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Haidar-Ahmad N, Manigat FO, Silué N, Pontier SM, Campbell-Valois FX. A Tale about Shigella: Evolution, Plasmid, and Virulence. Microorganisms 2023; 11:1709. [PMID: 37512882 PMCID: PMC10383432 DOI: 10.3390/microorganisms11071709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Shigella spp. cause hundreds of millions of intestinal infections each year. They target the mucosa of the human colon and are an important model of intracellular bacterial pathogenesis. Shigella is a pathovar of Escherichia coli that is characterized by the presence of a large invasion plasmid, pINV, which encodes the characteristic type III secretion system and icsA used for cytosol invasion and cell-to-cell spread, respectively. First, we review recent advances in the genetic aspects of Shigella, shedding light on its evolutionary history within the E. coli lineage and its relationship to the acquisition of pINV. We then discuss recent insights into the processes that allow for the maintenance of pINV. Finally, we describe the role of the transcription activators VirF, VirB, and MxiE in the major virulence gene regulatory cascades that control the expression of the type III secretion system and icsA. This provides an opportunity to examine the interplay between these pINV-encoded transcriptional activators and numerous chromosome-encoded factors that modulate their activity. Finally, we discuss novel chromosomal genes icaR, icaT, and yccE that are regulated by MxiE. This review emphasizes the notion that Shigella and E. coli have walked the fine line between commensalism and pathogenesis for much of their history.
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Affiliation(s)
- Nathaline Haidar-Ahmad
- Host-Microbe Interactions Laboratory, Centre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - France Ourida Manigat
- Host-Microbe Interactions Laboratory, Centre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Navoun Silué
- Host-Microbe Interactions Laboratory, Centre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Stéphanie M Pontier
- Centre de Recherche Santé Environnementale et Biodiversité de l'Outaouais (SEBO), CEGEP de l'Outaouais, Gatineau, QC J8Y 6M4, Canada
| | - François-Xavier Campbell-Valois
- Host-Microbe Interactions Laboratory, Centre for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Centre for Infection, Immunity and Inflammation, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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2
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Ibrahim AF, Glass K, Williamson DA, Polkinghorne BG, Ingle DJ, Wright R, Kirk MD. The changing epidemiology of shigellosis in Australia, 2001-2019. PLoS Negl Trop Dis 2023; 17:e0010450. [PMID: 36857390 DOI: 10.1371/journal.pntd.0010450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 03/13/2023] [Accepted: 02/14/2023] [Indexed: 03/02/2023] Open
Abstract
Shigellosis is an increasing cause of gastroenteritis in Australia, with prolonged outbreaks reported in remote Aboriginal and Torres Strait Islander (hereafter "First Nations") communities and among men who have sex with men (MSM) in major cities. To determine associations between Shigella species and demographic and geographic factors, we used multivariate negative binomial regression to analyse national case notifications of shigellosis from 2001 to 2019. Between 2001 and 2019, Australian states and territories reported 18,363 shigellosis cases to the National Notifiable Diseases Surveillance System (NNDSS), of which age, sex and organism information were available for >99% (18,327/18,363) of cases. Of the cases included in our analysis, 42% (7,649/18,327) were S. sonnei, 29% (5,267/18,327) were S. flexneri, 1% (214/18,327) were S. boydii, less than 1% (87/18,327) were S. dysenteriae, and species information was unknown for 28% (5,110/18,327) of cases. Males accounted for 54% (9,843/18,327) of cases, and the highest proportion of cases were in children aged 0-4 years (19%; 3,562/18,327). Crude annual notification rates ranged from 2.2 cases per 100,000 in 2003 and 2011 to 12.4 cases per 100,000 in 2019. Nationally, notification rates increased from 2001 to 2019 with yearly notification rate ratios of 1.04 (95% CI 1.02-1.07) for S. boydii and 1.05 (95% CI 1.04-1.06) for S. sonnei. Children aged 0-4 years had the highest burden of infection for S. flexneri, S. sonnei and S. boydii; and males had a higher notification rate for S. sonnei (notification rate ratio 1.24, 95% CI 1.15-1.33). First Nations Australians were disproportionately affected by shigellosis, with the notification rate in this population peaking in 2018 at 92.1 cases per 100,000 population. Over the study period, we also observed a shift in the testing method used to diagnose shigellosis, with culture independent diagnostic testing (CIDT) increasing from 2014; this also coincided with an increase in notifications of untyped Shigella. This change in testing methodology may have contributed to the observed increase in shigellosis notifications since 2014, with CIDT being more sensitive than culture dependent testing methods. The findings of this study provide important insights into the epidemiological characteristics of shigellosis in Australia, including identification of high-risk groups. This can be used to inform public health prevention and control strategies, such as targeted communication programs in First Nations communities and places with high levels of interaction between young children, such as childcare centres. Our study findings also highlight the implications of culture independent testing on shigellosis surveillance, particularly a reduction in the availability of species level information. This emphasises the continued importance of culture dependant testing for national surveillance of shigellosis.
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Liu W, Li W, Zheng H, Kwok LY, Sun Z. Genomics divergence of Lactococcus lactis subsp. lactis isolated from naturally fermented dairy products. Food Res Int 2022; 155:111108. [DOI: 10.1016/j.foodres.2022.111108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 12/13/2022]
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Toro CS, Salazar JC, Montero DA, Ugalde JA, Díaz J, Cádiz LA, Henríquez T, García C, Díaz P, Camponovo R, Hermosilla G, Ulloa MT. Antimicrobial Resistance Dynamics in Chilean Shigella sonnei Strains Within Two Decades: Role of Shigella Resistance Locus Pathogenicity Island and Class 1 and Class 2 Integrons. Front Microbiol 2022; 12:794470. [PMID: 35185820 PMCID: PMC8854971 DOI: 10.3389/fmicb.2021.794470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Shigellosis is an enteric infectious disease in which antibiotic treatment is effective, shortening the duration of symptoms and reducing the excretion of the pathogen into the environment. Shigella spp., the etiologic agent, are considered emerging pathogens with a high public health impact due to the increase and global spread of multidrug-resistant (MDR) strains. Since Shigella resistance phenotype varies worldwide, we present an overview of the resistance phenotypes and associated genetic determinants present in 349 Chilean S. sonnei strains isolated during the periods 1995–1997, 2002–2004, 2008–2009, and 2010–2013. We detected a great variability in antibiotic susceptibility patterns, finding 300 (86%) MDR strains. Mobile genetic elements (MGE), such as plasmids, integrons, and genomic islands, have been associated with the MDR phenotypes. The Shigella resistance locus pathogenicity island (SRL PAI), which encodes for ampicillin, streptomycin, chloramphenicol, and tetracycline resistance genes, was detected by PCR in 100% of the strains isolated in 2008–2009 but was less frequent in isolates from other periods. The presence or absence of SRL PAI was also differentiated by pulsed-field gel electrophoresis. An atypical class 1 integron which harbors the blaOXA–1-aadA1-IS1 organization was detected as part of SRL PAI. The dfrA14 gene conferring trimethoprim resistance was present in 98.8% of the 2008–2009 isolates, distinguishing them from the SRL-positive strains isolated before that. Thus, it seems an SRL-dfrA14 S. sonnei clone spread during the 2008–2009 period and declined thereafter. Besides these, SRL-negative strains harboring class 2 integrons with or without resistance to nalidixic acid were detected from 2011 onward, suggesting the circulation of another clone. Whole-genome sequencing of selected strains confirmed the results obtained by PCR and phenotypic analysis. It is highlighted that 70.8% of the MDR strains harbored one or more of the MGE evaluated, while 15.2% lacked both SRL PAI and integrons. These results underscore the temporal dynamics of antimicrobial resistance in S. sonnei strains circulating in Chile, mainly determined by the spread of MGE conferring MDR phenotypes. Since shigellosis is endemic in Chile, constant surveillance of antimicrobial resistance phenotypes and their genetic basis is a priority to contribute to public health policies.
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Affiliation(s)
- Cecilia S. Toro
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
- *Correspondence: Cecilia S. Toro,
| | - Juan Carlos Salazar
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - David A. Montero
- Programa Disciplinario de Inmunología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Juan Antonio Ugalde
- C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance, Santiago, Chile
| | - Janepsy Díaz
- Departamento de Estudios Científicos, Instituto de Salud Pública de Chile, Santiago, Chile
| | - Leandro A. Cádiz
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Tania Henríquez
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Camila García
- Escuela de Tecnología Médica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Patricia Díaz
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | | | - Germán Hermosilla
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - María Teresa Ulloa
- Programa de Microbiología y Micología, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
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Bengtsson RJ, Simpkin AJ, Pulford CV, Low R, Rasko DA, Rigden DJ, Hall N, Barry EM, Tennant SM, Baker KS. Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs. Nat Microbiol 2022; 7:251-261. [PMID: 35102306 PMCID: PMC8813619 DOI: 10.1038/s41564-021-01054-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/17/2021] [Indexed: 12/17/2022]
Abstract
AbstractShigella spp. are the leading bacterial cause of severe childhood diarrhoea in low- and middle-income countries (LMICs), are increasingly antimicrobial resistant and have no widely available licenced vaccine. We performed genomic analyses of 1,246 systematically collected shigellae sampled from seven countries in sub-Saharan Africa and South Asia as part of the Global Enteric Multicenter Study (GEMS) between 2007 and 2011, to inform control and identify factors that could limit the effectiveness of current approaches. Through contemporaneous comparison among major subgroups, we found that S. sonnei contributes ≥6-fold more disease than other Shigella species relative to its genomic diversity, and highlight existing diversity and adaptative capacity among S. flexneri that may generate vaccine escape variants in <6 months. Furthermore, we show convergent evolution of resistance against ciprofloxacin, the current WHO-recommended antimicrobial for the treatment of shigellosis, among Shigella isolates. This demonstrates the urgent need to integrate existing genomic diversity into vaccine and treatment plans for Shigella, providing a framework for the focused application of comparative genomics to guide vaccine development, and the optimization of control and prevention strategies for other pathogens relevant to public health policy considerations.
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6
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Yassine I, Lefèvre S, Hansen EE, Ruckly C, Carle I, Lejay-Collin M, Fabre L, Rafei R, Clermont D, de la Gandara MP, Dabboussi F, Thomson NR, Weill FX. Population structure analysis and laboratory monitoring of Shigella by core-genome multilocus sequence typing. Nat Commun 2022; 13:551. [PMID: 35087053 DOI: 10.1038/s41467-022-28121-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/06/2022] [Indexed: 11/18/2022] Open
Abstract
The laboratory surveillance of bacillary dysentery is based on a standardised Shigella typing scheme that classifies Shigella strains into four serogroups and more than 50 serotypes on the basis of biochemical tests and lipopolysaccharide O-antigen serotyping. Real-time genomic surveillance of Shigella infections has been implemented in several countries, but without the use of a standardised typing scheme. Here, we study over 4000 reference strains and clinical isolates of Shigella, covering all serotypes, with both the current serotyping scheme and the standardised EnteroBase core-genome multilocus sequence typing scheme (cgMLST). The Shigella genomes are grouped into eight phylogenetically distinct clusters, within the E. coli species. The cgMLST hierarchical clustering (HC) analysis at different levels of resolution (HC2000 to HC400) recognises the natural population structure of Shigella. By contrast, the serotyping scheme is affected by horizontal gene transfer, leading to a conflation of genetically unrelated Shigella strains and a separation of genetically related strains. The use of this cgMLST scheme will facilitate the transition from traditional phenotypic typing to routine whole-genome sequencing for the laboratory surveillance of Shigella infections. Lab-based surveillance of Shigella has traditionally been based on serotyping but increasing availability of whole genome sequencing could enable higher resolution typing. Here, the authors apply a core genome multilocus sequence typing scheme to Shigella sequence data and describe its population structure.
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Mai SNT, Bodhidatta L, Turner P, Wangchuk S, Ha Thanh T, Voong Vinh P, Pham DT, Rabaa MA, Thwaites GE, Thomson NR, Baker S, Chung The H. The evolutionary history of Shigella flexneri serotype 6 in Asia. Microb Genom 2021; 7. [PMID: 34904947 PMCID: PMC8767353 DOI: 10.1099/mgen.0.000736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Shigella flexneri serotype 6 is an understudied cause of diarrhoeal diseases in developing countries, and has been proposed as one of the major targets for vaccine development against shigellosis. Despite being named as S. flexneri, Shigella flexneri serotype 6 is phylogenetically distinct from other S. flexneri serotypes and more closely related to S. boydii. This unique phylogenetic relationship and its low sampling frequency have hampered genomic research on this pathogen. Herein, by utilizing whole genome sequencing (WGS) and analyses of Shigella flexneri serotype 6 collected from epidemiological studies (1987–2013) in four Asian countries, we revealed its population structure and evolutionary history in the region. Phylogenetic analyses supported the delineation of Asian Shigella flexneri serotype 6 into two phylogenetic groups (PG-1 and −2). Notably, temporal phylogenetic approaches showed that extant Asian S. flexneri serotype 6 could be traced back to an inferred common ancestor arising in the 18th century. The dominant lineage PG-1 likely emerged in the 1970s, which coincided with the times to most recent common ancestors (tMRCAs) inferred from other major Southeast Asian S. flexneri serotypes. Similar to other S. flexneri serotypes in the same period in Asia, genomic analyses showed that resistance to first-generation antimicrobials was widespread, while resistance to more recent first-line antimicrobials was rare. These data also showed a number of gene inactivation and gene loss events, particularly on genes related to metabolism and synthesis of cellular appendages, emphasizing the continuing role of reductive evolution in the adaptation of the pathogen to an intracellular lifestyle. Together, our findings reveal insights into the genomic evolution of the understudied Shigella flexneri serotype 6, providing a new piece in the puzzle of Shigella epidemiology and evolution.
