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Kushwaha SK, Narasimhan LP, Chithananthan C, Marathe SA. Clustered regularly interspaced short palindromic repeats-Cas system: diversity and regulation in Enterobacteriaceae. Future Microbiol 2022; 17:1249-1267. [PMID: 36006039 DOI: 10.2217/fmb-2022-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Insights into the arms race between bacteria and invading mobile genetic elements have revealed the intricacies of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system and the counter-defenses of bacteriophages. Incredible spacer diversity but significant spacer conservation among species/subspecies dictates the specificity of the CRISPR-Cas system. Researchers have exploited this feature to type/subtype the bacterial strains, devise targeted antimicrobials and regulate gene expression. This review focuses on the nuances of the CRISPR-Cas systems in Enterobacteriaceae that predominantly harbor type I-E and I-F CRISPR systems. We discuss the systems' regulation by the global regulators, H-NS, LeuO, LRP, cAMP receptor protein and other regulators in response to environmental stress. We further discuss the regulation of noncanonical functions like DNA repair pathways, biofilm formation, quorum sensing and virulence by the CRISPR-Cas system. The review comprehends multiple facets of the CRISPR-Cas system in Enterobacteriaceae including its diverse attributes, association with genetic features, regulation and gene regulatory mechanisms.
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Affiliation(s)
- Simran K Kushwaha
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, 333031, India
| | - Lakshmi P Narasimhan
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, 333031, India
| | - Chandrananthi Chithananthan
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, 333031, India
| | - Sandhya A Marathe
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani, Rajasthan, 333031, India
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2
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Nikiema MEM, Kakou-Ngazoa S, Ky/Ba A, Sylla A, Bako E, Addablah AYA, Ouoba JB, Sampo E, Gnada K, Zongo O, Traoré KA, Sanou A, Bonkoungou IJO, Ouédraogo R, Barro N, Sangaré L. Characterization of virulence factors of Salmonella isolated from human stools and street food in urban areas of Burkina Faso. BMC Microbiol 2021; 21:338. [PMID: 34895140 PMCID: PMC8665542 DOI: 10.1186/s12866-021-02398-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 11/24/2021] [Indexed: 01/19/2023] Open
Abstract
Background This study was undertaken to identify and functionally characterize virulence genes from Salmonella isolates in street food and stool cultures. From February 2017 to May 2018, clinical and food Salmonella strains were isolated in three regions in Burkina Faso. Salmonella was serotyped according to the White-Kauffmann-Le Minor method, and polymerase chain reaction (PCR) was used to detec invA, spvR, spvC, fimA and stn virulence genes commonly associated with salmonellosis in Sub-Saharan Africa. Results A total of 106 Salmonella isolates (77 human stools; 14 sandwiches) was analyzed using a serological identification with an O-group test reagent. The presence of Salmonella was confirmed in 86% (91/106) of the samples were reactive (OMA-positive/OMB-positive). Salmonella serogroup O:4,5 was the most common serogroup detected (40%; 36/91). Salmonella Enteritidis and Typhimurium represented 5.5% (5/91) and 3.3% (3/91), respectively and were identified only from clinical isolates. Furthermore, 14 serotypes of Salmonella (12/91 human strains and 2/15 sandwich strains) were evocative of Kentucky/Bargny serotype. For the genetic profile, 66% (70/106) of the Salmonella had invA and stn genes; 77.4% (82/106) had the fimA gene. The spvR gene was found in 36.8% (39/106) of the isolates while 48.1% (51/106) had the spvC gene. Among the identified Salmonella Enteritidis and Salmonella Typhimurium isolated from stools, the virulence genes detected were invA (3/5) versus (2/3), fimA (4/5) versus (3/3), stn (3/5) versus (2/3), spvR (4/5) versus (2/3) and spvC (3/5) versus (2/3), respectively. Conclusion This study reports the prevalence of Salmonella serotypes and virulence genes in clinical isolates and in street foods. It shows that food could be a significant source of Salmonella transmission to humans. Our results could help decision-making by the Burkina Faso health authority in the fight against street food-related diseases, in particular by training restaurateurs in food hygiene.
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Affiliation(s)
- Marguerite E M Nikiema
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA). Ecole Doctorale Sciences et Technologies, Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso. .,Plateforme de Biologie Moléculaire, Institut Pasteur de Côte d'Ivoire, Abidjan, Côte d'Ivoire. .,Service de Bactériologie-Virologie, CHU-Yalgado OUEDRAOGO, 03 BP 7022, Ouagadougou, Burkina Faso.
