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Pol S, Kallonen T, Mäklin T, Sar P, Hopkins J, Soeng S, Miliya T, Ling CL, Bentley SD, Corander J, Turner P. Exploring the pediatric nasopharyngeal bacterial microbiota with culture-based MALDI-TOF mass spectrometry and targeted metagenomic sequencing. mBio 2024; 15:e0078424. [PMID: 38682956 PMCID: PMC11237702 DOI: 10.1128/mbio.00784-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
The nasopharynx is an important reservoir of disease-associated and antimicrobial-resistant bacterial species. This proof-of-concept study assessed the utility of a combined culture, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and targeted metagenomic sequencing workflow for the study of the pediatric nasopharyngeal bacterial microbiota. Nasopharyngeal swabs and clinical metadata were collected from Cambodian children during a hospital outpatient visit and then biweekly for 12 weeks. Swabs were cultured on chocolate and blood-gentamicin agar, and all colony morphotypes were identified by MALDI-TOF MS. Metagenomic sequencing was done on a scrape of all colonies from a chocolate agar culture and processed using the mSWEEP pipeline. One hundred one children were enrolled, yielding 620 swabs. MALDI-TOF MS identified 106 bacterial species/40 genera: 20 species accounted for 88.5% (2,190/2,474) of isolates. Colonization by Moraxella catarrhalis (92.1% of children on ≥1 swab), Haemophilus influenzae (87.1%), and Streptococcus pneumoniae (83.2%) was particularly common. In S. pneumoniae-colonized children, a median of two serotypes [inter-quartile range (IQR) 1-2, range 1-4] was detected. For the 21 bacterial species included in the mSWEEP database and identifiable by MALDI-TOF, detection by culture + MALDI-TOF MS and culture + mSWEEP was highly concordant with a median species-level agreement of 96.9% (IQR 86.8%-98.8%). mSWEEP revealed highly dynamic lineage-level colonization patterns for S. pneumoniae which were quite different to those for S. aureus. A combined culture, MALDI-TOF MS, targeted metagenomic sequencing approach for the exploration of the young child nasopharyngeal microbiome was technically feasible, and each component yielded complementary data. IMPORTANCE The human upper respiratory tract is an important source of disease-causing and antibiotic-resistant bacteria. However, understanding the interactions and stability of these bacterial populations is technically challenging. We used a combination of approaches to determine colonization patterns over a 3-month period in 101 Cambodian children. The combined approach was feasible to implement, and each component gave complementary data to enable a better understanding of the complex patterns of bacterial colonization.
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Affiliation(s)
- Sreymom Pol
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Teemu Kallonen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Tommi Mäklin
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Poda Sar
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Jill Hopkins
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Sona Soeng
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Clare L Ling
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | | | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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2
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McHugh MP, Pettigrew KA, Taori S, Evans TJ, Leanord A, Gillespie SH, Templeton KE, Holden MTG. Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium. J Antimicrob Chemother 2024; 79:656-668. [PMID: 38323373 PMCID: PMC11090465 DOI: 10.1093/jac/dkae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/02/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND WGS is increasingly being applied to healthcare-associated vancomycin-resistant Enterococcus faecium (VREfm) outbreaks. Within-patient diversity could complicate transmission resolution if single colonies are sequenced from identified cases. OBJECTIVES Determine the impact of within-patient diversity on transmission resolution of VREfm. MATERIALS AND METHODS Fourteen colonies were collected from VREfm positive rectal screens, single colonies were collected from clinical samples and Illumina WGS was performed. Two isolates were selected for Oxford Nanopore sequencing and hybrid genome assembly to generate lineage-specific reference genomes. Mapping to closely related references was used to identify genetic variations and closely related genomes. A transmission network was inferred for the entire genome set using Phyloscanner. RESULTS AND DISCUSSION In total, 229 isolates from 11 patients were sequenced. Carriage of two or three sequence types was detected in 27% of patients. Presence of antimicrobial resistance genes and plasmids was variable within genomes from the same patient and sequence type. We identified two dominant sequence types (ST80 and ST1424), with two putative transmission clusters of two patients within ST80, and a single cluster of six patients within ST1424. We found transmission resolution was impaired using fewer than 14 colonies. CONCLUSIONS Patients can carry multiple sequence types of VREfm, and even within related lineages the presence of mobile genetic elements and antimicrobial resistance genes can vary. VREfm within-patient diversity could be considered in future to aid accurate resolution of transmission networks.
