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The changing epidemiology of shigellosis in Australia, 2001-2019. PLoS Negl Trop Dis 2023; 17:e0010450. [PMID: 36857390 PMCID: PMC10010521 DOI: 10.1371/journal.pntd.0010450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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Baruah N, Halder P, Koley H, Katti DS. Stable Recombinant Invasion Plasmid Antigen C (IpaC)-Based Single Dose Nanovaccine for Shigellosis. Mol Pharm 2022; 19:3884-3893. [PMID: 36122190 DOI: 10.1021/acs.molpharmaceut.2c00378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Shigellosis, caused by the bacteria Shigella, is the leading cause of bacterial diarrhea and the second leading cause of diarrheal death among children under the age of five. Unfortunately, Shigella strains have acquired resistance to antibiotics, and a commercial vaccine is yet to be available. We have previously demonstrated that Shigella dysenteriae serotype 1 (Sd1)-based recombinant, stabilized, "invasion plasmid antigen C" (IpaC; 42 kDa) protein can induce robust immune responses in BALB/c mice against a challenge of a high dose of heterologous Shigella when immunized via three intranasal doses of IpaC without an adjuvant. In this work, in order to reduce the frequency of dosing and increase possible patient compliance, based on our previous screening, the minimum protective dose of stabilized IpaC (20 μg) was encapsulated in biodegradable polymeric poly(lactide-co-glycolide) nanoparticles (∼370 nm) and intranasally administered in BALB/c mice in a single dose. Interestingly, a single intranasal dose of the developed vaccine particles encapsulating only 20 μg of Sd1 IpaC led to a temporal increase in the antibody production with an improved cytokine response compared to free IpaC administered three times as described in our previous report. Upon intraperitoneal challenge with a high dose of heterologous Shigella flexneri 2a (common in circulation), the immunized animals were protected from diarrhea, lethargy, and weight loss with ∼67% survival, while all the control animals died by 36 h of the challenge. Overall, the developed nanovaccine could be explored as a potential noninvasive, cross-protective, single-dose, single-antigen Shigella vaccine amenable for scale-up and eventual mass immunization.
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Affiliation(s)
- Namrata Baruah
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India.,The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Prolay Halder
- Division of Bacteriology, ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal 700010, India
| | - Hemanta Koley
- Division of Bacteriology, ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal 700010, India
| | - Dhirendra S Katti
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India.,The Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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Narayan C, Kant V, Mahajan JK, Mohan B, Taneja N. Differential dendritic immune cell responses to infection with various serotypes of Shigella. Indian J Med Microbiol 2022; 40:217-222. [DOI: 10.1016/j.ijmmb.2022.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 11/28/2022]
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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] [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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Mbuyi W M G, Makasa Mandja B, Kebela Ilunga B. [Spatio-temporal dynamics of bacillary dysentery outbreaks in Democratic Republic of the Congo, 1999-2013]. Rev Epidemiol Sante Publique 2021; 69:1-6. [PMID: 33518368 DOI: 10.1016/j.respe.2020.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/03/2020] [Accepted: 11/10/2020] [Indexed: 11/26/2022] Open
Abstract
PROBLEM STATEMENT From 1999 to 2013 in the Democratic RC, monitoring of bacillary dysentery in bloody diarrhea revealed an average rate of attack in 620 out of 100,000 inhabitants. Within the study period, biological confirmation was available in less than 1% of cases. A dozen dysentery outbreaks were confirmed in laboratories as shigellosis. In this study, our objective is to improve dysentery surveillance. METHODS A descriptive method based on epidemiological and biological data was applied, and a literature review was included. RESULTS According to historical research, the first dysentery epidemics occurred in the Mayombe Region in the early 1920s. Spatial dynamics show that the eastern part of the country experienced the highest number of attacks. Time series of bloody diarrhea in the country have revealed a decrease since 2005. No seasonality was found. CONCLUSION Shigellosis outbreaks have become rare and of low magnitude. Our results suggest a need for further exploration of the causes and determinants of high incidences of bloody diarrhea. Present-day diminution of shigellosis outbreaks calls for research into explanatory factors.
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Affiliation(s)
- G Mbuyi W M
- Direction de lutte contre la maladie/disease prevention and control center, ministère de la Santé publique/Public Health Ministry, Congo, République Démocratique du Congo.
| | - B Makasa Mandja
- Unité de recherche et de formation en écologie et contrôle des maladies infectieuses/infectious disease control and ecology training and research unit, faculté de médecine/faculty of medicine, université de Kinshasa/university of Kinshasa, République Démocratique du Congo.
| | - B Kebela Ilunga
- Direction de lutte contre la maladie/disease prevention and control center, ministère de la Santé publique/Public Health Ministry, Congo, République Démocratique du Congo.
