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Royer C, Patin NV, Jesser KJ, Peña-Gonzalez A, Hatt JK, Trueba G, Levy K, Konstantinidis KT. Comparison of metagenomic and traditional methods for diagnosis of E. coli enteric infections. mBio 2024; 15:e0342223. [PMID: 38488359 PMCID: PMC11005377 DOI: 10.1128/mbio.03422-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 02/23/2024] [Indexed: 04/11/2024] Open
Abstract
Diarrheagenic Escherichia coli, collectively known as DEC, is a leading cause of diarrhea, particularly in children in low- and middle-income countries. Diagnosing infections caused by different DEC pathotypes traditionally relies on the cultivation and identification of virulence genes, a resource-intensive and error-prone process. Here, we compared culture-based DEC identification with shotgun metagenomic sequencing of whole stool using 35 randomly drawn samples from a cohort of diarrhea-afflicted patients. Metagenomic sequencing detected the cultured isolates in 97% of samples, revealing, overall, reliable detection by this approach. Genome binning yielded high-quality E. coli metagenome-assembled genomes (MAGs) for 13 samples, and we observed that the MAG did not carry the diagnostic DEC virulence genes of the corresponding isolate in 60% of these samples. Specifically, two distinct scenarios were observed: diffusely adherent E. coli (DAEC) isolates without corresponding DAEC MAGs appeared to be relatively rare members of the microbiome, which was further corroborated by quantitative PCR (qPCR), and thus unlikely to represent the etiological agent in 3 of the 13 samples (~23%). In contrast, ETEC virulence genes were located on plasmids and largely escaped binning in associated MAGs despite being prevalent in the sample (5/13 samples or ~38%), revealing limitations of the metagenomic approach. These results provide important insights for diagnosing DEC infections and demonstrate how metagenomic methods can complement isolation efforts and PCR for pathogen identification and population abundance. IMPORTANCE Diagnosing enteric infections based on traditional methods involving isolation and PCR can be erroneous due to isolation and other biases, e.g., the most abundant pathogen may not be recovered on isolation media. By employing shotgun metagenomics together with traditional methods on the same stool samples, we show that mixed infections caused by multiple pathogens are much more frequent than traditional methods indicate in the case of acute diarrhea. Further, in at least 8.5% of the total samples examined, the metagenomic approach reliably identified a different pathogen than the traditional approach. Therefore, our results provide a methodology to complement existing methods for enteric infection diagnostics with cutting-edge, culture-independent metagenomic techniques, and highlight the strengths and limitations of each approach.
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Affiliation(s)
- C. Royer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - N. V. Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - K. J. Jesser
- Department of Environmental and Occupational Health, University of Washington, Seattle, Washington, USA
| | - A. Peña-Gonzalez
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotà, Colombia
| | - J. K. Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - G. Trueba
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - K. Levy
- Department of Environmental and Occupational Health, University of Washington, Seattle, Washington, USA
| | - K. T. Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
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Mustafa AS. Whole Genome Sequencing: Applications in Clinical Bacteriology. Med Princ Pract 2024; 33:185-197. [PMID: 38402870 DOI: 10.1159/000538002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/22/2024] [Indexed: 02/27/2024] Open
Abstract
The success in determining the whole genome sequence of a bacterial pathogen was first achieved in 1995 by determining the complete nucleotide sequence of Haemophilus influenzae Rd using the chain-termination method established by Sanger et al. in 1977 and automated by Hood et al. in 1987. However, this technology was laborious, costly, and time-consuming. Since 2004, high-throughput next-generation sequencing technologies have been developed, which are highly efficient, require less time, and are cost-effective for whole genome sequencing (WGS) of all organisms, including bacterial pathogens. In recent years, the data obtained using WGS technologies coupled with bioinformatics analyses of the sequenced genomes have been projected to revolutionize clinical bacteriology. WGS technologies have been used in the identification of bacterial species, strains, and genotypes from cultured organisms and directly from clinical specimens. WGS has also helped in determining resistance to antibiotics by the detection of antimicrobial resistance genes and point mutations. Furthermore, WGS data have helped in the epidemiological tracking and surveillance of pathogenic bacteria in healthcare settings as well as in communities. This review focuses on the applications of WGS in clinical bacteriology.
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Affiliation(s)
- Abu Salim Mustafa
- Department of Microbiology, College of Medicine, Kuwait University, Kuwait City, Kuwait
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Dwivedi-Yu JA, Oppler ZJ, Mitchell MW, Song YS, Brisson D. A fast machine-learning-guided primer design pipeline for selective whole genome amplification. PLoS Comput Biol 2023; 19:e1010137. [PMID: 37068103 PMCID: PMC10138271 DOI: 10.1371/journal.pcbi.1010137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 04/27/2023] [Accepted: 03/23/2023] [Indexed: 04/18/2023] Open
Abstract
Addressing many of the major outstanding questions in the fields of microbial evolution and pathogenesis will require analyses of populations of microbial genomes. Although population genomic studies provide the analytical resolution to investigate evolutionary and mechanistic processes at fine spatial and temporal scales-precisely the scales at which these processes occur-microbial population genomic research is currently hindered by the practicalities of obtaining sufficient quantities of the relatively pure microbial genomic DNA necessary for next-generation sequencing. Here we present swga2.0, an optimized and parallelized pipeline to design selective whole genome amplification (SWGA) primer sets. Unlike previous methods, swga2.0 incorporates active and machine learning methods to evaluate the amplification efficacy of individual primers and primer sets. Additionally, swga2.0 optimizes primer set search and evaluation strategies, including parallelization at each stage of the pipeline, to dramatically decrease program runtime. Here we describe the swga2.0 pipeline, including the empirical data used to identify primer and primer set characteristics, that improve amplification performance. Additionally, we evaluate the novel swga2.0 pipeline by designing primer sets that successfully amplify Prevotella melaninogenica, an important component of the lung microbiome in cystic fibrosis patients, from samples dominated by human DNA.
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Affiliation(s)
- Jane A. Dwivedi-Yu
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
- Facebook AI Research, 1 Rathbone Square, London, England
| | - Zachary J. Oppler
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew W. Mitchell
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Coriell Institute for Medical Research, Camden, New Jersey, United States of America
| | - Yun S. Song
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
- Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America
| | - Dustin Brisson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Joseph SJ, Bommana S, Ziklo N, Kama M, Dean D, Read TD. Patterns of within-host spread of Chlamydia trachomatis between vagina, endocervix and rectum revealed by comparative genomic analysis. Front Microbiol 2023; 14:1154664. [PMID: 37056744 PMCID: PMC10086254 DOI: 10.3389/fmicb.2023.1154664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
IntroductionChlamydia trachomatis, a gram-negative obligate intracellular bacterium, commonly causes sexually transmitted infections (STIs). Little is known about C. trachomatis transmission within the host, which is important for understanding disease epidemiology and progression.MethodsWe used RNA-bait enrichment and whole-genome sequencing to compare rectal, vaginal and endocervical samples collected at the same time from 26 study participants who attended Fijian Ministry of Health and Medical Services clinics and tested positive for C. trachomatis at each anatomic site.ResultsThe 78 C. trachomatis genomes from participants resolved into two major clades of the C. trachomatis phylogeny (the “prevalent urogenital and anorectal” clade and “non-prevalent urogenital and anorectal” clade). For 21 participants, genome sequences were almost identical in each anatomic site. For the other five participants, two distinct C. trachomatis strains were present in different sites; in two cases, the vaginal sample was a mixture of strains.DiscussionThe absence of large numbers of fixed SNPs between C. trachomatis genomes within many of the participants could indicate recent acquisition of infection prior to the clinic visit without sufficient time to accumulate significant genetic variation in different body sites. This model suggests that many C. trachomatis infections may be resolved relatively quickly in the Fijian population, possibly reflecting common prescription or over-the-counter antibiotics usage.
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Affiliation(s)
- Sandeep J. Joseph
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Sankhya Bommana
- Department of Pediatrics, University of California, San Francisco, Oakland, CA, United States
| | - Noa Ziklo
- Department of Pediatrics, University of California, San Francisco, Oakland, CA, United States
| | - Mike Kama
- Ministry of Health and Medical Services, Suva, Fiji
| | - Deborah Dean
- Department of Pediatrics, University of California, San Francisco, Oakland, CA, United States
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
- Department of Bioengineering, Joint Graduate Program, University of California, San Francisco, San Francisco, CA, United States
- Department of Bioengineering, Joint Graduate Program, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: Deborah Dean,
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States
- Timothy D. Read,
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Joseph SJ, Bommana S, Ziklo N, Kama M, Dean D, Read TD. Patterns of within-host spread of Chlamydia trachomatis between vagina, endocervix and rectum revealed by comparative genomic analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525576. [PMID: 36747780 PMCID: PMC9901013 DOI: 10.1101/2023.01.25.525576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Chlamydia trachomatis , a gram-negative obligate intracellular bacterium, commonly causes sexually transmitted infections (STIs). Little is known about C. trachomatis transmission within the host, which is important for understanding disease epidemiology and progression. We used RNA-bait enrichment and whole-genome sequencing to compare rectal, vaginal and endocervical samples collected at the same time from 26 study participants who attended Fijian Ministry of Health and Medical Services clinics and tested positive for C. trachomatis at each anatomic site. The 78 C. trachomatis genomes from participants were from two major clades of the C. trachomatis phylogeny (the "prevalent urogenital and anorecta"l clade and "non-prevalent urogenital and anorectal" clade). For 21 participants, genome sequences were almost identical in each anatomic site. For the other five participants, two distinct C. trachomatis strains were present in different sites; in two cases, the vaginal sample was a mixture of strains. The absence of large numbers of fixed SNPs between C. trachomatis strains within many of the participants could indicate recent acquisition of infection prior to the clinic visit without sufficient time to accumulate significant variation in the different body sites. This model suggests that many C. trachomatis infections may be resolved relatively quickly in the Fijian population, possibly reflecting common prescription or over-the-counter antibiotics usage. Importance Chlamydia trachomatis is a bacterial pathogen that causes millions of sexually transmitted infections (STIs) annually across the globe. Because C. trachomatis lives inside human cells, it has historically been hard to study. We know little about how the bacterium spreads between body sites. Here, samples from 26 study participants who had simultaneous infections in their vagina, rectum and endocervix were genetically analyzed using an improved method to extract C. trachomatis DNA directly from clinical samples for genome sequencing. By analyzing patterns of mutations in the genomes, we found that 21 participants shared very similar C. trachomatis strains in all three anatomic sites, suggesting recent infection and spread. For five participants two C. trachomatis strains were evident, indicating multiple infections. This study is significant in that improved enrichment methods for genome sequencing provides robust data to genetically trace patterns of C. trachomatis infection and transmission within an individual for epidemiologic and pathogenesis interrogations.
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Affiliation(s)
- Sandeep J. Joseph
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sankhya Bommana
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Noa Ziklo
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Mike Kama
- Ministry of Health and Medical Services, Suva, Fiji
| | - Deborah Dean
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA,Department of Medicine, University of California San Francisco, San Francisco, California, USA,Department of Bioengineering, Joint Graduate Program, University of California San Francisco and University of California Berkeley, San Francisco, California, USA,Bixby Center for Global Reproductive Health, University of California San Francisco, San Francisco, California, USA,Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, California, USA,Corresponding authors, contributed equally, DD: , TDR:
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA,Corresponding authors, contributed equally, DD: , TDR:
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Detection of Chlamydia trachomatis inside spermatozoa using flow cytometry: Effects of antibiotic treatment (before and after) on sperm count parameters. J Microbiol Methods 2022; 203:106604. [PMID: 36330892 DOI: 10.1016/j.mimet.2022.106604] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
There is increasing evidence that Chlamydia trachomatis (CT) infection can directly affect male fertility. However, only few have investigated the effects of CT on semen parameters, and mostly with inconclusive results. The main aims of this study were to identify CT inside spermatozoa, and the possible pre and post antibiotic treatment effects on the overall semen parameters. We developed a flow cytometric method for the detection of CT inside spermatozoa (SPI™). Briefly, sperm cells were fixed, membrane permeabilized and DNA was loosened using DNAse. Sperm cells were incubated with a primary monoclonal antibody against CT and with a secondary fluorescent antibody (vs primary), and analysed using a flow cytometer. Of 2415 infertile individuals, 48.61% were found positive for CT. 170 CT+ samples were included in the CT antibiotic treatment study. 78.82% (134/170) of the CT+ showed a significant reduction in the percentage of the iCT infected spermatozoa after the antibiotic treatment; 59.70% (80/134) decreased to non-detectable levels. Spermcount data were also recorded. Spermatozoa morphology (normal and teratozoospermia index, TZI) and motility (fast progressive and non-progressive spermatozoa) were statistically significant altered in CT+ pre-treatment vs control group. CT antibiotic treatment showed statistically significant effects on normal spermatozoa morphology, mid-piece and tail defects, and TZI. The study demonstrated that semen flow cytometric analysis of semen could be a valuable tool for faster and accurate identification of individuals with asymptomatic CT infection. It also identified a positive effect of antibiotic therapy on semen parameters, that could help males with infertility.
