101
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Lv Z, Zhang X, Zhao K, Du L, Wang X, Chu Y, Huang T. Co-immunization with DNA vaccines encoding yidR and IL-17 augments host immune response against Klebsiella pneumoniae infection in mouse model. Virulence 2024; 15:2345019. [PMID: 38656137 PMCID: PMC11057650 DOI: 10.1080/21505594.2024.2345019] [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: 08/10/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Klebsiella pneumoniae is an important gram-negative bacterium that causes severe respiratory and healthcare-associated infections. Although antibiotic therapy is applied to treat severe infections caused by K. pneumoniae, drug-resistant isolates pose a huge challenge to clinical practices owing to adverse reactions and the mismanagement of antibiotics. Several studies have attempted to develop vaccines against K. pneumoniae, but there are no licensed vaccines available for the control of K. pneumoniae infection. In the current study, we constructed a novel DNA vaccine, pVAX1-YidR, which encodes a highly conserved virulence factor YidR and a recombinant expression plasmid pVAX1-IL-17 encoding Interleukin-17 (IL-17) as a molecular adjuvant. Adaptive immune responses were assessed in immunized mice to compare the immunogenicity of the different vaccine schemes. The results showed that the targeted antigen gene was expressed in HEK293T cells using an immunofluorescence assay. Mice immunized with pVAX1-YidR elicited a high level of antibodies, induced strong cellular immune responses, and protected mice from K. pneumoniae challenge. Notably, co-immunization with pVAX1-YidR and pVAX1-IL-17 significantly augmented host adaptive immune responses and provided better protection against K. pneumoniae infections in vaccinated mice. Our study demonstrates that combined DNA vaccines and molecular adjuvants is a promising strategy to develop efficacious antibacterial vaccines against K. pneumoniae infections.
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Affiliation(s)
- Zheng Lv
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of pharmacy, Chengdu University, Chengdu, China
| | - Xuan Zhang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of pharmacy, Chengdu University, Chengdu, China
| | - Kelei Zhao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of pharmacy, Chengdu University, Chengdu, China
| | - Lianming Du
- Institute for Advanced Study, Chengdu University, Chengdu, China
| | - Xinrong Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of pharmacy, Chengdu University, Chengdu, China
| | - Yiwen Chu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of pharmacy, Chengdu University, Chengdu, China
| | - Ting Huang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of pharmacy, Chengdu University, Chengdu, China
- Antiinfective Agent Creation Engineering Research Centre of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, Chengdu, China
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102
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Hasan MK, Jeannine Brady L. Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes. J Struct Biol X 2024; 10:100106. [PMID: 39040530 PMCID: PMC11261784 DOI: 10.1016/j.yjsbx.2024.100106] [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: 02/23/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
K-Homology domain (KH domain) proteins bind single-stranded nucleic acids, influence protein-protein interactions of proteins that harbor them, and are found in all kingdoms of life. In concert with other functional protein domains KH domains contribute to a variety of critical biological activities, often within higher order machineries including membrane-localized protein complexes. Eukaryotic KH domain proteins are linked to developmental processes, morphogenesis, and growth regulation, and their aberrant expression is often associated with cancer. Prokaryotic KH domain proteins are involved in integral cellular activities including cell division and protein translocation. Eukaryotic and prokaryotic KH domains share structural features, but are differentiated based on their structural organizations. In this review, we explore the structure/function relationships of known examples of KH domain proteins, and highlight cases in which they function within or at membrane surfaces. We also summarize examples of KH domain proteins that influence bacterial virulence and pathogenesis. We conclude the article by discussing prospective research avenues that could be pursued to better investigate this largely understudied protein category.
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Affiliation(s)
- Md Kamrul Hasan
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - L. Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
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103
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Staudacher M, Hotz JF, Kriz R, Schefberger K, Schneider L, Spettel K, Starzengruber P, Hagemann JB, Leutzendorff A, Burgmann H, Lagler H. Differences in oxazolidinone resistance mechanisms and small colony variants emergence of Staphylococcus aureus induced in an in vitro resistance development model. Emerg Microbes Infect 2024; 13:2292077. [PMID: 38055244 PMCID: PMC10849000 DOI: 10.1080/22221751.2023.2292077] [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: 10/25/2022] [Accepted: 12/03/2023] [Indexed: 12/07/2023]
Abstract
Invasive Staphylococcus aureus infections are associated with a high burden of disease, case fatality rate and healthcare costs. Oxazolidinones such as linezolid and tedizolid are considered potential treatment choices for conditions involving methicillin resistance or penicillin allergies. Additionally, they are being investigated as potential inhibitors of toxins in toxin-mediated diseases. In this study, linezolid and tedizolid were evaluated in an in vitro resistance development model for induction of resistance in S. aureus. Whole genome sequencing was conducted to elucidate resistance mechanisms through the identification of causal mutations. After inducing resistance to both linezolid and tedizolid, several partially novel single nucleotide variants (SNVs) were detected in the rplC gene, which encodes the 50S ribosome protein L3 in S. aureus. These SNVs were found to decrease the binding affinity, potentially serving as the underlying cause for oxazolidinone resistance. Furthermore, in opposite to linezolid we were able to induce phenotypically small colony variants of S. aureus after induction of resistance with tedizolid for the first time in literature. In summary, even if different antibiotic concentrations were required and SNVs were detected, the principal capacity of S. aureus to develop resistance to oxazolidinones seems to differ between linezolid and tedizolid in-vivo but not in vitro. Stepwise induction of resistance seems to be a time and cost-effective tool for assessing resistance evolution. Inducted-resistant strains should be examined and documented for epidemiological reasons, if MICs start to rise or oxazolidinone-resistant S. aureus outbreaks become more frequent.
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Affiliation(s)
- Moritz Staudacher
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- Department of Angiology, Medical University of Vienna, Vienna, Austria
| | - Julian Frederic Hotz
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- Department of Neurology, Evangelic Hospital Vienna, Vienna, Austria
| | - Richard Kriz
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Katharina Schefberger
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Lisa Schneider
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Kathrin Spettel
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Peter Starzengruber
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | | | - Amelie Leutzendorff
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Heinz Burgmann
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Heimo Lagler
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
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104
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Wang H, Li H, Liu Z, Zhu Z, Cao Y. Activity of thonningianin A against Candida albicans in vitro and in vivo. Appl Microbiol Biotechnol 2024; 108:96. [PMID: 38212967 PMCID: PMC10784352 DOI: 10.1007/s00253-023-12996-1] [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: 09/06/2023] [Revised: 12/17/2023] [Accepted: 12/26/2023] [Indexed: 01/13/2024]
Abstract
Fungal infections are increasing rapidly, and antifungal agents used in clinics are limited. Therefore, novel antifungal agents with high efficiency are urgently required. In this study, we investigated the antifungal activity of thonningianin A (THA), a natural compound that is widely found in plants. We first determined the activity of THA against Candida albicans, one of the most common fungal pathogens, and found that THA showed antifungal activity against all C. albicans tested, including several fluconazole-resistant isolates. THA also inhibits the growth of non-Candida albicans species. In addition, THA displayed antibiofilm activity and could not only inhibit biofilm formation but also destroy mature biofilms. The in vivo antifungal efficacy of THA was confirmed in a Galleria mellonella infection model. Further studies revealed that THA could enhance intracellular reactive oxygen species (ROS) production and regulate the transcription of several redox-related genes. Specifically, caspase activity and expression of CaMCA1, a caspase-encoding gene in C. albicans, were remarkably increased upon THA treatment. Consistent with this, in the presence of THA, the Camca1 null mutant displayed higher survival rates and reduced caspase activity compared to the wild-type or CaMCA1-reintroduced strains, indicating an important role of CaMCA1 in the antifungal activity of THA. Taken together, our results indicate that THA possesses excellent antifungal activity and may be a promising novel antifungal candidate. KEY POINTS: • THA exhibits activity against Candida species, including fluconazole-resistant isolates • THA inhibits biofilm formation and destroys mature biofilm • Elevated ROS production and CaMCA1-mediated caspase activity are involved in the antifungal mechanisms of THA.
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Affiliation(s)
- Hui Wang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China
| | - Hui Li
- Department of Dermatology, Changhai Hospital, Naval Medical University, Shanghai, 200438, China
| | - ZhiWei Liu
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China
| | - ZhenYu Zhu
- School of Pharmacy, Naval Medical University, Shanghai, 200433, China.
| | - YingYing Cao
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China.
- Shanghai Engineering Research Center for Topical Chinese Medicine, Shanghai, 200443, China.
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105
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Larsen TG, Samaniego Castruita JA, Worning P, Westh H, Bartels MD. Within-host genomic evolution of methicillin-resistant Staphylococcus aureus in long-term carriers. Appl Microbiol Biotechnol 2024; 108:95. [PMID: 38212970 PMCID: PMC10784349 DOI: 10.1007/s00253-023-12932-3] [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: 08/01/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 01/13/2024]
Abstract
Assessing the genomic evolution of Staphylococcus aureus can help us understand how the bacteria adapt to its environment. In this study, we aimed to assess the mutation rate within 144 methicillin-resistant Staphylococcus aureus (MRSA) carriers with a carriage time from 4 to 11 years, including some carriers who belonged to the same households. We found that 23 of the 144 individuals had completely different MRSA types over time and were therefore not long-term carriers of the same MRSA. From the remaining 121 individuals, we performed whole-genome sequencing (WGS) on 424 isolates and then compared these pairwise using core genome multilocus sequence typing (cgMLST) and single-nucleotide polymorphism (SNP) analyses. We found a median within-host mutation rate in long-term MRSA carriers of 4.9 (3.4-6.9) SNPs/genome/year and 2.7 (1.8-4.2) allelic differences/genome/year, when excluding presumed recombination. Furthermore, we stratified the cohort into subgroups and found no significant difference between the median mutation rate of members of households, individuals with presumed continued exposure, e.g., from travel and persons without known continued exposure. Finally, we found that SNPs occurred at random within the genes in our cohort. KEY POINTS: • Median mutation rate within long-term MRSA carriers of 4.9 (3.4-6.9) SNPs/genome/year • Similar median mutation rates in subgroups (households, travelers) • No hotspots for SNPs within the genome.
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Affiliation(s)
- Tine Graakjær Larsen
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | | | - Peder Worning
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mette Damkjær Bartels
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
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106
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Liao H, Lyon CJ, Ying B, Hu T. Climate change, its impact on emerging infectious diseases and new technologies to combat the challenge. Emerg Microbes Infect 2024; 13:2356143. [PMID: 38767202 PMCID: PMC11138229 DOI: 10.1080/22221751.2024.2356143] [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: 02/06/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024]
Abstract
ABSTRACTImproved sanitation, increased access to health care, and advances in preventive and clinical medicine have reduced the mortality and morbidity rates of several infectious diseases. However, recent outbreaks of several emerging infectious diseases (EIDs) have caused substantial mortality and morbidity, and the frequency of these outbreaks is likely to increase due to pathogen, environmental, and population effects driven by climate change. Extreme or persistent changes in temperature, precipitation, humidity, and air pollution associated with climate change can, for example, expand the size of EID reservoirs, increase host-pathogen and cross-species host contacts to promote transmission or spillover events, and degrade the overall health of susceptible host populations leading to new EID outbreaks. It is therefore vital to establish global strategies to track and model potential responses of candidate EIDs to project their future behaviour and guide research efforts on early detection and diagnosis technologies and vaccine development efforts for these targets. Multi-disciplinary collaborations are demanding to develop effective inter-continental surveillance and modelling platforms that employ artificial intelligence to mitigate climate change effects on EID outbreaks. In this review, we discuss how climate change has increased the risk of EIDs and describe novel approaches to improve surveillance of emerging pathogens that pose the risk for EID outbreaks, new and existing measures that could be used to contain or reduce the risk of future EID outbreaks, and new methods to improve EID tracking during further outbreaks to limit disease transmission.
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Affiliation(s)
- Hongyan Liao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
- Center for Cellular and Molecular Diagnostics and Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics and Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, People’s Republic of China
| | - Tony Hu
- Center for Cellular and Molecular Diagnostics and Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, United States
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107
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Liu Y, Yuan J, Li Y, Bi Y, Prusky DB. The sensor protein AaSho1 regulates infection structures differentiation, osmotic stress tolerance and virulence via MAPK module AaSte11-AaPbs2-AaHog1 in Alternaria alternata. Comput Struct Biotechnol J 2024; 23:1594-1607. [PMID: 38680872 PMCID: PMC11047198 DOI: 10.1016/j.csbj.2024.04.031] [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: 01/20/2024] [Revised: 04/01/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
The high-osmolarity-sensitive protein Sho1 functions as a key membrane receptor in phytopathogenic fungi, which can sense and respond to external stimuli or stresses, and synergistically regulate diverse fungal biological processes through cellular signaling pathways. In this study, we investigated the biological functions of AaSho1 in Alternaria alternata, the causal agent of pear black spot. Targeted gene deletion revealed that AaSho1 is essential for infection structure differentiation, response to external stresses and synthesis of secondary metabolites. Compared to the wild-type (WT), the ∆AaSho1 mutant strain showed no significant difference in colony growth, morphology, conidial production and biomass accumulation. However, the mutant strain exhibited significantly reduced levels of melanin production, cellulase (CL) and ploygalacturonase (PG) activities, virulence, resistance to various exogenous stresses. Moreover, the appressorium and infection hyphae formation rates of the ∆AaSho1 mutant strain were significantly inhibited. RNA-Seq results showed that there were four branches including pheromone, cell wall stress, high osmolarity and starvation in the Mitogen-activated Protein Kinase (MAPK) cascade pathway. Furthermore, yeast two-hybrid experiments showed that AaSho1 activates the MAPK pathway via AaSte11-AaPbs2-AaHog1. These results suggest that AaSho1 of A. alternata is essential for fungal development, pathogenesis and osmotic stress response by activating the MAPK cascade pathway via Sho1-Ste11-Pbs2-Hog1.
