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Li W, Wang A. Genomic islands mediate environmental adaptation and the spread of antibiotic resistance in multiresistant Enterococci - evidence from genomic sequences. BMC Microbiol 2021; 21:55. [PMID: 33602143 PMCID: PMC7893910 DOI: 10.1186/s12866-021-02114-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background Genomic islands (GIs) play an important role in the chromosome diversity of Enterococcus. In the current study, we aimed to investigate the spread of GIs between Enterococcus strains and their correlation with antibiotic resistance genes (ARGs). Bitsliced Genomic Signature Indexes (BIGSI) were used to screen the NCBI Sequence Read Archive (SRA) for multiple resistant Enterococcus. A total of 37 pairs of raw reads were screened from 457,000 whole-genome sequences (WGS) in the SRA database, which come from 37 Enterococci distributed in eight countries. These raw reads were assembled for the prediction and analysis of GIs, ARGs, plasmids and prophages. Results The results showed that GIs were universal in Enterococcus, with an average of 3.2 GIs in each strain. Network analysis showed that frequent genetic information exchanges mediated by GIs occurred between Enterococcus strains. Seven antibiotic-resistant genomic islands (ARGIs) were found to carry one to three ARGs, mdtG, tetM, dfrG, lnuG, and fexA, in six strains. These ARGIs were involved in the spread of antibiotic resistance in 45.9% of the 37 strains, although there was no significant positive correlation between the frequency of GI exchanges and the number of ARGs each strain harboured (r = 0. 287, p = 0.085). After comprehensively analysing the genome data, we found that partial GIs were associated with multiple mobile genetic elements (transposons, integrons, prophages and plasmids) and had potential natural transformation characteristics. Conclusions All of these results based on genomic sequencing suggest that GIs might mediate the acquisition of some ARGs and might be involved in the high genome plasticity of Enterococcus through transformation, transduction and conjugation, thus providing a fitness advantage for Enterococcus hosts under complex environmental factors. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02114-4.
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Affiliation(s)
- Weiwei Li
- School of Life Science,
- Ludong University, Yantai, 264025, China.
| | - Ailan Wang
- School of Life Science,
- Ludong University, Yantai, 264025, China
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2
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Wang Y, Zhang Y, Cui Y, Sun Z, Zhou Z, Hu S, Li S, Liu M, Meng X, Xiao Y, Shi D, Bi D, Li Z. Identification of an Integrase That Responsible for Precise Integration and Excision of Riemerella anatipestifer Genomic Island. Front Microbiol 2019; 10:2099. [PMID: 31616389 PMCID: PMC6764341 DOI: 10.3389/fmicb.2019.02099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/26/2019] [Indexed: 12/19/2022] Open
Abstract
Riemerella anatipestifer is a Gram-negative, pathogenic bacterium, which is harmful to poultry. However, the genomic islands (GIs) in R. anatipestifer are not well-studied. In this study, a 10K genomic island was predicted by the bioinformatics analysis of R. anatipestifer ATCC 11845, which is widely found in other R. anatipestifer genomes. We had first reported the genomic island integration and excision function in R. anatipestifer. We successfully constructed the integration plasmid by using the integrase and 53 bp attP elements. The 10K GI was found integrated at the 53 bp attB located in the Arg-tRNA of the R. anatipestifer RA-YM chromosome. We identified an integrase that helped in the precise integration and excision in R. anatipestifer and elucidated the molecular mechanism of the 10K genomic island integration and excision. Furthermore, we provided a new method for the gene expression and construction of complementary strain.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yang Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yijie Cui
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhijian Sun
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zutao Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, China
| | - Sishun Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, China
| | - Shaowen Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, China
| | - Mei Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, China
| | - Xianrong Meng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, China
| | - Yuncai Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, China
| | - Deshi Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, China
| | - Dingren Bi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, China
| | - Zili Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, China
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3
