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Casiano González A, Pacheco Villanueva A, Castro-Alarcón N, Méndez J, Oropeza R, Martínez-Santos VI. A novel chaperone-effector-immunity system identified in uropathogenic Escherichia coli UMN026. PeerJ 2024; 12:e17336. [PMID: 38784397 PMCID: PMC11114119 DOI: 10.7717/peerj.17336] [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: 12/18/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
Background Urinary tract infections (UTIs) are very common worldwide. According to their symptomatology, these infections are classified as pyelonephritis, cystitis, or asymptomatic bacteriuria (AB). Approximately 75-95% of UTIs are caused by uropathogenic Escherichia coli (UPEC), which is an extraintestinal bacterium that possesses virulence factors for bacterial adherence and invasion in the urinary tract. In addition, UPEC possesses type 6 secretion systems (T6SS) as virulence mechanisms that can participate in bacterial competition and in bacterial pathogenicity. UPEC UMN026 carries three genes, namely, ECUMN_0231, ECUMN_0232, and ECUMN_0233, which encode three uncharacterized proteins related to the T6SS that are conserved in strains from phylogroups B2 and D and have been proposed as biomarkers of UTIs. Aim To analyze the frequency of the ECUMN_0231, ECUMN_0232, ECUMN_0233, and vgrG genes in UTI isolates, as well as their expression in Luria Bertani (LB) medium and urine; to determine whether these genes are related to UTI symptoms or bacterial competence and to identify functional domains on the putative proteins. Methods The frequency of the ECUMN and vgrG genes in 99 clinical isolates from UPEC was determined by endpoint PCR. The relationship between gene presence and UTI symptomatology was determined using the chi2 test, with p < 0.05 considered to indicate statistical significance. The expression of the three ECUMN genes and vgrG was analyzed by RT-PCR. The antibacterial activity of strain UMN026 was determined by bacterial competence assays. The identification of functional domains and the docking were performed using bioinformatic tools. Results The ECUMN genes are conserved in 33.3% of clinical isolates from patients with symptomatic and asymptomatic UTIs and have no relationship with UTI symptomatology. Of the ECUMN+ isolates, only five (15.15%, 5/33) had the three ECUMN and vgrG genes. These genes were expressed in LB broth and urine in UPEC UMN026 but not in all the clinical isolates. Strain UMN026 had antibacterial activity against UPEC clinical isolate 4014 (ECUMN-) and E. faecalis but not against isolate 4012 (ECUMN+). Bioinformatics analysis suggested that the ECUMN genes encode a chaperone/effector/immunity system. Conclusions The ECUMN genes are conserved in clinical isolates from symptomatic and asymptomatic patients and are not related to UTI symptoms. However, these genes encode a putative chaperone/effector/immunity system that seems to be involved in the antibacterial activity of strain UMN026.
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Affiliation(s)
- América Casiano González
- Microbiology Research Laboratory, Faculty of Chemical Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - Arantxa Pacheco Villanueva
- Microbiology Research Laboratory, Faculty of Chemical Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - Natividad Castro-Alarcón
- Microbiology Research Laboratory, Faculty of Chemical Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - Julio Méndez
- Department of Molecular Microbiology, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Ricardo Oropeza
- Department of Molecular Microbiology, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Maghembe RS, Magulye MA, Eilu E, Sekyanzi S, Mwesigwa S, Katagirya E. Chromosomal and plasmid-encoded virulence and multidrug resistance of Escherichia coli ST58/24 infecting a 2-year-old sickle cell patient with sepsis in Kampala Uganda, East Africa. Heliyon 2024; 10:e30187. [PMID: 38707307 PMCID: PMC11068601 DOI: 10.1016/j.heliyon.2024.e30187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024] Open
Abstract
Sepsis and drug resistance represent a complex of the most common global causes of mortality in intensive care units (ICUs) especially among patients with comorbidities. Extraintestinal pathogenic Escherichia coli (ExPEC) strains are highly implicated in systemic infections, with multidrug resistance exacerbating the risk of chronic conditions and patient mortality. The diversity of virulence and evolution of multidrug resistance are yet to be fully deciphered. In this work, we aimed at unveiling the pathogens and their genomic determinants of virulence and drug resistance relevant to increased sepsis in a sickle cell child admitted to ICU. From a rectal swab, we isolated a strain of E. coli from the patient and phenotypically tested it against a panel of selected beta lactams, fluoroquinolones, macrolides, aminoglycosides and colistin. We then sequenced the entire genome and integrated multiple bioinformatic pipelines to divulge the virulence and multidrug resistance profiles of the isolate. Our results revealed that the isolate belongs to the sequence type (ST) 58/24, which (ST58), is a known ExPEC. With the use of PathogenFinder, we were able to confirm that this isolate is a human pathogen (p = 0.936). The assembled chromosome and two plasmids encode virulence factors related to capsule (antiphagocytosis), serum survival and resistance, type 6 secretion system (T6SS), multiple siderophores (iron acquisition), and biosynthetic gene clusters for polyketides and nonribosomal peptides exhibiting host cell damaging activity in silico. The genome also harbors multidrug resistance genotypes including extended spectrum beta lactamase (ESBL) genes such as blaTEM-1A/B, sulfonamide resistance genes sul1/2, fluoroquinolone resistance genes dfrA5 and nonsynonymous mutations of the gene pmrB, conferring intrinsic colistin resistance. Conclusively, this pathogen holds the potential to cause systemic infection and might exacerbate sickle cell anemia in the patient. The virulence and multidrug resistance profiles are encoded by both the chromosome and plasmids. Genomic surveillance of pathogens with multidrug resistance among patients with commodities is crucial for effective disease management.
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Affiliation(s)
- Reuben S. Maghembe
- Department of Microbiologgy and Immunology, Faculty of Biomedical Sciences, Kampala International University, Western Campus, Ishaka, Uganda
- Department of Health and Biomedical Sciences, Didia Education and Health Organization, P. O. Box 113, Shinyanga, Tanzania
- Biological and Marine Sciences Unit, Faculty of Natural and Applied Sciences, Marian University College, P. O. Box 47, Bagamoyo, Tanzania
- Microbiology Section, Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag 00704, Gaborone, Botswana
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
| | - Maximilian A.K. Magulye
- Department of Health and Biomedical Sciences, Didia Education and Health Organization, P. O. Box 113, Shinyanga, Tanzania
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
| | - Emmanuel Eilu
- Department of Microbiologgy and Immunology, Faculty of Biomedical Sciences, Kampala International University, Western Campus, Ishaka, Uganda
| | - Simon Sekyanzi
- Department of Medical Microbiology, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
| | - Savannah Mwesigwa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, P. O. Box 7072, Kampala, Uganda
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Zhang P, Huguet-Tapia J, Peng Z, Liu S, Obasa K, Block AK, White FF. Genome analysis and hyphal movement characterization of the hitchhiker endohyphal Enterobacter sp. from Rhizoctonia solani. Appl Environ Microbiol 2024; 90:e0224523. [PMID: 38319098 PMCID: PMC10952491 DOI: 10.1128/aem.02245-23] [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: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
Bacterial-fungal interactions are pervasive in the rhizosphere. While an increasing number of endohyphal bacteria have been identified, little is known about their ecology and impact on the associated fungal hosts and the surrounding environment. In this study, we characterized the genome of an Enterobacter sp. Crenshaw (En-Cren), which was isolated from the generalist fungal pathogen Rhizoctonia solani, and examined the genetic potential of the bacterium with regard to the phenotypic traits associated with the fungus. Overall, the En-Cren genome size was typical for members of the genus and was capable of free-living growth. The genome was 4.6 MB in size, and no plasmids were detected. Several prophage regions and genomic islands were identified that harbor unique genes in comparison with phylogenetically closely related Enterobacter spp. Type VI secretion system and cyanate assimilation genes were identified from the bacterium, while some common heavy metal resistance genes were absent. En-Cren contains the key genes for indole-3-acetic acid (IAA) and phenylacetic acid (PAA) biosynthesis, and produces IAA and PAA in vitro, which may impact the ecology or pathogenicity of the fungal pathogen in vivo. En-Cren was observed to move along hyphae of R. solani and on other basidiomycetes and ascomycetes in culture. The bacterial flagellum is essential for hyphal movement, while other pathways and genes may also be involved.IMPORTANCEThe genome characterization and comparative genomics analysis of Enterobacter sp. Crenshaw provided the foundation and resources for a better understanding of the ecology and evolution of this endohyphal bacteria in the rhizosphere. The ability to produce indole-3-acetic acid and phenylacetic acid may provide new angles to study the impact of phytohormones during the plant-pathogen interactions. The hitchhiking behavior of the bacterium on a diverse group of fungi, while inhibiting the growth of some others, revealed new areas of bacterial-fungal signaling and interaction, which have yet to be explored.
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Affiliation(s)
- Peiqi Zhang
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Jose Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Zhao Peng
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- College of Plant Protection, Jilin Agricultural University, Changchun, Jilin, China
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Ken Obasa
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- High Plains Plant Disease Diagnostic Lab, Texas A&M AgriLife Extension Service, Amarillo, Texas, USA
| | - Anna K. Block
- Chemistry Research Unit, US Department of Agriculture-Agricultural Research Service, Gainesville, Florida, USA
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
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Peng M, Lin W, Zhou A, Jiang Z, Zhou F, Wang Z. High genetic diversity and different type VI secretion systems in Enterobacter species revealed by comparative genomics analysis. BMC Microbiol 2024; 24:26. [PMID: 38238664 PMCID: PMC10797944 DOI: 10.1186/s12866-023-03164-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/18/2023] [Indexed: 01/22/2024] Open
Abstract
The human-pathogenic Enterobacter species are widely distributed in diverse environmental conditions, however, the understanding of the virulence factors and genetic variations within the genus is very limited. In this study, we performed comparative genomics analysis of 49 strains originated from diverse niches and belonged to eight Enterobacter species, in order to further understand the mechanism of adaption to the environment in Enterobacter. The results showed that they had an open pan-genome and high genomic diversity which allowed adaptation to distinctive ecological niches. We found the number of secretion systems was the highest among various virulence factors in these Enterobacter strains. Three types of T6SS gene clusters including T6SS-A, T6SS-B and T6SS-C were detected in most Enterobacter strains. T6SS-A and T6SS-B shared 13 specific core genes, but they had different gene structures, suggesting they probably have different biological functions. Notably, T6SS-C was restricted to E. cancerogenus. We detected a T6SS gene cluster, highly similar to T6SS-C (91.2%), in the remote related Citrobacter rodenitum, suggesting that this unique gene cluster was probably acquired by horizontal gene transfer. The genomes of Enterobacter strains possess high genetic diversity, limited number of conserved core genes, and multiple copies of T6SS gene clusters with differentiated structures, suggesting that the origins of T6SS were not by duplication instead by independent acquisition. These findings provide valuable information for better understanding of the functional features of Enterobacter species and their evolutionary relationships.
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Affiliation(s)
- Mu Peng
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, China.
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China.
| | - Weiyuan Lin
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China
| | - Aifen Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Zhihui Jiang
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China
| | - Fangzhen Zhou
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China
| | - Zhiyong Wang
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China.
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Kjellin J, Lee D, Steinsland H, Dwane R, Barth Vedoy O, Hanevik K, Koskiniemi S. Colicins and T6SS-based competition systems enhance enterotoxigenic E. coli (ETEC) competitiveness. Gut Microbes 2024; 16:2295891. [PMID: 38149626 PMCID: PMC10761095 DOI: 10.1080/19490976.2023.2295891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023] Open
Abstract
Diarrheal diseases are still a significant problem for humankind, causing approximately half a million deaths annually. To cause diarrhea, enteric bacterial pathogens must first colonize the gut, which is a niche occupied by the normal bacterial microbiota. Therefore, the ability of pathogenic bacteria to inhibit the growth of other bacteria can facilitate the colonization process. Although enterotoxigenic Escherichia coli (ETEC) is one of the major causative agents of diarrheal diseases, little is known about the competition systems found in and used by ETEC and how they contribute to the ability of ETEC to colonize a host. Here, we collected a set of 94 fully assembled ETEC genomes by performing whole-genome sequencing and mining the NCBI RefSeq database. Using this set, we performed a comprehensive search for delivered bacterial toxins and investigated how these toxins contribute to ETEC competitiveness in vitro. We found that type VI secretion systems (T6SS) were widespread among ETEC (n = 47). In addition, several closely related ETEC strains were found to encode Colicin Ia and T6SS (n = 8). These toxins provide ETEC competitive advantages during in vitro competition against other E. coli, suggesting that the role of T6SS as well as colicins in ETEC biology has until now been underappreciated.