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Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics. Int J Mol Sci 2022; 23:ijms23179834. [PMID: 36077231 PMCID: PMC9456280 DOI: 10.3390/ijms23179834] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/21/2022] Open
Abstract
Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis.
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López-Pintor JM, Martínez-García L, Maruri A, Menéndez B, Puerta T, Rodríguez C, González-Alba JM, Rodríguez-Domínguez M, Galán JC. Quantification of plasmid copy number as surrogate marker of virulence among different invasive and non-invasive genotypes of Chlamydia trachomatis. Diagn Microbiol Infect Dis 2022; 102:115610. [DOI: 10.1016/j.diagmicrobio.2021.115610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 02/04/2023]
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Shetty S, Kouskouti C, Schoen U, Evangelatos N, Vishwanath S, Satyamoorthy K, Kainer F, Brand A. Diagnosis of Chlamydia trachomatis genital infections in the era of genomic medicine. Braz J Microbiol 2021; 52:1327-1339. [PMID: 34164797 PMCID: PMC8221097 DOI: 10.1007/s42770-021-00533-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 05/17/2021] [Indexed: 11/02/2022] Open
Abstract
PURPOSE Chlamydial genital infections constitute significant sexually transmitted infections worldwide. The often asymptomatic status of C. trachomatis (CT) infections leads to an increased burden on human reproductive health, especially in middle- and low-income settings. Early detection and management of these infections could play a decisive role in controlling this public health burden. The objective of this review is to provide an insight into the evolution of diagnostic methods for CT infections through the development of new molecular technologies, emphasizing on -omics' technologies and their significance as diagnostic tools both for effective patient management and control of disease transmission. METHODS Narrative review of the diagnostic methodologies of CT infections and the impact of the introduction of -omics' technologies on their diagnosis by review of the literature. RESULTS Various methodologies are discussed with respect to working principles, required specifications, advantages, and disadvantages. Implementing the most accurate methods in diagnosis is highlighted as the cornerstone in managing CT infections. CONCLUSION Diagnostics based on -omics' technologies are considered to be the most pertinent modalities in CT testing when compared to other available methods. There is a need to modify these effective and accurate diagnostic tools in order to render them more available and feasible in all settings, especially aiming on turning them to rapid point-of-care tests for effective patient management and disease control.
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Affiliation(s)
- Seema Shetty
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Madhav Nagar, Manipal, 576104, Karnataka, India.
- United Nations University - Maastricht Economics and Social Research Institute On Innovation and Technology (UNU-MERIT), Maastricht, 6211, AX, The Netherlands.
- Manipal Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
| | - Christina Kouskouti
- Department of Obstetrics and Perinatal Medicine, Klinik Hallerwiese, St. Johannis-Muhlgasse 19, 90419, Nuremberg, Germany
- Division of Maternal and Fetal Medicine Department of Obstetrics and Gynaecology, Mt. Sinai Hospital University of Toronto, Toronto, ON, Canada
| | - Uwe Schoen
- BioMedHeliX (Pty) Ltd., 3 Conifer Road, Cape Town, 8005, South Africa
| | - Nikolaos Evangelatos
- United Nations University - Maastricht Economics and Social Research Institute On Innovation and Technology (UNU-MERIT), Maastricht, 6211, AX, The Netherlands
- Interdepartmental Division of Critical Care Medicine, University of Toronto, ON, Canada
- Dr. TMA Pai Endowment Chair in Research Policy in Biomedical Sciences and Public Health, Prasanna School of Public Health (PSPH), Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Shashidhar Vishwanath
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Madhav Nagar, Manipal, 576104, Karnataka, India
- Manipal Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Franz Kainer
- Department of Obstetrics and Perinatal Medicine, Klinik Hallerwiese, St. Johannis-Muhlgasse 19, 90419, Nuremberg, Germany
| | - Angela Brand
- United Nations University - Maastricht Economics and Social Research Institute On Innovation and Technology (UNU-MERIT), Maastricht, 6211, AX, The Netherlands
- Dr. TMA Pai Endowment Chair in Public Health Genomics, Department of Public Health Genomics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- Department of International Health, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, 6229, GT, The Netherlands
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Manning C, O’Neill C, Clarke IN, Rebec M, Cliff PR, Marsh P. High-resolution genotyping of Lymphogranuloma Venereum (LGV) strains of Chlamydia trachomatis in London using multi-locus VNTR analysis-ompA genotyping (MLVA-ompA). PLoS One 2021; 16:e0254233. [PMID: 34237111 PMCID: PMC8266103 DOI: 10.1371/journal.pone.0254233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/22/2021] [Indexed: 12/02/2022] Open
Abstract
Background Lymphogranuloma venereum (LGV) is caused by Chlamydia trachomatis strains with ompA genotypes L1 to L3. An LGV epidemic associated with the L2b genotype has emerged in the past few decades amongst men who have sex with men (MSM). C. trachomatis genotypes can be discriminated by outer membrane protein A gene (ompA) sequencing, however this method has limited resolution. This study employed a high-resolution genotyping method, namely, multi-locus tandem repeat (VNTR) analysis with ompA sequencing (MLVA-ompA), to assess the distribution of LGV MLVA-ompA genotypes amongst individuals attending genitourinary medicine (GUM) clinics in London. Methods Clinical specimens were collected from individuals attending eight London-based GUM clinics. Specimens that tested positive for C. trachomatis by commercial nucleic acid amplification test (NAAT) were confirmed as LGV by pmpH real-time PCR. LGV-positive DNA extracts were subsequently genotyped using MLVA-ompA. Results Two hundred and thirty DNA extracts were confirmed as LGV, and 162 (70%) yielded complete MLVA-ompA genotypes. Six LGV MLVA-ompA genotypes were identified: 1.9.2b-L2, 1.9.3b-L2b, 1.9.2b-L2b, 1.9.2b-L2b/D, 1.4a.2b-L2b, and 5.9.2b-L1. The following LGV ompA genotypes were identified (in descending order of abundance): L2, L2b, L2b/D, and L1. Eight ompA sequences with the hybrid L2b/D profile were detected. The hybrid sequence was identical to the ompA of a recombinant L2b/D strain detected in Portugal in 2017. Conclusions The L2 ompA genotype was found to predominate in the London study population. The study detected an unusual hybrid L2b/D ompA profile that was previously reported in Portugal. We recommend further monitoring and surveillance of LGV strains within the UK population.
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Affiliation(s)
- Chloe Manning
- Department of Molecular Microbiology, Division of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- * E-mail:
| | - Colette O’Neill
- Department of Molecular Microbiology, Division of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ian N. Clarke
- Department of Molecular Microbiology, Division of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Monica Rebec
- Department of Microbiology, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London, United Kingdom
| | - Penelope R. Cliff
- Department of Infection Sciences, St Thomas’ Hospital, London, United Kingdom
| | - Peter Marsh
- Public Health England, Porton Down, Salisbury, United Kingdom
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Tryptophan Operon Diversity Reveals Evolutionary Trends among Geographically Disparate Chlamydia trachomatis Ocular and Urogenital Strains Affecting Tryptophan Repressor and Synthase Function. mBio 2021; 12:mBio.00605-21. [PMID: 33975934 PMCID: PMC8262981 DOI: 10.1128/mbio.00605-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The obligate intracellular pathogen Chlamydia trachomatis (Ct) is the leading cause of bacterial sexually transmitted infections and blindness globally. To date, Ct urogenital strains are considered tryptophan prototrophs, utilizing indole for tryptophan synthesis within a closed-conformation tetramer comprised of two α (TrpA)- and two β (TrpB)-subunits. In contrast, ocular strains are auxotrophs due to mutations in TrpA, relying on host tryptophan pools for survival. It has been speculated that there is strong selective pressure for urogenital strains to maintain a functional operon. Here, we performed genetic, phylogenetic, and novel functional modeling analyses of 595 geographically diverse Ct ocular, urethral, vaginal, and rectal strains with complete operon sequences. We found that ocular and urogenital, but not lymphogranuloma venereum, TrpA-coding sequences were under positive selection. However, vaginal and urethral strains exhibited greater nucleotide diversity and a higher ratio of nonsynonymous to synonymous substitutions [Pi(a)/Pi(s)] than ocular strains, suggesting a more rapid evolution of beneficial mutations. We also identified nonsynonymous amino acid changes for an ocular isolate with a urogenital backbone in the intergenic region between TrpR and TrpB at the exact binding site for YtgR-the only known iron-dependent transcription factor in Chlamydia-indicating that selective pressure has disabled the response to fluctuating iron levels. In silico effects on protein stability, ligand-binding affinity, and tryptophan repressor (TrpR) affinity for single-stranded DNA (ssDNA) measured by calculating free energy changes (ΔΔG) between Ct reference and mutant tryptophan operon proteins were also analyzed. We found that tryptophan synthase function was likely suboptimal compared to other bacterial tryptophan prototrophs and that a diversity of urogenital strain mutations rendered the synthase nonfunctional or inefficient. The novel mutations identified here affected active sites in an orthosteric manner but also hindered α- and β-subunit allosteric interactions from distant sites, reducing efficiency of the tryptophan synthase. Importantly, strains with mutant proteins were inclined toward energy conservation by exhibiting an altered affinity for their respective ligands compared to reference strains, indicating greater fitness. This is not surprising as l-tryptophan is one of the most energetically costly amino acids to synthesize. Mutations in the tryptophan repressor gene (trpR) among urogenital strains were similarly detrimental to function. Our findings indicate that urogenital strains are evolving more rapidly than previously recognized with mutations that impact tryptophan operon function in a manner that is energetically beneficial, providing a novel host-pathogen evolutionary mechanism for intracellular survival.IMPORTANCE Chlamydia trachomatis (Ct) is a major global public health concern causing sexually transmitted and ocular infections affecting over 130 million and 260 million people, respectively. Sequelae include infertility, preterm birth, ectopic pregnancy, and blindness. Ct relies on available host tryptophan pools and/or substrates to synthesize tryptophan to survive. Urogenital strains synthesize tryptophan from indole using their intact tryptophan synthase (TS). Ocular strains contain a trpA frameshift mutation that encodes a truncated TrpA with loss of TS function. We found that TS function is likely suboptimal compared to other tryptophan prototrophs and that urogenital stains contain diverse mutations that render TS nonfunctional/inefficient, evolve more rapidly than previously recognized, and impact operon function in a manner that is energetically beneficial, providing an alternative host-pathogen evolutionary mechanism for intracellular survival. Our research has broad scientific appeal since our approach can be applied to other bacteria that may explain evolution/survival in host-pathogen interactions.
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Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs. mSphere 2021; 6:6/2/e01302-20. [PMID: 33658279 PMCID: PMC8546720 DOI: 10.1128/msphere.01302-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chlamydia trachomatis, an obligately intracellular bacterium, is the most prevalent cause of bacterial sexually transmitted infections (STIs) worldwide. Numbers of U.S. infections of the urogenital tract and rectum have increased annually. Because C. trachomatis is not easily cultured, comparative genomic studies are limited, restricting our understanding of strain diversity and emergence among populations globally. While Agilent SureSelectXT target enrichment RNA bait libraries have been developed for whole-genome enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival, and rectal samples, public access to these libraries is not available. We therefore designed an RNA bait library (34,795 120-mer probes based on 85 genomes, versus 33,619 probes using 74 genomes in a previous one) to augment organism sequencing from clinical samples that can be shared with the scientific community, enabling comparison studies. We describe the library and limit of detection for genome copy input, and we present results of 100% efficiency and high-resolution determination of recombination and identical genomes within vaginal-rectal specimen pairs in women. This workflow provides a robust approach for discerning genomic diversity and advancing our understanding of the molecular epidemiology of contemporary C. trachomatis STIs across sample types, geographic populations, sexual networks, and outbreaks associated with proctitis/proctocolitis among women and men who have sex with men.IMPORTANCE Chlamydia trachomatis is an obligate intracellular bacterium that is not easily cultured, which limits our understanding of urogenital and rectal C. trachomatis transmission and impact on morbidity. To provide a publicly available workflow for whole-genome target enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival, and rectal specimens, we developed and report on an RNA bait library to enrich the organism from clinical samples for sequencing. We demonstrate an increased efficiency in the percentage of reads mapping to C. trachomatis and identified recombinant and identical C. trachomatis genomes in paired vaginal-rectal samples from women. Our workflow provides a robust genomic epidemiologic approach to advance our understanding of C. trachomatis strains causing ocular, urogenital, and rectal infections and to explore geo-sexual networks, outbreaks of colorectal infections among women and men who have sex with men, and the role of these strains in morbidity.
