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Lee H, Lee DG, Jo H, Heo YM, Baek C, Kim HB, Park G, Kang S, Lee W, Mun S, Han K. Comparative whole genome analysis of face-derived Streptococcus infantis CX-4 unravels the functions related to skin barrier. Genes Genomics 2024; 46:499-510. [PMID: 38453815 DOI: 10.1007/s13258-024-01495-w] [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: 12/10/2023] [Accepted: 01/21/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND The skin microbiome is essential in guarding against harmful pathogens and responding to environmental changes by generating substances useful in the cosmetic and pharmaceutical industries. Among these microorganisms, Streptococcus is a bacterial species identified in various isolation sources. In 2021, a strain of Streptococcus infantis, CX-4, was identified from facial skin and found to be linked to skin structure and elasticity. As the skin-derived strain differs from other S. infantis strains, which are usually of oral origin, it emphasizes the significance of bacterial variation by the environment. OBJECTIVE This study aims to explore the unique characteristics of the CX-4 compared to seven oral-derived Streptococcus strains based on the Whole-Genome Sequencing data, focusing on its potential role in skin health and its possible application in cosmetic strategies. METHODS The genome of the CX-4 strain was constructed using PacBio Sequencing, with the assembly performed using the SMRT protocol. Comparative whole-genome analysis was then performed with seven closely related strains, utilizing web-based tools like PATRIC, OrthoVenn3, and EggNOG-mapper, for various analyses, including protein association analysis using STRING. RESULTS Our analysis unveiled a substantial number of Clusters of Orthologous Groups in diverse functional categories in CX-4, among which sphingosine kinase (SphK) emerged as a unique product, exclusively present in the CX-4 strain. SphK is a critical enzyme in the sphingolipid metabolic pathway, generating sphingosine-1-phosphate. The study also brought potential associations with isoprene formation and retinoic acid synthesis, the latter being a metabolite of vitamin A, renowned for its crucial function in promoting skin cell growth, differentiation, and maintaining of skin barrier integrity. These findings collectively suggest the potential of the CX-4 strain in enhancing of skin barrier functionality. CONCLUSION Our research underscores the potential of the skin-derived S. infantis CX-4 strain by revealing unique bacterial compounds and their potential roles on human skin.
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Affiliation(s)
- Haeun Lee
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Dong-Geol Lee
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - HyungWoo Jo
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Young Mok Heo
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Chaeyun Baek
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Hye-Been Kim
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Geunhwa Park
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Seunghyun Kang
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Wooseok Lee
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Seyoung Mun
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
- Smart Animal Bio Institute, Dankook University, Cheonan, 31116, Republic of Korea
- Department of Cosmedical and Materials, Dankook University, Cheonan, 31116, Republic of Korea
| | - Kyudong Han
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
- Smart Animal Bio Institute, Dankook University, Cheonan, 31116, Republic of Korea.
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Xia F, Cheng J, Jiang M, Wang Z, Wen Z, Wang M, Ren J, Zhuge X. Genomics Analysis to Identify Multiple Genetic Determinants That Drive the Global Transmission of the Pandemic ST95 Lineage of Extraintestinal Pathogenic Escherichia coli (ExPEC). Pathogens 2022; 11:pathogens11121489. [PMID: 36558824 PMCID: PMC9781279 DOI: 10.3390/pathogens11121489] [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: 11/10/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is a pathogen that causes host extraintestinal diseases. The ST95 E. coli lineage is one of the dominant ExPEC lineages in humans and poultry. In this study, we took advantage of extensive E. coli genomes available through public open-access databases to construct a detailed understanding of the phylogeny and evolution of ST95. We used a high variability of accessory genomes to highlight the diversity and dynamic traits of ST95. Isolates from diverse hosts and geographic sources were randomly located on the phylogenetic tree, which suggested that there is no host specificity for ST95. The time-scaled phylogeny showed that ST95 is an ancient and long-lasting lineage. The virulence genes, resistance genes, and pathogenicity islands (PAIs) were characterized in ST95 pan-genomes to provide novel insights into the pathogenicity and multidrug resistance (MDR) genotypes. We found that a pool of large plasmids drives virulence and MDR. Based on the unique genes in the ST95 pan-genome, we designed a novel multiplex PCR reaction to rapidly detect ST95. Overall, our study addressed a gap in the current understanding of ST95 ExPEC genomes, with significant implications for recognizing the success and spread of ST95.
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Affiliation(s)
- Fufang Xia
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226019, China
| | - Jinlong Cheng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226019, China
| | - Min Jiang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226019, China
| | - Zhongxing Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226019, China
| | - Zhe Wen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Min Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226019, China
| | - Jianluan Ren
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (J.R.); (X.Z.)
| | - Xiangkai Zhuge
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226019, China
- Correspondence: (J.R.); (X.Z.)
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3
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Xia F, Jiang M, Wen Z, Wang Z, Wang M, Xu Y, Zhuge X, Dai J. Complete genomic analysis of ST117 lineage extraintestinal pathogenic Escherichia coli (ExPEC) to reveal multiple genetic determinants to drive its global transmission: ST117 E. coli as an emerging multidrug-resistant foodborne ExPEC with zoonotic potential. Transbound Emerg Dis 2022; 69:3256-3273. [PMID: 35945191 DOI: 10.1111/tbed.14678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 02/04/2023]
Abstract
Avian pathogenic Escherichia coli (APEC) is recognized as a primary source of foodborne extraintestinal pathogenic E. coli (ExPEC), which poses a significant risk of extraintestinal infections in humans. The potential of human infection with ST117 lineage APEC/ExPEC from poultry is particularly concerning. However, relatively few whole-genome studies have focused on ST117 as an emerging ExPEC lineage. In this study, the complete genomes of 11 avian ST117 isolates and the draft genomes of 20 ST117 isolates in China were sequenced to reveal the genomic islands and large plasmid composition of ST117 APEC. With reference to the extensive E. coli genomes available in public databases, large-scale comprehensive genomic analysis of the ST117 lineage APEC/ExPEC was performed to reveal the features of the ST117 pan-genome and population. The high variability of the accessory genome emphasized the diversity and dynamic traits of the ST117 pan-genome. ST117 isolates recovered from different hosts and geographic sources were randomly located on a phylogeny tree, suggesting that ST117 E. coli lacked host specificity. A time-scaled phylogeny tree showed that ST117 was a recent E. coli lineage with a relatively short evolutionary period. Further characterization of a wide diversity of ExPEC-related virulence genes, pathogenicity islands (PAIs), and resistance genes of the ST117 pan-genome provided insights into the virulence and resistance of ST117 APEC/ExPEC. The results suggested zoonotic potential of ST117 APEC/ExPEC between birds and humans. Moreover, genomic analysis showed that a pool of diverse plasmids drove the virulence and multidrug resistance of ST117 APEC/ExPEC. Several types of large plasmids were scattered across the ST117 isolates, but there was no strong plasmid-clade adaptation. Combined with the pan-genome analysis, a double polymerase chain reaction (PCR) method was designed for rapid and cost-effective detection of ST117 isolates from various avian and human APEC/ExPEC isolates. Overall, this study addressed a gap in current knowledge about the ST117 APEC/ExPEC genome, with significant implications to understand the success and spread of ST117 APEC/ExPEC.
