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Tan CY, Zeng K, Cui L, Lin RTP, Chen M. Diagnostic performance of rapid antigen tests (RAT) for COVID-19 and factors associated with RAT-negative results among RT-PCR-positive individuals during Omicron BA.2, BA.5 and XBB.1 predominance. BMC Infect Dis 2024; 24:504. [PMID: 38769524 DOI: 10.1186/s12879-024-09408-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/15/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND While numerous studies have evaluated the real-world performance of rapid antigen tests (RATs), data on the effect of Omicron sublineages such as XBB and reinfections on RAT performance is limited. We assessed the performance of RATs and factors associated with RAT-negative results among individuals who tested SARS-CoV-2-positive by reverse transcription-polymerase chain reaction (RT-PCR). METHODS We conducted a retrospective study among Singapore residents who underwent testing for SARS-CoV-2 with RAT (Acon Flowflex or SD Biosensor) and RT-PCR in the same clinical encounter between 9 May 2022 and 21 November 2022. RT-PCR served as a reference standard for RAT performance. Logistic regression was used to estimate the odds ratios (OR) of factors associated with negative RAT results among RT-PCR-positive cases. RESULTS Of 8,620 clinical encounters analysed, 3,519 (40.8%) were SARS-CoV-2-positive on RT-PCR. Overall sensitivity and specificity of RAT was 84.6% (95% CI 83.3-85.7%) and 99.4% (95% CI 99.1-99.6%) respectively. Acon Flowflex consistently achieved higher sensitivity and specificity than SD Biosensor test kit. Among RT-PCR-positive cases, individuals who had a previous documented SARS-CoV-2 infection, coinfection with another respiratory pathogen or tested ≥ 6 days from symptom onset had higher odds of testing RAT-negative, but the associations were attenuated after adjustment for cycle threshold values (proxy for viral load). There was no significant difference in RAT performance between Omicron sublineages BA.2, BA.5 and XBB.1. CONCLUSION Diagnostic performance of RAT was not affected by changes in predominant circulating Omicron sublineages. However, reinfection cases may be under ascertained by RAT. In individuals with a previous SARS-CoV-2 infection episode or symptom onset ≥ 6 days prior to testing, a confirmatory RT-PCR may be considered if there is high clinical suspicion.
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Affiliation(s)
- Celine Y Tan
- National Preventive Medicine Residency Programme, National University Health System, Singapore, Singapore.
- National Centre for Infectious Diseases, Singapore, Singapore.
| | - Kangwei Zeng
- National Centre for Infectious Diseases, Singapore, Singapore
- Ministry of Health, Singapore, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Mark Chen
- National Centre for Infectious Diseases, Singapore, Singapore
- Ministry of Health, Singapore, Singapore
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Teo JWP, Cheng JWS, Chew KL, Lin RTP. Whole genome characterization of Trichophyton indotineae isolated in Singapore. Med Mycol 2024; 62:myae012. [PMID: 38366631 DOI: 10.1093/mmy/myae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/18/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
Complete genome sequences from two Trichophyton indotineae isolates were obtained from a 23-year-old male presenting with tinea cruris after an overseas recreational water exposure and from a 53-year-old female patient with unknown travel history. Analysis of the squalene epoxidase gene and the cyp51 gene family showed an absence of mutations, correlating with phenotypic drug susceptibility. The Single Nucleotide Polymorphisms (SNPs) distance between both isolates was 92. Within the T. indotineae cluster, SNPs ranged from 7 to 182, suggesting a high genetic relatedness with other South Asian isolates. This study suggests that the prevalence of T. indotineae is under-reported and more widespread than previously thought.
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Affiliation(s)
- Jeanette W P Teo
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Janet W S Cheng
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Ka Lip Chew
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Raymond T P Lin
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Goh YS, Fong SW, Tay MZ, Rouers A, Chang ZW, Chavatte JM, Hor PX, Loh CY, Huang Y, Tan YJ, Wang B, Ngoh EZX, Mohd Salleh SN, Lee RTC, Lim G, Maurer-Stroh S, Wang CI, Leo YS, Lin RTP, Lam MC, Lye DC, Young BE, Ng LFP, Renia L. Author Correction: Higher Delta variant-specific neutralizing antibodies prevented infection in close contacts vaccinated with ancestral mRNA vaccines during the SARS-CoV-2 Delta wave. Sci Rep 2024; 14:1492. [PMID: 38233454 PMCID: PMC10794195 DOI: 10.1038/s41598-024-51484-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024] Open
Affiliation(s)
- Yun Shan Goh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Matthew Zirui Tay
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Angeline Rouers
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Zi Wei Chang
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Jean-Marc Chavatte
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Pei Xiang Hor
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Chiew Yee Loh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Yuling Huang
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Yong Jie Tan
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Bei Wang
- Singapore Immunology Network, A*STAR, Singapore, Singapore
| | | | | | - Raphael Tze Chuen Lee
- Bioinformatics Institute, A*STAR, Singapore, Singapore
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
| | | | - Sebastian Maurer-Stroh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
- Bioinformatics Institute, A*STAR, Singapore, Singapore
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Cheng-I Wang
- Singapore Immunology Network, A*STAR, Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - David C Lye
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute of Health Research, University of Liverpool, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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Goh YS, Fong SW, Tay MZ, Rouers A, Chang ZW, Chavatte JM, Hor PX, Loh CY, Huang Y, Tan YJ, Wang B, Ngoh EZX, Mohd Salleh SN, Lee RTC, Lim G, Maurer-Stroh S, Wang CI, Leo YS, Lin RTP, Lam MC, Lye DC, Young BE, Ng LFP, Renia L. Higher Delta variant-specific neutralizing antibodies prevented infection in close contacts vaccinated with ancestral mRNA vaccines during the SARS-CoV-2 Delta wave. Sci Rep 2023; 13:19331. [PMID: 37935965 PMCID: PMC10630438 DOI: 10.1038/s41598-023-46800-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/05/2023] [Indexed: 11/09/2023] Open
Abstract
Identification of the risk factors and the high-risk groups which are most vulnerable is critical in COVID-19 disease management at a population level. Evaluating the efficacy of vaccination against infections is necessary to determine booster vaccination strategies for better protection in high-risk groups. In this study, we recruited 158 mRNA-vaccinated individuals during the Delta wave of SARS-CoV-2 infections in Singapore and examined the antibody profiles of infected individuals. We found that, despite high exposure due to communal living conditions in proximity, 4% of individuals (6/158) had PCR-confirmed infections and 96% (152/158) remained uninfected. Time-course analysis of the antibody profile at the start and the end of quarantine period showed Delta-specific boosting of anti-spike antibody response in 57% of the uninfected individuals (86/152). In the remaining 43% of the uninfected individuals (66/152) with no Delta-specific antibody boost, we found a higher Delta-specific antibody response at the start of quarantine period, which correlated with higher Delta pseudovirus neutralizing capacity. Our findings indicate that a higher basal variant-specific antibody response in the mRNA-vaccinated individuals contributes to better protection against infections by the new emerging SARS-CoV-2 variants.
