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Yang Y, Wang P, Qaidi SE, Hardwidge PR, Huang J, Zhu G. Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance. Appl Microbiol Biotechnol 2024; 108:328. [PMID: 38717672 PMCID: PMC11078800 DOI: 10.1007/s00253-023-12971-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 05/12/2024]
Abstract
Pseudogenes are defined as "non-functional" copies of corresponding parent genes. The cognition of pseudogenes continues to be refreshed through accumulating and updating research findings. Previous studies have predominantly focused on mammals, but pseudogenes have received relatively less attention in the field of microbiology. Given the increasing recognition on the importance of pseudogenes, in this review, we focus on several aspects of microorganism pseudogenes, including their classification and characteristics, their generation and fate, their identification, their abundance and distribution, their impact on virulence, their ability to recombine with functional genes, the extent to which some pseudogenes are transcribed and translated, and the relationship between pseudogenes and viruses. By summarizing and organizing the latest research progress, this review will provide a comprehensive perspective and improved understanding on pseudogenes in microorganisms. KEY POINTS: • Concept, classification and characteristics, identification and databases, content, and distribution of microbial pseudogenes are presented. • How pseudogenization contribute to pathogen virulence is highlighted. • Pseudogenes with potential functions in microorganisms are discussed.
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Affiliation(s)
- Yi Yang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China
| | - Pengzhi Wang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China
| | - Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Jinlin Huang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Jiangsu Key Lab of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- College of Bioscience and Biotechnology, Yangzhou University, 12 East Wenhui Road Yangzhou, Jiangsu, 225009, China.
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China.
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China.
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Grote A, Piscon B, Manson AL, Adani B, Cohen H, Livny J, Earl AM, Gal-Mor O. Persistent Salmonella infections in humans are associated with mutations in the BarA/SirA regulatory pathway. Cell Host Microbe 2024; 32:79-92.e7. [PMID: 38211565 DOI: 10.1016/j.chom.2023.12.001] [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: 07/26/2022] [Revised: 10/04/2023] [Accepted: 12/06/2023] [Indexed: 01/13/2024]
Abstract
Several bacterial pathogens, including Salmonella enterica, can cause persistent infections in humans by mechanisms that are poorly understood. By comparing genomes of isolates longitudinally collected from 256 prolonged salmonellosis patients, we identified repeated mutations in global regulators, including the barA/sirA two-component regulatory system, across multiple patients and Salmonella serovars. Comparative RNA-seq analysis revealed that distinct mutations in barA/sirA led to diminished expression of Salmonella pathogenicity islands 1 and 4 genes, which are required for Salmonella invasion and enteritis. Moreover, barA/sirA mutants were attenuated in an acute salmonellosis mouse model and induced weaker transcription of host immune responses. In contrast, in a persistent infection mouse model, these mutants exhibited long-term colonization and prolonged shedding. Taken together, these findings suggest that selection of mutations in global virulence regulators facilitates persistent Salmonella infection in humans, by attenuating Salmonella virulence and inducing a weaker host inflammatory response.
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Affiliation(s)
- Alexandra Grote
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bar Piscon
- Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Boaz Adani
- Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Helit Cohen
- Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Ohad Gal-Mor
- Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Comparison of Phenotype and Genotype Virulence and Antimicrobial Factors of Salmonella Typhimurium Isolated from Human Milk. Int J Mol Sci 2023; 24:ijms24065135. [PMID: 36982209 PMCID: PMC10048834 DOI: 10.3390/ijms24065135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023] Open
Abstract
Salmonella is a common foodborne infection. Many serovars belonging to Salmonella enterica subsp. enterica are present in the gut of various animal species. They can cause infection in human infants via breast milk or cross-contamination with powdered milk. In the present study, Salmonella BO was isolated from human milk in accordance with ISO 6579-1:2017 standards and sequenced using whole-genome sequencing (WGS), followed by serosequencing and genotyping. The results also allowed its pathogenicity to be predicted. The WGS results were compared with the bacterial phenotype. The isolated strain was found to be Salmonella enterica subsp. enterica serovar Typhimurium 4:i:1,2_69M (S. Typhimurium 69M); it showed a very close similarity to S. enterica subsp. enterica serovar Typhimurium LT2. Bioinformatics sequence analysis detected eleven SPIs (SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-9, SPI-12, SPI-13, SPI-14, C63PI, CS54_island). Significant changes in gene sequences were noted, causing frameshift mutations in yeiG, rfbP, fumA, yeaL, ybeU (insertion) and lpfD, avrA, ratB, yacH (deletion). The sequences of several proteins were significantly different from those coded in the reference genome; their three-dimensional structure was predicted and compared with reference proteins. Our findings indicate the presence of a number of antimicrobial resistance genes that do not directly imply an antibiotic resistance phenotype.
