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Zhang S, Yang W, Xie Y, Zhao X, Chen H, Zhang L, Lin X. Quantitative proteomics investigating the intrinsic adaptation mechanism of Aeromonas hydrophila to streptomycin. Proteomics 2024; 24:e2300383. [PMID: 38700048 DOI: 10.1002/pmic.202300383] [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: 10/03/2023] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/05/2024]
Abstract
Aeromonas hydrophila, a prevalent pathogen in the aquaculture industry, poses significant challenges due to its drug-resistant strains. Moreover, residues of antibiotics like streptomycin, extensively employed in aquaculture settings, drive selective bacterial evolution, leading to the progressive development of resistance to this agent. However, the underlying mechanism of its intrinsic adaptation to antibiotics remains elusive. Here, we employed a quantitative proteomics approach to investigate the differences in protein expression between A. hydrophila under streptomycin (SM) stress and nonstress conditions. Notably, bioinformatics analysis unveiled the potential involvement of metal pathways, including metal cluster binding, iron-sulfur cluster binding, and transition metal ion binding, in influencing A. hydrophila's resistance to SM. Furthermore, we evaluated the sensitivity of eight gene deletion strains related to streptomycin and observed the potential roles of petA and AHA_4705 in SM resistance. Collectively, our findings enhance the understanding of A. hydrophila's response behavior to streptomycin stress and shed light on its intrinsic adaptation mechanism.
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Affiliation(s)
- Shuangziying Zhang
- College of JunCao Science and Ecology, School of Life Sciences, (Fujian Agriculture and Forestry University), Fuzhou, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, Fujian, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wenxiao Yang
- College of JunCao Science and Ecology, School of Life Sciences, (Fujian Agriculture and Forestry University), Fuzhou, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, Fujian, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuyue Xie
- College of JunCao Science and Ecology, School of Life Sciences, (Fujian Agriculture and Forestry University), Fuzhou, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, Fujian, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xinrui Zhao
- College of JunCao Science and Ecology, School of Life Sciences, (Fujian Agriculture and Forestry University), Fuzhou, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, Fujian, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Haoyu Chen
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, Fujian, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Lishan Zhang
- College of JunCao Science and Ecology, School of Life Sciences, (Fujian Agriculture and Forestry University), Fuzhou, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, Fujian, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiangmin Lin
- College of JunCao Science and Ecology, School of Life Sciences, (Fujian Agriculture and Forestry University), Fuzhou, Fujian, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, Fujian, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Kong Y, Jin P, Jia C, Qiao P, Zhang H, Dong Y, Yang Z, Zhou Y, Jung G, Hu J. A rapid real-time PCR assay for detecting Microdochium paspali causing sparse leaf patch on seashore paspalum and in environmental samples. PEST MANAGEMENT SCIENCE 2024. [PMID: 39300697 DOI: 10.1002/ps.8422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/29/2024] [Accepted: 09/05/2024] [Indexed: 09/22/2024]
Abstract
BACKGROUND Sparse leaf patch (SLP) is one of the most significant diseases affecting seashore paspalum (Paspalum vaginatum Sw.), caused by Microdochium paspali. Fast and accurate detection of this pathogen is crucial for effective disease management. However, conventional culture-based methods are time-consuming and often compromised by the presence of other saprophytic or endophytic fungi. RESULTS In this study, we developed a real-time fluorescent quantitative (q)PCR method based on the internal transcribed spacer (ITS) region of the ribosomal RNA gene to rapidly detect and quantify M. paspali. The qPCR assay demonstrated the ability to detect all 12 tested isolates of M. paspali, with no cross-reactions observed when tested against 30 isolates of other fungal pathogens from turfgrass samples. The detection limit of the qPCR method was as low as 3.65 × 102 copies μL-1 of M. paspali genomic DNA, and the entire detection process could be completed within 1 h. The fluorescence signal was detectable in the leaf tissues of seashore paspalum without apparent disease symptoms as early as 24 h postinoculation with M. paspali. Moreover, the qPCR method successfully detected M. paspali in both asymptomatic and symptomatic turfgrass samples, including leaf, stem, root and rhizosphere soil, indicating that this assay can significantly enhance the detection of M. paspali. CONCLUSION The study developed a rapid real-time qPCR assay for the detection of M. paspali causing SLP on seashore paspalum and in environmental samples, which has important implications for early warning and management of SLP. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Yixuan Kong
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Peiyuan Jin
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Chenchen Jia
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Panpan Qiao
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Huangwei Zhang
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Yinglu Dong
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Zhimin Yang
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Yuxin Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Geunhwa Jung
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, USA
| | - Jian Hu
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
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Marmitt M, Cauduro GP, Sbruzzi RC, Valiati VH. Evaluation of Differentially Expressed Candidate Genes in Benzo[a]pyrene Degradation by Burkholderia vietnamiensis G4. Mol Biotechnol 2024:10.1007/s12033-024-01284-6. [PMID: 39298104 DOI: 10.1007/s12033-024-01284-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/09/2024] [Indexed: 09/21/2024]
Abstract
Bacteria-mediated bioremediation is widely employed for its environmental benefits. The genus Burkholderia can degrade persistent organic compounds, however, little is known about its mechanisms. To increase this knowledge, Burkholderia vietnamiensis G4 bacteria were exposed to benzo[a]pyrene, a recalcitrant compound, and the expression of twelve genes of interest was analyzed at 1, 12 and 24 h. In addition, benzo[a]pyrene degradation, evaluation of cell viability and fluorescence emission of assimilated benzo[a]pyrene was performed over 28 days. The up-regulated genes were xre, paaE, livG and pckA at the three times, ACAD, atoB, bmoA and proV at 1 h and AstB at 12 h. These genes are important for bacterial survival in stress situations, breakdown and metabolization of organic compounds, and nutrient transport and uptake. Furthermore, a 52% reduction of the pollutant was observed, there was no significant variation in the viability rate of the cells, and fluorescence indicated an accumulation of benzo[a]pyrene after 24 h. Our study demonstrates the bacteria adaptability and ability to modulate the expression of genes at different times and as needed. This increases our understanding of biodegradation processes and opens new possibilities for using this bacterial strain as a tool for the bioremediation of contaminated areas.
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Affiliation(s)
- Marcela Marmitt
- Laboratory of Genetics and Molecular Biology, University of Vale Do Rio Dos Sinos, São Leopoldo, Rio Grande Do Sul, Brazil
| | - Guilherme Pinto Cauduro
- Laboratory of Genetics and Molecular Biology, University of Vale Do Rio Dos Sinos, São Leopoldo, Rio Grande Do Sul, Brazil
| | - Renan César Sbruzzi
- Laboratory of Genetics and Molecular Biology, University of Vale Do Rio Dos Sinos, São Leopoldo, Rio Grande Do Sul, Brazil
- Laboratory of Immunogenetics, Federal University of Rio Grande Do Sul, Porto Alegre, Rio Grande Do Sul, Brazil
| | - Victor Hugo Valiati
- Laboratory of Genetics and Molecular Biology, University of Vale Do Rio Dos Sinos, São Leopoldo, Rio Grande Do Sul, Brazil.
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Yu Q, Li H, Du L, Shen L, Zhang J, Yuan L, Yao H, Xiao H, Bai Q, Jia Y, Qiu J, Li Y. Transcriptional regulation of the yersiniabactin receptor fyuA gene by the ferric uptake regulator in Klebsiella pneumoniae NTUH-K2044. J Basic Microbiol 2024; 64:e2400001. [PMID: 38679904 DOI: 10.1002/jobm.202400001] [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: 01/03/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 05/01/2024]
Abstract
The ferric uptake regulator (Fur) is a global regulator that influences the expression of virulence genes in Klebsiella pneumoniae. Bioinformatics analysis suggests Fur may involve in iron acquisition via the identified regulatory box upstream of the yersiniabactin receptor gene fyuA. To observe the impact of the gene fyuA on the virulence of K. pneumoniae, the gene fyuA knockout strain and complementation strain were constructed and then conducted a series of phenotypic experiments including chrome azurol S (CAS) detection, crystal violet staining, and wax moth virulence experiment. To examine the regulatory relationship between Fur and the gene fyuA, green fluorescent protein (GFP) reporter gene fusion assay, real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR), gel migration assay (EMSA), and DNase I footprinting assay were used to clarify the regulatory mechanism of Fur on fyuA. CAS detection revealed that the gene fyuA could affect the generation of iron carriers in K. pneumoniae. Crystal violet staining experiment showed that fyuA could positively influence biofilm formation. Wax moth virulence experiment indicated that the deletion of the fyuA could weaken bacterial virulence. GFP reporter gene fusion experiment and RT-qPCR analysis revealed that Fur negatively regulated the expression of fyuA in iron-sufficient environment. EMSA experiment demonstrated that Fur could directly bind to the promoter region of fyuA, and DNase I footprinting assay further identified the specific binding site sequences. The study showed that Fur negatively regulated the transcriptional expression of fyuA by binding to upstream of the gene promoter region, and then affected the virulence of K. pneumoniae.
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Affiliation(s)
- Qian Yu
- School of Public Health, Chongqing Medical University, Chongqing, China
| | - Hailin Li
- School of Public Health, Chongqing Medical University, Chongqing, China
| | - Ling Du
- Chengdu Center for Disease Control and Prevention, Chengdu, Sichuan, China
| | - Lifei Shen
- Jiangbei District Center for Disease Control and Prevention, Jiangbei, Chongqing, China
| | - Jiaxue Zhang
- Jiangbei District Center for Disease Control and Prevention, Jiangbei, Chongqing, China
| | - Lingyue Yuan
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Huang Yao
- School of Public Health, Chongqing Medical University, Chongqing, China
| | - Hong Xiao
- School of Public Health, Chongqing Medical University, Chongqing, China
| | - Qunhua Bai
- School of Public Health, Chongqing Medical University, Chongqing, China
| | - Yan Jia
- School of Public Health, Chongqing Medical University, Chongqing, China
| | - Jingfu Qiu
- School of Public Health, Chongqing Medical University, Chongqing, China
| | - Yingli Li
- School of Public Health, Chongqing Medical University, Chongqing, China
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Muner JJ, de Oliveira PAA, Baboghlian J, Moura SC, de Andrade AG, de Oliveira MM, Campos YFD, Mançano ASF, Siqueira NMG, Pacheco T, Ferraz LFC. The transcriptional regulator Fur modulates the expression of uge, a gene essential for the core lipopolysaccharide biosynthesis in Klebsiella pneumoniae. BMC Microbiol 2024; 24:279. [PMID: 39061004 PMCID: PMC11282780 DOI: 10.1186/s12866-024-03418-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a Gram-negative pathogen that has become a threat to public health worldwide due to the emergence of hypervirulent and multidrug-resistant strains. Cell-surface components, such as polysaccharide capsules, fimbriae, and lipopolysaccharides (LPS), are among the major virulence factors for K. pneumoniae. One of the genes involved in LPS biosynthesis is the uge gene, which encodes the uridine diphosphate galacturonate 4-epimerase enzyme. Although essential for the LPS formation in K. pneumoniae, little is known about the mechanisms that regulate the expression of uge. Ferric uptake regulator (Fur) is an iron-responsive transcription factor that modulates the expression of capsular and fimbrial genes, but its role in LPS expression has not yet been identified. This work aimed to investigate the role of the Fur regulator in the expression of the K. pneumoniae uge gene and to determine whether the production of LPS by K. pneumoniae is modulated by the iron levels available to the bacterium. RESULTS Using bioinformatic analyses, a Fur-binding site was identified on the promoter region of the uge gene; this binding site was validated experimentally through Fur Titration Assay (FURTA) and DNA Electrophoretic Mobility Shift Assay (EMSA) techniques. RT-qPCR analyses were used to evaluate the expression of uge according to the iron levels available to the bacterium. The iron-rich condition led to a down-regulation of uge, while the iron-restricted condition resulted in up-regulation. In addition, LPS was extracted and quantified on K. pneumoniae cells subjected to iron-replete and iron-limited conditions. The iron-limited condition increased the amount of LPS produced by K. pneumoniae. Finally, the expression levels of uge and the amount of the LPS were evaluated on a K. pneumoniae strain mutant for the fur gene. Compared to the wild-type, the strain with the fur gene knocked out presented a lower LPS amount and an unchanged expression of uge, regardless of the iron levels. CONCLUSIONS Here, we show that iron deprivation led the K. pneumoniae cells to produce higher amount of LPS and that the Fur regulator modulates the expression of uge, a gene essential for LPS biosynthesis. Thus, our results indicate that iron availability modulates the LPS biosynthesis in K. pneumoniae through a Fur-dependent mechanism.
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Affiliation(s)
- José Júlio Muner
- Laboratório de Microbiologia Molecular e Clínica, Universidade São Francisco, Bragança Paulista, SP, Brazil
| | - Paloma Aparecida Alves de Oliveira
- Laboratório de Microbiologia Molecular e Clínica, Universidade São Francisco, Bragança Paulista, SP, Brazil
- Central Multiusuária de Análises Genômica e Transcriptômica (CmAGT), Universidade São Francisco, Bragança Paulista, SP, Brazil
| | - Juliana Baboghlian
- Laboratório de Microbiologia Molecular e Clínica, Universidade São Francisco, Bragança Paulista, SP, Brazil
| | - Stefany Casarin Moura
- Laboratório de Microbiologia Molecular e Clínica, Universidade São Francisco, Bragança Paulista, SP, Brazil
| | | | | | - Yasmin Ferreira de Campos
- Laboratório de Microbiologia Molecular e Clínica, Universidade São Francisco, Bragança Paulista, SP, Brazil
| | | | | | - Thaisy Pacheco
- Laboratório de Microbiologia Molecular e Clínica, Universidade São Francisco, Bragança Paulista, SP, Brazil
| | - Lúcio Fábio Caldas Ferraz
- Laboratório de Microbiologia Molecular e Clínica, Universidade São Francisco, Bragança Paulista, SP, Brazil.
