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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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Hasegawa LA, Vilela FP, Falcão JP. Antimicrobial resistance, virulence potential and genomic epidemiology of global genomes of the rare Salmonella enterica serovar Orion. Zoonoses Public Health 2024; 71:591-599. [PMID: 38702905 DOI: 10.1111/zph.13140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/06/2024] [Accepted: 04/24/2024] [Indexed: 05/06/2024]
Abstract
AIMS Our aim is to characterize through whole-genome sequencing (WGS) the antimicrobial resistance (AMR) and heavy metal tolerance (HMT) genes content, plasmid presence, virulence potential and genomic diversity of the rare non-typhoid Salmonella enterica serovar Orion (S. Orion) from 19 countries of the African, American, Eastern Mediterranean, European, Southeastern Asia and Western Pacific regions. METHODS AND RESULTS Totally 324 S. Orion genomes were screened for AMR, HMT and virulence genes, plasmids and Salmonella Pathogenicity Islands (SPIs). Genomic diversity was investigated using Multi-Locus Sequence Typing (MLST) and core-genome MLST (cgMLST). Efflux pump encoding genes mdsA and mdsB were present in all genomes analysed, while quinolone chromosomal point mutations and aminoglycoside, beta-lactam, colistin, lincosamide, macrolide, phenicol, sulphonamide, trimethoprim, tetracycline and disinfectant resistance genes were found in 0.3%-5.9%. A total of 17 genomes (5.2%) from Canada, the United Kingdom, the USA and Tanzania showed a potential multi-drug resistance profile. Gold tolerance genes golS and golT were detected in all genomes analysed, while arsenic, copper, mercury, silver and tellurium tolerance genes were found in 0.3%-35.5%. Col(MGD2) was the most frequently detected plasmid, in 15.4% of the genomes. Virulence genes related to adherence, macrophage induction, magnesium uptake, regulation, serum resistance, stress adaptation, type III secretion systems and six SPIs (1, 2, 3, 4, 5, 9, 12, 13, 14 and C63PI) were detected. ST639 was assigned to 89.2% of the S. Orion genomes, while cgMLST showed core-genome STs and clusters of strains specific by countries. CONCLUSION The high virulence factor frequencies, the genomic similarity among some non-clinical and clinical strains circulating worldwide and the presence of a strain carrying a resistance gene against a last resource antimicrobial like colistin, highlight the potential risk of S. Orion strains for public health and food safety and reinforce the importance to not underestimate the potential hazard of rare non-typhoid Salmonella serovars.
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Affiliation(s)
- Leticia Ayumi Hasegawa
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Ribeirao Preto, SP, Brazil
| | - Felipe Pinheiro Vilela
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Ribeirao Preto, SP, Brazil
| | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Ribeirao Preto, SP, Brazil
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Abdelhamid AG, Yousef AE. Egg-associated Salmonella enterica serovar Enteritidis: comparative genomics unveils phylogenetic links, virulence potential, and antimicrobial resistance traits. Front Microbiol 2023; 14:1278821. [PMID: 38029128 PMCID: PMC10667436 DOI: 10.3389/fmicb.2023.1278821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Salmonella enterica serovar Enteritidis (SE) remains a frequent cause of foodborne illnesses associated with the consumption of contaminated hen eggs. Such a food-pathogen association has been demonstrated epidemiologically, but the molecular basis for this association has not been explored. Comparative genomic analysis was implemented to decipher the phylogenomic characteristics, antimicrobial resistance, and virulence potential of eggs-associated SE. Analyzing 1,002 genomes belonging to 841 sequence types of food-isolated SE strains suggests a high genomic similarity within the egg-related lineage, which is phylogenetically close to SE strains isolated from poultry but is different from those isolated from beef. Core genome- and single nucleotide polymorphism (SNP)-based phylogeny of 74 SE strains of egg origin showcased two distinct sublineages. Time-scaled phylogeny supported the possibility of a common ancestor of egg-related SE lineages. Additionally, genome mining revealed frequent antibiotic resistance due to the presence of aac(6')-Iaa and mdsAB encoded on the genomes of egg-associated SE strains. For virulence gene profiling, 103-113 virulence determinants were identified in the egg-associated SE, which were comparable to 112 determinants found in human-associated SE, emphasizing the capacity of egg-associated strains to infect humans and cause diseases. The findings of this study proved the genomic similarity of egg-associated SE strains, and these were closely related to poultry strains. The egg-associated strains also harbor virulence genes equivalent to those found in human-associated SE strains. The analysis provided critical insights into the genetic structure, phylogenomics, dynamics of virulence, and antibiotic resistance of Salmonella Enteritidis, circulating in eggs and emphasizing the necessity of implementing anti-Salmonella intervention strategies, starting at the production stage of the poultry supply chain.