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Affiliation(s)
- Yongxiang Liu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
- College of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Jing Yuan
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Yongcai Li
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Yang Bi
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Dov B. Prusky
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
- Institute of Postharvest and Food Sciences, Agricultural Research Organization Volcani Center Information Center, Rishon LeZion, Israel
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108
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Wang T, Luo R, Zhang J, Lan J, Lu Z, Zhai H, Li LF, Sun Y, Qiu HJ. The African swine fever virus MGF300-4L protein is associated with viral pathogenicity by promoting the autophagic degradation of IKK β and increasing the stability of I κB α. Emerg Microbes Infect 2024; 13:2333381. [PMID: 38501350 PMCID: PMC11018083 DOI: 10.1080/22221751.2024.2333381] [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: 12/11/2023] [Accepted: 03/16/2024] [Indexed: 03/20/2024]
Abstract
African swine fever (ASF) is a highly contagious, often fatal viral disease caused by African swine fever virus (ASFV), which imposes a substantial economic burden on the global pig industry. When screening for the virus replication-regulating genes in the left variable region of the ASFV genome, we observed a notable reduction in ASFV replication following the deletion of the MGF300-4L gene. However, the role of MGF300-4L in ASFV infection remains unexplored. In this study, we found that MGF300-4L could effectively inhibit the production of proinflammatory cytokines IL-1β and TNF-α, which are regulated by the NF-κB signaling pathway. Mechanistically, we demonstrated that MGF300-4L interacts with IKKβ and promotes its lysosomal degradation via the chaperone-mediated autophagy. Meanwhile, the interaction between MGF300-4L and IκBα competitively inhibits the binding of the E3 ligase β-TrCP to IκBα, thereby inhibiting the ubiquitination-dependent degradation of IκBα. Remarkably, although ASFV encodes other inhibitors of NF-κB, the MGF300-4L gene-deleted ASFV (Del4L) showed reduced virulence in pigs, indicating that MGF300-4L plays a critical role in ASFV pathogenicity. Importantly, the attenuation of Del4L was associated with a significant increase in the production of IL-1β and TNF-α early in the infection of pigs. Our findings provide insights into the functions of MGF300-4L in ASFV pathogenicity, suggesting that MGF300-4L could be a promising target for developing novel strategies and live attenuated vaccines against ASF.
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Affiliation(s)
- Tao Wang
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Rui Luo
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Jing Zhang
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Jing Lan
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
- College of Animal Sciences, Yangtze University, Jingzhou, People’s Republic of China
| | - Zhanhao Lu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Huanjie Zhai
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Lian-Feng Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Yuan Sun
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
- College of Animal Sciences, Yangtze University, Jingzhou, People’s Republic of China
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109
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Xiang G, Zhao Z, Zhang S, Cai Y, He Y, Zeng J, Chen C, Huang B. Porin deficiency or plasmid copy number increase mediated carbapenem-resistant Escherichia coli resistance evolution. Emerg Microbes Infect 2024; 13:2352432. [PMID: 38712634 PMCID: PMC11107853 DOI: 10.1080/22221751.2024.2352432] [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: 12/13/2023] [Accepted: 05/02/2024] [Indexed: 05/08/2024]
Abstract
This study investigated resistance evolution mechanisms of conjugated plasmids and bacterial hosts under different concentrations of antibiotic pressure. Ancestral strain ECNX52 was constructed by introducing the blaNDM-5-carrying IncX3 plasmid into E. coli C600, and was subjected to laboratory evolution under different concentrations of meropenem pressure. Minimal inhibitory concentrations and conjugation frequency were determined. Fitness of these strains was assessed. Whole genome sequencing and transcriptional changes were performed. Ancestral host or plasmids were recombined with evolved hosts or plasmids to verify plasmid or host factors in resistance evolution. Role of the repA mutation on plasmid copy number was determined. Two out of the four clones (EM2N1 and EM2N3) exhibited four-fold increase in MIC when exposed to a continuous pressure of 2 μg/mL MEM (1/32 MIC), by down regulating expression of outer membrane protein ompF. Besides, all four clones displayed four-fold increase in MIC and higher conjugation frequency when subjected to a continuous pressure of 4 μg/mL MEM (1/16 MIC), attributing to increasing plasmid copy number generated by repA D140Y (GAT→TAT) mutation. Bacterial hosts and conjugative plasmids can undergo resistance evolution under certain concentrations of antimicrobial pressure by reducing the expression of outer membrane proteins or increasing plasmid copy numbers.
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Affiliation(s)
- Guoxiu Xiang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Zhiwei Zhao
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Shebin Zhang
- Department of Laboratory Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, People’s Republic of China
| | - Yimei Cai
- Department of Laboratory Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, People’s Republic of China
| | - Yuting He
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Jianming Zeng
- Department of Laboratory Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, People’s Republic of China
| | - Cha Chen
- Department of Laboratory Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, People’s Republic of China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
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110
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Nasser F, Gaudreau A, Lubega S, Zaker A, Xia X, Mer AS, D'Costa VM. Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter. Emerg Microbes Infect 2024; 13:2320929. [PMID: 38530969 DOI: 10.1080/22221751.2024.2320929] [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: 09/14/2023] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
The multi-drug resistant pathogen Acinetobacter baumannii has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, A. baumannii has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution. The epidemic multidrug-resistant A. baumannii ACICU harbours a plasmid encoding a Type IV Secretion System (T4SS) with homology to the E. coli F-plasmid, and plasmids with homologous gene clusters have been identified in several A. baumannii sequence types. However the genetic and host strain diversity, global distribution, and functional ability of this group of plasmids is not fully understood. Using systematic analysis, we show that pACICU2 belongs to a group of almost 120 T4SS-encoding plasmids within four different species of Acinetobacter and one strain of Klebsiella pneumoniae from human and environmental origin, and globally distributed across 20 countries spanning 4 continents. Genetic diversity was observed both outside and within the T4SS-encoding cluster, and 47% of plasmids harboured resistance determinants, with two plasmids harbouring eleven. Conjugation studies with an extensively drug-resistant (XDR) strain showed that the XDR plasmid could be successfully transferred to a more divergent A. baumanii, and transconjugants exhibited the resistance phenotype of the plasmid. Collectively, this demonstrates that these T4SS-encoding plasmids are globally distributed and more widespread among Acinetobacter than previously thought, and that they represent an important potential reservoir for future clinical concern.
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Affiliation(s)
- Farah Nasser
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Avery Gaudreau
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Shareefah Lubega
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Arvin Zaker
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Xuhua Xia
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
- Department of Biology, University of Ottawa, Ottawa, Canada
| | - Arvind S Mer
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Vanessa M D'Costa
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
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Chai X, Liu S, Liu C, Bai J, Meng J, Tian H, Han X, Han G, Xu X, Li Q. Surveillance of SARS-CoV-2 in wastewater by quantitative PCR and digital PCR: a case study in Shijiazhuang city, Hebei province, China. Emerg Microbes Infect 2024; 13:2324502. [PMID: 38465692 DOI: 10.1080/22221751.2024.2324502] [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: 12/13/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024]
Abstract
In this study, we reported the first long-term monitoring of SARS-CoV-2 in wastewater in Mainland China from November 2021 to October 2023. The city of Shijiazhuang was employed for this case study. We developed a triple reverse transcription droplet digital PCR (RT-ddPCR) method using triple primer-probes for simultaneous detection of the N1 gene, E gene, and Pepper mild mottle virus (PMMoV) to achieve accurate quantification of SARS-CoV-2 RNA in wastewater. Both the RT-ddPCR method and the commercial multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) method were implemented for the detection of SARS-CoV-2 in wastewater in Shijiazhuang City over a 24-month period. Results showed that SARS-CoV-2 was detected for the first time in the wastewater of Shijiazhuang City on 10 November 2022. The peak of COVID-19 cases occurred in the middle of December 2022, when the concentration of SARS-CoV-2 in the wastewater was highest. The trend of virus concentration increases and decreases forming a "long-tailed" shape in the COVID-19 outbreak and recession cycle. The results indicated that both multiplex RT-ddPCR and RT-qPCR are effective in detecting SARS-CoV-2 in wastewater, but RT-ddPCR is capable of detecting low concentrations of SARS-CoV-2 in wastewater which is more efficient. The SARS-CoV-2 abundance in wastewater is correlated to clinical data, outlining the public health utility of this work.HighlightsFirst long-term monitoring of SARS-CoV-2 in wastewater in Mainland ChinaCOVID-19 outbreak was tracked in Shijiazhuang City from outbreak to containmentWastewater was monitored simultaneously using RT-ddPCR and RT-qPCR methodsTriple primer-probe RT-ddPCR detects N1 and E genes of SARS-CoV-2 and PMMoV.
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Affiliation(s)
- Xiaoru Chai
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Shiyou Liu
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Chao Liu
- Shijiazhuang Qiaodong Sewage Treatment Plant, Shijiazhuang, People's Republic of China
| | - Jiaxuan Bai
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Juntao Meng
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Hong Tian
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Xu Han
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Guangyue Han
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Xiangdong Xu
- School of Public Health, Hebei Medical University, Shijiazhuang, People's Republic of China
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, People's Republic of China
| | - Qi Li
- Hebei Key Laboratory of Pathogens and Epidemiology of Infectious Diseases, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
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Tang CY, Gao C, Prasai K, Li T, Dash S, McElroy JA, Hang J, Wan XF. Prediction models for COVID-19 disease outcomes. Emerg Microbes Infect 2024; 13:2361791. [PMID: 38828796 PMCID: PMC11182058 DOI: 10.1080/22221751.2024.2361791] [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: 02/11/2024] [Accepted: 05/26/2024] [Indexed: 06/05/2024]
Abstract
SARS-CoV-2 has caused over 6.9 million deaths and continues to produce lasting health consequences. COVID-19 manifests broadly from no symptoms to death. In a retrospective cross-sectional study, we developed personalized risk assessment models that predict clinical outcomes for individuals with COVID-19 and inform targeted interventions. We sequenced viruses from SARS-CoV-2-positive nasopharyngeal swab samples between July 2020 and July 2022 from 4450 individuals in Missouri and retrieved associated disease courses, clinical history, and urban-rural classification. We integrated this data to develop machine learning-based predictive models to predict hospitalization, ICU admission, and long COVID.The mean age was 38.3 years (standard deviation = 21.4) with 55.2% (N = 2453) females and 44.8% (N = 1994) males (not reported, N = 4). Our analyses revealed a comprehensive set of predictors for each outcome, encompassing human, environment, and virus genome-wide genetic markers. Immunosuppression, cardiovascular disease, older age, cardiac, gastrointestinal, and constitutional symptoms, rural residence, and specific amino acid substitutions were associated with hospitalization. ICU admission was associated with acute respiratory distress syndrome, ventilation, bacterial co-infection, rural residence, and non-wild type SARS-CoV-2 variants. Finally, long COVID was associated with hospital admission, ventilation, and female sex.Overall, we developed risk assessment models that offer the capability to identify patients with COVID-19 necessitating enhanced monitoring or early interventions. Of importance, we demonstrate the value of including key elements of virus, host, and environmental factors to predict patient outcomes, serving as a valuable platform in the field of personalized medicine with the potential for adaptation to other infectious diseases.
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Affiliation(s)
- Cynthia Y. Tang
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
| | - Cheng Gao
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, Missouri, USA
| | - Kritika Prasai
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, Missouri, USA
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Shreya Dash
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Jane A. McElroy
- Family and Community Medicine, University of Missouri, Columbia, Missouri, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, Missouri, USA
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Souleiman Y, Ismail L, Eftimie R. Modeling and investigating malaria P. Falciparum and P. Vivax infections: Application to Djibouti data. Infect Dis Model 2024; 9:1095-1116. [PMID: 39006106 PMCID: PMC11245922 DOI: 10.1016/j.idm.2024.06.003] [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: 03/28/2024] [Revised: 06/03/2024] [Accepted: 06/14/2024] [Indexed: 07/16/2024] Open
Abstract
Malaria is an infectious and communicable disease, caused by one or more species of Plasmodium parasites. There are five species of parasites responsible for malaria in humans, of which two, Plasmodium Falciparum and Plasmodium Vivax, are the most dangerous. In Djibouti, the two species of Plasmodium are present in different proportions in the infected population: 77% of P. Falciparum and 33% of P. Vivax. In this study we present a new mathematical model describing the temporal dynamics of Plasmodium Falciparum and Plasmodium Vivax co-infection. We focus briefly on the well posedness of this model and on the calculation of the basic reproductive numbers for the infections with each Plasmodium species that help us understand the long-term dynamics of this model (i.e., existence and stability of various eqiuilibria). Then we use computational approaches to: (a) identify model parameters using real data on malaria infections in Djibouti; (b) illustrate the influence of different estimated parameters on the basic reproduction numbers; (c) perform global sensitivity and uncertainty analysis for the impact of various model parameters on the transient dynamics of infectious mosquitoes and infected humans, for infections with each of the Plasmodium species. The originality of this research stems from employing the FAST method and the LHS method to identify the key factors influencing the progression of the disease within the population of Djibouti. In addition, sensitivity analysis identified the most influential parameter for Falciparium and Vivax reproduction rates. Finally, the uncertainty analysis enabled us to understand the variability of certain parameters on the infected compartments.
