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Zhu J, Xu L, Zhang J, Wang Y, Yu H, Hao C, Cheng G, Liu D, Chen M. High catalytic nickel-platinum nanozyme enhancing colorimetric detection of Salmonella Typhimurium in milk. J Dairy Sci 2024:S0022-0302(24)01073-7. [PMID: 39154726 DOI: 10.3168/jds.2024-25111] [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: 05/02/2024] [Accepted: 07/18/2024] [Indexed: 08/20/2024]
Abstract
Colorimetric qualitative and sensitive quantitative detection of Salmonella Typhimurium (S. Typhimurium) holds significant importance for ensuring food safety and preventing foodborne illnesses. In the study, an ultra-high catalytic activity and biocompatible nickel-platinum nanoparticle (NiPt NP) nanozyme is successful synthesized to prepare a NLISA strategy for the detection of S. Typhimurium. The synthesized NiPt NPs exhibit high oxidase-like catalytic efficiency, with a Michaelis constant (Km) of 0.493 mM, similar to that of natural horseradish peroxidase (HRP). The maximal reaction velocity (Vmax) was determined to be 1.97 × 10-7 M·s-1 exhibiting a 1.97-fold higher than that of the HRP (1.0 × 10-7 M·s-1). Meanwhile, the antibody employed in this NiPt NPs-based NLISA exhibits exceptional capture efficacy, generating a stable immune complex with S. Typhimurium. The NiPt NPs-based NLISA demonstrates sensitivity, specificity, convenience, and cost-efficiency for the detection of S. Typhimurium. Under optimal conditions, this NiPt NPs-based NLISA demonstrates a quantitative range of 103∼106 cfu/mL with a detection limit as low as 103 cfu/mL. A single-blind experimental testing detects different concentrations of S. Typhimurium spiked skim milk, indicating the application potential of the proposed NLISA in real samples. In all, this research provides novel insights into the synthesis of nanozymes with excellent catalytic activity and their applications in S. Typhimurium biosensing.
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Affiliation(s)
- Jie Zhu
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221006, China
| | - Lingyue Xu
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221006, China
| | - Junlin Zhang
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221006, China
| | - Yuxin Wang
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221006, China
| | - Hongyue Yu
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221006, China
| | - Chuanchuan Hao
- The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221004, P.R. China; School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, PR China
| | - Guohui Cheng
- The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221004, P.R. China; School of Pharmacy, Xuzhou Medical University, Xuzhou 221004, PR China
| | - Daofeng Liu
- Jiangxi Province Key Laboratory of Diagnosing and Tracing of Foodborne Disease, Jiangxi Province Center for Disease Control and Prevention, 555 East Beijing Road, Nanchang 330029, China.
| | - Minghui Chen
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221006, China; The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221004, P.R. China.
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2
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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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3
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Onken A, Moyo S, Miraji MK, Bohlin J, Marijani M, Manyahi J, Kibwana KO, Müller F, Jenum PA, Abeid KA, Reimers M, Langeland N, Mørch K, Blomberg B. Predominance of multidrug-resistant Salmonella Typhi genotype 4.3.1 with low-level ciprofloxacin resistance in Zanzibar. PLoS Negl Trop Dis 2024; 18:e0012132. [PMID: 38630840 PMCID: PMC11057722 DOI: 10.1371/journal.pntd.0012132] [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: 10/06/2023] [Revised: 04/29/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Typhoid fever is a common cause of febrile illness in low- and middle-income countries. While multidrug-resistant (MDR) Salmonella Typhi (S. Typhi) has spread globally, fluoroquinolone resistance has mainly affected Asia. METHODS Consecutively, 1038 blood cultures were obtained from patients of all age groups with fever and/or suspicion of serious systemic infection admitted at Mnazi Mmoja Hospital, Zanzibar in 2015-2016. S. Typhi were analyzed with antimicrobial susceptibility testing and with short read (61 strains) and long read (9 strains) whole genome sequencing, including three S. Typhi strains isolated in a pilot study 2012-2013. RESULTS Sixty-three S. Typhi isolates (98%) were MDR carrying blaTEM-1B, sul1 and sul2, dfrA7 and catA1 genes. Low-level ciprofloxacin resistance was detected in 69% (43/62), with a single gyrase mutation gyrA-D87G in 41 strains, and a single gyrA-S83F mutation in the non-MDR strain. All isolates were susceptible to ceftriaxone and azithromycin. All MDR isolates belonged to genotype 4.3.1 lineage I (4.3.1.1), with the antimicrobial resistance determinants located on a composite transposon integrated into the chromosome. Phylogenetically, the MDR subgroup with ciprofloxacin resistance clusters together with two external isolates. CONCLUSIONS We report a high rate of MDR and low-level ciprofloxacin resistant S. Typhi circulating in Zanzibar, belonging to genotype 4.3.1.1, which is widespread in Southeast Asia and African countries and associated with low-level ciprofloxacin resistance. Few therapeutic options are available for treatment of typhoid fever in the study setting. Surveillance of the prevalence, spread and antimicrobial susceptibility of S. Typhi can guide treatment and control efforts.
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Affiliation(s)
- Annette Onken
- Department of Clinical Science, University of Medicine, Bergen, Norway
- National Centre for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
- Department of Microbiology, Vestre Viken Hospital Trust, Drammen, Norway
| | - Sabrina Moyo
- Department of Clinical Science, University of Medicine, Bergen, Norway
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - Jon Bohlin
- Department of methods and analysis, Section of modelling and bioinformatics, Domain of Infection Control, Oslo, Norway
- Center for Fertility and Health analysis, Norwegian Institute of Public Health, Oslo, Norway
| | - Msafiri Marijani
- Pathology Laboratory Department, Mnazi Mmoja Hospital, Zanzibar, Tanzania
| | - Joel Manyahi
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Kibwana Omar Kibwana
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Fredrik Müller
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Pål A. Jenum
- Department of Microbiology, Vestre Viken Hospital Trust, Drammen, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Khamis Ali Abeid
- Department of Pediatrics, Mnazi Mmoja Hospital, Zanzibar, Tanzania
| | - Marianne Reimers
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
| | - Nina Langeland
- Department of Clinical Science, University of Medicine, Bergen, Norway
- National Centre for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Kristine Mørch
- Department of Clinical Science, University of Medicine, Bergen, Norway
- National Centre for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Bjørn Blomberg
- Department of Clinical Science, University of Medicine, Bergen, Norway
- National Centre for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
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4
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Garcia JF, Morales-Cruz A, Cochetel N, Minio A, Figueroa-Balderas R, Rolshausen PE, Baumgartner K, Cantu D. Comparative Pangenomic Insights into the Distinct Evolution of Virulence Factors Among Grapevine Trunk Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:127-142. [PMID: 37934016 DOI: 10.1094/mpmi-09-23-0129-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
The permanent organs of grapevines (Vitis vinifera L.), like those of other woody perennials, are colonized by various unrelated pathogenic ascomycete fungi secreting cell wall-degrading enzymes and phytotoxic secondary metabolites that contribute to host damage and disease symptoms. Trunk pathogens differ in the symptoms they induce and the extent and speed of damage. Isolates of the same species often display a wide virulence range, even within the same vineyard. This study focuses on Eutypa lata, Neofusicoccum parvum, and Phaeoacremonium minimum, causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced 50 isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examination of genomic diversity and pangenome structure, we analyzed intraspecific conservation and variability of putative virulence factors, focusing on functions under positive selection and recent gene family dynamics of contraction and expansion. Our findings reveal contrasting distributions of putative virulence factors in the core, dispensable, and private genomes of each pangenome. For example, carbohydrate active enzymes (CAZymes) were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes of E. lata and P. minimum. The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthase genes in E. lata and P. minimum, glycosyltransferases in N. parvum). Our findings underscore the complexity of the genomic architecture in each species and provide insights into their adaptive strategies, enhancing our understanding of the underlying mechanisms of virulence. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jadran F Garcia
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, U.S.A
| | - Noé Cochetel
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Philippe E Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, U.S.A
| | - Kendra Baumgartner
- Crops Pathology and Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Davis, CA, U.S.A
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
- Genome Center, University of California, Davis, Davis, CA, U.S.A
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5
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Hajra D, Nair AV, Chakravortty D. Decoding the invasive nature of a tropical pathogen of concern: The invasive non-Typhoidal Salmonella strains causing host-restricted extraintestinal infections worldwide. Microbiol Res 2023; 277:127488. [PMID: 37716125 DOI: 10.1016/j.micres.2023.127488] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/18/2023]
Abstract
Invasive-Non-Typhoidal Salmonella (iNTS) are the major cause of health concern in the low-income, under-developed nations in Africa and Asia that lack proper sanitation facilities. Around 5% of the NTS cases give rise to invasive, extraintestinal diseases leading to focal infections like osteomyelitis, meningitis, osteoarthritis, endocarditis and neonatal sepsis. iNTS serovars like S. Typhimurium, S. Enteritidis, S. Dublin, S. Choleraesuis show a greater propensity to become invasive than others which hints at the genetic basis of their emergence. The major risk factors attributing to the invasive diseases include immune-compromised individuals having co-infection with malaria or HIV, or suffering from malnutrition. The rampant use of antibiotics leading to the emergence of multi-drug resistant strains poses a great challenge in disease management. An extensive understanding of the iNTS pathogenesis and its epidemiology will open up avenues for the development of new vaccination and therapeutic strategies to restrict the spread of this neglected disease.
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Affiliation(s)
- Dipasree Hajra
- Department of Microbiology & Cell Biology, Indian Institute of Science, India
| | - Abhilash Vijay Nair
- Department of Microbiology & Cell Biology, Indian Institute of Science, India
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6
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Carey ME, Dyson ZA, Ingle DJ, Amir A, Aworh MK, Chattaway MA, Chew KL, Crump JA, Feasey NA, Howden BP, Keddy KH, Maes M, Parry CM, Van Puyvelde S, Webb HE, Afolayan AO, Alexander AP, Anandan S, Andrews JR, Ashton PM, Basnyat B, Bavdekar A, Bogoch II, Clemens JD, da Silva KE, De A, de Ligt J, Diaz Guevara PL, Dolecek C, Dutta S, Ehlers MM, Francois Watkins L, Garrett DO, Godbole G, Gordon MA, Greenhill AR, Griffin C, Gupta M, Hendriksen RS, Heyderman RS, Hooda Y, Hormazabal JC, Ikhimiukor OO, Iqbal J, Jacob JJ, Jenkins C, Jinka DR, John J, Kang G, Kanteh A, Kapil A, Karkey A, Kariuki S, Kingsley RA, Koshy RM, Lauer AC, Levine MM, Lingegowda RK, Luby SP, Mackenzie GA, Mashe T, Msefula C, Mutreja A, Nagaraj G, Nagaraj S, Nair S, Naseri TK, Nimarota-Brown S, Njamkepo E, Okeke IN, Perumal SPB, Pollard AJ, Pragasam AK, Qadri F, Qamar FN, Rahman SIA, Rambocus SD, Rasko DA, Ray P, Robins-Browne R, Rongsen-Chandola T, Rutanga JP, Saha SK, Saha S, Saigal K, Sajib MSI, Seidman JC, Shakya J, Shamanna V, Shastri J, Shrestha R, Sia S, Sikorski MJ, Singh A, Smith AM, Tagg KA, Tamrakar D, Tanmoy AM, Thomas M, Thomas MS, Thomsen R, Thomson NR, Tupua S, Vaidya K, Valcanis M, Veeraraghavan B, Weill FX, Wright J, Dougan G, Argimón S, Keane JA, Aanensen DM, Baker S, Holt KE. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife 2023; 12:e85867. [PMID: 37697804 PMCID: PMC10506625 DOI: 10.7554/elife.85867] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/02/2023] [Indexed: 09/13/2023] Open
Abstract
Background The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. Funding No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).