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Affiliation(s)
- Ahmed G. Abdelhamid
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha, Egypt
| | - Ahmed E. Yousef
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
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Gu G, Pei H, Zhou A, Fan B, Zhou H, Choi A, Huang Z. A Comprehensive Study of Historical Detection Data for Pathogen Isolates from U.S. Cattle. Antibiotics (Basel) 2023; 12:1509. [PMID: 37887210 PMCID: PMC10604524 DOI: 10.3390/antibiotics12101509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Foodborne pathogens pose substantial health hazards and result in considerable economic losses in the U.S. Fortunately, the National Center for Biotechnology Information Pathogen Detection Isolates Browser (NPDIB) provides valuable access to antimicrobial resistance (AMR) genes and antimicrobial assay data. This study aimed to conduct the first comprehensive investigation of AMR genes in pathogens isolated from U.S. cattle over the past decade, driven by the urgent need to address the dangers of AMR specifically originating in pathogens isolated from U.S. cattle. In this study, around 28,000 pathogen isolate samples were extracted from the NPDIB and then analyzed using multivariate statistical methods, mainly principal component analysis (PCA) and hierarchical clustering (H-clustering). These approaches were necessary due to the high dimensions of the raw data. Specifically, PCA was utilized to reduce the dimensions of the data, converting it to a two-dimensional space, and H-clustering was used to better identify the differences among data points. The findings from this work highlighted Salmonella enterica and Escherichia coli as the predominant pathogens among the isolates, with E. coli being the more concerning pathogen due to its increasing prevalence in recent years. Moreover, tetracycline was observed as the most commonly resistant antimicrobial, with the resistance genes mdsA, mdsB, mdtM, blaEC, and acrF being the most prevalent in pathogen isolates from U.S. cattle. The occurrence of mdtM, blaEC, acrF, and glpT_E448k showed an increase in pathogens isolated from U.S. cattle in recent years. Furthermore, based on the data collected for the locations of AMR cases, Texas, California, and Nebraska were the major areas carrying major AMR genes or antimicrobials with detected resistance. The results from this study provide potential directions for targeted interventions to mitigate pathogens' antimicrobial resistance in U.S. cattle.
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Affiliation(s)
| | | | | | | | | | | | - Zuyi Huang
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA 19085, USA; (G.G.); (H.P.); (A.Z.); (B.F.); (H.Z.); (A.C.)
