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Klaper K, Tlapák H, Selb R, Jansen K, Heuer D. Integrated molecular, phenotypic and epidemiological surveillance of antimicrobial resistance in Neisseria gonorrhoeae in Germany. Int J Med Microbiol 2024; 314:151611. [PMID: 38309143 DOI: 10.1016/j.ijmm.2024.151611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/05/2024] Open
Abstract
Numbers of infections with Neisseria gonorrhoeae are among the top three sexually transmitted infections (STI) worldwide. In addition, the emergence and spread of antimicrobial resistance (AMR) in Neisseria gonorrhoeae pose an important public-health issue. The integration of genomic, phenotypic and epidemiological data to monitor Neisseria gonorrhoeae fosters our understanding of the emergence and spread of AMR in Neisseria gonorrhoeae and helps to inform therapy guidelines and intervention strategies. Thus, the Gonococcal resistance surveillance (Go-Surv-AMR) was implemented at the Robert Koch Institute in Germany in 2021 to obtain molecular, phenotypic and epidemiological data on Neisseria gonorrhoeae isolated in Germany. Here, we describe the structure and aims of Go-Surv-AMR. Furthermore, we point out future directions of Go-Surv-AMR to improve the integrated genomic surveillance of Neisseria gonorrhoeae. In this context we discuss current and prospective sequencing approaches and the information derived from their application. Moreover, we highlight the importance of combining phenotypic and WGS data to monitor the evolution of AMR in Neisseria gonorrhoeae in Germany. The implementation and constant development of techniques and tools to improve the genomic surveillance of Neisseria gonorrhoeae will be important in coming years.
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Affiliation(s)
- Kathleen Klaper
- Department Infectious Diseases, Unit 18 `Sexually transmitted bacterial pathogens and HIV´, Robert Koch Institute, Berlin, Germany
| | - Hana Tlapák
- Department Infectious Diseases, Unit 18 `Sexually transmitted bacterial pathogens and HIV´, Robert Koch Institute, Berlin, Germany
| | - Regina Selb
- Department of Infectious Disease Epidemiology, Unit 34 `'HIV/AIDS, STI and Blood-borne Infections´, Robert Koch Institute, Berlin, Germany
| | - Klaus Jansen
- Department of Infectious Disease Epidemiology, Unit 34 `'HIV/AIDS, STI and Blood-borne Infections´, Robert Koch Institute, Berlin, Germany
| | - Dagmar Heuer
- Department Infectious Diseases, Unit 18 `Sexually transmitted bacterial pathogens and HIV´, Robert Koch Institute, Berlin, Germany.
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2
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Sunkavalli A, McClure R, Genco C. Molecular Regulatory Mechanisms Drive Emergent Pathogenetic Properties of Neisseria gonorrhoeae. Microorganisms 2022; 10:922. [PMID: 35630366 PMCID: PMC9147433 DOI: 10.3390/microorganisms10050922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/05/2022] Open
Abstract
Neisseria gonorrhoeae is the causative agent of the sexually transmitted infection (STI) gonorrhea, with an estimated 87 million annual cases worldwide. N. gonorrhoeae predominantly colonizes the male and female genital tract (FGT). In the FGT, N. gonorrhoeae confronts fluctuating levels of nutrients and oxidative and non-oxidative antimicrobial defenses of the immune system, as well as the resident microbiome. One mechanism utilized by N. gonorrhoeae to adapt to this dynamic FGT niche is to modulate gene expression primarily through DNA-binding transcriptional regulators. Here, we describe the major N. gonorrhoeae transcriptional regulators, genes under their control, and how these regulatory processes lead to pathogenic properties of N. gonorrhoeae during natural infection. We also discuss the current knowledge of the structure, function, and diversity of the FGT microbiome and its influence on gonococcal survival and transcriptional responses orchestrated by its DNA-binding regulators. We conclude with recent multi-omics data and modeling tools and their application to FGT microbiome dynamics. Understanding the strategies utilized by N. gonorrhoeae to regulate gene expression and their impact on the emergent characteristics of this pathogen during infection has the potential to identify new effective strategies to both treat and prevent gonorrhea.
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Affiliation(s)
- Ashwini Sunkavalli
- Department of Immunology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA;
| | - Ryan McClure
- Pacific Northwest National Laboratory, Richland, WA 99354, USA;
| | - Caroline Genco
- Department of Immunology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA;
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3
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Calder A, Menkiti CJ, Çağdaş A, Lisboa Santos J, Streich R, Wong A, Avini AH, Bojang E, Yogamanoharan K, Sivanesan N, Ali B, Ashrafi M, Issa A, Kaur T, Latif A, Mohamed HAS, Maqsood A, Tamang L, Swager E, Stringer AJ, Snyder LAS. Virulence genes and previously unexplored gene clusters in four commensal Neisseria spp. isolated from the human throat expand the neisserial gene repertoire. Microb Genom 2020; 6. [PMID: 32845827 PMCID: PMC7643975 DOI: 10.1099/mgen.0.000423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Commensal non-pathogenic Neisseria spp. live within the human host alongside the pathogenic Neisseria meningitidis and Neisseria gonorrhoeae and due to natural competence, horizontal gene transfer within the genus is possible and has been observed. Four distinct Neisseria spp. isolates taken from the throats of two human volunteers have been assessed here using a combination of microbiological and bioinformatics techniques. Three of the isolates have been identified as Neisseria subflava biovar perflava and one as Neisseria cinerea. Specific gene clusters have been identified within these commensal isolate genome sequences that are believed to encode a Type VI Secretion System, a newly identified CRISPR system, a Type IV Secretion System unlike that in other Neisseria spp., a hemin transporter, and a haem acquisition and utilization system. This investigation is the first to investigate these systems in either the non-pathogenic or pathogenic Neisseria spp. In addition, the N. subflava biovar perflava possess previously unreported capsule loci and sequences have been identified in all four isolates that are similar to genes seen within the pathogens that are associated with virulence. These data from the four commensal isolates provide further evidence for a Neisseria spp. gene pool and highlight the presence of systems within the commensals with functions still to be explored.