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Affiliation(s)
- Si-Nguyen T Mai
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | | | - Paul Turner
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Sonam Wangchuk
- Royal Centre for Disease Control, Ministry of Health, Thimphu, Bhutan
| | - Tuyen Ha Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phat Voong Vinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Duy Thanh Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nicholas R Thomson
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,London School of Hygiene and Tropical Medicine, Bloomsbury, London WC1E 7HT, UK
| | - Stephen Baker
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases (CITIID), University of Cambridge, Cambridge, UK
| | - Hao Chung The
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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Tan L, Zhang C, Liu F, Chen P, Wei X, Li H, Yi G, Xu Y, Zheng X. Three-compartment septic tanks as sustainable on-site treatment facilities? Watch out for the potential dissemination of human-associated pathogens and antibiotic resistance. J Environ Manage 2021; 300:113709. [PMID: 34547574 DOI: 10.1016/j.jenvman.2021.113709] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Improved sanitation is critical important to reduce the spread of human deposited pathogens and antibiotic resistance genes (ARGs). In the China's rural "Toilet Revolution", three-compartment septic tanks (SPTs) are widely used as household domestic sewage treatment facilities. The effluents of SPTs are encouraged to be used as fertilizer in agriculture. However, whether SPT could eliminate fecal pathogens and ARGs is still unrevealed which is crucial in risk assessment of SPT effluent utilization. Herein, we employed metagenomic sequencing to investigate the pathogens and ARGs in rural household SPTs from Tianjin, China. We found that rural household SPT effluents conserved pathogens comparable to that of the influents. A total of 441 ARGs conferring resistance to 26 antibiotic classes were observed in rural household SPTs, with the relative abundance ranging from 709 to 1800 ppm. Results of metagenomic assembly indicated that some ARG-MGE-carrying contigs were carried by pathogens, which may pose risk to human and animal health after being introduced to the environment. This study raises the question of SPTs as sustainable on-site treatment facilities for rural domestic sewage and underscores the need for more attention to the propagation and dissemination of antibiotic-resistant pathogens from SPT to the environments, animals, and humans.
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Affiliation(s)
- Lu Tan
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Chunxue Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Fang Liu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Peizhen Chen
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Xiaocheng Wei
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Houyu Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Gao Yi
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yan Xu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
| | - Xiangqun Zheng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
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9
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Liu B, Guo X, Wang J, Wu P, Li S, Feng L, Liu B, Wang L. Development of a Molecular Serotyping Scheme for Morganella morganii. Front Microbiol 2021; 12:791165. [PMID: 34887844 PMCID: PMC8649690 DOI: 10.3389/fmicb.2021.791165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 12/02/2022] Open
Abstract
Morganella morganii, which is often regarded as a human commensal organism, can be an opportunistic pathogen, causing a variety of clinical infections with serious morbidity and mortality. An efficient and convenient method for subtyping and identifying M. morganii strains in epidemiological surveillance and control is urgently needed. Serotyping based on bacterial surface polysaccharide antigens (O-antigen or K-antigens) is a standard subtyping method for many gram-negative bacteria. Here, through whole genome sequencing and comparative genomics analysis of 27 strains, we developed a molecular serotyping scheme based on the genetic variation of O-antigen gene clusters (O-AGC) in M. morganii, and 11 distinct O-AGC types were identified. A conventional serotyping scheme was also developed by the production of antisera and agglutination experiments, which was shown to be perfectly consistent with the molecular serotyping scheme, confirming that the variation in M. morganii O-AGC correlated with phenotypic O-antigen diversification. Furthermore, a microsphere-based suspension array (MSA) with high specificity was developed based on the specific genes within each O-AGC type. The sensitivity of MSA was determined to be 0.1 ng of genomic DNA and 103 CFU of pure culture. We further analyzed 104 M. morganii genomes available in GenBank, and an additional six novel O-AGC types were identified, indicating that the extension of this molecular serotyping scheme is convenient. Our work provides an important tool for the detection and epidemiological surveillance of M. morganii, and this method has the potential to be widely utilized, especially for bacterial genera/species without an efficient typing approach.
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Affiliation(s)
- Bin Liu
- Tianjin Union Medical Center, TEDA Institute of Biological Sciences and Biotechnology, The Institute of Translational Medicine Research, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Nankai University, Ministry of Education, Tianjin, China
| | - Xi Guo
- Tianjin Union Medical Center, TEDA Institute of Biological Sciences and Biotechnology, The Institute of Translational Medicine Research, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Nankai University, Ministry of Education, Tianjin, China
| | - Jing Wang
- Tianjin Union Medical Center, TEDA Institute of Biological Sciences and Biotechnology, The Institute of Translational Medicine Research, Nankai University, Tianjin, China
| | - Pan Wu
- Tianjin Union Medical Center, TEDA Institute of Biological Sciences and Biotechnology, The Institute of Translational Medicine Research, Nankai University, Tianjin, China
| | - Shujie Li
- Tianjin Union Medical Center, TEDA Institute of Biological Sciences and Biotechnology, The Institute of Translational Medicine Research, Nankai University, Tianjin, China
| | - Lu Feng
- Tianjin Union Medical Center, TEDA Institute of Biological Sciences and Biotechnology, The Institute of Translational Medicine Research, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Nankai University, Ministry of Education, Tianjin, China
| | - Bin Liu
- Tianjin Union Medical Center, TEDA Institute of Biological Sciences and Biotechnology, The Institute of Translational Medicine Research, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Nankai University, Ministry of Education, Tianjin, China
| | - Lei Wang
- Tianjin Union Medical Center, TEDA Institute of Biological Sciences and Biotechnology, The Institute of Translational Medicine Research, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Nankai University, Ministry of Education, Tianjin, China
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10
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Baruah N, Ahamad N, Maiti S, Howlader DR, Bhaumik U, Patil VV, Chakrabarti MK, Koley H, Katti DS. Development of a Self-Adjuvanting, Cross-Protective, Stable Intranasal Recombinant Vaccine for Shigellosis. ACS Infect Dis 2021; 7:3182-3196. [PMID: 34734708 DOI: 10.1021/acsinfecdis.1c00345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
With the acquirement of antibiotic resistance, Shigella has resulted in multiple epidemics of shigellosis, an infectious diarrheal disease, causing thousands of deaths per year. Unfortunately, there are no licensed vaccines, primarily due to low or serotype-specific immunogenicity. Thus, conserved subunit vaccines utilizing recombinant invasion plasmid antigens (Ipa) have been explored as cross-protective vaccine candidates. However, achieving cross-protection against Shigella dysenteriae 1, which caused multiple pandemics/epidemics in the recent past, has been difficult. Therefore, a rational approach to improve cross-protection in the preparation for a possible pandemic should involve conserved proteins from S. dysenteriae 1 (Sd1). IpaC is one such conserved immunogenic protein that is less explored as an independent vaccine due to its instability/aggregation. Therefore, to improve cross-protection and potential immunogenicity and to be prepared for a future epidemic/pandemic, herein, we stabilized recombinant Sd1 IpaC, expressed without its chaperone, using a previously reported stabilizing detergent (LDAO) in a modified protocol and assessed its vaccine potential without an adjuvant. The protein assembled into heterogeneous complex spherical structures in the presence of LDAO and showed improved stability at storage temperatures of -80, -20, 4, 25, and 37 °C while providing enhanced yield and concentration. The protein could also be stably lyophilized and reconstituted, increasing the convenience of transportation and storage. Upon intranasal administration in BALB/c mice, the stabilized-IpaC-immunized groups generated significant antibody response and were not only protected against a high intraperitoneal dose of homologous S. dysenteriae 1 but also showed 100% survival against heterologous Shigella flexneri 2a without an adjuvant, while the control animals showed visible diarrhea (bloody-Sd1 challenge), lethargy, and weight loss with 0% survival. Overall, this work demonstrates that stabilized IpaC can be explored as a minimalist, self-adjuvanting, cross-protective, intranasal, single-antigen Shigella vaccine.
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Affiliation(s)
- Namrata Baruah
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Nadim Ahamad
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Suhrid Maiti
- Division of Bacteriology, ICMR-National Institute of Cholera & Enteric Diseases, P-33 CIT Road, Scheme-XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Debaki R. Howlader
- Division of Bacteriology, ICMR-National Institute of Cholera & Enteric Diseases, P-33 CIT Road, Scheme-XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Ushasi Bhaumik
- Division of Bacteriology, ICMR-National Institute of Cholera & Enteric Diseases, P-33 CIT Road, Scheme-XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Vinod V. Patil
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
| | - Manoj K. Chakrabarti
- Division of Bacteriology, ICMR-National Institute of Cholera & Enteric Diseases, P-33 CIT Road, Scheme-XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Hemanta Koley
- Division of Bacteriology, ICMR-National Institute of Cholera & Enteric Diseases, P-33 CIT Road, Scheme-XM, Beliaghata, Kolkata 700010, West Bengal, India
| | - Dhirendra S. Katti
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
- The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India
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11
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Schar D, Zhao C, Wang Y, Larsson DGJ, Gilbert M, Van Boeckel TP. Twenty-year trends in antimicrobial resistance from aquaculture and fisheries in Asia. Nat Commun 2021; 12:5384. [PMID: 34508079 PMCID: PMC8433129 DOI: 10.1038/s41467-021-25655-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/20/2021] [Indexed: 01/21/2023] Open
Abstract
Antimicrobial resistance (AMR) is a growing threat to human and animal health. However, in aquatic animals-the fastest growing food animal sector globally-AMR trends are seldom documented, particularly in Asia, which contributes two-thirds of global food fish production. Here, we present a systematic review and meta-analysis of 749 point prevalence surveys reporting antibiotic-resistant bacteria from aquatic food animals in Asia, extracted from 343 articles published in 2000-2019. We find concerning levels of resistance to medically important antimicrobials in foodborne pathogens. In aquaculture, the percentage of antimicrobial compounds per survey with resistance exceeding 50% (P50) plateaued at 33% [95% confidence interval (CI) 28 to 37%] between 2000 and 2018. In fisheries, P50 decreased from 52% [95% CI 39 to 65%] to 22% [95% CI 14 to 30%]. We map AMR at 10-kilometer resolution, finding resistance hotspots along Asia's major river systems and coastal waters of China and India. Regions benefitting most from future surveillance efforts are eastern China and India. Scaling up surveillance to strengthen epidemiological evidence on AMR and inform aquaculture and fisheries interventions is needed to mitigate the impact of AMR globally.
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Affiliation(s)
- Daniel Schar
- Spatial Epidemiology Laboratory, Université Libre de Bruxelles, Brussels, Belgium.
| | - Cheng Zhao
- Institute for Environmental Decisions, ETH Zurich, Zurich, Switzerland
| | - Yu Wang
- Institute for Environmental Decisions, ETH Zurich, Zurich, Switzerland
| | - D G Joakim Larsson
- Center for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute for Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Marius Gilbert
- Spatial Epidemiology Laboratory, Université Libre de Bruxelles, Brussels, Belgium
- Fonds National de la Recherche Scientifique, Brussels, Belgium
| | - Thomas P Van Boeckel
- Institute for Environmental Decisions, ETH Zurich, Zurich, Switzerland.
- Center for Diseases Dynamics, Economics, and Policy, New Delhi, India.
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12
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Hwang SB, Chelliah R, Kang JE, Rubab M, Banan-MwineDaliri E, Elahi F, Oh DH. Role of Recent Therapeutic Applications and the Infection Strategies of Shiga Toxin-Producing Escherichia coli. Front Cell Infect Microbiol 2021; 11:614963. [PMID: 34268129 PMCID: PMC8276698 DOI: 10.3389/fcimb.2021.614963] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/07/2021] [Indexed: 12/17/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a global foodborne bacterial pathogen that is often accountable for colon disorder or distress. STEC commonly induces severe diarrhea in hosts but can cause critical illnesses due to the Shiga toxin virulence factors. To date, there have been a significant number of STEC serotypes have been evolved. STECs vary from nausea and hemorrhoid (HC) to possible lethal hemolytic-based uremic syndrome (HUS), thrombotic thrombocytopenic purpura (TTP). Inflammation-based STEC is usually a foodborne illness with Shiga toxins (Stx 1 and 2) thought to be pathogenesis. The STEC's pathogenicity depends significantly on developing one or more Shiga toxins, which can constrain host cell protein synthesis leading to cytotoxicity. In managing STEC infections, antimicrobial agents are generally avoided, as bacterial damage and discharge of accumulated toxins are thought the body. It has also been documented that certain antibiotics improve toxin production and the development of these species. Many different groups have attempted various therapies, including toxin-focused antibodies, toxin-based polymers, synbiotic agents, and secondary metabolites remedies. Besides, in recent years, antibiotics' efficacy in treating STEC infections has been reassessed with some encouraging methods. Nevertheless, the primary role of synbiotic effectiveness (probiotic and prebiotic) against pathogenic STEC and other enteropathogens is less recognized. Additional studies are required to understand the mechanisms of action of probiotic bacteria and yeast against STEC infection. Because of the consensus contraindication of antimicrobials for these bacterial pathogens, the examination was focused on alternative remedy strategies for STEC infections. The rise of novel STEC serotypes and approaches employed in its treatment are highlighted.
