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Kalalah AA, Koenig SSK, Bono JL, Bosilevac JM, Eppinger M. Pathogenomes and virulence profiles of representative big six non-O157 serogroup Shiga toxin-producing Escherichia coli. Front Microbiol 2024; 15:1364026. [PMID: 38562479 PMCID: PMC10982417 DOI: 10.3389/fmicb.2024.1364026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Shiga toxin (Stx)-producing Escherichia coli (STEC) of non-O157:H7 serotypes are responsible for global and widespread human food-borne disease. Among these serogroups, O26, O45, O103, O111, O121, and O145 account for the majority of clinical infections and are colloquially referred to as the "Big Six." The "Big Six" strain panel we sequenced and analyzed in this study are reference type cultures comprised of six strains representing each of the non-O157 STEC serogroups curated and distributed by the American Type Culture Collection (ATCC) as a resource to the research community under panel number ATCC MP-9. The application of long- and short-read hybrid sequencing yielded closed chromosomes and a total of 14 plasmids of diverse functions. Through high-resolution comparative phylogenomics, we cataloged the shared and strain-specific virulence and resistance gene content and established the close relationship of serogroup O26 and O103 strains featuring flagellar H-type 11. Virulence phenotyping revealed statistically significant differences in the Stx-production capabilities that we found to be correlated to the strain's individual stx-status. Among the carried Stx1a, Stx2a, and Stx2d phages, the Stx2a phage is by far the most responsive upon RecA-mediated phage mobilization, and in consequence, stx2a + isolates produced the highest-level of toxin in this panel. The availability of high-quality closed genomes for this "Big Six" reference set, including carried plasmids, along with the recorded genomic virulence profiles and Stx-production phenotypes will provide a valuable foundation to further explore the plasticity in evolutionary trajectories in these emerging non-O157 STEC lineages, which are major culprits of human food-borne disease.
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Affiliation(s)
- Anwar A. Kalalah
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - Sara S. K. Koenig
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - James L. Bono
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
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Naidoo N, Zishiri OT. Comparative genomics analysis and characterization of Shiga toxin-producing Escherichia coli O157:H7 strains reveal virulence genes, resistance genes, prophages and plasmids. BMC Genomics 2023; 24:791. [PMID: 38124028 PMCID: PMC10731853 DOI: 10.1186/s12864-023-09902-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Escherichia coli O157:H7 is a foodborne pathogen that has been linked to global disease outbreaks. These diseases include hemorrhagic colitis and hemolytic uremic syndrome. It is vital to know the features that make this strain pathogenic to understand the development of disease outbreaks. In the current study, a comparative genomic analysis was carried out to determine the presence of structural and functional features of O157:H7 strains obtained from 115 National Center for Biotechnology Information database. These strains of interest were analysed in the following programs: BLAST Ring Image Generator, PlasmidFinder, ResFinder, VirulenceFinder, IslandViewer 4 and PHASTER. Five strains (ECP19-198, ECP19-798, F7508, F8952, H2495) demonstrated a great homology with Sakai because of a few regions missing. Five resistant genes were identified, however, Macrolide-associated resistance gene mdf(A) was commonly found in all genomes. Majority of the strains (97%) were positive for 15 of the virulent genes (espA, espB, espF, espJ, gad, chuA, eae, iss, nleA, nleB, nleC, ompT, tccP, terC and tir). The plasmid analysis demonstrated that the IncF group was the most prevalent in the strains analysed. The prophage and genomic island analysis showed a distribution of bacteriophages and genomic islands respectively. The results indicated that structural and functional features of the many O157:H7 strains differ and may be a result of obtaining mobile genetic elements via horizontal gene transfer. Understanding the evolution of O157:H7 strains pathogenicity in terms of their structural and functional features will enable the development of detection and control of transmission strategies.