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Affiliation(s)
- Alan Calder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Chukwuma Jude Menkiti
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Aylin Çağdaş
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Jefferson Lisboa Santos
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Ricarda Streich
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Alice Wong
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Amir H Avini
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Ebrima Bojang
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Karththeepan Yogamanoharan
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Nivetha Sivanesan
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Besma Ali
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Mariam Ashrafi
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Abdirizak Issa
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Tajinder Kaur
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Aisha Latif
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Hani A Sheik Mohamed
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Atifa Maqsood
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Laxmi Tamang
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Emily Swager
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Alex J Stringer
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
| | - Lori A S Snyder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Kingston upon Thames, KT1 2EE, UK
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4
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Hay ID, Lithgow T. Filamentous phages: masters of a microbial sharing economy. EMBO Rep 2019; 20:embr.201847427. [PMID: 30952693 DOI: 10.15252/embr.201847427] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/30/2019] [Accepted: 03/19/2019] [Indexed: 12/11/2022] Open
Abstract
Bacteriophage ("bacteria eaters") or phage is the collective term for viruses that infect bacteria. While most phages are pathogens that kill their bacterial hosts, the filamentous phages of the sub-class Inoviridae live in cooperative relationships with their bacterial hosts, akin to the principal behaviours found in the modern-day sharing economy: peer-to-peer support, to offset any burden. Filamentous phages impose very little burden on bacteria and offset this by providing service to help build better biofilms, or provision of toxins and other factors that increase virulence, or modified behaviours that provide novel motile activity to their bacterial hosts. Past, present and future biotechnology applications have been built on this phage-host cooperativity, including DNA sequencing technology, tools for genetic engineering and molecular analysis of gene expression and protein production, and phage-display technologies for screening protein-ligand and protein-protein interactions. With the explosion of genome and metagenome sequencing surveys around the world, we are coming to realize that our knowledge of filamentous phage diversity remains at a tip-of-the-iceberg stage, promising that new biology and biotechnology are soon to come.
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Affiliation(s)
- Iain D Hay
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Vic., Australia
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Spencer-Smith R, Gould SW, Pulijala M, Snyder LAS. Investigating Potential Chromosomal Rearrangements during Laboratory Culture of Neisseria gonorrhoeae. Microorganisms 2018; 6:microorganisms6010010. [PMID: 29361673 PMCID: PMC5874624 DOI: 10.3390/microorganisms6010010] [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: 12/01/2017] [Revised: 12/19/2017] [Accepted: 01/19/2018] [Indexed: 01/02/2023] Open
Abstract
Comparisons of genome sequence data between different strains and isolates of Neisseria spp., such as Neisseria gonorrhoeae, reveal that over the evolutionary history of these organisms, large scale chromosomal rearrangements have occurred. Factors within the genomes, such as repetitive sequences and prophage, are believed to have contributed to these observations. However, the timescale in which rearrangements occur is not clear, nor whether it might be expected for them to happen in the laboratory. In this study, N. gonorrhoeae was repeatedly passaged in the laboratory and assessed for large scale chromosomal rearrangements. Using gonococcal strain NCCP11945, for which there is a complete genome sequence, cultures were passaged for eight weeks in the laboratory. The resulting genomic DNA was assessed using Pulsed Field Gel Electrophoresis, comparing the results to the predicted results from the genome sequence data. Three cultures generated Pulsed Field Gel Electrophoresis patterns that varied from the genomic data and were further investigated for potential chromosomal rearrangements.
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Affiliation(s)
- Russell Spencer-Smith
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames KT1 2EE, UK.
- National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
| | - Simon W Gould
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames KT1 2EE, UK.
| | - Madhuri Pulijala
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames KT1 2EE, UK.
| | - Lori A S Snyder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames KT1 2EE, UK.
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6
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Affiliation(s)
- Søren A Ladefoged
- Department of Medical Microbiology and Immunology University of Aarhus, Denmark.,Department of Clinical Biochemistry University Hospital of Aarhus, Denmark
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The Pilin N-terminal Domain Maintains Neisseria gonorrhoeae Transformation Competence during Pilus Phase Variation. PLoS Genet 2016; 12:e1006069. [PMID: 27213957 PMCID: PMC4877100 DOI: 10.1371/journal.pgen.1006069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 04/29/2016] [Indexed: 02/06/2023] Open
Abstract
The obligate human pathogen Neisseria gonorrhoeae is the sole aetiologic agent of the sexually transmitted infection, gonorrhea. Required for gonococcal infection, Type IV pili (Tfp) mediate many functions including adherence, twitching motility, defense against neutrophil killing, and natural transformation. Critical for immune escape, the gonococcal Tfp undergoes antigenic variation, a recombination event at the pilE locus that varies the surface exposed residues of the major pilus subunit PilE (pilin) in the pilus fiber. This programmed recombination system has the potential to produce thousands of pilin variants and can produce strains with unproductive pilin molecules that are completely unable to form Tfp. Saturating mutagenesis of the 3' third of the pilE gene identified 68 unique single nucleotide mutations that each resulted in an underpiliated colony morphology. Notably, all isolates, including those with undetectable levels of pilin protein and no observable surface-exposed pili, retained an intermediate level of transformation competence not exhibited in ΔpilE strains. Site-directed, nonsense mutations revealed that only the first 38 amino acids of the mature pilin N-terminus (the N-terminal domain or Ntd) are required for transformation competence, and microscopy, ELISAs and pilus purification demonstrate that extended Tfp are not required for competence. Transformation in strains producing only the pilin Ntd has the same genetic determinants as wild-type transformation. The Ntd corresponds to the alternative product of S-pilin cleavage, a specific proteolysis unique to pathogenic Neisseria. Mutation of the S-pilin cleavage site demonstrated that S-pilin cleavage mediated release of the Ntd is required for competence when a strain produces unproductive pilin molecules that cannot assemble into a Tfp through mutation or antigenic variation. We conclude that S-pilin cleavage evolved as a mechanism to maintain competence in nonpiliated antigenic variants and suggest there are alternate forms of the Tfp assembly apparatus that mediate various functions including transformation.
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Abstract
The genus Neisseria contains two pathogenic species of prominant public health concern: Neisseria gonorrhoeae and Neisseria meningitidis. These pathogens display a notable ability to undergo frequent programmed recombination events. The recombination-mediated pathways of transformation and pilin antigenic variation in the Neisseria are well-studied systems that are critical for pathogenesis. Here we will detail the conserved and unique aspects of transformation and antigenic variation in the Neisseria. Transformation will be followed from initial DNA binding through recombination into the genome with consideration to the factors necessary at each step. Additional focus is paid to the unique type IV secretion system that mediates donation of transforming DNA in the pathogenic Neisseria. The pilin antigenic variation system uses programmed recombinations to alter a major surface determinant, which allows immune avoidance and promotes infection. We discuss the trans- and cis- acting factors which facilitate pilin antigenic variation and present the current understanding of the mechanisms involved in the process.
