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Dyson ZA, Ashton PM, Khanam F, Chunga Chirambo A, Shakya M, Meiring JE, Tonks S, Karkey A, Msefula C, Clemens JD, Dunstan SJ, Baker S, Dougan G, Pitzer VE, Basnyat B, Qadri F, Heyderman RS, Gordon MA, Pollard AJ, Holt KE. Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study. THE LANCET. MICROBE 2024:S2666-5247(24)00047-8. [PMID: 38996496 DOI: 10.1016/s2666-5247(24)00047-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND Enteric fever is a serious public health concern. The causative agents, Salmonella enterica serovars Typhi and Paratyphi A, frequently have antimicrobial resistance (AMR), leading to limited treatment options and poorer clinical outcomes. We investigated the genomic epidemiology, resistance mechanisms, and transmission dynamics of these pathogens at three urban sites in Africa and Asia. METHODS S Typhi and S Paratyphi A bacteria isolated from blood cultures of febrile children and adults at study sites in Dhaka (Bangladesh), Kathmandu (Nepal), and Blantyre (Malawi) during STRATAA surveillance were sequenced. Isolates were charactered in terms of their serotypes, genotypes (according to GenoTyphi and Paratype), molecular determinants of AMR, and population structure. We used phylogenomic analyses incorporating globally representative genomic data from previously published surveillance studies and ancestral state reconstruction to differentiate locally circulating from imported pathogen AMR variants. Clusters of sequences without any single-nucleotide variants in their core genome were identified and used to explore spatiotemporal patterns and transmission dynamics. FINDINGS We sequenced 731 genomes from isolates obtained during surveillance across the three sites between Oct 1, 2016, and Aug 31, 2019 (24 months in Dhaka and Kathmandu and 34 months in Blantyre). S Paratyphi A was present in Dhaka and Kathmandu but not Blantyre. S Typhi genotype 4.3.1 (H58) was common in all sites, but with different dominant variants (4.3.1.1.EA1 in Blantyre, 4.3.1.1 in Dhaka, and 4.3.1.2 in Kathmandu). Multidrug resistance (ie, resistance to chloramphenicol, co-trimoxazole, and ampicillin) was common in Blantyre (138 [98%] of 141 cases) and Dhaka (143 [32%] of 452), but absent from Kathmandu. Quinolone-resistance mutations were common in Dhaka (451 [>99%] of 452) and Kathmandu (123 [89%] of 138), but not in Blantyre (three [2%] of 141). Azithromycin-resistance mutations in acrB were rare, appearing only in Dhaka (five [1%] of 452). Phylogenetic analyses showed that most cases derived from pre-existing, locally established pathogen variants; 702 (98%) of 713 drug-resistant infections resulted from local circulation of AMR variants, not imported variants or recent de novo emergence; and pathogen variants circulated across age groups. 479 (66%) of 731 cases clustered with others that were indistinguishable by point mutations; individual clusters included multiple age groups and persisted for up to 2·3 years, and AMR determinants were invariant within clusters. INTERPRETATION Enteric fever was associated with locally established pathogen variants that circulate across age groups. AMR infections resulted from local transmission of resistant strains. These results form a baseline against which to monitor the impacts of control measures. FUNDING Wellcome Trust, Bill & Melinda Gates Foundation, EU Horizon 2020, and UK National Institute for Health and Care Research.
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Affiliation(s)
- Zoe A Dyson
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Philip M Ashton
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi; Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Farhana Khanam
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Angeziwa Chunga Chirambo
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi; Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Mila Shakya
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - James E Meiring
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Susan Tonks
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal; Centre for Tropical Medicine and Global Health, Medical Sciences Division, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - John D Clemens
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh; International Vaccine Institute, Seoul, South Korea
| | - Sarah J Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Stephen Baker
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Gordon Dougan
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal; Centre for Tropical Medicine and Global Health, Medical Sciences Division, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Robert S Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Melita A Gordon
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi; Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK; Kamuzu University of Health Sciences, Blantyre, Malawi; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
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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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Weyant C, Hooda Y, Munira SJ, Lo NC, Ryckman T, Tanmoy AM, Kanon N, Seidman JC, Garrett D, Saha SK, Goldhaber-Fiebert JD, Saha S, Andrews JR. Cost-effectiveness and public health impact of typhoid conjugate vaccine introduction strategies in Bangladesh. Vaccine 2024; 42:2867-2876. [PMID: 38531727 PMCID: PMC11033679 DOI: 10.1016/j.vaccine.2024.03.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024]
Abstract
PURPOSE Typhoid fever causes substantial morbidity and mortality in Bangladesh. The government of Bangladesh plans to introduce typhoid conjugate vaccines (TCV) in its expanded program on immunization (EPI) schedule. However, the optimal introduction strategy in addition to the costs and benefits of such a program are unclear. METHODS We extended an existing mathematical model of typhoid transmission to integrate cost data, clinical incidence data, and recently conducted serosurveys in urban, semi-urban, and rural areas. In our primary analysis, we evaluated the status quo (i.e., no vaccination) and eight vaccine introduction strategies including routine and 1-time campaign strategies, which differed by age groups targeted and geographic focus. Model outcomes included clinical incidence, seroincidence, deaths, costs, disability-adjusted life years (DALYs), and incremental cost-effectiveness ratios (ICERs) for each strategy. We adopted a societal perspective, 10-year model time horizon, and 3 % annual discount rate. We performed probabilistic, one-way, and scenario sensitivity analyses including adopting a healthcare perspective and alternate model time horizons. RESULTS We projected that all TCV strategies would be cost saving compared to the status quo. The preferred strategy was a nationwide introduction of TCV at 9-12 months of age with a single catch-up campaign for children ages 1-15, which was cost saving compared to all other strategies and the status quo. In the 10 years following implementation, we projected this strategy would avert 3.77 million cases (95 % CrI: 2.60 - 5.18), 11.31 thousand deaths (95 % CrI: 3.77 - 23.60), and save $172.35 million (95 % CrI: -14.29 - 460.59) compared to the status quo. Our findings were broadly robust to changes in parameter values and willingness-to-pay thresholds. CONCLUSIONS We projected that nationwide TCV introduction with a catch-up campaign would substantially reduce typhoid incidence and very likely be cost saving in Bangladesh.
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Affiliation(s)
- Christopher Weyant
- Department of Health Policy and Center for Health Policy, Stanford School of Medicine and Freeman Spogli Institute, Stanford University, Stanford, CA, United States.
| | - Yogesh Hooda
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | - Nathan C Lo
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Theresa Ryckman
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | | | - Naito Kanon
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | | | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh; Department of Microbiology, Bangladesh Shishu Hospital and Institute, Dhaka, Bangladesh
| | - Jeremy D Goldhaber-Fiebert
- Department of Health Policy and Center for Health Policy, Stanford School of Medicine and Freeman Spogli Institute, Stanford University, Stanford, CA, United States
| | - Senjuti Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, United States
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4
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Chowdhury AR, Mukherjee D, Chatterjee R, Chakravortty D. Defying the odds: Determinants of the antimicrobial response of Salmonella Typhi and their interplay. Mol Microbiol 2024; 121:213-229. [PMID: 38071466 DOI: 10.1111/mmi.15209] [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: 07/31/2023] [Revised: 11/12/2023] [Accepted: 11/27/2023] [Indexed: 02/12/2024]
Abstract
Salmonella Typhi, the invasive serovar of S. enterica subspecies enterica, causes typhoid fever in healthy human hosts. The emergence of antibiotic-resistant strains has consistently challenged the successful treatment of typhoid fever with conventional antibiotics. Antimicrobial resistance (AMR) in Salmonella is acquired either by mutations in the genomic DNA or by acquiring extrachromosomal DNA via horizontal gene transfer. In addition, Salmonella can form a subpopulation of antibiotic persistent (AP) cells that can survive at high concentrations of antibiotics. These have reduced the effectiveness of the first and second lines of antibiotics used to treat Salmonella infection. The recurrent and chronic carriage of S. Typhi in human hosts further complicates the treatment process, as a remarkable shift in the immune response from pro-inflammatory Th1 to anti-inflammatory Th2 is observed. Recent studies have also highlighted the overlap between AP, persistent infection (PI) and AMR. These incidents have revealed several areas of research. In this review, we have put forward a timeline for the evolution of antibiotic resistance in Salmonella and discussed the different mechanisms of the same availed by the pathogen at the genotypic and phenotypic levels. Further, we have presented a detailed discussion on Salmonella antibiotic persistence (AP), PI, the host and bacterial virulence factors that can influence PI, and how both AP and PI can lead to AMR.