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Affiliation(s)
- Yun Shan Goh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Matthew Zirui Tay
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Angeline Rouers
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Zi Wei Chang
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Jean-Marc Chavatte
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Pei Xiang Hor
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Chiew Yee Loh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Yuling Huang
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Yong Jie Tan
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
| | - Bei Wang
- Singapore Immunology Network, A*STAR, Singapore, Singapore
| | | | | | - Raphael Tze Chuen Lee
- Bioinformatics Institute, A*STAR, Singapore, Singapore
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
| | | | - Sebastian Maurer-Stroh
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
- Bioinformatics Institute, A*STAR, Singapore, Singapore
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Cheng-I Wang
- Singapore Immunology Network, A*STAR, Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - David C Lye
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Barnaby Edward Young
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute of Health Research, University of Liverpool, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos #05-13, Singapore, 138648, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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5
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Lim AYH, Ang MLT, Cho SSL, Ng DHL, Cutter J, Lin RTP. Implementation of national whole-genome sequencing of Mycobacterium tuberculosis, National Public Health Laboratory, Singapore, 2019-2022. Microb Genom 2023; 9. [PMID: 38010371 DOI: 10.1099/mgen.0.001139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
The National Tuberculosis Programme (NTBP) monitors the occurrence and spread of tuberculosis (TB) and multidrug-resistant TB (MDR-TB) in Singapore. Since 2020, whole-genome sequencing (WGS) of Mycobacterium tuberculosis isolates has been performed at the National Public Health Laboratory (NPHL) for genomic surveillance, replacing spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeats analysis (MIRU-VNTR). Four thousand three hundred and seven samples were sequenced from 2014 to January 2023, initially as research projects and later developed into a comprehensive public health surveillance programme. Currently, all newly diagnosed culture-positive cases of TB in Singapore are prospectively sent for WGS, which is used to perform lineage classification, predict drug resistance profiles and infer genetic relationships between TB isolates. This paper describes NPHL's operational and technical experiences with implementing the WGS service in an urban TB-endemic setting, focusing on cluster detection and genomic drug susceptibility testing (DST). Cluster detection: WGS has been used to guide contact tracing by detecting clusters and discovering unknown transmission networks. Examples have been clusters in a daycare centre, housing apartment blocks and a horse-racing betting centre. Genomic DST: genomic DST prediction (gDST) identifies mutations in core genes known to be associated with TB drug resistance catalogued in the TBProfiler drug resistance mutation database. Mutations are reported with confidence scores according to a standardized approach referencing NPHL's internal gDST confidence database, which is adapted from the World Health Organization (WHO) TB drug mutation catalogue. Phenotypic-genomic concordance was observed for the first-line drugs ranging from 2959/2998 (98.7 %) (ethambutol) to 2983/2996 (99.6 %) (rifampicin). Aspects of internal database management, reporting standards and caveats in results interpretation are discussed.
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Affiliation(s)
- Ansel Yi Herh Lim
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Michelle L T Ang
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Sharol S L Cho
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Deborah H L Ng
- National Tuberculosis Programme, National Centre for Infectious Diseases, Singapore, Singapore
| | - Jeffery Cutter
- National Tuberculosis Programme, National Centre for Infectious Diseases, Singapore, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
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Poh XY, Tan CW, Lee IR, Chavatte JM, Fong SW, Prince T, Hartley C, Yeoh AYY, Rao S, Chia PY, Ong SWX, Lee TH, Sadarangani SP, Lin RJH, Lim C, Teo J, Lim DRX, Chia W, Hiscox JA, Ng LFP, Ren EC, Lin RTP, Renia L, Lye DC, Wang LF, Young BE. Antibody Response of Heterologous vs Homologous Messenger RNA Vaccine Boosters Against the Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variant: Interim Results from the PRIBIVAC Study, a Randomized Clinical Trial. Clin Infect Dis 2022; 75:2088-2096. [PMID: 35543372 PMCID: PMC9129205 DOI: 10.1093/cid/ciac345] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Waning antibody levels post-vaccination and the emergence of variants of concern (VOCs) capable of evading protective immunity have raised the need for booster vaccinations. However, which combination of coronavirus disease 2019 (COVID-19) vaccines offers the strongest immune response against the Omicron variant is unknown. METHODS This randomized, participant-blinded, controlled trial assessed the reactogenicity and immunogenicity of different COVID-19 vaccine booster combinations. A total of 100 BNT162b2-vaccinated individuals were enrolled and randomized 1:1 to either homologous (BNT162b2 + BNT162b2 + BNT162b2; "BBB") or heterologous messenger RNA (mRNA) (BNT162b2 + BNT162b2 + mRNA-1273; "BBM") booster vaccine. The primary end point was the level of neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) wild-type and VOCs at day 28. RESULTS A total of 51 participants were allocated to BBB and 49 to BBM; 50 and 48, respectively, were analyzed for safety and immunogenicity outcomes. At day 28 post-boost, mean SARS-CoV-2 spike antibody titers were lower with BBB (22 382 IU/mL; 95% confidence interval [CI], 18 210 to 27 517) vs BBM (29 751 IU/mL; 95% CI, 25 281 to 35 011; P = .034) as was the median level of neutralizing antibodies: BBB 99.0% (interquartile range [IQR], 97.9% to 99.3%) vs BBM 99.3% (IQR, 98.8% to 99.5%; P = .021). On subgroup analysis, significant higher mean spike antibody titer, median surrogate neutralizing antibody level against all VOCs, and live Omicron neutralization titer were observed only in older adults receiving BBM. Both vaccines were well tolerated. CONCLUSIONS Heterologous mRNA-1273 booster vaccination compared with homologous BNT123b2 induced a stronger neutralizing response against the Omicron variant in older individuals. CLINICAL TRIALS REGISTRATION NCT05142319.
