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Kumari K, Aggarwal Y, Singh RP. Molecular characterization and in-depth genomic analysis to unravel the pathogenic features of an environmental isolate Enterobacter sp. S-33. Int Microbiol 2024; 27:1095-1110. [PMID: 38044418 DOI: 10.1007/s10123-023-00461-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/05/2023]
Abstract
Enterobacter species represent widely distributed opportunistic pathogens, commonly associated with plants and humans. In the present study, we performed a detailed molecular characterization as well as genomic study of a type VI secretion system (T6SS) bacterium belonging to member of the family Enterobacteriaceae and named Enterobacter sp. S-33. The comparative sequence analysis of the 16S rRNA gene showed that the strain was closely related to other Enterobacter species. The complete genome of the strain with a genome size of 4.6 Mbp and GC-content of 55.63% was obtained through high-quality sequencing. The genomic analysis with online tools unravelled the various genes belonging to the bacterial secretion system, antibiotic resistance, virulence, efflux pumps, etc. The isolate showed the motility behavior that contributes to Enterobacter persistence in a stressed environment and further supports infections. PCR amplification and further sequencing confirmed the presence of drug-efflux genes acrA, acrB, and outer membrane genes, viz. OmpA, OmpC, and OmpF. The cell surface hydrophobicity and co-aggregation assay against different bacterial strains illustrated its putative pathogenic nature. Genome mining identified various biosynthetic gene clusters (BGCs) corresponding to non-ribosomal proteins (NRPS), siderophore, and arylpolyene production. Briefly, genome sequencing and detailed characterization of environmental Enterobacter isolate will assist in understanding the epidemiology of Enterobacter species, and the further prevention and treatment of infectious diseases caused by these broad-host range species.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Yogender Aggarwal
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Rajnish Prakash Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India.
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2
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Abril AG, Calo-Mata P, Villa TG, Böhme K, Barros-Velázquez J, Sánchez-Pérez Á, Pazos M, Carrera M. Comprehensive shotgun proteomic characterization and virulence factors of seafood spoilage bacteria. Food Chem 2024; 448:139045. [PMID: 38537549 DOI: 10.1016/j.foodchem.2024.139045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/01/2024] [Accepted: 03/13/2024] [Indexed: 04/24/2024]
Abstract
This article summarizes the characterization, by shotgun proteomics, of 11 bacterial strains identified as responsible for seafood spoilage. A total of 4455 peptide spectrum matches, corresponding to 4299 peptides and 3817 proteins were identified. Analyses of data determined the functional pathways they are involved in. The proteins identified were integrated into a protein-protein network that involves 371 nodes and 3016 edges. Those proteins are implicated in energy pathways, peptidoglycan biosynthesis, spermidine/putrescine metabolism. An additional 773 peptides were characterized as virulence factors, that participates in bacterial pathogenesis; while 14 peptides were defined as biomarkers, as they can be used to differentiate the bacterial species present. This report represents the most extensive proteomic repository available in the field of seafood spoilage bacteria; the data substantially advances the understanding of seafood decay, as well as provides fundamental bases for the recognition of the bacteria existent in seafood that cause spoilage during food processing/storage.
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Affiliation(s)
- Ana G Abril
- Institute of Marine Research (IIM-CSIC), Department of Food Technology, Spanish National Research Council (CSIC), 36208 Vigo, Spain; Faculty of Pharmacy, University of Santiago de Compostela, Department of Microbiology and Parasitology, 15898 Santiago de Compostela, Spain.
| | - Pilar Calo-Mata
- School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, 27002 Lugo, Spain.
| | - Tomás G Villa
- Faculty of Pharmacy, University of Santiago de Compostela, Department of Microbiology and Parasitology, 15898 Santiago de Compostela, Spain.
| | - Karola Böhme
- School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, 27002 Lugo, Spain.
| | - Jorge Barros-Velázquez
- School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, 27002 Lugo, Spain.
| | - Ángeles Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia.
| | - Manuel Pazos
- Institute of Marine Research (IIM-CSIC), Department of Food Technology, Spanish National Research Council (CSIC), 36208 Vigo, Spain.
| | - Mónica Carrera
- Institute of Marine Research (IIM-CSIC), Department of Food Technology, Spanish National Research Council (CSIC), 36208 Vigo, Spain.
