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Moss S, Pretorius E, Ceesay S, Hutchins H, da Silva ET, Ndiath MO, Jones RT, Vasileva H, Phelan J, Acford-Palmer H, Collins E, Rodrigues A, Krishna S, Clark TG, Last A, Campino S. Genomic surveillance of Anopheles mosquitoes on the Bijagós Archipelago using custom targeted amplicon sequencing identifies mutations associated with insecticide resistance. Parasit Vectors 2024; 17:10. [PMID: 38178249 PMCID: PMC10768400 DOI: 10.1186/s13071-023-06085-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Insecticide resistance is reducing the efficacy of vector control interventions, consequently threatening efforts to control vector-borne diseases, including malaria. Investigating the prevalence of molecular markers of resistance is a useful tool for monitoring the spread of insecticide resistance in disease vectors. The Bijagós Archipelago (Bijagós) in Guinea-Bissau is a region of stable malaria transmission where insecticide-treated nets are the mainstay for malaria control. However, the prevalence of molecular markers of insecticide resistance in malaria vectors is not well understood. METHODS A total of 214 Anopheles mosquitoes were analysed from 13 islands across the Bijagós. These mosquitoes were collected using CDC light traps in November 2019, during the peak malaria transmission season. High-throughput multiplex amplicon sequencing was used to investigate the prevalence of 17 different molecular markers associated with insecticide resistance in four genes: vgsc, rdl, ace1 and gste2. RESULTS Of the 17 screened mutations, four were identified in mosquitoes from the Bijagós: vgsc L995F (12.2%), N1570Y (6.2%) and A1746S (0.7%) and rdl A269G (1.1%). This study is the first to report the L995F knock-down resistance (kdr)-west allele in Anopheles melas on the Archipelago. An additional eight non-synonymous single-nucleotide polymorphisms were identified across the four genes which have not been described previously. The prevalences of the vgsc L995F and N1570Y mutations were higher on Bubaque Island than on the other islands in this study; Bubaque is the most populous island in the archipelago, with the greatest population mobility and connection to continental Guinea-Bissau. CONCLUSIONS This study provides the first surveillance data for genetic markers present in malaria vectors from islands across the Bijagós Archipelago. Overall prevalence of insecticide resistance mutations was found to be low. However, the identification of the vgsc L995F and N1570Y mutations associated with pyrethroid resistance warrants further monitoring. This is particularly important as the mainstay of malaria control on the islands is the use of pyrethroid insecticide-treated nets.
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Affiliation(s)
- Sophie Moss
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Elizabeth Pretorius
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Sainey Ceesay
- Medical Research Council, The Gambia (MRCG), Fajara, Gambia
| | - Harry Hutchins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Eunice Teixeira da Silva
- Ministério de Saúde Pública, Bissau, Guinea-Bissau
- Projecto de Saúde Bandim, Bissau, Guinea-Bissau
| | | | - Robert T Jones
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Hristina Vasileva
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Holly Acford-Palmer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Emma Collins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Sanjeev Krishna
- Clinical Academic Group, Institute for Infection and Immunity, St. George's University Hospitals NHS Foundation Trust-St. George's University of London, London, UK
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon
- Institut Für Tropenmedizin Universitätsklinikum Tübingen, Tübingen, Germany
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Anna Last
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
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Sádlová J, Yeo M, Mateus DS, Phelan J, Hai LA, Bhattacharyya T, Kurtev S, Sebesta O, Myskova J, Seblova V, Andersson B, Florez de Sessions P, Volf P, Miles MA. Comparative genomics of Leishmania donovani progeny from genetic crosses in two sand fly species and impact on the diversity of diagnostic and vaccine candidates. PLoS Negl Trop Dis 2024; 18:e0011920. [PMID: 38295092 PMCID: PMC10830044 DOI: 10.1371/journal.pntd.0011920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
Sand fly transmitted Leishmania species are responsible for severe, wide ranging, visceral and cutaneous leishmaniases. Genetic exchange can occur among natural Leishmania populations and hybrids can now be produced experimentally, with limitations. Feeding Phlebotomus orientalis or Phlebotomus argentipes on two strains of Leishmania donovani yielded hybrid progeny, selected using double drug resistance and fluorescence markers. Fluorescence activated cell sorting of cultured clones derived from these hybrids indicated diploid progeny. Multilocus sequence typing of the clones showed hybridisation and nuclear heterozygosity, although with inheritance of single haplotypes in a kinetoplastid target. Comparative genomics showed diversity of clonal progeny between single chromosomes, and extraordinary heterozygosity across all 36 chromosomes. Diversity between progeny was seen for the HASPB antigen, which has been noted previously as having implications for design of a therapeutic vaccine. Genomic diversity seen among Leishmania strains and hybrid progeny is of great importance in understanding the epidemiology and control of leishmaniasis. As an outcome of this study we strongly recommend that wider biological archives of different Leishmania species from endemic regions should be established and made available for comparative genomics. However, in parallel, performance of genetic crosses and genomic comparisons should give fundamental insight into the specificity, diversity and limitations of candidate diagnostics, vaccines and drugs, for targeted control of leishmaniasis.
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Affiliation(s)
- Jovana Sádlová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Matthew Yeo
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - David S. Mateus
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Le Anh Hai
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Tapan Bhattacharyya
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Stefan Kurtev
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Ondrej Sebesta
- Laboratory of Confocal and Fluorescence Microscopy, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jitka Myskova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Veronika Seblova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Paola Florez de Sessions
- Genome Institute of Singapore, Biomedical Sciences Institutes, Agency for Science, Technology and Research, Singapore
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michael A. Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
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Derelle R, Lees J, Phelan J, Lalvani A, Arinaminpathy N, Chindelevitch L. fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing. Bioinformatics 2023; 39:btad648. [PMID: 37871178 PMCID: PMC10627351 DOI: 10.1093/bioinformatics/btad648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023] Open
Abstract
SUMMARY Fastlin is a bioinformatics tool designed for rapid Mycobacterium tuberculosis complex (MTBC) lineage typing. It utilizes an ultra-fast alignment-free approach to detect previously identified barcode single nucleotide polymorphisms associated with specific MTBC lineages. In a comprehensive benchmarking against existing tools, fastlin demonstrated high accuracy and significantly faster running times. AVAILABILITY AND IMPLEMENTATION fastlin is freely available at https://github.com/rderelle/fastlin and can easily be installed using Conda.
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Affiliation(s)
- Romain Derelle
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London W2 1PG, United Kingdom
| | - John Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London , London W12 0BZ, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus , Hinxton CB10 1SD, United Kingdom
| | - Jody Phelan
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Ajit Lalvani
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London W2 1PG, United Kingdom
| | - Nimalan Arinaminpathy
- NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London, London W2 1PG, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London , London W12 0BZ, United Kingdom
| | - Leonid Chindelevitch
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London , London W12 0BZ, United Kingdom
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Verboven L, Phelan J, Heupink TH, Van Rie A. Correction: TBProfiler for automated calling of the association with drug resistance of variants in Mycobacterium tuberculosis. PLoS One 2023; 18:e0293254. [PMID: 37847720 PMCID: PMC10581449 DOI: 10.1371/journal.pone.0293254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0279644.].
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Wang L, Campino S, Phelan J, Clark TG. Mixed infections in genotypic drug-resistant Mycobacterium tuberculosis. Sci Rep 2023; 13:17100. [PMID: 37816829 PMCID: PMC10564873 DOI: 10.1038/s41598-023-44341-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/06/2023] [Indexed: 10/12/2023] Open
Abstract
Tuberculosis disease (TB), caused by Mycobacterium tuberculosis, is a major global public health problem, resulting in more than 1 million deaths each year. Drug resistance (DR), including multi-drug (MDR-TB), is making TB control difficult and accounts for 16% of new and 48% of previously treated cases. To further complicate treatment decision-making, many clinical studies have reported patients harbouring multiple distinct strains of M. tuberculosis across the main lineages (L1 to L4). The extent to which drug-resistant strains can be deconvoluted within mixed strain infection samples is understudied. Here, we analysed M. tuberculosis isolates with whole genome sequencing data (n = 50,723), which covered the main lineages (L1 9.1%, L2 27.6%, L3 11.8%, L4 48.3%), with genotypic resistance to isoniazid (HR-TB; n = 9546 (29.2%)), rifampicin (RR-TB; n = 7974 (24.4%)), and at least MDR-TB (n = 5385 (16.5%)). TB-Profiler software revealed 531 (1.0%) isolates with potential mixed sub-lineage infections, including some with DR mutations (RR-TB 21/531; HR-TB 59/531; at least MDR-TB 173/531). To assist with the deconvolution of such mixtures, we adopted and evaluated a statistical Gaussian Mixture model (GMM) approach. By simulating 240 artificial mixtures of different ratios from empirical data across L1 to L4, a GMM approach was able to accurately estimate the DR profile of each lineage, with a low error rate for the estimated mixing proportions (mean squared error 0.012) and high accuracy for the DR predictions (93.5%). Application of the GMM model to the clinical mixtures (n = 531), found that 33.3% (188/531) of samples consisted of DR and sensitive lineages, 20.2% (114/531) consisted of lineages with only DR mutations, and 40.6% (229/531) consisted of lineages with genotypic pan-susceptibility. Overall, our work demonstrates the utility of combined whole genome sequencing data and GMM statistical analysis approaches for providing insights into mono and mixed M. tuberculosis infections, thereby potentially assisting diagnosis, treatment decision-making, drug resistance and transmission mapping for infection control.
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Affiliation(s)
- Linfeng Wang
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Jody Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
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Hackman J, Sheppard C, Phelan J, Jones-Warner W, Sobkowiak B, Shah S, Litt D, Fry NK, Toizumi M, Yoshida LM, Hibberd M, Miller E, Flasche S, Hué S. Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study. Wellcome Open Res 2023; 8:427. [PMID: 38638914 PMCID: PMC11024593 DOI: 10.12688/wellcomeopenres.19219.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 04/20/2024] Open
Abstract
Background: Inference on pneumococcal transmission has mostly relied on longitudinal studies which are costly and resource intensive. Therefore, we conducted a pilot study to test the ability to infer who infected whom from cross-sectional pneumococcal sequences using phylogenetic inference. Methods: Five suspected transmission pairs, for which there was epidemiological evidence of who infected whom, were selected from a household study. For each pair, Streptococcus pneumoniae full genomes were sequenced from nasopharyngeal swabs collected on the same day. The within-host genetic diversity of the pneumococcal population was used to infer the transmission direction and then cross-validated with the direction suggested by the epidemiological records. Results: The pneumococcal genomes clustered into the five households from which the samples were taken. The proportion of concordantly inferred transmission direction generally increased with increasing minimum genome fragment size and single nucleotide polymorphisms. We observed a larger proportion of unique polymorphic sites in the source bacterial population compared to that of the recipient in four of the five pairs, as expected in the case of a transmission bottleneck. The only pair that did not exhibit this effect was also the pair that had consistent discordant transmission direction compared to the epidemiological records suggesting potential misdirection as a result of false-negative sampling. Conclusions: This pilot provided support for further studies to test if the direction of pneumococcal transmission can be reliably inferred from cross-sectional samples if sequenced with sufficient depth and fragment length.
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Affiliation(s)
- Jada Hackman
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Carmen Sheppard
- Vaccine Preventable Bacteria Section, UK Health Security Agency, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - William Jones-Warner
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ben Sobkowiak
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Sonal Shah
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - David Litt
- Vaccine Preventable Bacteria Section, UK Health Security Agency, London, UK
| | - Norman K. Fry
- Vaccine Preventable Bacteria Section, UK Health Security Agency, London, UK
- Immunisation & Countermeasures Division, UK Health Security Agency, London, UK
| | - Michiko Toizumi
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Paediatric Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Lay-Myint Yoshida
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Paediatric Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Martin Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Elizabeth Miller
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Stefan Flasche
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Stéphane Hué
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
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Napier G, Couvin D, Refrégier G, Guyeux C, Meehan CJ, Sola C, Campino S, Phelan J, Clark TG. Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data. Sci Rep 2023; 13:11368. [PMID: 37443186 PMCID: PMC10345134 DOI: 10.1038/s41598-023-38384-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/07/2023] [Indexed: 07/15/2023] Open
Abstract
Bacterial strain-types in the Mycobacterium tuberculosis complex underlie tuberculosis disease, and have been associated with drug resistance, transmissibility, virulence, and host-pathogen interactions. Spoligotyping was developed as a molecular genotyping technique used to determine strain-types, though recent advances in whole genome sequencing (WGS) technology have led to their characterization using SNP-based sub-lineage nomenclature. Notwithstanding, spoligotyping remains an important tool and there is a need to study the congruence between spoligotyping-based and SNP-based sub-lineage assignation. To achieve this, an in silico spoligotype prediction method ("Spolpred2") was developed and integrated into TB-Profiler. Lineage and spoligotype predictions were generated for > 28 k isolates and the overlap between strain-types was characterized. Major spoligotype families detected were Beijing (25.6%), T (18.6%), LAM (13.1%), CAS (9.4%), and EAI (8.3%), and these broadly followed known geographic distributions. Most spoligotypes were perfectly correlated with the main MTBC lineages (L1-L7, plus animal). Conversely, at lower levels of the sub-lineage system, the relationship breaks down, with only 65% of spoligotypes being perfectly associated with a sub-lineage at the second or subsequent levels of the hierarchy. Our work supports the use of spoligotyping (membrane or WGS-based) for low-resolution surveillance, and WGS or SNP-based systems for higher-resolution studies.
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Affiliation(s)
- Gary Napier
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - David Couvin
- Institut Pasteur de la Guadeloupe, Les Abymes, Guadeloupe
| | - Guislaine Refrégier
- Université Paris-Saclay, Saint-Aubin, France
- CNRS, UMR ESE, AgroParisTech, 91405, Orsay, France
| | - Christophe Guyeux
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000, Besançon, France
| | | | - Christophe Sola
- Université Paris-Saclay, Saint-Aubin, France
- IAME, UMR1137, Université Paris-Cité, INSERM, Paris, France
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
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Mazumder R, Hussain A, Bhadra B, Phelan J, Campino S, Clark TG, Mondal D. Case report: A successfully treated case of community-acquired urinary tract infection due to Klebsiella aerogenes in Bangladesh. Front Med (Lausanne) 2023; 10:1206756. [PMID: 37435536 PMCID: PMC10330784 DOI: 10.3389/fmed.2023.1206756] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/05/2023] [Indexed: 07/13/2023] Open
Abstract
Klebsiella aerogenes, a nosocomial pathogen, is increasingly associated with extensive drug resistance and virulence profiles. It is responsible for high morbidity and mortality. This report describes the first successfully treated case of community-acquired urinary tract infection (UTI) caused by Klebsiella aerogenes in an elderly housewife with Type-2 diabetes (T2D) from Dhaka, Bangladesh. The patient was empirically treated with intravenous ceftriaxone (500 mg/8 h). However, she did not respond to the treatment. The urine culture and sensitivity tests, coupled with bacterial whole-genome sequencing (WGS) and analysis, revealed the bacteria to be K. aerogenes which was extensively drug-resistant but was susceptible to carbapenems and polymyxins. Based on these findings, meropenem (500 mg/8 h) was administered to the patient, who then responded to the treatment and recovered successfully without having a relapse. This case raises awareness of the importance of diagnosis of not-so-common etiological agents, correct identification of the pathogens, and targeted antibiotic therapy. In conclusion, correctly identifying etiological agents of UTI using WGS approaches that are otherwise difficult to diagnose could help improve the identification of infectious agents and improve the management of infectious diseases.