| | - Solange Kakou-Ngazoa
- Plateforme de Biologie Moléculaire, Institut Pasteur de Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Absatou Ky/Ba
- Laboratoire de Bactériologie-Virologie, CHU-Bogodogo, Ouagadougou, Burkina Faso
| | - Aboubacar Sylla
- Plateforme de Biologie Moléculaire, Institut Pasteur de Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Evariste Bako
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA). Ecole Doctorale Sciences et Technologies, Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso
| | | | - Jean Bienvenue Ouoba
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA). Ecole Doctorale Sciences et Technologies, Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso
| | - Emmanuel Sampo
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA). Ecole Doctorale Sciences et Technologies, Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso.,Hôpital Protestant Schiphra, 07 BP 5246, Ouagadougou, 07, Burkina Faso
| | - Kobo Gnada
- Centre MURAZ, Bobo-Dioulasso, Burkina Faso
| | - Oumarou Zongo
- Laboratoire de Biochimie et Immunologie Appliquées (LABIA), Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso
| | - Kuan Abdoulaye Traoré
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA). Ecole Doctorale Sciences et Technologies, Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso
| | - Adama Sanou
- Centre MURAZ, Bobo-Dioulasso, Burkina Faso.,Université Nazi Boni, 01 BP 1091, Bobo-Dioulasso, 01, Burkina Faso
| | - Isidore Juste Ouindgueta Bonkoungou
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA). Ecole Doctorale Sciences et Technologies, Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso
| | - Rasmata Ouédraogo
- Laboratoire de Bactériologie-Virologie, CHU-Pédiatrie Charles De Gaulle, 01 BP 1198 BP, Ouagadougou, 01, Burkina Faso
| | - Nicolas Barro
- Laboratoire de Biologie Moléculaire d'Epidémiologie et de Surveillance des Bactéries et Virus Transmis par les Aliments (LaBESTA). Ecole Doctorale Sciences et Technologies, Université Joseph Ki-Zerbo, 03 BP 7021, Ouagadougou, 03, Burkina Faso
| | - Lassana Sangaré
- Service de Bactériologie-Virologie, CHU-Yalgado OUEDRAOGO, 03 BP 7022, Ouagadougou, Burkina Faso
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3
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Mthembu TP, Zishiri OT, El Zowalaty ME. Detection and Molecular Identification of Salmonella Virulence Genes in Livestock Production Systems in South Africa. Pathogens 2019; 8:pathogens8030124. [PMID: 31405078 PMCID: PMC6789496 DOI: 10.3390/pathogens8030124] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/26/2019] [Accepted: 08/05/2019] [Indexed: 01/07/2023] Open
Abstract
Livestock are an important source of protein and food for humans, however opportunistic pathogens such as Salmonella spp. turn livestock into vehicles of foodborne diseases. This study investigated the prevalence of virulence genes in Salmonella spp. isolated from livestock production systems in two provinces of South Africa. During the period from May to August, 2018, a total of 361 faecal (189), oral (100), environmental (soil (36) and water (27)) and feed (9) samples were randomly collected from different animals (cattle, sheep, goats, pigs, ducks and chickens) that were housed in small-scale livestock production systems from Eastern Cape and KwaZulu-Natal Provinces in South Africa. Salmonella spp. were isolated and identified using microbiological and DNA molecular methods. Salmonella spp. were present in 29.0% of the samples of which 30.2% belonged to the Salmonella enterica species as confirmed by the positive amplification of the species specific iroB gene. Virulence genes that were screened from livestock-associated Salmonella were invA, iroB, spiC, pipD and int1. Statistically significant associations (p < 0.05) were established between the virulence genes, sampling location, animal host as well as the season when samples were collected. Furthermore, statistically significant (p < 0.05) positive correlations were observed between most of the virulence genes investigated. This is one of the recent studies to detect and investigate livestock-associated Salmonella spp. in South Africa. This study highlights the importance of continuous monitoring and surveillance for pathogenic salmonellae. It also demonstrated the detection and prevalence of virulent Salmonella spp. harbored by livestock in South Africa. This study demonstrated the potential risks of pathogenic Salmonella enterica to cause foodborne diseases and zoonotic infections from farm-to-fork continuum using the global one-health approach.
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Affiliation(s)
- Thobeka P Mthembu
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
| | - Oliver T Zishiri
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
| | - Mohamed E El Zowalaty
- Virology and Microbiology Research Group, College of Pharmacy City University College of Ajman, Al Tallah 2, Ajman, P.O. Box 18484, UAE.
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4
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Ashari KS, Roslan NS, Omar AR, Bejo MH, Ideris A, Mat Isa N. Genome sequencing and analysis of Salmonella enterica subsp. enterica serovar Stanley UPM 517: Insights on its virulence-associated elements and their potentials as vaccine candidates. PeerJ 2019; 7:e6948. [PMID: 31293824 PMCID: PMC6601603 DOI: 10.7717/peerj.6948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 04/05/2019] [Indexed: 12/12/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Stanley (S. Stanley) is a pathogen that contaminates food, and is related to Salmonella outbreaks in a variety of hosts such as humans and farm animals through products like dairy items and vegetables. Despite the fact that several vaccines of Salmonella strains had been constructed, none of them were developed according to serovar Stanley up to this day. This study presents results of genome sequencing and analysis on our S. Stanley UPM 517 strain taken from fecal swabs of 21-day-old healthy commercial chickens in Perak, Malaysia and used Salmonella enterica subsp. enterica serovar Typhimurium LT2 (S. Typhimurium LT2) as a reference to be compared with. First, sequencing and assembling of the Salmonella Stanley UPM 517 genome into a contiguous form were done. The work was then continued with scaffolding and gap filling. Annotation and alignment of the draft genome was performed with S. Typhimurium LT2. The other elements of virulence estimated in this study included Salmonella pathogenicity islands, resistance genes, prophages, virulence factors, plasmid regions, restriction-modification sites and the CRISPR-Cas system. The S. Stanley UPM 517 draft genome had a length of 4,736,817 bp with 4,730 coding sequence and 58 RNAs. It was discovered via genomic analysis on this strain that there were antimicrobial resistance properties toward a wide variety of antibiotics. Tcf and ste, the two fimbrial virulence clusters related with human and broiler intestinal colonizations which were not found in S. Typhimurium LT2, were atypically discovered in the S. Stanley UPM 517 genome. These clusters are involved in the intestinal colonization of human and broilers, respectively. There were seven Salmonella pathogenicity islands (SPIs) within the draft genome, which contained the virulence factors associated with Salmonella infection (except SPI-14). Five intact prophage regions, mostly comprising of the protein encoding Gifsy-1, Fels-1, RE-2010 and SEN34 prophages, were also encoded in the draft genome. Also identified were Type I–III restriction-modification sites and the CRISPR-Cas system of the Type I–E subtype. As this strain exhibited resistance toward numerous antibiotics, we distinguished several genes that had the potential for removal in the construction of a possible vaccine candidate to restrain and lessen the pervasiveness of salmonellosis and to function as an alternative to antibiotics.
