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Islam Sajib MS, Brunker K, Oravcova K, Everest P, Murphy ME, Forde T. Advances in Host Depletion and Pathogen Enrichment Methods for Rapid Sequencing-Based Diagnosis of Bloodstream Infection. J Mol Diagn 2024; 26:741-753. [PMID: 38925458 DOI: 10.1016/j.jmoldx.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/05/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
Bloodstream infection is a major cause of morbidity and death worldwide. Timely and appropriate treatment can reduce mortality among critically ill patients. Current diagnostic methods are too slow to inform precise antibiotic choice, leading to the prescription of empirical antibiotics, which may fail to cover the resistance profile of the pathogen, risking poor patient outcomes. Additionally, overuse of broad-spectrum antibiotics may lead to more resistant organisms, putting further pressure on the dwindling pipeline of antibiotics, and risk transmission of these resistant organisms in the health care environment. Therefore, rapid diagnostics are urgently required to better inform antibiotic choice early in the course of treatment. Sequencing offers great promise in reducing time to microbiological diagnosis; however, the amount of host DNA compared with the pathogen in patient samples presents a significant obstacle. Various host-depletion and bacterial-enrichment strategies have been used in samples, such as saliva, urine, or tissue. However, these methods have yet to be collectively integrated and/or extensively explored for rapid bloodstream infection diagnosis. Although most of these workflows possess individual strengths, their lack of analytical/clinical sensitivity and/or comprehensiveness demands additional improvements or synergistic application. This review provides a distinctive classification system for various methods based on their working principles to guide future research, and discusses their strengths and limitations and explores potential avenues for improvement to assist the reader in workflow selection.
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Affiliation(s)
- Mohammad S Islam Sajib
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom.
| | - Kirstyn Brunker
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom; Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Katarina Oravcova
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Paul Everest
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Michael E Murphy
- Department of Microbiology, National Health Service Greater Glasgow and Clyde, Glasgow, United Kingdom; School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, United Kingdom
| | - Taya Forde
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
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2
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Salazar JC, Vargas-Cely F, García-Luna JA, Ramirez LG, Bettin EB, Romero-Rosas N, Amórtegui MF, Silva S, Oviedo O, Vigil J, La Vake CJ, Galindo X, Ramirez JD, Martínez-Valencia AJ, Caimano MJ, Hennelly CM, Aghakhanian F, Moody MA, Seña AC, Parr JB, Hawley KL, López-Medina E, Radolf JD. Treponema pallidum genetic diversity and its implications for targeted vaccine development: A cross-sectional study of early syphilis cases in Southwestern Colombia. PLoS One 2024; 19:e0307600. [PMID: 39028747 PMCID: PMC11259262 DOI: 10.1371/journal.pone.0307600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 07/02/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Venereal syphilis, caused by the spirochete Treponema pallidum subsp. pallidum (TPA), is surging worldwide, underscoring the need for a vaccine with global efficacy. Vaccine development requires an understanding of syphilis epidemiology and clinical presentation as well as genomic characterization of TPA strains circulating within at-risk populations. The aim of this study was to describe the clinical, demographic, and molecular features of early syphilis cases in Cali, Colombia. METHODS AND FINDINGS We conducted a cross-sectional study to identify individuals with early syphilis (ES) in Cali, Colombia through a city-wide network of public health centers, private sector HIV clinics and laboratory databases from public health institutions. Whole blood (WB), skin biopsies (SB), and genital and oral lesion swabs were obtained for measurement of treponemal burdens by polA quantitative polymerase chain reaction (qPCR) and for whole-genome sequencing (WGS). Among 1,966 individuals screened, 128 participants met enrollment criteria: 112 (87%) with secondary (SS), 15 (12%) with primary (PS) and one with early latent syphilis; 66/128 (52%) self-reported as heterosexual, while 48 (38%) were men who have sex with men (MSM). Genital ulcer swabs had the highest polA copy numbers (67 copies/μl) by qPCR with a positivity rate (PR) of 73%, while SS lesions had 42 polA copies/μl with PR of 62%. WB polA positivity was more frequent in SS than PS (42% vs 7%, respectively; p = 0.009). Isolation of TPA from WB by rabbit infectivity testing (RIT) was achieved in 5 (56%) of 9 ES WB samples tested. WGS from 33 Cali patient samples, along with 10 other genomic sequences from South America (9 from Peru, 1 from Argentina) used as comparators, confirmed that SS14 was the predominant clade, and that half of all samples had mutations associated with macrolide (i.e., azithromycin) resistance. Variability in the outer membrane protein (OMP) and vaccine candidate BamA (TP0326) was mapped onto the protein's predicted structure from AlphaFold. Despite the presence of mutations in several extracellular loops (ECLs), ECL4, an immunodominant loop and proven opsonic target, was highly conserved in this group of Colombian and South American TPA isolates. CONCLUSIONS This study offers new insights into the sociodemographic and clinical features of venereal syphilis in a highly endemic area of Colombia and illustrates how genomic sequencing of regionally prevalent TPA strains can inform vaccine development.