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Affiliation(s)
- Atish Roy Chowdhury
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Debapriya Mukherjee
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Ritika Chatterjee
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, India
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5
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Hooda Y, Islam S, Kabiraj R, Rahman H, Sarkar H, da Silva KE, Raju RS, Luby SP, Andrews JR, Saha SK, Saha S. Old tools, new applications: Use of environmental bacteriophages for typhoid surveillance and evaluating vaccine impact. PLoS Negl Trop Dis 2024; 18:e0011822. [PMID: 38358956 PMCID: PMC10868810 DOI: 10.1371/journal.pntd.0011822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/27/2023] [Indexed: 02/17/2024] Open
Abstract
Typhoid-conjugate vaccines (TCVs) provide an opportunity to reduce the burden of typhoid fever, caused by Salmonella Typhi, in endemic areas. As policymakers design vaccination strategies, accurate and high-resolution data on disease burden is crucial. However, traditional blood culture-based surveillance is resource-extensive, prohibiting its large-scale and sustainable implementation. Salmonella Typhi is a water-borne pathogen, and here, we tested the potential of Typhi-specific bacteriophage surveillance in surface water bodies as a low-cost tool to identify where Salmonella Typhi circulates in the environment. In 2021, water samples were collected and tested for the presence of Salmonella Typhi bacteriophages at two sites in Bangladesh: urban capital city, Dhaka, and a rural district, Mirzapur. Salmonella Typhi-specific bacteriophages were detected in 66 of 211 (31%) environmental samples in Dhaka, in comparison to 3 of 92 (3%) environmental samples from Mirzapur. In the same year, 4,620 blood cultures at the two largest pediatric hospitals of Dhaka yielded 215 (5%) culture-confirmed typhoid cases, and 3,788 blood cultures in the largest hospital of Mirzapur yielded 2 (0.05%) cases. 75% (52/69) of positive phage samples were collected from sewage. All isolated phages were tested against a panel of isolates from different Salmonella Typhi genotypes circulating in Bangladesh and were found to exhibit a diverse killing spectrum, indicating that diverse bacteriophages were isolated. These results suggest an association between the presence of Typhi-specific phages in the environment and the burden of typhoid fever, and the potential of utilizing environmental phage surveillance as a low-cost tool to assist policy decisions on typhoid control.
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Affiliation(s)
- Yogesh Hooda
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | | | | | | | - Kesia E. da Silva
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | | | - Stephen P. Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jason R. Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Samir K. Saha
- Child Health Research Foundation, Dhaka, Bangladesh
- Department of Microbiology, Bangladesh Shishu Hospital and Institute, Dhaka, Bangladesh
| | - Senjuti Saha
- Child Health Research Foundation, Dhaka, Bangladesh
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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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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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8
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Irshad M, Mahmood SF. Extended drug-resistant Salmonella typhi osteomyelitis: a case report and literature review. THE EGYPTIAN JOURNAL OF INTERNAL MEDICINE 2022. [DOI: 10.1186/s43162-022-00173-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Background
Salmonella typhi infection commonly results in gastroenteritis, bacteremia with or without secondary seeding, or asymptomatic carrier stage. Few cases of Salmonella typhi bacteremia later result in seeding and ultimately lead to further complications including osteomyelitis and rarely vertebral osteomyelitis.
Case presentation
We are discussing a case of a 38-year-old Asian male patient, with no known comorbids. He presented with fever and backache for 4 weeks. Based on the magnetic resonance imaging (MRI) findings of the spine and positive blood cultures, a diagnosis of XDR Salmonella typhi (S. typhi) osteomyelitis (OM) was made. Patient was started on intravenous therapy as per culture report which was later modified according to treatment response.
Conclusion
S. typhi has a broad spectrum of clinical manifestations including osteomyelitis however to the best of our knowledge this is the first reported case of XDR S. typhi vertebral osteomyelitis. We describe the clinical course of the patient and review the literature regarding the treatment of S.typhi vertebral osteomyelitis with a special focus on XDR S. typhi. Treatment course and complications in view of this new resistant strain have to be reported in order to devise general guidelines for the management in such particular cases.
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9
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Persistence of Rare Salmonella Typhi Genotypes Susceptible to First-Line Antibiotics in the Remote Islands of Samoa. mBio 2022; 13:e0192022. [PMID: 36094088 PMCID: PMC9600463 DOI: 10.1128/mbio.01920-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
For decades, the remote island nation of Samoa (population ~200,000) has faced endemic typhoid fever despite improvements in water quality, sanitation, and economic development. We recently described the epidemiology of typhoid fever in Samoa from 2008 to 2019 by person, place, and time; however, the local Salmonella enterica serovar Typhi (S. Typhi) population structure, evolutionary origins, and genomic features remained unknown. Herein, we report whole genome sequence analyses of 306 S. Typhi isolates from Samoa collected between 1983 and 2020. Phylogenetics revealed a dominant population of rare genotypes 3.5.4 and 3.5.3, together comprising 292/306 (95.4%) of Samoan versus 2/4934 (0.04%) global S. Typhi isolates. Three distinct 3.5.4 genomic sublineages were identified, and their defining polymorphisms were determined. These dominant Samoan genotypes, which likely emerged in the 1970s, share ancestry with other 3.5 clade isolates from South America, Southeast Asia, and Oceania. Additionally, a 106-kb pHCM2 phenotypically cryptic plasmid, detected in a 1992 Samoan S. Typhi isolate, was identified in 106/306 (34.6%) of Samoan isolates; this is more than double the observed proportion of pHCM2-containing isolates in the global collection. In stark contrast with global S. Typhi trends, resistance-conferring polymorphisms were detected in only 15/306 (4.9%) of Samoan S. Typhi, indicating overwhelming susceptibility to antibiotics that are no longer effective in most of South and Southeast Asia. This country-level genomic framework can help local health authorities in their ongoing typhoid surveillance and control efforts, as well as fill a critical knowledge gap in S. Typhi genomic data from Oceania. IMPORTANCE In this study, we used whole genome sequencing and comparative genomics analyses to characterize the population structure, evolutionary origins, and genomic features of S. Typhi associated with decades of endemic typhoid fever in Samoa. Our analyses of Samoan isolates from 1983 to 2020 identified a rare S. Typhi population in Samoa that likely emerged around the early 1970s and evolved into sublineages that are presently dominant. The dominance of these endemic genotypes in Samoa is not readily explained by genomic content or widespread acquisition of antimicrobial resistance. These data establish the necessary framework for future genomic surveillance of S. Typhi in Samoa for public health benefit.
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10
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Yusof NY, Norazzman NII, Zaidi NFM, Azlan MM, Ghazali B, Najib MA, Malik AHA, Halim MAHA, Sanusi MNSM, Zainal AA, Aziah I. Prevalence of Antimicrobial Resistance Genes in Salmonella Typhi: A Systematic Review and Meta-Analysis. Trop Med Infect Dis 2022; 7:tropicalmed7100271. [PMID: 36288012 PMCID: PMC9611315 DOI: 10.3390/tropicalmed7100271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/23/2022] [Accepted: 09/25/2022] [Indexed: 11/16/2022] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi) that has developed resistance to many antimicrobials poses a serious challenge to public health. Hence, this study aimed to systematically determine the prevalence of antimicrobial resistance (AMR) in S. Typhi isolated from the environment and humans as well as to ascertain the spread of the selected AMR genes in S. Typhi. This systematic review and meta-analysis were performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines, and the study protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO). A total of 2353 studies were retrieved from three databases, of which 42 studies fulfilled the selection criteria. The pooled prevalence of AMR S. Typhi (using a random-effect model) was estimated at 84.8% (95% CI; 77.3−90.2), with high heterogeneity (I2: 95.35%, p-value < 0.001). The high estimated prevalence indicates that control methods should be improved immediately to prevent the spread of AMR among S. Typhi internationally.
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Affiliation(s)
- Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Correspondence: (N.Y.Y.); (I.A.)
| | - Nur Iffah Izzati Norazzman
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Nur Fatihah Mohd Zaidi
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Mawaddah Mohd Azlan
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Basyirah Ghazali
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Mohamad Ahmad Najib
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Abdul Hafiz Abdul Malik
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | | | | | - Annur Ashyqin Zainal
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Ismail Aziah
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Correspondence: (N.Y.Y.); (I.A.)
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11
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da Silva KE, Tanmoy AM, Pragasam AK, Iqbal J, Sajib MSI, Mutreja A, Veeraraghavan B, Tamrakar D, Qamar FN, Dougan G, Bogoch I, Seidman JC, Shakya J, Vaidya K, Carey ME, Shrestha R, Irfan S, Baker S, Luby SP, Cao Y, Dyson ZA, Garrett DO, John J, Kang G, Hooda Y, Saha SK, Saha S, Andrews JR. The international and intercontinental spread and expansion of antimicrobial-resistant Salmonella Typhi: a genomic epidemiology study. THE LANCET MICROBE 2022; 3:e567-e577. [PMID: 35750070 PMCID: PMC9329132 DOI: 10.1016/s2666-5247(22)00093-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/25/2022] Open
Abstract
Background The emergence of increasingly antimicrobial-resistant Salmonella enterica serovar Typhi (S Typhi) threatens to undermine effective treatment and control. Understanding where antimicrobial resistance in S Typhi is emerging and spreading is crucial towards formulating effective control strategies. Methods In this genomic epidemiology study, we sequenced the genomes of 3489 S Typhi strains isolated from prospective enteric fever surveillance studies in Nepal, Bangladesh, Pakistan, and India (between 2014 and 2019), and combined these with a global collection of 4169 S Typhi genome sequences isolated between 1905 and 2018 to investigate the temporal and geographical patterns of emergence and spread of antimicrobial-resistant S Typhi. We performed non-parametric phylodynamic analyses to characterise changes in the effective population size of fluoroquinolone-resistant, extensively drug-resistant (XDR), and azithromycin-resistant S Typhi over time. We inferred timed phylogenies for the major S Typhi sublineages and used ancestral state reconstruction methods to estimate the frequency and timing of international and intercontinental transfers. Findings Our analysis revealed a declining trend of multidrug resistant typhoid in south Asia, except for Pakistan, where XDR S Typhi emerged in 2016 and rapidly replaced less-resistant strains. Mutations in the quinolone-resistance determining region (QRDR) of S Typhi have independently arisen and propagated on at least 94 occasions, nearly all occurring in south Asia. Strains with multiple QRDR mutations, including triple mutants with high-level fluoroquinolone resistance, have been increasing in frequency and displacing strains with fewer mutations. Strains containing acrB mutations, conferring azithromycin resistance, emerged in Bangladesh around 2013 and effective population size of these strains has been steadily increasing. We found evidence of frequent international (n=138) and intercontinental transfers (n=59) of antimicrobial-resistant S Typhi, followed by local expansion and replacement of drug-susceptible clades. Interpretation Independent acquisition of plasmids and homoplastic mutations conferring antimicrobial resistance have occurred repeatedly in multiple lineages of S Typhi, predominantly arising in south Asia before spreading to other regions. Funding Bill & Melinda Gates Foundation.