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Affiliation(s)
- Xuan Ying Poh
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Chee Wah Tan
- Emerging Infectious Diseases Programme, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - I Russel Lee
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Jean-Marc Chavatte
- National Centre for Infectious Diseases, Singapore, Singapore
- National Public Health Laboratory, Singapore, Singapore
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Lab, Agency for Science Technology and Research, Singapore, Singapore
| | - Tessa Prince
- Department of Infection Biology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Catherine Hartley
- Department of Infection Biology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Aileen Y Y Yeoh
- Emerging Infectious Diseases Programme, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Suma Rao
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Po Ying Chia
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sean W X Ong
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tau Hong Lee
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Sapna P Sadarangani
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Ray J H Lin
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Clarissa Lim
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Jefanie Teo
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Daniel R X Lim
- National Centre for Infectious Diseases, Singapore, Singapore
- National Public Health Laboratory, Singapore, Singapore
| | - Wanni Chia
- Emerging Infectious Diseases Programme, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Julian A Hiscox
- A*STAR Infectious Diseases Lab, Agency for Science Technology and Research, Singapore, Singapore
- Department of Infection Biology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Lisa F P Ng
- A*STAR Infectious Diseases Lab, Agency for Science Technology and Research, Singapore, Singapore
- Department of Infection Biology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ee Chee Ren
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Immunology Network, Agency for Science Technology and Research, Singapore, Singapore
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore
- National Public Health Laboratory, Singapore, Singapore
| | - Laurent Renia
- A*STAR Infectious Diseases Lab, Agency for Science Technology and Research, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Lin-Fa Wang
- Emerging Infectious Diseases Programme, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Barnaby E Young
- National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
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7
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Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Global disparities in SARS-CoV-2 genomic surveillance. Nat Commun 2022; 13:7003. [PMID: 36385137 PMCID: PMC9667854 DOI: 10.1038/s41467-022-33713-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022] Open
Abstract
Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity.
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Affiliation(s)
- Anderson F Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
- Instituto Todos pela Saúde, São Paulo, SP, Brazil.
| | | | - Gytis Dudas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gabriel W Hassler
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale School of Medicine, Yale University, New Haven, CT, USA
| | | | - Joses Ho
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Charles N Agoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Lucy E Matkin
- Department of Biology, University of Oxford, Oxford, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | | | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Neta S Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Heather M Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Fernando R Spilki
- Feevale University, Institute of Health Sciences, Novo Hamburgo, RS, Brazil
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivan N Ivanov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivva Philipova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Christine V F Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nikita S D Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Ben Branda
- GISAID Global Data Science Initiative, Munich, Germany
| | - Céline Gurry
- GISAID Global Data Science Initiative, Munich, Germany
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Dhamari Naidoo
- Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India
| | - Karin J von Eije
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Mark D Perkins
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Maria van Kerkhove
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | | | - Ester C Sabino
- Instituto Todos pela Saúde, São Paulo, SP, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Royal Veterinary College, Hawkshead, UK
| | | | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Marc A Suchard
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nuno R Faria
- Department of Biology, University of Oxford, Oxford, UK.
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK.
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
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8
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Aw ZQ, Mok CK, Wong YH, Chen H, Mak TM, Lin RTP, Lye DC, Tan KS, Chu JJH. Early pathogenesis profiles across SARS-CoV-2 variants in K18-hACE2 mice revealed differential triggers of lung damages. Front Immunol 2022; 13:950666. [DOI: 10.3389/fimmu.2022.950666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022] Open
Abstract
The on-going COVID-19 pandemic has given rise to SARS-CoV-2 clades and variants with differing levels of symptoms and severity. To this end, we aim to systematically elucidate the changes in the pathogenesis as SARS-CoV-2 evolved from ancestral to the recent Omicron VOC, on their mechanisms (e.g. cytokine storm) resulting in tissue damage, using the established K18-hACE2 murine model. We reported that among the SARS-CoV-2 viruses tested, infection profiles were initially similar between viruses from early clades but started to differ greatly starting from VOC Delta, where the trend continues in Omicron. VOCs Delta and Omicron both accumulated a significant number of mutations, and when compared to VOCs Alpha, Beta, and earlier predecessors, showed reduced neurotropism and less apparent gene expression in cytokine storm associated pathways. They were shown to leverage on other pathways to cause tissue damage (or lack of in the case of Omicron). Our study highlighted the importance of elucidating the response profiles of individual SARS-CoV-2 iterations, as their propensity of severe infection via pathways like cytokine storm changes as more variant evolves. This will then affect the overall threat assessment of each variant as well as the use of immunomodulatory treatments as management of severe infections of each variant.
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9
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Lum FM, Torres-Ruesta A, Tay MZ, Lin RTP, Lye DC, Rénia L, Ng LFP. Monkeypox: disease epidemiology, host immunity and clinical interventions. Nat Rev Immunol 2022; 22:597-613. [PMID: 36064780 PMCID: PMC9443635 DOI: 10.1038/s41577-022-00775-4] [Citation(s) in RCA: 152] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2022] [Indexed: 12/11/2022]
Abstract
Monkeypox virus (MPXV), which causes disease in humans, has for many years been restricted to the African continent, with only a handful of sporadic cases in other parts of the world. However, unprecedented outbreaks of monkeypox in non-endemic regions have recently taken the world by surprise. In less than 4 months, the number of detected MPXV infections has soared to more than 48,000 cases, recording a total of 13 deaths. In this Review, we discuss the clinical, epidemiological and immunological features of MPXV infections. We also highlight important research questions and new opportunities to tackle the ongoing monkeypox outbreak. In this Review, Ng and colleagues examine the clinical, epidemiological and immunological aspects of monkeypox virus (MPXV) infections, with a focus on mechanisms of host immunity to MPXV. The authors also consider the unique epidemiological and pathological characteristics of the current non-endemic outbreak of the virus and discuss vaccines, therapeutics and outstanding research questions.
