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Li HZ, Li WJ, Wang ZJ, Chen QL, Staal Jensen MK, Qiao M, Cui L. Integrating Multiple Bacterial Phenotypes and Bayesian Network for Analyzing Health Risks of Pathogens in Plastisphere. Anal Chem 2024; 96:11374-11382. [PMID: 38949233 DOI: 10.1021/acs.analchem.4c01433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Plastic pollution represents a critical threat to soil ecosystems and even humans, as plastics can serve as a habitat for breeding and refuging pathogenic microorganisms against stresses. However, evaluating the health risk of plastispheres is difficult due to the lack of risk factors and quantification model. Here, DNA sequencing, single-cell Raman-D2O labeling, and transformation assay were used to quantify key risk factors of plastisphere, including pathogen abundance, phenotypic resistance to various stresses (antibiotic and pesticide), and ability to acquire antibiotic resistance genes. A Bayesian network model was newly introduced to integrate these three factors and infer their causal relationships. Using this model, the risk of pathogen in the plastisphere is found to be nearly 3 magnitudes higher than that in free-living state. Furthermore, this model exhibits robustness for risk prediction, even in the absence of one factor. Our framework offers a novel and practical approach to assessing the health risk of plastispheres, contributing to the management of plastic-related threats to human health.
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Affiliation(s)
- Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Wen-Jing Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Jian Wang
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14850, United States
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Mia Kristine Staal Jensen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Min Qiao
- Research Center for Eco-Environmental Sciences Chinese Academy of Sciences, Beijing 100085, China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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Kareem BO, Gazioglu O, Mueller Brown K, Habtom M, Glanville DG, Oggioni MR, Andrew PW, Ulijasz AT, Hiller NL, Yesilkaya H. Environmental and genetic regulation of Streptococcus pneumoniae galactose catabolic pathways. Nat Commun 2024; 15:5171. [PMID: 38886409 PMCID: PMC11183247 DOI: 10.1038/s41467-024-49619-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Efficient utilization of nutrients is crucial for microbial survival and virulence. The same nutrient may be utilized by multiple catabolic pathways, indicating that the physical and chemical environments for induction as well as their functional roles may differ. Here, we study the tagatose and Leloir pathways for galactose catabolism of the human pathogen Streptococcus pneumoniae. We show that galactose utilization potentiates pneumococcal virulence, the induction of galactose catabolic pathways is influenced differentially by the concentration of galactose and temperature, and sialic acid downregulates galactose catabolism. Furthermore, the genetic regulation and in vivo induction of each pathway differ, and both galactose catabolic pathways can be turned off with a galactose analogue in a substrate-specific manner, indicating that galactose catabolic pathways can be potential drug targets.
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Affiliation(s)
- Banaz O Kareem
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
- Department of Basic Medical Sciences, College of Medicine, University of Sulaimani, Sulaimani, Iraq
| | - Ozcan Gazioglu
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Karina Mueller Brown
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Medhanie Habtom
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - David G Glanville
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Marco R Oggioni
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
- Department of Pharmacy and Biotechnology, Bologna, Italy
| | - Peter W Andrew
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Andrew T Ulijasz
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - N Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Hasan Yesilkaya
- Department of Respiratory Sciences, University of Leicester, Leicester, UK.
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Torres M, Paszti S, Eberl L. Shedding light on bacteria-host interactions with the aid of TnSeq approaches. mBio 2024; 15:e0039024. [PMID: 38722161 PMCID: PMC11237515 DOI: 10.1128/mbio.00390-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024] Open
Abstract
Bacteria are highly adaptable and grow in diverse niches, where they often interact with eukaryotic organisms. These interactions with different hosts span the entire spectrum from symbiosis to pathogenicity and thus determine the lifestyle of the bacterium. Knowledge of the genetic determinants involved in animal and plant host colonization by pathogenic and mutualistic bacteria is not only crucial to discover new drug targets for disease management but also for developing novel biostimulant strategies. In the last decades, significant progress in genome-wide high-throughput technologies such as transposon insertion sequencing has led to the identification of pathways that enable efficient host colonization. However, the extent to which similar genes play a role in this process in different bacteria is yet unclear. This review highlights the commonalities and specificities of bacterial determinants important for bacteria-host interaction.
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Affiliation(s)
- Marta Torres
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
| | - Sarah Paszti
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
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Carhuaricra-Huaman D, Gonzalez IHL, Ramos PL, da Silva AM, Setubal JC. Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths ( Bradypus variegatus), the first from a non-human host. PeerJ 2024; 12:e17206. [PMID: 38584940 PMCID: PMC10999152 DOI: 10.7717/peerj.17206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Kerstersia gyiorum is a Gram-negative bacterium found in various animals, including humans, where it has been associated with various infections. Knowledge of the basic biology of K. gyiorum is essential to understand the evolutionary strategies of niche adaptation and how this organism contributes to infectious diseases; however, genomic data about K. gyiorum is very limited, especially from non-human hosts. In this work, we sequenced 12 K. gyiorum genomes isolated from healthy free-living brown-throated sloths (Bradypus variegatus) in the Parque Estadual das Fontes do Ipiranga (São Paulo, Brazil), and compared them with genomes from isolates of human origin, in order to gain insights into genomic diversity, phylogeny, and host specialization of this species. Phylogenetic analysis revealed that these K. gyiorum strains are structured according to host. Despite the fact that sloth isolates were sampled from a single geographic location, the intra-sloth K. gyiorum diversity was divided into three clusters, with differences of more than 1,000 single nucleotide polymorphisms between them, suggesting the circulation of various K. gyiorum lineages in sloths. Genes involved in mobilome and defense mechanisms against mobile genetic elements were the main source of gene content variation between isolates from different hosts. Sloth-specific K. gyiorum genome features include an IncN2 plasmid, a phage sequence, and a CRISPR-Cas system. The broad diversity of defense elements in K. gyiorum (14 systems) may prevent further mobile element flow and explain the low amount of mobile genetic elements in K. gyiorum genomes. Gene content variation may be important for the adaptation of K. gyiorum to different host niches. This study furthers our understanding of diversity, host adaptation, and evolution of K. gyiorum, by presenting and analyzing the first genomes of non-human isolates.
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Affiliation(s)
| | - Irys H L Gonzalez
- Coordenadoria de Fauna Silvestre, Secretaria do Meio Ambiente, São Paulo, SP, Brazil
| | - Patricia L Ramos
- Coordenadoria de Fauna Silvestre, Secretaria do Meio Ambiente, São Paulo, SP, Brazil
| | - Aline M da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Joao C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
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Jiang F, Ruan Y, Chen XH, Yu HL, Cheng T, Duan XY, Liu YG, Zhang HY, Zhang QY. Metabolites of pathogenic microorganisms database (MPMdb) and its seed metabolite applications. Microbiol Spectr 2024; 12:e0234223. [PMID: 38391229 PMCID: PMC10986615 DOI: 10.1128/spectrum.02342-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Seed metabolites are the combination of essential compounds required by an organism across various potential environmental conditions. The seed metabolites screening framework based on the network topology approach can capture important biological information of species. This study aims to identify comprehensively the relationship between seed metabolites and pathogenic bacteria. A large-scale data set was compiled, describing the seed metabolite sets and metabolite sets of 124,192 pathogenic strains from 34 genera, by constructing genome-scale metabolic models. The enrichment analysis method was used to screen the specific seed metabolites of each species/genus of pathogenic bacteria. The metabolites of pathogenic microorganisms database (MPMdb) (http://qyzhanglab.hzau.edu.cn/MPMdb/) was established for browsing, searching, predicting, or downloading metabolites and seed metabolites of pathogenic microorganisms. Based on the MPMdb, taxonomic and phylogenetic analyses of pathogenic bacteria were performed according to the function of seed metabolites and metabolites. The results showed that the seed metabolites could be used as a feature for microorganism chemotaxonomy, and they could mirror the phylogeny of pathogenic bacteria. In addition, our screened specific seed metabolites of pathogenic bacteria can be used not only for further tapping the nutritional resources and identifying auxotrophies of pathogenic bacteria but also for designing targeted bactericidal compounds by combining with existing antimicrobial agents.IMPORTANCEMetabolites serve as key communication links between pathogenic microorganisms and hosts, with seed metabolites being crucial for microbial growth, reproduction, external communication, and host infection. However, the large-scale screening of metabolites and the identification of seed metabolites have always been the main technical bottleneck due to the low throughput and costly analysis. Genome-scale metabolic models have become a recognized research paradigm to investigate the metabolic characteristics of species. The developed metabolites of pathogenic microorganisms database in this study is committed to systematically predicting and identifying the metabolites and seed metabolites of pathogenic microorganisms, which could provide a powerful resource platform for pathogenic bacteria research.
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Affiliation(s)
- Feng Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Yao Ruan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xiao-Hui Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Hai-Long Yu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Ting Cheng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xin-Ya Duan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Yan-Guang Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Qing-Ye Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
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Wenner N, Zhu X, Rowe WPM, Händler K, Hinton JCD. Succinate utilisation by Salmonella is inhibited by multiple regulatory systems. PLoS Genet 2024; 20:e1011142. [PMID: 38457455 DOI: 10.1371/journal.pgen.1011142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/26/2024] [Accepted: 01/19/2024] [Indexed: 03/10/2024] Open
Abstract
Succinate is a potent immune signalling molecule that is present in the mammalian gut and within macrophages. Both of these infection niches are colonised by the pathogenic bacterium Salmonella enterica serovar Typhimurium during infection. Succinate is a C4-dicarboyxlate that can serve as a source of carbon for bacteria. When succinate is provided as the sole carbon source for in vitro cultivation, Salmonella and other enteric bacteria exhibit a slow growth rate and a long lag phase. This growth inhibition phenomenon was known to involve the sigma factor RpoS, but the genetic basis of the repression of bacterial succinate utilisation was poorly understood. Here, we use an experimental evolution approach to isolate fast-growing mutants during growth of S. Typhimurium on succinate containing minimal medium. Our approach reveals novel RpoS-independent systems that inhibit succinate utilisation. The CspC RNA binding protein restricts succinate utilisation, an inhibition that is antagonised by high levels of the small regulatory RNA (sRNA) OxyS. We discovered that the Fe-S cluster regulatory protein IscR inhibits succinate utilisation by repressing the C4-dicarboyxlate transporter DctA. Furthermore, the ribose operon repressor RbsR is required for the complete RpoS-driven repression of succinate utilisation, suggesting a novel mechanism of RpoS regulation. Our discoveries shed light on the redundant regulatory systems that tightly regulate the utilisation of succinate. We speculate that the control of central carbon metabolism by multiple regulatory systems in Salmonella governs the infection niche-specific utilisation of succinate.
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Affiliation(s)
- Nicolas Wenner
- Clinical Infection, Microbiology & Immunology, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Xiaojun Zhu
- Clinical Infection, Microbiology & Immunology, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Will P M Rowe
- Clinical Infection, Microbiology & Immunology, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Kristian Händler
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Jay C D Hinton
- Clinical Infection, Microbiology & Immunology, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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Xi W, Zhang X, Zhu X, Wang J, Xue H, Pan H. Distribution patterns and influential factors of pathogenic bacteria in freshwater aquaculture sediments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:16028-16047. [PMID: 38308166 DOI: 10.1007/s11356-024-31897-y] [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: 08/07/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Pathogenic bacteria, the major causative agents of aquaculture diseases, are a serious impediment to the aquaculture industry. However, the bioinformatics of pathogenic bacteria and virulence factors (VFs) in sediments, an important component of freshwater aquaculture ecosystems, are not well characterized. In this study, 20 sediment samples were collected from fish pond sediments (FPS), shrimp field sediments (SFS), fish pond sediment control (FPSC), and shrimp field sediment control (SFSC). Molecular biological information was obtained on a total of 173 pathogenic bacteria, 1093 virulence factors (VFs), and 8475 mobile genetic elements (MGEs) from these samples. The results indicated that (1) aquaculture patterns and sediment characteristics can affect the distribution of pathogenic bacteria. According to the results of the Kruskal-Wallis H test, except for Mycobacterium gilvum, there were significant differences (P < 0.05) among the four sediment types in the average abundance of major pathogenic bacteria (top 30 in abundance), and the average abundance of major pathogenic bacteria in the four sediment types followed the following pattern: FPS > SFS > FPSC > SFSC. (2) Pathogenic bacteria are able to implement a variety of complex pathogenic mechanisms such as adhesion, invasion, immune evasion, and metabolic regulation in the host because they carry a variety of VFs such as type IV pili, HSI-I, Alginate, Colibactin, and Capsule. According to the primary classification of the Virulence Factor Database (VFDB), the abundance of VFs in all four types of sediments showed the following pattern: offensive VFs > non-specific VFs > defensive VFs > regulation of virulence-related genes. (3) Total organic carbon (TOC), total phosphorus (TP), available phosphorus (AP), nitrite, and nitrate were mostly only weakly positively correlated with the major pathogenic bacteria and could promote the growth of pathogenic bacteria to some extent, whereas ammonia was significantly positively correlated with most of the major pathogenic bacteria and could play an important role in promoting the growth and reproduction of pathogenic bacteria. (4) Meanwhile, there was also a significant positive correlation between CAZyme genes and major pathogenic bacteria (0.62 ≤ R ≤ 0.89, P < 0.05). This suggests that these pathogenic bacteria could be the main carriers of CAZyme genes and, to some extent, gained a higher level of metabolic activity by degrading organic matter in the sediments to maintain their competitive advantage. (5) Worryingly, the results of correlation analyses indicated that MGEs in aquaculture sediments could play an important role in the spread of VFs (R = 0.82, P < 0.01), and in particular, plasmids (R = 0.75, P < 0.01) and integrative and conjugative elements (ICEs, R = 0.65, P < 0.05) could be these major vectors of VFs. The results of this study contribute to a comprehensive understanding of the health of freshwater aquaculture sediments and provide a scientific basis for aquaculture management and conservation.