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Affiliation(s)
- Juan C. Salazar
- Department of Pediatrics, University of Connecticut School of Medicine, Farmington, CT, United States of America
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, United States of America
- Division of Infectious Diseases, Connecticut Children’s, Hartford, CT, United States of America
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
| | - Fabio Vargas-Cely
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
| | - Jonny A. García-Luna
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
- Universidad ICESI, Cali, Colombia
- Division of Dermatology, School of Medicine, Universidad del Valle, Cali, Colombia
| | - Lady G. Ramirez
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
- Universidad ICESI, Cali, Colombia
| | - Everton B. Bettin
- Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, United States of America
| | - Nelson Romero-Rosas
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
| | - María F. Amórtegui
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
| | - Sebastián Silva
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
| | - Oscar Oviedo
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
| | - Julie Vigil
- Department of Pediatrics, University of Connecticut School of Medicine, Farmington, CT, United States of America
| | - Carson J. La Vake
- Department of Pediatrics, University of Connecticut School of Medicine, Farmington, CT, United States of America
| | | | - Jose D. Ramirez
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
| | - Alvaro J. Martínez-Valencia
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
- Universidad ICESI, Cali, Colombia
| | - Melissa J. Caimano
- Department of Pediatrics, University of Connecticut School of Medicine, Farmington, CT, United States of America
- Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, United States of America
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States of America
| | - Christopher M. Hennelly
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States of America
| | - Farhang Aghakhanian
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States of America
| | - M. Anthony Moody
- Duke Human Vaccine Institute, Durham, NC, United States of America
- Department of Pediatrics, Duke University Medical Center, Durham, NC, United States of America
- Department of Integrative Immunology, Duke University Medical Center, Durham, NC, United States of America
| | - Arlene C. Seña
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States of America
| | - Jonathan B. Parr
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States of America
| | - Kelly L. Hawley
- Department of Pediatrics, University of Connecticut School of Medicine, Farmington, CT, United States of America
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, United States of America
- Division of Infectious Diseases, Connecticut Children’s, Hartford, CT, United States of America
- Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, United States of America
| | - Eduardo López-Medina
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
- Centro de Estudios en Infectología Pediátrica (CEIP), Cali, Colombia
| | - Justin D. Radolf
- Department of Pediatrics, University of Connecticut School of Medicine, Farmington, CT, United States of America
- Department of Immunology, University of Connecticut School of Medicine, Farmington, CT, United States of America
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
- Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, United States of America
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, United States of America
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3
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Long DR, Bryson-Cahn C, Waalkes A, Holmes EA, Penewit K, Tavolaro C, Bellabarba C, Zhang F, Chan JD, Fang FC, Lynch JB, Salipante SJ. Contribution of the patient microbiome to surgical site infection and antibiotic prophylaxis failure in spine surgery. Sci Transl Med 2024; 16:eadk8222. [PMID: 38598612 DOI: 10.1126/scitranslmed.adk8222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
Abstract
Despite modern antiseptic techniques, surgical site infection (SSI) remains a leading complication of surgery. However, the origins of SSI and the high rates of antimicrobial resistance observed in these infections are poorly understood. Using instrumented spine surgery as a model of clean (class I) skin incision, we prospectively sampled preoperative microbiomes and postoperative SSI isolates in a cohort of 204 patients. Combining multiple forms of genomic analysis, we correlated the identity, anatomic distribution, and antimicrobial resistance profiles of SSI pathogens with those of preoperative strains obtained from the patient skin microbiome. We found that 86% of SSIs, comprising a broad range of bacterial species, originated endogenously from preoperative strains, with no evidence of common source infection among a superset of 1610 patients. Most SSI isolates (59%) were resistant to the prophylactic antibiotic administered during surgery, and their resistance phenotypes correlated with the patient's preoperative resistome (P = 0.0002). These findings indicate the need for SSI prevention strategies tailored to the preoperative microbiome and resistome present in individual patients.