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Affiliation(s)
- Su-bin Hwang
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Ramachandran Chelliah
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Ji Eun Kang
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Momna Rubab
- School of Food and Agricultural Sciences, University of Management and Technology, Lahore, Pakistan
| | - Eric Banan-MwineDaliri
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Fazle Elahi
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
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13
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Pakbin B, Didban A, Monfared YK, Mahmoudi R, Peymani A, Modabber MR. Antibiotic susceptibility and genetic relatedness of Shigella species isolated from food and human stool samples in Qazvin, Iran. BMC Res Notes 2021; 14:144. [PMID: 33865447 PMCID: PMC8052664 DOI: 10.1186/s13104-021-05554-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/02/2021] [Indexed: 01/25/2023] Open
Abstract
Objective The aim of this study was to investigate the genetic relatedness and antimicrobial resistance among Shigella species isolated from food and stool samples. Using cross sectional study method, Shigella spp. were isolated from food and clinical samples using culture-based, biochemical and serological methods. Antimicrobial susceptibility and genetic relatedness among the isolates were evaluated using disk diffusion and RAPD-PCR methods respectively. Results The prevalence of Shigella spp. were 4.84 and 7.7% in food and stool samples respectively. All food isolates were Sh. sonnei. 91.42% of the Shigella stool isolates were Sh. sonnei. 62.5% of food isolates were resistant to tetracycline. 46.8, 50 and 65.8% of clinical isolates were resistant to imipenem, amikacin and azithromycin respectively. 50 and 85.7% of the food and clinical isolates respectively were MDR. Dendrogram generated by RAPD-PCR showed that the isolates from food and stool samples were categorized in a same group. Close genetic relatedness between MDR Shigella isolates from food and clinical samples indicate that foods can be considered as one of the main vehicles for transmission of MDR Shigella to human causing acute diseases. Survey of MDR Shigella among food and clinical samples is strongly suggested to be implemented.
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Affiliation(s)
- Babak Pakbin
- Children Growth Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Bahonar Blvd., P.O. Box: 34185-754, Qazvin, Iran.,Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Abdollah Didban
- Children Growth Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Bahonar Blvd., P.O. Box: 34185-754, Qazvin, Iran.
| | | | - Razzagh Mahmoudi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Amir Peymani
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mohammad Reza Modabber
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
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14
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Chung The H, Bodhidatta L, Pham DT, Mason CJ, Ha Thanh T, Voong Vinh P, Turner P, Hem S, Dance DAB, Newton PN, Phetsouvanh R, Davong V, Thwaites GE, Thomson NR, Baker S, Rabaa MA. Evolutionary histories and antimicrobial resistance in Shigella flexneri and Shigella sonnei in Southeast Asia. Commun Biol 2021; 4:353. [PMID: 33742111 PMCID: PMC7979695 DOI: 10.1038/s42003-021-01905-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/10/2021] [Indexed: 01/31/2023] Open
Abstract
Conventional disease surveillance for shigellosis in developing country settings relies on serotyping and low-resolution molecular typing, which fails to contextualise the evolutionary history of the genus. Here, we interrogated a collection of 1,804 Shigella whole genome sequences from organisms isolated in four continental Southeast Asian countries (Thailand, Vietnam, Laos, and Cambodia) over three decades to characterise the evolution of both S. flexneri and S. sonnei. We show that S. sonnei and each major S. flexneri serotype are comprised of genetically diverse populations, the majority of which were likely introduced into Southeast Asia in the 1970s-1990s. Intranational and regional dissemination allowed widespread propagation of both species across the region. Our data indicate that the epidemiology of S. sonnei and the major S. flexneri serotypes were characterised by frequent clonal replacement events, coinciding with changing susceptibility patterns against contemporaneous antimicrobials. We conclude that adaptation to antimicrobial pressure was pivotal to the recent evolutionary trajectory of Shigella in Southeast Asia.
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Affiliation(s)
- Hao Chung The
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ladaporn Bodhidatta
- grid.413910.e0000 0004 0419 1772Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Duy Thanh Pham
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Carl J. Mason
- grid.413910.e0000 0004 0419 1772Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Tuyen Ha Thanh
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phat Voong Vinh
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Paul Turner
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK ,grid.459332.a0000 0004 0418 5364Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Sopheak Hem
- grid.418537.cMedical Biology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - David A. B. Dance
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK ,grid.416302.20000 0004 0484 3312Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos ,grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK
| | - Paul N. Newton
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK ,grid.416302.20000 0004 0484 3312Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos ,grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK
| | - Rattanaphone Phetsouvanh
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK ,grid.416302.20000 0004 0484 3312Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Viengmon Davong
- grid.416302.20000 0004 0484 3312Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Guy E. Thwaites
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nicholas R. Thomson
- grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK ,grid.10306.340000 0004 0606 5382The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Stephen Baker
- grid.5335.00000000121885934The Department of Medicine, University of Cambridge, Cambridge, UK
| | - Maia A. Rabaa
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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15
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Sváb D, Falgenhauer L, Horváth B, Maróti G, Falgenhauer J, Chakraborty T, Tóth I. Genome Analysis of a Historical Shigella dysenteriae Serotype 1 Strain Carrying a Conserved Stx Prophage Region. Front Microbiol 2021; 11:614793. [PMID: 33488558 PMCID: PMC7819885 DOI: 10.3389/fmicb.2020.614793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/09/2020] [Indexed: 11/13/2022] Open
Abstract
Shigella dysenteriae are significant agents of bacillary dysentery, accounting for a considerable number of illnesses with high morbidity worldwide. The Shiga toxin (Stx) encoded by a defective prophage is the key virulence factor of S. dysenteriae type 1 (SD1) strains. Here we present the full genome sequence of an SD1 strain HNCMB 20080 isolated in 1954, compare it to other sequenced SD1 genomes, and assess the diversity of Stx-prophages harbored by previously sequenced SD1 strains. The genome of HNCMB 20080 consists of a chromosome sized 4,393,622 bp containing 5,183 CDSs, as well as two small plasmids. Comparative genomic analysis revealed a high degree of uniformity among SD1 genomes, including the structure of Stx prophage regions, which we found to form two subgroups termed PT-I and PT-II. All PT-I strains are members of the sequence type (ST) 146 or ST260, while the only PT-II harboring strain, Sd1617 proved to be ST untypeable. In accordance with data from previous reports, the Stx1 prophage could not be induced from HNCMB 20080. Our cumulative data do not support the notion that stx-harboring phages in STEC are derived from historical SD1 isolates.
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Affiliation(s)
- Domonkos Sváb
- Institue for Veterinary Medical Research, Centre for Agricultural Research, Martonvásár, Hungary
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany.,German Centre for Infection Research, Site Giessen-Marburg-Langen, Giessen, Germany
| | | | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary.,Faculty of Water Sciences, University of Public Service, Baja, Hungary
| | - Jane Falgenhauer
- German Centre for Infection Research, Site Giessen-Marburg-Langen, Giessen, Germany.,Institute for Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany.,Institute for Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - István Tóth
- Institue for Veterinary Medical Research, Centre for Agricultural Research, Martonvásár, Hungary
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16
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van den Beld MJC, Reubsaet FAG, Pijnacker R, Harpal A, Kuiling S, Heerkens EM, Hoeve-Bakker BJA(D, Noomen RCEA, Hendriks ACA, Borst D, van der Heide H, Kooistra-Smid AMD(M, Rossen JWA. A Multifactorial Approach for Surveillance of Shigella spp. and Entero-Invasive Escherichia coli Is Important for Detecting (Inter)national Clusters. Front Microbiol 2020; 11:564103. [PMID: 33193150 PMCID: PMC7604320 DOI: 10.3389/fmicb.2020.564103] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/22/2020] [Indexed: 01/08/2023] Open
Abstract
Shigella spp. and entero-invasive Escherichia coli (EIEC) can cause mild diarrhea to dysentery. In Netherlands, although shigellosis is a notifiable disease, there is no laboratory surveillance for Shigella spp. and EIEC in place. Consequently, the population structure for circulating Shigella spp. and EIEC isolates is not known. This study describes the phenotypic and serological characteristics, the phenotypic and genetic antimicrobial resistance (AMR) profiles, the virulence gene profiles, the classic multi-locus sequence types (MLST) and core genome (cg)MLST types, and the epidemiology of 414 Shigella spp. and EIEC isolates collected during a cross-sectional study in Netherlands in 2016 and 2017. S. sonnei (56%), S. flexneri (25%), and EIEC (15%) were detected predominantly in Netherlands, of which the EIEC isolates were most diverse according to their phenotypical profile, O-types, MLST types, and cgMLST clades. Virulence gene profiling showed that none of the isolates harbored Shiga toxin genes. Most S. flexneri and EIEC isolates possessed nearly all virulence genes examined, while these genes were only detected in approximately half of the S. sonnei isolates, probably due to loss of the large invasion plasmid upon subculturing. Phenotypical resistance correlated well with the resistant genotype, except for the genes involved in resistance to aminoglycosides. A substantial part of the characterized isolates was resistant to antimicrobials advised for treatment, i.e., 73% was phenotypically resistant to co-trimoxazole and 19% to ciprofloxacin. AMR was particularly observed in isolates from male patients who had sex with men (MSM) or from patients that had traveled to Asia. Furthermore, isolates related to international clusters were also circulating in Netherlands. Travel-related isolates formed clusters with isolates from patients without travel history, indicating their emergence into the Dutch population. In conclusion, laboratory surveillance using whole genome sequencing as high-resolution typing technique and for genetic characterization of isolates complements the current epidemiological surveillance, as the latter is not sufficient to detect all (inter)national clusters, emphasizing the importance of multifactorial public health approaches.
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Affiliation(s)
- Maaike J. C. van den Beld
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Frans A. G. Reubsaet
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Roan Pijnacker
- Infectious Diseases, Epidemiology and Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Airien Harpal
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Sjoerd Kuiling
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Evy M. Heerkens
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - B. J. A. (Dieneke) Hoeve-Bakker
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Ramón C. E. A. Noomen
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Amber C. A. Hendriks
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Dyogo Borst
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Han van der Heide
- Infectious Disease Research, Diagnostics and Laboratory Surveillance, Centre for Infectious disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - A. M. D. (Mirjam) Kooistra-Smid
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Medical Microbiology, Certe, Groningen, Netherlands
| | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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17
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Zhang W, Zhao Y, Wang W, Peng J, Li Y, Shangguan Y, Ouyang G, Xu M, Wang S, Wei J, Wei H, Li W, Yang Z. Colloidal Surface Engineering: Growth of Layered Double Hydroxides with Intrinsic Oxidase-Mimicking Activities to Fight Against Bacterial Infection in Wound Healing. Adv Healthc Mater 2020; 9:e2000092. [PMID: 32729238 DOI: 10.1002/adhm.202000092] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 07/07/2020] [Indexed: 11/08/2022]
Abstract
Colloidal surface engineering is of particular importance to impart modular functionalities to the colloidal systems. Here, a layer of Mn/Ni layered hydroxides (Mn/Ni(OH)x LDHs) can be successfully coated on various colloidal particles, such as silica spheres, silica rods, ferrite nanocrystal supraparticles, as well as FeOOH nanorods. Such layered hydroxides have intrinsic oxidase-mimetic activities, as demonstrated by catalytic oxidation of tetramethyl benzidine in the presence of oxygen. Furthermore, Mn/Ni(OH)x LDHs structure seems to capture bacteria (both Gram positive and Gram negative) and exhibit antibacterial properties in vitro. Moreover, local delivery of Mn/Ni-LDH structure fights against infection and reverses delayed wound healing procedures in mice models. Importantly, such hierarchical structures may have strong adhesive properties to the bacteria, which may maximize the contact between Mn/Ni(OH)x LDHs and the bacteria's surface. Overall, the present versatile colloidal surface engineering strategy will bring new insights in the field of antibiotics for its high efficiency toward antibacterial activity.