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Affiliation(s)
- Jonas Kjellin
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Danna Lee
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Hans Steinsland
- CISMAC, Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Rachel Dwane
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Oda Barth Vedoy
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Norway
- National centre for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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Maurya S, Arya CK, Parmar N, Sathyanarayanan N, Joshi CG, Ramanathan G. Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF. Arch Microbiol 2023; 206:6. [PMID: 38015256 DOI: 10.1007/s00203-023-03729-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P. DMF) that was isolated from a domestic wastewater treatment plant in Kanpur, India (26.4287 °N, 80.3891 °E) based on its ability to degrade a recalcitrant organic solvent N, N-dimethylformamide (DMF). The results reveal a genome size of 4,202,269 base pairs (bp) with a G + C content of 67.9%. The assembled genome comprises 4141 coding sequences (CDS), 46 RNA sequences, and 2 CRISPRs. Interestingly, catabolic operons related to the conventional marine-based methylated amines (MAs) degradation pathway were functionally annotated within the genome of an obligated aerobic heterotroph that is P. DMF. The genomic data-based characterization presented here for the novel heterotroph P. DMF aims to improve the understanding of the phenotypic gene products, enzymes, and pathways involved with greater emphasis on facultative methylotrophic motility-based latent pathogenicity.
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Affiliation(s)
- Shiwangi Maurya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Chetan Kumar Arya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Nidhi Parmar
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Nitish Sathyanarayanan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, 560065, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Gurunath Ramanathan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
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Liu W, Li M, Cao S, Ishaq HM, Zhao H, Yang F, Liu L. The Biological and Regulatory Role of Type VI Secretion System of Klebsiella pneumoniae. Infect Drug Resist 2023; 16:6911-6922. [PMID: 37928603 PMCID: PMC10624183 DOI: 10.2147/idr.s426657] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/30/2023] [Indexed: 11/07/2023] Open
Abstract
Bacteria communicate with their surroundings through diverse secretory systems, and the recently discovered Type VI Secretion System (T6SS) has gained significant attention. Klebsiella pneumoniae (K. pneumoniae), an opportunistic pathogen known for causing severe infections in both hospital and animal settings, possesses this intriguing T6SS. This system equips K. pneumoniae with a formidable armory of protein-based weaponry, enabling the delivery of toxins into neighboring cells, thus granting a substantial competitive advantage. Remarkably, the T6SS has also been associated with K. pneumoniae's ability to form biofilms and acquire resistance against antibiotics. However, the precise effects of the T6SS on K. pneumoniae's functions remain inadequately studied, despite research efforts to understand the intricacies of these mechanisms. This comprehensive review aims to provide an overview of the current knowledge regarding the biological functions and regulatory mechanisms of the T6SS in K. pneumoniae.
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Affiliation(s)
- Wenke Liu
- Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, People’s Republic of China
| | - Min Li
- Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, People’s Republic of China
| | - Shiwen Cao
- Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, People’s Republic of China
| | - Hafiz Muhammad Ishaq
- Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Huajie Zhao
- Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, People’s Republic of China
| | - Fan Yang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, People’s Republic of China
| | - Liang Liu
- Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, People’s Republic of China
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Carter MQ, Quiñones B, Laniohan N, Carychao D, Pham A, He X, Cooley M. Pathogenicity assessment of Shiga toxin-producing Escherichia coli strains isolated from wild birds in a major agricultural region in California. Front Microbiol 2023; 14:1214081. [PMID: 37822735 PMCID: PMC10562709 DOI: 10.3389/fmicb.2023.1214081] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) consists of diverse strains differing in genetic make-up and virulence potential. To better understand the pathogenicity potential of STEC carried by the wildlife, three STEC and one E. coli strains isolated from wild birds near a major agricultural region in California were selected for comparative pathogenomic analyses. Three American crow (Corvus brachyrhynchos) strains, RM9088, RM9513, and RM10410, belonging to phylogroup A with serotypes O109:H48, O9:H30, and O113:H4, respectively, and a red-winged blackbird (Agelaius phoeniceus) strain RM14516 in phylogroup D with serotype O17:H18, were examined. Shiga toxin genes were identified in RM9088 (stx1a), RM10410 (stx1a + stx2d), and RM14516 (stx2a). Unlike STEC O157:H7 strain EDL933, none of the avian STEC strains harbored the pathogenicity islands OI-122, OI-57, and the locus of enterocyte effacement, therefore the type III secretion system biogenesis genes and related effector genes were absent in the three avian STEC genomes. Interestingly, all avian STEC strains exhibited greater (RM9088 and RM14516) or comparable (RM10410) cytotoxicity levels compared with EDL933. Comparative pathogenomic analyses revealed that RM9088 harbored numerous genes encoding toxins, toxins delivery systems, and adherence factors, including heat-labile enterotoxin, serine protease autotransporter toxin Pic, type VI secretion systems, protein adhesin Paa, fimbrial adhesin K88, and colonization factor antigen I. RM9088 also harbored a 36-Kb high pathogenicity island, which is related to iron acquisition and pathogenicity in Yersinia spp. Strain RM14516 carried an acid fitness island like the one in EDL933, containing a nine gene cluster involved in iron acquisition. Genes encoding extracellular serine protease EspP, subtilase cytotoxin, F1C fimbriae, and inverse autotransporter adhesin IatC were only detected in RM14516, and genes encoding serine protease autotransporter EspI and P fimbriae were only identified in RM10410. Although all curli genes were present in avian STEC strains, production of curli fimbriae was only detected for RM9088 and RM14516. Consistently, strong, moderate, and little biofilms were observed for RM9088, RM14516, and RM10410, respectively. Our study revealed novel combinations of virulence factors in two avian strains, which exhibited high level of cytotoxicity and strong biofilm formation. Comparative pathogenomics is powerful in assessing pathogenicity and health risk of STEC strains.
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Affiliation(s)
- Michelle Qiu Carter
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Beatriz Quiñones
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Nicole Laniohan
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Diana Carychao
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Antares Pham
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Xiaohua He
- Foodborne Toxin Detection and Prevention Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Michael Cooley
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
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Smith JA, Holmes DE, Woodard TL, Li Y, Liu X, Wang LY, Meier D, Schwarz IA, Lovley DR. Detrimental impact of the Geobacter metallireducens type VI secretion system on direct interspecies electron transfer. Microbiol Spectr 2023; 11:e0094123. [PMID: 37650614 PMCID: PMC10580878 DOI: 10.1128/spectrum.00941-23] [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: 03/02/2023] [Accepted: 07/02/2023] [Indexed: 09/01/2023] Open
Abstract
Direct interspecies electron transfer (DIET) is important in anaerobic communities of environmental and practical significance. Other than the need for close physical contact for electrical connections, the interactions of DIET partners are poorly understood. Type VI secretion systems (T6SSs) typically kill competitive microbes. Surprisingly, Geobacter metallireducens highly expressed T6SS genes when DIET-based co-cultures were initiated with Geobacter sulfurreducens. T6SS gene expression was lower when the electron shuttle anthraquinone-2,6-disulfonate was added to alleviate the need for interspecies contact. Disruption of hcp, the G. metallireducens gene for the main T6SS needle-tube protein subunit, and the most highly upregulated gene in DIET-grown cells eliminated the long lag periods required for the initiation of DIET. The mutation did not aid DIET in the presence of granular-activated carbon (GAC), consistent with the fact that DIET partners do not make physical contact when electrically connected through conductive materials. The hcp-deficient mutant also established DIET quicker with Methanosarcina barkeri. However, the mutant also reduced Fe(III) oxide faster than the wild-type strain, a phenotype not expected from the loss of the T6SS. Quantitative PCR revealed greater gene transcript abundance for key components of extracellular electron transfer in the hcp-deficient mutant versus the wild-type strain, potentially accounting for the faster Fe(III) oxide reduction and impact on DIET. The results highlight that interspecies interactions beyond electrical connections may influence DIET effectiveness. The unexpected increase in the expression of genes for extracellular electron transport components when hcp was deleted emphasizes the complexities in evaluating the electromicrobiology of highly adaptable Geobacter species. IMPORTANCE Direct interspecies electron transfer is an alternative to the much more intensively studied process of interspecies H2 transfer as a mechanism for microbes to share electrons during the cooperative metabolism of energy sources. DIET is an important process in anaerobic soils and sediments generating methane, a significant greenhouse gas. Facilitating DIET can accelerate and stabilize the conversion of organic wastes to methane biofuel in anaerobic digesters. Therefore, a better understanding of the factors controlling how fast DIET partnerships are established is expected to lead to new strategies for promoting this bioenergy process. The finding that when co-cultured with G. sulfurreducens, G. metallireducens initially expressed a type VI secretion system, a behavior not conducive to interspecies cooperation, illustrates the complexity of establishing syntrophic relationships.
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Affiliation(s)
- Jessica A. Smith
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Dawn E. Holmes
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Trevor L. Woodard
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - Yang Li
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- School of Ocean Science and Technology, Dalian University of Technology, Panjin, Liaoning, China
| | - Xinying Liu
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, China
| | - Li-Ying Wang
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - David Meier
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - Ingrid A. Schwarz
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
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Azam MW, Zarrilli R, Khan AU. Updates on the Virulence Factors Produced by Multidrug-Resistant Enterobacterales and Strategies to Control Their Infections. Microorganisms 2023; 11:1901. [PMID: 37630461 PMCID: PMC10456890 DOI: 10.3390/microorganisms11081901] [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: 03/15/2023] [Revised: 07/06/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
The Enterobacterales order is a massive group of Gram-negative bacteria comprised of pathogenic and nonpathogenic members, including beneficial commensal gut microbiota. The pathogenic members produce several pathogenic or virulence factors that enhance their pathogenic properties and increase the severity of the infection. The members of Enterobacterales can also develop resistance against the common antimicrobial agents, a phenomenon called antimicrobial resistance (AMR). Many pathogenic Enterobacterales members are known to possess antimicrobial resistance. This review discusses the virulence factors, pathogenicity, and infections caused by multidrug-resistant Enterobacterales, especially E. coli and some other bacterial species sharing similarities with the Enterobacterales members. We also discuss both conventional and modern approaches used to combat the infections caused by them. Understanding the virulence factors produced by the pathogenic bacteria will help develop novel strategies and methods to treat infections caused by them.
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Affiliation(s)
- Mohd W. Azam
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy
| | - Asad U. Khan
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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11
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Lin YL, Smith SN, Kanso E, Septer AN, Rycroft CH. A subcellular biochemical model for T6SS dynamics reveals winning competitive strategies. PNAS NEXUS 2023; 2:pgad195. [PMID: 37441614 PMCID: PMC10335733 DOI: 10.1093/pnasnexus/pgad195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 07/15/2023]
Abstract
The type VI secretion system (T6SS) is a broadly distributed interbacterial weapon that can be used to eliminate competing bacterial populations. Although unarmed target populations are typically used to study T6SS function in vitro, bacteria most likely encounter other T6SS-armed competitors in nature. However, the connection between subcellular details of the T6SS and the outcomes of such mutually lethal battles is not well understood. Here, we incorporate biological data derived from natural competitors of Vibrio fischeri light organ symbionts to build a biochemical model for T6SS at the single-cell level, which we then integrate into an agent-based model (ABM). Using the ABM, we isolate and experiment with strain-specific physiological differences between competitors in ways not possible with biological samples to identify winning strategies for T6SS-armed populations. Through in vitro experiments, we discover that strain-specific differences exist in T6SS activation speed. ABM simulations corroborate that faster activation is dominant in determining survival during competition. Once competitors are fully activated, the energy required for T6SS creates a tipping point where increased weapon building and firing becomes too costly to be advantageous. Through ABM simulations, we identify the threshold where this transition occurs in the T6SS parameter space. We also find that competitive outcomes depend on the geometry of the battlefield: unarmed target cells survive at the edges of a range expansion where unlimited territory can be claimed. Alternatively, competitions within a confined space, much like the light organ crypts where natural V. fischeri compete, result in the rapid elimination of the unarmed population.
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Affiliation(s)
| | | | - Eva Kanso
- Department of Aerospace and Mechanical Engineering, University of Southern California, 3650 McClintock Ave, Los Angeles, CA 90089, USA
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12
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Gong J, Yu J, Yin S, Ke J, Wu J, Liu C, Luo Z, Cheng WM, Xie Y, Chen Y, He Z, Lan P. Mesenteric Adipose Tissue-Derived Klebsiella variicola Disrupts Intestinal Barrier and Promotes Colitis by Type VI Secretion System. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205272. [PMID: 36802200 PMCID: PMC10131791 DOI: 10.1002/advs.202205272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Mesenteric adipose tissue (MAT) in Crohn's disease (CD) is associated with transmural inflammation. Extended mesenteric excision can reduce surgical recurrence and improve long-term outcomes, indicating that MAT plays an important role in the pathogenesis of CD. Bacterial translocation has been reported to occur in the MAT of patients with CD (CD-MAT), but the mechanisms by which translocated bacteria lead to intestinal colitis remain unclear. Here it is shown that members of Enterobacteriaceae are highly enriched in CD-MAT compared with non-CD controls. Viable Klebsiella variicola in Enterobacteriaceae is isolated exclusively in CD-MAT and can induce a pro-inflammatory response in vitro and exacerbates colitis both in dextran sulfate sodium (DSS)-induced colitis mice model and IL-10-/- spontaneous colitis mice model. Mechanistically, active type VI secretion system (T6SS) is identified in the genome of K. variicola, which can impair the intestinal barrier by inhibiting the zonula occludens (ZO-1) expression. Dysfunction of T6SS by CRISPR interference system alleviates the inhibitory effect of K. variicola on ZO-1 expression and attenuated colitis in mice. Overall, these findings demonstrate that a novel colitis-promoting bacteria exist in the mesenteric adipose tissue of CD, opening a new therapeutic avenue for colitis management.