- Central Multiusuária de Análises Genômica e Transcriptômica (CmAGT), Universidade São Francisco, Bragança Paulista, SP, Brazil.
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Liu GL, Wu SL, Sun Z, Xing MD, Chi ZM, Liu YJ. ι-Carrageenan catabolism is initiated by key sulfatases in the marine bacterium Pseudoalteromonas haloplanktis LL1. Appl Environ Microbiol 2024; 90:e0025524. [PMID: 38874338 PMCID: PMC11267874 DOI: 10.1128/aem.00255-24] [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: 02/13/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024] Open
Abstract
Marine bacteria contribute substantially to cycle macroalgae polysaccharides in marine environments. Carrageenans are the primary cell wall polysaccharides of red macroalgae. The carrageenan catabolism mechanism and pathways are still largely unclear. Pseudoalteromonas is a representative bacterial genus that can utilize carrageenan. We previously isolated the strain Pseudoalteromonas haloplanktis LL1 that could grow on ι-carrageenan but produce no ι-carrageenase. Here, through a combination of bioinformatic, biochemical, and genetic analyses, we determined that P. haloplanktis LL1 processed a desulfurization-depolymerization sequential pathway for ι-carrageenan utilization, which was initiated by key sulfatases PhSulf1 and PhSulf2. PhSulf2 acted as an endo/exo-G4S (4-O-sulfation-β-D-galactopyranose) sulfatase, while PhSulf1 was identified as a novel endo-DA2S sulfatase that could function extracellularly. Because of the unique activity of PhSulf1 toward ι-carrageenan rather than oligosaccharides, P. haloplanktis LL1 was considered to have a distinct ι-carrageenan catabolic pathway compared to other known ι-carrageenan-degrading bacteria, which mainly employ multifunctional G4S sulfatases and exo-DA2S (2-O-sulfation-3,6-anhydro-α-D-galactopyranose) sulfatase for sulfate removal. Furthermore, we detected widespread occurrence of PhSulf1-encoding gene homologs in the global ocean, indicating the prevalence of such endo-acting DA2S sulfatases as well as the related ι-carrageenan catabolism pathway. This research provides valuable insights into the enzymatic processes involved in carrageenan catabolism within marine ecological systems.IMPORTANCECarrageenan is a type of linear sulfated polysaccharide that plays a significant role in forming cell walls of marine algae and is found extensively distributed throughout the world's oceans. To the best of our current knowledge, the ι-carrageenan catabolism in marine bacteria either follows the depolymerization-desulfurization sequential process initiated by ι-carrageenase or starts from the desulfurization step catalyzed by exo-acting sulfatases. In this study, we found that the marine bacterium Pseudoalteromonas haloplanktis LL1 processes a distinct pathway for ι-carrageenan catabolism employing a specific endo-acting DA2S-sulfatase PhSulf1 and a multifunctional G4S sulfatase PhSulf2. The unique PhSulf1 homologs appear to be widely present on a global scale, indicating the indispensable contribution of the marine bacteria containing the distinct ι-carrageenan catabolism pathway. Therefore, this study would significantly enrich our understanding of the molecular mechanisms underlying carrageenan utilization, providing valuable insights into the intricate roles of marine bacteria in polysaccharide cycling in marine environments.
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Affiliation(s)
- Guang-Lei Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- MOE Key Laboratory of Evolution and Marine Biodiversity, Qingdao, China
| | - Sheng-Lei Wu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Zhe Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- MOE Key Laboratory of Evolution and Marine Biodiversity, Qingdao, China
| | - Meng-Dan Xing
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- MOE Key Laboratory of Evolution and Marine Biodiversity, Qingdao, China
| | - Zhen-Ming Chi
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- MOE Key Laboratory of Evolution and Marine Biodiversity, Qingdao, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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Charfi R, Tazi A, Sereme Y, Plainvert C, Poupet H, Doloy A, Guyonnet C, Morand P, Loubinoux J, Poyart C, Mammeri H. High-level expression of chromosomally encoded SHV-1 β-lactamase reduces the susceptibility to cefiderocol of clinical isolates of Klebsiella pneumoniae. J Antimicrob Chemother 2024; 79:1711-1714. [PMID: 38785356 DOI: 10.1093/jac/dkae143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024] Open
Affiliation(s)
- Rym Charfi
- Hôpitaux Universitaires Paris Centre, Site Cochin, Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Asmaa Tazi
- Hôpitaux Universitaires Paris Centre, Site Cochin, Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Paris, France
- Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR8104, Paris, France
| | - Youssouf Sereme
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, Laboratory of Bacteriology, 75015 Paris, France
| | - Céline Plainvert
- Hôpitaux Universitaires Paris Centre, Site Cochin, Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Paris, France
- Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR8104, Paris, France
| | - Hélène Poupet
- Hôpitaux Universitaires Paris Centre, Site Cochin, Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Alexandra Doloy
- Hôpitaux Universitaires Paris Centre, Site Cochin, Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Cécile Guyonnet
- Hôpitaux Universitaires Paris Centre, Site Cochin, Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Paris, France
- Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR8104, Paris, France
| | - Philippe Morand
- Hôpitaux Universitaires Paris Centre, Site Cochin, Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Paris, France
- Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR8104, Paris, France
| | - Julien Loubinoux
- Hôpitaux Universitaires Paris Centre, Site Cochin, Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Claire Poyart
- Hôpitaux Universitaires Paris Centre, Site Cochin, Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Paris, France
- Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR8104, Paris, France
| | - Hedi Mammeri
- Hôpitaux Universitaires Paris Centre, Site Cochin, Service de Bactériologie, Assistance Publique Hôpitaux de Paris, Paris, France
- Université Paris Cité, INSERM, CNRS, Institut Necker Enfants Malades, Laboratory of Bacteriology, 75015 Paris, France
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8
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Barrio-Pujante A, Bleriot I, Blasco L, Fernández-Garcia L, Pacios O, Ortiz-Cartagena C, Cuenca FF, Oteo-Iglesias J, Tomás M. Regulation of anti-phage defense mechanisms by using cinnamaldehyde as a quorum sensing inhibitor. Front Microbiol 2024; 15:1416628. [PMID: 38989015 PMCID: PMC11233531 DOI: 10.3389/fmicb.2024.1416628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024] Open
Abstract
Background Multidrug-resistant bacteria and the shortage of new antibiotics constitute a serious health problem. This problem has led to increased interest in the use of bacteriophages, which have great potential as antimicrobial agents but also carry the risk of inducing resistance. The objective of the present study was to minimize the development of phage resistance in Klebsiella pneumoniae strains by inhibiting quorum sensing (QS) and thus demonstrate the role of QS in regulating defense mechanisms. Results Cinnamaldehyde (CAD) was added to K. pneumoniae cultures to inhibit QS and thus demonstrate the role of the signaling system in regulating the anti-phage defense mechanism. The QS inhibitory activity of CAD in K. pneumoniae was confirmed by a reduction in the quantitative expression of the lsrB gene (AI-2 pathway) and by proteomic analysis. The infection assays showed that the phage was able to infect a previously resistant K. pneumoniae strain in the cultures to which CAD was added. The results were confirmed using proteomic analysis. Thus, anti-phage defense-related proteins from different systems, such as cyclic oligonucleotide-based bacterial anti-phage signaling systems (CBASS), restriction-modification (R-M) systems, clustered regularly interspaced short palindromic repeat-Cas (CRISPR-Cas) system, and bacteriophage control infection (BCI), were present in the cultures with phage but not in the cultures with phage and CAD. When the QS and anti-phage defense systems were inhibited by the combined treatment, proteins related to phage infection and proliferation, such as the tail fiber protein, the cell division protein DamX, and the outer membrane channel protein TolC, were detected. Conclusion Inhibition of QS reduces phage resistance in K. pneumoniae, resulting in the infection of a previously resistant strain by phage, with a significant increase in phage proliferation and a significant reduction in bacterial growth. QS inhibitors could be considered for therapeutic application by including them in phage cocktails or in phage-antibiotic combinations to enhance synergistic effects and reduce the emergence of antimicrobial resistance.
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Affiliation(s)
- Antonio Barrio-Pujante
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Inés Bleriot
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Lucía Blasco
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Laura Fernández-Garcia
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Olga Pacios
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Concha Ortiz-Cartagena
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Felipe Fernández Cuenca
- Unidad Clínica de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario Virgen Macarena, Instituto de Biomedicina de Sevilla (Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla), Sevilla, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- MEPRAM, Proyecto de Medicina de Precisión Contra las Resistencias Antimicrobianas, Madrid, Spain
| | - Jesús Oteo-Iglesias
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- MEPRAM, Proyecto de Medicina de Precisión Contra las Resistencias Antimicrobianas, Madrid, Spain
- Laboratorio de Referencia e Investigación de Resistencias a Antibióticos e Infecciones Sanitarias, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María Tomás
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) the Behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
- MEPRAM, Proyecto de Medicina de Precisión Contra las Resistencias Antimicrobianas, Madrid, Spain
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Wetthasinghe L, Ng HF, Ngeow YF, Chew KS, Lee WS. Navigating the intricacies of RT-qPCR data analysis in gene expression studies. Funct Integr Genomics 2024; 24:115. [PMID: 38910215 DOI: 10.1007/s10142-024-01393-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Affiliation(s)
- Linah Wetthasinghe
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang, Selangor, 43000, Malaysia
| | - Hien Fuh Ng
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang, Selangor, 43000, Malaysia.
| | - Yun Fong Ngeow
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang, Selangor, 43000, Malaysia
| | - Kee Seang Chew
- Department of Paediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Wilayah Persekutuan, Kuala Lumpur, 50603, Malaysia
| | - Way Seah Lee
- Dr. Wu Lien-Teh Centre for Research in Communicable Diseases, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long, Kajang, Selangor, 43000, Malaysia
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10
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Vialetto E, Miele S, Goren MG, Yu J, Yu Y, Collias D, Beamud B, Osbelt L, Lourenço M, Strowig T, Brisse S, Barquist L, Qimron U, Bikard D, Beisel C. Systematic interrogation of CRISPR antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity. Nucleic Acids Res 2024; 52:6079-6091. [PMID: 38661215 PMCID: PMC11162776 DOI: 10.1093/nar/gkae281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 03/24/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
CRISPR-Cas systems can be utilized as programmable-spectrum antimicrobials to combat bacterial infections. However, how CRISPR nucleases perform as antimicrobials across target sites and strains remains poorly explored. Here, we address this knowledge gap by systematically interrogating the use of CRISPR antimicrobials using multidrug-resistant and hypervirulent strains of Klebsiella pneumoniae as models. Comparing different Cas nucleases, DNA-targeting nucleases outperformed RNA-targeting nucleases based on the tested targets. Focusing on AsCas12a that exhibited robust targeting across different strains, we found that the elucidated modes of escape varied widely, restraining opportunities to enhance killing. We also encountered individual guide RNAs yielding different extents of clearance across strains, which were linked to an interplay between improper gRNA folding and strain-specific DNA repair and survival. To explore features that could improve targeting across strains, we performed a genome-wide screen in different K. pneumoniae strains that yielded guide design rules and trained an algorithm for predicting guide efficiency. Finally, we showed that Cas12a antimicrobials can be exploited to eliminate K. pneumoniae when encoded in phagemids delivered by T7-like phages. Altogether, our results highlight the importance of evaluating antimicrobial activity of CRISPR antimicrobials across relevant strains and define critical parameters for efficient CRISPR-based targeting.
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Affiliation(s)
- Elena Vialetto
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Solange Miele
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Moran G Goren
- Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Jiaqi Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Yanying Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Daphne Collias
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Beatriz Beamud
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Lisa Osbelt
- Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Till Strowig
- Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
- University of Würzburg, Medical Faculty, 97080 Würzburg, Germany
| | - Udi Qimron
- Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - David Bikard
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- University of Würzburg, Medical Faculty, 97080 Würzburg, Germany
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11
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Horn J, Höhn P, Strotmann J, Majchrzak-Stiller B, Buchholz M, Uhl W, Herzog T. Next-generation microbiological testing in intraabdominal infections with PCR technology. Langenbecks Arch Surg 2024; 409:108. [PMID: 38570375 PMCID: PMC10990981 DOI: 10.1007/s00423-024-03298-9] [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: 11/13/2023] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
PURPOSE Intraabdominal infections (IAI) are increasing worldwide and are a major contributor to morbidity and mortality. Among IAI, the number of multi-drug resistant organisms (MDRO) is increasing globally. We tested the Unyvero A50® for intraabdominal infections, compared the detected microorganisms and antibiotic resistance, and compared the results with those of routine microbiology. METHODS We prospectively compared samples obtained from surgical patients using PCR-based Unyvero IAI cartridges against routine microbiology for the detection of microorganisms. Additionally, we identified clinical parameters that correlated with the microbiological findings. Data were analyzed using the t-test and Mann-Whitney U test. RESULTS Sixty-two samples were analyzed. The PCR system identified more microorganisms, mostly Bacteroides species, Escherichia coli, and Enterococcus spp. For bacterial resistance, the PCR system results were fully concordant with those of routine microbiology, resulting in a sensitivity, specificity, and positive and negative predictive value (PPV, NPV) of 100%. The sensitivity, specificity, PPV, and NPV for the detection of microorganisms were 74%, 58%, 60%, and 72%, respectively. CRP levels were significantly higher in patients with detectable microorganisms. We identified more microorganisms and bacterial resistance in hospital-acquired intra-abdominal infections by using the PCR system. DISCUSSION IAI warrants early identification of the microorganisms involved and their resistance to allow for adequate antibiotic therapy. PCR systems enable physicians to rapidly adjust their antibiotic treatment. Conventional microbiological culture and testing remain essential for determining the minimal growth inhibition concentrations for antibiotic therapy.