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12
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Noor M, Rahim F, Amin S, Ullah R, Zafar S. A Patient With Fever, Loose Motions and Jaundice: Hickam’s Dictum or Occam's Razor. Cureus 2022; 14:e23295. [PMID: 35464514 PMCID: PMC9013503 DOI: 10.7759/cureus.23295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2022] [Indexed: 11/23/2022] Open
Abstract
Infectious diseases like malaria, typhoid, leptospirosis, and dengue fever are the leading causes of morbidity and mortality in developing countries like Pakistan. Although rare, it is possible to have coinfection with organisms that are endemic in a region, causing diagnostic and therapeutic dilemmas. Leptospirosis is caused by Gram-negative spirochetes. Leptospira are widely distributed and are transmitted by contamination of water and food by the urine of infected animals like rodents. Leptospirosis is characterized by fever, body aches, abdominal pain, and hepatic and renal involvement. Laboratory abnormalities include cytopenia, elevated bilirubin, alanine aminotransferase, and abnormal renal function tests. Typhoid fever is caused by Salmonella typhi (S. typhi), which is transmitted by fecal contamination of drinking water and food items. The clinical manifestations of typhoid fever include fever, abdominal pain, and diarrhea. Laboratory abnormalities include cytopenia and mildly deranged liver function tests. A strain of S. typhi resistant to all antibiotics except azithromycin and carbapenems was isolated in 2016 in Pakistan. Most of the clinical manifestations and laboratory abnormalities of leptospirosis and typhoid fever overlap. There have been case reports of coinfection of S. typhi and Leptospira, but there is no report of coinfection of extensively drug-resistant (XDR) S. typhi and Leptospira. We present a case of a 20-year-old man with fever, loose motions, and jaundice from Peshawar, Pakistan who had coinfection of Leptospira and XDR S. typhi. The attending physicians should adopt Hickam’s dictum instead of Occam's razor approach.
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13
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Hou J, Mao D, Zhang Y, Huang R, Li L, Wang X, Luo Y. Long-term spatiotemporal variation of antimicrobial resistance genes within the Serratia marcescens population and transmission of S. marcescens revealed by public whole-genome datasets. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127220. [PMID: 34844350 DOI: 10.1016/j.jhazmat.2021.127220] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/05/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
The development of antimicrobial resistance (AMR) is accelerated by the selective pressure exerted by the widespread use of antimicrobial drugs, posing an increasing danger to public health. However, long-term spatiotemporal variation in AMR genes in microorganisms, particularly in bacterial pathogens in response to antibiotic consumption, is not fully understood. Here, we used the NCBI RefSeq database to collect 478 whole-genome sequences for Serratia marcescens ranging from 1961 up to 2019, to document global long-term AMR trends in S. marcescens populations. In total, 100 AMR gene subtypes (16 AMR gene types) were detected in the genomes of S. marcescens populations. We identified 3 core resistance genes in S. marcescens genomes, and a high diversity of AMR genes was observed in S. marcescens genomes after corresponding antibiotics were discovered and introduced into clinical practice, suggesting the adaptation of S. marcescens populations to challenges with therapeutic antibiotics. Our findings indicate spatiotemporal variation of AMR genes in S. marcescens populations in relation to antibiotic consumption and suggest the potential transmission of S. marcescens isolates harboring AMR genes among countries and between the environment and the clinic, representing a public health threat that necessitates international solidarity to overcome.
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Affiliation(s)
- Jie Hou
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yulin Zhang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Ruiyang Huang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Linyun Li
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Xiaolong Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China.
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14
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Akter T, Chakma M, Tanzina AY, Rumi MH, Shimu MSS, Saleh MA, Mahmud S, Sami SA, Emran TB. Curcumin Analogues as a Potential Drug against Antibiotic Resistant Protein, β-Lactamases and L, D-Transpeptidases Involved in Toxin Secretion in Salmonella typhi: A Computational Approach. BIOMEDINFORMATICS 2021; 2:77-100. [DOI: 10.3390/biomedinformatics2010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Typhoid fever caused by the bacteria Salmonella typhi gained resistance through multidrug-resistant S. typhi strains. One of the reasons behind β-lactam antibiotic resistance is -lactamase. L, D-Transpeptidases is responsible for typhoid fever as it is involved in toxin release that results in typhoid fever in humans. A molecular modeling study of these targeted proteins was carried out by various methods, such as homology modeling, active site prediction, prediction of disease-causing regions, and by analyzing the potential inhibitory activities of curcumin analogs by targeting these proteins to overcome the antibiotic resistance. The five potent drug candidate compounds were identified to be natural ligands that can inhibit those enzymes compared to controls in our research. The binding affinity of both the Go-Y032 and NSC-43319 were found against β-lactamase was −7.8 Kcal/mol in AutoDock, whereas, in SwissDock, the binding energy was −8.15 and −8.04 Kcal/mol, respectively. On the other hand, the Cyclovalone and NSC-43319 had an equal energy of −7.60 Kcal/mol in AutoDock, whereas −7.90 and −8.01 Kcal/mol in SwissDock against L, D-Transpeptidases. After the identification of proteins, the determination of primary and secondary structures, as well as the gene producing area and homology modeling, was accomplished. The screened drug candidates were further evaluated in ADMET, and pharmacological properties along with positive drug-likeness properties were observed for these ligand molecules. However, further in vitro and in vivo experiments are required to validate these in silico data to develop novel therapeutics against antibiotic resistance.
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15
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VanOeffelen M, Nguyen M, Aytan-Aktug D, Brettin T, Dietrich EM, Kenyon RW, Machi D, Mao C, Olson R, Pusch GD, Shukla M, Stevens R, Vonstein V, Warren AS, Wattam AR, Yoo H, Davis JJ. A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes. Brief Bioinform 2021; 22:bbab313. [PMID: 34379107 PMCID: PMC8575023 DOI: 10.1093/bib/bbab313] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/18/2021] [Accepted: 07/20/2021] [Indexed: 11/14/2022] Open
Abstract
Antimicrobial resistance (AMR) is a major global health threat that affects millions of people each year. Funding agencies worldwide and the global research community have expended considerable capital and effort tracking the evolution and spread of AMR by isolating and sequencing bacterial strains and performing antimicrobial susceptibility testing (AST). For the last several years, we have been capturing these efforts by curating data from the literature and data resources and building a set of assembled bacterial genome sequences that are paired with laboratory-derived AST data. This collection currently contains AST data for over 67 000 genomes encompassing approximately 40 genera and over 100 species. In this paper, we describe the characteristics of this collection, highlighting areas where sampling is comparatively deep or shallow, and showing areas where attention is needed from the research community to improve sampling and tracking efforts. In addition to using the data to track the evolution and spread of AMR, it also serves as a useful starting point for building machine learning models for predicting AMR phenotypes. We demonstrate this by describing two machine learning models that are built from the entire dataset to show where the predictive power is comparatively high or low. This AMR metadata collection is freely available and maintained on the Bacterial and Viral Bioinformatics Center (BV-BRC) FTP site ftp://ftp.bvbrc.org/RELEASE_NOTES/PATRIC_genomes_AMR.txt.