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Vilela FP, Rodrigues DDP, Allard MW, Falcão JP. The rare Salmonella enterica serovar Isangi: genomic characterization of the antimicrobial resistance, virulence potential and epidemiology of Brazilian strains in comparison to global isolates. J Med Microbiol 2023; 72. [PMID: 37462464 DOI: 10.1099/jmm.0.001736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
Introduction. Salmonella enterica serovar Isangi (S. Isangi) is a rare non-typhoidal serovar, related to invasive nosocomial infections in various countries and to increasing antimicrobial resistance rates.Gap statement. Despite existing reports on S. Isangi, there is a lack of information of specific traits regarding this serovar, which could be improved through genomic analyses.Aim. Our goals were to characterize the antimicrobial resistance, virulence potential and genomic relatedness of 11 S. Isangi strains from Brazil in comparison to 185 genomes of global isolates using whole-genome sequencing (WGS) data.Methodology. Phenotypic resistance was determined by disc-diffusion. The search for resistance genes, plasmids, prophages, Salmonella pathogenicity islands (SPIs) and virulence genes, plus multi-locus sequence typing (MLST) and core-genome MLST (cgMLST) were performed using WGS.Results. Brazilian S. Isangi strains showed phenotypic resistance to nalidixic acid, ciprofloxacin and streptomycin, and harboured antimicrobial resistance [qnrB19, aac(6')-Iaa, mdsAB] and heavy metal tolerance (arsD, golST) genes. Col(pHAD28) and IncFII(S) plasmids, virulence genes related to adherence, macrophage induction, magnesium uptake, regulation and type III secretion systems, 12 SPIs and eight prophages were detected. The 185 additional global genomes analysed harboured resistance genes against 11 classes of antimicrobial compounds, 22 types of plasmids, 32 prophages, 14 SPIs, and additional virulence genes related to serum resistance, stress adaptation and toxins. Sequence type (ST)216 was assigned to genomes from Brazil and other countries, while ST335 was the most frequent ST, especially among South African genomes. cgMLST showed that Brazilian genomes were more closely related to genomes from European and African countries, the USA and Taiwan, while the majority of South African genomes were more closely related among each other.Conclusion. The presence of S. Isangi strains from Brazil and different countries showing a close genomic correlation, antimicrobial resistance profiles to drugs used in human therapy and a large number of virulence determinants reinforced the need for stronger initiatives to monitor rare non-typhoidal Salmonella serovars such as S. Isangi in order to prevent its dissemination among human and non-human sources.
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Affiliation(s)
- Felipe Pinheiro Vilela
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Av. do Café, s/n, 14040-903, Ribeirão Preto, SP, Brazil
| | | | - Marc William Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Juliana Pfrimer Falcão
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Av. do Café, s/n, 14040-903, Ribeirão Preto, SP, Brazil
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Zhou K, Sun L, Zhang X, Xu X, Mi K, Ma W, Zhang L, Huang L. Salmonella antimicrobials inherited and the non-inherited resistance: mechanisms and alternative therapeutic strategies. Front Microbiol 2023; 14:1176317. [PMID: 37303797 PMCID: PMC10249997 DOI: 10.3389/fmicb.2023.1176317] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/24/2023] [Indexed: 06/13/2023] Open
Abstract
Salmonella spp. is one of the most important foodborne pathogens. Typhoid fever and enteritis caused by Salmonella enterica are associated with 16-33 million infections and 500,000 to 600,000 deaths annually worldwide. The eradication of Salmonella is becoming increasingly difficult because of its remarkable capacity to counter antimicrobial agents. In addition to the intrinsic and acquired resistance of Salmonella, increasing studies indicated that its non-inherited resistance, which commonly mentioned as biofilms and persister cells, plays a critical role in refractory infections and resistance evolution. These remind the urgent demand for new therapeutic strategies against Salmonella. This review starts with escape mechanisms of Salmonella against antimicrobial agents, with particular emphasis on the roles of the non-inherited resistance in antibiotic failure and resistance evolution. Then, drug design or therapeutic strategies that show impressive effects in overcoming Salmonella resistance and tolerance are summarized completely, such as overcoming the barrier of outer membrane by targeting MlaABC system, reducing persister cells by limiting hydrogen sulfide, and applying probiotics or predatory bacteria. Meanwhile, according to the clinical practice, the advantages and disadvantages of above strategies are discussed. Finally, we further analyze how to deal with this tricky problems, thus can promote above novel strategies to be applied in the clinic as soon as possible. We believed that this review will be helpful in understanding the relationships between tolerance phenotype and resistance of Salmonella as well as the efficient control of antibiotic resistance.