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Affiliation(s)
- Khalidah Syahirah Ashari
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | | | - Abdul Rahman Omar
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohd Hair Bejo
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Aini Ideris
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Nurulfiza Mat Isa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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5
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Ilyas B, Tsai CN, Coombes BK. Evolution of Salmonella-Host Cell Interactions through a Dynamic Bacterial Genome. Front Cell Infect Microbiol 2017; 7:428. [PMID: 29034217 PMCID: PMC5626846 DOI: 10.3389/fcimb.2017.00428] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/19/2017] [Indexed: 11/13/2022] Open
Abstract
Salmonella Typhimurium has a broad arsenal of genes that are tightly regulated and coordinated to facilitate adaptation to the various host environments it colonizes. The genome of Salmonella Typhimurium has undergone multiple gene acquisition events and has accrued changes in non-coding DNA that have undergone selection by regulatory evolution. Together, at least 17 horizontally acquired pathogenicity islands (SPIs), prophage-associated genes, and changes in core genome regulation contribute to the virulence program of Salmonella. Here, we review the latest understanding of these elements and their contributions to pathogenesis, emphasizing the regulatory circuitry that controls niche-specific gene expression. In addition to an overview of the importance of SPI-1 and SPI-2 to host invasion and colonization, we describe the recently characterized contributions of other SPIs, including the antibacterial activity of SPI-6 and adhesion and invasion mediated by SPI-4. We further discuss how these fitness traits have been integrated into the regulatory circuitry of the bacterial cell through cis-regulatory evolution and by a careful balance of silencing and counter-silencing by regulatory proteins. Detailed understanding of regulatory evolution within Salmonella is uncovering novel aspects of infection biology that relate to host-pathogen interactions and evasion of host immunity.
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Affiliation(s)
- Bushra Ilyas
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Caressa N Tsai
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Brian K Coombes
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
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6
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Echeverz M, García B, Sabalza A, Valle J, Gabaldón T, Solano C, Lasa I. Lack of the PGA exopolysaccharide in Salmonella as an adaptive trait for survival in the host. PLoS Genet 2017; 13:e1006816. [PMID: 28542593 PMCID: PMC5464674 DOI: 10.1371/journal.pgen.1006816] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/08/2017] [Accepted: 05/12/2017] [Indexed: 12/22/2022] Open
Abstract
Many bacteria build biofilm matrices using a conserved exopolysaccharide named PGA or PNAG (poly-β-1,6-N-acetyl-D-glucosamine). Interestingly, while E. coli and other members of the family Enterobacteriaceae encode the pgaABCD operon responsible for PGA synthesis, Salmonella lacks it. The evolutionary force driving this difference remains to be determined. Here, we report that Salmonella lost the pgaABCD operon after the divergence of Salmonella and Citrobacter clades, and previous to the diversification of the currently sequenced Salmonella strains. Reconstitution of the PGA machinery endows Salmonella with the capacity to produce PGA in a cyclic dimeric GMP (c-di-GMP) dependent manner. Outside the host, the PGA polysaccharide does not seem to provide any significant benefit to Salmonella: resistance against chlorine treatment, ultraviolet light irradiation, heavy metal stress and phage infection remained the same as in a strain producing cellulose, the main biofilm exopolysaccharide naturally produced by Salmonella. In contrast, PGA production proved to be deleterious to Salmonella survival inside the host, since it increased susceptibility to bile salts and oxidative stress, and hindered the capacity of S. Enteritidis to survive inside macrophages and to colonize extraintestinal organs, including the gallbladder. Altogether, our observations indicate that PGA is an antivirulence factor whose loss may have been a necessary event during Salmonella speciation to permit survival inside the host. During bacterial evolution, specific traits that optimize the organism’s fitness are selected. The production of exopolysaccharides is widespread among bacteria in which they play a protective shielding role as main constituents of biofilms. In contrast to closely related siblings, Salmonella has lost the capacity to produce the exopolysaccharide PGA. Our study reveals that Salmonella lost pga genes, and that the driving force for such a loss may have been the detrimental impact that PGA has during Salmonella invasion of internal organs where it augments the susceptibility to bile salts and oxygen radicals, reducing bacterial survival inside macrophages and rendering Salmonella avirulent. These results suggest that gene-loss has played an important role during Salmonella evolution.
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Affiliation(s)
- Maite Echeverz
- Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain
| | - Begoña García
- Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain
| | - Amaia Sabalza
- Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain
| | - Jaione Valle
- Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Cristina Solano
- Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain
- * E-mail: (CS); (IL)
| | - Iñigo Lasa
- Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain
- * E-mail: (CS); (IL)
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7
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Kubera A, Thamchaipenet A, Shoham M. Biofilm inhibitors targeting the outer membrane protein A of Pasteurella multocida in swine. BIOFOULING 2017; 33:14-23. [PMID: 27892689 DOI: 10.1080/08927014.2016.1259415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/06/2016] [Indexed: 06/06/2023]
Abstract
Pasteurella multocida (Pm) is the causative agent of atrophic rhinitis in swine. This study aimed to discover biofilm inhibitors against swine Pm to counteract antibiotic resistance and decrease virulence. The virulence factor outer membrane protein A (OmpA) was targeted. A library of drugs approved by the Food and Drug Administration (FDA) was used to perform virtual screening against PmOmpA. The top-scoring compounds had no effect on the growth of Pm serotype A or D. Mycophenolate mofetil showed the highest efficacy in inhibiting biofilm formation by Pm serotype A, with an IC50 of 7.3 nM. For Pm serotype D, indocyanine green showed the highest effect at an IC50 of 11.7 nM. Nevertheless, these compounds had no effect on an established biofilm of Pm. This study offers an alternative way to prevent biofilm formation by Pm that could also be applied to other pathogens.
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Affiliation(s)
- Anchanee Kubera
- a Department of Genetics , Faculty of Science, Kasetsart University , Bangkok , Thailand
- b Centre for Advanced Studies in Tropical Natural Resources , Kasetsart University , Bangkok , Thailand
| | - Arinthip Thamchaipenet
- a Department of Genetics , Faculty of Science, Kasetsart University , Bangkok , Thailand
- b Centre for Advanced Studies in Tropical Natural Resources , Kasetsart University , Bangkok , Thailand
| | - Menachem Shoham
- c Department of Biochemistry , Case Western Reserve University , Cleveland, OH , USA
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Bakour S, Sankar SA, Rathored J, Biagini P, Raoult D, Fournier PE. Identification of virulence factors and antibiotic resistance markers using bacterial genomics. Future Microbiol 2016; 11:455-66. [PMID: 26974504 DOI: 10.2217/fmb.15.149] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In recent years, the number of multidrug-resistant bacteria has increased rapidly and several epidemics were signaled in different regions of the world. Faced with this situation that presents a major global public health concern, the development and the use of new and rapid technologies is more than urgent. The use of the next-generation sequencing platforms by microbiologists and infectious disease specialists has allowed great progress in the medical field. Here, we review the usefulness of whole-genome sequencing for the detection of virulence and antibiotic resistance associated genes.