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Affiliation(s)
- Wendi Zhang
- Key Laboratory of Colloid and Interface Chemistry Ministry of Education, School of Chemistry and Chemical Engineering Shandong University Jinan Shandong 250100 P. R. China
| | - Yunpeng Zhao
- Department of Orthopedics Qilu Hospital, Cheeloo College of Medicine Shandong University Jinan Shandong 250012 P. R. China
| | - Wenhan Wang
- Department of Orthopedics Qilu Hospital, Cheeloo College of Medicine Shandong University Jinan Shandong 250012 P. R. China
- Cheeloo College of Medicine Shandong University Jinan Shandong 250012 P. R. China
| | - Jiangfan Peng
- Cheeloo College of Medicine Shandong University Jinan Shandong 250012 P. R. China
| | - Yuanming Li
- Cheeloo College of Medicine Shandong University Jinan Shandong 250012 P. R. China
| | - Yangtao Shangguan
- Cheeloo College of Medicine Shandong University Jinan Shandong 250012 P. R. China
| | - Gege Ouyang
- Cheeloo College of Medicine Shandong University Jinan Shandong 250012 P. R. China
| | - Mingyang Xu
- Cheeloo College of Medicine Shandong University Jinan Shandong 250012 P. R. China
| | - Shuping Wang
- Key Laboratory of Colloid and Interface Chemistry Ministry of Education, School of Chemistry and Chemical Engineering Shandong University Jinan Shandong 250100 P. R. China
| | - Jingjing Wei
- Key Laboratory of Colloid and Interface Chemistry Ministry of Education, School of Chemistry and Chemical Engineering Shandong University Jinan Shandong 250100 P. R. China
| | - Huiying Wei
- Key Laboratory of Colloid and Interface Chemistry Ministry of Education, School of Chemistry and Chemical Engineering Shandong University Jinan Shandong 250100 P. R. China
| | - Weiwei Li
- Department of Pathology Qilu Hospital, Cheeloo College of Medicine Shandong University Jinan Shandong 250012 P. R. China
| | - Zhijie Yang
- Key Laboratory of Colloid and Interface Chemistry Ministry of Education, School of Chemistry and Chemical Engineering Shandong University Jinan Shandong 250100 P. R. China
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18
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Taitt CR, Leski TA, Prouty MG, Ford GW, Heang V, House BL, Levin SY, Curry JA, Mansour A, Mohammady HE, Wasfy M, Tilley DH, Gregory MJ, Kasper MR, Regeimbal J, Rios P, Pimentel G, Danboise BA, Hulseberg CE, Odundo EA, Ombogo AN, Cheruiyot EK, Philip CO, Vora GJ. Tracking Antimicrobial Resistance Determinants in Diarrheal Pathogens: A Cross-Institutional Pilot Study. Int J Mol Sci 2020; 21:ijms21165928. [PMID: 32824772 PMCID: PMC7460656 DOI: 10.3390/ijms21165928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Infectious diarrhea affects over four billion individuals annually and causes over a million deaths each year. Though not typically prescribed for treatment of uncomplicated diarrheal disease, antimicrobials serve as a critical part of the armamentarium used to treat severe or persistent cases. Due to widespread over- and misuse of antimicrobials, there has been an alarming increase in global resistance, for which a standardized methodology for geographic surveillance would be highly beneficial. To demonstrate that a standardized methodology could be used to provide molecular surveillance of antimicrobial resistance (AMR) genes, we initiated a pilot study to test 130 diarrheal pathogens (Campylobacter spp., Escherichia coli, Salmonella, and Shigella spp.) from the USA, Peru, Egypt, Cambodia, and Kenya for the presence/absence of over 200 AMR determinants. We detected a total of 55 different determinants conferring resistance to ten different categories of antimicrobials: genes detected in ≥ 25 samples included blaTEM, tet(A), tet(B), mac(A), mac(B), aadA1/A2, strA, strB, sul1, sul2, qacEΔ1, cmr, and dfrA1. The number of determinants per strain ranged from none (several Campylobacter spp. strains) to sixteen, with isolates from Egypt harboring a wider variety and greater number of genes per isolate than other sites. Two samples harbored carbapenemase genes, blaOXA-48 or blaNDM. Genes conferring resistance to azithromycin (ere(A), mph(A)/mph(K), erm(B)), a first-line therapeutic for severe diarrhea, were detected in over 10% of all Enterobacteriaceae tested: these included >25% of the Enterobacteriaceae from Egypt and Kenya. Forty-six percent of the Egyptian Enterobacteriaceae harbored genes encoding CTX-M-1 or CTX-M-9 families of extended-spectrum β-lactamases. Overall, the data provide cross-comparable resistome information to establish regional trends in support of international surveillance activities and potentially guide geospatially informed medical care.
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Affiliation(s)
- Chris R. Taitt
- US Naval Research Laboratory, Center for Biomolecular Science & Engineering, Washington, DC 20375, USA; (T.A.L.); (G.J.V.)
- Correspondence: ; Tel.: +1-011-202-404-4208
| | - Tomasz A. Leski
- US Naval Research Laboratory, Center for Biomolecular Science & Engineering, Washington, DC 20375, USA; (T.A.L.); (G.J.V.)
| | - Michael G. Prouty
- US Naval Medical Research Unit No. 2-Phnom Penh, Blvd Kim Il Sung, Khan Toul Kork, Phnom Penh, Cambodia; (M.G.P.); (G.W.F.); (V.H.)
| | - Gavin W. Ford
- US Naval Medical Research Unit No. 2-Phnom Penh, Blvd Kim Il Sung, Khan Toul Kork, Phnom Penh, Cambodia; (M.G.P.); (G.W.F.); (V.H.)
| | - Vireak Heang
- US Naval Medical Research Unit No. 2-Phnom Penh, Blvd Kim Il Sung, Khan Toul Kork, Phnom Penh, Cambodia; (M.G.P.); (G.W.F.); (V.H.)
| | - Brent L. House
- US Naval Medical Research Unit No. 3, Naval Air Station Sigonella, 95030 Sigonella, Italy; (B.L.H.); (S.Y.L.); (J.A.C.); (A.M.); (H.E.M.); (M.W.)
| | - Samuel Y. Levin
- US Naval Medical Research Unit No. 3, Naval Air Station Sigonella, 95030 Sigonella, Italy; (B.L.H.); (S.Y.L.); (J.A.C.); (A.M.); (H.E.M.); (M.W.)
| | - Jennifer A. Curry
- US Naval Medical Research Unit No. 3, Naval Air Station Sigonella, 95030 Sigonella, Italy; (B.L.H.); (S.Y.L.); (J.A.C.); (A.M.); (H.E.M.); (M.W.)
| | - Adel Mansour
- US Naval Medical Research Unit No. 3, Naval Air Station Sigonella, 95030 Sigonella, Italy; (B.L.H.); (S.Y.L.); (J.A.C.); (A.M.); (H.E.M.); (M.W.)
| | - Hanan El Mohammady
- US Naval Medical Research Unit No. 3, Naval Air Station Sigonella, 95030 Sigonella, Italy; (B.L.H.); (S.Y.L.); (J.A.C.); (A.M.); (H.E.M.); (M.W.)
| | - Momtaz Wasfy
- US Naval Medical Research Unit No. 3, Naval Air Station Sigonella, 95030 Sigonella, Italy; (B.L.H.); (S.Y.L.); (J.A.C.); (A.M.); (H.E.M.); (M.W.)
| | - Drake Hamilton Tilley
- US Naval Medical Research Unit No. 6 Peru, Lima 07001, Peru; (D.H.T.); (M.J.G.); (M.R.K.); (J.R.); (P.R.); (G.P.)
| | - Michael J. Gregory
- US Naval Medical Research Unit No. 6 Peru, Lima 07001, Peru; (D.H.T.); (M.J.G.); (M.R.K.); (J.R.); (P.R.); (G.P.)
| | - Matthew R. Kasper
- US Naval Medical Research Unit No. 6 Peru, Lima 07001, Peru; (D.H.T.); (M.J.G.); (M.R.K.); (J.R.); (P.R.); (G.P.)
| | - James Regeimbal
- US Naval Medical Research Unit No. 6 Peru, Lima 07001, Peru; (D.H.T.); (M.J.G.); (M.R.K.); (J.R.); (P.R.); (G.P.)
| | - Paul Rios
- US Naval Medical Research Unit No. 6 Peru, Lima 07001, Peru; (D.H.T.); (M.J.G.); (M.R.K.); (J.R.); (P.R.); (G.P.)
| | - Guillermo Pimentel
- US Naval Medical Research Unit No. 6 Peru, Lima 07001, Peru; (D.H.T.); (M.J.G.); (M.R.K.); (J.R.); (P.R.); (G.P.)
| | - Brook A. Danboise
- US Army Medical Research Directorate-Africa/Kenya, Kericho 20200, Kenya; (B.A.D.); (C.E.H.); (E.A.O.); (A.N.O.); (E.K.C.); (C.O.P.)
| | - Christine E. Hulseberg
- US Army Medical Research Directorate-Africa/Kenya, Kericho 20200, Kenya; (B.A.D.); (C.E.H.); (E.A.O.); (A.N.O.); (E.K.C.); (C.O.P.)
| | - Elizabeth A. Odundo
- US Army Medical Research Directorate-Africa/Kenya, Kericho 20200, Kenya; (B.A.D.); (C.E.H.); (E.A.O.); (A.N.O.); (E.K.C.); (C.O.P.)
| | - Abigael N. Ombogo
- US Army Medical Research Directorate-Africa/Kenya, Kericho 20200, Kenya; (B.A.D.); (C.E.H.); (E.A.O.); (A.N.O.); (E.K.C.); (C.O.P.)
| | - Erick K. Cheruiyot
- US Army Medical Research Directorate-Africa/Kenya, Kericho 20200, Kenya; (B.A.D.); (C.E.H.); (E.A.O.); (A.N.O.); (E.K.C.); (C.O.P.)
| | - Cliff O. Philip
- US Army Medical Research Directorate-Africa/Kenya, Kericho 20200, Kenya; (B.A.D.); (C.E.H.); (E.A.O.); (A.N.O.); (E.K.C.); (C.O.P.)
| | - Gary J. Vora
- US Naval Research Laboratory, Center for Biomolecular Science & Engineering, Washington, DC 20375, USA; (T.A.L.); (G.J.V.)
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Hawkey J, Monk JM, Billman-Jacobe H, Palsson B, Holt KE. Impact of insertion sequences on convergent evolution of Shigella species. PLoS Genet 2020; 16:e1008931. [PMID: 32644999 PMCID: PMC7373316 DOI: 10.1371/journal.pgen.1008931] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 07/21/2020] [Accepted: 06/15/2020] [Indexed: 12/31/2022] Open
Abstract
Shigella species are specialised lineages of Escherichia coli that have converged to become human-adapted and cause dysentery by invading human gut epithelial cells. Most studies of Shigella evolution have been restricted to comparisons of single representatives of each species; and population genomic studies of individual Shigella species have focused on genomic variation caused by single nucleotide variants and ignored the contribution of insertion sequences (IS) which are highly prevalent in Shigella genomes. Here, we investigate the distribution and evolutionary dynamics of IS within populations of Shigella dysenteriae Sd1, Shigella sonnei and Shigella flexneri. We find that five IS (IS1, IS2, IS4, IS600 and IS911) have undergone expansion in all Shigella species, creating substantial strain-to-strain variation within each population and contributing to convergent patterns of functional gene loss within and between species. We find that IS expansion and genome degradation are most advanced in S. dysenteriae and least advanced in S. sonnei; and using genome-scale models of metabolism we show that Shigella species display convergent loss of core E. coli metabolic capabilities, with S. sonnei and S. flexneri following a similar trajectory of metabolic streamlining to that of S. dysenteriae. This study highlights the importance of IS to the evolution of Shigella and provides a framework for the investigation of IS dynamics and metabolic reduction in other bacterial species.
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Affiliation(s)
- Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Jonathan M. Monk
- Department of Bioengineering, University of California, San Diego, San Diego, California, United States of America
| | - Helen Billman-Jacobe
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Bernhard Palsson
- Department of Bioengineering, University of California, San Diego, San Diego, California, United States of America
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- The London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Abstract
Diarrhea has long been recognized as an important cause of mortality during childhood. In parallel with ensuring access to proven care practices is the imperative to apply modern advances in medicine, science, and technology to accelerate progress against diarrheal disease, particularly in developing countries where the burden of avoidable harm is the greatest. In order to highlight achievements and identify outstanding areas of need, we reviewed the landscape of recent innovations that have significance for the study and clinical management of pediatric diarrhea in low resource settings.
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Affiliation(s)
- Rajiv S. Jumani
- Novartis Institute for Tropical Diseases, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Jonathan M. Spector
- Novartis Institute for Tropical Diseases, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Rasa Izadnegahdar
- Bill and Melinda Gates Foundation, 440 5th Ave N, Seattle, Washington 98109, United States
| | - Paul Kelly
- Blizard Institute, Barts and The London School of Medicine, Queen Mary University of London, Turner Street, London E1 2AD, United Kingdom
- Tropical Gastroenterology and Nutrition group, University of Zambia School of Medicine, Nationalist Road, Lusaka, Zambia
| | - Thierry T. Diagana
- Novartis Institute for Tropical Diseases, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Ujjini H. Manjunatha
- Novartis Institute for Tropical Diseases, 5300 Chiron Way, Emeryville, California 94608, United States
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22
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Cerf-Bensussan N. Microbiology and immunology: An ideal partnership for a tango at the gut surface-A tribute to Philippe Sansonetti. Cell Microbiol 2019; 21:e13097. [PMID: 31414516 PMCID: PMC7027583 DOI: 10.1111/cmi.13097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/02/2019] [Accepted: 08/12/2019] [Indexed: 12/12/2022]
Abstract
Over the past 20 years, the highly dynamic interactions that take place between hosts and the gut microbiota have emerged as a major determinant in health and disease. The complexity of the gut microbiota represents, however, a considerable challenge, and reductionist approaches are indispensable to define the contribution of individual bacteria to host responses and to dissect molecular mechanisms. In this tribute to Philippe Sansonetti, I would like to show how rewarding collaborations with microbiologists have guided our team of immunologists in the study of host–microbiota interactions and, thanks to the use of controlled colonisation experiments in gnotobiotic mice, toward the demonstration that segmented filamentous bacteria (SFB) are indispensable to drive the post‐natal maturation of the gut immune barrier in mice. The work led with Philippe Sansonetti to set up in vitro culture conditions has been one important milestone that laid the ground for in‐depth characterization of the molecular attributes of this unusual symbiont. Recent suggestions that SFB may be present in the human microbiota encourage further cross‐fertilising interactions between microbiologists and immunologists to define whether results from mice can be translated to humans and, if so, how SFB may be used to promote human intestinal defences against enteropathogens. Nurturing the competences to pursue this inspiring project is one legacy of Philippe Sansonetti.
