Department of Tropical Medicine, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, South Korea
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2
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Gao RF, Wang Y, Wang Y, Wang ZW, Zhang GM. Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristics. PLoS One 2022; 17:e0272435. [PMID: 35930552 PMCID: PMC9355198 DOI: 10.1371/journal.pone.0272435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
In this study, we sequenced a bacteria isolate Pandoraea sp. 892iso isolated from a Phytophthora rubi strain which is an important plant pathogenic oomycete, identified through genome and combined the data with existing genomic data from other 28 the genus of Pandoraea species. Next, we conducted a comparative genomic analysis of the genome structure, evolutionary relationships, and pathogenic characteristics of Pandoraea species. Our results identified Pandoraea sp. 892iso as Pandoraea sputorum at both the genome and gene levels. At the genome level, we carried out phylogenetic analysis of single-copy, gene co-linearity, ANI (average nucleotide identity) and AAI (average amino acid identity) indices, rpoB similarity, MLSA phylogenetic analysis, and genome-to-genome distance calculator calculations to identify the relationship between Pandoraea sp. 892iso and P. sputorum. At the gene level, the quorum sensing genes ppnI and ppnR and the OXA-159 gene were assessed. It is speculated that Pandoraea sp. 892iso is the endosymbiont of the Oomycetes strain of Phytophthora rubi.
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Affiliation(s)
- Rui-Fang Gao
- Animal & Plant Inspection and Quarantine Technology Center of Shenzhen Customs District P.R. China, Shenzhen, China
- Shenzhen Key Laboratory for Research & Development on Detection Technology of Alien Pests, Shenzhen Academy of Inspection and Quarantine, Shenzhen, China
- * E-mail:
| | - Ying Wang
- Animal & Plant Inspection and Quarantine Technology Center of Shenzhen Customs District P.R. China, Shenzhen, China
- Shenzhen Key Laboratory for Research & Development on Detection Technology of Alien Pests, Shenzhen Academy of Inspection and Quarantine, Shenzhen, China
| | - Ying Wang
- Animal & Plant Inspection and Quarantine Technology Center of Shenzhen Customs District P.R. China, Shenzhen, China
- Shenzhen Key Laboratory for Research & Development on Detection Technology of Alien Pests, Shenzhen Academy of Inspection and Quarantine, Shenzhen, China
| | | | - Gui-Ming Zhang
- Animal & Plant Inspection and Quarantine Technology Center of Shenzhen Customs District P.R. China, Shenzhen, China
- Shenzhen Key Laboratory for Research & Development on Detection Technology of Alien Pests, Shenzhen Academy of Inspection and Quarantine, Shenzhen, China
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3
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Singh S, Sahu C, Patel SS, Garg A, Ghoshal U. Pandoraea apista Bacteremia in a COVID-Positive Man: A Rare Coinfection Case Report from North India. J Lab Physicians 2021; 13:192-194. [PMID: 34483568 PMCID: PMC8409125 DOI: 10.1055/s-0041-1730847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pandoraea apista
is a novel gram-negative bacillus usually isolated from respiratory specimens of cystic fibrosis patients. Few cases of bacteremia have also been reported due to this rare pathogen. Emergence of multidrug-resistant isolates of this bacillus is of grave concern. Here, we report a very interesting and unusual case of
Pandoraea apista
bacteremia in a coronavirus disease (COVID)–positive elderly diabetic man suffering from pneumonia. Prompt isolation and antibiotic sensitivity testing guided the patient’s treatment and yielded favorable outcome. The need of automated methods for identification and sensitivity testing limits the reporting of this rare but important pathogen in hospital settings. Detailed research work and studies are needed in this direction to better understand this pathogen and its clinical manifestations for better patient outcome.