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Affiliation(s)
- Wenxiang Xi
- Hubei Key Laboratory of Petroleum Geochemistry and Environment, Yangtze University, Wuhan, 430100, Hubei, China
- College of Resources and Environment, Yangtze University, Wuhan, 430100, Hubei, China
| | - Xun Zhang
- China Coal Mine Construction Group Co., LTD, Hefei, 230071, Anhui, China
| | - Xianbin Zhu
- Hubei Key Laboratory of Petroleum Geochemistry and Environment, Yangtze University, Wuhan, 430100, Hubei, China
- College of Resources and Environment, Yangtze University, Wuhan, 430100, Hubei, China
| | - Jiaming Wang
- Hubei Key Laboratory of Petroleum Geochemistry and Environment, Yangtze University, Wuhan, 430100, Hubei, China
- College of Resources and Environment, Yangtze University, Wuhan, 430100, Hubei, China
| | - Han Xue
- Hubei Key Laboratory of Petroleum Geochemistry and Environment, Yangtze University, Wuhan, 430100, Hubei, China
- College of Resources and Environment, Yangtze University, Wuhan, 430100, Hubei, China
| | - Hongzhong Pan
- Hubei Key Laboratory of Petroleum Geochemistry and Environment, Yangtze University, Wuhan, 430100, Hubei, China.
- College of Resources and Environment, Yangtze University, Wuhan, 430100, Hubei, China.
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Li C, Song J, Chen Q, Ge D, Li Q, Yang Y. Whole-genome shotgun sequencing unravels the influence of environmental microbial co-infections on the treatment efficacy for severe pediatric infectious diseases. Front Microbiol 2024; 15:1308871. [PMID: 38328429 PMCID: PMC10847551 DOI: 10.3389/fmicb.2024.1308871] [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: 10/08/2023] [Accepted: 01/03/2024] [Indexed: 02/09/2024] Open
Abstract
Background The microbiome plays a pivotal role in mediating immune deviation during the development of early-life viral infections. Recurrent infections in children are considered a risk factor for disease development. This study delves into the metagenomics of the microbiome in children suffering from severe infections, seeking to identify potential sources of these infections. Aims The aim of this study was to identify the specific microorganisms and factors that significantly influence the treatment duration in patients suffering from severe infections. We sought to understand how these microbial communities and other variables may affect the treatment duration and the use of antibiotics of these patients with severe infections. Method Whole-genome shotgun sequencing was conducted on samples collected from children aged 0-14 years with severe infections, admitted to the Pediatrics Department of Xiamen First Hospital. The Kraken2 algorithm was used for taxonomic identification from sequence reads, and linear mixed models were employed to identify significant microorganisms influencing treatment duration. Colwellia, Cryptococcus, and Citrobacter were found to significantly correlate with the duration of clinical treatment. Further analysis using propensity score matching (PSM) and rank-sum test identified clinical indicators significantly associated with the presence of these microorganisms. Results Using a linear mixed model after removed the outliers, we identified that the abundance of Colwellia, Cryptococcus, and Citrobacter significantly influences the treatment duration. The presence of these microorganisms is associated with a longer treatment duration for patients. Furthermore, these microorganisms were found to impact various clinical measures. Notably, an increase in hospitalization durations and medication costs was observed in patients with these microorganisms. In patients with Colwellia, Cryptococcus, and Citrobacter, we discover significant differences in platelets levels. We also find that in patients with Cryptococcus, white blood cells, hemoglobin, and neutrophils levels are lower. Conclusion These findings suggest that Colwellia, Cryptococcus, and Citrobacter, particularly Cryptococcus, could potentially contribute to the severity of infections observed in this cohort, possibly as co-infections. These microorganisms warrant further investigation into their pathogenic roles and mechanisms of action, as their presence in combination with disease-causing organisms may have a synergistic effect on disease severity. Understanding the interplay between these microorganisms and pathogenic agents could provide valuable insights into the complex nature of severe pediatric infections and guide the development of targeted therapeutic strategies.
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Affiliation(s)
- Chengxin Li
- Department of Pediatrics, Pediatric Key Laboratory of Xiamen, The First Affiliated Hospital of Xiamen University, Institute of Pediatrics, School of Medicine, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Jing Song
- Department of Pediatrics, Pediatric Key Laboratory of Xiamen, The First Affiliated Hospital of Xiamen University, Institute of Pediatrics, School of Medicine, Xiamen University, Xiamen, China
| | - Qihong Chen
- Department of Pediatrics, Pediatric Key Laboratory of Xiamen, The First Affiliated Hospital of Xiamen University, Institute of Pediatrics, School of Medicine, Xiamen University, Xiamen, China
| | - Dandan Ge
- Department of Pediatrics, Pediatric Key Laboratory of Xiamen, The First Affiliated Hospital of Xiamen University, Institute of Pediatrics, School of Medicine, Xiamen University, Xiamen, China
| | - Qiyuan Li
- Department of Pediatrics, Pediatric Key Laboratory of Xiamen, The First Affiliated Hospital of Xiamen University, Institute of Pediatrics, School of Medicine, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Yungang Yang
- Department of Pediatrics, Pediatric Key Laboratory of Xiamen, The First Affiliated Hospital of Xiamen University, Institute of Pediatrics, School of Medicine, Xiamen University, Xiamen, China
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Okon EM, Okocha RC, Taiwo AB, Michael FB, Bolanle AM. Dynamics of co-infection in fish: A review of pathogen-host interaction and clinical outcome. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 4:100096. [PMID: 37250211 PMCID: PMC10213192 DOI: 10.1016/j.fsirep.2023.100096] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 04/09/2023] [Accepted: 05/15/2023] [Indexed: 05/31/2023] Open
Abstract
Co-infections can affect the transmission of a pathogen within a population and the pathogen's virulence, ultimately affecting the disease's dynamics. In addition, co-infections can potentially affect the host's immunological responses, clinical outcomes, survival, and disease control efficacy. Co-infections significantly impact fish production and can change several fish diseases' progression and severity. However, the effect of co-infection has only recently garnered limited attention in aquatic animals such as fish, and there is currently a dearth of studies on this topic. This study, therefore, presents an in-depth summary of the dynamics of co-infection in fish. This study reviewed the co-infection of fish pathogens, the interaction of pathogens and fish, clinical outcomes and impacts on fish immune responses, and fish survival. Most studies described the prevalence of co-infections in fish, with various parameters influencing their outcomes. Bacterial co-infection increased fish mortality, ulcerative dermatitis, and intestinal haemorrhage. Viral co-infection resulted in osmoregulatory effects, increased mortality and cytopathic effect (CPE). More severe histological alterations and clinical symptoms were related to the co-infection of fish than in single-infected fish. In parasitic co-infection, there was increased mortality, high kidney swelling index, and severe necrotic alterations in the kidney, liver, and spleen. In other cases, there were more severe kidney lesions, cartilage destruction and displacement. There was a dearth of information on mitigating co-infections in fish. Therefore, further studies on the mitigation strategies of co-infections in fish will provide valuable insights into this research area. Also, more research on the immunology of co-infection specific to each fish pathogen class (bacteria, viruses, fungi, and parasites) is imperative. The findings from such studies would provide valuable information on the relationship between fish immune systems and targeted responses.
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Affiliation(s)
| | - Reuben Chukwuka Okocha
- Department of Animal Science, College of Agricultural Sciences, Landmark University, P.M.B. 1001 Omu-Aran, Kwara State, Nigeria
- Climate Action Research Group, Landmark University SDG 13, Nigeria
| | | | - Falana Babatunde Michael
- Department of Animal Science, College of Agricultural Sciences, Landmark University, P.M.B. 1001 Omu-Aran, Kwara State, Nigeria
- Life Below Water Research Group, Landmark University SDG 14, Nigeria
| | - Adeniran Moji Bolanle
- Department of Animal Science, College of Agricultural Sciences, Landmark University, P.M.B. 1001 Omu-Aran, Kwara State, Nigeria
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Murray GGR, Hossain ASMM, Miller EL, Bruchmann S, Balmer AJ, Matuszewska M, Herbert J, Hadjirin NF, Mugabi R, Li G, Ferrando ML, Fernandes de Oliveira IM, Nguyen T, Yen PLK, Phuc HD, Zaw Moe A, Su Wai T, Gottschalk M, Aragon V, Valentin-Weigand P, Heegaard PMH, Vrieling M, Thein Maw M, Thidar Myint H, Tun Win Y, Thi Hoa N, Bentley SD, Clavijo MJ, Wells JM, Tucker AW, Weinert LA. The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs. Proc Natl Acad Sci U S A 2023; 120:e2307773120. [PMID: 37963246 PMCID: PMC10666105 DOI: 10.1073/pnas.2307773120] [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: 05/22/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023] Open
Abstract
The expansion and intensification of livestock production is predicted to promote the emergence of pathogens. As pathogens sometimes jump between species, this can affect the health of humans as well as livestock. Here, we investigate how livestock microbiota can act as a source of these emerging pathogens through analysis of Streptococcus suis, a ubiquitous component of the respiratory microbiota of pigs that is also a major cause of disease on pig farms and an important zoonotic pathogen. Combining molecular dating, phylogeography, and comparative genomic analyses of a large collection of isolates, we find that several pathogenic lineages of S. suis emerged in the 19th and 20th centuries, during an early period of growth in pig farming. These lineages have since spread between countries and continents, mirroring trade in live pigs. They are distinguished by the presence of three genomic islands with putative roles in metabolism and cell adhesion, and an ongoing reduction in genome size, which may reflect their recent shift to a more pathogenic ecology. Reconstructions of the evolutionary histories of these islands reveal constraints on pathogen emergence that could inform control strategies, with pathogenic lineages consistently emerging from one subpopulation of S. suis and acquiring genes through horizontal transfer from other pathogenic lineages. These results shed light on the capacity of the microbiota to rapidly evolve to exploit changes in their host population and suggest that the impact of changes in farming on the pathogenicity and zoonotic potential of S. suis is yet to be fully realized.
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Affiliation(s)
- Gemma G. R. Murray
- Department of Genetics, Evolution and Environment, University College London, LondonWC1E 6BT, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | | | - Eric L. Miller
- Department of Biology, Haverford College, Haverford, PA19041
| | - Sebastian Bruchmann
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | - Andrew J. Balmer
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
- Department of Medicine, University of Cambridge, CambridgeCB2 2QQ, United Kingdom
| | - Josephine Herbert
- Centre for Enzyme Innovation, University of Portsmouth, PortsmouthPO1 2DD, United Kingdom
| | - Nazreen F. Hadjirin
- Nuffield Department of Population Health, University of Oxford, OxfordOX3 7LF, United Kingdom
| | - Robert Mugabi
- College of Veterinary Medicine, Iowa State University, Ames, IA50011
| | - Ganwu Li
- College of Veterinary Medicine, Iowa State University, Ames, IA50011
| | - Maria Laura Ferrando
- Animal Sciences Department, Wageningen University, 6700 AHWageningen, The Netherlands
| | | | - Thanh Nguyen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phung L. K. Yen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho D. Phuc
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Aung Zaw Moe
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Thiri Su Wai
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Marcelo Gottschalk
- Département de Pathologie et Microbiologie, Université de Montréal, QuébecJ2S 2M2, Canada
| | - Virginia Aragon
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Barcelona08193, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona08193, Spain
| | - Peter Valentin-Weigand
- Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover30559, Germany
| | - Peter M. H. Heegaard
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Manouk Vrieling
- Wageningen Bioveterinary Research, 8221 RALelystad, The Netherlands
| | - Min Thein Maw
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | | | - Ye Tun Win
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7LG, United Kingdom
- Microbiology Department and Center for Tropical Medicine Research, Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, CambridgeCB10 1RQ, United Kingdom
| | - Maria J. Clavijo
- College of Veterinary Medicine, Iowa State University, Ames, IA50011
| | - Jerry M. Wells
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
- Animal Sciences Department, Wageningen University, 6700 AHWageningen, The Netherlands
| | - Alexander W. Tucker
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | - Lucy A. Weinert
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
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11
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Obolski U, Swarthout TD, Kalizang'oma A, Mwalukomo TS, Chan JM, Weight CM, Brown C, Cave R, Cornick J, Kamng'ona AW, Msefula J, Ercoli G, Brown JS, Lourenço J, Maiden MC, French N, Gupta S, Heyderman RS. The metabolic, virulence and antimicrobial resistance profiles of colonising Streptococcus pneumoniae shift after PCV13 introduction in urban Malawi. Nat Commun 2023; 14:7477. [PMID: 37978177 PMCID: PMC10656543 DOI: 10.1038/s41467-023-43160-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Streptococcus pneumoniae causes substantial mortality among children under 5-years-old worldwide. Polysaccharide conjugate vaccines (PCVs) are highly effective at reducing vaccine serotype disease, but emergence of non-vaccine serotypes and persistent nasopharyngeal carriage threaten this success. We investigated the hypothesis that following vaccine, adapted pneumococcal genotypes emerge with the potential for vaccine escape. We genome sequenced 2804 penumococcal isolates, collected 4-8 years after introduction of PCV13 in Blantyre, Malawi. We developed a pipeline to cluster the pneumococcal population based on metabolic core genes into "Metabolic genotypes" (MTs). We show that S. pneumoniae population genetics are characterised by emergence of MTs with distinct virulence and antimicrobial resistance (AMR) profiles. Preliminary in vitro and murine experiments revealed that representative isolates from emerging MTs differed in growth, haemolytic, epithelial infection, and murine colonisation characteristics. Our results suggest that in the context of PCV13 introduction, pneumococcal population dynamics had shifted, a phenomenon that could further undermine vaccine control and promote spread of AMR.
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Affiliation(s)
- Uri Obolski
- Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Todd D Swarthout
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | - Akuzike Kalizang'oma
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
| | | | - Jia Mun Chan
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
| | - Caroline M Weight
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
- Faculty of Health and Medicine, Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Comfort Brown
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
| | - Rory Cave
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom
| | - Jen Cornick
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi
- Clinical Infection, Microbiology and Immunology, Institute of Infection Veterinary & Ecological Science, University of Liverpool, Liverpool, United Kingdom
| | | | | | - Giuseppe Ercoli
- UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Jeremy S Brown
- UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Universidade Católica Portuguesa, Faculty of Medicine, Biomedical Research Centre, Lisbon, Portugal
| | - Martin C Maiden
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Neil French
- Clinical Infection, Microbiology and Immunology, Institute of Infection Veterinary & Ecological Science, University of Liverpool, Liverpool, United Kingdom
| | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Robert S Heyderman
- Malawi Liverpool Wellcome Programme, Blantyre, Malawi.