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Shikov AE, Belousova ME, Belousov MV, Nizhnikov AA, Antonets KS. Salmonella-Based Biorodenticides: Past Applications and Current Contradictions. Int J Mol Sci 2022; 23:ijms232314595. [PMID: 36498920 PMCID: PMC9736839 DOI: 10.3390/ijms232314595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/03/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
Abstract
The idea of using pathogens to control pests has existed since the end of the 19th century. Enterobacteria from the genus Salmonella, discovered at that time, are the causative agents of many serious diseases in mammals often leading to death. Mostly, the strains of Salmonella are able to infect a wide spectrum of hosts belonging to vertebrates, but some of them show host restriction. Several strains of these bacteria have been used as biorodenticides due to the host restriction until they were banned in many countries in the second part of the 20th century. The main reason for the ban was their potential pathogenicity for some domestic animals and poultry and the outbreaks of gastroenteritis in humans. Since that time, a lot of data regarding the host specificity and host restriction of different strains of Salmonella have been accumulated, and the complexity of the molecular mechanisms affecting it has been uncovered. In this review, we summarize the data regarding the history of studying and application of Salmonella-based rodenticides, discuss molecular systems controlling the specificity of Salmonella interactions within its multicellular hosts at different stages of infection, and attempt to reconstruct the network of genes and their allelic variants which might affect the host-restriction mechanisms.
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Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Maria E. Belousova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia
| | - Mikhail V. Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia
- Correspondence:
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Feng Y, Wang Z, Chien KY, Chen HL, Liang YH, Hua X, Chiu CH. "Pseudo-pseudogenes" in bacterial genomes: Proteogenomics reveals a wide but low protein expression of pseudogenes in Salmonella enterica. Nucleic Acids Res 2022; 50:5158-5170. [PMID: 35489061 PMCID: PMC9122581 DOI: 10.1093/nar/gkac302] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 12/03/2022] Open
Abstract
Pseudogenes (genes disrupted by frameshift or in-frame stop codons) are ubiquitously present in the bacterial genome and considered as nonfunctional fossil. Here, we used RNA-seq and mass-spectrometry technologies to measure the transcriptomes and proteomes of Salmonella enterica serovars Paratyphi A and Typhi. All pseudogenes’ mRNA sequences remained disrupted, and were present at comparable levels to their intact homologs. At the protein level, however, 101 out of 161 pseudogenes suggested successful translation, with their low expression regardless of growth conditions, genetic background and pseudogenization causes. The majority of frameshifting detected was compensatory for -1 frameshift mutations. Readthrough of in-frame stop codons primarily involved UAG; and cytosine was the most frequent base adjacent to the codon. Using a fluorescence reporter system, fifteen pseudogenes were confirmed to express successfully in vivo in Escherichia coli. Expression of the intact copy of the fifteen pseudogenes in S. Typhi affected bacterial pathogenesis as revealed in human macrophage and epithelial cell infection models. The above findings suggest the need to revisit the nonstandard translation mechanism as well as the biological role of pseudogenes in the bacterial genome.