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Affiliation(s)
- Sofiane Bakour
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Senthil Alias Sankar
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Jaishriram Rathored
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Philippe Biagini
- UMR CNRS 7268 Equipe "Emergence et coévolution virale," Etablissement Français du Sang Alpes-Méditerranée et Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille
| | - Didier Raoult
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Pierre-Edouard Fournier
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
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9
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Wang J, Qiu S, Xu X, Su W, Li P, Liang B, Ma Q, Yang C, Qi L, Li H, Yi S, Wu Z, Wang L, Hao R, Song H, Sun Y. Emergence of ONPG-negative Shigella sonnei in Shanghai, China. Diagn Microbiol Infect Dis 2015; 83:338-40. [PMID: 26403725 DOI: 10.1016/j.diagmicrobio.2015.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/08/2015] [Accepted: 08/17/2015] [Indexed: 11/30/2022]
Abstract
Shigella sonnei has become predominant species causing shigellosis in Shanghai. Two hundred ninety-three S. sonnei were isolated in sentinel hospitals of Shanghai in 2011. We found an emergence of 8 strains of S. sonnei with negative phenotype for o-nitrophenyl-β-d-galactopyranoside in late August, which showed distinct pulsed-field gel electrophoresis patterns from the other 285 S. sonnei and had genes deletion in lac and mhp operons.
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Affiliation(s)
- Jian Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Shaofu Qiu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Xuebin Xu
- Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, China
| | - Wenli Su
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Peng Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Beibei Liang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Qiuxia Ma
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Chaojie Yang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Lihua Qi
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Hao Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Shengjie Yi
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Zhihao Wu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Ligui Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Rongzhang Hao
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Hongbin Song
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China.
| | - Yansong Sun
- Department of Science and Technology, Academy of Military Medical Sciences, Beijing, China.
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Leonard SR, Lacher DW, Lampel KA. Acquisition of the lac operon by Salmonella enterica. BMC Microbiol 2015; 15:173. [PMID: 26303940 PMCID: PMC4549013 DOI: 10.1186/s12866-015-0511-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/17/2015] [Indexed: 12/05/2022] Open
Abstract
Background Classical bacteriological characteristics of Salmonella enterica indicate that the members of this species are unable to utilize lactose as a carbon source. However, lactose-fermenting (Lac+) strains of several Salmonella serovars have been isolated from different foodborne outbreaks as well as different geographical regions worldwide. In the present study, we sequenced the genomes of 13 Lac + S. enterica isolates and characterized the lac region, comparing it to the lac region in other enteric bacterial species. Results Genetic analysis of the lac operons in the S. enterica genomes revealed that they all contain intact lacI, lacZ, and lacY genes. However, lacA was truncated in all of the S. enterica subsp. enterica isolates, encoding a 56 amino acid peptide rather than the full length 220 amino acid LacA protein. Molecular analyses of the 13 isolates revealed that the lac operon resided on a plasmid in some strains and in others was integrated into the bacterial chromosome. In most cases, an insertion sequence flanked at least one end of the operon. Interestingly, the S. enterica Montevideo and S. enterica Senftenberg isolates were found to harbor a plasmid with a high degree of sequence similarity to a plasmid from Klebsiella pneumoniae strain NK29 that also harbors the lac operon. In addition, two S. enterica Tennessee isolates carried two copies of the lac operon. Phylogenetic analysis based on lacIZY gene sequences determines distinct clusters, and reveals a greater correlation between lacIZY sequence and flanking organization than with either bacterial species or genomic location. Conclusions Our results indicate that the lac region is highly mobile among Enterobacteriaceae and demonstrate that the Lac + S. enterica subsp. enterica serovars acquired the lac region through parallel events. The acquisition of the lac operon by several S. enterica serovars may be indicative of environmental adaptation by these bacteria. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0511-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susan R Leonard
- Division of Molecular Biology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
| | - David W Lacher
- Division of Molecular Biology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
| | - Keith A Lampel
- Division of Molecular Biology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
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Loss of the lac Operon Contributes to Salmonella Invasion of Epithelial Cells Through Derepression of Flagellar Synthesis. Curr Microbiol 2014; 70:315-23. [DOI: 10.1007/s00284-014-0720-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 09/18/2014] [Indexed: 12/12/2022]
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12
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Lahiri C, Pawar S, Sabarinathan R, Ashraf MI, Chand Y, Chakravortty D. Interactome analyses of Salmonella pathogenicity islands reveal SicA indispensable for virulence. J Theor Biol 2014; 363:188-97. [PMID: 25128737 DOI: 10.1016/j.jtbi.2014.08.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/13/2014] [Accepted: 08/05/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Serovars of Salmonella enterica, namely Typhi and Typhimurium, reportedly, are the bacterial pathogens causing systemic infections like gastroenteritis and typhoid fever. To elucidate the role and importance in such infection, the proteins of the Type III secretion system of Salmonella pathogenicity islands and two component signal transduction systems, have been mainly focused. However, the most indispensable of these virulent ones and their hierarchical role has not yet been studied extensively. RESULTS We have adopted a theoretical approach to build an interactome comprising the proteins from the Salmonella pathogeneicity islands (SPI) and two component signal transduction systems. This interactome was then analyzed by using network parameters like centrality and k-core measures. An initial step to capture the fingerprint of the core network resulted in a set of proteins which are involved in the process of invasion and colonization, thereby becoming more important in the process of infection. These proteins pertained to the Inv, Org, Prg, Sip, Spa, Ssa and Sse operons along with chaperone protein SicA. Amongst them, SicA was figured out to be the most indispensable protein from different network parametric analyses. Subsequently, the gene expression levels of all these theoretically identified important proteins were confirmed by microarray data analysis. Finally, we have proposed a hierarchy of the proteins involved in the total infection process. This theoretical approach is the first of its kind to figure out potential virulence determinants encoded by SPI for therapeutic targets for enteric infection. CONCLUSIONS A set of responsible virulent proteins was identified and the expression level of their genes was validated by using independent, published microarray data. The result was a targeted set of proteins that could serve as sensitive predictors and form the foundation for a series of trials in the wet-lab setting. Understanding these regulatory and virulent proteins would provide insight into conditions which are encountered by this intracellular enteric pathogen during the course of infection. This would further contribute in identifying novel targets for antimicrobial agents.