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Affiliation(s)
- Razib Mazumder
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Arif Hussain
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Bithika Bhadra
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Jody Phelan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dinesh Mondal
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
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Vanheer LN, Mahamar A, Manko E, Niambele SM, Sanogo K, Youssouf A, Dembele A, Diallo M, Maguiraga SO, Phelan J, Osborne A, Spadar A, Smit MJ, Bousema T, Drakeley C, Clark TG, Stone W, Dicko A, Campino S. Genome-wide genetic variation and molecular surveillance of drug resistance in Plasmodium falciparum isolates from asymptomatic individuals in Ouélessébougou, Mali. Sci Rep 2023; 13:9522. [PMID: 37308503 DOI: 10.1038/s41598-023-36002-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/27/2023] [Indexed: 06/14/2023] Open
Abstract
Sequence analysis of Plasmodium falciparum parasites is informative in ensuring sustained success of malaria control programmes. Whole-genome sequencing technologies provide insights into the epidemiology and genome-wide variation of P. falciparum populations and can characterise geographical as well as temporal changes. This is particularly important to monitor the emergence and spread of drug resistant P. falciparum parasites which is threatening malaria control programmes world-wide. Here, we provide a detailed characterisation of genome-wide genetic variation and drug resistance profiles in asymptomatic individuals in South-Western Mali, where malaria transmission is intense and seasonal, and case numbers have recently increased. Samples collected from Ouélessébougou, Mali (2019-2020; n = 87) were sequenced and placed in the context of older Malian (2007-2017; n = 876) and African-wide (n = 711) P. falciparum isolates. Our analysis revealed high multiclonality and low relatedness between isolates, in addition to increased frequencies of molecular markers for sulfadoxine-pyrimethamine and lumefantrine resistance, compared to older Malian isolates. Furthermore, 21 genes under selective pressure were identified, including a transmission-blocking vaccine candidate (pfCelTOS) and an erythrocyte invasion locus (pfdblmsp2). Overall, our work provides the most recent assessment of P. falciparum genetic diversity in Mali, a country with the second highest burden of malaria in West Africa, thereby informing malaria control activities.
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Affiliation(s)
- Leen N Vanheer
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
| | - Almahamoudou Mahamar
- Malaria Research and Training Centre, Faculty of Pharmacy and Faculty of Medicine and Dentistry, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Emilia Manko
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Sidi M Niambele
- Malaria Research and Training Centre, Faculty of Pharmacy and Faculty of Medicine and Dentistry, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Koualy Sanogo
- Malaria Research and Training Centre, Faculty of Pharmacy and Faculty of Medicine and Dentistry, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Ahamadou Youssouf
- Malaria Research and Training Centre, Faculty of Pharmacy and Faculty of Medicine and Dentistry, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Adama Dembele
- Malaria Research and Training Centre, Faculty of Pharmacy and Faculty of Medicine and Dentistry, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Makonon Diallo
- Malaria Research and Training Centre, Faculty of Pharmacy and Faculty of Medicine and Dentistry, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Seydina O Maguiraga
- Malaria Research and Training Centre, Faculty of Pharmacy and Faculty of Medicine and Dentistry, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Jody Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ashley Osborne
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anton Spadar
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Merel J Smit
- Department of Medical Microbiology and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Teun Bousema
- Department of Medical Microbiology and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Chris Drakeley
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - William Stone
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Alassane Dicko
- Malaria Research and Training Centre, Faculty of Pharmacy and Faculty of Medicine and Dentistry, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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10
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Scott DAV, Benavente E, Libiseller-Egger J, Fedorov D, Phelan J, Ilina E, Tikhonova P, Kudryavstev A, Galeeva J, Clark T, Lewin A. Bayesian compositional regression with microbiome features via variational inference. BMC Bioinformatics 2023; 24:210. [PMID: 37217852 PMCID: PMC10201722 DOI: 10.1186/s12859-023-05219-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/02/2023] [Indexed: 05/24/2023] Open
Abstract
The microbiome plays a key role in the health of the human body. Interest often lies in finding features of the microbiome, alongside other covariates, which are associated with a phenotype of interest. One important property of microbiome data, which is often overlooked, is its compositionality as it can only provide information about the relative abundance of its constituting components. Typically, these proportions vary by several orders of magnitude in datasets of high dimensions. To address these challenges we develop a Bayesian hierarchical linear log-contrast model which is estimated by mean field Monte-Carlo co-ordinate ascent variational inference (CAVI-MC) and easily scales to high dimensional data. We use novel priors which account for the large differences in scale and constrained parameter space associated with the compositional covariates. A reversible jump Monte Carlo Markov chain guided by the data through univariate approximations of the variational posterior probability of inclusion, with proposal parameters informed by approximating variational densities via auxiliary parameters, is used to estimate intractable marginal expectations. We demonstrate that our proposed Bayesian method performs favourably against existing frequentist state of the art compositional data analysis methods. We then apply the CAVI-MC to the analysis of real data exploring the relationship of the gut microbiome to body mass index.
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Affiliation(s)
- Darren A. V. Scott
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Ernest Benavente
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Julian Libiseller-Egger
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Dmitry Fedorov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Jody Phelan
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Elena Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Polina Tikhonova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Bioinformatics and Genomics Intercollege Graduate Program, Huck Institutes of Life Sciences, Pennsylvania State University, Pennsylvania, USA
| | | | - Julia Galeeva
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Taane Clark
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
| | - Alex Lewin
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
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11
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Moss S, Mańko E, Vasileva H, Da Silva ET, Goncalves A, Osborne A, Phelan J, Rodrigues A, Djata P, D'Alessandro U, Mabey D, Krishna S, Last A, Clark TG, Campino S. Population dynamics and drug resistance mutations in Plasmodium falciparum on the Bijagós Archipelago, Guinea-Bissau. Sci Rep 2023; 13:6311. [PMID: 37072433 PMCID: PMC10113324 DOI: 10.1038/s41598-023-33176-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/08/2023] [Indexed: 05/03/2023] Open
Abstract
Following integrated malaria control interventions, malaria burden on the Bijagós Archipelago has significantly decreased. Understanding the genomic diversity of circulating Plasmodium falciparum malaria parasites can assist infection control, through identifying drug resistance mutations and characterising the complexity of population structure. This study presents the first whole genome sequence data for P. falciparum isolates from the Bijagós Archipelago. Amplified DNA from P. falciparum isolates sourced from dried blood spot samples of 15 asymptomatic malaria cases were sequenced. Using 1.3 million SNPs characterised across 795 African P. falciparum isolates, population structure analyses revealed that isolates from the archipelago cluster with samples from mainland West Africa and appear closely related to mainland populations; without forming a separate phylogenetic cluster. This study characterises SNPs associated with antimalarial drug resistance on the archipelago. We observed fixation of the PfDHFR mutations N51I and S108N, associated with resistance to sulphadoxine-pyrimethamine, and the continued presence of PfCRT K76T, associated with chloroquine resistance. These data have relevance for infection control and drug resistance surveillance; particularly considering expected increases in antimalarial drug use following updated WHO recommendations, and the recent implementation of seasonal malaria chemoprevention and mass drug administration in the region.
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Affiliation(s)
- Sophie Moss
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
| | - Emilia Mańko
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Hristina Vasileva
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Eunice Teixeira Da Silva
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Ministry of Public Health, Bissau, Guinea-Bissau
| | - Adriana Goncalves
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ashley Osborne
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Paulo Djata
- National Malaria Control Programme, Ministry of Public Health, Bissau, Guinea-Bissau
| | | | - David Mabey
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Sanjeev Krishna
- Clinical Academic Group, Institute for Infection and Immunity, and St. George's University Hospitals NHS Foundation Trust, St. George's University of London, London, UK
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon
- Institut Für Tropenmedizin Universitätsklinikum Tübingen, Tübingen, Germany
| | - Anna Last
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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12
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Kristan M, Acford-Palmer H, Campos MO, Collins EL, Phelan J, Portwood NM, Pelloquin B, Clarke S, Lines J, Clark TG, Walker T, Campino S, Messenger LA. Towards environmental detection, quantification, and molecular characterization of Anopheles stephensi and Aedes aegypti from experimental larval breeding sites. Sci Rep 2023; 13:2729. [PMID: 36792622 PMCID: PMC9932160 DOI: 10.1038/s41598-023-29657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
The invasion and establishment of An. stephensi mosquitoes in the Horn of Africa represents a significant regional threat, which may jeopardise malaria control, particularly in urban areas which were formally free from disease transmission. Novel vector surveillance methods are urgently needed, both agnostic to mosquito larval morphology, and simple to implement at the sampling stage. Using new multiplex TaqMan assays, specifically targeting An. stephensi and Ae. aegypti, we validated the use of environmental DNA (eDNA) for simultaneous vector detection in shared artificial breeding sites. Study findings demonstrated that An. stephensi and Ae. aegypti eDNA deposited by as few as one second instar larva in 1L of water was detectable. Characterization of molecular insecticide resistance mechanisms, using novel amplicon-sequencing panels for both vector species, was possible from eDNA shed by as few as 16-32 s instar larvae in 50 ml of water. An. stephensi eDNA, derived from emergent pupae for 24 h, was remarkably stable, and still detectable ~ 2 weeks later. eDNA surveillance has the potential to be implemented in local endemic communities and at points of country entry, to monitor the spread of invasive vector species. Further studies are required to validate the feasibility of this technique under field conditions.
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Affiliation(s)
- Mojca Kristan
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Holly Acford-Palmer
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Monica Oliveira Campos
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Emma L Collins
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Jody Phelan
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Natalie M Portwood
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Bethanie Pelloquin
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Sian Clarke
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Jo Lines
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Taane G Clark
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thomas Walker
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Susana Campino
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Louisa A Messenger
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
- Department of Environmental and Occupational Health, School of Public Health, University of Nevada, Las Vegas, NV, USA.
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13
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Phelan J, Gomez-Gonzalez PJ, Andreu N, Omae Y, Toyo-Oka L, Yanai H, Miyahara R, Nedsuwan S, de Sessions PF, Campino S, Sallah N, Parkhill J, Smittipat N, Palittapongarnpim P, Mushiroda T, Kubo M, Tokunaga K, Mahasirimongkol S, Hibberd ML, Clark TG. Genome-wide host-pathogen analyses reveal genetic interaction points in tuberculosis disease. Nat Commun 2023; 14:549. [PMID: 36725857 PMCID: PMC9892022 DOI: 10.1038/s41467-023-36282-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
The genetics underlying tuberculosis (TB) pathophysiology are poorly understood. Human genome-wide association studies have failed so far to reveal reproducible susceptibility loci, attributed in part to the influence of the underlying Mycobacterium tuberculosis (Mtb) bacterial genotype on the outcome of the infection. Several studies have found associations of human genetic polymorphisms with Mtb phylo-lineages, but studies analysing genome-genome interactions are needed. By implementing a phylogenetic tree-based Mtb-to-human analysis for 714 TB patients from Thailand, we identify eight putative genetic interaction points (P < 5 × 10-8) including human loci DAP and RIMS3, both linked to the IFNγ cytokine and host immune system, as well as FSTL5, previously associated with susceptibility to TB. Many of the corresponding Mtb markers are lineage specific. The genome-to-genome analysis reveals a complex interactome picture, supports host-pathogen adaptation and co-evolution in TB, and has potential applications to large-scale studies across many TB endemic populations matched for host-pathogen genomic diversity.
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Affiliation(s)
- Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Nuria Andreu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Yosuke Omae
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Licht Toyo-Oka
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideki Yanai
- Fukujuji Hospital and Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Reiko Miyahara
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | | | | | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Neneh Sallah
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nat Smittipat
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Prasit Palittapongarnpim
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | | | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Surakameth Mahasirimongkol
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom.
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14
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Verboven L, Phelan J, Heupink TH, Van Rie A. TBProfiler for automated calling of the association with drug resistance of variants in Mycobacterium tuberculosis. PLoS One 2022; 17:e0279644. [PMID: 36584023 PMCID: PMC9803136 DOI: 10.1371/journal.pone.0279644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
Following a huge global effort, the first World Health Organization (WHO)-endorsed catalogue of 17,356 variants in the Mycobacterium tuberculosis complex along with their classification as associated with resistance (interim), not associated with resistance (interim) or uncertain significance was made public In June 2021. This marks a critical step towards the application of next generation sequencing (NGS) data for clinical care. Unfortunately, the variant format used makes it difficult to look up variants when NGS data is generated by other bioinformatics pipelines. Furthermore, the large number of variants of uncertain significance in the catalogue hamper its useability in clinical practice. We successfully converted 98.3% of variants from the WHO catalogue format to the standardized HGVS format. We also created TBProfiler version 4.4.0 to automate the calling of all variants located in the tier 1 and 2 candidate resistance genes along with their classification when listed in the WHO catalogue. Using a representative sample of 339 clinical isolates from South Africa containing 691 variants in a tier 1 or 2 gene, TBProfiler classified 105 (15%) variants as conferring resistance, 72 (10%) as not conferring resistance and 514 (74%) as unclassified, with an average of 29 unclassified variants per isolate. Using a second cohort of 56 clinical isolates from a TB outbreak in Spain containing 21 variants in the tier 1 and 2 genes, TBProfiler classified 13 (61.9%) as unclassified, 7 (33.3%) as not conferring resistance, and a single variant (4.8%) classified as conferring resistance. Continued global efforts using standardized methods for genotyping, phenotyping and bioinformatic analyses will be essential to ensure that knowledge on genomic variants translates into improved patient care.