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Affiliation(s)
- Natalie Naidoo
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
| | - Oliver T Zishiri
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa
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Genomic Insights and Functional Analysis Reveal Plant Growth Promotion Traits of Paenibacillus mucilaginosus G78. Genes (Basel) 2023; 14:genes14020392. [PMID: 36833318 PMCID: PMC9956331 DOI: 10.3390/genes14020392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/21/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Paenibacillus mucilaginosus has widely been reported as a plant growth-promoting rhizobacteria (PGPR). However, the important genomic insights into plant growth promotion in this species remain undescribed. In this study, the genome of P. mucilaginosus G78 was sequenced using Illumina NovaSeq PE150. It contains 8,576,872 bp with a GC content of 58.5%, and was taxonomically characterized. Additionally, a total of 7337 genes with 143 tRNAs, 41 rRNAs, and 5 ncRNAs were identified. This strain can prohibit the growth of the plant pathogen, but also has the capability to form biofilm, solubilize phosphate, and produce IAA. Twenty-six gene clusters encoding secondary metabolites were identified, and the genotypic characterization indirectly proved its resistant ability to ampicillin, bacitracin, polymyxin and chloramphenicol. The putative exopolysaccharide biosynthesis and biofilm formation gene clusters were explored. According to the genetic features, the potential monosaccharides of its exopolysaccharides for P. mucilaginosus G78 may include glucose, mannose, galactose, fucose, that can probably be acetylated and pyruvated. Conservation of the pelADEFG compared with other 40 Paenibacillus species suggests that Pel may be specific biofilm matrix component in P. mucilaginosus. Several genes relevant to plant growth-promoting traits, i.e., IAA production and phosphate solubilization are well conserved compared with other 40 other Paenibacillus strains. The current study can benefit for understanding the plant growth-promoting traits of P. mucilaginosus as well as its potential application in agriculture as PGPR.
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Zhang B, Zhao W, Gao B, Shan C, Wang X, Wan Q, Deng J, Cha J, Chen B, Han D, Gao L, Ao P, Zhao R, Xiao P, Lv L, Gao H. Whole Genome Sequencing and Biological Characteristics of Two Strains of Porcine Escherichia coli Isolated from Saba Pigs. Curr Microbiol 2022; 79:182. [PMID: 35508821 DOI: 10.1007/s00284-022-02873-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/11/2022] [Indexed: 11/24/2022]
Abstract
Escherichia coli (E. coli) is an important pathogen that causes diarrhea and death in piglets. In this work, whole genome sequencing of two E. coli strains (ZB-1, ZWW-1) isolated from Saba pigs. And focus on the relationship between drug resistance, pathogenic phenotype and genotype of the two strains. This study analyzed the drug susceptibility of the two strains. The LD50 values, tissue bacterial load and intestinal pathological changes in mice infected with the two strains. The differences in gene functions such as drug resistance, virulence, and unique genes between the two strains, as well as the genetic evolutionary relationship of housekeeping genes were analyzed. The results showed that the two strains had the same resistance phenotype to most drugs. The LD50 value, tissue load, and pathological changes in mice infected with strain ZB-1 revealed that this strain was more virulent and pathogenic than strain ZWW-1. In addition, the housekeeping genes contained in the two strains are in the same large branch as E. coli of different species, and the genetic evolution is stable. All of them carry EPEC-type strain-specific virulence genes escV and ent, indicating that they are all new members of EPEC-type strains. This study laid the foundation for understanding the genetic background and biological characteristics of E. coli from Saba pigs.
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Affiliation(s)
- Bo Zhang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Weiwei Zhao
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Bin Gao
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Chunlan Shan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xi Wang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Quan Wan
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Jing Deng
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Jinglong Cha
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Bingxun Chen
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Dongmei Han
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Libo Gao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Pingxing Ao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Ru Zhao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Peng Xiao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China.
| | - Longbao Lv
- Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
| | - Hong Gao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China.
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Bai Z, Zhang S, Wang X, Aslam MZ, Wang W, Li H, Dong Q. Genotyping Based on CRISPR Loci Diversity and Pathogenic Potential of Diarrheagenic Escherichia coli. Front Microbiol 2022; 13:852662. [PMID: 35308371 PMCID: PMC8924505 DOI: 10.3389/fmicb.2022.852662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/26/2022] [Indexed: 11/23/2022] Open
Abstract
Diarrheagenic Escherichia coli (DEC) can cause epidemic diarrhea worldwide. The pathogenic potential of different strains is diverse and the continuous emergence of pathogenic strains has brought serious harm to public health. Accurately distinguishing and identifying DEC with different virulence is necessary for epidemiological surveillance and investigation. Clustered regularly interspaced short palindromic repeats (CRISPR) typing is a new molecular method that can distinguish pathogenic bacteria excellently and has shown great promise in DEC typing. The purpose of this study was to investigate the discrimination of CRISPR typing method for DEC and explore the pathogenicity potential of DEC based on CRISPR types (CT). The whole genome sequences of 789 DEC strains downloaded from the database were applied CRISPR typing and serotyping. The D value (Simpson’s index) with 0.9709 determined that CRISPR typing had a higher discrimination. Moreover, the same H antigen strains with different O seemed to share more identical spacers. Further analyzing the strains CRISPR types and the number of virulence genes, it was found that there was a significant correlation between the CRISPR types and the number of virulence genes (p < 0.01). The strains with the largest number of virulence genes concentrated in CT25 and CT56 and the number of virulence genes in CT264 was the least, indicating that the pathway potential of different CRISPR types was variable. Combined with the Caco-2 cell assay of the laboratory strains, the invasion capacity of STEC strains of different CRISPR types was different and there was no significant difference in the invasion rate between different CRISPR type strains (p > 0.05). In the future, with the increase of the number of strains that can be studied experimentally, the relationship between CRISPR types and adhesion and invasion capacities will be further clarified.