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Affiliation(s)
- Junli Gong
- Department of Colorectal SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
- Guangdong Institute of GastroenterologyGuangzhouGuangdong510655P. R. China
| | - Jing Yu
- Department of Colorectal SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
| | - Shengmei Yin
- School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510275P. R. China
| | - Jia Ke
- Department of Colorectal SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
| | - Jinjie Wu
- Department of Colorectal SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
| | - Chen Liu
- Department of Colorectal SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
- Guangdong Institute of GastroenterologyGuangzhouGuangdong510655P. R. China
| | - Zhanhao Luo
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
- Guangdong Institute of GastroenterologyGuangzhouGuangdong510655P. R. China
| | - Wai Ming Cheng
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
- Guangdong Institute of GastroenterologyGuangzhouGuangdong510655P. R. China
| | - Yaozu Xie
- Department of Colorectal SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
| | - Yuan Chen
- School of MedicineSun Yat‐sen UniversityGuangzhouGuangdong510275P. R. China
| | - Zhen He
- Department of Colorectal SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
| | - Ping Lan
- Department of Colorectal SurgeryThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat‐sen UniversityGuangzhouGuangdong510655P. R. China
- Guangdong Institute of GastroenterologyGuangzhouGuangdong510655P. R. China
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13
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Du Q, Xu Q, Pan F, Shi Y, Yu F, Zhang T, Jiang J, Liu W, Pan X, Han D, Zhang H. Association between Intestinal Colonization and Extraintestinal Infection with Carbapenem-Resistant Klebsiella pneumoniae in Children. Microbiol Spectr 2023; 11:e0408822. [PMID: 36916927 PMCID: PMC10100809 DOI: 10.1128/spectrum.04088-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/15/2023] [Indexed: 03/16/2023] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a critical public health threat. However, the association between intestinal colonization and parenteral infection among pediatric patients has not been elucidated. We collected 8 fecal CRKP strains and 10 corresponding CRKP strains responsible for extraintestinal infection from eight patients who did not manifest infection upon admission to the hospital. Paired isolates showed identical resistance to antimicrobials and identical virulence in vitro and in vivo. wzi capsule typing, multilocus sequence typing, and whole-genome sequencing (WGS) indicated high similarity between paired colonizing and infecting isolates. Mutations between colonizing and infecting isolate pairs found by WGS had a distinctive molecular signature of a high proportion of complex structural variants. The mutated genes were involved in pathways associated with infection-related physiological and pathogenic functions, including antibiotic resistance, virulence, and response to the extracellular environment. The latter is important for bacterial infection of environmental niches. Various mutations related to antibiotic resistance, virulence, and colonization that were not associated with any particular mutational hot spot correlated with an increased risk of extraintestinal infection. Notably, novel subclone carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) KL19-ST15 exhibited hypervirulence in experimental assays that reflected the severe clinical symptoms of two patients infected with the clonal strains. Taken together, our findings indicate the association between CRKP intestinal colonization and extraintestinal infection, suggesting that active screening for colonization on admission could decrease infection risk in children. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKP) causes an increasing number of nosocomial infections, which can be life-threatening, as carbapenems are last-resort antibiotics. K. pneumoniae is part of the healthy human microbiome, and this provides a potential advantage for infection. This study demonstrated that CRKP intestinal colonization is strongly linked to extraintestinal infection, based on the evidence given by whole-genome sequencing data and phenotypic assays of antimicrobial resistance and virulence. Apart from these findings, our in-depth analysis of point mutations and chromosome structural variants in patient-specific infecting isolates compared with colonizing isolates may contribute insights into bacterial adaptation underlying CRKP infection. In addition, a novel subclone of carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) was observed in the study. This finding highlights the importance of CRKP active surveillance among children, targeting in particular the novel high-risk CR-hvKP clone.
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Affiliation(s)
- Qingqing Du
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Xu
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Fen Pan
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingying Shi
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fangyuan Yu
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tiandong Zhang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Jiang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenxin Liu
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaozhou Pan
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dingding Han
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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14
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Cho THS, Pick K, Raivio TL. Bacterial envelope stress responses: Essential adaptors and attractive targets. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119387. [PMID: 36336206 DOI: 10.1016/j.bbamcr.2022.119387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/05/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
Millions of deaths a year across the globe are linked to antimicrobial resistant infections. The need to develop new treatments and repurpose of existing antibiotics grows more pressing as the growing antimicrobial resistance pandemic advances. In this review article, we propose that envelope stress responses, the signaling pathways bacteria use to recognize and adapt to damage to the most vulnerable outer compartments of the microbial cell, are attractive targets. Envelope stress responses (ESRs) support colonization and infection by responding to a plethora of toxic envelope stresses encountered throughout the body; they have been co-opted into virulence networks where they work like global positioning systems to coordinate adhesion, invasion, microbial warfare, and biofilm formation. We highlight progress in the development of therapeutic strategies that target ESR signaling proteins and adaptive networks and posit that further characterization of the molecular mechanisms governing these essential niche adaptation machineries will be important for sparking new therapeutic approaches aimed at short-circuiting bacterial adaptation.
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Affiliation(s)
- Timothy H S Cho
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Kat Pick
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Tracy L Raivio
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
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15
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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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Identification of novel genes involved in the biofilm formation process of Avian Pathogenic Escherichia coli (APEC). PLoS One 2022; 17:e0279206. [PMID: 36534660 PMCID: PMC9762606 DOI: 10.1371/journal.pone.0279206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Avian pathogenic Escherichia coli (APEC) is the etiological agent of avian colibacillosis, a leading cause of economic loss to the poultry industry worldwide. APEC causes disease using a diverse repertoire of virulence factors and has the ability to form biofilms, which contributes to the survival and persistence of APEC in harsh environments. The objective of this study was to identify genes most widespread and important in APEC that contribute to APEC biofilm formation. Using the characterized APEC O18 as the template strain, a total of 15,660 mutants were randomly generated using signature tagged mutagenesis and evaluated for decreased biofilm formation ability using the crystal violet assay. Biofilm deficient mutants were sequenced, and a total of 547 putative biofilm formation genes were identified. Thirty of these genes were analyzed by PCR for prevalence among 109 APEC isolates and 104 avian fecal E. coli (AFEC) isolates, resulting in nine genes with significantly greater prevalence in APEC than AFEC. The expression of these genes was evaluated in the wild-type APEC O18 strain using quantitative real-time PCR (qPCR) in both the exponential growth phase and the mature biofilm phase. To investigate the role of these genes in biofilm formation, isogenic mutants were constructed and evaluated for their biofilm production and planktonic growth abilities. Four of the mutants (rfaY, rfaI, and two uncharacterized genes) displayed significantly decreased biofilm formation, and of those four, one (rfaI) displayed significantly decreased growth compared to the wild type. Overall, this study identified novel genes that may be important in APEC and its biofilm formation. The data generated from this study will benefit further investigation into the mechanisms of APEC biofilm formation.
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17
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Carter MQ, Laniohan N, Pham A, Quiñones B. Comparative genomic and phenotypic analyses of the virulence potential in Shiga toxin-producing Escherichia coli O121:H7 and O121:H10. Front Cell Infect Microbiol 2022; 12:1043726. [PMID: 36506028 PMCID: PMC9729726 DOI: 10.3389/fcimb.2022.1043726] [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: 09/13/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) O121 is among the top six non-O157 serogroups that are most frequently associated with severe disease in humans. While O121:H19 is predominant, other O121 serotypes have been frequently isolated from environmental samples, but their virulence repertoire is poorly characterized. Here, we sequenced the complete genomes of two animal isolates belonging to O121:H7 and O121:H10 and performed comparative genomic analysis with O121:H19 to assess their virulence potential. Both O121:H7 and O121:H10 strains carry a genome comparable in size with the O121:H19 genomes and belong to phylogroup B1. However, both strains appear to have evolved from a different lineage than the O121:H19 strains according to the core genes-based phylogeny and Multi Locus Sequence Typing. A systematic search of over 300 E. coli virulence genes listed in the Virulence Factor DataBase revealed a total of 73 and 71 in O121:H7 and O121:H10 strains, respectively, in comparison with an average of 135 in the O121:H19 strains. This variation in the virulence genes repertoire was mainly attributed to the reduction in the number of genes related to the Type III Secretion System in the O121:H7 and O121:H10 strains. Compared to the O121:H19 strains, the O121:H7 strain carries more adherence and toxin genes while the O121:H10 strain carries more genes related to the Type VI Secretion System. Although both O121:H7 and O121:H10 strains carry the large virulence plasmid pEHEC, they do not harbor all pEHEC virulence genes in O121:H19. Furthermore, unlike the O121:H19 strains, neither the O121:H7 nor O121:H10 strain carried the Locus of Enterocyte Effacement, OI-122, nor the tellurite resistance island. Although an incomplete Locus of Adhesion and Autoaggregation (LAA) was identified in the O121:H7 and O121:H10 strains, a limited number of virulence genes were present. Consistently, both O121:H7 and O121:H10 strains displayed significant reduced cytotoxicity than either the O157:H7 strain EDL933 or the O121:H19 strain RM8352. In fact, the O121:H7 strain RM8082 appeared to cause minimal cytotoxicity to Vero cells. Our study demonstrated distinct evolutionary lineages among the strains of serotypes O121:H19, O121:H10, and O121:H7 and suggested reduced virulence potentials in STEC strains of O121:H10 and O121:H7.
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18
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Dubinsky V, Reshef L, Rabinowitz K, Wasserberg N, Dotan I, Gophna U. Escherichia coli Strains from Patients with Inflammatory Bowel Diseases have Disease-specific Genomic Adaptations. J Crohns Colitis 2022; 16:1584-1597. [PMID: 35560165 DOI: 10.1093/ecco-jcc/jjac071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIMS Escherichia coli is over-abundant in the gut microbiome of patients with inflammatory bowel disease [IBD]. Here, we aimed to identify IBD-specific genomic functions of diverse E. coli lineages. METHODS We investigated E. coli genomes from patients with ulcerative colitis [UC], Crohn's disease [CD] or a pouch, and healthy subjects. The majority of genomes were reconstructed from metagenomic samples, including newly sequenced faecal metagenomes. Clinical metadata were collected. Functional analysis at the gene and mutation level were performed and integrated with IBD phenotypes and biomarkers. RESULTS Overall, 530 E. coli genomes were analysed. The E. coli B2 lineage was more prevalent in UC compared with other IBD phenotypes. Genomic metabolic capacities varied across E. coli lineages and IBD phenotypes. Host mucin utilisation enzymes were present in a single lineage and depleted in patients with a pouch, whereas those involved in inulin hydrolysis were enriched in patients with a pouch. E. coli strains from patients with UC were twice as likely to encode the genotoxic molecule colibactin than strains from patients with CD or a pouch. Strikingly, patients with a pouch showed the highest inferred E. coli growth rates, even in the presence of antibiotics. Faecal calprotectin did not correlate with the relative abundance of E. coli. Finally, we identified multiple IBD-specific non-synonymous mutations in E. coli genes encoding for bacterial cell envelope components. CONCLUSIONS Comparative genomics indicates that E. coli is a commensal species adapted to the overactive mucosal immune milieu in IBD, rather than causing it. Our results reveal mutations that may lead to attenuated antigenicity in some E. coli strains.