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Affiliation(s)
- Lennert Verboven
- Torch Consortium FAMPOP Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- ADReM Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Tim H. Heupink
- Torch Consortium FAMPOP Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Annelies Van Rie
- Torch Consortium FAMPOP Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
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15
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Hargreaves JR, Langan SM, Oswald WE, Halliday KE, Sturgess J, Phelan J, Nguipdop-Djomo P, Ford B, Allen E, Sundaram N, Ireland G, Poh J, Ijaz S, Diamond I, Rourke E, Dawe F, Judd A, Warren-Gash C, Clark TG, Glynn JR, Edmunds WJ, Bonell C, Mangtani P, Ladhani SN. Epidemiology of SARS-CoV-2 infection among staff and students in a cohort of English primary and secondary schools during 2020-2021. Lancet Reg Health Eur 2022; 21:100471. [PMID: 36035630 PMCID: PMC9398464 DOI: 10.1016/j.lanepe.2022.100471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background There remains uncertainty about the epidemiology of SARS-CoV-2 among school students and staff and the extent to which non-pharmaceutical-interventions reduce the risk of school settings. Methods We conducted an open cohort study in a sample of 59 primary and 97 secondary schools in 15 English local authority areas that were implementing government guidance to schools open during the pandemic. We estimated SARS-CoV-2 infection prevalence among those attending school, antibody prevalence, and antibody negative to positive conversion rates in staff and students over the school year (November 2020-July 2021). Findings 22,585 staff and students participated. SARS-CoV-2 infection prevalence among those attending school was highest during the first two rounds of testing in the autumn term, ranging from 0.7% (95% CI 0.2, 1.2) among primary staff in November 2020 to 1.6% (95% CI 0.9, 2.3) among secondary staff in December 2020. Antibody conversion rates were highest in the autumn term. Infection patterns were similar between staff and students, and between primary and secondary schools. The prevalence of nucleoprotein antibodies increased over the year and was lower among students than staff. SARS-CoV-2 infection prevalence in the North-West region was lower among secondary students attending school on normal school days than the regional estimate for secondary school-age children. Interpretation SARS-CoV-2 infection prevalence in staff and students attending school varied with local community infection rates. Non-pharmaceutical interventions intended to prevent infected individuals attending school may have partially reduced the prevalence of infection among those on the school site. Funding UK Department of Health and Social Care.
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Affiliation(s)
- James R. Hargreaves
- Department of Public Health, Environments and Society, Faculty of Public Health and Policy, London School of Hygiene & Tropical Medicine, London, UK
| | - Sinéad M. Langan
- Department of Non-communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - William E. Oswald
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Katherine E. Halliday
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Joanna Sturgess
- Department of Medical Statistics, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Patrick Nguipdop-Djomo
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Benjamin Ford
- Office for National Statistics, Government Buildings, Newport, UK
| | - Elizabeth Allen
- Department of Medical Statistics, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Neisha Sundaram
- Department of Global Health and Development, Faculty of Public Health and Policy, London School of Hygiene & Tropical Medicine, London, UK
| | - Georgina Ireland
- National Infection Service, UK Health Security Agency, London, UK
| | - John Poh
- National Infection Service, UK Health Security Agency, London, UK
| | - Samreen Ijaz
- National Infection Service, UK Health Security Agency, London, UK
| | - Ian Diamond
- Office for National Statistics, Government Buildings, Newport, UK
| | - Emma Rourke
- Office for National Statistics, Government Buildings, Newport, UK
| | - Fiona Dawe
- Office for National Statistics, Government Buildings, Newport, UK
| | - Alison Judd
- Office for National Statistics, Government Buildings, Newport, UK
| | - Charlotte Warren-Gash
- Department of Non-communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Taane G. Clark
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Judith R. Glynn
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - W. John Edmunds
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Chris Bonell
- Department of Public Health, Environments and Society, Faculty of Public Health and Policy, London School of Hygiene & Tropical Medicine, London, UK
| | - Punam Mangtani
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Shamez N. Ladhani
- National Infection Service, UK Health Security Agency, London, UK
- Paediatric Infectious Diseases Research Group, St George's University of London, London, UK
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16
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Campos M, Phelan J, Spadar A, Collins E, Gonçalves A, Pelloquin B, Vaselli NM, Meiwald A, Clark E, Stica C, Orsborne J, Sylla M, Edi C, Camara D, Mohammed AR, Afrane YA, Kristan M, Walker T, Gomez LF, Messenger LA, Clark TG, Campino S. High-throughput barcoding method for the genetic surveillance of insecticide resistance and species identification in Anopheles gambiae complex malaria vectors. Sci Rep 2022; 12:13893. [PMID: 35974073 PMCID: PMC9381500 DOI: 10.1038/s41598-022-17822-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/01/2022] [Indexed: 12/30/2022] Open
Abstract
Surveillance of malaria vector species and the monitoring of insecticide resistance are essential to inform malaria control strategies and support the reduction of infections and disease. Genetic barcoding of mosquitoes is a useful tool to assist the high-throughput surveillance of insecticide resistance, discriminate between sibling species and to detect the presence of Plasmodium infections. In this study, we combined multiplex PCR, custom designed dual indexing, and Illumina next generation sequencing for high throughput single nucleotide polymorphism (SNP)-profiling of four species from the Anopheles (An.) gambiae complex (An. gambiae sensu stricto, An. coluzzii, An. arabiensis and An. melas). By amplifying and sequencing only 14 genetic fragments (500 bp each), we were able to simultaneously detect Plasmodium infection; insecticide resistance-conferring SNPs in ace1, gste2, vgsc and rdl genes; the partial sequences of nuclear ribosomal internal transcribed spacers (ITS1 and ITS2) and intergenic spacers (IGS), Short INterspersed Elements (SINE), as well as mitochondrial genes (cox1 and nd4) for species identification and genetic diversity. Using this amplicon sequencing approach with the four selected An. gambiae complex species, we identified a total of 15 non-synonymous mutations in the insecticide target genes, including previously described mutations associated with resistance and two new mutations (F1525L in vgsc and D148E in gste2). Overall, we present a reliable and cost-effective high-throughput panel for surveillance of An. gambiae complex mosquitoes in malaria endemic regions.
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Affiliation(s)
- Monica Campos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Emma Collins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Adéritow Gonçalves
- Laboratório de Entomologia Médica, Instituto Nacional de Saúde Pública, Praia, 719, Cabo Verde
| | - Bethanie Pelloquin
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- School of Tropical Medicine and Global Health, University of Nagasaki, Nagasaki, Japan
| | - Natasha Marcella Vaselli
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anne Meiwald
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Emma Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Caleb Stica
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - James Orsborne
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Moussa Sylla
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland
| | - Constant Edi
- Centre Suisse de Recherches Scientifiques en Cote d'Ivoire, Abidjan, Côte d'Ivoire
| | - Denka Camara
- Programme National de Lutte Contre le Paludisme, Ministère de la Santé, BP. 595, Conakry, Guinea
| | - Abdul Rahim Mohammed
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Yaw Asare Afrane
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Mojca Kristan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Thomas Walker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Louisa A Messenger
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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Elias R, Spadar A, Phelan J, Melo-Cristino J, Lito L, Pinto M, Gonçalves L, Campino S, Clark TG, Duarte A, Perdigão J. A phylogenomic approach for the analysis of colistin resistance associated genes in Klebsiella pneumoniae, its mutational diversity and implications for phenotypic resistance. Int J Antimicrob Agents 2022; 59:106581. [DOI: 10.1016/j.ijantimicag.2022.106581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/17/2022] [Accepted: 03/27/2022] [Indexed: 11/05/2022]
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Coll F, Gouliouris T, Bruchmann S, Phelan J, Raven KE, Clark TG, Parkhill J, Peacock SJ. PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies. Commun Biol 2022; 5:266. [PMID: 35338232 PMCID: PMC8956664 DOI: 10.1038/s42003-022-03194-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) are increasingly being applied to investigate the genetic basis of bacterial traits. However, approaches to perform power calculations for bacterial GWAS are limited. Here we implemented two alternative approaches to conduct power calculations using existing collections of bacterial genomes. First, a sub-sampling approach was undertaken to reduce the allele frequency and effect size of a known and detectable genotype-phenotype relationship by modifying phenotype labels. Second, a phenotype-simulation approach was conducted to simulate phenotypes from existing genetic variants. We implemented both approaches into a computational pipeline (PowerBacGWAS) that supports power calculations for burden testing, pan-genome and variant GWAS; and applied it to collections of Enterococcus faecium, Klebsiella pneumoniae and Mycobacterium tuberculosis. We used this pipeline to determine sample sizes required to detect causal variants of different minor allele frequencies (MAF), effect sizes and phenotype heritability, and studied the effect of homoplasy and population diversity on the power to detect causal variants. Our pipeline and user documentation are made available and can be applied to other bacterial populations. PowerBacGWAS can be used to determine sample sizes required to find statistically significant associations, or the associations detectable with a given sample size. We recommend to perform power calculations using existing genomes of the bacterial species and population of study.
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Affiliation(s)
- Francesc Coll
- Department of Infection Biology, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Theodore Gouliouris
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Jody Phelan
- Department of Infection Biology, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Kathy E Raven
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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19
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Darboe S, Bradbury RS, Phelan J, Kanteh A, Muhammad AK, Worwui A, Yang S, Nwakanma D, Perez-Sepulveda B, Kariuki S, Kwambana-Adams B, Antonio M. Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia. Microb Genom 2022; 8:000785. [PMID: 35302932 PMCID: PMC9176284 DOI: 10.1099/mgen.0.000785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/24/2022] [Indexed: 11/18/2022] Open
Abstract
Non-typhoidal Salmonella associated with multidrug resistance cause invasive disease in sub-Saharan Africa. Specific lineages of serovars Typhimurium and Enteritidis have been implicated. Here we characterized the genomic diversity of 100 clinical non-typhoidal Salmonella collected from 93 patients in 2001 from the eastern, and in 2006-2018 from the western regions of The Gambia respectively. A total of 93 isolates (64 invasive, 23 gastroenteritis and six other sites) representing a single infection episode were phenotypically tested for antimicrobial susceptibility using the Kirby-Bauer disc diffusion technique. Whole genome sequencing of 100 isolates was performed using Illumina, and the reads were assembled and analysed using SPAdes. The Salmonella in Silico Typing Resource (SISTR) was used for serotyping. SNP differences among the 93 isolates were determined using Roary, and phylogenetic analysis was performed in the context of 495 African strains from the European Nucleotide Archive. Salmonella serovars Typhimurium (26/64; 30.6 %) and Enteritidis (13/64; 20.3 %) were associated with invasive disease, whilst other serovars were mainly responsible for gastroenteritis (17/23; 73.9 %). The presence of three major serovar Enteritidis clades was confirmed, including the invasive West African clade, which made up more than half (11/16; 68.8 %) of the genomes. Multidrug resistance was confined among the serovar Enteritidis West African clade. The presence of this epidemic virulent clade has potential for spread of resistance and thus important implications for systematic patient management. Surveillance and epidemiological investigations to inform control are warranted.
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Affiliation(s)
- Saffiatou Darboe
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | | | - Jody Phelan
- London School of Hygiene and Tropical Medicine, London, UK
| | - Abdoulie Kanteh
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | - Abdul-Khalie Muhammad
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | - Archibald Worwui
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | - Shangxin Yang
- University of California, Los Angeles, California, USA
| | - Davis Nwakanma
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | | | | | - Brenda Kwambana-Adams
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
- University College London, London, UK
| | - Martin Antonio
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
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20
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Deelder W, Napier G, Campino S, Palla L, Phelan J, Clark TG. A modified decision tree approach to improve the prediction and mutation discovery for drug resistance in Mycobacterium tuberculosis. BMC Genomics 2022; 23:46. [PMID: 35016609 PMCID: PMC8753810 DOI: 10.1186/s12864-022-08291-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Drug resistant Mycobacterium tuberculosis is complicating the effective treatment and control of tuberculosis disease (TB). With the adoption of whole genome sequencing as a diagnostic tool, machine learning approaches are being employed to predict M. tuberculosis resistance and identify underlying genetic mutations. However, machine learning approaches can overfit and fail to identify causal mutations if they are applied out of the box and not adapted to the disease-specific context. We introduce a machine learning approach that is customized to the TB setting, which extracts a library of genomic variants re-occurring across individual studies to improve genotypic profiling. RESULTS We developed a customized decision tree approach, called Treesist-TB, that performs TB drug resistance prediction by extracting and evaluating genomic variants across multiple studies. The application of Treesist-TB to rifampicin (RIF), isoniazid (INH) and ethambutol (EMB) drugs, for which resistance mutations are known, demonstrated a level of predictive accuracy similar to the widely used TB-Profiler tool (Treesist-TB vs. TB-Profiler tool: RIF 97.5% vs. 97.6%; INH 96.8% vs. 96.5%; EMB 96.8% vs. 95.8%). Application of Treesist-TB to less understood second-line drugs of interest, ethionamide (ETH), cycloserine (CYS) and para-aminosalisylic acid (PAS), led to the identification of new variants (52, 6 and 11, respectively), with a high number absent from the TB-Profiler library (45, 4, and 6, respectively). Thereby, Treesist-TB had improved predictive sensitivity (Treesist-TB vs. TB-Profiler tool: PAS 64.3% vs. 38.8%; CYS 45.3% vs. 30.7%; ETH 72.1% vs. 71.1%). CONCLUSION Our work reinforces the utility of machine learning for drug resistance prediction, while highlighting the need to customize approaches to the disease-specific context. Through applying a modified decision learning approach (Treesist-TB) across a range of anti-TB drugs, we identified plausible resistance-encoding genomic variants with high predictive ability, whilst potentially overcoming the overfitting challenges that can affect standard machine learning applications.
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Affiliation(s)
- Wouter Deelder
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Dalberg Advisors, 7 Rue de Chantepoulet, CH-1201, Geneva, Switzerland
| | - Gary Napier
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Susana Campino
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Luigi Palla
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, Rome, Italy
| | - Jody Phelan
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Taane G Clark
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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21
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Gröschel MI, Owens M, Freschi L, Vargas R, Marin MG, Phelan J, Iqbal Z, Dixit A, Farhat MR. GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning. Genome Med 2021; 13:138. [PMID: 34461978 PMCID: PMC8407037 DOI: 10.1186/s13073-021-00953-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/12/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Multidrug-resistant Mycobacterium tuberculosis (Mtb) is a significant global public health threat. Genotypic resistance prediction from Mtb DNA sequences offers an alternative to laboratory-based drug-susceptibility testing. User-friendly and accurate resistance prediction tools are needed to enable public health and clinical practitioners to rapidly diagnose resistance and inform treatment regimens. RESULTS We present Translational Genomics platform for Tuberculosis (GenTB), a free and open web-based application to predict antibiotic resistance from next-generation sequence data. The user can choose between two potential predictors, a Random Forest (RF) classifier and a Wide and Deep Neural Network (WDNN) to predict phenotypic resistance to 13 and 10 anti-tuberculosis drugs, respectively. We benchmark GenTB's predictive performance along with leading TB resistance prediction tools (Mykrobe and TB-Profiler) using a ground truth dataset of 20,408 isolates with laboratory-based drug susceptibility data. All four tools reliably predicted resistance to first-line tuberculosis drugs but had varying performance for second-line drugs. The mean sensitivities for GenTB-RF and GenTB-WDNN across the nine shared drugs were 77.6% (95% CI 76.6-78.5%) and 75.4% (95% CI 74.5-76.4%), respectively, and marginally higher than the sensitivities of TB-Profiler at 74.4% (95% CI 73.4-75.3%) and Mykrobe at 71.9% (95% CI 70.9-72.9%). The higher sensitivities were at an expense of ≤ 1.5% lower specificity: Mykrobe 97.6% (95% CI 97.5-97.7%), TB-Profiler 96.9% (95% CI 96.7 to 97.0%), GenTB-WDNN 96.2% (95% CI 96.0 to 96.4%), and GenTB-RF 96.1% (95% CI 96.0 to 96.3%). Averaged across the four tools, genotypic resistance sensitivity was 11% and 9% lower for isoniazid and rifampicin respectively, on isolates sequenced at low depth (< 10× across 95% of the genome) emphasizing the need to quality control input sequence data before prediction. We discuss differences between tools in reporting results to the user including variants underlying the resistance calls and any novel or indeterminate variants CONCLUSIONS: GenTB is an easy-to-use online tool to rapidly and accurately predict resistance to anti-tuberculosis drugs. GenTB can be accessed online at https://gentb.hms.harvard.edu , and the source code is available at https://github.com/farhat-lab/gentb-site .
