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Carey ME, Thi Nguyen TN, Tran DHN, Dyson ZA, Keane JA, Pham Thanh D, Mylona E, Nair S, Chattaway M, Baker S. The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi. Commun Biol 2024; 7:775. [PMID: 38942806 PMCID: PMC11213900 DOI: 10.1038/s42003-024-06451-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 06/13/2024] [Indexed: 06/30/2024] Open
Abstract
Antimicrobial resistance (AMR) poses a serious threat to the clinical management of typhoid fever. AMR in Salmonella Typhi (S. Typhi) is commonly associated with the H58 lineage, a lineage that arose comparatively recently before becoming globally disseminated. To better understand when and how H58 emerged and became dominant, we performed detailed phylogenetic analyses on contemporary genome sequences from S. Typhi isolated in the period spanning the emergence. Our dataset, which contains the earliest described H58 S. Typhi organism, indicates that ancestral H58 organisms were already multi-drug resistant (MDR). These organisms emerged spontaneously in India in 1987 and became radially distributed throughout South Asia and then globally in the ensuing years. These early organisms were associated with a single long branch, possessing mutations associated with increased bile tolerance, suggesting that the first H58 organism was generated during chronic carriage. The subsequent use of fluoroquinolones led to several independent mutations in gyrA. The ability of H58 to acquire and maintain AMR genes continues to pose a threat, as extensively drug-resistant (XDR; MDR plus resistance to ciprofloxacin and third generation cephalosporins) variants, have emerged recently in this lineage. Understanding where and how H58 S. Typhi originated and became successful is key to understand how AMR drives successful lineages of bacterial pathogens. Additionally, these data can inform optimal targeting of typhoid conjugate vaccines (TCVs) for reducing the potential for emergence and the impact of new drug-resistant variants. Emphasis should also be placed upon the prospective identification and treatment of chronic carriers to prevent the emergence of new drug resistant variants with the ability to spread efficiently.
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Affiliation(s)
- Megan E Carey
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK.
- IAVI, Chelsea & Westminster Hospital, London, UK.
| | - To Nguyen Thi Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | | | - Zoe A Dyson
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jacqueline A Keane
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Elli Mylona
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Satheesh Nair
- United Kingdom Health Security Agency, Gastrointestinal Bacteria Reference Unit, London, UK
| | - Marie Chattaway
- United Kingdom Health Security Agency, Gastrointestinal Bacteria Reference Unit, London, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- IAVI, Chelsea & Westminster Hospital, London, UK
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Webster E, Palanco Lopez P, Kirchhelle C. Shifting targets: typhoid's transformation from an environmental to a vaccine-preventable disease, 1940-2019. THE LANCET. INFECTIOUS DISEASES 2024; 24:e232-e244. [PMID: 37995738 DOI: 10.1016/s1473-3099(23)00500-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 11/25/2023]
Abstract
160 years after the discovery of its waterborne transmission and 120 years after the development of the first-generation of vaccines, typhoid fever remains a major health threat globally. In this Historical Review, we use WHO's Institutional Repository for Information Sharing to examine changes in typhoid control policy from January, 1940, to December, 2019. We used a mixed-methods approach in the analysis of infection control priorities, combining semi-inductive thematic coding with historical analysis to show major thematic shifts in typhoid control policy, away from water, sanitation, and hygiene (WASH)-based control towards vaccine-based interventions concurrent with declining attention to the disease. Documentary analysis shows that, although international planners never officially disavowed WASH and low-income countries persistently lobbied for WASH, vaccines emerged as a permanent stopgap while meaningful support of sustained WASH strengthening lost momentum-with serious, long-term ramifications for typhoid control.
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Affiliation(s)
- Emily Webster
- Department of Philosophy, Durham University, Durham, UK; Department of Philosophy, University of Johannesburg, Johannesburg, South Africa
| | | | - Claas Kirchhelle
- School of History, University College Dublin, Dublin, Ireland; Oxford Vaccine Group, University of Oxford, Oxford, UK.