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Affiliation(s)
- Julian Horn
- Department of General and Visceral Surgery, St. Josef-Hospital Bochum, Ruhr University Bochum, Gudrunstraße 56, 44791, Bochum, Germany.
| | - Philipp Höhn
- Department of General and Visceral Surgery, Division of Molecular and Clinical Research, St. Josef-Hospital Bochum, Ruhr University Bochum, Gudrunstraße 56, 44791, Bochum, Germany
| | - Johanna Strotmann
- Department of General and Visceral Surgery, Division of Molecular and Clinical Research, St. Josef-Hospital Bochum, Ruhr University Bochum, Gudrunstraße 56, 44791, Bochum, Germany
| | - Britta Majchrzak-Stiller
- Department of General and Visceral Surgery, Division of Molecular and Clinical Research, St. Josef-Hospital Bochum, Ruhr University Bochum, Gudrunstraße 56, 44791, Bochum, Germany
| | - Marie Buchholz
- Department of General and Visceral Surgery, Division of Molecular and Clinical Research, St. Josef-Hospital Bochum, Ruhr University Bochum, Gudrunstraße 56, 44791, Bochum, Germany
| | - Waldemar Uhl
- Department of General and Visceral Surgery, St. Josef-Hospital Bochum, Ruhr University Bochum, Gudrunstraße 56, 44791, Bochum, Germany
| | - Torsten Herzog
- Department of General Surgery and Visceral Surgery, Klinikum Vest, Ruhr University Bochum, Recklinghausen, Germany
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12
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Ding L, Yang Z, Sun B. Understanding blaNDM-1 gene regulation in CRKP infections: toward novel antimicrobial strategies for hospital-acquired pneumonia. Mol Med 2024; 30:29. [PMID: 38395744 PMCID: PMC10893750 DOI: 10.1186/s10020-024-00794-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND The escalating challenge of Carbapenem-resistant Klebsiella pneumoniae (CRKP) in hospital-acquired pneumonia (HAP) is closely linked to the blaNDM-1 gene. This study explores the regulatory mechanisms of blaNDM-1 expression and aims to enhance antibacterial tactics to counteract the spread and infection of resistant bacteria. METHODS KP and CRKP strains were isolated from HAP patients' blood samples. Transcriptomic sequencing (RNA-seq) identified significant upregulation of blaNDM-1 gene expression in CRKP strains. Bioinformatics analysis revealed blaNDM-1 gene involvement in beta-lactam resistance pathways. CRISPR-Cas9 was used to delete the blaNDM-1 gene, restoring sensitivity. In vitro and in vivo experiments demonstrated enhanced efficacy with Imipenem and Thanatin or Subatan combination therapy. RESULTS KP and CRKP strains were isolated with significant upregulation of blaNDM-1 in CRKP strains identified by RNA-seq. The Beta-lactam resistance pathway was implicated in bioinformatics analysis. Knockout of blaNDM-1 reinstated sensitivity in CRKP strains. Further, co-treatment with Imipenem, Thanatin, or Subactam markedly improved antimicrobial effectiveness. CONCLUSION Silencing blaNDM-1 in CRKP strains from HAP patients weakens their Carbapenem resistance and optimizes antibacterial strategies. These results provide new theoretical insights and practical methods for treating resistant bacterial infections.
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Affiliation(s)
- Liang Ding
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Chongchuan District, Nantong, 226001, Jiangsu Province, China
| | - Zheng Yang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Chongchuan District, Nantong, 226001, Jiangsu Province, China
| | - Baier Sun
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Chongchuan District, Nantong, 226001, Jiangsu Province, China.
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13
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de Oliveira PAA, Baboghlian J, Ramos COA, Mançano ASF, Porcari ADM, Girardello R, Ferraz LFC. Selection and validation of reference genes suitable for gene expression analysis by Reverse Transcription Quantitative real-time PCR in Acinetobacter baumannii. Sci Rep 2024; 14:3830. [PMID: 38360762 PMCID: PMC10869792 DOI: 10.1038/s41598-024-51499-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024] Open
Abstract
Acinetobacter baumannii is a Gram-negative bacterium considered an emerging multi-drug-resistant pathogen. Furthermore, this bacterium can survive in extreme environmental conditions, which makes it a frequent cause of nosocomial infection outbreaks. Gene expression analyses by Reverse Transcription Quantitative real-time PCR (RT-qPCR) depend on a reference gene, also called an endogenous gene, which is used to normalize the generated data and thus ensure an accurate analysis with minimal errors. Currently, gene expression analyses in A. baumannii are compromised, as there are no reports in the literature describing the identification of validated reference genes for use in RT-qPCR analyses. For this reason, we selected twelve candidate reference genes of A. baumannii and assessed their expression profile under different experimental and culture conditions. The expression stability of the candidate genes was evaluated by using statistical algorithms such as BestKeeper, geNorm, NormFinder, Delta CT, and RefFinder, in order to identify the most suitable candidate reference genes for RT-qPCR analyses. The statistical analyses indicated rpoB, rpoD, and fabD genes as the most adequate to ensure accurate normalization of RT-qPCR data in A. baumannii. The accuracy of the proposed reference genes was validated by using them to normalize the expression of the ompA gene, encoding the outer membrane protein A, in A. baumannii sensible and resistant to the antibiotic polymyxin. The present work provides suitable reference genes for precise RT-qPCR data normalization on future gene expression studies with A. baumannii.
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Affiliation(s)
| | - Juliana Baboghlian
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, SP, CEP 12916-900, Brazil
| | | | | | - Andréia de Melo Porcari
- Laboratório Multidisciplinar de Pesquisa, Universidade São Francisco, Bragança Paulista, SP, CEP 12916-900, Brazil
| | - Raquel Girardello
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, SP, CEP 12916-900, Brazil
| | - Lúcio Fábio Caldas Ferraz
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, SP, CEP 12916-900, Brazil.
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14
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Leung PB, Matanza XM, Roche B, Ha KP, Cheung HC, Appleyard S, Collins T, Flanagan O, Marteyn BS, Clements A. Shigella sonnei utilises colicins during inter-bacterial competition. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001434. [PMID: 38376387 PMCID: PMC10924462 DOI: 10.1099/mic.0.001434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/25/2024] [Indexed: 02/21/2024]
Abstract
The mammalian colon is one of the most densely populated habitats currently recognised, with 1011-1013 commensal bacteria per gram of colonic contents. Enteric pathogens must compete with the resident intestinal microbiota to cause infection. Among these enteric pathogens are Shigella species which cause approximately 125 million infections annually, of which over 90 % are caused by Shigella flexneri and Shigella sonnei. Shigella sonnei was previously reported to use a Type VI Secretion System (T6SS) to outcompete E. coli and S. flexneri in in vitro and in vivo experiments. S. sonnei strains have also been reported to harbour colicinogenic plasmids, which are an alternative anti-bacterial mechanism that could provide a competitive advantage against the intestinal microbiota. We sought to determine the contribution of both T6SS and colicins to the anti-bacterial killing activity of S. sonnei. We reveal that whilst the T6SS operon is present in S. sonnei, there is evidence of functional degradation of the system through SNPs, indels and IS within key components of the system. We created strains with synthetically inducible T6SS operons but were still unable to demonstrate anti-bacterial activity of the T6SS. We demonstrate that the anti-bacterial activity observed in our in vitro assays was due to colicin activity. We show that S. sonnei no longer displayed anti-bacterial activity against bacteria that were resistant to colicins, and removal of the colicin plasmid from S. sonnei abrogated anti-bacterial activity of S. sonnei. We propose that the anti-bacterial activity demonstrated by colicins may be sufficient for niche competition by S. sonnei within the gastrointestinal environment.
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Affiliation(s)
- P. B. Leung
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
| | - X. M. Matanza
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
| | - B. Roche
- Universite de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, CNRS UPR9002, F-67000 Strasbourg, France
| | - K. P. Ha
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
| | - H. C. Cheung
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
| | - S. Appleyard
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
| | - T. Collins
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
| | - O. Flanagan
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
| | - B. S. Marteyn
- Universite de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, CNRS UPR9002, F-67000 Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), F-67000 Strasbourg, France
- Institut Pasteur, Université de Paris, Inserm U1225, Unité de Pathogenèse des Infections Vasculaires, F-75015 Paris, France
| | - A. Clements
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW72AZ, UK
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15
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Delik E, Eroğlu B, Tefon-Öztürk BE. Evaluation of the in vitro effects of concentrations of antibiotics on three Enterobacteriaceae isolates. World J Microbiol Biotechnol 2024; 40:73. [PMID: 38240926 PMCID: PMC10799096 DOI: 10.1007/s11274-023-03877-w] [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: 11/21/2023] [Accepted: 12/17/2023] [Indexed: 01/22/2024]
Abstract
Due to the misuse and overuse of antibiotics, bacteria are now exposed to sub-minimum inhibitory concentrations (sub-MICs) of antibiotics in various environments. In recent years, exposure of bacteria to sub-MICs of antibiotics has led to the widespread emergence of antibiotic-resistant bacteria. In this study, three bacterial species from the Enterobacteriaceae family (Raoultella ornithinolytica, Pantoea agglomerans and Klebsiella quasivariicola) were isolated from water. The antibiotic susceptibility of these bacteria to 16 antibiotics was then investigated. The effects of sub-MICs of four selected antibiotics (kanamycin, chloramphenicol, meropenem, and ciprofloxacin) on the growth, biofilm formation, surface polysaccharide production, siderophore production, morphology, and expression of the translational/transcriptional regulatory transformer gene rfaH of these bacteria were analysed. The MICs of kanamycin, chloramphenicol, meropenem, and ciprofloxacin were determined to be 1, 2, 0.03 and 0.03 µg/mL for R. ornithinolytica; 0.6, 6, 0.03 and 0.05 µg/mL for P. agglomerans; and 2, 5, 0.04 and 0.2 µg/mL for K. quasivariicola. The growth kinetics and biofilm formation ability decreased for all three isolates at sub-MICs. The surface polysaccharides of R. ornithinolytica and P. agglomerans increased at sub-MICs. There was no significant change in the siderophore activities of the bacterial isolates, with the exception of MIC/2 meropenem in R. ornithinolytica and MIC/2 kanamycin in K. quasivariicola. It was observed that the sub-MICs of meropenem and ciprofloxacin caused significant changes in bacterial morphology. In addition, the expression of rfaH in R. ornithinolytica and K. quasivariicola increased with the sub-MICs of the selected antibiotics.
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Affiliation(s)
- Eda Delik
- Biology Department, Faculty of Science, Akdeniz University, 07070, Antalya, Turkey
| | - Berfin Eroğlu
- Biology Department, Faculty of Science, Akdeniz University, 07070, Antalya, Turkey
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16
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Lu P, Bai R, Gao T, Chen J, Jiang K, Zhu Y, Lu Y, Zhang S, Xu F, Zhao H. Systemic metabolic engineering of Enterobacter aerogenes for efficient 2,3-butanediol production. Appl Microbiol Biotechnol 2024; 108:146. [PMID: 38240862 PMCID: PMC10798932 DOI: 10.1007/s00253-023-12911-8] [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: 07/18/2023] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 01/22/2024]
Abstract
2,3-Butanediol (2,3-BDO) is an important gateway molecule for many chemical derivatives. Currently, microbial production is gradually being recognized as a green and sustainable alternative to petrochemical synthesis, but the titer, yield, and productivity of microbial 2,3-BDO remain suboptimal. Here, we used systemic metabolic engineering strategies to debottleneck the 2,3-BDO production in Enterobacter aerogenes. Firstly, the pyruvate metabolic network was reconstructed by deleting genes for by-product synthesis to improve the flux toward 2,3-BDO synthesis, which resulted in a 90% increase of the product titer. Secondly, the 2,3-BDO productivity of the IAM1183-LPCT/D was increased by 55% due to the heterologous expression of DR1558 which boosted cell resistance to abiotic stress. Thirdly, carbon sources were optimized to further improve the yield of target products. The IAM1183-LPCT/D showed the highest titer of 2,3-BDO from sucrose, 20% higher than that from glucose, and the yield of 2,3-BDO reached 0.49 g/g. Finally, the titer of 2,3-BDO of IAM1183-LPCT/D in a 5-L fermenter reached 22.93 g/L, 85% higher than the wild-type strain, and the titer of by-products except ethanol was very low. KEY POINTS: Deletion of five key genes in E. aerogenes improved 2,3-BDO production The titer of 2,3-BDO was increased by 90% by regulating metabolic flux Response regulator DR1558 was expressed to increase 2,3-BDO productivity.
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Affiliation(s)
- Ping Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ruoxuan Bai
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ting Gao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jiale Chen
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ke Jiang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yalun Zhu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ye Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Shuting Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Fangxu Xu
- Liaoning Province Key Laboratory of Cordyceps Militaris With Functional Value, Experimental Teaching Center, Shenyang Normal University, Shenyang, 110034, China
| | - Hongxin Zhao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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17
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Dede B, Reeves EP, Walter M, Bach W, Amann R, Meyerdierks A. Bacterial chemolithoautotrophy in ultramafic plumes along the Mid-Atlantic Ridge. THE ISME JOURNAL 2024; 18:wrae165. [PMID: 39163484 PMCID: PMC11411561 DOI: 10.1093/ismejo/wrae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/10/2024] [Accepted: 08/19/2024] [Indexed: 08/22/2024]
Abstract
Hydrothermal vent systems release reduced chemical compounds that act as an important energy source in the deep sea. Chemolithoautotrophic microbes inhabiting hydrothermal plumes oxidize these compounds, in particular, hydrogen and reduced sulfur, to obtain the energy required for CO2 fixation. Here, we analysed the planktonic communities of four hydrothermal systems located along the Mid-Atlantic Ridge: Irinovskoe, Semenov-2, Logatchev-1, and Ashadze-2, by combining long-read 16S rRNA gene analysis, fluorescence in situ hybridization, meta-omics, and thermodynamic calculations. Sulfurimonas and SUP05 dominated the microbial communities in these hydrothermal plumes. Investigation of Sulfurimonas and SUP05 MAGs, and their gene transcription in plumes indicated a niche partitioning driven by hydrogen and sulfur. In addition to sulfur and hydrogen oxidation, a novel SAR202 clade inhabiting the plume, here referred to as genus Carboxydicoccus, harbours the capability for CO oxidation and CO2 fixation via reverse TCA cycle. Both pathways were also highly transcribed in other hydrogen-rich plumes, including the Von Damm vent field. Carboxydicoccus profundi reached up to 4% relative abundance (1.0 x 103 cell ml- 1) in Irinovskoe non-buoyant plume and was also abundant in non-hydrothermally influenced deep-sea metagenomes (up to 5 RPKM). Therefore, CO, which is probably not sourced from the hydrothermal fluids (1.9-5.8 μM), but rather from biological activities within the rising fluid, may serve as a significant energy source in hydrothermal plumes. Taken together, this study sheds light on the chemolithoautotrophic potential of the bacterial community in Mid-Atlantic Ridge plumes.