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Affiliation(s)
- Nadine Cerf-Bensussan
- Laboratory of Intestinal Immunity, INSERM UMR 1163, Institut Imagine, Paris, France.,Université de Paris, Paris, France
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23
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Pasqua M, Grossi M, Zennaro A, Fanelli G, Micheli G, Barras F, Colonna B, Prosseda G. The Varied Role of Efflux Pumps of the MFS Family in the Interplay of Bacteria with Animal and Plant Cells. Microorganisms 2019; 7:microorganisms7090285. [PMID: 31443538 PMCID: PMC6780985 DOI: 10.3390/microorganisms7090285] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022] Open
Abstract
Efflux pumps represent an important and large group of transporter proteins found in all organisms. The importance of efflux pumps resides in their ability to extrude a wide range of antibiotics, resulting in the emergence of multidrug resistance in many bacteria. Besides antibiotics, multidrug efflux pumps can also extrude a large variety of compounds: Bacterial metabolites, plant-produced compounds, quorum-sensing molecules, and virulence factors. This versatility makes efflux pumps relevant players in interactions not only with other bacteria, but also with plant or animal cells. The multidrug efflux pumps belonging to the major facilitator superfamily (MFS) are widely distributed in microbial genomes and exhibit a large spectrum of substrate specificities. Multidrug MFS efflux pumps are present either as single-component transporters or as tripartite complexes. In this review, we will summarize how the multidrug MFS efflux pumps contribute to the interplay between bacteria and targeted host cells, with emphasis on their role in bacterial virulence, in the colonization of plant and animal host cells and in biofilm formation. We will also address the complexity of these interactions in the light of the underlying regulatory networks required for the effective activation of efflux pump genes.
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Affiliation(s)
- Martina Pasqua
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Via dei Sardi 70, 00185 Rome, Italy
| | - Milena Grossi
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Via dei Sardi 70, 00185 Rome, Italy
| | - Alessandro Zennaro
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Via dei Sardi 70, 00185 Rome, Italy
| | - Giulia Fanelli
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Via dei Sardi 70, 00185 Rome, Italy
| | - Gioacchino Micheli
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche (CNR), P.le A. Moro 5, 00185 Roma, Italy
| | - Frederic Barras
- Département de Microbiologie, Institut Pasteur, 75015 Paris, France
- Équipe de Recherche Labellisée (ERL) Microbiology, Centre National de la Recherche Scientifique (CNRS), 13009 Marseille, France
| | - Bianca Colonna
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Via dei Sardi 70, 00185 Rome, Italy
| | - Gianni Prosseda
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Via dei Sardi 70, 00185 Rome, Italy.
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Abstract
Many pathogens that caused devastating disease throughout human history, such as Yersinia pestis, Mycobacterium tuberculosis, and Mycobacterium leprae, remain problematic today. Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously understudied resource. This minireview brings together example studies which have utilized ancient DNA, individual historical isolates (both extant and dead) and collections of historical isolates. The studies span human history and highlight the contribution that sequencing and analysis of historical bacterial genomes have made to a wide variety of fields. From providing retrospective diagnosis, to uncovering epidemiological pathways and characterizing genetic diversity, there is clear evidence for the utility of historical isolate studies in understanding disease today. Studies utilizing historical isolate collections, such as those from the National Collection of Type Cultures, the American Type Culture Collection, and the Institut Pasteur, offer enhanced insight since they typically span a wide time period encompassing important historical events and are useful for the investigating the phylodynamics of pathogens. Furthermore, historical sequencing studies are particularly useful for looking into the evolution of antimicrobial resistance, a major public health concern. In summary, although there are limitations to working with historical bacterial isolates, especially when utilizing ancient DNA, continued improvement in molecular and sequencing technologies and the resourcefulness of investigators mean this area of study will continue to expand and contribute to the understanding of pathogens.
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Abstract
PURPOSE OF REVIEW Diarrhoea is a major global health problem, and recent studies have confirmed Shigella as a major contributor to this burden. Here, we review recent advances in Shigella research; focusing on their epidemiology, pathogenesis, antimicrobial resistance, and the role of the gut microbiome during infection. RECENT FINDINGS Enhanced epidemiological data, combined with new generation diagnostics, has highlighted a greater burden of Shigella disease than was previously estimated, which is not restricted to vulnerable populations in low-middle income countries. As we gain an ever more detailed insight into the orchestrated mechanisms that Shigella exploit to trigger infection, we can also begin to appreciate the complex role of the gut microbiome in preventing and inducing such infections. The use of genomics, in combination with epidemiological data and laboratory investigations, has unravelled the evolution and spread of various species. Such measures have identified resistance to antimicrobials as a key contributor to the success of specific clones. SUMMARY We need to apply novel findings towards sustainable approaches for treating and preventing Shigella infections. Vaccines and alternative treatments are under development and may offer an opportunity to reduce the burden of Shigella disease and restrict the mobility of antimicrobial resistant clones.
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26
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Smith AM. Review of molecular subtyping methodologies used to investigate outbreaks due to multidrug-resistant enteric bacterial pathogens in sub-Saharan Africa. Afr J Lab Med 2019; 8:760. [PMID: 31205868 PMCID: PMC6556818 DOI: 10.4102/ajlm.v8i1.760] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 09/25/2018] [Indexed: 01/05/2023] Open
Abstract
Background In sub-Saharan Africa, molecular epidemiological investigation of outbreaks caused by antimicrobial-resistant enteric bacterial pathogens have mostly been described for Salmonella species, Vibrio cholerae, Shigella species and Escherichia coli. For these organisms, I reviewed all publications describing the use of molecular subtyping methodologies to investigate outbreaks caused by multidrug-resistant (MDR) enteric bacterial infections. Objectives To describe the use of molecular subtyping methodologies to investigate outbreaks caused by MDR enteric bacterial pathogens in sub-Saharan Africa and to describe the current status of molecular subtyping capabilities in the region. Methods A PubMed database literature search (English language only) was performed using the search strings: ‘Africa outbreak MDR’, ‘Africa outbreak multi’, ‘Africa outbreak multidrug’, ‘Africa outbreak multi drug’, ‘Africa outbreak resistance’, ‘Africa outbreak resistant’, ‘Africa outbreak drug’, ‘Africa outbreak antibiotic’, ‘Africa outbreak antimicrobial’. These search strings were used in combination with genus and species names of the organisms listed above. All results were included in the review. Results The year 1991 saw one of the first reports describing the use of molecular subtyping methodologies in sub-Saharan Africa; this included the use of plasmid profiling to characterise Salmonella Enteritidis. To date, several methodologies have been used; pulsed-field gel electrophoresis analysis and multilocus sequence typing have been the most commonly used methodologies. Investigations have particularly highlighted the emergence and spread of MDR clones; these include Salmonella Typhi H58 and Salmonella Typhimurium ST313 clones. In recent times, whole-genome sequencing (WGS) analysis approaches have increasingly been used. Conclusion Traditional molecular subtyping methodologies are still commonly used and still have their place in investigations; however, WGS approaches have increasingly been used and are slowly gaining a stronghold. African laboratories need to start adapting their molecular surveillance methodologies to include WGS, as it is foreseen that WGS analysis will eventually replace all traditional methodologies.
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Affiliation(s)
- Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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27
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Allué-Guardia A, Koenig SSK, Quirós P, Muniesa M, Bono JL, Eppinger M. Closed Genome and Comparative Phylogenetic Analysis of the Clinical Multidrug Resistant Shigella sonnei Strain 866. Genome Biol Evol 2018; 10:2241-2247. [PMID: 30060169 PMCID: PMC6128377 DOI: 10.1093/gbe/evy168] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 01/10/2023] Open
Abstract
Shigella sonnei is responsible for the majority of shigellosis infections in the US with over 500,000 cases reported annually. Here, we present the complete genome of the clinical multidrug resistant (MDR) strain 866, which is highly susceptible to bacteriophage infections. The strain has a circular chromosome of 4.85 Mb and carries a 113 kb MDR plasmid. This IncB/O/K/Z-type plasmid, termed p866, confers resistance to five different classes of antibiotics including ß-lactamase, sulfonamide, tetracycline, aminoglycoside, and trimethoprim. Comparative analysis of the plasmid architecture and gene inventory revealed that p866 shares its plasmid backbone with previously described IncB/O/K/Z-type Shigella spp. and Escherichia coli plasmids, but is differentiated by the insertion of antibiotic resistance cassettes, which we found associated with mobile genetic elements such as Tn3, Tn7, and Tn10. A whole genome-derived phylogenetic reconstruction showed the evolutionary relationships of S. sonnei strain 866 and the four established Shigella species, highlighting the clonal nature of S. sonnei.
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Affiliation(s)
- Anna Allué-Guardia
- Department of Biology, University of Texas at San Antonio.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio
| | - Sara S K Koenig
- Department of Biology, University of Texas at San Antonio.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio
| | - Pablo Quirós
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Spain
| | - James L Bono
- Agricultural Research Service, United States Department of Agriculture, U.S. Meat Animal Research Center, Clay Center, Nebraska
| | - Mark Eppinger
- Department of Biology, University of Texas at San Antonio.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio
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28
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Pérez-Losada M, Arenas M, Castro-Nallar E. Microbial sequence typing in the genomic era. Infect Genet Evol 2018; 63:346-359. [PMID: 28943406 PMCID: PMC5908768 DOI: 10.1016/j.meegid.2017.09.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 12/18/2022]
Abstract
Next-generation sequencing (NGS), also known as high-throughput sequencing, is changing the field of microbial genomics research. NGS allows for a more comprehensive analysis of the diversity, structure and composition of microbial genes and genomes compared to the traditional automated Sanger capillary sequencing at a lower cost. NGS strategies have expanded the versatility of standard and widely used typing approaches based on nucleotide variation in several hundred DNA sequences and a few gene fragments (MLST, MLVA, rMLST and cgMLST). NGS can now accommodate variation in thousands or millions of sequences from selected amplicons to full genomes (WGS, NGMLST and HiMLST). To extract signals from high-dimensional NGS data and make valid statistical inferences, novel analytic and statistical techniques are needed. In this review, we describe standard and new approaches for microbial sequence typing at gene and genome levels and guidelines for subsequent analysis, including methods and computational frameworks. We also present several applications of these approaches to some disciplines, namely genotyping, phylogenetics and molecular epidemiology.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal; Children's National Medical Center, Washington, DC 20010, USA.
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago 8370146, Chile
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29
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Terry LM, Barker CR, Day MR, Greig DR, Dallman TJ, Jenkins C. Antimicrobial resistance profiles of Shigella dysenteriae isolated from travellers returning to the UK, 2004-2017. J Med Microbiol 2018; 67:1022-1030. [PMID: 29957175 DOI: 10.1099/jmm.0.000779] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Antimicrobial resistance (AMR) profiles of 754 strains of Shigella dysenteriae isolated between 2004 and 2017 from UK travellers reporting symptoms of gastrointestinal (GI) disease were reviewed to look for evidence of emerging AMR associated with travellers' diarrhoea. METHODOLOGY A travel history was provided for 72.7 % (548/754) of cases, of which 90.9 % (498/548) reported travel outside the UK within 7 days of onset of symptoms, and 9.1 % (50/498) reported no travel in that time frame. During the course of this study, whole genome sequencing (WGS) was implemented for GI disease surveillance, and we compared phenotypic AMR profiles with those derived from WGS data (n=133).Results/Key findings. The phenotypic and genotypic AMR results correlated well, with 90.1 % (121/133) isolates having concordant results to 10 classes of antimicrobials. Resistance to the first-line drugs commonly used in the treatment of shigellosis was observed throughout the study (ampicillin, 54.1%; chloramphenicol, 33.7 %; sulphonamides, 76.0 %; trimethoprim, 80.0%). Between 2004 and 2017, resistance to all classes of antimicrobials (except the phenicols) increased. The proportion of isolates exhibiting reduced susceptibility to ciprofloxacin increased from 3.8 % in 2004 to 75.7 % in 2017, and this was significantly associated with cases reporting travel to Asia compared to Africa (P<0.001). Of the 201 sequenced isolates, 3.0 % (20/201) had either blaCTX-M-15 or blaCMY-4. CONCLUSIONS Increasing MDR, along with resistance to the fluroquinolones and the third generation cephalosporins, in Shigella dysenteriae causing travellers' diarrhoea provides further evidence for the need to regulatethe use of antimicrobial agents and continuous monitoring of emerging AMR.