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Affiliation(s)
| | - Marcus Nguyen
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA
| | - Derya Aytan-Aktug
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Thomas Brettin
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL, USA
| | - Emily M Dietrich
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL, USA
| | - Ronald W Kenyon
- Biocomplexity Institute and Initiative, University of Virginia, Virginia, USA
| | - Dustin Machi
- Biocomplexity Institute and Initiative, University of Virginia, Virginia, USA
| | - Chunhong Mao
- Biocomplexity Institute and Initiative, University of Virginia, Virginia, USA
| | - Robert Olson
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA
| | - Gordon D Pusch
- Fellowship for Interpretation of Genomes, Burr Ridge, IL, USA
| | - Maulik Shukla
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA
| | - Rick Stevens
- Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL, USA
- Department of Computer Science, University of Chicago, Chicago, IL, USA
| | | | - Andrew S Warren
- Biocomplexity Institute and Initiative, University of Virginia, Virginia, USA
| | - Alice R Wattam
- Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA
- Biocomplexity Institute and Initiative, University of Virginia, Virginia, USA
| | - Hyunseung Yoo
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA
| | - James J Davis
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA
- Northwestern Argonne Institute for Science and Engineering, Evanston, IL, USA
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16
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Wan Makhtar WR, Bharudin I, Samsulrizal NH, Yusof NY. Whole Genome Sequencing Analysis of Salmonella enterica Serovar Typhi: History and Current Approaches. Microorganisms 2021; 9:microorganisms9102155. [PMID: 34683476 PMCID: PMC8538346 DOI: 10.3390/microorganisms9102155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 12/27/2022] Open
Abstract
In recent years, the advance in whole-genome sequencing technology has changed the study of infectious diseases. The emergence of genome sequencing has improved the understanding of infectious diseases, which has revamped many fields, such as molecular microbiology, epidemiology, infection control, and vaccine production. In this review we discuss the findings of Salmonella enterica serovar Typhi genomes, publicly accessible from the initial complete genome to the recent update of Salmonella enterica serovar Typhi genomes, which has greatly improved Salmonella enterica serovar Typhi and other pathogen genomic research. Significant information on genetic changes, evolution, antimicrobial resistance, virulence, pathogenesis, and investigation from the genome sequencing of S. Typhi is also addressed. This review will gather information on the variation of the Salmonella enterica serovar Typhi genomes and hopefully facilitate our understanding of their genome evolution, dynamics of adaptation, and pathogenesis for the development of the typhoid point-of-care diagnostics, medications, and vaccines.
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Affiliation(s)
- Wan Ratmaazila Wan Makhtar
- Reconstructive Sciences Unit, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia;
| | - Izwan Bharudin
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia UKM, Bangi 43600, Malaysia;
| | - Nurul Hidayah Samsulrizal
- Department of Plant Science, Kuliyyah of Science, International Islamic University Malaysia, Kuantan 25200, Malaysia;
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Correspondence:
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17
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Rahman SIA, Nguyen TNT, Khanam F, Thomson NR, Dyson ZA, Taylor-Brown A, Chowdhury EK, Dougan G, Baker S, Qadri F. Genetic diversity of Salmonella Paratyphi A isolated from enteric fever patients in Bangladesh from 2008 to 2018. PLoS Negl Trop Dis 2021; 15:e0009748. [PMID: 34648506 PMCID: PMC8516307 DOI: 10.1371/journal.pntd.0009748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 08/22/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The proportion of enteric fever cases caused by Salmonella Paratyphi A is increasing and may increase further as we begin to introduce typhoid conjugate vaccines (TCVs). While numerous epidemiological and genomic studies have been conducted for S. Typhi, there are limited data describing the genomic epidemiology of S. Paratyphi A in especially in endemic settings, such as Bangladesh. PRINCIPAL FINDINGS We conducted whole genome sequencing (WGS) of 67 S. Paratyphi A isolated between 2008 and 2018 from eight enteric disease surveillance sites across Bangladesh. We performed a detailed phylogenetic analysis of these sequence data incorporating sequences from 242 previously sequenced S. Paratyphi A isolates from a global collection and provided evidence of lineage migration from neighboring countries in South Asia. The data revealed that the majority of the Bangladeshi S. Paratyphi A isolates belonged to the dominant global lineage A (67.2%), while the remainder were either lineage C (19.4%) or F (13.4%). The population structure was relatively homogenous across the country as we did not find any significant lineage distributions between study sites inside or outside Dhaka. Our genomic data showed presence of single point mutations in gyrA gene either at codon 83 or 87 associated with decreased fluoroquinolone susceptibility in all Bangladeshi S. Paratyphi A isolates. Notably, we identified the pHCM2- like cryptic plasmid which was highly similar to S. Typhi plasmids circulating in Bangladesh and has not been previously identified in S. Paratyphi A organisms. SIGNIFICANCE This study demonstrates the utility of WGS to monitor the ongoing evolution of this emerging enteric pathogen. Novel insights into the genetic structure of S. Paratyphi A will aid the understanding of both regional and global circulation patterns of this emerging pathogen and provide a framework for future genomic surveillance studies.
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Affiliation(s)
- Sadia Isfat Ara Rahman
- Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - To Nguyen Thi Nguyen
- Oxford University Clinical Research Unit, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Farhana Khanam
- Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Nicholas R. Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Infection Biology, Faculty of Infections and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Zoe A. Dyson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Infection Biology, Faculty of Infections and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Alyce Taylor-Brown
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Emran Kabir Chowdhury
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Gordon Dougan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Stephen Baker
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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18
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Saha S, Saha SK. Invasive Bacterial Vaccine-Preventable Disease Surveillance: Successes and Lessons Learned in Bangladesh for a Sustainable Path Forward. J Infect Dis 2021; 224:S293-S298. [PMID: 34469550 PMCID: PMC8409528 DOI: 10.1093/infdis/jiab129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have made considerable progress in setting and scaling up surveillance systems to drive evidence-based policy decisions, but the recent epidemics highlight that current systems are not optimally designed. Good surveillance systems should be coordinated, comprehensive, and adaptive. They should generate data in real time for immediate analysis and intervention, whether for endemic diseases or potential epidemics. Such systems are especially needed in low-resource settings where disease burden is the highest, but tracking systems are the weakest here due to competing priorities and constraints on available resources. In this article, using the examples of 3 large, and mostly successful, infectious disease surveillance studies in Bangladesh, we identify 2 core limitations—the pathogen bias and the vaccine bias—in the way current surveillance programs are designed for low-resource settings. We highlight the strengths of the current Global Invasive Bacterial Vaccine Preventable Disease Surveillance Network of the World Health Organization and present case studies from Bangladesh to illustrate how this surveillance platform can be leveraged to overcome its limitations. Finally, we propose a set of criteria for building a comprehensive infectious disease surveillance system with the hope of encouraging current systems to use the limited resources as optimally as possible to generate the maximum amount of knowledge.
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Affiliation(s)
- Senjuti Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh.,Dhaka Shishu Hospital, Dhaka, Bangladesh.,Bangladesh Institute of Child Health, Dhaka, Bangladesh
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Reply to Fabre et al. 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:genes12081147. [PMID: 34440321 PMCID: PMC8392857 DOI: 10.3390/genes12081147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 11/17/2022] Open
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20
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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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21
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Molecular Characterization of Fluoroquinolone-Resistant Bartonella bacilliformis. Pathogens 2021; 10:pathogens10070876. [PMID: 34358026 PMCID: PMC8308817 DOI: 10.3390/pathogens10070876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 11/17/2022] Open
Abstract
The presence of amino acid changes in GyrA, GyrB, ParC, ParE, and in a proposed chromosomal chloramphenicol acetyl transferase (CAT), as well as mutations at 23S rRNA, were established by PCR and sequencing in 38 B. bacilliformis clinical isolates from four different areas in Peru. Eighteen out of 24 (75%) isolates showing ciprofloxacin resistance for both disk-diffusion and e-test presented amino acid substitutions in GyrA (G89C, six isolates, A91V, 1 isolate) GyrB (S474F, 10 isolates) or both (GyrA D95N and GyrB S474F, one isolate). Two out of 14 susceptible isolates presented amino acid substitutions at GyrB (S474F) or a double substitution GyrA D95N and GyrB S474F. Of note, ciprofloxacin-resistant isolates were recovered in the four areas studied. No amino acid change was observed at ParC or ParE. Only one isolate showed chloramphenicol resistance, but no alteration was present in either 23S rRNA or CAT. B. bacilliformis resistant to quinolones are extended throughout Peru, with amino acid substitutions at GyrA or GyrB as the main, albeit not exclusive, cause. B. bacilliformis seems to have an apparent facility to develop mutations on GyrB outside the classical positions 91, 95 of GyrA and 85, 88 of ParC.
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22
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Britto CD, Dyson ZA, Mathias S, Bosco A, Dougan G, Jose S, Nagaraj S, Holt KE, Pollard AJ. Persistent circulation of a fluoroquinolone-resistant Salmonella enterica Typhi clone in the Indian subcontinent. J Antimicrob Chemother 2021; 75:337-341. [PMID: 31665304 PMCID: PMC7223262 DOI: 10.1093/jac/dkz435] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/16/2019] [Accepted: 09/23/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The molecular structure of circulating enteric fever pathogens was studied using hospital-based genomic surveillance in a tertiary care referral centre in South India as a first genomic surveillance study, to our knowledge, of blood culture-confirmed enteric fever in the region. METHODS Blood culture surveillance was conducted at St John's Medical College Hospital, Bengaluru, between July 2016 and June 2017. The bacterial isolates collected were linked to demographic variables of patients and subjected to WGS. The resulting pathogen genomic data were also globally contextualized to gauge possible phylogeographical patterns. RESULTS Hospital-based genomic surveillance for enteric fever in Bengaluru, India, identified 101 Salmonella enterica Typhi and 14 S. Paratyphi A in a 1 year period. Ninety-six percent of isolates displayed non-susceptibility to fluoroquinolones. WGS showed the dominant pathogen was S. Typhi genotype 4.3.1.2 (H58 lineage II). A fluoroquinolone-resistant triple-mutant clone of S. Typhi 4.3.1.2 previously associated with gatifloxacin treatment failure in Nepal was implicated in 18% of enteric fever cases, indicating ongoing inter-regional circulation. CONCLUSIONS Enteric fever in South India continues to be a major public health issue and is strongly associated with antimicrobial resistance. Robust microbiological surveillance is necessary to direct appropriate treatment and preventive strategies. Of particular concern is the emergence and expansion of the highly fluoroquinolone-resistant triple-mutant S. Typhi clone and its ongoing inter- and intra-country transmission in South Asia, which highlights the need for regional coordination of intervention strategies, including vaccination and longer-term strategies such as improvements to support hygiene and sanitation.