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Affiliation(s)
- Bledina Dede
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Eoghan P Reeves
- Department of Earth Science and Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Maren Walter
- Institute of Environmental Physics, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Wolfgang Bach
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Geoscience Department, University of Bremen, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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18
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Rashid FZM, Crémazy FGE, Hofmann A, Forrest D, Grainger DC, Heermann DW, Dame RT. The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli. Nat Commun 2023; 14:7478. [PMID: 37978176 PMCID: PMC10656529 DOI: 10.1038/s41467-023-43322-y] [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: 11/03/2022] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
Nucleoid associated proteins (NAPs) maintain the architecture of bacterial chromosomes and regulate gene expression. Thus, their role as transcription factors may involve three-dimensional chromosome re-organisation. While this model is supported by in vitro studies, direct in vivo evidence is lacking. Here, we use RT-qPCR and 3C-qPCR to study the transcriptional and architectural profiles of the H-NS (histone-like nucleoid structuring protein)-regulated, osmoresponsive proVWX operon of Escherichia coli at different osmolarities and provide in vivo evidence for transcription regulation by NAP-mediated chromosome re-modelling in bacteria. By consolidating our in vivo investigations with earlier in vitro and in silico studies that provide mechanistic details of how H-NS re-models DNA in response to osmolarity, we report that activation of proVWX in response to a hyperosmotic shock involves the destabilization of H-NS-mediated bridges anchored between the proVWX downstream and upstream regulatory elements (DRE and URE), and between the DRE and ygaY that lies immediately downstream of proVWX. The re-establishment of these bridges upon adaptation to hyperosmolarity represses the operon. Our results also reveal additional structural features associated with changes in proVWX transcript levels such as the decompaction of local chromatin upstream of the operon, highlighting that further complexity underlies the regulation of this model operon. H-NS and H-NS-like proteins are wide-spread amongst bacteria, suggesting that chromosome re-modelling may be a typical feature of transcriptional control in bacteria.
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Affiliation(s)
- Fatema-Zahra M Rashid
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, 2333CC, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, 2333CC, The Netherlands
| | - Frédéric G E Crémazy
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands
- Laboratoire Infection et Inflammation, INSERM, UVSQ, Université Paris-Saclay, Versailles, 78180, France
| | - Andreas Hofmann
- Statistical Physics and Theoretical Biophysics, Heidelberg University, Heidelberg, D-69120, Germany
| | - David Forrest
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - David C Grainger
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Dieter W Heermann
- Statistical Physics and Theoretical Biophysics, Heidelberg University, Heidelberg, D-69120, Germany
| | - Remus T Dame
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, 2333CC, The Netherlands.
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, 2333CC, The Netherlands.
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19
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Liu Y, Zhong W, Feng S, Tang Z, Zhang Y, Ai L, Xiong Z. Identification of new reference genes for colony counting by reverse-transcription quantitative PCR in Bifidobacterium animalis. J Dairy Sci 2023; 106:7477-7485. [PMID: 37641239 DOI: 10.3168/jds.2022-23000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/12/2023] [Indexed: 08/31/2023]
Abstract
Bifidobacterium animalis, one of the predominant bacteria in the intestines of humans and other mammals, is widely added to dairy products. We employed RNA sequencing to analyze gene expression variance on a genome-wide scale and found stable reference genes (RG) in B. animalis. A total of 1,665 genes were identified by analyzing the data from the transcriptome under 4 different conditions, and 13 probable candidate RG with variation coefficient values <0.1 were validated using reverse-transcription quantitative PCR (RT-qPCR). The amplification efficiency of candidate RG were ranging from 94.16% to 126.25%. We integrated the analysis results of BestKeeper, geNorm, NormFinder, and RefFinder algorithms and revealed that rplD and atpA comprehensive ranked 1.68 and 2.82, respectively, which were more stable than traditional RG. Compared with plate count (1.58 × 106 cfu/mL), the concentrations of B. animalis AR668 by RT-qPCR using rplD, atpA, and 16S rRNA as RG were 2.27 × 106, 2.24 × 106, and 6.66 × 106 cfu/mL, respectively, after 10 h of fermentation in fermented skim milk. It suggested that rplD and atpA as RG can be accurate for colony counting of B. animalis. Our study provides the foundation for more accurate analysis of colony counting by RT-qPCR of B. animalis in dairy foods.
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Affiliation(s)
- Yaping Liu
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Wanting Zhong
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Shuo Feng
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Ziteng Tang
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yingzhi Zhang
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Lianzhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Zhiqiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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20
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Hu CM, Zhou CL, Wan JN, Guo T, Ji GY, Luo SZ, Ji KP, Cao Y, Tan Q, Bao DP, Yang RH. Selection and validation of internal control genes for quantitative real-time RT‒qPCR normalization of Phlebopus portentosus gene expression under different conditions. PLoS One 2023; 18:e0288982. [PMID: 37756330 PMCID: PMC10530043 DOI: 10.1371/journal.pone.0288982] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 07/03/2023] [Indexed: 09/29/2023] Open
Abstract
Phlebopus portentosus (Berk. and Broome) Boedijn is an attractive edible mushroom and is considered the only bolete for which artificial cultivation in vitro has been achieved. Gene expression analysis has become widely used in research on edible fungi and is important for elucidating the functions of genes involved in complex biological processes. Selecting appropriate reference genes is crucial to ensuring reliable RT‒qPCR gene expression analysis results. In our study, a total of 12 candidate control genes were selected from 25 traditional housekeeping genes based on their expression stability in 9 transcriptomes of 3 developmental stages. These genes were further evaluated using geNorm, NormFinder, and RefFinder under different conditions and developmental stages. The results revealed that MSF1 domain-containing protein (MSF1), synaptobrevin (SYB), mitogen-activated protein kinase genes (MAPK), TATA-binding protein 1 (TBP1), and SPRY domain protein (SPRY) were the most stable reference genes in all sample treatments, while elongation factor 1-alpha (EF1), actin and ubiquitin-conjugating enzyme (UBCE) were the most unstably expressed. The gene SYB was selected based on the transcriptome results and was identified as a novel reference gene in P. portentosus. This is the first detailed study on the identification of reference genes in this fungus and may provide new insights into selecting genes and quantifying gene expression.
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Affiliation(s)
- Chen-Menghui Hu
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungal Resources and Utilization (South), Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chen-Li Zhou
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungal Resources and Utilization (South), Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jia-Ning Wan
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungal Resources and Utilization (South), Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ting Guo
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungal Resources and Utilization (South), Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Guang-Yan Ji
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Shun-Zhen Luo
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Kai-Ping Ji
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Yang Cao
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Qi Tan
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungal Resources and Utilization (South), Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Da-Peng Bao
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungal Resources and Utilization (South), Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Rui-Heng Yang
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungal Resources and Utilization (South), Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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21
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Nucci A, Janaszkiewicz J, Rocha EPC, Rendueles O. Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola. MICROLIFE 2023; 4:uqad038. [PMID: 37781688 PMCID: PMC10540941 DOI: 10.1093/femsml/uqad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 10/03/2023]
Abstract
Klebsiella variicola is an emergent human pathogen causing diverse infections, some of which in the urinary tract. However, little is known about the evolution and maintenance of genetic diversity in this species, the molecular mechanisms and their population dynamics. Here, we characterized the emergence of a novel rdar-like (rough and dry) morphotype which is contingent both on the genetic background and the environment. We show that mutations in either the nitrogen assimilation control gene (nac) or the type III fimbriae regulator, mrkH, suffice to generate rdar-like colonies. These morphotypes are primarily selected for the reduced inter-cellular aggregation as a result of MrkH loss-of-function which reduces type 3 fimbriae expression. Additionally, these clones also display increased growth rate and reduced biofilm formation. Direct competitions between rdar and wild type clones show that mutations in mrkH provide large fitness advantages. In artificial urine, the morphotype is under strong negative frequency-dependent selection and can socially exploit wild type strains. An exhaustive search for mrkH mutants in public databases revealed that ca 8% of natural isolates analysed had a truncated mrkH gene many of which were due to insertions of IS elements, including a reported clinical isolate with rdar morphology. These strains were rarely hypermucoid and often isolated from human, mostly from urine and blood. The decreased aggregation of these mutants could have important clinical implications as we hypothesize that such clones could better disperse within the host allowing colonisation of other body sites and potentially leading to systemic infections.
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Affiliation(s)
- Amandine Nucci
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Juliette Janaszkiewicz
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Olaya Rendueles
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
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22
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Jiang K, Bai R, Gao T, Lu P, Zhang J, Zhang S, Xu F, Wang S, Zhao H. Optimization of hydrogen production in Enterobacter aerogenes by Complex I peripheral fragments destruction and maeA overexpression. Microb Cell Fact 2023; 22:137. [PMID: 37496040 PMCID: PMC10373349 DOI: 10.1186/s12934-023-02155-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023] Open
Abstract
As a concentrated energy source with high added value, hydrogen has great development prospects, with special emphasis on sustainable microbial production as a replacement for traditional fossil fuels. In this study, λ-Red recombination was used to alter the activity of Complex I by single and combined knockout of nuoE, nuoF and nuoG. In addition, the conversion of malic to pyruvic acid was promoted by overexpressing the maeA gene, which could increase the content of NADH and formic acid in the bacterial cells. Compared to the original strain, hydrogen production was 65% higher in the optimized strain IAM1183-EFG/M, in which the flux of the formic acid pathway was increased by 257%, the flux of the NADH pathway was increased by 13%, and the content of metabolites also changed significantly. In further bioreactor, the total hydrogen production of the scale-up IAM1183-EFG/M after 44 h of fermentation was 4.76 L, which increased by 18% compared with the starting strain. This study provides a new direction for future exploration of microbial hydrogen production by combinatorial modification of multiple genes.
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Affiliation(s)
- Ke Jiang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ruoxuan Bai
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ting Gao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ping Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jingya Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Shuting Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Fangxu Xu
- Shenyang Functional Cordyceps militaris Industrial Technology Research Institute, Shenyang, 110034, China
- Liaoning Province Key Laboratory of Cordyceps Militaris with Functional Value, Experimental Teaching Center, Shenyang Normal University, Shenyang, 110034, China
| | - Shenghou Wang
- Shenyang Functional Cordyceps militaris Industrial Technology Research Institute, Shenyang, 110034, China
- Liaoning Province Key Laboratory of Cordyceps Militaris with Functional Value, Experimental Teaching Center, Shenyang Normal University, Shenyang, 110034, China
| | - Hongxin Zhao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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23
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Mironova AV, Karimova AV, Bogachev MI, Kayumov AR, Trizna EY. Alterations in Antibiotic Susceptibility of Staphylococcus aureus and Klebsiella pneumoniae in Dual Species Biofilms. Int J Mol Sci 2023; 24:ijms24108475. [PMID: 37239822 DOI: 10.3390/ijms24108475] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
In the last decades, it has been shown that biofilm-associated infections in most cases are caused by rather two or even more pathogens than by single microorganisms. Due to intermicrobial interactions in mixed communities, bacteria change their gene expression profile, in turn leading to alterations in the biofilm structure and properties, as well as susceptibility to antimicrobials. Here, we report the alterations of antimicrobials efficiency in mixed biofilms of Staphylococcus aureus-Klebsiella pneumoniae in comparison with mono-species biofilms of each counterpart and discuss possible mechanisms of these alterations. In cell clumps detached from dual-species biofilms, S. aureus became insensitive to vancomycin, ampicillin, and ceftazidime compared to solely S. aureus cell clumps. In turn, the increased efficiency of amikacin and ciprofloxacin against both bacteria could be observed, compared to mono-species biofilms of each counterpart. Scanning electron microscopy and confocal microscopy indicate the porous structure of the dual-species biofilm, and differential fluorescent staining revealed an increased number of polysaccharides in the matrix, in turn leading to more loose structure and thus apparently providing increased permeability of the dual-species biofilm to antimicrobials. The qRT-PCR showed that ica operon in S. aureus became repressed in mixed communities, and polysaccharides are produced mainly by K. pneumoniae. While the molecular trigger of these changes remains undiscovered, detailed knowledge of the alterations in antibiotic susceptibility to given drugs opens doors for treatment correction options for S. aureus-K. pneumoniae biofilm-associated infections.