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Affiliation(s)
- Fufang Xia
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, Jiangsu, P.R. China.,MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Min Jiang
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, Jiangsu, P.R. China.,MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhe Wen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhongxing Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, Jiangsu, P.R. China.,MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Min Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, Jiangsu, P.R. China
| | - Yudian Xu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiangkai Zhuge
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, Jiangsu, P.R. China
| | - Jianjun Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,College of Pharmacy, China Pharmaceutical University, Nanjing, China
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4
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Zhang R, Yang T, Zhang Q, Liu D, Elhadidy M, Ding T. Whole-genome sequencing: a perspective on sensing bacterial risk for food safety. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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5
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Ko KKK, Chng KR, Nagarajan N. Metagenomics-enabled microbial surveillance. Nat Microbiol 2022; 7:486-496. [PMID: 35365786 DOI: 10.1038/s41564-022-01089-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022]
Abstract
Lessons learnt from the COVID-19 pandemic include increased awareness of the potential for zoonoses and emerging infectious diseases that can adversely affect human health. Although emergent viruses are currently in the spotlight, we must not forget the ongoing toll of morbidity and mortality owing to antimicrobial resistance in bacterial pathogens and to vector-borne, foodborne and waterborne diseases. Population growth, planetary change, international travel and medical tourism all contribute to the increasing frequency of infectious disease outbreaks. Surveillance is therefore of crucial importance, but the diversity of microbial pathogens, coupled with resource-intensive methods, compromises our ability to scale-up such efforts. Innovative technologies that are both easy to use and able to simultaneously identify diverse microorganisms (viral, bacterial or fungal) with precision are necessary to enable informed public health decisions. Metagenomics-enabled surveillance methods offer the opportunity to improve detection of both known and yet-to-emerge pathogens.
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Affiliation(s)
- Karrie K K Ko
- Laboratory of Metagenomic Technologies and Microbial Systems, Genome Institute of Singapore, Singapore, Singapore.,Department of Microbiology, Singapore General Hospital, Singapore, Singapore.,Department of Molecular Pathology, Singapore General Hospital, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National Univerisity of Singapore, Singapore, Singapore
| | - Kern Rei Chng
- Laboratory of Metagenomic Technologies and Microbial Systems, Genome Institute of Singapore, Singapore, Singapore.,National Centre for Food Science, Singapore Food Agency, Singapore, Singapore
| | - Niranjan Nagarajan
- Laboratory of Metagenomic Technologies and Microbial Systems, Genome Institute of Singapore, Singapore, Singapore. .,Yong Loo Lin School of Medicine, National Univerisity of Singapore, Singapore, Singapore.
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6
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Vesga P, Augustiny E, Keel C, Maurhofer M, Vacheron J. Phylogenetically closely related pseudomonads isolated from arthropods exhibit differential insect-killing abilities and genetic variations in insecticidal factors. Environ Microbiol 2021; 23:5378-5394. [PMID: 34190383 PMCID: PMC8519069 DOI: 10.1111/1462-2920.15623] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/12/2021] [Accepted: 06/02/2021] [Indexed: 01/07/2023]
Abstract
Strains belonging to the Pseudomonas protegens and Pseudomonas chlororaphis species are able to control soilborne plant pathogens and to kill pest insects by producing virulence factors such as toxins, chitinases, antimicrobials or two‐partner secretion systems. Most insecticidal Pseudomonas described so far were isolated from roots or soil. It is unknown whether these bacteria naturally occur in arthropods and how they interact with them. Therefore, we isolated P. protegens and P. chlororaphis from various healthy insects and myriapods, roots and soil collected in an agricultural field and a neighbouring grassland. The isolates were compared for insect killing, pathogen suppression and host colonization abilities. Our results indicate that neither the origin of isolation nor the phylogenetic position mirror the degree of insecticidal activity. Pseudomonas protegens strains appeared homogeneous regarding phylogeny, biocontrol and insecticidal capabilities, whereas P. chlororaphis strains were phylogenetically and phenotypically more heterogenous. A phenotypic and genomic analysis of five closely related P. chlororaphis isolates displaying varying levels of insecticidal activity revealed variations in genes encoding insecticidal factors that may account for the reduced insecticidal activity of certain isolates. Our findings point towards an adaption to insects within closely related pseudomonads and contribute to understand the ecology of insecticidal Pseudomonas.
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Affiliation(s)
- Pilar Vesga
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.,Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Eva Augustiny
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Monika Maurhofer
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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7
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Turner WC, Kamath PL, van Heerden H, Huang YH, Barandongo ZR, Bruce SA, Kausrud K. The roles of environmental variation and parasite survival in virulence-transmission relationships. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210088. [PMID: 34109041 PMCID: PMC8170194 DOI: 10.1098/rsos.210088] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Disease outbreaks are a consequence of interactions among the three components of a host-parasite system: the infectious agent, the host and the environment. While virulence and transmission are widely investigated, most studies of parasite life-history trade-offs are conducted with theoretical models or tractable experimental systems where transmission is standardized and the environment controlled. Yet, biotic and abiotic environmental factors can strongly affect disease dynamics, and ultimately, host-parasite coevolution. Here, we review research on how environmental context alters virulence-transmission relationships, focusing on the off-host portion of the parasite life cycle, and how variation in parasite survival affects the evolution of virulence and transmission. We review three inter-related 'approaches' that have dominated the study of the evolution of virulence and transmission for different host-parasite systems: (i) evolutionary trade-off theory, (ii) parasite local adaptation and (iii) parasite phylodynamics. These approaches consider the role of the environment in virulence and transmission evolution from different angles, which entail different advantages and potential biases. We suggest improvements to how to investigate virulence-transmission relationships, through conceptual and methodological developments and taking environmental context into consideration. By combining developments in life-history evolution, phylogenetics, adaptive dynamics and comparative genomics, we can improve our understanding of virulence-transmission relationships across a diversity of host-parasite systems that have eluded experimental study of parasite life history.