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Affiliation(s)
- Carl D Britto
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Zoe A Dyson
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia.,Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Ashish Bosco
- St John's Medical College Hospital, Bengaluru, India
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sanju Jose
- St John's Medical College Hospital, Bengaluru, India
| | | | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia.,Department of Infection Biology, Faculty of Infections and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK
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23
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A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch. Nat Commun 2021; 12:2879. [PMID: 34001879 PMCID: PMC8128892 DOI: 10.1038/s41467-021-23091-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022] Open
Abstract
As whole-genome sequencing capacity becomes increasingly decentralized, there is a growing opportunity for collaboration and the sharing of surveillance data within and between countries to inform typhoid control policies. This vision requires free, community-driven tools that facilitate access to genomic data for public health on a global scale. Here we present the Pathogenwatch scheme for Salmonella enterica serovar Typhi (S. Typhi), a web application enabling the rapid identification of genomic markers of antimicrobial resistance (AMR) and contextualization with public genomic data. We show that the clustering of S. Typhi genomes in Pathogenwatch is comparable to established bioinformatics methods, and that genomic predictions of AMR are highly concordant with phenotypic susceptibility data. We demonstrate the public health utility of Pathogenwatch with examples selected from >4,300 public genomes available in the application. Pathogenwatch provides an intuitive entry point to monitor of the emergence and spread of S. Typhi high risk clones. Whole genome sequencing data are increasingly becoming routinely available but generating actionable insights is challenging. Here, the authors describe Pathogenwatch, a web tool for genomic surveillance of S. Typhi, and demonstrate its use for antimicrobial resistance assignment and strain risk assessment.
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24
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Jacob JJ, Pragasam AK, Vasudevan K, Veeraraghavan B, Kang G, John J, Nagvekar V, Mutreja A. Salmonella Typhi acquires diverse plasmids from other Enterobacteriaceae to develop cephalosporin resistance. Genomics 2021; 113:2171-2176. [PMID: 33965548 PMCID: PMC8276774 DOI: 10.1016/j.ygeno.2021.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/22/2021] [Accepted: 05/04/2021] [Indexed: 11/25/2022]
Abstract
Background Recent reports have established the emergence and dissemination of extensively drug resistant (XDR) H58 Salmonella Typhi clone in Pakistan. In India where typhoid fever is endemic, only sporadic cases of ceftriaxone resistant S. Typhi are reported. This study aimed at elucidating the phylogenetic evolutionary framework of ceftriaxone resistant S. Typhi isolates from India to predict their potential dissemination. Methods Five ceftriaxone resistant S. Typhi isolates from three tertiary care hospitals in India were sequenced on an Ion Torrent Personal Genome Machine (PGM). A core genome single-nucleotide-polymorphism (SNP) based phylogeny of the isolates in comparison to the global collection of MDR and XDR S. Typhi isolates was built. Two of five isolates were additionally sequenced using Oxford Nanopore MinION to completely characterize the plasmid and understand its transmission dynamics within Enterobacteriaceae. Results Comparative genomic analysis and detailed plasmid characterization indicate that while in Pakistan (4.3.1 lineage I) the XDR trait is associated with blaCTX-M-15 gene on IncY plasmid, in India (4.3.1 lineage II), the ceftriaxone resistance is due to short term persistence of resistance plasmids such as IncX3 (blaSHV-12) or IncN (blaTEM-1B + blaDHA-1). Conclusion Considering the selection pressure exerted by the extensive use of ceftriaxone in India, there are potential risks for the occurrence of plasmid transmission events in the predominant H58 lineages. Therefore, continuous monitoring of S. Typhi lineages carrying plasmid-mediated cephalosporin resistant genes is vital not just for India but also globally. S. Typhi to develop cephalosporin resistance by acquiring diverse plasmids from other Enterobacteriaceae. Independent acquisition of drug-resistant plasmids such as IncX3 and IncN with genes encoding beta-lactamases in H58 lineage II of S. Typhi. A short-term persistence of drug-resistant plasmids in H58 lineage II can be the reason for the sporadic cases cephalosporin resistant S. Typhi in India. Plasmid acquisition and maintenance of cephalosporin resistant S. Typhi appears to be specific to the phylogenetic lineage. Critical strategies in monitoring and control of cephalosporin resistant S. Typhi is needed to tackle further public health crisis.
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Affiliation(s)
- Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Agila Kumari Pragasam
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India.
| | - Gagandeep Kang
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jacob John
- Department of Community Health, Christian Medical College, Vellore, Tamil Nadu, India
| | - Vasant Nagvekar
- Department of Physician/Internal Medicine, Lilavati Hospital & Research Centre, Mumbai, India
| | - Ankur Mutreja
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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Javaid N, Sultana Q, Rasool K, Gandra S, Ahmad F, Chaudhary SU, Mirza S. Trends in antimicrobial resistance amongst pathogens isolated from blood and cerebrospinal fluid cultures in Pakistan (2011-2015): A retrospective cross-sectional study. PLoS One 2021; 16:e0250226. [PMID: 33901205 PMCID: PMC8075205 DOI: 10.1371/journal.pone.0250226] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/02/2021] [Indexed: 12/29/2022] Open
Abstract
While antimicrobial resistance (AMR) continues to be a major public health problem in Pakistan, data regarding trends of resistance among pathogenic bacteria remains scarce, with few studies presenting long-term trends in AMR. This study was therefore designed to analyze long-term AMR trends at a national level in Pakistan. We report here results of a comprehensive analysis of resistance, among pathogens isolated from blood and cerebrospinal fluid (CSF), between 2011 and 2015. Susceptibility data was obtained from a local laboratory with collection points all across Pakistan (Chughtai Laboratory). Resistance proportions to most commonly used antimicrobials were calculated for each pathogen over a period of five years. While Acinetobacter species demonstrated highest resistance rates to all tested antimicrobials, a sharp increase in carbapenem resistance was the most noticeable (50%-95%) between 2011-2015. Our results also highlight the presence of third and fourth generation cephalosporins resistance in Salmonella enterica serovar Typhi in Pakistan. Interestingly, where rise in AMR was being observed in some major invasive pathogens, decreasing resistance trends were observed in Staphylococcus aureus, against commonly used antimicrobials. Overall pathogens isolated from blood and CSF between 2011-2015, showed an increase in resistance towards commonly used antimicrobials.
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Affiliation(s)
- Nida Javaid
- Department of Biology, School of Science and Engineering, Lahore University of Management Science, Lahore, Pakistan
| | - Qamar Sultana
- Department of Microbiology, Chughtai Lab/Chughtai Institute of Pathology, Lahore, Pakistan
| | - Karam Rasool
- Department of Microbiology, Chughtai Lab/Chughtai Institute of Pathology, Lahore, Pakistan
| | - Sumanth Gandra
- Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MI, United States of America
| | - Fayyaz Ahmad
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Shaper Mirza
- Department of Biology, School of Science and Engineering, Lahore University of Management Science, Lahore, Pakistan
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26
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Sajib MSI, Tanmoy AM, Hooda Y, Rahman H, Andrews JR, Garrett DO, Endtz HP, Saha SK, Saha S. Tracking the Emergence of Azithromycin Resistance in Multiple Genotypes of Typhoidal Salmonella. mBio 2021; 12:e03481-20. [PMID: 33593966 PMCID: PMC8545119 DOI: 10.1128/mbio.03481-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/05/2021] [Indexed: 11/29/2022] Open
Abstract
The rising prevalence of antimicrobial resistance in Salmonella enterica serovars Typhi and Paratyphi A, causative agents of typhoid and paratyphoid, have led to fears of untreatable infections. Of specific concern is the emerging resistance against azithromycin, the only remaining oral drug to treat extensively drug resistant (XDR) typhoid. Since the first report of azithromycin resistance from Bangladesh in 2019, cases have been reported from Nepal, India, and Pakistan. The genetic basis of this resistance is a single point mutation in the efflux pump AcrB (R717Q/L). Here, we report 38 additional cases of azithromycin-resistant (AzmR) Salmonella Typhi and Paratyphi A isolated in Bangladesh between 2016 and 2018. Using genomic analysis of 56 AzmR isolates from South Asia with AcrB-R717Q/L, we confirm that this mutation has spontaneously emerged in different Salmonella Typhi and Paratyphi A genotypes. The largest cluster of AzmR Typhi belonged to genotype 4.3.1.1; Bayesian analysis predicts the mutation to have emerged sometime in 2010. A travel-related Typhi isolate with AcrB-R717Q belonging to 4.3.1.1 was isolated in the United Kingdom, increasing fears of global spread. For real-time detection of AcrB-R717Q/L, we developed an extraction-free, rapid, and low-cost mismatch amplification mutation assay (MAMA). Validation of MAMA using 113 AzmR and non-AzmR isolates yielded >98% specificity and sensitivity versus phenotypic and whole-genome sequencing assays currently used for azithromycin resistance detection. With increasing azithromycin use, AcrB-R717Q/L is likely to be acquired by XDR strains. The proposed tool for active detection and surveillance of this mutation may detect pan-oral drug resistance early, giving us a window to intervene.IMPORTANCE In the early 1900s, with mortality of ∼30%, typhoid and paratyphoid ravaged parts of the world; with improved water, sanitation, and hygiene in resource-rich countries and the advent of antimicrobials, mortality dwindled to <1%. Today, the burden rests disproportionately on South Asia, where the primary means for combatting the disease is antimicrobials. However, prevalence of antimicrobial resistance is rising and, in 2016, an extensively drug resistant Typhi strain triggered an ongoing outbreak in Pakistan, leaving only one oral drug, azithromycin, to treat it. Since the description of emergence of azithromycin resistance, conferred by a point mutation in acrB (AcrB-R717Q/L) in 2019, there have been increasing numbers of reports. Using genomics and Bayesian analysis, we illustrate that this mutation emerged in approximately 2010 and has spontaneously arisen multiple times. Emergence of pan-oral drug resistant Salmonella Typhi is imminent. We developed a low-cost, rapid PCR tool to facilitate real-time detection and prevention policies.