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Affiliation(s)
- Anna V Mironova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Agniya V Karimova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Mikhail I Bogachev
- Biomedical Engineering Research Centre, St. Petersburg Electrotechnical University, 197022 St. Petersburg, Russia
| | - Airat R Kayumov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Elena Y Trizna
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
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24
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Liu Z, Zhu C, Sun J, Zhang Z, Zhao S, Shi W, Wang W, Zhao B. Influence of rootstock on endogenous hormones and color change in Cabernet Sauvignon grapes. Sci Rep 2023; 13:6608. [PMID: 37095085 PMCID: PMC10125983 DOI: 10.1038/s41598-023-33089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 04/06/2023] [Indexed: 04/26/2023] Open
Abstract
Different rootstocks for grapes can significantly affect fruit color and quality, possibly by affecting hormone contents, related genetic pathways, and fruit coloring mechanisms in skin. 'Cabernet Sauvignon' was grafted to '5BB', 'SO4', '140R', 'CS', '3309M' and 'Vitis riparia' rootstocks, with self-rooting seedlings as the control (CS/CS), and sampled from the early stage of veraison to the ripening stage. The effects of rootstock on the contents of gibberellin (GA3), auxin (IAA), and abscisic acid (ABA) in grape skin were determined alongside the expression levels of eight anthocyanin synthesis related genes using real-time fluorescence quantitative PCR methods. The rootstock cultivars exhibited accelerated fruit color change, and the CS/140R combination resulted in grapes with more color than the control group in the same period. With the development of fruit, the IAA and GA3 contents in the skin of different rootstock combinations showed trends of increasing initially, then decreasing, while the ABA content decreased initially and then increased. During the verasion (28 July), the various 'Cabernet Sauvignon' rootstock combinations exhibited varying degrees of increases in GA3, ABA, and IAA contents; correlation analysis showed that, at the start of veraison, the expression levels of the anthocyanin synthesis-related genes VvCHS, VvDFR, and VvUFGT had strong positive correlations with hormone contents, which indicated they are key genes involved in the endogenous hormone responsive anthocyanin biosynthesis pathway. The results of this study showed that rootstock regulates the fruit coloring process by influencing the metabolism level of peel hormones in the 'Cabernet Sauvignon' grape.
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Affiliation(s)
- Zhiyu Liu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China
- The Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of the Xinjiang Production and Construction, Xinjiang, China
| | - Chunmei Zhu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China
- The Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of the Xinjiang Production and Construction, Xinjiang, China
| | - Junli Sun
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China
- The Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of the Xinjiang Production and Construction, Xinjiang, China
| | - Zhijun Zhang
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China
- The Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of the Xinjiang Production and Construction, Xinjiang, China
| | - Shucheng Zhao
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China
| | - Wenchao Shi
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China
- The Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of the Xinjiang Production and Construction, Xinjiang, China
| | - Wei Wang
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China
| | - Baolong Zhao
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003, China.
- The Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of the Xinjiang Production and Construction, Xinjiang, China.
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25
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Mu J, Wang Y, Wang M, Zhang D, Liu M. Identification of reliable reference genes for gene expression studies in mouse models under microplastics stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 252:114569. [PMID: 36696727 DOI: 10.1016/j.ecoenv.2023.114569] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Microplastics (MPs) and nanoplastics (NPs) have been deemed to be newly emerged contaminants interfering with various physiological processes closely related with gene expression alteration. Reverse transcriptase quantitative real-time polymerase chain reaction (RT-qPCR) serves as a powerful tool to assess gene expression, however highly dependent on a reliable reference gene. Therefore, it is necessary to identify stable reference genes for gene expression study under MP or NP stress. We constructed a mouse model postexposure to polypropylene microplastics (PP-MPs) to assess PP-MPs bioaccumulation in kidney, evaluate the kidney pathological changes, and then explore potential reference genes via RT-qPCR. Although the hematoxylin-eosin staining showed no obvious damage in kidney tissues, we observed significant PP-MPs accumulation in kidney using Raman spectra analysis supported by spectral multivariate analysis. The expression of 19 candidate reference genes were examined, including the commonly used ones of β-actin, glyceraldehyde 3-phosphate dehydrogenase (Gapdh), Cytochrome c oxidase subunit 4I1 (Cox4i), Histocompatibility 13 (H13) and ribosomal protein. Their expression stability and reliability were assessed by the combination of four algorithms including geNorm, NormFinder, BestKeeper and Delta Cq. The geNorm analysis revealed that the top three genes with the lowest variability were Cox4il, Rps9 and Gapdh, whereas NormFinder results ranked Rps3, Cox4il and Rps18 as the top three ones. Rpl15, Cox4i1 and Rps3 were the most reliable reference genes in BestKeeper results, and Delta Cq proposed Rps3 and Cox4il as the stable genes. The overall ranking indicated by GMR value gave the five most stable reference genes (Cox4i1, Rps3, Rps9, Rps18 and Gapdh). Three genes associated with different biochemical processes (Atp5f1, Crebbp and Dele1) were chosen to verify the characterized reference genes using the least stable gene as a control, exhibiting different expression profiles and implying the essentiality to select the reliable reference genes. Our results documented the expression fluctuations of acknowledged reference gene (Ubc) and proposed a set of reliable reference genes for future studies of gene expression profiles in MP treated mouse models.
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Affiliation(s)
- Ju Mu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, PR China
| | - Yu Wang
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou 310053, PR China
| | - Miao Wang
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, PR China
| | - Dayi Zhang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Changchun 130021, PR China; College of New Energy and Environment, Jilin University, Changchun 130021, PR China.
| | - Mingying Liu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, PR China.
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Klebsiella pneumoniae carrying multiple alleles of antigen 43-encoding gene of Escherichia coli associated with biofilm formation. Eur J Clin Microbiol Infect Dis 2023; 42:371-377. [PMID: 36695920 PMCID: PMC9899198 DOI: 10.1007/s10096-023-04552-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/14/2023] [Indexed: 01/26/2023]
Abstract
A clinical strain of Klebsiella pneumoniae typed as sequence type 307 carrying three different alleles of the flu gene encoding the Escherichia coli virulence factor antigen 43 associated with biofilm formation was detected and characterized. The flu alleles are located in the chromosome inside putative integrative conjugative elements. The strain displays the phenotypes associated with Ag43, i.e. bi-phasic colony morphology and enhanced biofilm production. Furthermore, the strain produces low amount of capsule known to affect Ag43 function. Analysis of 1431 worldwide deposited genomes revealed that 3.7% Klebsiella pneumoniae carry one or two flu alleles.
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Daoud L, Al-Marzooq F, Moubareck CA, Ghazawi A, Collyns T. Elucidating the effect of iron acquisition systems in Klebsiella pneumoniae on susceptibility to the novel siderophore-cephalosporin cefiderocol. PLoS One 2022; 17:e0277946. [PMID: 36580460 PMCID: PMC9799297 DOI: 10.1371/journal.pone.0277946] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/08/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Cefiderocol (CFDC) is a novel siderophore-cephalosporin, effective against multidrug-resistant Gram-negative bacteria. As it has a siderophore side chain, it can utilize iron acquisition systems for penetration of the bacterial outer membrane. We aimed to elucidate the role of siderophores and iron uptake receptors in defining Klebsiella pneumoniae susceptibility to CFDC. METHODS Initially, 103 K. pneumoniae strains were characterized for susceptibility to different antibiotics including CFDC. CFDC minimum inhibitory concentrations (MIC) were determined in iron-depleted and iron-enriched conditions. Iron uptake genes including siderophores, their receptors, ferric citrate (fecA) and iron uptake (kfu) receptors were detected by PCR in all the strains. For 10 selected strains, gene expression was tested in iron-depleted media with or without CFDC treatment and compared to expression in iron-enriched conditions. RESULTS CFDC exhibited 96.1% susceptibility, being superior to all the other antibiotics (MIC50: 0.5 and MIC90: 4 μg/ml). Only three strains (2.9%) were intermediately susceptible and a pandrug resistant strain (0.97%) was resistant to CFDC (MIC: 8 and 256 μg/ml, respectively). The presence of kfu and fecA had a significant impact on CFDC MIC, especially when co-produced, and if coupled with yersiniabactin receptor (fyuA). CFDC MICs were negatively correlated with enterobactin receptor (fepA) expression and positively correlated with expression of kfu and fecA. Thus, fepA was associated with increased susceptibility to CFDC, while kfu and fecA were associated with reduced susceptibility to CFDC. CFDC MICs increased significantly in iron-enriched media, with reduced expression of siderophore receptors, hence, causing less drug uptake. CONCLUSION Iron acquisition systems have a significant impact on CFDC activity, and their altered expression is a factor leading to reduced susceptibility. Iron concentration is also a major player affecting CFDC susceptibility; therefore, it is essential to explore possible ways to improve the drug activity to facilitate its use to treat infections in iron-rich sites.
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Affiliation(s)
- Lana Daoud
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Farah Al-Marzooq
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- * E-mail:
| | | | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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Remodeling of the Enterococcal Cell Envelope during Surface Penetration Promotes Intrinsic Resistance to Stress. mBio 2022; 13:e0229422. [PMID: 36354750 PMCID: PMC9765498 DOI: 10.1128/mbio.02294-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Enterococcus faecalis is a normal commensal of the human gastrointestinal tract (GIT). However, upon disruption of gut homeostasis, this nonmotile bacterium can egress from its natural niche and spread to distal organs. While this translocation process can lead to life-threatening systemic infections, the underlying mechanisms remain largely unexplored. Our prior work showed that E. faecalis migration across diverse surfaces requires the formation of matrix-covered multicellular aggregates and the synthesis of exopolysaccharides, but how enterococcal cells are reprogrammed during this process is unknown. Whether surface penetration endows E. faecalis with adaptive advantages is also uncertain. Here, we report that surface penetration promotes the generation of a metabolically and phenotypically distinct E. faecalis population with an enhanced capacity to endure various forms of extracellular stress. Surface-invading enterococci demonstrated major ultrastructural alterations in their cell envelope characterized by increased membrane glycolipid content. These changes were accompanied by marked induction of specific transcriptional programs enhancing cell envelope biogenesis and glycolipid metabolism. Notably, the surface-invading population demonstrated superior tolerance to membrane-damaging antimicrobials, including daptomycin and β-defensins produced by epithelial cells. Genetic mutations impairing glycolipid biosynthesis sensitized E. faecalis to envelope stressors and reduced the ability of this bacterium to penetrate semisolid surfaces and translocate through human intestinal epithelial cell monolayers. Our study reveals that surface penetration induces distinct transcriptional, metabolic, and ultrastructural changes that equip E. faecalis with enhanced capacity to resist external stressors and thrive in its surrounding environment. IMPORTANCE Enterococcus faecalis inhabits the GIT of multiple organisms, where its establishment could be mediated by the formation of biofilm-like aggregates. In susceptible individuals, this bacterium can overgrow and breach intestinal barriers, a process that may lead to lethal systemic infections. While the formation of multicellular aggregates promotes E. faecalis migration across surfaces, little is known about the metabolic and physiological states of the enterococci encased in these surface-penetrating structures. The present study reveals that E. faecalis cells capable of migrating through semisolid surfaces genetically reprogram their metabolism toward increased cell envelope and glycolipid biogenesis, which confers superior tolerance to membrane-damaging agents. E. faecalis's success as a pathobiont depends on its antimicrobial resistance, as well as on its rapid adaptability to overcome multiple environmental challenges. Thus, targeting adaptive genetic and/or metabolic pathways induced during E. faecalis surface penetration may be useful to better confront infections by this bacterium in the clinic.
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Lin TH, Wu CC, Tseng CY, Fang JH, Lin CT. Effects of gallic acid on capsular polysaccharide biosynthesis in Klebsiella pneumoniae. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1255-1262. [PMID: 34326026 DOI: 10.1016/j.jmii.2021.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Klebsiella pneumoniae is a gram-negative opportunistic pathogen that causes diseases mostly in immunocompromised individuals. Recently, hypervirulent K. pneumoniae strains also cause severe disease in healthy individuals. Capsular polysaccharide (CPS) is the major virulence determinant in hypervirulent K. pneumoniae and protects the cell against the bactericidal activity of the immune system. Gallic acid (GA), a natural phenolic compound, is known to exhibit wide spectrum antibacterial activity; however, its effect on hypervirulent K. pneumoniae remains largely unresolved. We aimed to identify the effects of GA on CPS biosynthesis in hypervirulent K. pneumoniae. METHODS Antibacterial activity of GA was evaluated by counting colonies. CPS amount was determined by glucuronic acid content. The transcriptions of cps gene cluster were measured by quantitative real time PCR (qRT-PCR) and the β-galactosidase activity. The effect of GA on the resistance of K. pneumoniae to streptonigrin (SNG), an iron-activated antibiotic, was evaluated. The effect of GA on the resistance of K. pneumoniae to serum killing and phagocytosis by macrophages was observed. RESULTS GA inhibited the growth and CPS biosynthesis in K. pneumoniae. GA may affect the iron availability in K. pneumoniae, thus possibly repressing the cps transcription. In addition, GA reduced the resistance of K. pneumoniae to serum killing and enhanced its susceptibility to phagocytosis. CONCLUSION GA possesses bactericidal activity and inhibits the CPS biosynthesis in hypervirulent K. pneumoniae, thereby facilitating pathogen clearance by the host immune system. Therefore, GA may represent a promising strategy for the prevention or treatment of patients with hypervirulent K. pneumoniae infections.
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Affiliation(s)
- Tien-Huang Lin
- Division of Urology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan; Post-Baccalaureate Chinese Medicine, Tzu Chi University, Hualien, Taiwan.
| | - Chien-Chen Wu
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan.
| | - Cheng-Yin Tseng
- Graduate Institute of Chinese Medicine, China Medical University, Taichung, Taiwan; Section of Infectious Disease, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan.
| | - Jing-Han Fang
- School of Post-Baccalaureate Chinese Medicine, China Medical University, Taichung, Taiwan.
| | - Ching-Ting Lin
- School of Chinese Medicine, China Medical University, Taichung, Taiwan.