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Affiliation(s)
- Chandrajit Lahiri
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.
| | - Shrikant Pawar
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
| | | | - Md Izhar Ashraf
- B.S. Abdur Rahman University, Vandalur, Chennai 600048, India.
| | - Yamini Chand
- Department of Bioinformatics, Karunya University, Coimbatore 641114, India.
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.
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Chakraborty S, Chaudhuri D, Balakrishnan A, Chakravortty D. Salmonella methylglyoxal detoxification by STM3117-encoded lactoylglutathione lyase affects virulence in coordination with Salmonella pathogenicity island 2 and phagosomal acidification. MICROBIOLOGY-SGM 2014; 160:1999-2017. [PMID: 24961952 DOI: 10.1099/mic.0.078998-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Intracellular pathogens such as Salmonella enterica serovar Typhimurium (S. Typhimurium) manipulate their host cells through the interplay of various virulence factors. A multitude of such virulence factors are encoded on the genome of S. Typhimurium and are usually organized in pathogenicity islands. The virulence-associated genomic stretch of STM3117-3120 has structural features of pathogenicity islands and is present exclusively in non-typhoidal serovars of Salmonella. It encodes metabolic enzymes predicted to be involved in methylglyoxal metabolism. STM3117-encoded lactoylglutathione lyase significantly impacts the proliferation of intracellular Salmonella. The deletion mutant of STM3117 (Δlgl) fails to grow in epithelial cells but hyper-replicates in macrophages. This difference in proliferation outcome was the consequence of failure to detoxify methylglyoxal by Δlgl, which was also reflected in the form of oxidative DNA damage and upregulation of kefB in the mutant. Within macrophages, the toxicity of methylglyoxal adducts elicits the potassium efflux channel (KefB) in the mutant which subsequently modulates the acidification of mutant-containing vacuoles (MCVs). The perturbation in the pH of the MCV milieu and bacterial cytosol enhances the Salmonella pathogenicity island 2 translocation in Δlgl, increasing its net growth within macrophages. In epithelial cells, however, the maturation of Δlgl-containing vacuoles were affected as these non-phagocytic cells maintain less acidic vacuoles compared to those in macrophages. Remarkably, ectopic expression of Toll-like receptors 2 and 4 on epithelial cells partially restored the survival of Δlgl. This study identified a novel metabolic enzyme in S. Typhimurium whose activity during intracellular infection within a given host cell type differentially affected the virulence of the bacteria.
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Affiliation(s)
- Sangeeta Chakraborty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Debalina Chaudhuri
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Arjun Balakrishnan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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14
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Abstract
Attenuated Salmonella vaccines can be administered orally to deliver recombinant antigens to mucosal surfaces inducing a protective immune response against a variety of targeted pathogens. A number of exciting new approaches and technologies for attenuated Salmonella vaccines have been developed recently. However, a disconnect remains between results obtained with mice in preclinical studies and results obtained in human clinical trials. This is due to an incomplete understanding of Salmonella Typhi interactions with human hosts and inadequate animal models available for study. In this review, the authors describe recent progress in identifying important differences underlying S. Typhi-host interactions, the development of novel approaches to vaccine design and six recent clinical trials evaluating Salmonella-vectored vaccines.
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Affiliation(s)
- Kenneth L Roland
- The Biodesign Institute, Arizona State University, 1001 S. McAllister Avenue, Tempe, AZ 85287-5401, USA
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15
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Louwen R, Staals RHJ, Endtz HP, van Baarlen P, van der Oost J. The role of CRISPR-Cas systems in virulence of pathogenic bacteria. Microbiol Mol Biol Rev 2014; 78:74-88. [PMID: 24600041 PMCID: PMC3957734 DOI: 10.1128/mmbr.00039-13] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are present in many bacterial and archaeal genomes. Since the discovery of the typical CRISPR loci in the 1980s, well before their physiological role was revealed, their variable sequences have been used as a complementary typing tool in diagnostic, epidemiologic, and evolutionary analyses of prokaryotic strains. The discovery that CRISPR spacers are often identical to sequence fragments of mobile genetic elements was a major breakthrough that eventually led to the elucidation of CRISPR-Cas as an adaptive immunity system. Key elements of this unique prokaryotic defense system are small CRISPR RNAs that guide nucleases to complementary target nucleic acids of invading viruses and plasmids, generally followed by the degradation of the invader. In addition, several recent studies have pointed at direct links of CRISPR-Cas to regulation of a range of stress-related phenomena. An interesting example concerns a pathogenic bacterium that possesses a CRISPR-associated ribonucleoprotein complex that may play a dual role in defense and/or virulence. In this review, we describe recently reported cases of potential involvement of CRISPR-Cas systems in bacterial stress responses in general and bacterial virulence in particular.
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16
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Pei Y, Parreira VR, Roland KL, Curtiss R, Prescott JF. Assessment of attenuated Salmonella vaccine strains in controlling experimental Salmonella Typhimurium infection in chickens. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2014; 78:23-30. [PMID: 24396177 PMCID: PMC3878005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 03/15/2013] [Indexed: 06/03/2023]
Abstract
Salmonella hold considerable promise as vaccine delivery vectors for heterologous antigens in chickens. Such vaccines have the potential additional benefit of also controlling Salmonella infection in immunized birds. As a way of selecting attenuated strains with optimal immunogenic potential as antigen delivery vectors, this study screened 20 novel Salmonella Typhimurium vaccine strains, differing in mutations associated with delayed antigen synthesis and delayed attenuation, for their efficacy in controlling colonization by virulent Salmonella Typhimurium, as well as for their persistence in the intestine and the spleen. Marked differences were observed between strains in these characteristics, which provide the basis for selection for further study as vaccine vectors.