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Affiliation(s)
- Martin P McHugh
- School of Medicine, University of St Andrews, St Andrews, UK
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | | | - Surabhi Taori
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Thomas J Evans
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Alistair Leanord
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, UK
| | | | - Kate E Templeton
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
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3
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Fan J, Khan J, Singh NP, Pibiri GE, Patro R. Fulgor: a fast and compact k-mer index for large-scale matching and color queries. Algorithms Mol Biol 2024; 19:3. [PMID: 38254124 PMCID: PMC10810250 DOI: 10.1186/s13015-024-00251-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
The problem of sequence identification or matching-determining the subset of reference sequences from a given collection that are likely to contain a short, queried nucleotide sequence-is relevant for many important tasks in Computational Biology, such as metagenomics and pangenome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resource-efficient solution to this problem is of utmost importance. This poses the threefold challenge of representing the reference collection with a data structure that is efficient to query, has light memory usage, and scales well to large collections. To solve this problem, we describe an efficient colored de Bruijn graph index, arising as the combination of a k-mer dictionary with a compressed inverted index. The proposed index takes full advantage of the fact that unitigs in the colored compacted de Bruijn graph are monochromatic (i.e., all k-mers in a unitig have the same set of references of origin, or color). Specifically, the unitigs are kept in the dictionary in color order, thereby allowing for the encoding of the map from k-mers to their colors in as little as 1 + o(1) bits per unitig. Hence, one color per unitig is stored in the index with almost no space/time overhead. By combining this property with simple but effective compression methods for integer lists, the index achieves very small space. We implement these methods in a tool called Fulgor, and conduct an extensive experimental analysis to demonstrate the improvement of our tool over previous solutions. For example, compared to Themisto-the strongest competitor in terms of index space vs. query time trade-off-Fulgor requires significantly less space (up to 43% less space for a collection of 150,000 Salmonella enterica genomes), is at least twice as fast for color queries, and is 2-6[Formula: see text] faster to construct.
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Affiliation(s)
- Jason Fan
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Jamshed Khan
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Noor Pratap Singh
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | | | - Rob Patro
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA.
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4
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Pibiri GE, Fan J, Patro R. Meta-colored compacted de Bruijn graphs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.550101. [PMID: 37546988 PMCID: PMC10401949 DOI: 10.1101/2023.07.21.550101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
MOTIVATION The colored compacted de Bruijn graph (c-dBG) has become a fundamental tool used across several areas of genomics and pangenomics. For example, it has been widely adopted by methods that perform read mapping or alignment, abundance estimation, and subsequent downstream analyses. These applications essentially regard the c-dBG as a map from k-mers to the set of references in which they appear. The c-dBG data structure should retrieve this set -- the color of the k-mer -- efficiently for any given k-mer, while using little memory. To aid retrieval, the colors are stored explicitly in the data structure and take considerable space for large reference collections, even when compressed. Reducing the space of the colors is therefore of utmost importance for large-scale sequence indexing. RESULTS We describe the meta-colored compacted de Bruijn graph (Mac-dBG) -- a new colored de Bruijn graph data structure where colors are represented holistically, i.e., taking into account their redundancy across the whole collection being indexed, rather than individually as atomic integer lists. This allows the factorization and compression of common sub-patterns across colors. While optimizing the space of our data structure is NP-hard, we propose a simple heuristic algorithm that yields practically good solutions. Results show that the Mac-dBG data structure improves substantially over the best previous space/time trade-off, by providing remarkably better compression effectiveness for the same (or better) query efficiency. This improved space/time trade-off is robust across different datasets and query workloads. Code availability: A C++17 implementation of the Mac-dBG is publicly available on GitHub at: https://github.com/jermp/fulgor.