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Description of an unusual Neisseria meningitidis isolate containing and expressing Neisseria gonorrhoeae-Specific 16S rRNA gene sequences. J Clin Microbiol 2013; 51:3199-206. [PMID: 23863567 DOI: 10.1128/jcm.00309-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
An apparently rare Neisseria meningitidis isolate containing one copy of a Neisseria gonorrhoeae 16S rRNA gene is described herein. This isolate was identified as N. meningitidis by biochemical identification methods but generated a positive signal with Gen-Probe Aptima assays for the detection of Neisseria gonorrhoeae. Direct 16S rRNA gene sequencing of the purified isolate revealed mixed bases in signature regions that allow for discrimination between N. meningitidis and N. gonorrhoeae. The mixed bases were resolved by sequencing individually PCR-amplified single copies of the genomic 16S rRNA gene. A total of 121 discrete sequences were obtained; 92 (76%) were N. meningitidis sequences, and 29 (24%) were N. gonorrhoeae sequences. Based on the ratio of species-specific sequences, the N. meningitidis strain seems to have replaced one of its four intrinsic 16S rRNA genes with the gonococcal gene. Fluorescence in situ hybridization (FISH) probes specific for meningococcal and gonococcal rRNA were used to demonstrate the expression of the rRNA genes. Interestingly, the clinical isolate described here expresses both N. meningitidis and N. gonorrhoeae 16S rRNA genes, as shown by positive FISH signals with both probes. This explains why the probes for N. gonorrhoeae in the Gen-Probe Aptima assays cross-react with this N. meningitidis isolate. The N. meningitidis isolate described must have obtained N. gonorrhoeae-specific DNA through interspecies recombination.
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10
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Multiplex bead suspension array for screening Neisseria gonorrhoeae antibiotic resistance genetic determinants in noncultured clinical samples. J Mol Diagn 2012; 15:116-29. [PMID: 23159594 DOI: 10.1016/j.jmoldx.2012.08.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 08/15/2012] [Accepted: 08/24/2012] [Indexed: 11/22/2022] Open
Abstract
The increasing threat of antibiotic-resistant Neisseria gonorrhoeae highlights the need for new diagnostic options. A high-throughput multiplex bead suspension array assay was developed for profiling 29 N. gonorrhoeae genomic mutations and 2 plasmid genes conferring resistance to 6 antimicrobial agents: penicillin, ciprofloxacin, cefixime, tetracycline, azithromycin, and spectinomycin. The three steps of this assay include amplification of 12 N. gonorrhoeae chromosomal and plasmid loci, multiplex allele-specific primer extension reaction, and multiplex bead suspension array detection. Antibiotic resistance genetic determinants were identified successfully in 239 cervicovaginal N. gonorrhoeae-positive noncultured swab samples. This molecular assay can be used for detection of gonococci in clinical specimens, molecular typing, mutation profiling, and predictive assessment of N. gonorrhoeae susceptibility to antibiotics without the need for culture.
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Ouzounova-Raykova V, Jordanov D, El-Tibi M, Mitov I. Gonococcal infection in symptomatic and asymptomatic persons seeking medical clinics in Sofia--a 3-year study 2008-2010. APMIS 2011; 119:864-7. [PMID: 22085362 DOI: 10.1111/j.1600-0463.2011.02769.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The aim was to determine the prevalence of gonococcal infection and to compare the results with those received by other researchers, because in Bulgaria a good medical practice for the laboratory confirmation, report and therapy is lacking. A total of 617 specimens from symptomatic and asymptomatic persons attending clinics in Sofia from January 2008 to December 2010 were tested by culture and in-house PCR. Using PCR Neisseria gonorrhoeae was identified in six urethral (6.25%) and eight (1.54%) cervical specimens. By applying culture method, N. gonorrhoeae positive result was found in 12 swabs--one cervical and one urethral swab less. The positive results correspond predominantly to persons with genital complains and suspicions for gonococcal or other sexually transmitted infection. This is the first study in Bulgaria since 1989 and determines the prevalence of N. gonorrhoeae to 2.3% over a 3-year period. Detection by culture was slightly less sensitive than by nucleic acid amplification test (NAAT). Continuous monitoring of gonorrhea by culture and NAAT is important for public health in Bulgaria.
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12
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Abstract
The sexually transmitted pathogen, Neisseria gonorrhoeae, undergoes natural transformation at high frequency. This property has led to the rapid dissemination of antibiotic resistance markers and to the panmictic structure of the gonococcal population. However, high-frequency transformation also makes N. gonorrhoeae one of the easiest bacterial species to manipulate genetically in the laboratory. Techniques have been developed that result in transformation frequencies >50%, allowing the identification of mutants by screening and without selection. Constructs have been created to take advantage of this high-frequency transformation, facilitating genetic mutation, complementation, and heterologous gene expression. Techniques are described for genetic manipulation of N. gonorrhoeae, as well as for growth of this fastidious organism.
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Affiliation(s)
- Joseph P Dillard
- Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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13
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Munson E, Firmani MA. Molecular diagnosis ofNeisseria gonorrhoeaeinfection in the United States. ACTA ACUST UNITED AC 2009; 3:327-43. [DOI: 10.1517/17530050902860229] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Lee SH, Vigliotti VS, Pappu S. Molecular tests for human papillomavirus (HPV), Chlamydia trachomatis and Neisseria gonorrhoeae in liquid-based cytology specimen. BMC Womens Health 2009; 9:8. [PMID: 19358733 PMCID: PMC2672071 DOI: 10.1186/1472-6874-9-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 04/09/2009] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Laboratory detection of Human papillomavirus (HPV), Chlamydia trachomatis and Neisseria gonorrhoeae in liquid-based cervicovaginal cytology specimens is now based on identification of the DNA sequences unique to these infectious agents. However, current commercial test kits rely on nucleotide probe hybridization to determine DNA sequences, which may lead to diagnostic errors due to cross-reactivity. The aim of this study was to find a practical approach to perform automated Sanger DNA sequencing in clinical laboratories for validation of the DNA tests for these three infectious agents. METHODS A crude proteinase K digest of 5% of the cells collected in a liquid-based cervicovaginal cytology specimen was used for the detection of DNA molecules specific for HPV, C trachomatis and N gonorrhoeae, and for preparation of materials suitable for direct automated DNA sequencing. Several sets of commercially available polymerase chain reaction (PCR) primers were used to prepare nested PCR amplicons for direct DNA sequencing. RESULTS Some variants of HPV-16 and HPV-31 were found to share an at least 34-base long sequence homology downstream of the GP5+ binding site, and all HPV-6 and HPV-11 variants shared an upstream 34-base sequence including part of the GP5+ primer. Accurate HPV genotyping frequently required more than 34-bases for sequence alignments to distinguish some of the HPV genotype variants with closely related sequences in this L1 gene hypervariable region. Using the automated Sanger DNA sequencing method for parallel comparative studies on split samples and to retest the residues of samples previously tested positive for C trachomatis and/or for N gonorrhoeae, we also found false-negative and false-positive results as reported by two commercial nucleic acid test kits. CONCLUSION Identification of a signature DNA sequence by the automated Sanger method is useful for validation of HPV genotyping and for molecular testing of C trachomatis and N gonorrhoeae in liquid-based cervicovaginal Papanicolaou (Pap) cytology specimens for clinical laboratories with experience in molecular biology to increase the specificity of these DNA-based tests. However, even a highly specific test for high-risk HPV genotyping may have unacceptably low positive predictive values for precancer lesion in populations with a low cervical cancer prevalence rate.