- Mucosal Pathogens Research Group, Research Department of Infection, Division of Infection & Immunity, University College London, London, United Kingdom.
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12
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Li XY, Zeng ZX, Cheng ZX, Wang YL, Yuan LJ, Zhai ZY, Gong W. Common pathogenic bacteria-induced reprogramming of the host proteinogenic amino acids metabolism. Amino Acids 2023; 55:1487-1499. [PMID: 37814028 PMCID: PMC10689525 DOI: 10.1007/s00726-023-03334-w] [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: 04/02/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023]
Abstract
Apart from cancer, metabolic reprogramming is also prevalent in other diseases, such as bacterial infections. Bacterial infections can affect a variety of cells, tissues, organs, and bodies, leading to a series of clinical diseases. Common Pathogenic bacteria include Helicobacter pylori, Salmonella enterica, Mycobacterium tuberculosis, Staphylococcus aureus, and so on. Amino acids are important and essential nutrients in bacterial physiology and support not only their proliferation but also their evasion of host immune defenses. Many pathogenic bacteria or opportunistic pathogens infect the host and lead to significant changes in metabolites, especially the proteinogenic amino acids, to inhibit the host's immune mechanism to achieve its immune evasion and pathogenicity. Here, we review the regulation of host metabolism, while host cells are infected by some common pathogenic bacteria, and discuss how amino acids of metabolic reprogramming affect bacterial infections, revealing the potential adjunctive application of amino acids alongside antibiotics.
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Affiliation(s)
- Xiao-Yue Li
- The First School of Clinical Medicine, Southern Medical University, Guangdong, 510515, China
| | - Zi-Xin Zeng
- The First School of Clinical Medicine, Southern Medical University, Guangdong, 510515, China
| | - Zhi-Xing Cheng
- The First School of Clinical Medicine, Southern Medical University, Guangdong, 510515, China
| | - Yi-Lin Wang
- The First School of Clinical Medicine, Southern Medical University, Guangdong, 510515, China
| | - Liang-Jun Yuan
- The First School of Clinical Medicine, Southern Medical University, Guangdong, 510515, China
| | - Zhi-Yong Zhai
- Shenzhen Hospital, Southern Medical University, Shenzhen Clinical Medical College, Southern Medical University, Guangdong, 518101, China.
| | - Wei Gong
- Shenzhen Hospital, Southern Medical University, Shenzhen Clinical Medical College, Southern Medical University, Guangdong, 518101, China.
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13
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Wiesmann CL, Wang NR, Zhang Y, Liu Z, Haney CH. Origins of symbiosis: shared mechanisms underlying microbial pathogenesis, commensalism and mutualism of plants and animals. FEMS Microbiol Rev 2023; 47:fuac048. [PMID: 36521845 PMCID: PMC10719066 DOI: 10.1093/femsre/fuac048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/17/2023] Open
Abstract
Regardless of the outcome of symbiosis, whether it is pathogenic, mutualistic or commensal, bacteria must first colonize their hosts. Intriguingly, closely related bacteria that colonize diverse hosts with diverse outcomes of symbiosis have conserved host-association and virulence factors. This review describes commonalities in the process of becoming host associated amongst bacteria with diverse lifestyles. Whether a pathogen, commensal or mutualist, bacteria must sense the presence of and migrate towards a host, compete for space and nutrients with other microbes, evade the host immune system, and change their physiology to enable long-term host association. We primarily focus on well-studied taxa, such as Pseudomonas, that associate with diverse model plant and animal hosts, with far-ranging symbiotic outcomes. Given the importance of opportunistic pathogens and chronic infections in both human health and agriculture, understanding the mechanisms that facilitate symbiotic relationships between bacteria and their hosts will help inform the development of disease treatments for both humans, and the plants we eat.
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Affiliation(s)
- Christina L Wiesmann
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nicole R Wang
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yue Zhang
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zhexian Liu
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Cara H Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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14
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Cutri A, Shrout JD, Bohn PW. Metabolic and Oxidative Stress Effects on the Spectroelectrochemical Behavior of Single Pseudomonas aeruginosa Cells. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:659-666. [PMID: 37886305 PMCID: PMC10598847 DOI: 10.1021/cbmi.3c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen capable of causing a wide range of diseases in immunocompromised patients. In order to better understand P. aeruginosa behavior and virulence and to advance drug therapies to combat infection, it would be beneficial to understand how P. aeruginosa cells survive stressful conditions, especially environmental stressors. Here, we report on a strategy that measures potential-dependent fluorescence of individual P. aeruginosa cells, as a sentinel, for cellular response to starvation, hunger, and oxidative stress. This is accomplished using a micropore electrode array capable of trapping large numbers of isolated, vertically oriented cells at well-defined spatial positions in order to study large arrays of single cells in parallel. We find that conditions promoting either starvation or oxidative stress produce discernible changes in the fluorescence response, demonstrated by an increase in the prevalence of fluorescence transients, one of three canonical spectroelectrochemical behaviors exhibited by single P. aeruginosa cells. In contrast, more modest nutrient limitations have little to no effect on the spectroelectrochemical response when compared to healthy cells in the stationary phase. These findings demonstrate the capabilities of micropore electrode arrays for studying the behavior of single microbial cells under conditions where the intercellular spacing, orientation, and chemical environment of the cells are controlled. Realizing single-cell studies under such well-defined conditions makes it possible to study fundamental stress responses with unprecedented control.
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Affiliation(s)
- Allison
R. Cutri
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
| | - Joshua D. Shrout
- Department
of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department
of Biological Sciences, University of Notre
Dame, Notre Dame, Indiana 46556, United
States
| | - Paul W. Bohn
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
- Department
of Chemical and Biomolecular Engineering, University of Notre Dame, Notre
Dame, Indiana 46556, United States
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15
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Smith HB, Lee K, Freeman MJ, Stevenson DM, Amador-Noguez D, Sauer JD. Listeria monocytogenes requires DHNA-dependent intracellular redox homeostasis facilitated by Ndh2 for survival and virulence. Infect Immun 2023; 91:e0002223. [PMID: 37754681 PMCID: PMC10580952 DOI: 10.1128/iai.00022-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/09/2023] [Indexed: 09/28/2023] Open
Abstract
Listeria monocytogenes is a remarkably well-adapted facultative intracellular pathogen that can thrive in a wide range of ecological niches. L. monocytogenes maximizes its ability to generate energy from diverse carbon sources using a respiro-fermentative metabolism that can function under both aerobic and anaerobic conditions. Cellular respiration maintains redox homeostasis by regenerating NAD+ while also generating a proton motive force. The end products of the menaquinone (MK) biosynthesis pathway are essential to drive both aerobic and anaerobic cellular respirations. We previously demonstrated that intermediates in the MK biosynthesis pathway, notably 1,4-dihydroxy-2-naphthoate (DHNA), are required for the survival and virulence of L. monocytogenes independent of their role in respiration. Furthermore, we found that restoration of NAD+/NADH ratio through expression of water-forming NADH oxidase could rescue phenotypes associated with DHNA deficiency. Here, we extend these findings to demonstrate that endogenous production or direct supplementation of DHNA restored both the cellular redox homeostasis and metabolic output of fermentation in L. monocytogenes. Furthermore, exogenous supplementation of DHNA rescues the in vitro growth and ex vivo virulence of L. monocytogenes DHNA-deficient mutants. Finally, we demonstrate that exogenous DHNA restores redox balance in L. monocytogenes specifically through the recently annotated NADH dehydrogenase Ndh2, independent of its role in the extracellular electron transport pathway. These data suggest that the production of DHNA may represent an additional layer of metabolic adaptability by L. monocytogenes to drive energy metabolism in the absence of respiration-favorable conditions.
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Affiliation(s)
- Hans B. Smith
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kijeong Lee
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Matthew J. Freeman
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David M. Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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16
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Jaroensuk J, Chuaboon L, Kesornpun C, Chaiyen P. Enzymes in riboflavin biosynthesis: Potential antibiotic drug targets. Arch Biochem Biophys 2023; 748:109762. [PMID: 37739114 DOI: 10.1016/j.abb.2023.109762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
The rapid resistance of pathogens to antibiotics has emerged as a major threat to global health. Identification of new antibiotic targets is thus needed for developing alternative drugs. Genes encoding enzymes involved in the biosynthesis of riboflavin and flavin cofactors (FMN/FAD) are attractive targets because these enzymatic reactions are necessary for most bacteria to synthesize flavin cofactors for use in their central metabolic reactions. Moreover, humans lack most of these enzymes because we uptake riboflavin from our diet. This review discusses the current knowledge of enzymes involved in bacterial biosynthesis of riboflavin and other flavin cofactors, as well as the functions of the FMN riboswitch. Here, we highlight recent progress in the structural and mechanistic characterization, and inhibition of GTP cyclohydrolase II (GCH II), lumazine synthase (LS), riboflavin synthase (RFS), FAD synthetase (FADS), and FMN riboswitch, which have been identified as plausible antibiotic targets. As the structures and functions of these enzymes and regulatory systems are not completely understood, they are attractive as subjects for future in-depth biochemical and biophysical analysis.
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Affiliation(s)
- Juthamas Jaroensuk
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Wangchan, Rayong, 21210, Thailand
| | - Litavadee Chuaboon
- School of Pharmacy and Biomass and Oil Palm Center of Excellence, Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Chatchai Kesornpun
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Wangchan, Rayong, 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Wangchan, Rayong, 21210, Thailand.
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17
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Chang YT, Ko HT, Wu PL, Kumar R, Wang HC, Lu HP. Gut microbiota of Pacific white shrimp ( Litopenaeus vannamei) exhibits distinct responses to pathogenic and non-pathogenic Vibrio parahaemolyticus. Microbiol Spectr 2023; 11:e0118023. [PMID: 37750710 PMCID: PMC10580984 DOI: 10.1128/spectrum.01180-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/11/2023] [Indexed: 09/27/2023] Open
Abstract
Acute hepatopancreatic necrosis disease (AHPND), a high-mortality-rate shrimp disease, is caused by specific Vibrio parahaemolyticus (Vp) strains with a plasmid encoding the PirABVp toxins. As a bacterial pathogen, the invasion of AHPND-causing Vp might impose pressure on commensal microbiota in the shrimp gut, while the relationship between the pathogenesis of AHPND and the dysbiosis of gut bacterial communities remains unclear. Here we explored the temporal changes of shrimp gut microbiota in response to AHPND-causing and non-AHPND-causing Vp strains, with the non-infected controls as a baseline of the shrimp gut microbiota. The diversity and composition of bacterial communities from 168 gut samples (covering three treatments at seven time points with eight individuals per set) were investigated using 16S rRNA gene metabarcoding with high-throughput sequencing. The results showed that (i) species diversity of gut bacterial communities declined in Vp-infected shrimp, independent of the strain pathogenicity; (ii) taxonomic compositions of gut bacterial communities were significantly different between shrimp infected by AHPND-causing and non-AHPND-causing Vp strains; (iii) short-term (within 6 hours) compositional shifts in the gut microbiota were found only in AHPND-causing Vp-infected shrimp; (iv) the gut microbiota of AHPND-causing Vp-infected shrimp was enriched with genera Photobacterium and Vibrio, with a decline in Candidatus Bacilliplasma; and (v) functional predictions suggested the loss of normal metabolism due to compositional shifts in the gut microbiota. Our work reveals distinct features of community dynamics in shrimp gut microbiota, associated with pathogenic versus non-pathogenic Vibrio infections, providing a new perspective of the pathogenesis of AHPND. IMPORTANCE Shrimp production is continually threatened by newly emerging diseases, such as AHPND, which is caused by specific Vp strains. Previous studies on the pathogenesis of AHPND have mainly focused on the histopathology and immune responses of the host. However, more attention needs to be paid to the gut microbiota, which acts as the first barrier to pathogen colonization. In this study, we revealed that shrimp gut microbiota responded differently to pathogenic and non-pathogenic Vp strains, with bacterial genera Photobacterium and Vibrio enriched in pathogenic Vp-infected shrimp, and Candidatus Bacilliplasma enriched in non-pathogenic Vp-infected shrimp. Moreover, functional predictions suggested that changes in taxonomic compositions would further affect normal metabolic functions, emphasizing the importance of sustaining an equilibrium in the gut microbiota. Several biomarkers associated with specific microbial taxa and functional pathways were identified in our data sets, which help predict the incidence of disease outcomes.