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Affiliation(s)
- Lauren M Terry
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
| | - Clare R Barker
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
| | - Martin R Day
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
| | - David R Greig
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
| | - Timothy J Dallman
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
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Duchene S, Duchene DA, Geoghegan JL, Dyson ZA, Hawkey J, Holt KE. Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods. BMC Evol Biol 2018; 18:95. [PMID: 29914372 PMCID: PMC6006949 DOI: 10.1186/s12862-018-1210-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 06/05/2018] [Indexed: 12/04/2022] Open
Abstract
Background Recent developments in sequencing technologies make it possible to obtain genome sequences from a large number of isolates in a very short time. Bayesian phylogenetic approaches can take advantage of these data by simultaneously inferring the phylogenetic tree, evolutionary timescale, and demographic parameters (such as population growth rates), while naturally integrating uncertainty in all parameters. Despite their desirable properties, Bayesian approaches can be computationally intensive, hindering their use for outbreak investigations involving genome data for a large numbers of pathogen isolates. An alternative to using full Bayesian inference is to use a hybrid approach, where the phylogenetic tree and evolutionary timescale are estimated first using maximum likelihood. Under this hybrid approach, demographic parameters are inferred from estimated trees instead of the sequence data, using maximum likelihood, Bayesian inference, or approximate Bayesian computation. This can vastly reduce the computational burden, but has the disadvantage of ignoring the uncertainty in the phylogenetic tree and evolutionary timescale. Results We compared the performance of a fully Bayesian and a hybrid method by analysing six whole-genome SNP data sets from a range of bacteria and simulations. The estimates from the two methods were very similar, suggesting that the hybrid method is a valid alternative for very large datasets. However, we also found that congruence between these methods is contingent on the presence of strong temporal structure in the data (i.e. clocklike behaviour), which is typically verified using a date-randomisation test in a Bayesian framework. To reduce the computational burden of this Bayesian test we implemented a date-randomisation test using a rapid maximum likelihood method, which has similar performance to its Bayesian counterpart. Conclusions Hybrid approaches can produce reliable inferences of evolutionary timescales and phylodynamic parameters in a fraction of the time required for fully Bayesian analyses. As such, they are a valuable alternative in outbreak studies involving a large number of isolates. Electronic supplementary material The online version of this article (10.1186/s12862-018-1210-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastian Duchene
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3020, Australia.
| | - David A Duchene
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Zoe A Dyson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3020, Australia
| | - Jane Hawkey
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3020, Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3020, Australia
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Zeng H, Zhang J, Wu Q, He W, Wu H, Ye Y, Li C, Ling N, Chen M, Wang J, Cai S, Lei T, Ding Y, Xue L. Reconstituting the History of Cronobacter Evolution Driven by Differentiated CRISPR Activity. Appl Environ Microbiol 2018; 84:e00267-18. [PMID: 29523551 PMCID: PMC5930372 DOI: 10.1128/aem.00267-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/05/2018] [Indexed: 01/18/2023] Open
Abstract
Cronobacter strains harboring the CRISPR-Cas system are important foodborne pathogens causing serious neonatal infections. However, the specific role of the CRISPR-Cas system in bacterial evolution remains relatively unexplored. In this study, we investigated the impact of the CRISPR-Cas system on Cronobacter evolution and obtained 137 new whole-genome Cronobacter sequences by next-generation sequencing technology. Among the strains examined (n = 240), 90.6% (193/213) of prevalent species Cronobacter sakazakii, Cronobactermalonaticus, and Cronobacterdublinensis strains had intact CRISPR-Cas systems. Two rare species, Cronobactercondimenti (n = 2) and Cronobacteruniversalis (n = 6), lacked and preserved the CRISPR-Cas system at a low frequency (1/6), respectively. These results suggest that the presence of one CRISPR-Cas system is important for a Cronobacter species to maintain genome homeostasis for survival. The Cronobacter ancestral strain is likely to have harbored both subtype I-E and I-F CRISPR-Cas systems; during the long evolutionary process, subtype I-E was retained while subtype I-F selectively degenerated in Cronobacter species and was even lost by the major Cronobacter pathovars. Moreover, significantly higher CRISPR activity was observed in the plant-associated species Cdublinensis than in the virulence-related species C. sakazakii and Cmalonaticus Similar spacers of CRISPR arrays were rarely found among species, suggesting intensive change through adaptive acquisition and loss. Differentiated CRISPR activity appears to be the product of environmental selective pressure and might contribute to the bidirectional divergence and speciation of CronobacterIMPORTANCE This study reports the evolutionary history of Cronobacter under the selective pressure of the CRISPR-Cas system. One CRISPR-Cas system in Cronobacter is important for maintaining genome homeostasis, whereas two types of systems may be redundant and not conducive to acquiring beneficial DNA for environmental adaptation and pathogenicity. Differentiated CRISPR activity has contributed to the bidirectional divergence and genetic diversity of Cronobacter This perspective makes a significant contribution to the literature by providing new insights into CRISPR-Cas systems in general, while further expanding the roles of CRISPR beyond conferring adaptive immunity and demonstrating a link to adaptation and species divergence in a genus. Moreover, our study provides new insights into the balance between genome homeostasis and the uptake of beneficial DNA related to CRISPR-based activity in the evolution of Cronobacter.
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Affiliation(s)
- Haiyan Zeng
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Jumei Zhang
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Qingping Wu
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Wenjing He
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Haoming Wu
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Yingwang Ye
- School of Food Science and Technology, Hefei University of Technology, Hefei, China
| | - Chengsi Li
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Na Ling
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Moutong Chen
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Shuzhen Cai
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Tao Lei
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Yu Ding
- Department of Food Science & Technology, Jinan University, Guangzhou, China
| | - Liang Xue
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
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Baker KS, Dallman TJ, Field N, Childs T, Mitchell H, Day M, Weill FX, Lefèvre S, Tourdjman M, Hughes G, Jenkins C, Thomson N. Genomic epidemiology of Shigella in the United Kingdom shows transmission of pathogen sublineages and determinants of antimicrobial resistance. Sci Rep 2018; 8:7389. [PMID: 29743642 PMCID: PMC5943296 DOI: 10.1038/s41598-018-25764-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/27/2018] [Indexed: 12/11/2022] Open
Abstract
Shigella are globally important diarrhoeal pathogens that are endemic in low-to-middle income nations and also occur in high income nations, typically in travellers or community-based risk-groups. Shigella phylogenetics reveals population structures that are more reliable than those built with traditional typing methods, and has identified sublineages associated with specific geographical regions or patient groups. Genomic analyses reveal temporal increases in Shigella antimicrobial resistance (AMR) gene content, which is frequently encoded on mobile genetic elements. Here, we whole genome sequenced representative subsamples of S. flexneri 2a and S. sonnei (n = 366) from the United Kingdom from 2008 to 2014, and analysed these alongside publicly available data to make qualitative insights on the genomic epidemiology of shigellosis and its AMR within the broader global context. Combined phylogenetic, epidemiological and genomic anlayses revealed the presence of domestically-circulating sublineages in patient risk-groups and the importation of travel-related sublineages from both Africa and Asia, including ciprofloxacin-resistant sublineages of both species from Asia. Genomic analyses revealed common AMR determinants among travel-related and domestically-acquired isolates, and the evolution of mutations associated with reduced quinolone susceptibility in domestically-circulating sublineages. Collectively, this study provides unprecedented insights on the contribution and mobility of endemic and travel-imported sublineages and AMR determinants responsible for disease in a high-income nation.
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Affiliation(s)
- Kate S Baker
- Institute for Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom.
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England, London, NW9 5HT, United Kingdom
| | - Nigel Field
- Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, UCL, London, United Kingdom
| | - Tristan Childs
- Centre for Infectious Disease Surveillance and Control, National Infection Service, Public Health England, London, NW9 5HT, United Kingdom
| | - Holly Mitchell
- Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, UCL, London, United Kingdom
| | - Martin Day
- Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England, London, NW9 5HT, United Kingdom
| | | | - Sophie Lefèvre
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | - Mathieu Tourdjman
- Santé Publique France, the French Public Health Agency, Saint-Maurice, France
| | - Gwenda Hughes
- Department of HIV and STIs, National Infection Service, Public Health England, London, NW9 5HT, United Kingdom
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England, London, NW9 5HT, United Kingdom
| | - Nicholas Thomson
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom.
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom.
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Baker KS, Dallman TJ, Field N, Childs T, Mitchell H, Day M, Weill FX, Lefèvre S, Tourdjman M, Hughes G, Jenkins C, Thomson N. Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species. Nat Commun 2018; 9:1462. [PMID: 29654279 PMCID: PMC5899146 DOI: 10.1038/s41467-018-03949-8] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/21/2018] [Indexed: 11/22/2022] Open
Abstract
Horizontal gene transfer has played a role in developing the global public health crisis of antimicrobial resistance (AMR). However, the dynamics of AMR transfer through bacterial populations and its direct impact on human disease is poorly elucidated. Here, we study parallel epidemic emergences of multiple Shigella species, a priority AMR organism, in men who have sex with men to gain insight into AMR emergence and spread. Using genomic epidemiology, we show that repeated horizontal transfer of a single AMR plasmid among Shigella enhanced existing and facilitated new epidemics. These epidemic patterns contrasted with slighter, slower increases in disease caused by organisms with vertically inherited (chromosomally encoded) AMR. This demonstrates that horizontal transfer of AMR directly affects epidemiological outcomes of globally important AMR pathogens and highlights the need for integration of genomic analyses into all areas of AMR research, surveillance and management.
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Affiliation(s)
- Kate S Baker
- Institute for Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England, London, NW9 5HT, UK
| | - Nigel Field
- Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, UCL, London, WC1E 6BT, UK
| | - Tristan Childs
- Centre for Infectious Disease Surveillance and Control, National Infection Service, Public Health England, London, NW9 5HT, UK
| | - Holly Mitchell
- Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, UCL, London, WC1E 6BT, UK
| | - Martin Day
- Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England, London, NW9 5HT, UK
| | | | - Sophie Lefèvre
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | - Mathieu Tourdjman
- Santé Publique France, the French Public Health Agency, Saint-Maurice, 94415, France
| | - Gwenda Hughes
- Department of HIV and STIs, National Infection Service, Public Health England, London, NW9 5HT, UK
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England, London, NW9 5HT, UK
| | - Nicholas Thomson
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
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Abstract
Shigella are ranked among the most prevalent aetiologies of diarrhoeal disease worldwide, disproportionately affecting young children in developing countries and high-risk communities in developed settings. Antimicrobial treatment, most commonly with fluoroquinolones, is currently recommended for Shigella infections to alleviate symptoms and control disease transmission. Resistance to fluoroquinolones has emerged in differing Shigella species (S. dysenteriae, flexneri and sonnei) since the turn of the 21st century, originating in endemic areas, and latterly spreading into non-endemic regions. Despite occurring independently, the emergence of fluoroquinolone resistance in these different Shigella species shares striking similarities regarding their epidemiology and resistance mechanisms. Here, we review and discuss the current epidemiology of fluoroquinolone-resistant Shigella species, particularly in the light of recent genomic insights.
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Affiliation(s)
- Hao Chung The
- Enteric Infections, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- Enteric Infections, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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Hwang SB, Choi JG, Wei S, Park BJ, Chelliah R, Oh DH. In vivo screening platform for shiga toxin-producing Escherichia coli (STEC) using Caenorhabditis elegans as a model. PLoS One 2018; 13:e0193277. [PMID: 29489863 DOI: 10.1371/journal.pone.0193277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 02/07/2018] [Indexed: 01/02/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) strains are the main cause of bacillary dysentery, although STEC strains generally induce milder disease symptoms compared to Shigella species. This study aimed to determine the virulence of STEC using the nematode Caenorhabditis elegans as a model host. Worm killing, fertility and bacterial colonisation assays were performed to examine the potential difference in the virulence of STEC strains compared to that of the control E. coli OP50 strains on which worms were fed. A statistically significant difference in the survival rates of C. elegans was observed in that the STEC strains caused death in 8–10 days and the E. coli OP50 strains caused death in 15 days. STEC strains severely reduced the fertility of the worms. The intestinal load of bacteria in the adult stage nematodes harbouring the E. coli OP50 strains was found to be 3.5 log CFU mL-1. In contrast, the STEC strains E15, E18 and E22 harboured 4.1, 4.2 and 4.7 log CFU ml−1 per nematode, respectively. The heat-killed STEC strains significantly increased the longevity of the worms compared to the non-heated STEC strains. In addition, PCR-based genomic profiling of shiga toxin genes, viz., stx1 and stx2, identified in selected STEC strains revealed that these toxins may be associated with the virulence of the STEC strains. This study demonstrated that C. elegans is an effective model to examine and compare the pathogenicity and virulence variation of STEC strains to that of E. coli OP50 strains.
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Weill FX, Domman D, Njamkepo E, Tarr C, Rauzier J, Fawal N, Keddy KH, Salje H, Moore S, Mukhopadhyay AK, Bercion R, Luquero FJ, Ngandjio A, Dosso M, Monakhova E, Garin B, Bouchier C, Pazzani C, Mutreja A, Grunow R, Sidikou F, Bonte L, Breurec S, Damian M, Njanpop-Lafourcade BM, Sapriel G, Page AL, Hamze M, Henkens M, Chowdhury G, Mengel M, Koeck JL, Fournier JM, Dougan G, Grimont PAD, Parkhill J, Holt KE, Piarroux R, Ramamurthy T, Quilici ML, Thomson NR. Genomic history of the seventh pandemic of cholera in Africa. Science 2017; 358:785-789. [DOI: 10.1126/science.aad5901] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/10/2017] [Indexed: 11/02/2022]
Abstract
The seventh cholera pandemic has heavily affected Africa, although the origin and continental spread of the disease remain undefined. We used genomic data from 1070 Vibrio cholerae O1 isolates, across 45 African countries and over a 49-year period, to show that past epidemics were attributable to a single expanded lineage. This lineage was introduced at least 11 times since 1970, into two main regions, West Africa and East/Southern Africa, causing epidemics that lasted up to 28 years. The last five introductions into Africa, all from Asia, involved multidrug-resistant sublineages that replaced antibiotic-susceptible sublineages after 2000. This phylogenetic framework describes the periodicity of lineage introduction and the stable routes of cholera spread, which should inform the rational design of control measures for cholera in Africa.
