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Shi L, Zhang Y, Zhan Y, Wang X, Xu J, Wang H, Zeng M, Lu Z. Genomic characteristics of antimicrobial resistance and virulence factors of carbapenem-resistant Stutzerimonas nitrititolerans isolated from the clinical specimen. BMC Microbiol 2024; 24:386. [PMID: 39358682 PMCID: PMC11448376 DOI: 10.1186/s12866-024-03546-4] [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: 10/26/2023] [Accepted: 09/24/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Stutzerimonas nitrititolerans (S. nitrititolerans) is a rare human pathogenic bacterium and has been inadequately explored at the genomic level. Here, we report the first case of carbapenem-resistant S. nitrititolerans isolated from the peritoneal dialysis fluid of a patient with chronic renal failure. This study analyzed the genomic features, antimicrobial resistance, and virulence factors of the isolated strain through whole genome sequencing (WGS). METHODS The bacterial isolate from the peritoneal dialysis fluid was named PDI170223, and preliminary identification was conducted through Matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI-TOF MS). WGS of the strain PDI170223 was performed using the Illumina platform, and a phylogenetic tree was constructed based on the 16S rRNA gene sequences. Antimicrobial susceptibility test (AST) was conducted using the TDR-200B2 automatic bacteria identification/drug sensitivity tester. RESULTS S. nitrititolerans may emerge as a human pathogen due to its numerous virulence genes, including those encoding toxins, and those involved in flagellum and biofilm formation. The AST results revealed that the strain is multidrug- and carbapenem-resistant. The antimicrobial resistance genes of S. nitrititolerans are complex and diverse, including efflux pump genes and β⁃lactam resistance genes. CONCLUSION The analysis of virulence factors and antimicrobial resistance of S. nitrititolerans provides clinical insight into the pathogenicity and potential risks of this bacterium. It is crucial to explore the mechanisms through which S. nitrititolerans causes diseases and maintains its antimicrobial resistance, thereby contributing to development of effective treatment and prevention strategies.
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Affiliation(s)
- Lifeng Shi
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingmiao Zhang
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Zhan
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiuling Wang
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Xu
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Hui Wang
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ming Zeng
- Hubei Center for Clinical Laboratory, Wuhan, China.
| | - Zhongxin Lu
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China.
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Tang R, Wang J, Zhan Y, Wu K, Wang H, Lu Z. Hemodialysis catheter-related infection caused by Pannonibacter phragmitetus: a rare case report in China. Front Cell Infect Microbiol 2022; 12:926154. [PMID: 35959368 PMCID: PMC9362148 DOI: 10.3389/fcimb.2022.926154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Pannonibacter phragmitetus (P. phragmitetus) is rarely related with human disease. We reported a case of catheter-related infection caused by P. phragmitetus in a 68-year-old woman on hemodialysis. The patient developed recurrent fever during hemodialysis and blood cultures were positive for P. phragmitetus. The patient’s body temperature returned to normal after intravenous cefoperazone/sulbactam treatment, and the hemodialysis catheter was locked with gentamicin and urokinase. The potential anti-infective treatment against P. phragmitetus was discussed.
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Affiliation(s)
- Ruizhi Tang
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Wang
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Zhan
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kaifu Wu
- Department of Radiology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Wang
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhongxin Lu
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Research Institute of Wuhan, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Zhongxin Lu,
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Gallardo A, Del Carmen Merino Bueno M, Merino CS, Laurés AMS, de la Torre-Fernández M, Álvarez ES. First case of bacteriemia caused by Pannonibacter phragmitetus in a haemodialysis patient. Nefrologia 2022; 42:209-210. [PMID: 36153918 DOI: 10.1016/j.nefroe.2020.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 08/19/2020] [Indexed: 06/16/2023] Open
Affiliation(s)
- Anna Gallardo
- Nefrología, Hospital San Agustín, Avilés, Asturias, Spain.
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Gallardo A, Merino Bueno MDC, Sango Merino C, Suárez Laurés AM, de la Torre-Fernández M, Sánchez Álvarez E. First case of bacteriemia caused by Pannonibacter phragmitetus in a haemodialysis patient. Nefrologia 2020; 42:S0211-6995(20)30183-1. [PMID: 33388179 DOI: 10.1016/j.nefro.2020.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 08/19/2020] [Indexed: 11/28/2022] Open
Affiliation(s)
- Anna Gallardo
- Nefrología, Hospital San Agustín, Avilés, Asturias. España.