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Domman D, Ruis C, Dorman MJ, Shakya M, Chain PSG. Novel Insights Into the Spread of Enteric Pathogens Using Genomics. J Infect Dis 2020; 221:S319-S330. [PMID: 31538189 DOI: 10.1093/infdis/jiz220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/19/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daryl Domman
- Bioscience Division, Los Alamos National Laboratory, New Mexico
| | - Christopher Ruis
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Matthew J Dorman
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, New Mexico
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Evaluation of in vitro and in vivo antibiotic efficacy against a novel bioluminescent Shigella flexneri. Sci Rep 2019; 9:13567. [PMID: 31537849 PMCID: PMC6753072 DOI: 10.1038/s41598-019-49729-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Shigella spp., the bacteria responsible for shigellosis, are one of the leading causes of diarrheal morbidity and mortality amongst children. There is a pressing need for the development of novel therapeutics, as resistance of Shigella to many currently used antibiotics is rapidly emerging. This paper describes the development of robust in vitro and in vivo tools to study antibiotic efficacy against Shigella flexneri. A novel bioluminescent S. flexneri strain (S. flexneri lux1) was generated, which can be used in a mammalian epithelial cell co-culture assay to evaluate antibiotic intracellular and extracellular efficacy. In addition, the S. flexneri lux1 strain was used with an intraperitoneal (IP) murine model of shigellosis to test the efficacy of ciprofloxacin and ampicillin. Both antibiotics significantly reduced the observed radiance from the gastrointestinal tissue of infected mice compared to vehicle control. Furthermore, plated gastrointestinal tissue homogenate confirmed antibiotic treatment significantly reduced the S. flexneri infection. However, in contrast to the results generated with tissue homogenate, the radiance data was not able to distinguish between the efficacy of ampicillin and ciprofloxacin. Compared to traditional methods, these models can be utilized for efficient screening of novel antibiotics aiding in the discovery of new treatments against shigellosis.
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Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes. J Clin Microbiol 2019; 57:JCM.00100-19. [PMID: 31092597 DOI: 10.1128/jcm.00100-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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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Thomas AK, Preetha S, Omanakuttan A, Vidyullata L, Ashokan A, Rajachandran V, Chattopadhyay S. Mutational convergence acts as a major player in adaptive parallel evolution of Shigella spp. Sci Rep 2019; 9:3252. [PMID: 30824790 PMCID: PMC6397287 DOI: 10.1038/s41598-019-39810-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 01/25/2019] [Indexed: 12/17/2022] Open
Abstract
Shigella spp., emerging from multiple origins of Escherichia coli, poses a significant health threat as a causative agent of bacillary dysentery. While multiple serotypes of four different species have evolved via independent lineages, Shigella spp. are designated as a single pathotype, primarily because of their common mode of pathogenesis. Convergent horizontal transfer events have so far been attributed to the commonalities in the evolution of virulence across diverse lineages. However, the role of mutational convergence in such parallel evolution is not yet well understood. Here we have carried out a genome-wide analysis of Shigella strains from all four species to detect the core genes (i.e. the ones present in all analyzed strains) acquiring convergent mutations of evolutionarily recent origin. Simulation studies show non-neutral accumulation of these convergent mutations across species, suggesting their adaptive role in the evolution of Shigella virulence. S. dysenteriae strain 197, representing highly virulent type 1 (Sd1) clone, carries excessively high number of core genes with recent convergent mutations compared to other analyzed strains. We propose that this high frequency of adaptive convergence in S. dysenteriae strain 197 could be linked to recent re-emergence of the Sd1 clone and its increased resistance to antimicrobials.
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Affiliation(s)
- Achsah K Thomas
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, Kerala, India
| | - Sruthy Preetha
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, Kerala, India
| | - Anjana Omanakuttan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, Kerala, India
| | - Lakkaraju Vidyullata
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, Kerala, India
| | - Anjaly Ashokan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, Kerala, India
| | - Vyshakh Rajachandran
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, Kerala, India
| | - Sujay Chattopadhyay
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, 690 525, Kerala, India.