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Affiliation(s)
- Yahyeh Souleiman
- Centre de Recherche en Mathématiques et Numérique (CRMN), University of the Djibouti, Campus Balbala, Djibouti
| | - Liban Ismail
- Centre de Recherche en Mathématiques et Numérique (CRMN), University of the Djibouti, Campus Balbala, Djibouti
| | - Raluca Eftimie
- Laboratoire Mathématiques de Besançon (LMB), University of Bourgogne Franche-Comté, Besançon, France
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114
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Yang X, Zeng J, Wang D, Zhou Q, Yu X, Wang Z, Bai T, Luan G, Xu Y. NagZ modulates the virulence of E. cloacae by acting through the gene of unknown function, ECL_03795. Virulence 2024; 15:2367652. [PMID: 38912723 PMCID: PMC11197897 DOI: 10.1080/21505594.2024.2367652] [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: 02/19/2024] [Accepted: 06/09/2024] [Indexed: 06/25/2024] Open
Abstract
β-N-acetylglucosaminidase (NagZ), a cytosolic glucosaminidase, plays a pivotal role in peptidoglycan recycling. Previous research demonstrated that NagZ knockout significantly eradicated AmpC-dependent β-lactam resistance in Enterobacter cloacae. However, NagZ's role in the virulence of E. cloacae remains unclear. Our study, incorporating data on mouse and Galleria mellonella larval mortality rates, inflammation markers, and histopathological examinations, revealed a substantial reduction in the virulence of E. cloacae following NagZ knockout. Transcriptome sequencing uncovered differential gene expression between NagZ knockout and wild-type strains, particularly in nucleotide metabolism pathways. Further investigation demonstrated that NagZ deletion led to a significant increase in cyclic diguanosine monophosphate (c-di-GMP) levels. Additionally, transcriptome sequencing and RT-qPCR confirmed significant differences in the expression of ECL_03795, a gene with an unknown function but speculated to be involved in c-di-GMP metabolism due to its EAL domain known for phosphodiesterase activity. Interestingly, in ECL_03795 knockout strains, a notable reduction in the virulence was observed, and virulence was rescued upon complementation with ECL_03795. Consequently, our study suggests that NagZ's function on virulence is partially mediated through the ECL_03795→c-di-GMP pathway, providing insight into the development of novel therapies and strongly supporting the interest in creating highly efficient NagZ inhibitors.
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Affiliation(s)
- Xianggui Yang
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Jun Zeng
- Division of Pulmonary and Critical Care Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Dan Wang
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Qin Zhou
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Xuejing Yu
- Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhenguo Wang
- Department of Stomatology, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Tingting Bai
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Guangxin Luan
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Ying Xu
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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115
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Liu Z, Guo Z, Zhou J, Guo X, Chen Y. Biotic interactions and environmental modifications determine symbiotic microbial diversity and stability. Comput Struct Biotechnol J 2024; 23:2717-2726. [PMID: 39040687 PMCID: PMC11260581 DOI: 10.1016/j.csbj.2024.05.047] [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: 12/24/2023] [Revised: 05/09/2024] [Accepted: 05/28/2024] [Indexed: 07/24/2024] Open
Abstract
Taking amphibians as island models, we examined the effects of interspecific interaction on the diversity and stability of microbial ecological. As skin area increased, the diversity and stability of skin microbes decreased, but the strength of negative interactions increased significantly. In contrast, as gut area increased, the diversity and stability of gut microbes increased, but the strength of interactions remained constant. These results indicate that microbial interactions are affected by habitat properties. When living in fluctuating environments without strong filtering, microorganisms can enhance their negative interactions with other taxa by changing the pH of their surroundings. In contrast, the pH of the gut is relatively stable, and colonized microorganisms cannot alter the gut pH and inhibit other colonizers. This study demonstrates that in the field of microbiology, diversity and stability are predominantly influenced by the intensity of interspecies interactions. The findings in this study deepen our understanding of microbial diversity and stability and provide a mechanistic link between species interactions, biodiversity, and stability in microbial ecosystems.
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Affiliation(s)
- Zhidong Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zeguang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuecheng Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youhua Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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116
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Fan L, Wang Y, Huang H, Wang Z, Liang C, Yang X, Ye P, Lin J, Shi W, Zhou Y, Yan H, Long Z, Wang Z, Liu L, Qian J. RNA binding motif 4 inhibits the replication of ebolavirus by directly targeting 3'-leader region of genomic RNA. Emerg Microbes Infect 2024; 13:2300762. [PMID: 38164794 PMCID: PMC10773643 DOI: 10.1080/22221751.2023.2300762] [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: 09/29/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Ebola virus (EBOV) belongs to Filoviridae family possessing single-stranded negative-sense RNA genome, which is a serious threat to human health. Nowadays, no therapeutics have been proven to be successful in efficiently decreasing the mortality rate. RNA binding proteins (RBPs) are reported to participate in maintaining cell integrity and regulation of viral replication. However, little is known about whether and how RBPs participate in regulating the life cycle of EBOV. In our study, we found that RNA binding motif protein 4 (RBM4) inhibited the replication of EBOV in HEK293T and Huh-7 cells by suppressing viral mRNA production. Such inhibition resulted from the direct interaction between the RRM1 domain of RBM4 and the "CU" enrichment elements located in the PE1 and TSS of the 3'-leader region within the viral genome. Simultaneously, RBM4 could upregulate the expression of some cytokines involved in the host innate immune responses to synergistically exert its antiviral function. The findings therefore suggest that RBM4 might serve as a novel target of anti-EBOV strategy.
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Affiliation(s)
- Linjin Fan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Yulong Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Hongxin Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Zequn Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Chudan Liang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Xiaofeng Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Pengfei Ye
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Jingyan Lin
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Wendi Shi
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Yuandong Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Huijun Yan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Zhenyu Long
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zhongyi Wang
- Beijing Institute of Biotechnology, Beijing, People’s Republic of China
| | - Linna Liu
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Jun Qian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
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117
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Zheng X, Xia C, Liu M, Wu H, Yan J, Zhang Z, Huang Y, Gu Q, Li P. Role of folic acid in regulating gut microbiota and short-chain fatty acids based on an in vitro fermentation model. Appl Microbiol Biotechnol 2024; 108:40. [PMID: 38175236 DOI: 10.1007/s00253-023-12825-5] [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: 02/24/2023] [Revised: 10/04/2023] [Accepted: 10/14/2023] [Indexed: 01/05/2024]
Abstract
Folic acid deficiency is common worldwide and is linked to an imbalance in gut microbiota. However, based on model animals used to study the utilization of folic acid by gut microbes, there are challenges of reproducibility and individual differences. In this study, an in vitro fecal slurry culture model of folic acid deficiency was established to investigate the effects of supplementation with 5-methyltetrahydrofolate (MTHF) and non-reduced folic acid (FA) on the modulation of gut microbiota. 16S rRNA sequencing results revealed that both FA (29.7%) and MTHF (27.9%) supplementation significantly reduced the relative abundance of Bacteroidetes compared with control case (34.3%). MTHF supplementation significantly improved the relative abundance of Firmicutes by 4.49%. Notably, compared with the control case, FA and MTHF supplementation promoted an increase in fecal levels of Lactobacillus, Bifidobacterium, and Pediococcus. Short-chain fatty acid (SCFA) analysis showed that folic acid supplementation decreased acetate levels and increased fermentative production of isobutyric acid. The in vitro fecal slurry culture model developed in this study can be utilized as a model of folic acid deficiency in humans to study the gut microbiota and demonstrate that exogenous folic acid affects the composition of the gut microbiota and the level of SCFAs. KEY POINTS: • Establishment of folic acid deficiency in an in vitro culture model. • Folic acid supplementation regulates intestinal microbes and SCFAs. • Connections between microbes and SCFAs after adding folic acid are built.
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Affiliation(s)
- Xiaogu Zheng
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, People's Republic of China
| | - Chenlan Xia
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, People's Republic of China
| | - Manman Liu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, People's Republic of China
| | - Hongchen Wu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, People's Republic of China
| | - Jiaqian Yan
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, People's Republic of China
| | - Zihao Zhang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, People's Republic of China
| | - Yingjie Huang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, People's Republic of China
| | - Qing Gu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, People's Republic of China
| | - Ping Li
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, People's Republic of China.
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118
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Tenório BG, Kollath DR, Gade L, Litvintseva AP, Chiller T, Jenness JS, Stajich JE, Matute DR, Hanzlicek AS, Barker BM, Teixeira MDM. Tracing histoplasmosis genomic epidemiology and species occurrence across the USA. Emerg Microbes Infect 2024; 13:2315960. [PMID: 38465644 DOI: 10.1080/22221751.2024.2315960] [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: 11/08/2023] [Accepted: 02/04/2024] [Indexed: 03/12/2024]
Abstract
ABSTRACTHistoplasmosis is an endemic mycosis in North America frequently reported along the Ohio and Mississippi River Valleys, although autochthonous cases occur in non-endemic areas. In the United States, the disease is provoked by two genetically distinct clades of Histoplasma capsulatum sensu lato, Histoplasma mississippiense (Nam1) and H. ohiense (Nam2). To bridge the molecular epidemiological gap, we genotyped 93 Histoplasma isolates (62 novel genomes) including clinical, environmental, and veterinarian samples from a broader geographical range by whole-genome sequencing, followed by evolutionary and species niche modelling analyses. We show that histoplasmosis is caused by two major lineages, H. ohiense and H. mississippiense; with sporadic cases caused by H. suramericanum in California and Texas. While H. ohiense is prevalent in eastern states, H. mississipiense was found to be prevalent in the central and western portions of the United States, but also geographically overlapping in some areas suggesting that these species might co-occur. Species Niche Modelling revealed that H. ohiense thrives in places with warmer and drier conditions, while H. mississippiense is endemic to areas with cooler temperatures and more precipitation. In addition, we predicted multiple areas of secondary contact zones where the two species co-occur, potentially facilitating gene exchange and hybridization. This study provides the most comprehensive understanding of the genomic epidemiology of histoplasmosis in the USA and lays a blueprint for the study of invasive fungal diseases.
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Affiliation(s)
| | - Daniel R Kollath
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Tom Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jeff S Jenness
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason E Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - Andrew S Hanzlicek
- MiraVista Diagnostics, Indianapolis, IN, USA
- Department of Veterinary Clinical Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Marcus de Melo Teixeira
- Faculty of Medicine, University of Brasília, Brasília, Brazil
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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119
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Hertz S, Anderson JM, Nielsen HL, Schachtschneider C, McCauley KE, Özçam M, Larsen L, Lynch SV, Nielsen H. Fecal microbiota is associated with extraintestinal manifestations in inflammatory bowel disease. Ann Med 2024; 56:2338244. [PMID: 38648495 PMCID: PMC11036898 DOI: 10.1080/07853890.2024.2338244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/17/2024] [Indexed: 04/25/2024] Open
Abstract
INTRODUCTION A large proportion of patients with inflammatory bowel disease (IBD) experience IBD-related inflammatory conditions outside of the gastrointestinal tract, termed extraintestinal manifestations (EIMs) which further decreases quality of life and, in extreme cases, can be life threatening. The pathogenesis of EIMs remains unknown, and although gut microbiota alterations are a well-known characteristic of patients with IBD, its relationship with EIMs remains sparsely investigated. This study aimed to compare the gut microbiota of patients with IBD with and without EIMs. METHODS A total of 131 Danish patients with IBD were included in the study, of whom 86 had a history of EIMs (IBD-EIM) and 45 did not (IBD-C). Stool samples underwent 16S rRNA sequencing. Amplicon sequence variants (ASVs) were mapped to the Silva database. Diversity indices and distance matrices were compared between IBD-EIM and IBD-C. Differentially abundant ASVs were identified using a custom multiple model statistical analysis approach, and modules of co-associated bacteria were identified using sparse correlations for compositional data (SparCC) and related to patient EIM status. RESULTS Patients with IBD and EIMs exhibited increased disease activity, body mass index, increased fecal calprotectin levels and circulating monocytes and neutrophils. Microbiologically, IBD-EIM exhibited lower fecal microbial diversity than IBD-C (Mann-Whitney's test, p = .01) and distinct fecal microbiota composition (permutational multivariate analysis of variance; weighted UniFrac, R2 = 0.018, p = .01). A total of 26 ASVs exhibited differential relative abundances between IBD-EIM and IBD-C, including decreased Agathobacter and Blautia and increased Eggerthella lenta in the IBD-EIM group. SparCC analysis identified 27 bacterial co-association modules, three of which were negatively related to EIM (logistic regression, p < .05) and included important health-associated bacteria, such as Agathobacter and Faecalibacterium. CONCLUSIONS The fecal microbiota in IBD patients with EIMs is distinct from that in IBD patients without EIM and could be important for EIM pathogenesis.