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Affiliation(s)
- Wendy C. Turner
- US Geological Survey, Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Pauline L. Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Henriette van Heerden
- Faculty of Veterinary Science, Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort, South Africa
| | - Yen-Hua Huang
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zoe R. Barandongo
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Spencer A. Bruce
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Kyrre Kausrud
- Section for Epidemiology, Norwegian Veterinary Institute, Ullevålsveien 68, 0454 Oslo, Norway
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8
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Gil-Gil T, Ochoa-Sánchez LE, Baquero F, Martínez JL. Antibiotic resistance: Time of synthesis in a post-genomic age. Comput Struct Biotechnol J 2021; 19:3110-3124. [PMID: 34141134 PMCID: PMC8181582 DOI: 10.1016/j.csbj.2021.05.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 12/20/2022] Open
Abstract
Antibiotic resistance has been highlighted by international organizations, including World Health Organization, World Bank and United Nations, as one of the most relevant global health problems. Classical approaches to study this problem have focused in infected humans, mainly at hospitals. Nevertheless, antibiotic resistance can expand through different ecosystems and geographical allocations, hence constituting a One-Health, Global-Health problem, requiring specific integrative analytic tools. Antibiotic resistance evolution and transmission are multilayer, hierarchically organized processes with several elements (from genes to the whole microbiome) involved. However, their study has been traditionally gene-centric, each element independently studied. The development of robust-economically affordable whole genome sequencing approaches, as well as other -omic techniques as transcriptomics and proteomics, is changing this panorama. These technologies allow the description of a system, either a cell or a microbiome as a whole, overcoming the problems associated with gene-centric approaches. We are currently at the time of combining the information derived from -omic studies to have a more holistic view of the evolution and spread of antibiotic resistance. This synthesis process requires the accurate integration of -omic information into computational models that serve to analyse the causes and the consequences of acquiring AR, fed by curated databases capable of identifying the elements involved in the acquisition of resistance. In this review, we analyse the capacities and drawbacks of the tools that are currently in use for the global analysis of AR, aiming to identify the more useful targets for effective corrective interventions.
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Affiliation(s)
- Teresa Gil-Gil
- Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain
| | | | - Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain
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9
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Carvalho R, Aburjaile F, Canario M, Nascimento AMA, Chartone-Souza E, de Jesus L, Zamyatnin AA, Brenig B, Barh D, Ghosh P, Goes-Neto A, Figueiredo HCP, Soares S, Ramos R, Pinto A, Azevedo V. Genomic Characterization of Multidrug-Resistant Escherichia coli BH100 Sub-strains. Front Microbiol 2021; 11:549254. [PMID: 33584554 PMCID: PMC7874104 DOI: 10.3389/fmicb.2020.549254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 12/09/2020] [Indexed: 01/17/2023] Open
Abstract
The rapid emergence of multidrug-resistant (MDR) bacteria is a global health problem. Mobile genetic elements like conjugative plasmids, transposons, and integrons are the major players in spreading resistance genes in uropathogenic Escherichia coli (UPEC) pathotype. The E. coli BH100 strain was isolated from the urinary tract of a Brazilian woman in 1974. This strain presents two plasmids carrying MDR cassettes, pBH100, and pAp, with conjugative and mobilization properties, respectively. However, its transposable elements have not been characterized. In this study, we attempted to unravel the factors involved in the mobilization of virulence and drug-resistance genes by assessing genomic rearrangements in four BH100 sub-strains (BH100 MG2014, BH100 MG2017, BH100L MG2017, and BH100N MG2017). Therefore, the complete genomes of the BH100 sub-strains were achieved through Next Generation Sequencing and submitted to comparative genomic analyses. Our data shows recombination events between the two plasmids in the sub-strain BH100 MG2017 and between pBH100 and the chromosome in BH100L MG2017. In both cases, IS3 and IS21 elements were detected upstream of Tn21 family transposons associated with MDR genes at the recombined region. These results integrated with Genomic island analysis suggest pBH100 might be involved in the spreading of drug resistance through the formation of resistance islands. Regarding pathogenicity, our results reveal that BH100 strain is closely related to UPEC strains and contains many IS3 and IS21-transposase-enriched genomic islands associated with virulence. This study concludes that those IS elements are vital for the evolution and adaptation of BH100 strain.
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Affiliation(s)
- Rodrigo Carvalho
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Flavia Aburjaile
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | - Marcus Canario
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Andréa M A Nascimento
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Edmar Chartone-Souza
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luis de Jesus
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Andrey A Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Debmalya Barh
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Institute of Integrative Omics and Applied Biotechnology, Purba Medinipur, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Aristoteles Goes-Neto
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Henrique C P Figueiredo
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Siomar Soares
- Departmento de Microbiologia, Imunologia e Parasitologia, Universidade Federal do Triangulo Mineiro, Uberaba, Brazil
| | | | - Anne Pinto
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vasco Azevedo
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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10
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Molecular Characterization of Cronobacter sakazakii Strains Isolated from Powdered Milk. Foods 2020; 10:foods10010020. [PMID: 33374633 PMCID: PMC7822459 DOI: 10.3390/foods10010020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/14/2020] [Accepted: 12/19/2020] [Indexed: 12/21/2022] Open
Abstract
Cronobacter spp. are opportunistic pathogens of the Enterobacteriaceae family. The organism causes infections in all age groups, but the most serious cases occur in outbreaks related to neonates with meningitis and necrotizing enterocolitis. The objective was to determine the in silico and in vitro putative virulence factors of six Cronobacter sakazakii strains isolated from powdered milk (PM) in the Czech Republic. Strains were identified by MALDI-TOF MS and whole-genome sequencing (WGS). Virulence and resistance genes were detected with the Ridom SeqSphere+ software task template and the Comprehensive Antibiotic Resistance Database (CARD) platform. Adherence and invasion ability were performed using the mouse neuroblastoma (N1E-115 ATCCCRL-2263) cell line. The CRISPR-Cas system was searched with CRISPRCasFinder. Core genome MLST identified four different sequence types (ST1, ST145, ST245, and ST297) in six isolates. Strains 13755-1B and 1847 were able to adhere in 2.2 and 3.2 × 106 CFU/mL, while 0.00073% invasion frequency was detected only in strain 1847. Both strains 13755-1B and 1847 were positive for three (50.0%) and four virulence genes, respectively. The cpa gene was not detected. Twenty-eight genes were detected by WGS and grouped as flagellar or outer membrane proteins, chemotaxis, hemolysins, and invasion, plasminogen activator, colonization, transcriptional regulator, and survival in macrophages. The colistin-resistance-encoding mcr-9.1 and cephalothin-resis-encoding blaCSA genes and IncFII(pECLA) and IncFIB(pCTU3) plasmids were detected. All strains exhibited CRISPR matrices and four of them two type I-E and I-F matrices. Combined molecular methodologies improve Cronobacter spp. decision-making for health authorities to protect the population.
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11
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Papkou A, Hedge J, Kapel N, Young B, MacLean RC. Efflux pump activity potentiates the evolution of antibiotic resistance across S. aureus isolates. Nat Commun 2020; 11:3970. [PMID: 32769975 PMCID: PMC7414891 DOI: 10.1038/s41467-020-17735-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/14/2020] [Indexed: 11/23/2022] Open
Abstract
The rise of antibiotic resistance in many bacterial pathogens has been driven by the spread of a few successful strains, suggesting that some bacteria are genetically pre-disposed to evolving resistance. Here, we test this hypothesis by challenging a diverse set of 222 isolates of Staphylococcus aureus with the antibiotic ciprofloxacin in a large-scale evolution experiment. We find that a single efflux pump, norA, causes widespread variation in evolvability across isolates. Elevated norA expression potentiates evolution by increasing the fitness benefit provided by DNA topoisomerase mutations under ciprofloxacin treatment. Amplification of norA provides a further mechanism of rapid evolution in isolates from the CC398 lineage. Crucially, chemical inhibition of NorA effectively prevents the evolution of resistance in all isolates. Our study shows that pre-existing genetic diversity plays a key role in shaping resistance evolution, and it may be possible to predict which strains are likely to evolve resistance and to optimize inhibitor use to prevent this outcome.