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Affiliation(s)
- Zhiye Bai
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Shiqin Zhang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xiang Wang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Muhammad Zohaib Aslam
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Wen Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, MOA Laboratory of Quality and Safety Risk Assessment for Agro-products (Hangzhou), Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongmei Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Qingli Dong
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
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6
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Comparative Pathogenomics of Escherichia coli: Polyvalent Vaccine Target Identification through Virulome Analysis. Infect Immun 2021; 89:e0011521. [PMID: 33941580 PMCID: PMC8281228 DOI: 10.1128/iai.00115-21] [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: 02/07/2023] Open
Abstract
Comparative genomics of bacterial pathogens has been useful for revealing potential virulence factors. Escherichia coli is a significant cause of human morbidity and mortality worldwide but can also exist as a commensal in the human gastrointestinal tract. With many sequenced genomes, it has served as a model organism for comparative genomic studies to understand the link between genetic content and potential for virulence. To date, however, no comprehensive analysis of its complete “virulome” has been performed for the purpose of identifying universal or pathotype-specific targets for vaccine development. Here, we describe the construction of a pathotype database of 107 well-characterized completely sequenced pathogenic and nonpathogenic E. coli strains, which we annotated for major virulence factors (VFs). The data are cross referenced for patterns against pathotype, phylogroup, and sequence type, and the results were verified against all 1,348 complete E. coli chromosomes in the NCBI RefSeq database. Our results demonstrate that phylogroup drives many of the “pathotype-associated” VFs, and ExPEC-associated VFs are found predominantly within the B2/D/F/G phylogenetic clade, suggesting that these phylogroups are better adapted to infect human hosts. Finally, we used this information to propose polyvalent vaccine targets with specificity toward extraintestinal strains, targeting key invasive strategies, including immune evasion (group 2 capsule), iron acquisition (FyuA, IutA, and Sit), adherence (SinH, Afa, Pap, Sfa, and Iha), and toxins (Usp, Sat, Vat, Cdt, Cnf1, and HlyA). While many of these targets have been proposed before, this work is the first to examine their pathotype and phylogroup distribution and how they may be targeted together to prevent disease.
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Duong VT, Tu LTP, Tuyen HT, Nhi LTQ, Campbell JI, Van Minh P, Le Phuc H, Chau TTH, Ngoc NM, Vi LL, Jenkins C, Okeke I, Higginson E, Baker S. Novel multiplex real-time PCR assays reveal a high prevalence of diarrhoeagenic Escherichia coli pathotypes in healthy and diarrhoeal children in the south of Vietnam. BMC Microbiol 2020; 20:192. [PMID: 32620076 PMCID: PMC7333254 DOI: 10.1186/s12866-020-01878-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/25/2020] [Indexed: 08/30/2023] Open
Abstract
Background Diarrhoeagenic Escherichia coli (DEC) infections are common in children in low-middle income countries (LMICs). However, detecting the various DEC pathotypes is complex as they cannot be differentiated by classical microbiology. We developed four multiplex real-time PCR assays were to detect virulence markers of six DEC pathotypes; specificity was tested using DEC controls and other enteric pathogens. PCR amplicons from the six E. coli pathotypes were purified and amplified to be used to optimize PCR reactions and to calculate reproducibility. After validation, these assays were applied to clinical samples from healthy and diarrhoeal Vietnamese children and associated with clinical data. Results The multiplex real-time PCRs were found to be reproducible, and specific. At least one DEC variant was detected in 34.7% (978/2815) of the faecal samples from diarrhoeal children; EAEC, EIEC and atypical EPEC were most frequent Notably, 41.2% (205/498) of samples from non-diarrhoeal children was positive with a DEC pathotype. In this population, only EIEC, which was detected in 34.3% (99/289) of diarrhoeal samples vs. 0.8% (4/498) non-diarrhoeal samples (p < 0.001), was significantly associated with diarrhoea. Multiplex real-time PCR when applied to clinical samples is an efficient and high-throughput approach to DEC pathotypes. Conclusions This approach revealed high carriage rates of DEC pathotypes among Vietnamese children. We describe a novel diagnostic approach for DEC, which provides baseline data for future surveillance studies assessing DEC burden in LMICs.