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3
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Benyamini P. Phylogenetic Tracing of Evolutionarily Conserved Zonula Occludens Toxin Reveals a "High Value" Vaccine Candidate Specific for Treating Multi-Strain Pseudomonas aeruginosa Infections. Toxins (Basel) 2024; 16:271. [PMID: 38922165 PMCID: PMC11209546 DOI: 10.3390/toxins16060271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/09/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
Extensively drug-resistant Pseudomonas aeruginosa infections are emerging as a significant threat associated with adverse patient outcomes. Due to this organism's inherent properties of developing antibiotic resistance, we sought to investigate alternative strategies such as identifying "high value" antigens for immunotherapy-based purposes. Through extensive database mining, we discovered that numerous Gram-negative bacterial (GNB) genomes, many of which are known multidrug-resistant (MDR) pathogens, including P. aeruginosa, horizontally acquired the evolutionarily conserved gene encoding Zonula occludens toxin (Zot) with a substantial degree of homology. The toxin's genomic footprint among so many different GNB stresses its evolutionary importance. By employing in silico techniques such as proteomic-based phylogenetic tracing, in conjunction with comparative structural modeling, we discovered a highly conserved intermembrane associated stretch of 70 amino acids shared among all the GNB strains analyzed. The characterization of our newly identified antigen reveals it to be a "high value" vaccine candidate specific for P. aeruginosa. This newly identified antigen harbors multiple non-overlapping B- and T-cell epitopes exhibiting very high binding affinities and can adopt identical tertiary structures among the least genetically homologous P. aeruginosa strains. Taken together, using proteomic-driven reverse vaccinology techniques, we identified multiple "high value" vaccine candidates capable of eliciting a polarized immune response against all the P. aeruginosa genetic variants tested.
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Affiliation(s)
- Payam Benyamini
- Department of Health Sciences at Extension, University of California Los Angeles, 1145 Gayley Ave., Los Angeles, CA 90024, USA
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4
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de Melo AG, Morency C, Moineau S. Virulence-associated factors as targets for phage infection. Curr Opin Microbiol 2024; 79:102471. [PMID: 38569419 DOI: 10.1016/j.mib.2024.102471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024]
Abstract
Bacterial pathogens can infect a wide range of hosts and pose a threat to public and animal health as well as to agriculture. The emergence of antibiotic-resistant strains has increased this risk by making the treatment of bacterial infections even more challenging. Pathogenic bacteria thrive in various ecological niches, but they can also be specifically targeted and killed by bacteriophages (phages). Lytic phages are now investigated and even used, in some cases, as alternatives or complements to antibiotics for preventing or treating bacterial infections (phage therapy). As such, it is key to identify factors responsible for phage specificity and efficiency. Here, we review recent advances in virulence-associated factors that are targeted by phages. We highlight components of the bacterial cell surface, effector systems, and motility structures exploited by phages and the effects of phages on cell aggregation and communication. We also look at the fitness trade-off of phage resistance.
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Affiliation(s)
- Alessandra G de Melo
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Québec City, QC G1V 0A6, Canada
| | - Carlee Morency
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Québec City, QC G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Québec City, QC G1V 0A6, Canada; Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, QC G1V 0A6, Canada.
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5
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Afsharian M, Asadi S, Danesh C, Sedighi R, Karimi K, Miladi N, Miladi R, Azizi M, Madadi-Goli N, Ahmadi K, Zamanian MH. The Abundance of Plasmid-Mediated Quinolone Resistance Genes in Enterobacter cloacae Strains Isolated from Clinical Specimens in Kermanshah, Iran. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2024; 2024:8849097. [PMID: 38623587 PMCID: PMC11018368 DOI: 10.1155/2024/8849097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/07/2024] [Accepted: 03/23/2024] [Indexed: 04/17/2024]
Abstract
Background Enterobacter cloacae (E. cloacae) is one of the most common Enterobacteriaceae causing nosocomial infections. Plasmid-mediated quinolone resistance (PMQR) determinants have been considered recently. This study evaluated the abundance of PMQR genes in strains of E. cloacae obtained from clinical samples in Kermanshah, Iran. Methods In this descriptive cross-sectional study, after collecting 113 isolates of E. cloacae, their identity was confirmed using specific biochemical tests. After determining their drug resistance patterns using disc diffusion, the phenotypic frequency of extended-spectrum beta-lactamase (ESBL)-producing isolates was measured by the double-disk synergy test (DDST) method. The isolates were examined for the presence of qnrA, qnrB, qnrS, and aac(6')-Ib-cr genes by the polymerase chain reaction (PCR) assay. Results The antibiotic resistance rate of E. cloacae isolates varied from 9.7% to 60.2%; among them, 78% were multidrug-resistant (MDR). The highest quinolone resistance was observed in ESBL-producing strains of E. cloacae. The frequency of positive isolates for PMQR and ESBL was 79.6% and 57.5%, respectively. The genes aac(6')-ib-cr (70.8%) and qnrB (38.1%) had the highest frequency among other genes. The number of isolates simultaneously carrying 2 and 3 genes was 64 and 5 isolates, respectively. Conclusion The obtained results indicate a high degree of quinolone resistance among ESBL-producing E. cloacae strains. Nevertheless, there was a significant relationship between the PMQR gene and ESBL-positive isolates. Therefore, special attention should be paid to molecular epidemiological studies on antibiotic resistance to quinolones and beta-lactamases in these strains.