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Kotloff KL, Riddle MS, Platts-Mills JA, Pavlinac P, Zaidi AKM. Shigellosis. Lancet 2018; 391:801-812. [PMID: 29254859 DOI: 10.1016/s0140-6736(17)33296-8] [Citation(s) in RCA: 307] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 08/10/2017] [Accepted: 09/15/2017] [Indexed: 01/02/2023]
Abstract
Shigellosis is a clinical syndrome caused by invasion of the epithelium lining the terminal ileum, colon, and rectum by Shigella species. Although infections occur globally, and in people of all ages, endemic infections among children aged 1-4 years living in low-income and middle-income settings constitute most of the disease burden. The versatile manifestations of these highly contagious organisms range from acute watery diarrhoea to fulminant dysentery characterised by frequent scant bloody stools with fever, prostration, and abdominal cramps. A broad array of uncommon, but often severe, intestinal and extraintestinal complications can occur. Despite marked reductions in mortality during the past three decades, there are roughly 164 000 annual deaths attributable to shigellosis. Intercontinental dissemination of multiresistant shigella strains, facilitated by travellers and men who have sex with men, has prompted new recommendations for antibiotic therapy. Awareness of disease burden and the emerging threats posed by shigella have accelerated interest in development of shigella vaccines, many of which are being tested in clinical trials.
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Affiliation(s)
- Karen L Kotloff
- Departments of Pediatrics and Medicine, Center for Vaccine Development, Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Mark S Riddle
- Naval Medical Research Center, Silver Spring, MD, USA; Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Patricia Pavlinac
- Department of Global Health, Global Center for Integrated Health of Women, Adolescents and Children (Global WACh), University of Washington, Seattle, WA, USA
| | - Anita K M Zaidi
- Enteric and Diarrheal Diseases Programme, Bill & Melinda Gates Foundation, Seattle, WA, USA
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Abstract
Many biological agents have been strategic pathogenic agents throughout history. Some have even changed history as a consequence of early discoveries of their use as weapons of war. Many of these bioagents can be easily isolated from the environment, and some have recently been genetically manipulated to become more pathogenic for biowarfare. However, it is difficult to determine accidental outbreaks of disease from intentional exposures. In this review, we examine how molecular tools have been used in combination with forensic research to resolve cases of unusual outbreaks and trace the source of the biocrime. New technologies are also discussed in terms of their crucial role impacting forensic science. The anthrax event of 2001 serves as an example of the real threat of bioterrorism and the employment of bioagents as weapons against a population. The Amerithrax investigation has given us lessons of the highest resolution possible with new technologies capable of distinguishing isolates at the base-pair level of sensitivity. In addition, we discuss the implications of proper sanitation to avoid waterborne diseases. The use of new methods in forensic science and health-related surveillance will be invaluable in determining the source of any new disease outbreak, and these data will allow for a quick response to any type of public health threat, whether accidental or purposely initiated.
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Mattock E, Blocker AJ. How Do the Virulence Factors of Shigella Work Together to Cause Disease? Front Cell Infect Microbiol 2017; 7:64. [PMID: 28393050 PMCID: PMC5364150 DOI: 10.3389/fcimb.2017.00064] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/21/2017] [Indexed: 01/01/2023] Open
Abstract
Shigella is the major cause of bacillary dysentery world-wide. It is divided into four species, named S. flexneri, S. sonnei, S. dysenteriae, and S. boydii, which are distinct genomically and in their ability to cause disease. Shigellosis, the clinical presentation of Shigella infection, is characterized by watery diarrhea, abdominal cramps, and fever. Shigella's ability to cause disease has been attributed to virulence factors, which are encoded on chromosomal pathogenicity islands and the virulence plasmid. However, information on these virulence factors is not often brought together to create a detailed picture of infection, and how this translates into shigellosis symptoms. Firstly, Shigella secretes virulence factors that induce severe inflammation and mediate enterotoxic effects on the colon, producing the classic watery diarrhea seen early in infection. Secondly, Shigella injects virulence effectors into epithelial cells via its Type III Secretion System to subvert the host cell structure and function. This allows invasion of epithelial cells, establishing a replicative niche, and causes erratic destruction of the colonic epithelium. Thirdly, Shigella produces effectors to down-regulate inflammation and the innate immune response. This promotes infection and limits the adaptive immune response, causing the host to remain partially susceptible to re-infection. Combinations of these virulence factors may contribute to the different symptoms and infection capabilities of the diverse Shigella species, in addition to distinct transmission patterns. Further investigation of the dominant species causing disease, using whole-genome sequencing and genotyping, will allow comparison and identification of crucial virulence factors and may contribute to the production of a pan-Shigella vaccine.