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Affiliation(s)
- Sin Hang Lee
- Department of Pathology, Milford Hospital, Milford, Connecticut, USA
| | | | - Suri Pappu
- Department of Pathology, Milford Hospital, Milford, Connecticut, USA
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15
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Dillard JP. Genetic manipulation of Neisseria gonorrhoeae. CURRENT PROTOCOLS IN MICROBIOLOGY 2008; Chapter 4:Unit 4A.2. [PMID: 18770590 DOI: 10.1002/9780471729259.mc04a02s00] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The sexually-transmitted pathogen, Neisseria gonorrhoeae, undergoes natural transformation at high frequency. This property has led to the rapid dissemination of antibiotic resistance markers and to the panmictic structure of the gonococcal population. However, high frequency transformation also makes N. gonorrhoeae one of the easiest bacterial species to manipulate genetically in the laboratory. Techniques have been developed that result in transformation frequencies >50%, allowing the identification of mutants by screening and without selection. Constructs have been created to take advantage of this high frequency transformation, facilitating genetic mutation, complementation, and heterologous gene expression. Techniques are described for genetic manipulation of N. gonorrhoeae, as well as for growth of this fastidious organism.
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Affiliation(s)
- Joseph P Dillard
- University of Wisconsin-Madison Medical School, Madison, Wisconsin, USA
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16
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Whiley DM, Garland SM, Harnett G, Lum G, Smith DW, Tabrizi SN, Sloots TP, Tapsall JW. Exploring 'best practice' for nucleic acid detection of Neisseria gonorrhoeae. Sex Health 2008; 5:17-23. [PMID: 18361850 DOI: 10.1071/sh07050] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 12/12/2007] [Indexed: 11/23/2022]
Abstract
Nucleic acid detection tests (NADT) have considerable benefits for the detection of Neisseria gonorrhoeae (GC), including high sensitivity across a range of specimen types and use under widely differing settings and conditions. However, sexual health practitioners and others who use data generated by NADT for GC should be aware of some important limitations of these tests. False-positive results caused by cross reaction with commensal Neisseria species have been observed in many assays, and have lead to unacceptably low positive-predictive values in some patient populations. Further, false-negative results can be caused by GC sequence variation, with some gonococci lacking certain NADT target sequences. This review examines the issues associated with gonococcal NADT and considers best practice for use of these assays based on current knowledge. We emphasise the need for supplementary testing and extensive assay validation, and suggest appropriate strategies for these requirements irrespective of the setting in which they are used. Further, we highlight the need to maintain culture-based testing for certain specimen sites as well as for antimicrobial resistance surveillance.
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Affiliation(s)
- David M Whiley
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Brisbane, Qld 4029, Australia
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17
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Whiley DM, Anderson TP, Barratt K, Beaman MH, Buda PJ, Carter M, Freeman K, Hallsworth P, Limnios EA, Lum G, Merien F, Vernel-Pauillac F, Tapsall JW, Witt MJ, Nissen MD, Sloots TP. Evidence that the gonococcal porA pseudogene is present in a broad range of Neisseria gonorrhoeae strains; suitability as a diagnostic target. Pathology 2006; 38:445-8. [PMID: 17008285 DOI: 10.1080/00313020600928253] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AIMS The primary aim of the study was to determine if the gonococcal porA pseudogene is a stable sequence target for the detection of Neisseria gonorrhoeae by PCR. METHODS A total of 240 gonococcal strains from various geographic locations were tested by porA pseudogene PCR. In addition, porA pseudogene PCR positivity rates were compared with established gonococcal assays in three Australian states. RESULTS All N. gonorrhoeae isolates provided positive results in the porA pseudogene PCR. Positivity rates compared favourably with established gonococcal assays, with increased N. gonorrhoeae detection in the Northern Territory and Western Australia. CONCLUSIONS The results of this multicentre study provide further evidence that the porA pseudogene is highly conserved across a diverse range N. gonorrhoeae strains and is a suitable PCR target for routine detection of N. gonorrhoeae.
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Affiliation(s)
- David M Whiley
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand.
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18
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Whiley DM, Tapsall JW, Sloots TP. Nucleic acid amplification testing for Neisseria gonorrhoeae: an ongoing challenge. J Mol Diagn 2006; 8:3-15. [PMID: 16436629 PMCID: PMC1871692 DOI: 10.2353/jmoldx.2006.050045] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2005] [Indexed: 11/20/2022] Open
Abstract
Nucleic acid amplification tests (NAATs) for the detection of Neisseria gonorrhoeae became available in the early 1990s. Although offering several advantages over traditional detection methods, N. gonorrhoeae NAATs do have some limitations. These include cost, risk of carryover contamination, inhibition, and inability to provide antibiotic resistance data. In addition, there are sequence-related limitations that are unique to N. gonorrhoeae NAATs. In particular, false-positive results are a major consideration. These primarily stem from the frequent horizontal genetic exchange occurring within the Neisseria genus, leading to commensal Neisseria species acquiring N. gonorrhoeae genes. Furthermore, some N. gonorrhoeae subtypes may lack specific sequences targeted by a particular NAAT. Therefore, NAAT false-negative results because of sequence variation may occur in some gonococcal populations. Overall, the N. gonorrhoeae species continues to present a considerable challenge for molecular diagnostics. The need to evaluate N. gonorrhoeae NAATs before their use in any new patient population and to educate physicians on the limitations of these tests is emphasized in this review.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital & Health Service District, Herston Road, Herston, Queensland, Australia 4029.