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Affiliation(s)
- Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Zoe A Dyson
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Danielle J Ingle
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
| | | | - Mabel K Aworh
- Nigeria Field Epidemiology and Laboratory Training ProgrammeAbujaNigeria
- College of Veterinary Medicine, North Carolina State UniversityRaleighUnited States
| | | | - Ka Lip Chew
- National University HospitalSingaporeSingapore
| | - John A Crump
- Centre for International Health, University of OtagoDunedinNew Zealand
| | - Nicholas A Feasey
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
- Malawi-Liverpool Wellcome Programme, Kamuzu University of Health SciencesBlantyreMalawi
| | - Benjamin P Howden
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne at Doherty Institute for Infection and ImmunityMelbourneAustralia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Christopher M Parry
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
| | - Sandra Van Puyvelde
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- University of AntwerpAntwerpBelgium
| | - Hattie E Webb
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Ayorinde Oluwatobiloba Afolayan
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Shalini Anandan
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Philip M Ashton
- Malawi-Liverpool Wellcome ProgrammeBlantyreMalawi
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Buddha Basnyat
- Oxford University Clinical Research Unit NepalKathmanduNepal
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of TorontoTorontoCanada
| | - John D Clemens
- International Vaccine InstituteSeoulRepublic of Korea
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
- UCLA Fielding School of Public HealthLos AngelesUnited States
- Korea UniversitySeoulRepublic of Korea
| | - Kesia Esther da Silva
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Anuradha De
- Topiwala National Medical CollegeMumbaiIndia
| | - Joep de Ligt
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | | | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Shanta Dutta
- ICMR - National Institute of Cholera & Enteric DiseasesKolkataIndia
| | - Marthie M Ehlers
- Department of Medical Microbiology, Faculty of Health Sciences, University of PretoriaPretoriaSouth Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory ServicePretoriaSouth Africa
| | | | | | - Gauri Godbole
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | - Melita A Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Andrew R Greenhill
- Federation University AustraliaChurchillAustralia
- Papua New Guinea Institute of Medical ResearchGorokaPapua New Guinea
| | - Chelsey Griffin
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Madhu Gupta
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | | | - Robert S Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | - Juan Carlos Hormazabal
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomedico, Instituto de Salud Publica de Chile (ISP)SantiagoChile
| | - Odion O Ikhimiukor
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Claire Jenkins
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | - Jacob John
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Gagandeep Kang
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Abdoulie Kanteh
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Arti Kapil
- All India Institute of Medical SciencesDelhiIndia
| | | | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research InstituteNairobiKenya
| | | | | | - AC Lauer
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Myron M Levine
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
| | | | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Grant Austin Mackenzie
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Tapfumanei Mashe
- National Microbiology Reference LaboratoryHarareZimbabwe
- World Health OrganizationHarareZimbabwe
| | | | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | | | - Satheesh Nair
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | | | | | - Iruka N Okeke
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of OxfordOxfordUnited Kingdom
- The NIHR Oxford Biomedical Research CentreOxfordUnited Kingdom
| | | | - Firdausi Qadri
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
| | - Farah N Qamar
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | | | - Savitra Devi Rambocus
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - David A Rasko
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | - Pallab Ray
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | - Roy Robins-Browne
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
- Murdoch Children’s Research Institute, Royal Children’s HospitalParkvilleAustralia
| | | | | | | | | | | | - Mohammad Saiful Islam Sajib
- Child Health Research FoundationDhakaBangladesh
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of GlasgowGlasgowUnited Kingdom
| | | | - Jivan Shakya
- Dhulikhel HospitalDhulikhelNepal
- Institute for Research in Science and TechnologyKathmanduNepal
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | - Jayanthi Shastri
- Topiwala National Medical CollegeMumbaiIndia
- Kasturba Hospital for Infectious DiseasesMumbaiIndia
| | - Rajeev Shrestha
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | - Sonia Sia
- Research Institute for Tropical Medicine, Department of HealthMuntinlupa CityPhilippines
| | - Michael J Sikorski
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | | | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable DiseasesJohannesburgSouth Africa
| | - Kaitlin A Tagg
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Dipesh Tamrakar
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | | | - Maria Thomas
- Christian Medical College, LudhianaLudhianaIndia
| | | | | | | | - Siaosi Tupua
- Ministry of Health, Government of SamoaApiaSamoa
| | | | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | | | - Jackie Wright
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Jacqueline A Keane
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
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7
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Sim EM, Wang Q, Howard P, Kim R, Lim L, Hope K, Sintchenko V. Persistent Salmonella enterica serovar Typhi sub-populations within host interrogated by whole genome sequencing and metagenomics. PLoS One 2023; 18:e0289070. [PMID: 37611017 PMCID: PMC10446203 DOI: 10.1371/journal.pone.0289070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/10/2023] [Indexed: 08/25/2023] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi) causes typhoid fever and, in some cases, chronic carriage after resolution of acute disease. This study examined sequential isolates of S. Typhi from a single host with persistent asymptomatic infection. These isolates, along with another S. Typhi isolate recovered from a household contact with typhoid fever, were subjected to whole genome sequencing and analysis. In addition, direct sequencing of the bile fluid from the host with persistent infection was also performed. Comparative analysis of isolates revealed three sub-populations of S. Typhi with distinct genetic patterns. Metagenomic sequencing recognised only two of the three sub-populations within the bile fluid. The detection and investigation of insertion sequences IS10R and associated deletions complemented analysis of single nucleotide polymorphisms. These findings improve our understanding of within-host dynamics of S. Typhi in cases of persistent infection and inform epidemiological investigations of transmission events associated with chronic carriers.
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Affiliation(s)
- Eby M. Sim
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology- Public Health, Westmead Hospital, Westmead, New South Wales, Australia
| | - Qinning Wang
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
| | - Peter Howard
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
| | - Rady Kim
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
| | - Ling Lim
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
| | - Kirsty Hope
- Health Protection, New South Wales Ministry of Health, North Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology- Public Health, Westmead Hospital, Westmead, New South Wales, Australia
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8
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Fu Y, M’ikanatha NM, Dudley EG. Whole-Genome Subtyping Reveals Population Structure and Host Adaptation of Salmonella Typhimurium from Wild Birds. J Clin Microbiol 2023; 61:e0184722. [PMID: 37249426 PMCID: PMC10281135 DOI: 10.1128/jcm.01847-22] [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: 12/14/2022] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
Within-host evolution of bacterial pathogens can lead to host-associated variants of the same species or serovar. Identification and characterization of closely related variants from diverse host species are crucial to public health and host-pathogen adaptation research. However, the work remained largely underexplored at a strain level until the advent of whole-genome sequencing (WGS). Here, we performed WGS-based subtyping and analyses of Salmonella enterica serovar Typhimurium (n = 787) from different wild birds across 18 countries over a 75-year period. We revealed seven avian host-associated S. Typhimurium variants/lineages. These lineages emerged globally over short timescales and presented genetic features distinct from S. Typhimurium lineages circulating among humans and domestic animals. We further showed that, in terms of virulence, host adaptation of these variants was driven by genome degradation. Our results provide a snapshot of the population structure and genetic diversity of S. Typhimurium within avian hosts. We also demonstrate the value of WGS-based subtyping and analyses in unravelling closely related variants at the strain level.
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Affiliation(s)
- Yezhi Fu
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | | | - Edward G. Dudley
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- E. coli Reference Center, The Pennsylvania State University, University Park, Pennsylvania, USA
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9
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Vanderslott S, Kumar S, Adu-Sarkodie Y, Qadri F, Zellweger RM. Typhoid Control in an Era of Antimicrobial Resistance: Challenges and Opportunities. Open Forum Infect Dis 2023; 10:S47-S52. [PMID: 37274528 PMCID: PMC10236512 DOI: 10.1093/ofid/ofad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
Historically, typhoid control has been achieved with water and sanitation interventions. Today, in an era of rising antimicrobial resistance (AMR), two World Health Organization-prequalified vaccines are available to accelerate control in the shorter term. Meanwhile, water and sanitation interventions could be implemented in the longer term to sustainably prevent typhoid in low- and middle-income countries. This article first approaches typhoid control from a historical perspective, subsequently presents how vaccination could complement water and sanitation activities, and finally discusses the challenges and opportunities for impactful control of typhoid infection. It also addresses data blind spots and knowledge gaps to focus on for typhoid control and to ultimately progress towards elimination. This article presents a synthesis of discussions held in December 2021 during a roundtable session at the "12th International Conference on Typhoid and Other Invasive Salmonelloses".
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Affiliation(s)
- Samantha Vanderslott
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom and NIHR Oxford Biomedical Research Centre, Oxford, Oxfordshire, United Kingdom
| | - Supriya Kumar
- Enteric and Diarrheal Diseases, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Yaw Adu-Sarkodie
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Raphaël M Zellweger
- Correspondence: Raphaël M. Zellweger, MSc, PhD, Epidemiology , Public Health & Impact, International Vaccine Institute, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea. ()
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10
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Li X, Cao H, Chen JHK, Ng YZ, Fung KK, Cheng VCC, Ho PL. Genomic Investigation of Salmonella Typhi in Hong Kong Revealing the Predominance of Genotype 3.2.2 and the First Case of an Extensively Drug-Resistant H58 Genotype. Microorganisms 2023; 11:microorganisms11030667. [PMID: 36985239 PMCID: PMC10058776 DOI: 10.3390/microorganisms11030667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023] Open
Abstract
Typhoid fever is a notable disease in Hong Kong. We noticed two local cases of typhoid fever caused by Salmonella Typhi within a two-week period in late 2022, which had no apparent epidemiological linkage except for residing in the same region of Hong Kong. A phylogenetic study of Salmonella Typhi isolates from Hong Kong Island from 2020 to 2022 was performed, including a whole-genome analysis, the typing of plasmids, and the analysis of antibiotic-resistance genes (ARGs), to identify the dominant circulating strain and the spread of ARGs. A total of seven isolates, from six local cases and an imported case, were identified from positive blood cultures in two hospitals in Hong Kong. Five antibiotic-sensitive strains of genotype 3.2.2 were found, which clustered with another 30 strains originating from Southeast Asia. Whole-genome sequencing revealed clonal transmission between the two index cases. The remaining two local cases belong to genotype 2.3.4 and genotype 4.3.1.1.P1 (also known as the H58 lineage). The genotype 4.3.1.1.P1 strain has an extensively drug-resistant (XDR) phenotype (co-resistance to ampicillin, chloramphenicol, ceftriaxone, ciprofloxacin, and co-trimoxazole). Although the majority of local strains belong to the non-H58 genotype 3.2.2 with a low degree of antibiotic resistance, the introduction of XDR strains with the global dissemination of the H58 lineage remains a concern.
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Affiliation(s)
- Xin Li
- Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Department of Microbiology, Queen Mary Hospital, Hong Kong SAR, China
| | - Huiluo Cao
- Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | | | - Yuey-Zhun Ng
- Department of Microbiology, Queen Mary Hospital, Hong Kong SAR, China
| | - Ka-Kin Fung
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong SAR, China
| | | | - Pak-Leung Ho
- Department of Microbiology, and Carol Yu Centre for Infection, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Department of Microbiology, Queen Mary Hospital, Hong Kong SAR, China
- Correspondence:
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11
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Gupta MK, Vadde R. Next-generation development and application of codon model in evolution. Front Genet 2023; 14:1091575. [PMID: 36777719 PMCID: PMC9911445 DOI: 10.3389/fgene.2023.1091575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
To date, numerous nucleotide, amino acid, and codon substitution models have been developed to estimate the evolutionary history of any sequence/organism in a more comprehensive way. Out of these three, the codon substitution model is the most powerful. These models have been utilized extensively to detect selective pressure on a protein, codon usage bias, ancestral reconstruction and phylogenetic reconstruction. However, due to more computational demanding, in comparison to nucleotide and amino acid substitution models, only a few studies have employed the codon substitution model to understand the heterogeneity of the evolutionary process in a genome-scale analysis. Hence, there is always a question of how to develop more robust but less computationally demanding codon substitution models to get more accurate results. In this review article, the authors attempted to understand the basis of the development of different types of codon-substitution models and how this information can be utilized to develop more robust but less computationally demanding codon substitution models. The codon substitution model enables to detect selection regime under which any gene or gene region is evolving, codon usage bias in any organism or tissue-specific region and phylogenetic relationship between different lineages more accurately than nucleotide and amino acid substitution models. Thus, in the near future, these codon models can be utilized in the field of conservation, breeding and medicine.