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Affiliation(s)
- Fok-Moon Lum
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Anthony Torres-Ruesta
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Matthew Z Tay
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, Singapore, Singapore.,National Centre for Infectious Diseases, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - David C Lye
- National Centre for Infectious Diseases, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Tan Tock Seng Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Laurent Rénia
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK. .,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
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10
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Poh XY, Lee IR, Lim C, Teo J, Rao S, Chia PY, Ong SWX, Lee TH, Lin RJH, Ng LFP, Ren EC, Lin RTP, Wang LF, Renia L, Lye DC, Young BE. Evaluation of the safety and immunogenicity of different COVID-19 vaccine combinations in healthy individuals: study protocol for a randomized, subject-blinded, controlled phase 3 trial [PRIBIVAC]. Trials 2022; 23:498. [PMID: 35710572 PMCID: PMC9201789 DOI: 10.1186/s13063-022-06345-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/23/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Over 2021, COVID-19 vaccination programs worldwide focused on raising population immunity through the primary COVID-19 vaccine series. In Singapore, two mRNA vaccines (BNT162b2 and mRNA-1273) and the inactivated vaccine CoronaVac are currently authorized under the National Vaccination Programme for use as the primary vaccination series. More than 90% of the Singapore population has received at least one dose of a COVID-19 vaccine as of December 2021. With the demonstration that vaccine effectiveness wanes in the months after vaccination, and the emergence of Omicron which evades host immunity from prior infection and/or vaccination, attention in many countries has shifted to how best to maintain immunity through booster vaccinations. METHODS The objectives of this phase 3, randomized, subject-blinded, controlled clinical trial are to assess the safety and immunogenicity of heterologous boost COVID-19 vaccine regimens (intervention groups 1-4) compared with a homologous boost regimen (control arm) in up to 600 adult volunteers. As non-mRNA vaccine candidates may enter the study at different time points depending on vaccine availability and local regulatory approval, participants will be randomized at equal probability to the available intervention arms at the time of randomization. Eligible participants will have received two doses of a homologous mRNA vaccine series with BNT162b2 or mRNA-1273 at least 6 months prior to enrolment. Participants will be excluded if they have a history of confirmed SARS or SARS-CoV-2 infection, are immunocompromised, or are pregnant. Participants will be monitored for adverse events and serious adverse events by physical examinations, laboratory tests and self-reporting. Blood samples will be collected at serial time points [pre-vaccination/screening (day - 14 to day 0), day 7, day 28, day 180, day 360 post-vaccination] for assessment of antibody and cellular immune parameters. Primary endpoint is the level of anti-SARS-CoV-2 spike immunoglobulins at day 28 post-booster and will be measured against wildtype SARS-CoV-2 and variants of concern. Comprehensive immune profiling of the humoral and cellular immune response to vaccination will be performed. DISCUSSION This study will provide necessary data to understand the quantity, quality, and persistence of the immune response to a homologous and heterologous third booster dose of COVID-19 vaccines. This is an important step in developing COVID-19 vaccination programs beyond the primary series. TRIAL REGISTRATION ClinicalTrials.gov NCT05142319 . Registered on 2 Dec 2021.
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Affiliation(s)
- Xuan Ying Poh
- National Centre for Infectious Diseases, Singapore, Singapore
| | - I Russel Lee
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Clarissa Lim
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Jefanie Teo
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Suma Rao
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Po Ying Chia
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sean W X Ong
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Tau Hong Lee
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Ray J H Lin
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Lab, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ee Chee Ren
- Singapore Immunology Network, A*STAR, Singapore, Singapore
| | | | - Lin-Fa Wang
- Duke-NUS Medical School, Singapore, Singapore
| | - Laurent Renia
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- A*STAR Infectious Diseases Lab, Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Barnaby E Young
- National Centre for Infectious Diseases, Singapore, Singapore.
- Tan Tock Seng Hospital, Singapore, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
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11
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Mauldin MR, McCollum AM, Nakazawa YJ, Mandra A, Whitehouse ER, Davidson W, Zhao H, Gao J, Li Y, Doty J, Yinka-Ogunleye A, Akinpelu A, Aruna O, Naidoo D, Lewandowski K, Afrough B, Graham V, Aarons E, Hewson R, Vipond R, Dunning J, Chand M, Brown C, Cohen-Gihon I, Erez N, Shifman O, Israeli O, Sharon M, Schwartz E, Beth-Din A, Zvi A, Mak TM, Ng YK, Cui L, Lin RTP, Olson VA, Brooks T, Paran N, Ihekweazu C, Reynolds MG. Exportation of Monkeypox Virus From the African Continent. J Infect Dis 2022; 225:1367-1376. [PMID: 32880628 PMCID: PMC9016419 DOI: 10.1093/infdis/jiaa559] [Citation(s) in RCA: 168] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The largest West African monkeypox outbreak began September 2017, in Nigeria. Four individuals traveling from Nigeria to the United Kingdom (n = 2), Israel (n = 1), and Singapore (n = 1) became the first human monkeypox cases exported from Africa, and a related nosocomial transmission event in the United Kingdom became the first confirmed human-to-human monkeypox transmission event outside of Africa. METHODS Epidemiological and molecular data for exported and Nigerian cases were analyzed jointly to better understand the exportations in the temporal and geographic context of the outbreak. RESULTS Isolates from all travelers and a Bayelsa case shared a most recent common ancestor and traveled to Bayelsa, Delta, or Rivers states. Genetic variation for this cluster was lower than would be expected from a random sampling of genomes from this outbreak, but data did not support direct links between travelers. CONCLUSIONS Monophyly of exportation cases and the Bayelsa sample, along with the intermediate levels of genetic variation, suggest a small pool of related isolates is the likely source for the exported infections. This may be the result of the level of genetic variation present in monkeypox isolates circulating within the contiguous region of Bayelsa, Delta, and Rivers states, or another more restricted, yet unidentified source pool.