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Affiliation(s)
- Mandana Afsharian
- Department of Infectious Disease, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Somayeh Asadi
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Camellia Danesh
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Reza Sedighi
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Kohsar Karimi
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Nooshin Miladi
- Department of Pediatrics, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ronak Miladi
- Department of Infectious Disease, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Azizi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Nahid Madadi-Goli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Kamal Ahmadi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Hossein Zamanian
- Department of Infectious Disease, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
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6
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Abril AG, Calo-Mata P, Villa TG, Böhme K, Barros-Velázquez J, Sánchez-Pérez Á, Pazos M, Carrera M. High-Resolution Comparative and Quantitative Proteomics of Biogenic-Amine-Producing Bacteria and Virulence Factors Present in Seafood. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4448-4463. [PMID: 38364257 PMCID: PMC10906483 DOI: 10.1021/acs.jafc.3c06607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 02/18/2024]
Abstract
The presence of biogenic amines (histamine, tyramine, putrescine, and cadaverine) in seafood is a significant concern for food safety. This review describes for the first time a shotgun quantitative proteomics strategy to evaluate and compare foodborne strains of bacteria that produce biogenic amines in seafoods. This approach recognized 35,621 peptide spectrum matches, belonging to 20,792 peptides, and 4621 proteins. It allowed the determination of functional pathways and the classification of the strains into hierarchical clusters. The study identified a protein-protein interaction network involving 1160 nodes/10,318 edges. Proteins were related to energy pathways, spermidine biosynthesis, and putrescine metabolism. Label-free quantitative proteomics allowed the identification of differentially regulated proteins in specific strains such as putrescine aminotransferase, arginine decarboxylase, and l-histidine-binding protein. Additionally, 123 peptides were characterized as virulence factors and 299 peptide biomarkers were selected to identify bacterial species in fish products. This study presents the most extensive proteomic repository and progress in the science of food biogenic bacteria and could be applied in the food industry for the detection of bacterial contamination that produces histamine and other biogenic amines during food processing/storage.
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Affiliation(s)
- Ana G. Abril
- Department
of Food Technology, Spanish National Research
Council (CSIC), Institute of Marine Research (IIM-CSIC), 36208 Vigo, Spain
- Department
of Microbiology and Parasitology, Faculty
of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain
| | - Pilar Calo-Mata
- Department
of Analytical Chemistry, Nutrition and Food Science, Food Technology
Division, School of Veterinary Sciences,
University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Tomás G. Villa
- Department
of Microbiology and Parasitology, Faculty
of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain
| | - Karola Böhme
- Department
of Analytical Chemistry, Nutrition and Food Science, Food Technology
Division, School of Veterinary Sciences,
University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Jorge Barros-Velázquez
- Department
of Analytical Chemistry, Nutrition and Food Science, Food Technology
Division, School of Veterinary Sciences,
University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Ángeles Sánchez-Pérez
- Sydney
School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Manuel Pazos
- Department
of Food Technology, Spanish National Research
Council (CSIC), Institute of Marine Research (IIM-CSIC), 36208 Vigo, Spain
| | - Mónica Carrera
- Department
of Food Technology, Spanish National Research
Council (CSIC), Institute of Marine Research (IIM-CSIC), 36208 Vigo, Spain
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7
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Shah M, Anwar A, Qasim A, Jaan S, Sarfraz A, Ullah R, Ali EA, Nishan U, Shehroz M, Zaman A, Ojha SC. Proteome level analysis of drug-resistant Prevotella melaninogenica for the identification of novel therapeutic candidates. Front Microbiol 2023; 14:1271798. [PMID: 37808310 PMCID: PMC10556700 DOI: 10.3389/fmicb.2023.1271798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/30/2023] [Indexed: 10/10/2023] Open
Abstract
The management of infectious diseases has become more critical due to the development of novel pathogenic strains with enhanced resistance. Prevotella melaninogenica, a gram-negative bacterium, was found to be involved in various infections of the respiratory tract, aerodigestive tract, and gastrointestinal tract. The need to explore novel drug and vaccine targets against this pathogen was triggered by the emergence of antimicrobial resistance against reported antibiotics to combat P. melaninogenica infections. The study involves core genes acquired from 14 complete P. melaninogenica strain genome sequences, where promiscuous drug and vaccine candidates were explored by state-of-the-art subtractive proteomics and reverse vaccinology approaches. A stringent bioinformatics analysis enlisted 18 targets as novel, essential, and non-homologous to humans and having druggability potential. Moreover, the extracellular and outer membrane proteins were subjected to antigenicity, allergenicity, and physicochemical analysis for the identification of the candidate proteins to design multi-epitope vaccines. Two candidate proteins (ADK95685.1 and ADK97014.1) were selected as the best target for the designing of a vaccine construct. Lead B- and T-cell overlapped epitopes were joined to generate potential chimeric vaccine constructs in combination with adjuvants and linkers. Finally, a prioritized vaccine construct was found to have stable interactions with the human immune cell receptors as confirmed by molecular docking and MD simulation studies. The vaccine construct was found to have cloning and expression ability in the bacterial cloning system. Immune simulation ensured the elicitation of significant immune responses against the designed vaccine. In conclusion, our study reported novel drug and vaccine targets and designed a multi-epitope vaccine against the P. melaninogenica infection. Further experimental validation will help open new avenues in the treatment of this multi-drug-resistant pathogen.