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Affiliation(s)
- Matthias I Gröschel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Martin Owens
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Maximilian G Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Zamin Iqbal
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 ISD, UK
| | - Avika Dixit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA.
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22
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Tunstall T, Phelan J, Eccleston C, Clark TG, Furnham N. Structural and Genomic Insights Into Pyrazinamide Resistance in Mycobacterium tuberculosis Underlie Differences Between Ancient and Modern Lineages. Front Mol Biosci 2021; 8:619403. [PMID: 34422898 PMCID: PMC8372558 DOI: 10.3389/fmolb.2021.619403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/14/2021] [Indexed: 11/30/2022] Open
Abstract
Resistance to drugs used to treat tuberculosis disease (TB) continues to remain a public health burden, with missense point mutations in the underlying Mycobacterium tuberculosis bacteria described for nearly all anti-TB drugs. The post-genomics era along with advances in computational and structural biology provide opportunities to understand the interrelationships between the genetic basis and the structural consequences of M. tuberculosis mutations linked to drug resistance. Pyrazinamide (PZA) is a crucial first line antibiotic currently used in TB treatment regimens. The mutational promiscuity exhibited by the pncA gene (target for PZA) necessitates computational approaches to investigate the genetic and structural basis for PZA resistance development. We analysed 424 missense point mutations linked to PZA resistance derived from ∼35K M. tuberculosis clinical isolates sourced globally, which comprised the four main M. tuberculosis lineages (Lineage 1-4). Mutations were annotated to reflect their association with PZA resistance. Genomic measures (minor allele frequency and odds ratio), structural features (surface area, residue depth and hydrophobicity) and biophysical effects (change in stability and ligand affinity) of point mutations on pncA protein stability and ligand affinity were assessed. Missense point mutations within pncA were distributed throughout the gene, with the majority (>80%) of mutations with a destabilising effect on protomer stability and on ligand affinity. Active site residues involved in PZA binding were associated with multiple point mutations highlighting mutational diversity due to selection pressures at these functionally important sites. There were weak associations between genomic measures and biophysical effect of mutations. However, mutations associated with PZA resistance showed statistically significant differences between structural features (surface area and residue depth), but not hydrophobicity score for mutational sites. Most interestingly M. tuberculosis lineage 1 (ancient lineage) exhibited a distinct protein stability profile for mutations associated with PZA resistance, compared to modern lineages.
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Affiliation(s)
- Tanushree Tunstall
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jody Phelan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Charlotte Eccleston
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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23
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Deelder W, Benavente ED, Phelan J, Manko E, Campino S, Palla L, Clark TG. Using deep learning to identify recent positive selection in malaria parasite sequence data. Malar J 2021; 20:270. [PMID: 34126997 PMCID: PMC8201710 DOI: 10.1186/s12936-021-03788-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/29/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Malaria, caused by Plasmodium parasites, is a major global public health problem. To assist an understanding of malaria pathogenesis, including drug resistance, there is a need for the timely detection of underlying genetic mutations and their spread. With the increasing use of whole-genome sequencing (WGS) of Plasmodium DNA, the potential of deep learning models to detect loci under recent positive selection, historically signals of drug resistance, was evaluated. METHODS A deep learning-based approach (called "DeepSweep") was developed, which can be trained on haplotypic images from genetic regions with known sweeps, to identify loci under positive selection. DeepSweep software is available from https://github.com/WDee/Deepsweep . RESULTS Using simulated genomic data, DeepSweep could detect recent sweeps with high predictive accuracy (areas under ROC curve > 0.95). DeepSweep was applied to Plasmodium falciparum (n = 1125; genome size 23 Mbp) and Plasmodium vivax (n = 368; genome size 29 Mbp) WGS data, and the genes identified overlapped with two established extended haplotype homozygosity methods (within-population iHS, across-population Rsb) (~ 60-75% overlap of hits at P < 0.0001). DeepSweep hits included regions proximal to known drug resistance loci for both P. falciparum (e.g. pfcrt, pfdhps and pfmdr1) and P. vivax (e.g. pvmrp1). CONCLUSION The deep learning approach can detect positive selection signatures in malaria parasite WGS data. Further, as the approach is generalizable, it may be trained to detect other types of selection. With the ability to rapidly generate WGS data at low cost, machine learning approaches (e.g. DeepSweep) have the potential to assist parasite genome-based surveillance and inform malaria control decision-making.
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Affiliation(s)
- Wouter Deelder
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Dalberg Advisors, 7 Rue de Chantepoulet, CH-1201, Geneva, Switzerland
| | | | - Jody Phelan
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Emilia Manko
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Susana Campino
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Luigi Palla
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, Rome, Italy
| | - Taane G Clark
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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24
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Benavente ED, Manko E, Phelan J, Campos M, Nolder D, Fernandez D, Velez-Tobon G, Castaño AT, Dombrowski JG, Marinho CRF, Aguiar ACC, Pereira DB, Sriprawat K, Nosten F, Moon R, Sutherland CJ, Campino S, Clark TG. Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa. Nat Commun 2021; 12:3160. [PMID: 34039976 PMCID: PMC8154914 DOI: 10.1038/s41467-021-23422-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/28/2021] [Indexed: 12/30/2022] Open
Abstract
Despite the high burden of Plasmodium vivax malaria in South Asian countries, the genetic diversity of circulating parasite populations is not well described. Determinants of antimalarial drug susceptibility for P. vivax in the region have not been characterised. Our genomic analysis of global P. vivax (n = 558) establishes South Asian isolates (n = 92) as a distinct subpopulation, which shares ancestry with some East African and South East Asian parasites. Signals of positive selection are linked to drug resistance-associated loci including pvkelch10, pvmrp1, pvdhfr and pvdhps, and two loci linked to P. vivax invasion of reticulocytes, pvrbp1a and pvrbp1b. Significant identity-by-descent was found in extended chromosome regions common to P. vivax from India and Ethiopia, including the pvdbp gene associated with Duffy blood group binding. Our investigation provides new understanding of global P. vivax population structure and genomic diversity, and genetic evidence of recent directional selection in this important human pathogen.
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Affiliation(s)
- Ernest Diez Benavente
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Emilia Manko
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Monica Campos
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Debbie Nolder
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Public Health England Malaria Reference Laboratory, London School of Hygiene & Tropical Medicine, London, UK
| | - Diana Fernandez
- Grupo Malaria, Facultad de Medicina, Universidad de Antioquia, Antioquia, Colombia
| | - Gabriel Velez-Tobon
- Grupo Malaria, Facultad de Medicina, Universidad de Antioquia, Antioquia, Colombia
| | | | - Jamille G Dombrowski
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Claudio R F Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Anna Caroline C Aguiar
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Robert Moon
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Colin J Sutherland
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Public Health England Malaria Reference Laboratory, London School of Hygiene & Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Taane G Clark
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
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25
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Spadar A, Perdigão J, Phelan J, Charleston J, Modesto A, Elias R, de Sessions PF, Hibberd ML, Campino S, Duarte A, Clark TG. Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals. Sci Rep 2021; 11:6491. [PMID: 33753763 PMCID: PMC7985491 DOI: 10.1038/s41598-021-85724-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
Klebsiella pneumoniae is an important nosocomial infectious agent with a high antimicrobial resistance (AMR) burden. The application of long read sequencing technologies is providing insights into bacterial chromosomal and putative extra-chromosomal genetic elements (PEGEs) associated with AMR, but also epigenetic DNA methylation, which is thought to play a role in cleavage of foreign DNA and expression regulation. Here, we apply the PacBio sequencing platform to eight Portuguese hospital isolates, including one carbapenemase producing isolate, to identify methylation motifs. The resulting assembled chromosomes were between 5.2 and 5.5Mbp in length, and twenty-six PEGEs were found. Four of our eight samples carry blaCTX-M-15, a dominant Extended Spectrum Beta Lactamase in Europe. We identified methylation motifs that control Restriction-Modification systems, including GATC of the DNA adenine methylase (Dam), which methylates N6-methyladenine (m6A) across all our K. pneumoniae assemblies. There was a consistent lack of methylation by Dam of the GATC motif downstream of two genes: fosA, a locus associated with low level fosfomycin resistance, and tnpB transposase on IncFIB(K) plasmids. Overall, we have constructed eight high quality reference genomes of K. pneumoniae, with insights into horizontal gene transfer and methylation m6A motifs.
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Affiliation(s)
- Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - James Charleston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ana Modesto
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Rita Elias
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | | | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Aida Duarte
- Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Almada, Portugal
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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Grignard L, Nolder D, Sepulveda N, Berhane A, Mihreteab S, Kaaya R, Phelan J, Moser K, van Schalkwyk DA, Campino S, Parr JB, Juliano JJ, Chiodini P, Cunningham J, Sutherland CJ, Drakeley C, Beshir KB. Corrigendum to 'A novel multiplex qPCR assay for detection of Plasmodium falciparum with histidine-rich protein 2 and 3 (pfhrp2 and pfhrp3) deletions in polyclonal infections'. EBioMedicine 2021; 65:103261. [PMID: 33639399 PMCID: PMC7921491 DOI: 10.1016/j.ebiom.2021.103261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Lynn Grignard
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Debbie Nolder
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom; PHE Malaria Reference Laboratory, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Nuno Sepulveda
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom; Centre of Statistics and Applications of University of Lisbon, Portugal
| | - Araia Berhane
- Communicable Diseases Control Division, Ministry of Health, Eritrea
| | - Selam Mihreteab
- Communicable Diseases Control Division, Ministry of Health, Eritrea
| | - Robert Kaaya
- Kilimanjaro Christian Medical University College, Tanzania
| | - Jody Phelan
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Kara Moser
- University of North Carolina at Chapel Hill, United States
| | - Donelly A van Schalkwyk
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Susana Campino
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | | | | | - Peter Chiodini
- PHE Malaria Reference Laboratory, London School of Hygiene & Tropical Medicine, United Kingdom; UCL Hospital for Tropical Diseases, United Kingdom
| | | | - Colin J Sutherland
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Chris Drakeley
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Khalid B Beshir
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom.
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Mason KE, Palla L, Pearce N, Phelan J, Cummins S. Genetic risk of obesity as a modifier of associations between neighbourhood environment and body mass index: an observational study of 335 046 UK Biobank participants. BMJ Nutr Prev Health 2021; 3:247-255. [PMID: 33521535 PMCID: PMC7841812 DOI: 10.1136/bmjnph-2020-000107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 11/10/2022] Open
Abstract
Background There is growing recognition that recent global increases in obesity are the product of a complex interplay between genetic and environmental factors. However, in gene-environment studies of obesity, ‘environment’ usually refers to individual behavioural factors that influence energy balance, whereas more upstream environmental factors are overlooked. We examined gene-environment interactions between genetic risk of obesity and two neighbourhood characteristics likely to be associated with obesity (proximity to takeaway/fast-food outlets and availability of physical activity facilities). Methods We used data from 335 046 adults aged 40–70 in the UK Biobank cohort to conduct a population-based cross-sectional study of interactions between neighbourhood characteristics and genetic risk of obesity, in relation to body mass index (BMI). Proximity to a fast-food outlet was defined as distance from home address to nearest takeaway/fast-food outlet, and availability of physical activity facilities as the number of formal physical activity facilities within 1 km of home address. Genetic risk of obesity was operationalised by weighted Genetic Risk Scores of 91 or 69 single nucleotide polymorphisms (SNP), and by six individual SNPs considered separately. Multivariable, mixed-effects models with product terms for the gene-environment interactions were estimated. Results After accounting for likely confounding, the association between proximity to takeaway/fast-food outlets and BMI was stronger among those at increased genetic risk of obesity, with evidence of an interaction with polygenic risk scores (p=0.018 and p=0.028 for 69-SNP and 91-SNP scores, respectively) and in particular with a SNP linked to MC4R (p=0.009), a gene known to regulate food intake. We found very little evidence of gene-environment interaction for the availability of physical activity facilities. Conclusions Individuals at an increased genetic risk of obesity may be more sensitive to exposure to the local fast-food environment. Ensuring that neighbourhood residential environments are designed to promote a healthy weight may be particularly important for those with greater genetic susceptibility to obesity.
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Affiliation(s)
- Kate E Mason
- Department of Public Health, Policy and Systems, University of Liverpool, Liverpool, UK.,Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Luigi Palla
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, UK.,Department of Global Health, University of Nagasaki, Nagasaki, Japan
| | - Neil Pearce
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody Phelan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Steven Cummins
- Department of Public Health, Environments and Society, London School of Hygiene and Tropical Medicine, London, UK
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28
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Napier G, Campino S, Merid Y, Abebe M, Woldeamanuel Y, Aseffa A, Hibberd ML, Phelan J, Clark TG. Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies. Genome Med 2020; 12:114. [PMID: 33317631 PMCID: PMC7734807 DOI: 10.1186/s13073-020-00817-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/03/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tuberculosis, caused by bacteria in the Mycobacterium tuberculosis complex (MTBC), is a major global public health burden. Strain-specific genomic diversity in the known lineages of MTBC is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Fast and accurate tracking of MTBC strains is therefore crucial for infection control, and our previous work developed a 62-single nucleotide polymorphism (SNP) barcode to inform on the phylogenetic identity of 7 human lineages and 64 sub-lineages. METHODS To update this barcode, we analysed whole genome sequencing data from 35,298 MTBC isolates (~ 1 million SNPs) covering 9 main lineages and 3 similar animal-related species (M. tuberculosis var. bovis, M. tuberculosis var. caprae and M. tuberculosis var. orygis). The data was partitioned into training (N = 17,903, 50.7%) and test (N = 17,395, 49.3%) sets and were analysed using an integrated phylogenetic tree and population differentiation (FST) statistical approach. RESULTS By constructing a phylogenetic tree on the training MTBC isolates, we characterised 90 lineages or sub-lineages or species, of which 30 are new, and identified 421 robust barcoding mutations, of which a minimal set of 90 was selected that included 20 markers from the 62-SNP barcode. The barcoding SNPs (90 and 421) discriminated perfectly the 86 MTBC isolate (sub-)lineages in the test set and could accurately reconstruct the clades across the combined 35k samples. CONCLUSIONS The validated 90 SNPs can be used for the rapid diagnosis and tracking of MTBC strains to assist public health surveillance and control. To facilitate this, the SNP markers have now been incorporated into the TB-Profiler informatics platform ( https://github.com/jodyphelan/TBProfiler ).