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12
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Burrows H, Antillón M, Gauld JS, Kim JH, Mogasale V, Ryckman T, Andrews JR, Lo NC, Pitzer VE. Comparison of model predictions of typhoid conjugate vaccine public health impact and cost-effectiveness. Vaccine 2023; 41:965-975. [PMID: 36586741 PMCID: PMC9880559 DOI: 10.1016/j.vaccine.2022.12.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/31/2022]
Abstract
Models are useful to inform policy decisions on typhoid conjugate vaccine (TCV) deployment in endemic settings. However, methodological choices can influence model-predicted outcomes. To provide robust estimates for the potential public health impact of TCVs that account for structural model differences, we compared four dynamic and one static mathematical model of typhoid transmission and vaccine impact. All models were fitted to a common dataset of age-specific typhoid fever cases in Kolkata, India. We evaluated three TCV strategies: no vaccination, routine vaccination at 9 months of age, and routine vaccination at 9 months with a one-time catch-up campaign (ages 9 months to 15 years). The primary outcome was the predicted percent reduction in symptomatic typhoid cases over 10 years after vaccine introduction. For three models with economic analyses (Models A-C), we also compared the incremental cost-effectiveness ratios (ICERs), calculated as the incremental cost (US$) per disability-adjusted life-year (DALY) averted. Routine vaccination was predicted to reduce symptomatic cases by 10-46 % over a 10-year time horizon under an optimistic scenario (95 % initial vaccine efficacy and 19-year mean duration of protection), and by 2-16 % under a pessimistic scenario (82 % initial efficacy and 6-year mean protection). Adding a catch-up campaign predicted a reduction in incidence of 36-90 % and 6-35 % in the optimistic and pessimistic scenarios, respectively. Vaccine impact was predicted to decrease as the relative contribution of chronic carriers to transmission increased. Models A-C all predicted routine vaccination with or without a catch-up campaign to be cost-effective compared to no vaccination, with ICERs varying from $95-789 per DALY averted; two models predicted the ICER of routine vaccination alone to be greater than with the addition of catch-up campaign. Despite differences in model-predicted vaccine impact and cost-effectiveness, routine vaccination plus a catch-up campaign is likely to be impactful and cost-effective in high incidence settings such as Kolkata.
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Affiliation(s)
- Holly Burrows
- Yale School of Public Health, Yale University, New Haven, CT, USA.
| | - Marina Antillón
- Yale School of Public Health, Yale University, New Haven, CT, USA; Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Jillian S Gauld
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Jong-Hoon Kim
- Public Health, Access, and Vaccine Epidemiology (PAVE) Unit, International Vaccine Institute, Seoul, Republic of Korea
| | - Vittal Mogasale
- Policy and Economic Research Department, International Vaccine Institute, Seoul 08826, Republic of Korea
| | - Theresa Ryckman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nathan C Lo
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
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13
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Genome-Wide Searching Single Nucleotide-Polymorphisms (SNPs) and SNPs-Targeting a Multiplex Primer for Identification of Common Salmonella Serotypes. Pathogens 2022; 11:pathogens11101075. [PMID: 36297133 PMCID: PMC9611365 DOI: 10.3390/pathogens11101075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 12/04/2022] Open
Abstract
A rapid and high-quality single-nucleotide polymorphisms (SNPs)-based method was developed to improve detection and reduce salmonellosis burden. In this study, whole-genome sequence (WGS) was used to investigate SNPs, the most common genetic marker for identifying bacteria. SNP-sites encompassing 15 sets of primers (666–863 bp) were selected and used to amplify the target Salmonella serovar strains, and the amplified products were sequenced. The prevalent Salmonella enterica subspecies enterica serovars, including Typhimurium; Enteritidis, Agona, enterica, Typhi, and Abony, were amplified and sequenced. The amplified sequences of six Salmonella serovars with 15 sets of SNP-sites encompassing primers were aligned, explored SNPs, and SNPs-carrying primers (23 sets) were designed to develop a multiplex PCR marker (m-PCR). Each primer exists in at least two SNPs bases at the 3′ end of each primer, such as one was wild, and another was a mismatched base by transition or transversion mutation. Thus, twenty-three sets of SNP primers (242–670 bp), including 13 genes (SBG, dedA, yacG, mrcB, mesJ, metN, rihA/B, modA, hutG, yehX, ybiY, moeB, and sopA), were developed for PCR confirmation of target Salmonella serovar strains. Finally, the SNPs in four genes, including fliA gene (S. Enteritidis), modA (S. Agona and S. enterica), sopA (S. Abony), and mrcB (S. Typhimurium and S. Typhi), were used for detection markers of six target Salmonella serotypes. We developed an m-PCR primer set in which Salmonella serovars were detected in a single reaction. Nevertheless, m-PCR was validated with 21 Salmonella isolates (at least one isolate was taken from one positive animal fecal, and n = 6 reference Salmonella strains) and non-Salmonella bacteria isolates. The SNP-based m-PCR method would identify prevalent Salmonella serotypes, minimize the infection, and control outbreaks.
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14
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McCann N, Scott P, Parry CM, Brown M. Antimicrobial agents for the treatment of enteric fever chronic carriage: A systematic review. PLoS One 2022; 17:e0272043. [PMID: 35905082 PMCID: PMC9337697 DOI: 10.1371/journal.pone.0272043] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 07/13/2022] [Indexed: 11/18/2022] Open
Abstract
Background
Chronic carriage of S. Typhi or S. Paratyphi is an important source of enteric fever transmission. Existing guidance and treatment options for this condition are limited. This systematic review aims to assess the evidence concerning the efficacy of different antimicrobials in treating enteric fever chronic carriage.
Methods
We searched major bibliographic databases using relevant keywords between 1946 and September 2021. We included all interventional studies that included patients with confirmed enteric fever chronic carriage and deployed an antimicrobial that remains in clinical practice today. Case reports and case series of under 10 patients were excluded. Two reviewers screened abstracts, selected articles for final inclusion and quality-assessed the included studies for risk of bias. Extracted data was analysed, with pooling of data and eradication rates for each antimicrobial calculated. As only one randomised controlled trial was identified, no meta-analysis was performed.
Results
Of the 593 papers identified by the initial search, a total of eight studies met the inclusion criteria and were included in the systematic review. Evidence was identified for the use of fluoroquinolones and amoxicillin/ampicillin in the treatment for enteric fever chronic carriage. Fluoroquinolones were superior to amoxicillin/ampicillin with 92% of patients achieving eradication after one antimicrobial course compared to 68% (p = 0.02). The quality of included studies was poor, and all were carried out before 1990.
Conclusion
This review identified fluoroquinolones and amoxicillin/ampicillin as treatment options for enteric fever chronic carriage, with fluoroquinolones the more effective option. However, this evidence pre-dates rises in antimicrobial resistance in enteric fever and therefore the significance of these findings to today’s practice is unclear. Further research is needed to investigate whether these antimicrobials remain appropriate treatment options or whether alternative interventions are more effective.
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Affiliation(s)
- Naina McCann
- UCL Faculty of Population Health Sciences, University College London (UCL), London, United Kingdom
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, United Kingdom
- * E-mail: ,
| | - Peter Scott
- UCL Faculty of Population Health Sciences, University College London (UCL), London, United Kingdom
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Christopher M. Parry
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Alder Hey Children’s NHS Foundation Trust, Liverpool, United Kingdom
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Michael Brown
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, United Kingdom
- Clinical Research Dept, London School of Hygiene & Tropical Medicine, London, United Kingdom
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15
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Davies MR, Duchene S, Valcanis M, Jenkins AP, Jenney A, Rosa V, Hayes AJ, Strobel AG, McIntyre L, Lacey JA, Klemm EJ, Wong VK, Sahukhan A, Thomson H, Page A, Hocking D, Wang N, Tudravu L, Rafai E, Dougan G, Howden BP, Crump JA, Mulholland K, Strugnell RA. Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2022; 24:100488. [PMID: 35769175 PMCID: PMC9234096 DOI: 10.1016/j.lanwpc.2022.100488] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Typhoid fever is endemic in some Pacific Island Countries including Fiji and Samoa yet genomic surveillance is not routine in such settings. Previous studies suggested imports of the global H58 clade of Salmonella enterica var Typhi (Salmonella Typhi) contribute to disease in these countries which, given the MDR potential of H58, does not auger well for treatment. The objective of the study was to define the genomic epidemiology of Salmonella Typhi in Fiji. METHODS Genomic sequencing approaches were implemented to study the distribution of 255 Salmonella Typhi isolates from the Central Division of Fiji. We augmented epidemiological surveillance and Bayesian phylogenomic approaches with a multi-year typhoid case-control study to define geospatial patterns among typhoid cases. FINDINGS Genomic analyses showed Salmonella Typhi from Fiji resolved into 2 non-H58 genotypes with isolates from the two dominant ethnic groups, the Indigenous (iTaukei) and non-iTaukei genetically indistinguishable. Low rates of international importation of clones was observed and overall, there were very low levels an antibiotic resistance within the endemic Fijian typhoid genotypes. Genomic epidemiological investigations were able to identify previously unlinked case clusters. Bayesian phylodynamic analyses suggested that genomic variation within the larger endemic Salmonella Typhi genotype expanded at discreet times, then contracted. INTERPRETATION Cyclones and flooding drove 'waves' of typhoid outbreaks in Fiji which, through population aggregation, poor sanitation and water safety, and then mobility of the population, spread clones more widely. Minimal international importations of new typhoid clones suggest that targeted local intervention strategies may be useful in controlling endemic typhoid infection. These findings add to our understanding of typhoid transmission networks in an endemic island country with broad implications, particularly across Pacific Island Countries. FUNDING This work was supported by the Coalition Against Typhoid through the Bill and Melinda Gates Foundation [grant number OPP1017518], the Victorian Government, the National Health and Medical Research Council Australia, the Australian Research Council, and the Fiji Ministry of Health and Medical Services.
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Affiliation(s)
- Mark R. Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Aaron P. Jenkins
- Centre for Ecosystem Management, Edith Cowan University, Western Australia
- School of Public Health, University of Sydney, Sydney, NSW, Australia
| | - Adam Jenney
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
- College of Medicine, Nursing and Health Sciences, Fiji National University, Suva, Fiji
| | - Varanisese Rosa
- Fiji Centre for Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Andrew J. Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Aneley Getahun Strobel
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Liam McIntyre
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Jake A. Lacey
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Victoria, Australia
| | - Elizabeth J. Klemm
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Vanessa K. Wong
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Aalisha Sahukhan
- Fiji Centre for Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Helen Thomson
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
| | - Andrew Page
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom
| | - Dianna Hocking
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | | | - Eric Rafai
- Fiji Ministry of Health and Medical Services, Suva, Fiji
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - John A. Crump
- Centre for International Health, Otago Medical School, University of Otago, Dunedin, New Zealand
| | - Kim Mulholland
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
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16
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Pan J, Li W, Ni J, Wu K, Konigsberg I, Rivera CE, Tincher C, Gregory C, Zhou X, Doak TG, Lee H, Wang Y, Gao X, Lynch M, Long H. Rates of Mutations and Transcript Errors in the Foodborne Pathogen Salmonella enterica subsp. enterica. Mol Biol Evol 2022; 39:msac081. [PMID: 35446958 PMCID: PMC9040049 DOI: 10.1093/molbev/msac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Because errors at the DNA level power pathogen evolution, a systematic understanding of the rate and molecular spectra of mutations could guide the avoidance and treatment of infectious diseases. We thus accumulated tens of thousands of spontaneous mutations in 768 repeatedly bottlenecked lineages of 18 strains from various geographical sites, temporal spread, and genetic backgrounds. Entailing over ∼1.36 million generations, the resultant data yield an average mutation rate of ∼0.0005 per genome per generation, with a significant within-species variation. This is one of the lowest bacterial mutation rates reported, giving direct support for a high genome stability in this pathogen resulting from high DNA-mismatch-repair efficiency and replication-machinery fidelity. Pathogenicity genes do not exhibit an accelerated mutation rate, and thus, elevated mutation rates may not be the major determinant for the diversification of toxin and secretion systems. Intriguingly, a low error rate at the transcript level is not observed, suggesting distinct fidelity of the replication and transcription machinery. This study urges more attention on the most basic evolutionary processes of even the best-known human pathogens and deepens the understanding of their genome evolution.