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Affiliation(s)
- Vu Thuy Duong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - Le Thi Phuong Tu
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ha Thanh Tuyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Le Thi Quynh Nhi
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - James I Campbell
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Pham Van Minh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Tran Thi Hong Chau
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Lu Lan Vi
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Claire Jenkins
- National Infection Service, Public Health England, England, UK
| | - Iruka Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Ellen Higginson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) Department of Medicine, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AW, UK.
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Gut Microbiota Alterations from Three-Strain Yogurt Formulation Treatments in Slow-Transit Constipation. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2020; 2020:4583973. [PMID: 32148595 PMCID: PMC7049856 DOI: 10.1155/2020/4583973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 12/28/2019] [Accepted: 01/27/2020] [Indexed: 02/07/2023]
Abstract
The objective of this study was to evaluate the effects of a three-strain yogurt formulation in slow-transit constipation (STC) patients. Each individual in both treatment groups consumed 250 mL of the formulated yogurt daily for a week (7 days), and fecal samples were collected for gut microbiota and short-chain fatty acid (SCFA) analyses. A significant increase in the defection frequency (p < 0.001) and bacterial diversity (p=0.027) at the 100% sequence homology level and a decrease in the concentrations of acetic acid (p=0.014), propionic acid (p=0.019), and butanoic acid (p=0.005) were observed after the STC patients consumed three-strain yogurt formulation. In addition, the consumption of the three-strain yogurt formulation significantly altered the composition of the intestinal bacteria in the STC patients. The relative abundances of 23 genera in the top dominating genera were altered significantly after the STC patients consumed the yogurt. In summary, the consumption of 250 mL day− the three-strain yogurt formulation described in this study can play a role in improving the symptoms of STC.
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Zhao W, Yu D, Cheng J, Wang Y, Yang Z, Yao X, Luo Y. Identification and pathogenicity analysis of Streptococcus equinus FMD1, a beta-hemolytic strain isolated from forest musk deer lung. J Vet Med Sci 2019; 82:172-176. [PMID: 31902837 PMCID: PMC7041976 DOI: 10.1292/jvms.19-0566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Streptococcus spp. cause a wide range of diseases in animals and humans.
A Streptococcus strain (FMD1) was isolated from forest musk deer lung. To
identify the bacterium at the species level and investigate its pathogenicity, whole
genome sequencing and experimental infections of mice were performed. The genome had
97.63% average nucleotide identity with the S. equinus strain. Through
virulence gene analysis, a beta-hemolysin/cytolysin genome island was found in the FMD1
genome, which contained 12 beta-hemolysin/cytolysin-related genes. Hemolytic reaction and
histopathological analysis established the strain’s pathogenicity in mice. This is the
first report of a beta-hemolytic S. equinus strain in forest musk deer
identified based on phenotypic and genotypic analyzes; this strategy could be useful for
analyzing pathogens affecting rare animals.
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Affiliation(s)
- Wei Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
| | - Dong Yu
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
| | - JianGuo Cheng
- Sichuan Institute of Musk Deer Breeding, Dujiangyan 611830, Sichuan Province, China
| | - Yin Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
| | - ZeXiao Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
| | - XuePing Yao
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
| | - Yan Luo
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang 611130, Sichuan Province, China
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Reis-Cunha JL, Bartholomeu DC, Manson AL, Earl AM, Cerqueira GC. ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database. PLoS One 2019; 14:e0223364. [PMID: 31577829 PMCID: PMC6774505 DOI: 10.1371/journal.pone.0223364] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/19/2019] [Indexed: 01/18/2023] Open
Abstract
Background Prophages play a significant role in prokaryotic evolution, often altering the function of the cell that they infect via transfer of new genes e.g., virulence or antibiotic resistance factors, inactivation of existing genes or by modifying gene expression. Recently, phage therapy has gathered renewed interest as a promising alternative to control bacterial infections. Cataloging the repertoire of prophages in large collections of species’ genomes is an important initial step in understanding their evolution and potential therapeutic utility. However, current widely-used tools for identifying prophages within bacterial genome sequences are mainly web-based, can have long response times, and do not scale to keep pace with the many thousands of genomes currently being sequenced routinely. Methodology In this work, we present ProphET, an easy to install prophage predictor to be used in Linux operation system, without the constraints associated with a web-based tool. ProphET predictions rely on similarity searches against a database of prophage genes, taking as input a bacterial genome sequence in FASTA format and its corresponding gene annotation in GFF. ProphET identifies prophages in three steps: similarity search, calculation of the density of prophage genes, and edge refinement. ProphET performance was evaluated and compared with other phage predictors based on a set of 54 bacterial genomes containing 267 manually annotated prophages. Findings and conclusions ProphET identifies prophages in bacterial genomes with high precision and offers a fast, highly scalable alternative to widely-used web-based applications for prophage detection.