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Affiliation(s)
- Gary Napier
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Yared Merid
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Hawassa University College of Medicine and Health Sciences, Hawassa, Ethiopia
| | - Markos Abebe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Yimtubezinash Woldeamanuel
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Martin L. Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
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29
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Perdigão J, Caneiras C, Elias R, Modesto A, Spadar A, Phelan J, Campino S, Clark TG, Costa E, Saavedra MJ, Duarte A. Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain. Microorganisms 2020; 8:E1986. [PMID: 33322205 PMCID: PMC7763156 DOI: 10.3390/microorganisms8121986] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
The evolutionary epidemiology, resistome, virulome and mobilome of thirty-one multidrug resistant Klebsiella pneumoniae clinical isolates from the northern Vila Real region of Portugal were characterized using whole-genome sequencing and bioinformatic analysis. The genomic population structure was dominated by two main sequence types (STs): ST147 (n = 17; 54.8%) and ST15 (n = 6; 19.4%) comprising four distinct genomic clusters. Two main carbapenemase coding genes were detected (blaKPC-3 and blaOXA-48) along with additional extended-spectrum β-lactamase coding loci (blaCTX-M-15, blaSHV-12, blaSHV-27, and blaSHV-187). Moreover, whole genome sequencing enabled the identification of one Klebsiella variicola KPC-3 producer isolate previously misidentified as K. pneumoniae, which in addition to the blaKPC-3 carbapenemase gene, bore the chromosomal broad spectrum β-lactamase blaLEN-2 coding gene, oqxAB and fosA resistance loci. The blaKPC-3 genes were located in a Tn4401b transposon (K. variicolan = 1; K. pneumoniaen = 2) and Tn4401d isoform (K. pneumoniaen = 28). Overall, our work describes the first report of a blaKPC-3 producing K. variicola, as well as the detection of this species during infection control measures in surveillance cultures from infected patients. It also highlights the importance of additional control measures to overcome the clonal dissemination of carbapenemase producing clones.
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Affiliation(s)
- João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-033 Lisboa, Portugal; (J.P.); (R.E.); (A.M.)
| | - Cátia Caneiras
- Laboratory of Microbiology Research in Environmental Health (EnviHealthMicro Lab), Institute of Environmental Health (ISAMB), Faculty of Medicine, Universidade de Lisboa, 1649-026 Lisboa, Portugal;
- Institute of Preventive Medicine and Public Health (IMP&SP), Faculty of Medicine, Universidade de Lisboa, 1649-026 Lisboa, Portugal
- Department of Microbiology and Immunology, Faculty of Pharmacy, Universidade de Lisboa, 1649-033 Lisboa, Portugal
| | - Rita Elias
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-033 Lisboa, Portugal; (J.P.); (R.E.); (A.M.)
| | - Ana Modesto
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-033 Lisboa, Portugal; (J.P.); (R.E.); (A.M.)
| | - Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; (A.S.); (J.P.); (S.C.); (T.G.C.)
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; (A.S.); (J.P.); (S.C.); (T.G.C.)
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; (A.S.); (J.P.); (S.C.); (T.G.C.)
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; (A.S.); (J.P.); (S.C.); (T.G.C.)
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Eliana Costa
- Serviço de Patologia Clínica, Centro Hospitalar de Trás-os-Montes e Alto Douro, 5000-508 Vila Real, Portugal;
| | - Maria José Saavedra
- Laboratory Medical Microbiology, Department of Veterinary Sciences, CITAB-Centre for the Research and Technology Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal;
| | - Aida Duarte
- Department of Microbiology and Immunology, Faculty of Pharmacy, Universidade de Lisboa, 1649-033 Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, 2829-511 Monte da Caparica, Portugal
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30
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Perdigão J, Silva C, Maltez F, Machado D, Miranda A, Couto I, Rabna P, Florez de Sessions P, Phelan J, Pain A, McNerney R, Hibberd ML, Mokrousov I, Clark TG, Viveiros M, Portugal I. Emergence of multidrug-resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing. Emerg Microbes Infect 2020; 9:1342-1353. [PMID: 32538300 PMCID: PMC7473242 DOI: 10.1080/22221751.2020.1774425] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 04/17/2020] [Accepted: 05/14/2020] [Indexed: 11/22/2022]
Abstract
The Beijing genotype comprises a highly disseminated strain type that is frequently associated with multidrug resistant (MDR) tuberculosis (TB) and increased transmissibility but, countries such as Portugal and Guinea-Bissau fall outside the regions phylogeographically associated with this specific genotype. Nevertheless, recent data shows that this genotype might be gradually emerging in these two countries as an underlying cause of primary MDR-TB. Here, we describe the emergence of Mycobacterium tuberculosis Beijing strains associated with MDR-TB in Portugal and Guinea-Bissau demonstrating the presence of the well described superclusters 100-32 and 94-32 in Portugal and Guinea-Bissau, respectively. Genome-wide analysis and comparison with a global genomic dataset of M. tuberculosis Beijing strains, revealed the presence of two genomic clusters encompassing isolates from Portugal and Guinea-Bissau, GC1 (n = 121) and GC2 (n = 39), both of which bore SNP signatures compatible with the 100-32/B0/W148 and 94-32/Central Asia Outbreak clades, respectively. Moreover, GC2 encompasses a cross-border cluster between Portugal, Guinea-Bissau and Brazil thus supporting migration-associated introduction of MDR-TB and subsequent clonal expansion at the community-level. The comparison with global Beijing datasets demonstrates the global reach of the disease and its complex dissemination across multiple countries while in parallel there are clear microevolutionary trajectories towards extensively drug resistant TB.
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Affiliation(s)
- João Perdigão
- iMed.ULisboa – Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Carla Silva
- iMed.ULisboa – Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Fernando Maltez
- Serviço de Doenças Infecciosas, Hospital de Curry Cabral-CHLC, Lisboa, Portugal
| | - Diana Machado
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Anabela Miranda
- National Mycobacterium Reference Laboratory, Instituto Nacional de Saúde Dr. Ricardo Jorge, Porto, Portugal
| | - Isabel Couto
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Paulo Rabna
- Instituto Nacional de Saúde Pública/Projecto de Saúde de Bandim (INASA/PSB), Bissau,Guiné-Bissau
| | | | - Jody Phelan
- London School of Hygiene & Tropical Medicine, London, UK
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Ruth McNerney
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St Petersburg Pasteur Institute, St Petersburg, Russia
| | - Taane G. Clark
- London School of Hygiene & Tropical Medicine, London, UK
| | - Miguel Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Isabel Portugal
- iMed.ULisboa – Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
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31
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Tunstall T, Portelli S, Phelan J, Clark TG, Ascher DB, Furnham N. Combining structure and genomics to understand antimicrobial resistance. Comput Struct Biotechnol J 2020; 18:3377-3394. [PMID: 33294134 PMCID: PMC7683289 DOI: 10.1016/j.csbj.2020.10.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 02/07/2023] Open
Abstract
Antimicrobials against bacterial, viral and parasitic pathogens have transformed human and animal health. Nevertheless, their widespread use (and misuse) has led to the emergence of antimicrobial resistance (AMR) which poses a potentially catastrophic threat to public health and animal husbandry. There are several routes, both intrinsic and acquired, by which AMR can develop. One major route is through non-synonymous single nucleotide polymorphisms (nsSNPs) in coding regions. Large scale genomic studies using high-throughput sequencing data have provided powerful new ways to rapidly detect and respond to such genetic mutations linked to AMR. However, these studies are limited in their mechanistic insight. Computational tools can rapidly and inexpensively evaluate the effect of mutations on protein function and evolution. Subsequent insights can then inform experimental studies, and direct existing or new computational methods. Here we review a range of sequence and structure-based computational tools, focussing on tools successfully used to investigate mutational effect on drug targets in clinically important pathogens, particularly Mycobacterium tuberculosis. Combining genomic results with the biophysical effects of mutations can help reveal the molecular basis and consequences of resistance development. Furthermore, we summarise how the application of such a mechanistic understanding of drug resistance can be applied to limit the impact of AMR.
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Affiliation(s)
- Tanushree Tunstall
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Stephanie Portelli
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Australia
| | - Jody Phelan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - David B. Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Australia
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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32
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Grignard L, Nolder D, Sepúlveda N, Berhane A, Mihreteab S, Kaaya R, Phelan J, Moser K, van Schalkwyk DA, Campino S, Parr JB, Juliano JJ, Chiodini P, Cunningham J, Sutherland CJ, Drakeley C, Beshir KB. A novel multiplex qPCR assay for detection of Plasmodium falciparum with histidine-rich protein 2 and 3 (pfhrp2 and pfhrp3) deletions in polyclonal infections. EBioMedicine 2020; 55:102757. [PMID: 32403083 PMCID: PMC7218259 DOI: 10.1016/j.ebiom.2020.102757] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/13/2020] [Accepted: 03/30/2020] [Indexed: 11/02/2022] Open
Abstract
BACKGROUND Many health facilities in malaria endemic countries are dependent on Rapid diagnostic tests (RDTs) for diagnosis and some National Health Service (NHS) hospitals without expert microscopists rely on them for diagnosis out of hours. The emergence of P. falciparum lacking the gene encoding histidine-rich protein 2 and 3 (HRP2 and HRP3) and escaping RDT detection threatens progress in malaria control and elimination. Currently, confirmation of RDT negative due to the deletion of pfhrp2 and pfhrp3, which encodes a cross-reactive protein isoform, requires a series of PCR assays. These tests have different limits of detection and many laboratories have reported difficulty in confirming the absence of the deletions with certainty. METHODS We developed and validated a novel and rapid multiplex real time quantitative (qPCR) assay to detect pfhrp2, pfhrp3, confirmatory parasite and human reference genes simultaneously. We also applied the assay to detect pfhrp2 and pfhrp3 deletion in 462 field samples from different endemic countries and UK travellers. RESULTS The qPCR assay demonstrated diagnostic sensitivity of 100% (n = 19, 95% CI= (82.3%; 100%)) and diagnostic specificity of 100% (n = 31; 95% CI= (88.8%; 100%)) in detecting pfhrp2 and pfhrp3 deletions. In addition, the assay estimates P. falciparum parasite density and accurately detects pfhrp2 and pfhrp3 deletions masked in polyclonal infections. We report pfhrp2 and pfhrp3 deletions in parasite isolates from Kenya, Tanzania and in UK travellers. INTERPRETATION The new qPCR is easily scalable to routine surveillance studies in countries where P. falciparum parasites lacking pfhrp2 and pfhrp3 are a threat to malaria control.
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Affiliation(s)
- Lynn Grignard
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Debbie Nolder
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom; PHE Malaria Reference Laboratory, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Nuno Sepúlveda
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom; Centre of Statistics and Applications of University of Lisbon, Portugal
| | - Araia Berhane
- Communicable Diseases Control Division, Ministry of Health, Eritrea
| | - Selam Mihreteab
- Communicable Diseases Control Division, Ministry of Health, Eritrea
| | - Robert Kaaya
- Kilimanjaro Christian Medical University College, Tanzania
| | - Jody Phelan
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Kara Moser
- University of North Carolina at Chapel Hill, United States
| | - Donelly A van Schalkwyk
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Susana Campino
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | | | | | - Peter Chiodini
- PHE Malaria Reference Laboratory, London School of Hygiene & Tropical Medicine, United Kingdom; UCL Hospital for Tropical Diseases, United Kingdom
| | | | - Colin J Sutherland
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Chris Drakeley
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Khalid B Beshir
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, United Kingdom.
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33
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Doyle RM, O'Sullivan DM, Aller SD, Bruchmann S, Clark T, Coello Pelegrin A, Cormican M, Diez Benavente E, Ellington MJ, McGrath E, Motro Y, Phuong Thuy Nguyen T, Phelan J, Shaw LP, Stabler RA, van Belkum A, van Dorp L, Woodford N, Moran-Gilad J, Huggett JF, Harris KA. Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study. Microb Genom 2020; 6:e000335. [PMID: 32048983 PMCID: PMC7067211 DOI: 10.1099/mgen.0.000335] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/17/2020] [Indexed: 01/21/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a threat to public health. Clinical microbiology laboratories typically rely on culturing bacteria for antimicrobial-susceptibility testing (AST). As the implementation costs and technical barriers fall, whole-genome sequencing (WGS) has emerged as a 'one-stop' test for epidemiological and predictive AST results. Few published comparisons exist for the myriad analytical pipelines used for predicting AMR. To address this, we performed an inter-laboratory study providing sets of participating researchers with identical short-read WGS data from clinical isolates, allowing us to assess the reproducibility of the bioinformatic prediction of AMR between participants, and identify problem cases and factors that lead to discordant results. We produced ten WGS datasets of varying quality from cultured carbapenem-resistant organisms obtained from clinical samples sequenced on either an Illumina NextSeq or HiSeq instrument. Nine participating teams ('participants') were provided these sequence data without any other contextual information. Each participant used their choice of pipeline to determine the species, the presence of resistance-associated genes, and to predict susceptibility or resistance to amikacin, gentamicin, ciprofloxacin and cefotaxime. We found participants predicted different numbers of AMR-associated genes and different gene variants from the same clinical samples. The quality of the sequence data, choice of bioinformatic pipeline and interpretation of the results all contributed to discordance between participants. Although much of the inaccurate gene variant annotation did not affect genotypic resistance predictions, we observed low specificity when compared to phenotypic AST results, but this improved in samples with higher read depths. Had the results been used to predict AST and guide treatment, a different antibiotic would have been recommended for each isolate by at least one participant. These challenges, at the final analytical stage of using WGS to predict AMR, suggest the need for refinements when using this technology in clinical settings. Comprehensive public resistance sequence databases, full recommendations on sequence data quality and standardization in the comparisons between genotype and resistance phenotypes will all play a fundamental role in the successful implementation of AST prediction using WGS in clinical microbiology laboratories.