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Affiliation(s)
- Vadim Dubinsky
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Leah Reshef
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Keren Rabinowitz
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Nir Wasserberg
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel.,Colorectal Unit, Division of Surgery, Rabin Medical Center, Petah-Tikva, Israel
| | - Iris Dotan
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Uri Gophna
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
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19
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Hcp Proteins of the Type VI Secretion System Promote Avian Pathogenic E. coli DE205B (O2:K1) to Induce Meningitis in Rats. Life (Basel) 2022; 12:life12091353. [PMID: 36143390 PMCID: PMC9503490 DOI: 10.3390/life12091353] [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: 07/05/2022] [Revised: 08/09/2022] [Accepted: 08/21/2022] [Indexed: 11/16/2022] Open
Abstract
Avian pathogenic Escherichia coli (APEC) is an important extra-intestinal pathogenic E. coli (ExPEC), which often causes systemic infection in poultry and causes great economic loss to the breeding industry. In addition, as a major source of human ExPEC infection, the potential zoonotic risk of APEC has been an ongoing concern. Previous studies have pointed out that APEC is a potential zoonotic pathogen, which has high homology with human pathogenic E. coli such as uro-pathogenic E. coli (UPEC) and neonatal meningitis E. coli (NMEC), shares multiple virulence factors and can cause mammalian diseases. Previous studies have reported that O18 and O78 could cause different degrees of meningitis in neonatal rats, and different serotypes had different degrees of zoonotic risk. Here, we compared APEC DE205B (O2:K1) with NMEC RS218 (O18:K1:H7) by phylogenetic analysis and virulence gene identification to analyze the potential risk of DE205B in zoonotic diseases. We found that DE205B possessed a variety of virulence factors associated with meningitis and, through phylogenetic analysis, had high homology with RS218. DE205B could colonize the cerebrospinal fluid (CSF) of rats, and cause meningitis and nerve damage. Symptoms and pathological changes in the brain were similar to RS218. In addition, we found that DE205B had a complete T6SS, of which Hcp protein was its important structural protein. Hcp1 induced cytoskeleton rearrangement in human brain microvascular endothelial cells (HBMECs), and Hcp2 was mainly involved in the invasion of DE205B in vitro. In the meningitis model of rats, deletion of hcp2 gene reduced survival in the blood and the brain invasiveness of DE205B. Compared with WT group, Δhcp2 group induced lower inflammation and neutrophils infiltration in brain tissue, alleviating the process of meningitis. Together, these results suggested that APEC DE205B had close genetic similarities to NMEC RS218, and a similar mechanism in causing meningitis and being a risk for zoonosis. This APEC serotype provided a basis for zoonotic research.
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Kim SK, Lee JB, Yoon JW. Characterization of transcriptional activities at a divergent promoter of the type VI secretion system in enterohemorrhagic Escherichia coli O157:H7. J Microbiol 2022; 60:928-934. [DOI: 10.1007/s12275-022-2109-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/16/2022] [Accepted: 05/30/2022] [Indexed: 10/15/2022]
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21
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Sycz Z, Wojnicz D, Tichaczek-Goska D. Does Secondary Plant Metabolite Ursolic Acid Exhibit Antibacterial Activity against Uropathogenic Escherichia coli Living in Single- and Multispecies Biofilms? Pharmaceutics 2022; 14:pharmaceutics14081691. [PMID: 36015317 PMCID: PMC9415239 DOI: 10.3390/pharmaceutics14081691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/18/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
Multispecies bacterial biofilms are the often cause of chronic recurrent urinary tract infections within the human population. Eradicating such a complex bacterial consortium with standard pharmacotherapy is often unsuccessful. Therefore, plant-derived compounds are currently being researched as an alternative strategy to antibiotic therapy for preventing bacterial biofilm formation and facilitating its eradication. Therefore, our research aimed to determine the effect of secondary plant metabolite ursolic acid (UA) on the growth and survival, the quantity of exopolysaccharides formed, metabolic activity, and morphology of uropathogenic Gram-negative rods living in single- and mixed-species biofilms at various stages of their development. Spectrophotometric methods were used for biofilm mass formation and metabolic activity determination. The survival of bacteria was established using the serial dilution assay. The decrease in survival and inhibition of biofilm creation, both single- and multispecies, as well as changes in the morphology of bacterial cells were noticed. As UA exhibited better activity against young biofilms, the use of UA-containing formulations, especially during the initial steps of urinary tract infection, seems to be reasonable. However, the future direction should be a thorough understanding of the mechanisms of UA activity as a bioactive substance.
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Barbé S, Figàs-Segura À, Benada M, Navarro-Herrero I, Sampaio TM, Biosca EG, Marco-Noales E. Plant-associated microbiota as a source of antagonistic bacteria against the phytopathogen Erwinia amylovora. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:559-569. [PMID: 35403335 DOI: 10.1111/1758-2229.13064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Control of bacterial plant diseases is a major concern, as they affect economically important species and spread easily, such as the case of fire blight of rosaceous caused by Erwinia amylovora. In the search for alternatives to the use of agrochemicals and antibiotics, this work presents a screening of natural bacterial antagonists of this relevant and devastating phytopathogen. We recovered bacterial isolates from different plant tissues and geographical origins and then selected those with the strongest ability to reduce fire blight symptoms ex vivo and remarkable in vitro antagonistic activity against E. amylovora. None of them elicited a hypersensitivity reaction in tobacco leaves, most produced several hydrolytic enzymes and presented other biocontrol and/or plant growth-promoting activities, such as siderophore production and phosphate solubilization. These isolates, considered as biocontrol candidates, were identified by 16S rRNA sequencing as Pseudomonas rhizosphaerae, Curtobacterium flaccumfaciens, Enterobacter cancerogenus, Pseudomonas azotoformans, Rosenbergiella epipactidis and Serratia plymuthica. This is the first time that the last five bacterial species are reported to have biocontrol potential against E. amylovora.
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Affiliation(s)
- Silvia Barbé
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315 km 10.7, 46113 Moncada, Valencia, Spain
| | - Àngela Figàs-Segura
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner, 50, 46100 Burjassot, Valencia, Spain
| | - M'hamed Benada
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315 km 10.7, 46113 Moncada, Valencia, Spain
- Faculty of Natural Sciences, Earth and the Universe, 8 Mai 1945 University, Guelma, Algeria
| | - Inmaculada Navarro-Herrero
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315 km 10.7, 46113 Moncada, Valencia, Spain
| | - Telma Maria Sampaio
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315 km 10.7, 46113 Moncada, Valencia, Spain
| | - Elena G Biosca
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner, 50, 46100 Burjassot, Valencia, Spain
| | - Ester Marco-Noales
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315 km 10.7, 46113 Moncada, Valencia, Spain
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Host–Bacterial Interactions: Outcomes of Antimicrobial Peptide Applications. MEMBRANES 2022; 12:membranes12070715. [PMID: 35877918 PMCID: PMC9317001 DOI: 10.3390/membranes12070715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/04/2023]
Abstract
The bacterial membrane is part of a secretion system which plays an integral role to secrete proteins responsible for cell viability and pathogenicity; pathogenic bacteria, for example, secrete virulence factors and other membrane-associated proteins to invade the host cells through various types of secretion systems (Type I to Type IX). The bacterial membrane can also mediate microbial communities’ communication through quorum sensing (QS), by secreting auto-stimulants to coordinate gene expression. QS plays an important role in regulating various physiological processes, including bacterial biofilm formation while providing increased virulence, subsequently leading to antimicrobial resistance. Multi-drug resistant (MDR) bacteria have emerged as a threat to global health, and various strategies targeting QS and biofilm formation have been explored by researchers worldwide. Since the bacterial secretion systems play such a crucial role in host–bacterial interactions, this review intends to outline current understanding of bacterial membrane systems, which may provide new insights for designing approaches aimed at antimicrobials discovery. Various mechanisms pertaining interaction of the bacterial membrane with host cells and antimicrobial agents will be highlighted, as well as the evolution of bacterial membranes in evasion of antimicrobial agents. Finally, the use of antimicrobial peptides (AMPs) as a cellular device for bacterial secretion systems will be discussed as emerging potential candidates for the treatment of multidrug resistance infections.
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The Evolution of a Specialized, Highly Virulent Fish Pathogen through Gene Loss and Acquisition of Host-Specific Survival Mechanisms. Appl Environ Microbiol 2022; 88:e0022222. [PMID: 35862683 PMCID: PMC9317898 DOI: 10.1128/aem.00222-22] [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] [Indexed: 01/06/2023] Open
Abstract
Photobacterium damselae comprises two subspecies, P. damselae subsp. damselae and P. damselae subsp. piscicida, that contrast remarkably despite their taxonomic relationship. The former is opportunistic and free-living but can cause disease in compromised individuals from a broad diversity of taxa, while the latter is a highly specialized, primary fish pathogen. Here, we employ new closed curated genome assemblies from Australia to estimate the global phylogenetic structure of the species P. damselae. We identify genes responsible for the shift from an opportunist to a host-adapted fish pathogen, potentially via an arthropod vector as fish-to-fish transmission was not achieved in repeated cohabitation challenges despite high virulence for Seriola lalandi. Acquisition of ShdA adhesin and of thiol peroxidase may have allowed the environmental, generalist ancestor to colonize zooplankton and to occasionally enter in fish host sentinel cells. As dependence on the host has increased, P. damselae has lost nonessential genes, such as those related to nitrite and sulfite reduction, urea degradation, a type 6 secretion system (T6SS) and several toxin-antitoxin (TA) systems. Similar to the evolution of Yersinia pestis, the loss of urease may be the crucial event that allowed the pathogen to stably colonize zooplankton vectors. Acquisition of host-specific genes, such as those required to form a sialic acid capsule, was likely necessary for the emergent P. damselae subsp. piscicida to become a highly specialized, facultative intracellular fish pathogen. Processes that have shaped P. damselae subsp. piscicida from subsp. damselae are similar to those underlying evolution of Yersinia pestis from Y. pseudotuberculosis. IMPORTANCEPhotobacterium damselae subsp. damselae is a ubiquitous marine bacterium and opportunistic pathogen of compromised hosts of diverse taxa. In contrast, its sister subspecies P. damselae subsp. piscicida (Pdp) is highly virulent in fish. Pdp has evolved from a single subclade of Pdd through gene loss and acquisition. We show that fish-to-fish transmission does not occur in repeated infection models in the primary host, Seriola lalandi, and present genomic evidence for vector-borne transmission, potentially via zooplankton. The broad genomic changes from generalist Pdd to specialist Pdp parallel those of the environmental opportunist Yersinia pseudotuberculosis to vector-borne plague bacterium Y. pestis and demonstrate that evolutionary processes in bacterial pathogens are universal between the terrestrial and marine biosphere.
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Tantoso E, Eisenhaber B, Kirsch M, Shitov V, Zhao Z, Eisenhaber F. To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131. BMC Biol 2022; 20:146. [PMID: 35710371 PMCID: PMC9205054 DOI: 10.1186/s12915-022-01347-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Escherichia coli (E. coli) has been one of the most studied model organisms in the history of life sciences. Initially thought just to be commensal bacteria, E. coli has shown wide phenotypic diversity including pathogenic isolates with great relevance to public health. Though pangenome analysis has been attempted several times, there is no systematic functional characterization of the E. coli subgroups according to the gene profile. RESULTS Systematically scanning for optimal parametrization, we have built the E. coli pangenome from 1324 complete genomes. The pangenome size is estimated to be ~25,000 gene families (GFs). Whereas the core genome diminishes as more genomes are added, the softcore genome (≥95% of strains) is stable with ~3000 GFs regardless of the total number of genomes. Apparently, the softcore genome (with a 92% or 95% generation threshold) can define the genome of a bacterial species listing the critically relevant, evolutionarily most conserved or important classes of GFs. Unsupervised clustering of common E. coli sequence types using the presence/absence GF matrix reveals distinct characteristics of E. coli phylogroups B1, B2, and E. We highlight the bi-lineage nature of B1, the variation of the secretion and of the iron acquisition systems in ST11 (E), and the incorporation of a highly conserved prophage into the genome of ST131 (B2). The tail structure of the prophage is evolutionarily related to R2-pyocin (a tailocin) from Pseudomonas aeruginosa PAO1. We hypothesize that this molecular machinery is highly likely to play an important role in protecting its own colonies; thus, contributing towards the rapid rise of pandemic E. coli ST131. CONCLUSIONS This study has explored the optimized pangenome development in E. coli. We provide complete GF lists and the pangenome matrix as supplementary data for further studies. We identified biological characteristics of different E. coli subtypes, specifically for phylogroups B1, B2, and E. We found an operon-like genome region coding for a tailocin specific for ST131 strains. The latter is a potential killer weapon providing pandemic E. coli ST131 with an advantage in inter-bacterial competition and, suggestively, explains their dominance as human pathogen among E. coli strains.
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Affiliation(s)
- Erwin Tantoso
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Miles Kirsch
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,Present address: Northeastern University, Boston, USA
| | - Vladimir Shitov
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Zhiya Zhao
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,Present address: The University of Cambridge, Cambridge, UK
| | - Frank Eisenhaber
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore. .,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore. .,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, 637551, Singapore, Republic of Singapore.