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Martin RM, Bachman MA. Colonization, Infection, and the Accessory Genome of Klebsiella pneumoniae. Front Cell Infect Microbiol 2018; 8:4. [PMID: 29404282 PMCID: PMC5786545 DOI: 10.3389/fcimb.2018.00004] [Citation(s) in RCA: 474] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/05/2018] [Indexed: 12/22/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative pathogen that has a large accessory genome of plasmids and chromosomal gene loci. This accessory genome divides K. pneumoniae strains into opportunistic, hypervirulent, and multidrug-resistant groups and separates K. pneumoniae from two closely related species, Klebsiella variicola and Klebsiella quasipneumoniae. Some strains of K. pneumoniae act as opportunistic pathogens, infecting critically ill and immunocompromised patients. These K. pneumoniae are a common cause of health-care associated infections including pneumonia, urinary tract infections (UTIs), and bloodstream infections. K. variicola and K. quasipneumoniae are often clinically indistinguishable from opportunistic K. pneumoniae. Other strains of K. pneumoniae are hypervirulent, infecting healthy people in community settings and causing severe infections including pyogenic liver abscess, endophthalmitis, and meningitis. A third group of K. pneumoniae encode carbapenemases, making them highly antibiotic-resistant. These strains act as opportunists but are exceedingly difficult to treat. All of these groups of K. pneumoniae and related species can colonize the gastrointestinal tract, and the accessory genome may determine if a colonizing strain remains asymptomatic or progresses to cause disease. This review will explore the associations between colonization and infection with opportunistic, antibiotic-resistant, and hypervirulent K. pneumoniae strains and the role of the accessory genome in distinguishing these groups and related species. As K. pneumoniae infections become progressively more difficult to treat in the face of antibiotic resistance and hypervirulent strains, an increased understanding of the epidemiology and pathogenesis of these bacteria is vital.
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Affiliation(s)
| | - Michael A. Bachman
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
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Marcoleta AE, Berríos-Pastén C, Nuñez G, Monasterio O, Lagos R. Klebsiella pneumoniae Asparagine tDNAs Are Integration Hotspots for Different Genomic Islands Encoding Microcin E492 Production Determinants and Other Putative Virulence Factors Present in Hypervirulent Strains. Front Microbiol 2016; 7:849. [PMID: 27375573 PMCID: PMC4891358 DOI: 10.3389/fmicb.2016.00849] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/23/2016] [Indexed: 01/09/2023] Open
Abstract
Due to the developing of multi-resistant and invasive hypervirulent strains, Klebsiella pneumoniae has become one of the most urgent bacterial pathogen threats in the last years. Genomic comparison of a growing number of sequenced isolates has allowed the identification of putative virulence factors, proposed to be acquirable mainly through horizontal gene transfer. In particular, those related with synthesizing the antibacterial peptide microcin E492 (MccE492) and salmochelin siderophores were found to be highly prevalent among hypervirulent strains. The determinants for the production of both molecules were first reported as part of a 13-kbp segment of K. pneumoniae RYC492 chromosome, and were cloned and characterized in E. coli. However, the genomic context of this segment in K. pneumoniae remained uncharacterized. In this work, we provided experimental and bioinformatics evidence indicating that the MccE492 cluster is part of a highly conserved 23-kbp genomic island (GI) named GIE492, that was integrated in a specific asparagine-tRNA gene (asn-tDNA) and was found in a high proportion of isolates from liver abscesses sampled around the world. This element resulted to be unstable and its excision frequency increased after treating bacteria with mitomycin C and upon the overexpression of the island-encoded integrase. Besides the MccE492 genetic cluster, it invariably included an integrase-coding gene, at least seven protein-coding genes of unknown function, and a putative transfer origin that possibly allows this GI to be mobilized through conjugation. In addition, we analyzed the asn-tDNA loci of all the available K. pneumoniae assembled chromosomes to evaluate them as GI-integration sites. Remarkably, 73% of the strains harbored at least one GI integrated in one of the four asn-tDNA present in this species, confirming them as integration hotspots. Each of these tDNAs was occupied with different frequencies, although they were 100% identical. Also, we identified a total of 47 asn-tDNA-associated GIs that were classified into 12 groups of homology differing in theencoded functionalities but sharing with GIE492 a conserved recombination module and potentially its mobility features. Most of these GIs encoded factors with proven or potential role in pathogenesis, constituting a major reservoir of virulence factors in this species.