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Affiliation(s)
- Emily Mattock
- Faculty of Biomedical Sciences, Schools of Cellular and Molecular Medicine and Biochemistry, University of Bristol Bristol, UK
| | - Ariel J Blocker
- Faculty of Biomedical Sciences, Schools of Cellular and Molecular Medicine and Biochemistry, University of Bristol Bristol, UK
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Cimmino T, Le Page S, Raoult D, Rolain JM. Contemporary challenges and opportunities in the diagnosis and outbreak detection of multidrug-resistant infectious disease. Expert Rev Mol Diagn 2016; 16:1163-1175. [PMID: 27690721 DOI: 10.1080/14737159.2016.1244005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The dissemination of multi-drug resistant bacteria (MDRB) has become a major public health concern worldwide because of the increase in infections caused by MDRB, the difficulty in treating them, and expenditures in patient care. Areas covered: We have reviewed challenges and contemporary opportunities for rapidly confronting infections caused by MDRB in the 21st century, including surveillance, detection, identification of resistance mechanisms, and action steps. Expert commentary: In this context, the first critical point for clinical microbiologists is to be able to rapidly detect an abnormal event, an outbreak and/or the spread of a MDRB with surveillance tools so that healthcare policies and therapies adapted to a new stochastic event that will certainly occur again in the future can be implemented.
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Affiliation(s)
- Teresa Cimmino
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Stéphanie Le Page
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Didier Raoult
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Jean-Marc Rolain
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
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Staphylococcus aureus Protein A Mediates Interspecies Interactions at the Cell Surface of Pseudomonas aeruginosa. mBio 2016; 7:mBio.00538-16. [PMID: 27222468 PMCID: PMC4895107 DOI: 10.1128/mbio.00538-16] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
While considerable research has focused on the properties of individual bacteria, relatively little is known about how microbial interspecies interactions alter bacterial behaviors and pathogenesis. Staphylococcus aureus frequently coinfects with other pathogens in a range of different infectious diseases. For example, coinfection by S. aureus with Pseudomonas aeruginosa occurs commonly in people with cystic fibrosis and is associated with higher lung disease morbidity and mortality. S. aureus secretes numerous exoproducts that are known to interact with host tissues, influencing inflammatory responses. The abundantly secreted S. aureus staphylococcal protein A (SpA) binds a range of human glycoproteins, immunoglobulins, and other molecules, with diverse effects on the host, including inhibition of phagocytosis of S. aureus cells. However, the potential effects of SpA and other S. aureus exoproducts on coinfecting bacteria have not been explored. Here, we show that S. aureus-secreted products, including SpA, significantly alter two behaviors associated with persistent infection. We found that SpA inhibited biofilm formation by specific P. aeruginosa clinical isolates, and it also inhibited phagocytosis by neutrophils of all isolates tested. Our results indicate that these effects were mediated by binding to at least two P. aeruginosa cell surface structures—type IV pili and the exopolysaccharide Psl—that confer attachment to surfaces and to other bacterial cells. Thus, we found that the role of a well-studied S. aureus exoproduct, SpA, extends well beyond interactions with the host immune system. Secreted SpA alters multiple persistence-associated behaviors of another common microbial community member, likely influencing cocolonization and coinfection with other microbes. Bacteria rarely exist in isolation, whether on human tissues or in the environment, and they frequently coinfect with other microbes. However, relatively little is known about how microbial interspecies interactions alter bacterial behaviors and pathogenesis. We identified a novel interaction between two bacterial species that frequently infect together—Staphylococcus aureus and Pseudomonas aeruginosa. We show that the S. aureus-secreted protein staphylococcal protein A (SpA), which is well-known for interacting with host targets, also binds to specific P. aeruginosa cell surface molecules and alters two persistence-associated P. aeruginosa behaviors: biofilm formation and uptake by host immune cells. Because S. aureus frequently precedes P. aeruginosa in chronic infections, these findings reveal how microbial community interactions can impact persistence and host interactions during coinfections.