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Affiliation(s)
- Matthew R Mauldin
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andrea M McCollum
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yoshinori J Nakazawa
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Anna Mandra
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Erin R Whitehouse
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Whitni Davidson
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hui Zhao
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jinxin Gao
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yu Li
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jeffrey Doty
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | | | - Olusola Aruna
- International Health Regulations Strengthening Project, Global Public Health, Public Health England, London, United Kingdom
| | - Dhamari Naidoo
- World Health Organization Country Office, Abuja, Nigeria
| | | | | | | | - Emma Aarons
- Public Health England, London, United Kingdom
| | | | | | | | - Meera Chand
- Public Health England, London, United Kingdom
| | - Colin Brown
- Public Health England, London, United Kingdom
| | - Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Biology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Noam Erez
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ohad Shifman
- Department of Biochemistry and Molecular Biology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Biology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Melamed Sharon
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Eli Schwartz
- Institute of Tropical Medicine, Chaim Sheba Medical Center, Tel Hashomer, Israel
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Biology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Biology, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Tze Minn Mak
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Yi Kai Ng
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Lin Cui
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Victoria A Olson
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tim Brooks
- Public Health England, London, United Kingdom
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | | | - Mary G Reynolds
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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12
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Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MU, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Global disparities in SARS-CoV-2 genomic surveillance. medRxiv 2021:2021.08.21.21262393. [PMID: 34462754 PMCID: PMC8404891 DOI: 10.1101/2021.08.21.21262393] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Genomic sequencing provides critical information to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments and vaccines, and guide public health responses. To investigate the spatiotemporal heterogeneity in the global SARS-CoV-2 genomic surveillance, we estimated the impact of sequencing intensity and turnaround times (TAT) on variant detection in 167 countries. Most countries submit genomes >21 days after sample collection, and 77% of low and middle income countries sequenced <0.5% of their cases. We found that sequencing at least 0.5% of the cases, with a TAT <21 days, could be a benchmark for SARS-CoV-2 genomic surveillance efforts. Socioeconomic inequalities substantially impact our ability to quickly detect SARS-CoV-2 variants, and undermine the global pandemic preparedness.
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Affiliation(s)
- Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Instituto Todos pela Saúde, São Paulo, São Paulo, Brazil
| | - Elizaveta Semenova
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Mathematics, Imperial College London, London, UK
| | - Gytis Dudas
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Gabriel W. Hassler
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | | | - Joses Ho
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
| | - Houriiyah Tegally
- KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kenya
| | | | - Lucy E. Matkin
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom
| | | | | | | | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales 2145, Australia
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Israel
| | - Heather M Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, Michigan, USA
| | - Tulio de Oliveira
- KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | | | | | | | - Fernando R. Spilki
- Feevale University, Institute of Health Sciences, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D’Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivan N. Ivanov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivva Philipova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Christine V. F. Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nikita S. D. Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Céline Gurry
- GISAID Global Data Science Initiative, Munich, Germany
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore
| | - Dhamari Naidoo
- Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India
| | - Karin J von Eije
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Mark D. Perkins
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Maria van Kerkhove
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | | | - Ester C. Sabino
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Royal Veterinary College, Hawkshead, United Kingdom
| | - Christopher Dye
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Marc A. Suchard
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nuno R. Faria
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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13
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Chew KL, Octavia S, Lai D, Lin RTP, Teo JWP. Staphylococcus singaporensis sp. nov., a new member of the Staphylococcus aureus complex, isolated from human clinical specimens. Int J Syst Evol Microbiol 2021; 71. [PMID: 34698625 DOI: 10.1099/ijsem.0.005067] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Staphylococcus argenteus and Staphylococcus schweitzeri are the newest members of the Staphylococcus aureus complex. The number of clinical reports attributed to these new S. aureus complex members is limited. In a retrospective clinical laboratory study conducted over a 4-month period investigating the prevalence of S. argenteus and S. schweitzeri, a total of 43 isolates were selected. Phylogeny based on core-gene multilocus sequence typing (MLST) analysis confirmed that 37 were S. argenteus but a genetically distinct clade of six isolates was identified. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses further supported the classification of these six isolates as a separate species. When compared to S. aureus complex reference genomes, the ANI values were ≤94 % and the dDDH values were <53 %. Based on the seven-gene S. aureus MLST scheme, the six isolates belong to five novel allelic profiles (ST6105, ST6106, ST6107, ST6108 and ST109). Their clinical infection features were similar to S. aureus. Skin and soft tissue infections presented in four out of the six cases. Routine clinical diagnostic identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and biochemical profiling does not differentiate these new members from the rest of the complex. Genotypic analysis suggests that the six isolates belong to a novel species, Staphylococcus singaporensis sp. nov. with isolate SS21T (=DSM 111408T=NCTC14419T) designated as the type strain.
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Affiliation(s)
- Ka Lip Chew
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Sophie Octavia
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore.,Present address: Environmental Health Institute, National Environment Agency, Singapore, Singapore
| | - Deborah Lai
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Raymond T P Lin
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore.,National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Jeanette W P Teo
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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14
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Ong SWX, Chiew CJ, Ang LW, Mak TM, Cui L, Toh MPHS, Lim YD, Lee PH, Lee TH, Chia PY, Maurer-Stroh S, Lin RTP, Leo YS, Lee VJ, Lye DC, Young BE. Clinical and Virological Features of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants of Concern: A Retrospective Cohort Study Comparing B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta). Clin Infect Dis 2021; 75:e1128-e1136. [PMID: 34423834 PMCID: PMC8522361 DOI: 10.1093/cid/ciab721] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The impact of SARS-CoV-2 variants of concern (VOCs) on disease severity is unclear. In this retrospective study, we compared the outcomes of patients infected with B.1.1.7, B.1.351, and B.1.617.2 with wild-type strains from early 2020. METHODS National surveillance data from January to May 2021 were obtained and outcomes in relation to VOCs were explored. Detailed patient-level data from all patients with VOC infection admitted to our center between December 2020 and May 2021 were analyzed. Clinical outcomes were compared with a cohort of 846 patients admitted from January to April 2020. RESULTS A total of 829 patients in Singapore in the study period were infected with these 3 VOCs. After adjusting for age and sex, B.1.617.2 was associated with higher odds of oxygen requirement, intensive care unit admission, or death (adjusted odds ratio [aOR], 4.90; 95% confidence interval [CI]: 1.43-30.78). Of these patients, 157 were admitted to our center. After adjusting for age, sex, comorbidities, and vaccination, the aOR for pneumonia with B.1.617.2 was 1.88 (95% CI: .95-3.76) compared with wild-type. These differences were not seen with B.1.1.7 and B.1.351. Vaccination status was associated with decreased severity. B.1.617.2 was associated with significantly lower polymerase chain reaction cycle threshold (Ct) values and longer duration of Ct value ≤30 (median duration 18 days for B.1.617.2, 13 days for wild-type). CONCLUSIONS B.1.617.2 was associated with increased severity of illness, and with lower Ct values and longer viral shedding. These findings provide impetus for the rapid implementation of vaccination programs.