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Affiliation(s)
- Dustin R Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Chloe Bryson-Cahn
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Elizabeth A Holmes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Celeste Tavolaro
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Carlo Bellabarba
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Fangyi Zhang
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jeannie D Chan
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Pharmacy, Harborview Medical Center, University of Washington School of Pharmacy, Seattle, WA 98104, USA
| | - Ferric C Fang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Clinical Microbiology Laboratory, Harborview Medical Center, Seattle, WA 98104, USA
| | - John B Lynch
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
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4
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Peng Y, Williams MM, Xiaoli L, Simon A, Fueston H, Tondella ML, Weigand MR. Strengthening Bordetella pertussis genomic surveillance by direct sequencing of residual positive specimens. J Clin Microbiol 2024; 62:e0165323. [PMID: 38445858 PMCID: PMC11005353 DOI: 10.1128/jcm.01653-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024] Open
Abstract
Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent methods to diagnose infectious diseases has resulted in few isolates available for WGS. Here, we report a novel culture-independent approach to genome characterization of Bordetella pertussis, the causative agent of pertussis and a paradigm for insufficient genomic surveillance due to limited culture of clinical isolates. Sequencing libraries constructed directly from residual pertussis-positive diagnostic nasopharyngeal specimens were hybridized with biotinylated RNA "baits" targeting B. pertussis fragments within complex mixtures that contained high concentrations of host and microbial background DNA. Recovery of B. pertussis genome sequence data was evaluated with mock and pooled negative clinical specimens spiked with reducing concentrations of either purified DNA or inactivated cells. Targeted enrichment increased the yield of B. pertussis sequencing reads up to 90% while simultaneously decreasing host reads to less than 10%. Filtered sequencing reads provided sufficient genome coverage to perform characterization via whole-genome single nucleotide polymorphisms and whole-genome multilocus sequencing typing. Moreover, these data were concordant with sequenced isolates recovered from the same specimens such that phylogenetic reconstructions from either consistently clustered the same putatively linked cases. The optimized protocol is suitable for nasopharyngeal specimens with diagnostic IS481 Ct < 35 and >10 ng DNA. Routine implementation of these methods could strengthen surveillance and study of pertussis resurgence by capturing additional cases with genomic characterization.