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Affiliation(s)
- Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Weiyi Li
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Kun Wu
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Iain Konigsberg
- Division of Biomedical Informatics & Personalized Medicine, Department of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Caitlyn E. Rivera
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Clayton Tincher
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Colin Gregory
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Xia Zhou
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Thomas G. Doak
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47405, USA
| | - Heewook Lee
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ 85281, USA
| | - Yan Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of Life Science, Shandong University, No. 72 Binhai Road, Qingdao, Shandong Province 266237, China
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, 5 Yushan Road, Qingdao, Shandong Province 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
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17
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Foster N, Tang Y, Berchieri A, Geng S, Jiao X, Barrow P. Revisiting Persistent Salmonella Infection and the Carrier State: What Do We Know? Pathogens 2021; 10:1299. [PMID: 34684248 PMCID: PMC8537056 DOI: 10.3390/pathogens10101299] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
One characteristic of the few Salmonella enterica serovars that produce typhoid-like infections is that disease-free persistent infection can occur for months or years in a small number of individuals post-convalescence. The bacteria continue to be shed intermittently which is a key component of the epidemiology of these infections. Persistent chronic infection occurs despite high levels of circulating specific IgG. We have reviewed the information on the basis for persistence in S. Typhi, S. Dublin, S. Gallinarum, S. Pullorum, S. Abortusovis and also S. Typhimurium in mice as a model of persistence. Persistence appears to occur in macrophages in the spleen and liver with shedding either from the gall bladder and gut or the reproductive tract. The involvement of host genetic background in defining persistence is clear from studies with the mouse but less so with human and poultry infections. There is increasing evidence that the organisms (i) modulate the host response away from the typical Th1-type response normally associated with immune clearance of an acute infection to Th2-type or an anti-inflammatory response, and that (ii) the bacteria modulate transformation of macrophage from M1 to M2 type. The bacterial factors involved in this are not yet fully understood. There are early indications that it might be possible to remodulate the response back towards a Th1 response by using cytokine therapy.
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Affiliation(s)
- Neil Foster
- SRUC Aberdeen Campus, Craibstone Estate, Ferguson Building, Aberdeen AB21 9YA, UK
| | - Ying Tang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518055, China;
| | - Angelo Berchieri
- Departamento de Patologia Veterinária, Faculdade de Ciências Agrárias e Veterinárias, Univ Estadual Paulista, Via de Acesso Paulo Donato Castellane, s/n, 14884-900 Jaboticabal, SP, Brazil;
| | - Shizhong Geng
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (S.G.); (X.J.)
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (S.G.); (X.J.)
| | - Paul Barrow
- School of Veterinary Medicine, University of Surrey, Daphne Jackson Road, Guildford GU2 7AL, UK;
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18
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Comment on Tanmoy et al. CRISPR-Cas Diversity in Clinical Salmonella enterica Serovar Typhi Isolates from South Asian Countries. Genes 2020, 11, 1365. Genes (Basel) 2021; 12:genes12081142. [PMID: 34440320 PMCID: PMC8391509 DOI: 10.3390/genes12081142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/06/2021] [Indexed: 11/17/2022] Open
Abstract
Tanmoy et al. [...].
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19
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Mashe T, Leekitcharoenphon P, Mtapuri-Zinyowera S, Kingsley RA, Robertson V, Tarupiwa A, Kock MM, Makombe EP, Chaibva BV, Manangazira P, Phiri I, Nyadundu S, Chigwena CT, Mufoya LP, Thilliez G, Midzi S, Mwamakamba LW, Hamblion EL, Matheu J, Jensen JD, Aarestrup FM, Hendriksen RS, Ehlers MM. Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019. J Antimicrob Chemother 2021; 76:1160-1167. [PMID: 33347558 DOI: 10.1093/jac/dkaa519] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/11/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Typhoid fever, caused by S. enterica ser. Typhi, continues to be a substantial health burden in developing countries. Little is known of the genotypic diversity of S. enterica ser. Typhi in Zimbabwe, but this is key for understanding the emergence and spread of this pathogen and devising interventions for its control. OBJECTIVES To report the molecular epidemiology of S. enterica ser. Typhi outbreak strains circulating from 2012 to 2019 in Zimbabwe, using comparative genomics. METHODS A review of typhoid cases records from 2012 to 2019 in Zimbabwe was performed. The phylogenetic relationship of outbreak isolates from 2012 to 2019 and emergence of antibiotic resistance was investigated by whole-genome sequence analysis. RESULTS A total 22 479 suspected typhoid cases, 760 confirmed cases were reported from 2012 to 2019 and 29 isolates were sequenced. The majority of the sequenced isolates were predicted to confer resistance to aminoglycosides, β-lactams, phenicols, sulphonamides, tetracycline and fluoroquinolones (including qnrS detection). The qnrS1 gene was associated with an IncN (subtype PST3) plasmid in 79% of the isolates. Whole-genome SNP analysis, SNP-based haplotyping and resistance determinant analysis showed that 93% of the isolates belonged to a single clade represented by multidrug-resistant H58 lineage I (4.3.1.1), with a maximum pair-wise distance of 22 SNPs. CONCLUSIONS This study has provided detailed genotypic characterization of the outbreak strain, identified as S. Typhi 4.3.1.1 (H58). The strain has reduced susceptibility to ciprofloxacin due to qnrS carried by an IncN (subtype PST3) plasmid resulting from ongoing evolution to full resistance.
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Affiliation(s)
- Tapfumanei Mashe
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Pimlapas Leekitcharoenphon
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens Genomics, FAO Reference Laboratory for Antimicrobial Resistance and European Union Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | | | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich, UK.,University of East Anglia, Norwich, UK
| | - V Robertson
- Medical Microbiology, University of Zimbabwe, Zimbabwe
| | - Andrew Tarupiwa
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Marleen M Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,National Health Laboratory Service, Tshwane Academic Divisions, Pretoria, South Africa
| | - Evidence P Makombe
- Gweru Provincial Hospital, Ministry of Health and Child Care, Gweru, Zimbabwe
| | | | - Portia Manangazira
- Ministry of Health and Child Care, Epidemiology and Disease Control, Zimbabwe
| | - Isaac Phiri
- Ministry of Health and Child Care, Epidemiology and Disease Control, Zimbabwe
| | - Simon Nyadundu
- Provincial Medical Directorate Offices, Midlands Province, Ministry of Health and Child Care, Gweru, Zimbabwe
| | | | | | | | | | - Lusubilo W Mwamakamba
- World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo
| | - Esther L Hamblion
- World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo
| | | | - Jacob D Jensen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens Genomics, FAO Reference Laboratory for Antimicrobial Resistance and European Union Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens Genomics, FAO Reference Laboratory for Antimicrobial Resistance and European Union Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Rene S Hendriksen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens Genomics, FAO Reference Laboratory for Antimicrobial Resistance and European Union Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Marthie M Ehlers
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,National Health Laboratory Service, Tshwane Academic Divisions, Pretoria, South Africa
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20
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Didelot X, Siveroni I, Volz EM. Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies. Mol Biol Evol 2021; 38:307-317. [PMID: 32722797 PMCID: PMC8480190 DOI: 10.1093/molbev/msaa193] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Phylogenetic dating is one of the most powerful and commonly used methods of drawing epidemiological interpretations from pathogen genomic data. Building such trees requires considering a molecular clock model which represents the rate at which substitutions accumulate on genomes. When the molecular clock rate is constant throughout the tree then the clock is said to be strict, but this is often not an acceptable assumption. Alternatively, relaxed clock models consider variations in the clock rate, often based on a distribution of rates for each branch. However, we show here that the distributions of rates across branches in commonly used relaxed clock models are incompatible with the biological expectation that the sum of the numbers of substitutions on two neighboring branches should be distributed as the substitution number on a single branch of equivalent length. We call this expectation the additivity property. We further show how assumptions of commonly used relaxed clock models can lead to estimates of evolutionary rates and dates with low precision and biased confidence intervals. We therefore propose a new additive relaxed clock model where the additivity property is satisfied. We illustrate the use of our new additive relaxed clock model on a range of simulated and real data sets, and we show that using this new model leads to more accurate estimates of mean evolutionary rates and ancestral dates.
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Affiliation(s)
- Xavier Didelot
- School of Life Sciences, University of Warwick, Coventry, United Kingdom.,Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Igor Siveroni
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Erik M Volz
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
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21
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Bose D, Mukhopadhyay S. The hunt for a yet unknown: Common molecular signature in some genetically monomorphic enterobacteria. J Basic Microbiol 2021; 61:524-546. [PMID: 33991346 DOI: 10.1002/jobm.202000630] [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: 11/24/2020] [Revised: 04/04/2021] [Accepted: 04/22/2021] [Indexed: 11/09/2022]
Abstract
Mark Achtman introduced the term "genetically monomorphic bacteria" (GM bacteria) for some human and plant pathogens. They displayed a great uniformity in terms of their "genetic" properties. This "uniformity" poses a challenge to microbiologists. To address these problems, we used CodonW and IslandViewer 3 as analytical tools and took Escherichia coli, Salmonella, and Shigella strains as a model organisms. We hypothesized that GM bacterium contains a common molecular signature among them. We have found a significant correlation regarding the number of protein-coding genes, predicted highly expressed genes, and the highest length of gene in this regard. On the other hand, the correspondence analysis of pathogenicity-related genes identified by IslandViewer 3 displayed a somewhat unique pattern in GM bacteria. The probable pathogenic genes are clustered into two separate groups, which is a hallmark of some pattern. Similar genes of non-monomorphic pathogenic strain clustered almost similarly, but the clusters are joined together, they are not completely separated. These features, in our considered view, may be considered as codon usages signatures of these bacteria, and E. coli in particular.
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Affiliation(s)
- Debadin Bose
- Department of Botany, Kabi Nazrul College, Murarai, West Bengal, India
| | - Subhasis Mukhopadhyay
- Distributed Information Centre for Bioinformatics, Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Calcutta, West Bengal, India
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22
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Pragasam AK, Pickard D, Wong V, Dougan G, Kang G, Thompson A, John J, Balaji V, Mutreja A. Phylogenetic Analysis Indicates a Longer Term Presence of the Globally Distributed H58 Haplotype of Salmonella Typhi in Southern India. Clin Infect Dis 2021; 71:1856-1863. [PMID: 32003431 PMCID: PMC7643746 DOI: 10.1093/cid/ciz1112] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 01/29/2019] [Indexed: 12/28/2022] Open
Abstract
Background Typhoid fever caused by Salmonella Typhi is a major public health concern in low-/middle-income countries. A recent study of 1900 global S. Typhi indicated that South Asia might be the site of the original emergence of the most successful and hypervirulent clone belonging to the 4.3.1 genotype. However, this study had limited samples from India. Methods We analyzed 194 clinical S. Typhi, temporal representatives from those isolated from blood and bone marrow cultures in southern India, over 26 years (1991–2016). Antimicrobial resistance (AMR) testing was performed for most common clinical agents. Whole-genome sequencing and SNP-level analysis was conducted. Comparative genomics of Vellore isolates was performed to infer transmission and AMR events. Results We identified multidrug-resistance (MDR)–associated clade 4.3.1 as the dominant genotype. We detected 4.3.1 S. Typhi as early as 1991, the earliest to be reported form India, and the majority were fluoroquinolone resistant and not MDR. MDR was not detected at all in other genotypes circulating in Vellore. Comparison with global S. Typhi showed 2 Vellore subgroups (I and II) that were phylogenetically highly related to previously described South Asia (subgroup I, II) and Southeast Asia (subgroup II) clades. Conclusions 4.3.1 S. Typhi has dominated in Vellore for 2 decades. Our study would assist public health agencies in better tracking of transmission and persistence of this successful clade in India and globally. It informs clinicians of the AMR pattern of circulating clone, which would add confidence to their prophylactic/treatment decision making and facilitate efficient patient care.