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Affiliation(s)
- Andrei Papkou
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3PS, UK.
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland.
| | - Jessica Hedge
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3PS, UK
| | - Natalia Kapel
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3PS, UK
| | - Bernadette Young
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - R Craig MacLean
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3PS, UK.
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12
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Gonçalves OS, de Queiroz MV, Santana MF. Potential evolutionary impact of integrative and conjugative elements (ICEs) and genomic islands in the Ralstonia solanacearum species complex. Sci Rep 2020; 10:12498. [PMID: 32719415 PMCID: PMC7385641 DOI: 10.1038/s41598-020-69490-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/13/2020] [Indexed: 11/09/2022] Open
Abstract
Ralstonia solanacearum, a soil-borne plant pathogen, encompasses a large number of strains known as R. solanacearum species complex (RSSC). Although it has been suggested that mobile genetic elements (MGEs) may play an important role in the RSSC genome, the evolutionary impact of these elements remains unknown. Here, we identified and analysed Integrative and Conjugative Elements (ICEs) and Genomic Islands (GIs) in the 121 genomes published for Ralstonia spp., including RSSC strains and three other non-plant pathogenic Ralstonia spp. Our results provided a dataset of 12 ICEs and 31 GIs distributed throughout Ralstonia spp. Four novel ICEs in RSSC were found. Some of these elements cover 5% of the host genome and carry accessory genes with a potential impact on the fitness and pathogenicity of RSSC. In addition, phylogenetic analysis revealed that these MGEs clustered to the same species, but there is evidence of strains from different countries that host the same element. Our results provide novel insight into the RSSC adaptation, opening new paths to a better understanding of how these elements affect this soil-borne plant pathogen.
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Affiliation(s)
- Osiel Silva Gonçalves
- Departamento de Microbiologia, Instituto de Bsiotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Marisa Vieira de Queiroz
- Departamento de Microbiologia, Instituto de Bsiotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Mateus Ferreira Santana
- Departamento de Microbiologia, Instituto de Bsiotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil.
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13
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Determining antimicrobial resistance profiles and identifying novel mutations of Neisseria gonorrhoeae genomes obtained by multiplexed MinION sequencing. SCIENCE CHINA. LIFE SCIENCES 2020; 63:1063-1070. [PMID: 31784935 DOI: 10.1007/s11427-019-1558-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/25/2019] [Indexed: 01/19/2023]
Abstract
Gonorrhea is one of the most common sexually transmitted diseases worldwide. To cure infection and prevent transmission, timely and appropriate antimicrobial therapy is necessary. Unfortunately, Neisseria gonorrhoeae, the etiological agent of gonorrhea, has acquired nearly all known mechanisms of antimicrobial resistance (AMR), thereby compromising the efficacy of antimicrobial therapy. Treatment failure resulting from AMR has become a global public health concern. Whole-genome sequencing is an effective method to determine the AMR characteristics of N. gonorrhoeae. Compared with next-generation sequencing, the MinION sequencer (Oxford Nanopore Technologies (ONT)) has the advantages of long read length and portability. Based on a pilot study using MinION to sequence the genome of N. gonorrhoeae, we optimized the workflow of sequencing and data analysis in the current study. Here we sequenced nine isolates within one flow cell using a multiplexed sequencing strategy. After hybrid assembly with Illumina reads, nine integral circular chromosomes were obtained. By using the online tool Pathogenwatch and a BLAST-based workflow, we acquired complete AMR profiles related to seven classes of antibiotics. We also evaluated the performance of ONT-only assemblies. Most AMR determinants identified by ONT-only assemblies were the same as those identified by hybrid assemblies. Moreover, one of the nine assemblies indicated a potentially novel antimicrobial-related mutation located in mtrR which results in a frame-shift, premature stop codon, and truncated peptide. In addition, this is the first study using the MinION sequencer to obtain complete genome sequences of N. gonorrhoeae strains which are epidemic in China. This study shows that complete genome sequences and antimicrobial characteristics of N. gonorrhoeae can be obtained using the MinION sequencer in a simple and cost-effective manner, with hardly any knowledge of bioinformatics required. More importantly, this strategy provides us with a potential approach to discover new AMR determinants.
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14
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Domman D, Ruis C, Dorman MJ, Shakya M, Chain PSG. Novel Insights Into the Spread of Enteric Pathogens Using Genomics. J Infect Dis 2020; 221:S319-S330. [PMID: 31538189 DOI: 10.1093/infdis/jiz220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/19/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daryl Domman
- Bioscience Division, Los Alamos National Laboratory, New Mexico
| | - Christopher Ruis
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Matthew J Dorman
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, New Mexico
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15
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Hospitalization costs for patients colonized with carbapenemase-producing Enterobacterales during an Australian outbreak. J Hosp Infect 2020; 105:146-153. [PMID: 32179134 DOI: 10.1016/j.jhin.2020.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/05/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND Carbapenem-producing Enterobacterales are an expanding group of Gram-negative bacteria that are resistant to carbapenems and cause over 9000 cases of hospital-associated infections in the USA. Efforts to quantify the economic and societal burden to healthcare are important to inform resource planning to implement infection control programmes. AIM We estimated the healthcare costs during an outbreak of carbapenemase-producing Escherichia coli OXA-181 in Australia. We aimed to understand the economic burden to hospitals of patients who are asymptomatically colonized with high-risk bacteria. METHODS Hospital admissions data and associated costs were obtained from the State Health Department. Colonized patients were matched to non-colonized patients on age, sex, admission ward and diagnostic category. Mean healthcare costs and length of stay were examined using generalized linear models and accounted for time-dependent bias, patient age and ward location. FINDINGS On average, colonized patients had six times higher mean costs (AU$155,784; 95% confidence interval (CI): AU$77,892-285,604) than non-colonized patients (AU$25,964). Mean costs for those aged 75-79 years were 50% lower (P=0.02) compared with the youngest subgroup, 35-39 years of age. The mean extended length of stay was 12 days (95% CI: 3-21) for colonized patients. Nursing care was the main driver of overall costs for colonized (44%) and non-colonized (39%) patients. CONCLUSION Patients colonized with carbapenem-producing Enterobacterales during an official hospital outbreak incurred higher costs than non-colonized patients. Although infected patients incur substantial economic burden to hospitals, the costs incurred by colonized patients is also high.