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15
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Njamkepo E, Fawal N, Tran-Dien A, Hawkey J, Strockbine N, Jenkins C, Talukder KA, Bercion R, Kuleshov K, Kolínská R, Russell JE, Kaftyreva L, Accou-Demartin M, Karas A, Vandenberg O, Mather AE, Mason CJ, Page AJ, Ramamurthy T, Bizet C, Gamian A, Carle I, Sow AG, Bouchier C, Wester AL, Lejay-Collin M, Fonkoua MC, Le Hello S, Blaser MJ, Jernberg C, Ruckly C, Mérens A, Page AL, Aslett M, Roggentin P, Fruth A, Denamur E, Venkatesan M, Bercovier H, Bodhidatta L, Chiou CS, Clermont D, Colonna B, Egorova S, Pazhani GP, Ezernitchi AV, Guigon G, Harris SR, Izumiya H, Korzeniowska-Kowal A, Lutyńska A, Gouali M, Grimont F, Langendorf C, Marejková M, Peterson LAM, Perez-Perez G, Ngandjio A, Podkolzin A, Souche E, Makarova M, Shipulin GA, Ye C, Žemličková H, Herpay M, Grimont PAD, Parkhill J, Sansonetti P, Holt KE, Brisse S, Thomson NR, Weill FX. Global phylogeography and evolutionary history of Shigella dysenteriae type 1. Nat Microbiol 2016; 1:16027. [PMID: 27572446 DOI: 10.1038/nmicrobiol.2016.27] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 02/03/2016] [Indexed: 11/09/2022]
Abstract
Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease.
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Affiliation(s)
- Elisabeth Njamkepo
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | - Nizar Fawal
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | - Alicia Tran-Dien
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | - Jane Hawkey
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,School of Agriculture and Veterinary Science, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nancy Strockbine
- Centers for Disease Control and Prevention, Escherichia and Shigella Reference Unit, Atlanta, Georgia 30333, USA
| | - Claire Jenkins
- Public Health England, Gastrointestinal Bacteria Reference Unit, Colindale NW9 5HT, UK
| | - Kaisar A Talukder
- icddr,b, Enteric and Food Microbiology Laboratory, Dhaka 1212, Bangladesh
| | - Raymond Bercion
- Institut Pasteur de Bangui, BP 923, Bangui, République Centrafricaine.,Institut Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Konstantin Kuleshov
- Federal Budget Institute of Science, Central Research Institute for Epidemiology, Moscow 111123, Russia
| | - Renáta Kolínská
- Czech National Collection of Type Cultures (CNCTC), National Institute of Public Health, Prague 10, Czech Republic
| | - Julie E Russell
- Public Health England, National Collection of Type Cultures, Porton Down SP4 0JG, UK
| | - Lidia Kaftyreva
- Pasteur Institute of St Petersburg, St Petersburg 197101, Russia
| | - Marie Accou-Demartin
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | - Andreas Karas
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Olivier Vandenberg
- Department of Microbiology, LHUB-ULB, Brussels University Hospitals Laboratory, 1000 Brussels, Belgium.,Environmental Health Research Centre, Public Health School, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Alison E Mather
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Carl J Mason
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok 10400, Thailand
| | - Andrew J Page
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | | | - Chantal Bizet
- Institut Pasteur, Collection de l'Institut Pasteur (CIP), 75724 Paris Cedex 15, France
| | - Andrzej Gamian
- Polish Collection of Microorganisms, Institute of Immunology and Experimental Therapy, 53-114 Wroclaw, Poland
| | - Isabelle Carle
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | | | | | - Astrid Louise Wester
- Department of Foodborne Infections, Norwegian Institute of Public Health, Nydalen 0403, Oslo, Norway
| | - Monique Lejay-Collin
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | | | - Simon Le Hello
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | - Martin J Blaser
- Departments of Medicine and Microbiology, New York University Langone Medical Center, New York, New York 10016, USA
| | | | - Corinne Ruckly
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | - Audrey Mérens
- Biology Department and Infection Control Unit, Bégin Military Hospital, 94160 Saint-Mandé, France
| | | | - Martin Aslett
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | | | - Angelika Fruth
- Divison of Enteropathogenic Bacteria and Legionella, Robert Koch Institut, 38855 Wernigerode, Germany
| | - Erick Denamur
- INSERM, IAME, UMR 1137, Univ. Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, 75018 Paris, France
| | - Malabi Venkatesan
- Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA
| | - Hervé Bercovier
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Ladaporn Bodhidatta
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok 10400, Thailand
| | - Chien-Shun Chiou
- Center of Research and Diagnostics, Centers for Disease Control, Taichung 40855, Taiwan
| | - Dominique Clermont
- Institut Pasteur, Collection de l'Institut Pasteur (CIP), 75724 Paris Cedex 15, France
| | - Bianca Colonna
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie C Darwin, Sapienza Università di Roma, 00185, Roma, Italy
| | - Svetlana Egorova
- Pasteur Institute of St Petersburg, St Petersburg 197101, Russia
| | - Gururaja P Pazhani
- National Institute of Cholera and Enteric Diseases (NICED), Kolkata, West Bengal 700010, India
| | | | - Ghislaine Guigon
- Institut Pasteur, Genotyping of Pathogens and Public Health Platform, 75724 Paris Cedex 15, France
| | | | - Hidemasa Izumiya
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | | | - Anna Lutyńska
- Department of Sera and Vaccines Evaluation, National Institute of Public Health-National Institute of Hygiene, 00-791 Warsaw, Poland
| | - Malika Gouali
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | - Francine Grimont