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Affiliation(s)
- Agila Kumari Pragasam
- Department of Clinical Microbiology, Christian Medical College, Vellore, India.,Department of Medicine, Univesity of Cambridge, Cambridge, United Kingdom
| | - Derek Pickard
- Department of Medicine, Univesity of Cambridge, Cambridge, United Kingdom
| | - Vanessa Wong
- Department of Medicine, Univesity of Cambridge, Cambridge, United Kingdom
| | - Gordon Dougan
- Department of Medicine, Univesity of Cambridge, Cambridge, United Kingdom.,Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Gagandeep Kang
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Andrew Thompson
- Department of Medicine, Univesity of Cambridge, Cambridge, United Kingdom
| | - Jacob John
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | | | - Ankur Mutreja
- Department of Medicine, Univesity of Cambridge, Cambridge, United Kingdom.,Wellcome Sanger Institute, Hinxton, United Kingdom
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23
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Enteric Fever Diagnosis: Current Challenges and Future Directions. Pathogens 2021; 10:pathogens10040410. [PMID: 33915749 PMCID: PMC8065732 DOI: 10.3390/pathogens10040410] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/23/2021] [Accepted: 03/27/2021] [Indexed: 12/21/2022] Open
Abstract
Enteric fever is a life-threatening systemic febrile disease caused by Salmonella enterica serovars Typhi and Paratyphi (S. Typhi and S. Paratyphi). Unfortunately, the burden of the disease remains high primarily due to the global spread of various drug-resistant Salmonella strains despite continuous advancement in the field. An accurate diagnosis is critical for effective control of the disease. However, enteric fever diagnosis based on clinical presentations is challenging due to overlapping symptoms with other febrile illnesses that are also prevalent in endemic areas. Current laboratory tests display suboptimal sensitivity and specificity, and no diagnostic methods are available for identifying asymptomatic carriers. Several research programs have employed systemic approaches to identify more specific biomarkers for early detection and asymptomatic carrier detection. This review discusses the pros and cons of currently available diagnostic tests for enteric fever, the advancement of research toward improved diagnostic tests, and the challenges of discovering new ideal biomarkers and tests.
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24
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Jamilah J, Hatta M, Natzir R, Umar F, Sjahril R, Agus R, Junita AR, Dwiyanti R, Primaguna MR, Sabir M. Analysis of existence of multidrug-resistant H58 gene in Salmonella enterica serovar Typhi isolated from typhoid fever patients in Makassar, Indonesia. New Microbes New Infect 2020; 38:100793. [PMID: 33294191 PMCID: PMC7695904 DOI: 10.1016/j.nmni.2020.100793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 11/02/2022] Open
Abstract
The surveillance of multidrug-resistant (MDR) H58 typhoid is highly important, especially in endemic areas. MDR strain detection is needed by using a simple PCR technique that only uses a pair of primers. This is conducted considering the detection of Salmonella Typhi strains that have been carried out so far are only using antimicrobial sensitivity tests to determine microbial resistance phenotypically and to determine genotypically using complex molecular techniques. We aimed to analyse the existence of Salmonella Typhi MDR H58 in patients with typhoid fever in Makassar, Indonesia. A total of 367 blood samples of typhoid fever patients were collected from April 2018 until April 2019. The blood sample was cultured, then confirmed via simple PCR. All of the confirmed samples were tested for susceptibility against antibiotics and molecularly analysed for MDR H58 existence using a simple PCR technique. We found 7% (27/367) of the samples to be positive by both blood culture and PCR. All 27 isolates were found to be sensitive to sulfamethoxazole/trimethoprim. The lowest drug sensitivities were to amoxicillin, at one (3.7%) of 27 isolates, and ampicillin, at 13 (48.1%) of 27 isolates. Salmonella Typhi H58 PCR results showed that one (3.7%) of 27 isolates carried a positive fragment of 993 bp that led to the H58 strain, since the deletion flanks this fragment. The isolate was also found to be resistant to amoxicillin and fluoroquinolone according to a sensitivity test. Further molecular analysis needs to be conducted to examine the single isolate that carried the 933 bp fragment.
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Affiliation(s)
- J Jamilah
- Alauddin State Islamic University, Makassar, Indonesia.,Postgraduate Program of Medical Science, Indonesia
| | - M Hatta
- Molecular Biology and Immunology Laboratory, Indonesia
| | - R Natzir
- Department of Biochemistry, Indonesia
| | - F Umar
- Postgraduate Program of Medical Science, Indonesia.,Makassar Medical State Laboratory, Indonesian Ministry of Health, Makassar, Indonesia
| | - R Sjahril
- Department of Medical Microbiology, Indonesia
| | - R Agus
- Laboratory of Genetics, Department of Biology, Faculty of Science, University of Hasanuddin, Makassar, Indonesia
| | - A R Junita
- Molecular Biology and Immunology Laboratory, Indonesia
| | - R Dwiyanti
- Department of Medical Microbiology, Faculty of Medicine, Tadulako University, Palu, Indonesia
| | - M R Primaguna
- Department of Internal Medicine, Faculty of Medicine, Indonesia
| | - M Sabir
- Department of Medical Microbiology, Faculty of Medicine, Tadulako University, Palu, Indonesia
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25
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Gallbladder carriage generates genetic variation and genome degradation in Salmonella Typhi. PLoS Pathog 2020; 16:e1008998. [PMID: 33085725 PMCID: PMC7605710 DOI: 10.1371/journal.ppat.1008998] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/02/2020] [Accepted: 09/21/2020] [Indexed: 11/19/2022] Open
Abstract
Despite recent advances in typhoid fever control, asymptomatic carriage of Salmonella Typhi in the gallbladder remains poorly understood. Aiming to understand if S. Typhi becomes genetically adapted for long-term colonisation in the gallbladder, we performed whole genome sequencing on a collection of S. Typhi isolated from the gallbladders of typhoid carriers. These sequences were compared to contemporaneously sampled sequences from organisms isolated from the blood of acute patients within the same population. We found that S. Typhi carriage was not restricted to any particular genotype or conformation of antimicrobial resistance genes, but was largely reflective of S. Typhi circulating in the general population. However, gallbladder isolates showed a higher genetic variability than acute isolates, with median pairwise SNP distances of 21 and 13 SNPs (p = 2.8x10-9), respectively. Within gallbladder isolates of the predominant H58 genotype, variation was associated with a higher prevalence of nonsense mutations. Notably, gallbladder isolates displayed a higher frequency of non-synonymous mutations in genes encoding hypothetical proteins, membrane lipoproteins, transport/binding proteins, surface antigens, and carbohydrate degradation. Specifically, we identified several gallbladder-specific non-synonymous mutations involved in LPS synthesis and modification, with some isolates lacking the Vi capsular polysaccharide vaccine target due to the 134Kb deletion of SPI-7. S. Typhi is under strong selective pressure in the human gallbladder, which may be reflected phylogenetically by long terminal branches that may distinguish organisms from chronic and acute infections. Our work shows that selective pressures asserted by the hostile environment of the human gallbladder generate new antigenic variants and raises questions regarding the role of carriage in the epidemiology of typhoid fever. Salmonella Typhi is the bacterium that causes typhoid. Salmonella Typhi is infamous for being able to be carried in the gallbladder, with Typhoid Mary being the best-known example of a typhoid carrier. Despite having new tools for typhoid control, we have made little progress in understanding this disease process. Aiming to understand if Salmonella Typhi is adapted for long-term survival in the gallbladder, we sequenced the genomes of 24 Salmonella Typhi isolated from the gallbladders of typhoid carriers. We compared these genomes to Salmonella Typhi from acute typhoid patients within the same population. The carriage of Salmonella Typhi was not restricted to any specific genotype or resistance to antibiotics, but reflective of the organisms causing acute disease. However, gallbladder isolates had higher genetic variability than acute isolates, with a higher frequency of mutations changing the amino acid sequences of hypothetical proteins, membrane lipoproteins, transport/binding proteins, surface antigens, and carbohydrate degradation. We identified several gallbladder-specific mutations involved in polysaccharide synthesis on the bacterial surface. Our work shows that selective pressures asserted by the hostile environment of the human gallbladder generates genetic variation, which is not observed in acute isolates, raising questions regarding the role of carriage in the epidemiology of typhoid.
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26
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Acosta-Alonzo CB, Erovenko IV, Lancaster A, Oh H, Rychtář J, Taylor D. High endemic levels of typhoid fever in rural areas of Ghana may stem from optimal voluntary vaccination behaviour. Proc Math Phys Eng Sci 2020; 476:20200354. [PMID: 33071586 PMCID: PMC7544331 DOI: 10.1098/rspa.2020.0354] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/04/2020] [Indexed: 01/24/2023] Open
Abstract
Typhoid fever has long established itself endemically in rural Ghana despite the availability of cheap and effective vaccines. We used a game-theoretic model to investigate whether the low vaccination coverage in Ghana could be attributed to rational human behaviour. We adopted a version of an epidemiological model of typhoid fever dynamics, which accounted not only for chronic life-long carriers but also for a short-cycle transmission in the immediate environment and a long-cycle transmission via contamination of the water supply. We calibrated the model parameters based on the known incidence data. We found that unless the (perceived) cost of vaccination is negligible, the individually optimal population vaccination rate falls significantly short of the societally optimal population vaccination rate needed to reach herd immunity. We expressed both the herd immunity and the optimal equilibrium vaccination rates in terms of only a few observable parameters such as the incidence rate, demographics, vaccine waning rate and the perceived cost of vaccination relative to the cost of infection. This allowed us not to rely on other uncertain epidemiological model parameters and, in particular, to bypass uncertainties about the role of the carriers in the transmission.
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Affiliation(s)
| | - Igor V. Erovenko
- Department of Mathematics and Statistics, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Aaleah Lancaster
- Department of Mathematics and Computer Science, Bennett College, Greensboro, NC 27401, USA
| | - Hyunju Oh
- Division of Mathematics and Computer Science, University of Guam, Mangilao, Guam 96923, USA
| | - Jan Rychtář
- Department of Mathematics and Applied Mathematics, Virginia Commonwealth University, Richmond, VA 23284-2014, USA
| | - Dewey Taylor
- Department of Mathematics and Applied Mathematics, Virginia Commonwealth University, Richmond, VA 23284-2014, USA
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27
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Arriola LA, Cooper A, Weyrich LS. Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Measurement of Typhim Vi® IgG antibodies in healthy donors as a tool for the diagnostic of patients with antibody deficiencies. Clin Immunol 2020; 215:108416. [DOI: 10.1016/j.clim.2020.108416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/05/2020] [Accepted: 04/07/2020] [Indexed: 10/24/2022]
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Abstract
Multiple drug (antibiotic) resistance (MDR) has become a major threat to the treatment of typhoid and other infectious diseases. Since the 1970s, this threat has increased in Salmonella enterica serovar Typhi, driven in part by the emergence of successful genetic clades, such as haplotype H58, associated with the MDR phenotype. H58 S. Typhi can express multiple antibiotic resistance determinants while retaining the ability to efficiently transmit and persist within the human population. The recent identification of extensively drug resistant S. Typhi only highlights the dangers of ignoring this threat. Here we discuss the evolution of the S. Typhi MDR phenotype and consider options for management.