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Affiliation(s)
- Ye Feng
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Zeyu Wang
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Kun-Yi Chien
- Graduate Institute of Biomedical Sciences, Chang Gung University College of Medicine, Taoyuan, Republic of China
| | - Hsiu-Ling Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Republic of China
| | - Yi-Hua Liang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Republic of China
| | - Xiaoting Hua
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Cheng-Hsun Chiu
- Graduate Institute of Biomedical Sciences, Chang Gung University College of Medicine, Taoyuan, Republic of China.,Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Republic of China.,Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Republic of China
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Li Q, Li Z, Fei X, Tian Y, Zhou G, Hu Y, Wang S, Shi H. The role of TolA, TolB, and TolR in cell morphology, OMVs production, and virulence of Salmonella Choleraesuis. AMB Express 2022; 12:5. [PMID: 35075554 PMCID: PMC8787014 DOI: 10.1186/s13568-022-01347-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/15/2022] [Indexed: 01/12/2023] Open
Abstract
The Tol–Pal system of Gram-negative bacteria is necessary for maintaining outer membrane integrity. It is a multiprotein complex of five envelope proteins, TolQ, TolR, TolA, TolB, and Pal. These proteins were first investigated in E. coli, and subsequently been identified in many other bacterial genera. However, the function of the Tol–Pal system in Salmonella Choleraesuis pathogenesis is still unclear. Here, we reported the role of three of these proteins in the phenotype and biology of S. Choleraesuis. We found that mutations in tolA, tolB, and tolR caused severe damage to the cell wall, which was supported by observing the microstructure of spherical forms, long chains, flagella defects, and membrane blebbing. We confirmed that all the mutants significantly decreased S. Choleraesuis survival when exposed to sodium deoxycholate and exhibited a high sensitivity to vancomycin, which may be explained by the disruption of envelope integrity. In addition, tolA, tolB, and tolR mutants displayed attenuated virulence in a mouse infection model. This could be interpreted as a series of defective phenotypes in the mutants, such as severe defects in envelope integrity, growth, and motility. Further investigation showed that all the genes participate in outer membrane vesicles (OMVs) biogenesis. Interestingly, immunization with OMVs from ΔtolB efficiently enhanced murine viability in contrast to OMVs from the wild-type S. Choleraesuis, suggesting its potential use in vaccination strategies. Collectively, this study provides an insight into the biological role of the S. Choleraesuis Tol–Pal system.
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Zhang Y, Liu K, Zhang Z, Tian S, Liu M, Li X, Han Y, Zhu K, Liu H, Yang C, Liu H, Du X, Wang Q, Wang H, Yang M, Wang L, Song H, Yang H, Xiang Y, Qiu S. A Severe Gastroenteritis Outbreak of Salmonella enterica Serovar Enteritidis Linked to Contaminated Egg Fried Rice, China, 2021. Front Microbiol 2021; 12:779749. [PMID: 34880847 PMCID: PMC8645860 DOI: 10.3389/fmicb.2021.779749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 10/22/2021] [Indexed: 12/04/2022] Open
Abstract
Salmonella contamination of eggs and egg shells has been identified as a public health problem worldwide. Here, we reported an outbreak of severe gastrointestinal symptoms caused by Salmonella enterica serovar Enteritidis (S. enteritidis) in China. We evaluated the outbreak by using epidemiological surveys, routine laboratory testing methods, and whole genome sequencing (WGS). This outbreak occurred in a canteen in Beijing, during March 9–11, 2021, 225 of the 324 diners who have eaten at the canteen showed gastrointestinal symptoms. The outbreak had characteristical epidemiological and clinical features. It caused a very high attack rate (69.4%) in a short incubation time. All patients developed diarrhea and high fever, accompanied by abdominal pain (62.3%), nausea (50.4%), and vomiting (62.7%). The average frequency of diarrhea was 12.4 times/day, and the highest frequency of diarrhea was as high as 50 times/day. The average fever temperature was 39.4°C, and the highest fever temperature was 42°C. Twenty strains of S. enteritidis were recovered, including 19 from the patients samples, and one from remained egg fried rice. Antibiotic susceptibility test showed that the 20 outbreak strains all had the same resistance pattern. PFGE results demonstrated that all 20 strains bore completely identical bands. Phylogenetic analysis based on WGS revealed that all 20 outbreak strains were tightly clustered together. So the pathogenic source of this food poisoning incident may was contaminated egg fried rice. Resistance gene analysis showed that the outbreak strains are all multi-drug resistant strains. Virulence gene analysis indicated that these outbreak strains carried a large number of virulence genes, including 2 types of Salmonella pathogenicity islands (SPI-1 and SPI-2). Other important virulence genes were also carried by the outbreak strains, such as pefABCD, rck and shdA. And the shdA gene was not in other strains located in the same evolutionary branch as the outbreak strain. We speculated that this is a significant reason for the serious symptoms of gastroenteritis in this outbreak. This outbreak caused by S. enteritidis suggested government should strengthen monitoring of the prevalence of outbreak clone strains, and take measures to mitigate the public health threat posed by contaminated eggs.