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Affiliation(s)
- Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Amna Anwar
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Aqsa Qasim
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Samavia Jaan
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Asifa Sarfraz
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Riaz Ullah
- Medicinal Aromatic and Poisonous Plants Research Center, College of Pharmacy King Saud University, Riyadh, Saudi Arabia
| | - Essam A. Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science and Technology, Kohat, Pakistan
| | - Muhammad Shehroz
- Department of Bioinformatics, Kohsar University Murree, Murree, Pakistan
| | - Aqal Zaman
- Department of Microbiology and Molecular Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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8
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Astley RA, Mursalin MH, Coburn PS, Livingston ET, Nightengale JW, Bagaruka E, Hunt JJ, Callegan MC. Ocular Bacterial Infections: A Ten-Year Survey and Review of Causative Organisms Based on the Oklahoma Experience. Microorganisms 2023; 11:1802. [PMID: 37512974 PMCID: PMC10386592 DOI: 10.3390/microorganisms11071802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Ocular infections can be medical emergencies that result in permanent visual impairment or blindness and loss of quality of life. Bacteria are a major cause of ocular infections. Effective treatment of ocular infections requires knowledge of which bacteria are the likely cause of the infection. This survey of ocular bacterial isolates and review of ocular pathogens is based on a survey of a collection of isolates banked over a ten-year span at the Dean McGee Eye Institute in Oklahoma. These findings illustrate the diversity of bacteria isolated from the eye, ranging from common species to rare and unique species. At all sampled sites, staphylococci were the predominant bacteria isolated. Pseudomonads were the most common Gram-negative bacterial isolate, except in vitreous, where Serratia was the most common Gram-negative bacterial isolate. Here, we discuss the range of ocular infections that these species have been documented to cause and treatment options for these infections. Although a highly diverse spectrum of species has been isolated from the eye, the majority of infections are caused by Gram-positive species, and in most infections, empiric treatments are effective.
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Affiliation(s)
- Roger A Astley
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Md Huzzatul Mursalin
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Phillip S Coburn
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Erin T Livingston
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - James W Nightengale
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Eddy Bagaruka
- Department of Biology, Oklahoma Christian University, Edmond, OK 73013, USA
| | - Jonathan J Hunt
- Department of Biology, Oklahoma Christian University, Edmond, OK 73013, USA
| | - Michelle C Callegan
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
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9
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Zhou G, Wang Q, Wang Y, Wen X, Peng H, Peng R, Shi Q, Xie X, Li L. Outer Membrane Porins Contribute to Antimicrobial Resistance in Gram-Negative Bacteria. Microorganisms 2023; 11:1690. [PMID: 37512863 PMCID: PMC10385648 DOI: 10.3390/microorganisms11071690] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/30/2023] Open
Abstract
Gram-negative bacteria depend on their cell membranes for survival and environmental adaptation. They contain two membranes, one of which is the outer membrane (OM), which is home to several different outer membrane proteins (Omps). One class of important Omps is porins, which mediate the inflow of nutrients and several antimicrobial drugs. The microorganism's sensitivity to antibiotics, which are predominantly targeted at internal sites, is greatly influenced by the permeability characteristics of porins. In this review, the properties and interactions of five common porins, OmpA, OmpC, OmpF, OmpW, and OmpX, in connection to porin-mediated permeability are outlined. Meanwhile, this review also highlighted the discovered regulatory characteristics and identified molecular mechanisms in antibiotic penetration through porins. Taken together, uncovering porins' functional properties will pave the way to investigate effective agents or approaches that use porins as targets to get rid of resistant gram-negative bacteria.
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Affiliation(s)
- Gang Zhou
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qian Wang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yingsi Wang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xia Wen
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Hong Peng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Ruqun Peng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qingshan Shi
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xiaobao Xie
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Liangqiu Li
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
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10
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Hyams Y, Rubin-Blum M, Rosner A, Brodsky L, Rinkevich Y, Rinkevich B. Physiological changes during torpor favor association with Endozoicomonas endosymbionts in the urochordate Botrylloides leachii. Front Microbiol 2023; 14:1072053. [PMID: 37323901 PMCID: PMC10264598 DOI: 10.3389/fmicb.2023.1072053] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
Environmental perturbations evoke down-regulation of metabolism in some multicellular organisms, leading to dormancy, or torpor. Colonies of the urochordate Botrylloides leachii enter torpor in response to changes in seawater temperature and may survive for months as small vasculature remnants that lack feeding and reproductive organs but possess torpor-specific microbiota. Upon returning to milder conditions, the colonies rapidly restore their original morphology, cytology and functionality while harboring re-occurring microbiota, a phenomenon that has not been described in detail to date. Here we investigated the stability of B. leachii microbiome and its functionality in active and dormant colonies, using microscopy, qPCR, in situ hybridization, genomics and transcriptomics. A novel lineage of Endozoicomonas, proposed here as Candidatus Endozoicomonas endoleachii, was dominant in torpor animals (53-79% read abundance), and potentially occupied specific hemocytes found only in torpid animals. Functional analysis of the metagenome-assembled genome and genome-targeted transcriptomics revealed that Endozoicomonas can use various cellular substrates, like amino acids and sugars, potentially producing biotin and thiamine, but also expressing various features involved in autocatalytic symbiosis. Our study suggests that the microbiome can be linked to the metabolic and physiological states of the host, B. leachii, introducing a model organism for the study of symbioses during drastic physiological changes, such as torpor.