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Hooda Y, Islam S, Kabiraj R, Rahman H, Sarkar H, da Silva KE, Raju RS, Luby SP, Andrews JR, Saha SK, Saha S. Old tools, new applications: Use of environmental bacteriophages for typhoid surveillance and evaluating vaccine impact. PLoS Negl Trop Dis 2024; 18:e0011822. [PMID: 38358956 PMCID: PMC10868810 DOI: 10.1371/journal.pntd.0011822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/27/2023] [Indexed: 02/17/2024] Open
Abstract
Typhoid-conjugate vaccines (TCVs) provide an opportunity to reduce the burden of typhoid fever, caused by Salmonella Typhi, in endemic areas. As policymakers design vaccination strategies, accurate and high-resolution data on disease burden is crucial. However, traditional blood culture-based surveillance is resource-extensive, prohibiting its large-scale and sustainable implementation. Salmonella Typhi is a water-borne pathogen, and here, we tested the potential of Typhi-specific bacteriophage surveillance in surface water bodies as a low-cost tool to identify where Salmonella Typhi circulates in the environment. In 2021, water samples were collected and tested for the presence of Salmonella Typhi bacteriophages at two sites in Bangladesh: urban capital city, Dhaka, and a rural district, Mirzapur. Salmonella Typhi-specific bacteriophages were detected in 66 of 211 (31%) environmental samples in Dhaka, in comparison to 3 of 92 (3%) environmental samples from Mirzapur. In the same year, 4,620 blood cultures at the two largest pediatric hospitals of Dhaka yielded 215 (5%) culture-confirmed typhoid cases, and 3,788 blood cultures in the largest hospital of Mirzapur yielded 2 (0.05%) cases. 75% (52/69) of positive phage samples were collected from sewage. All isolated phages were tested against a panel of isolates from different Salmonella Typhi genotypes circulating in Bangladesh and were found to exhibit a diverse killing spectrum, indicating that diverse bacteriophages were isolated. These results suggest an association between the presence of Typhi-specific phages in the environment and the burden of typhoid fever, and the potential of utilizing environmental phage surveillance as a low-cost tool to assist policy decisions on typhoid control.
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Affiliation(s)
- Yogesh Hooda
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | | | | | | | - Kesia E. da Silva
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | | | - Stephen P. Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jason R. Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Samir K. Saha
- Child Health Research Foundation, Dhaka, Bangladesh
- Department of Microbiology, Bangladesh Shishu Hospital and Institute, Dhaka, Bangladesh
| | - Senjuti Saha
- Child Health Research Foundation, Dhaka, Bangladesh
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Abbas A, Laverde R, Yap A, Stephens CQ, Samad L, Seyi-Olajide JO, Ameh EA, Ozgediz D, Lakhoo K, Bickler SW, Meara JG, Bundy D, Jamison DT, Klazura G, Sykes A, Philipo GS. Routine Pediatric Surgical Emergencies: Incidence, Morbidity, and Mortality During the 1st 8000 Days of Life-A Narrative Review. World J Surg 2023; 47:3419-3428. [PMID: 37341797 PMCID: PMC10694096 DOI: 10.1007/s00268-023-07097-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2023] [Indexed: 06/22/2023]
Abstract
BACKGROUND Many potentially treatable non-congenital and non-traumatic surgical conditions can occur during the first 8000 days of life and an estimated 85% of children in low- and middle-income countries (LMICs) will develop one before 15 years old. This review summarizes the common routine surgical emergencies in children from LMICs and their effects on morbidity and mortality. METHODS A narrative review was undertaken to assess the epidemiology, treatment, and outcomes of common surgical emergencies that present within the first 8000 days (or 21.9 years) of life in LMICs. Available data on pediatric surgical emergency care in LMICs were aggregated. RESULTS Outside of trauma, acute appendicitis, ileal perforation secondary to typhoid fever, and intestinal obstruction from intussusception and hernias continue to be the most common abdominal emergencies among children in LMICs. Musculoskeletal infections also contribute significantly to the surgical burden in children. These "neglected" conditions disproportionally affect children in LMICs and are due to delays in seeking care leading to late presentation and preventable complications. Pediatric surgical emergencies also necessitate heavy resource utilization in LMICs, where healthcare systems are already under strain. CONCLUSIONS Delays in care and resource limitations in LMIC healthcare systems are key contributors to the complicated and emergent presentation of pediatric surgical disease. Timely access to surgery can not only prevent long-term impairments but also preserve the impact of public health interventions and decrease costs in the overall healthcare system.