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Affiliation(s)
- Andrés E Marcoleta
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Camilo Berríos-Pastén
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Gonzalo Nuñez
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Octavio Monasterio
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Rosalba Lagos
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
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Prediction of Type II Toxin-Antitoxin Loci in Klebsiella pneumoniae Genome Sequences. Interdiscip Sci 2015; 8:143-149. [PMID: 26662948 DOI: 10.1007/s12539-015-0135-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/10/2015] [Accepted: 05/26/2015] [Indexed: 10/22/2022]
Abstract
Klebsiella pneumoniae is an increasingly important bacterial pathogen to human. This Gram-negative bacterium species has become a serious concern due to its dramatic increase in the levels of multiple antibiotic resistances, particularly to carbapenems. The toxin-antitoxin (TA) system has recently been reported to be involved in the formation of drug-tolerant persister cells. The type II TA system is composed of a stable toxin protein and a relatively unstable antitoxin protein that is able to inhibit the toxin. Here, we examine the type II TA locus distribution and compare the TA diversity throughout ten completely sequenced K. pneumoniae genomes by using bioinformatics approaches. Two hundred and twelve putative type II TA loci were identified in 30 replicons of these K. pneumoniae strains. The amino acid sequence similarity-based grouping shows that these loci distribute differently not only among different K. pneumoniae strains isolated from diverse sources, but also between their chromosomes and plasmids.
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Roach DJ, Burton JN, Lee C, Stackhouse B, Butler-Wu SM, Cookson BT, Shendure J, Salipante SJ. A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota. PLoS Genet 2015; 11:e1005413. [PMID: 26230489 PMCID: PMC4521703 DOI: 10.1371/journal.pgen.1005413] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/02/2015] [Indexed: 01/05/2023] Open
Abstract
Bacterial whole genome sequencing holds promise as a disruptive technology in clinical microbiology, but it has not yet been applied systematically or comprehensively within a clinical context. Here, over the course of one year, we performed prospective collection and whole genome sequencing of nearly all bacterial isolates obtained from a tertiary care hospital's intensive care units (ICUs). This unbiased collection of 1,229 bacterial genomes from 391 patients enables detailed exploration of several features of clinical pathogens. A sizable fraction of isolates identified as clinically relevant corresponded to previously undescribed species: 12% of isolates assigned a species-level classification by conventional methods actually qualified as distinct, novel genomospecies on the basis of genomic similarity. Pan-genome analysis of the most frequently encountered pathogens in the collection revealed substantial variation in pan-genome size (1,420 to 20,432 genes) and the rate of gene discovery (1 to 152 genes per isolate sequenced). Surprisingly, although potential nosocomial transmission of actively surveilled pathogens was rare, 8.7% of isolates belonged to genomically related clonal lineages that were present among multiple patients, usually with overlapping hospital admissions, and were associated with clinically significant infection in 62% of patients from which they were recovered. Multi-patient clonal lineages were particularly evident in the neonatal care unit, where seven separate Staphylococcus epidermidis clonal lineages were identified, including one lineage associated with bacteremia in 5/9 neonates. Our study highlights key differences in the information made available by conventional microbiological practices versus whole genome sequencing, and motivates the further integration of microbial genome sequencing into routine clinical care.