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Affiliation(s)
- Ronan M. Doyle
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
- Microbiology Department, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Denise M. O'Sullivan
- Molecular and Cell Biology Team, National Measurement Laboratory, Queens Road, Teddington, Middlesex, UK
| | - Sean D. Aller
- Institute for Infection and Immunity, St George’s, University of London, Cranmer Terrace, London, UK
| | - Sebastian Bruchmann
- Pathogen Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Taane Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Andreu Coello Pelegrin
- Clinical Unit, bioMérieux, La Balme Les Grottes, France
- Vaccine and Infectious Disease Institute, Laboratory of Medical Microbiology, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Ernest Diez Benavente
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Elaine McGrath
- Carbapenemase-Producing Enterobacterales Reference Laboratory, Department of Medical Microbiology, University Hospital Galway, Galway, Ireland
| | - Yair Motro
- School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Thi Phuong Thuy Nguyen
- Department of BiNano Technology, College of BiNano Technology, Gachon University, Seoul, Republic of Korea
| | - Jody Phelan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Liam P. Shaw
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | | | - Lucy van Dorp
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK
| | - Neil Woodford
- NIS Laboratories, National Infection Service, Public Health England, London, UK
| | - Jacob Moran-Gilad
- School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jim F. Huggett
- Molecular and Cell Biology Team, National Measurement Laboratory, Queens Road, Teddington, Middlesex, UK
- School of Biosciences and Medicine, Faculty of Health and Medical Science, University of Surrey, Guildford, UK
| | - Kathryn A. Harris
- Microbiology Department, Great Ormond Street Hospital NHS Foundation Trust, London, UK
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Higgins M, Ravenhall M, Ward D, Phelan J, Ibrahim A, Forrest MS, Clark TG, Campino S. PrimedRPA: primer design for recombinase polymerase amplification assays. Bioinformatics 2019; 35:682-684. [PMID: 30101342 PMCID: PMC6379019 DOI: 10.1093/bioinformatics/bty701] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/31/2018] [Accepted: 08/07/2018] [Indexed: 11/26/2022] Open
Abstract
Summary Recombinase polymerase amplification (RPA), an isothermal nucleic acid amplification method, is enhancing our ability to detect a diverse array of pathogens, thereby assisting the diagnosis of infectious diseases and the detection of microorganisms in food and water. However, new bioinformatics tools are needed to automate and improve the design of the primers and probes sets to be used in RPA, particularly to account for the high genetic diversity of circulating pathogens and cross detection of genetically similar organisms. PrimedRPA is a python-based package that automates the creation and filtering of RPA primers and probe sets. It aligns several sequences to identify conserved targets, and filters regions that cross react with possible background organisms. Availability and implementation PrimedRPA was implemented in Python 3 and supported on Linux and MacOS and is freely available from http://pathogenseq.lshtm.ac.uk/PrimedRPA.html. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthew Higgins
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - Matt Ravenhall
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - Daniel Ward
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - Jody Phelan
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | - Amy Ibrahim
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine (LSHTM), London, UK
| | | | - Taane G Clark
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine (LSHTM), London, UK.,Department of Infectious Disease Epidemiology, LSHTM, London, UK
| | - Susana Campino
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine (LSHTM), London, UK
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35
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Deelder W, Christakoudi S, Phelan J, Benavente ED, Campino S, McNerney R, Palla L, Clark TG. Machine Learning Predicts Accurately Mycobacterium tuberculosis Drug Resistance From Whole Genome Sequencing Data. Front Genet 2019; 10:922. [PMID: 31616478 PMCID: PMC6775242 DOI: 10.3389/fgene.2019.00922] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/02/2019] [Indexed: 11/25/2022] Open
Abstract
Background: Tuberculosis disease, caused by Mycobacterium tuberculosis, is a major public health problem. The emergence of M. tuberculosis strains resistant to existing treatments threatens to derail control efforts. Resistance is mainly conferred by mutations in genes coding for drug targets or converting enzymes, but our knowledge of these mutations is incomplete. Whole genome sequencing (WGS) is an increasingly common approach to rapidly characterize isolates and identify mutations predicting antimicrobial resistance and thereby providing a diagnostic tool to assist clinical decision making. Methods: We applied machine learning approaches to 16,688 M. tuberculosis isolates that have undergone WGS and laboratory drug-susceptibility testing (DST) across 14 antituberculosis drugs, with 22.5% of samples being multidrug resistant and 2.1% being extensively drug resistant. We used non-parametric classification-tree and gradient-boosted-tree models to predict drug resistance and uncover any associated novel putative mutations. We fitted separate models for each drug, with and without "co-occurrent resistance" markers known to be causing resistance to drugs other than the one of interest. Predictive performance was measured using sensitivity, specificity, and the area under the receiver operating characteristic curve, assuming DST results as the gold standard. Results: The predictive performance was highest for resistance to first-line drugs, amikacin, kanamycin, ciprofloxacin, moxifloxacin, and multidrug-resistant tuberculosis (area under the receiver operating characteristic curve above 96%), and lowest for third-line drugs such as D-cycloserine and Para-aminosalisylic acid (area under the curve below 85%). The inclusion of co-occurrent resistance markers led to improved performance for some drugs and superior results when compared to similar models in other large-scale studies, which had smaller sample sizes. Overall, the gradient-boosted-tree models performed better than the classification-tree models. The mutation-rank analysis detected no new single nucleotide polymorphisms linked to drug resistance. Discordance between DST and genotypically inferred resistance may be explained by DST errors, novel rare mutations, hetero-resistance, and nongenomic drivers such as efflux-pump upregulation. Conclusion: Our work demonstrates the utility of machine learning as a flexible approach to drug resistance prediction that is able to accommodate a much larger number of predictors and to summarize their predictive ability, thus assisting clinical decision making and single nucleotide polymorphism detection in an era of increasing WGS data generation.
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Affiliation(s)
- Wouter Deelder
- Faculties of Epidemiology & Population Health and Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Dalberg Advisors, Geneva, Switzerland
| | - Sofia Christakoudi
- Faculties of Epidemiology & Population Health and Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Epidemiology and Biostatistics Department, Imperial College London, St Mary’s Campus, London, United Kingdom
| | - Jody Phelan
- Faculties of Epidemiology & Population Health and Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Ernest Diez Benavente
- Faculties of Epidemiology & Population Health and Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Faculties of Epidemiology & Population Health and Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Ruth McNerney
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Luigi Palla
- Faculties of Epidemiology & Population Health and Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Faculties of Epidemiology & Population Health and Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Ajawatanawong P, Yanai H, Smittipat N, Disratthakit A, Yamada N, Miyahara R, Nedsuwan S, Imasanguan W, Kantipong P, Chaiyasirinroje B, Wongyai J, Plitphonganphim S, Tantivitayakul P, Phelan J, Parkhill J, Clark TG, Hibberd ML, Ruangchai W, Palittapongarnpim P, Juthayothin T, Thawornwattana Y, Viratyosin W, Tongsima S, Mahasirimongkol S, Tokunaga K, Palittapongarnpim P. A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages. Sci Rep 2019; 9:13718. [PMID: 31548561 PMCID: PMC6757101 DOI: 10.1038/s41598-019-50078-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 08/27/2019] [Indexed: 11/08/2022] Open
Abstract
Global Mycobacterium tuberculosis population comprises 7 major lineages. The Beijing strains, particularly the ones classified as Modern groups, have been found worldwide, frequently associated with drug resistance, younger ages, outbreaks and appear to be expanding. Here, we report analysis of whole genome sequences of 1170 M. tuberculosis isolates together with their patient profiles. Our samples belonged to Lineage 1-4 (L1-L4) with those of L1 and L2 being equally dominant. Phylogenetic analysis revealed several new or rare sublineages. Differential associations between sublineages of M. tuberculosis and patient profiles, including ages, ethnicity, HIV (human immunodeficiency virus) infection and drug resistance were demonstrated. The Ancestral Beijing strains and some sublineages of L4 were associated with ethnic minorities while L1 was more common in Thais. L2.2.1.Ancestral 4 surprisingly had a mutation that is typical of the Modern Beijing sublineages and was common in Akha and Lahu tribes who have migrated from Southern China in the last century. This may indicate that the evolutionary transition from the Ancestral to Modern Beijing sublineages might be gradual and occur in Southern China, where the presence of multiple ethnic groups might have allowed for the circulations of various co-evolving sublineages which ultimately lead to the emergence of the Modern Beijing strains.
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Affiliation(s)
- Pravech Ajawatanawong
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | - Hideki Yanai
- Fukujuji Hospital, Japan Anti-Tuberculosis Association (JATA), Kiyose, Japan
| | - Nat Smittipat
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Areeya Disratthakit
- Department of Medical Sciences, Ministry of Public Health, Tiwanon Road, Nonthaburi, Thailand
| | - Norio Yamada
- Research Institute of Tuberculosis, JATA, Kiyose, Japan
| | - Reiko Miyahara
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Supalert Nedsuwan
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | - Worarat Imasanguan
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | - Pacharee Kantipong
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | | | | | - Supada Plitphonganphim
- Department of Biostatistics, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Pornpen Tantivitayakul
- Department of Oral Microbiology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Jody Phelan
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Taane G Clark
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Wuthiwat Ruangchai
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | | | - Tada Juthayothin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Yuttapong Thawornwattana
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | - Wasna Viratyosin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | | | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Prasit Palittapongarnpim
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand.
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand.
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37
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Perdigão J, Modesto A, Pereira AL, Neto O, Matos V, Godinho A, Phelan J, Charleston J, Spadar A, de Sessions PF, Hibberd M, Campino S, Costa A, Fernandes F, Ferreira F, Correia AB, Gonçalves L, Clark TG, Duarte A. Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital. Microb Genom 2019; 7:000349. [PMID: 32234124 PMCID: PMC8627661 DOI: 10.1099/mgen.0.000349] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/14/2020] [Indexed: 01/08/2023] Open
Abstract
Klebsiella pneumoniae has emerged as an important nosocomial pathogen, with whole-genome sequencing (WGS) significantly improving our ability to characterize associated outbreaks. Our study sought to perform a genome-wide analysis of multiclonal K. pneumoniae isolates (n=39; 23 patients) producing extended spectrum beta-lactamases and/or carbapenemases sourced between 2011 and 2016 in a Portuguese tertiary-care hospital. All isolates showed resistance to third-generation cephalosporins and six isolates (five patients) were also carbapenem resistant. Genome-wide-based phylogenetic analysis revealed a topology representing ongoing dissemination of three main sequence-type (ST) clades (ST15, ST147 and ST307) and transmission across different wards, compatible with missing links that can take the form of undetected colonized patients. Two carbapenemase-coding genes were detected: blaKPC-3, located on a Tn4401d transposon, and blaGES-5 on a novel class 3 integron. Additionally, four genes coding for ESBLs (blaBEL-1, blaCTX-M-8, blaCTX-M-15 and blaCTX-M-32) were also detected. ESBL horizontal dissemination across five clades is highlighted by the similar genetic environments of blaCTX-M-15 gene upstream of ISEcp1 on a Tn3-like transposon. Overall, this study provides a high-resolution genome-wide perspective on the epidemiology of ESBL and carbapenemase-producing K. pneumoniae in a healthcare setting while contributing for the adoption of appropriate intervention and prevention strategies.
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Affiliation(s)
- João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - Ana Modesto
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - A. L. Pereira
- Clinical Pathology Unit. Hospital SAMS, Lisboa, Portugal
| | - O. Neto
- Infection Control Commission, Hospital SAMS, Lisboa, Portugal
| | - V. Matos
- Infection Control Commission, Hospital SAMS, Lisboa, Portugal
| | - A. Godinho
- Infection Control Commission, Hospital SAMS, Lisboa, Portugal
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - James Charleston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Martin Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - A. Costa
- Intensive Care Medicine Unit, Hospital SAMS, Lisboa, Portugal
| | - F. Fernandes
- Intensive Care Medicine Unit, Hospital SAMS, Lisboa, Portugal
| | - F. Ferreira
- Intensive Care Medicine Unit, Hospital SAMS, Lisboa, Portugal
| | - A. B. Correia
- Clinical Pathology Unit. Hospital SAMS, Lisboa, Portugal
| | | | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Aida Duarte
- Faculty of Pharmacy, Universidade de Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Portugal
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38
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Oppong YEA, Phelan J, Perdigão J, Machado D, Miranda A, Portugal I, Viveiros M, Clark TG, Hibberd ML. Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance. BMC Genomics 2019; 20:252. [PMID: 30922221 PMCID: PMC6440112 DOI: 10.1186/s12864-019-5615-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 03/15/2019] [Indexed: 12/30/2022] Open
Abstract
Background Continuing evolution of the Mycobacterium tuberculosis (Mtb) complex genomes associated with resistance to anti-tuberculosis drugs is threatening tuberculosis disease control efforts. Both multi- and extensively drug resistant Mtb (MDR and XDR, respectively) are increasing in prevalence, but the full set of Mtb genes involved are not known. There is a need for increased sensitivity of genome-wide approaches in order to elucidate the genetic basis of anti-microbial drug resistance and gain a more detailed understanding of Mtb genome evolution in a context of widespread antimicrobial therapy. Population structure within the Mtb complex, due to clonal expansion, lack of lateral gene transfer and low levels of recombination between lineages, may be reducing statistical power to detect drug resistance associated variants. Results To investigate the effect of lineage-specific effects on the identification of drug resistance associations, we applied genome-wide association study (GWAS) and convergence-based (PhyC) methods to multiple drug resistance phenotypes of a global dataset of Mtb lineages 2 and 4, using both lineage-wise and combined approaches. We identify both well-established drug resistance variants and novel associations; uniquely identifying associations for both lineage-specific and -combined GWAS analyses. We report 17 potential novel associations between antimicrobial resistance phenotypes and Mtb genomic variants. Conclusions For GWAS, both lineage-specific and -combined analyses are useful, whereas PhyC may perform better in contexts of greater diversity. Unique associations with XDR in lineage-specific analyses provide evidence of diverging evolutionary trajectories between lineages 2 and 4 in response to antimicrobial drug therapy. Electronic supplementary material The online version of this article (10.1186/s12864-019-5615-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yaa E A Oppong
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Jody Phelan
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - João Perdigão
- iMed.ULisboa - Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Diana Machado
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Anabela Miranda
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | - Isabel Portugal
- iMed.ULisboa - Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Miguel Viveiros
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Taane G Clark
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.,Faculty of Epidemiology and Population Health, LSHTM, London, UK
| | - Martin L Hibberd
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
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Campos MC, Dombrowski JG, Phelan J, Marinho CRF, Hibberd M, Clark TG, Campino S. Zika might not be acting alone: Using an ecological study approach to investigate potential co-acting risk factors for an unusual pattern of microcephaly in Brazil. PLoS One 2018; 13:e0201452. [PMID: 30110370 PMCID: PMC6093667 DOI: 10.1371/journal.pone.0201452] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 07/16/2018] [Indexed: 01/14/2023] Open
Abstract
Zika virus infections can cause a range of neurologic disorders including congenital microcephaly. However, while Zika infections have been notified across all regions in Brazil, there has been an unusual number of congenital microcephaly case notifications concentrated in the Northeast of the country. To address this observation, we investigated epidemiological data (2014–2016) on arbovirus co-distribution, environmental and socio-economic factors for each region in Brazil. Data on arbovirus reported cases and microcephaly were collected from several Brazilian Ministry of Health databases for each Federal unit. These were complemented by environmental management, social economic and Aedes aegypti infestation index data, extracted from multiple databases. Spatial time “ecological” analysis on the number of arboviruses transmitted by Aedes mosquitoes in Brazil show that the distribution of dengue and Zika was widespread in the whole country, with higher incidence in the West-Central region. However, reported chikungunya cases were higher in the Northeast, the region also with the highest number of microcephaly cases registered. Social economic factors (human development index and poverty index) and environmental management (water supply/storage and solid waste management) pointed the Northeast as the less wealthy region. The Northeast is also the region with the highest risk of Aedes aegypti house infestation due to the man-made larval habitats. In summary, the results of our ecological analysis support the hypothesis that the unusual distribution of microcephaly might not be due to Zika infection alone and could be accentuated by poverty and previous or co-infection with other pathogens. Our study reinforces the link between poverty and the risk of disease and the need to understand the effect on pathogenesis of sequential exposure to arboviruses and co-viral infections. Comprehensive large-scale cohort studies are required to corroborate our findings. We recommend that the list of infectious diseases screened, particularly during pregnancy, be regularly updated to include and effectively differentiate all viruses from ongoing outbreaks.