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Affiliation(s)
- Sandra Hertz
- Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline Moltzau Anderson
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Hans Linde Nielsen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Claire Schachtschneider
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Kathryn E. McCauley
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Mustafa Özçam
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Lone Larsen
- Department of Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Aalborg University, Aalborg, Denmark
| | - Susan V. Lynch
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Henrik Nielsen
- Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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Galvez-Llompart M, Hierrezuelo J, Blasco M, Zanni R, Galvez J, de Vicente A, Pérez-García A, Romero D. Targeting bacterial growth in biofilm conditions: rational design of novel inhibitors to mitigate clinical and food contamination using QSAR. J Enzyme Inhib Med Chem 2024; 39:2330907. [PMID: 38651823 DOI: 10.1080/14756366.2024.2330907] [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: 10/25/2023] [Accepted: 03/06/2024] [Indexed: 04/25/2024] Open
Abstract
Antimicrobial resistance (AMR) is a pressing global issue exacerbated by the abuse of antibiotics and the formation of bacterial biofilms, which cause up to 80% of human bacterial infections. This study presents a computational strategy to address AMR by developing three novel quantitative structure-activity relationship (QSAR) models based on molecular topology to identify potential anti-biofilm and antibacterial agents. The models aim to determine the chemo-topological pattern of Gram (+) antibacterial, Gram (-) antibacterial, and biofilm formation inhibition activity. The models were applied to the virtual screening of a commercial chemical database, resulting in the selection of 58 compounds. Subsequent in vitro assays showed that three of these compounds exhibited the most promising antibacterial activity, with potential applications in enhancing food and medical device safety.
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Affiliation(s)
- Maria Galvez-Llompart
- Department of Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine, Faculty of Pharmacy, University of Valencia, Burjassot, Spain
- Department of Physical Chemistry, University of Valencia, Burjassot, Spain
- Department of Microbiology, Faculty of Science, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga, Spain
| | - Jesús Hierrezuelo
- Department of Microbiology, Faculty of Science, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga, Spain
| | - Mariluz Blasco
- Department of Microbiology, Faculty of Science, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga, Spain
| | - Riccardo Zanni
- Department of Physical Chemistry, University of Valencia, Burjassot, Spain
| | - Jorge Galvez
- Department of Physical Chemistry, University of Valencia, Burjassot, Spain
| | - Antonio de Vicente
- Department of Microbiology, Faculty of Science, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga, Spain
| | - Alejandro Pérez-García
- Department of Microbiology, Faculty of Science, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga, Spain
| | - Diego Romero
- Department of Microbiology, Faculty of Science, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, IHSM-UMA-CSIC, University of Málaga, Málaga, Spain
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Xi Y, Li X, Liu L, Xiu F, Yi X, Chen H, You X. Sneaky tactics: Ingenious immune evasion mechanisms of Bartonella. Virulence 2024; 15:2322961. [PMID: 38443331 PMCID: PMC10936683 DOI: 10.1080/21505594.2024.2322961] [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: 12/18/2023] [Accepted: 02/20/2024] [Indexed: 03/07/2024] Open
Abstract
Gram-negative Bartonella species are facultative intracellular bacteria that can survive in the harsh intracellular milieu of host cells. They have evolved strategies to evade detection and degradation by the host immune system, which ensures their proliferation in the host. Following infection, Bartonella alters the initial immunogenic surface-exposed proteins to evade immune recognition via antigen or phase variation. The diverse lipopolysaccharide structures of certain Bartonella species allow them to escape recognition by the host pattern recognition receptors. Additionally, the survival of mature erythrocytes and their resistance to lysosomal fusion further complicate the immune clearance of this species. Certain Bartonella species also evade immune attacks by producing biofilms and anti-inflammatory cytokines and decreasing endothelial cell apoptosis. Overall, these factors create a challenging landscape for the host immune system to rapidly and effectively eradicate the Bartonella species, thereby facilitating the persistence of Bartonella infections and creating a substantial obstacle for therapeutic interventions. This review focuses on the effects of three human-specific Bartonella species, particularly their mechanisms of host invasion and immune escape, to gain new perspectives in the development of effective diagnostic tools, prophylactic measures, and treatment options for Bartonella infections.
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Affiliation(s)
- Yixuan Xi
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, University of South China, Hengyang, China
| | - Xinru Li
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, University of South China, Hengyang, China
| | - Lu Liu
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, University of South China, Hengyang, China
| | - Feichen Xiu
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, University of South China, Hengyang, China
| | - Xinchao Yi
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, University of South China, Hengyang, China
| | - Hongliang Chen
- Chenzhou NO.1 People’s Hospital, The Affiliated Chenzhou Hospital, Hengyang Medical College, University of South China, ChenZhou, China
| | - Xiaoxing You
- Institute of Pathogenic Biology, Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, University of South China, Hengyang, China
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Xu J, Chen L, Pang S, Zhang Q, Deng S, Zhu J, Chen X, Langford PR, Huang Q, Zhou R, Li L. HylS', a fragment of truncated hyaluronidase of Streptococcus suis, contributes to immune evasion by interaction with host complement factor C3b. Virulence 2024; 15:2306691. [PMID: 38251716 PMCID: PMC10854370 DOI: 10.1080/21505594.2024.2306691] [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: 07/04/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Pathogenic bacteria have evolved many strategies to evade surveillance and attack by complements. Streptococcus suis is an important zoonotic pathogen that infects humans and pigs. Hyaluronidase (HylA) has been reported to be a potential virulence factor of S. suis. However, in this study, it was discovered that the genomic region encoding HylA of the virulent S. suis strain SC19 and other ST1 strains was truncated into four fragments when aligned with a strain containing intact HylA and possessing hyaluronidase activity. As a result, SC19 had no hyaluronidase activity, but one truncated HylA fragment, designated as HylS,' directly interacted with complement C3b, as confirmed by western ligand blotting, pull-down, and ELISA assays. The deposition of C3b and membrane attack complex (MAC) formation on the surface of a HylS'-deleted mutant (ΔhylS') was significantly increased compared to wild-type SC19. In human sera and whole blood, ΔhylS' survival was significantly reduced compared to that in SC19. The resistance of ΔhylS' to macrophages and human polymorphonuclear neutrophil PMNs also decreased. In a mouse infection model, ΔhylS' showed reduced lethality and lower bacterial load in the organs compared to that of SC19. We conclude that the truncated hyaluronidase HylS' fragment contributes to complement evasion and the pathogenesis of S. suis.
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Affiliation(s)
- Jiajia Xu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Long Chen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Siqi Pang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Qiuhong Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Simin Deng
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Jiaqi Zhu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
| | - Xiabing Chen
- Institute of Animal Husbandry and Veterinary Science, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Paul R Langford
- Section of Paediatric Infectious Disease, Imperial College London, St Mary’s Campus, London, UK
| | - Qi Huang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
- International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan, Hubei, China
| | - Rui Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
- International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan, Hubei, China
| | - Lu Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, China
- International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan, Hubei, China
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Zanditenas E, Ankri S. Unraveling the interplay between unicellular parasites and bacterial biofilms: Implications for disease persistence and antibiotic resistance. Virulence 2024; 15:2289775. [PMID: 38058008 PMCID: PMC10761080 DOI: 10.1080/21505594.2023.2289775] [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: 07/26/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023] Open
Abstract
Bacterial biofilms have attracted significant attention due to their involvement in persistent infections, food and water contamination, and infrastructure corrosion. This review delves into the intricate interactions between bacterial biofilms and unicellular parasites, shedding light on their impact on biofilm formation, structure, and function. Unicellular parasites, including protozoa, influence bacterial biofilms through grazing activities, leading to adaptive changes in bacterial communities. Moreover, parasites like Leishmania and Giardia can shape biofilm composition in a grazing independent manner, potentially influencing disease outcomes. Biofilms, acting as reservoirs, enable the survival of protozoan parasites against environmental stressors and antimicrobial agents. Furthermore, these biofilms may influence parasite virulence and stress responses, posing challenges in disease treatment. Interactions between unicellular parasites and fungal-containing biofilms is also discussed, hinting at complex microbial relationships in various ecosystems. Understanding these interactions offers insights into disease mechanisms and antibiotic resistance dissemination, paving the way for innovative therapeutic strategies and ecosystem-level implications.
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Affiliation(s)
- Eva Zanditenas
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
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Wei Y, Li G, Wang Z, Qian K, Zhang S, Zhang L, Lei C, Hu S. Development and characterization of a novel neutralizing scFv vectored immunoprophylaxis against botulinum toxin type A. J Drug Target 2024; 32:213-222. [PMID: 38164940 DOI: 10.1080/1061186x.2023.2301418] [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: 05/17/2023] [Accepted: 10/18/2023] [Indexed: 01/03/2024]
Abstract
Botulinum toxin is a protein toxin secreted by Clostridium botulinum that is strongly neurotoxic. Due to its characteristics of being super toxic, quick acting, and difficult to prevent, the currently reported antiviral studies focusing on monoclonal antibodies have limited effectiveness. Therefore, for the sake of effectively prevention and treatment of botulism and to maintain country biosecurity as well as the health of the population, in this study, we intend to establish a single chain antibody (scFv) targeting the carboxyl terminal binding functional domain of the botulinum neurotoxin heavy chain (BONT/AHc) of botulinum neurotoxin type A, and explore the value of a new passive immune method in antiviral research which based on adeno-associated virus (AAV) mediated vector immunoprophylaxis (VIP) strategy. The scFv small-molecular single-chain antibody sequenced, designed, constructed, expressed and purified by hybridoma has high neutralising activity and affinity level, which can lay a good foundation for the modification and development of antibody engineering drugs. In vivo experiments, AAV-mediated scFv engineering drug has good anti-BONT/A toxin neutralisation ability, has advantages of simple operation, stable expression and good efficacy, and may be one of the effective treatment strategies for long-term prevention and protection of BONT/A botulinum neurotoxin.
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Affiliation(s)
- Yongpeng Wei
- Department of Biophysics, College of Basic Medical Sciences, Second Military Medical University, Shanghai, China
- Hepatic Surgery Department V, The Third Affiliated Hospital, Second Military Medical University, Shanghai, China
| | - Guangyao Li
- Department of Biophysics, College of Basic Medical Sciences, Second Military Medical University, Shanghai, China
- Department of Biomedical Engineering, College of Basic Medical Sciences, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Zhuo Wang
- Department of Biophysics, College of Basic Medical Sciences, Second Military Medical University, Shanghai, China
- Hepatic Surgery Department V, The Third Affiliated Hospital, Second Military Medical University, Shanghai, China
| | - Kewen Qian
- Department of Biophysics, College of Basic Medical Sciences, Second Military Medical University, Shanghai, China
- Department of Biomedical Engineering, College of Basic Medical Sciences, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Shuyi Zhang
- Department of Biophysics, College of Basic Medical Sciences, Second Military Medical University, Shanghai, China
| | - Lingling Zhang
- Department of Central Laboratory, Clinical Research Center of Changhai Hospital, Shanghai, China
| | - Changhai Lei
- Department of Biophysics, College of Basic Medical Sciences, Second Military Medical University, Shanghai, China
| | - Shi Hu
- Department of Biomedical Engineering, College of Basic Medical Sciences, Naval Medical University (Second Military Medical University), Shanghai, China
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Colson P, Fantini J, Delerce J, Bader W, Levasseur A, Pontarotti P, Devaux C, Raoult D. "Outlaw" mutations in quasispecies of SARS-CoV-2 inhibit replication. Emerg Microbes Infect 2024; 13:2368211. [PMID: 38916498 PMCID: PMC11207925 DOI: 10.1080/22221751.2024.2368211] [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: 11/09/2023] [Accepted: 06/10/2024] [Indexed: 06/26/2024]
Abstract
The evolution of SARS-CoV-2, the agent of COVID-19, has been remarkable for its high mutation potential, leading to the appearance of variants. Some mutations have never appeared in the published genomes, which represent consensus, or bona fide genomes. Here we tested the hypothesis that mutations that did not appear in consensus genomes were, in fact, as frequent as the mutations that appeared during the various epidemic episodes, but were not expressed because lethal. To identify these mutations, we analysed the genomes of 90 nasopharyngeal samples and the quasispecies determined by next-generation sequencing. Mutations observed in the quasispecies and not in the consensus genomes were considered to be lethal, what we called "outlaw" mutations. Among these mutations, we analysed the 21 most frequent. Eight of these "outlaws" were in the RNA polymerase and we were able to use a structural biology model and molecular dynamics simulations to demonstrate the functional incapacity of these mutated RNA polymerases. Three other mutations affected the spike, a major protein involved in the pathogenesis of COVID-19. Overall, by analysing the SARS-CoV-2 quasispecies obtained during sequencing, this method made it possible to identify "outlaws," showing areas that could potentially become the target of treatments.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Jacques Fantini
- INSERM UMR UA 16, Aix-Marseille Université, Marseille, France
| | | | - Wahiba Bader
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS), Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS), Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, Marseille, France
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Coutant F, Touret F, Pin JJ, Alonzo M, Baronti C, Munier S, Attia M, de Lamballerie X, Ferry T, Miossec P. Neutralizing and enhancing monoclonal antibodies in SARS-CoV-2 convalescent patients: lessons from early variant infection and impact on shaping emerging variants. Emerg Microbes Infect 2024; 13:2307510. [PMID: 38240255 PMCID: PMC10829827 DOI: 10.1080/22221751.2024.2307510] [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: 10/03/2023] [Accepted: 01/16/2024] [Indexed: 02/01/2024]
Abstract
Serological studies of COVID-19 convalescent patients have identified polyclonal lineage-specific and cross-reactive antibodies (Abs), with varying effector functions against virus variants. Individual specificities of anti-SARS-CoV-2 Abs and their impact on infectivity by other variants have been little investigated to date. Here, we dissected at a monoclonal level neutralizing and enhancing Abs elicited by early variants and how they affect infectivity of emerging variants. B cells from 13 convalescent patients originally infected by D614G or Alpha variants were immortalized to isolate 445 naturally-produced anti-SARS-CoV-2 Abs. Monoclonal antibodies (mAbs) were tested for their abilities to impact the cytopathic effect of D614G, Delta, and Omicron (BA.1) variants. Ninety-eight exhibited robust neutralization against at least one of the three variant types, while 309 showed minimal or no impact on infectivity. Thirty-eight mAbs enhanced infectivity of SARS-CoV-2. Infection with D614G/Alpha variants generated variant-specific (65 neutralizing Abs, 35 enhancing Abs) and cross-reactive (18 neutralizing Abs, 3 enhancing Abs) mAbs. Interestingly, among the neutralizing mAbs with cross-reactivity restricted to two of the three variants tested, none demonstrated specific neutralization of the Delta and Omicron variants. In contrast, cross-reactive mAbs enhancing infectivity (n = 3) were found exclusively specific to Delta and Omicron variants. Notably, two mAbs that amplified in vitro the cytopathic effect of the Delta variant also exhibited neutralization against Omicron. These findings shed light on functional diversity of cross-reactive Abs generated during SARS-CoV-2 infection and illustrate how the balance between neutralizing and enhancing Abs facilitate variant emergence.