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19
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Snyder LAS, Davies JK, Ryan CS, Saunders NJ. Comparative overview of the genomic and genetic differences between the pathogenic Neisseria strains and species. Plasmid 2005; 54:191-218. [PMID: 16024078 DOI: 10.1016/j.plasmid.2005.04.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Revised: 04/18/2005] [Accepted: 04/21/2005] [Indexed: 01/19/2023]
Abstract
The availability of complete genome sequences from multiple pathogenic Neisseria strains and species has enabled a comprehensive survey of the genomic and genetic differences occurring within these species. In this review, we describe the chromosomal rearrangements that have occurred, and the genomic islands and prophages that have been identified in the various genomes. We also describe instances where specific genes are present or absent, other instances where specific genes have been inactivated, and situations where there is variation in the version of a gene that is present. We also provide an overview of mosaic genes present in these genomes, and describe the variation systems that allow the expression of particular genes to be switched ON or OFF. We have also described the presence and location of mobile non-coding elements in the various genomes. Finally, we have reviewed the incidence and properties of various extra-chromosomal elements found within these species. The overall impression is one of genomic variability and instability, resulting in increased functional flexibility within these species.
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Affiliation(s)
- Lori A S Snyder
- Bacterial Pathogenesis and Functional Genomics Group, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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20
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Whiley DM, Buda PP, Freeman K, Pattle NI, Bates J, Sloots TP. A real-time PCR assay for the detection of Neisseria gonorrhoeae in genital and extragenital specimens. Diagn Microbiol Infect Dis 2005; 52:1-5. [PMID: 15878435 DOI: 10.1016/j.diagmicrobio.2004.12.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Accepted: 12/20/2004] [Indexed: 11/23/2022]
Abstract
A Neisseria gonorrhoeae LightCycler (NGpapLC) assay targeting the porA pseudogene was compared with bacterial culture for detection of N. gonorrhoeae in 636 clinical specimens (216 cervical, 185 urethral, 196 throat, and 39 rectal swab specimens). The specificity of the NGpapLC assay was further investigated by testing a bacterial reference panel comprising several Neisseria species. Overall, 19 (3.0%) specimens were positive and 613 (96.4%) specimens were negative by both methods. Four (0.6%) specimens were positive by the NGpapLC assay only. For the cervical and urethral swabs, the NGpapLC provided 100% sensitivity and 100% specificity compared with bacterial culture. Following discrepant analysis, the clinical sensitivity and specificity of the NGpapLC for throat and rectal swabs was also 100%. For the bacterial panel, only N. gonorrhoeae isolates provided positive results. The results show the NGpapLC assay is suitable for use on a range of clinical specimens and could improve detection of pharyngeal N. gonorrhoeae.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Queensland 4029, Australia
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21
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Jose J, Otto GW, Meyer TF. The integration site of the iga gene in commensal Neisseria sp. Mol Genet Genomics 2003; 269:197-204. [PMID: 12720087 DOI: 10.1007/s00438-002-0799-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2002] [Accepted: 12/04/2002] [Indexed: 11/30/2022]
Abstract
An IgA1 protease is produced by the human pathogens Neisseria gonorrhoeae and N. meningitidis but not by related non-pathogenic, commensal, Neisseria species. In this study, the chromosomal iga locus was characterized in the N. gonorrhoeae strain MS11 and compared to corresponding loci in N. meningitidis and commensal Neisseria species. In N. gonorrhoeae, the genes trpB and ksgA were found immediately downstream of iga. In addition to comL and comA, a homolog of the Escherichia coli YFII gene was identified upstream of iga. Each gene in the iga region (YFII and comL, comA and iga, and trpB and ksgA) is transcribed in the opposite direction to its neighbors. The comL/ comA and iga/ trpB pairs each have a transcriptional terminator in the correct position for joint use. These terminators contain the common gonococcal DNA uptake sequence (DUS). A highly conserved direct repeat of 25 bp located immediately adjacent to the iga gene in N. gonorrhoeae was also found in N. meningitidis. In Southern hybridization experiments, no homology to iga was detectable in the chromosomal DNAs of the commensal species N. mucosa, N. lactamica, N. flavescens, N. cinerea, N. subflava, N. flava, N. sicca or N. elongata. When N. gonorrhoeae comL and trpB were used as probes, signals were detected on the same restriction fragment in six of the eight species. This indicated that commensal Neisseria species share a possible integration site for the iga gene between comA and trpB. The region between comA and trpB was therefore amplified by PCR. The fragment obtained from N. lactamica showed a high degree of homology to gonococcal comA and trpB, respectively, but iga was replaced by a sequence of 13 bp that shows no homology to any known gonococcal sequence. Our data suggest that iga was acquired by a common ancestor of N. gonorrhoeae and N. meningitidis rather than being distributed by horizontal gene transfer. N. lactamica, which is more closely related to N. gonorrhoeae than other commensals, may have lost iga by deletion.
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Affiliation(s)
- J Jose
- Abteilung Molekulare Biologie, Max-Planck-Institut für Infektionsbiologie, Schumannstrasse 20/21, 10117 Berlin, Germany
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22
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Palmer HM, Mallinson H, Wood RL, Herring AJ. Evaluation of the specificities of five DNA amplification methods for the detection of Neisseria gonorrhoeae. J Clin Microbiol 2003; 41:835-7. [PMID: 12574295 PMCID: PMC149679 DOI: 10.1128/jcm.41.2.835-837.2003] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intragenus specificities of five molecular diagnostic methods for Neisseria gonorrhoeae were determined. Three assays were considered suboptimal. Molecular detection of N. gonorrhoeae from sites where other Neisseria spp. commonly occur or from any site in low-prevalence settings should be confirmed by a test targeting a different genetic locus.
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Affiliation(s)
- H M Palmer
- Genitourinary Infections Reference Laboratory, Public Health Laboratory, Bristol Royal Infirmary, Bristol, BS2 8HW, United Kingdom.