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Affiliation(s)
- Yosef Hyams
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Maxim Rubin-Blum
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Leonid Brodsky
- Tauber Bioinformatics Research Center, University of Haifa, Haifa, Israel
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Yuval Rinkevich
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, Munich, Germany
| | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
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Abril AG, Calo-Mata P, Böhme K, Villa TG, Barros-Velázquez J, Pazos M, Carrera M. Shotgun Proteomics Analysis, Functional Networks, and Peptide Biomarkers for Seafood-Originating Biogenic-Amine-Producing Bacteria. Int J Mol Sci 2023; 24:ijms24097704. [PMID: 37175409 PMCID: PMC10178689 DOI: 10.3390/ijms24097704] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Biogenic amine-producing bacteria are responsible for the production of basic nitrogenous compounds (histamine, cadaverine, tyramine, and putrescine) following the spoilage of food due to microorganisms. In this study, we adopted a shotgun proteomics strategy to characterize 15 foodborne strains of biogenic-amine-producing bacteria. A total of 10,673 peptide spectrum matches belonging to 4081 peptides and corresponding to 1811 proteins were identified. Relevant functional pathways were determined, and strains were differentiated into hierarchical clusters. An expected protein-protein interaction network was created (260 nodes/1973 interactions). Most of the determined proteins were associated with networks/pathways of energy, putrescine metabolism, and host-virus interaction. Additionally, 556 peptides were identified as virulence factors. Moreover, 77 species-specific peptide biomarkers corresponding to 64 different proteins were proposed to identify 10 bacterial species. This represents a major proteomic dataset of biogenic-amine-producing strains. These results may also be suitable for new treatments for food intoxication and for tracking microbial sources in foodstuffs.
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Affiliation(s)
- Ana González Abril
- Department of Food Technology, Spanish National Research Council (CSIC), Institute of Marine Research (IIM-CSIC), 36208 Vigo, Spain
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Karola Böhme
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Tomás G Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Manuel Pazos
- Department of Food Technology, Spanish National Research Council (CSIC), Institute of Marine Research (IIM-CSIC), 36208 Vigo, Spain
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council (CSIC), Institute of Marine Research (IIM-CSIC), 36208 Vigo, Spain
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12
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Akshay SD, Nayak S, Deekshit VK, Rohit A, Maiti B. Differential expression of outer membrane proteins and quinolone resistance determining region mutations can lead to ciprofloxacin resistance in Salmonella Typhi. Arch Microbiol 2023; 205:136. [PMID: 36961627 DOI: 10.1007/s00203-023-03485-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/17/2023] [Accepted: 03/13/2023] [Indexed: 03/25/2023]
Abstract
Multi-drug resistance in Salmonella Typhi remains a public health concern globally. This study aimed to investigate the function of quinolone resistance determining region (QRDR) of gyrA and parC in ciprofloxacin (CIP) resistant isolates and examine the differential expression of outer membrane proteins (OMPs) on exposure to sub-lethal concentrations of CIP in S. Typhi. The CIP-resistant isolates were screened for mutations in the QRDR and analyzed for bacterial growth. Furthermore, major OMPs encoding genes such as ompF, lamB, yaeT, tolC, ompS1, and phoE were examined for differential expression under the sub-lethal concentrations of CIP by real-time PCR and SDS-PAGE. Notably, our study has shown a single-point mutation in gyrA at codon 83 (Ser83-tyrosine and Ser83-phenylalanine), also the rare amino acid substitution in parC gene at codon 80 (Glu80-glycine) in CIP-resistant isolates. Additionally, CIP-resistant isolates showed moderate growth compared to susceptible isolates. Although most of the OMP-encoding genes (tolC, ompS1, and phoE) showed some degree of upregulation, a significant level of upregulation (p < 0.05) was observed only for yaeT. However, ompF and lamB genes were down-regulated compared to CIP-susceptible isolates. Whereas OMPs profiling using SDS-PAGE did not show any changes in the banding pattern. These results provide valuable information on the QRDR mutation, and the difference in the growth, and expression of OMP-encoding genes in resistant and susceptible isolates of S. Typhi. This further provides insight into the involvement of QRDR mutation and OMPs associated with CIP resistance in S. Typhi.
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Affiliation(s)
- Sadanand Dangari Akshay
- Division of Infectious Diseases, Nitte (Deemed to Be University), Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Srajana Nayak
- Division of Infectious Diseases, Nitte (Deemed to Be University), Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Vijaya Kumar Deekshit
- Division of Infectious Diseases, Nitte (Deemed to Be University), Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Anusha Rohit
- Division of Infectious Diseases, Nitte (Deemed to Be University), Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India
- Department of Microbiology, The Madras Medical Mission, 4-A, Dr, Mogappair, Chennai, Tamil Nadu, 600037, India
| | - Biswajit Maiti
- Division of Infectious Diseases, Nitte (Deemed to Be University), Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India.