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Affiliation(s)
- Yaowen Zhang
- School of Public Health, Zhengzhou University, Zhengzhou, China.,Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kangkang Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Zhenbiao Zhang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Sai Tian
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Meiling Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xinge Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yiran Han
- School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Kunpeng Zhu
- School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Hongbo Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Chaojie Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbo Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xinying Du
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Qi Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hui Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Mingjuan Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Ligui Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbin Song
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Haiyan Yang
- School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Ying Xiang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Shaofu Qiu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
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Lerminiaux NA, MacKenzie KD, Cameron ADS. Salmonella Pathogenicity Island 1 (SPI-1): The Evolution and Stabilization of a Core Genomic Type Three Secretion System. Microorganisms 2020; 8:microorganisms8040576. [PMID: 32316180 PMCID: PMC7232297 DOI: 10.3390/microorganisms8040576] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 11/16/2022] Open
Abstract
Salmonella Pathogenicity Island 1 (SPI-1) encodes a type three secretion system (T3SS), effector proteins, and associated transcription factors that together enable invasion of epithelial cells in animal intestines. The horizontal acquisition of SPI-1 by the common ancestor of all Salmonella is considered a prime example of how gene islands potentiate the emergence of new pathogens with expanded niche ranges. However, the evolutionary history of SPI-1 has attracted little attention. Here, we apply phylogenetic comparisons across the family Enterobacteriaceae to examine the history of SPI-1, improving the resolution of its boundaries and unique architecture by identifying its composite gene modules. SPI-1 is located between the core genes fhlA and mutS, a hotspot for the gain and loss of horizontally acquired genes. Despite the plasticity of this locus, SPI-1 demonstrates stable residency of many tens of millions of years in a host genome, unlike short-lived homologous T3SS and effector islands including Escherichia ETT2, Yersinia YSA, Pantoea PSI-2, Sodalis SSR2, and Chromobacterium CPI-1. SPI-1 employs a unique series of regulatory switches, starting with the dedicated transcription factors HilC and HilD, and flowing through the central SPI-1 regulator HilA. HilA is shared with other T3SS, but HilC and HilD may have their evolutionary origins in Salmonella. The hilA, hilC, and hilD gene promoters are the most AT-rich DNA in SPI-1, placing them under tight control by the transcriptional repressor H-NS. In all Salmonella lineages, these three promoters resist amelioration towards the genomic average, ensuring strong repression by H-NS. Hence, early development of a robust and well-integrated regulatory network may explain the evolutionary stability of SPI-1 compared to T3SS gene islands in other species.
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Affiliation(s)
- Nicole A. Lerminiaux
- Department of Biology, Faculty of Science, University of Regina, Regina, SK S4S 0A2, Canada; (N.A.L.); (K.D.M.)
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, SK S4S 0A2, Canada
| | - Keith D. MacKenzie
- Department of Biology, Faculty of Science, University of Regina, Regina, SK S4S 0A2, Canada; (N.A.L.); (K.D.M.)
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, SK S4S 0A2, Canada
| | - Andrew D. S. Cameron
- Department of Biology, Faculty of Science, University of Regina, Regina, SK S4S 0A2, Canada; (N.A.L.); (K.D.M.)
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, SK S4S 0A2, Canada
- Correspondence:
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Zhang D, Zhuang L, Wang C, Zhang P, Zhang T, Shao H, Han X, Gong J. Virulence Gene Distribution of Salmonella Pullorum Isolates Recovered from Chickens in China (1953-2015). Avian Dis 2019; 62:431-436. [PMID: 31119928 DOI: 10.1637/11927-071318-resnote.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/05/2022]
Abstract
Salmonella enterica subspecies enterica serovar Gallinarum biovar Pullorum (Salmonella Pullorum) has strict host specificity for poultry, and pullorum disease seriously threatens the poultry industry. Virulence genes play a central role in Salmonella pathogenicity, but very few reports are available on the distribution of virulence genes in Salmonella Pullorum. In this study, we investigated 304 Salmonella Pullorum isolates recovered from chickens in China between 1953 and 2015 for the presence of 25 Salmonella virulence genes (invA, orgA, prgH, sitC, spaN, sifA, spiA, ttrC, mgtB, misL, siiE, spi4D, pipA, sipB, sopB, sefA, cdtB, pagC, shdA, msgA, lpfC, tolC, iroN, pefA, and spvB), including pathogenicity island genes, fimbriae genes, and virulence plasmid genes. PCR showed that 15 of the 25 virulence genes were present in all isolates tested, whereas cdtB was not present in any isolate. The presence rates of the remaining genes ranged from 97.7% to 99.7%. The variation rates of these virulence genes was low, and no significant differences were identified in the distribution of virulence genes over time. On the basis of the distribution of these virulence genes, the 304 Salmonella Pullorum isolates were divided into 10 virulence genotypes. The major genotype, which comprised 93.4% of all isolates, included isolates that carried 24 of the virulence genes assessed. The results of this study will help in the characterization of Salmonella Pullorum and in the study of the correlation between virulence genotypes and pathogenicity.