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Affiliation(s)
- Yi-Ting Chang
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Hao-Ting Ko
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Ping-Lun Wu
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Ramya Kumar
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- International Center for Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Han-Ching Wang
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- International Center for Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Hsiao-Pei Lu
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
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18
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Kang DY, Kim A, Kim JN. CcpA and CodY Regulate CRISPR-Cas System of Streptococcus mutans. Microbiol Spectr 2023; 11:e0182623. [PMID: 37367300 PMCID: PMC10434267 DOI: 10.1128/spectrum.01826-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/05/2023] [Indexed: 06/28/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are widely recognized as bacterial adaptive immune systems against invading viruses and bacteriophages. The oral pathogen Streptococcus mutans encodes two CRISPR-Cas loci (CRISPR1-Cas and CRISPR2-Cas), and their expression under environmental conditions is still under investigation. In this study, we investigated the transcriptional regulation of cas operons by CcpA and CodY, two global regulators that contribute to carbohydrate and (p)ppGpp metabolism. The possible promoter regions for cas operons and the binding sites for CcpA and CodY in the promoter regions of both CRISPR-Cas loci were predicted using computational algorithms. We found that CcpA could directly bind to the upstream region of both cas operons, and detected an allosteric interaction of CodY within the same region. The binding sequences of the two regulators were identified through footprinting analysis. Our results showed that the promoter activity of CRISPR1-Cas was enhanced under fructose-rich conditions, while deletion of the ccpA gene led to reduced activity of the CRISPR2-Cas promoter under the same conditions. Additionally, deletion of the CRISPR systems resulted in a significant decrease in fructose uptake ability compared to the parental strain. Interestingly, the accumulation of guanosine tetraphosphate (ppGpp) was reduced in the presence of mupirocin, which induces a stringent response, in the CRISPR1-Cas-deleted (ΔCR1cas) and both CRISPR-Cas-deleted (ΔCRDcas) mutant strains. Furthermore, the promoter activity of both CRISPRs was enhanced in response to oxidative or membrane stress, while the CRISPR1 promoter activity was reduced under low-pH conditions. Collectively, our findings demonstrate that the transcription of the CRISPR-Cas system is directly regulated by the binding of CcpA and CodY. These regulatory actions play a crucial role in modulating glycolytic processes and exerting effective CRISPR-mediated immunity in response to nutrient availability and environmental cues. IMPORTANCE An effective immune system has evolved not only in eukaryotic organisms but also in microorganisms, enabling them to rapidly detect and neutralize foreign invaders in the environment. Specifically, the CRISPR-Cas system in bacterial cells is established through a complex and sophisticated regulatory mechanism involving specific factors. In this study, we demonstrate that the expression of two CRISPR systems in S. mutans can be controlled by two global regulators, CcpA and CodY, which play critical roles in carbohydrate metabolism and amino acid biosynthesis. Importantly, our results show that the expression of the CRISPR-Cas system in S. mutans influences (p)ppGpp production during the stringent response, which is a gene expression regulatory response that aids in environmental stress adaptation. This transcriptional regulation by these regulators enables a CRISPR-mediated immune response in a host environment with limited availability of carbon sources or amino acids, while ensuring efficient carbon flux and energy expenditure to support multiple metabolic processes.
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Affiliation(s)
- Da-Young Kang
- Department of Integrated Biological Science, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
| | - Andy Kim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Jeong Nam Kim
- Department of Integrated Biological Science, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
- Department of Microbiology, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
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19
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Gil-Gil T, Cuesta T, Hernando-Amado S, Reales-Calderón JA, Corona F, Linares JF, Martínez JL. Virulence and Metabolism Crosstalk: Impaired Activity of the Type Three Secretion System (T3SS) in a Pseudomonas aeruginosa Crc-Defective Mutant. Int J Mol Sci 2023; 24:12304. [PMID: 37569678 PMCID: PMC10419072 DOI: 10.3390/ijms241512304] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous nosocomial opportunistic pathogen that harbors many virulence determinants. Part of P. aeruginosa success colonizing a variety of habitats resides in its metabolic robustness and plasticity, which are the basis of its capability of adaptation to different nutrient sources and ecological conditions, including the infected host. Given this situation, it is conceivable that P. aeruginosa virulence might be, at least in part, under metabolic control, in such a way that virulence determinants are produced just when needed. Indeed, it has been shown that the catabolite repression control protein Crc, which together with the RNA chaperon Hfq regulates the P. aeruginosa utilization of carbon sources at the post-transcriptional level, also regulates, directly or indirectly, virulence-related processes in P. aeruginosa. Among them, Crc regulates P. aeruginosa cytotoxicity, likely by modulating the activity of the Type III Secretion System (T3SS), which directly injects toxins into eukaryotic host cells. The present work shows that the lack of Crc produces a Type III Secretion-defective phenotype in P. aeruginosa. The observed impairment is a consequence of a reduced expression of the genes encoding the T3SS, together with an impaired secretion of the proteins involved. Our results support that the impaired T3SS activity of the crc defective mutant is, at least partly, a consequence of a defective protein export, probably due to a reduced proton motive force. This work provides new information about the complex regulation of the expression and the activity of the T3SS in P. aeruginosa. Our results highlight the need of a robust bacterial metabolism, which is defective in the ∆crc mutant, to elicit complex and energetically costly virulence strategies, as that provided by the T3SS.
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Affiliation(s)
- Teresa Gil-Gil
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Trinidad Cuesta
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Sara Hernando-Amado
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Jose Antonio Reales-Calderón
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Fernando Corona
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Juan F. Linares
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - José L. Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
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20
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Yoon CK, Lee SH, Zhang J, Lee HY, Kim MK, Seok YJ. HPr prevents FruR-mediated facilitation of RNA polymerase binding to the fru promoter in Vibrio cholerae. Nucleic Acids Res 2023; 51:5432-5448. [PMID: 36987873 PMCID: PMC10287919 DOI: 10.1093/nar/gkad220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/17/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Phosphorylation state-dependent interactions of the phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) components with transcription factors play a key role in carbon catabolite repression (CCR) by glucose in bacteria. Glucose inhibits the PTS-dependent transport of fructose and is preferred over fructose in Vibrio cholerae, but the mechanism is unknown. We have recently shown that, contrary to Escherichia coli, the fructose-dependent transcriptional regulator FruR acts as an activator of the fru operon in V. cholerae and binding of the FruR-fructose 1-phosphate (F1P) complex to an operator facilitates RNA polymerase (RNAP) binding to the fru promoter. Here we show that, in the presence of glucose, dephosphorylated HPr, a general PTS component, binds to FruR. Whereas HPr does not affect DNA-binding affinity of FruR, regardless of the presence of F1P, it prevents the FruR-F1P complex from facilitating the binding of RNAP to the fru promoter. Structural and biochemical analyses of the FruR-HPr complex identify key residues responsible for the V. cholerae-specific FruR-HPr interaction not observed in E. coli. Finally, we reveal how the dephosphorylated HPr interacts with FruR in V. cholerae, whereas the phosphorylated HPr binds to CcpA, which is a global regulator of CCR in Bacillus subtilis and shows structural similarity to FruR.
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Affiliation(s)
- Chang-Kyu Yoon
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Korea
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
| | - Seung-Hwan Lee
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Korea
| | - Jing Zhang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea
| | - Hye-Young Lee
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Korea
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
| | - Min-Kyu Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea
| | - Yeong-Jae Seok
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Korea
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21
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Chen EC, Freel Meyers CL. DXP Synthase Function in a Bacterial Metabolic Adaptation and Implications for Antibacterial Strategies. Antibiotics (Basel) 2023; 12:antibiotics12040692. [PMID: 37107054 PMCID: PMC10135061 DOI: 10.3390/antibiotics12040692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Pathogenic bacteria possess a remarkable ability to adapt to fluctuating host environments and cause infection. Disturbing bacterial central metabolism through inhibition of 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) has the potential to hinder bacterial adaptation, representing a new antibacterial strategy. DXPS functions at a critical metabolic branchpoint to produce the metabolite DXP, a precursor to pyridoxal-5-phosphate (PLP), thiamin diphosphate (ThDP) and isoprenoids presumed essential for metabolic adaptation in nutrient-limited host environments. However, specific roles of DXPS in bacterial adaptations that rely on vitamins or isoprenoids have not been studied. Here we investigate DXPS function in an adaptation of uropathogenic E. coli (UPEC) to d-serine (d-Ser), a bacteriostatic host metabolite that is present at high concentrations in the urinary tract. UPEC adapt to d-Ser by producing a PLP-dependent deaminase, DsdA, that converts d-Ser to pyruvate, pointing to a role for DXPS-dependent PLP synthesis in this adaptation. Using a DXPS-selective probe, butyl acetylphosphonate (BAP), and leveraging the toxic effects of d-Ser, we reveal a link between DXPS activity and d-Ser catabolism. We find that UPEC are sensitized to d-Ser and produce sustained higher levels of DsdA to catabolize d-Ser in the presence of BAP. In addition, BAP activity in the presence of d-Ser is suppressed by β-alanine, the product of aspartate decarboxylase PanD targeted by d-Ser. This BAP-dependent sensitivity to d-Ser marks a metabolic vulnerability that can be exploited to design combination therapies. As a starting point, we show that combining inhibitors of DXPS and CoA biosynthesis displays synergy against UPEC grown in urine where there is increased dependence on the TCA cycle and gluconeogenesis from amino acids. Thus, this study provides the first evidence for a DXPS-dependent metabolic adaptation in a bacterial pathogen and demonstrates how this might be leveraged for development of antibacterial strategies against clinically relevant pathogens.
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Affiliation(s)
- Eric C. Chen
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins School of Medicine, Baltimore, MD 21201, USA
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins School of Medicine, Baltimore, MD 21201, USA
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22
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Dresen M, Valentin-Weigand P, Berhanu Weldearegay Y. Role of Metabolic Adaptation of Streptococcus suis to Host Niches in Bacterial Fitness and Virulence. Pathogens 2023; 12:pathogens12040541. [PMID: 37111427 PMCID: PMC10144218 DOI: 10.3390/pathogens12040541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Streptococcus suis, both a common colonizer of the porcine upper respiratory tract and an invasive pig pathogen, successfully adapts to different host environments encountered during infection. Whereas the initial infection mainly occurs via the respiratory tract, in a second step, the pathogen can breach the epithelial barrier and disseminate within the whole body. Thereby, the pathogen reaches other organs such as the heart, the joints, or the brain. In this review, we focus on the role of S. suis metabolism for adaptation to these different in vivo host niches to encounter changes in nutrient availability, host defense mechanisms and competing microbiota. Furthermore, we highlight the close link between S. suis metabolism and virulence. Mutants deficient in metabolic regulators often show an attenuation in infection experiments possibly due to downregulation of virulence factors, reduced resistance to nutritive or oxidative stress and to phagocytic activity. Finally, metabolic pathways as potential targets for new therapeutic strategies are discussed. As antimicrobial resistance in S. suis isolates has increased over the last years, the development of new antibiotics is of utmost importance to successfully fight infections in the future.
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Affiliation(s)
- Muriel Dresen
- Institute for Microbiology, University of Veterinary Medicine Hannover, 30173 Hannover, Germany
| | - Peter Valentin-Weigand
- Institute for Microbiology, University of Veterinary Medicine Hannover, 30173 Hannover, Germany
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23
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Kim J, Kim BS. Bacterial Sialic Acid Catabolism at the Host–Microbe Interface. J Microbiol 2023; 61:369-377. [PMID: 36972004 DOI: 10.1007/s12275-023-00035-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023]
Abstract
Sialic acids consist of nine-carbon keto sugars that are commonly found at the terminal end of mucins. This positional feature of sialic acids contributes to host cell interactions but is also exploited by some pathogenic bacteria in evasion of host immune system. Moreover, many commensals and pathogens use sialic acids as an alternative energy source to survive within the mucus-covered host environments, such as the intestine, vagina, and oral cavity. Among the various biological events mediated by sialic acids, this review will focus on the processes necessary for the catabolic utilization of sialic acid in bacteria. First of all, transportation of sialic acid should be preceded before its catabolism. There are four types of transporters that are used for sialic acid uptake; the major facilitator superfamily (MFS), the tripartite ATP-independent periplasmic C4-dicarboxilate (TRAP) multicomponent transport system, the ATP binding cassette (ABC) transporter, and the sodium solute symporter (SSS). After being moved by these transporters, sialic acid is degraded into an intermediate of glycolysis through the well-conserved catabolic pathway. The genes encoding the catabolic enzymes and transporters are clustered into an operon(s), and their expression is tightly controlled by specific transcriptional regulators. In addition to these mechanisms, we will cover some researches about sialic acid utilization by oral pathogens.
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Affiliation(s)
- Jaeeun Kim
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Byoung Sik Kim
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul, 03760, Republic of Korea.
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24
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Carrilero L, Urwin L, Ward E, Choudhury NR, Monk IR, Turner CE, Stinear TP, Corrigan RM. Stringent Response-Mediated Control of GTP Homeostasis Is Required for Long-Term Viability of Staphylococcus aureus. Microbiol Spectr 2023; 11:e0044723. [PMID: 36877013 PMCID: PMC10101089 DOI: 10.1128/spectrum.00447-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 03/07/2023] Open
Abstract
Staphylococcus aureus is an opportunistic bacterial pathogen that often results in difficult-to-treat infections. One mechanism used by S. aureus to enhance survival during infection is the stringent response. This is a stress survival pathway that utilizes the nucleotides (p)ppGpp to reallocate bacterial resources, shutting down growth until conditions improve. Small colony variants (SCVs) of S. aureus are frequently associated with chronic infections, and this phenotype has previously been linked to a hyperactive stringent response. Here, we examine the role of (p)ppGpp in the long-term survival of S. aureus under nutrient-restricted conditions. When starved, a (p)ppGpp-null S. aureus mutant strain ((p)ppGpp0) initially had decreased viability. However, after 3 days we observed the presence and dominance of a population of small colonies. Similar to SCVs, these small colony isolates (p0-SCIs) had reduced growth but remained hemolytic and sensitive to gentamicin, phenotypes that have been tied to SCVs previously. Genomic analysis of the p0-SCIs revealed mutations arising within gmk, encoding an enzyme in the GTP synthesis pathway. We show that a (p)ppGpp0 strain has elevated levels of GTP, and that the mutations in the p0-SCIs all lower Gmk enzyme activity and consequently cellular GTP levels. We further show that in the absence of (p)ppGpp, cell viability can be rescued using the GuaA inhibitor decoyinine, which artificially lowers the intracellular GTP concentration. Our study highlights the role of (p)ppGpp in GTP homeostasis and underscores the importance of nucleotide signaling for long-term survival of S. aureus in nutrient-limiting conditions, such as those encountered during infections. IMPORTANCE Staphylococcus aureus is a human pathogen that upon invasion of a host encounters stresses, such as nutritional restriction. The bacteria respond by switching on a signaling cascade controlled by the nucleotides (p)ppGpp. These nucleotides function to shut down bacterial growth until conditions improve. Therefore, (p)ppGpp are important for bacterial survival and have been implicated in promoting chronic infections. Here, we investigate the importance of (p)ppGpp for long-term survival of bacteria in nutrient-limiting conditions similar to those in a human host. We discovered that in the absence of (p)ppGpp, bacterial viability decreases due to dysregulation of GTP homeostasis. However, the (p)ppGpp-null bacteria were able to compensate by introducing mutations in the GTP synthesis pathway that led to a reduction in GTP build-up and a rescue of viability. This study therefore highlights the importance of (p)ppGpp for the regulation of GTP levels and for long-term survival of S. aureus in restricted environments.