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13
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Qasim A, Jaan S, Wara TU, Shehroz M, Nishan U, Shams S, Shah M, Ojha SC. Computer-aided genomic data analysis of drug-resistant Neisseria gonorrhoeae for the Identification of alternative therapeutic targets. Front Cell Infect Microbiol 2023; 13:1017315. [PMID: 37033487 PMCID: PMC10080061 DOI: 10.3389/fcimb.2023.1017315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/02/2023] [Indexed: 04/11/2023] Open
Abstract
Neisseria gonorrhoeae is an emerging multidrug resistance pathogen that causes sexually transmitted infections in men and women. The N. gonorrhoeae has demonstrated an emerging antimicrobial resistance against reported antibiotics, hence fetching the attention of researchers to address this problem. The present in-silico study aimed to find putative novel drug and vaccine targets against N. gonorrhoeae infection by the application of bioinformatics approaches. Core genes set of 69 N. gonorrhoeae strains was acquired from complete genome sequences. The essential and non-homologous metabolic pathway proteins of N. gonorrhoeae were identified. Moreover, different bioinformatics databases were used for the downstream analysis. The DrugBank database scanning identified 12 novel drug targets in the prioritized list. They were preferred as drug targets against this bacterium. A viable vaccine is unavailable so far against N. gonorrhoeae infection. In the current study, two outer-membrane proteins were prioritized as vaccine candidates via reverse vaccinology approach. The top lead B and T-cells overlapped epitopes were utilized to generate a chimeric vaccine construct combined with immune-modulating adjuvants, linkers, and PADRE sequences. The top ranked prioritized vaccine construct (V7) showed stable molecular interaction with human immune cell receptors as inferred during the molecular docking and MD simulation analyses. Considerable response for immune cells was interpreted by in-silico immune studies. Additional tentative validation is required to ensure the effectiveness of the prioritized vaccine construct against N. gonorrhoeae infection. The identified proteins can be used for further rational drug and vaccine designing to develop potential therapeutic entities against the multi-drug resistant N. gonorrhoeae.
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Affiliation(s)
- Aqsa Qasim
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Samavia Jaan
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Tehreem Ul Wara
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Shehroz
- Department of Bioinformatics, Kohsar University, Murree, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
- *Correspondence: Suvash Chandra Ojha, ; Mohibullah Shah, ;
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- *Correspondence: Suvash Chandra Ojha, ; Mohibullah Shah, ;
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14
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Bolourchi N, Fereshteh S, Noori Goodarzi N, Badmasti F. Subtractive genomic analysis for computational identification of putative immunogenic targets against clinical Enterobacter cloacae complex. PLoS One 2022; 17:e0275749. [PMID: 36228013 PMCID: PMC9560131 DOI: 10.1371/journal.pone.0275749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022] Open
Abstract
Background Enterobacter is a major nosocomial genus of Enterobacteriaceae responsible for a variety of nosocomial infections, particularly in prolonged hospitalized patients in the intensive care units. Since current antibiotics have failed treating colistin- and carbapenem-resistant Enterobacteriaceae, efforts are underway to find suitable alternative strategies. Therefore, this study conducted a reverse vaccinology (RV) to identify novel and putative immunogenic targets using core proteome of 20 different sequence types (STs) of clinical Enterobacter spp. Moreover, we introduced a structural-based approach for exploration of potential vaccine candidates against the Enterobacteriaceae family using their conserved domain analysis. Results A number of 2616 core coding sequences (CDSs) were retrieved from 20 clinical strains of Enterobacter spp. with a similarity of ≥ 50%. Nine proteins with a score of ≥ 20 considered as the shortlisted proteins based on the quartile scoring method, including three TonB-dependent receptors, WP_008500981.1, WP_058690971.1 and WP_058679571.1; one YjbH domain-containing protein, WP_110108068.1; three flagellar proteins, WP_088207510.1, WP_033145204.1 and WP_058679632.1; one spore-coat U domain-containing protein, WP_039266612.1; and one DD-metalloendopeptidase family protein, WP_025912449.1. In this study, proteins WP_058690971.1 and WP_110108068.1 were detected as the top candidates with regard to immune stimulation and interactions with TLRs. However, their efficacy is remaining to be evaluated experimentally. Conclusions Our investigation introduced common ferrichrome porins with high sequence similarity as potential vaccine candidates against the Enterobacteriaceae family. These proteins belong to the iron acquisition system and possess all criteria of suitable vaccine targets. Therefore, they need to be specifically paid attention for vaccine development against clinically important members of Enterobacteriaceae family.