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13
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Kim JH, Oh SW. Pretreatment methods for nucleic acid-based rapid detection of pathogens in food: A review. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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14
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Pilo S, Zizelski Valenci G, Rubinstein M, Pichadze L, Scharf Y, Dveyrin Z, Rorman E, Nissan I. High-resolution multilocus sequence typing for Chlamydia trachomatis: improved results for clinical samples with low amounts of C. trachomatis DNA. BMC Microbiol 2021; 21:28. [PMID: 33461496 PMCID: PMC7814548 DOI: 10.1186/s12866-020-02077-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 12/20/2020] [Indexed: 11/17/2022] Open
Abstract
Background Several Multilocus Sequence Typing (MLST) schemes have been developed for Chlamydia trachomatis. Bom’s MLST scheme for MLST is based on nested PCR amplification and sequencing of five hypervariable genes and ompA. In contrast to other Chlamydia MLST schemes, Bom’s MLST scheme gives higher resolution and phylogenetic trees that are comparable to those from whole genome sequencing. However, poor results have been obtained with Bom’s MLST scheme in clinical samples with low concentrations of Chlamydia DNA. Results In this work, we present an improved version of the scheme that is based on the same genes and MLST database as Bom’s MLST scheme, but with newly designed primers for nested-1 and nested-2 steps under stringent conditions. Furthermore, we introduce a third primer set for the sequencing step, which considerably improves the performance of the assay. The improved primers were tested in-silico using a dataset of 141 Whole Genome Sequences (WGS) and in a comparative analysis of 32 clinical samples. Based on cycle threshold and melting curve analysis values obtained during Real-Time PCR of nested-1 & 2 steps, we developed a simple scoring scheme and flow chart that allow identification of reaction inhibitors as well as to predict with high accuracy amplification success. The improved MLST version was used to obtain a genovars distribution in patients attending an STI clinic in Tel Aviv. Conclusions The newly developed MLST version showed great improvement of assay results for samples with very low concentrations of Chlamydia DNA. A similar concept could be applicable to other MLST schemes. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02077-y.
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Affiliation(s)
- Shlomo Pilo
- Ministry of Health, National Public Health Laboratory, Tel Aviv, Israel
| | | | - Mor Rubinstein
- Ministry of Health, National Public Health Laboratory, Tel Aviv, Israel
| | - Lea Pichadze
- Ministry of Health, National Public Health Laboratory, Tel Aviv, Israel
| | - Yael Scharf
- Ministry of Health, National Public Health Laboratory, Tel Aviv, Israel
| | - Zeev Dveyrin
- Ministry of Health, National Public Health Laboratory, Tel Aviv, Israel
| | - Efrat Rorman
- Ministry of Health, National Public Health Laboratory, Tel Aviv, Israel
| | - Israel Nissan
- Ministry of Health, National Public Health Laboratory, Tel Aviv, Israel.
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15
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Wang Q, Feng J, Zhang J, Shi L, Jin Z, Liu D, Wu B, Chen J. Diagnosis of complication in lung transplantation by TBLB + ROSE + mNGS. Open Med (Wars) 2020; 15:968-980. [PMID: 33313416 PMCID: PMC7706120 DOI: 10.1515/med-2020-0232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 07/26/2020] [Accepted: 09/02/2020] [Indexed: 11/18/2022] Open
Abstract
Lung transplantation is a potentially life-saving therapy for patients with terminal respiratory illnesses. Long-term survival is limited by the development of a variety of opportunistic infections and rejection. Optimal means of differential diagnosis of infection and rejection have not been established. With these challenges in mind, we tried to use transbronchial lung biopsy (TBLB) rapid on-site cytological evaluation (ROSE), metagenomic next-generation sequencing (mNGS), and routine histologic examination to timely distinguish infection and rejection, and accurately detect etiologic pathogens. We reviewed the medical records of all patients diagnosed with infection or rejection by these means from December 2017 to September 2018 in our center. We identified seven recipients whose clinical course was complicated by infection or rejection. Three patients were diagnosed with acute rejection, organizing pneumonia, and acute fibrinoid organizing pneumonia, respectively. Four of the seven patients were diagnosed with infections, including Pneumocystis carinii pneumonia, cytomegalovirus, Aspergillus, and bacterial pneumonia. These patients recovered after proper treatment. TBLB + ROSE + mNGS might be a good method to accurately detect etiologic pathogens, which may help us to facilitate the use of targeted and precision medicine therapy in postoperative complications and avoid unnecessary potential adverse effects of drugs.
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Affiliation(s)
- Qing Wang
- Respiratory Department of Kunming Municipal First People’s Hospital, Kunming 650000, China
- Graduate School, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Jing Feng
- Respiratory Department of Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Ji Zhang
- Respiratory Department of Lung Transplant Center, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi 214023, China
| | - Lingzhi Shi
- Respiratory Department of Lung Transplant Center, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi 214023, China
| | - Zhixian Jin
- Respiratory Department of Kunming Municipal First People’s Hospital, Kunming 650000, China
| | - Dong Liu
- Respiratory Department of Lung Transplant Center, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi 214023, China
| | - Bo Wu
- Respiratory Department of Lung Transplant Center, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi 214023, China
| | - Jingyu Chen
- Respiratory Department of Lung Transplant Center, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi 214023, China
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Abstract
This paper provides an overview of the current knowledge of chlamydiae. These intracellular microorganisms belonging to the Chlamydiaceae family are widely distributed throughout the world. Constant development of culture-independent approaches for characterisation of microbial genomes enables new discoveries in the field of Chlamydia. The number of new taxa is continuously increasing as well as the range of hosts. New species and genotypes are constantly being discovered, particularly new avian and reptilian agents, which are discussed in this article. Interestingly, wild animals are the main hosts for new Chlamydia species including different species of bird, turtle and snake. The availability of next-generation sequencing opens up a new prospect for research and leads to deeper knowledge of these interesting microorganisms about which much is still to discover.
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17
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Pickering H, Chernet A, Sata E, Zerihun M, Williams CA, Breuer J, Nute AW, Haile M, Zeru T, Tadesse Z, Bailey RL, Callahan EK, Holland MJ, Nash SD. Genomics of Ocular Chlamydia trachomatis after 5 years of SAFE interventions for trachoma in Amhara, Ethiopia. J Infect Dis 2020; 225:994-1004. [PMID: 33034349 PMCID: PMC8922003 DOI: 10.1093/infdis/jiaa615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/30/2020] [Indexed: 12/18/2022] Open
Abstract
To eliminate trachoma as a public health problem, the WHO recommends the SAFE (Surgery, Antibiotics, Facial cleanliness, and Environmental improvement) strategy. As part of the SAFE strategy in the Amhara Region, Ethiopia, the Trachoma Control Program distributed over 124 million doses of antibiotic between 2007 and 2015. Despite this, trachoma remained hyperendemic in many districts and a considerable level of Chlamydia trachomatis (Ct) infection was evident. We utilised residual material from Abbott m2000 Ct diagnostic tests to sequence 99 ocular Ct samples from Amhara and investigated the role of Ct genomic variation in continued transmission of Ct. Sequences were typical of ocular Ct, at the whole-genome level and in tissue tropism-associated genes. There was no evidence of macrolide-resistance in this population. Polymorphism around ompA gene was associated with village-level trachomatous inflammation-follicular prevalence. Greater ompA diversity at the district-level was associated with increased Ct infection prevalence. We found no evidence for Ct genomic variation contributing to continued transmission of Ct after treatment, adding to evidence that azithromycin does not drive acquisition of macrolide resistance in Ct. Increased Ct infection in areas with more ompA variants requires longitudinal investigation to understand what impact this may have on treatment success and host immunity.
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Affiliation(s)
- Harry Pickering
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, UK
| | | | | | | | | | - Judith Breuer
- Division of Infection and Immunity, University College London, UK
| | | | | | - Taye Zeru
- Amhara Public Health Institute Bahir Dar, Ethiopia
| | | | - Robin L Bailey
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, UK
| | | | - Martin J Holland
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, UK
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18
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Hyeon JY, Mann DA, Wang J, Kim WK, Deng X. Rapid detection of Salmonella in poultry environmental samples using real-time PCR coupled with immunomagnetic separation and whole genome amplification. Poult Sci 2020; 98:6973-6979. [PMID: 31347691 PMCID: PMC8913963 DOI: 10.3382/ps/pez425] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/11/2019] [Indexed: 11/23/2022] Open
Abstract
We evaluated the combination of immunomagnetic separation (IMS), multiple displacement amplification (MDA), and real-time PCR to detect Salmonella from poultry environmental samples. The limits of detection (LODs) of IMS-MDA real-time PCR with different culture enrichment hours (0, 4, 6, and 8 h) were determined in artificially inoculated litter samples from a specific pathogen-free (SPF) poultry farm. In addition, Salmonella detection rate of IMS-MDA real-time PCR with 8-h culture enrichment was compared with that of conventional real-time PCR and culture-based detection by analyzing 174 poultry environmental samples (boot swabs, drag swabs, and litter), and the levels of Salmonella in the samples were quantified using the most probably number method. The LODs of IMS-MDA real-time PCR with 0, 4 to 6, and 8-h enrichment were 10, 1, and 0.1 CFU/g, respectively. Salmonella was detected in 25 of the 174 environmental samples (14.4%) by IMS-MDA real-time PCR, compared with 24 (13.8%) by conventional real-time PCR and 19 (10.9%) by culturing. Cohen's kappa index indicated strong concordance (0.79) between IMS-MDA real-time PCR and culture detection. We demonstrated the potential of the IMS-MDA real-time PCR assay as a faster and more sensitive alternative to culture-based Salmonella detection from poultry environmental samples.
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Affiliation(s)
- Ji-Yeon Hyeon
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA 30223
| | - David A Mann
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA 30223
| | - Jinquan Wang
- Department of Poultry Science, University of Georgia, Athens, GA 30602
| | - Woo Kyun Kim
- Department of Poultry Science, University of Georgia, Athens, GA 30602
| | - Xiangyu Deng
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA 30223
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19
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Abstract
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the requirement for in vitro culturing, is attractive in terms of time- and labor-saving, especially in the case of slow growing, or obligate intracellular pathogens, such as Chlamydia trachomatis. However clinical samples typically contain too low levels of pathogen nucleic acid, plus relatively high levels of human and natural microbiota DNA/RNA, to make this a viable option. Using a combination of whole-genome enrichment and deep sequencing, which has been proven to be a nonmutagenic approach, we can capture all known variation found within C. trachomatis genomes. The method is a consistent and sensitive tool that enables rapid whole-genome sequencing of C. trachomatis directly from clinical samples and has the potential to be adapted to other pathogens with a similar clonal nature.
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20
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Optimizing DNA Extraction Methods for Nanopore Sequencing of Neisseria gonorrhoeae Directly from Urine Samples. J Clin Microbiol 2020; 58:JCM.01822-19. [PMID: 31852766 PMCID: PMC7041563 DOI: 10.1128/jcm.01822-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/06/2019] [Indexed: 12/17/2022] Open
Abstract
Empirical gonorrhea treatment at initial diagnosis reduces onward transmission. However, increasing resistance to multiple antibiotics may necessitate waiting for culture-based diagnostics to select an effective treatment. There is a need for same-day culture-free diagnostics that identify infection and detect antimicrobial resistance. We investigated if Nanopore sequencing can detect sufficient Neisseria gonorrhoeae DNA to reconstruct whole genomes directly from urine samples. Empirical gonorrhea treatment at initial diagnosis reduces onward transmission. However, increasing resistance to multiple antibiotics may necessitate waiting for culture-based diagnostics to select an effective treatment. There is a need for same-day culture-free diagnostics that identify infection and detect antimicrobial resistance. We investigated if Nanopore sequencing can detect sufficient Neisseria gonorrhoeae DNA to reconstruct whole genomes directly from urine samples. We used N. gonorrhoeae-spiked urine samples and samples from gonorrhea infections to determine optimal DNA extraction methods that maximize the amount of N. gonorrhoeae DNA sequenced while minimizing contaminating host DNA. In simulated infections, the Qiagen UCP pathogen mini kit provided the highest ratio of N. gonorrhoeae to human DNA and the most consistent results. Depletion of human DNA with saponin increased N. gonorrhoeae yields in simulated infections but decreased yields in clinical samples. In 10 urine samples from men with symptomatic urethral gonorrhea, ≥92.8% coverage of an N. gonorrhoeae reference genome was achieved in all samples, with ≥93.8% coverage breath at ≥10-fold depth in 7 (70%) samples. In simulated infections, if ≥104 CFU/ml of N. gonorrhoeae was present, sequencing of the large majority of the genome was frequently achieved. N. gonorrhoeae could also be detected from urine in cobas PCR medium tubes and from urethral swabs and in the presence of simulated Chlamydia coinfection. Using Nanopore sequencing of urine samples from men with urethral gonorrhea, sufficient data can be obtained to reconstruct whole genomes in the majority of samples without the need for culture.