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Affiliation(s)
- Frédéric Coutant
- Immunogenomics and Inflammation Research Team, University of Lyon, Edouard Herriot Hospital, Lyon, France
- Immunology Department, Lyon-Sud Hospital, Hospices Civils of Lyon, Pierre-Bénite, France
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France
| | - Jean-Jacques Pin
- Eurobio Scientific/Dendritics – Edouard Herriot Hospital, Lyon, France
| | - Marina Alonzo
- Immunogenomics and Inflammation Research Team, University of Lyon, Edouard Herriot Hospital, Lyon, France
| | - Cécile Baronti
- Unité des Virus Émergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France
| | - Sandie Munier
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Molecular Genetics of RNA Viruses Unit, Paris, France
| | - Mikaël Attia
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Molecular Genetics of RNA Viruses Unit, Paris, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille University - IRD 190 - Inserm 1207), Marseille, France
| | - Tristan Ferry
- Department of Infectious and Tropical Diseases, Hospices Civils of Lyon - Croix-Rousse Hospital, Lyon, France
- CIRI, Inserm U1111, CNRS, UMR5308, ENS Lyon, Université Claude Bernard Lyon I, Lyon, France
| | - Pierre Miossec
- Immunogenomics and Inflammation Research Team, University of Lyon, Edouard Herriot Hospital, Lyon, France
- Department of Immunology and Rheumatology, Edouard Herriot Hospital, Lyon, France
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Xie M, Ye L, Chen K, Xu Q, Yang C, Chen X, Chan EWC, Li F, Chen S. Clinical use of tigecycline may contribute to the widespread dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae strains. Emerg Microbes Infect 2024; 13:2306957. [PMID: 38240375 PMCID: PMC10829843 DOI: 10.1080/22221751.2024.2306957] [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: 10/22/2023] [Accepted: 01/14/2024] [Indexed: 02/01/2024]
Abstract
The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) poses grave threats to human health. These strains increased dramatically in clinical settings in China in the past few years but not in other parts of the world. Four isogenic K. pneumoniae strains, including classical K. pneumoniae, carbapenem-resistant K. pneumoniae (CRKP), hypervirulent K. pneumoniae (hvKP) and CR-hvKP, were created and subjected to phenotypic characterization, competition assays, mouse sepsis model and rat colonization tests to investigate the mechanisms underlying the widespread nature of CR-hvKP in China. Acquisition of virulence plasmid led to reduced fitness and abolishment of colonization in the gastrointestinal tract, which may explain why hvKP is not clinically prevalent after its emergence for a long time. However, tigecycline treatment facilitated the colonization of hvKP and CR-hvKP and reduced the population of Lactobacillus spp. in animal gut microbiome. Feeding with Lactobacillus spp. could significantly reduce the colonization of hvKP and CR-hvKP in the animal gastrointestinal tract. Our data implied that the clinical use of tigecycline to treat carbapenem-resistant K. pneumoniae infections facilitated the high spread of CR-hvKP in clinical settings in China and demonstrated that Lactobacillus spp. was a potential candidate for anticolonization strategy against CR-hvKP.
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Affiliation(s)
- Miaomiao Xie
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Lianwei Ye
- 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 Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Qi 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
| | - Chen 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
| | - Xiangnan 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
| | - 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, Kowloon, Hong Kong
| | - Fuyong Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Sheng Chen
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong
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Sharma S, Chaurasia S, Dinday S, Srivastava G, Singh A, Chanotiya CS, Ghosh S. High-level biosynthesis of enantiopure germacrene D in yeast. Appl Microbiol Biotechnol 2024; 108:50. [PMID: 38183482 PMCID: PMC10789846 DOI: 10.1007/s00253-023-12885-7] [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: 06/22/2023] [Revised: 09/18/2023] [Accepted: 09/30/2023] [Indexed: 01/08/2024]
Abstract
Germacrene D, a sesquiterpenoid compound found mainly in plant essential oils at a low level as (+) and/or (-) enantiomeric forms, is an ingredient for the fragrance industry, but a process for the sustainable supply of enantiopure germacrene D is not yet established. Here, we demonstrate metabolic engineering in yeast (Saccharomyces cerevisiae) achieving biosynthesis of enantiopure germacrene D at a high titer. To boost farnesyl pyrophosphate (FPP) flux for high-level germacrene D biosynthesis, a background yeast chassis (CENses5C) was developed by genomic integration of the expression cassettes for eight ergosterol pathway enzymes that sequentially converted acetyl-CoA to FPP and by replacing squalene synthase promoter with a copper-repressible promoter, which restricted FPP flux to the competing pathway. Galactose-induced expression of codon-optimized plant germacrene D synthases led to 13-30 fold higher titers of (+) or (-)-germacrene D in CENses5C than the parent strain CEN.PK2.1C. Furthermore, genomic integration of germacrene D synthases in GAL80, LPP1 and rDNA loci generated CENses8(+D) and CENses8(-D) strains, which produced 41.36 µg/ml and 728.87 µg/ml of (+) and (-)-germacrene D, respectively, without galactose supplementation. Moreover, coupling of mitochondrial citrate pool to the cytosolic acetyl-CoA, by expressing a codon-optimized ATP-citrate lyase of oleaginous yeast, resulted in 137.71 µg/ml and 815.81 µg/ml of (+) or (-)-germacrene D in CENses8(+D)* and CENses8(-D)* strains, which were 67-120 fold higher titers than in CEN.PK2.1C. In fed-batch fermentation, CENses8(+D)* and CENses8(-D)* produced 290.28 µg/ml and 2519.46 µg/ml (+) and (-)-germacrene D, respectively, the highest titers in shake-flask fermentation achieved so far. KEY POINTS: • Engineered S. cerevisiae produced enantiopure (+) and (-)-germacrene D at high titers • Engineered strain produced up to 120-fold higher germacrene D than the parental strain • Highest titers of enantiopure (+) and (-)-germacrene D achieved so far in shake-flask.
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Affiliation(s)
- Shubha Sharma
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Seema Chaurasia
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Sandeep Dinday
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India
| | - Gaurav Srivastava
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Anamika Singh
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Chandan Singh Chanotiya
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Phytochemistry Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India
| | - Sumit Ghosh
- Plant Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, 226015, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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129
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Venkatachalam S, Jabir T, Vipindas PV, Krishnan KP. Ecological significance of Candidatus ARS69 and Gemmatimonadota in the Arctic glacier foreland ecosystems. Appl Microbiol Biotechnol 2024; 108:128. [PMID: 38229335 DOI: 10.1007/s00253-023-12991-6] [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: 07/07/2023] [Revised: 11/08/2023] [Accepted: 12/28/2023] [Indexed: 01/18/2024]
Abstract
The Gemmatimonadota phylum has been widely detected in diverse natural environments, yet their specific ecological roles in many habitats remain poorly investigated. Similarly, the Candidatus ARS69 phylum has been identified only in a few habitats, and literature on their metabolic functions is relatively scarce. In the present study, we investigated the ecological significance of phyla Ca. ARS69 and Gemmatimonadota in the Arctic glacier foreland (GF) ecosystems through genome-resolved metagenomics. We have reconstructed the first high-quality metagenome-assembled genome (MAG) belonging to Ca. ARS69 and 12 other MAGs belonging to phylum Gemmatimonadota from the three different Arctic GF samples. We further elucidated these two groups phylogenetic lineage and their metabolic function through phylogenomic and pangenomic analysis. The analysis showed that all the reconstructed MAGs potentially belonged to novel species. The MAGs belonged to Ca. ARS69 consist about 8296 gene clusters, of which only about 8% of single-copy core genes (n = 980) were shared among them. The study also revealed the potential ecological role of Ca. ARS69 is associated with carbon fixation, denitrification, sulfite oxidation, and reduction biochemical processes in the GF ecosystems. Similarly, the study demonstrates the widespread distribution of different classes of Gemmatimonadota across wide ranges of ecosystems and their metabolic functions, including in the polar region. KEY POINTS: • Glacier foreland ecosystems act as a natural laboratory to study microbial community structure. • We have reconstructed 13 metagenome-assembled genomes from the soil samples. • All the reconstructed MAGs belonged to novel species with different metabolic processes. • Ca. ARS69 and Gemmatimonadota MAGs were found to participate in carbon fixation and denitrification processes.
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Affiliation(s)
- Siddarthan Venkatachalam
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India.
| | - Thajudeen Jabir
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| | - Puthiya Veettil Vipindas
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
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130
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Wohlers H, Zentgraf L, van der Sande L, Holtmann D. Metabolic engineering of Shewanella oneidensis to produce glutamate and itaconic acid. Appl Microbiol Biotechnol 2024; 108:36. [PMID: 38183472 PMCID: PMC10771365 DOI: 10.1007/s00253-023-12879-5] [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: 06/20/2023] [Revised: 11/17/2023] [Accepted: 11/24/2023] [Indexed: 01/08/2024]
Abstract
Shewanella oneidensis is a gram-negative bacterium known for its unique respiratory capabilities, which allow it to utilize a wide range of electron acceptors, including solid substrates such as electrodes. For a future combination of chemical production and electro-fermentation, the goal of this study was to expand its product spectrum. S. oneidensis was metabolically engineered to optimize its glutamate production and to enable production of itaconic acid. By deleting the glutamate importer gltS for a reduced glutamate uptake and pckA/ptA to redirect the carbon flux towards the TCA cycle, a ∆3 mutant was created. In combination with the plasmid pG2 carrying the glutamate dehydrogenase gdhA and a specific glutamate exporter NCgl1221 A111V, a 72-fold increase in glutamate concentration compared to the wild type was achieved. Along with overexpression of gdhA and NCgl1221 A111V, the deletion of gltS and pckA/ptA as well as the deletion of all three genes (∆3) was examined for their impact on growth and lactate consumption. This showed that the redirection of the carbon flux towards the TCA cycle is possible. Furthermore, we were able to produce itaconic acid for the first time with a S. oneidensis strain. A titer of 7 mM was achieved after 48 h. This suggests that genetic optimization with an expression vector carrying a cis-aconitate decarboxylase (cadA) and a aconitate hydratase (acnB) along with the proven redirection of the carbon flux to the TCA cycle enabled the production of itaconic acid, a valuable platform chemical used in the production of a variety of products. KEY POINTS: •Heterologous expression of gdhA and NCgl1221_A111V leads to higher glutamate production. •Deletion of ackA/pta redirects carbon flux towards TCA cycle. •Heterologous expression of cadA and acnB enables itaconic acid production.
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Affiliation(s)
- Hannah Wohlers
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390, Giessen, Germany
- DECHEMA-Forschungsinstitut, Microbial Biotechnology, Theodor-Heuss-Allee 25, 60486, Frankfurt Am Main, Germany
| | - Laura Zentgraf
- DECHEMA-Forschungsinstitut, Microbial Biotechnology, Theodor-Heuss-Allee 25, 60486, Frankfurt Am Main, Germany
| | - Lisa van der Sande
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390, Giessen, Germany
- Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Karlsruhe, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Dirk Holtmann
- Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Karlsruhe, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.