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | | | - Monika Marejková
- National Reference Laboratory for E. coli and Shigella, National Institute of Public Health, Prague 10, Czech Republic
| | - Lorea A M Peterson
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Guillermo Perez-Perez
- Departments of Medicine and Microbiology, New York University Langone Medical Center, New York, New York 10016, USA
| | | | - Alexander Podkolzin
- Federal Budget Institute of Science, Central Research Institute for Epidemiology, Moscow 111123, Russia
| | - Erika Souche
- Institut Pasteur, Bioinformatics platform, 75724 Paris Cedex 15, France
| | - Mariia Makarova
- Pasteur Institute of St Petersburg, St Petersburg 197101, Russia
| | - German A Shipulin
- Federal Budget Institute of Science, Central Research Institute for Epidemiology, Moscow 111123, Russia
| | - Changyun Ye
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing 102206, China
| | - Helena Žemličková
- Czech National Collection of Type Cultures (CNCTC), National Institute of Public Health, Prague 10, Czech Republic.,Department of Clinical Microbiology, Faculty of Medicine and University Hospital, Charles University, 500 05, Hradec Kralove, Czech Republic
| | - Mária Herpay
- Hungarian National Collection of Medical Bacteria, National Center for Epidemiology, H-1097 Budapest, Hungary
| | - Patrick A D Grimont
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France
| | | | - Philippe Sansonetti
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 75724 Paris Cedex 15, France
| | - Kathryn E Holt
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sylvain Brisse
- Institut Pasteur, Genotyping of Pathogens and Public Health Platform, 75724 Paris Cedex 15, France.,Institut Pasteur, Microbial Evolutionary Genomics Unit, 75724 Paris Cedex 15, France.,CNRS, UMR 3525, 75015 Paris, France
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK.,London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - François-Xavier Weill
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.,Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
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16
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The HC, Thanh DP, Holt KE, Thomson NR, Baker S. The genomic signatures of Shigella evolution, adaptation and geographical spread. Nat Rev Microbiol 2016; 14:235-50. [PMID: 26923111 DOI: 10.1038/nrmicro.2016.10] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Shigella spp. are some of the key pathogens responsible for the global burden of diarrhoeal disease. These facultative intracellular bacteria belong to the family Enterobacteriaceae, together with other intestinal pathogens, such as Escherichia coli and Salmonella spp. The genus Shigella comprises four different species, each consisting of several serogroups, all of which show phenotypic similarity, including invasive pathogenicity. DNA sequencing suggests that this similarity results from the convergent evolution of different Shigella spp. founders. Here, we review the evolutionary relationships between Shigella spp. and E . coli, and we highlight how the genomic plasticity of these bacteria and their acquisition of a distinctive virulence plasmid have enabled the development of such highly specialized pathogens. Furthermore, we discuss the insights that genotyping and whole-genome sequencing have provided into the phylogenetics and intercontinental spread of Shigella spp.
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Affiliation(s)
- Hao Chung The
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam
| | - Kathryn E Holt
- Centre for Systems Genomics, University of Melbourne.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Nicholas R Thomson
- Bacterial Genomics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.,Centre for Tropical Medicine and Global Health, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, UK.,Department of Pathogen and Molecular Biology, The London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
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17
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Pettengill EA, Pettengill JB, Binet R. Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation. Front Microbiol 2016; 6:1573. [PMID: 26834722 PMCID: PMC4718091 DOI: 10.3389/fmicb.2015.01573] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 12/28/2015] [Indexed: 12/30/2022] Open
Abstract
As a leading cause of bacterial dysentery, Shigella represents a significant threat to public health and food safety. Related, but often overlooked, enteroinvasive Escherichia coli (EIEC) can also cause dysentery. Current typing methods have limited ability to identify and differentiate between these pathogens despite the need for rapid and accurate identification of pathogens for clinical treatment and outbreak response. We present a comprehensive phylogeny of Shigella and EIEC using whole genome sequencing of 169 samples, constituting unparalleled strain diversity, and observe a lack of monophyly between Shigella and EIEC and among Shigella taxonomic groups. The evolutionary relationships in the phylogeny are supported by analyses of population structure and hierarchical clustering patterns of translated gene homolog abundance. Lastly, we identified a panel of 254 single nucleotide polymorphism (SNP) markers specific to each phylogenetic cluster for more accurate identification of Shigella and EIEC. Our findings show that Shigella and EIEC are not distinct evolutionary groups within the E. coli genus and, thus, EIEC as a group is not the ancestor to Shigella. The multiple analyses presented provide evidence for reconsidering the taxonomic placement of Shigella. The SNP markers offer more discriminatory power to molecular epidemiological typing methods involving these bacterial pathogens.