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Affiliation(s)
- François-Xavier Weill
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Daryl Domman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Elisabeth Njamkepo
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | - Cheryl Tarr
- Centers for Disease Control and Prevention, Escherichia and Shigella Reference Unit, Atlanta, GA 30333, USA
| | - Jean Rauzier
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | - Nizar Fawal
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | - Karen H. Keddy
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg 2131, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Henrik Salje
- Institut Pasteur, Mathematical Modelling of Infectious Diseases, Paris, 75015, France
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Sandra Moore
- Laboratoire de Parasitologie-Mycologie, CHU Timone, Université de la Méditerranée, Marseille, 13385, France
| | - Asish K. Mukhopadhyay
- National Institute of Cholera and Enteric Diseases (NICED), Kolkata, West Bengal 700010, India
| | - Raymond Bercion
- Institut Pasteur de Bangui, BP 923, Bangui, Central African Republic
- Institut Pasteur de Dakar, BP 220, Dakar, Senegal
| | | | | | - Mireille Dosso
- Bacteriology and Virology Department, Institut Pasteur, Abidjan, Côte d'Ivoire
| | - Elena Monakhova
- Rostov-on-Don Research Institute for Plague Control, Rostov-on-Don, 344022, Russia
| | - Benoit Garin
- Institut Pasteur de Dakar, BP 220, Dakar, Senegal
| | | | - Carlo Pazzani
- University of Bari “A. Moro”, Department of Biology, Bari, 70126, Italy
| | - Ankur Mutreja
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0SP, UK
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana 121001, India
| | | | - Fati Sidikou
- Centre de Recherche Medicale et Sanitaire (CERMES), BP 10887, Niamey, Niger
| | | | - Sébastien Breurec
- Institut Pasteur de Bangui, BP 923, Bangui, Central African Republic
| | - Maria Damian
- Cantacuzino National Institute of Research-Development for Microbiology and Immunology, Bucharest, Romania
| | | | - Guillaume Sapriel
- Université de Versailles Saint-Quentin-en-Yvelines, UFR des sciences de la santé Simone Veil, Montigny-le-Bretonneux, 78180, France
- Atelier de Bioinformatique, ISYEB, UMR 7205, Paris, 75005, France
| | | | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), EDST-FSP, Université Libanaise, Tripoli, Lebanon
| | | | - Goutam Chowdhury
- National Institute of Cholera and Enteric Diseases (NICED), Kolkata, West Bengal 700010, India
| | - Martin Mengel
- Agence de Médecine Préventive (AMP), Paris, 75015, France
| | - Jean-Louis Koeck
- Centre Hospitalier des Armées Bouffard, Djibouti, Republic of Djibouti
| | | | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0SP, UK
| | - Patrick A. D. Grimont
- Institut Pasteur, Unité Biodiversité des Bactéries Pathogènes Emergentes, Paris, 75015, France
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Kathryn E. Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Renaud Piarroux
- Laboratoire de Parasitologie-Mycologie, CHU Timone, Université de la Méditerranée, Marseille, 13385, France
| | | | - Marie-Laure Quilici
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
- Institut Pasteur, Unité du Choléra et des Vibrions, Paris, 75015, France
| | - Nicholas R. Thomson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Pérez-Losada M. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. Infect Genet Evol 2017; 63:295-306. [PMID: 28951202 DOI: 10.1016/j.meegid.2017.09.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
Mutation and recombination drive the evolution of most pathogens by generating the genetic variants upon which selection operates. Those variants can, for example, confer resistance to host immune systems and drug therapies or lead to epidemic outbreaks. Given their importance, diverse evolutionary studies have investigated the abundance and consequences of mutation and recombination in pathogen populations. However, some controversies persist regarding the contribution of each evolutionary force to the development of particular phenotypic observations (e.g., drug resistance). In this study, we revise the importance of mutation and recombination in the evolution of pathogens at both intra-host and inter-host levels. We also describe state-of-the-art analytical methodologies to detect and quantify these two evolutionary forces, including biases that are often ignored in evolutionary studies. Finally, we present some of our former studies involving pathogenic taxa where mutation and recombination played crucial roles in the recovery of pathogenic fitness, the generation of interspecific genetic diversity, or the design of centralized vaccines. This review also illustrates several common controversies and pitfalls in the analysis and in the evaluation and interpretation of mutation and recombination outcomes.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain; Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Catarina Branco
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Nadine Castelhano
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago, Chile.
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, Washington, DC, United States; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal.
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Hall G, Kurosawa S, Stearns-Kurosawa DJ. Shiga Toxin Therapeutics: Beyond Neutralization. Toxins (Basel) 2017; 9:toxins9090291. [PMID: 28925976 PMCID: PMC5618224 DOI: 10.3390/toxins9090291] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 01/04/2023] Open
Abstract
Ribotoxic Shiga toxins are the primary cause of hemolytic uremic syndrome (HUS) in patients infected with Shiga toxin-producing enterohemorrhagic Escherichia coli (STEC), a pathogen class responsible for epidemic outbreaks of gastrointestinal disease around the globe. HUS is a leading cause of pediatric renal failure in otherwise healthy children, resulting in a mortality rate of 10% and a chronic morbidity rate near 25%. There are currently no available therapeutics to prevent or treat HUS in STEC patients despite decades of work elucidating the mechanisms of Shiga toxicity in sensitive cells. The preclinical development of toxin-targeted HUS therapies has been hindered by the sporadic, geographically dispersed nature of STEC outbreaks with HUS cases and the limited financial incentive for the commercial development of therapies for an acute disease with an inconsistent patient population. The following review considers potential therapeutic targeting of the downstream cellular impacts of Shiga toxicity, which include the unfolded protein response (UPR) and the ribotoxic stress response (RSR). Outcomes of the UPR and RSR are relevant to other diseases with large global incidence and prevalence rates, thus reducing barriers to the development of commercial drugs that could improve STEC and HUS patient outcomes.
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Affiliation(s)
- Gregory Hall
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Shinichiro Kurosawa
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Deborah J Stearns-Kurosawa
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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Hazen TH, Michalski J, Nagaraj S, Okeke IN, Rasko DA. Characterization of a Large Antibiotic Resistance Plasmid Found in Enteropathogenic Escherichia coli Strain B171 and Its Relatedness to Plasmids of Diverse E. coli and Shigella Strains. Antimicrob Agents Chemother 2017; 61:e00995-17. [PMID: 28674052 DOI: 10.1128/AAC.00995-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/26/2017] [Indexed: 11/20/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) is a leading cause of severe infantile diarrhea in developing countries. Previous research has focused on the diversity of the EPEC virulence plasmid, whereas less is known regarding the genetic content and distribution of antibiotic resistance plasmids carried by EPEC. A previous study demonstrated that in addition to the virulence plasmid, reference EPEC strain B171 harbors a second, larger plasmid that confers antibiotic resistance. To further understand the genetic diversity and dissemination of antibiotic resistance plasmids among EPEC strains, we describe the complete sequence of an antibiotic resistance plasmid from EPEC strain B171. The resistance plasmid, pB171_90, has a completed sequence length of 90,229 bp, a GC content of 54.55%, and carries protein-encoding genes involved in conjugative transfer, resistance to tetracycline (tetA), sulfonamides (sulI), and mercury, as well as several virulence-associated genes, including the transcriptional regulator hha and the putative calcium sequestration inhibitor (csi). In silico detection of the pB171_90 genes among 4,798 publicly available E. coli genome assemblies indicates that the unique genes of pB171_90 (csi and traI) are primarily restricted to genomes identified as EPEC or enterotoxigenic E. coli However, conserved regions of the pB171_90 plasmid containing genes involved in replication, stability, and antibiotic resistance were identified among diverse E. coli pathotypes. Interestingly, pB171_90 also exhibited significant similarity with a sequenced plasmid from Shigella dysenteriae type I. Our findings demonstrate the mosaic nature of EPEC antibiotic resistance plasmids and highlight the need for additional sequence-based characterization of antibiotic resistance plasmids harbored by pathogenic E. coli.
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Griffiths E, Dooley D, Graham M, Van Domselaar G, Brinkman FSL, Hsiao WWL. Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance. Front Microbiol 2017; 8:1068. [PMID: 28694792 PMCID: PMC5483436 DOI: 10.3389/fmicb.2017.01068] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/29/2017] [Indexed: 11/18/2022] Open
Abstract
Globalization of food networks increases opportunities for the spread of foodborne pathogens beyond borders and jurisdictions. High resolution whole-genome sequencing (WGS) subtyping of pathogens promises to vastly improve our ability to track and control foodborne disease, but to do so it must be combined with epidemiological, clinical, laboratory and other health care data (called “contextual data”) to be meaningfully interpreted for regulatory and health interventions, outbreak investigation, and risk assessment. However, current multi-jurisdictional pathogen surveillance and investigation efforts are complicated by time-consuming data re-entry, curation and integration of contextual information owing to a lack of interoperable standards and inconsistent reporting. A solution to these challenges is the use of ‘ontologies’ - hierarchies of well-defined and standardized vocabularies interconnected by logical relationships. Terms are specified by universal IDs enabling integration into highly regulated areas and multi-sector sharing (e.g., food and water microbiology with the veterinary sector). Institution-specific terms can be mapped to a given standard at different levels of granularity, maximizing comparability of contextual information according to jurisdictional policies. Fit-for-purpose ontologies provide contextual information with the auditability required for food safety laboratory accreditation. Our research efforts include the development of a Genomic Epidemiology Ontology (GenEpiO), and Food Ontology (FoodOn) that harmonize important laboratory, clinical and epidemiological data fields, as well as existing food resources. These efforts are supported by a global consortium of researchers and stakeholders worldwide. Since foodborne diseases do not respect international borders, uptake of such vocabularies will be crucial for multi-jurisdictional interpretation of WGS results and data sharing.
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Affiliation(s)
- Emma Griffiths
- Department of Molecular Biology and Biochemistry, Simon Fraser University, VancouverBC, Canada
| | - Damion Dooley
- Department of Pathology and Laboratory Medicine, University of British Columbia, VancouverBC, Canada
| | - Morag Graham
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada.,Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, WinnipegMB, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada.,Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, WinnipegMB, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, VancouverBC, Canada
| | - William W L Hsiao
- Department of Pathology and Laboratory Medicine, University of British Columbia, VancouverBC, Canada.,British Columbia Centre for Disease Control Public Health Laboratory, VancouverBC, Canada
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Baker KS, Campos J, Pichel M, Della Gaspera A, Duarte-Martínez F, Campos-Chacón E, Bolaños-Acuña HM, Guzmán-Verri C, Mather AE, Diaz Velasco S, Zamudio Rojas ML, Forbester JL, Connor TR, Keddy KH, Smith AM, López de Delgado EA, Angiolillo G, Cuaical N, Fernández J, Aguayo C, Morales Aguilar M, Valenzuela C, Morales Medrano AJ, Sirok A, Weiler Gustafson N, Diaz Guevara PL, Montaño LA, Perez E, Thomson NR. Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses. Clin Microbiol Infect 2017; 23:845-853. [PMID: 28389276 PMCID: PMC5667938 DOI: 10.1016/j.cmi.2017.03.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/16/2017] [Accepted: 03/27/2017] [Indexed: 12/31/2022]
Abstract
Objectives Shigella sonnei is a globally important diarrhoeal pathogen tracked through the surveillance network PulseNet Latin America and Caribbean (PNLA&C), which participates in PulseNet International. PNLA&C laboratories use common molecular techniques to track pathogens causing foodborne illness. We aimed to demonstrate the possibility and advantages of transitioning to whole genome sequencing (WGS) for surveillance within existing networks across a continent where S. sonnei is endemic. Methods We applied WGS to representative archive isolates of S. sonnei (n = 323) from laboratories in nine PNLA&C countries to generate a regional phylogenomic reference for S. sonnei and put this in the global context. We used this reference to contextualise 16 S. sonnei from three Argentinian outbreaks, using locally generated sequence data. Assembled genome sequences were used to predict antimicrobial resistance (AMR) phenotypes and identify AMR determinants. Results S. sonnei isolates clustered in five Latin American sublineages in the global phylogeny, with many (46%, 149 of 323) belonging to previously undescribed sublineages. Predicted multidrug resistance was common (77%, 249 of 323), and clinically relevant differences in AMR were found among sublineages. The regional overview showed that Argentinian outbreak isolates belonged to distinct sublineages and had different epidemiologic origins. Conclusions Latin America contains novel genetic diversity of S. sonnei that is relevant on a global scale and commonly exhibits multidrug resistance. Retrospective passive surveillance with WGS has utility for informing treatment, identifying regionally epidemic sublineages and providing a framework for interpretation of prospective, locally sequenced outbreaks.