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16
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Santos-Cortez RLP, Bhutta MF, Earl JP, Hafrén L, Jennings M, Mell JC, Pichichero ME, Ryan AF, Tateossian H, Ehrlich GD. Panel 3: Genomics, precision medicine and targeted therapies. Int J Pediatr Otorhinolaryngol 2020; 130 Suppl 1:109835. [PMID: 32007292 PMCID: PMC7155947 DOI: 10.1016/j.ijporl.2019.109835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
OBJECTIVE To review the most recent advances in human and bacterial genomics as applied to pathogenesis and clinical management of otitis media. DATA SOURCES PubMed articles published since the last meeting in June 2015 up to June 2019. REVIEW METHODS A panel of experts in human and bacterial genomics of otitis media was formed. Each panel member reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a merged draft was created. The panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019, discussed the review and refined the content. A final draft was made, circulated, and approved by the panel members. CONCLUSION Trans-disciplinary approaches applying pan-omic technologies to identify human susceptibility to otitis media and to understand microbial population dynamics, patho-adaptation and virulence mechanisms are crucial to the development of novel, personalized therapeutics and prevention strategies for otitis media. IMPLICATIONS FOR PRACTICE In the future otitis media prevention strategies may be augmented by mucosal immunization, combination vaccines targeting multiple pathogens, and modulation of the middle ear microbiome. Both treatment and vaccination may be tailored to an individual's otitis media phenotype as defined by molecular profiles obtained by using rapidly developing techniques in microbial and host genomics.
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Affiliation(s)
- Regie Lyn P. Santos-Cortez
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, 12700 E. 19 Ave., Aurora, CO 80045, USA
| | - Mahmood F. Bhutta
- Department of ENT, Royal Sussex County Hospital, Eastern Road, Brighton BN2 5BE, UK
| | - Joshua P. Earl
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
| | - Lena Hafrén
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Tukholmankatu 8A, 00290 Helsinki, Finland
| | - Michael Jennings
- Institute for Glycomics, Gold Coast campus, Griffith University, QLD 4222, Australia
| | - Joshua C. Mell
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
| | - Michael E. Pichichero
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, 1425 Portland Ave., Rochester, NY 14621, USA
| | - Allen F. Ryan
- Department of Surgery/Otolaryngology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Hilda Tateossian
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell, Oxford, Didcot OX11 0RD, UK
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
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17
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Lacey JA, James TB, Tong SYC, Davies MR. Whole Genome Sequence Analysis and Population Genomics of Group A Streptococci. Methods Mol Biol 2020; 2136:81-111. [PMID: 32430815 DOI: 10.1007/978-1-0716-0467-0_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Whole-genome sequencing (WGS) is used to determine the genetic composition of an organism. This fast-moving field is continually evolving through technical advancements and the development of new bioinformatic tools for analyzing genomic data; however, the basic principles and processes for defining and processing high-quality genome sequence information remain unchanged. Here, we introduce some considerations and describe some commonly used bioinformatic steps for processing raw genome sequence data to generate genome assemblies through to understanding basic population genomics.
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Affiliation(s)
- Jake A Lacey
- Doherty Department, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Taylah B James
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Steven Y C Tong
- Doherty Department, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Division of Global and Tropical Health, Menzies School of Health Research, Division of Global and Tropical Health, Darwin, NT, Australia
- Victorian Infectious Disease Service, The Royal Melbourne Hospital, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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18
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Hanafiah A, Lopes BS. Genetic diversity and virulence characteristics of Helicobacter pylori isolates in different human ethnic groups. INFECTION GENETICS AND EVOLUTION 2019; 78:104135. [PMID: 31837482 DOI: 10.1016/j.meegid.2019.104135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 12/03/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023]
Abstract
Helicobacter pylori is the most predominant bacterium in almost 50% of the world's population and colonization causes a persistent inflammatory response leading to chronic gastritis. It shows high genetic diversity and individuals generally harbour a distinct bacterial population. With the advancement of whole-genome sequencing technology, new H. pylori subpopulations have been identified that show admixture between various H. pylori strains. Genotypic variation of H. pylori may be related to the presence of virulence factors among strains and is associated with different outcomes of infection in different individuals. This review summarizes the genetic diversity in H. pylori strain populations and its virulence characteristics responsible for variable outcomes in different ethnic groups.
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Affiliation(s)
- Alfizah Hanafiah
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia.
| | - Bruno S Lopes
- Department of Medical Microbiology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, 0:025 Polwarth Building, Aberdeen AB25 2ZD, United Kingdom.
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19
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Uncovering Bifidobacteria via Targeted Sequencing of the Mammalian Gut Microbiota. Microorganisms 2019; 7:microorganisms7110535. [PMID: 31698863 PMCID: PMC6920958 DOI: 10.3390/microorganisms7110535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022] Open
Abstract
Bifidobacteria are among the most prevalent gut commensals in mammals, playing crucial functional roles that start from their early colonization of the infant gastrointestinal tract and last throughout the life span of their host. Metagenomic approaches have been employed to unveil the genetic features of bifidobacteria in order to understand how they participate in the correct development of a healthy microbiome. Nevertheless, their low relative abundance in many environmental samples may represent a major limitation for metagenomics approaches. To overcome this restriction, we applied an enrichment method that allows amplification of bifidobacterial DNA obtained from human or animal fecal samples for up to 26,500-fold, resulting in the metagenomic reconstruction of genomes belonging to bifidobacterial strains, present at very low abundance in collected samples. Functional predictions of the genes from these reconstructed genomes allows us to identify unique signatures among members of the same bifidobacterial species, highlighting genes correlated with the uptake of nutrients and adhesion to the intestinal mucosa.
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20
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A large-scale whole-genome comparison shows that experimental evolution in response to antibiotics predicts changes in naturally evolved clinical Pseudomonas aeruginosa. Antimicrob Agents Chemother 2019:AAC.01619-19. [PMID: 31570397 DOI: 10.1128/aac.01619-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes a wide range of acute and chronic infections. An increasing number of isolates have mutations that make them antibiotic resistant, making treatment difficult. To identify resistance-associated mutations we experimentally evolved the antibiotic sensitive strain P. aeruginosa PAO1 to become resistant to three widely used anti-pseudomonal antibiotics, ciprofloxacin, meropenem and tobramycin. Mutants could tolerate up to 2048-fold higher concentrations of antibiotic than strain PAO1. Genome sequences were determined for thirteen mutants for each antibiotic. Each mutant had between 2 and 8 mutations. For each antibiotic at least 8 genes were mutated in multiple mutants, demonstrating the genetic complexity of resistance. For all three antibiotics mutations arose in genes known to be associated with resistance, but also in genes not previously associated with resistance. To determine the clinical relevance of mutations uncovered in this study we analysed the corresponding genes in 558 isolates of P. aeruginosa from patients with chronic lung disease and in 172 isolates from the general environment. Many genes identified through experimental evolution had predicted function-altering changes in clinical isolates but not in environmental isolates, showing that mutated genes in experimentally evolved bacteria can predict those that undergo mutation during infection. Additionally, large deletions of up to 479kb arose in experimentally evolved meropenem resistant mutants and large deletions were present in 87 of the clinical isolates. These findings significantly advance understanding of antibiotic resistance in P. aeruginosa and demonstrate the validity of experimental evolution in identifying clinically-relevant resistance-associated mutations.