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21
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Parmar NR, Perera SR, Wang J, Levett PN, Minion J, Dillon JAR. Characterization of antimicrobial resistance genes from Neisseria gonorrhoeae positive remnant Aptima urine specimens. Future Microbiol 2020; 14:1559-1571. [PMID: 31992068 DOI: 10.2217/fmb-2019-0161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Aim: To ascertain the antimicrobial resistance and strain types (STs) of Neisseria gonorrhoeae from 50 remnant Aptima urine specimens using molecular methods. Methods: Mutations predictive of resistance to six antibiotics were identified in eight genes. STs were determined using NG-MAST and NG-STAR. Results: All eight antimicrobial resistance genes could be characterized in 36 specimens. A total of 17 specimens were predicted to be susceptible to all antibiotics, including ceftriaxone. Decreased susceptibility to cefixime and ciprofloxacin resistance was predicted in 11 specimens (PBP2 type 34.001). Overall, 38/50 specimens were predicted to be ciprofloxacin susceptible; three were azithromycin resistant. Nineteen NG-MAST and 21 NG-STAR STs were noted. Conclusion: Molecular analysis of remnant Aptima specimens enabled the prediction of emerging gonococcal cefixime and azithromycin resistance which would otherwise have been undetected.
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Affiliation(s)
- Nidhi R Parmar
- Department of Biochemistry, Microbiology, & Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.,Vaccine & Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK, S7N 5E3, Canada
| | - Sumudu R Perera
- Department of Biochemistry, Microbiology, & Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.,Vaccine & Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK, S7N 5E3, Canada
| | - Jin Wang
- Vaccine & Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK, S7N 5E3, Canada
| | - Paul N Levett
- Roy Romanow Provincial Laboratory, 5 Research Drive, Regina, SK, S4S 0A4, Canada
| | - Jessica Minion
- Roy Romanow Provincial Laboratory, 5 Research Drive, Regina, SK, S4S 0A4, Canada
| | - Jo-Anne R Dillon
- Department of Biochemistry, Microbiology, & Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.,Vaccine & Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK, S7N 5E3, Canada
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22
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Preiswerk B, Imkamp F, Vorburger D, Hömke RV, Keller PM, Wagner K. Mycoplasma penetrans bacteremia in an immunocompromised patient detected by metagenomic sequencing: a case report. BMC Infect Dis 2020; 20:7. [PMID: 31900105 PMCID: PMC6942334 DOI: 10.1186/s12879-019-4723-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/22/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycoplasma sp. are well recognized as etiological agents of respiratory and sexually transmitted disease. Mycoplasma penetrans, a species of Mycoplasma sp., has been frequently detected in HIV-positive patients and associated with the progression of HIV-associated disease. To date, there is only a single case report describing M. penetrans as the causative agent of a severe respiratory tract infection in a HIV-negative patient. CASE PRESENTATION In this report, we describe the case of M. penetrans bacteremia in a HIV-negative, 38-year-old, female, immunocompromised, solid organ transplant patient (combined kidney and pancreas transplantation in 2016), who was admitted to our hospital with anemic uterine bleeding and fever of 38.3 °C. Several hours before her admission at our university hospital, a latex bladder catheter was inserted into her uterus and she complained about fatigue, dizziness and ongoing vaginal bleeding. Laboratory examination showed severe anemia, but microbiological examination was inconspicuous (culture negative vaginal and cervical smears, negative urine culture). Bacterial blood cultures showed a growth signal after 4 h, but microscopic examination with Gram staining and subcultures on different agar media did not identify bacterial pathogens. To identify the bacterial cause of malignancy in the patient, metagenomic sequencing of the blood culture was performed that identified M. penetrans. CONCLUSION Metagenomic sequencing identified M. penetrans in an immunosuppressed patient with culture-negative bacteremia. Clinicians should be aware of the opportunistic potential of M. penetrans that may cause severe infections in certain vulnerable patient populations and the limitations of culture and Gram staining for confirming the presence of fastidious bacterial pathogens like Mycoplasma spp.
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Affiliation(s)
- Benjamin Preiswerk
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Present Address: Triemli Hospital Zurich, Zurich, Switzerland
| | - Frank Imkamp
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Denise Vorburger
- Department of Gynecology, University Hospital Zurich, Zurich, Switzerland
| | - Rico V Hömke
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Peter M Keller
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Present Address: Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Karoline Wagner
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland. .,Laboratory Medicine, University Hospital of Basel, Petersgraben 4, 4031, Basel, Switzerland.
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23
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Alkhidir AAI, Holland MJ, Elhag WI, Williams CA, Breuer J, Elemam AE, El Hussain KMK, Ournasseir MEH, Pickering H. Whole-genome sequencing of ocular Chlamydia trachomatis isolates from Gadarif State, Sudan. Parasit Vectors 2019; 12:518. [PMID: 31685017 PMCID: PMC6829945 DOI: 10.1186/s13071-019-3770-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trachoma, caused by ocular Chlamydia trachomatis, is the leading infectious cause of blindness worldwide. Sudan first reported trachoma in the 1930s and has since been consistently endemic. Ocular C. trachomatis previously isolated from trachoma patients in Sudan in 1963 was antigenically identical to an isolate from Saudi Arabia (A/SA1). No contemporary ocular C. trachomatis whole genome sequences have been reported from Sudan. METHODS This study sequenced twenty ocular C. trachomatis isolates to improve understanding of pathogen diversity in North-East Africa and examine for genomic variation specific to Sudan, possibly related to the persistence of trachoma in surveyed communities. High quality, whole genome sequences were obtained from 12/20 isolates. RESULTS All isolates were serovar A and had tarP and trpA sequences typical of classical, ocular C. trachomatis isolates. The Sudanese isolates formed a closely related subclade within the T2-trachoma clade of C. trachomatis phylogeny distinct from geographically disparate ocular isolates, with little intra-population diversity. We found 333 SNPs that were conserved in Sudanese ocular isolates but rare compared to other ocular C. trachomatis populations, which were focused in two genomic loci (CTA0172-CTA0173 and CTA0482). CONCLUSIONS Limited intra-population diversity and geographical clustering of ocular C. trachomatis suggests minimal transmission between and slow diversification within trachoma-endemic communities. However, diversity may have been higher pre-treatment in these communities. Over-representation of Sudan-specific SNPs in three genes suggests they may have an impact on C. trachomatis growth and transmission in this population.
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Affiliation(s)
| | - Martin J Holland
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
| | - Wafa Ibrahim Elhag
- Faculty of Medical Laboratory Sciences, Al-Neelain University, Khartoum, Sudan
| | | | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK.,Microbiology, Virology, and Infection Control, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | | | | | | | - Harry Pickering
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, UK
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24
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Harding-Esch EM, Holland MJ, Schémann JF, Sillah A, Sarr B, Christerson L, Pickering H, Molina-Gonzalez S, Sarr I, Andreasen AA, Jeffries D, Grundy C, Mabey DCW, Herrmann B, Bailey RL. Impact of a single round of mass drug administration with azithromycin on active trachoma and ocular Chlamydia trachomatis prevalence and circulating strains in The Gambia and Senegal. Parasit Vectors 2019; 12:497. [PMID: 31640755 PMCID: PMC6805539 DOI: 10.1186/s13071-019-3743-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/09/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mass drug administration (MDA) with azithromycin is a cornerstone of the trachoma elimination strategy. Although the global prevalence of active trachoma has declined considerably, prevalence persists or even increases in some communities and districts. To increase understanding of MDA impact, we investigated the prevalence of active trachoma and ocular C. trachomatis prevalence, organism load, and circulating strains at baseline and one-year post-MDA in The Gambia and Senegal. METHODS Pre- and one-year post-MDA, children aged 0-9 years were examined for clinical signs of trachoma in six Gambian and 12 Senegalese villages. Ocular swabs from each child's right conjunctiva were tested for evidence of ocular C. trachomatis infection and organism load (ompA copy number), and ompA and multi-locus sequence typing (MLST) was performed. RESULTS A total of 1171 children were examined at baseline and follow-up in The Gambia. Active trachoma prevalence decreased from 23.9% to 17.7%, whereas ocular C. trachomatis prevalence increased from 3.0% to 3.8%. In Senegal, 1613 and 1771 children were examined at baseline and follow-up, respectively. Active trachoma prevalence decreased from 14.9% to 8.0%, whereas ocular C. trachomatis prevalence increased from 1.8% to 3.6%. Higher organism load was associated with having active trachoma and severe inflammation. Sequence typing demonstrated that all Senegalese samples were genovar A, whereas Gambian samples were a mix of genovars A and B. MLST provided evidence of clustering at village and household levels and demonstrated differences of strain variant frequencies in Senegal, indicative of an "outbreak". MLST, including partial ompA typing, provided greater discriminatory power than complete ompA typing. CONCLUSIONS We found that one round of MDA led to an overall decline in active trachoma prevalence but no impact on ocular C. trachomatis infection, with heterogeneity observed between villages studied. This could not be explained by MDA coverage or number of different circulating strains pre- and post-MDA. The poor correlation between active trachoma and infection prevalence supports the need for further work on alternative indicators to clinical signs for diagnosing ocular C. trachomatis infection. MLST typing has potential molecular epidemiology utility, including better understanding of transmission dynamics, although relationship to whole-genome sequence variability requires further exploration.
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Affiliation(s)
- Emma M. Harding-Esch
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Martin J. Holland
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
- Medical Research Council Laboratories, PO Box 273, Fajara, Banjul, The Gambia
| | | | - Ansumana Sillah
- National Eye Health Programme, Ministry of Health and Social Welfare, Kanifing, The Gambia
| | - Boubacar Sarr
- Programme National de Lutte Contre la Cécité, Ministère de la Santé, BP 3817, Dakar, Sénégal
| | - Linus Christerson
- Department of Clinical Microbiology, Uppsala University, Uppsala, Sweden
| | - Harry Pickering
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | | | - Isatou Sarr
- Medical Research Council Laboratories, PO Box 273, Fajara, Banjul, The Gambia
| | - Aura A. Andreasen
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - David Jeffries
- Medical Research Council Laboratories, PO Box 273, Fajara, Banjul, The Gambia
| | - Chris Grundy
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - David C. W. Mabey
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Bjorn Herrmann
- Department of Clinical Microbiology, Uppsala University, Uppsala, Sweden
| | - Robin L. Bailey
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
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Hadfield J, Bénard A, Domman D, Thomson N. The Hidden Genomics of Chlamydia trachomatis. Curr Top Microbiol Immunol 2019; 412:107-131. [PMID: 29071471 DOI: 10.1007/82_2017_39] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The application of whole-genome sequencing has moved us on from sequencing single genomes to defining unravelling population structures in different niches, and at the -species, -serotype or even -genus level, and in local, national and global settings. This has been instrumental in cataloguing and revealing a huge a range of diversity in this bacterium, when at first we thought there was little. Genomics has challenged assumptions, added insight, as well as confusion and glimpses of truths. What is clear is that at a time when we start to realise the extent and nature of the diversity contained within a genus or a species like this, the huge depth of knowledge communities have developed, through cell biology, as well as the new found molecular approaches will be more precious than ever to link genotype to phenotype. Here we detail the technological developments and insights we have seen during the relatively short time since we began to see the hidden genome of Chlamydia trachomatis.