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Affiliation(s)
- Alizeh Abbas
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ruth Laverde
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Ava Yap
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
| | - Caroline Q Stephens
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Lubna Samad
- Global Surgery Programs, Interactive Research & Development, Karachi, Pakistan
| | | | - Emmanuel A Ameh
- Division of Pediatric Surgery, Department of Surgery, National Hospital, Abuja, Nigeria
| | - Doruk Ozgediz
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Kokila Lakhoo
- Department of Pediatric Surgery, University of Oxford and Oxford University Hospitals, Oxford, UK
| | - Stephen W Bickler
- Division of Pediatric Surgery, Department of Surgery, University of California San Diego School of Medicine, 9500 Gilman Drive #0739, La Jolla, San Diego, CA, 92093-0739, USA
| | - John G Meara
- Program in Global Surgery and Social Change, Harvard Medical School, Boston, MA, USA
| | - Donald Bundy
- Global Research Consortium for School Health and Nutrition, London School of Hygiene and Tropical Medicine, London, UK
| | - Dean T Jamison
- Institute for Global Health Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Greg Klazura
- Loyola University Medical Center, Chicago, IL, USA
| | - Alicia Sykes
- Naval Medical Center San Diego, San Diego, CA, USA
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Ikhimiukor OO, Oaikhena AO, Afolayan AO, Fadeyi A, Kehinde A, Ogunleye VO, Aboderin AO, Oduyebo OO, Elikwu CJ, Odih EE, Komolafe I, Argimón S, Egwuenu A, Adebiyi I, Sadare OA, Okwor T, Kekre M, Underwood A, Ihekweazu C, Aanensen DM, Okeke IN. Genomic characterization of invasive typhoidal and non-typhoidal Salmonella in southwestern Nigeria. PLoS Negl Trop Dis 2022; 16:e0010716. [PMID: 36026470 PMCID: PMC9455843 DOI: 10.1371/journal.pntd.0010716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 09/08/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022] Open
Abstract
Background Salmonellosis causes significant morbidity and mortality in Africa. Information on lineages of invasive Salmonella circulating in Nigeria is sparse. Methods Salmonella enterica isolated from blood (n = 60) and cerebrospinal fluid (CSF, n = 3) between 2016 and 2020 from five tertiary hospitals in southwest Nigeria were antimicrobial susceptibility-tested and Illumina-sequenced. Genomes were analysed using publicly-available bioinformatic tools. Results Isolates and sequence types (STs) from blood were S. Typhi [ST1, n = 1 and ST2, n = 43] and invasive non-typhoidal Salmonella (iNTS) (S. Enteritidis [ST11, n = 7], S. Durham [ST10, n = 2], S. Rissen [ST8756, n = 2], S. Chester [ST2063, n = 1], S. Dublin [ST10, n = 1], S. Infantis [ST603, n = 1], S. Telelkebir [ST8757, n = 1] and S. Typhimurium [ST313, n = 1]). S. Typhi ST2 (n = 2) and S. Adabraka ST8757 (n = 1) were recovered from CSF. Most S. Typhi belonged to genotype 3.1.1 (n = 44), carried an IncY plasmid, had several antibiotic resistance genes (ARGs) including blaTEM-1 (n = 38), aph(6)-Id (n = 32), tet(A) (n = 33), sul2 (n = 32), dfrA14 (n = 30) as well as quinolone resistance-conferring gyrA_S83Y single-nucleotide polymorphisms (n = 37). All S. Enteritidis harboured aph(3”)-Ib, blaTEM-1, catA1, dfrA7, sul1, sul2, tet(B) genes, and a single ARG, qnrB19, was detected in S. Telelkebir. Typhoidal toxins cdtB, pltA and pltB were detected in S. Typhi, Rissen, Chester, and Telelkebir. Conclusion Most invasive salmonelloses in southwest Nigeria are vaccine-preventable infections due to multidrug-resistant, West African dominant S. Typhi lineage 3.1.1. Invasive NTS serovars, including some harbouring typhoidal toxin or resistance genes, represented a third of the isolates emphasizing the need for better diagnosis and surveillance. Whole genome sequencing of 63 invasive Salmonella from 5 tertiary hospitals in Nigeria revealed multiple serovars including a dominant antibiotic-resistance-gene harbouring S. Typhi 3.1.1 genotype comprising a gyrA_S83Y and IncY plasmid. We also report invasive non-typhoidal Salmonella harbouring typhoidal toxins.
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Affiliation(s)
- Odion O. Ikhimiukor
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Anderson O. Oaikhena
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Ayorinde O. Afolayan
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Abayomi Fadeyi
- Department of Medical Microbiology and Parasitology, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Aderemi Kehinde
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Veronica O. Ogunleye
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Aaron O. Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - Oyinlola O. Oduyebo
- Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Charles J. Elikwu
- Department of Medical Microbiology, School of Basic Clinical Sciences, Benjamin Carson College of Health and Medical Sciences, Babcock University & Teaching Hospital, Ilishan-Remo, Ogun State, Nigeria
| | - Erkison Ewomazino Odih
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Ifeoluwa Komolafe
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | | | - Ini Adebiyi
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Oluwadamilola A. Sadare
- Department of Medical Microbiology, School of Basic Clinical Sciences, Benjamin Carson College of Health and Medical Sciences, Babcock University & Teaching Hospital, Ilishan-Remo, Ogun State, Nigeria
| | - Tochi Okwor
- Nigeria Centre for Disease Control, Jabi, Abuja, Nigeria
| | - Mihir Kekre
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | | | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Iruka N. Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
- * E-mail:
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