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Affiliation(s)
- Sweta Singh
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Chinmoy Sahu
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Sangram Singh Patel
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Atul Garg
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Ujjala Ghoshal
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
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Bayjanov JR, Ekkelenkamp MB, Rogers MR, Cantón R, Benaissa-Trouw BJ, Díez-Aguilar M, Tunney M, Fluit AC. Whole-genome analysis of Pandoraea species strains from cystic fibrosis patients. Future Microbiol 2019; 14:1357-1367. [PMID: 31762328 DOI: 10.2217/fmb-2019-0038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Aim: Genetic characterization of Pandoraea strains recovered from cystic fibrosis patients. Materials & methods: The whole-genome sequence of 12 Pandoraea strains was determined using Illumina technology. The position of the strains within the genus Pandoraea was analyzed using selected partial gene sequences, core genome multi-locus sequence typing and average nucleotide identity analysis. Furthermore, the sequences were annotated. Results: The results show that some strains previously identified as Pandoraea pnomenusa, Pandoraea sputorum, Pandoraea oxalativorans and Pandoraea pulmonicola belong to novel species. The strains did not harbor acquired antibiotic resistance genes but encoded an OXA-type ß-lactamase. Conclusion: The taxonomy of the genus Pandoraea needs to be revised.
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Affiliation(s)
- Jumamurat R Bayjanov
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Miquel B Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Malbert Rc Rogers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal & Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Barry J Benaissa-Trouw
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - María Díez-Aguilar
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal & Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Michael Tunney
- Department of Pulmonology, Queen's University Belfast, Northern Ireland, UK
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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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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6
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Lin C, Luo N, Xu Q, Zhang J, Cai M, Zheng G, Yang P. Pneumonia due to Pandoraea Apista after evacuation of traumatic intracranial hematomas:a case report and literature review. BMC Infect Dis 2019; 19:869. [PMID: 31640582 PMCID: PMC6805617 DOI: 10.1186/s12879-019-4420-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/28/2019] [Indexed: 11/21/2022] Open
Abstract
Background Pandoraea species is a newly described genus, which is multidrug resistant and difficult to identify. Clinical isolates are mostly cultured from cystic fibrosis (CF) patients. CF is a rare disease in China, which makes Pandoraea a total stranger to Chinese physicians. Pandoraea genus is reported as an emerging pathogen in CF patients in most cases. However, there are few pieces of evidence that confirm Pandoraea can be more virulent in non-CF patients. The pathogenicity of Pandoraea genus is poorly understood, as well as its treatment. The incidence of Pandoraea induced infection in non-CF patients may be underestimated and it’s important to identify and understand these organisms. Case presentation We report a 44-years-old man who suffered from pneumonia and died eventually. Before his condition deteriorated, a Gram-negative bacilli was cultured from his sputum and identified as Pandoraea Apista by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS). Conclusion Pandoraea spp. is an emerging opportunistic pathogen. The incidences of Pandoraea related infection in non-CF patients may be underestimated due to the difficulty of identification. All strains of Pandoraea show multi-drug resistance and highly variable susceptibility. To better treatment, species-level identification and antibiotic susceptibility test are necessary.
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Affiliation(s)
- Chuanzhong Lin
- Department of Pharmacy, Huadu District People's Hospital of Guangzhou, Southern Medical University, Guangzhou, China.,Department of Pharmacy, The First Affiliated Hospital of Medicine School, Zhejiang University, Hangzhou, China
| | - Ning Luo
- Department of Pharmacy, Huadu District People's Hospital of Guangzhou, Southern Medical University, Guangzhou, China
| | - Qiang Xu
- Department of Pharmacy, The First Affiliated Hospital of Medicine School, Zhejiang University, Hangzhou, China
| | - Jianjun Zhang
- Department of Pharmacy, Zhejiang provincial hospital of TCM, Hangzhou, China
| | - Mengting Cai
- Department of Pharmacy, Meizhou People's Hospital, Meizhou, China
| | - Guanhao Zheng
- Department of Pharmacy, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Ping Yang
- Department of Pharmacy, The First Affiliated Hospital of Medicine School, Zhejiang University, Hangzhou, China.
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Host-symbiont specificity determined by microbe-microbe competition in an insect gut. Proc Natl Acad Sci U S A 2019; 116:22673-22682. [PMID: 31636183 DOI: 10.1073/pnas.1912397116] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Despite the omnipresence of specific host-symbiont associations with acquisition of the microbial symbiont from the environment, little is known about how the specificity of the interaction evolved and is maintained. The bean bug Riptortus pedestris acquires a specific bacterial symbiont of the genus Burkholderia from environmental soil and harbors it in midgut crypts. The genus Burkholderia consists of over 100 species, showing ecologically diverse lifestyles, and including serious human pathogens, plant pathogens, and nodule-forming plant mutualists, as well as insect mutualists. Through infection tests of 34 Burkholderia species and 18 taxonomically diverse bacterial species, we demonstrate here that nonsymbiotic Burkholderia and even its outgroup Pandoraea could stably colonize the gut symbiotic organ and provide beneficial effects to the bean bug when inoculated on aposymbiotic hosts. However, coinoculation revealed that the native symbiont always outcompeted the nonnative bacteria inside the gut symbiotic organ, explaining the predominance of the native Burkholderia symbiont in natural bean bug populations. Hence, the abilities for colonization and cooperation, usually thought of as specific traits of mutualists, are not unique to the native Burkholderia symbiont but, to the contrary, competitiveness inside the gut is a derived trait of the native symbiont lineage only and was thus critical in the evolution of the insect gut symbiont.