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Koju R, Miao S, Liang B, Joshi DR, Bai Y, Liu R, Qu J. Transcriptional and metabolic response against hydroxyethane-(1,1-bisphosphonic acid) on bacterial denitrification by a halophilic Pannonibacter sp. strain DN. CHEMOSPHERE 2020; 252:126478. [PMID: 32197179 DOI: 10.1016/j.chemosphere.2020.126478] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 06/10/2023]
Abstract
Biological denitrification is an environmentally sound pathway for the elimination of nitrogen pollution in wastewater treatment. Extreme environmental conditions, such as the co-existence of toxic organic pollutants, can affect biological denitrification. However, the potential underlying mechanism remains largely unexplored. Herein, the effect of a model pollutant, hydroxyethane-(1,1-bisphosphonic acid) (HEDP), a widely applied and consumed bisphosphonate, on microbial denitrification was investigated by exploring the metabolic and transcriptional responses of an isolated denitrifier, Pannonibacter sp. strain DN. Results showed that nitrate removal efficiency decreased from 85% to 50% with an increase in HEDP concentration from 0 to 3.5 mM, leading to nitrite accumulation of 204 mg L-1 in 3.5 mM HEDP. This result was due to the lower bacterial population count and reduction in the live cell percentage. Further investigation revealed that HEDP caused a decrease in membrane potential from 0.080 ± 0.005 to 0.020 ± 0.002 with the increase in HEDP from 0 to 3.5 mM. This hindered electron transfer, which is required for nitrate transformation into nitrogen gas. Moreover, transcriptional profiling indicated that HEDP enhanced the genes involved in ROS (O2-) scavenging, thus protecting cells against oxidative stress damage. However, the suppression of genes responsible for the production of NADH/FADH2 in tricarboxylic acid cycle (TCA), NADH catalyzation (NADH dehydrogenase) in (electron transport chain) ETC system and denitrifying genes, especially nor and nir, in response to 2.5 mM HEDP were identified as the key factor inhibiting transfer of electron from TCA cycle to denitrifying enzymes through ETC system.
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Affiliation(s)
- Rashmi Koju
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiyu Miao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Liang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Dev Raj Joshi
- Central Department of Microbiology, Tribhuvan University, Kritipur, 44613, Nepal
| | - Yaohui Bai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Beijing, 100085, China.
| | - Ruiping Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Beijing, 100085, China
| | - Juihui Qu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Beijing, 100085, China
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Wang X, Zhu H, Shutes B, Fu B, Yan B, Yu X, Wen H, Chen X. Identification and denitrification characteristics of a salt-tolerant denitrifying bacterium Pannonibacter phragmitetus F1. AMB Express 2019; 9:193. [PMID: 31797109 PMCID: PMC6890923 DOI: 10.1186/s13568-019-0918-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 11/10/2022] Open
Abstract
A salt-tolerant denitrifying bacterium F1 was isolated in this study, which has high nitrite (NO2--N) and nitrate (NO3--N) removal abilities. The salt tolerance capacity of strain F1 was further verified and the effects of initial pH, initial NaNO2 concentration and inoculation size on the denitrification capacity of strain F1 under saline conditions were evaluated. Strain F1 was identified as Pannonibacter phragmitetus and named Pannonibacter phragmitetus F1. This strain can tolerate NaCl concentrations up to 70 g/L, and its most efficient denitrification capacity was observed at NaCl concentrations of 0-10 g/L. Under non-saline condition, the removal percentages of NO2--N and NO3--N by strain Pannonibacter phragmitetus F1 at pH of 10 and inoculation size of 5% were 100% and 83%, respectively, after cultivation for 5 days. Gas generation was observed during the cultivation, indicating that an efficient denitrification performance was achieved. When pH was 10 and the inoculation size was 5%, both the highest removal percentages of NO2--N (99%) and NO3--N (95%) by strain Pannonibacter phragmitetus F1 were observed at NaCl concentration of 10 g/L. When the NaCl concentration was 10 g/L, strain Pannonibacter phragmitetus F1 can adapt to a wide range of neutral and alkaline environments (pH of 7-10) and is highly tolerant of NaNO2 concentration (0.4-1.6 g/L). In conclusion, strain Pannonibacter phragmitetus F1 has a great potential to be applied in the treatment of saline wastewater containing high nitrogen concentrations, e.g. coastal aquaculture wastewater.