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21
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Whole-genome sequencing of Neisseria gonorrhoeae in a forensic transmission case. Forensic Sci Int Genet 2019; 42:141-146. [PMID: 31319352 DOI: 10.1016/j.fsigen.2019.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 07/02/2019] [Accepted: 07/02/2019] [Indexed: 11/21/2022]
Abstract
Molecular epidemiology and phylogenetic analyses are frequently used in the investigation of viral transmission cases in forensic contexts. Here, we present the methods and results of the analysis of a bacterial transmission episode in an alleged child abuse case using complete genome sequences obtained by high-throughput sequencing (HTS) methods. We obtained genomes of Neisseria gonorrhoeae from the victim, the suspect, and 29 unrelated controls. The analysis of the genomes revealed that the victim and suspect isolates had identical sequences in both the bacterial chromosome and the single plasmid present in them. One of the local controls was very similar (differing in only 2 SNPs) to the case sequences, but the remaining controls were very divergent. Additional cases of identity and very high similarity among controls were observed occasionally, pointing at recent transmission cases. These results were more discriminative than the previous molecular epidemiology analyses performed at the hospital's Microbiology Service, as Multi-Locus Sequence Typing (MLST) could not distinguish between the suspect/victim and the controls isolates, and Pulse Field Gel Electrophoresis (PFGE) was not able to distinguish between the suspect/victim and one of the local controls. These results lead us to conclude that complete bacterial genome sequences obtained with HTS technologies may be a valuable tool for establishing recent transmission cases and, although more studies are needed, they have a great potential for being used in forensic analyses.
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22
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Chen SL. Genomic Insights Into the Distribution and Evolution of Group B Streptococcus. Front Microbiol 2019; 10:1447. [PMID: 31316488 PMCID: PMC6611187 DOI: 10.3389/fmicb.2019.01447] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 06/11/2019] [Indexed: 01/31/2023] Open
Abstract
Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a bacteria with truly protean biology. It infects a variety of hosts, among which the most commonly studied are humans, cattle, and fish. GBS holds a singular position in the history of bacterial genomics, as it was the substrate used to describe one of the first major conceptual advances of comparative genomics, the idea of the pan-genome. In this review, I describe a brief history of GBS and the major contributions of genomics to understanding its genome plasticity and evolution as well as its molecular epidemiology, focusing on the three hosts mentioned above. I also discuss one of the major recent paradigm shifts in our understanding of GBS evolution and disease burden: foodborne GBS can cause invasive infections in humans.
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Affiliation(s)
- Swaine L Chen
- Division of Infectious Diseases, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Infectious Diseases Group, Genome Institute of Singapore, Singapore, Singapore
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23
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Lugli GA, Milani C, Duranti S, Alessandri G, Turroni F, Mancabelli L, Tatoni D, Ossiprandi MC, van Sinderen D, Ventura M. Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches. Genome Biol 2019; 20:96. [PMID: 31097033 PMCID: PMC6524291 DOI: 10.1186/s13059-019-1711-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 05/07/2019] [Indexed: 02/07/2023] Open
Abstract
Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method.
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Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Giulia Alessandri
- Department of Veterinary Medical Science, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Danilo Tatoni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Maria Cristina Ossiprandi
- Department of Veterinary Medical Science, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy. .,Microbiome Research Hub, University of Parma, Parma, Italy.
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24
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Abstract
ABSTRACT
The rapid development of genomics and other “-omics” approaches has significantly impacted how we have investigated host-pathogen interactions since the turn of the millennium. Technologies such as next-generation sequencing, stem cell biology, and high-throughput proteomics have transformed the scale and sensitivity with which we interrogate biological samples. These approaches are impacting experimental design in the laboratory and transforming clinical management in health care systems. Here, we review this area from the perspective of research on bacterial pathogens.
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25
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Uncovering carbohydrate metabolism through a genotype-phenotype association study of 56 lactic acid bacteria genomes. Appl Microbiol Biotechnol 2019; 103:3135-3152. [PMID: 30830251 PMCID: PMC6447522 DOI: 10.1007/s00253-019-09701-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/14/2019] [Accepted: 02/14/2019] [Indexed: 11/09/2022]
Abstract
Owing to their unique potential to ferment carbohydrates, both homo- and heterofermentative lactic acid bacteria (LAB) are widely used in the food industry. Deciphering the genetic basis that determine the LAB fermentation type, and hence carbohydrate utilization, is paramount to optimize LAB industrial processes. Deep sequencing of 24 LAB species and comparison with 32 publicly available genome sequences provided a comparative data set including five major LAB genera for further analysis. Phylogenomic reconstruction confirmed Leuconostoc and Pediococcus species as independently emerging from the Lactobacillus genus, within one of the three phylogenetic clades identified. These clades partially grouped LABs according to their fermentation types, suggesting that some metabolic capabilities were independently acquired during LAB evolution. In order to apply a genome-wide association study (GWAS) at the multigene family level, utilization of 49 carbohydrates was also profiled for these 56 LAB species. GWAS results indicated that obligately heterofermentative species lack 1-phosphofructokinase, required for d-mannose degradation in the homofermentative pathway. Heterofermentative species were found to often contain the araBAD operon, involved in l-arabinose degradation, which is important for heterofermentation. Taken together, our results provide helpful insights into the genetic determinants of LAB carbohydrate metabolism, and opens for further experimental research, aiming at validating the role of these candidate genes for industrial applications.
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26
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Wang Y, Jia B, Xu X, Zhang L, Wei C, Ou H, Cui Y, Shi C, Shi X. Comparative Genomic Analysis and Characterization of Two Salmonella enterica Serovar Enteritidis Isolates From Poultry With Notably Different Survival Abilities in Egg Whites. Front Microbiol 2018; 9:2111. [PMID: 30245675 PMCID: PMC6137255 DOI: 10.3389/fmicb.2018.02111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022] Open
Abstract
Salmonellaenterica serovar Enteritidis (Salmonella Enteritidis) is a globally important foodborne pathogen, and the contaminated chicken eggs are the major source of salmonellosis in humans. Salmonella Enteritidis strains are differentially susceptible to the hostile environment of egg whites. Strains with superior survival ability in egg whites are more likely to contaminate eggs and consequently infect humans. However, the genetic basis for this phenotype is unclear. We characterized two Salmonella Enteritidis strains isolated from chicken meat that had similar genetic backgrounds but large differences in survival ability in egg whites. Although genome comparisons indicated that the gene content and genomic synteny were highly conserved, variations including six insertions or deletions (INDELs) and 70 single nucleotide polymorphisms (SNPs) were observed between the two genomes. Of these, 38 variations including four INDELs and 34 non-synonymous SNPs (nsSNP) were annotated to result in amino acid substitutions or INDELs in coding proteins. These variations were located in 38 genes involved in lysozyme inhibition, vitamin biosynthesis, cell division and DNA damage response, osmotic and oxidative protection, iron-related functions, cell envelope maintenance, amino acid and carbohydrate metabolism, antimicrobial resistance, and type III secretion system. We carried out allelic replacements for two nsSNPs in bioC (biotin synthesis) and pliC (lysozyme inhibition), and two INDELs in ftsK and yqiJ (DNA damage response) by homologous recombination, and these replacements did not alter the bacterial survival ability in egg whites. However, the bacterial survival ability in egg whites was reduced when deletion mutation of the genes bioC and pliC occurred. This study provides initial correlations between observed genotypes and phenotypes and serves as an important caveat for further functional studies.