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Evaluation of candidate reference genes stability for gene expression analysis by reverse transcription qPCR in Clostridium perfringens. Sci Rep 2022; 12:19434. [PMID: 36372839 PMCID: PMC9659559 DOI: 10.1038/s41598-022-23804-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 11/06/2022] [Indexed: 11/14/2022] Open
Abstract
Identification of stable reference genes for normalization purposes is necessary for obtaining reliable and accurate results of reverse transcription quantitative polymerase chain reaction (RT-qPCR) analyses. To our knowledge, no reference gene(s) have been validated for this purpose in Clostridium perfringens. In this study, the expression profile of ten candidate reference genes from three strains of C. perfringens were assessed for stability under various experimental conditions using geNorm in qbase + . These stability rankings were then compared to stability assessments evaluated by BestKeeper, NormFinder, delta Ct, and RefFinder algorithms. When comparing all the analyses; gyrA, ftsZ, and recA were identified within the most stable genes under the different experimental conditions and were further tested as a set of reference genes for normalization of alpha toxin gene expression over a 22-h period. Depending on the condition, rpoA and rho might also be suitable to include as part of the reference set. Although commonly used for the purpose of normalizing RT-qPCR data, the 16S rRNA gene (rrs) was found to be an unsuitable gene to be used as a reference. This work provides a framework for the selection of a suitable stable reference gene set for data normalization of C. perfringens gene expression.
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Lu P, Gao T, Bai R, Yang J, Xu Y, Chu W, Jiang K, Zhang J, Xu F, Zhao H. Regulation of carbon flux and NADH/NAD + supply to enhance 2,3-butanediol production in Enterobacter aerogenes. J Biotechnol 2022; 358:67-75. [PMID: 36087783 DOI: 10.1016/j.jbiotec.2022.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/23/2022] [Accepted: 09/05/2022] [Indexed: 10/31/2022]
Abstract
As a valuable platform chemical, 2,3-Butanediol (2,3-BDO) has a variety of industrial applications, and its microbial production is particularly attractive as an alternative to petroleum-based production. In this study, the regulation of intracellular carbon flux and NADH/NAD+ was used to increase the 2,3-BDO production of Enterobacter aerogenes. The genes encoding lactate dehydrogenase (ldh) and pyruvate formate lyase (pfl) were disrupted using the λ-Red recombination method and CRISPR-Cas9 to reduce the production of several byproducts and the consumption of NADH. Knockout of ldh or pfl increased intracellular NADH/NAD+ by 111 % and 113 %, respectively. Moreover, two important genes in the 2,3-BDO biosynthesis pathway, acetolactate synthase (budB) and acetoin reductase (budC), were overexpressed in E. aerogenes to further amply the metabolic flux toward 2,3-BDO production. And the overexpression of budB or budC increased intracellular NADH/NAD+ by 46 % and 57 %, respectively. In shake-flask cultivation with sucrose as carbon source, the 2,3-BDO titer of the IAM1183-LPBC was 3.55 times that of the wild type. In the 5-L fermenter, the maximal 2,3-BDO production produced by the IAM1183-LPBC was 2.88 times that of the original strain. This work offers new ideas for promoting the biosynthesis of 2,3-BDO for industrial applications.
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Affiliation(s)
- Ping Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Ting Gao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Ruoxuan Bai
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jiayao Yang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yudong Xu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Wanying Chu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Ke Jiang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jingya Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Fangxu Xu
- Liaoning Province Key Laboratory of Cordyceps Militaris with Functional Value, Experimental Teaching Center, Shenyang Normal University, Shenyang 110034, China
| | - Hongxin Zhao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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Conserved FimK Truncation Coincides with Increased Expression of Type 3 Fimbriae and Cultured Bladder Epithelial Cell Association in Klebsiella quasipneumoniae. J Bacteriol 2022; 204:e0017222. [PMID: 36005809 PMCID: PMC9487511 DOI: 10.1128/jb.00172-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella spp. commonly cause both uncomplicated urinary tract infection (UTI) and recurrent UTI (rUTI). Klebsiella quasipneumoniae, a relatively newly defined species of Klebsiella, has been shown to be metabolically distinct from Klebsiella pneumoniae, but its type 1 and type 3 fimbriae have not been studied. K. pneumoniae uses both type 1 and type 3 fimbriae to attach to host epithelial cells. The type 1 fimbrial operon is well conserved between Escherichia coli and K. pneumoniae apart from fimK, which is unique to Klebsiella spp. FimK contains an N-terminal DNA binding domain and a C-terminal phosphodiesterase (PDE) domain that has been hypothesized to cross-regulate type 3 fimbriae expression via modulation of cellular levels of cyclic di-GMP. Here, we find that a conserved premature stop codon in K. quasipneumoniae fimK results in truncation of the C-terminal PDE domain and that K quasipneumoniae strain KqPF9 cultured bladder epithelial cell association and invasion are dependent on type 3 but not type 1 fimbriae. Further, we show that basal expression of both type 1 and type 3 fimbrial operons as well as cultured bladder epithelial cell association is elevated in KqPF9 relative to uropathogenic K. pneumoniae TOP52. Finally, we show that complementation of KqPF9ΔfimK with the TOP52 fimK allele reduced type 3 fimbrial expression and cultured bladder epithelial cell attachment. Taken together these data suggest that the C-terminal PDE of FimK can modulate type 3 fimbrial expression in K. pneumoniae and its absence in K. quasipneumoniae may lead to a loss of type 3 fimbrial cross-regulation. IMPORTANCE K. quasipneumoniae is often indicated as the cause of opportunistic infections, including urinary tract infection, which affects >50% of women worldwide. However, the virulence factors of K. quasipneumoniae remain uninvestigated. Prior to this work, K. quasipneumoniae and K. pneumoniae had only been distinguished phenotypically by metabolic differences. This work contributes to the understanding of K. quasipneumoniae by evaluating the contribution of type 1 and type 3 fimbriae, which are critical colonization factors encoded by all Klebsiella spp., to K. quasipneumoniae bladder epithelial cell attachment in vitro. We observe clear differences in bladder epithelial cell attachment and regulation of type 3 fimbriae between uropathogenic K. pneumoniae and K. quasipneumoniae that coincide with a structural difference in the fimbrial regulatory gene fimK.
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Gual-de-Torrella A, Delgado-Valverde M, Pérez-Palacios P, Oteo-Iglesias J, Rojo-Molinero E, Macià MD, Oliver A, Pascual Á, Fernández-Cuenca F. Prevalence of the fimbrial operon mrkABCD, mrkA expression, biofilm formation and effect of biocides on biofilm formation in carbapenemase-producing Klebsiella pneumoniae isolates belonging or not to high-risk clones. Int J Antimicrob Agents 2022; 60:106663. [PMID: 35995073 DOI: 10.1016/j.ijantimicag.2022.106663] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 11/03/2021] [Accepted: 08/11/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND The role of mrkA adhesin expression, biofilm production, biofilm viability and biocides in the biofilms of carbapenemase-producing K. pneumoniae isolates was investigated. METHODS Seventeen isolates representing different sequence types and carbapenemases were investigated. mrkA expression was determined by real-time RT-PCR. Biofilm production (25°C and 37°C, with and without humidity) was determined by the crystal violet assay. The effect of isopropanol, povidone-iodine, sodium hypochlorite, chlorhexidine digluconate, benzalkonium chloride, ethanol and triclosan on biofilms was determined. The effect of povidone-iodine on biofilm biomass and thickness was also determined by Confocal Laser Scanning Microscopy (CLSM). RESULTS mrkA expression ranged 28.2-1.3 (high or intermediate-level; 64% of HR clones) and 21.5-1.3 (50% of non-HR clones). At 25°C biofilm formation was observed in 41% of isolates (absence of humidity) and 35% of isolates (presence of humidity), whereas at 37°C it was observed in 76% of isolates, with and without humidity. At 25°C biofilm producers were more frequently observed in HR clones (45% with humidity and 55% without humidity) than non-HR clones (17% with and without humidity). Biofilm viability from day 21 was higher at 25°C than 37°C. The greatest decrease in biofilm formation was observed with povidone iodine (29% decrease), which also decrease biofilm thickness. CONCLUSIONS Biofilm formation in carbapenemase-producing K. pneumoniae is related to mrkA expression. Biofilm formation is affected by temperature (37°C>25°C) whereas humidity has little effect. Biofilm viability is affected by temperature (25°C>37°C). At 25°C, HR clones are more frequently biofilm producers than non-HR clones. Povidone-iodine can decrease biofilm production and biofilm thickness.
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Affiliation(s)
- Ana Gual-de-Torrella
- UGC Enfermedades Infecciosas, Microbiología Clínica y Medicina Preventiva. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla; Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena, CSIC, Universidad de Sevilla, Seville, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Mercedes Delgado-Valverde
- UGC Enfermedades Infecciosas, Microbiología Clínica y Medicina Preventiva. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla; Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena, CSIC, Universidad de Sevilla, Seville, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Patricia Pérez-Palacios
- UGC Enfermedades Infecciosas, Microbiología Clínica y Medicina Preventiva. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla; Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena, CSIC, Universidad de Sevilla, Seville, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain; Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Estrella Rojo-Molinero
- Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma de Mallorca, Spain
| | - María Dolores Macià
- Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma de Mallorca, Spain
| | - Antonio Oliver
- Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma de Mallorca, Spain
| | - Álvaro Pascual
- UGC Enfermedades Infecciosas, Microbiología Clínica y Medicina Preventiva. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla; Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena, CSIC, Universidad de Sevilla, Seville, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain; Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
| | - Felipe Fernández-Cuenca
- UGC Enfermedades Infecciosas, Microbiología Clínica y Medicina Preventiva. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla; Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain.
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High prevalence of mgrB-mediated colistin resistance among carbapenem-resistant Klebsiella pneumoniae is associated with biofilm formation, and can be overcome by colistin-EDTA combination therapy. Sci Rep 2022; 12:12939. [PMID: 35902639 PMCID: PMC9334626 DOI: 10.1038/s41598-022-17083-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/20/2022] [Indexed: 12/02/2022] Open
Abstract
The global prevalence of colistin-resistant Klebsiella pneumoniae (ColRkp) facilitated by chromosomal and plasmid-mediated Ara4N or PEtN-remodeled LPS alterations has steadily increased with increased colistin usage for treating carbapenem-resistant K. pneumoniae (CRkp). Our study demonstrated the rising trend of ColRkp showing extensively and pandrug-resistant characteristics among CRkp, with a prevalence of 28.5%, which was mediated by chromosomal mgrB, pmrB, or phoQ mutations (91.5%), and plasmid-mediated mcr-1.1, mcr-8.1, mcr-8.2 alone or in conjunction with R256G PmrB (8.5%). Several genetic alterations in mgrB (85.1%) with increased expressions of Ara4N-related phoPQ and pmrK were critical for establishing colistin resistance in our isolates. In this study, we discovered the significant associations between extensively drug-resistant bacteria (XDR) and pandrug-resistant bacteria (PDR) ColRkp in terms of moderate, weak or no biofilm-producing abilities, and altered expressions of virulence factors. These ColRkp would therefore be very challenging to treat, emphasizing for innovative therapy to combat these infections. Regardless of the underlying colistin-resistant mechanisms, colistin-EDTA combination therapy in this study produced potent synergistic effects in both in vitro and in vivo murine bacteremia, with no ColRkp regrowth and improved animal survival, implying the significance of colistin-EDTA combination therapy as systemic therapy for unlocking colistin resistance in ColRkp-associated bacteremia.
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Li S, Zhou Y, Yuan T, Feng Z, Zhang Z, Wu Y, Xie Q, Wang J, Li Q, Deng Z, Yu Y, Yuan X. Selection of internal reference gene for normalization of reverse transcription-quantitative polymerase chain reaction analysis in Mycoplasma hyopneumoniae. Front Vet Sci 2022; 9:934907. [PMID: 35937288 PMCID: PMC9355380 DOI: 10.3389/fvets.2022.934907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Mycoplasma hyopneumoniae is the etiological agent of swine enzootic pneumonia (EP), which resulting in considerable economic losses in pig farming globally. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is a major tool for gene expression studies. However, no internal reference genes for normalization of RT-qPCR data of M. hyopneumoniae have been reported. The aim of this study was to screen the most stable genes for RT-qPCR analysis in M. hyopneumoniae under different conditions. Therefore, a total of 13 candidate internal reference genes (rpoC, Lipo, sgaB, oppB, hypo621, oppF, gyrB, uvrA, P146, prfA, proS, gatB, and hypo499) of M. hyopneumoniae filtered according to the reported quantitative proteomic analysis and the 16S rRNA internal reference gene frequently used in other bacteria were selected for RT-qPCR analysis. The mRNAs from different virulence strains (168, 168 L, J, NJ, and LH) at five different growth phases were extracted. The corresponding cycle threshold (Ct) values of the 25 reverse transcribed cDNAs using the 14 candidate genes were determined. Different internal reference genes or combinations were then screened for expression stability analysis using various statistical tools and algorithms, including geNorm, BestKeeper, and NormFinder software, to ensure the reliability of the analysis. Through further comprehensive evaluation of the RefFinder software, it is concluded that the gatB gene was the most suitable internal reference gene for samples of the different virulence strains in different growth phases for M. hyopneumoniae, followed by prfA, hypo499, and gyrB.