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Affiliation(s)
- Kaixiang Zhou
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
| | - Lei Sun
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
| | - Xuehua Zhang
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
| | - Xiangyue Xu
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
| | - Kun Mi
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
| | - Wenjin Ma
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
| | - Lan Zhang
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
| | - Lingli Huang
- Department of Veterinary Medicine Science, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Wuhan, Hubei, China
- MOA Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, Hubei, China
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Vilela FP, Dos Prazeres Rodrigues D, Allard MW, Falcão JP. Genomic analyses of drug-resistant Salmonella enterica serovar Heidelberg strains isolated from meat and related sources between 2013 and 2017 in the south region of Brazil. Curr Genet 2023; 69:141-152. [PMID: 36920496 DOI: 10.1007/s00294-023-01264-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023]
Abstract
Salmonella enterica serovar Heidelberg (S. Heidelberg) is a zoonotic, ubiquitous, and worldwide-distributed pathogen, responsible for gastroenteritis in humans caused by the consumption of contaminated food. In this study, 11 S. Heidelberg strains isolated from chicken and bovine meat, drag swab, and animal feed between 2013 and 2017 in states of the southern region of Brazil were characterized by whole-genome sequencing (WGS) analyses. Antimicrobial resistance against 18 antimicrobials was determined by disk-diffusion and ciprofloxacin's minimum inhibitory concentration by Etest®. The search for resistance and virulence genes, plasmids, Salmonella Pathogenicity Islands (SPIs) plus multi-locus sequence typing (MLST), and single-nucleotide polymorphisms (SNPs) analyses was conducted using WGS data. All strains harbored resistance genes fosA7, aac(6')-Iaa, sul2, tet(A), blaCMY-2, mdsA, and mdsB, and point mutations in gyrA and parC. All strains showed a phenotypic multidrug-resistant profile, with resistant or intermediate resistant profiles against 14 antimicrobials tested. Plasmids ColpVC, IncC, IncX1, and IncI1-I(Alpha) were detected. Virulence genes related to adherence, macrophage induction, magnesium uptake, regulation, and type III secretion systems plus 10 SPIs were detected. All strains were assigned to ST15 and belonged to two SNP clusters showing high similarity to isolates from the United Kingdom, Chile, Germany, the Netherlands, China, South Africa, and South Korea. In conclusion, the presence of multidrug-resistant S. Heidelberg strains in Brazil showing a global genomic relationship may alert for the necessity of stronger surveillance measures by food safety and public health authorities to limit its spread to humans and animals through foods.
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Affiliation(s)
- Felipe Pinheiro Vilela
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, Av. do Café, s/n, Bloco S-Sala 41, Ribeirão Preto, SP, 14040-903, Brazil
| | | | - Marc William Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, Av. do Café, s/n, Bloco S-Sala 41, Ribeirão Preto, SP, 14040-903, Brazil.
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Vilela FP, Rodrigues DDP, Allard MW, Falcão JP. Genomic characterization and antimicrobial resistance profiles of Salmonella enterica serovar Infantis isolated from food, humans and veterinary-related sources in Brazil. J Appl Microbiol 2021; 132:3327-3342. [PMID: 34958707 DOI: 10.1111/jam.15430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 01/07/2023]
Abstract
AIMS To characterize the genetic relatedness, phenotypic and genotypic antimicrobial resistance and plasmid content of 80 Salmonella Infantis strains isolated from food, humans and veterinary sources from 2013 to 2018 in Brazil. METHODS AND RESULTS Pulsed-field gel electrophoresis and single-nucleotide polymorphism analysis showed major clusters containing 50% and 38.8% of the strains studied respectively. Multilocus sequence typing assigned all strains to ST32. Disk-diffusion revealed that 90% of the strains presented resistant or intermediate resistant profiles and 38.8% displayed multidrug resistance. Resistance genes for aminoglycosides (aac(6')-Iaa; aadA12; aph(3″-Ib; aph(6)-Id), β-lactams (blaTEM-1 ; blaCTX-M-8 ; blaCMY-2 ), trimethoprim (dfrA8), tetracycline (tet(A)), amphenicols (floR), sulfonamide (sul2), efflux pumps (mdsA; mdsB), chromosomal point mutations in gyrB, parC, acrB and pmrA were detected. Strains harboured IncI, IncF, IncX, IncQ, IncN and IncR plasmids. CONCLUSIONS The presence of a prevalent S. Infantis subtype in Brazil and the high antimicrobial resistance rates reinforced the potential hazard of this serovar for the public health and food safety fields. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study characterizing a large set of S. Infantis from Brazil by whole-genome sequencing, which provided a better local and global comprehension about the distribution and characteristics of this serovar of importance in the food, human and veterinary fields.