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5
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Tarracchini C, Alessandri G, Fontana F, Rizzo SM, Lugli GA, Bianchi MG, Mancabelli L, Longhi G, Argentini C, Vergna LM, Anzalone R, Viappiani A, Turroni F, Taurino G, Chiu M, Arboleya S, Gueimonde M, Bussolati O, van Sinderen D, Milani C, Ventura M. Genetic strategies for sex-biased persistence of gut microbes across human life. Nat Commun 2023; 14:4220. [PMID: 37452041 PMCID: PMC10349097 DOI: 10.1038/s41467-023-39931-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023] Open
Abstract
Although compositional variation in the gut microbiome during human development has been extensively investigated, strain-resolved dynamic changes remain to be fully uncovered. In the current study, shotgun metagenomic sequencing data of 12,415 fecal microbiomes from healthy individuals are employed for strain-level tracking of gut microbiota members to elucidate its evolving biodiversity across the human life span. This detailed longitudinal meta-analysis reveals host sex-related persistence of strains belonging to common, maternally-inherited species, such as Bifidobacterium bifidum and Bifidobacterium longum subsp. longum. Comparative genome analyses, coupled with experiments including intimate interaction between microbes and human intestinal cells, show that specific bacterial glycosyl hydrolases related to host-glycan metabolism may contribute to more efficient colonization in females compared to males. These findings point to an intriguing ancient sex-specific host-microbe coevolution driving the selective persistence in women of key microbial taxa that may be vertically passed on to the next generation.
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Affiliation(s)
- Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- GenProbio srl, Parma, Italy
| | - Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Massimiliano Giovanni Bianchi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Laura Maria Vergna
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Giuseppe Taurino
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Martina Chiu
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Silvia Arboleya
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, CSIC, 33300, Villaviciosa, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, CSIC, 33300, Villaviciosa, Spain
| | - Ovidio Bussolati
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, T12YT20, Cork, Ireland
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy.
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy.
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6
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Fan J, Singh NP, Khan J, Pibiri GE, Patro R. Fulgor: A fast and compact k-mer index for large-scale matching and color queries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539895. [PMID: 37214944 PMCID: PMC10197524 DOI: 10.1101/2023.05.09.539895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The problem of sequence identification or matching - determining the subset of references from a given collection that are likely to contain a query nucleotide sequence - is relevant for many important tasks in Computational Biology, such as metagenomics and pan-genome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resourceefficient solution to this problem is of utmost importance. The reference collection should therefore be pre-processed into an index for fast queries. This poses the threefold challenge of designing an index that is efficient to query, has light memory usage, and scales well to large collections. To solve this problem, we describe how recent advancements in associative, order-preserving, k-mer dictionaries can be combined with a compressed inverted index to implement a fast and compact colored de Bruijn graph data structure. This index takes full advantage of the fact that unitigs in the colored de Bruijn graph are monochromatic (all k-mers in a unitig have the same set of references of origin, or "color"), leveraging the order-preserving property of its dictionary. In fact, k-mers are kept in unitig order by the dictionary, thereby allowing for the encoding of the map from k-mers to their inverted lists in as little as 1+o(1) bits per unitig. Hence, one inverted list per unitig is stored in the index with almost no space/time overhead. By combining this property with simple but effective compression methods for inverted lists, the index achieves very small space. We implement these methods in a tool called Fulgor. Compared to Themisto, the prior state of the art, Fulgor indexes a heterogeneous collection of 30,691 bacterial genomes in 3.8× less space, a collection of 150,000 Salmonella enterica genomes in approximately 2× less space, is at least twice as fast for color queries, and is 2 - 6× faster to construct.
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Affiliation(s)
- Jason Fan
- Department of Computer Science, University of Maryland, College Park, MD 20440, USA
| | - Noor Pratap Singh
- Department of Computer Science, University of Maryland, College Park, MD 20440, USA
| | - Jamshed Khan
- Department of Computer Science, University of Maryland, College Park, MD 20440, USA
| | | | - Rob Patro
- Department of Computer Science, University of Maryland, College Park, MD 20440, USA
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7
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Herold M, Hock L, Penny C, Walczak C, Djabi F, Cauchie HM, Ragimbeau C. Metagenomic Strain-Typing Combined with Isolate Sequencing Provides Increased Resolution of the Genetic Diversity of Campylobacter jejuni Carriage in Wild Birds. Microorganisms 2023; 11:microorganisms11010121. [PMID: 36677413 PMCID: PMC9860660 DOI: 10.3390/microorganisms11010121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023] Open
Abstract
As the world's leading cause of human gastro-enteritis, the food- and waterborne pathogen Campylobacter needs to be intensively monitored through a One Health approach. Particularly, wild birds have been hypothesized to contribute to the spread of human clinical recurring C. jejuni genotypes across several countries. A major concern in studying epidemiological dynamics is resolving the large genomic diversity of strains circulating in the environment and various reservoirs, challenging to achieve with isolation techniques. Here, we applied a passive-filtration method to obtain isolates and in parallel recovered genotypes from metagenomic sequencing data from associated filter sweeps. For genotyping mixed strains, a reference-based computational workflow to predict allelic profiles of nine extended-MLST loci was utilized. We validated the pipeline by sequencing artificial mixtures of C. jejuni strains and observed the highest prediction accuracy when including obtained isolates as references. By analyzing metagenomic samples, we were able to detect over 20% additional genetic diversity and observed an over 50% increase in the potential to connect genotypes across wild-bird samples. With an optimized filtration method and a computational approach for genotyping strain mixtures, we provide the foundation for future studies assessing C. jejuni diversity in environmental and clinical settings at improved throughput and resolution.