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131
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Van Le V, Kang M, Ko SR, Park CY, Lee JJ, Choi IC, Oh HM, Ahn CY. Response of particle-attached and free-living bacterial communities to Microcystis blooms. Appl Microbiol Biotechnol 2024; 108:42. [PMID: 38183480 DOI: 10.1007/s00253-023-12828-2] [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: 03/24/2023] [Revised: 07/29/2023] [Accepted: 11/13/2023] [Indexed: 01/08/2024]
Abstract
The massive proliferation of Microcystis threatens freshwater ecosystems and degrades water quality globally. Understanding the mechanisms that contribute to Microcystis growth is crucial for managing Microcystis blooms. The lifestyles of bacteria can be classified generally into two groups: particle-attached (PA; > 3 µm) and free-living (FL; 0.2-3.0 µm). However, little is known about the response of PA and FL bacteria to Microcystis blooms. Using 16S rRNA gene high-throughput sequencing, we investigated the stability, assembly process, and co-occurrence patterns of PA and FL bacterial communities during distinct bloom stages. PA bacteria were phylogenetically different from their FL counterparts. Microcystis blooms substantially influenced bacterial communities. The time decay relationship model revealed that Microcystis blooms might increase the stability of both PA and FL bacterial communities. A contrasting community assembly mechanism was observed between the PA and FL bacterial communities. Throughout Microcystis blooms, homogeneous selection was the major assembly process that impacted the PA bacterial community, whereas drift explained much of the turnover of the FL bacterial community. Both PA and FL bacterial communities could be separated into modules related to different phases of Microcystis blooms. Microcystis blooms altered the assembly process of PA and FL bacterial communities. PA bacterial community appeared to be more responsive to Microcystis blooms than FL bacteria. Decomposition of Microcystis blooms may enhance cooperation among bacteria. Our findings highlight the importance of studying bacterial lifestyles to understand their functions in regulating Microcystis blooms. KEY POINTS: • Microcystis blooms alter the assembly process of PA and FL bacterial communities • Microcystis blooms increase the stability of both PA and FL bacterial communities • PA bacteria seem to be more responsive to Microcystis blooms than FL bacteria.
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Affiliation(s)
- Ve Van Le
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Mingyeong Kang
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
| | - Chan-Yeong Park
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jay Jung Lee
- Geum River Environment Research Center, National Institute of Environmental Research, Chungbuk, 29027, Republic of Korea
| | - In-Chan Choi
- Geum River Environment Research Center, National Institute of Environmental Research, Chungbuk, 29027, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea.
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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132
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Wen S, Zhao Y, Qi X, Cai M, Huang K, Liu H, Kong DX. Conformational plasticity of SpyCas9 induced by AcrIIA4 and AcrIIA2: Insights from molecular dynamics simulation. Comput Struct Biotechnol J 2024; 23:537-548. [PMID: 38235361 PMCID: PMC10791570 DOI: 10.1016/j.csbj.2023.12.030] [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: 07/14/2023] [Revised: 12/06/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
CRISPR-Cas9 systems constitute bacterial adaptive immune systems that protect against phage infections. Bacteriophages encode anti-CRISPR proteins (Acrs) that mitigate the bacterial immune response. However, the structural basis for their inhibitory actions from a molecular perspective remains elusive. In this study, through microsecond atomistic molecular dynamics simulations, we demonstrated the remarkable flexibility of Streptococcus pyogenes Cas9 (SpyCas9) and its conformational adaptability during interactions with AcrIIA4 and AcrIIA2. Specifically, we demonstrated that the binding of AcrIIA4 and AcrIIA2 to SpyCas9 induces a conformational rearrangement that causes spatial separation between the nuclease and cleavage sites, thus making the endonuclease inactive. This separation disrupts the transmission of signals between the protospacer adjacent motif recognition and nuclease domains, thereby impeding the efficient processing of double-stranded DNA. The simulation also reveals that AcrIIA4 and AcrIIA2 cause different structural variations of SpyCas9. Our research illuminates the precise mechanisms underlying the suppression of SpyCas9 by AcrIIA4 and AcrIIA2, thus presenting new possibilities for controlling genome editing with higher accuracy.
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Affiliation(s)
- Shuixiu Wen
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Yuxin Zhao
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Xinyu Qi
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Mingzhu Cai
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Kaisheng Huang
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Hui Liu
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - De-Xin Kong
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
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133
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Nlandu Y, Tannor EK, Bafemika T, Makulo JR. Kidney damage associated with COVID-19: from the acute to the chronic phase. Ren Fail 2024; 46:2316885. [PMID: 38561236 PMCID: PMC10986440 DOI: 10.1080/0886022x.2024.2316885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-COV-2) infection is well established as a systemic disease including kidney damage. The entry point into the renal cell remains the angiotensin-converting enzyme 2 (ACE-2) receptor and the spectrum of renal lesions is broad, with a clear predominance of structural and functional tubular lesions. The most common form of glomerular injury is collapsing glomerulopathy (CG), which is strongly associated with apolipoprotein L1(APOL-1) risk variants. These acute lesions, which are secondary to the direct or indirect effects of SARS-CoV-2, can progress to chronicity and are specific to long COVID-19 in the absence of any other cause. Residual inflammation associated with SARS-CoV-2 infection, in addition to acute kidney injury (AKI) as a transitional state with or without severe histological lesions, may be responsible for greater kidney function decline in mild-to-moderate COVID-19. This review discusses the evidence for renal histological markers of chronicity in COVID-19 patients and triggers of low-grade inflammation that may explain the decline in kidney function in the post-COVID-19 period.
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Affiliation(s)
- Yannick Nlandu
- Nephrology Unit, Kinshasa University Hospital, Kinshasa, Democratic Republic of the Congo
| | - Elliot Koranteng Tannor
- Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Directorate of Medicine, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Titilope Bafemika
- Renal Unit, Uniosun Teaching Hospital Osogbo, Osun State University, Osogbo, Osun State, Nigeria
| | - Jean-Robert Makulo
- Nephrology Unit, Kinshasa University Hospital, Kinshasa, Democratic Republic of the Congo
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134
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Wang F, Sun H, Kang C, Yan J, Chen J, Feng X, Yang B. Genomic island-encoded regulatory proteins in enterohemorrhagic Escherichia coli O157:H7. Virulence 2024; 15:2313407. [PMID: 38357901 PMCID: PMC10877973 DOI: 10.1080/21505594.2024.2313407] [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: 10/24/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is an important zoonotic pathogen that is a major cause of foodborne diseases in most developed and developing countries and can cause uncomplicated diarrhoea, haemorrhagic colitis, and haemolytic uraemic syndrome. O islands (OIs), which are unique genomic islands in EHEC O157:H7, are composed of 177 isolated genomic features and harbour 26% of the total genes that are absent in the non-pathogenic E. coli K-12 genome. In the last twenty years, many OI-encoded proteins have been characterized, including proteins regulating virulence, motility, and acid resistance. Given the critical role of regulatory proteins in the systematic and hierarchical regulation of bacterial biological processes, this review summarizes the OI-encoded regulatory proteins in EHEC O157:H7 characterized to date, emphasizing OI-encoded regulatory proteins for bacterial virulence, motility, and acid resistance. This summary will be significant for further exploration and understanding of the virulence and pathogenesis of EHEC O157:H7.
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Affiliation(s)
- Fang Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- Intensive Care Unit, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Hongmin Sun
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Chenbo Kang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Jun Yan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Jingnan Chen
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Xuequan Feng
- Tianjin First Central Hospital, Nankai University, Tianjin, China
| | - Bin Yang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
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135
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Wang CZ, Zhang YJ, Chu YF, Zhong LG, Xu JP, Liang LY, Long TF, Fang LX, Sun J, Liao XP, Zhou YF. Tobramycin-resistant small colony variant mutant of Salmonella enterica serovar Typhimurium shows collateral sensitivity to nitrofurantoin. Virulence 2024; 15:2356692. [PMID: 38797966 PMCID: PMC11135859 DOI: 10.1080/21505594.2024.2356692] [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: 02/05/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
The increasing antibiotic resistance poses a significant global health challenge, threatening our ability to combat infectious diseases. The phenomenon of collateral sensitivity, whereby resistance to one antibiotic is accompanied by increased sensitivity to another, offers potential avenues for novel therapeutic interventions against infections unresponsive to classical treatments. In this study, we elucidate the emergence of tobramycin (TOB)-resistant small colony variants (SCVs) due to mutations in the hemL gene, which render S. Typhimurium more susceptible to nitrofurantoin (NIT). Mechanistic studies demonstrate that the collateral sensitivity in TOB-resistant S. Typhimurium SCVs primarily stems from disruptions in haem biosynthesis. This leads to dysfunction in the electron transport chain (ETC) and redox imbalance, ultimately inducing lethal accumulation of reactive oxygen species (ROS). Additionally, the upregulation of nfsA/B expressions facilitates the conversion of NIT prodrug into its active form, promoting ROS-mediated bacterial killing and contributing to this collateral sensitivity pattern. Importantly, alternative NIT therapy demonstrates a significant reduction of bacterial load by more than 2.24-log10 cfu/g in the murine thigh infection and colitis models. Our findings corroborate the collateral sensitivity of S. Typhimurium to nitrofurans as a consequence of evolving resistance to aminoglycosides. This provides a promising approach for treating infections due to aminoglycoside-resistant strains.
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Affiliation(s)
- Chang-Zhen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Yue-Jun Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Yue-Fei Chu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Long-Gen Zhong
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Jin-Peng Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Liu-Yan Liang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Teng-Fei Long
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Liang-Xing Fang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Jian Sun
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xiao-Ping Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Yu-Feng Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
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Zhu J, Wang J, Kang W, Zhang X, Kerdsin A, Yao H, Zheng H, Wu Z. Streptococcus suis serotype 4: a population with the potential pathogenicity in humans and pigs. Emerg Microbes Infect 2024; 13:2352435. [PMID: 38703011 PMCID: PMC11097711 DOI: 10.1080/22221751.2024.2352435] [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: 01/10/2024] [Accepted: 05/02/2024] [Indexed: 05/06/2024]
Abstract
Streptococcus suis is a major bacterial pathogen in pigs and an emerging zoonotic pathogen. Different S. suis serotypes exhibit diverse characteristics in population structure and pathogenicity. Surveillance data highlight the significance of S. suis serotype 4 (SS4) in swine streptococcusis, a pathotype causing human infections. However, except for a few epidemiologic studies, the information on SS4 remains limited. In this study, we investigated the population structure, pathogenicity, and antimicrobial characteristics of SS4 based on 126 isolates, including one from a patient with septicemia. We discovered significant diversities within this population, clustering into six minimum core genome (MCG) groups (1, 2, 3, 4, 7-2, and 7-3) and five lineages. Two main clonal complexes (CCs), CC17 and CC94, belong to MCG groups 1 and 3, respectively. Numerous important putative virulence-associated genes are present in these two MCG groups, and 35.00% (7/20) of pig isolates from CC17, CC94, and CC839 (also belonging to MCG group 3) were highly virulent (mortality rate ≥ 80%) in zebrafish and mice, similar to the human isolate ID36054. Cytotoxicity assays showed that the human and pig isolates of SS4 strains exhibit significant cytotoxicity to human cells. Antimicrobial susceptibility testing showed that 95.83% of strains isolated from our labs were classified as multidrug-resistant. Prophages were identified as the primary vehicle for antibiotic resistance genes. Our study demonstrates the public health threat posed by SS4, expanding the understanding of SS4 population structure and pathogenicity characteristics and providing valuable information for its surveillance and prevention.
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Affiliation(s)
- Jinlu Zhu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People’s Republic of China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, People’s Republic of China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing, People’s Republic of China
| | - Jianping Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Weiming Kang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Xiyan Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Huochun Yao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People’s Republic of China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, People’s Republic of China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing, People’s Republic of China
| | - Han Zheng
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Zongfu Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People’s Republic of China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, People’s Republic of China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing, People’s Republic of China
- Guangdong Provincial Key Laboratory of Research on the Technology of Pig-breeding and Pig-disease Prevention, Guangzhou, People’s Republic of China
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137
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Chanket W, Pipatthana M, Sangphukieo A, Harnvoravongchai P, Chankhamhaengdecha S, Janvilisri T, Phanchana M. The complete catalog of antimicrobial resistance secondary active transporters in Clostridioides difficile: evolution and drug resistance perspective. Comput Struct Biotechnol J 2024; 23:2358-2374. [PMID: 38873647 PMCID: PMC11170357 DOI: 10.1016/j.csbj.2024.05.027] [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: 02/08/2024] [Revised: 05/01/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024] Open
Abstract
Secondary active transporters shuttle substrates across eukaryotic and prokaryotic membranes, utilizing different electrochemical gradients. They are recognized as one of the antimicrobial efflux pumps among pathogens. While primary active transporters within the genome of C. difficile 630 have been completely cataloged, the systematical study of secondary active transporters remains incomplete. Here, we not only identify secondary active transporters but also disclose their evolution and role in drug resistance in C. difficile 630. Our analysis reveals that C. difficile 630 carries 147 secondary active transporters belonging to 27 (super)families. Notably, 50 (34%) of them potentially contribute to antimicrobial resistance (AMR). AMR-secondary active transporters are structurally classified into five (super)families: the p-aminobenzoyl-glutamate transporter (AbgT), drug/metabolite transporter (DMT) superfamily, major facilitator (MFS) superfamily, multidrug and toxic compound extrusion (MATE) family, and resistance-nodulation-division (RND) family. Surprisingly, complete RND genes found in C. difficile 630 are likely an evolutionary leftover from the common ancestor with the diderm. Through protein structure comparisons, we have potentially identified six novel AMR-secondary active transporters from DMT, MATE, and MFS (super)families. Pangenome analysis revealed that half of the AMR-secondary transporters are accessory genes, which indicates an important role in adaptive AMR function rather than innate physiological homeostasis. Gene expression profile firmly supports their ability to respond to a wide spectrum of antibiotics. Our findings highlight the evolution of AMR-secondary active transporters and their integral role in antibiotic responses. This marks AMR-secondary active transporters as interesting therapeutic targets to synergize with other antibiotic activity.