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Affiliation(s)
- James Hadfield
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Angèle Bénard
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Daryl Domman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Nicholas Thomson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
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26
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Exploring bacterial resistome and resistance dessemination: an approach of whole genome sequencing. Future Med Chem 2019; 11:247-260. [PMID: 30801197 DOI: 10.4155/fmc-2018-0201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
For several decades antibiotics are used to combat against pathogenic bacteria, but their misuse and overuse have caused the emergence of resistant bacteria. The scarcities of effective antibiotics along with unavailability of alternative solutions have exacerbated bacterial infections and mortality rate. This review provides the concept of bacterial resistome and mechanisms of resistance. It has also described the utility of whole genome sequencing in identifying resistance and its dissemination in association with available bioinformatics tools and databases. Moreover, the whole genome sequencing methodology described in this review will help to select effective antibiotics, maintain unparalleled surveillance of resistance and provide early diagnosis during resistance outbreaks. The provided information could be used to control infection caused by resistant microorganisms.
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Methods in Metagenomics and Environmental Biotechnology. NANOSCIENCE AND BIOTECHNOLOGY FOR ENVIRONMENTAL APPLICATIONS 2019. [DOI: 10.1007/978-3-319-97922-9_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Hawken SE, Snitkin ES. Genomic epidemiology of multidrug-resistant Gram-negative organisms. Ann N Y Acad Sci 2019; 1435:39-56. [PMID: 29604079 PMCID: PMC6167210 DOI: 10.1111/nyas.13672] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 02/13/2018] [Accepted: 02/17/2018] [Indexed: 12/12/2022]
Abstract
The emergence and spread of antibiotic-resistant Gram-negative bacteria (rGNB) across global healthcare networks presents a significant threat to public health. As the number of effective antibiotics available to treat these resistant organisms dwindles, it is essential that we devise more effective strategies for controlling their proliferation. Recently, whole-genome sequencing has emerged as a disruptive technology that has transformed our understanding of the evolution and epidemiology of diverse rGNB species, and it has the potential to guide strategies for controlling the evolution and spread of resistance. Here, we review specific areas in which genomics has already made a significant impact, including outbreak investigations, regional epidemiology, clinical diagnostics, resistance evolution, and the study of epidemic lineages. While highlighting early successes, we also point to the next steps needed to translate this technology into strategies to improve public health and clinical medicine.
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Affiliation(s)
- Shawn E Hawken
- Department of Microbiology and Immunology, University of Michigan Medical School, Michigan, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Michigan, USA
- Division of Infectious Diseases/Department of Medicine, University of Michigan Medical School, Michigan, USA
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Bachmann NL, Rockett RJ, Timms VJ, Sintchenko V. Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics. Front Public Health 2018; 6:363. [PMID: 30619804 PMCID: PMC6299010 DOI: 10.3389/fpubh.2018.00363] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022] Open
Abstract
Whole genome sequencing (WGS) plays an increasing role in communicable disease control through high-resolution outbreak tracing, laboratory surveillance and diagnostics. However, WGS has traditionally relied on microbial culture in order to obtain pathogen specific DNA for sequencing. This has severely limited the application of whole genome sequencing on pathogens with fastidious culturing requirements. In addition, the widespread adoption of culture-independent diagnostic tests has reduced availability of cultured isolates for confirmatory testing and surveillance. These recent developments have created demand for the implementation of techniques enabling direct sequencing of microbial genomes in clinical samples without having to culture an isolate. However, sequencing of specific organisms from clinical samples can be affected by high levels of contaminating DNA from the host and other commensal microorganisms. Several methods have been introduced for selective lysis of host cells and/or separate specific organisms from a clinical sample. This review examines the different approaches for sample preparation that have been used in diagnostic and public health laboratories for metagenomic sequencing.
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Affiliation(s)
- Nathan L. Bachmann
- Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
- Centenary Institute, University of Sydney, Camperdown, NSW, Australia
| | - Rebecca J. Rockett
- Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Verlaine Joy Timms
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, NSW, Australia
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Hyeon JY, Mann DA, Townsend AM, Deng X. Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples. J Vis Exp 2018. [PMID: 30417889 DOI: 10.3791/58612] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Quasi-metagenomics sequencing refers to the sequencing-based analysis of modified microbiomes of food and environmental samples. In this protocol, microbiome modification is designed to concentrate genomic DNA of a target foodborne pathogen contaminant to facilitate the detection and subtyping of the pathogen in a single workflow. Here, we explain and demonstrate the sample preparation steps for the quasi-metagenomics analysis of Salmonella enterica from representative food and environmental samples including alfalfa sprouts, ground black pepper, ground beef, chicken breast and environmental swabs. Samples are first subjected to the culture enrichment of Salmonella for a shortened and adjustable duration (4-24 h). Salmonella cells are then selectively captured from the enrichment culture by immunomagnetic separation (IMS). Finally, multiple displacement amplification (MDA) is performed to amplify DNA from IMS-captured cells. The DNA output of this protocol can be sequenced by high throughput sequencing platforms. An optional quantitative PCR analysis can be performed to replace sequencing for Salmonella detection or assess the concentration of Salmonella DNA before sequencing.
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Patiño LH, Camargo M, Muñoz M, Ríos-Chaparro DI, Patarroyo MA, Ramírez JD. Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis. Front Microbiol 2018; 9:1854. [PMID: 30186244 PMCID: PMC6113918 DOI: 10.3389/fmicb.2018.01854] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/24/2018] [Indexed: 11/21/2022] Open
Abstract
Multilocus sequence typing (MLST) has become a useful tool for studying the genetic diversity of important public health pathogens, such as Chlamydia trachomatis (Ct). Four MLST schemes have been proposed for Ct (data available from Chlamydiales MLST databases). However, the lack of a sole standardized scheme represents the greatest limitation regarding typing this species. This study was thus aimed at evaluating the usefulness of the four MLST schemes available for Ct, describing each molecular marker's pattern and its contribution toward a description of intra-specific genetic diversity and population structure. The markers for each scheme, showed a variable power of dicrimination, exhibiting in some cases over estimation in the determination of Sequence Types (STs). However, individual analysis of each locus's typing efficiency and discrimination power led to identifying 8 markers as having a suitable pattern for intra-specific typing. analyzing the 8 candidate markers gave a combination of 3 of these loci as an optimal scheme for identifying a large amount of STs, maximizing discrimination power whilst maintaining suitable typing efficiency. One scheme was compared against core genome phylogenies, finding a higher typing resolution through the last approach. These results confirm once again that although complete genome data, in particular from core genome MLST (cgMLST) allow a high resolution clustering for Ct isolates. There are combinations of molecular markers that could generate equivalent results, with the advantage of representing an easy implementation strategy and lower costs leading to contribute to the monitoring and molecular epidemiology of Ct.
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Affiliation(s)
- Luz H. Patiño
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Ph.D. Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Milena Camargo
- Ph.D. Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Dora I. Ríos-Chaparro
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Manuel A. Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan D. Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
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Patel JG, Patel BJ, Patel SS, Raval SH, Parmar RS, Joshi DV, Chauhan HC, Chandel BS, Patel BK. Metagenomic of clinically diseased and healthy broiler affected with respiratory disease complex. Data Brief 2018; 19:82-85. [PMID: 29892620 PMCID: PMC5993000 DOI: 10.1016/j.dib.2018.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/03/2018] [Indexed: 10/25/2022] Open
Abstract
In recent past, the respiratory infection has emerged as a great challenge to the poultry farmers. Various pathogens including Avian pneumovirus (APV), Avian influenza virus (AIV), Infectious bronchitis virus (IBV) and Newcastle disease virus (NDV), Avibacterium paragallinarum, Ornithobacterium rhinotracheale (ORT), Mycoplasma synoviae (MS), Mycoplasma gallisepticum (MG) and Avian pathogenic Escherichia coli (APEC) are involved in the respiratory disease complex in birds [1], [2] (Bradbury, 1984; Roussan et al., 2008). Hence, respiratory disease complex is the most serious disease affecting to poultry and causes heavy economic losses in the poultry industry worldwide [3] (Murthy et al., 2008). In recent years, metagenomics is powerful analyzing tool for detection of pathogens directly from clinical samples without any prior knowledge of the organism in a given sample [4], [5] (Schuster, 2008; Pereira et al., 2010). High throughput Next-Generation-Sequencing technology was used for sequencing the isolated genomic DNA. These data provides an insight about taxonomic and functional status of microorganisms responsible for causing respiratory infection in broiler. The data of these metagenome are available in the BioSample Submission Portal as Bioproject PRJNA339659 and SRA accession number SRR5997823, SRR5992854, SRR6037376, SRR6024702, SRR6012248 and SRR6008913.
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Affiliation(s)
- J G Patel
- Department of Veterinary Pathology, College of Veterinary Science and Anima Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - B J Patel
- Department of Veterinary Pathology, College of Veterinary Science and Anima Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - S S Patel
- Department of Veterinary Microbiology, College of Veterinary Science and Animal, Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - S H Raval
- Department of Veterinary Pathology, College of Veterinary Science and Anima Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - R S Parmar
- Department of Veterinary Pathology, College of Veterinary Science and Anima Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - D V Joshi
- Department of Veterinary Pathology, College of Veterinary Science and Anima Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - H C Chauhan
- Department of Veterinary Microbiology, College of Veterinary Science and Animal, Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - B S Chandel
- Department of Animal Biotechnology, College of Veterinary Science and Animal, Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - B K Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal, Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
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Pillonel T, Bertelli C, Greub G. Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle. Front Microbiol 2018. [PMID: 29515524 PMCID: PMC5826181 DOI: 10.3389/fmicb.2018.00079] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Chlamydiae phylum exclusively encompasses bacteria sharing a similar obligate intracellular life cycle. Existing 16S rDNA data support a high diversity within the phylum, however genomic data remain scarce owing to the difficulty in isolating strains using culture systems with eukaryotic cells. Yet, Chlamydiae genome data extracted from large scale metagenomic studies might help fill this gap. This work compares 33 cultured and 27 environmental, uncultured chlamydial genomes, in order to clarify the phylogenetic relatedness of the new chlamydial clades and to investigate the genetic diversity of the Chlamydiae phylum. The analysis of published chlamydial genomes from metagenomics bins and single cell sequencing allowed the identification of seven new deeply branching chlamydial clades sharing genetic hallmarks of parasitic Chlamydiae. Comparative genomics suggests important biological differences between those clades, including loss of many proteins involved in cell division in the genus Similichlamydia, and loss of respiratory chain and tricarboxylic acid cycle in several species. Comparative analyses of chlamydial genomes with two proteobacterial orders, the Rhizobiales and the Rickettsiales showed that genomes of different Rhizobiales families are much more similar than genomes of different Rickettsiales families. On the other hand, the chlamydial 16S rRNAs exhibit a higher sequence conservation than their Rickettsiales counterparts, while chlamydial proteins exhibit increased sequence divergence. Studying the diversity and genome plasticity of the entire Chlamydiae phylum is of major interest to better understand the emergence and evolution of this ubiquitous and ancient clade of obligate intracellular bacteria.
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Affiliation(s)
- Trestan Pillonel
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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Hyeon JY, Li S, Mann DA, Zhang S, Li Z, Chen Y, Deng X. Quasimetagenomics-Based and Real-Time-Sequencing-Aided Detection and Subtyping of Salmonella enterica from Food Samples. Appl Environ Microbiol 2018; 84:e02340-17. [PMID: 29196295 PMCID: PMC5795075 DOI: 10.1128/aem.02340-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 11/28/2017] [Indexed: 11/20/2022] Open
Abstract
Metagenomics analysis of food samples promises isolation-independent detection and subtyping of foodborne bacterial pathogens in a single workflow. The selective concentration of Salmonella genomic DNA by immunomagnetic separation (IMS) and multiple displacement amplification (MDA) shortened the time for culture enrichment of Salmonella-spiked raw chicken breast samples by over 12 h while permitting serotyping and high-fidelity single nucleotide polymorphism (SNP) typing of the pathogen using short shotgun sequencing reads. The herein-termed quasimetagenomics approach was evaluated on Salmonella-spiked lettuce and black peppercorn samples as well as retail chicken parts naturally contaminated with different serotypes of Salmonella Culture enrichment of between 8 and 24 h was required for detecting and subtyping naturally occurring Salmonella from unspiked chicken parts compared with 4- to 12-h culture enrichment when Salmonella-spiked food samples were analyzed, indicating the likely need for longer culture enrichment to revive low levels of stressed or injured Salmonella cells in food. A further acceleration of the workflow was achieved by real-time nanopore sequencing. After 1.5 h of analysis on a potable sequencer, sufficient data were generated from sequencing the IMS-MDA products of a cultured-enriched lettuce sample to enable serotyping and robust phylogenetic placement of the inoculated isolate.IMPORTANCE Both culture enrichment and next-generation sequencing remain time-consuming processes for food testing, whereas rapid methods for pathogen detection are widely available. Our study demonstrated a substantial acceleration of these processes by the use of immunomagnetic separation (IMS) with multiple displacement amplification (MDA) and real-time nanopore sequencing. In one example, the combined use of the two methods delivered a less than 24-h turnaround time from the collection of a Salmonella-contaminated lettuce sample to the phylogenetic identification of the pathogen. An improved efficiency such as this is important for further expanding the use of whole-genome and metagenomics sequencing in the microbial analysis of food. Our results suggest the potential of the quasimetagenomics approach in areas where rapid detection and subtyping of foodborne pathogens are important, such as for foodborne outbreak response and the precision tracking and monitoring of foodborne pathogens in production environments and supply chains.