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Affiliation(s)
- Yanhui Peng
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M. Williams
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Ashley Simon
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Heather Fueston
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria L. Tondella
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael R. Weigand
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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5
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Weeber P, Singh N, Lapierre P, Mingle L, Wroblewski D, Nazarian EJ, Haas W, Weiss D, Musser KA. A novel hybridization capture method for direct whole genome sequencing of clinical specimens to inform Legionnaires' disease investigations. J Clin Microbiol 2024; 62:e0130523. [PMID: 38511938 PMCID: PMC11005328 DOI: 10.1128/jcm.01305-23] [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: 10/06/2023] [Accepted: 02/14/2024] [Indexed: 03/22/2024] Open
Abstract
The unprecedented precision and resolution of whole genome sequencing (WGS) can provide definitive identification of infectious agents for epidemiological outbreak tracking. WGS approaches, however, are frequently impeded by low pathogen DNA recovery from available primary specimens or unculturable samples. A cost-effective hybrid capture assay for Legionella pneumophila WGS analysis directly on primary specimens was developed. DNA from a diverse range of sputum and autopsy specimens PCR-positive for L. pneumophila serogroup 1 (LPSG1) was enriched with this method, and WGS was performed. All tested specimens were determined to be enriched for Legionella reads (up to 209,000-fold), significantly improving the discriminatory power to compare relatedness when no clinical isolate was available. We found the WGS data from some enriched specimens to differ by less than five single-nucleotide polymorphisms (SNPs) when compared to the WGS data of a matched culture isolate. This testing and analysis retrospectively provided previously unconfirmed links to environmental sources for clinical specimens of sputum and autopsy lung tissue. The latter provided the additional information needed to identify the source of these culture-negative cases associated with the South Bronx 2015 Legionnaires' disease (LD) investigation in New York City. This new method provides a proof of concept for future direct clinical specimen hybrid capture enrichment combined with WGS and bioinformatic analysis during outbreak investigations.IMPORTANCELegionnaires' disease (LD) is a severe and potentially fatal type of pneumonia primarily caused by inhalation of Legionella-contaminated aerosols from man-made water or cooling systems. LD remains extremely underdiagnosed as it is an uncommon form of pneumonia and relies on clinicians including it in the differential and requesting specialized testing. Additionally, it is challenging to obtain clinical lower respiratory specimens from cases with LD, and when available, culture requires specialized media and growth conditions, which are not available in all microbiology laboratories. In the current study, a method for Legionella pneumophila using hybrid capture by RNA baiting was developed, which allowed us to generate sufficient genome resolution from L. pneumophila serogroup 1 PCR-positive clinical specimens. This new approach offers an additional tool for surveillance of future LD outbreaks where isolation of Legionella is not possible and may help solve previously unanswered questions from past LD investigations.
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Affiliation(s)
- Phillip Weeber
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Navjot Singh
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Lisa Mingle
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Danielle Wroblewski
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Wolfgang Haas
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Don Weiss
- New York City Department of Health and Mental Hygiene, New York, New York, USA
| | - Kimberlee A. Musser
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
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6
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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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7
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Pilling OA, Reis-Cunha JL, Grace CA, Berry ASF, Mitchell MW, Yu JA, Malekshahi CR, Krespan E, Go CK, Lombana C, Song YS, Amorim CF, Lago AS, Carvalho LP, Carvalho EM, Brisson D, Scott P, Jeffares DC, Beiting DP. Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies. PLoS Pathog 2023; 19:e1011230. [PMID: 36940219 PMCID: PMC10063166 DOI: 10.1371/journal.ppat.1011230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 03/30/2023] [Accepted: 02/22/2023] [Indexed: 03/21/2023] Open
Abstract
In Brazil, Leishmania braziliensis is the main causative agent of the neglected tropical disease, cutaneous leishmaniasis (CL). CL presents on a spectrum of disease severity with a high rate of treatment failure. Yet the parasite factors that contribute to disease presentation and treatment outcome are not well understood, in part because successfully isolating and culturing parasites from patient lesions remains a major technical challenge. Here we describe the development of selective whole genome amplification (SWGA) for Leishmania and show that this method enables culture-independent analysis of parasite genomes obtained directly from primary patient skin samples, allowing us to circumvent artifacts associated with adaptation to culture. We show that SWGA can be applied to multiple Leishmania species residing in different host species, suggesting that this method is broadly useful in both experimental infection models and clinical studies. SWGA carried out directly on skin biopsies collected from patients in Corte de Pedra, Bahia, Brazil, showed extensive genomic diversity. Finally, as a proof-of-concept, we demonstrated that SWGA data can be integrated with published whole genome data from cultured parasite isolates to identify variants unique to specific geographic regions in Brazil where treatment failure rates are known to be high. SWGA provides a relatively simple method to generate Leishmania genomes directly from patient samples, unlocking the potential to link parasite genetics with host clinical phenotypes.