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Affiliation(s)
- Laura Carrilero
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Lucy Urwin
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Ezra Ward
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Naznin R. Choudhury
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Ian R. Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Claire E. Turner
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca M. Corrigan
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
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25
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Lange T, Kasper L, Gresnigt MS, Brunke S, Hube B. "Under Pressure" - How fungi evade, exploit, and modulate cells of the innate immune system. Semin Immunol 2023; 66:101738. [PMID: 36878023 PMCID: PMC10109127 DOI: 10.1016/j.smim.2023.101738] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Indexed: 03/06/2023]
Abstract
The human immune system uses an arsenal of effector mechanisms to prevent and counteract infections. Yet, some fungal species are extremely successful as human pathogens, which can be attributed to a wide variety of strategies by which these fungi evade, exploit, and modulate the immune system. These fungal pathogens normally are either harmless commensals or environmental fungi. In this review we discuss how commensalism, but also life in an environmental niche without human contact, can drive the evolution of diverse and specialized immune evasion mechanisms. Correspondingly, we discuss the mechanisms contributing to the ability of these fungi to cause superficial to life-threatening infections.
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Affiliation(s)
- Theresa Lange
- Department of Microbial Pathogenicity Mechanisms, Hans Knoell Institute, Jena, Germany
| | - Lydia Kasper
- Department of Microbial Pathogenicity Mechanisms, Hans Knoell Institute, Jena, Germany
| | - Mark S Gresnigt
- Junior Research Group Adaptive Pathogenicity Strategies, Hans Knoell Institute, Jena, Germany
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Hans Knoell Institute, Jena, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Hans Knoell Institute, Jena, Germany; Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
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26
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Shrestha GS, Vijay AK, Stapleton F, White A, Pickford R, Carnt N. Human tear metabolites associated with nucleoside-signalling pathways in bacterial keratitis. Exp Eye Res 2023; 228:109409. [PMID: 36775205 DOI: 10.1016/j.exer.2023.109409] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/17/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
OBJECTIVE The study aimed to profile and quantify tear metabolites associated with bacterial keratitis using both untargeted and targeted metabolomic platforms. METHODS Untargeted metabolomic analysis using liquid-chromatography-Q Exactive-HF mass-spectrometry explored tear metabolites significantly associated with bacterial keratitis (n = 6) compared to healthy participants (n = 6). Differential statistics and principal component analysis determined meaningful metabolite differences between cases and controls. Purines and nucleosides were further quantified and compared between 15 cases and 15 controls in the targeted metabolomic platform using TSQ quantum access triple quadrupole mass spectrometry. Compound quantification was done by plotting the calibration curves and the difference in the compound levels was evaluated using the Wilcoxon rank-sum test. RESULTS In the untargeted analysis, 49 tear metabolites (27 upregulated and 22 downregulated) were differentially expressed between cases and controls. The untargeted analysis indicated that the purine metabolism pathway was the most affected by bacterial keratitis. Metabolite quantification in the targeted analysis further confirmed the upregulation of xanthine (P = 0.02) and downregulation of adenine (P < 0.0001), adenosine (P < 0.0001) and cytidine (P < 0.0001) in the tears of participants with bacterial keratitis compared to that of healthy participants. CONCLUSIONS Bacterial keratitis significantly changes the tear metabolite profile, including five major compound classes such as indoles, amino acids, nucleosides, carbohydrates, and steroids. This study also indicates that tear fluids can be used to map the metabolic pathways and uncover metabolic markers associated with bacterial keratitis. Conceivably, the inhibition of nucleoside synthesis may contribute to the pathophysiology of bacterial keratitis because nucleosides are required for maintaining cellular energy homeostasis and immune adaptability.
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Affiliation(s)
| | | | - Fiona Stapleton
- School of Optometry and Vision Science, UNSW Sydney, Australia
| | - Andrew White
- Department of Ophthalmology, Westmead Hospital, University of Sydney, Australia; Westmead Institute for Medical Research, University of Sydney, Australia
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, UNSW Sydney, Australia
| | - Nicole Carnt
- School of Optometry and Vision Science, UNSW Sydney, Australia; Westmead Institute for Medical Research, University of Sydney, Australia; Institute of Ophthalmology, University College London, United Kingdom
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The Pathogen Aeromonas salmonicida achromogenes Induces Fast Immune and Microbiota Modifications in Rainbow Trout. Microorganisms 2023; 11:microorganisms11020539. [PMID: 36838503 PMCID: PMC9964013 DOI: 10.3390/microorganisms11020539] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/27/2023] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Environmental stressors can disrupt the relationship between the microbiota and the host and lead to the loss of its functions. Among them, bacterial infection caused by Aeromonas salmonicida, the causative agent of furunculosis, results in high mortality in salmonid aquaculture. Here, rainbow trout were exposed to A. salmonicida achromogenes and its effects on the taxonomic composition and structure of the microbiota was assessed on different epithelia (gills, skin, and caudal fin) at 6 and 72 h post-infection (hpi) using the V1-V3 region of the 16S rRNA sequencing. Moreover, the infection by the pathogen and immune gene responses were evaluated in the head kidney by qPCR. Our results suggested that α-diversity was highly diverse but predominated by a few taxa while β-diversity was affected very early by infection in the gills after 6 h, subsequently affecting the microbiota of the skin and caudal fin. A dysbiosis of the microbiota and an increase in genera known to be opportunistic pathogens (Aeromonas, Pseudomonas) were also identified. Furthermore, an increase in pro-inflammatory cytokines and virulence protein array (vapa) was observed in trout head kidney as soon as 6 hpi and remained elevated until 72 hpi, while the anti-inflammatory genes seemed repressed. This study suggests that the infection by A. salmonicida achromogenes can alter fish microbiota of gills in the few hours post-infection. This result can be useful to develop a non-invasive technique to prevent disease outbreak in aquaculture.
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28
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Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates. mSphere 2023; 8:e0049522. [PMID: 36794931 PMCID: PMC10117131 DOI: 10.1128/msphere.00495-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering and mortality and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last 10 years from 16 French broiler farms. Comparative genomics, genome-wide association studies, and the measured susceptibility to serum, biofilm-forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate the origin of the isolates or the phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically, and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of E. cecorum cluster into a few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of E. cecorum belong mainly to one phylogenetic clade. IMPORTANCE Enterococcus cecorum is an important pathogen of poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated E. cecorum isolates. To address this need, we performed whole-genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first data set on the genetic diversity and resistome of E. cecorum strains circulating in France, we pinpoint an epidemic lineage that is probably also circulating elsewhere that should be targeted preferentially by preventive strategies in order to reduce the burden of E. cecorum-related diseases.
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29
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Couchoud C, Bertrand X, Bourgeon M, Piton G, Valot B, Hocquet D. Genome-based typing reveals rare events of patient contamination with Pseudomonas aeruginosa from other patients and sink traps in a medical intensive care unit. J Hosp Infect 2023; 134:63-70. [PMID: 36738994 DOI: 10.1016/j.jhin.2023.01.010] [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: 10/18/2022] [Revised: 01/03/2023] [Accepted: 01/18/2023] [Indexed: 02/05/2023]
Abstract
AIM We used genome-based typing data with the aim of identifying the routes of acquisition of Pseudomonas aeruginosa by patients hospitalized in a medical intensive care unit (MICU) over a long period in a non-epidemic context. METHODS This monocentric prospective study took place over 10 months in 2019 in a 15-bed MICU that applies standard precautions of hygiene. Lockable sink traps installed at all water points of use were bleach disinfected twice a week. We sampled all sink traps weekly to collect 404 P. aeruginosa environmental isolates and collected all P. aeruginosa isolates (N = 115) colonizing or infecting patients (N = 65). All isolates had their phenotypic resistance profile determined and their genome sequenced, from which we identified resistance determinants and assessed the population structure of the collection at the nucleotide level to identify events of P. aeruginosa transmission. FINDINGS All sink traps were positive for P. aeruginosa, each sink trap being colonized for several months by one or more clones. The combination of genomic and spatiotemporal data identified one potential event of P. aeruginosa transmission from a sink trap to a patient (1/65, 1.5%) and six events of patient cross-transmission, leading to the contamination of five patients (5/65, 7.7%). All transmitted isolates were fully susceptible to β-lactams and aminoglycosides. CONCLUSIONS Genome-based typing revealed the contamination of patients by P. aeruginosa originating from sink traps to be infrequent (1.5%) in an MICU with sink trap-bleaching measures, and that only 7.7% of the patients acquired P. aeruginosa originating from another patient.
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Affiliation(s)
- C Couchoud
- Hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France; Chrono-environnement UMR6249, CNRS Université de Franche-Comté, F-25000, Besançon, France
| | - X Bertrand
- Hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France; Chrono-environnement UMR6249, CNRS Université de Franche-Comté, F-25000, Besançon, France
| | - M Bourgeon
- Hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France; Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Universitaire, Besançon, France
| | - G Piton
- Service de Médecine Intensive Réanimation, Centre Hospitalier Universitaire, Besançon, France; EA3920, Université de Franche-Comté, Besançon, France
| | - B Valot
- Chrono-environnement UMR6249, CNRS Université de Franche-Comté, F-25000, Besançon, France; Bioinformatique et Big Data Au Service de La Santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
| | - D Hocquet
- Hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France; Chrono-environnement UMR6249, CNRS Université de Franche-Comté, F-25000, Besançon, France; Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Universitaire, Besançon, France; Bioinformatique et Big Data Au Service de La Santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France.
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30
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Das Q, Hasted TL, Lepp D, Yin X, Tang J, Chalmers G, Ross K, Boerlin P, Diarra MS. Transcriptional profiling of extraintestinal Escherichia coli exposed to cranberry pomace extracts alone or in combination with ceftriaxone. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2022.957099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) includes several serotypes that have been associated with colibacillosis in poultry, as well as urinary tract infections and newborn meningitis in humans. This study investigated the antimicrobial activities of ceftriaxone (AXO) and cranberry pomace extracts (CRAN) alone or in combination (CC) against multidrug-resistant (MDR) ExPEC from broiler. The growth-inhibitory activity of CRAN and synergy tests by a checkerboard method were determined in cation-adjusted Mueller–Hinton broth (CAMHB). The transcriptomic profile of the MDR E. coli O7:H18 (ST38) grown in CAMHB supplemented with sub-inhibitory concertation of CRAN and AXO alone or in combination was obtained by RNA-seq. The MIC of CRAN for all isolates was 16 mg/mL. An additive activity was observed between 4 mg/mL of CRAN and 4 μg/mL of AXO. Compared to the control, the transcriptomic analysis revealed that 4 mg/ml of (1/4MIC) CRAN and its combination with 4 μg/mL of (1/8MIC) AXO (CC) exposures resulted in 727 and 712 differentially expressed genes, respectively (false discovery rate < 0.001 and log2-fold change > 2), in the studied E. coli. Major virulence genes including adhesins (fim, flg, csg, and yad), protectins (omp, tra, waa, and hly), secretion systems (hof, pho, and vir), and quorum sensing (lsr), which are energetically expensive for bacteria, were downregulated. Most importantly, 1/4MIC of CRAN or CC downregulated the β-lactamase blaCMY-2 and efflux pump including tolC, mdtEIJ, gadEW, and their regulator gene evgS, while upregulating the cysteine biosynthesis and oxidative stress-related regulatory genes including cys, dmlA, sbp, nrdGHI, soxSR, and rpoH. Downregulation of multiple enzymes involved in TCA cycles and upregulation of Fe–S cluster coordinated by Cys and Isc proteins reflect the regulation of energy metabolism of the studied E. coli upon CRAN or CC exposure. The downregulation of outer membrane protein genes that control permeability barriers, along with different antimicrobial resistance genes, demonstrates that CRAN may have the unique potential to enhance the antimicrobial activities of third-generation cephalosporins such as AXO against MDR E. coli.
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Necrotizing Enterocolitis: The Role of Hypoxia, Gut Microbiome, and Microbial Metabolites. Int J Mol Sci 2023; 24:ijms24032471. [PMID: 36768793 PMCID: PMC9917134 DOI: 10.3390/ijms24032471] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/15/2023] [Accepted: 01/17/2023] [Indexed: 02/01/2023] Open
Abstract
Necrotizing enterocolitis (NEC) is a life-threatening disease that predominantly affects very low birth weight preterm infants. Development of NEC in preterm infants is accompanied by high mortality. Surgical treatment of NEC can be complicated by short bowel syndrome, intestinal failure, parenteral nutrition-associated liver disease, and neurodevelopmental delay. Issues surrounding pathogenesis, prevention, and treatment of NEC remain unclear. This review summarizes data on prenatal risk factors for NEC, the role of pre-eclampsia, and intrauterine growth retardation in the pathogenesis of NEC. The role of hypoxia in NEC is discussed. Recent data on the role of the intestinal microbiome in the development of NEC, and features of the metabolome that can serve as potential biomarkers, are presented. The Pseudomonadota phylum is known to be associated with NEC in preterm neonates, and the role of other bacteria and their metabolites in NEC pathogenesis is also discussed. The most promising approaches for preventing and treating NEC are summarized.
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Smith HB, Lee K, Stevenson DM, Amador-Noguez D, Sauer JD. Listeria monocytogenes requires DHNA-dependent intracellular redox homeostasis facilitated by Ndh2 for survival and virulence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.524026. [PMID: 36711537 PMCID: PMC9882099 DOI: 10.1101/2023.01.13.524026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Listeria monocytogenes is a remarkably well-adapted facultative intracellular pathogen that can thrive in a wide range of ecological niches. L. monocytogenes maximizes its ability to generate energy from diverse carbon sources using a respiro-fermentative metabolism that can function under both aerobic and anaerobic conditions. Cellular respiration maintains redox homeostasis by regenerating NAD + while also generating a proton motive force (PMF). The end products of the menaquinone (MK) biosynthesis pathway are essential to drive both aerobic and anaerobic cellular respiration. We previously demonstrated that intermediates in the MK biosynthesis pathway, notably 1,4-dihydroxy-2-naphthoate (DHNA), are required for the survival and virulence of L. monocytogenes independent of their role in respiration. Furthermore, we found that restoration of NAD + /NADH ratio through expression of water-forming NADH oxidase (NOX) could rescue phenotypes associated with DHNA deficiency. Here we extend these findings to demonstrate that endogenous production or direct supplementation of DHNA restored both the cellular redox homeostasis and metabolic output of fermentation in L. monocytogenes . Further, exogenous supplementation of DHNA rescues the in vitro growth and ex vivo virulence of L. monocytogenes DHNA-deficient mutants. Finally, we demonstrate that exogenous DHNA restores redox balance in L. monocytogenes specifically through the recently annotated NADH dehydrogenase Ndh2, independent of the extracellular electron transport (EET) pathway. These data suggest that the production of DHNA may represent an additional layer of metabolic adaptability by L. monocytogenes to drive energy metabolism in the absence of respiration-favorable conditions.