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Chai L, Ding C, Tang C, Yang W, Yang Z, Wang Y, Liao Q, Li J. Discerning three novel chromate reduce and transport genes of highly efficient Pannonibacter phragmitetus BB: From genome to gene and protein. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 162:139-146. [PMID: 29990725 DOI: 10.1016/j.ecoenv.2018.06.090] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 06/22/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
Here, Pannonibacter phragmitetus BB was investigated at genomic, genetic and protein levels to explore molecular mechanisms of chromium biotransformation, respectively. The results of Miseq sequencing uncovered that a high-qualified bacterial genome draft was achieved with 5.07 Mb in length. Three novel genes involved in chromate reduce and transport, named nitR, chrA1 and chrA2, were identified by alignment, annotation and phylogenetic tree analyses, which encode a chromate reductase (NitR) and two chromate transporters (ChrA1 and ChrA2). Reverse transcription real-time polymerase chain reaction (RT-qPCR) analyses showed that the relative quantitative transcription of the three genes as the maximum reduction rate of Cr(VI) were significantly up-regulated with the increasing initial Cr(VI) concentrations. However, at the maximum cell growth points nitR was in a low transcription level, while the transcription of chrA1 and chrA2 were hold at a relatively high level and decreased with the increasing initial Cr(VI) concentrations. The ex-situ chromate reducing activity of NitR was revealed a Vmax of 34.46 µmol/min/mg enzyme and Km of 14.55 µmol/L, suggesting feasibility of the reaction with Cr(VI) as substrate. The multiple alignment demonstrates that NitR is potentially a nicotinamide adenine dinucleotide phosphate (NADPH) dependent flavin mononucleotide (FMN) reductase of Class I chromate reductases. Our results will prompt a large-scaled bioremediation on the contaminated soils and water by Pannonibacter phragmitetus BB, taking advantage of uncovering its molecular mechanisms of chromium biotransformation.
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Affiliation(s)
- Liyuan Chai
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, 410083 Changsha, China
| | - Chunlian Ding
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China
| | - Chongjian Tang
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, 410083 Changsha, China
| | - Weichun Yang
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, 410083 Changsha, China
| | - Zhihui Yang
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, 410083 Changsha, China
| | - Yangyang Wang
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China; College of Environment and Planning, Henan University, 475004 Kaifeng, China
| | - Qi Liao
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, 410083 Changsha, China.
| | - Jiawei Li
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China
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Zhou Y, Jiang T, Hu S, Wang M, Ming D, Chen S. Genomic insights of Pannonibacter phragmitetus strain 31801 isolated from a patient with a liver abscess. Microbiologyopen 2017; 6. [PMID: 28857514 PMCID: PMC5727363 DOI: 10.1002/mbo3.515] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/04/2017] [Accepted: 06/13/2017] [Indexed: 12/22/2022] Open
Abstract
Pannonibacter phragmitetus is a bioremediation reagent for the detoxification of heavy metals and polycyclic aromatic compounds (PAHs) while it rarely infects healthy populations. However, infection by the opportunistic pathogen P. phragmitetus complicates diagnosis and treatments, and poses a serious threat to immunocompromised patients owing to its multidrug resistance. Unfortunately, genome features, antimicrobial resistance, and virulence potentials in P. phragmitetus have not been reported before. A predominant colony (31801) was isolated from a liver abscess patient, indicating that it accounted for the infection. To investigate its infection mechanism(s) in depth, we sequenced this bacterial genome and tested its antimicrobial resistance. Average nucleotide identity (ANI) analysis assigned the bacterium to the species P. phragmitetus (ANI, >95%). Comparative genomics analyses among Pannonibacter spp. representing the different living niches were used to describe the Pannonibacter pan‐genomes and to examine virulence factors, prophages, CRISPR arrays, and genomic islands. Pannonibacter phragmitetus 31801 consisted of one chromosome and one plasmid, while the plasmid was absent in other Pannonibacter isolates. Pannonibacter phragmitetus 31801 may have a great infection potential because a lot of genes encoding toxins, flagellum formation, iron uptake, and virulence factor secretion systems in its genome. Moreover, the genome has 24 genomic islands and 2 prophages. A combination of antimicrobial susceptibility tests and the detailed antibiotic resistance gene analysis provide useful information about the drug resistance mechanisms and therefore can be used to guide the treatment strategy for the bacterial infection.
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Affiliation(s)
- Yajun Zhou
- Yun Leung Laboratory for Molecular Diagnostics, School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Tao Jiang
- Yun Leung Laboratory for Molecular Diagnostics, School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Shaohua Hu
- Yun Leung Laboratory for Molecular Diagnostics, School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Mingxi Wang
- Yun Leung Laboratory for Molecular Diagnostics, School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China.,Institute of Nanomedicine Technology and Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, China
| | - Desong Ming
- Department of Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Fujian, China
| | - Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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