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Affiliation(s)
- Yanyan Wang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Ben Jia
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuebin Xu
- Department of Microbiology, Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Lida Zhang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Chaochun Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hongyu Ou
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Cui
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xianming Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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Branchu P, Bawn M, Kingsley RA. Genome Variation and Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Pathovariants. Infect Immun 2018; 86:e00079-18. [PMID: 29784861 PMCID: PMC6056856 DOI: 10.1128/iai.00079-18] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Salmonella enterica serovar Typhimurium is one of approximately 2,500 distinct serovars of the genus Salmonella but is exceptional in its wide distribution in the environment, livestock, and wild animals. S Typhimurium causes a large proportion of nontyphoidal Salmonella (NTS) infections, accounting for a quarter of infections, second only to S. enterica serovar Enteritidis in incidence. S Typhimurium was once considered the archetypal broad-host-range Salmonella serovar due to its wide distribution in livestock and wild animals, and much of what we know of the interaction of Salmonella with the host comes from research using a small number of laboratory strains of the serovar (LT2, SL1344, and ATCC 14028). But it has become clear that these strains do not reflect the genotypic or phenotypic diversity of S Typhimurium. Here, we review the epidemiological record of S Typhimurium and studies of the host-pathogen interactions of diverse strains of S Typhimurium. We present the concept of distinct pathovariants of S Typhimurium that exhibit diversity of host range, distribution in the environment, pathogenicity, and risk to food safety. We review recent evidence from whole-genome sequencing that has revealed the extent of genomic diversity of S Typhimurium pathovariants, the genomic basis of differences in the level of risk to human and animal health, and the molecular epidemiology of prominent strains. An improved understanding of the impact of genome variation of bacterial pathogens on pathogen-host and pathogen-environment interactions has the potential to improve quantitative risk assessment and reveal how new pathogens evolve.
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Affiliation(s)
- Priscilla Branchu
- Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, United Kingdom
| | - Matt Bawn
- Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, United Kingdom
- Earlham Institute, Norwich Research Park, Colney, Norwich, United Kingdom
| | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, United Kingdom
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28
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Pathogenic flora composition and overview of the trends used for bacterial pathogenicity identifications. Microb Pathog 2018; 121:139-146. [DOI: 10.1016/j.micpath.2018.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 04/28/2018] [Accepted: 05/04/2018] [Indexed: 11/19/2022]
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Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence. ISME JOURNAL 2018; 12:2518-2531. [PMID: 29942073 DOI: 10.1038/s41396-018-0199-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/29/2018] [Accepted: 03/20/2018] [Indexed: 12/17/2022]
Abstract
Since the discovery of the human pathogen Helicobacter pylori, various other Helicobacter species have been identified in the stomach of domesticated and wild mammals. To better understand the evolutionary history of these ecologically similar but genetically distinct species, we analyzed 108 gastric Helicobacter genomes and included 54 enterohepatic Helicobacter genomes for comparison purposes. An admixture analysis supported the presence of an ecological barrier, preventing the genetic exchange between the gastric and enterohepatic Helicobacter species, and unraveled many gene flow events within and across species residing in the stomach. As pets can be colonized by multiple gastric Helicobacter species, the genetic exchange between the canine and feline strains was evident, with H. heilmannii and H. bizzozeronii showing the highest interspecies recombination. An admixture between H. pylori (in particular, the ancestral African strains), H. acinonychis from wild felines and H. cetorum from marine mammals was also identified. Because these latter species do not share the same host, this phenomenon is most likely a remaining signal of shared ancestry. A reconstruction of the time of divergence of the gastric Helicobacter spp. revealed that the domestic animal-related Helicobacter species evolved in parallel with H. pylori and its two closest relatives (H. acinonychis and H. cetorum), rather than together.
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30
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Rantsiou K, Kathariou S, Winkler A, Skandamis P, Saint-Cyr MJ, Rouzeau-Szynalski K, Amézquita A. Next generation microbiological risk assessment: opportunities of whole genome sequencing (WGS) for foodborne pathogen surveillance, source tracking and risk assessment. Int J Food Microbiol 2017; 287:3-9. [PMID: 29246458 DOI: 10.1016/j.ijfoodmicro.2017.11.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 10/16/2017] [Accepted: 11/12/2017] [Indexed: 12/11/2022]
Abstract
Whole genome sequencing (WGS) of important foodborne pathogens is a technology under development, but is already employed in routine surveillance by public health agencies and is being increasingly exploited in tracing transmission routes and identifying contamination events (source tracking) that take place in the farm-to-fork continuum. Furthermore, data generated from WGS, complemented by other -omics data, have the potential to be integrated into and strengthen microbiological risk assessment. In this paper, we discuss the contribution of WGS in diverse areas important to food safety and public health. Additionally, an outlook of future WGS applications, which should contribute to our understanding of the ecology and physiology of foodborne microorganisms, is presented.
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Affiliation(s)
- Kalliopi Rantsiou
- Department of Agriculture, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco, Italy.
| | - Sophia Kathariou
- North Carolina State University, Department of Food, Bioprocessing and Nutrition Sciences, Raleigh, NC, USA
| | - Annet Winkler
- Mondelez International, Kraft Foods R&D, Unterbiberger St. 15, D-81737 Munich, Germany
| | - Panos Skandamis
- Laboratory of Food Quality Control & Hygiene, Department of Food Science & Technology, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | | | | | - Alejandro Amézquita
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
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31
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Pseudogenization of the Secreted Effector Gene sseI Confers Rapid Systemic Dissemination of S. Typhimurium ST313 within Migratory Dendritic Cells. Cell Host Microbe 2017; 21:182-194. [PMID: 28182950 DOI: 10.1016/j.chom.2017.01.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/14/2016] [Accepted: 01/18/2017] [Indexed: 12/23/2022]
Abstract
Genome degradation correlates with host adaptation and systemic disease in Salmonella. Most lineages of the S. enterica subspecies Typhimurium cause gastroenteritis in humans; however, the recently emerged ST313 lineage II pathovar commonly causes systemic bacteremia in sub-Saharan Africa. ST313 lineage II displays genome degradation compared to gastroenteritis-associated lineages; yet, the mechanisms and causal genetic differences mediating these infection phenotypes are largely unknown. We find that the ST313 isolate D23580 hyperdisseminates from the gut to systemic sites, such as the mesenteric lymph nodes (MLNs), via CD11b+ migratory dendritic cells (DCs). This hyperdissemination was facilitated by the loss of sseI, which encodes an effector that inhibits DC migration in gastroenteritis-associated isolates. Expressing functional SseI in D23580 reduced the number of infected migratory DCs and bacteria in the MLN. Our study reveals a mechanism linking pseudogenization of effectors with the evolution of niche adaptation in a bacterial pathogen.