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Affiliation(s)
- Emily A Pettengill
- Division of Microbiology, Office of Regulatory Science, U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition College Park, MD, USA
| | - James B Pettengill
- Division of Public Health Informatics and Analytics, Office of Analytics and Outreach, U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition College Park, MD, USA
| | - Rachel Binet
- Division of Microbiology, Office of Regulatory Science, U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition College Park, MD, USA
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18
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Chung The H, Rabaa MA, Thanh DP, Ruekit S, Wangchuk S, Dorji T, Tshering KP, Nguyen TNT, Vinh PV, Thanh TH, Minh CNN, Turner P, Sar P, Thwaites G, Holt KE, Thomson NR, Bodhidatta L, Jeffries Mason C, Baker S. Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan. Microb Genom 2015; 1:e000042. [PMID: 28348825 PMCID: PMC5320628 DOI: 10.1099/mgen.0.000042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/19/2015] [Indexed: 11/26/2022] Open
Abstract
Shigella sonnei is a major contributor to the global burden of diarrhoeal disease, generally associated with dysenteric diarrhoea in developed countries but also emerging in developing countries. The reason for the recent success of S. sonnei is unknown, but is likely catalysed by its ability to acquire resistance against multiple antimicrobials. Between 2011 and 2013, S. sonnei exhibiting resistance to fluoroquinolones, the first-line treatment recommended for shigellosis, emerged in Bhutan. Aiming to reconstruct the introduction and establishment of fluoroquinolone-resistant S. sonnei populations in Bhutan, we performed whole-genome sequencing on 71 S. sonnei samples isolated in Bhutan between 2011 and 2013.We found that these strains represented an expansion of a clade within the previously described lineage III, found specifically in Central Asia. Temporal phylogenetic reconstruction demonstrated that all of the sequenced Bhutanese S. sonnei diverged from a single ancestor that was introduced into Bhutan around 2006. Our data additionally predicted that fluoroquinolone resistance, conferred by mutations in gyrA and parC, arose prior to the introduction of the founder strain into Bhutan. Once established in Bhutan, these S. sonnei had access to a broad gene pool, as indicated by the acquisition of extended-spectrum β-lactamase-encoding plasmids and genes encoding type IV pili. The data presented here outline a model for the introduction and maintenance of fluoroquinolone-resistant S. sonnei in a new setting. Given the current circulation of fluoroquinolone-resistant S. sonnei in Asia, we speculate that this pattern of introduction is being recapitulated across the region and beyond.
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Affiliation(s)
- Hao Chung The
- The Hospital for Tropical Diseases, OUCRU, Ho Chi Minh City, Vietnam
| | - Maia A Rabaa
- The Hospital for Tropical Diseases, OUCRU, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Oxford University, Oxford, UK
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, OUCRU, Ho Chi Minh City, Vietnam
| | | | - Sonam Wangchuk
- Public Health Laboratory, Department of Public Health, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Tshering Dorji
- Public Health Laboratory, Department of Public Health, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Kinzang Pem Tshering
- Department of Pediatrics, Jigme Dorji Wangchuk Referral Hospital, Kawa Jangsa, Thimphu, Bhutan
| | | | - Phat Voong Vinh
- The Hospital for Tropical Diseases, OUCRU, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- The Hospital for Tropical Diseases, OUCRU, Ho Chi Minh City, Vietnam
| | | | - Paul Turner
- Centre for Tropical Medicine, Oxford University, Oxford, UK.,Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Poda Sar
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Guy Thwaites
- The Hospital for Tropical Diseases, OUCRU, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Oxford University, Oxford, UK
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicholas R Thomson
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK.,The London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - Stephen Baker
- The Hospital for Tropical Diseases, OUCRU, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine, Oxford University, Oxford, UK.,The London School of Hygiene and Tropical Medicine, London, UK
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19
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Connor TR, Barker CR, Baker KS, Weill FX, Talukder KA, Smith AM, Baker S, Gouali M, Pham Thanh D, Jahan Azmi I, Dias da Silveira W, Semmler T, Wieler LH, Jenkins C, Cravioto A, Faruque SM, Parkhill J, Wook Kim D, Keddy KH, Thomson NR. Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri. eLife 2015; 4:e07335. [PMID: 26238191 PMCID: PMC4522646 DOI: 10.7554/elife.07335] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/04/2015] [Indexed: 12/15/2022] Open
Abstract
Shigella flexneri is the most common cause of bacterial dysentery in low-income countries. Despite this, S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on serotyping reactions developed over half-a-century ago. Here we combine whole genome sequencing with geographical and temporal data to examine the natural history of the species. Our analysis subdivides S. flexneri into seven phylogenetic groups (PGs); each containing two-or-more serotypes and characterised by distinct virulence gene complement and geographic range. Within the S. flexneri PGs we identify geographically restricted sub-lineages that appear to have persistently colonised regions for many decades to over 100 years. Although we found abundant evidence of antimicrobial resistance (AMR) determinant acquisition, our dataset shows no evidence of subsequent intercontinental spread of antimicrobial resistant strains. The pattern of colonisation and AMR gene acquisition suggest that S. flexneri has a distinct life-cycle involving local persistence.