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Muneeswari R, Iyappan S, Swathi KV, Vinu R, Ramani K, Sekaran G. Biocatalytic lipoprotein bioamphiphile induced treatment of recalcitrant hydrocarbons in petroleum refinery oil sludge through transposon technology. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128520. [PMID: 35228072 DOI: 10.1016/j.jhazmat.2022.128520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/04/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
The present investigation employed transposon technology to enhance the degradation of recalcitrant petroleum hydrocarbons present in petroleum oil sludge by using biosurfactant hyper-producing strain Enterobacter xiangfangensis STP-3. Out of 2500 transposon induced mutants, mutants M257E.xiangfangensis and M916E.xiangfangensis hyper-produce biocatalytic lipoprotein biosurfactant by1.98 and 2.34 fold higher than wild-type strain. Transposon induced mutation also modified the amino acid composition which improved the hydrophobicity and thermal stability of the biosurfactants produced by mutants, compared to the wild-type biosurfactant. GC-MS and LC-MS-MS revealed that biosurfactants have pentameric lipid moiety and esterase as protein moiety. Increased biosurfactant hydrophobicity and yield by the mutants resulted in the enhanced bioavailability of petroleum hydrocarbons, thereby mutants M257E.xiangfangensis and M916E.xiangfangensis demonstrated better petroleum oil sludge degradation by 82% and 88% respectively, than wild-type (72%). Disrupted genes vgr G and pgm M in M257E.xiangfangensis and M916E.xiangfangensis respectively hyper-produce biosurfactant by competitive pathway inhibition and increased precursor availability mechanism. Hyper-production of biosurfactant was also validated by comparing the expression of biosynthetic genes ent E, ent F and est using qPCR. This is the first report on the application of transposon technology to hyper-produce biosurfactant for the effective bioremediation of hydrocarbon contaminated environments.
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Affiliation(s)
- R Muneeswari
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kancheepuram District, Kattankulathur 603203, Tamil Nadu, India
| | - S Iyappan
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kancheepuram District, Kattankulathur 603203, Tamil Nadu, India
| | - K V Swathi
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kancheepuram District, Kattankulathur 603203, Tamil Nadu, India
| | - R Vinu
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - K Ramani
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kancheepuram District, Kattankulathur 603203, Tamil Nadu, India.
| | - G Sekaran
- SRM Institute of Science and Technology, Ramapuram 600089, Tamil Nadu, India
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Moran-Garcia N, Lopez-Saucedo C, Becerra A, Meza-Segura M, Hernandez-Cazares F, Guerrero-Baez J, Galindo-Gómez S, Tsutsumi V, Schnoor M, Méndez-Tenorio A, Nataro JP, Estrada-Garcia T. A Novel Adult Murine Model of Typical Enteroaggregative Escherichia coli Infection Reveals Microbiota Dysbiosis, Mucus Secretion, and AAF/II-Mediated Expression and Localization of β-Catenin and Expression of MUC1 in Ileum. Front Cell Infect Microbiol 2022; 12:885191. [PMID: 35706909 PMCID: PMC9190437 DOI: 10.3389/fcimb.2022.885191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Typical enteroaggregative Escherichia coli (tEAEC) is a diarrheagenic E. coli pathotype associated with pediatric and traveler’s diarrhea. Even without diarrhea, EAEC infections in children also lead to increased gut inflammation and growth shortfalls. EAEC strain’s defining phenotype is the aggregative adherence pattern on epithelial cells attributable to the aggregative adherence fimbriae (AAF). EAEC only causes diarrhea in humans; therefore, not much is known of the exact intestinal region of infection and damage or its interactions with intestinal enterocytes in vivo and in situ. This study aimed to develop a new tEAEC mouse model of infection, characterize the microbiota of infected mice, and evaluate in situ the expression of host adherence and surface molecules triggering EAEC infection and the role of the EAEC AAF-II in adherence. Six-week-old C57BL/6 mice, without previous antibiotic treatment, were orally challenged with EAEC 042 strain or EAEC 042 AAF-II mutant (ΔAAF/II) strain, or DAEC-MXR strain (diffusely adherent E. coli clinical isolate), and with saline solution (control group). Paraffin sections of the colon and ileum were stained with H&E and periodic acid-Schiff. ZO-1, β-catenin, MUC1, and bacteria were analyzed by immunofluorescence. EAEC-infected mice, in comparison with DAEC-MXR-infected and control mice, significantly lost weight during the first 3 days. After 7 days post-infection, mucus production was increased in the colon and ileum, ZO-1 localization remained unaltered, and morphological alterations were more pronounced in the ileum since increased expression and apical localization of β-catenin in ileal enterocytes were observed. EAEC-infected mice developed dysbiosis 21 days post-infection. At 4 days post-infection, EAEC strain 042 formed a biofilm on ileal villi and increased the expression and apical localization of β-catenin in ileal enterocytes; these effects were not seen in animals infected with the 042 ΔAAF/II strain. At 3 days post-infection, MUC1 expression on ileal enterocytes was mainly detectable among infected mice and colocalized with 042 strains on the enterocyte surface. We developed a novel mouse model of EAEC infection, which mimics human infection, not an illness, revealing that EAEC 042 exerts its pathogenic effects in the mouse ileum and causes dysbiosis. This model is a unique tool to unveil early molecular mechanisms of EAEC infection in vivo and in situ.
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Affiliation(s)
| | | | - Adriana Becerra
- Department of Molecular Biomedicine, CINVESTAV-IPN, Mexico City, Mexico
| | - Mario Meza-Segura
- Department of Molecular Biomedicine, CINVESTAV-IPN, Mexico City, Mexico
| | | | | | - Silvia Galindo-Gómez
- Department of Infectomics and Molecular Pathogenesis, CINVESTAV-IPN, Mexico City, Mexico
| | - Víctor Tsutsumi
- Department of Infectomics and Molecular Pathogenesis, CINVESTAV-IPN, Mexico City, Mexico
| | - Michael Schnoor
- Department of Molecular Biomedicine, CINVESTAV-IPN, Mexico City, Mexico
| | - Alfonso Méndez-Tenorio
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - James P. Nataro
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Teresa Estrada-Garcia
- Department of Molecular Biomedicine, CINVESTAV-IPN, Mexico City, Mexico
- *Correspondence: Teresa Estrada-Garcia,
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Antimicrobial resistance and genetic background of non-typhoidal Salmonella enterica strains isolated from human infections in São Paulo, Brazil (2000-2019). Braz J Microbiol 2022; 53:1249-1262. [PMID: 35446010 PMCID: PMC9433476 DOI: 10.1007/s42770-022-00748-8] [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: 12/11/2021] [Accepted: 03/30/2022] [Indexed: 11/02/2022] Open
Abstract
Salmonella enterica causes Salmonellosis, an important infection in humans and other animals. The number of multidrug-resistant (MDR) phenotypes associated with Salmonella spp. isolates is increasing worldwide, causing public health concern. Here, we aim to characterize the antimicrobial-resistant phenotype of 789 non-typhoidal S. enterica strains isolated from human infections in the state of São Paulo, Brazil, along 20 years (2000-2019). Among the non-susceptible isolates, 31.55, 14.06, and 13.18% were resistant to aminoglycosides, tetracycline, and β-lactams, respectively. Moreover, 68 and 11 isolates were considered MDR and Extended Spectrum β-Lactamase (ESBL) producers, respectively, whereas one isolate was colistin-resistant. We selected four strains to obtain a draft of the Genome Sequence; one S. Infantis (ST32), one S. Enteritidis (ST11), one S. I 4,[5],12:i:- (ST19), and one S. Typhimurium (ST313). Among them, three presented at least one of the following antimicrobial resistance genes (AMR) linked to mobile DNA: blaTEM-1B, dfrA1, tetA, sul1, floR, aac(6')-laa, and qnrE1. This is the first description of the plasmid-mediated quinolone resistance (PMQR) gene qnrE1 in a clinical isolate of S. I 4,[5],12:i:-. The S. Typhimurium is a colistin-resistant isolate, but did not harbor mcr genes, but it presented mutations within the mgrB, pmrB, and pmrC regions that might be linked to the colistin-resistant phenotype. The virulence pattern of the four isolates resembled the virulence pattern of the highly pathogenic S. Typhimurium UK-1 reference strain in assays involving the in vivo Galleria mellonella model. In conclusion, most isolates studied here are susceptible, but a small percentage present an MDR or ESBL-producer and pathogenic phenotype. Sequence analyses revealed plasmid-encoded AMR genes, such as β-lactam and fluoroquinolone resistance genes, indicating that these characteristics can be potentially disseminated among other bacterial strains.
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Liyanapathiranage P, Jones JB, Potnis N. Mutation of a Single Core Gene, tssM, of Type VI Secretion System of Xanthomonas perforans Influences Virulence, Epiphytic Survival, and Transmission During Pathogenesis on Tomato. PHYTOPATHOLOGY 2022; 112:752-764. [PMID: 34543058 DOI: 10.1094/phyto-02-21-0069-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Xanthomonas perforans is a seedborne hemibiotrophic pathogen that successfully establishes infection in the phyllosphere of tomato. While most studies investigating mechanistic basis of pathogenesis have focused on successful apoplastic growth, factors important during asymptomatic colonization in the early stages of disease development are not well understood. In this study, we show that tssM gene of the type VI secretion system cluster i3* (T6SS-i3*) plays a significant role during initial asymptomatic epiphytic colonization at different stages during the life cycle of the pathogen. Mutation in a core gene, tssM of T6SS-i3*, imparted higher aggressiveness to the pathogen, as indicated by higher overall disease severity, higher in planta growth, and shorter latent infection period compared with the wild-type upon dip inoculation of 4- to 5-week-old tomato plants. Contribution of tssM toward aggressiveness was evident during vertical transmission from seed to seedling, with wild-type showing reduced disease severity as well as lower in planta populations on seedlings compared with the mutant. Presence of functional TssM offered higher epiphytic fitness as well as higher dissemination potential to the pathogen when tested in an experimental setup mimicking transplant house high-humidity conditions. We showed higher osmotolerance being one mechanism by which TssM offers higher epiphytic fitness. Taken together, these data reveal that functional TssM plays a larger role in offering ecological advantage to the pathogen. TssM prolongs the association of hemibiotrophic pathogen with the host, minimizing overall disease severity yet facilitating successful dissemination.
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Affiliation(s)
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
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30
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Pankratov TA, Nikitin PA, Patutina EO. Genome Analysis of Two Lichen Bacteriobionts, Lichenibacterium ramalinae and Lichenibacterium minor: Toxin‒Antitoxin Systems and Secretion Proteins. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722020096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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31
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Liu Z, Zhao Y, Sossah FL, Okorley BA, Amoako DG, Liu P, Sheng H, Li D, Li Y. Characterization, Pathogenicity, Phylogeny, and Comparative Genomic Analysis of Pseudomonas tolaasii Strains Isolated from Various Mushrooms in China. PHYTOPATHOLOGY 2022; 112:521-534. [PMID: 34293910 DOI: 10.1094/phyto-12-20-0550-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Since 2016, devastating bacterial blotch affecting the fruiting bodies of Agaricus bisporus, Cordyceps militaris, Flammulina filiformis, and Pleurotus ostreatus in China has caused severe economic losses. We isolated 102 bacterial strains and characterized them polyphasically. We identified the causal agent as Pseudomonas tolaasii and confirmed the pathogenicity of the strains. A host range test further confirmed the pathogen's ability to infect multiple hosts. This is the first report in China of bacterial blotch in C. militaris caused by P. tolaasii. Whole-genome sequences were generated for three strains: Pt11 (6.48 Mb), Pt51 (6.63 Mb), and Pt53 (6.80 Mb), and pangenome analysis was performed with 13 other publicly accessible P. tolaasii genomes to determine their genetic diversity, virulence, antibiotic resistance, and mobile genetic elements. The pangenome of P. tolaasii is open, and many more gene families are likely to emerge with further genome sequencing. Multilocus sequence analysis using the sequences of four common housekeeping genes (glns, gyrB, rpoB, and rpoD) showed high genetic variability among the P. tolaasii strains, with 115 strains clustered into a monophyletic group. The P. tolaasii strains possess various genes for secretion systems, virulence factors, carbohydrate-active enzymes, toxins, secondary metabolites, and antimicrobial resistance genes that are associated with pathogenesis and adapted to different environments. The myriad of insertion sequences, integrons, prophages, and genome islands encoded in the strains may contribute to genome plasticity, virulence, and antibiotic resistance. These findings advance understanding of the determinants of virulence, which can be targeted for the effective control of bacterial blotch disease.
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Affiliation(s)
- Zhenghui Liu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
- Department of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yitong Zhao
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Frederick L Sossah
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Benjamin A Okorley
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
- Crop Science Department, University of Ghana, Legon, Accra, Ghana
| | - Daniel G Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Peibin Liu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Hongyan Sheng
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Dan Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Ministry of Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Ministry of Science and Technology, Jilin Agricultural University, Changchun 130118, China
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Nagakubo T. Biological Functions and Applications of Virus-Related Bacterial Nanoparticles: A Review. Int J Mol Sci 2022; 23:ijms23052595. [PMID: 35269736 PMCID: PMC8910223 DOI: 10.3390/ijms23052595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/25/2022] Open
Abstract
Accumulating evidence suggests that microorganisms produce various nanoparticles that exhibit a variety of biological functions. The structure of these bacterial nanoparticles ranges from membrane vesicles composed of membrane lipids to multicomponent proteinaceous machines. Of bacterial nanoparticles, bacterial phage tail-like nanoparticles, associated with virus-related genes, are found in bacteria from various environments and have diverse functions. Extracellular contractile injection systems (eCISs), a type of bacterial phage tail-like nanostructure, have diverse biological functions that mediate the interactions between the producer bacteria and target eukaryote. Known gram-negative bacterial eCISs can act as protein translocation systems and inject effector proteins that modulate eukaryotic cellular processes by attaching to the target cells. Further investigation of the functions of eCISs will facilitate the application of these nanomachines as nano-sized syringes in the field of nanomedicine and vaccine development. This review summarises the recent progress in elucidating the structures and biological functions of nanoparticles that resemble the tail components of phages that infect bacteria and discusses directions for future research to improve the clinical applicability of virus-related bacterial nanoparticles.