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Affiliation(s)
- Zoe A Dyson
- Department of Medicine, University of Cambridge, Hinxton, Cambridge, United Kingdom
| | - Elizabeth J Klemm
- Department of Medicine, University of Cambridge, Hinxton, Cambridge, United Kingdom.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sophie Palmer
- Department of Medicine, University of Cambridge, Hinxton, Cambridge, United Kingdom
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Hinxton, Cambridge, United Kingdom.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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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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Hooda Y, Sajib MSI, Rahman H, Luby SP, Bondy-Denomy J, Santosham M, Andrews JR, Saha SK, Saha S. Molecular mechanism of azithromycin resistance among typhoidal Salmonella strains in Bangladesh identified through passive pediatric surveillance. PLoS Negl Trop Dis 2019; 13:e0007868. [PMID: 31730615 PMCID: PMC6881056 DOI: 10.1371/journal.pntd.0007868] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 11/27/2019] [Accepted: 10/24/2019] [Indexed: 12/11/2022] Open
Abstract
Background With the rise in fluoroquinolone-resistant Salmonella Typhi and the recent emergence of ceftriaxone resistance, azithromycin is one of the last oral drugs available against typhoid for which resistance is uncommon. Its increasing use, specifically in light of the ongoing outbreak of extensively drug-resistant (XDR) Salmonella Typhi (resistant to chloramphenicol, ampicillin, cotrimoxazole, streptomycin, fluoroquinolones and third-generation cephalosporins) in Pakistan, places selective pressure for the emergence and spread of azithromycin-resistant isolates. However, little is known about azithromycin resistance in Salmonella, and no molecular data are available on its mechanism. Methods and findings We conducted typhoid surveillance in the two largest pediatric hospitals of Bangladesh from 2009–2016. All typhoidal Salmonella strains were screened for azithromycin resistance using disc diffusion and resistance was confirmed using E-tests. In total, we identified 1,082 Salmonella Typhi and Paratyphi A strains; among these, 13 strains (12 Typhi, 1 Paratyphi A) were azithromycin-resistant (MIC range: 32–64 μg/ml) with the first case observed in 2013. We sequenced the resistant strains, but no molecular basis of macrolide resistance was identified by the currently available antimicrobial resistance prediction tools. A whole genome SNP tree, made using RAxML, showed that the 12 Typhi resistant strains clustered together within the 4.3.1.1 sub-clade (H58 lineage 1). We found a non-synonymous single-point mutation exclusively in these 12 strains in the gene encoding AcrB, an efflux pump that removes small molecules from bacterial cells. The mutation changed the conserved amino acid arginine (R) at position 717 to a glutamine (Q). To test the role of R717Q present in azithromycin-resistant strains, we cloned acrB from azithromycin-resistant and sensitive strains, expressed them in E. coli, Typhi and Paratyphi A strains and tested their azithromycin susceptibility. Expression of AcrB-R717Q in E. coli and Typhi strains increased the minimum inhibitory concentration (MIC) for azithromycin by 11- and 3-fold respectively. The azithromycin-resistant Paratyphi A strain also contained a mutation at R717 (R717L), whose introduction in E. coli and Paratyphi A strains increased MIC by 7- and 3-fold respectively, confirming the role of R717 mutations in conferring azithromycin resistance. Conclusions This report confirms 12 azithromycin-resistant Salmonella Typhi strains and one Paratyphi A strain. The molecular basis of this resistance is one mutation in the AcrB protein at position 717. This is the first report demonstrating the impact of this non-synonymous mutation in conferring macrolide resistance in a clinical setting. With increasing azithromycin use, strains with R717 mutations may spread and be acquired by XDR strains. An azithromycin-resistant XDR strain would shift enteric fever treatment from outpatient departments, where patients are currently treated with oral azithromycin, to inpatient departments to be treated with injectable antibiotics like carbapenems, thereby further burdening already struggling health systems in endemic regions. Moreover, with the dearth of novel antimicrobials in the horizon, we risk losing our primary defense against widespread mortality from typhoid. In addition to rolling out the WHO prequalified typhoid conjugate vaccine in endemic areas to decrease the risk of pan-resistant Salmonella Typhi strains, it is also imperative to implement antimicrobial stewardship and water sanitation and hygiene intervention to decrease the overall burden of enteric fever. With the outbreak of extensively resistant (XDR) typhoid fever in Pakistan, azithromycin has become the last oral drug to treat typhoid. Although no azithromycin resistant XDR isolate has been reported to date, the increasing use of azithromycin and the clear historical record of widespread dissemination of resistance to all previously widely used antimicrobials by typhoidal Salmonella, suggest we will soon face strains resistant to all oral antibiotics. This makes it imperative to elucidate the mechanism of azithromycin resistance in typhoidal Salmonella. We tested 1,082 typhoidal Salmonella isolates from the two largest pediatric hospitals of Bangladesh and identified 13 azithromycin-resistant isolates. Using comparative genomics, we identified a mutation in a specific protein called AcrB that makes these isolates resistant to azithromycin. All azithromycin-resistant strains were susceptible to cephalosporin but resistant to all other oral antibiotics. The Pakistan outbreak strain is resistant to all common oral antibiotics and only susceptible to azithromycin. Acquisition of the plasmid that confers cephalosporin resistance in XDR strains by the Bangladeshi azithromycin-resistant strains or rise of the AcrB mutation in the XDR strains could be the end of oral treatment for typhoid. This poses serious threats to the health system of LMICs where typhoid is endemic. Currently, the majority of typhoid patients are prescribed oral treatment in the outpatient department, but an azithromycin-resistant XDR strain would shift enteric fever treatment from outpatient departments to inpatient departments to be treated with injectable antibiotics like carbapenems, further burdening already struggling health systems in endemic regions. Moreover, with the dearth of novel antimicrobials in the horizon, we risk losing our primary defense against widespread mortality from enteric fever.
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Affiliation(s)
- Yogesh Hooda
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Mohammad S. I. Sajib
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Hafizur Rahman
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Stephen P. Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Mathuram Santosham
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, 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, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
- Bangladesh Institute of Child Health, Dhaka Shishu Hospital, Dhaka, Bangladesh
- * E-mail: (SKS); (SS)
| | - Senjuti Saha
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail: (SKS); (SS)
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Baldi M, Barquero Calvo E, Hutter SE, Walzer C. Salmonellosis detection and evidence of antibiotic resistance in an urban raccoon population in a highly populated area, Costa Rica. Zoonoses Public Health 2019; 66:852-860. [PMID: 31359623 PMCID: PMC6852039 DOI: 10.1111/zph.12635] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/20/2019] [Accepted: 06/30/2019] [Indexed: 11/28/2022]
Abstract
Wild animals are involved in zoonotic disease transmission cycles. These are generally complex and poorly understood, especially among animals adapted to life in human ecosystems. Raccoons are reservoirs and effective carriers for infectious agents such as Salmonella throughout different environments and contribute to the transference of resistance genes. This study examined the presence of circulating Salmonella sp. in a population of raccoons in a tropical urban environment and evaluated resistance to antibiotics commonly used to treat salmonellosis. A total of 97 raccoons of different ages and sex were included in this study. 49% (38-60 CI) of the faecal samples were positive for Salmonella spp. The study identified 15 circulating serovars with the most prevalent being S. Hartford (7/15), S. Typhimurium (4/15) and S. Bovismorbificans (4/15). These serovars correspond to the serovars detected in humans with clinical symptoms in Costa Rica. 9.5% of the Salmonella strains recovered demonstrated ciprofloxacin resistance, and 7.1% showed resistance to nalidixic acid. This study provides evidence of multiple Salmonella serovars circulating in a population of urban raccoons in Costa Rica. Furthermore, the study confirms the existence of antimicrobial resistance to two antibiotics used to treat human salmonellosis. The findings emphasize the role of the raccoon as a reservoir of Salmonella in the Greater Metropolitan Area of Costa Rica (GAM) and stress the need for active monitoring of the presence and possible spread in antibiotic resistance due to this peri-domestic carnivore.
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Affiliation(s)
- Mario Baldi
- Research Institute of Wildlife EcologyUniversity of Veterinary MedicineViennaAustria
- Tropical Diseases Research Program, School of Veterinary MedicineNational UniversityHerediaCosta Rica
| | - Elías Barquero Calvo
- Tropical Diseases Research Program, School of Veterinary MedicineNational UniversityHerediaCosta Rica
| | - Sabine E. Hutter
- Institute of Veterinary Public HealthUniversity of Veterinary, MedicineViennaAustria
- National Animal Health Service (SENASA)Ministry of Agriculture and Livestock (MAG)HerediaCosta Rica
| | - Chris Walzer
- Research Institute of Wildlife EcologyUniversity of Veterinary MedicineViennaAustria
- Wildlife Conservation SocietyWildlife Health ProgramBronxNYUSA
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Abstract
We combine methodology from history and genetics to reconstruct the biosocial history of antimicrobial resistance (AMR) in the bacterium Salmonella enterica serovar Typhi (S. Typhi). We show how evolutionary divergence in S. Typhi was driven by rising global antibiotic use and by the neglect of typhoid outside of high-income countries. Although high-income countries pioneered 1960s precautionary antibiotic regulations to prevent selection for multidrug resistance, new antibiotic classes, typhoid's cultural status as a supposedly ancient disease of "undeveloped" countries, limited international funding, and narrow biosecurity agendas helped fragment effective global collective action for typhoid control. Antibiotic-intensive compensation for weak water and healthcare systems subsequently fueled AMR selection in low- and middle-income countries but often remained invisible due to lacking surveillance capabilities. The recent rise of extensively drug-resistant typhoid bears the biosocial footprint of more than half a century of antibiotic-intensive international neglect.
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Affiliation(s)
- Claas Kirchhelle
- Wellcome Unit for the History of Medicine/Oxford Martin School, University of Oxford, Addenbrooke’s Hospital, United Kingdom
| | - Zoe Anne Dyson
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, United Kingdom
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, United Kingdom
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Ingle DJ, Nair S, Hartman H, Ashton PM, Dyson ZA, Day M, Freedman J, Chattaway MA, Holt KE, Dallman TJ. Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers. PLoS Negl Trop Dis 2019; 13:e0007620. [PMID: 31513580 PMCID: PMC6741848 DOI: 10.1371/journal.pntd.0007620] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 07/09/2019] [Indexed: 11/30/2022] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi) is the causative agent of typhoid fever, a systemic human infection with a burden exceeding 20 million cases each year that occurs disproportionately among children in low and middle income countries. Antimicrobial therapy is the mainstay for treatment, but resistance to multiple agents is common. Here we report genotypes and antimicrobial resistance (AMR) determinants detected from routine whole-genome sequencing (WGS) of 533 S. Typhi isolates referred to Public Health England between April 2014 and March 2017, 488 (92%) of which had accompanying patient travel information obtained via an enhanced surveillance questionnaire. The majority of cases involved S. Typhi 4.3.1 (H58) linked with travel to South Asia (59%). Travel to East and West Africa were associated with genotypes 4.3.1 and 3.3.1, respectively. Point mutations in the quinolone resistance determining region (QRDR), associated with reduced susceptibility to fluoroquinolones, were very common (85% of all cases) but the frequency varied significantly by region of travel: 95% in South Asia, 43% in East Africa, 27% in West Africa. QRDR triple mutants, resistant to ciprofloxacin, were restricted to 4.3.1 lineage II and associated with travel to India, accounting for 23% of cases reporting travel to the country. Overall 24% of isolates were MDR, however the frequency varied significantly by region and country of travel: 27% in West Africa, 52% in East Africa, 55% in Pakistan, 24% in Bangladesh, 3% in India. MDR determinants were plasmid-borne (IncHI1 PST2 plasmids) in S. Typhi 3.1.1 linked to West Africa, but in all other regions MDR was chromosomally integrated in 4.3.1 lineage I. We propose that routine WGS data from travel-associated cases in industrialised countries could serve as informal sentinel AMR genomic surveillance data for countries where WGS is not available or routinely performed. Our data demonstrate how routine WGS data produced by Public Health England can be further mined for informal passive surveillance of Salmonella Typhi circulating in different geographical regions where typhoid is endemic. We have shown the public health utility of a simplified approach to WGS reporting based on the GenoTyphi genotyping framework and nomenclature, which doesn’t require the generation of a phylogenetic tree or other phylogenetic analysis. These approaches yielded results consistent with previously reported antimicrobial resistance (AMR) patterns of S. Typhi, including prevalence of multi-drug resistant (MDR) and fluoroquinolone resistance in different regions in association with different pathogen variants. These data provide a rationale and framework for the extraction and reporting of geographically stratified genotype and AMR data from public health labs in non-endemic countries. Prospective analysis and reporting of such data could potentially detect shifts in regional S. Typhi populations, such as replacement or spread of different subclades and the emergence and dissemination of MDR, fluoroquinolone resistant and/or extensively drug resistant S. Typhi, providing valuable data to inform typhoid control measures in low and middle income countries that are still building their genomics capacity.