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Affiliation(s)
- Mohammad S I Sajib
- Child Health Research Foundation, Dhaka, Bangladesh
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Arif M Tanmoy
- Child Health Research Foundation, Dhaka, Bangladesh
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yogesh Hooda
- Child Health Research Foundation, Dhaka, Bangladesh
- MRC-Laboratory Molecular Biology, Cambridge, United Kingdom
| | | | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | | | - Hubert P Endtz
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
- Fondation Mérieux and Centre International de Recherche en Infectiologie, INSERM, Lyon, France
| | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh
- Department of Microbiology, Dhaka Shishu Hospital, Dhaka, Bangladesh
- Bangladesh Institute of Child Health, Dhaka, Bangladesh
| | - Senjuti Saha
- Child Health Research Foundation, Dhaka, Bangladesh
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Duy PT, Dongol S, Giri A, Nguyen To NT, Dan Thanh HN, Nhu Quynh NP, Duc Trung P, Thwaites GE, Basnyat B, Baker S, Rabaa MA, Karkey A. The emergence of azithromycin-resistant Salmonella Typhi in Nepal. JAC Antimicrob Resist 2020; 2:dlaa109. [PMID: 34223059 PMCID: PMC8210228 DOI: 10.1093/jacamr/dlaa109] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/10/2020] [Indexed: 11/12/2022] Open
Abstract
Background Typhoid fever remains a significant cause of morbidity and mortality in Asia and Africa. The emergence of azithromycin resistance in South Asia is concerning, as azithromycin is one of the last effective oral drugs for treating typhoid. Objectives To describe the molecular mechanism and phylogenetics of azithromycin-resistant (AzithR) Salmonella Typhi isolates from Patan Hospital, Kathmandu, Nepal. Methods Whole-genome sequences of three AzithR S. Typhi isolates (MIC >256 mg/L) were analysed and compared with a global collection to investigate the azithromycin resistance mechanism and phylogenetic structure. Clinical information is reported for one of the three patients infected with AzithR S. Typhi. Results The three AzithR isolates belonged to the H58 lineage and were genetically identical; they were distantly related to contemporaneous S. Typhi from Nepal and AzithR S. Typhi recently described in Bangladesh. Azithromycin resistance was mediated by a non-synonymous mutation in the acrB gene (R717L). The three AzithR isolates showed reduced susceptibility to ciprofloxacin (double mutation in the gyrA: S83F and D87G), and were susceptible to ampicillin, chloramphenicol and co-trimoxazole. Clinical information from one patient suggested non-response to azithromycin treatment. Conclusions This is the first molecular description of AzithR S. Typhi in Nepal. These organisms showed no phylogenetic link to AzithR S. Typhi in Bangladesh. Our data suggest that increasing use of azithromycin may pose a strong selective pressure driving the emergence of AzithR S. Typhi in South Asia. Further investigations are needed to evaluate treatment responses to azithromycin, predict evolutionary trajectories, and track the transmission of these organisms.
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Affiliation(s)
- Pham Thanh Duy
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | | | - Nguyen Thi Nguyen To
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho Ngoc Dan Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Pham Nhu Quynh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Pham Duc Trung
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy E Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Maia A Rabaa
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
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CRISPR-Cas Diversity in Clinical Salmonella enterica Serovar Typhi Isolates from South Asian Countries. Genes (Basel) 2020; 11:genes11111365. [PMID: 33218076 PMCID: PMC7698835 DOI: 10.3390/genes11111365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 12/26/2022] Open
Abstract
Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), is a global health concern and its treatment is problematic due to the rise in antimicrobial resistance (AMR). Rapid detection of patients infected with AMR positive S. Typhi is, therefore, crucial to prevent further spreading. Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated genes (CRISPR-Cas), is an adaptive immune system that initially was used for typing purposes. Later, it was discovered to play a role in defense against phages and plasmids, including ones that carry AMR genes, and, at present, it is being explored for its usage in diagnostics. Despite the availability of whole-genome sequences (WGS), very few studied the CRISPR-Cas system of S. Typhi, let alone in typing purposes or relation to AMR. In the present study, we analyzed the CRISPR-Cas system of S. Typhi using WGS data of 1059 isolates obtained from Bangladesh, India, Nepal, and Pakistan in combination with demographic data and AMR status. Our results reveal that the S. Typhi CRISPR loci can be classified into two groups: A (evidence level >2) and B (evidence level ≤2), in which we identified a total of 47 unique spacers and 15 unique direct repeats. Further analysis of the identified spacers and repeats demonstrated specific patterns that harbored significant associations with genotype, demographic characteristics, and AMR status, thus raising the possibility of their usage as biomarkers. Potential spacer targets were identified and, interestingly, the phage-targeting spacers belonged to the group-A and plasmid-targeting spacers to the group-B CRISPR loci. Further analyses of the spacer targets led to the identification of an S. Typhi protospacer adjacent motif (PAM) sequence, TTTCA/T. New cas-genes known as DinG, DEDDh, and WYL were also discovered in the S. Typhi genome. However, a specific variant of the WYL gene was only identified in the extensively drug-resistant (XDR) lineage from Pakistan and ciprofloxacin-resistant lineage from Bangladesh. From this work, we conclude that there are strong correlations between variations identified in the S. Typhi CRISPR-Cas system and endemic AMR positive S. Typhi isolates.
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Troisi M, Andreano E, Sala C, Kabanova A, Rappuoli R. Vaccines as remedy for antimicrobial resistance and emerging infections. Curr Opin Immunol 2020; 65:102-106. [PMID: 33289646 DOI: 10.1016/j.coi.2020.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/27/2020] [Accepted: 09/15/2020] [Indexed: 12/29/2022]
Abstract
Life expectancy has grown tremendously. This incredible achievement for mankind has been obtained mostly thanks to three pillars: hygiene, antibiotics and vaccines. They represent one of the most effective forms of medical intervention. From Jenner's work to new vaccines, immunization has reduced the consequences of infectious diseases. In the last years antimicrobial resistance (AMR) as well as emerging infectious diseases have been rated as major threats for our society, as their toll is forecasted to drastically impinge on human health and economies. Indeed, recently, the whole world has experienced such problems because of the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of Covid-19. Herein, we propose an excursus through the three main pillars (hygiene, antibiotics and vaccination) that contributed to improving life expectancy, their clinical and economic impact and the role of vaccines to fight AMR-related diseases and emerging infectious diseases like Covid-19.
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Affiliation(s)
- Marco Troisi
- Monoclonal Antibody Discovery Laboratory, Fondazione Toscana Life Sciences, Siena, Italy; University of Siena, Department of Biotechnology, Chemistry and Pharmacy, Siena, Italy
| | - Emanuele Andreano
- Monoclonal Antibody Discovery Laboratory, Fondazione Toscana Life Sciences, Siena, Italy
| | - Claudia Sala
- Monoclonal Antibody Discovery Laboratory, Fondazione Toscana Life Sciences, Siena, Italy
| | - Anna Kabanova
- Monoclonal Antibody Discovery Laboratory, Fondazione Toscana Life Sciences, Siena, Italy; Tumour Immunology Unit, Fondazione Toscana Life Sciences, Siena, Italy
| | - Rino Rappuoli
- Monoclonal Antibody Discovery Laboratory, Fondazione Toscana Life Sciences, Siena, Italy; GSK, Siena, Italy; Imperial College, London, United Kingdom.
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30
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Jaillard M, Palmieri M, van Belkum A, Mahé P. Interpreting k-mer-based signatures for antibiotic resistance prediction. Gigascience 2020; 9:giaa110. [PMID: 33068113 PMCID: PMC7568433 DOI: 10.1093/gigascience/giaa110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 07/23/2020] [Accepted: 09/16/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Recent years have witnessed the development of several k-mer-based approaches aiming to predict phenotypic traits of bacteria on the basis of their whole-genome sequences. While often convincing in terms of predictive performance, the underlying models are in general not straightforward to interpret, the interplay between the actual genetic determinant and its translation as k-mers being generally hard to decipher. RESULTS We propose a simple and computationally efficient strategy allowing one to cope with the high correlation inherent to k-mer-based representations in supervised machine learning models, leading to concise and easily interpretable signatures. We demonstrate the benefit of this approach on the task of predicting the antibiotic resistance profile of a Klebsiella pneumoniae strain from its genome, where our method leads to signatures defined as weighted linear combinations of genetic elements that can easily be identified as genuine antibiotic resistance determinants, with state-of-the-art predictive performance. CONCLUSIONS By enhancing the interpretability of genomic k-mer-based antibiotic resistance prediction models, our approach improves their clinical utility and hence will facilitate their adoption in routine diagnostics by clinicians and microbiologists. While antibiotic resistance was the motivating application, the method is generic and can be transposed to any other bacterial trait. An R package implementing our method is available at https://gitlab.com/biomerieux-data-science/clustlasso.