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Affiliation(s)
- Toshiki Nagakubo
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Japan;
- Microbiology Research Centre for Sustainability (MiCS), University of Tsukuba, Tsukuba 305-8577, Japan
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Wang J, Pang H, Yin L, Zeng F, Wang N, Hoare R, Monaghan SJ, Li W, Jian J. A Comprehensive Analysis of the Lysine Acetylome in the Aquatic Animals Pathogenic Bacterium Vibrio mimicus. Front Microbiol 2022; 13:816968. [PMID: 35250932 PMCID: PMC8891801 DOI: 10.3389/fmicb.2022.816968] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Protein lysine acetylation is an evolutionarily conserved post-translational modification (PTM), which is dynamic and reversible, playing a crucial regulatory role in almost every aspect of metabolism, of both eukaryotes and prokaryotes. Several global lysine acetylome studies have been carried out in various bacteria, but thus far, there have been no reports of lysine acetylation for the commercially important aquatic animal pathogen Vibrio mimicus. In the present study, we used anti-Ac-K antibody beads to highly sensitive immune-affinity purification and combined high-resolution LC-MS/MS to perform the first global lysine acetylome analysis in V. mimicus, leading to the identification of 1,097 lysine-acetylated sites on 582 proteins, and more than half (58.4%) of the acetylated proteins had only one site. The analysis of acetylated modified peptide motifs revealed six significantly enriched motifs, namely, KacL, KacR, L(-2) KacL, LKacK, L(-7) EKac, and IEKac. In addition, bioinformatic assessments state clearly that acetylated proteins have a hand in many important biological processes in V. mimicus, such as purine metabolism, ribosome, pyruvate metabolism, glycolysis/gluconeogenesis, the TCA cycle, and so on. Moreover, 13 acetylated proteins were related to the virulence of V. mimicus. To sum up, this is a comprehensive analysis whole situation protein lysine acetylome in V. mimicus and provides an important foundation for in-depth study of the biological function of lysine acetylation in V. mimicus.
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Affiliation(s)
- Junlin Wang
- Fisheries College of Guangdong Ocean University and Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals and Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes, Zhanjiang, China
| | - Huanying Pang
- Fisheries College of Guangdong Ocean University and Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals and Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes, Zhanjiang, China
- *Correspondence: Huanying Pang,
| | - Linlin Yin
- Fisheries College of Guangdong Ocean University and Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals and Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes, Zhanjiang, China
| | - Fuyuan Zeng
- Fisheries College of Guangdong Ocean University and Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals and Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes, Zhanjiang, China
| | - Na Wang
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Rowena Hoare
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Sean J. Monaghan
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Wanxin Li
- School of Public Health, Fujian Medical University, Fuzhou, China
- Wanxin Li, ,
| | - Jichang Jian
- Fisheries College of Guangdong Ocean University and Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals and Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes, Zhanjiang, China
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Ragab W, Kawato S, Nozaki R, Kondo H, Hirono I. Comparative genome analyses of five Vibrio penaeicida strains provide insights into their virulence-related factors. Microb Genom 2022; 8. [PMID: 35171089 PMCID: PMC8942037 DOI: 10.1099/mgen.0.000766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Vibrio penaeicida (family Vibrionaceae) is an important bacterial pathogen that affects Japanese shrimp aquaculture. Only two whole-genome sequences of V. penaeicida are publicly available, which has hampered our understanding of the pathogenesis of shrimp vibriosis caused by this bacterium. To gain insight into the genetic features, evolution and pathogenicity of V. penaeicida, we sequenced five V. penaeicida strains (IFO 15640T, IFO 15641, IFO 15642, TUMSAT-OK1 and TUMSAT-OK2) and performed comparative genomic analyses. Virulence factors and mobile genetic elements were detected. Furthermore, average nucleotide identities (ANIs), clusters of orthologous groups and phylogenetic relationships were evaluated. The V. penaeicida genome consists of two circular chromosomes. Chromosome I sizes ranged from 4.1 to 4.3 Mb, the GC content ranged from 43.9 to 44.1 %, and the number of predicted protein-coding sequences (CDSs) ranged from 3620 to 3782. Chromosome II sizes ranged from 2.2 to 2.4 Mb, the GC content ranged from 43.5 to 43.8 %, and the number of predicted CDSs ranged from 1992 to 2273. All strains except IFO 15641 harboured one plasmid, having sizes that ranged from 150 to 285 kb. All five genomes had typical virulence factors, including adherence, anti-phagocytosis, flagella-related proteins and toxins (repeats-in-toxin and thermolabile haemolysin). The genomes also contained factors responsible for iron uptake and the type II, IV and VI secretion systems. The genome of strain TUMSAT-OK2 tended to encode more prophage regions than the other strains, whereas the genome of strain IFO 15640T had the highest number of regions encoding genomic islands. For comparative genome analysis, we used V. penaeicida (strain CAIM 285T) as a reference strain. ANIs between strain CAIM 285T and the five V. penaeicida strains were >95 %, which indicated that these strains belong to the same species. Orthology cluster analysis showed that strains TUMSAT-OK1 and TUMSAT-OK2 had the greatest number of shared gene clusters, followed by strains CAIM 285T and IFO 15640T. These strains were also the most closely related to each other in a phylogenetic analysis. This study presents the first comparative genome analysis of V. penaeicida and these results will be useful for understanding the pathogenesis of this bacterium.
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Affiliation(s)
- Wafaa Ragab
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Satoshi Kawato
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Reiko Nozaki
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
- *Correspondence: Ikuo Hirono,
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Amaya FA, Blondel CJ, Barros-Infante MF, Rivera D, Moreno-Switt AI, Santiviago CA, Pezoa D. Identification of Type VI Secretion Systems Effector Proteins That Contribute to Interbacterial Competition in Salmonella Dublin. Front Microbiol 2022; 13:811932. [PMID: 35222335 PMCID: PMC8867033 DOI: 10.3389/fmicb.2022.811932] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
The Type VI Secretion System (T6SS) is a multiprotein device that has emerged as an important fitness and virulence factor for many Gram-negative bacteria through the injection of effector proteins into prokaryotic or eukaryotic cells via a contractile mechanism. While some effector proteins specifically target bacterial or eukaryotic cells, others can target both types of cells (trans-kingdom effectors). In Salmonella, five T6SS gene clusters have been identified within pathogenicity islands SPI-6, SPI-19, SPI-20, SPI-21, and SPI-22, which are differentially distributed among serotypes. Salmonella enterica serotype Dublin (S. Dublin) is a cattle-adapted pathogen that harbors both T6SSSPI-6 and T6SSSPI-19. Interestingly, while both systems have been linked to virulence and host colonization in S. Dublin, an antibacterial activity has not been detected for T6SSSPI-6 in this serotype. In addition, there is limited information regarding the repertoire of effector proteins encoded within T6SSSPI-6 and T6SSSPI-19 gene clusters in S. Dublin. In the present study, we demonstrate that T6SSSPI-6 and T6SSSPI-19 of S. Dublin CT_02021853 contribute to interbacterial competition. Bioinformatic and comparative genomic analyses allowed us to identify genes encoding three candidate antibacterial effectors located within SPI-6 and two candidate effectors located within SPI-19. Each antibacterial effector gene is located upstream of a gene encoding a hypothetic immunity protein, thus conforming an effector/immunity (E/I) module. Of note, the genes encoding these effectors and immunity proteins are widely distributed in Salmonella genomes, suggesting a relevant role in interbacterial competition and virulence. Finally, we demonstrate that E/I modules SED_RS01930/SED_RS01935 (encoded in SPI-6), SED_RS06235/SED_RS06230, and SED_RS06335/SED_RS06340 (both encoded in SPI-19) contribute to interbacterial competition in S. Dublin CT_02021853.
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Affiliation(s)
- Fernando A. Amaya
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Carlos J. Blondel
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | | | - Dácil Rivera
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Andrea I. Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Initiative on Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Carlos A. Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
- *Correspondence: Carlos A. Santiviago, David Pezoa,
| | - David Pezoa
- Escuela de Medicina Veterinaria, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- *Correspondence: Carlos A. Santiviago, David Pezoa,
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Castelli M, Lanzoni O, Giovannini M, Lebedeva N, Gammuto L, Sassera D, Melekhin M, Potekhin A, Fokin S, Petroni G. 'Candidatus Gromoviella agglomerans', a novel intracellular Holosporaceae parasite of the ciliate Paramecium showing marked genome reduction. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:34-49. [PMID: 34766443 DOI: 10.1111/1758-2229.13021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Holosporales are an alphaproteobacterial lineage encompassing bacteria obligatorily associated with multiple diverse eukaryotes. For most representatives, little is known on the interactions with their hosts. In this study, we characterized a novel Holosporales symbiont of the ciliate Paramecium polycaryum. This bacterium inhabits the host cytoplasm, frequently forming quite large aggregates. Possibly due to such aggregates, host cells sometimes displayed lethal division defects. The symbiont was also able to experimentally stably infect another Paramecium polycaryum strain. The bacterium is phylogenetically related with symbionts of other ciliates and diplonemids, forming a putatively fast-evolving clade within the family Holosporaceae. Similarly to many close relatives, it presents a very small genome (<600 kbp), and, accordingly, a limited predicted metabolism, implying a heavy dependence on Paramecium, thanks also to some specialized membrane transporters. Characterized features, including the presence of specific secretion systems, are overall suggestive of a mild parasitic effect on the host. From an evolutionary perspective, a potential ancestral trend towards pronounced genome reduction and possibly linked to parasitism could be inferred, at least among fast-evolving Holosporaceae, with some lineage-specific traits. Interestingly, similar convergent features could be observed in other host-associated lineages, in particular Rickettsiales among Alphaproteobacteria.
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Affiliation(s)
- Michele Castelli
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
| | - Olivia Lanzoni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | | | - Natalia Lebedeva
- Centre of Core Facilities "Culture Collections of Microorganisms", Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Davide Sassera
- Dipartimento di Biologia e Biotecnologie, Università degli studi di Pavia, Pavia, Italy
| | - Maksim Melekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
- Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Sergei Fokin
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
- Department of Invertebrate Zoology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Giulio Petroni
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
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Genome analysis of Pseudomonas sp. 14A reveals metabolic capabilities to support epiphytic behavior. World J Microbiol Biotechnol 2022; 38:49. [DOI: 10.1007/s11274-022-03238-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/19/2022] [Indexed: 11/26/2022]
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Rodríguez-Santiago J, Rodríguez-Medina N, Tamayo-Legorreta EM, Silva-Sánchez J, Téllez-Sosa J, Duran-Bedolla J, Aguilar-Vera A, Lecona-Valera AN, Garza-Ramos U, Alpuche-Aranda C. Molecular and Genomic Insights of mcr-1-Producing Escherichia coli Isolates from Piglets. Antibiotics (Basel) 2022; 11:antibiotics11020157. [PMID: 35203760 PMCID: PMC8868104 DOI: 10.3390/antibiotics11020157] [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: 12/18/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
The use of colistin in food-producing animals favors the emergence and spread of colistin-resistant strains. Here, we investigated the occurrence and molecular mechanisms of colistin resistance among E. coli isolates from a Mexican piglet farm. A collection of 175 cephalosporin-resistant colonies from swine fecal samples were recovered. The colistin resistance phenotype was identified by rapid polymyxin test and the mcr-type genes were screened by PCR. We assessed the colistin-resistant strains by antimicrobial susceptibility test, pulse-field gel electrophoresis, plasmid profile, and mating experiments. Whole-Genome Sequencing data was used to explore the resistome, virulome, and mobilome of colistin-resistant strains. A total of four colistin-resistant E. coli were identified from the cefotaxime-resistant colonies. All harbored the plasmid-borne mcr-1 gene, which was located on conjugative 170-kb IncHI-2 plasmid co-carrying ESBLs genes. Thus, high antimicrobial resistance rates were observed for several antibiotic families. In the RC2-007 strain, the mcr-1 gene was located as part of a prophage carried on non-conjugative 100-kb-plasmid, which upon being transformed into K. variicola strain increased the polymyxin resistance 2-fold. The genomic analysis showed a broad resistome and virulome. Our findings suggest that colistin resistance followed independent acquisition pathways as clonal and non-genetically related mcr-1-harboring strains were identified. These E. coli isolates represent a reservoir of antibiotic resistance and virulence genes in animals for human consumption which could be potentially propagated into other interfaces.