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Affiliation(s)
- Olivia A. Pilling
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - João L. Reis-Cunha
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Cooper A. Grace
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Alexander S. F. Berry
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew W. Mitchell
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jane A. Yu
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
| | - Clara R. Malekshahi
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Elise Krespan
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Christina K. Go
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Cláudia Lombana
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 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
| | - Camila F. Amorim
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alexsandro S. Lago
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, Brazil
| | - Lucas P. Carvalho
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, Brazil
| | - Edgar M. Carvalho
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, Brazil
| | - Dustin Brisson
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Phillip Scott
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Daniel C. Jeffares
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Daniel P. Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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8
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Lieberman NAP, Armstrong TD, Chung B, Pfalmer D, Hennelly CM, Haynes A, Romeis E, Wang QQ, Zhang RL, Kou CX, Ciccarese G, Conte ID, Cusini M, Drago F, Nakayama SI, Lee K, Ohnishi M, Konda KA, Vargas SK, Eguiluz M, Caceres CF, Klausner JD, Mitja O, Rompalo A, Mulcahy F, Hook EW, Hoffman IF, Matoga MM, Zheng H, Yang B, Lopez-Medina E, Ramirez LG, Radolf JD, Hawley KL, Salazar JC, Lukehart SA, Seña AC, Parr JB, Giacani L, Greninger AL. High-throughput nanopore sequencing of Treponema pallidum tandem repeat genes arp and tp0470 reveals clade-specific patterns and recapitulates global whole genome phylogeny. Front Microbiol 2022; 13:1007056. [PMID: 36204625 PMCID: PMC9531955 DOI: 10.3389/fmicb.2022.1007056] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Sequencing of most Treponema pallidum genomes excludes repeat regions in tp0470 and the tp0433 gene, encoding the acidic repeat protein (arp). As a first step to understanding the evolution and function of these genes and the proteins they encode, we developed a protocol to nanopore sequence tp0470 and arp genes from 212 clinical samples collected from ten countries on six continents. Both tp0470 and arp repeat structures recapitulate the whole genome phylogeny, with subclade-specific patterns emerging. The number of tp0470 repeats is on average appears to be higher in Nichols-like clade strains than in SS14-like clade strains. Consistent with previous studies, we found that 14-repeat arp sequences predominate across both major clades, but the combination and order of repeat type varies among subclades, with many arp sequence variants limited to a single subclade. Although strains that were closely related by whole genome sequencing frequently had the same arp repeat length, this was not always the case. Structural modeling of TP0470 suggested that the eight residue repeats form an extended α-helix, predicted to be periplasmic. Modeling of the ARP revealed a C-terminal sporulation-related repeat (SPOR) domain, predicted to bind denuded peptidoglycan, with repeat regions possibly incorporated into a highly charged β-sheet. Outside of the repeats, all TP0470 and ARP amino acid sequences were identical. Together, our data, along with functional considerations, suggests that both TP0470 and ARP proteins may be involved in T. pallidum cell envelope remodeling and homeostasis, with their highly plastic repeat regions playing as-yet-undetermined roles.