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Affiliation(s)
- Danielle J. Ingle
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- * E-mail:
| | - Satheesh Nair
- Gastrointestinal Bacteria Reference Unit, Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kingdom
| | - Hassan Hartman
- Gastrointestinal Bacteria Reference Unit, Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kingdom
| | - Philip M. Ashton
- Gastrointestinal Bacteria Reference Unit, Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kingdom
| | - Zoe A. Dyson
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Martin Day
- Gastrointestinal Bacteria Reference Unit, Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kingdom
| | - Joanne Freedman
- Travel Migrant and Health Department, Public Health England, 61 Colindale Avenue, London, United Kingdom
| | - Marie A. Chattaway
- Gastrointestinal Bacteria Reference Unit, Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kingdom
| | - Kathryn E. Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
- London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Timothy J. Dallman
- Gastrointestinal Bacteria Reference Unit, Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kingdom
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Bakeer MS, Youssef MI, Elshazly HM, Abdel-Samiee M, El-Gendy AA, Abouzed M, Othman W, Abdelkareem M, Abozeid M, Awad SM, Khalil FO, Bedair HM, Diab KA, Seif AS, Youssef MF, Sakr AA, Abdelsameea E. On-treatment improvement of an emerging psychosomatic depressive disorder among salmonella carriers: a multicenter experience from Egypt. Infect Drug Resist 2019; 12:2573-2582. [PMID: 31686865 PMCID: PMC6709802 DOI: 10.2147/idr.s206642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022] Open
Abstract
Background As physicians in a referral hospital, we observed the association between history of enteric fever and somatic disorders associated with low mood. At the Al-Hussein University Hospital, Cairo and the National Liver Institute Hospital, Menoufia, we receive patients from all over Egypt, including rural areas where enteric fever is endemic. Aim Here in, 60 Egyptian patients referred to us for evaluation of different somatic disorders are reported. Methods After extensive evaluations, the patients' symptoms were function-related. Also, their typhoid carrier states were documented, and the severity of depression using Hamilton-D (HAM-D) questionnaire was evaluated and recorded. All patients were treated with ceftriaxone, 2 gm, IV, daily for 15 days. The clinical evaluation and Hamilton score were reassessed at the end of the treatment and 6 weeks thereafter. The patients did not receive any anti-depressant nor anti-anxiety treatment during their course. Typhoid carrier was defined by documenting the history of typhoid fever that was diagnosed by culturing the Salmonella species, and not by serology, isolated from stool culture along with febrile condition, plus the absence of fever in the past 3 weeks. The Widal test was not accepted as a criterion for enrollment. Results Patients showed clinically significant improvement in the somatic complaints, and their HAM-D score immediately post-treatment that was consolidated for 6 weeks post-treatment completion. Conclusion In this study, the typhoid carrier was associated with the psychosomatic depression that improved by antibiotic therapy.
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Affiliation(s)
| | | | - Helmy M Elshazly
- Hepatology and Gastroenterology Department, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - Mohamed Abdel-Samiee
- Hepatology and Gastroenterology Department, National Liver Institute, Menoufia University, Menoufia, Egypt
| | | | - M Abouzed
- Psychiatry Department, Al-Azhar University, Cairo, Egypt
| | - Warda Othman
- Hepatology and Gastroenterology Department, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - Mervat Abdelkareem
- Hepatology and Gastroenterology Department, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - Mai Abozeid
- Hepatology and Gastroenterology Department, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - Samah Mohammed Awad
- Clinical Microbiology and Immunology and Molecular Microbiology in Liver and GIT Department, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - Fatma O Khalil
- Clinical Microbiology and Immunology and Molecular Microbiology in Liver and GIT Department, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - Hanan M Bedair
- Clinical Pathology Department, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - Karema A Diab
- Clinical Pathology Department, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - A S Seif
- Tropical Medicine Hepatology and Gastroenterology Department, Shebin Elkom Teaching Hospital, Menoufia, Egypt
| | - Marwa F Youssef
- Epidemiology and Preventive Medicine Department, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - Ayman Ahmed Sakr
- Tropical Medicine Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Eman Abdelsameea
- Hepatology and Gastroenterology Department, National Liver Institute, Menoufia University, Menoufia, Egypt
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Liao J, Orsi RH, Carroll LM, Kovac J, Ou H, Zhang H, Wiedmann M. Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica. BMC Evol Biol 2019; 19:132. [PMID: 31226931 PMCID: PMC6588947 DOI: 10.1186/s12862-019-1457-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 06/11/2019] [Indexed: 12/28/2022] Open
Abstract
Background The emergence of antimicrobial-resistant (AMR) strains of the important human and animal pathogen Salmonella enterica poses a growing threat to public health. Here, we studied the genome-wide evolution of 90 S. enterica AMR isolates, representing one host adapted serotype (S. Dublin) and two broad host range serotypes (S. Newport and S. Typhimurium). Results AMR S. Typhimurium had a large effective population size, a large and diverse genome, AMR profiles with high diversity, and frequent positive selection and homologous recombination. AMR S. Newport showed a relatively low level of diversity and a relatively clonal population structure. AMR S. Dublin showed evidence for a recent population bottleneck, and the genomes were characterized by a larger number of genes and gene ontology terms specifically absent from this serotype and a significantly higher number of pseudogenes as compared to other two serotypes. Approximately 50% of accessory genes, including specific AMR and putative prophage genes, were significantly over- or under-represented in a given serotype. Approximately 65% of the core genes showed phylogenetic clustering by serotype, including the AMR gene aac (6′)-Iaa. While cell surface proteins were shown to be the main target of positive selection, some proteins with possible functions in AMR and virulence also showed evidence for positive selection. Homologous recombination mainly acted on prophage-associated proteins. Conclusions Our data indicates a strong association between genome content of S. enterica and serotype. Evolutionary patterns observed in S. Typhimurium are consistent with multiple emergence events of AMR strains and/or ecological success of this serotype in different hosts or habitats. Evolutionary patterns of S. Newport suggested that antimicrobial resistance emerged in one single lineage, Lineage IIC. A recent population bottleneck and genome decay observed in AMR S. Dublin are congruent with its narrow host range. Finally, our results suggest the potentially important role of positive selection in the evolution of antimicrobial resistance, host adaptation and serotype diversification in S. enterica. Electronic supplementary material The online version of this article (10.1186/s12862-019-1457-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingqiu Liao
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA.,Graduate Field of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Renato Hohl Orsi
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Laura M Carroll
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hongyu Ou
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hailong Zhang
- Department of Computer Science & Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Martin Wiedmann
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA.
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Palmer M, Venter SN, Coetzee MP, Steenkamp ET. Prokaryotic species are sui generis evolutionary units. Syst Appl Microbiol 2019; 42:145-158. [DOI: 10.1016/j.syapm.2018.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 12/25/2022]
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Emergence of dominant multidrug-resistant bacterial clades: Lessons from history and whole-genome sequencing. Proc Natl Acad Sci U S A 2019; 115:12872-12877. [PMID: 30559200 DOI: 10.1073/pnas.1717162115] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Antibiotic resistance in bacteria has emerged as a global challenge over the past 90 years, compromising our ability to effectively treat infections. There has been a dramatic increase in antibiotic resistance-associated determinants in bacterial populations, driven by the mobility and infectious nature of such determinants. Bacterial genome flexibility and antibiotic-driven selection are at the root of the problem. Genome evolution and the emergence of highly successful multidrug-resistant clades in different pathogens have made this a global challenge. Here, we describe some of the factors driving the origin, evolution, and spread of the antibiotic resistance genotype.
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The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa. Nat Commun 2018; 9:5094. [PMID: 30504848 PMCID: PMC6269545 DOI: 10.1038/s41467-018-07370-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/18/2018] [Indexed: 11/18/2022] Open
Abstract
There is paucity of data regarding the geographical distribution, incidence, and phylogenetics of multi-drug resistant (MDR) Salmonella Typhi in sub-Saharan Africa. Here we present a phylogenetic reconstruction of whole genome sequenced 249 contemporaneous S. Typhi isolated between 2008-2015 in 11 sub-Saharan African countries, in context of the 2,057 global S. Typhi genomic framework. Despite the broad genetic diversity, the majority of organisms (225/249; 90%) belong to only three genotypes, 4.3.1 (H58) (99/249; 40%), 3.1.1 (97/249; 39%), and 2.3.2 (29/249; 12%). Genotypes 4.3.1 and 3.1.1 are confined within East and West Africa, respectively. MDR phenotype is found in over 50% of organisms restricted within these dominant genotypes. High incidences of MDR S. Typhi are calculated in locations with a high burden of typhoid, specifically in children aged <15 years. Antimicrobial stewardship, MDR surveillance, and the introduction of typhoid conjugate vaccines will be critical for the control of MDR typhoid in Africa. Typhoid fever is caused by the bacterium Salmonella Typhi. Here, Park et al. analyse the genomes of 249 S. Typhi isolates from 11 sub-Saharan African countries, identifying genes and plasmids associated with antibiotic resistance and showing that multi-drug resistance is highly pervasive in sub-Saharan Africa.
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40
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Salmonella enterica Phylogeny Based on Whole-Genome Sequencing Reveals Two New Clades and Novel Patterns of Horizontally Acquired Genetic Elements. mBio 2018; 9:mBio.02303-18. [PMID: 30482836 PMCID: PMC6282209 DOI: 10.1128/mbio.02303-18] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Rapid improvements in nucleotide sequencing access and affordability have led to a drastic increase in availability of genetic information. This information will improve the accuracy of molecular descriptions, including serovars, within S. enterica. Although the concept of serovars continues to be useful, it may have more significant limitations than previously understood. Furthermore, the discrete absence or presence of specific genes can be an unstable indicator of phylogenetic identity. Whole-genome sequencing provides more rigorous tools for assessing the distributions of these genes. Our phylogenetic and genetic content analyses reveal how active genetic elements are dynamically distributed within a species, allowing us to better understand genetic reservoirs and underlying bacterial evolution. Using whole-genome sequence (WGS) data from the GenomeTrakr network, a globally distributed network of laboratories sequencing foodborne pathogens, we present a new phylogeny of Salmonella enterica comprising 445 isolates from 266 distinct serovars and originating from 52 countries. This phylogeny includes two previously unidentified S. enterica subsp. enterica clades. Serovar Typhi is shown to be nested within clade A. Our findings are supported by both phylogenetic support, based on a core genome alignment, and Bayesian approaches, based on single-nucleotide polymorphisms. Serovar assignments were refined by in silico analysis using SeqSero. More than 10% of serovars were either polyphyletic or paraphyletic. We found variable genetic content in these isolates relating to gene mobilization and virulence factors which have different distributions within clades. Gifsy-1- and Gifsy-2-like phages appear more prevalent in clade A; other viruses are more evenly distributed. Our analyses reveal IncFII is the predominant plasmid replicon in S. enterica. Few core or clade-defining virulence genes are observed, and their distributions appear probabilistic in nature. Together, these patterns demonstrate that genetic exchange within S. enterica is more extensive and frequent than previously realized, which significantly alters how we view the genetic structure of the bacterial species.
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Ja'afar JN, Bhore SJ, Phua KK. Non-specificity of sequence characterised amplified region as an alternative molecular epidemiology marker for the identification of Salmonella enterica subspecies enterica serovar Typhi. BMC Res Notes 2018; 11:766. [PMID: 30373642 PMCID: PMC6206845 DOI: 10.1186/s13104-018-3870-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/19/2018] [Indexed: 12/30/2022] Open
Abstract
Objective Identification of Salmonella Typhi by conventional culture techniques is labour-intensive, time consuming, and lack sensitivity and specificity unlike high-throughput epidemiological markers that are highly specific but are not affordable for low-resource settings. SCAR, obtained from RAPD technique, is an affordable, reliable and reproducible method for developing genetic markers. Hence, this study investigated the use of SCAR as an alternative molecular epidemiological marker for easy identification of S. Typhi in low-resource settings. Results One hundred and twenty RAPD primers were screened through RAPD-PCR against a panel of common enterobacteriaceae for the best RAPD band pattern discrimination to develop SCAR primers that were used to develop a RAPD-SCAR PCR. Of this number, 10 were selected based on their calculated indices of discrimination. Four RAPD primers, SBSA02, SBSA03, SBSD08 and SBSD11 produced suitable bands ranging from 900 to 2500 bp. However, only SBSD11 was found to be specific for S. Typhi, and was cloned, sequenced and used to design new SCAR primers. The primers were used to amplify a panel of organisms to evaluate its specificity. However, the amplified regions were similar to other non-Typhi genomes denoting a lack of specificity of the primers as a marker for S. Typhi.
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Affiliation(s)
- Ja'afar Nuhu Ja'afar
- Enteric Diseases Research Cluster, Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, USM, George Town, Penang, Malaysia. .,Department of Biotechnology, School of Life Sciences, Modibbo Adama University of Technology (MAUTECH), Yola, PMB 2076, Adamawa State, Nigeria.
| | - Subhash Janardhan Bhore
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, 08100, Bedong, Kedah, Malaysia
| | - Kia Kien Phua
- Enteric Diseases Research Cluster, Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, USM, George Town, Penang, Malaysia.