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Affiliation(s)
- Monica C. Campos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
| | - Jamille G. Dombrowski
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Claudio R. F. Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Martin Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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40
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Palittapongarnpim P, Ajawatanawong P, Viratyosin W, Smittipat N, Disratthakit A, Mahasirimongkol S, Yanai H, Yamada N, Nedsuwan S, Imasanguan W, Kantipong P, Chaiyasirinroje B, Wongyai J, Toyo-Oka L, Phelan J, Parkhill J, Clark TG, Hibberd ML, Ruengchai W, Palittapongarnpim P, Juthayothin T, Tongsima S, Tokunaga K. Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates. Sci Rep 2018; 8:11597. [PMID: 30072734 PMCID: PMC6072702 DOI: 10.1038/s41598-018-29986-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/20/2018] [Indexed: 12/19/2022] Open
Abstract
Tuberculosis presents a global health challenge. Mycobacterium tuberculosis is divided into several lineages, each with a different geographical distribution. M. tuberculosis lineage 1 (L1) is common in the high-burden areas in East Africa and Southeast Asia. Although the founder effect contributes significantly to the phylogeographic profile, co-evolution between the host and M. tuberculosis may also play a role. Here, we reported the genomic analysis of 480 L1 isolates from patients in northern Thailand. The studied bacterial population was genetically diverse, allowing the identification of a total of 18 sublineages distributed into three major clades. The majority of isolates belonged to L1.1 followed by L1.2.1 and L1.2.2. Comparison of the single nucleotide variant (SNV) phylogenetic tree and the clades defined by spoligotyping revealed some monophyletic clades representing EAI2_MNL, EAI2_NTM and EAI6_BGD1 spoligotypes. Our work demonstrates that ambiguity in spoligotype assignment could be partially resolved if the entire DR region is investigated. Using the information to map L1 diversity across Southeast Asia highlighted differences in the dominant strain-types in each individual country, despite extensive interactions between populations over time. This finding supported the hypothesis that there is co-evolution between the bacteria and the host, and have implications for tuberculosis disease control.
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Affiliation(s)
- Prasit Palittapongarnpim
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand.
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand.
| | - Pravech Ajawatanawong
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | - Wasna Viratyosin
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Nat Smittipat
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Areeya Disratthakit
- Department of Medical Sciences, Ministry of Public Health, Tiwanon Road, Nonthaburi, Thailand
| | | | - Hideki Yanai
- TB-HIV Research Foundation, Chiangrai, Thailand
- Fukujuji Hospital, Japan Anti-tuberculosis Association (JATA), Kiyose, Japan
| | - Norio Yamada
- Research Institute of Tuberculosis, JATA, Kiyose, Japan
| | - Supalert Nedsuwan
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | - Worarat Imasanguan
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | - Pacharee Kantipong
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | | | | | - Licht Toyo-Oka
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Jody Phelan
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Taane G Clark
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Wuthiwat Ruengchai
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | | | - Tada Juthayothin
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Sissades Tongsima
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
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Herman LS, Fornace K, Phelan J, Grigg MJ, Anstey NM, William T, Moon RW, Blackman MJ, Drakeley CJ, Tetteh KKA. Identification and validation of a novel panel of Plasmodium knowlesi biomarkers of serological exposure. PLoS Negl Trop Dis 2018; 12:e0006457. [PMID: 29902183 PMCID: PMC6001954 DOI: 10.1371/journal.pntd.0006457] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/17/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Plasmodium knowlesi is the most common cause of malaria in Malaysian Borneo, with reporting limited to clinical cases presenting to health facilities and scarce data on the true extent of transmission. Serological estimations of transmission have been used with other malaria species to garner information about epidemiological patterns. However, there are a distinct lack of suitable serosurveillance tools for this neglected disease. METHODOLOGY/PRINCIPAL FINDINGS Using in silico tools, we designed and expressed four novel P. knowlesi protein products to address the distinct lack of suitable serosurveillance tools: PkSERA3 antigens 1 and 2, PkSSP2/TRAP and PkTSERA2 antigen 1. Antibody prevalence to these antigens was determined by ELISA for three time-points post-treatment from a hospital-based clinical treatment trial in Sabah, East Malaysia (n = 97 individuals; 241 total samples for all time points). Higher responses were observed for the PkSERA3 antigen 2 (67%, 65/97) across all time-points (day 0: 36.9% 34/92; day 7: 63.8% 46/72; day 28: 58.4% 45/77) with significant differences between the clinical cases and controls (n = 55, mean plus 3 SD) (day 0 p<0.0001; day 7 p<0.0001; day 28 p<0.0001). Using boosted regression trees, we developed models to classify P. knowlesi exposure (cross-validated AUC 88.9%; IQR 86.1-91.3%) and identified the most predictive antibody responses. CONCLUSIONS/SIGNIFICANCE The PkSERA3 antigen 2 had the highest relative variable importance in all models. Further validation of these antigens is underway to determine the specificity of these tools in the context of multi-species infections at the population level.
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Affiliation(s)
- Lou S. Herman
- Department Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kimberly Fornace
- Department Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jody Phelan
- Department Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew J. Grigg
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Nicholas M. Anstey
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Timothy William
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
- Clinical Research Centre, Queen Elizabeth Hospital, Kota Kinabalu, Sabah, Malaysia
- Jesselton Medical Centre, Kota Kinabalu, Sabah, Malaysia
| | - Robert W. Moon
- Department Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michael J. Blackman
- Department Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Malaria Biochemistry Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Chris J. Drakeley
- Department Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kevin K. A. Tetteh
- Department Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Sepúlveda N, Phelan J, Diez-Benavente E, Campino S, Clark TG, Hopkins H, Sutherland C, Drakeley CJ, Beshir KB. Global analysis of Plasmodium falciparum histidine-rich protein-2 (pfhrp2) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis. Infect Genet Evol 2018; 62:211-219. [PMID: 29729386 DOI: 10.1016/j.meegid.2018.04.039] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/24/2018] [Accepted: 04/29/2018] [Indexed: 02/02/2023]
Abstract
Many rapid diagnostic tests (RDT) used on suspected malaria cases are based on the detection of the protein encoded by the Plasmodium falciparum histidine-rich protein-2 (pfhrp2) gene, which shares a high sequence homology with pfhrp3 in the 3D7 reference genome. Parasite isolates showing pfhrp2 and pfhrp3 gene deletions have been emerging over the years, but a comprehensive genetic analysis of these variants is still lacking. With this purpose, genomic data from experimental P. falciparum genetic crosses between different laboratory lines (3D7, HB3, DD2, 7G8 and GB4) were first analysed (n = 98). The frequency of pfhrp2 deletions was consistent with a Mendelian prediction in HB3 × DD2 (56.7%; 95%CI = (39.5%-72.9%)). Moreover, the pfhrp2 and pfhrp3 deletions segregated independently of each other in the same genetic cross. Analysis of 3D7 × HB3 and 7G8 × GB4 estimated the probability of spontaneously generating a pfhrp2 deletion during sexual recombination to be up to 6.2%. Next, whole genome sequence data from 1970 P. falciparum isolates collected globally were analysed. Nine samples displayed depth of coverage consistent with pfhrp2 deletions (0.5%), but the corresponding split-read analysis could not confirm deletions in seven of these samples. Twenty-eight isolates had evidence of pfhrp3 deletions (1.4%), which are widespread in Southeast Asia. Finally, a meta-analysis of published data revealed a positive mean association between the frequencies of pfhrp2 and pfhrp3 deletions in Africa and South America. This result suggested a shared selective pressure acting on these genetic variants. In conclusion, evidence of genetic selection on both pfhrp2 and pfhrp3 deletions was presented, but experimental crosses do not provide evidence of a fitness cost of these variants. Further work is urgently needed to accurately determine the prevalence and the degree of association between these genetic variants, and the respective impact on diagnostic accuracy of many in-use RDT.
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Affiliation(s)
- Nuno Sepúlveda
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom; Centre of Statistics and its Applications of University of Lisbon, Faculdade de Ciências da Universidade de Lisboa, Bloco C6 - Piso 4, Campo Grande, 1749-016 Lisboa, Portugal.
| | - Jody Phelan
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Ernest Diez-Benavente
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Susana Campino
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Taane G Clark
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Heidi Hopkins
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Colin Sutherland
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Chris J Drakeley
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Khalid B Beshir
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
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43
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Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, Abdallah AM, Alghamdi S, Alsomali M, Ahmed AO, Portelli S, Oppong Y, Alves A, Bessa TB, Campino S, Caws M, Chatterjee A, Crampin AC, Dheda K, Furnham N, Glynn JR, Grandjean L, Ha DM, Hasan R, Hasan Z, Hibberd ML, Joloba M, Jones-López EC, Matsumoto T, Miranda A, Moore DJ, Mocillo N, Panaiotov S, Parkhill J, Penha C, Perdigão J, Portugal I, Rchiad Z, Robledo J, Sheen P, Shesha NT, Sirgel FA, Sola C, Sousa EO, Streicher EM, Van Helden P, Viveiros M, Warren RM, McNerney R, Pain A, Clark TG. Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nat Genet 2018; 50:764. [PMID: 29674744 DOI: 10.1038/s41588-018-0074-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article initially published, the URL listed for TubercuList was incorrect. The correct URL is https://mycobrowser.epfl.ch/. The error has been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Grant A Hill-Cawthorne
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Sydney Emerging Infections and Biosecurity Institute and School of Public Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Mridul B Nair
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Shahjahan Ali
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdallah M Abdallah
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mona Alsomali
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdallah O Ahmed
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Stephanie Portelli
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Yaa Oppong
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Adriana Alves
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | | | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, UK.,Pham Ngoc Thach Hospital for TB and Lung Diseases, Ho Chi Minh City, Vietnam
| | | | - Amelia C Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.,Karonga Prevention Study, Chilumba, Karonga, Malawi
| | - Keertan Dheda
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Nicholas Furnham
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.,Karonga Prevention Study, Chilumba, Karonga, Malawi
| | - Louis Grandjean
- Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Dang Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Diseases, Ho Chi Minh City, Vietnam
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edward C Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
| | | | - Anabela Miranda
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | - David J Moore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nora Mocillo
- Reference Laboratory of Tuberculosis Control, Buenos Aires, Argentina
| | - Stefan Panaiotov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Carlos Penha
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - João Perdigão
- iMed.ULisboa-Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Portugal
- iMed.ULisboa-Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Zineb Rchiad
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jaime Robledo
- Corporación para Investigaciones Biológicas, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Patricia Sheen
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | | | - Frik A Sirgel
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Christophe Sola
- Institute for Integrative Cell Biology, CEA, CNRS, Université Paris-Saclay, Orsay, France
| | - Erivelton Oliveira Sousa
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil.,Laboratorio Central de Saúde Pública Professor Gonçalo Moniz, Salvador, Brazil
| | - Elizabeth M Streicher
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Paul Van Helden
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Robert M Warren
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. .,Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa.
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia. .,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. .,Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
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Last AR, Pickering H, Roberts CH, Coll F, Phelan J, Burr SE, Cassama E, Nabicassa M, Seth-Smith HMB, Hadfield J, Cutcliffe LT, Clarke IN, Mabey DCW, Bailey RL, Clark TG, Thomson NR, Holland MJ. Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity. Genome Med 2018; 10:15. [PMID: 29482619 PMCID: PMC5828069 DOI: 10.1186/s13073-018-0521-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 02/13/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Chlamydia trachomatis (Ct) is the most common infectious cause of blindness and bacterial sexually transmitted infection worldwide. Ct strain-specific differences in clinical trachoma suggest that genetic polymorphisms in Ct may contribute to the observed variability in severity of clinical disease. METHODS Using Ct whole genome sequences obtained directly from conjunctival swabs, we studied Ct genomic diversity and associations between Ct genetic polymorphisms with ocular localization and disease severity in a treatment-naïve trachoma-endemic population in Guinea-Bissau, West Africa. RESULTS All Ct sequences fall within the T2 ocular clade phylogenetically. This is consistent with the presence of the characteristic deletion in trpA resulting in a truncated non-functional protein and the ocular tyrosine repeat regions present in tarP associated with ocular tissue localization. We have identified 21 Ct non-synonymous single nucleotide polymorphisms (SNPs) associated with ocular localization, including SNPs within pmpD (odds ratio, OR = 4.07, p* = 0.001) and tarP (OR = 0.34, p* = 0.009). Eight synonymous SNPs associated with disease severity were found in yjfH (rlmB) (OR = 0.13, p* = 0.037), CTA0273 (OR = 0.12, p* = 0.027), trmD (OR = 0.12, p* = 0.032), CTA0744 (OR = 0.12, p* = 0.041), glgA (OR = 0.10, p* = 0.026), alaS (OR = 0.10, p* = 0.032), pmpE (OR = 0.08, p* = 0.001) and the intergenic region CTA0744-CTA0745 (OR = 0.13, p* = 0.043). CONCLUSIONS This study demonstrates the extent of genomic diversity within a naturally circulating population of ocular Ct and is the first to describe novel genomic associations with disease severity. These findings direct investigation of host-pathogen interactions that may be important in ocular Ct pathogenesis and disease transmission.