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Affiliation(s)
- Malte Herold
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
- Epidemiology and Microbial Genomics, Laboratoire National de Santé (LNS), 1 rue Louis Rech, L-3555 Dudelange, Luxembourg
- Correspondence:
| | - Louise Hock
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Christian Penny
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Cécile Walczak
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Fatu Djabi
- Epidemiology and Microbial Genomics, Laboratoire National de Santé (LNS), 1 rue Louis Rech, L-3555 Dudelange, Luxembourg
| | - Henry-Michel Cauchie
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Catherine Ragimbeau
- Epidemiology and Microbial Genomics, Laboratoire National de Santé (LNS), 1 rue Louis Rech, L-3555 Dudelange, Luxembourg
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8
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Mäklin T, Thorpe HA, Pöntinen AK, Gladstone RA, Shao Y, Pesonen M, McNally A, Johnsen PJ, Samuelsen Ø, Lawley TD, Honkela A, Corander J. Strong pathogen competition in neonatal gut colonisation. Nat Commun 2022; 13:7417. [PMID: 36456554 PMCID: PMC9715557 DOI: 10.1038/s41467-022-35178-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
Opportunistic bacterial pathogen species and their strains that colonise the human gut are generally understood to compete against both each other and the commensal species colonising this ecosystem. Currently we are lacking a population-wide quantification of strain-level colonisation dynamics and the relationship of colonisation potential to prevalence in disease, and how ecological factors might be modulating these. Here, using a combination of latest high-resolution metagenomics and strain-level genomic epidemiology methods we performed a characterisation of the competition and colonisation dynamics for a longitudinal cohort of neonatal gut microbiomes. We found strong inter- and intra-species competition dynamics in the gut colonisation process, but also a number of synergistic relationships among several species belonging to genus Klebsiella, which includes the prominent human pathogen Klebsiella pneumoniae. No evidence of preferential colonisation by hospital-adapted pathogen lineages in either vaginal or caesarean section birth groups was detected. Our analysis further enabled unbiased assessment of strain-level colonisation potential of extra-intestinal pathogenic Escherichia coli (ExPEC) in comparison with their propensity to cause bloodstream infections. Our study highlights the importance of systematic surveillance of bacterial gut pathogens, not only from disease but also from carriage state, to better inform therapies and preventive medicine in the future.
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Affiliation(s)
- Tommi Mäklin
- grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Harry A. Thorpe
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Anna K. Pöntinen
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway ,grid.412244.50000 0004 4689 5540Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Rebecca A. Gladstone
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Yan Shao
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire UK
| | - Maiju Pesonen
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Alan McNally
- grid.6572.60000 0004 1936 7486Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Pål J. Johnsen
- grid.10919.300000000122595234Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- grid.412244.50000 0004 4689 5540Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway ,grid.10919.300000000122595234Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Trevor D. Lawley
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire UK
| | - Antti Honkela
- grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Jukka Corander
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway ,grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire UK ,grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
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9
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Mouftah SF, Pascoe B, Calland JK, Mourkas E, Tonkin N, Lefevre C, Deuker D, Smith S, Wickenden H, Hitchings MD, Sheppard SK, Elhadidy M. Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance. Microb Genom 2022; 8. [PMID: 35675117 PMCID: PMC9455717 DOI: 10.1099/mgen.0.000834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Campylobacter is the most common cause of bacterial gastroenteritis worldwide, and diarrhoeal disease is a major cause of child morbidity, growth faltering and mortality in low- and middle-income countries. Despite evidence of high incidence and differences in disease epidemiology, there is limited genomic data from studies in developing countries. In this study, we aimed to quantify the extent of gene sharing in local and global populations. We characterized the genetic diversity and accessory-genome content of a collection of Campylobacter isolates from the Cairo metropolitan area, Egypt. In total, 112 Campylobacter isolates were collected from broiler carcasses (n=31), milk and dairy products (n=24), and patients suffering from gastroenteritis (n=57). Among the most common sequence types (STs), we identified the globally disseminated host generalist ST-21 clonal complex (CC21) and the poultry specialists CC206, CC464 and CC48. Notably, CC45 and the cattle-specialist CC42 were under-represented, with a total absence of CC61. Core- and accessory-genome sharing was compared among isolates from Egypt and a comparable collection from the UK (Oxford). Lineage-specific accessory-genome sharing was significantly higher among isolates from the same country, particularly CC21, which demonstrated greater local geographical clustering. In contrast, no geographical clustering was noted in either the core or accessory genome of CC828, suggesting a highly admixed population. A greater proportion of Campylobacter coli isolates were multidrug resistant compared to Campylobacter jejuni. Our results suggest that there is more horizontal transfer of accessory genes between strains in Egypt. This has strong implications for controlling the spread of antimicrobial resistance among this important pathogen.