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Affiliation(s)
- Wannarat Chanket
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Methinee Pipatthana
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Apiwat Sangphukieo
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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138
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Liu Z, Lu L, Jiang S. Receptor-binding domain-associated serotypes of SARS-CoV-2. Emerg Microbes Infect 2024; 13:2309968. [PMID: 38264798 PMCID: PMC10866045 DOI: 10.1080/22221751.2024.2309968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024]
Affiliation(s)
- Zezhong Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, School of Pharmacy, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, School of Pharmacy, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, School of Pharmacy, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
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139
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Choi N, Choi E, Cho YJ, Kim MJ, Choi HW, Lee EJ. A shared mechanism of multidrug resistance in laboratory-evolved uropathogenic Escherichia coli. Virulence 2024; 15:2367648. [PMID: 38899601 PMCID: PMC11195483 DOI: 10.1080/21505594.2024.2367648] [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: 12/26/2023] [Accepted: 06/09/2024] [Indexed: 06/21/2024] Open
Abstract
The emergence of multidrug-resistant bacteria poses a significant threat to human health, necessitating a comprehensive understanding of their underlying mechanisms. Uropathogenic Escherichia coli (UPEC), the primary causative agent of urinary tract infections, is frequently associated with multidrug resistance and recurrent infections. To elucidate the mechanism of resistance of UPEC to beta-lactam antibiotics, we generated ampicillin-resistant UPEC strains through continuous exposure to low and high levels of ampicillin in the laboratory, referred to as Low AmpR and High AmpR, respectively. Whole-genome sequencing revealed that both Low and High AmpR strains contained mutations in the marR, acrR, and envZ genes. The High AmpR strain exhibited a single additional mutation in the nlpD gene. Using protein modeling and qRT-PCR analyses, we validated the contributions of each mutation in the identified genes to antibiotic resistance in the AmpR strains, including a decrease in membrane permeability, increased expression of multidrug efflux pump, and inhibition of cell lysis. Furthermore, the AmpR strain does not decrease the bacterial burden in the mouse bladder even after continuous antibiotic treatment in vivo, implicating the increasing difficulty in treating host infections caused by the AmpR strain. Interestingly, ampicillin-induced mutations also result in multidrug resistance in UPEC, suggesting a common mechanism by which bacteria acquire cross-resistance to other classes of antibiotics.
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Affiliation(s)
- Nakjun Choi
- Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Eunna Choi
- Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Yong-Joon Cho
- Department of Molecular Bioscience, Multidimensional Genomics Research Center, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea
| | - Min Jung Kim
- Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Hae Woong Choi
- Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Eun-Jin Lee
- Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
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140
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Hao Z, Hu S, Huang J, Hu J, Zhang Z, Li H, Yan W. Confounding amplifies the effect of environmental factors on COVID-19. Infect Dis Model 2024; 9:1163-1174. [PMID: 39035783 PMCID: PMC11260012 DOI: 10.1016/j.idm.2024.06.005] [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: 03/15/2024] [Revised: 05/26/2024] [Accepted: 06/16/2024] [Indexed: 07/23/2024] Open
Abstract
The global COVID-19 pandemic has severely impacted human health and socioeconomic development, posing an enormous public health challenge. Extensive research has been conducted into the relationship between environmental factors and the transmission of COVID-19. However, numerous factors influence the development of pandemic outbreaks, and the presence of confounding effects on the mechanism of action complicates the assessment of the role of environmental factors in the spread of COVID-19. Direct estimation of the role of environmental factors without removing the confounding effects will be biased. To overcome this critical problem, we developed a Double Machine Learning (DML) causal model to estimate the debiased causal effects of the influencing factors in the COVID-19 outbreaks in Chinese cities. Comparative experiments revealed that the traditional multiple linear regression model overestimated the impact of environmental factors. Environmental factors are not the dominant cause of widespread outbreaks in China in 2022. In addition, by further analyzing the causal effects of environmental factors, it was verified that there is significant heterogeneity in the role of environmental factors. The causal effect of environmental factors on COVID-19 changes with the regional environment. It is therefore recommended that when exploring the mechanisms by which environmental factors influence the spread of epidemics, confounding factors must be handled carefully in order to obtain clean quantitative results. This study offers a more precise representation of the impact of environmental factors on the spread of the COVID-19 pandemic, as well as a framework for more accurately quantifying the factors influencing the outbreak.
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Affiliation(s)
- Zihan Hao
- College of Atmospheric Sciences, Lanzhou University, Lanzhoum, 730000, China
| | - Shujuan Hu
- College of Atmospheric Sciences, Lanzhou University, Lanzhoum, 730000, China
| | - Jianping Huang
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jiaxuan Hu
- College of Atmospheric Sciences, Lanzhou University, Lanzhoum, 730000, China
| | - Zhen Zhang
- College of Atmospheric Sciences, Lanzhou University, Lanzhoum, 730000, China
| | - Han Li
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Wei Yan
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou, 730000, China
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141
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Lu R, Luo XM. The role of gut microbiota in different murine models of systemic lupus erythematosus. Autoimmunity 2024; 57:2378876. [PMID: 39014962 DOI: 10.1080/08916934.2024.2378876] [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: 04/30/2024] [Accepted: 07/07/2024] [Indexed: 07/18/2024]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by immune system dysfunction that can lead to serious health issues and mortality. Recent investigations highlight the role of gut microbiota alterations in modulating inflammation and disease severity in SLE. This review specifically summaries the variations in gut microbiota composition across various murine models of lupus. By focusing on these differences, we aim to elucidate the intricate relationship between gut microbiota dysbiosis and the development and progression of SLE in preclinical settings.
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Affiliation(s)
- Ran Lu
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Xin M Luo
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
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142
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Hu Y, Wang Y, Hu X, Chao H, Li S, Ni Q, Zhu Y, Hu Y, Zhao Z, Chen M. T4SEpp: A pipeline integrating protein language models to predict bacterial type IV secreted effectors. Comput Struct Biotechnol J 2024; 23:801-812. [PMID: 38328004 PMCID: PMC10847861 DOI: 10.1016/j.csbj.2024.01.015] [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: 09/21/2023] [Revised: 01/20/2024] [Accepted: 01/20/2024] [Indexed: 02/09/2024] Open
Abstract
Many pathogenic bacteria use type IV secretion systems (T4SSs) to deliver effectors (T4SEs) into the cytoplasm of eukaryotic cells, causing diseases. The identification of effectors is a crucial step in understanding the mechanisms of bacterial pathogenicity, but this remains a major challenge. In this study, we used the full-length embedding features generated by six pre-trained protein language models to train classifiers predicting T4SEs and compared their performance. We integrated three modules into a model called T4SEpp. The first module searched for full-length homologs of known T4SEs, signal sequences, and effector domains; the second module fine-tuned a machine learning model using data for a signal sequence feature; and the third module used the three best-performing pre-trained protein language models. T4SEpp outperformed other state-of-the-art (SOTA) software tools, achieving ∼0.98 accuracy at a high specificity of ∼0.99, based on the assessment of an independent validation dataset. T4SEpp predicted 13 T4SEs from Helicobacter pylori, including the well-known CagA and 12 other potential ones, among which eleven could potentially interact with human proteins. This suggests that these potential T4SEs may be associated with the pathogenicity of H. pylori. Overall, T4SEpp provides a better solution to assist in the identification of bacterial T4SEs and facilitates studies of bacterial pathogenicity. T4SEpp is freely accessible at https://bis.zju.edu.cn/T4SEpp.
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Affiliation(s)
- Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yejun Wang
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
- Department of Cell Biology and Genetics, College of Basic Medicine, Shenzhen University Medical School, Shenzhen, China
| | - Xiaotian Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Sida Li
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qinyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yanyan Zhu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yixue Hu
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
| | - Ziyi Zhao
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
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143
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Chen B, Liu G, Chen Q, Wang H, Liu L, Tang K. Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes. Comput Struct Biotechnol J 2024; 23:406-416. [PMID: 38235362 PMCID: PMC10792170 DOI: 10.1016/j.csbj.2023.12.025] [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: 06/15/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024] Open
Abstract
Members of the phylum Bacteroidetes play a key role in the marine carbon cycle through their degradation of polysaccharides via carbohydrate-active enzymes (CAZymes) and polysaccharide utilization loci (PULs). The discovery of novel CAZymes and PULs is important for our understanding of the marine carbon cycle. In this study, we isolated and identified a potential new genus of the family Catalimonadaceae, in the phylum Bacteroidetes, from the southwest Indian Ocean. Strain TK19036, the type strain of the new genus, is predicted to encode CAZymes that are relatively abundant in marine Bacteroidetes genomes. Tunicatimonas pelagia NBRC 107804T, Porifericola rhodea NBRC 107748T and Catalinimonas niigatensis NBRC 109829T, which exhibit 16 S rRNA similarities exceeding 90% with strain TK19036, and belong to the same family, were selected as reference strains. These organisms possess a highly diverse repertoire of CAZymes and PULs, which may enable them to degrade a wide range of polysaccharides, especially pectin and alginate. In addition, some secretory CAZymes in strain TK19036 and its relatives were predicted to be transported by type IX secretion system (T9SS). Further, to the best of our knowledge, we propose the first reported "hybrid" PUL targeting alginates in T. pelagia NBRC 107804T. Our findings provide new insights into the polysaccharide degradation capacity of marine Bacteroidetes, and suggest that T9SS may play a more important role in this process than previously believed.
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Affiliation(s)
- Beihan Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Guohua Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Quanrui Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Huanyu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Le Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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144
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Sakurada Y, Matsuda Y, Motohashi K, Hasegawa T, Otsuka Y, Nakano Y, Tokumasu K, Yamamoto K, Sunada N, Honda H, Hagiya H, Ueda K, Otsuka F. Clinical characteristics of female long COVID patients with menstrual symptoms: a retrospective study from a Japanese outpatient clinic. J Psychosom Obstet Gynaecol 2024; 45:2305899. [PMID: 38270210 DOI: 10.1080/0167482x.2024.2305899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/07/2024] [Indexed: 01/26/2024] Open
Abstract
PURPOSE To elucidate the impact of long COVID on menstruation and mental health, medical records of patients with long COVID were evaluated. METHODS Symptoms of long COVID, QOL, mental health, and related endocrine data were compared between two groups with and without menstrual disturbances. RESULTS Of 349 female patients who visited our clinic between February 2021 and March 2023, 223 patients with long COVID (aged 18-50 years) were included. Forty-four (19.7%) of the patients had menstrual symptoms associated with long COVID. The patients with menstrual symptoms were older than those without menstrual symptoms (42.5 vs. 38 years). The percentage of patients with menstrual symptoms was higher during the Omicron phase (24%) than during the Preceding (13%) and Delta (12%) phases. Cycle irregularity was the most frequent (in 63.6% of the patients), followed by severe pain (25%), heavy bleeding (20.5%), perimenopausal symptoms (18.2%), and premenstrual syndrome (15.9%). Fatigue and depression were the most frequent complications. Scores for fatigue and for QOL were significantly worse in long COVID patients with menstrual symptoms. Results of endocrine examinations showed significantly increased cortisol levels in patients with menstrual complaints. CONCLUSION Long COVID has an impact on menstrual conditions and on QOL related to menstrual conditions.
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Affiliation(s)
- Yasue Sakurada
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yui Matsuda
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kanon Motohashi
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Toru Hasegawa
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yuki Otsuka
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yasuhiro Nakano
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kazuki Tokumasu
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Koichiro Yamamoto
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Naruhiko Sunada
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hiroyuki Honda
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hideharu Hagiya
- Department of Infectious Diseases, Okayama University Hospital, Okayama, Japan
| | - Keigo Ueda
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Fumio Otsuka
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Department of Infectious Diseases, Okayama University Hospital, Okayama, Japan
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145
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Liu F, Yang J, Zhang Y, Yang S, Zhang Y, Chen Y, Shao Y, Gao D, Yuan Z, Zhang Y. Mulches assist degraded soil recovery via stimulating biogeochemical cycling: metagenomic analysis. Appl Microbiol Biotechnol 2024; 108:20. [PMID: 38159114 DOI: 10.1007/s00253-023-12824-6] [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: 02/24/2023] [Revised: 11/07/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024]
Abstract
Soil degradation of urban greening has caused soil fertility loss and soil organic carbon depletion. Organic mulches are made from natural origin materials, and represent a cost-effective and environment-friendly remediation method for urban greening. To reveal the effects of organic mulch on soil physicochemical characteristics and fertility, we selected a site that was covered with organic mulch for 6 years and a nearby lawn-covered site. The results showed that soil organic matter, total nitrogen, and available phosphorus levels were improved, especially at a depth of 0-20 cm. The activities of cellulase, invertase, and dehydrogenase in soil covered with organic mulch were 17.46%, 78.98%, and 283.19% higher than those under lawn, respectively. The marker genes of fermentation, aerobic respiration, methanogenesis, and methane oxidation were also enriched in the soil under organic mulch. Nitrogen cycling was generally repressed by the organic mulch, but the assimilatory nitrate and nitrite reduction processes were enhanced. The activity of alkaline phosphatase was 12.63% higher in the mulch-covered soil, and functional genes involved in phosphorus cycling were also enriched. This study presents a comprehensive investigation of the influence of organic mulch on soil microbes and provides a deeper insight into the recovery strategy for soil degradation following urban greening. KEY POINTS: • Long-term cover with organic mulches assists soil recovery from degradation • Soil physical and chemical properties were changed by organic mulches • Organic mulches enhanced genes involved in microbially mediated C and P cycling • Soil organic matter was derived from decomposition of organic mulch and carbon fixation • N cycling was repressed by mulches, except for assimilatory NO2- and NO3- reductions.