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Affiliation(s)
- Ji-Yeon Hyeon
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, Georgia, USA
| | - Shaoting Li
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, Georgia, USA
| | - David A Mann
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, Georgia, USA
| | - Shaokang Zhang
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, Georgia, USA
| | - Zhen Li
- Washington State Department of Health, Public Health Laboratories, Shoreline, Washington, USA
| | - Yi Chen
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA
| | - Xiangyu Deng
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, Georgia, USA
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Versteeg B, Bruisten SM, Pannekoek Y, Jolley KA, Maiden MCJ, van der Ende A, Harrison OB. Genomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease. BMC Genomics 2018; 19:130. [PMID: 29426279 PMCID: PMC5810182 DOI: 10.1186/s12864-018-4522-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/31/2018] [Indexed: 12/02/2022] Open
Abstract
Background Chlamydia trachomatis (Ct) plasmid has been shown to encode genes essential for infection. We evaluated the population structure of Ct using whole-genome sequence data (WGS). In particular, the relationship between the Ct genome, plasmid and disease was investigated. Results WGS data from 157 Ct isolates deposited in the Chlamydiales pubMLST database (http://pubMLST.org/chlamydiales/) were annotated with 902 genes including the core and accessory genome. Plasmid associated genes were annotated and a plasmid MLST scheme was defined allowing plasmid sequence types to be determined. Plasmid allelic variation was investigated. Phylogenetic relationships were examined using the Genome Comparator tool available in pubMLST. Phylogenetic analyses identified four distinct Ct core genome clusters and six plasmid clusters, with a strong association between the chromosomal genotype and plasmid. This in turn was linked to ompA genovars and disease phenotype. Horizontal genetic transfer of plasmids was observed for three urogenital-associated isolates, which possessed plasmids more commonly found in isolates resulting from ocular infections. The pgp3 gene was identified as the most polymorphic plasmid gene and pgp4 was the most conserved. Conclusion A strong association between chromosomal genome, plasmid type and disease was observed, consistent with previous studies. This suggests co-evolution of the Ct chromosome and their plasmids, but we confirmed that plasmid transfer can occur between isolates. These data provide a better understanding of the genetic diversity occurring across the Ct genome in association with the plasmid content. Electronic supplementary material The online version of this article (10.1186/s12864-018-4522-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bart Versteeg
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands.
| | - Sylvia M Bruisten
- Public Health Laboratory, Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands.,Amsterdam Infection & Immunity Institute, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Yvonne Pannekoek
- Amsterdam Infection & Immunity Institute, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Keith A Jolley
- Peter Medawar building, Department of Zoology, University of Oxford, Oxford, UK
| | - Martin C J Maiden
- Peter Medawar building, Department of Zoology, University of Oxford, Oxford, UK
| | - Arie van der Ende
- Amsterdam Infection & Immunity Institute, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Odile B Harrison
- Peter Medawar building, Department of Zoology, University of Oxford, Oxford, UK
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Piñeiro L, Isaksson J, Zapico M, Cilla G, Herrmann B. Chlamydia trachomatis genotypes A and B from urogenital specimens of patients in Spain: molecular characterization. Clin Microbiol Infect 2018; 24:910.e5-910.e8. [PMID: 29427803 DOI: 10.1016/j.cmi.2018.01.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/11/2018] [Accepted: 01/23/2018] [Indexed: 01/10/2023]
Abstract
OBJECTIVES Chlamydia trachomatis ompA genotypes A and B, primarily associated with trachoma, were unexpectedly detected in urogenital samples of patients in Spain, a trachoma-free country. In this study, we aimed to explain this finding using analysis of organotropism-related genes and a multilocus sequence typing (MLST) technique. METHODS C. trachomatis genotypes A or B were detected in 8/930 (0.9%) infection episodes between 2006 and 2012. In these strains, organotropism-related genes (polymorphic membrane protein gene H, tryptophan synthase gene A, CTA0934, and cytotoxin) were studied. Further, the strains were analysed by MLST, using a polymerase chain reaction that amplifies five highly variable genomic loci (hctB, CT058, CT144, CT172, and pbpB). Amplicons were sequenced and phylogenetic analysis was conducted. RESULTS Seven strains were detected in the eight infection episodes (in one patient, an identical strain being found in two episodes). Analysis of organotropism-related genes showed that these strains shared genetic features characteristic of genitotropic genotypes but not of trachoma strains. Three strains of genotype A showed a unique and new MLST-sequence type (ST551, allele profile 8-8-2-27-69). The four strains of genotype B belonged to ST138. CONCLUSIONS C. trachomatis ompA genotypes A and B associated with trachoma, but detected sporadically in urogenital samples in trachoma-free countries, may be the result of recombination between strains adapted to trachoma and strains adapted to sexual transmission.
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Affiliation(s)
- L Piñeiro
- Microbiology Department, Hospital Universitario Donostia-Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain.
| | - J Isaksson
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - M Zapico
- Microbiology Department, Hospital Universitario Donostia-Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain
| | - G Cilla
- Microbiology Department, Hospital Universitario Donostia-Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain; Biomedical Research Centre Network for Respiratory Diseases (CIBERES), San Sebastián, Spain
| | - B Herrmann
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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Abstract
The expanding field of bacterial genomics has revolutionized our understanding of microbial diversity, biology and phylogeny. For most species, DNA extracted from culture material is used as the template for genome sequencing; however, the majority of microbes are actually uncultivable, and others, such as obligate intracellular bacteria, require laborious tissue culture to yield sufficient genomic material for sequencing. Chlamydiae are one such group of obligate intracellular microbes whose characterization has been hampered by this requirement. To circumvent these challenges, researchers have developed culture-independent sample preparation methods that can be applied to the sample directly or to genomic material extracted from the sample. These methods, which encompass both targeted [immunomagnetic separation-multiple displacement amplification (IMS-MDA) and sequence capture] and non-targeted approaches (host methylated DNA depletion-microbial DNA enrichment and cell-sorting-MDA), have been applied to a range of clinical and environmental samples to generate whole genomes of novel chlamydial species and strains. This review aims to provide an overview of the application, advantages and limitations of these targeted and non-targeted approaches in the chlamydial context. The methods discussed also have broad application to other obligate intracellular bacteria or clinical and environmental samples.
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Affiliation(s)
- Alyce Taylor-Brown
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Australia
| | - Danielle Madden
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Australia
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Australia
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Smelov V, Vrbanac A, van Ess EF, Noz MP, Wan R, Eklund C, Morgan T, Shrier LA, Sanders B, Dillner J, de Vries HJC, Morre SA, Dean D. Chlamydia trachomatis Strain Types Have Diversified Regionally and Globally with Evidence for Recombination across Geographic Divides. Front Microbiol 2017; 8:2195. [PMID: 29180986 PMCID: PMC5693916 DOI: 10.3389/fmicb.2017.02195] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/25/2017] [Indexed: 11/17/2022] Open
Abstract
Chlamydia trachomatis (Ct) is the leading cause of bacterial sexually transmitted diseases worldwide. The Ct Multi Locus Sequence Typing (MLST) scheme is effective in differentiating strain types (ST), deciphering transmission patterns and treatment failure, and identifying recombinant strains. Here, we analyzed 323 reference and clinical samples, including 58 samples from Russia, an area that has not previously been represented in Ct typing schemes, to expand our knowledge of the global diversification of Ct STs. The 323 samples resolved into 84 unique STs, a 3.23 higher typing resolution compared to the gold standard single locus ompA genotyping. Our MLST scheme showed a high discriminatory index, D, of 0.98 (95% CI 0.97-0.99) confirming the validity of this method for typing. Phylogenetic analyses revealed distinct branches for the phenotypic diseases of lymphogranuloma venereum, urethritis and cervicitis, and a sub-branch for ocular trachoma. Consistent with these findings, single nucleotide polymorphisms were identified that significantly correlated with each phenotype. While the overall number of unique STs per region was comparable across geographies, the number of STs was greater for Russia with a significantly higher ST/sample ratio of 0.45 (95% CI: 0.35-0.53) compared to Europe or the Americas (p < 0.009), which may reflect a higher level of sexual mixing with the introduction of STs from other regions and/or reassortment of alleles. Four STs were found to be significantly associated with a particular geographic region. ST23 [p = 0.032 (95% CI: 1-23)], ST34 [p = 0.019 (95% CI: 1.1-25)]; and ST19 [p = 0.001 (95% CI: 1.7-34.7)] were significantly associated with Netherlands compared to Russia or the Americas, while ST 30 [p = 0.031 (95% CI: 1.1-17.8)] was significantly associated with the Americas. ST19 was significantly associated with Netherlands and Russia compared with the Americans [p = 0.001 (95% CI: 1.7-34.7) and p = 0.006 (95% CI: 1.5-34.6), respectively]. Additionally, recombinant strains were ubiquitous in the data set [106 (32.8%)], although Europe had a significantly higher number than Russia or the Americas (p < 0.04), the majority of which were from Amsterdam [43 (87.8%) of 49)]. The higher number of recombinants in Europe indicates selective pressure and/or adaptive diversification that will require additional studies to elucidate.
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Affiliation(s)
- Vitaly Smelov
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- Karolinska Institute, Stockholm, Sweden
- North-Western State Medical University named after I.I. Mechnikov, St. Petersburg, Russia
| | - Alison Vrbanac
- UCSF Benioff Children’s Hospital Oakland Research Institute, Oakland, CA, United States
| | - Eleanne F. van Ess
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, Netherlands
| | - Marlies P. Noz
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, Netherlands
| | - Raymond Wan
- UCSF Benioff Children’s Hospital Oakland Research Institute, Oakland, CA, United States
| | | | - Tyler Morgan
- UCSF Benioff Children’s Hospital Oakland Research Institute, Oakland, CA, United States
| | - Lydia A. Shrier
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
| | - Blake Sanders
- UCSF Benioff Children’s Hospital Oakland Research Institute, Oakland, CA, United States
| | | | - Henry J. C. de Vries
- Center for Infection and Immunology Amsterdam, Academic Medical Center, Amsterdam, Netherlands
- Department of Dermatology, Academic Medical Center, Amsterdam, Netherlands
- STI Outpatient Clinic, Public Health Service of Amsterdam (GGD Amsterdam), Amsterdam, Netherlands
| | - Servaas A. Morre
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, Netherlands
- Institute of Public Health Genomics, Department of Genetics and Cell Biology, Research Institute GROW (School for Oncology and Developmental Biology), Faculty of Health, Medicine and Life Sciences, University of Maastricht, Maastricht, Netherlands
| | - Deborah Dean
- UCSF Benioff Children’s Hospital Oakland Research Institute, Oakland, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
- Department of Bioengineering, University of California, San Francisco, San Francisco, CA, United States
- Departments of Medicine and Pediatrics, University of California, San Francisco, San Francisco, CA, United States
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Tagini F, Greub G. Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review. Eur J Clin Microbiol Infect Dis 2017; 36:2007-2020. [PMID: 28639162 PMCID: PMC5653721 DOI: 10.1007/s10096-017-3024-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/22/2017] [Indexed: 12/11/2022]
Abstract
In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. Herein, we reviewed the literature on the use of WGS for the most commonly encountered pathogens in clinical microbiology laboratories: Escherichia coli and other Enterobacteriaceae, Staphylococcus aureus and coagulase-negative staphylococci, streptococci and enterococci, mycobacteria and Chlamydia trachomatis. For each pathogen group, we focused on five different aspects: the genome characteristics, the most common genomic approaches and the clinical uses of WGS for (i) typing and outbreak analysis, (ii) virulence investigation and (iii) in silico antimicrobial susceptibility testing. Of all the clinical usages, the most frequent and straightforward usage was to type bacteria and to trace outbreaks back. A next step toward standardisation was made thanks to the development of several new genome-wide multi-locus sequence typing systems based on WGS data. Although virulence characterisation could help in various particular clinical settings, it was done mainly to describe outbreak strains. An increasing number of studies compared genotypic to phenotypic antibiotic susceptibility testing, with mostly promising results. However, routine implementation will preferentially be done in the workflow of particular pathogens, such as mycobacteria, rather than as a broadly applicable generic tool. Overall, concrete uses of WGS in routine clinical microbiology or infection control laboratories were done, but the next big challenges will be the standardisation and validation of the procedures and bioinformatics pipelines in order to reach clinical standards.