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Affiliation(s)
- Felipe Pinheiro Vilela
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Ribeirão Preto, SP, Brazil
| | | | - Marc William Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Juliana Pfrimer Falcão
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Ribeirão Preto, SP, Brazil
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Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
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Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
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Mycobacterium tuberculosis Rv0191 is an efflux pump of major facilitator superfamily transporter regulated by Rv1353c. Arch Biochem Biophys 2019; 667:59-66. [DOI: 10.1016/j.abb.2019.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 02/06/2023]
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Jo I, Kim JS, Xu Y, Hyun J, Lee K, Ha NC. Recent paradigm shift in the assembly of bacterial tripartite efflux pumps and the type I secretion system. J Microbiol 2019; 57:185-194. [PMID: 30806976 DOI: 10.1007/s12275-019-8520-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/26/2018] [Accepted: 01/10/2019] [Indexed: 01/15/2023]
Abstract
Tripartite efflux pumps and the type I secretion system of Gram-negative bacteria are large protein complexes that span the entire cell envelope. These complexes expel antibiotics and other toxic substances or transport protein toxins from bacterial cells. Elucidating the binary and ternary complex structures at an atomic resolution are crucial to understanding the assembly and working mechanism. Recent advances in cryoelectron microscopy along with the construction of chimeric proteins drastically shifted the assembly models. In this review, we describe the current assembly models from a historical perspective and emphasize the common assembly mechanism for the assembly of diverse tripartite pumps and type I secretion systems.
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Affiliation(s)
- Inseong Jo
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin-Sik Kim
- Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, Liaoning, 116600, P. R. China
| | - Jaekyung Hyun
- Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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Chiok KL, Paul NC, Adekanmbi EO, Srivastava SK, Shah DH. Dimethyl adenosine transferase (KsgA) contributes to cell-envelope fitness in Salmonella Enteritidis. Microbiol Res 2018; 216:108-119. [PMID: 30269850 DOI: 10.1016/j.micres.2018.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/17/2018] [Accepted: 08/21/2018] [Indexed: 01/02/2023]
Abstract
We previously reported that inactivation of a universally conserved dimethyl adenosine transferase (KsgA) attenuates virulence and increases sensitivity to oxidative and osmotic stress in Salmonella Enteritidis. Here, we show a role of KsgA in cell-envelope fitness as a potential mechanism underlying these phenotypes in Salmonella. We assessed structural integrity of the cell-envelope by transmission electron microscopy, permeability barrier function by determining intracellular accumulation of ethidium bromide and electrophysical properties by dielectrophoresis, an electrokinetic tool, in wild-type and ksgA knock-out mutants of S. Enteritidis. Deletion of ksgA resulted in disruption of the structural integrity, permeability barrier and distorted electrophysical properties of the cell-envelope. The cell-envelope fitness defects were alleviated by expression of wild-type KsgA (WT-ksgA) but not by its catalytically inactive form (ksgAE66A), suggesting that the dimethyl transferase activity of KsgA is important for cell-envelope fitness in S. Enteritidis. Upon expression of WT-ksgA and ksgAE66A in inherently permeable E. coli cells, the former strengthened and the latter weakened the permeability barrier, suggesting that KsgA also contributes to the cell-envelope fitness in E. coli. Lastly, expression of ksgAE66A exacerbated the cell-envelope fitness defects, resulting in impaired S. Enteritidis interactions with human intestinal epithelial cells, and human and avian phagocytes. This study shows that KsgA contributes to cell-envelope fitness and opens new avenues to modulate cell-envelopes via use of KsgA-antagonists.