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Affiliation(s)
- Hans B. Smith
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, 53706, United States of America
| | - Kijeong Lee
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, 53706, United States of America
| | - David M. Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, United States of America
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, United States of America
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, 53706, United States of America
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33
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Muhammad AY, Amonov M, Murugaiah C, Baig AA, Yusoff M. Intestinal colonization against Vibrio cholerae: host and microbial resistance mechanisms. AIMS Microbiol 2023; 9:346-374. [PMID: 37091815 PMCID: PMC10113163 DOI: 10.3934/microbiol.2023019] [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: 01/08/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
Vibrio cholerae is a non-invasive enteric pathogen known to cause a major public health problem called cholera. The pathogen inhabits the aquatic environment while outside the human host, it is transmitted into the host easily through ingesting contaminated food and water containing the vibrios, thus causing diarrhoea and vomiting. V. cholerae must resist several layers of colonization resistance mechanisms derived from the host or the gut commensals to successfully survive, grow, and colonize the distal intestinal epithelium, thus causing an infection. The colonization resistance mechanisms derived from the host are not specific to V. cholerae but to all invading pathogens. However, some of the gut commensal-derived colonization resistance may be more specific to the pathogen, making it more challenging to overcome. Consequently, the pathogen has evolved well-coordinated mechanisms that sense and utilize the anti-colonization factors to modulate events that promote its survival and colonization in the gut. This review is aimed at discussing how V. cholerae interacts and resists both host- and microbe-specific colonization resistance mechanisms to cause infection.
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Affiliation(s)
| | - Malik Amonov
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Malaysia
- * Correspondence: ; Tel: +60189164478
| | | | - Atif Amin Baig
- University Institute of Public Health, Faculty of Allied Health Sciences, The University of Lahore, Pakistan
| | - Marina Yusoff
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Malaysia
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Ormazábal A, Pierdominici-Sottile G, Palma J. Recognition and Binding of RsmE to an AGGAC Motif of RsmZ: Insights from Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:6614-6627. [PMID: 35470666 DOI: 10.1021/acs.jcim.2c00037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
CsrA/RsmE is a post-transcriptional regulator protein widely distributed in bacteria. It impedes the expression of target mRNAs by attaching their 5' untranslated region. The translation is restored by small, noncoding RNAs that sequester CsrA/RsmE acting as sponges. In both cases, the protein recognizes and attaches to specific AGGAX and AXGGAX motifs, where X refers to any nucleotide. RsmZ of Pseudomonas protegens is one of these small RNAs. The structures of some of its complexes with RsmE were disclosed a few years ago. We have used umbrella sampling simulations to force the unbinding of RsmE from the AGGAC motif located in the single-stranded region sited between stem loops 2 and 3 of RsmZ. The calculations unveiled the identity of the main residues and nucleotides involved in the process. They also showed that the region adopts a hairpin-like conformation during the initial stages of the binding. The ability to acquire this conformation requires that the region has a length of at least nine nucleotides. Besides, we performed standard molecular dynamics simulations of the isolated fragments, analyzed their typical conformations, and characterized their movements. This analysis revealed that the free molecules oscillate along specific collective coordinates that facilitate the initial stages of the binding. The results strongly suggest that the flexibility of the single-stranded region of RsmZ crucially affects the ability of its binding motif to catch RsmE.
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Affiliation(s)
- Agustín Ormazábal
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Sáenz Peña 352, Bernal B1876BXD, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina
| | - Gustavo Pierdominici-Sottile
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Sáenz Peña 352, Bernal B1876BXD, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina
| | - Juliana Palma
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Sáenz Peña 352, Bernal B1876BXD, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina
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Systems-Wide Dissection of Organic Acid Assimilation in Pseudomonas aeruginosa Reveals a Novel Path To Underground Metabolism. mBio 2022; 13:e0254122. [PMID: 36377867 PMCID: PMC9765439 DOI: 10.1128/mbio.02541-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The human pathogen Pseudomonas aeruginosa (Pa) is one of the most frequent and severe causes of nosocomial infection. This organism is also a major cause of airway infections in people with cystic fibrosis (CF). Pa is known to have a remarkable metabolic plasticity, allowing it to thrive under diverse environmental conditions and ecological niches; yet, little is known about the central metabolic pathways that sustain its growth during infection or precisely how these pathways operate. In this work, we used a combination of 'omics approaches (transcriptomics, proteomics, metabolomics, and 13C-fluxomics) and reverse genetics to provide systems-level insight into how the infection-relevant organic acids succinate and propionate are metabolized by Pa. Moreover, through structural and kinetic analysis of the 2-methylcitrate synthase (2-MCS; PrpC) and its paralogue citrate (CIT) synthase (GltA), we show how these two crucial enzymatic steps are interconnected in Pa organic acid assimilation. We found that Pa can rapidly adapt to the loss of GltA function by acquiring mutations in a transcriptional repressor, which then derepresses prpC expression. Our findings provide a clear example of how "underground metabolism," facilitated by enzyme substrate promiscuity, "rewires" Pa metabolism, allowing it to overcome the loss of a crucial enzyme. This pathogen-specific knowledge is critical for the advancement of a model-driven framework to target bacterial central metabolism. IMPORTANCE Pseudomonas aeruginosa is an opportunistic human pathogen that, due to its unrivalled resistance to antibiotics, ubiquity in the built environment, and aggressiveness in infection scenarios, has acquired the somewhat dubious accolade of being designated a "critical priority pathogen" by the WHO. In this work, we uncover the pathways and mechanisms used by P. aeruginosa to grow on a substrate that is abundant at many infection sites: propionate. We found that if the organism is prevented from metabolizing propionate, the substrate turns from being a convenient nutrient source into a potent poison, preventing bacterial growth. We further show that one of the enzymes involved in these reactions, 2-methylcitrate synthase (PrpC), is promiscuous and can moonlight for another essential enzyme in the cell (citrate synthase). Indeed, mutations that abolish citrate synthase activity (which would normally prevent the cell from growing) can be readily overcome if the cell acquires additional mutations that increase the expression of PrpC. This is a nice example of the evolutionary utility of so-called "underground metabolism."
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36
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Hudson J, Egan S. Opportunistic diseases in marine eukaryotes: Could Bacteroidota be the next threat to ocean life? Environ Microbiol 2022; 24:4505-4518. [PMID: 35706128 PMCID: PMC9804302 DOI: 10.1111/1462-2920.16094] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 01/05/2023]
Abstract
Bacteria within the phylum Bacteroidota (Bacteroidetes) are known to cause devastating and widespread disease outbreaks in marine eukaryotic hosts. However, with few pathogens described in detail, their prevalence and virulence strategies remain largely unknown. Here, we systematically reviewed the literature to evaluate the current understanding of Bacteroidota that cause disease in marine hosts. Isolates affiliated with the genera Tenacibaculum and Aquimarina (Flavobacteriaceae) were the most widely reported and characterized pathogens. Although cultured isolates were predominantly Flavobacteriia, culture-independent studies also found classes Bacteroidia, Cytophagia and Sphingobacteriia associated with disease. We found that pathogenic marine Bacteroidota largely conformed to an opportunistic lifestyle but could also act as secondary pathogens or were involved in polymicrobial diseases. Many diseases were also associated with an environmental stressor, especially those affecting coral, macroalgae and fish. Key virulence traits included the production of adhesins and host tissue-degrading enzymes. Overall, the nature of disease involving Bacteroidota pathogens appears to be an outcome of complex host-pathogen-environment interactions; however, our understanding of virulence remains limited by the lack of functional characterization studies. This is concerning as Bacteroidota have the potential to emerge as a serious threat to marine ecosystems and aquaculture industries, driven by global changes in ocean conditions.
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Affiliation(s)
- Jennifer Hudson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyAustralia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyAustralia
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37
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Johnston ML, Bonett EM, DeColli AA, Freel Meyers CL. Antibacterial Target DXP Synthase Catalyzes the Cleavage of d-Xylulose 5-Phosphate: a Study of Ketose Phosphate Binding and Ketol Transfer Reaction. Biochemistry 2022; 61:1810-1823. [PMID: 35998648 PMCID: PMC9531112 DOI: 10.1021/acs.biochem.2c00274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial enzyme 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) catalyzes the formation of DXP from pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) in a thiamin diphosphate (ThDP)-dependent manner. In addition to its role in isoprenoid biosynthesis, DXP is required for ThDP and pyridoxal phosphate biosynthesis. Due to its function as a branch-point enzyme and its demonstrated substrate and catalytic promiscuity, we hypothesize that DXPS could be key for bacterial adaptation in the dynamic metabolic landscape during infection. Prior work in the Freel Meyers laboratory has illustrated that DXPS displays relaxed specificity toward donor and acceptor substrates and varies acceptor specificity according to the donor used. We have reported that DXPS forms dihydroxyethyl (DHE)ThDP from ketoacid or aldehyde donor substrates via decarboxylation and deprotonation, respectively. Here, we tested other DHE donors and found that DXPS cleaves d-xylulose 5-phosphate (X5P) at C2-C3, producing DHEThDP through a third mechanism involving d-GAP elimination. We interrogated DXPS-catalyzed reactions using X5P as a donor substrate and illustrated (1) production of a semi-stable enzyme-bound intermediate and (2) O2, H+, and d-erythrose 4-phosphate act as acceptor substrates, highlighting a new transketolase-like activity of DXPS. Furthermore, we examined X5P binding to DXPS and suggest that the d-GAP binding pocket plays a crucial role in X5P binding and turnover. Overall, this study reveals a ketose-cleavage reaction catalyzed by DXPS, highlighting the remarkable flexibility for donor substrate usage by DXPS compared to other C-C bond-forming enzymes.
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Affiliation(s)
- Melanie L. Johnston
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eucolona M. Bonett
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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38
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Fischer F, Vorontsov E, Turlin E, Malosse C, Garcia C, Tabb DL, Chamot-Rooke J, Percudani R, Vinella D, De Reuse H. Expansion of nickel binding- and histidine-rich proteins during gastric adaptation of Helicobacter species. METALLOMICS : INTEGRATED BIOMETAL SCIENCE 2022; 14:6674772. [PMID: 36002005 DOI: 10.1093/mtomcs/mfac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/17/2022] [Indexed: 11/14/2022]
Abstract
Acquisition and homeostasis of essential metals during host colonization by bacterial pathogens rely on metal uptake, trafficking and storage proteins. How these factors have evolved within bacterial pathogens is poorly defined. Urease, a nickel enzyme, is essential for Helicobacter pylori to colonize the acidic stomach. Our previous data suggest that acquisition of nickel transporters and a Histidine-rich protein (HRP) involved in nickel storage in H. pylori and gastric Helicobacter spp. have been essential evolutionary events for gastric colonization. Using bioinformatics, proteomics and phylogenetics, we extended this analysis to determine how evolution has framed the repertoire of HRPs among 39 Epsilonproteobacteria; 18 gastric and 11 non-gastric enterohepatic (EH) Helicobacter spp., as well as 10 other Epsilonproteobacteria. We identified a total of 213 HRPs distributed in 22 protein families named orthologous groups (OG) with His-rich domains, including 15 newly described OGs. Gastric Helicobacter spp. are enriched in HRPs (7.7 ± 1.9 HRPs/strain) as compared to EH Helicobacter spp. (1.9 ± 1.0 HRPs/strain) with a particular prevalence of HRPs with C-terminal Histidine-rich domains in gastric species. The expression and nickel-binding capacity of several HRPs was validated in five gastric Helicobacter spp. We established the evolutionary history of new HRP families, such as the periplasmic HP0721-like proteins and the HugZ-type heme-oxygenases. The expansion of Histidine-rich extensions in gastric Helicobacter spp. proteins is intriguing but can tentatively be associated with the presence of the urease nickel-enzyme. We conclude that this HRP expansion is associated with unique properties of organisms that rely on large intracellular nickel amounts for their survival.