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Tabatabaei M, Dastbarsar M, Moslehi MA. Isolation and identification of Pandoraea spp. From bronchoalveolar lavage of cystic fibrosis patients in Iran. Ital J Pediatr 2019; 45:118. [PMID: 31477148 PMCID: PMC6720371 DOI: 10.1186/s13052-019-0687-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 07/23/2019] [Indexed: 01/17/2023] Open
Abstract
Background Pandoraea species are gram negative, motile, non-spore forming, rod shaped and oxidase positive, obligate aerobes bacteria, and have one polar flagellum. Most of Pandoraea species are associated with lung infections in cystic fibrosis patients. Cystic fibrosis is the most prevalent autosomal recessive hereditary disease in the world that affects various organs of the body. The main important cause of death in these patients is lung involvement. This study was conducted to isolate and identify Pandoraea bacterium from bronchoalveolar lavage and sputum samples of cystic fibrosis patients in Shiraz, Iran. Methods In this research 31 samples of bronchoalveolar lavage and sputum were examined by culture and PCR method. Then confirmed isolates were evaluated for susceptibility to different antibiotics and ability to produce biofilm. Results The results of this study after cultivation, purification and DNA extraction led to the isolation of 4 Pandoraea bacterium by PCR using specific primers. Antibiotic susceptibility test were indicated all isolates were resistant to gentamicin, amikacin and imipenem and susceptible to ciprofloxacin, trimethoprim-sulfumethoxazole, piperacillin and tetracycline. Ability to create biofilm was indicated by some of Pandoraea isolates. According to findings of this study, ability to synthesis biofilm by Pandoraea isolates and resistance to some antibiotics are very important. Conclusions Our study notes the role of P. pnomenusa as an emerging pathogen that can cause chronic lung colonization in CF patients. Identification tools need to be accurate and must be based on molecular techniques. Also our findings should raise awareness about antibiotic resistance in cystic fibrosis patients in Iran and ability of including bacterial agents to produce biofilm is an alarm for public health. Thus clinicians should exercise caution about finding of clinical relevance of this pathogen to the infection and prescribing antibiotics, especially in cases of children infections.
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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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See-Too WS, Ambrose M, Malley R, Ee R, Mulcahy E, Manche E, Lazenby J, McEwan B, Pagnon J, Chen JW, Chan KG, Turnbull L, Whitchurch CB, Roddam LF. Pandoraea fibrosis sp. nov., a novel Pandoraea species isolated from clinical respiratory samples. Int J Syst Evol Microbiol 2019; 69:645-651. [DOI: 10.1099/ijsem.0.003147] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wah Seng See-Too
- 1Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Mark Ambrose
- 2School of Medicine, Faculty of Health, University of Tasmania, Tasmania 7001, Australia
| | - Roslyn Malley
- 2School of Medicine, Faculty of Health, University of Tasmania, Tasmania 7001, Australia
- 3Department of Pathology, Royal Hobart Hospital, Tasmania 7001, Australia
| | - Robson Ee
- 1Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Emily Mulcahy
- 2School of Medicine, Faculty of Health, University of Tasmania, Tasmania 7001, Australia
- 3Department of Pathology, Royal Hobart Hospital, Tasmania 7001, Australia
| | - Emily Manche
- 2School of Medicine, Faculty of Health, University of Tasmania, Tasmania 7001, Australia
| | - James Lazenby
- 4The ithree Institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Belinda McEwan
- 5Department of Microbiology and Infectious Disease, Royal Hobart Hospital, Tasmania 7001, Australia
| | - Joanne Pagnon
- 2School of Medicine, Faculty of Health, University of Tasmania, Tasmania 7001, Australia
| | - Jian Woon Chen
- 1Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Kok Gan Chan
- 1Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
- 6International Genome Centre, Jiangsu University, Zhenjiang, PR China
| | - Lynne Turnbull
- 4The ithree Institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Cynthia B. Whitchurch
- 4The ithree Institute, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Louise F. Roddam
- 2School of Medicine, Faculty of Health, University of Tasmania, Tasmania 7001, Australia