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Affiliation(s)
- Kim Lam Chiok
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164-7040, USA
| | - Narayan C Paul
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164-7040, USA
| | - Ezekiel O Adekanmbi
- Department of Chemical and Materials Engineering, University of Idaho, Moscow, Idaho 83844-1021, USA
| | - Soumya K Srivastava
- Department of Chemical and Materials Engineering, University of Idaho, Moscow, Idaho 83844-1021, USA
| | - Devendra H Shah
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164-7040, USA; Paul Allen School for Global Animal Health, Washington State University, Pullman, WA 99164-7040, USA.
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Wang Z, Fan G, Hryc CF, Blaza JN, Serysheva II, Schmid MF, Chiu W, Luisi BF, Du D. An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump. eLife 2017; 6. [PMID: 28355133 PMCID: PMC5404916 DOI: 10.7554/elife.24905] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/14/2017] [Indexed: 12/12/2022] Open
Abstract
Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell envelope. Here, we report the near-atomic resolution cryoEM structures of the Escherichia coli AcrAB-TolC multidrug efflux pump in resting and drug transport states, revealing a quaternary structural switch that allosterically couples and synchronizes initial ligand binding with channel opening. Within the transport-activated state, the channel remains open even though the pump cycles through three distinct conformations. Collectively, our data provide a dynamic mechanism for the assembly and operation of the AcrAB-TolC pump. DOI:http://dx.doi.org/10.7554/eLife.24905.001
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Affiliation(s)
- Zhao Wang
- National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, United States.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, The University of Texas Health Science Center at Houston Medical School, Houston, United States
| | - Corey F Hryc
- National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, United States.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States.,Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, United States
| | - James N Blaza
- MRC Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, The University of Texas Health Science Center at Houston Medical School, Houston, United States
| | - Michael F Schmid
- National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, United States.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States
| | - Wah Chiu
- National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, United States.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States.,Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, United States
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Dijun Du
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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14
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Song S, Lee B, Yeom JH, Hwang S, Kang I, Cho JC, Ha NC, Bae J, Lee K, Kim YH. MdsABC-Mediated Pathway for Pathogenicity in Salmonella enterica Serovar Typhimurium. Infect Immun 2015; 83:4266-76. [PMID: 26283336 PMCID: PMC4598412 DOI: 10.1128/iai.00653-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/11/2015] [Indexed: 12/20/2022] Open
Abstract
MdsABC is a Salmonella-specific tripartite efflux pump that has been implicated in the virulence of Salmonella enterica serovar Typhimurium; however, little is known about the virulence factors associated with this pump. We observed MdsABC expression-dependent alterations in the degree of resistance to extracellular oxidative stress and macrophage-mediated killing. Thin-layer chromatography and tandem mass spectrometry analyses revealed that overexpression of MdsABC led to increased secretion of 1-palmitoyl-2-stearoyl-phosphatidylserine (PSPS), affecting the ability of the bacteria to invade and survive in host cells. Overexpression of MdsABC and external addition of PSPS similarly rendered the mdsABC deletion strain resistant to diamide. Diagonal gel analysis showed that PSPS treatment reduced the diamide-mediated formation of disulfide bonds, particularly in the membrane fraction of the bacteria. Salmonella infection of macrophages induced the upregulation of MdsABC expression and led to an increase of intracellular bacterial number and host cell death, similar to the effects of MdsABC overexpression and PSPS pretreatment on the mdsABC deletion strain. Our study shows that MdsABC mediates a previously uncharacterized pathway that involves PSPS as a key factor for the survival and virulence of S. Typhimurium in phagocytic cells.