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32
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Lourenço J, Watkins ER, Obolski U, Peacock SJ, Morris C, Maiden MCJ, Gupta S. Lineage structure of Streptococcus pneumoniae may be driven by immune selection on the groEL heat-shock protein. Sci Rep 2017; 7:9023. [PMID: 28831154 PMCID: PMC5567354 DOI: 10.1038/s41598-017-08990-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/20/2017] [Indexed: 12/29/2022] Open
Abstract
Populations of Streptococcus pneumoniae (SP) are typically structured into groups of closely related organisms or lineages, but it is not clear whether they are maintained by selection or neutral processes. Here, we attempt to address this question by applying a machine learning technique to SP whole genomes. Our results indicate that lineages evolved through immune selection on the groEL chaperone protein. The groEL protein is part of the groESL operon and enables a large range of proteins to fold correctly within the physical environment of the nasopharynx, thereby explaining why lineage structure is so stable within SP despite high levels of genetic transfer. SP is also antigenically diverse, exhibiting a variety of distinct capsular serotypes. Associations exist between lineage and capsular serotype but these can be easily perturbed, such as by vaccination. Overall, our analyses indicate that the evolution of SP can be conceptualized as the rearrangement of modular functional units occurring on several different timescales under different pressures: some patterns have locked in early (such as the epistatic interactions between groESL and a constellation of other genes) and preserve the differentiation of lineages, while others (such as the associations between capsular serotype and lineage) remain in continuous flux.
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Affiliation(s)
- José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
| | | | - Uri Obolski
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Samuel J Peacock
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | | | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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33
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Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome. ISME JOURNAL 2017; 11:2848-2863. [PMID: 28837129 PMCID: PMC5702742 DOI: 10.1038/ismej.2017.139] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/05/2017] [Accepted: 07/14/2017] [Indexed: 12/12/2022]
Abstract
The influence of unicellular eukaryotic microorganisms on human gut health and disease is still largely unexplored. Blastocystis spp. commonly colonize the gut, but its clinical significance and ecological role are currently unsettled. We have developed a high-sensitivity bioinformatic pipeline to detect Blastocystis subtypes (STs) from shotgun metagenomics, and applied it to 12 large data sets, comprising 1689 subjects of different geographic origin, disease status and lifestyle. We confirmed and extended previous observations on the high prevalence the microrganism in the population (14.9%), its non-random and ST-specific distribution, and its ability to cause persistent (asymptomatic) colonization. These findings, along with the higher prevalence observed in non-westernized individuals, the lack of positive association with any of the disease considered, and decreased presence in individuals with dysbiosis associated with colorectal cancer and Crohn's disease, strongly suggest that Blastocystis is a component of the healthy gut microbiome. Further, we found an inverse association between body mass index and Blastocystis, and strong co-occurrence with archaeal organisms (Methanobrevibacter smithii) and several bacterial species. The association of specific microbial community structures with Blastocystis was confirmed by the high predictability (up to 0.91 area under the curve) of the microorganism colonization based on the species-level composition of the microbiome. Finally, we reconstructed and functionally profiled 43 new draft Blastocystis genomes and discovered a higher intra subtype variability of ST1 and ST2 compared with ST3 and ST4. Altogether, we provide an in-depth epidemiologic, ecological, and genomic analysis of Blastocystis, and show how metagenomics can be crucial to advance population genomics of human parasites.
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34
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Tran TT, Miller WR, Shamoo Y, Arias CA. Targeting cell membrane adaptation as a novel antimicrobial strategy. Curr Opin Microbiol 2016; 33:91-96. [PMID: 27458841 DOI: 10.1016/j.mib.2016.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/01/2016] [Accepted: 07/05/2016] [Indexed: 01/19/2023]
Abstract
Emergence of antibiotic resistance is an example of the incredible plasticity of bacteria to survive in all environments. The search for new antibiotics active against traditional targets is more challenging due not only to the lack of novel natural products to fulfill the current clinical needs against multidrug-resistant (MDR) bacteria, but also for the possible 'collateral' effects on the human microbiota. Thus, non-traditional approaches to combat MDR bacteria have been proposed. Here, we discuss the possibility of targeting the membrane response to the antibiotic attack (cell membrane adaptation) as a viable strategy to increase the activity of current antimicrobials, enhance the activity of the innate immune system and prevent development of resistance during therapy using the three-component regulatory system LiaFSR of enterococci as a model.
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Affiliation(s)
- Truc T Tran
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas McGovern Medical School, Houston, TX, United States; Center for Antibiotic Resistance and Microbial Genomics, University of Texas McGovern Medical School, Houston, TX, United States
| | - William R Miller
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas McGovern Medical School, Houston, TX, United States; Center for Antibiotic Resistance and Microbial Genomics, University of Texas McGovern Medical School, Houston, TX, United States
| | - Yousif Shamoo
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX, United States
| | - Cesar A Arias
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas McGovern Medical School, Houston, TX, United States; Center for Antibiotic Resistance and Microbial Genomics, University of Texas McGovern Medical School, Houston, TX, United States; Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia; International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia.
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35
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Rusconi B, Sanjar F, Koenig SSK, Mammel MK, Tarr PI, Eppinger M. Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks. Front Microbiol 2016; 7:985. [PMID: 27446025 PMCID: PMC4928038 DOI: 10.3389/fmicb.2016.00985] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 06/08/2016] [Indexed: 01/29/2023] Open
Abstract
Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and long-term evolution and can complement currently employed typing schemes for outbreak ex- and inclusion, diagnostics, surveillance, and forensic studies.
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Affiliation(s)
- Brigida Rusconi
- South Texas Center for Emerging Infectious Diseases, University of Texas at San AntonioSan Antonio, TX, USA; Department of Biology, University of Texas at San AntonioSan Antonio, TX, USA
| | - Fatemeh Sanjar
- South Texas Center for Emerging Infectious Diseases, University of Texas at San AntonioSan Antonio, TX, USA; Department of Biology, University of Texas at San AntonioSan Antonio, TX, USA
| | - Sara S K Koenig
- South Texas Center for Emerging Infectious Diseases, University of Texas at San AntonioSan Antonio, TX, USA; Department of Biology, University of Texas at San AntonioSan Antonio, TX, USA
| | - Mark K Mammel
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration Laurel, MD, USA
| | - Phillip I Tarr
- Department of Pediatrics, Washington University School of Medicine St. Louis, MO, USA
| | - Mark Eppinger
- South Texas Center for Emerging Infectious Diseases, University of Texas at San AntonioSan Antonio, TX, USA; Department of Biology, University of Texas at San AntonioSan Antonio, TX, USA
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