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Affiliation(s)
- Negin Bolourchi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Narjes Noori Goodarzi
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
- * E-mail:
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15
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Hussain HI, Aqib AI, Seleem MN, Shabbir MA, Hao H, Iqbal Z, Kulyar MFEA, Zaheer T, Li K. Genetic basis of molecular mechanisms in β-lactam resistant gram-negative bacteria. Microb Pathog 2021; 158:105040. [PMID: 34119627 PMCID: PMC8445154 DOI: 10.1016/j.micpath.2021.105040] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/25/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022]
Abstract
Antibiotic-resistant bacteria are considered one of the major global threats to human and animal health. The most harmful among the resistant bacteria are β-lactamase producing Gram-negative species (β-lactamases). β-lactamases constitute a paradigm shift in the evolution of antibiotic resistance. Therefore, it is imperative to present a comprehensive review of the mechanisms responsible for developing antimicrobial resistance. Resistance due to β-lactamases develops through a variety of mechanisms, and the number of resistant genes are involved that can be transferred between bacteria, mostly via plasmids. Over time, these new molecular-based resistance mechanisms have been progressively disclosed. The present review article provides information on the recent findings regarding the molecular mechanisms of resistance to β-lactams in Gram-negative bacteria, including CTX-M-type ESBLs with methylase activity, plasmids harbouring phages with β-lactam resistance genes, the co-presence of β-lactam resistant genes of unique combinations and the presence of β-lactam and non-β-lactam antibiotic-resistant genes in the same bacteria. Keeping in view, the molecular level resistance development, multifactorial and coordinated measures may be taken to counter the challenge of rapidly increasing β-lactam resistance.
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Affiliation(s)
- Hafiz Iftikhar Hussain
- Department of Pathology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan
| | - Amjad Islam Aqib
- Department of Medicine, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan.
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, USA
| | | | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zahid Iqbal
- Department of Pharmacology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China.
| | | | - Tean Zaheer
- Department of Parasitology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, PR China.
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16
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Interplay between ESKAPE Pathogens and Immunity in Skin Infections: An Overview of the Major Determinants of Virulence and Antibiotic Resistance. Pathogens 2021; 10:pathogens10020148. [PMID: 33540588 PMCID: PMC7912840 DOI: 10.3390/pathogens10020148] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/16/2022] Open
Abstract
The skin is the largest organ in the human body, acting as a physical and immunological barrier against pathogenic microorganisms. The cutaneous lesions constitute a gateway for microbial contamination that can lead to chronic wounds and other invasive infections. Chronic wounds are considered as serious public health problems due the related social, psychological and economic consequences. The group of bacteria known as ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter sp.) are among the most prevalent bacteria in cutaneous infections. These pathogens have a high level of incidence in hospital environments and several strains present phenotypes of multidrug resistance. In this review, we discuss some important aspects of skin immunology and the involvement of ESKAPE in wound infections. First, we introduce some fundamental aspects of skin physiology and immunology related to cutaneous infections. Following this, the major virulence factors involved in colonization and tissue damage are highlighted, as well as the most frequently detected antimicrobial resistance genes. ESKAPE pathogens express several virulence determinants that overcome the skin's physical and immunological barriers, enabling them to cause severe wound infections. The high ability these bacteria to acquire resistance is alarming, particularly in the hospital settings where immunocompromised individuals are exposed to these pathogens. Knowledge about the virulence and resistance markers of these species is important in order to develop new strategies to detect and treat their associated infections.
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17
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Patil A, Banerji R, Kanojiya P, Koratkar S, Saroj S. Bacteriophages for ESKAPE: role in pathogenicity and measures of control. Expert Rev Anti Infect Ther 2021; 19:845-865. [PMID: 33261536 DOI: 10.1080/14787210.2021.1858800] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
INTRODUCTION The quest to combat bacterial infections has dreaded humankind for centuries. Infections involving ESKAPE (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) impose therapeutic challenges due to the emergence of antimicrobial drug resistance. Recently, investigations with bacteriophages have led to the development of novel strategies against ESKAPE infections. Also, bacteriophages have been demonstrated to be instrumental in the dissemination of virulence markers in ESKAPE pathogens. AREAS COVERED The review highlights the potential of bacteriophage in and against the pathogenicity of antibiotic-resistant ESKAPE pathogens. The review also emphasizes the challenges of employing bacteriophage in treating ESKAPE pathogens and the knowledge gap in the bacteriophage mediated antibiotic resistance and pathogenicity in ESKAPE infections. EXPERT OPINION Bacteriophage infection can kill the host bacteria but in survivors can transfer genes that contribute toward the survival of the pathogens in the host and resistance toward multiple antimicrobials. The knowledge on the dual role of bacteriophages in the treatment and pathogenicity will assist in the prediction and development of novel therapeutics targeting antimicrobial-resistant ESKAPE. Therefore, extensive investigations on the efficacy of synthetic bacteriophage, bacteriophage cocktails, and bacteriophage in combination with antibiotics are needed to develop effective therapeutics against ESKAPE infections.