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Affiliation(s)
- Sean Wei Xiang Ong
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Calvin J Chiew
- National Centre for Infectious Diseases, Singapore, Singapore,Ministry of Health, Singapore, Singapore
| | - Li Wei Ang
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Tze Minn Mak
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Matthias Paul H S Toh
- National Centre for Infectious Diseases, Singapore, Singapore,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | | | - Pei Hua Lee
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tau Hong Lee
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Po Ying Chia
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore,A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore,Department of Biological Sciences, National University of Singapore, Singapore
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yee Sin Leo
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vernon J Lee
- Ministry of Health, Singapore, Singapore,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Barnaby Edward Young
- Correspondence: Barnaby Young, National Centre for Infectious Diseases, 16 Jln Tan Tock Seng, Singapore 308442 ()
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15
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Chew KL, Octavia S, Lai D, Lin RTP, Teo JWP. Genomic Characterization of Klebsiella quasipneumoniae from Clinical Specimens in Singapore. Antimicrob Agents Chemother 2021; 65:e0041221. [PMID: 34060897 PMCID: PMC8284435 DOI: 10.1128/aac.00412-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/24/2021] [Indexed: 11/20/2022] Open
Abstract
A total of 1,281 specimens from 1,024 patients were screened. Phylogenetic analysis classified 44 of these isolates as Klebsiella quasipneumoniae subsp. similipneumoniae (44/1,281 [3.4%]) and the remaining three as K. quasipneumoniae subsp. quasipneumoniae. The most common specimen source was urine (21/47 [44.7%]) followed by blood (14/47 [29.8%]). K. quasipneumoniae isolates were nonclonal. Carbapenemase-encoding genes (blaNDM and blaOXA-181) were detected in only two isolates (2/47 [4.3%]). K. quasipneumoniae appears to cause a spectrum of infections similar to those of K. pneumoniae, although higher rates of susceptibility to many commonly tested antimicrobials and low prevalence of virulence genes were demonstrated.
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Affiliation(s)
- Ka Lip Chew
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Sophie Octavia
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Deborah Lai
- Department of Pathology, Singapore General Hospital, Singapore
| | - Raymond T. P. Lin
- Department of Laboratory Medicine, National University Hospital, Singapore
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Jeanette W. P. Teo
- Department of Laboratory Medicine, National University Hospital, Singapore
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16
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Octavia S, Xu W, Ng OT, Marimuthu K, Venkatachalam I, Cheng B, Lin RTP, Teo JWP. Identification of AbaR4 Acinetobacter baumannii resistance island in clinical isolates of blaOXA-23-positive Proteus mirabilis. J Antimicrob Chemother 2021; 75:521-525. [PMID: 31725155 DOI: 10.1093/jac/dkz472] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/01/2019] [Accepted: 10/14/2019] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES bla OXA-23 is a class D carbapenemase-encoding gene typical of the Acinetobacter genus. However, its occurrence in the Enterobacteriaceae is uncommon. Here we provide the genome characterization of blaOXA-23-positive Proteus mirabilis. METHODS In Singapore, a national surveillance of carbapenem non-susceptible clinical Enterobacteriaceae has enabled the collection of OXA-23 bearing isolates. Three clinical P. mirabilis were whole-genome sequenced using Oxford Nanopore MinION and Illumina platforms. The sequence accuracy of MinION long-read contigs was enhanced by polishing with Illumina-derived short-read data. RESULTS In two P. mirabilis genomes, blaOXA-23 was detected as two copies, present on the chromosome and on a 60018 bp plasmid. blaOXA-23 was associated with the classic Acinetobacter composite transposon Tn2006, bounded by two copies of ISAba1 bracketing the carbapenemase gene. The Tn2006 itself was embedded within an Acinetobacter baumannii AbaR4 resistance island. In the chromosome, the AbaR4 was found integrated into the comM gene, which is also the preferred 'hotspot' in A. baumannii. In the plasmid, AbaR4 integrated into a putative colicin gene. CONCLUSIONS Our description of an A. baumannii AbaR4 encoding blaOXA-23 in P. mirabilis is to our knowledge the first description of an Acinetobacter resistance island in Proteus and suggests that P. mirabilis may be a reservoir for this class D carbapenemase gene.
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Affiliation(s)
- Sophie Octavia
- National Public Health Laboratory, Ministry of Health, Singapore.,National Centre for Infectious Diseases, Singapore
| | - Weizhen Xu
- National Centre for Infectious Diseases, Singapore.,Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore
| | - Oon Tek Ng
- National Public Health Laboratory, Ministry of Health, Singapore.,National Centre for Infectious Diseases, Singapore.,Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore.,Nanyang Technological University, Lee Kong Chian School of Medicine, Singapore
| | - Kalisvar Marimuthu
- National Centre for Infectious Diseases, Singapore.,Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore.,National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | - Indumathi Venkatachalam
- Singapore General Hospital, Department of Infectious Diseases and Department of Infection Prevention & Epidemiology, Singapore
| | - Bernadette Cheng
- National University Hospital, Department of Laboratory Medicine, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, Ministry of Health, Singapore.,National Centre for Infectious Diseases, Singapore.,National University Hospital, Department of Laboratory Medicine, Singapore
| | - Jeanette W P Teo
- National University Hospital, Department of Laboratory Medicine, Singapore
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17
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Abstract
Global travel has led to intermittent importation of multidrug-resistant Salmonellaenterica serovar Typhi into industrialized countries. We detected azithromycin-resistant Salmonella Typhi in Singapore, of which 2 isolates were likely locally acquired. Ongoing vigilance and surveillance to minimize the public health risk for this serious pathogen is needed.