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Affiliation(s)
- A. R. Last
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - H. Pickering
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - C. h. Roberts
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - F. Coll
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - J. Phelan
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - S. E. Burr
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, Gambia
| | - E. Cassama
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea-Bissau
| | - M. Nabicassa
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea-Bissau
| | - H. M. B. Seth-Smith
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Clinical Microbiology, Universitätsspital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - J. Hadfield
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - L. T. Cutcliffe
- Molecular Microbiology Group, University of Southampton Medical School, Southampton, UK
| | - I. N. Clarke
- Molecular Microbiology Group, University of Southampton Medical School, Southampton, UK
| | - D. C. W. Mabey
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - R. L. Bailey
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - T. G. Clark
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - N. R. Thomson
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - M. J. Holland
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
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Shah N, Jackson L, Phelan J, Corton M. 16: Anterior and medial thigh anatomy in female cadavers: Clinical applications to transobturator tape sling excision. Am J Obstet Gynecol 2018. [DOI: 10.1016/j.ajog.2017.12.200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, Abdallah AM, Alghamdi S, Alsomali M, Ahmed AO, Portelli S, Oppong Y, Alves A, Bessa TB, Campino S, Caws M, Chatterjee A, Crampin AC, Dheda K, Furnham N, Glynn JR, Grandjean L, Minh Ha D, Hasan R, Hasan Z, Hibberd ML, Joloba M, Jones-López EC, Matsumoto T, Miranda A, Moore DJ, Mocillo N, Panaiotov S, Parkhill J, Penha C, Perdigão J, Portugal I, Rchiad Z, Robledo J, Sheen P, Shesha NT, Sirgel FA, Sola C, Oliveira Sousa E, Streicher EM, Helden PV, Viveiros M, Warren RM, McNerney R, Pain A, Clark TG. Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nat Genet 2018; 50:307-316. [PMID: 29358649 DOI: 10.1038/s41588-017-0029-0] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 12/01/2017] [Indexed: 12/30/2022]
Abstract
To characterize the genetic determinants of resistance to antituberculosis drugs, we performed a genome-wide association study (GWAS) of 6,465 Mycobacterium tuberculosis clinical isolates from more than 30 countries. A GWAS approach within a mixed-regression framework was followed by a phylogenetics-based test for independent mutations. In addition to mutations in established and recently described resistance-associated genes, novel mutations were discovered for resistance to cycloserine, ethionamide and para-aminosalicylic acid. The capacity to detect mutations associated with resistance to ethionamide, pyrazinamide, capreomycin, cycloserine and para-aminosalicylic acid was enhanced by inclusion of insertions and deletions. Odds ratios for mutations within candidate genes were found to reflect levels of resistance. New epistatic relationships between candidate drug-resistance-associated genes were identified. Findings also suggest the involvement of efflux pumps (drrA and Rv2688c) in the emergence of resistance. This study will inform the design of new diagnostic tests and expedite the investigation of resistance and compensatory epistatic mechanisms.
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Affiliation(s)
- Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Grant A Hill-Cawthorne
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Sydney Emerging Infections and Biosecurity Institute and School of Public Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Mridul B Nair
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Shahjahan Ali
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdallah M Abdallah
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mona Alsomali
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdallah O Ahmed
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Stephanie Portelli
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Yaa Oppong
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Adriana Alves
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | | | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, UK
- Pham Ngoc Thach Hospital for TB and Lung Diseases, Ho Chi Minh City, Vietnam
| | | | - Amelia C Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Karonga Prevention Study, Chilumba, Karonga, Malawi
| | - Keertan Dheda
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Nicholas Furnham
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Karonga Prevention Study, Chilumba, Karonga, Malawi
| | - Louis Grandjean
- Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Dang Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Diseases, Ho Chi Minh City, Vietnam
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edward C Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
| | | | - Anabela Miranda
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | - David J Moore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nora Mocillo
- Reference Laboratory of Tuberculosis Control, Buenos Aires, Argentina
| | - Stefan Panaiotov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Carlos Penha
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - João Perdigão
- iMed.ULisboa-Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Portugal
- iMed.ULisboa-Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Zineb Rchiad
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jaime Robledo
- Corporación para Investigaciones Biológicas, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Patricia Sheen
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | | | - Frik A Sirgel
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Christophe Sola
- Institute for Integrative Cell Biology, CEA, CNRS, Université Paris-Saclay, Orsay, France
| | - Erivelton Oliveira Sousa
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Laboratorio Central de Saúde Pública Professor Gonçalo Moniz, Salvador, Brazil
| | - Elizabeth M Streicher
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Paul Van Helden
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Robert M Warren
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa.
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
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Phelan J, de Sessions PF, Tientcheu L, Perdigao J, Machado D, Hasan R, Hasan Z, Bergval IL, Anthony R, McNerney R, Antonio M, Portugal I, Viveiros M, Campino S, Hibberd ML, Clark TG. Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally. Sci Rep 2018; 8:160. [PMID: 29317751 PMCID: PMC5760664 DOI: 10.1038/s41598-017-18188-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/07/2017] [Indexed: 11/30/2022] Open
Abstract
DNA methylation is an epigenetic modification of the genome involved in regulating crucial cellular processes, including transcription and chromosome stability. Advances in PacBio sequencing technologies can be used to robustly reveal methylation sites. The methylome of the Mycobacterium tuberculosis complex is poorly understood but may be involved in virulence, hypoxic survival and the emergence of drug resistance. In the most extensive study to date, we characterise the methylome across the 4 major lineages of M. tuberculosis and 2 lineages of M. africanum, the leading causes of tuberculosis disease in humans. We reveal lineage-specific methylated motifs and strain-specific mutations that are abundant globally and likely to explain loss of function in the respective methyltransferases. Our work provides a set of sixteen new complete reference genomes for the Mycobacterium tuberculosis complex, including complete lineage 5 genomes. Insights into lineage-specific methylomes will further elucidate underlying biological mechanisms and other important phenotypes of the epi-genome.
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Affiliation(s)
- Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Leopold Tientcheu
- Vaccines and Immunity Theme, Medical Research Council Unit, Fajara, The Gambia
| | - Joao Perdigao
- iMed.ULisboa - Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Diana Machado
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Indra L Bergval
- Royal Tropical Institute, KIT Biomedical Research, Amsterdam, The Netherlands
| | - Richard Anthony
- Royal Tropical Institute, KIT Biomedical Research, Amsterdam, The Netherlands
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Cape Town, South Africa
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council Unit, Fajara, The Gambia
| | - Isabel Portugal
- iMed.ULisboa - Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
- Genome Institute of Singapore, Biopolis, Singapore.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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48
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Saxena D, Li Y, Devota A, Pushalkar S, Abrams W, Barber C, Corby P, Poles M, Phelan J, Malamud D. Modulation of the orodigestive tract microbiome in HIV-infected patients. Oral Dis 2017; 22 Suppl 1:73-8. [PMID: 27109275 DOI: 10.1111/odi.12392] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
More than 37 million people are living with human immunodeficiency virus 1 (HIV), and more people than ever received lifesaving antiretroviral therapy worldwide. HIV-1 infection disrupts the intestinal immune system, leading to microbial translocation and systemic immune activation. We investigated the impact of HIV-1 infection on the GI microbiome and its association with host immune activation. The data indicated that the microbiome was different in HIV-positive and HIV-negative individuals. The initial sequence analysis of saliva indicated that there were major differences in the phyla of Bacteroidetes, Firmicutes, Proteobacteria, and TM7. Phylum Tenericutes was only seen in HIV-positive saliva. At the family level, we identified differences in Streptococcacea, Prevotellaceae, Porphyromonadaceae, and Neisseriaceae, whereas data from various sites in GI tract indicated that Prevotella melaninigencia, Fusobacterium necrophorum, Burkholderia, Bradyrhizobium, Ralstonia, and Eubacterium biforme were predominant but differentially present at various sites. Furthermore, there was a decrease in seven proteins associated with the alternative complement pathway and an increase in 6 proteins associated with the lectin and classical complement pathways. The correlation with a shift in complement pathways suggests that compromised immunity could be responsible for the observed dysbiosis in the GI microbiome.
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Affiliation(s)
- D Saxena
- Department of Basic Science, New York University College of Dentistry, New York, NY, USA
| | - Y Li
- Department of Basic Science, New York University College of Dentistry, New York, NY, USA
| | - A Devota
- Department of Basic Science, New York University College of Dentistry, New York, NY, USA
| | - S Pushalkar
- Department of Basic Science, New York University College of Dentistry, New York, NY, USA
| | - W Abrams
- Department of Basic Science, New York University College of Dentistry, New York, NY, USA
| | - C Barber
- Department of Basic Science, New York University College of Dentistry, New York, NY, USA
| | - P Corby
- Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - M Poles
- Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - J Phelan
- Department of Basic Science, New York University College of Dentistry, New York, NY, USA
| | - D Malamud
- Department of Basic Science, New York University College of Dentistry, New York, NY, USA.,Department of Medicine, New York University School of Medicine, New York, NY, USA
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49
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de Oliveira TC, Rodrigues PT, Menezes MJ, Gonçalves-Lopes RM, Bastos MS, Lima NF, Barbosa S, Gerber AL, Loss de Morais G, Berná L, Phelan J, Robello C, de Vasconcelos ATR, Alves JMP, Ferreira MU. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax. PLoS Negl Trop Dis 2017; 11:e0005824. [PMID: 28759591 PMCID: PMC5552344 DOI: 10.1371/journal.pntd.0005824] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/10/2017] [Accepted: 07/20/2017] [Indexed: 01/15/2023] Open
Abstract
Background The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax. Methods We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences), Peru (PER, n = 23), Colombia (COL, n = 31), and Mexico (MEX, n = 19). Principal findings/Conclusions We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10−4 and 6.2 × 10−4) as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed) in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o) gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092). Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically diverse sites. Further genome-wide analyses are required to test the demographic scenario suggested by our data. Plasmodium vivax is the most common human malaria parasite in the Americas, but how and when this species arrived in the New World remains unclear. Here we describe high-quality whole-genome sequence data for nine P. vivax isolates from Brazil, a country that accounts for 37% of the malaria burden in this continent, and compare these data with additional publicly available P. vivax genomes from Brazil, Peru, Colombia, and Mexico. P. vivax populations from the New World were found to be as diverse as their counterparts from areas with substantially higher malaria transmission, such as Southeast Asia, and to carry several non-synonymous substitutions in candidate drug-resistance genes. Moreover, genome-wide patterns of linkage disequilibrium between pairs of polymorphic sites are consistent with very frequent outcrossing in these populations. Interestingly, local P. vivax is more polymorphic, with less between-population differentiation, than sympatric populations of P. falciparum, possibly as a result of different demographic histories of these two species in the Americas. We hypothesize that local P. vivax lineages originated from successive migratory waves and subsequent admixture between parasites from geographically diverse sites.
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Affiliation(s)
- Thais C. de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Priscila T. Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria José Menezes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Raquel M. Gonçalves-Lopes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Melissa S. Bastos
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nathália F. Lima
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Susana Barbosa
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandra L. Gerber
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - Guilherme Loss de Morais
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - Luisa Berná
- Unit of Molecular Biology, Pasteur Institute of Montevideo, Montevideo, Uruguay
| | - Jody Phelan
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Carlos Robello
- Unit of Molecular Biology, Pasteur Institute of Montevideo, Montevideo, Uruguay
| | - Ana Tereza R. de Vasconcelos
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - João Marcelo P. Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- * E-mail:
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50
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Sengstake S, Bergval IL, Schuitema AR, de Beer JL, Phelan J, de Zwaan R, Clark TG, van Soolingen D, Anthony RM. Pyrazinamide resistance-conferring mutations in pncA and the transmission of multidrug resistant TB in Georgia. BMC Infect Dis 2017; 17:491. [PMID: 28697808 PMCID: PMC5506614 DOI: 10.1186/s12879-017-2594-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/05/2017] [Indexed: 11/28/2022] Open
Abstract
Background The ongoing epidemic of multidrug-resistant tuberculosis (MDR-TB) in Georgia highlights the need for more effective control strategies. A new regimen to treat MDR-TB that includes pyrazinamide (PZA) is currently being evaluated and PZA resistance status will largely influence the success of current and future treatment strategies. PZA susceptibility testing was not routinely performed at the National Reference Laboratory (NRL) in Tbilisi between 2010 and September 2015. We here provide a first insight into the prevalence of PZA resistant TB in this region. Methods Phenotypic susceptibility to PZA was determined in a convenience collection of well-characterised TB patient isolates collected at the NRL in Tbilisi between 2012 and 2013. In addition, the pncA gene was sequenced and whole genome sequencing was performed on two isolates. Results Out of 57 isolates tested 33 (57.9%) showed phenotypic drug resistance to PZA and had a single pncA mutation. All of these 33 isolates were MDR-TB strains. pncA mutations were absent in all but one of the 24 PZA susceptible isolate. In total we found 18 polymorphisms in the pncA gene. From the two major MDR-TB clusters represented (94–32 and 100–32), 10 of 15, 67.0% and 13 of 14, 93.0% strains, respectively were PZA resistant. We also identified a member of the potentially highly transmissive clade A strain carrying the characteristic I6L substitution in PncA. Another strain with the same MLVA type as the clade A strain acquired a different mutation in pncA and was genetically more distantly related suggesting that different branches of this particular lineage have been introduced into this region. Conclusion In this high MDR-TB setting more than half of the tested MDR-TB isolates were resistant to PZA. As PZA is part of current and planned MDR-TB treatment regimens this is alarming and deserves the attention of health authorities. Based on our typing and sequence analysis results we conclude that PZA resistance is the result of primary transmission as well as acquisition within the patient and recommend prospective genotyping and PZA resistance testing in high MDR-TB settings. This is of utmost importance in order to preserve bacterial susceptibility to PZA to help protect (new) second line drugs in PZA containing regimens.
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Affiliation(s)
- Sarah Sengstake
- Royal Tropical Institute, KIT Biomedical Research, Meibergdreef 39, 1105 AZ, Amsterdam, The Netherlands. .,Unit of Mycobacteriology, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000, Antwerp, Belgium.
| | - Indra L Bergval
- Royal Tropical Institute, KIT Biomedical Research, Meibergdreef 39, 1105 AZ, Amsterdam, The Netherlands.,Centre for Zoonoses and Environmental Microbiology, Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), PO Box 1, 3720 BA, Bilthoven, The Netherlands
| | - Anja R Schuitema
- Royal Tropical Institute, KIT Biomedical Research, Meibergdreef 39, 1105 AZ, Amsterdam, The Netherlands
| | - Jessica L de Beer
- Mycobacteria Diagnostic Laboratory for Bacteriology and Parasitology (BPD) Center for Infectious Disease Research, Diagnostics and Perinatal Screening (IDS) National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
| | - Jody Phelan
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK
| | - Rina de Zwaan
- Mycobacteria Diagnostic Laboratory for Bacteriology and Parasitology (BPD) Center for Infectious Disease Research, Diagnostics and Perinatal Screening (IDS) National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
| | - Taane G Clark
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK.,Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT, London, UK
| | - Dick van Soolingen
- Mycobacteria Diagnostic Laboratory for Bacteriology and Parasitology (BPD) Center for Infectious Disease Research, Diagnostics and Perinatal Screening (IDS) National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
| | - Richard M Anthony
- Royal Tropical Institute, KIT Biomedical Research, Meibergdreef 39, 1105 AZ, Amsterdam, The Netherlands.,Mycobacteria Diagnostic Laboratory for Bacteriology and Parasitology (BPD) Center for Infectious Disease Research, Diagnostics and Perinatal Screening (IDS) National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
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