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Affiliation(s)
- Frédéric Fischer
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, UMR CNRS 6047, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE.,Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, Université de Strasbourg, Institut de Physiologie et Chimie Biologiques, 4 allée Konrad Roentgen, 67084 Strasbourg, FRANCE
| | - Egor Vorontsov
- Institut Pasteur, Department of Structural Biology and Chemistry, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology Unit, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE.,Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Box 413, 40530 Gothenburg, SWEDEN
| | - Evelyne Turlin
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, UMR CNRS 6047, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE
| | - Christian Malosse
- Institut Pasteur, Department of Structural Biology and Chemistry, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology Unit, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE
| | - Camille Garcia
- Institut Pasteur, Department of Structural Biology and Chemistry, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology Unit, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE
| | - David L Tabb
- Institut Pasteur, Department of Structural Biology and Chemistry, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology Unit, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE
| | - Julia Chamot-Rooke
- Institut Pasteur, Department of Structural Biology and Chemistry, Université Paris Cité, CNRS UAR 2024, Mass Spectrometry for Biology Unit, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, ITALY
| | - Daniel Vinella
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, UMR CNRS 6047, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE
| | - Hilde De Reuse
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, UMR CNRS 6047, 28 rue du Dr Roux 75724 PARIS Cedex 15 FRANCE
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Henriot CP, Martak D, Genet S, Bornette G, Hocquet D. Origin, fluxes, and reservoirs of Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa in aquatic ecosystems of a French floodplain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155353. [PMID: 35460768 DOI: 10.1016/j.scitotenv.2022.155353] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
The release and spread of opportunistic pathogens - some of which are resistant to antibiotics - in the environment is a major public health challenge worldwide. In this study, we found evidence of the origin of such microorganisms and characterized their dispersal and survival in floodplain ecosystems to understand their fate in the environment. We determined the concentrations of Escherichia coli, extended-spectrum β-lactamases (ESBL)-producing E. coli, Klebsiella pneumoniae, ESBL-producing K. pneumoniae, and Pseudomonas aeruginosa in a floodplain of Eastern France using a culture-based method. Furthermore, we assessed the population structure of E. coli isolates by quadruplex PCR, their plasmid replicon content by PCR-based replicon typing, and the nature of their blaESBL genes by PCR and sequencing. The main aquatic ecosystems of the floodplain (river, tributaries, riverine wetlands, and groundwater) were sampled monthly over a one-year cycle. The majority of E. coli isolates retrieved in the studied floodplain were likely of human origin. Moreover, contamination of floodplain aquatic ecosystems by opportunistic pathogens mainly resulted from hydrological fluxes during high-flow periods, suggesting that dispersal and dilution predominated. During low-flow periods, E. coli may be able to survive for several months in isolated ecosystems in which it may find favourable conditions to thrive. The most nutrient-rich and isolated wetlands are consequently potential pathogen reservoirs. The production of ESBL was not a disadvantage for E. coli in low-anthropized floodplain ecosystems.
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Affiliation(s)
- Charles P Henriot
- UMR CNRS 6249 Chrono-environnement, Université de Bourgogne Franche-Comté, 16 Route de Gray, 25030 Besançon, France.
| | - Daniel Martak
- UMR CNRS 6249 Chrono-environnement, Université de Bourgogne Franche-Comté, 16 Route de Gray, 25030 Besançon, France; Hygiène Hospitalière, Centre Hospitalier Universitaire de Besançon, 3 boulevard Fleming, 25030 Besançon, France
| | - Salomé Genet
- UMR CNRS 6249 Chrono-environnement, Université de Bourgogne Franche-Comté, 16 Route de Gray, 25030 Besançon, France
| | - Gudrun Bornette
- UMR CNRS 6249 Chrono-environnement, Université de Bourgogne Franche-Comté, 16 Route de Gray, 25030 Besançon, France
| | - Didier Hocquet
- UMR CNRS 6249 Chrono-environnement, Université de Bourgogne Franche-Comté, 16 Route de Gray, 25030 Besançon, France; Hygiène Hospitalière, Centre Hospitalier Universitaire de Besançon, 3 boulevard Fleming, 25030 Besançon, France; Centre de Ressources Biologiques Filière Microbiologie de Besançon, Centre Hospitalier Universitaire, 3 boulevard Fleming, 25030 Besançon, France
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40
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Rath A, Rautenschlein S, Rzeznitzeck J, Lalk M, Methling K, Rychlik I, Peh E, Kittler S, Waldmann KH, von Altrock A. Investigation on the colonisation of Campylobacter strains in the pig intestine depending on available metabolites. Comp Immunol Microbiol Infect Dis 2022; 88:101865. [PMID: 35914481 DOI: 10.1016/j.cimid.2022.101865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 10/16/2022]
Abstract
Campylobacter (C.) spp. represent one of the most important causes for food-borne bacterial pathogen in humans worldwide. The aim of this study was to investigate metabolic requirements of two Campylobacter strains of different species based on substrate utilisation (in vitro). Based on these results, a correlation between the colonisation and the available substrates in different intestinal sections was recorded using an animal model. Campylobacter coli (ST-5777) and C. jejuni (ST-122) were used to inoculate 16 pigs, respectively, and one group of 16 pigs was used as control. The strains differed significantly in substrate utilisation - C. coli was able to metabolise various substrates (acetate, asparagine, serine, fucose, and propionate), while C. jejuni only utilised serine. Metabolomic analysis of intestinal content from different gut sections showed the presence of all previously tested metabolites, except for fucose. A significantly larger amount of glucose was found in the jejunum of those pigs infected with C. coli, while neither strain utilised it in vitro. The analysis of the intestinal contents revealed a very low proportion of Campylobacterales in the total microbiome, suggesting that the small percentage of the inoculated Campylobacter strains in the gut microflora of the animals is too low to cause differences between the control and infected groups in the composition of the metabolome. Nevertheless, knowledge of specific nutritional requirements of the pathogens combined with proof of different metabolites in the intestinal segments may provide clues about the site of colonisation in the host and improve our understanding of this zoonotic germ.
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Affiliation(s)
- Alexandra Rath
- Clinic for Swine and Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany.
| | - Silke Rautenschlein
- Clinic for Poultry, University of Veterinary Medicine Hannover Foundation, 30559 Hannover, Germany
| | - Janina Rzeznitzeck
- Clinic for Poultry, University of Veterinary Medicine Hannover Foundation, 30559 Hannover, Germany
| | - Michael Lalk
- Institute for Pharmaceutical Biology, University of Greifswald, Greifswald, Germany
| | - Karen Methling
- Institute for Pharmaceutical Biology, University of Greifswald, Greifswald, Germany
| | - Ivan Rychlik
- Veterinary Research Institute, Brno, Czech Republic
| | - Elisa Peh
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Sophie Kittler
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Karl-Heinz Waldmann
- Clinic for Swine and Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany
| | - Alexandra von Altrock
- Clinic for Swine and Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany
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Djahanschiri B, Di Venanzio G, Distel JS, Breisch J, Dieckmann MA, Goesmann A, Averhoff B, Göttig S, Wilharm G, Feldman MF, Ebersberger I. Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex. PLoS Genet 2022; 18:e1010020. [PMID: 35653398 PMCID: PMC9162365 DOI: 10.1371/journal.pgen.1010020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/04/2022] [Indexed: 11/19/2022] Open
Abstract
Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for the world-wide spread of multi- and pan-drug resistant bacteria. Aiding the urgent demand for novel therapeutic targets, comparative genomics studies between pathogens and their apathogenic relatives shed light on the genetic basis of human-pathogen interaction. Yet, existing studies are limited in taxonomic scope, sensing of the phylogenetic signal, and resolution by largely analyzing genes independent of their organization in functional gene clusters. Here, we explored more than 3,000 Acinetobacter genomes in a phylogenomic framework integrating orthology-based phylogenetic profiling and microsynteny conservation analyses. We delineate gene clusters in the type strain A. baumannii ATCC 19606 whose evolutionary conservation indicates a functional integration of the subsumed genes. These evolutionarily stable gene clusters (ESGCs) reveal metabolic pathways, transcriptional regulators residing next to their targets but also tie together sub-clusters with distinct functions to form higher-order functional modules. We shortlisted 150 ESGCs that either co-emerged with the pathogenic ACB clade or are preferentially found therein. They provide a high-resolution picture of genetic and functional changes that coincide with the manifestation of the pathogenic phenotype in the ACB clade. Key innovations are the remodeling of the regulatory-effector cascade connecting LuxR/LuxI quorum sensing via an intermediate messenger to biofilm formation, the extension of micronutrient scavenging systems, and the increase of metabolic flexibility by exploiting carbon sources that are provided by the human host. We could show experimentally that only members of the ACB clade use kynurenine as a sole carbon and energy source, a substance produced by humans to fine-tune the antimicrobial innate immune response. In summary, this study provides a rich and unbiased set of novel testable hypotheses on how pathogenic Acinetobacter interact with and ultimately infect their human host. It is a comprehensive resource for future research into novel therapeutic strategies. The spread of multi- and pan-drug resistant bacterial pathogens is a worldwide threat to human health. Understanding the genetics of host colonization and infection can substantially help in devising novel ways of treatment. Acinetobacter baumannii, a nosocomial pathogen ranked top by the World Health Organization in the list of bacteria for which novel therapeutic approaches are needed, is a prime example. Here, we have carved out the genetic make-up that distinguishes A. baumannii and its pathogenic next relatives from other and mostly apathogenic Acinetobacter species. We found a rich spectrum of pathways and regulatory modules that reveal how the pathogens have modified biofilm formation, iron scavenging, and their carbohydrate metabolism to adapt to their human host. Among these, the capability to metabolize kynurenine is particularly intriguing. Humans produce this substance to contain bacterial invaders and to fine-tune the innate immune response. But A. baumannii and closely related pathogens found a way to feed on kynurenine. This suggests that the pathogens might be able to dysregulate the human immune response. In summary, our study substantially deepens the understanding of how a highly critical pathogen interacts with its host, which substantially eases the identification of novel targets for innovative therapeutic strategies.
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Affiliation(s)
- Bardya Djahanschiri
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gisela Di Venanzio
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jesus S. Distel
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Jennifer Breisch
- Inst. of Molecular Biosciences, Department of Molecular Microbiology and Bioenergetics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Gießen, Gießen, Germany
| | - Beate Averhoff
- Inst. of Molecular Biosciences, Department of Molecular Microbiology and Bioenergetics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stephan Göttig
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | | | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Inst. of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIKF), Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
- * E-mail:
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Comparative Metabolic Characterization of Extraintestinal Pathogenic Escherichia coli Blood Isolates from Saudi Arabia. J Trop Med 2022; 2022:1745835. [PMID: 35677619 PMCID: PMC9170502 DOI: 10.1155/2022/1745835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/13/2022] [Accepted: 05/18/2022] [Indexed: 11/25/2022] Open
Abstract
Background The prevalence of bloodstream infections caused by extraintestinal pathogenic Escherichia coli (ExPEC) has increased substantially. E. coli ST131 is one of the dominant ExPEC clones among E. coli bacteremia population. Metabolism can trigger the pathogenesis of some bacterial isolates, and here we evaluated and compared the metabolic traits of E. coli bacteremia isolates including β-lactamase (BL)/extended-spectrum β-lactamase (ESBL)-positive and ESBL-negative isolates and ST131 and non-ST131 isolates. Methods The metabolic profiles of thirty E. coli isolates, obtained from blood samples for hospitalized individuals at a tertiary healthcare facility in Riyadh, were determined using HiMedia carbohydrate test strips. The difference in the utilization ability between isolate groups was then statistically assessed. Results Our data found that non-BL/ESBL producers were of low metabolic capacity compared with ESBL-positive isolates although the difference remained insignificant. Higher levels of utilization for some carbohydrates, such as fructose and trehalose, were detected among ST131 isolates when compared with non-ST131, and ST131 was also significantly associated with metabolizing rhamnose. The mean bio-score of both isolate groups was insignificant. We showed no link between metabolism and antimicrobial susceptibility profiles among tested blood isolates. Conclusion ST131 blood isolates were slightly higher in their carbohydrate utilization activity than non-ST131. More importantly, ST131 isolates were significantly capable of metabolizing rhamnose. Future research should focus on the factors that might drive the success of major ExPEC clones such as ST131.
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Desruelle AV, de Maistre S, Gaillard S, Richard S, Tardivel C, Martin JC, Blatteau JE, Boussuges A, Rives S, Risso JJ, Vallee N. Cecal Metabolomic Fingerprint of Unscathed Rats: Does It Reflect the Good Response to a Provocative Decompression? Front Physiol 2022; 13:882944. [PMID: 35655958 PMCID: PMC9152359 DOI: 10.3389/fphys.2022.882944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/27/2022] [Indexed: 11/23/2022] Open
Abstract
On one side, decompression sickness (DCS) with neurological disorders lead to a reshuffle of the cecal metabolome of rats. On the other side, there is also a specific and different metabolomic signature in the cecum of a strain of DCS-resistant rats, that are not exposed to hyperbaric protocol. We decide to study a conventional strain of rats that resist to an accident-provoking hyperbaric exposure, and we hypothesize that the metabolomic signature put forward may correspond to a physiological response adapted to the stress induced by diving. The aim is to verify and characterize whether the cecal compounds of rats resistant to the provocative dive have a cecal metabolomic signature different from those who do not dive. 35 asymptomatic diver rats are selected to be compared to 21 rats non-exposed to the hyperbaric protocol. Because our aim is essentially to study the differences in the cecal metabolome associated with the hyperbaric exposure, about half of the rats are fed soy and the other half of maize in order to better rule out the effect of the diet itself. Lower levels of IL-1β and glutathione peroxidase (GPX) activity are registered in blood of diving rats. No blood cell mobilization is noted. Conventional and ChemRICH approaches help the metabolomic interpretation of the 185 chemical compounds analyzed in the cecal content. Statistical analysis show a panel of 102 compounds diet related. 19 are in common with the hyperbaric protocol effect. Expression of 25 compounds has changed in the cecal metabolome of rats resistant to the provocative dive suggesting an alteration of biliary acids metabolism, most likely through actions on gut microbiota. There seem to be also weak changes in allocations dedicated to various energy pathways, including hormonal reshuffle. Some of the metabolites may also have a role in regulating inflammation, while some may be consumed for the benefit of oxidative stress management.