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Affiliation(s)
- João L. Reis-Cunha
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- * E-mail: (JLR-C); (GCC)
| | - Daniella C. Bartholomeu
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Abigail L. Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Gustavo C. Cerqueira
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Personal Genome Diagnostics, Baltimore, Maryland, United States of America
- * E-mail: (JLR-C); (GCC)
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ISOLATION, IDENTIFICATION, AND GENOME ANALYSIS OF LUNG PATHOGENIC KLEBSIELLA PNEUMONIAE (LPKP) IN FOREST MUSK DEER. J Zoo Wildl Med 2019; 48:1039-1048. [PMID: 29297821 DOI: 10.1638/2016-0241.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Klebsiella pneumoniae is an important pathogen commonly associated with opportunistic infections. In this study, lung pathogenic K. pneumoniae (LPKP) was isolated and identified from suppurative pneumoniae in forest musk deer by conventional methods and by 16S ribosomal RNA sequence analysis. Median lethal dose and histopathologic analysis were used to demonstrate pathogenicity of the organism in mice. Furthermore, a draft genome of LPKP was sequenced, and its virulence genes were detected. One hundred and twenty-two virulence genes encoded determinant of capsule polysaccharide (CPS), lipopolysaccharide, fimbriae, outer membrane proteins, iron acquisition, and urease. In particular, 20 CPS-related genes were highly conserved in LPKP, K. pneumoniae U, K. pneumoniae NTUH-KP35, and K. pneumoniae KP-1. All of the strains were identified as capsular type K54. This is the first report of capsular type K54 K. pneumoniae causing suppurative pneumonia in an animal. The results of this study provided the basis for understanding the pathogenicity of LPKP and laid a foundation for the development of vaccines for the capsular type K54 K. pneumoniae disease.
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Forde BM, McAllister LJ, Paton JC, Paton AW, Beatson SA. SMRT sequencing reveals differential patterns of methylation in two O111:H- STEC isolates from a hemolytic uremic syndrome outbreak in Australia. Sci Rep 2019; 9:9436. [PMID: 31263188 PMCID: PMC6602927 DOI: 10.1038/s41598-019-45760-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 05/23/2019] [Indexed: 11/21/2022] Open
Abstract
In 1995 a severe haemolytic-uremic syndrome (HUS) outbreak in Adelaide occurred. A recent genomic analysis of Shiga toxigenic Escherichia coli (STEC) O111:H- strains 95JB1 and 95NR1 from this outbreak found that the more virulent isolate, 95NR1, harboured two additional copies of the Shiga toxin 2 (Stx2) genes encoded within prophage regions. The structure of the Stx2-converting prophages could not be fully resolved using short-read sequence data alone and it was not clear if there were other genomic differences between 95JB1 and 95NR1. In this study we have used Pacific Biosciences (PacBio) single molecule real-time (SMRT) sequencing to characterise the genome and methylome of 95JB1 and 95NR1. We completely resolved the structure of all prophages including two, tandemly inserted, Stx2-converting prophages in 95NR1 that were absent from 95JB1. Furthermore we defined all insertion sequences and found an additional IS1203 element in the chromosome of 95JB1. Our analysis of the methylome of 95NR1 and 95JB1 identified hemi-methylation of a novel motif (5′-CTGCm6AG-3′) in more than 4000 sites in the 95NR1 genome. These sites were entirely unmethylated in the 95JB1 genome, and included at least 177 potential promoter regions that could contribute to regulatory differences between the strains. IS1203 mediated deactivation of a novel type IIG methyltransferase in 95JB1 is the likely cause of the observed differential patterns of methylation between 95NR1 and 95JB1. This study demonstrates the capability of PacBio SMRT sequencing to resolve complex prophage regions and reveal the genetic and epigenetic heterogeneity within a clonal population of bacteria.