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Affiliation(s)
- Thomas R Connor
- Cardiff School of Biosciences, Cardiff, United Kingdom
- Pathogen Genomics, Wellcome Trust Sanger Centre, Cambridge, United Kingdom
| | | | - Kate S Baker
- Pathogen Genomics, Wellcome Trust Sanger Centre, Cambridge, United Kingdom
| | | | - Kaisar Ali Talukder
- Centre for Food and Water Borne Diseases, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Malika Gouali
- Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Paris, France
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ishrat Jahan Azmi
- Centre for Food and Water Borne Diseases, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Wanderley Dias da Silveira
- Department of Genetics, Evolution, and Bioagents, Institute of Biology, University of Campinas, São Paulo, Brazil
| | - Torsten Semmler
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie University, Berlin, Germany
- Robert Koch Institute, Berlin, Germany
| | - Lothar H Wieler
- Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie University, Berlin, Germany
- Robert Koch Institute, Berlin, Germany
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, United Kingdom
| | | | - Shah M Faruque
- Centre for Food and Water Borne Diseases, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Centre, Cambridge, United Kingdom
| | - Dong Wook Kim
- Department of Pharmacy, School of Pharmacy, Hanyang University, Ansan, Republic of Korea
| | - Karen H Keddy
- Centre for Enteric Diseases, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicholas R Thomson
- Pathogen Genomics, Wellcome Trust Sanger Centre, Cambridge, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
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20
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Kaur G, Sathyabama S, Arora A, Verma S, Mubin N, Agrewala JN, Mayilraj S. Genome sequencing, annotation and comparative genomic analysis of Shigella dysenteriae strain SD1D. Gut Pathog 2014; 6:28. [PMID: 25028600 PMCID: PMC4099087 DOI: 10.1186/1757-4749-6-28] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/02/2014] [Indexed: 11/15/2022] Open
Abstract
Background Shigellosis is an acute form of gastroenteritis caused by the bacteria belonging to the genus Shigella. It is the most common cause of morbidity and mortality in children. Shigella belongs to the family Enterobactericeae, which is a Gram-negative and rod shaped bacterium. In the present study, we report the draft genome of Shigella dysenteriae strain SD1D, which was isolated from the stool sample of a healthy individual. Results Based on 16S rRNA gene sequence and phylogenetic analysis, the strain SD1D was identified as Shigella dysenteriae. The draft genome of SD1D consisted of 45, 93, 159 bp with a G + C content of 50.7%, 4, 960 predicted CDSs, 75 tRNAs and 2 rRNAs. The final assembly contained 146 contigs of total length 45, 93, 159 bp with N50 contig length of 77, 053 bp; the largest contig assembled measured 3, 85, 550 bp. Conclusions We have for the first time performed the whole genome sequencing of Shigella dysenteriae strain SD1D. The comparative genomic analysis revealed several genes responsible for the pathogenesis, virulence, defense, resistance to antibiotics and toxic compounds, multidrug resistance efflux pumps and other genomic features of the bacterium.
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Affiliation(s)
- Gurwinder Kaur
- Microbial Type Culture Collection and Gene bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Sathyaseelan Sathyabama
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Amit Arora
- Microbial Type Culture Collection and Gene bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Sheenam Verma
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Nida Mubin
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Javed N Agrewala
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
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