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Affiliation(s)
- Shiyang Li
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
- Key Laboratory of Veterinary Biological Engineering and Technology, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Yanqing Zhou
- Key Laboratory of Veterinary Biological Engineering and Technology, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Nanjing, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Ting Yuan
- Key Laboratory of Veterinary Biological Engineering and Technology, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Zhixin Feng
- Key Laboratory of Veterinary Biological Engineering and Technology, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Nanjing, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhenzhen Zhang
- Key Laboratory of Veterinary Biological Engineering and Technology, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Yuzi Wu
- Key Laboratory of Veterinary Biological Engineering and Technology, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Qingyun Xie
- Key Laboratory of Veterinary Biological Engineering and Technology, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Jia Wang
- Key Laboratory of Veterinary Biological Engineering and Technology, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Nanjing, China
| | - Quan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zhibang Deng
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Yanfei Yu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
- Key Laboratory of Veterinary Biological Engineering and Technology, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Nanjing, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- *Correspondence: Yanfei Yu
| | - Xiaomin Yuan
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
- Xiaomin Yuan
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High Osmotic Stress Increases OmpK36 Expression through the Regulation of KbvR to Decrease the Antimicrobial Resistance of Klebsiella pneumoniae. Microbiol Spectr 2022; 10:e0050722. [PMID: 35658577 PMCID: PMC9241633 DOI: 10.1128/spectrum.00507-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella pneumoniae is a pathogen known for its high frequency of antimicrobial resistance. Responses to various environmental stresses during its life can influence the resistance to antibiotics. Here, we demonstrate the role and mechanism of KbvR regulator in the response to environmental osmotic stress and in the effect of osmotic stress on antimicrobial resistance. The kbvR mutant strain exhibited increasing tolerance to high osmotic stress and certain antibiotics, including β-lactams. The expression levels of KbvR and outer membrane porin OmpK36 were upregulated in response to high osmotic stress in the wild type (WT), and the deletion of kbvR decreased the expression level of ompK36. The membrane permeability of the kbvR mutant strain was decreased, which was partly restored through the upregulated expression of OmpK36. The DNA affinity purification sequencing (DAP-seq) and microscale thermophoresis (MST) assay disclosed the binding of KbvR to the promoter of the ompK36 gene, indicating that KbvR directly and positively regulated the expression of OmpK36. The high osmotic stress increased the susceptibility to β-lactams and the expression of ompK36 in the WT strain. However, the increased ompK36 expression and the susceptibility to β-lactams in the kbvR mutant strain under high osmotic stress were lower than those of WT. In conclusion, our study has identified that high osmotic stress in the environment influenced the resistance of K. pneumoniae to antibiotics and that the regulation of KbvR with OmpR on the expression of OmpK36 was involved in countering high osmotic stress to change the antimicrobial resistance. IMPORTANCEKlebsiella pneumoniae is considered a global threat because of the rising prevalence of multidrug-resistant strains and their optimal adaptation to clinical environments and the human host. The sensing and adaption abilities of bacteria to the environmental osmotic stress can change the expression of their outer membrane porins, membrane permeability, and resistance to antibiotics. This study reports that KbvR is a newly found regulator that can be upregulated under high osmotic stress and directly regulate the expression of OmpK36 to change the resistance of K. pneumoniae to β-lactam antibiotics. The results demonstrate how adaptation to high osmotic stress changes the sensitivity of K. pneumoniae to antibiotics. The mechanism can be used to sensitize bacteria to antibiotics and highlight new potential strategies for exploiting shared constraints in governing adaptation to diverse environmental challenges.
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Spring S, Rohde M, Bunk B, Spröer C, Will SE, Neumann-Schaal M. New insights into the energy metabolism and taxonomy of Deferribacteres revealed by the characterization of a new isolate from a hypersaline microbial mat. Environ Microbiol 2022; 24:2543-2575. [PMID: 35415868 DOI: 10.1111/1462-2920.15999] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/04/2022] [Indexed: 12/13/2022]
Abstract
Strain L21-Ace-BEST , isolated from a lithifying cyanobacterial mat, could be assigned to a novel species and genus within the Deferribacteres. It is an important model organism for the study of anaerobic acetate degradation under hypersaline conditions. The metabolism of strain L21-Ace-BEST was characterized by biochemical studies, comparative genome analyses, and the evaluation of gene expression patterns. The central metabolic pathway is the citric acid cycle, which is mainly controlled by the enzyme succinyl-CoA:acetate-CoA transferase. The potential use of a reversed oxidative citric acid cycle to fix CO2 has been revealed through genome analysis. However, no autotrophic growth was detected in this strain, whereas sulfide and H2 can be used mixotrophically. Preferred electron acceptors for the anaerobic oxidation of acetate are nitrate, fumarate and DMSO, while oxygen can be utilized only under microoxic conditions. Aerotolerant growth by fermentation was observed at higher oxygen concentrations. The redox cycling of sulfur/sulfide enables the generation of reducing power for the assimilation of acetate during growth and could prevent the over-reduction of cells in stationary phase. Extracellular electron transfer appears to be an essential component of the respiratory metabolism in this clade of Deferribacteres and may be involved in the reduction of nitrite to ammonium. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Braunschweig, Germany
| | - Boyke Bunk
- Department Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Eva Will
- Research Group Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Research Group Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Antimicrobial Susceptibility Testing: A Comprehensive Review of Currently Used Methods. Antibiotics (Basel) 2022; 11:antibiotics11040427. [PMID: 35453179 PMCID: PMC9024665 DOI: 10.3390/antibiotics11040427] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Antimicrobial resistance (AMR) has emerged as a major threat to public health globally. Accurate and rapid detection of resistance to antimicrobial drugs, and subsequent appropriate antimicrobial treatment, combined with antimicrobial stewardship, are essential for controlling the emergence and spread of AMR. This article reviews common antimicrobial susceptibility testing (AST) methods and relevant issues concerning the advantages and disadvantages of each method. Although accurate, classic technologies used in clinical microbiology to profile antimicrobial susceptibility are time-consuming and relatively expensive. As a result, physicians often prescribe empirical antimicrobial therapies and broad-spectrum antibiotics. Although recently developed AST systems have shown advantages over traditional methods in terms of testing speed and the potential for providing a deeper insight into resistance mechanisms, extensive validation is required to translate these methodologies to clinical practice. With a continuous increase in antimicrobial resistance, additional efforts are needed to develop innovative, rapid, accurate, and portable diagnostic tools for AST. The wide implementation of novel devices would enable the identification of the optimal treatment approaches and the surveillance of antibiotic resistance in health, agriculture, and the environment, allowing monitoring and better tackling the emergence of AMR.
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Arora-Williams K, Holder C, Secor M, Ellis H, Xia M, Gnanadesikan A, Preheim SP. Abundant and persistent sulfur-oxidizing microbial populations are responsive to hypoxia in the Chesapeake Bay. Environ Microbiol 2022; 24:2315-2332. [PMID: 35304940 PMCID: PMC9310604 DOI: 10.1111/1462-2920.15976] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 03/07/2022] [Accepted: 03/12/2022] [Indexed: 01/04/2023]
Abstract
The number, size and severity of aquatic low‐oxygen dead zones are increasing worldwide. Microbial processes in low‐oxygen environments have important ecosystem‐level consequences, such as denitrification, greenhouse gas production and acidification. To identify key microbial processes occurring in low‐oxygen bottom waters of the Chesapeake Bay, we sequenced both 16S rRNA genes and shotgun metagenomic libraries to determine the identity, functional potential and spatiotemporal distribution of microbial populations in the water column. Unsupervised clustering algorithms grouped samples into three clusters using water chemistry or microbial communities, with extensive overlap of cluster composition between methods. Clusters were strongly differentiated by temperature, salinity and oxygen. Sulfur‐oxidizing microorganisms were found to be enriched in the low‐oxygen bottom water and predictive of hypoxic conditions. Metagenome‐assembled genomes demonstrate that some of these sulfur‐oxidizing populations are capable of partial denitrification and transcriptionally active in a prior study. These results suggest that microorganisms capable of oxidizing reduced sulfur compounds are a previously unidentified microbial indicator of low oxygen in the Chesapeake Bay and reveal ties between the sulfur, nitrogen and oxygen cycles that could be important to capture when predicting the ecosystem response to remediation efforts or climate change.
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Affiliation(s)
- Keith Arora-Williams
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Christopher Holder
- Department of Earth and Planetary Sciences, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Maeve Secor
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Hugh Ellis
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Meng Xia
- Department of Natural Sciences, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | - Anand Gnanadesikan
- Department of Earth and Planetary Sciences, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Sarah P Preheim
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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Xu C, Dong N, Chen K, Yang X, Zeng P, Hou C, Chi Chan EW, Yao X, Chen S. Bactericidal, anti-biofilm, and anti-virulence activity of vitamin C against carbapenem-resistant hypervirulent Klebsiella pneumoniae. iScience 2022; 25:103894. [PMID: 35243252 PMCID: PMC8873610 DOI: 10.1016/j.isci.2022.103894] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/15/2021] [Accepted: 02/04/2022] [Indexed: 12/27/2022] Open
Affiliation(s)
- Chen Xu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Ning Dong
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Kaichao Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Xuemei Yang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Ping Zeng
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Changshun Hou
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Edward Wai Chi Chan
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Xi Yao
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
- Corresponding author
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Shen L, Zhang J, Xue J, Du L, Yuan L, Nie H, Dai S, Yu Q, Li Y. Regulation of ECP fimbriae-related genes by the transcriptional regulator RcsAB in Klebsiella pneumoniae NTUH-K2044. J Basic Microbiol 2022; 62:593-603. [PMID: 35132658 DOI: 10.1002/jobm.202100595] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 01/06/2022] [Accepted: 01/15/2022] [Indexed: 11/11/2022]
Abstract
Klebsiella pneumoniae is one of the major pathogens causing nosocomial infections. The regulator of capsule synthesis (Rcs) system is a complex signal transduction pathway that is involved in the regulation of virulence factors of K. pneumoniae as an important transcriptional regulator. The RcsAB box-like sequence was found to be present in the promoter-proximal regions of ykgK, one of the ECP fimbriae-related genes, which suggested the expression of ECP fimbriae may be regulated by RcsAB. The ykgK gene in K. pneumoniae has 86% similarity to the ecpR gene in Escherichia coli. Nucleotide sequence alignment revealed a similar ECP fimbriae gene cluster including six genes in K. pneumoniae, which was proved to be on the same operon in this study. The electrophoretic mobility shift assay and DNase I assay, relative fluorescence expression, β-galactosidase activity, and relative gene expression of ykgK in the wild-type and mutant strains were performed to determine the transcriptional regulation mechanism of RcsAB on ECP fimbriae. The mutant ΔykgK and complementary strain ΔykgK/cΔykgK were constructed to complete the Galleria mellonella larvae infection experiment and biofilm formation assay. This study showed that RcsAB binds directly to the promoter region of the ykgK gene to positively regulate ECP fimbriae-related gene clusters, and then positively affect the biofilm formation.
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Affiliation(s)
- Lifei Shen
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Jiaxue Zhang
- Chongqing Jiangbei District Center for Disease Control and Prevention, Chongqing, China
| | - Jian Xue
- Zunyi Medical and Pharmaceutical College, Zunyi, China
| | - Ling Du
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Lingyue Yuan
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Hao Nie
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Sue Dai
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Qian Yu
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Yingli Li
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
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42
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OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1578-1585. [DOI: 10.1093/jac/dkac078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/16/2022] [Indexed: 11/14/2022] Open
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Early Response of Antimicrobial Resistance and Virulence Genes Expression in Classical, Hypervirulent, and Hybrid hvKp-MDR Klebsiella pneumoniae on Antimicrobial Stress. Antibiotics (Basel) 2021; 11:antibiotics11010007. [PMID: 35052884 PMCID: PMC8773033 DOI: 10.3390/antibiotics11010007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/16/2022] Open
Abstract
Klebsiella pneumoniae is an increasingly important hospital pathogen. Classical K. pneumoniae (cKp) and hypervirulent K. pneumoniae (hvKp) are two distinct evolutionary genetic lines. The recently ongoing evolution of K. pneumoniae resulted in the generation of hybrid hvKP-MDR strains. K. pneumoniae distinct isolates (n = 70) belonged to 20 sequence types with the prevalence of ST395 (27.1%), ST23 (18.6%), ST147 (15.7%), and ST86 (7.1%), and 17 capsular types with the predominance of K2 (31.4%), K57 (18.6%), K64 (10.0%), K1 (5.7%) were isolated from patients of the Moscow neurosurgery ICU in 2014-2019. The rate of multi-drug resistant (MDR) and carbapenem-resistant phenotypes were 84.3% and 45.7%, respectively. Whole-genome sequencing of five selected strains belonging to cKp (ST395K47 and ST147K64), hvKp (ST86K2), and hvKp-MDR (ST23K1 and ST23K57) revealed blaSHV, blaTEM, blaCTX, blaOXA-48, and blaNDM beta-lactamase genes; acr, oqx, kpn, kde, and kex efflux genes; and K. pneumoniae virulence genes. Selective pressure of 100 mg/L ampicillin or 10 mg/L ceftriaxone induced changes of expression levels for named genes in the strains belonging to cKp, hvKp, and hybrid hvKp-MDR. Obtained results seem to be important for epidemiologists and clinicians for enhancing knowledge about hospital pathogens.
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Masood KI, Umar S, Hasan Z, Farooqi J, Razzak SA, Jabeen N, Rao J, Shakoor S, Hasan R. Lipid A-Ara4N as an alternate pathway for (colistin) resistance in Klebsiella pneumonia isolates in Pakistan. BMC Res Notes 2021; 14:449. [PMID: 34906210 PMCID: PMC8670247 DOI: 10.1186/s13104-021-05867-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/29/2021] [Indexed: 11/23/2022] Open
Abstract
Objectives This study aimed to explore mechanism of colistin resistance amongst Klebsiella pneumoniae isolates through plasmid mediated mcr-1 gene in Pakistan. Carbapenem and Colistin resistant K. pneumoniae isolates (n = 34) stored at − 80 °C as part of the Aga Khan University Clinical Laboratory strain bank were randomly selected and subjected to mcr-1 gene PCR. To investigate mechanisms of resistance, other than plasmid mediated mcr-1 gene, whole genome sequencing was performed on 8 clinical isolates, including 6 with colistin resistance (MIC > 4 μg/ml) and 2 with intermediate resistance to colistin (MIC > 2 μg/ml). Results RT-PCR conducted revealed absence of mcr-1 gene in all isolates tested. Whole genome sequencing results revealed modifications in Lipid A-Ara4N pathway. Modifications in Lipid A-Ara4N pathway were detected in ArnA_ DH/FT, UgdH, ArnC and ArnT genes. Mutation in ArnA_ DH/FT gene were detected in S3, S5, S6 and S7 isolates. UgdH gene modifications were found in all isolates except S3, mutations in ArnC were present in all except S1, S2 and S8 and ArnT were detected in all except S4 and S7. In the absence of known mutations linked with colistin resistance, lipid pathway modifications may possibly explain the phenotype resistance to colistin, but this needs further exploration. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05867-3.