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Affiliation(s)
| | | | | | - Pierre Mahé
- bioMérieux, Chemin de l'Orme, 69280 Marcy l'Etoile, France
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31
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A Race against Time: Reduced Azithromycin Susceptibility in Salmonella enterica Serovar Typhi in Pakistan. mSphere 2020; 5:5/4/e00215-20. [PMID: 32699118 PMCID: PMC7376502 DOI: 10.1128/msphere.00215-20] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance is an ongoing issue in the treatment of typhoid fever. Resistance to first-line antimicrobials and extensively drug resistant (XDR) Salmonella Typhi isolates in Pakistan have left azithromycin as the only remaining effective oral treatment. Here, we report the emergence of organisms with a single point mutation in acrB gene, implicated in azithromycin resistance, in a S. Typhi isolate from Pakistan. The isolation of this organism is worrisome and highlights the significance of the introduction of typhoid conjugate vaccine in South Asia.IMPORTANCE The emergence of XDR Salmonella Typhi in Pakistan has left azithromycin as the only viable oral treatment option. Here, we report the detection of an azithromycin resistance-associated mutation in one S. Typhi isolate. This finding is important because any possible spread of azithromycin resistance in S. Typhi isolates would make it nearly impossible to treat in outpatient settings due to the need of injectable antibiotics. Our findings also signify the importance of introduction of typhoid conjugate vaccine in regions of endemicity such as Pakistan.
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Reviving the "Moore Swab": a Classic Environmental Surveillance Tool Involving Filtration of Flowing Surface Water and Sewage Water To Recover Typhoidal Salmonella Bacteria. Appl Environ Microbiol 2020; 86:AEM.00060-20. [PMID: 32332133 PMCID: PMC7301852 DOI: 10.1128/aem.00060-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The “Moore swab” is a classic environmental surveillance tool whereby a gauze pad tied with string is suspended in flowing water or wastewater contaminated with human feces and harboring enteric pathogens that pose a human health threat. In contrast to single volume “grab” samples, Moore swabs act as continuous filters to “trap” microorganisms, which are subsequently isolated and confirmed using appropriate laboratory methods. Continuous filtration is valuable for the isolation of transiently present pathogens such as human-restricted Salmonella enterica serovars Typhi and Paratyphi A and B. The “Moore swab” is a classic environmental surveillance tool whereby a gauze pad tied with string is suspended in flowing water or wastewater contaminated with human feces and harboring enteric pathogens that pose a human health threat. In contrast to single volume “grab” samples, Moore swabs act as continuous filters to “trap” microorganisms, which are subsequently isolated and confirmed using appropriate laboratory methods. Continuous filtration is valuable for the isolation of transiently present pathogens such as human-restricted Salmonella enterica serovars Typhi and Paratyphi A and B. The technique was first proposed (1948) to trace Salmonella Paratyphi B systematically through sewers to pinpoint the residence of a chronic carrier responsible for sporadic outbreaks of paratyphoid fever. From 1948 to 1986, Moore swabs proved instrumental to identify long-term human reservoirs (chronic carriers) and long-cycle environmental transmission pathways of S. Typhi and Paratyphi, for example, to decipher endemic transmission in Santiago, Chile, during the 1980s. Despite limitations such as intermittent shedding of typhoidal Salmonella by humans and the effects of dilution, S. Typhi and S. Paratyphi have been recovered from sewers, surface waters, irrigation canals, storm drains, flush toilets, and septic tanks by using Moore swabs. Driven by the emergence of multiple antibiotic-resistant S. Typhi and S. Paratyphi A strains that limit treatment options, several countries are embarking on accelerated typhoid control programs using vaccines and environmental interventions. Moore swabs, which are regaining appreciation as important components of the public health/environmental microbiology toolbox, can enhance environmental surveillance for typhoidal Salmonella, thereby contributing to the control of typhoid fever.
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Vandenberg O, Durand G, Hallin M, Diefenbach A, Gant V, Murray P, Kozlakidis Z, van Belkum A. Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies. Clin Microbiol Rev 2020; 33:e00057-19. [PMID: 32102900 PMCID: PMC7048017 DOI: 10.1128/cmr.00057-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Clinical microbiology is experiencing revolutionary advances in the deployment of molecular, genome sequencing-based, and mass spectrometry-driven detection, identification, and characterization assays. Laboratory automation and the linkage of information systems for big(ger) data management, including artificial intelligence (AI) approaches, also are being introduced. The initial optimism associated with these developments has now entered a more reality-driven phase of reflection on the significant challenges, complexities, and health care benefits posed by these innovations. With this in mind, the ongoing process of clinical laboratory consolidation, covering large geographical regions, represents an opportunity for the efficient and cost-effective introduction of new laboratory technologies and improvements in translational research and development. This will further define and generate the mandatory infrastructure used in validation and implementation of newer high-throughput diagnostic approaches. Effective, structured access to large numbers of well-documented biobanked biological materials from networked laboratories will release countless opportunities for clinical and scientific infectious disease research and will generate positive health care impacts. We describe why consolidation of clinical microbiology laboratories will generate quality benefits for many, if not most, aspects of the services separate institutions already provided individually. We also define the important role of innovative and large-scale diagnostic platforms. Such platforms lend themselves particularly well to computational (AI)-driven genomics and bioinformatics applications. These and other diagnostic innovations will allow for better infectious disease detection, surveillance, and prevention with novel translational research and optimized (diagnostic) product and service development opportunities as key results.
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Affiliation(s)
- Olivier Vandenberg
- Innovation and Business Development Unit, LHUB-ULB, Groupement Hospitalier Universitaire de Bruxelles (GHUB), Université Libre de Bruxelles, Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Géraldine Durand
- bioMérieux, Microbiology Research and Development, La Balme Les Grottes, France
| | - Marie Hallin
- Department of Microbiology, LHUB-ULB, Groupement Hospitalier Universitaire de Bruxelles (GHUB), Université Libre de Bruxelles, Brussels, Belgium
| | - Andreas Diefenbach
- Department of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Labor Berlin, Charité-Vivantes GmbH, Berlin, Germany
| | - Vanya Gant
- Department of Clinical Microbiology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Patrick Murray
- BD Life Sciences Integrated Diagnostic Solutions, Scientific Affairs, Sparks, Maryland, USA
| | - Zisis Kozlakidis
- Laboratory Services and Biobank Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, La Balme Les Grottes, France
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Rahman SIA, Dyson ZA, Klemm EJ, Khanam F, Holt KE, Chowdhury EK, Dougan G, Qadri F. Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016. PLoS Negl Trop Dis 2020; 14:e0008036. [PMID: 32106221 PMCID: PMC7064254 DOI: 10.1371/journal.pntd.0008036] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 03/10/2020] [Accepted: 01/08/2020] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Multi-drug resistant typhoid fever remains an enormous public health threat in low and middle-income countries. However, we still lack a detailed understanding of the epidemiology and genomics of S. Typhi in many regions. Here we have undertaken a detailed genomic analysis of typhoid in urban Dhaka, Bangladesh to unravel the population structure and antimicrobial resistance patterns in S. Typhi isolated between 2004-2016. PRINCIPAL FINDINGS Whole genome sequencing of 202 S. Typhi isolates obtained from three study locations in urban Dhaka revealed a diverse range of S. Typhi genotypes and AMR profiles. The bacterial population within Dhaka were relatively homogenous with little stratification between different healthcare facilities or age groups. We also observed evidence of exchange of Bangladeshi genotypes with neighboring South Asian countries (India, Pakistan and Nepal) suggesting these are circulating throughout the region. This analysis revealed a decline in H58 (genotype 4.3.1) isolates from 2011 onwards, coinciding with a rise in a diverse range of non-H58 genotypes and a simultaneous rise in isolates with reduced susceptibility to fluoroquinolones, potentially reflecting a change in treatment practices. We identified a novel S. Typhi genotype, subclade 3.3.2 (previously defined only to clade level, 3.3), which formed two localized clusters (3.3.2.Bd1 and 3.3.2.Bd2) associated with different mutations in the Quinolone Resistance Determining Region (QRDR) of gene gyrA. SIGNIFICANCE Our analysis of S. Typhi isolates from urban Dhaka, Bangladesh isolated over a twelve year period identified a diverse range of AMR profiles and genotypes. The observed increase in non-H58 genotypes associated with reduced fluoroquinolone susceptibility may reflect a change in treatment practice in this region and highlights the importance of continued molecular surveillance to monitor the ongoing evolution of AMR in Dhaka. We have defined new genotypes and lineages of Bangladeshi S. Typhi which will facilitate the identification of these emerging AMR clones in future surveillance efforts.