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18
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Chew KL, Octavia S, Jureen R, Lin RTP, Teo JWP. Targeted amplification and MinION nanopore sequencing of key azole and echinocandin resistance determinants of clinically relevant Candida spp. from blood culture bottles. Lett Appl Microbiol 2021; 73:286-293. [PMID: 34060660 DOI: 10.1111/lam.13516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/29/2021] [Accepted: 05/21/2021] [Indexed: 12/19/2022]
Abstract
The objective of the study was to evaluate the use of targeted multiplex Nanopore MinION amplicon re-sequencing of key Candida spp. from blood culture bottles to identify azole and echinocandin resistance associated SNPs. Targeted PCR amplification of azole (ERG11 and ERG3) and echinocandin (FKS) resistance-associated loci was performed on positive blood culture media. Sequencing was performed using MinION nanopore device with R9.4.1 Flow Cells. Twenty-eight spiked blood cultures (ATCC strains and clinical isolates) and 12 prospectively collected positive blood cultures with candidaemia were included. Isolate species included Candida albicans, Candida glabrata, Candida krusei, Candida parapsilosis, Candida tropicalis and Candida auris. SNPs that were identified on ERG and FKS genes using Snippy tool and CLC Genomic Workbench were correlated with phenotypic testing by broth microdilution (YeastOne™ Sensititre). Illumina whole-genome-sequencing and Sanger-sequencing were also performed as confirmatory testing of the mutations identified from nanopore sequencing data. There was a perfect agreement of the resistance-associated mutations detected by MinION-nanopore-sequencing compared to phenotypic testing for acquired resistance (16 with azole resistance; 3 with echinocandin resistance), and perfect concordance of the nanopore sequence mutations to Illumina and Sanger data. Mutations with no known association with phenotypic drug resistance and novel mutations were also detected.
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Affiliation(s)
- K L Chew
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - S Octavia
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - R Jureen
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - R T P Lin
- Department of Laboratory Medicine, National University Hospital, Singapore.,National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - J W P Teo
- Department of Laboratory Medicine, National University Hospital, Singapore
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19
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Sim JXY, Gan ES, Tan HC, Choy MM, Wong HM, Tan BH, Kee T, Ho QY, Thangaraju S, Lin RTP, Ooi EE, Low JGH. Aviremic organ transplant dengue virus transmission - A case report. Am J Transplant 2021; 21:1944-1947. [PMID: 33583132 DOI: 10.1111/ajt.16540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 01/25/2023]
Abstract
Dengue virus (DENV), a mosquito-borne pathogen, causes systemic infections. There are no clear guidelines regarding the screening of donor blood is used in endemic countries to prevent blood transfusion or transplant-associated dengue. DENV has been shown to be detected in urine samples even when DENV viremia is undetectable. We describe an incident of transplant-associated dengue where the donor tested negative for DENV viremia but positive for DENV viuria resulting in the transmission of DENV to our two kidney recipients. Both recipients resolved DENV infection uneventfully, with no adverse impact on the renal graft. Our findings raise the consideration for revised screening recommendations in endemic countries to include DENV RT-PCR in the urine.
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Affiliation(s)
- Jean X Y Sim
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore.,Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore
| | - Esther S Gan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Hwee C Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Milly M Choy
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Hei M Wong
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore.,Department of Infection Prevention and Epidemiology, Singapore General Hospital, Singapore, Singapore
| | - Ban H Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore.,SingHealth Duke-NUS Transplant Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Terence Kee
- SingHealth Duke-NUS Transplant Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.,Department of Renal Medicine, Singapore General Hospital, Singapore, Singapore
| | - Quan Y Ho
- SingHealth Duke-NUS Transplant Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.,Department of Renal Medicine, Singapore General Hospital, Singapore, Singapore
| | - Sobhana Thangaraju
- SingHealth Duke-NUS Transplant Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.,Department of Renal Medicine, Singapore General Hospital, Singapore, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
| | - Eng E Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Jenny G-H Low
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
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20
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Octavia S, Chew KL, Lin RTP, Teo JWP. Whole genome sequencing of Salmonella enterica serovar Saintpaul for elucidating the mechanisms of resistance to third generation cephalosporins. Pathology 2021; 53:768-772. [PMID: 33840533 DOI: 10.1016/j.pathol.2020.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 12/01/2020] [Accepted: 12/07/2020] [Indexed: 11/28/2022]
Abstract
An increase in the number of Salmonella enterica serovar Saintpaul observed in Singapore in 2015-2016 in humans was accompanied by increased resistance to third generation cephalosporins. We aimed to understand the genetic mechanisms contributing to this resistance. Whole genome sequencing using MiSeq was performed on 49 S. Saintpaul isolates collected between 2014-2016. Nanopore sequencing was also performed in an attempt to obtain a full genome of the plasmids. All but one S. Saintpaul isolates sequenced belonged to a single sequence type based on an in silico 7-gene multi-locus sequence typing scheme suggesting a clonal lineage. In total 27/49 were resistant to third generation cephalosporins as confirmed by the broth microdilution method; the resistance was due to the presence of either blaCTX-M-55 (n=23), blaCTX-M-27 (n=1) or blaCMY-2 (n=3) carried on a plasmid. Two isolates were also found to carry the mcr-1 gene on a different plasmid. Our study showed that all S. Saintpaul isolates resistant to third generation cephalosporins carried either blaCTX-M-55, blaCTX-M-27 or blaCMY-2 on a plasmid. Continuous monitoring of Salmonella serovars is warranted to track the potential spread of these plasmids.