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Affiliation(s)
- Kiran Iqbal Masood
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Seema Umar
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Joveria Farooqi
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Safina Abdul Razzak
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Nazish Jabeen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Jason Rao
- Health Security Partners, Washington, DC, 20009, USA
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan. .,Department of Infection Biology, Faculty Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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45
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Sun D, Ge X, Tang S, Liu Y, Sun J, Zhou Y, Luo L, Xu Z, Zhou W, Sheng J. Bacterial Characteristics of Intestinal Tissues From Patients With Crohn's Disease. Front Cell Infect Microbiol 2021; 11:711680. [PMID: 34869050 PMCID: PMC8635149 DOI: 10.3389/fcimb.2021.711680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Background and Aims It is believed that intestinal bacteria play an indispensable role in promoting intestinal inflammation. However, the characteristics of these tissue-associated bacteria remain elusive. The aim of this study is to explore the bacterial loads, compositions, and structures in the noninflamed mucosa, inflamed mucosa, and creeping fat taken from patients with Crohn’s disease (CD). Methods Noninflamed mucosa, inflamed mucosa, and creeping fat samples were obtained from 10 surgical patients suffering from CD. Total bacterial DNA was extracted in a sterile environment using aseptic techniques. The V3–V4 regions of bacterial 16S rDNA were amplified and analysed using standard microbiological methods. qPCR was used to confirm the change in abundance of specific species in additional 30 independent samples. Results Inflamed mucosa exhibited the highest bacterial load (3.8 and 12 times more than that of non-inflamed mucosa and creeping fat) and species diversity. The relative abundance of Proteobacteria was dominant in most samples and was negatively associated with Firmicutes. Moreover, the relative abundances of Methylobacterium and Leifsonia in creeping fat significantly increased more than twice as much as other tissue types. The bacterial community structure analysis showed that the bacterial samples from the same individual clustered more closely. Conclusion This study reveals the significant differences in bacterial load, species diversity, and composition among different intestinal tissue types of CD patients and confirms that the bacterial samples from the same individual are highly correlated. Our findings will shed light on fully revealing the characteristics of tissue-associated bacteria and their roles in CD pathogenesis.
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Affiliation(s)
- Desen Sun
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China.,Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China.,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, China
| | - Xiaolong Ge
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China.,Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shasha Tang
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yaxin Liu
- Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Sun
- Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuping Zhou
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Liang Luo
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengping Xu
- Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Zhou
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinghao Sheng
- Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China.,Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Nale JY, Al-Tayawi TS, Heaphy S, Clokie MRJ. Impact of Phage CDHS-1 on the Transcription, Physiology and Pathogenicity of a Clostridioides difficile Ribotype 027 Strain, R20291. Viruses 2021; 13:v13112262. [PMID: 34835068 PMCID: PMC8619979 DOI: 10.3390/v13112262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 01/05/2023] Open
Abstract
All known Clostridioides difficile phages encode integrases rendering them potentially able to lyse or lysogenise bacterial strains. Here, we observed the infection of the siphovirus, CDHS-1 on a ribotype 027 strain, R20291 and determined the phage and bacterial gene expression profiles, and impacts of phage infection on bacterial physiology and pathogenicity. Using RNA-seq and RT-qPCR we analysed transcriptomic changes during early, mid-log and late phases of phage replication at an MOI of 10. The phage has a 20 min latent period, takes 80 min to lyse cells and a burst size of ~37. All phage genes are highly expressed during at least one time point. The Cro/C1-transcriptional regulator, ssDNA binding protein and helicase are expressed early, the holin is expressed during the mid-log phase and structural proteins are expressed from mid-log to late phase. Most bacterial genes, particularly the metabolism and toxin production/regulatory genes, were downregulated from early phage replication. Phage-resistant strains and lysogens showed reduced virulence during Galleria mellonella colonization as ascertained by the larval survival and expression of growth (10), reproduction (2) and infection (2) marker genes. These data suggest that phage infection both reduces colonization and negatively impacts bacterial pathogenicity, providing encouraging data to support the development of this phage for therapy to treat C. difficile infection.
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Malvidin Protects against and Repairs Peptic Ulcers in Mice by Alleviating Oxidative Stress and Inflammation. Nutrients 2021; 13:nu13103312. [PMID: 34684313 PMCID: PMC8537945 DOI: 10.3390/nu13103312] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 12/29/2022] Open
Abstract
Peptic ulcer episodes cause damage to the stomach and intestine, with inflammatory cell infiltration and oxidative stress as the main players. In this study, we investigated the potential of anthocyanidin malvidin for preventive and curative peptic ulcer treatment. The anthocyanidin effects were examined in gastric ulcer mouse models induced by ethanol, non-steroidal anti-inflammatory drugs (NSAIDs), ischemia-reperfusion (IR), acetic acid and duodenal ulcer induced by polypharmacy. Expression levels of oxidative and inflammatory genes were measured to investigate the mechanism of anthocyanin activity. At a dose of 5 mg·kg−1, Malvidin prevented gastric ulcer induction by ethanol, NSAID and repaired the tissue after 6 days of IR. Moreover, the anthocyanidin accelerated the healing of acetic acid-induced ulcer, increased the gene expression of EGF and COX-1, and downregulated MMP-9. Anthocyanin treatment mitigated the effect of polypharmacy on inflammation and oxidative stress observed in the intestine. Additionally, the compound downregulated cytokine expression and TLR4 and upregulated HMOX-1 and IL-10, exhibiting protective activity in the mouse gut. Malvidin thus prevented gastric and duodenal ulcers due to prominent anti-inflammatory and antioxidative effects on the gastrointestinal tract that were related to gene expression modulation and an increase in endogenous defense mechanisms.
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Arizzi M, Morra S, Gilardi G, Pugliese M, Gullino ML, Valetti F. Improving sustainable hydrogen production from green waste: [FeFe]-hydrogenases quantitative gene expression RT-qPCR analysis in presence of autochthonous consortia. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:182. [PMID: 34530890 PMCID: PMC8444407 DOI: 10.1186/s13068-021-02028-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 08/28/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Bio-hydrogen production via dark fermentation of low-value waste is a potent and simple mean of recovering energy, maximising the harvesting of reducing equivalents to produce the cleanest fuel amongst renewables. Following several position papers from companies and public bodies, the hydrogen economy is regaining interest, especially in combination with circular economy and the environmental benefits of short local supply chains, aiming at zero net emission of greenhouse gases (GHG). The biomasses attracting the largest interest are agricultural and urban green wastes (pruning of trees, collected leaves, grass clippings from public parks and boulevards), which are usually employed in compost production, with some concerns over the GHG emission during the process. Here, an alternative application of green wastes, low-value compost and intermediate products (partially composted but unsuitable for completing the process) is studied, pointing at the autochthonous microbial consortium as an already selected source of implementation for biomass degradation and hydrogen production. The biocatalysts investigated as mainly relevant for hydrogen production were the [FeFe]-hydrogenases expressed in Clostridia, given their very high turnover rates. RESULTS Bio-hydrogen accumulation was related to the modulation of gene expression of multiple [FeFe]-hydrogenases from two strains (Clostridium beijerinckii AM2 and Clostridium tyrobutyricum AM6) isolated from the same waste. Reverse Transcriptase quantitative PCR (RT-qPCR) was applied over a period of 288 h and the RT-qPCR results showed that C. beijerinckii AM2 prevailed over C. tyrobutyricum AM6 and a high expression modulation of the 6 different [FeFe]-hydrogenase genes of C. beijerinckii in the first 23 h was observed, sustaining cumulative hydrogen production of 0.6 to 1.2 ml H2/g VS (volatile solids). These results are promising in terms of hydrogen yields, given that no pre-treatment was applied, and suggested a complex cellular regulation, linking the performance of dark fermentation with key functional genes involved in bio-H2 production in presence of the autochthonous consortium, with different roles, time, and mode of expression of the involved hydrogenases. CONCLUSIONS An applicative outcome of the hydrogenases genes quantitative expression analysis can be foreseen in optimising (on the basis of the acquired functional data) hydrogen production from a nutrient-poor green waste and/or low added value compost, in a perspective of circular bioeconomy.
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Affiliation(s)
- M Arizzi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
- Acea Engineering Laboratories Research Innovation SpA, Roma, Italy
| | - S Morra
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - G Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
| | - M Pugliese
- Centre of Competence for Innovation in Agro-Environmental Field (Agroinnova) and DiSAFA, University of Torino, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
- AgriNewTech Srl, Via Livorno 60, 10140, Torino, Italy
| | - M L Gullino
- Centre of Competence for Innovation in Agro-Environmental Field (Agroinnova) and DiSAFA, University of Torino, Largo Paolo Braccini 2, 10095, Grugliasco, TO, Italy
- AgriNewTech Srl, Via Livorno 60, 10140, Torino, Italy
| | - F Valetti
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy.
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Mulyanti D, Soewandhi SN, Riani C. Insertion of prpoD_rpoS fragment enhances expression of recombinant protein by dps auto-inducible promoter in Escherichia coli. Mol Biol Rep 2021; 48:5833-5845. [PMID: 34342815 DOI: 10.1007/s11033-021-06562-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Nowadays, recombinant therapeutic proteins have been widely produced and consumed. For the safety and effectiveness of the protein production, an auto-inducible expression vector is required to replace inducer interference, which is uneconomic and could be harmful. In this research, an auto-inducible expression plasmid, pCAD2_sod (a pBR322 derivate plasmid), which was under dps (RpoS-dependent gene) promoter control, was modified to provide RpoS at earlier phase. Hence, accumulates more target protein and resulting a new plasmid, pCAD2+_sod. pCAD2_sod had been constructed to automatically induces the expression of recombinant superoxide dismutase (SOD) from Staphylococcus equorum (rMnSODSeq) in the stationary growth phase of Escherichia coli. This work aimed to obtain pCAD2+_sod and determine the expression level of rMnSODSeq on mRNA and protein level. METHOD AND RESULTS A synthetic rpoS coding region under rpoD promoter control (prpoD_rpoS) was inserted to pCAD2_sod and generated pCAD2+_sod. The rMnSODSeq (24.3 kDa) produced from pCAD2+_sod was ~ 1.5 fold higher at 37 °C and more intense at 43 °C compared to that from pCAD2_sod, likewise shifted to earlier phase (after 1 h of incubation), as shown in the SDS-PAGE. The dismutase activity was also retained after zymography assay. The mRNA level from pCAD2+_sod was determined by qPCR and gave quantification cycle (Cq) values of cDNA lowest among others. It made the relative quantification (RQ) of the mRNA expression towards rho reference gene were high. CONCLUSIONS The prpoD_rpoS insertion shifts and increases the rMnSODSeq production from stationary to exponential phase. The pCAD2+_sod plasmid is potential for further recombinant protein productions.
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Affiliation(s)
- Dina Mulyanti
- School of Pharmacy, Bandung Institute of Technology, Ganesha 10, Bandung, 40132, Indonesia.,Department of Pharmacy, Bandung Islamic University, Ranggagading 8, Bandung, 40116, Indonesia
| | | | - Catur Riani
- School of Pharmacy, Bandung Institute of Technology, Ganesha 10, Bandung, 40132, Indonesia.
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Pacheco T, Gomes AÉI, Siqueira NMG, Assoni L, Darrieux M, Venter H, Ferraz LFC. SdiA, a Quorum-Sensing Regulator, Suppresses Fimbriae Expression, Biofilm Formation, and Quorum-Sensing Signaling Molecules Production in Klebsiella pneumoniae. Front Microbiol 2021; 12:597735. [PMID: 34234747 PMCID: PMC8255378 DOI: 10.3389/fmicb.2021.597735] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 04/26/2021] [Indexed: 12/24/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative pathogen that has become a worldwide concern due to the emergence of multidrug-resistant isolates responsible for various invasive infectious diseases. Biofilm formation constitutes a major virulence factor for K. pneumoniae and relies on the expression of fimbrial adhesins and aggregation of bacterial cells on biotic or abiotic surfaces in a coordinated manner. During biofilm aggregation, bacterial cells communicate with each other through inter- or intra-species interactions mediated by signallng molecules, called autoinducers, in a mechanism known as quorum sensing (QS). In most Gram-negative bacteria, intra-species communication typically involves the LuxI/LuxR system: LuxI synthase produces N-acyl homoserine lactones (AHLs) as autoinducers and the LuxR transcription factor is their cognate receptor. However, K. pneumoniae does not produce AHL but encodes SdiA, an orphan LuxR-type receptor that responds to exogenous AHL molecules produced by other bacterial species. While SdiA regulates several cellular processes and the expression of virulence factors in many pathogens, the role of this regulator in K. pneumoniae remains unknown. In this study, we describe the characterization of sdiA mutant strain of K. pneumoniae. The sdiA mutant strain has increased biofilm formation, which correlates with the increased expression of type 1 fimbriae, thus revealing a repressive role of SdiA in fimbriae expression and bacterial cell adherence and aggregation. On the other hand, SdiA acts as a transcriptional activator of cell division machinery assembly in the septum, since cells lacking SdiA regulator exhibited a filamentary shape rather than the typical rod shape. We also show that K. pneumoniae cells lacking SdiA regulator present constant production of QS autoinducers at maximum levels, suggesting a putative role for SdiA in the regulation of AI-2 production. Taken together, our results demonstrate that SdiA regulates cell division and the expression of virulence factors such as fimbriae expression, biofilm formation, and production of QS autoinducers in K. pneumoniae.
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Affiliation(s)
- Thaisy Pacheco
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Ana Érika Inácio Gomes
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | | | - Lucas Assoni
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Michelle Darrieux
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Lúcio Fábio Caldas Ferraz
- Laboratório de Biologia Molecular de Microrganismos, Universidade São Francisco, Bragança Paulista, Brazil
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