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Chen WM, Xie PB, Hsu MY, Sheu SY. Parvibium lacunae gen. nov., sp. nov., a new member of the family Alcaligenaceae isolated from a freshwater pond. Int J Syst Evol Microbiol 2018; 68:1291-1299. [PMID: 29498621 DOI: 10.1099/ijsem.0.002667] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated KMB9T was isolated from a freshwater pond in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain KMB9T were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, motile by means of a monopolar flagellum, non-spore-forming and rods surrounded by a thick capsule and forming white-coloured colonies. Growth occurred at 20-40 °C (optimum, 25-37 °C), at pH 6.5-7.5 (optimum, pH 7.0) and with 0-0.5 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene and four housekeeping gene sequences (recA, rpoA, rpoB and atpD) showed that strain KMB9T forms a distinct phyletic line within the family Alcaligenaceae, and the levels of 16S rRNA gene sequence similarity to its closest relatives with validly published names were less than 93.3 %. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8. The major polyamine was putrescine. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and several uncharacterized aminophospholipids, aminolipids, phospholipids and lipids. The genomic DNA G+C content of strain KMB9T was 54.5 mol%. On the basis of the genotypic and phenotypic data, strain KMB9T represents a novel species of a new genus in the family Alcaligenaceae, for which the name Parvibium lacunae gen. nov., sp. nov. is proposed. The type strain is KMB9T (=BCRC 81053T=LMG 30055T=KCTC 52814T).
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Affiliation(s)
- Wen-Ming Chen
- Department of Seafood Science, Laboratory of Microbiology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Pei-Bei Xie
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Ming-Yuan Hsu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
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Kostygov AY, Butenko A, Nenarokova A, Tashyreva D, Flegontov P, Lukeš J, Yurchenko V. Genome of Ca. Pandoraea novymonadis, an Endosymbiotic Bacterium of the Trypanosomatid Novymonas esmeraldas. Front Microbiol 2017; 8:1940. [PMID: 29046673 PMCID: PMC5632650 DOI: 10.3389/fmicb.2017.01940] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/21/2017] [Indexed: 12/22/2022] Open
Abstract
We have sequenced, annotated, and analyzed the genome of Ca. Pandoraea novymonadis, a recently described bacterial endosymbiont of the trypanosomatid Novymonas esmeraldas. When compared with genomes of its free-living relatives, it has all the hallmarks of the endosymbionts’ genomes, such as significantly reduced size, extensive gene loss, low GC content, numerous gene rearrangements, and low codon usage bias. In addition, Ca. P. novymonadis lacks mobile elements, has a strikingly low number of pseudogenes, and almost all genes are single copied. This suggests that it already passed the intensive period of host adaptation, which still can be observed in the genome of Polynucleobacter necessarius, a certainly recent endosymbiont. Phylogenetically, Ca. P. novymonadis is more related to P. necessarius, an intracytoplasmic bacterium of free-living ciliates, than to Ca. Kinetoplastibacterium spp., the only other known endosymbionts of trypanosomatid flagellates. As judged by the extent of the overall genome reduction and the loss of particular metabolic abilities correlating with the increasing dependence of the symbiont on its host, Ca. P. novymonadis occupies an intermediate position P. necessarius and Ca. Kinetoplastibacterium spp. We conclude that the relationships between Ca. P. novymonadis and N. esmeraldas are well-established, although not as fine-tuned as in the case of Strigomonadinae and their endosymbionts.
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Affiliation(s)
- Alexei Y Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia.,Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia.,Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czechia
| | - Anna Nenarokova
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czechia.,Faculty of Sciences, University of South Bohemia, České Budějovice, Czechia
| | - Daria Tashyreva
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czechia
| | - Pavel Flegontov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia.,Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czechia.,Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czechia.,Faculty of Sciences, University of South Bohemia, České Budějovice, Czechia
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia.,Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czechia.,Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czechia
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