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Affiliation(s)
- Anne-Virginie Desruelle
- Institut de Recherche Biomédicale des Armées, Equipe de Recherche Subaquatique Opérationnelle, Toulon Cedex, France
| | - Sébastien de Maistre
- Service de Médecine Hyperbare Expertise Plongée, Hôpital d'Instruction des Armées Sainte-Anne, Toulon Cedex, France
| | | | | | - Catherine Tardivel
- C2VN, INRAE, INSERM, BIOMET, Aix Marseille University, Faculté de Médecine La Timone, Marseille, France
| | - Jean-Charles Martin
- C2VN, INRAE, INSERM, BIOMET, Aix Marseille University, Faculté de Médecine La Timone, Marseille, France
| | - Jean-Eric Blatteau
- Service de Médecine Hyperbare Expertise Plongée, Hôpital d'Instruction des Armées Sainte-Anne, Toulon Cedex, France
| | - Alain Boussuges
- Institut de Recherche Biomédicale des Armées, Equipe de Recherche Subaquatique Opérationnelle, Toulon Cedex, France
| | - Sarah Rives
- Institut de Recherche Biomédicale des Armées, Equipe de Recherche Subaquatique Opérationnelle, Toulon Cedex, France
| | - Jean-Jacques Risso
- Institut de Recherche Biomédicale des Armées, Equipe de Recherche Subaquatique Opérationnelle, Toulon Cedex, France
| | - Nicolas Vallee
- Institut de Recherche Biomédicale des Armées, Equipe de Recherche Subaquatique Opérationnelle, Toulon Cedex, France
- *Correspondence: Nicolas Vallee,
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Niemiec MJ, Kapitan M, Himmel M, Döll K, Krüger T, Köllner TG, Auge I, Kage F, Alteri CJ, Mobley HL, Monsen T, Linde S, Nietzsche S, Kniemeyer O, Brakhage AA, Jacobsen ID. Augmented Enterocyte Damage During Candida albicans and Proteus mirabilis Coinfection. Front Cell Infect Microbiol 2022; 12:866416. [PMID: 35651758 PMCID: PMC9149288 DOI: 10.3389/fcimb.2022.866416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/15/2022] [Indexed: 12/24/2022] Open
Abstract
The human gut acts as the main reservoir of microbes and a relevant source of life-threatening infections, especially in immunocompromised patients. There, the opportunistic fungal pathogen Candida albicans adapts to the host environment and additionally interacts with residing bacteria. We investigated fungal-bacterial interactions by coinfecting enterocytes with the yeast Candida albicans and the Gram-negative bacterium Proteus mirabilis resulting in enhanced host cell damage. This synergistic effect was conserved across different P. mirabilis isolates and occurred also with non-albicans Candida species and C. albicans mutants defective in filamentation or candidalysin production. Using bacterial deletion mutants, we identified the P. mirabilis hemolysin HpmA to be the key effector for host cell destruction. Spatially separated coinfections demonstrated that synergism between Candida and Proteus is induced by contact, but also by soluble factors. Specifically, we identified Candida-mediated glucose consumption and farnesol production as potential triggers for Proteus virulence. In summary, our study demonstrates that coinfection of enterocytes with C. albicans and P. mirabilis can result in increased host cell damage which is mediated by bacterial virulence factors as a result of fungal niche modification via nutrient consumption and production of soluble factors. This supports the notion that certain fungal-bacterial combinations have the potential to result in enhanced virulence in niches such as the gut and might therefore promote translocation and dissemination.
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Affiliation(s)
- Maria Joanna Niemiec
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
- Center for Sepsis Control and Care, Jena, Germany
| | - Mario Kapitan
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
- Center for Sepsis Control and Care, Jena, Germany
| | - Maximilian Himmel
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Kristina Döll
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Thomas Krüger
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Tobias G. Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Isabel Auge
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Franziska Kage
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Christopher J. Alteri
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Harry L.T. Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Tor Monsen
- Department Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Susanne Linde
- Center for Electron Microscopy, University Hospital, Jena, Germany
| | - Sandor Nietzsche
- Center for Electron Microscopy, University Hospital, Jena, Germany
| | - Olaf Kniemeyer
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Axel A. Brakhage
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Ilse D. Jacobsen
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
- Center for Sepsis Control and Care, Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
- *Correspondence: Ilse D. Jacobsen,
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Sauvage S, Gaviard C, Tahrioui A, Coquet L, Le H, Alexandre S, Ben Abdelkrim A, Bouffartigues E, Lesouhaitier O, Chevalier S, Jouenne T, Hardouin J. Impact of Carbon Source Supplementations on Pseudomonas aeruginosa Physiology. J Proteome Res 2022; 21:1392-1407. [PMID: 35482949 DOI: 10.1021/acs.jproteome.1c00936] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen highly resistant to a wide range of antimicrobial agents, making its infections very difficult to treat. Since microorganisms need to perpetually adapt to their surrounding environment, understanding the effect of carbon sources on P. aeruginosa physiology is therefore essential to avoid increasing drug-resistance and better fight this pathogen. By a global proteomic approach and phenotypic assays, we investigated the impact of various carbon source supplementations (glucose, glutamate, succinate, and citrate) on the physiology of the P. aeruginosa PA14 strain. A total of 581 proteins were identified as differentially expressed in the 4 conditions. Most of them were more abundant in citrate supplementation and were involved in virulence, motility, biofilm development, and antibiotic resistance. Phenotypic assays were performed to check these hypotheses. By coupling all this data, we highlight the importance of the environment in which the bacterium evolves on its metabolism, and thus the necessity to better understand the metabolic pathways implied in its adaptative response according to the nutrient availability.
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Affiliation(s)
- Salomé Sauvage
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Charlotte Gaviard
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Ali Tahrioui
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Laurent Coquet
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Hung Le
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France
| | - Stéphane Alexandre
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France
| | - Ahmed Ben Abdelkrim
- Lactanet, Valacta, 555 Boul des Anciens-Combattants, Sainte-Anne-de-Bellevue, Québec H9X 3R4, Canada
| | - Emeline Bouffartigues
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Sylvie Chevalier
- Laboratoire de microbiologie signaux et microenvironnement, LMSM EA4312, 55 rue Saint-Germain, 27000 Evreux, France
| | - Thierry Jouenne
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Normandie Université, UNIROUEN, INSA, CNRS Polymers, Biopolymers, Surface Laboratory, 76821 Mont-Saint-Aignan cedex, France.,PISSARO Proteomic Facility, IRIB, 76820 Mont-Saint-Aignan, France
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Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing Escherichia coli O145:H28. Microorganisms 2022; 10:microorganisms10050866. [PMID: 35630311 PMCID: PMC9144400 DOI: 10.3390/microorganisms10050866] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 01/27/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) O145:H28 can cause severe disease in humans and is a predominant serotype in STEC O145 environmental isolates. Here, comparative genomics was applied to a set of clinical and environmental strains to systematically evaluate the pathogenicity potential in environmental strains. While the core genes-based tree separated all O145:H28 strains from the non O145:H28 reference strains, it failed to segregate environmental strains from the clinical. In contrast, the accessory genes-based tree placed all clinical strains in the same clade regardless of their genotypes or serotypes, apart from the environmental strains. Loss-of-function mutations were common in the virulence genes examined, with a high frequency in genes related to adherence, autotransporters, and the type three secretion system. Distinct differences in pathogenicity islands LEE, OI-122, and OI-57, the acid fitness island, and the tellurite resistance island were detected between the O145:H28 and reference strains. A great amount of genetic variation was detected in O145:H28, which was mainly attributed to deletions, insertions, and gene acquisition at several chromosomal “hot spots”. Our study demonstrated a distinct virulence gene repertoire among the STEC O145:H28 strains originating from the same geographical region and revealed unforeseen contributions of loss-of-function mutations to virulence evolution and genetic diversification in STEC.
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Emwas AH, Szczepski K, Al-Younis I, Lachowicz JI, Jaremko M. Fluxomics - New Metabolomics Approaches to Monitor Metabolic Pathways. Front Pharmacol 2022; 13:805782. [PMID: 35387341 PMCID: PMC8977530 DOI: 10.3389/fphar.2022.805782] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/24/2022] [Indexed: 12/18/2022] Open
Abstract
Fluxomics is an innovative -omics research field that measures the rates of all intracellular fluxes in the central metabolism of biological systems. Fluxomics gathers data from multiple different -omics fields, portraying the whole picture of molecular interactions. Recently, fluxomics has become one of the most relevant approaches to investigate metabolic phenotypes. Metabolic flux using 13C-labeled molecules is increasingly used to monitor metabolic pathways, to probe the corresponding gene-RNA and protein-metabolite interaction networks in actual time. Thus, fluxomics reveals the functioning of multi-molecular metabolic pathways and is increasingly applied in biotechnology and pharmacology. Here, we describe the main fluxomics approaches and experimental platforms. Moreover, we summarize recent fluxomic results in different biological systems.
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Affiliation(s)
- Abdul-Hamid Emwas
- King Abdullah University of Science and Technology, Core Labs, Thuwal, Saudi Arabia
| | - Kacper Szczepski
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Inas Al-Younis
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Joanna Izabela Lachowicz
- Department of Medical Sciences and Public Health, University of Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Hao F, Xie X, Feng Z, Chen R, Wei Y, Liu J, Xiong Q, Shao G, Lin J. NADH oxidase of Mycoplasma hyopneumoniae functions as a potential mediator of virulence. BMC Vet Res 2022; 18:126. [PMID: 35366872 PMCID: PMC8976378 DOI: 10.1186/s12917-022-03230-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/25/2022] [Indexed: 12/03/2022] Open
Abstract
Background Mycoplasma hyopneumoniae (M. hyopneumoniae) is the etiological agent of enzootic pneumonia, a highly infectious swine respiratory disease that distributed worldwide. The pathogenesis and virulence factors of M. hyopneumoniae are not fully clarified. As an important virulence factor of bacteria, nicotinamide adenine dinucleotide (NADH) oxidase (NOX) participates in host-pathogen interaction, however, the function of NOX involved in the pathogenesis of M. hyopneumoniae is not clear. Results In this study, significant differences in NOX transcription expression levels among different strains of M. hyopneumoniae differed in virulence were identified, suggesting that NOX may be correlated with M. hyopneumoniae virulence. The nox gene of M. hyopneumoniae was cloned and expressed in Escherichia coli, and polyclonal antibodies against recombinant NOX (rNOX) were prepared. We confirmed the enzymatic activity of rNOX based on its capacity to oxidize NADH to NAD+. Flow cytometry analysis demonstrated the surface localization of NOX, and subcellular localization analysis further demonstrated that NOX exists in both the cytoplasm and cell membrane. rNOX was depicted to mediate adhesion to immortalized porcine bronchial epithelial cells (hTERT-PBECs). Pre-neutralizing M. hyopneumoniae with anti-rNOX antibody resulted in a more than 55% reduction in the adhesion rate of high- and low-virulence M. hyopneumoniae strains to hTERT-PBECs. Moreover, a significant difference appeared in the decline in CCU50 titer between virulent (168) and virulence-attenuated (168L) strains. NOX not only recognized and interacted with host fibronectin but also induced cellular oxidative stress and apoptosis in hTERT-PBECs. The release of lactate dehydrogenase by NOX in hTERT-PBECs was positively correlated with the virulence of M. hyopneumoniae strains. Conclusions NOX is considered to be a potential virulence factor of M. hyopneumoniae and may play a significant role in mediating its pathogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03230-7.
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Jang FH, Wong C, Choo J, Aun Sia ES, Mujahid A, Müller M. Increased transfer of trace metals and Vibrio sp. from biodegradable microplastics to catfish Clarias gariepinus. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 298:118850. [PMID: 35041899 DOI: 10.1016/j.envpol.2022.118850] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Microplastic ingestion has been documented in various aquatic species. This causes physical damage, and additionally contaminated microplastics transfer attached pollutants and microbial pathogens to ingesting organisms. Continued metal accumulation can lead to toxicity and adverse health effects; attached microbial pathogens can cause dysbiosis - which lowers host immunity and promotes infections. Catfish, Clarias gariepinus, are a major food source in Southeast Asia, a hotspot of plastic pollution. This study aimed to quantify the transfer of the trace metals copper (Cu) and lead (Pb) -at environmentally relevant concentrations-from microplastics (polyamide 12, PA12, and polylactic acid, PLA) to catfish. Fish were reared for three months and exposed to seven different combinations of feed, supplemented with plastics and metals. At monthly intervals, fish gills, intestines, liver, and edible muscles were analysed for Cu and Pb concentrations using ICP-OES, and the intestines content assessed for Vibrio sp.. Our results showed that biodegradable PLA transferred higher amounts of metals to catfish than expected and also led to increased Vibrio counts in the intestines compared to PA12. Trace metal accumulation was significantly different in varying tissues, with highest concentrations observed in the gills, followed by liver, intestines, and lastly edible muscles. The results of this study further support the existing evidence that microplastics act as efficient shuttles to concentrate and transfer metals. They also indicate that their uptake can cause dysbiosis (increased numbers of Vibrio sp.). Most importantly, however, our study highlights that biodegradable polymers, such as PLA, could actually pose a greater environmental threat when ingested compared to the more common polymers such as PA12.
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Affiliation(s)
- Faddrine Holt Jang
- Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak, 93350, Kuching, Sarawak, Malaysia
| | - Changi Wong
- Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak, 93350, Kuching, Sarawak, Malaysia
| | - Jenny Choo
- Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak, 93350, Kuching, Sarawak, Malaysia
| | - Edwin Sien Aun Sia
- Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak, 93350, Kuching, Sarawak, Malaysia
| | - Aazani Mujahid
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Moritz Müller
- Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak, 93350, Kuching, Sarawak, Malaysia.
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50
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Chang JD, Vaughan EE, Liu CG, Jelinski JW, Terwilliger AL, Maresso AW. Metabolic profiling reveals nutrient preferences during carbon utilization in Bacillus species. Sci Rep 2021; 11:23917. [PMID: 34903830 PMCID: PMC8669014 DOI: 10.1038/s41598-021-03420-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/29/2021] [Indexed: 11/18/2022] Open
Abstract
The genus Bacillus includes species with diverse natural histories, including free-living nonpathogenic heterotrophs such as B. subtilis and host-dependent pathogens such as B. anthracis (the etiological agent of the disease anthrax) and B. cereus, a cause of food poisoning. Although highly similar genotypically, the ecological niches of these three species are mutually exclusive, which raises the untested hypothesis that their metabolism has speciated along a nutritional tract. Here, we developed a pipeline for quantitative total assessment of the use of diverse sources of carbon for general metabolism to better appreciate the "culinary preferences" of three distinct Bacillus species, as well as related Staphylococcus aureus. We show that each species has widely varying metabolic ability to utilize diverse sources of carbon that correlated to their ecological niches. This approach was applied to the growth and survival of B. anthracis in a blood-like environment and find metabolism shifts from sugar to amino acids as the preferred source of energy. Finally, various nutrients in broth and host-like environments are identified that may promote or interfere with bacterial metabolism during infection.
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Affiliation(s)
- James D Chang
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Ellen E Vaughan
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Carmen Gu Liu
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph W Jelinski
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Austen L Terwilliger
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony W Maresso
- The Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
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