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Affiliation(s)
- Brian M Forde
- Australian Infectious Diseases Centre, The University of Queensland, Brisbane, QLD, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lauren J McAllister
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - James C Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Adrienne W Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Scott A Beatson
- Australian Infectious Diseases Centre, The University of Queensland, Brisbane, QLD, Australia. .,Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
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Haddad N, Johnson N, Kathariou S, Métris A, Phister T, Pielaat A, Tassou C, Wells-Bennik MH, Zwietering MH. Next generation microbiological risk assessment—Potential of omics data for hazard characterisation. Int J Food Microbiol 2018; 287:28-39. [DOI: 10.1016/j.ijfoodmicro.2018.04.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 03/31/2018] [Accepted: 04/10/2018] [Indexed: 12/18/2022]
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14
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Berger M, Berger P, Denamur E, Mellmann A, Dobrindt U. Core elements of the vegetative replication control of the Inc1 plasmid pO104_90 of Escherichia coli O104:H4 also regulate its transfer frequency. Int J Med Microbiol 2018; 308:962-968. [DOI: 10.1016/j.ijmm.2018.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/25/2018] [Accepted: 07/10/2018] [Indexed: 01/18/2023] Open
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15
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Shridhar PB, Patel IR, Gangiredla J, Noll LW, Shi X, Bai J, Elkins CA, Strockbine NA, Nagaraja TG. Genetic Analysis of Virulence Potential of Escherichia coli O104 Serotypes Isolated From Cattle Feces Using Whole Genome Sequencing. Front Microbiol 2018; 9:341. [PMID: 29545780 PMCID: PMC5838399 DOI: 10.3389/fmicb.2018.00341] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/12/2018] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli O104:H4, a Shiga toxin-producing hybrid pathotype that was implicated in a major foodborne outbreak in Germany in 2011, has not been detected in cattle. However, serotypes of O104, other than O104:H4, have been isolated from cattle feces, with O104:H7 being the most predominant. In this study, we investigated, based on whole genome sequence analyses, the virulence potential of E. coli O104 strains isolated from cattle feces, since cattle are asymptomatic carriers of E. coli O104. The genomes of ten bovine E. coli O104 strains (six O104:H7, one O104:H8, one O104:H12, and two O104:H23) and five O104:H7 isolated from human clinical cases were sequenced. Of all the bovine O104 serotypes (H7, H8, H12, and H23) that were included in the study, only E. coli O104:H7 serotype possessed Shiga toxins. Four of the six bovine O104:H7 strains and one of the five human strains carried stx1c. Three human O104 strains carried stx2, two were of subtype 2a, and one was 2d. Genomes of stx carrying bovine O104:H7 strains were larger than the stx-negative strains of O104:H7 or other serotypes. The genome sizes were proportional to the number of genes carried on the mobile genetic elements (phages, prophages, transposable elements and plasmids). Both bovine and human strains were negative for intimin and other genes associated with the type III secretory system and non-LEE encoded effectors. Plasmid-encoded virulence genes (ehxA, epeA, espP, katP) were also present in bovine and human strains. All O104 strains were negative for antimicrobial resistance genes, except one human strain. Phylogenetic analysis indicated that bovine E. coli O104 strains carrying the same flagellar antigen clustered together and STEC strains clustered separately from non-STEC strains. One of the human O104:H7 strains was phylogenetically closely related to and belonged to the same sequence type (ST-1817) as the bovine O104:H7 STEC strains. This suggests that the bovine feces could be a source of human illness caused by E. coli O104:H7 serotype. Because bovine O104:H7 strains carried virulence genes similar to human clinical strains and one of the human clinical strains was phylogenetically related to bovine strains, the serotype has the potential to be a diarrheagenic pathogen in humans.