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Affiliation(s)
| | | | | | | | - John F. Prescott
- Address all correspondence to Dr. John F. Prescott; telephone: (519) 824-4120 ext. 54716; fax: (519) 824-5930; e-mail:
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17
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Abstract
The emergence of new pathogens and the exploitation of novel pathogenic niches by bacteria typically require the horizontal transfer of virulence factors and subsequent adaptation--a "fine-tuning" process--for the successful incorporation of these factors into the microbe's genome. The function of newly acquired virulence factors may be hindered by the expression of genes already present in the bacterium. Occasionally, certain genes must be inactivated or deleted for full expression of the pathogen phenotype to occur. These genes are known as antivirulence genes (AVGs). Originally identified in Shigella, AVGs have improved our understanding of pathogen evolution and provided a novel approach to drug and vaccine development. In this review, we revisit the AVG definition and update the list of known AVGs, which now includes genes from pathogens such as Salmonella, Yersinia pestis, and the virulent Francisella tularensis subspecies. AVGs encompass a wide variety of different roles within the microbe, including genes involved in metabolism, biofilm synthesis, lipopolysaccharide modification, and host vasoconstriction. More recently, the use of one of these AVGs (lpxL) as a potential vaccine candidate highlights the practical application of studying AVG inactivation in microbial pathogens.
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18
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Garai P, Gnanadhas DP, Chakravortty D. Salmonella enterica serovars Typhimurium and Typhi as model organisms: revealing paradigm of host-pathogen interactions. Virulence 2012; 3:377-88. [PMID: 22722237 PMCID: PMC3478240 DOI: 10.4161/viru.21087] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The lifestyle of intracellular pathogens has always questioned the skill of a microbiologist in the context of finding the permanent cure to the diseases caused by them. The best tool utilized by these pathogens is their ability to reside inside the host cell, which enables them to easily bypass the humoral immunity of the host, such as the complement system. They further escape from the intracellular immunity, such as lysosome and inflammasome, mostly by forming a protective vacuole-bound niche derived from the host itself. Some of the most dreadful diseases are caused by these vacuolar pathogens, for example, tuberculosis by Mycobacterium or typhoid fever by Salmonella. To deal with such successful pathogens therapeutically, the knowledge of a host-pathogen interaction system becomes primarily essential, which further depends on the use of a model system. A well characterized pathogen, namely Salmonella, suits the role of a model for this purpose, which can infect a wide array of hosts causing a variety of diseases. This review focuses on various such aspects of research on Salmonella which are useful for studying the pathogenesis of other intracellular pathogens.
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Affiliation(s)
- Preeti Garai
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research and Biosafety Laboratories, Indian Institute of Science, Bangalore, India
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19
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Archetti M, Scheuring I, Hoffman M, Frederickson ME, Pierce NE, Yu DW. Economic game theory for mutualism and cooperation. Ecol Lett 2011; 14:1300-12. [DOI: 10.1111/j.1461-0248.2011.01697.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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20
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Fookes M, Schroeder GN, Langridge GC, Blondel CJ, Mammina C, Connor TR, Seth-Smith H, Vernikos GS, Robinson KS, Sanders M, Petty NK, Kingsley RA, Bäumler AJ, Nuccio SP, Contreras I, Santiviago CA, Maskell D, Barrow P, Humphrey T, Nastasi A, Roberts M, Frankel G, Parkhill J, Dougan G, Thomson NR. Salmonella bongori provides insights into the evolution of the Salmonellae. PLoS Pathog 2011; 7:e1002191. [PMID: 21876672 PMCID: PMC3158058 DOI: 10.1371/journal.ppat.1002191] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 06/21/2011] [Indexed: 02/05/2023] Open
Abstract
The genus Salmonella contains two species, S. bongori and S. enterica. Compared to the well-studied S. enterica there is a marked lack of information regarding the genetic makeup and diversity of S. bongori. S. bongori has been found predominantly associated with cold-blooded animals, but it can infect humans. To define the phylogeny of this species, and compare it to S. enterica, we have sequenced 28 isolates representing most of the known diversity of S. bongori. This cross-species analysis allowed us to confidently differentiate ancestral functions from those acquired following speciation, which include both metabolic and virulence-associated capacities. We show that, although S. bongori inherited a basic set of Salmonella common virulence functions, it has subsequently elaborated on this in a different direction to S. enterica. It is an established feature of S. enterica evolution that the acquisition of the type III secretion systems (T3SS-1 and T3SS-2) has been followed by the sequential acquisition of genes encoding secreted targets, termed effectors proteins. We show that this is also true of S. bongori, which has acquired an array of novel effector proteins (sboA-L). All but two of these effectors have no significant S. enterica homologues and instead are highly similar to those found in enteropathogenic Escherichia coli (EPEC). Remarkably, SboH is found to be a chimeric effector protein, encoded by a fusion of the T3SS-1 effector gene sopA and a gene highly similar to the EPEC effector nleH from enteropathogenic E. coli. We demonstrate that representatives of these new effectors are translocated and that SboH, similarly to NleH, blocks intrinsic apoptotic pathways while being targeted to the mitochondria by the SopA part of the fusion. This work suggests that S. bongori has inherited the ancestral Salmonella virulence gene set, but has adapted by incorporating virulence determinants that resemble those employed by EPEC.