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Affiliation(s)
- Saemee Song
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Boeun Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Ji-Hyun Yeom
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Soonhye Hwang
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon, Republic of Korea
| | - Nam-Chul Ha
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Jeehyeon Bae
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Yong-Hak Kim
- Department of Microbiology, Catholic University of Daegu School of Medicine, Daegu, Republic of Korea
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15
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Molecular architecture of the bacterial tripartite multidrug efflux pump focusing on the adaptor bridging model. J Microbiol 2015; 53:355-64. [DOI: 10.1007/s12275-015-5248-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 05/18/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
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16
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Symmons MF, Marshall RL, Bavro VN. Architecture and roles of periplasmic adaptor proteins in tripartite efflux assemblies. Front Microbiol 2015; 6:513. [PMID: 26074901 PMCID: PMC4446572 DOI: 10.3389/fmicb.2015.00513] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/08/2015] [Indexed: 12/12/2022] Open
Abstract
Recent years have seen major advances in the structural understanding of the different components of tripartite efflux assemblies, which encompass the multidrug efflux (MDR) pumps and type I secretion systems. The majority of these investigations have focused on the role played by the inner membrane transporters and the outer membrane factor (OMF), leaving the third component of the system – the Periplasmic Adaptor Proteins (PAPs) – relatively understudied. Here we review the current state of knowledge of these versatile proteins which, far from being passive linkers between the OMF and the transporter, emerge as active architects of tripartite assemblies, and play diverse roles in the transport process. Recognition between the PAPs and OMFs is essential for pump assembly and function, and targeting this interaction may provide a novel avenue for combating multidrug resistance. With the recent advances elucidating the drug efflux and energetics of the tripartite assemblies, the understanding of the interaction between the OMFs and PAPs is the last piece remaining in the complete structure of the tripartite pump assembly puzzle.
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Affiliation(s)
- Martyn F Symmons
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Robert L Marshall
- Institute of Microbiology and Infection, University of Birmingham Birmingham, UK
| | - Vassiliy N Bavro
- Institute of Microbiology and Infection, University of Birmingham Birmingham, UK
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Functional analysis of Vibrio vulnificus RND efflux pumps homologous to Vibrio cholerae VexAB and VexCD, and to Escherichia coli AcrAB. J Microbiol 2015; 53:256-61. [PMID: 25740377 DOI: 10.1007/s12275-015-5037-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 01/28/2015] [Accepted: 01/29/2015] [Indexed: 01/05/2023]
Abstract
Resistance-nodulation-division (RND) efflux pumps are associated with multidrug resistance in many gram-negative pathogens. The genome of Vibrio vulnificus encodes 11 putative RND pumps homologous to those of Vibrio cholerae and Escherichia coli. In this study, we analyzed three putative RND efflux pumps, showing homology to V. cholerae VexAB and VexCD and to E. coli AcrAB, for their functional roles in multidrug resistance of V. vulnificus. Deletion of the vexAB homolog resulted in increased susceptibility of V. vulnificus to bile acid, acriflavine, ethidium bromide, and erythromycin, whereas deletion of acrAB homologs rendered V. vulnificus more susceptible to acriflavine only. Deletion of vexCD had no effect on susceptibility of V. vulnificus to these chemicals. Upon exposure to these antibacterial chemicals, expression of tolCV1 and tolCV2, which are putative outer membrane factors of RND efflux pumps, was induced, whereas expression levels of vexAB, vexCD, and acrAB homologs were not significantly changed. Our results show that the V. vulnificus homologs of VexAB largely contributed to in vitro antimicrobial resistance with a broad substrate specificity that was partially redundant with the AcrAB pump homologs.
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