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23
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Liu SV, Saunders NJ, Jeffries A, Rest RF. Genome analysis and strain comparison of correia repeats and correia repeat-enclosed elements in pathogenic Neisseria. J Bacteriol 2002; 184:6163-73. [PMID: 12399486 PMCID: PMC151967 DOI: 10.1128/jb.184.22.6163-6173.2002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole genome sequences of Neisseria meningitidis strains Z2491 and MC58 and Neisseria gonorrhoeae FA1090 were analyzed for Correia repeats (CR) and CR-enclosed elements (CREE). A total of 533, 516, and 256 copies of CR and 270, 261, and 102 copies of CREE were found in these three genomes, respectively. The lengths of CREE range from 28 to 348 bp, and the lengths of multicopy CREE appear mainly in the ranges of 154 to 156 bp and 105 to 107 bp. The distribution of CREE lengths is similar between the two N. meningitidis genomes, with a greater number of 154- to 156-bp CREE (163 and 152 copies in N. meningitidis strain Z2491 and N. meningitidis strain MC58, respectively) than 105- to 107-bp CREE (72 and 77 copies). In the N. gonorrhoeae strain FA1090 genome there are relatively more 105- to 107-bp CREE (51 copies) than 154- to 156-bp CREE (36 copies). The genomic distribution of 107-bp CREE also shows similarity between the two N. meningitidis strains (15 copies share the same loci) and differences between N. meningitidis strains and N. gonorrhoeae FA1090 (only one copy is located in the same locus). Detailed sequence analysis showed that both the terminal inverted repeats and the core regions of CREE are composed of distinct basic sequence blocks. Direct TA dinucleotide repeats exist at the termini of all CREE. A survey of DNA sequence upstream of the sialyltransferase gene, lst, in several Neisseria isolates showed that 5 N. meningitidis strains contain a 107-bp CREE in this region but 25 N. gonorrhoeae strains show an exact absence of a 105-bp sequence block (i.e., the 107-bp CREE without a 5' TA dinucleotide) in the same region. Whole-genome sequence analysis confirmed that this 105-bp indel exists in many homologous 107-bp CREE loci. Thus, we postulate that all CREE are made of target TA with indels of various lengths. Analysis of 107-bp CREE revealed that they exist predominantly in intergenic regions and are often near virulence, metabolic, and transporter genes. The abundance of CREE in Neisseria genomes suggests that they may have played a role in genome organization, function, and evolution. Their differential distribution in different pathogenic Neisseria strains may contribute to the distinct behaviors of each Neisseria species.
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Affiliation(s)
- Shi V Liu
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19129, USA
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24
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Seib KL, Peak IRA, Jennings MP. Phase variable restriction-modification systems in Moraxella catarrhalis. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 2002; 32:159-65. [PMID: 11821238 DOI: 10.1111/j.1574-695x.2002.tb00548.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A repetitive DNA motif was used as a marker to identify novel genes in the mucosal pathogen Moraxella catarrhalis. There is a high prevalence of such repetitive motifs in virulence genes that display phase variable expression. Two repeat containing loci were identified using a digoxigenin-labelled 5'-(CAAC)6-3' oligonucleotide probe. The repeats are located in the methylase components of two distinct type III restriction-modification (R-M) systems. We suggest that the phase variable nature of these R-M systems indicates that they have an important role in the biology of M. catarrhalis.
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Affiliation(s)
- Kate L Seib
- Department of Microbiology and Parasitology, The University of Queensland, Brisbane, Qld 4072, Australia
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25
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Hamilton HL, Schwartz KJ, Dillard JP. Insertion-duplication mutagenesis of neisseria: use in characterization of DNA transfer genes in the gonococcal genetic island. J Bacteriol 2001; 183:4718-26. [PMID: 11466274 PMCID: PMC99525 DOI: 10.1128/jb.183.16.4718-4726.2001] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We created plasmids for use in insertion-duplication mutagenesis (IDM) of Neisseria gonorrhoeae. This mutagenesis method has the advantage that it requires only a single cloning step prior to transformation into gonococci. Chromosomal DNA cloned into the plasmid directs insertion into the chromosome at the site of homology by a single-crossover (Campbell-type) recombination event. Two of the vectors contain an erythromycin resistance gene, ermC, with a strong promoter and in an orientation such that transcription will proceed into the cloned insert. Thus, these plasmids can be used to create insertions that are effectively nonpolar on the transcription of downstream genes. In addition to the improved ermC, the vector contains two copies of the neisserial DNA uptake sequence to facilitate high-frequency DNA uptake during transformation. Using various chromosomal DNA insert sizes, we have determined that even small inserts can target insertion mutation by this method and that the insertions are stably maintained in the gonococcal chromosome. We have used IDM to create knockouts in two genes in the gonococcal genetic island (GGI) and to clone additional regions of the GGI by a chromosome-walking procedure. Phenotypic characterization of traG and traH mutants suggests a role for the encoded proteins in DNA secretion by a novel type IV secretion system.
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MESH Headings
- Chromosomes, Bacterial/genetics
- Cloning, Molecular/methods
- Crossing Over, Genetic
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- Drug Resistance, Microbial/genetics
- Erythromycin
- Genetic Vectors
- Methyltransferases/genetics
- Models, Genetic
- Mutagenesis, Insertional/methods
- Neisseria gonorrhoeae/genetics
- Plasmids
- Polymerase Chain Reaction
- Recombination, Genetic
- Restriction Mapping
- Transformation, Bacterial
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Affiliation(s)
- H L Hamilton
- Department of Medical Microbiology and Immunology, University of Wisconsin- Madison Medical School, Madison, Wisconsin 53706, USA
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26
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Tosta CE. Coevolutionary networks: a novel approach to understanding the relationships of humans with the infectious agents. Mem Inst Oswaldo Cruz 2001; 96:415-25. [PMID: 11313655 DOI: 10.1590/s0074-02762001000300024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Human organism is interpenetrated by the world of microorganisms, from the conception until the death. This interpenetration involves different levels of interactions between the partners including trophic exchanges, bi-directional cell signaling and gene activation, besides genetic and epigenetic phenomena, and tends towards mutual adaptation and coevolution. Since these processes are critical for the survival of individuals and species, they rely on the existence of a complex organization of adaptive systems aiming at two apparently conflicting purposes: the maintenance of the internal coherence of each partner, and a mutually advantageous coexistence and progressive adaptation between them. Humans possess three adaptive systems: the nervous, the endocrine and the immune system, each internally organized into subsystems functionally connected by intraconnections, to maintain the internal coherence of the system. The three adaptive systems aim at the maintenance of the internal coherence of the organism and are functionally linked by interconnections, in such way that what happens to one is immediately sensed by the others. The different communities of infectious agents that live within the organism are also organized into functional networks. The members of each community are linked by intraconnections, represented by the mutual trophic, metabolic and other influences, while the different infectious communities affect each other through interconnections. Furthermore, by means of its adaptive systems, the organism influences and is influenced by the microbial communities through the existence of transconnections. It is proposed that these highly complex and dynamic networks, involving gene exchange and epigenetic phenomena, represent major coevolutionary forces for humans and microorganisms.