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Affiliation(s)
- Di Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225125, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225002, China
| | - Linlin Zhuang
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Chengming Wang
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn AL 36849
| | - Ping Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225125, China
| | - Tengfei Zhang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Huabin Shao
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Xiangan Han
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China,
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225125, China, .,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225002, China,
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10
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Rakov AV, Mastriani E, Liu SL, Schifferli DM. Association of Salmonella virulence factor alleles with intestinal and invasive serovars. BMC Genomics 2019; 20:429. [PMID: 31138114 PMCID: PMC6540521 DOI: 10.1186/s12864-019-5809-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 05/20/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The role of Salmonella virulence factor (VF) allelic variation in modulating pathogenesis or host specificity has only been demonstrated in a few cases, mostly through serendipitous findings. Virulence factor (VF) alleles from Salmonella enterica subsp. enterica genomes were compared to identify potential associations with the host-adapted invasive serovars Typhi, Dublin, Choleraesuis, and Gallinarum, and with the broad host-range intestinal serovars Typhimurium, Enteritidis, and Newport. RESULTS Through a bioinformatics analysis of 500 Salmonella genomes, we have identified allelic variants of 70 VFs, many of which are associated with either one of the four host-adapted invasive Salmonella serovars or one of the three broad host-range intestinal serovars. In addition, associations between specific VF alleles and intra-serovar clusters, sequence types (STs) and/or host-adapted FimH adhesins were identified. Moreover, new allelic VF associations with non-typhoidal S. Enteritidis and S. Typhimurium (NTS) or invasive NTS (iNTS) were detected. CONCLUSIONS By analogy to the previously shown association of specific FimH adhesin alleles with optimal binding by host adapted Salmonella serovars, lineages or strains, we predict that some of the identified association of other VF alleles with host-adapted serovars, lineages or strains will reflect specific contributions to host adaptation and/or pathogenesis. The identification of these allelic associations will support investigations of the biological impact of VF alleles and better characterize the role of allelic variation in Salmonella pathogenesis. Most relevant functional experiments will test the potential causal contribution of the detected FimH-associated VF variants in host adapted virulence.
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Affiliation(s)
- Alexey V. Rakov
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania USA
- Present Address: Somov Institute of Epidemiology and Microbiology, Vladivostok, Russia
| | - Emilio Mastriani
- Systemomics Center, College of Pharmacy, Genomics Research Center, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Harbin Medical University, Harbin, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Systemomics Center, College of Pharmacy, Genomics Research Center, State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Harbin Medical University, Harbin, China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Dieter M. Schifferli
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania USA
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11
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Nevermann J, Silva A, Otero C, Oyarzún DP, Barrera B, Gil F, Calderón IL, Fuentes JA. Identification of Genes Involved in Biogenesis of Outer Membrane Vesicles (OMVs) in Salmonella enterica Serovar Typhi. Front Microbiol 2019; 10:104. [PMID: 30778340 PMCID: PMC6369716 DOI: 10.3389/fmicb.2019.00104] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/17/2019] [Indexed: 12/26/2022] Open
Abstract
Outer membrane vesicles (OMVs) are nano-sized proteoliposomes discharged from the cell envelope of Gram-negative bacteria. OMVs normally contain toxins, enzymes and other factors, and are used as vehicles in a process that has been considered a generalized, evolutionarily conserved delivery system among bacteria. Furthermore, OMVs can be used in biotechnological applications that require delivery of biomolecules, such as vaccines, remarking the importance of their study. Although it is known that Salmonella enterica serovar Typhi (S. Typhi), the etiological agent of typhoid fever in humans, delivers toxins (e.g., HlyE) via OMVs, there are no reports identifying genetic determinants of the OMV biogenesis in this serovar. In the present work, and with the aim to identify genes participating in OMV biogenesis in S. Typhi, we screened 15,000 random insertion mutants for increased HlyE secretion. We found 9 S. Typhi genes (generically called zzz genes) determining an increased HlyE secretion that were also involved in OMV biogenesis. The genes corresponded to ompA, nlpI, and tolR (envelope stability), rfaE and waaC (LPS synthesis), yipP (envC), mrcB (synthesis and remodeling of peptidoglycan), degS (stress sensor serine endopeptidase) and hns (global transcriptional regulator). We found that S. Typhi Δzzz mutants were prone to secrete periplasmic, functional proteins with a relatively good envelope integrity. In addition, we showed that zzz genes participate in OMV biogenesis, modulating different properties such as OMV size distribution, OMV yield and OMV protein cargo.