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Affiliation(s)
- F Tagini
- Institute of Microbiology, Department of Laboratory, University of Lausanne & University Hospital, Lausanne, Switzerland
| | - G Greub
- Institute of Microbiology, Department of Laboratory, University of Lausanne & University Hospital, Lausanne, Switzerland.
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40
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Sadhasivam A, Vetrivel U. Genome-wide codon usage profiling of ocular infective Chlamydia trachomatis serovars and drug target identification. J Biomol Struct Dyn 2017. [PMID: 28627970 DOI: 10.1080/07391102.2017.1343685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Chlamydia trachomatis (C.t) is a Gram-negative obligate intracellular bacteria and is a major causative of infectious blindness and sexually transmitted diseases. Among the varied serovars of this organism, A, B and C are reported as prominent ocular pathogens. Genomic studies of these strains shall aid in deciphering potential drug targets and genomic influence on pathogenesis. Hence, in this study we performed deep statistical profiling of codon usage in these serovars. The overall base composition analysis reveals that these serovars are over biased to AU than GC. Similarly, relative synonymous codon usage also showed preference towards A/U ending codons. Parity Rule 2 analysis inferred unequal distribution of AT and GC, indicative of other unknown factors acting along with mutational pressure to influence codon usage bias (CUB). Moreover, absolute quantification of CUB also revealed lower bias across these serovars. The effect of natural selection on CUB was also confirmed by neutrality plot, reinforcing natural selection under mutational pressure turned to be a pivotal role in shaping the CUB in the strains studied. Correspondence analysis (COA) clarified that, C.t C/TW-3 to show a unique trend in codon usage variation. Host influence analysis on shaping the codon usage pattern also inferred some speculative relativity. In a nutshell, our finding suggests that mutational pressure is the dominating factor in shaping CUB in the strains studied, followed by natural selection. We also propose potential drug targets based on cumulative analysis of strand bias, CUB and human non-homologue screening.
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Affiliation(s)
- Anupriya Sadhasivam
- a Centre for Bioinformatics , Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya , Chennai 600 006 , Tamil Nadu , India
| | - Umashankar Vetrivel
- a Centre for Bioinformatics , Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya , Chennai 600 006 , Tamil Nadu , India
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41
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Abstract
Recent advances in genome sequencing of single microbial cells enable the assignment of functional roles to members of the human microbiome that cannot currently be cultured. This approach can reveal the genomic basis of phenotypic variation between closely related strains and can be applied to the targeted study of immunogenic bacteria in disease.
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Affiliation(s)
- Andrew C Tolonen
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA. .,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA. .,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA. .,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, 02139, USA.
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42
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Hadfield J, Harris SR, Seth-Smith HMB, Parmar S, Andersson P, Giffard PM, Schachter J, Moncada J, Ellison L, Vaulet MLG, Fermepin MR, Radebe F, Mendoza S, Ouburg S, Morré SA, Sachse K, Puolakkainen M, Korhonen SJ, Sonnex C, Wiggins R, Jalal H, Brunelli T, Casprini P, Pitt R, Ison C, Savicheva A, Shipitsyna E, Hadad R, Kari L, Burton MJ, Mabey D, Solomon AW, Lewis D, Marsh P, Unemo M, Clarke IN, Parkhill J, Thomson NR. Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion. Genome Res 2017; 27:1220-1229. [PMID: 28588068 PMCID: PMC5495073 DOI: 10.1101/gr.212647.116] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 04/27/2017] [Indexed: 01/26/2023]
Abstract
Chlamydia trachomatis is the world's most prevalent bacterial sexually transmitted infection and leading infectious cause of blindness, yet it is one of the least understood human pathogens, in part due to the difficulties of in vitro culturing and the lack of available tools for genetic manipulation. Genome sequencing has reinvigorated this field, shedding light on the contemporary history of this pathogen. Here, we analyze 563 full genomes, 455 of which are novel, to show that the history of the species comprises two phases, and conclude that the currently circulating lineages are the result of evolution in different genomic ecotypes. Temporal analysis indicates these lineages have recently expanded in the space of thousands of years, rather than the millions of years as previously thought, a finding that dramatically changes our understanding of this pathogen's history. Finally, at a time when almost every pathogen is becoming increasingly resistant to antimicrobials, we show that there is no evidence of circulating genomic resistance in C. trachomatis.
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Affiliation(s)
- James Hadfield
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Simon R Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Helena M B Seth-Smith
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Surendra Parmar
- Public Health England, Public Health Laboratory Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QW, United Kingdom
| | - Patiyan Andersson
- Menzies School of Health Research, Darwin, Northern Territory 0810, Australia
| | - Philip M Giffard
- Menzies School of Health Research, Darwin, Northern Territory 0810, Australia.,School of Psychological and Clinical Sciences, Charles Darwin University, Darwin 0909, Australia
| | - Julius Schachter
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California 94110, USA
| | - Jeanne Moncada
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California 94110, USA
| | - Louise Ellison
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - María Lucía Gallo Vaulet
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Microbiología Clínica, Buenos Aires C1113AAD, Argentina
| | - Marcelo Rodríguez Fermepin
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Microbiología Clínica, Buenos Aires C1113AAD, Argentina
| | - Frans Radebe
- Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, National Health Laboratory Service, 2192 Johannesburg, South Africa
| | - Suyapa Mendoza
- Jefe Laboratorio de ITS, Laboratorio Nacional de Vigilancia, FM1100, Honduras
| | - Sander Ouburg
- Department of Medical Microbiology and Infection Control, Laboratory of Immunogenetics, VU University Medical Center, 1081 HZ Amsterdam, The Netherlands
| | - Servaas A Morré
- Department of Medical Microbiology and Infection Control, Laboratory of Immunogenetics, VU University Medical Center, 1081 HZ Amsterdam, The Netherlands.,Department of Genetics and Cell Biology, Institute of Public Health Genomics, School for Oncology & Developmental Biology (GROW), Faculty of Health, Medicine and Life Sciences, University of Maastricht, 6229 ER Maastricht, The Netherlands
| | - Konrad Sachse
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), 07743 Jena, Germany
| | - Mirja Puolakkainen
- Department of Virology, University of Helsinki and Helsinki University Hospital, University of Helsinki, 00014 Helsinki, Finland
| | - Suvi J Korhonen
- Department of Virology, University of Helsinki and Helsinki University Hospital, University of Helsinki, 00014 Helsinki, Finland
| | - Chris Sonnex
- Public Health England, Public Health Laboratory Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QW, United Kingdom
| | - Rebecca Wiggins
- Department of Biology, University of York, York CB2 2QQ, United Kingdom
| | - Hamid Jalal
- Public Health England, Public Health Laboratory Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QW, United Kingdom
| | - Tamara Brunelli
- Clinical Chemistry and Microbiology Laboratory, Santo Stefano Hospital, ASL4, 59100 Prato, Italy
| | - Patrizia Casprini
- Clinical Chemistry and Microbiology Laboratory, Santo Stefano Hospital, ASL4, 59100 Prato, Italy
| | - Rachel Pitt
- Sexually Transmitted Bacteria Reference Unit, Microbiological Services, Public Health England, London NW9 5HT, United Kingdom
| | - Cathy Ison
- Sexually Transmitted Bacteria Reference Unit, Microbiological Services, Public Health England, London NW9 5HT, United Kingdom
| | - Alevtina Savicheva
- Laboratory of Microbiology, D.O. Ott Research Institute of Obstetrics and Gynecology, St. Petersburg, Russia 199034
| | - Elena Shipitsyna
- Laboratory of Microbiology, D.O. Ott Research Institute of Obstetrics and Gynecology, St. Petersburg, Russia 199034.,WHO Collaborating Centre for Gonorrhoea and other STIs, Faculty of Medicine and Health, Örebro University Hospital, SE-701 85 Örebro, Sweden
| | - Ronza Hadad
- WHO Collaborating Centre for Gonorrhoea and other STIs, Faculty of Medicine and Health, Örebro University Hospital, SE-701 85 Örebro, Sweden
| | - Laszlo Kari
- Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, USA
| | - Matthew J Burton
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - David Mabey
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Anthony W Solomon
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - David Lewis
- Centre for HIV and Sexually Transmitted Infections, National Institute for Communicable Diseases, National Health Laboratory Service, 2192 Johannesburg, South Africa.,Centre for Infectious Diseases and Microbiology and Marie Bashir Institute for Infectious Diseases and Biosecurity, Westmead Clinical School, University of Sydney, Sydney 2192, Australia
| | - Peter Marsh
- Public Health England, Public Health Laboratory Southampton, Southampton General Hospital, Southampton SO16 6YD, United Kingdom
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, Faculty of Medicine and Health, Örebro University Hospital, SE-701 85 Örebro, Sweden
| | - Ian N Clarke
- Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton SO16 6YD, United Kingdom
| | - Julian Parkhill
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Nicholas R Thomson
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.,Department of Pathogen Molecular Biology, The London School of Hygiene and Tropical Medicine, London WC1 7HT, United Kingdom
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43
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Hyeon JY, Deng X. Rapid detection of Salmonella in raw chicken breast using real-time PCR combined with immunomagnetic separation and whole genome amplification. Food Microbiol 2017; 63:111-116. [DOI: 10.1016/j.fm.2016.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 11/11/2016] [Accepted: 11/15/2016] [Indexed: 01/30/2023]
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44
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Rawre J, Juyal D, Dhawan B. Molecular typing of Chlamydia trachomatis: An overview. Indian J Med Microbiol 2017; 35:17-26. [PMID: 28303813 DOI: 10.4103/ijmm.ijmm_16_341] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Urogenital infection due to Chlamydia trachomatis (CT) is one of the most common bacterial sexually transmitted infections (STIs) and is a major public health problem worldwide. Molecular characterisation of CT is important for understanding the pathophysiological mechanisms of chlamydial disease and its transmission dynamics in sexual networks. Traditionally, strain typing of CT was based on serotyping methods characterising the major outer membrane protein (MOMP). With the advent of polymerase chain reaction and sequencing the era of molecular typing began. Molecular characterization of CT strains is based on sequence analysis of ompA gene encoding MOMP. However, in due course of time, improvements were made to enhance the discriminatory power of sequencing and quality of epidemiological information. New high-resolution genotyping methods using multiple loci such as multilocus sequence typing (MLST) and multiple loci variable number of tandem repeats (MLVA) were developed but were unable to differentiate mixed infections (MIs). The development of DNA-hybridisation methods emerged as a major breakthrough in detecting MIs. Although MLST and MLVA are more discriminative than other genotyping methods, they are laborious and expensive. DNA microarray technique is an affordable alternative for genotyping. Since recombination is widespread in the CT genome, ompA is not a reliable marker for phylogenetic studies; hence, whole genome sequencing may provide maximum phylogenetic resolution of CT strains. A descriptive review is provided of the various molecular CT typing methods. The vital information gained can be used for formulating screening programmes, targeted prevention and optimising therapeutic measures aiming to reduce disease transmission.