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Affiliation(s)
- K S Baker
- University of Liverpool, Department of Functional and Comparative Genomics, Liverpool, England, United Kingdom; Wellcome Trust Sanger Institute, Pathogen Variation Programme, Hinxton, England, United Kingdom.
| | - J Campos
- Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
| | - M Pichel
- Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
| | - A Della Gaspera
- Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
| | - F Duarte-Martínez
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), Costa Rica
| | - E Campos-Chacón
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), Costa Rica
| | - H M Bolaños-Acuña
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (Inciensa), Costa Rica
| | - C Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica; Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - A E Mather
- Wellcome Trust Sanger Institute, Pathogen Variation Programme, Hinxton, England, United Kingdom; University of Cambridge, Department of Veterinary Medicine, Cambridge, England, United Kingdom
| | | | | | - J L Forbester
- Wellcome Trust Sanger Institute, Pathogen Variation Programme, Hinxton, England, United Kingdom
| | - T R Connor
- Organisms and Environment Division, Cardiff University School of Biosciences, Sir Martin Evans Building, Cardiff, Wales, United Kingdom
| | - K H Keddy
- Centre for Enteric Diseases, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - E A López de Delgado
- Department of Bacteriology, National Institute of Hygiene 'Rafael Rangel', Ciudad University, Los Chaguaramos, Venezuela
| | - G Angiolillo
- Department of Bacteriology, National Institute of Hygiene 'Rafael Rangel', Ciudad University, Los Chaguaramos, Venezuela
| | - N Cuaical
- Department of Bacteriology, National Institute of Hygiene 'Rafael Rangel', Ciudad University, Los Chaguaramos, Venezuela
| | - J Fernández
- Molecular Genetics Laboratory, Institute of Public Health of Chile, Santiago, Chile
| | - C Aguayo
- Molecular Genetics Laboratory, Institute of Public Health of Chile, Santiago, Chile
| | - M Morales Aguilar
- Department of Foodborne Diseases, National Health Laboratory of Guatemala, Laboratorio Nacional de Salud, Barcenas, Guatemala
| | - C Valenzuela
- Department of Foodborne Diseases, National Health Laboratory of Guatemala, Laboratorio Nacional de Salud, Barcenas, Guatemala
| | - A J Morales Medrano
- Department of Foodborne Diseases, National Health Laboratory of Guatemala, Laboratorio Nacional de Salud, Barcenas, Guatemala
| | - A Sirok
- Bacteriology Laboratory, Departamento de Laboratorios de Salud Pública (DLSP), Ministerio de Salud Pública (MSP), Montevideo, Uruguay
| | - N Weiler Gustafson
- Department of Bacteriology, Laboratorio Central de Salud Pública, Asuncion, Paraguay
| | - P L Diaz Guevara
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - L A Montaño
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - E Perez
- Pan American Health Organization/World Health Organization, Department of Health Emergencies, Washington, DC, United States
| | - N R Thomson
- Wellcome Trust Sanger Institute, Pathogen Variation Programme, Hinxton, England, United Kingdom; London School of Hygiene and Tropical Medicine, London, England, United Kingdom.
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Imamura D, Morita M, Sekizuka T, Mizuno T, Takemura T, Yamashiro T, Chowdhury G, Pazhani GP, Mukhopadhyay AK, Ramamurthy T, Miyoshi SI, Kuroda M, Shinoda S, Ohnishi M. Comparative genome analysis of VSP-II and SNPs reveals heterogenic variation in contemporary strains of Vibrio cholerae O1 isolated from cholera patients in Kolkata, India. PLoS Negl Trop Dis 2017; 11:e0005386. [PMID: 28192431 DOI: 10.1371/journal.pntd.0005386] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 03/14/2017] [Accepted: 02/04/2017] [Indexed: 12/20/2022] Open
Abstract
Cholera is an acute diarrheal disease and a major public health problem in many developing countries in Asia, Africa, and Latin America. Since the Bay of Bengal is considered the epicenter for the seventh cholera pandemic, it is important to understand the genetic dynamism of Vibrio cholerae from Kolkata, as a representative of the Bengal region. We analyzed whole genome sequence data of V. cholerae O1 isolated from cholera patients in Kolkata, India, from 2007 to 2014 and identified the heterogeneous genomic region in these strains. In addition, we carried out a phylogenetic analysis based on the whole genome single nucleotide polymorphisms to determine the genetic lineage of strains in Kolkata. This analysis revealed the heterogeneity of the Vibrio seventh pandemic island (VSP)-II in Kolkata strains. The ctxB genotype was also heterogeneous and was highly related to VSP-II types. In addition, phylogenetic analysis revealed the shifts in predominant strains in Kolkata. Two distinct lineages, 1 and 2, were found between 2007 and 2010. However, the proportion changed markedly in 2010 and lineage 2 strains were predominant thereafter. Lineage 2 can be divided into four sublineages, I, II, III and IV. The results of this study indicate that lineages 1 and 2-I were concurrently prevalent between 2007 and 2009, and lineage 2-III observed in 2010, followed by the predominance of lineage 2-IV in 2011 and continued until 2014. Our findings demonstrate that the epidemic of cholera in Kolkata was caused by several distinct strains that have been constantly changing within the genetic lineages of V. cholerae O1 in recent years. Seven cholera pandemics have been recorded throughout history, and the sixth, and presumably earlier pandemics, emerged from the Bay of Bengal. The seventh pandemic strain also appeared and spread from this area to different area of the world. Thus, the Bay of Bengal has always been considered the epicenter of cholera pandemics. In this report, we characterized the V. cholerae strains isolated from patients with cholera in Kolkata as a representative area of the Bay of Bengal between 2007 and 2014. The analysis revealed that the cholera epidemics were caused by several distinct V. cholerae O1 strains and that the predominant strains have genetically changed several times in recent years.
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Duchêne S, Holt KE, Weill FX, Le Hello S, Hawkey J, Edwards DJ, Fourment M, Holmes EC. Genome-scale rates of evolutionary change in bacteria. Microb Genom 2016; 2:e000094. [PMID: 28348834 PMCID: PMC5320706 DOI: 10.1099/mgen.0.000094] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 10/24/2016] [Indexed: 01/26/2023] Open
Abstract
Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host–pathogen associations and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with ‘ancient DNA’ data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from approximately 10−5 to 10−8 nucleotide substitutions per site year−1. This variation was negatively associated with sampling time, with this relationship best described by an exponential decay curve. To avoid potential estimation biases, such time-dependency should be considered when inferring evolutionary time-scales in bacteria.
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Affiliation(s)
- Sebastian Duchêne
- 1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.,2Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC 3010, Australia.,3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kathryn E Holt
- 2Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC 3010, Australia.,3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | | | - Simon Le Hello
- 4Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris 75015, France
| | - Jane Hawkey
- 2Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC 3010, Australia.,3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - David J Edwards
- 2Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC 3010, Australia.,3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Mathieu Fourment
- 1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- 1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
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Argimón S, Abudahab K, Goater RJE, Fedosejev A, Bhai J, Glasner C, Feil EJ, Holden MTG, Yeats CA, Grundmann H, Spratt BG, Aanensen DM. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb Genom 2016; 2:e000093. [PMID: 28348833 PMCID: PMC5320705 DOI: 10.1099/mgen.0.000093] [Citation(s) in RCA: 333] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 10/19/2016] [Indexed: 11/18/2022] Open
Abstract
Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data. There is, therefore, a need for flexible, interactive software that presents the population genomic outputs and associated data in a user-friendly manner for a wide range of end users, from trained bioinformaticians to front-line epidemiologists and health workers. Here, we present Microreact, a web application for the easy visualization of datasets consisting of any combination of trees, geographical, temporal and associated metadata. Data files can be uploaded to Microreact directly via the web browser or by linking to their location (e.g. from Google Drive/Dropbox or via API), and an integrated visualization via trees, maps, timelines and tables provides interactive querying of the data. The visualization can be shared as a permanent web link among collaborators, or embedded within publications to enable readers to explore and download the data. Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets.
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Affiliation(s)
- Silvia Argimón
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Khalil Abudahab
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Richard J E Goater
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Artemij Fedosejev
- 2Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - Jyothish Bhai
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Corinna Glasner
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Edward J Feil
- 3The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | | | - Corin A Yeats
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK.,2Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - Hajo Grundmann
- 5Department of Infection Prevention and Hospital Hygiene, University Medical Centre Freiburg, Freiburg, Germany
| | - Brian G Spratt
- 2Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - David M Aanensen
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK.,2Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
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Moriel DG, Tan L, Goh KG, Phan MD, Ipe DS, Lo AW, Peters KM, Ulett GC, Beatson SA, Schembri MA. A Novel Protective Vaccine Antigen from the Core Escherichia coli Genome. mSphere 2016; 1:e00326-16. [PMID: 27904885 DOI: 10.1128/mSphere.00326-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 12/21/2022] Open
Abstract
E. coli is a multifaceted pathogen of major significance to global human health and an important contributor to increasing antibiotic resistance. Given the paucity of therapies still effective against multidrug-resistant pathogenic E. coli strains, novel treatment and prevention strategies are urgently required. In this study, we defined the core and accessory components of the E. coli genome by examining a large collection of draft and completely sequenced strains available from public databases. This data set was mined by employing a reverse-vaccinology approach in combination with proteomics to identify putative broadly protective vaccine antigens. One such antigen was identified that was highly immunogenic and induced protection in a mouse model of bacteremia. Overall, our study provides a genomic and proteomic framework for the selection of novel vaccine antigens that could mediate broad protection against pathogenic E. coli. Escherichia coli is a versatile pathogen capable of causing intestinal and extraintestinal infections that result in a huge burden of global human disease. The diversity of E. coli is reflected by its multiple different pathotypes and mosaic genome composition. E. coli strains are also a major driver of antibiotic resistance, emphasizing the urgent need for new treatment and prevention measures. Here, we used a large data set comprising 1,700 draft and complete genomes to define the core and accessory genome of E. coli and demonstrated the overlapping relationship between strains from different pathotypes. In combination with proteomic investigation, this analysis revealed core genes that encode surface-exposed or secreted proteins that represent potential broad-coverage vaccine antigens. One of these antigens, YncE, was characterized as a conserved immunogenic antigen able to protect against acute systemic infection in mice after vaccination. Overall, this work provides a genomic blueprint for future analyses of conserved and accessory E. coli genes. The work also identified YncE as a novel antigen that could be exploited in the development of a vaccine against all pathogenic E. coli strains—an important direction given the high global incidence of infections caused by multidrug-resistant strains for which there are few effective antibiotics. IMPORTANCEE. coli is a multifaceted pathogen of major significance to global human health and an important contributor to increasing antibiotic resistance. Given the paucity of therapies still effective against multidrug-resistant pathogenic E. coli strains, novel treatment and prevention strategies are urgently required. In this study, we defined the core and accessory components of the E. coli genome by examining a large collection of draft and completely sequenced strains available from public databases. This data set was mined by employing a reverse-vaccinology approach in combination with proteomics to identify putative broadly protective vaccine antigens. One such antigen was identified that was highly immunogenic and induced protection in a mouse model of bacteremia. Overall, our study provides a genomic and proteomic framework for the selection of novel vaccine antigens that could mediate broad protection against pathogenic E. coli.
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Di Martino ML, Falconi M, Micheli G, Colonna B, Prosseda G. The Multifaceted Activity of the VirF Regulatory Protein in the Shigella Lifestyle. Front Mol Biosci 2016; 3:61. [PMID: 27747215 PMCID: PMC5041530 DOI: 10.3389/fmolb.2016.00061] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/15/2016] [Indexed: 12/20/2022] Open
Abstract
Shigella is a highly adapted human pathogen, mainly found in the developing world and causing a severe enteric syndrome. The highly sophisticated infectious strategy of Shigella banks on the capacity to invade the intestinal epithelial barrier and cause its inflammatory destruction. The cellular pathogenesis and clinical presentation of shigellosis are the sum of the complex action of a large number of bacterial virulence factors mainly located on a large virulence plasmid (pINV). The expression of pINV genes is controlled by multiple environmental stimuli through a regulatory cascade involving proteins and sRNAs encoded by both the pINV and the chromosome. The primary regulator of the virulence phenotype is VirF, a DNA-binding protein belonging to the AraC family of transcriptional regulators. The virF gene, located on the pINV, is expressed only within the host, mainly in response to the temperature transition occurring when the bacterium transits from the outer environment to the intestinal milieu. VirF then acts as anti-H-NS protein and directly activates the icsA and virB genes, triggering the full expression of the invasion program of Shigella. In this review we will focus on the structure of VirF, on its sophisticated regulation, and on its role as major player in the path leading from the non-invasive to the invasive phenotype of Shigella. We will address also the involvement of VirF in mechanisms aimed at withstanding adverse conditions inside the host, indicating that this protein is emerging as a global regulator whose action is not limited to virulence systems. Finally, we will discuss recent observations conferring VirF the potential of a novel antibacterial target for shigellosis.
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Affiliation(s)
- Maria Letizia Di Martino
- Dipartimento di Biologia e Biotecnologie C. Darwin, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma Roma, Italy
| | - Maurizio Falconi
- Laboratorio di Genetica Molecolare e dei Microrganismi, Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino Camerino, Italy
| | - Gioacchino Micheli
- Istituto di Biologia e Patologia Molecolari, Consilglio Nazionale Delle Richerche Roma, Italy
| | - Bianca Colonna
- Dipartimento di Biologia e Biotecnologie C. Darwin, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma Roma, Italy
| | - Gianni Prosseda
- Dipartimento di Biologia e Biotecnologie C. Darwin, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma Roma, Italy
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