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Affiliation(s)
- C E Tosta
- Laboratório de Imunologia Celular, Faculdade de Medicina, Universidade de Brasília, Brasília, DF, 70910-900, Brasil.
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27
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Abstract
Inversions and translocations distinguish the genomes of closely related bacterial species, but most of these rearrangements preserve the relationship between the rearranged fragments and the axis of chromosome replication. Within species, such rearrangements are found less frequently, except in the case of clinical isolates of human pathogens, where rearrangements are very frequent.
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Affiliation(s)
- D Hughes
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, S-751 24 Uppsala, Sweden.
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28
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Schneider D, Duperchy E, Coursange E, Lenski RE, Blot M. Long-term experimental evolution in Escherichia coli. IX. Characterization of insertion sequence-mediated mutations and rearrangements. Genetics 2000; 156:477-88. [PMID: 11014799 PMCID: PMC1461276 DOI: 10.1093/genetics/156.2.477] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
As part of a long-term evolution experiment, two populations of Escherichia coli B adapted to a glucose minimal medium for 10,000 generations. In both populations, multiple IS-associated mutations arose that then went to fixation. We identify the affected genetic loci and characterize the molecular events that produced nine of these mutations. All nine were IS-mediated events, including simple insertions as well as recombination between homologous elements that generated inversions and deletions. Sequencing DNA adjacent to the insertions indicates that the affected genes are involved in central metabolism (knockouts of pykF and nadR), cell wall synthesis (adjacent to the promoter of pbpA-rodA), and ill-defined functions (knockouts of hokB-sokB and yfcU). These genes are candidates for manipulation and competition experiments to determine whether the mutations were beneficial or merely hitchhiked to fixation.
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Affiliation(s)
- D Schneider
- Laboratoire Plasticité et Expression des Génomes Microbiens, Université Joseph Fourier, 38041 Grenoble Cedex 9, France.
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29
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Le Bourgeois P, Daveran-Mingot ML, Ritzenthaler P. Genome plasticity among related ++Lactococcus strains: identification of genetic events associated with macrorestriction polymorphisms. J Bacteriol 2000; 182:2481-91. [PMID: 10762249 PMCID: PMC111311 DOI: 10.1128/jb.182.9.2481-2491.2000] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genomic diversity of nine strains of the Lactococcus lactis subsp. cremoris (NCDO712, NCDO505, NCDO2031, NCDO763, MMS36, C2, LM0230, LM2301, and MG1363) was studied by macrorestriction enzyme analysis using pulsed-field gel electrophoresis. These strains were considered adequate for the investigation of genomic plasticity because they have been described as belonging to the same genetic lineage. Comparison of ApaI and SmaI genome fingerprints of each strain revealed the presence of several macrorestriction fragment length polymorphisms (RFLPs), despite a high degree of similarity of the generated restriction patterns. The physical map of the MG1363 chromosome was used to establish a genome map of the other strains and allocate the RFLPs to five regions. Southern hybridization analysis correlated the polymorphic regions with genetic events such as chromosomal inversion, integration of prophage DNA, and location of the transposon-like structures carrying conjugative factor or oligopeptide transport system.
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Affiliation(s)
- P Le Bourgeois
- Laboratoire de Microbiologie et Génétique Moléculaire du CNRS, Université Paul Sabatier, 31062 Toulouse, France
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30
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Abstract
We determined the genomic organization of 14 clinical strains of Bordetella pertussis isolated over an 18-month period in Alberta, Canada. The maps of these 14 strains, while demonstrating general similarity of gene order, display a number of examples of genomic rearrangements in the form of large chromosomal inversions.
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Affiliation(s)
- S Stibitz
- Division of Bacterial Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892, USA.
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31
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Kahler CM, Stephens DS. Genetic basis for biosynthesis, structure, and function of meningococcal lipooligosaccharide (endotoxin). Crit Rev Microbiol 1999; 24:281-334. [PMID: 9887366 DOI: 10.1080/10408419891294216] [Citation(s) in RCA: 123] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The exclusive human pathogen Neisseria meningitidis expresses lipooligosaccharide (LOS), an endotoxin that is structurally distinct from the lipopolysaccharides (LPS) of enteric Gram-negative bacilli. Differences that appear to be biologically important occur in the composition and attachment of acyl chains to lipid A, phosphorylation patterns of lipid A, and the incorporation and phosphorylation of sugar residues in the LOS inner core. Further, unlike most enteric LPS, only two to five sugar residues are attached to the meningococcal LOS inner core, and there are no multiple repeating units of O-antigens. In contrast to Escherichia coli, where the LPS biosynthesis genes are organized as large operons, the meningococcal LOS biosynthesis genes are organized into small operons or are located individually in the chromosome. Some of these genetic loci in meningococci and gonococci display polymorphisms caused by localized chromosomal rearrangements. One mechanism of antigenic variation of meningococci LOS is the regulation of glycosyltransferase activity by slipped strand mispairing of homopolymeric tracts within the 5' end of the genes encoding these enzymes, resulting in the addition of different sugar residues to the LOS molecule. Meningococcal LOS is a critical virulence factor in N. meningitidis infections and is involved in many aspects of pathogenesis, including the colonization of the human nasopharynx, survival after bloodstream invasion, and the inflammation associated with the morbidity and mortality of meningococcemia and meningitis. Meningococcal LOS, which is a component of serogroup B meningococcal vaccines currently in clinical trials, has been proposed as a candidate for a new generation of meningococcal vaccines. The rapidly expanding knowledge of the genetic basis for biosynthesis, structure, and regulation of meningococcal LOS provides insights into unique endotoxin structures and the precise role of LOS in the pathogenesis of meningococcal disease.