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Chien SC, Iap TH, Chiu YR, Shie SS, Chen CJ. Microbiological features of indigenous typhoid cases in Taiwan and relatedness to imported cases, 2001-2014: A cross-sectional analysis. Travel Med Infect Dis 2018; 27:92-98. [PMID: 30300755 DOI: 10.1016/j.tmaid.2018.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Typhoid fever was rare in Taiwan but approximately two-thirds of the cases were indigenous. The transmission source of the indigenous cases and the relatedness to the imported cases remained unknown. METHODS Patients with any site culture positive for Salmonella enterica serovar Typhi were identified in a teaching hospital during 2001-2014. The isolates were determined for antibiotic susceptibilities, pulsed-field gel electrophoresis (PFGE) types and single nucleotide polymorphisms (SNP) types. RESULTS A total of 64 typhoid episodes were identified in 63 patients. Seventeen episodes (26.6%) were imported and a majority (10, 58.8%) of them were from Indonesia. The clinical manifestations, outcomes of patients and antibiograms of isolates were similar between indigenous and imported cases. 63.3% of the isolates were ciprofloxacin-resistant. The distributions of PFGE and SNP types did not differ significantly between indigenous and imported isolates, either (P = 0.191 and 0.124, respectively). Identical PFGE pattern could be identified in indigenous isolates appearing at certain time frames, indicating outbreaks due to local transmission of certain Typhi strains. CONCLUSIONS The imported cases of typhoid fever from Southeast Asia were the major sources of indigenous S. Typhi infections in Taiwan. Small-scale outbreaks occurred due to local transmission of the strains after their importation.
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Affiliation(s)
- Shao-Chieh Chien
- School of Medicine, College of Medicine, Chang Gung University, 333, Taoyuan, Taiwan
| | - Tsong-Him Iap
- School of Medicine, College of Medicine, Chang Gung University, 333, Taoyuan, Taiwan
| | - Yin-Rong Chiu
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, 333, Taoyuan, Taiwan
| | - Shian-Sen Shie
- School of Medicine, College of Medicine, Chang Gung University, 333, Taoyuan, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital, 333, Taoyuan, Taiwan
| | - Chih-Jung Chen
- School of Medicine, College of Medicine, Chang Gung University, 333, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, 333, Taoyuan, Taiwan.
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Pérez-Losada M, Arenas M, Castro-Nallar E. Microbial sequence typing in the genomic era. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 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] [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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Gori M, Ebranati E, Scaltriti E, Huedo P, Ciceri G, Tanzi E, Pontello M, Zehender G, Pongolini S, Bolzoni L. High-resolution diffusion pattern of human infections by Salmonella enterica serovar Napoli in Northern Italy explained through phylogeography. PLoS One 2018; 13:e0202573. [PMID: 30133519 PMCID: PMC6104998 DOI: 10.1371/journal.pone.0202573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/06/2018] [Indexed: 01/31/2023] Open
Abstract
Salmonella enterica serovar Napoli (serovar Napoli) is an emerging cause of human salmonellosis in Northern Italy. No specific reservoirs of serovar Napoli have been identified in Italy, so far. However, the environment, especially surface waters, has been hypothesized as an important source of infection based on the observation that genotypically different clusters of serovar Napoli are detected in different geographical macro-areas. To further support the hypothesis of a spatially-restricted pattern of serovar Napoli diffusion, a spatial segregation of serovar Napoli lineages should be observed also at smaller geographical scale. However, classical genotyping techniques used for Salmonella, such as pulsed-field gel electrophoresis (PFGE), did not possess enough discriminatory power to highlight spatial clustering of serovar Napoli within the macro-areas. To this purpose, we performed phylogeographical analyses based on genome-wide single nucleotide polymorphisms to test whether spatio-temporal evolution patterns of serovar Napoli in Northern Italy could be recognized with high geographical resolution, i.e. at local level. Specifically, we analyzed the local spread of the main PFGE clonal group, responsible for more than 60% of human infections in the study area, that did not show any geographical differentiation by PFGE within Northern Italy, i.e. the macro-area considered in the study. Both discrete and continuous phylogeography highlighted the existence of two main geographically-restricted clades: a Southern clade corresponding to the Po Valley and a Northern clade corresponding to the Pre-Alps area. Furthermore, the phylogeographical analyses suggested that the most probable site of origin of the clone was in an area of the Po Valley at the confluence of the Po and Ticino rivers, one of the most important Italian wetlands. These findings provide further support to the hypothesis that environmental transmission may play an important role in the ecology of serovar Napoli.
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Affiliation(s)
- Maria Gori
- Department of Health Sciences, University of Milan, Milano, Italy
| | - Erika Ebranati
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milano, Italy
| | - Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, Parma, Italy
| | - Pol Huedo
- Department of Health Sciences, University of Milan, Milano, Italy
| | - Giulia Ciceri
- Department of Biomedical Sciences for Health, University of Milan, Milano, Italy
| | - Elisabetta Tanzi
- Department of Biomedical Sciences for Health, University of Milan, Milano, Italy
- CRC-Coordinated Research Center “EpiSoMI”, University of Milan, Milano, Italy
| | - Mirella Pontello
- Department of Health Sciences, University of Milan, Milano, Italy
- CRC-Coordinated Research Center “EpiSoMI”, University of Milan, Milano, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milano, Italy
- CRC-Coordinated Research Center “EpiSoMI”, University of Milan, Milano, Italy
| | - Stefano Pongolini
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, Parma, Italy
| | - Luca Bolzoni
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, Parma, Italy
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Hiyoshi H, Tiffany CR, Bronner DN, Bäumler AJ. Typhoidal Salmonella serovars: ecological opportunity and the evolution of a new pathovar. FEMS Microbiol Rev 2018; 42:527-541. [DOI: 10.1093/femsre/fuy024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/19/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Hirotaka Hiyoshi
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Connor R Tiffany
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Denise N Bronner
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medial Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
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Djeghout B, Saha S, Sajib MSI, Tanmoy AM, Islam M, Kay GL, Langridge GC, Endtz HP, Wain J, Saha SK. Ceftriaxone-resistant Salmonella Typhi carries an IncI1-ST31 plasmid encoding CTX-M-15. J Med Microbiol 2018; 67:620-627. [PMID: 29616895 DOI: 10.1099/jmm.0.000727] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Ceftriaxone is the drug of choice for typhoid fever and the emergence of resistant Salmonella Typhi raises major concerns for treatment. There are an increasing number of sporadic reports of ceftriaxone-resistant S. Typhi and limiting the risk of treatment failure in the patient and outbreaks in the community must be prioritized. This study describes the use of whole genome sequencing to guide outbreak identification and case management. METHODOLOGY An isolate of ceftriaxone-resistant S. Typhi from the blood of a child taken in 2000 at the Popular Diagnostic Center, Dhaka, Bangladesh was subjected to whole genome sequencing, using an Illumina NextSeq 500 and analysis using Geneious software.Results/Key findings. Comparison with other ceftriaxone-resistant S. Typhi revealed an isolate from the Democratic Republic of the Congo in 2015 as the closest relative but no evidence of an outbreak. A plasmid belonging to incompatibility group I1 (IncI1-ST31) which included blaCTX-M-15 (ceftriaxone resistance) associated with ISEcp-1 was identified. High similarity (90 %) was seen with pS115, an IncI1 plasmid from S. Enteritidis, and with pESBL-EA11, an incI1 plasmid from E. coli (99 %) showing that S. Typhi has access to ceftriaxone resistance through the acquisition of common plasmids. CONCLUSIONS The transmission of ceftriaxone resistance from E. coli to S. Typhi is of concern because of clinical resistance to ceftriaxone, the main stay of typhoid treatment. Whole genome sequencing, albeit several years after the isolation, demonstrated the success of containment but clinical trials with alternative agents are urgently required.
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Affiliation(s)
- Bilal Djeghout
- Laboratory of Microbiology and Virology, Department of Biomedical Sciences, University of Sassari, V. le San Pietro 43/B, 07100 Sassari, Italy
| | - Senjuti Saha
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh.,Bangladesh Institute of Child Health, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Mohammad Saiful Islam Sajib
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh.,Bangladesh Institute of Child Health, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Arif Mohammad Tanmoy
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh.,Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Maksuda Islam
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh.,Bangladesh Institute of Child Health, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Gemma L Kay
- Medical Microbiology Research Laboratory, Norwich Medical School, University of East Anglia, Norwich, NR4 7UQ, UK
| | - Gemma C Langridge
- Medical Microbiology Research Laboratory, Norwich Medical School, University of East Anglia, Norwich, NR4 7UQ, UK
| | - Hubert P Endtz
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, the Netherlands.,Laboratoire des Pathogènes Émergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, Lyon, France
| | - John Wain
- Medical Microbiology Research Laboratory, Norwich Medical School, University of East Anglia, Norwich, NR4 7UQ, UK
| | - Samir K Saha
- Bangladesh Institute of Child Health, Dhaka Shishu Hospital, Dhaka, Bangladesh.,Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
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Atterby C, Mourkas E, Méric G, Pascoe B, Wang H, Waldenström J, Sheppard SK, Olsen B, Järhult JD, Ellström P. The Potential of Isolation Source to Predict Colonization in Avian Hosts: A Case Study in Campylobacter jejuni Strains From Three Bird Species. Front Microbiol 2018; 9:591. [PMID: 29651281 PMCID: PMC5884941 DOI: 10.3389/fmicb.2018.00591] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/14/2018] [Indexed: 12/28/2022] Open
Abstract
Campylobacter jejuni is the primary cause of bacterial gastroenteritis worldwide, infecting humans mostly through consumption of contaminated poultry. C. jejuni is common in the gut of wild birds, and shows distinct strain-specific association to particular bird species. This contrasts with farm animals, in which several genotypes co-exist. It is unclear if the barriers restricting transmission between host species of such specialist strains are related to environmental factors such as contact between host species, bacterial survival in the environment, etc., or rather to strain specific adaptation to the intestinal environment of specific hosts. We compared colonization dynamics in vivo between two host-specific C. jejuni from a song thrush (ST-1304 complex) and a mallard (ST-995), and a generalist strain from chicken (ST-21 complex) in a wild host, the mallard (Anas platyrhynchos). In 18-days infection experiments, the song thrush strain showed only weak colonization and was cleared from all birds after 10 days, whereas both mallard and chicken strains remained stable. When the chicken strain was given 4 days prior to co-infection of the same birds with a mallard strain, it was rapidly outcompeted by the latter. In contrast, when the mallard strain was given 4 days prior to co-infection with the chicken strain, the mallard strain remained and expansion of the chicken strain was delayed. Our results suggest strain-specific differences in the ability of C. jejuni to colonize mallards, likely associated with host origin. This difference might explain observed host association patterns in C. jejuni from wild birds.
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Affiliation(s)
- Clara Atterby
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Evangelos Mourkas
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden.,Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Guillaume Méric
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Ben Pascoe
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom.,MRC CLIMB Consortium, Bath, United Kingdom
| | - Helen Wang
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Samuel K Sheppard
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom.,MRC CLIMB Consortium, Bath, United Kingdom
| | - Björn Olsen
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Josef D Järhult
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Patrik Ellström
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
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Ancient balancing selection on heterocyst function in a cosmopolitan cyanobacterium. Nat Ecol Evol 2018; 2:510-519. [DOI: 10.1038/s41559-017-0435-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 11/29/2017] [Indexed: 11/08/2022]
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Abstract
The coevolution of intracellular bacteria with their eukaryotic hosts has presented these pathogens with numerous challenges for their evolutionary progress and survival. Chief among these is the ability to exit from host cells, an event that is fundamentally linked to pathogen dissemination and transmission. Recent years have witnessed a major expansion of research in this area, and this chapter summarizes our current understanding of the spectrum of exit strategies that are exploited by intracellular pathogens. Clear themes regarding the mechanisms of microbial exit have emerged and are most easily conceptualized as (i) lysis of the host cell, (ii) nonlytic exit of free bacteria, and (iii) release of microorganisms into membrane-encased compartments. The adaptation of particular exit strategies is closely linked with additional themes in microbial pathogenesis, including host cell death, manipulation of host signaling pathways, and coincident activation of proinflammatory responses. This chapter will explore the molecular determinants used by intracellular pathogens to promote host cell escape and the infectious advantages each exit pathway may confer, and it will provide an evolutionary framework for the adaptation of these mechanisms.
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Hauck S, Maiden MCJ. Clonally Evolving Pathogenic Bacteria. MOLECULAR MECHANISMS OF MICROBIAL EVOLUTION 2018. [DOI: 10.1007/978-3-319-69078-0_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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