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Affiliation(s)
- Shaimaa F Mouftah
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Ben Pascoe
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK.,Chiang Mai University, Chiang Mai, Thailand
| | - Jessica K Calland
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | - Evangelos Mourkas
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | - Naomi Tonkin
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | - Charlotte Lefevre
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK.,Present address: Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Danielle Deuker
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK.,Present address: Nuffield Department of Medicine, Jenner Institute, University of Oxford, Oxford, UK
| | - Sunny Smith
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | - Harry Wickenden
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK
| | | | - Samuel K Sheppard
- Milner Centre of Evolution, University of Bath, Claverton Down, Bath, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - Mohamed Elhadidy
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.,Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
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10
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Tonkin-Hill G, Ling C, Chaguza C, Salter SJ, Hinfonthong P, Nikolaou E, Tate N, Pastusiak A, Turner C, Chewapreecha C, Frost SDW, Corander J, Croucher NJ, Turner P, Bentley SD. Pneumococcal within-host diversity during colonization, transmission and treatment. Nat Microbiol 2022; 7:1791-1804. [PMID: 36216891 PMCID: PMC9613479 DOI: 10.1038/s41564-022-01238-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022]
Abstract
Characterizing the genetic diversity of pathogens within the host promises to greatly improve surveillance and reconstruction of transmission chains. For bacteria, it also informs our understanding of inter-strain competition and how this shapes the distribution of resistant and sensitive bacteria. Here we study the genetic diversity of Streptococcus pneumoniae within 468 infants and 145 of their mothers by deep sequencing whole pneumococcal populations from 3,761 longitudinal nasopharyngeal samples. We demonstrate that deep sequencing has unsurpassed sensitivity for detecting multiple colonization, doubling the rate at which highly invasive serotype 1 bacteria were detected in carriage compared with gold-standard methods. The greater resolution identified an elevated rate of transmission from mothers to their children in the first year of the child's life. Comprehensive treatment data demonstrated that infants were at an elevated risk of both the acquisition and persistent colonization of a multidrug-resistant bacterium following antimicrobial treatment. Some alleles were enriched after antimicrobial treatment, suggesting that they aided persistence, but generally purifying selection dominated within-host evolution. Rates of co-colonization imply that in the absence of treatment, susceptible lineages outcompeted resistant lineages within the host. These results demonstrate the many benefits of deep sequencing for the genomic surveillance of bacterial pathogens.
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Affiliation(s)
- Gerry Tonkin-Hill
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Blindern, Norway
| | - Clare Ling
- grid.10223.320000 0004 1937 0490Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chrispin Chaguza
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.47100.320000000419368710Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT USA
| | - Susannah J. Salter
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Pattaraporn Hinfonthong
- grid.10223.320000 0004 1937 0490Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Elissavet Nikolaou
- grid.48004.380000 0004 1936 9764Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK ,grid.1058.c0000 0000 9442 535XInfection and Immunity, Murdoch Children’s Research Institute, Melbourne, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria Australia
| | - Natalie Tate
- grid.48004.380000 0004 1936 9764Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Claudia Turner
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK ,grid.459332.a0000 0004 0418 5364Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Claire Chewapreecha
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.10223.320000 0004 1937 0490Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Simon D. W. Frost
- grid.419815.00000 0001 2181 3404Microsoft Research, Redmond, WA USA ,grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK
| | - Jukka Corander
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Blindern, Norway ,grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Nicholas J. Croucher
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Paul Turner
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK ,grid.459332.a0000 0004 0418 5364Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Stephen D. Bentley
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
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