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Affiliation(s)
- Maria Fookes
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gunnar N. Schroeder
- Centre for Molecular Microbiology and Infection, Division of Cell and Molecular Biology, Imperial College London, London, United Kingdom
| | - Gemma C. Langridge
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Carlos J. Blondel
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Caterina Mammina
- Dept. Sciences for Health Promotion “G. D'Alessandro”, University of Palermo, Palermo, Italy
| | - Thomas R. Connor
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Helena Seth-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Georgios S. Vernikos
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Keith S. Robinson
- Centre for Molecular Microbiology and Infection, Division of Cell and Molecular Biology, Imperial College London, London, United Kingdom
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nicola K. Petty
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Robert A. Kingsley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, United State of America
| | - Sean-Paul Nuccio
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, United State of America
| | - Inés Contreras
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Carlos A. Santiviago
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Duncan Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paul Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
| | - Tom Humphrey
- National Centre for Zoonosis Research, University of Liverpool, Leahurst Campus, Neston, Wirral, United Kingdom
| | | | - Mark Roberts
- Institute of Comparative Medicine, Faculty of Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Gad Frankel
- Centre for Molecular Microbiology and Infection, Division of Cell and Molecular Biology, Imperial College London, London, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nicholas R. Thomson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- * E-mail:
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21
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FliZ acts as a repressor of the ydiV gene, which encodes an anti-FlhD4C2 factor of the flagellar regulon in Salmonella enterica serovar typhimurium. J Bacteriol 2011; 193:5191-8. [PMID: 21804009 DOI: 10.1128/jb.05441-11] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
YdiV acts as an anti-FlhD4C2 factor, which negatively regulates the class 2 flagellar operons in poor medium in Salmonella enterica serovar Typhimurium. On the other hand, one of the class 2 flagellar genes, fliZ, encodes a positive regulator of the class 2 operons. In this study, we found that the FliZ-dependent activation of class 2 operon expression was more profound in poor medium than in rich medium and not observed in the ydiV mutant background. Transcription of the ydiV gene was shown to increase in the fliZ mutant. Purified FliZ protein was shown in vitro to bind to the promoter region of the nlpC gene, which is located just upstream of the ydiV gene, and to repress its transcription. These results indicate that FliZ is a repressor of the nlpC-ydiV operon and activates the class 2 operons by repressing ydiV expression. Therefore, the fliZ and ydiV genes form a regulatory loop.
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22
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Shelburne SA, Sahasrobhajane P, Suber B, Keith DB, Davenport MT, Horstmann N, Kumaraswami M, Olsen RJ, Brennan RG, Musser JM. Niche-specific contribution to streptococcal virulence of a MalR-regulated carbohydrate binding protein. Mol Microbiol 2011; 81:500-14. [PMID: 21645132 DOI: 10.1111/j.1365-2958.2011.07708.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Low G+C Gram-positive bacteria typically contain multiple LacI/GalR regulator family members, which often have highly similar amino-terminal DNA binding domains, suggesting significant overlap in target DNA sequences. The LacI/GalR family regulator catabolite control protein A (CcpA) is a global regulator of the Group A Streptococcus (GAS) transcriptome and contributes to GAS virulence in diverse infection sites. Herein, we studied the role of the maltose repressor (MalR), another LacI/GalR family member, in GAS global gene expression and virulence. MalR inactivation reduced GAS colonization of the mouse oropharynx but did not detrimentally affect invasive infection. The MalR transcriptome was limited to only 25 genes, and a highly conserved MalR DNA-binding sequence was identified. Variation of the MalR binding sequence significantly reduced MalR binding in vitro. In contrast, CcpA bound to the same DNA sequences as MalR but tolerated variation in the promoter sequences with minimal change in binding affinity. Inactivation of pulA, a MalR regulated gene which encodes a cell surface carbohydrate binding protein, significantly reduced GAS human epithelial cell adhesion and mouse oropharyngeal colonization but did not affect GAS invasive disease. These data delineate a molecular mechanism by which hierarchical regulation of carbon source utilization influences bacterial pathogenesis in a site-specific fashion.
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Affiliation(s)
- Samuel A Shelburne
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, TX 77030, USA.
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The ferritin-like protein Dps protects Salmonella enterica serotype Enteritidis from the Fenton-mediated killing mechanism of bactericidal antibiotics. Int J Antimicrob Agents 2011; 37:261-5. [PMID: 21295952 DOI: 10.1016/j.ijantimicag.2010.11.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 10/26/2010] [Accepted: 11/22/2010] [Indexed: 11/20/2022]
Abstract
Dps is a ferritin-like protein with DNA-binding properties that is capable of affording protection during oxidative stress and during times of nutritional deprivation. Here we present evidence that in exponentially growing Salmonella enterica serotype Enteritidis, Dps is vital for protection against the common killing mechanism of bactericidal antibiotics, a mechanism manifested by hydroxyl radical production via the Fenton reaction. A dps deletion mutant ('dps mutant') was hypersensitive to the bactericidal antibiotics streptomycin, nalidixic acid, norfloxacin and rifampicin compared with its parental strain. However, the observed discrepancy in survivability between the dps mutant and the parental strain following exposure to bactericidal antibiotics was fully alleviated when drug-exposed cultures were treated with an iron chelator, confirming that Fenton-mediated oxidative stress was a major factor in the reduced survival rate of the dps mutant. In addition, deletion of the DNA damage-induced repair protein RecA further intensified the killing capacity of bactericidal antibiotics in a Δdps (i.e. dps deletion) background, implying that Dps and RecA may operate in a synergistic manner to protect against the common killing mechanism of bactericidal antibiotics. The relevance of this work is demonstrated by the need for new and increasingly effective bactericidal therapies. Targeting Dps may represent a means to increase the potency of bactericidal antibiotics in S. enterica and other bacterial pathogens alike.