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Affiliation(s)
- C M Kahler
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30303, USA
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32
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Daveran-Mingot ML, Campo N, Ritzenthaler P, Le Bourgeois P. A natural large chromosomal inversion in Lactococcus lactis is mediated by homologous recombination between two insertion sequences. J Bacteriol 1998; 180:4834-42. [PMID: 9733685 PMCID: PMC107507 DOI: 10.1128/jb.180.18.4834-4842.1998] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Comparative analysis of chromosomal macrorestriction polymorphism of the two closely related Lactococcus lactis subsp. cremoris strains MG1363 and NCDO763 revealed the presence of a large inversion covering half of the genome. To determine what kind of genetic element could be implicated in this rearrangement, the two inversion junctions of MG1363 and NCDO763 chromosomes were cloned and characterized. Nucleotide sequence analysis showed the presence of one copy of the lactococcal IS905 element in each junction. Each copy of this element contained the same nucleotide mutation that inactivates the putative transposase. Comparison of the sequences surrounding the insertion sequence demonstrated that the large inversion arose from a single-step homologous recombination event between the two defective copies of the IS905 element. The large inversion presumably conferred no selective disadvantage on strain NCDO763 because this rearrangement did not alter the oriC-terC symmetry of the chromosome and the local genetic environment.
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Affiliation(s)
- M L Daveran-Mingot
- Laboratoire de Microbiologie et Génétique Moléculaire du CNRS, Université Paul Sabatier, 31062 Toulouse, France
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33
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Badía J, Ibáñez E, Sabaté M, Baldomà L, Aguilar J. A rare 920-kilobase chromosomal inversion mediated by IS1 transposition causes constitutive expression of the yiaK-S operon for carbohydrate utilization in Escherichia coli. J Biol Chem 1998; 273:8376-81. [PMID: 9525947 DOI: 10.1074/jbc.273.14.8376] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The regulator of the yiaK-S operon, currently assigned a carbohydrate utilization function in Escherichia coli, is inactivated by a genome rearrangement that leads to the constitutive expression of the operon. The yiaK-S constitutive cells acquire the ability to utilize the rare pentose L-lyxose. Restriction analysis and sequencing of the regulator gene indicate that it is disrupted by foreign DNA. The insert consists of a large inverted fragment of DNA of 920 kilobases flanked by two IS1 elements with opposite polarity. One corresponds to that found naturally at min 0.4 of the bacterial chromosome and the other to a new copy transposed into the regulator gene located at min 80.6. This insertion-inversion could be the result of the intramolecular transposition mechanism itself, a gene rearrangement rarely originated by IS1. Alternatively, it could be attributed to the homologous recombination between the IS1 at min 0.4 and the IS1 transposed intermolecularly into the yiaK-S regulator gene. The participation of a rare IS1-mediated inversion in the evolution of a stable phenotype is thus identified.
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Affiliation(s)
- J Badía
- Department of Biochemistry, School of Pharmacy, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain
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34
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Abstract
Current efforts to completely sequence the meningococcal and gonocococcal genomes raise the question whether the lessons learned from the sequenced strains may be safely extrapolated to other members of these species, or whether, in view of the fact that Neisseriae are highly recombinogenic and exhibit a high degree of horizontal intra- and interspecies genetic transfer, only clone-specific conclusions are valid. From the known physical and genetic maps of each of two gonococcal and meningococcal strains, it would appear that both species exhibit a species-specific conservation in their genetic organization while the interspecies comparison revealed several rearrangements, although still with a high overall similarity. However, these data contrast with other evidence suggesting intra-species rearrangements, such as the nonconserved I-CeuI macrorestriction patterns of different meningococcal and other neisserial strains. Since I-CeuI cuts within the 23S-rRNA sequence, the restriction pattern should give reliable information on the distribution of rrn loci in the neisserial genomes. Further studies are warranted to answer these questions.
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Affiliation(s)
- W Bautsch
- Institute of Medical Microbiology, Hannover Medical School, Germany.
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35
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Fussenegger M, Rudel T, Barten R, Ryll R, Meyer TF. Transformation competence and type-4 pilus biogenesis in Neisseria gonorrhoeae--a review. Gene 1997; 192:125-34. [PMID: 9224882 DOI: 10.1016/s0378-1119(97)00038-3] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In Neisseria gonorrhoea (Ngo), the processes of type-4 pilus biogenesis and DNA transformation are functionally linked and play a pivotal role in the life style of this strictly human pathogen. The assembly of pili from its main subunit pilin (PilE) is a prerequisite for gonococcal infection since it allows the first contact to epithelial cells in conjunction with the pilus tip-associated PilC protein. While the components of the pilus and its assembly machinery are either directly or indirectly involved in the transport of DNA across the outer membrane, other factors unrelated to pilus biogenesis appear to facilitate further DNA transfer across the murein layer (ComL, Tpc) and the inner membrane (ComA) before the transforming DNA is rescued in the recipient bacterial chromosome in a RecA-dependent manner. Interestingly, PilE is essential for the first step of transformation, i.e., DNA uptake, and is itself also subject to transformation-mediated phase and antigenic variation. This short-term adaptive mechanism allows Ngo to cope with changing micro-environments in the host as well as to escape the immune response during the course of infection. Given the fact that Ngo has no ecological niche other than man, horizontal genetic exchange is essential for a successful co-evolution with the host. Horizontal exchange gives rise to heterogeneous populations harboring clones which better withstand selective forces within the host. Such extended horizontal exchange is reflected by a high genome plasticity, the existence of mosaic genes and a low linkage disequilibrium of genetic loci within the neisserial population. This led to the concept that rather than regarding individual Neisseria species as independent traits, they comprise a collective of species interconnected via horizontal exchange and relying on a common gene pool.
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Affiliation(s)
- M Fussenegger
- Max-Planck-Institut für Biologie, Abteilung Infektionsbiologie, Tübingen, Germany
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Rozsa FW, Meyer TF, Fussenegger M. Inversion of Moraxella lacunata type 4 pilin gene sequences by a Neisseria gonorrhoeae site-specific recombinase. J Bacteriol 1997; 179:2382-8. [PMID: 9079926 PMCID: PMC178977 DOI: 10.1128/jb.179.7.2382-2388.1997] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A plasmid library of Neisseria gonorrhoeae sequences was screened for the ability to mediate recombinations on a sequence containing the Moraxella lacunata type 4 pilin gene invertible region in Escherichia coli. A plasmid containing the N. gonorrhoeae sequence encoding the putative recombinase (gcr) was identified and sequenced. Plasmids containing gcr were able to mediate site-specific recombinations despite a weak amino acid homology to Piv, the native M. lacunata pilin gene invertase. The gcr gene is present only in pathogenic strains of Neisseria tested; however, in our assays gene knockouts of gcr did not alter the variation of surface features that play a role in the pathogenesis of N. gonorrhoeae.
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Affiliation(s)
- F W Rozsa
- Department of Microbiology, Biozentrum, University of Basel, Switzerland.
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