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Affiliation(s)
- Fengqin Liu
- College of Life Sciences, Henan Agricultural University, No. 63 Agricultural Road, Zhengzhou, 450002, China
| | - Jiale Yang
- College of Life Sciences, Henan Agricultural University, No. 63 Agricultural Road, Zhengzhou, 450002, China
| | - Yu Zhang
- College of Life Sciences, Henan Agricultural University, No. 63 Agricultural Road, Zhengzhou, 450002, China
| | - Shuilian Yang
- College of Resources and Environmental Sciences, Henan Agricultural University, No. 63 Agricultural Road, Zhengzhou, 450002, China
| | - Yifan Zhang
- College of Life Sciences, Henan Agricultural University, No. 63 Agricultural Road, Zhengzhou, 450002, China
| | - Yun Chen
- College of Life Sciences, Henan Agricultural University, No. 63 Agricultural Road, Zhengzhou, 450002, China
| | - Yizhen Shao
- College of Life Sciences, Henan Agricultural University, No. 63 Agricultural Road, Zhengzhou, 450002, China
| | - Dawen Gao
- College of Environment and Energy Engineering, Engineering and Architecture, Beijing University of Civil, Beijing, 100044, China
| | - Zhiliang Yuan
- College of Life Sciences, Henan Agricultural University, No. 63 Agricultural Road, Zhengzhou, 450002, China.
| | - Yupeng Zhang
- College of Resources and Environmental Sciences, Henan Agricultural University, No. 63 Agricultural Road, Zhengzhou, 450002, China.
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146
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Liu F, Wang ZK, Li MY, Zhang XL, Cai FC, Wang XD, Gao XF, Li W. Characterization of biliary and duodenal microbiota in patients with primary and recurrent choledocholithiasis. Health Inf Sci Syst 2024; 12:29. [PMID: 38584761 PMCID: PMC10994894 DOI: 10.1007/s13755-023-00267-2] [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: 04/24/2023] [Accepted: 12/27/2023] [Indexed: 04/09/2024] Open
Abstract
Purpose To explore the biliary and duodenal microbiota features associated with the formation and recurrence of choledocholithiasis (CDL). Methods We prospectively recruited patients with primary (P-CDL, n = 29) and recurrent CDL (R-CDL, n = 27) for endoscopic retrograde cholangiopancreatography (ERCP). Duodenal mucosa (DM), bile and bile duct stones (BDS) samples were collected in P- and R-CDL patients. DM samples were also collected in 8 healthy controls (HC). The microbiota profile analysis was performed with 16S rRNA gene sequencing. Results Short-course antibiotic application before ERCP showed no significant effects in alpha and beta diversities of the biliary and duodenal microbiota in CDL. Alpha diversity showed no difference between DM and bile samples in CDL. The duodenal microbial richness and diversity was lower in both P- and R-CDL than HC. The biliary microbiota composition showed a high similarity between P- and R-CDL. Fusobacterium and Enterococcus were higher abundant in DM, bile, and BDS samples of R-CDL than P-CDL, as well as Escherichia and Klebsiella in bile samples of R-CDL. The enriched duodenal and biliary bacteria in CDL were closely associated with cholecystectomy, inflammation and liver dysfunction. The bile-associated microbiota of R-CDL expressed enhanced capacity of D-glucuronide and D-glucuronate degradation, implicating an elevated level of β-glucuronidase probably produced by enriched Escherichia and Klebsiella in bile. Conclusions The duodenal microbiota was in an imbalance in CDL. The duodenal microbiota was probably the main source of the biliary microbiota and was closely related to CDL formation and recurrence. Enterococcus, Fusobacterium, Escherichia and Klebsiella might contribute to CDL recurrence. Clinical trials The study was registered at the Chinese Clinical Trial Registry (https://www.chictr.org.cn/index.html, ChiCTR2000033940). Supplementary Information The online version contains supplementary material available at 10.1007/s13755-023-00267-2.
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Affiliation(s)
- Fang Liu
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China
| | - Zi-Kai Wang
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China
| | - Ming-Yang Li
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China
| | - Xiu-li Zhang
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China
| | - Feng-Chun Cai
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China
| | - Xiang-Dong Wang
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China
| | - Xue-Feng Gao
- Integrative Microecology Clinical Center, Shenzhen Key Laboratory of Gastrointestinal Microbiota and Disease, Shenzhen Clinical Research Center for Digestive Disease, Shenzhen Technology Research Center of Gut Microbiota Transplantation, The Clinical Innovation & Research Center, Shenzhen Hospital, Southern Medical University, Shenzhen, 518000 Guangdong China
| | - Wen Li
- Medical School of Chinese PLA, Beijing, China
- Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China
- Minimally Invasive Digestive Disease Center, Beijing and Shenzhen United Family Hospital, Beijing, China
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147
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Wu XQ, Zhao L, Zhao YL, He XY, Zou L, Zhao YY, Li X. Traditional Chinese medicine improved diabetic kidney disease through targeting gut microbiota. PHARMACEUTICAL BIOLOGY 2024; 62:423-435. [PMID: 38757785 PMCID: PMC11104709 DOI: 10.1080/13880209.2024.2351946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024]
Abstract
CONTEXT Diabetic kidney disease (DKD) affects nearly 40% of diabetic patients, often leading to end-stage renal disease that requires renal replacement therapies, such as dialysis and transplantation. The gut microbiota, an integral aspect of human evolution, plays a crucial role in this condition. Traditional Chinese medicine (TCM) has shown promising outcomes in ameliorating DKD by addressing the gut microbiota. OBJECTIVE This review elucidates the modifications in gut microbiota observed in DKD and explores the impact of TCM interventions on correcting microbial dysregulation. METHODS We searched relevant articles from databases including Web of Science, PubMed, ScienceDirect, Wiley, and Springer Nature. The following keywords were used: diabetic kidney disease, diabetic nephropathy, gut microbiota, natural product, TCM, Chinese herbal medicine, and Chinese medicinal herbs. Rigorous criteria were applied to identify high-quality studies on TCM interventions against DKD. RESULTS Dysregulation of the gut microbiota, including Lactobacillus, Streptococcus, and Clostridium, has been observed in individuals with DKD. Key indicators of microbial dysregulation include increased uremic solutes and decreased short-chain fatty acids. Various TCM therapies, such as formulas, tablets, granules, capsules, and decoctions, exhibit unique advantages in regulating the disordered microbiota to treat DKD. CONCLUSION This review highlights the importance of targeting the gut-kidney axis to regulate microbial disorders, their metabolites, and associated signaling pathways in DKD. The Qing-Re-Xiao-Zheng formula, the Shenyan Kangfu tablet, the Huangkui capsule, and the Bekhogainsam decoction are potential candidates to address the gut-kidney axis. TCM interventions offer a significant therapeutic approach by targeting microbial dysregulation in patients with DKD.
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Affiliation(s)
- Xia-Qing Wu
- Faculty of Life Science & Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Lei Zhao
- Department of General Practice, Xi’an International Medical Center Hospital, Xi’an, Shaanxi, China
| | - Yan-Long Zhao
- Faculty of Life Science & Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Xin-Yao He
- Faculty of Life Science & Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Liang Zou
- School of Food and Bioengineering, Chengdu University, Chengdu, Sichuan, China
| | - Ying-Yong Zhao
- Faculty of Life Science & Medicine, Northwest University, Xi’an, Shaanxi, China
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Xia Li
- Faculty of Life Science & Medicine, Northwest University, Xi’an, Shaanxi, China
- Department of General Practice, Xi’an International Medical Center Hospital, Xi’an, Shaanxi, China
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148
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Hu M, Ge J, Jiang Y, Sun X, Guo D, Gu Y. Advances and perspectives in genetic expression and operation for the oleaginous yeast Yarrowia lipolytica. Synth Syst Biotechnol 2024; 9:618-626. [PMID: 38784195 PMCID: PMC11109602 DOI: 10.1016/j.synbio.2024.05.003] [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: 01/14/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
The utilization of industrial biomanufacturing has emerged as a viable and sustainable alternative to fossil-based resources for producing functional chemicals. Moreover, advancements in synthetic biology have created new opportunities for the development of innovative cell factories. Notably, Yarrowia lipolytica, an oleaginous yeast that is generally regarded as safe, possesses several advantageous characteristics, including the ability to utilize inexpensive renewable carbon sources, well-established genetic backgrounds, and mature genetic manipulation methods. Consequently, there is increasing interest in manipulating the metabolism of this yeast to enhance its potential as a biomanufacturing platform. Here, we reviewed the latest developments in genetic expression strategies and manipulation tools related to Y. lipolytica, particularly focusing on gene expression, chromosomal operation, CRISPR-based tool, and dynamic biosensors. The purpose of this review is to serve as a valuable reference for those interested in the development of a Y. lipolytica microbial factory.
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Affiliation(s)
- Mengchen Hu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jianyue Ge
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yaru Jiang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Dongshen Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
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149
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Otesteanu CF, Caldelari R, Heussler V, Sznitman R. Machine learning for predicting Plasmodium liver stage development in vitro using microscopy imaging. Comput Struct Biotechnol J 2024; 24:334-342. [PMID: 38690550 PMCID: PMC11059334 DOI: 10.1016/j.csbj.2024.04.029] [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: 12/08/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Abstract
Malaria, a significant global health challenge, is caused by Plasmodium parasites. The Plasmodium liver stage plays a pivotal role in the establishment of the infection. This study focuses on the liver stage development of the model organism Plasmodium berghei, employing fluorescent microscopy imaging and convolutional neural networks (CNNs) for analysis. Convolutional neural networks have been recently proposed as a viable option for tasks such as malaria detection, prediction of host-pathogen interactions, or drug discovery. Our research aimed to predict the transition of Plasmodium-infected liver cells to the merozoite stage, a key development phase, 15 hours in advance. We collected and analyzed hourly imaging data over a span of at least 38 hours from 400 sequences, encompassing 502 parasites. Our method was compared to human annotations to validate its efficacy. Performance metrics, including the area under the receiver operating characteristic curve (AUC), sensitivity, and specificity, were evaluated on an independent test dataset. The outcomes revealed an AUC of 0.873, a sensitivity of 84.6%, and a specificity of 83.3%, underscoring the potential of our CNN-based framework to predict liver stage development of P. berghei. These findings not only demonstrate the feasibility of our methodology but also could potentially contribute to the broader understanding of parasite biology.
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Affiliation(s)
- Corin F. Otesteanu
- Artificial Intelligence in Medicine group, University of Bern, Switzerland
| | - Reto Caldelari
- Institute of Cell Biology, University of Bern, Switzerland
| | | | - Raphael Sznitman
- Artificial Intelligence in Medicine group, University of Bern, Switzerland
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150
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Chen A, Fang N, Zhang Z, Wen Y, Shen Y, Zhang Y, Zhang L, Zhao G, Ding J, Li J. Structural basis of the monkeypox virus mRNA cap N7 methyltransferase complex. Emerg Microbes Infect 2024; 13:2369193. [PMID: 38873898 PMCID: PMC11212559 DOI: 10.1080/22221751.2024.2369193] [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: 02/20/2024] [Accepted: 06/12/2024] [Indexed: 06/15/2024]
Abstract
The global outbreak of Mpox, caused by the monkeypox virus (MPXV), has attracted international attention and become another major infectious disease event after COVID-19. The mRNA cap N7 methyltransferase (RNMT) of MPXV methylates the N7 position of the added guanosine to the 5'-cap structure of mRNAs and plays a vital role in evading host antiviral immunity. MPXV RNMT is composed of the large subunit E1 and the small subunit E12. How E1 and E12 of MPXV assembly remains unclear. Here, we report the crystal structures of E12, the MTase domain of E1 with E12 (E1CTD-E12) complex, and the E1CTD-E12-SAM ternary complex, revealing the detailed conformations of critical residues and the structural changes upon E12 binding to E1. Functional studies suggest that E1CTD N-terminal extension (Asp545-Arg562) and the small subunit E12 play an essential role in the binding process of SAM. Structural comparison of the AlphaFold2-predicted E1, E1CTD-E12 complex, and the homologous D1-D12 complex of vaccinia virus (VACV) indicates an allosteric activating effect of E1 in MPXV. Our findings provide the structural basis for the MTase activity stimulation of the E1-E12 complex and suggest a potential interface for screening the anti-poxvirus inhibitors.
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Affiliation(s)
- Anke Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, People’s Republic of China
| | - Ning Fang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, People’s Republic of China
| | - Zhifei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, People’s Republic of China
| | - Yiqing Wen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, People’s Republic of China
| | - Yajie Shen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, People’s Republic of China
| | - Yanjie Zhang
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, People’s Republic of China
| | - Lu Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Guoping Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Jin Ding
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, People’s Republic of China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, People’s Republic of China
- Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
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