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Affiliation(s)
- Sadia Isfat Ara Rahman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Zoe A. Dyson
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Elizabeth J. Klemm
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Farhana Khanam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infection Biology, Faculty of Infections and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Emran Kabir Chowdhury
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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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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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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Meyer Sauteur PM, Stevens MJA, Paioni P, Wüthrich D, Egli A, Stephan R, Berger C, Bloemberg GV. Siblings with typhoid fever: An investigation of intrafamilial transmission, clonality, and antibiotic susceptibility. Travel Med Infect Dis 2019; 34:101498. [PMID: 31580900 DOI: 10.1016/j.tmaid.2019.101498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/27/2019] [Accepted: 09/28/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Typhoid fever usually manifests as an acute disease. However, asymptomatic carriage with Salmonella Typhi may occur. This study investigated a family setting of severe typhoid fever in Switzerland months after return from Bangladesh. METHOD Standard microbiological procedures were performed. Testing for S. Typhi IgM antibodies was done using a novel immunochromographic lateral flow assay. Whole genome sequencing (WGS) followed by comparative core genome multilocus sequence typing (cgMLST) was performed on the S. Typhi isolates. RESULTS Four months after returning from a visit to Bangladesh sibling 1 (9 months) was diagnosed with a S. Typhi meningitis and sibling 3 (8 years) was identified as asymptomatic S. Typhi carrier. Sibling 2 (2 years) was retrospectively diagnosed with typhoid fever by IgM serology at the time point of admission to the hospital. Parents were asymptomatic and culture-negative. WGS analysis of family S. Typhi isolates showed clonality and strongest homology with S. Typhi strains occurring in Bangladesh. The S. Typhi strain showed resistance against fluoroquinolones. A 4-week course of ceftriaxone resulted in full recovery of sibling 1. S. Typhi was eradicated from sibling 3 following azithromycin treatment for 14 days. CONCLUSION S. Typhi, acquired from a visit to Bangladesh, was most likely transmitted within the family from one brother as asymptomatic shedder to his 9-month-old brother who manifested S. Typhi meningitis as a very rare and life-threatening presentation of typhoid fever. S. Typhi infection should be considered even in case of uncommon manifestations and irrespective of the interval between disease presentation and travel to an endemic area.
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Affiliation(s)
- Patrick M Meyer Sauteur
- Division of Infectious Diseases and Hospital Epidemiology, University Children's Hospital Zurich, Switzerland
| | - Marc J A Stevens
- Institute for Food Safety and Hygiene, University of Zurich, Switzerland
| | - Paolo Paioni
- Division of Infectious Diseases and Hospital Epidemiology, University Children's Hospital Zurich, Switzerland
| | - Daniel Wüthrich
- Clinical Bacteriology & Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Adrian Egli
- Clinical Bacteriology & Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Roger Stephan
- Swiss National Center for Enteropathogenic Bacteria and Listeria (NENT), Institute for Food Safety and Hygiene, University of Zurich, Switzerland
| | - Christoph Berger
- Division of Infectious Diseases and Hospital Epidemiology, University Children's Hospital Zurich, Switzerland
| | - Guido V Bloemberg
- Swiss National Center for Enteropathogenic Bacteria and Listeria (NENT), Institute for Food Safety and Hygiene, University of Zurich, Switzerland.
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Wang KY, Lee DJ, Shie SS, Chen CJ. Population structure and transmission modes of indigenous typhoid in Taiwan. BMC Med Genomics 2019; 12:126. [PMID: 31481113 PMCID: PMC6724314 DOI: 10.1186/s12920-019-0576-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/29/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Indigenous typhoid fever was continuing to be identified in Taiwan which has not been endemic for the enteric fever for more than 20 years. The source and transmission by which the local patients acquired typhoid and the population structure of the indigenous typhoid strains remain not well characterized. METHODS During 2001 and 2014, non-duplicated clinical Salmonella enterica serovar Typhi isolates in a hospital were analyzed by whole-genome sequencing (WGS) and determined for pulsotypes. Maximum likelihood phylogeny was constructed by nucleotide alterations in core genomes and compared to the framework of global typhoid strains. Potential source and transmission were traced by correlating the phylogeny and the temporal relationship between isolates. RESULTS A total of 43 S. Typhi isolates from indigenous cases were analyzed and a majority (39, 90.7%) of them were belonged to six WGS-defined genotypes prevailing mainly in Southeast Asia. Genotype 3.4.0 and a multidrug-resistant type 4.3.1 (also known as pandemic H58 haplotype) were associated respectively with two solitary small-scale outbreaks, implying a transmission mode of importation followed by outbreak. Twelve isolates with nearly identical core genomes were belonged to genotype 3.2.1 but were categorized into three different pulsotypes. The 3.2.1 isolates were identified across 13 years and involved in three clusters and a sporadic case, indicating sustained local transmission of the same strain. The remaining indigenous isolates belonging to three genotypes (2.1, 3.1.2, and 3.0.0) were of substantial genetic diversity and isolated at different time points, indicating independent event of each case. CONCLUSIONS Indigenous typhoid in Taiwan occurred mainly with the forms of small-scale outbreaks or sporadic events likely by contracting imported strains which prevailed in Southeast Asia. Sustained local transmission of certain strain was also evident by WGS analysis, but not by conventional pulsotyping, highlighting the importance of continuing molecular surveillance of typhoid fever with adequate tools in the non-endemic region.
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Affiliation(s)
- Kai-Yu Wang
- School of medicine, College of Medicine, Chang Gung University, 333, Taoyuan, Taiwan
| | - De-Jen Lee
- Physical Education Office, Chang Gung University, 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 Paediatrics, Chang Gung Memorial Hospital, Linkou, No. 5, Fu-Shin Street, Kweishan, 333, Taoyuan, Taiwan. .,Department of Pediatrics, Xiamen Chang Gung Hospital, Xiamen, Fujian, China.
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Typhoidal Salmonella strains in Pakistan: an impending threat of extensively drug-resistant Salmonella Typhi. Eur J Clin Microbiol Infect Dis 2019; 38:2145-2149. [DOI: 10.1007/s10096-019-03658-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 07/22/2019] [Indexed: 10/26/2022]
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Lima NCB, Tanmoy AM, Westeel E, de Almeida LGP, Rajoharison A, Islam M, Endtz HP, Saha SK, de Vasconcelos ATR, Komurian-Pradel F. Analysis of isolates from Bangladesh highlights multiple ways to carry resistance genes in Salmonella Typhi. BMC Genomics 2019; 20:530. [PMID: 31253105 PMCID: PMC6599262 DOI: 10.1186/s12864-019-5916-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/20/2019] [Indexed: 12/12/2022] Open
Abstract
Background Typhoid fever, caused by Salmonella Typhi, follows a fecal-oral transmission route and is a major global public health concern, especially in developing countries like Bangladesh. Increasing emergence of antimicrobial resistance (AMR) is a serious issue; the list of treatments for typhoid fever is ever-decreasing. In addition to IncHI1-type plasmids, Salmonella genomic island (SGI) 11 has been reported to carry AMR genes. Although reports suggest a recent reduction in multidrug resistance (MDR) in the Indian subcontinent, the corresponding genomic changes in the background are unknown. Results Here, we assembled and annotated complete closed chromosomes and plasmids for 73 S. Typhi isolates using short-length Illumina reads. S. Typhi had an open pan-genome, and the core genome was smaller than previously reported. Considering AMR genes, we identified five variants of SGI11, including the previously reported reference sequence. Five plasmids were identified, including the new plasmids pK91 and pK43; pK43and pHCM2 were not related to AMR. The pHCM1, pPRJEB21992 and pK91 plasmids carried AMR genes and, along with the SGI11 variants, were responsible for resistance phenotypes. pK91 also contained qnr genes, conferred high ciprofloxacin resistance and was related to the H58-sublineage Bdq, which shows the same phenotype. The presence of plasmids (pHCM1 and pK91) and SGI11 were linked to two H58-lineages, Ia and Bd. Loss of plasmids and integration of resistance genes in genomic islands could contribute to the fitness advantage of lineage Ia isolates. Conclusions Such events may explain why lineage Ia is globally widespread, while the Bd lineage is locally restricted. Further studies are required to understand how these S. Typhi AMR elements spread and generate new variants. Preventive measures such as vaccination programs should also be considered in endemic countries; such initiatives could potentially reduce the spread of AMR. Electronic supplementary material The online version of this article (10.1186/s12864-019-5916-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicholas Costa Barroso Lima
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil.,Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Arif M Tanmoy
- Department of Medical Microbiology & Infectious Diseases, Erasmus MC, Rotterdam, the Netherlands.,Fondation Mérieux - Laboratoire des Pathogènes Emergents, Lyon, France.,Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, 1207, Bangladesh
| | - Emilie Westeel
- Fondation Mérieux - Laboratoire des Pathogènes Emergents, Lyon, France
| | | | - Alain Rajoharison
- Fondation Mérieux - Laboratoire des Pathogènes Emergents, Lyon, France
| | - Maksuda Islam
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, 1207, Bangladesh
| | - Hubert P Endtz
- Department of Medical Microbiology & Infectious Diseases, Erasmus MC, Rotterdam, the Netherlands.,Fondation Mérieux - Laboratoire des Pathogènes Emergents, Lyon, France
| | - Samir K Saha
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, 1207, Bangladesh.,Bangladesh Institute of Child Health, Dhaka Shishu Hospital, Dhaka, 1207, Bangladesh
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