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Affiliation(s)
- Jan Nevermann
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Andrés Silva
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Carolina Otero
- Escuela de Química y Farmacia, Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Diego P Oyarzún
- Center of Applied Nanosciences, Universidad Andres Bello, Santiago, Chile
| | - Boris Barrera
- Unidad de Microbiología, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Fernando Gil
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Iván L Calderón
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Juan A Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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12
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Yap KP, Thong KL. Salmonella Typhi genomics: envisaging the future of typhoid eradication. Trop Med Int Health 2017; 22:918-925. [PMID: 28544285 DOI: 10.1111/tmi.12899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Next-generation whole-genome sequencing has revolutionised the study of infectious diseases in recent years. The availability of genome sequences and its understanding have transformed the field of molecular microbiology, epidemiology, infection treatments and vaccine developments. We review the key findings of the publicly accessible genomes of Salmonella enterica serovar Typhi since the first complete genome to the most recent release of thousands of Salmonella Typhi genomes, which remarkably shape the genomic research of S. Typhi and other pathogens. Important new insights acquired from the genome sequencing of S. Typhi, pertaining to genomic variations, evolution, population structure, antibiotic resistance, virulence, pathogenesis, disease surveillance/investigation and disease control are discussed. As the numbers of sequenced genomes are increasing at an unprecedented rate, fine variations in the gene pool of S. Typhi are captured in high resolution, allowing deeper understanding of the pathogen's evolutionary trends and its pathogenesis, paving the way to bringing us closer to eradication of typhoid through effective vaccine/treatment development.
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Affiliation(s)
- Kien-Pong Yap
- Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kwai Lin Thong
- Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
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13
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Carreño A, Aros AE, Otero C, Polanco R, Gacitúa M, Arratia-Pérez R, Fuentes JA. Substituted bidentate and ancillary ligands modulate the bioimaging properties of the classical Re(i) tricarbonyl core with yeasts and bacteria. NEW J CHEM 2017. [DOI: 10.1039/c6nj03792e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Six classical rhenium(i) tricarbonyl complexes were investigated for their ability to be used as dyes for bioimaging in walled cells.
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Affiliation(s)
- Alexander Carreño
- Center of Applied Nanosciences (CENAP)
- Universidad Andres Bello
- Santiago
- Chile
- Núcleo Milenio de Ingeniería Molecular para Catálisis y Biosensores (MECB)
| | - Alejandra E. Aros
- Núcleo Milenio de Ingeniería Molecular para Catálisis y Biosensores (MECB)
- ICM
- Chile
- Laboratorio de Genética y Patogénesis Bacteriana
- Facultad de Ciencias Biológicas
| | - Carolina Otero
- Center for Integrative Medicine and Innovative Science (CIMIS)
- Facultad de Medicina
- Universidad Andres Bello
- Santiago
- Chile
| | - Rubén Polanco
- Centro de Biotecnología Vegetal
- Facultad de Ciencias Biológicas
- Universidad Andres Bello
- Santiago
- Chile
| | - Manuel Gacitúa
- Center of Applied Ecology and Sustainability (CAPES)
- Universidad Adolfo Ibáñez
- Peñalolén
- Chile
| | - Ramiro Arratia-Pérez
- Center of Applied Nanosciences (CENAP)
- Universidad Andres Bello
- Santiago
- Chile
- Núcleo Milenio de Ingeniería Molecular para Catálisis y Biosensores (MECB)
| | - Juan A. Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana
- Facultad de Ciencias Biológicas
- Universidad Andrés Bello
- Santiago
- Chile
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14
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Ortega A, Villagra N, Urrutia I, Valenzuela L, Talamilla-Espinoza A, Hidalgo A, Rodas P, Gil F, Calderón I, Paredes-Sabja D, Mora G, Fuentes J. Lose to win: marT pseudogenization in Salmonella enterica serovar Typhi contributed to the surV -dependent survival to H 2 O 2 , and inside human macrophage-like cells. INFECTION GENETICS AND EVOLUTION 2016; 45:111-121. [DOI: 10.1016/j.meegid.2016.08.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 08/17/2016] [Accepted: 08/22/2016] [Indexed: 02/06/2023]