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Affiliation(s)
- Pragathi B Shridhar
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS, United States
| | - Isha R Patel
- Division of Molecular Biology, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Laurel, MD, United States
| | - Jayanthi Gangiredla
- Division of Molecular Biology, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Laurel, MD, United States
| | - Lance W Noll
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS, United States
| | - Xiaorong Shi
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS, United States
| | - Jianfa Bai
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS, United States.,Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, United States
| | - Christopher A Elkins
- Division of Molecular Biology, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Laurel, MD, United States
| | - Nancy A Strockbine
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - T G Nagaraja
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS, United States
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16
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Draft Genome Sequences of Escherichia coli O104 Strains of Bovine and Human Origin. GENOME ANNOUNCEMENTS 2017; 5:5/33/e00630-17. [PMID: 28818887 PMCID: PMC5604760 DOI: 10.1128/genomea.00630-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cattle harbor and shed in their feces several Escherichia coli O104 serotypes. All O104 strains examined were intimin negative and belonged to the B1 phylogroup, and some were Shiga toxigenic. We report here the genome sequences of bovine O104:H7 (n = 5), O104:H23 (n = 2), O104:H8 (n = 1), and O104:H12 (n = 1) isolates and human clinical isolates of O104:H7 (n = 5).
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17
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Montero DA, Velasco J, Del Canto F, Puente JL, Padola NL, Rasko DA, Farfán M, Salazar JC, Vidal R. Locus of Adhesion and Autoaggregation (LAA), a pathogenicity island present in emerging Shiga Toxin-producing Escherichia coli strains. Sci Rep 2017; 7:7011. [PMID: 28765569 PMCID: PMC5539235 DOI: 10.1038/s41598-017-06999-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/22/2017] [Indexed: 02/03/2023] Open
Abstract
Shiga Toxin-producing Escherichia coli (STEC) are a group of foodborne pathogens associated with diarrhea, dysentery, hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS). Shiga toxins are the major virulence factor of these pathogens, however adhesion and colonization to the human intestine is required for STEC pathogenesis. A subset of STEC strains carry the Locus of Enterocyte Effacement (LEE) pathogenicity island (PAI), which encodes genes that mediate the colonization of the human intestine. While LEE-positive STEC strains have traditionally been associated with human disease, the burden of disease caused by STEC strains that lacks LEE (LEE-negative) has increased recently in several countries; however, in the absence of LEE, the molecular pathogenic mechanisms by STEC strains are unknown. Here we report a 86-kb mosaic PAI composed of four modules that encode 80 genes, including novel and known virulence factors associated with adherence and autoaggregation. Therefore, we named this PAI as Locus of Adhesion and Autoaggregation (LAA). Phylogenomic analysis using whole-genome sequences of STEC strains available in the NCBI database indicates that LAA PAI is exclusively present in a subset of emerging LEE-negative STEC strains, including strains isolated from HC and HUS cases. We suggest that the acquisition of this PAI is a recent evolutionary event, which may contribute to the emergence of these STEC.
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Affiliation(s)
- David A Montero
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Juliana Velasco
- Servicio de Urgencia Infantil, Hospital Clínico de la Universidad de Chile "Dr. José Joaquín Aguirre", Santiago, Chile
| | - Felipe Del Canto
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Jose L Puente
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Nora L Padola
- Centro de Investigación Veterinaria Tandil, CONICET-CIC, Facultad de Ciencias Veterinarias, UNCPBA, Tandil, Argentina
| | - David A Rasko
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Mauricio Farfán
- Centro de Estudios Moleculares, Departamento de Pediatría, Hospital Dr. Luis Calvo Mackenna, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Juan C Salazar
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Roberto Vidal
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago, Chile.
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18
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Plasmids from Shiga Toxin-Producing Escherichia coli Strains with Rare Enterohemolysin Gene (ehxA) Subtypes Reveal Pathogenicity Potential and Display a Novel Evolutionary Path. Appl Environ Microbiol 2016; 82:6367-6377. [PMID: 27542930 DOI: 10.1128/aem.01839-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/11/2016] [Indexed: 12/27/2022] Open
Abstract