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Affiliation(s)
- Jonathan Rodríguez-Santiago
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Nadia Rodríguez-Medina
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Elsa María Tamayo-Legorreta
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Jesús Silva-Sánchez
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Juan Téllez-Sosa
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Josefina Duran-Bedolla
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Alejandro Aguilar-Vera
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62100, Morelos, Mexico;
| | - Alba Neri Lecona-Valera
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Ulises Garza-Ramos
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
- Correspondence: (U.G.-R.); (C.A.-A.)
| | - Celia Alpuche-Aranda
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
- Correspondence: (U.G.-R.); (C.A.-A.)
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Li J, Hu WW, Qu GX, Li XR, Xiang Y, Jiang P, Luo JQ, He WH, Jin YJ, Shi Q. Characterization of a Type VI Secretion System vgrG2 Gene in the Pathogenicity of Burkholderia thailandensis BPM. Front Microbiol 2022; 12:811343. [PMID: 35069514 PMCID: PMC8767068 DOI: 10.3389/fmicb.2021.811343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/13/2021] [Indexed: 11/17/2022] Open
Abstract
Burkholderia thailandensis is a clinically underestimated conditional pathogen in the genus Burkholderia, the pathogenicity of the infection caused by B. thailandensis remains poorly understood. According to previous studies, Type-VI secretion system (T6SS) is a protein secreting device widely existing in Gram-negative bacilli. Valine-glycine repeat protein G (VgrG) is not only an important component of T6SS, but also a virulence factor of many Gram-negative bacilli. In one of our previous studies, a unique T6SS vgrG gene (vgrG2 gene) was present in a virulent B. thailandensis strain BPM (BPM), but not in the relatively avirulent B. thailandensis strain E264 (E264). Meanwhile, transcriptome analysis of BPM and E264 showed that the vgrG2 gene was strongly expressed in BPM, but not in E264. Therefore, we identified the function of the vgrG2 gene by constructing the mutant and complemented strains in this study. In vitro, the vgrG2 gene was observed to be involved in the interactions with host cells. The animal model experiment showed that the deletion of vgrG2 gene significantly led to the decrease in the lethality of BPM and impaired its ability to trigger host immune response. In conclusion, our study provides a new perspective for studying the pathogenicity of B. thailandensis and lays the foundation for discovering the potential T6SS effectors.
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Affiliation(s)
- Jin Li
- M.O.E. Key Laboratory of Laboratory Medicine Diagnostics, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Wei-Wei Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guo-Xin Qu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Xiao-Rong Li
- M.O.E. Key Laboratory of Laboratory Medicine Diagnostics, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Yi Xiang
- M.O.E. Key Laboratory of Laboratory Medicine Diagnostics, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Peng Jiang
- M.O.E. Key Laboratory of Laboratory Medicine Diagnostics, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Jiang-Qiao Luo
- M.O.E. Key Laboratory of Laboratory Medicine Diagnostics, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Wen-Huan He
- M.O.E. Key Laboratory of Laboratory Medicine Diagnostics, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Yu-Jia Jin
- M.O.E. Key Laboratory of Laboratory Medicine Diagnostics, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Qiong Shi
- M.O.E. Key Laboratory of Laboratory Medicine Diagnostics, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
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Comparative Genomics of Typical and Atypical Aeromonas salmonicida Complete Genomes Revealed New Insights into Pathogenesis Evolution. Microorganisms 2022; 10:microorganisms10010189. [PMID: 35056638 PMCID: PMC8780938 DOI: 10.3390/microorganisms10010189] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/05/2022] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
Aeromonas salmonicida is a global distributed Gram-negative teleost pathogen, affecting mainly salmonids in fresh and marine environments. A. salmonicida strains are classified as typical or atypical depending on their origin of isolation and phenotype. Five subspecies have been described, where A. salmonicida subsp. salmonicida is the only typical subspecies, and the subsp. achromogenes, masoucida, smithia, and pectinolytica are considered atypical. Genomic differences between A. salmonicida subsp. salmonicida isolates and their relationship with the current classification have not been explored. Here, we sequenced and compared the complete closed genomes of four virulent strains to elucidate their molecular diversity and pathogenic evolution using the more accurate genomic information so far. Phenotypes, biochemical, and enzymatic profiles were determined. PacBio and MiSeq sequencing platforms were utilized for genome sequencing. Comparative genomics showed that atypical strains belong to the subsp. salmonicida, with 99.55% ± 0.25% identity with each other, and are closely related to typical strains. The typical strain A. salmonicida J223 is closely related to typical strains, with 99.17% identity with the A. salmonicida A449. Genomic differences between atypical and typical strains are strictly related to insertion sequences (ISs) activity. The absence and presence of genes encoding for virulence factors, transcriptional regulators, and non-coding RNAs are the most significant differences between typical and atypical strains that affect their phenotypes. Plasmidome plays an important role in A. salmonicida virulence and genome plasticity. Here, we determined that typical strains harbor a larger number of plasmids and virulence-related genes that contribute to its acute virulence. In contrast, atypical strains harbor a single, large plasmid and a smaller number of virulence genes, reflected by their less acute virulence and chronic infection. The relationship between phenotype and A. salmonicida subspecies’ taxonomy is not evident. Comparative genomic analysis based on completed genomes revealed that the subspecies classification is more of a reflection of the ecological niche occupied by bacteria than their divergences at the genomic level except for their accessory genome.
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Sørensen PE, Baig S, Stegger M, Ingmer H, Garmyn A, Butaye P. Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli. Front Microbiol 2021; 12:782757. [PMID: 34966369 PMCID: PMC8711792 DOI: 10.3389/fmicb.2021.782757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/23/2021] [Indexed: 01/19/2023] Open
Abstract
Avian pathogenic Escherichia coli (APEC) is one of the most important bacterial pathogens affecting poultry worldwide. The emergence of multidrug-resistant pathogens has renewed the interest in the therapeutic use of bacteriophages (phages). However, a major concern for the successful implementation of phage therapy is the emergence of phage-resistant mutants. The understanding of the phage-host interactions, as well as underlying mechanisms of resistance, have shown to be essential for the development of a successful phage therapy. Here, we demonstrate that the strictly lytic Escherichia phage vB_EcoM-P10 rapidly selected for resistance in the APEC ST95 O1 strain AM621. Whole-genome sequence analysis of 109 spontaneous phage-resistant mutant strains revealed 41 mutants with single-nucleotide polymorphisms (SNPs) in their core genome. In 32 of these, a single SNP was detected while two SNPs were identified in a total of nine strains. In total, 34 unique SNPs were detected. In 42 strains, including 18 strains with SNP(s), gene losses spanning 17 different genes were detected. Affected by genetic changes were genes known to be involved in phage resistance (outer membrane protein A, lipopolysaccharide-, O- antigen-, or cell wall-related genes) as well as genes not previously linked to phage resistance, including two hypothetical genes. In several strains, we did not detect any genetic changes. Infecting phages were not able to overcome the phage resistance in host strains. However, interestingly the initial infection was shown to have a great fitness cost for several mutant strains, with up to ∼65% decrease in overall growth. In conclusion, this study provides valuable insights into the phage-host interaction and phage resistance in APEC. Although acquired resistance to phages is frequently observed in pathogenic E. coli, it may be associated with loss of fitness, which could be exploited in phage therapy.
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Affiliation(s)
- Patricia E. Sørensen
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Sharmin Baig
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - An Garmyn
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
| | - Patrick Butaye
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
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Malone M, Radzieta M, Peters TJ, Dickson HG, Schwarzer S, Jensen SO, Lavery LA. Host-microbe metatranscriptome reveals differences between acute and chronic infections in diabetes-related foot ulcers. APMIS 2021; 130:751-762. [PMID: 34888950 DOI: 10.1111/apm.13200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/07/2021] [Indexed: 12/13/2022]
Abstract
Virtually all diabetes-related foot ulcers (DRFUs) will become colonized by microorganisms that may increase the risk of developing an infection. The reasons why some ulcerations develop acute clinical infections (AI-DRFUs) whilst others develop chronic infection (CI-DRFUs) and the preceding host-microbe interactions in vivo remain largely unknown. Establishing that acute and chronic infections are distinct processes requires demonstrating that these are two different strategies employed by microbes when interacting with a host. In this study, dual-RNA seq was employed to differentiate the host-microbe metatranscriptome between DRFUs that had localized chronic infection or acute clinical infection. Comparison of the host metatranscriptome in AI-DRFUs relative to CI-DRFUs identified upregulated differentially expressed genes (DEGs) that functioned as regulators of vascular lymphatic inflammatory responses, T-cell signalling and olfactory receptors. Conversely, CI-DRFUs upregulated DEGs responsible for cellular homeostasis. Gene set enrichment analysis using Hallmark annotations revealed enrichment of immune and inflammatory profiles in CI-DRFUs relative to AI-DRFUs. Analysis of the microbial metatranscriptome identified the DEGs being enriched within AI-DRFUs relative to CI-DRFUs included several toxins, two-component systems, bacterial motility, secretion systems and genes encoding for energy metabolism. Functions relevant to DRFU pathology were further explored, including biofilm and bacterial pathogenesis. This identified that the expression of biofilm-associated genes was higher within CI-DRFUs compared to that of AI-DRFUs, with mucR being the most highly expressed gene. Collectively, these data provide insights into the host-microbe function in two clinically-distinct infective phenotypes that affect DRFUs. The data reveal that bacteria in acutely infected DRFUs prioritize motility over biofilm and demonstrate greater pathogenicity and mechanisms, which likely subvert host cellular and immune pathways to establish infection. Upregulation of genes for key vascular inflammatory mediators in acutely infected ulcers may contribute, in part, to the clinical picture of a red, hot, swollen foot, which differentiates an acutely infected ulcer from that of a chronic infection.
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Affiliation(s)
- Matthew Malone
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Sydney, NSW, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Michael Radzieta
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Sydney, NSW, Australia.,Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Timothy J Peters
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,University of New South Wales, Sydney, NSW, Australia
| | - Hugh G Dickson
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Sydney, NSW, Australia.,South Western Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Saskia Schwarzer
- South West Sydney Limb Preservation and Wound Research, South Western Sydney LHD, Sydney, NSW, Australia
| | - Slade O Jensen
- Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Lawrence A Lavery
- Department of Plastic Surgery, University of Texas Southwestern Medical Centre, Dallas, TX, USA
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The two-component system FleS/FleR represses H1-T6SS via c-di-GMP signaling in Pseudomonas aeruginosa. Appl Environ Microbiol 2021; 88:e0165521. [PMID: 34731046 DOI: 10.1128/aem.01655-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The type VI secretion system (T6SS) is an important translocation apparatus that is widely employed by Gram-negative bacteria to deliver toxic effectors into eukaryotic and prokaryotic target cells, causing host damage and providing competitive advantages in polymicrobial environments. The genome of P. aeruginosa harbors three T6SS clusters (H1-T6SS, H2-T6SS, H3-T6SS). Activities of these systems are tightly regulated by a complicated signaling network which remains largely elusive. In this study, we focused on a previously characterized two-component system FleS/FleR and performed comparative transcriptome analysis between the PAO1 wild-type strain and its isogenic ΔfleR mutant, which revealed the important role of FleS/FleR in regulating multiple physiological pathways including T6SS. Gene expression and bacterial killing assays showed that the expression and activity of H1-T6SS are repressed in the wild-type strain owing to the high intracellular c-di-GMP content. Further explorations demonstrated that c-di-GMP relies on the transcription factor FleQ to repress H1-T6SS and its synthesis is controlled by a global regulator AmrZ which is induced by the active FleS/FleR. Interestingly, FleS/FleR regulates H1-T6SS in PAO1 is independent of RetS which is known to regulate H1-T6SS by controlling the central post-transcriptional factor RsmA. Together, our results identified a novel regulator of H1-T6SS and provided detailed mechanisms of this signaling pathway in PAO1. IMPORTANCE P. aeruginosa is an opportunistic human pathogen distributed widely in the environment. The genome of this pathogen contains three T6SS clusters which contribute significantly to its virulence. Understanding the complex regulatory network that controls the activity of T6SS is essential for the development of effective therapeutic treatments for P. aeruginosa infections. In this study, transcriptome analysis led to the identification of a novel regulator FleS/FleR which inversely regulates H1-T6SS and H2-T6SS in P. aeruginosa PAO1. We further revealed a detailed FleS/FleR-mediated regulatory pathway of H1-T6SS in PAO1 which involves two additional transcriptional regulators AmrZ and FleQ and the second messenger c-di-GMP, providing important implications to develop novel anti-infective strategies and antimicrobial drugs.