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Affiliation(s)
- Jyoti Rawre
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Deepak Juyal
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Benu Dhawan
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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45
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Taylor-Brown A, Pillonel T, Bridle A, Qi W, Bachmann NL, Miller TL, Greub G, Nowak B, Seth-Smith HMB, Vaughan L, Polkinghorne A. Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilized by these intracellular bacteria. Environ Microbiol 2017; 19:1899-1913. [PMID: 28205377 DOI: 10.1111/1462-2920.13694] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/02/2017] [Accepted: 02/07/2017] [Indexed: 12/12/2022]
Abstract
Several Chlamydiales families are associated with epitheliocystis, a common condition of the fish gill epithelium. These families share common ancestors with the Chlamydiaceae and environmental Chlamydiae. Due to the lack of culture systems, little is known about the biology of these chlamydial fish pathogens. We investigated epitheliocystis in cultured Orange-spotted grouper (Epinephelus coioides) from North Queensland, Australia. Basophilic inclusions were present in the gills of 22/31 fish and the presence of the chlamydial pathogen in the cysts was confirmed by in situ hybridization. Giant grouper (Epinephelus lanceolatus) cultured in the same systems were epitheliocystis free. 16S rRNA gene sequencing revealed a novel member of the Candidatus Parilichlamydiaceae: Ca. Similichlamydia epinephelii. Using metagenomic approaches, we obtained an estimated 68% of the chlamydial genome, revealing that this novel chlamydial pathogen shares a number of key pathogenic hallmarks with the Chlamydiaceae, including an intact Type III Secretion system and several chlamydial virulence factors. This provides additional evidence that these pathogenic mechanisms were acquired early in the evolution of this unique bacterial phylum. The identification and genomic characterization of Ca. S. epinephelii provides new opportunities to study the biology of distantly-related chlamydial pathogens while shining a new light on the evolution of pathogenicity of the Chlamydiaceae.
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Affiliation(s)
- Alyce Taylor-Brown
- Centre for Animal Health Innovation, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
| | - Trestan Pillonel
- Institute of Microbiology, University of Lausanne, Lausanne, CH-1011, Switzerland
| | - Andrew Bridle
- Institute of Marine and Antarctic Studies, University of Tasmania, Newnham, Tasmania, 7248, Australia
| | - Weihong Qi
- Functional Genomics Centre, University of Zurich, Zurich, CH-8057, Switzerland
| | - Nathan L Bachmann
- Centre for Animal Health Innovation, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
| | - Terrence L Miller
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Marine and Environmental Sciences, James Cook University, Cairns, Queensland, 4878, Australia
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne, Lausanne, CH-1011, Switzerland
| | - Barbara Nowak
- Institute of Marine and Antarctic Studies, University of Tasmania, Newnham, Tasmania, 7248, Australia
| | - Helena M B Seth-Smith
- Functional Genomics Centre, University of Zurich, Zurich, CH-8057, Switzerland.,Institute of Veterinary Pathology, University of Zurich, Zurich, CH-8057, Switzerland
| | - Lloyd Vaughan
- Institute of Veterinary Pathology, University of Zurich, Zurich, CH-8057, Switzerland
| | - Adam Polkinghorne
- Centre for Animal Health Innovation, Faculty of Science, Engineering and Education, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
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46
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Battilani M, De Arcangeli S, Balboni A, Dondi F. Genetic diversity and molecular epidemiology of Anaplasma. INFECTION GENETICS AND EVOLUTION 2017; 49:195-211. [PMID: 28122249 DOI: 10.1016/j.meegid.2017.01.021] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 01/18/2017] [Accepted: 01/19/2017] [Indexed: 11/25/2022]
Abstract
Anaplasma are obligate intracellular bacteria of cells of haematopoietic origin and are aetiological agents of tick-borne diseases of both veterinary and medical interest common in both tropical and temperate regions. The recent disclosure of their zoonotic potential has greatly increased interest in the study of these bacteria, leading to the recent reorganisation of Rickettsia taxonomy and to the possible discovery of new species belonging to the genus Anaplasma. This review is particularly focused on the common and unique characteristics of Anaplasma marginale and Anaplasma phagocytophilum, with an emphasis on genetic diversity and evolution, and the main distinguishing features of the diseases caused by the different Anaplasma spp. are described as well.
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Affiliation(s)
- Mara Battilani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum - University of Bologna, Via Tolara di Sopra, 50, 40064 Ozzano Emilia, Bo, Italy.
| | - Stefano De Arcangeli
- Department of Veterinary Medical Sciences, Alma Mater Studiorum - University of Bologna, Via Tolara di Sopra, 50, 40064 Ozzano Emilia, Bo, Italy
| | - Andrea Balboni
- Department of Veterinary Medical Sciences, Alma Mater Studiorum - University of Bologna, Via Tolara di Sopra, 50, 40064 Ozzano Emilia, Bo, Italy
| | - Francesco Dondi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum - University of Bologna, Via Tolara di Sopra, 50, 40064 Ozzano Emilia, Bo, Italy
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47
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Brown AC, Christiansen MT. Whole-Genome Enrichment Using RNA Probes and Sequencing of Chlamydia trachomatis Directly from Clinical Samples. Methods Mol Biol 2017; 1616:1-22. [PMID: 28600759 DOI: 10.1007/978-1-4939-7037-7_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography, and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the requirement for in vitro culturing, is attractive in terms of time- and labor-saving, especially in the case of slow-growing, or obligate intracellular pathogens, such as Chlamydia trachomatis. However clinical samples typically contain too low levels of pathogen nucleic acid, plus relatively high levels of human and natural microbiota DNA/RNA, to make this a viable option. Using a combination of whole-genome enrichment and deep sequencing, which has been proven to be a non-mutagenic approach, we can capture all known variations found within C. trachomatis genomes. The method is a consistent and sensitive tool that enables rapid whole-genome sequencing of C. trachomatis directly from clinical samples and has the potential to be adapted to other pathogens with a similar clonal nature.
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Affiliation(s)
- Amanda Claire Brown
- Oxford Gene Technology, Oxford, OX5 1PF, UK.
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, 14853, USA.
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48
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Miller RR, Uyaguari-Diaz M, McCabe MN, Montoya V, Gardy JL, Parker S, Steiner T, Hsiao W, Nesbitt MJ, Tang P, Patrick DM. Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects. PLoS One 2016; 11:e0165691. [PMID: 27806082 PMCID: PMC5091812 DOI: 10.1371/journal.pone.0165691] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/17/2016] [Indexed: 12/24/2022] Open
Abstract
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating disease causing indefinite fatigue. ME/CFS has long been hypothesised to have an infectious cause; however, no specific infectious agent has been identified. We used metagenomics to analyse the RNA from plasma samples from 25 individuals with ME/CFS and compare their microbial content to technical controls as well as three control groups: individuals with alternatively diagnosed chronic Lyme syndrome (N = 13), systemic lupus erythematosus (N = 11), and healthy controls (N = 25). We found that the majority of sequencing reads were removed during host subtraction, thus there was very low microbial RNA content in the plasma. The effects of sample batching and contamination during sample processing proved to outweigh the effects of study group on microbial RNA content, as the few differences in bacterial or viral RNA abundance we did observe between study groups were most likely caused by contamination and batch effects. Our results highlight the importance of including negative controls in all metagenomic analyses, since there was considerable overlap between bacterial content identified in study samples and control samples. For example, Proteobacteria, Firmicutes, Actinobacteria, and Bacteriodes were found in both study samples and plasma-free negative controls. Many of the taxonomic groups we saw in our plasma-free negative control samples have previously been associated with diseases, including ME/CFS, demonstrating how incorrect conclusions may arise if controls are not used and batch effects not accounted for.
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Affiliation(s)
- Ruth R. Miller
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Miguel Uyaguari-Diaz
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Mark N. McCabe
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Vincent Montoya
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Jennifer L. Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Shoshana Parker
- Centre for Health Evaluation and Outcome Sciences, Vancouver, British Columbia, Canada
| | - Theodore Steiner
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - William Hsiao
- British Columbia Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - David M. Patrick
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- * E-mail:
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Culture-independent genomic characterisation of Candidatus Chlamydia sanzinia, a novel uncultivated bacterium infecting snakes. BMC Genomics 2016; 17:710. [PMID: 27595750 PMCID: PMC5011893 DOI: 10.1186/s12864-016-3055-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent molecular studies have revealed considerably more diversity in the phylum Chlamydiae than was previously thought. Evidence is growing that many of these novel chlamydiae may be important pathogens in humans and animals. A significant barrier to characterising these novel chlamydiae is the requirement for culturing. We recently identified a range of novel uncultured chlamydiae in captive snakes in Switzerland, however, nothing is known about their biology. Using a metagenomics approach, the aim of this study was to characterise the genome of a novel chlamydial taxon from the choana of a captive snake. In doing so, we propose a new candidate species in the genus Chlamydia (Candidatus Chlamydia sanzinia) and reveal new information about the biological diversity of this important group of pathogens. RESULTS We identified two chlamydial genomic contigs: a 1,113,073 bp contig, and a 7,504 bp contig, representing the chromosome and plasmid of Ca. Chlamydia sanzinia strain 2742-308, respectively. The 998 predicted coding regions include an expanded repertoire of outer membrane proteins (Pmps and Omps), some of which exhibited frameshift mutations, as well as several chlamydial virulence factors such as the translocating actin-recruitment phosphoprotein (Tarp) and macrophage inhibition potentiator (Mip). A suite of putative inclusion membrane proteins were also predicted. Notably, no evidence of a traditional chlamydial plasticity zone was identified. Phylogenetically, Ca. Chlamydia sanzinia forms a clade with C. pneumoniae and C. pecorum, distinct from former "Chlamydophila" species. CONCLUSIONS Genomic characterisation of a novel uncultured chlamydiae from the first reptilian host has expanded our understanding of the diversity and biology of a genus that was thought to be the most well-characterised in this unique phylum. It is anticipated that this method will be suitable for characterisation of other novel chlamydiae.
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Gharsallah H, Bom RJM, Bruisten SM, Himschoot M, Frikha-Gargouri O, Hammami A. Identification of a dominant Chlamydia trachomatis strain in patients attending sexual transmitted infection clinic and female sex workers in Tunisia using a high resolution typing method. INFECTION GENETICS AND EVOLUTION 2016; 44:444-449. [PMID: 27497657 DOI: 10.1016/j.meegid.2016.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 07/11/2016] [Accepted: 08/03/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND The distribution of Chlamydia trachomatis genotypes in Tunisia was previously studied using the reverse hybridization method. In this study, we used multilocus sequence typing (MLST) to describe Chlamydia trachomatis genetic diversity among heterosexual populations in Tunisia. The obtained sequence types (STs) were compared with those from a heterosexual population from Amsterdam, the Netherlands. METHODS Clinical Tunisian patients and female sex workers provided 107 Chlamydia trachomatis positive samples that were used for MLST. Samples from 256 heterosexuals visiting the Amsterdam STI clinic were included as a reference group. Six highly variable genetic regions including the ompA gene were amplified and sequenced. The ST numbers were derived from a Chlamydia typing database (http://mlstdb.uu.se) and used to draw minimum spanning trees. RESULTS ompA sequencing detected 7 genotypes among the Tunisian populations of which genotype E was the most prevalent (66.3%). This genotype E resolved into 23 different STs and among these the ST3 was predominant (53.5%). MLST displayed 43 STs, of which 28 (65%) were new in the database. Minimum spanning tree analysis of all Tunisian samples identified 4 clusters of which one formed a clonal cluster with samples presenting the most prevalent ST3. When comparing samples from the Tunisian and Dutch populations in one minimum spanning tree, there was little overlap between the Chlamydia trachomatis samples. CONCLUSION The CT-hrMLST scheme allowed us to identify that the Tunisian distribution was dominated by one genotype E (ST3) strain which is also highly prevalent in many other countries worldwide.
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Affiliation(s)
- Houda Gharsallah
- Department of Microbiology and research laboratory "Microorganismes et Pathologies Humaines", Habib Bourguiba University Hospital, Medical School of Sfax, Avenue Majida Boulila 3000, University of Sfax, Tunisia.
| | - Reinier J M Bom
- Public Health Laboratory, Public Health Service of Amsterdam (GGD Amsterdam), Nieuwe Achtergracht 100, 1018 WT Amsterdam, The Netherlands.
| | - Sylvia M Bruisten
- Public Health Laboratory, Public Health Service of Amsterdam (GGD Amsterdam), Nieuwe Achtergracht 100, 1018 WT Amsterdam, The Netherlands.
| | - Michelle Himschoot
- Public Health Laboratory, Public Health Service of Amsterdam (GGD Amsterdam), Nieuwe Achtergracht 100, 1018 WT Amsterdam, The Netherlands.
| | - Olfa Frikha-Gargouri
- Department of Microbiology and research laboratory "Microorganismes et Pathologies Humaines", Habib Bourguiba University Hospital, Medical School of Sfax, Avenue Majida Boulila 3000, University of Sfax, Tunisia; Biopesticides Team, Centre of Biotechnology of Sfax, Road of Sidi Mansour Km 6, 3018 Sfax, Tunisia.
| | - Adnene Hammami
- Department of Microbiology and research laboratory "Microorganismes et Pathologies Humaines", Habib Bourguiba University Hospital, Medical School of Sfax, Avenue Majida Boulila 3000, University of Sfax, Tunisia.
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