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Affiliation(s)
- Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Thaddeus D. Armstrong
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Benjamin Chung
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Daniel Pfalmer
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Christopher M. Hennelly
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Austin Haynes
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Emily Romeis
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Qian-Qiu Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Rui-Li Zhang
- Department of Dermatology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cai-Xia Kou
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Giulia Ciccarese
- Section of Dermatology, Department of Health Sciences, San Martino University Hospital, Genoa, Italy
| | - Ivano Dal Conte
- Sexual Health Center, Department of Prevention, ASL Città di Torino, Turin, Italy
| | - Marco Cusini
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Drago
- Section of Dermatology, Department of Health Sciences, San Martino University Hospital, Genoa, Italy
| | - Shu-ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kelika A. Konda
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Silver K. Vargas
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- School of Public Health and Administration “Carlos Vidal Layseca”, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maria Eguiluz
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Carlos F. Caceres
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Jeffrey D. Klausner
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Oriol Mitja
- Fight Aids and Infectious Diseases Foundation, Hospital Germans Trias i Pujol, Barcelona, Spain
- Lihir Medical Centre, International SOS, Londolovit, Papua New Guinea
| | - Anne Rompalo
- Department of Infectious Diseases, Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - Fiona Mulcahy
- Department of Genito Urinary Medicine and Infectious Diseases, St. James’s Hospital, Dublin, Ireland
| | - Edward W. Hook
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Irving F. Hoffman
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- UNC Project-Malawi, Lilongwe, Malawi
| | - Mitch M. Matoga
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- UNC Project-Malawi, Lilongwe, Malawi
| | - Heping Zheng
- Dermatology Hospital of Southern Medical University, Guangzhou, China
- Institute for Global Health and Sexually Transmitted Infections, Guangzhou, China
| | - Bin Yang
- Dermatology Hospital of Southern Medical University, Guangzhou, China
- Institute for Global Health and Sexually Transmitted Infections, Guangzhou, China
| | - Eduardo Lopez-Medina
- Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM), Cali, Colombia
- Centro de Estudios en Infectología Pediátrica (CEIP), Cali, Colombia
| | - Lady G. Ramirez
- Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM), Cali, Colombia
- Universidad ICESI, Cali, Colombia
| | - Justin D. Radolf
- Department of Medicine, UConn Health, Farmington, CT, United States
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, United States
| | - Kelly L. Hawley
- Department of Medicine, UConn Health, Farmington, CT, United States
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Division of Infectious Diseases and Immunology, Connecticut Children’s Medical Center, Hartford, CT, United States
| | - Juan C. Salazar
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Division of Infectious Diseases and Immunology, Connecticut Children’s Medical Center, Hartford, CT, United States
| | - Sheila A. Lukehart
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Global Health, University of Washington School of Medicine, Seattle, WA, United States
| | - Arlene C. Seña
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jonathan B. Parr
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lorenzo Giacani
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Global Health, University of Washington School of Medicine, Seattle, WA, United States
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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Kojima N, Konda KA, Klausner JD. Notes on syphilis vaccine development. Front Immunol 2022; 13:952284. [PMID: 35967432 PMCID: PMC9365935 DOI: 10.3389/fimmu.2022.952284] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
The quest for a syphilis vaccine to provide protection from infection or disease began not long after the isolation of the first Treponema pallidum subspecies pallidum (T. pallidum) strain in 1912. Yet, a practical and effective vaccine formulation continues to elude scientists. Over the last few years, however, efforts toward developing a syphilis vaccine have increased thanks to an improved understanding of the repertoire of T. pallidum outer membrane proteins (OMPs), which are the most likely syphilis vaccine candidates. More has been also learned about the molecular mechanisms behind pathogen persistence and immune evasion. Published vaccine formulations based on a subset of the pathogen's OMPs have conferred only partial protection upon challenge of immunized laboratory animals, primarily rabbits. Nonetheless, those experiments have improved our approach to the choice of immunization regimens, adjuvants, and vaccine target selection, although significant knowledge gaps remain. Herein, we provide a brief overview on current technologies and approaches employed in syphilis vaccinology, and possible future directions to develop a vaccine that could be pivotal to future syphilis control and elimination initiatives.
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Affiliation(s)
- Noah Kojima
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Kelika A. Konda
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States
- Centro de Investigación Interdisciplinaria en Sexualidad Sida y Sociedad, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jeffrey D. Klausner
- Departments of Medicine and Population and Public Health Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, CA, United States
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