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Affiliation(s)
- David J. Roach
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Joshua N. Burton
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Bethany Stackhouse
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Susan M. Butler-Wu
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Brad T. Cookson
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Stephen J. Salipante
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
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Abstract
La synthèse des protéines, également appelée traduction, est assurée dans chaque cellule par des machines moléculaires très sophistiquées : les ribosomes. Compte tenu de l’immense quantité de données biologiques à traiter, il arrive régulièrement que ces machines se bloquent et mettent en péril la survie de la cellule. Chez les bactéries, le principal processus de sauvetage des ribosomes bloqués est la trans-traduction. Il est assuré par un acide ribonucléique (ARN) hybride, l’ARN transfert-messager (ARNtm), associé à une petite protéine basique, SmpB (small protein B). Plusieurs autres systèmes de contrôle qualité ont récemment été mis en évidence, révélant un réseau de maintien de la survie cellulaire très sophistiqué. Cette machinerie du contrôle qualité de la synthèse protéique est une cible très prometteuse pour le développement de futurs antibiotiques.
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Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum. J Bacteriol 2012; 194:1841-2. [PMID: 22408243 DOI: 10.1128/jb.00043-12] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Klebsiella pneumoniae is an important pathogen commonly associated with opportunistic infections. Here we report the genome sequence of a strain, HS11286, isolated from human sputum in 2011 in Shanghai, China. It contains one chromosome (5.3 Mb), three multidrug resistance plasmids (∼110 kb), including a carbapenemase producer, and three small plasmids (∼3 kb).
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van Aartsen JJ, Stahlhut SG, Harrison EM, Crosatti M, Ou HY, Krogfelt KA, Struve C, Rajakumar K. Characterization of a novel chaperone/usher fimbrial operon present on KpGI-5, a methionine tRNA gene-associated genomic island in Klebsiella pneumoniae. BMC Microbiol 2012; 12:59. [PMID: 22520965 PMCID: PMC3419637 DOI: 10.1186/1471-2180-12-59] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 04/20/2012] [Indexed: 01/11/2023] Open
Abstract
Background Several strain-specific Klebsiella pneumoniae virulence determinants have been described, though these have almost exclusively been linked with hypervirulent liver abscess-associated strains. Through PCR interrogation of integration hotspots, chromosome walking, island-tagging and fosmid-based marker rescue we captured and sequenced KpGI-5, a novel genomic island integrated into the met56 tRNA gene of K. pneumoniae KR116, a bloodstream isolate from a patient with pneumonia and neutropenic sepsis. Results The 14.0 kb KpGI-5 island exhibited a genome-anomalous G + C content, possessed near-perfect 46 bp direct repeats, encoded a γ1-chaperone/usher fimbrial cluster (fim2) and harboured seven other predicted genes of unknown function. Transcriptional analysis demonstrated expression of three fim2 genes, and suggested that the fim2A-fim2K cluster comprised an operon. As fimbrial systems are frequently implicated in pathogenesis, we examined the role of fim2 by analysing KR2107, a streptomycin-resistant derivative of KR116, and three isogenic mutants (Δfim, Δfim2 and ΔfimΔfim2) using biofilm assays, human cell adhesion assays and pair-wise competition-based murine models of intestinal colonization, lung infection and ascending urinary tract infection. Although no statistically significant role for fim2 was demonstrable, liver and kidney CFU counts for lung and urinary tract infection models, respectively, hinted at an ordered gradation of virulence: KR2107 (most virulent), KR2107∆fim2, KR2107∆fim and KR2107∆fim∆fim2 (least virulent). Thus, despite lack of statistical evidence there was a suggestion that fim and fim2 contribute additively to virulence in these murine infection models. However, further studies would be necessary to substantiate this hypothesis. Conclusion Although fim2 was present in 13% of Klebsiella spp. strains investigated, no obvious in vitro or in vivo role for the locus was identified, although there were subtle hints of involvement in urovirulence and bacterial dissemination from the respiratory tract. Based on our findings and on parallels with other fimbrial systems, we propose that fim2 has the potential to contribute beneficially to pathogenesis and/or environmental persistence of Klebsiella strains, at least under specific yet-to-be identified conditions.
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Affiliation(s)
- Jon J van Aartsen
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK
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