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15
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Velásquez JC, Hidalgo AA, Villagra N, Santiviago CA, Mora GC, Fuentes JA. SPI-9 of Salmonella enterica serovar Typhi is constituted by an operon positively regulated by RpoS and contributes to adherence to epithelial cells in culture. Microbiology (Reading) 2016; 162:1367-1378. [DOI: 10.1099/mic.0.000319] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Juan C. Velásquez
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, República 217, Santiago, Chile
| | - Alejandro A. Hidalgo
- Laboratorio de Patogénesis Molecular y Antimicrobianos, Facultad de Medicina, Universidad Andres Bello, Echaurren 183, Santiago, Chile
| | - Nicolás Villagra
- Laboratorio de Patogénesis Molecular y Antimicrobianos, Facultad de Medicina, Universidad Andres Bello, Echaurren 183, Santiago, Chile
| | - Carlos A. Santiviago
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont 964, Independencia, Santiago, Chile
| | - Guido C. Mora
- Laboratorio de Patogénesis Molecular y Antimicrobianos, Facultad de Medicina, Universidad Andres Bello, Echaurren 183, Santiago, Chile
| | - Juan A. Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, República 217, Santiago, Chile
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16
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Yap KP, Ho WS, Gan HM, Chai LC, Thong KL. Global MLST of Salmonella Typhi Revisited in Post-genomic Era: Genetic Conservation, Population Structure, and Comparative Genomics of Rare Sequence Types. Front Microbiol 2016; 7:270. [PMID: 26973639 PMCID: PMC4774407 DOI: 10.3389/fmicb.2016.00270] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/19/2016] [Indexed: 11/16/2022] Open
Abstract
Typhoid fever, caused by Salmonella enterica serovar Typhi, remains an important public health burden in Southeast Asia and other endemic countries. Various genotyping methods have been applied to study the genetic variations of this human-restricted pathogen. Multilocus sequence typing (MLST) is one of the widely accepted methods, and recently, there is a growing interest in the re-application of MLST in the post-genomic era. In this study, we provide the global MLST distribution of S. Typhi utilizing both publicly available 1,826 S. Typhi genome sequences in addition to performing conventional MLST on S. Typhi strains isolated from various endemic regions spanning over a century. Our global MLST analysis confirms the predominance of two sequence types (ST1 and ST2) co-existing in the endemic regions. Interestingly, S. Typhi strains with ST8 are currently confined within the African continent. Comparative genomic analyses of ST8 and other rare STs with genomes of ST1/ST2 revealed unique mutations in important virulence genes such as flhB, sipC, and tviD that may explain the variations that differentiate between seemingly successful (widespread) and unsuccessful (poor dissemination) S. Typhi populations. Large scale whole-genome phylogeny demonstrated evidence of phylogeographical structuring and showed that ST8 may have diverged from the earlier ancestral population of ST1 and ST2, which later lost some of its fitness advantages, leading to poor worldwide dissemination. In response to the unprecedented increase in genomic data, this study demonstrates and highlights the utility of large-scale genome-based MLST as a quick and effective approach to narrow the scope of in-depth comparative genomic analysis and consequently provide new insights into the fine scale of pathogen evolution and population structure.
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Affiliation(s)
- Kien-Pong Yap
- Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Wing S Ho
- Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Han M Gan
- School of Science, Monash University Malaysia Bandar Sunway, Malaysia
| | - Lay C Chai
- Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Kwai L Thong
- Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
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17
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Pseudogenization of sopA and sopE2 is functionally linked and contributes to virulence of Salmonella enterica serovar Typhi. INFECTION GENETICS AND EVOLUTION 2015; 33:131-42. [DOI: 10.1016/j.meegid.2015.04.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/13/2015] [Accepted: 04/21/2015] [Indexed: 12/11/2022]
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