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Affiliation(s)
- Amrita Patil
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, Lavale, Pune Maharashtra, India
| | - Rajashri Banerji
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, Lavale, Pune Maharashtra, India
| | - Poonam Kanojiya
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, Lavale, Pune Maharashtra, India
| | - Santosh Koratkar
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, Lavale, Pune Maharashtra, India
| | - Sunil Saroj
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, Lavale, Pune Maharashtra, India
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18
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Dogan Guzel F, Pletzer D, Norouz Dizaji A, Al-Nahas K, Bajrai M, Winterhalter M. Towards understanding single-channel characteristics of OccK8 purified from Pseudomonas aeruginosa. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:87-98. [PMID: 33481046 DOI: 10.1007/s00249-021-01498-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/10/2021] [Indexed: 10/22/2022]
Abstract
Antibiotic resistance in Gram-negative bacteria causes serious health issues worldwide. Bacteria employ several resistance mechanisms to cope with antimicrobials. One of their strategies is to reduce the permeability of antibiotics either through general diffusion porins or substrate-specific channels. In this study, one of the substrate-specific channels from Pseudomonas aeruginosa, OccK8 (also known as OprE), was investigated using single-channel electrophysiology. The study also includes the investigation of permeability properties of several amino acids with different charged groups (i.e. arginine, glycine and glutamic acid) through OccK8. We observed four different conformations of the same OccK8 channel when inserted in lipid bilayers. This is in contrast to previous studies where heterologous expressed OccK8 in E. coli showed only one conformation. We hypothesized that the difference in our study was due to the expression and purification of the native channel from P. aeruginosa. The single-channel uptake characteristics of the porin showed that negatively charged glutamic acid preferentially interacted with the channel while the positively charged arginine molecule showed infrequent interaction with OccK8. The neutral amino acid glycine did not show any interaction at the physiological conditions.
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Affiliation(s)
- Fatma Dogan Guzel
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Ankara Yildirim Beyazit University, 06010, Ankara, Turkey.
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany.
| | - Daniel Pletzer
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Araz Norouz Dizaji
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Ankara Yildirim Beyazit University, 06010, Ankara, Turkey
| | - Kareem Al-Nahas
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Mawadah Bajrai
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Mathias Winterhalter
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
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19
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Searching for putative virulence factors in the genomes of Shewanella indica and Shewanella algae. Arch Microbiol 2020; 203:683-692. [PMID: 33040180 DOI: 10.1007/s00203-020-02060-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/12/2020] [Accepted: 09/30/2020] [Indexed: 12/16/2022]
Abstract
Bacterial pathogens are a major threat to both humans and animals worldwide. It is crucial to understand the mechanisms of various disease processes at the molecular level. Shewanella species are widespread in the environment and some are considered as emerging opportunistic human and marine mammal pathogens. In this study, putative virulence factors on the genome of Shewanella indica BW, a bacterium isolated from the Bryde's whale (Balaenoptera edeni), were determined. Additionally, for comparative purposes, putative virulence factors from two other S. indica and ten S. algae strains were also determined using the Pathosystems Resource Integration Center (PATRIC) pipeline. We confirmed the presence of previously reported virulence factors and we are proposing several new candidate virulence factors. Interestingly, the putative virulence factors were very similar between the two species with the exception of microbial collagenase which was present in all S. algae genomes, but absent in all S. indica genomes.
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20
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Ferrand A, Vergalli J, Pagès JM, Davin-Regli A. An Intertwined Network of Regulation Controls Membrane Permeability Including Drug Influx and Efflux in Enterobacteriaceae. Microorganisms 2020; 8:E833. [PMID: 32492979 PMCID: PMC7355843 DOI: 10.3390/microorganisms8060833] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 12/19/2022] Open
Abstract
The transport of small molecules across membranes is a pivotal step for controlling the drug concentration into the bacterial cell and it efficiently contributes to the antibiotic susceptibility in Enterobacteriaceae. Two types of membrane transports, passive and active, usually represented by porins and efflux pumps, are involved in this process. Importantly, the expression of these transporters and channels are modulated by an armamentarium of tangled regulatory systems. Among them, Helix-turn-Helix (HTH) family regulators (including the AraC/XylS family) and the two-component systems (TCS) play a key role in bacterial adaptation to environmental stresses and can manage a decrease of porin expression associated with an increase of efflux transporters expression. In the present review, we highlight some recent genetic and functional studies that have substantially contributed to our better understanding of the sophisticated mechanisms controlling the transport of small solutes (antibiotics) across the membrane of Enterobacteriaceae. This information is discussed, taking into account the worrying context of clinical antibiotic resistance and fitness of bacterial pathogens. The localization and relevance of mutations identified in the respective regulation cascades in clinical resistant strains are discussed. The possible way to bypass the membrane/transport barriers is described in the perspective of developing new therapeutic targets to combat bacterial resistance.
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Affiliation(s)
| | | | | | - Anne Davin-Regli
- UMR_MD1, U-1261, Aix-Marseille University, INSERM, SSA, IRBA, MCT, Faculté de Pharmacie, 27 Bd Jean Moulin, 13385 Marseille CEDEX 05, France; (A.F.); (J.V.); (J.-M.P.)
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