Most Shiga toxin-producing Escherichia coli (STEC) strains associated with severe disease, such as hemolytic-uremic syndrome (HUS), carry large enterohemolysin-encoding (ehxA) plasmids, e.g., pO157 and pO103, that contribute to STEC clinical manifestations. Six ehxA subtypes (A through F) exist that phylogenetically cluster into eae-positive (B, C, F), a mix of eae-positive (E) and eae-negative (A), and a third, more distantly related, cluster of eae-negative (D) STEC strains. While subtype B, C, and F plasmids share a number of virulence traits that are distinct from those of subtype A, sequence data have not been available for subtype D and E plasmids. Here, we determined and compared the genetic composition of four subtype D and two subtype E plasmids to establish their evolutionary relatedness among ehxA subtypes and define their potential role in pathogenicity. We found that subtype D strains carry one exceptionally large plasmid (>200 kbp) that carries a variety of virulence genes that are associated with enterotoxigenic and enterohemorrhagic E. coli, which, quite possibly, enables these strains to cause disease despite being food isolates. Our data offer further support for the hypothesis that this subtype D plasmid represents a novel virulence plasmid, sharing very few genetic features with other plasmids; we conclude that these plasmids have evolved from a different evolutionary lineage than the plasmids carrying the other ehxA subtypes. In contrast, the 50-kbp plasmids of subtype E (pO145), although isolated from HUS outbreak strains, carried only few virulence-associated determinants, suggesting that the clinical presentation of subtype E strains is largely a result of chromosomally encoded virulence factors. IMPORTANCE Bacterial plasmids are known to be key agents of change in microbial populations, promoting the dissemination of various traits, such as drug resistance and virulence. This study determined the genetic makeup of virulence plasmids from rare enterohemolysin subtype D and E Shiga toxin-producing E. coli strains. We demonstrated that ehxA subtype D plasmids represent a novel E. coli virulence plasmid, and although subtype D plasmids were derived from nonclinical isolates, they encoded a variety of virulence determinants that are associated with pathogenic E. coli In contrast, subtype E plasmids, isolated from strains recovered from severely ill patients, carry only a few virulence determinants. The results of this study reemphasize the plasticity and vast diversity among E. coli plasmids. This work demonstrates that, although E. coli strains of certain serogroups may not be frequently associated with disease, they should not be underestimated in protecting human health and food safety.
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Lozinak KA, Jani N, Gangiredla J, Patel I, Elkins CA, Hu Z, Kassim PA, Myers RA, Laksanalamai P. Investigation of potential Shiga toxin producing Escherichia coli (STEC) associated with a local foodborne outbreak using multidisciplinary approaches. FOOD SCIENCE AND HUMAN WELLNESS 2016. [DOI: 10.1016/j.fshw.2016.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Molecular characterization and phylogeny of Shiga toxin–producing Escherichia coli isolates obtained from two Dutch regions using whole genome sequencing. Clin Microbiol Infect 2016; 22:642.e1-9. [DOI: 10.1016/j.cmi.2016.03.028] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 03/17/2016] [Accepted: 03/25/2016] [Indexed: 11/19/2022]
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21
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Ruhe ZC, Nguyen JY, Chen AJ, Leung NY, Hayes CS, Low DA. CDI Systems Are Stably Maintained by a Cell-Contact Mediated Surveillance Mechanism. PLoS Genet 2016; 12:e1006145. [PMID: 27355474 PMCID: PMC4927057 DOI: 10.1371/journal.pgen.1006145] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 06/07/2016] [Indexed: 11/17/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) systems are widespread amongst Gram-negative bacteria where they play important roles in inter-cellular competition and biofilm formation. CDI+ bacteria use cell-surface CdiA proteins to bind neighboring bacteria and deliver C-terminal toxin domains. CDI+ cells also express CdiI immunity proteins that specifically neutralize toxins delivered from adjacent siblings. Genomic analyses indicate that cdi loci are commonly found on plasmids and genomic islands, suggesting that these Type 5 secretion systems are spread through horizontal gene transfer. Here, we examine whether CDI toxin and immunity activities serve to stabilize mobile genetic elements using a minimal F plasmid that fails to partition properly during cell division. This F plasmid is lost from Escherichia coli populations within 50 cell generations, but is maintained in ~60% of the cells after 100 generations when the plasmid carries the cdi gene cluster from E. coli strain EC93. By contrast, the ccdAB "plasmid addiction" module normally found on F exerts only a modest stabilizing effect. cdi-dependent plasmid stabilization requires the BamA receptor for CdiA, suggesting that plasmid-free daughter cells are inhibited by siblings that retain the CDI+ plasmid. In support of this model, the CDI+ F plasmid is lost rapidly from cells that carry an additional cdiI immunity gene on a separate plasmid. These results indicate that plasmid stabilization occurs through elimination of non-immune cells arising in the population via plasmid loss. Thus, genetic stabilization reflects a strong selection for immunity to CDI. After long-term passage for more than 300 generations, CDI+ plasmids acquire mutations that increase copy number and result in 100% carriage in the population. Together, these results show that CDI stabilizes genetic elements through a toxin-mediated surveillance mechanism in which cells that lose the CDI system are detected and eliminated by their siblings.
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Affiliation(s)
- Zachary C Ruhe
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Josephine Y Nguyen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Annette J Chen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Nicole Y Leung
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - David A Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California, United States of America
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