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Abstract
The gut microbiota plays a crucial role in susceptibility to enteric pathogens, including Citrobacter rodentium, a model extracellular mouse pathogen that colonizes the colonic mucosa. C. rodentium infection outcomes vary between mouse strains, with C57BL/6 and C3H/HeN mice clearing and succumbing to the infection, respectively. Kanamycin (Kan) treatment at the peak of C57BL/6 mouse infection with Kan-resistant C. rodentium resulted in relocalization of the pathogen from the colonic mucosa and cecum to solely the cecal luminal contents; cessation of the Kan treatment resulted in rapid clearance of the pathogen. We now show that in C3H/HeN mice, following Kan-induced displacement of C. rodentium to the cecum, the pathogen stably colonizes the cecal lumens of 65% of the mice in the absence of continued antibiotic treatment, a phenomenon that we term antibiotic-induced bacterial commensalization (AIBC). AIBC C. rodentium was well tolerated by the host, which showed few signs of inflammation; passaged AIBC C. rodentium robustly infected naive C3H/HeN mice, suggesting that the AIBC state is transient and did not select for genetically avirulent C. rodentium mutants. Following withdrawal of antibiotic treatment, 35% of C3H/HeN mice were able to prevent C. rodentium commensalization in the gut lumen. These mice presented a bloom of a commensal species, Citrobacter amalonaticus, which inhibited the growth of C. rodentiumin vitro in a contact-dependent manner and the luminal growth of AIBC C. rodentiumin vivo. Overall, our data suggest that commensal species can confer colonization resistance to closely related pathogenic species.
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Leclercq SO, Branger M, Smith DGE, Germon P. Lipopolysaccharide core type diversity in the Escherichia coli species in association with phylogeny, virulence gene repertoire and distribution of type VI secretion systems. Microb Genom 2021; 7. [PMID: 34586053 PMCID: PMC8715443 DOI: 10.1099/mgen.0.000652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli is a very versatile species for which diversity has been explored from various perspectives highlighting, for example, phylogenetic groupings and pathovars, as well as a wide range of O serotypes. The highly variable O-antigen, the most external part of the lipopolysaccharide (LPS) component of the outer membrane of E. coli, is linked to the innermost lipid A through the core region of LPS of which five different structures, denominated K-12, R1, R2, R3 and R4, have been characterized so far. The aim of the present study was to analyse the prevalence of these LPS core types in the E. coli species and explore their distribution in the different E. coli phylogenetic groups and in relationship with the virulence gene repertoire. Results indicated an uneven distribution of core types between the different phylogroups, with phylogroup A strains being the most diverse in terms of LPS core types, while phylogroups B1, D and E strains were dominated by the R3 type, and phylogroups B2 and C strains were dominated by the R1 type. Strains carrying the LEE virulence operon were mostly of the R3 type whatever the phylogroup while, within phylogroup B2, strains carrying a K-12 core all belonged to the complex STc131, one of the major clones of extraintestinal pathogenic E. coli (ExPEC) strains. The origin of this uneven distribution is discussed but remains to be fully explained, as well as the consequences of carrying a specific core type on the wider aspects of bacterial phenotype.
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Affiliation(s)
| | - Maxime Branger
- UMR ISP, INRAE, Université François Rabelais de Tours, F-37380 Nouzilly, France
| | - David G E Smith
- Institute for Biological Chemistry, Biophysics and Bioengineering (IB3), Riccarton Campus, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Pierre Germon
- UMR ISP, INRAE, Université François Rabelais de Tours, F-37380 Nouzilly, France
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Sibinelli-Sousa S, de Araújo-Silva AL, Hespanhol JT, Bayer-Santos E. Revisiting the steps of Salmonella gut infection with a focus on antagonistic interbacterial interactions. FEBS J 2021; 289:4192-4211. [PMID: 34546626 DOI: 10.1111/febs.16211] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/12/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022]
Abstract
A commensal microbial community is established in the mammalian gut during its development, and these organisms protect the host against pathogenic invaders. The hallmark of noninvasive Salmonella gut infection is the induction of inflammation via effector proteins secreted by the type III secretion system, which modulate host responses to create a new niche in which the pathogen can overcome the colonization resistance imposed by the microbiota. Several studies have shown that endogenous microbes are important to control Salmonella infection by competing for resources. However, there is limited information about antimicrobial mechanisms used by commensals and pathogens during these in vivo disputes for niche control. This review aims to revisit the steps that Salmonella needs to overcome during gut colonization-before and after the induction of inflammation-to achieve an effective infection. We focus on a series of reported and hypothetical antagonistic interbacterial interactions in which both contact-independent and contact-dependent mechanisms might define the outcome of the infection.
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Affiliation(s)
| | | | - Julia Takuno Hespanhol
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil
| | - Ethel Bayer-Santos
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil
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Bao Y, Verdegaal AA, Anderson BW, Barry NA, He J, Gao X, Goodman AL. A Common Pathway for Activation of Host-Targeting and Bacteria-Targeting Toxins in Human Intestinal Bacteria. mBio 2021; 12:e0065621. [PMID: 34465018 PMCID: PMC8406203 DOI: 10.1128/mbio.00656-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 08/02/2021] [Indexed: 11/26/2022] Open
Abstract
Human gut microbes exhibit a spectrum of cooperative and antagonistic interactions with their host and also with other microbes. The major Bacteroides host-targeting virulence factor, Bacteroides fragilis toxin (BFT), is produced as an inactive protoxin by enterotoxigenic B. fragilis strains. BFT is processed by the conserved bacterial cysteine protease fragipain (Fpn), which is also encoded in B. fragilis strains that lack BFT. In this report, we identify a secreted antibacterial protein (fragipain-activated bacteriocin 1 [Fab1]) and its cognate immunity protein (resistance to fragipain-activated bacteriocin 1 [RFab1]) in enterotoxigenic and nontoxigenic strains of B. fragilis. Although BFT and Fab1 share no sequence identity, Fpn also activates the Fab1 protoxin, resulting in its secretion and antibacterial activity. These findings highlight commonalities between host- and bacterium-targeting toxins in intestinal bacteria and suggest that antibacterial antagonism may promote the conservation of pathways that activate host-targeting virulence factors. IMPORTANCE The human intestine harbors a highly complex microbial community; interpersonal variation in this community can impact pathogen susceptibility, metabolism, and other aspects of health. Here, we identified and characterized a commensal-targeting antibacterial protein encoded in the gut microbiome. Notably, a shared pathway activates this antibacterial toxin and a host-targeting toxin. These findings highlight unexpected commonalities between host- and bacterium-targeting toxins in intestinal bacteria.
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Affiliation(s)
- Yiqiao Bao
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, New Haven, Connecticut, USA
| | - Andrew A. Verdegaal
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, New Haven, Connecticut, USA
| | - Brent W. Anderson
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, New Haven, Connecticut, USA
| | - Natasha A. Barry
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, New Haven, Connecticut, USA
| | - Jing He
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Andrew L. Goodman
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, New Haven, Connecticut, USA
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Inhibiting Type VI Secretion System Activity with a Biomimetic Peptide Designed To Target the Baseplate Wedge Complex. mBio 2021; 12:e0134821. [PMID: 34372705 PMCID: PMC8406304 DOI: 10.1128/mbio.01348-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Human health is threatened by bacterial infections that are increasingly resistant to multiple drugs. A recently emerged strategy consists of disarming pathogenic bacteria by targeting and blocking their virulence factors. The type VI secretion system (T6SS) is a widespread secretion nanomachine encoded and employed by pathogenic strains to establish their virulence process during host invasion. Given the conservation of T6SS in several human bacterial pathogens, the discovery of an effective broad-spectrum T6SS virulence blocker represents an attractive target for development of antivirulence therapies. Here, we identified and validated a protein-protein interaction interface, TssK-TssG, as a key factor in the assembly of the T6SS baseplate (BP) complex in the pathogen enteroaggregative Escherichia coli (EAEC). In silico and biochemical studies revealed that the determinants of the interface are broadly conserved among pathogenic species, suggesting a role for this interface as a target for T6SS inhibition. Based on the high-resolution structure of the TssKFGE wedge complex, we rationally designed a biomimetic cyclic peptide (BCP) that blocks the assembly of the EAEC BP complex and inhibits the function of T6SS in bacterial cultures. Our BCP is the first compound completely designed from prior structural knowledge with anti-T6SS activity that can be used as a model to target human pathogens.
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Armand-Lefèvre L, Rondinaud E, Desvillechabrol D, Mullaert J, Clermont O, Petitjean M, Ruppe E, Cokelaer T, Bouchier C, Tenaillon O, Ma L, Nooroya Y, Matheron S, The Voyag-R Study Group, Andremont A, Denamur E, Kennedy SP. Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad. Microb Genom 2021; 7. [PMID: 34279212 PMCID: PMC8477403 DOI: 10.1099/mgen.0.000576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Travel to tropical regions is associated with high risk of acquiring extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) that are typically cleared in less than 3 months following return. The conditions leading to persistent carriage that exceeds 3 months in some travellers require investigation. Whole-genome sequencing (Illumina MiSeq) was performed on the 82 ESBL-E isolates detected upon return and 1, 2, 3, 6 and 12 months later from the stools of 11 long-term (>3 months) ESBL-E carriers following travel abroad. One to five different ESBL Escherichia coli strains were detected per traveller upon return, and this diminished to one after 3 months. Long-term carriage was due to the presence of the same ESBL E. coli strain, for more than 3 months, in 9 out of 11 travellers, belonging to epidemic sequence type complexes (STc 10, 14, 38, 69, 131 and 648). The mean carriage duration of strains belonging to phylogroups B2/D/F, associated with extra-intestinal virulence, was higher than that for commensal-associated A/B1/E phylogroups (3.5 vs 0.5 months, P=0.021). Genes encoding iron capture systems (fyuA, irp), toxins (senB, sat), adhesins (flu, daaF, afa/nfaE, pap, ecpA) and colicin (cjrA) were more often present in persistent strains than in transient ones. Single-nucleotide polymorphism (SNP) analysis in persistent strains showed a maximum divergence of eight SNPs over 12 months without signs of adaptation. Genomic plasticity was observed during the follow-up with the loss or gain of mobile genetic elements such as plasmids, integrons and/or transposons that may contain resistance genes at different points in the follow-up. Long-term colonization of ESBL-E following travel is primarily due to the acquisition of E. coli strains belonging to epidemic clones and harbouring ‘virulence genes’, allowing good adaptation to the intestinal microbiota.
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Affiliation(s)
- Laurence Armand-Lefèvre
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France.,Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Emilie Rondinaud
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France.,Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Dimitri Desvillechabrol
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F-75015 Paris, France
| | - Jimmy Mullaert
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Olivier Clermont
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Marie Petitjean
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Etienne Ruppe
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France.,Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Thomas Cokelaer
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F-75015 Paris, France.,Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, F-75015 Paris, France
| | - Christiane Bouchier
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F-75015 Paris, France
| | | | - Laurence Ma
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F-75015 Paris, France
| | - Yasmine Nooroya
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Sophie Matheron
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France.,Service de Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France
| | | | - Antoine Andremont
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France.,Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Erick Denamur
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France.,Laboratoire de Génétique Moléculaire, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France
| | - Sean P Kennedy
- Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, F-75015 Paris, France
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Distribution of type VI secretion system (T6SS) in clinical Klebsiella pneumoniae strains from a Chinese hospital and its potential relationship with virulence and drug resistance. Microb Pathog 2021; 162:105085. [PMID: 34252554 DOI: 10.1016/j.micpath.2021.105085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 11/23/2022]
Abstract
OBJECTIVES The type VI secretion system (T6SS) in Klebsiella pneumoniae strains isolated from the bloodstream, intestinal, the pyogenic liver abscess has been reported. Here we aimed to characterize T6SS in 248 Klebsiella pneumoniae isolates with all kinds of specimens from a Chinese hospital and to investigate the potential association of T6SS with virulence and drug resistance. METHODS T6SS genes, capsular serotyping genes, drug resistance genes, and virulence genes were identified by polymerase chain reaction (PCR). Antibiotic susceptibilities were examined by the disk diffusion method. To assess biofilm formation of these clinical Klebsiella pneumoniae isolates, 96-well microtiter plate assays were performed. MLST was used to analyze the genotypes of these Klebsiella pneumoniae isolates. RESULTS The frequency of T6SS genes among the clinical Klebsiella pneumoniae isolates was 72.2%. The T6SS-positive isolates displayed higher resistance to piperacillin-tazobactam, ciprofloxacin, levofloxacin, meropenem than the T6SS-negative isolates (P < 0.05). The T6SS-positive isolates formed significantly more biofilm mass than the T6SS-negative isolates (mean ± standard deviation [SD], 0.3 ± 0.09 vs.0.16 ± 0.06; P < 0.01). Compared to the T6SS-negative isolates, the T6SS-positive isolates had a higher frequency of virulence genes (rmpA, fimH, entB, kfu, ybtS) and the pLVPK-like plasmid (P < 0.05). CONCLUSION In conclusion, the prevalence of the type VI secretion system is high in clinical Klebsiella pneumoniae isolates in a Chinese teaching hospital. T6SS-positive strains show higher biofilm-forming activity with high drug resistance and exhibit higher virulence potential.
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