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Comparison of a regulated delayed antigen synthesis system with in vivo-inducible promoters for antigen delivery by live attenuated Salmonella vaccines. Infect Immun 2010; 79:937-49. [PMID: 21134969 DOI: 10.1128/iai.00445-10] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Induction of strong immune responses against a vectored antigen in hosts immunized with live attenuated Salmonella vaccines is related in part to the amount of antigen delivered and the overall fitness of the Salmonella vector in relation to its ability to stimulate the host immune system. Constitutive high-level antigen synthesis causes a metabolic burden to the vaccine vector strain that can reduce the vaccine strain's ability to interact with host lymphoid tissues, resulting in a compromised immune response. A solution to this problem is the use of systems that regulate antigen gene expression, permitting high levels of antigen synthesis only after the vaccine strain has reached its target tissues. In vivo-inducible promoters (IVIPs) are often used to accomplish this. We recently developed an alternative strategy, a regulated delayed antigen synthesis (RDAS) system, in which the LacI-repressible P(trc) promoter controls antigen gene expression by adding arabinose. In this paper, we compared the RDAS system with two commonly used IVIPs, P(ssaG) and P(pagC). Three nearly identical plasmids, differing only in the promoter used to direct transcription of the pneumococcal pspA gene, P(trc), P(ssaG), or P(pagC), were constructed and introduced into isogenic Salmonella vaccine strains with or without arabinose-inducible LacI synthesis. Mice immunized with the RDAS strain developed slightly higher titers of mucosal and serum anti-PspA antibodies than P(pagC)-immunized mice, while titers in mice immunized with the P(ssaG) strain were 100-fold lower. Both the RDAS and P(pagC) strains conferred similar levels of protection against Streptococcus pneumoniae challenge, significantly greater than those for the P(ssaG) strain or controls. Thus, RDAS provides another choice for inclusion in the live vaccine design to increase immunogenicity.
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25
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Archetti M, Ubeda F, Fudenberg D, Green J, Pierce NE, Yu DW. Let the right one in: a microeconomic approach to partner choice in mutualisms. Am Nat 2010; 177:75-85. [PMID: 21091210 DOI: 10.1086/657622] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
One of the main problems impeding the evolution of cooperation is partner choice. When information is asymmetric (the quality of a potential partner is known only to himself), it may seem that partner choice is not possible without signaling. Many mutualisms, however, exist without signaling, and the mechanisms by which hosts might select the right partners are unclear. Here we propose a general mechanism of partner choice, "screening," that is similar to the economic theory of mechanism design. Imposing the appropriate costs and rewards may induce the informed individuals to screen themselves according to their types and therefore allow a noninformed individual to establish associations with the correct partners in the absence of signaling. Several types of biological symbioses are good candidates for screening, including bobtail squid, ant-plants, gut microbiomes, and many animal and plant species that produce reactive oxygen species. We describe a series of diagnostic tests for screening. Screening games can apply to the cases where by-products, partner fidelity feedback, or host sanctions do not apply, therefore explaining the evolution of mutualism in systems where it is impossible for potential symbionts to signal their cooperativeness beforehand and where the host does not punish symbiont misbehavior.
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Affiliation(s)
- Marco Archetti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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Salmonella vaccine vectors displaying delayed antigen synthesis in vivo to enhance immunogenicity. Infect Immun 2010; 78:3969-80. [PMID: 20605977 DOI: 10.1128/iai.00444-10] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We have developed a regulated delayed antigen synthesis (RDAS) system for use in recombinant attenuated Salmonella vaccine (RASV) strains to enhance immune responses by reducing the adverse effects of high-level antigen synthesis. This system includes a chromosomal repressor gene, lacI, expressed from the arabinose-regulated araC PBAD promoter. LacI serves to regulate expression from a plasmid promoter, Ptrc, that directs antigen synthesis. In the presence of arabinose LacI is produced, which binds to Ptrc, blocking antigen synthesis. In vivo, an arabinose-poor environment, the concentration of LacI decreases with each cell division, allowing increased antigen synthesis. To optimize the system and for comparison, we altered the lacI ribosome-binding site, start codon, and/or codon content to construct RDAS strains chi9095, chi9959, and chi9241, synthesizing from low to high levels of LacI, respectively, and non-RDAS strain chi9555 as a control. We evaluated this system with two test antigens, the green fluorescent protein for initial in vitro assessment and the Streptococcus pneumoniae PspA protein for validation of our system in mice. All RASV strains expressing PspA generated high antilipopolysaccharide antibody titers, indicating that expression of lacI did not interfere with the capacity to induce an immune response. Strain chi9241 induced significantly higher anti-PspA IgG and IgA antibody titers than strain chi9555, which expressed PspA constitutively. Anti-PspA antibody titers were inversely correlated to the level of LacI synthesis. Strain chi9241 also induced significantly greater protective efficacy against challenge with virulent S. pneumoniae. These results suggest that regulated delayed antigen synthesis is useful for improving immunogenicity of RASV strains.
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A pathoadaptive deletion in an enteroaggregative Escherichia coli outbreak strain enhances virulence in a Caenorhabditis elegans model. Infect Immun 2010; 78:4068-76. [PMID: 20584976 DOI: 10.1128/iai.00014-10] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) strains are important diarrheal pathogens. EAEC strains are defined by their characteristic stacked-brick pattern of adherence to epithelial cells but show heterogeneous virulence and have different combinations of adhesin and toxin genes. Pathoadaptive deletions in the lysine decarboxylase (cad) genes have been noted among hypervirulent E. coli subtypes of Shigella and enterohemorrhagic E. coli. To test the hypothesis that cad deletions might account for heterogeneity in EAEC virulence, we developed a Caenorhabditis elegans pathogenesis model. Well-characterized EAEC strains were shown to colonize and kill C. elegans, and differences in virulence could be measured quantitatively. Of 49 EAEC strains screened for lysine decarboxylase activity, 3 tested negative. Most notable is isolate 101-1, which was recovered in Japan, from the largest documented EAEC outbreak. EAEC strain 101-1 was unable to decarboxylate lysine in vitro due to deletions in cadA and cadC, which, respectively, encode lysine decarboxylase and a transcriptional activator of the cadAB genes. Strain 101-1 was significantly more lethal to C. elegans than control strain OP50. Lethality was attenuated when the lysine decarboxylase defect was complemented from a multicopy plasmid and in single copy. In addition, restoring lysine decarboxylase function produced derivatives of 101-1 deficient in aggregative adherence to cultured human epithelial cells. Lysine decarboxylase inactivation is pathoadapative in an important EAEC outbreak strain, and deletion of cad genes could produce hypervirulent EAEC lineages in the future. These results suggest that loss, as well as gain, of genetic material can account for heterogeneous virulence among EAEC strains.
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