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Affiliation(s)
- Sophie Octavia
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore.
| | - Ka Lip Chew
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore; Department of Laboratory Medicine, National University Hospital, Singapore
| | - Jeanette W P Teo
- Department of Laboratory Medicine, National University Hospital, Singapore
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21
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Puah SH, Young BE, Chia PY, Ho VK, Loh J, Gokhale RS, Tan SY, Sewa DW, Kalimuddin S, Tan CK, Pada SKMS, Cove ME, Chai LYA, Parthasarathy P, Ho BCH, Ng JJ, Ling LM, Abisheganaden JA, Lee VJM, Tan CH, Lin RTP, Leo YS, Lye DC, Yeo TW. Clinical features and predictors of severity in COVID-19 patients with critical illness in Singapore. Sci Rep 2021; 11:7477. [PMID: 33820944 PMCID: PMC8021583 DOI: 10.1038/s41598-021-81377-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 12/14/2020] [Indexed: 01/10/2023] Open
Abstract
We aim to describe a case series of critically and non-critically ill COVID-19 patients in Singapore. This was a multicentered prospective study with clinical and laboratory details. Details for fifty uncomplicated COVID-19 patients and ten who required mechanical ventilation were collected. We compared clinical features between the groups, assessed predictors of intubation, and described ventilatory management in ICU patients. Ventilated patients were significantly older, reported more dyspnea, had elevated C-reactive protein and lactate dehydrogenase. A multivariable logistic regression model identified respiratory rate (aOR 2.83, 95% CI 1.24–6.47) and neutrophil count (aOR 2.39, 95% CI 1.34–4.26) on admission as independent predictors of intubation with area under receiver operating characteristic curve of 0.928 (95% CI 0.828–0.979). Median APACHE II score was 19 (IQR 17–22) and PaO2/FiO2 ratio before intubation was 104 (IQR 89–129). Median peak FiO2 was 0.75 (IQR 0.6–1.0), positive end-expiratory pressure 12 (IQR 10–14) and plateau pressure 22 (IQR 18–26) in the first 24 h of ventilation. Median duration of ventilation was 6.5 days (IQR 5.5–13). There were no fatalities. Most COVID-19 patients in Singapore who required mechanical ventilation because of ARDS were extubated with no mortality.
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Affiliation(s)
| | - Barnaby Edward Young
- Tan Tock Seng Hospital, Singapore, Singapore.,National Centre for Infectious Diseases, Singapore, Singapore.,Lee Kong Chian School of Medicine, Novena Campus Clinical Sciences Building, 11 Mandalay Rd, Singapore, 308232, Singapore
| | - Po Ying Chia
- Tan Tock Seng Hospital, Singapore, Singapore.,National Centre for Infectious Diseases, Singapore, Singapore.,Lee Kong Chian School of Medicine, Novena Campus Clinical Sciences Building, 11 Mandalay Rd, Singapore, 308232, Singapore
| | - Vui Kian Ho
- Sengkang General Hospital, Singapore, Singapore
| | - Jiashen Loh
- Sengkang General Hospital, Singapore, Singapore
| | | | - Seow Yen Tan
- Singapore General Hospital, Singapore, Singapore
| | - Duu Wen Sewa
- Singapore General Hospital, Singapore, Singapore
| | - Shirin Kalimuddin
- Singapore General Hospital, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | | | - Surinder K M S Pada
- Ng Teng Fong General Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Matthew Edward Cove
- National University Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Louis Yi Ann Chai
- National University Hospital, Singapore, Singapore.,Yong Loo Lin School of Medicine, Singapore, Singapore
| | | | | | | | - Li Min Ling
- Tan Tock Seng Hospital, Singapore, Singapore.,National Centre for Infectious Diseases, Singapore, Singapore.,Lee Kong Chian School of Medicine, Novena Campus Clinical Sciences Building, 11 Mandalay Rd, Singapore, 308232, Singapore
| | - John A Abisheganaden
- Tan Tock Seng Hospital, Singapore, Singapore.,Lee Kong Chian School of Medicine, Novena Campus Clinical Sciences Building, 11 Mandalay Rd, Singapore, 308232, Singapore
| | - Vernon J M Lee
- Ministry of Health, Singapore, Singapore.,Saw Swee Hock School of Public Health, Singapore, Singapore
| | - Cher Heng Tan
- Tan Tock Seng Hospital, Singapore, Singapore.,Lee Kong Chian School of Medicine, Novena Campus Clinical Sciences Building, 11 Mandalay Rd, Singapore, 308232, Singapore
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore.,Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Yee Sin Leo
- Tan Tock Seng Hospital, Singapore, Singapore.,National Centre for Infectious Diseases, Singapore, Singapore.,Lee Kong Chian School of Medicine, Novena Campus Clinical Sciences Building, 11 Mandalay Rd, Singapore, 308232, Singapore.,Yong Loo Lin School of Medicine, Singapore, Singapore.,Saw Swee Hock School of Public Health, Singapore, Singapore
| | - David C Lye
- Tan Tock Seng Hospital, Singapore, Singapore.,National Centre for Infectious Diseases, Singapore, Singapore.,Lee Kong Chian School of Medicine, Novena Campus Clinical Sciences Building, 11 Mandalay Rd, Singapore, 308232, Singapore.,Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Tsin Wen Yeo
- Tan Tock Seng Hospital, Singapore, Singapore. .,National Centre for Infectious Diseases, Singapore, Singapore. .,Lee Kong Chian School of Medicine, Novena Campus Clinical Sciences Building, 11 Mandalay Rd, Singapore, 308232, Singapore. .,Menzies School of Health Research, Charles Darwin University, Darwin, Australia.
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22
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Chew KL, Lin RTP, Teo JWP. Absence of mecC methicillin-resistant Staphylococcus aureus in a tertiary hospital in Singapore. Pathology 2021; 53:808. [PMID: 33642097 DOI: 10.1016/j.pathol.2020.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/02/2020] [Accepted: 11/13/2020] [Indexed: 11/24/2022]
Affiliation(s)
- Ka Lip Chew
- Department of Laboratory Medicine, National University Hospital, Singapore.
| | - Raymond T P Lin
- Department of Laboratory Medicine, National University Hospital, Singapore; National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Jeanette W P Teo
- Department of Laboratory Medicine, National University Hospital, Singapore
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Tan GSE, Ding Y, Cui L, Mak TM, Mok CK, Kurup A, Parthasarathy P, Chia WN, Wang LF, Lin RTP, Leo YS, Vasoo S. Positive RT-PCR detected in patients recovered from COVID-19. Ann Acad Med Singap 2021; 50:191-194. [PMID: 33733267 DOI: 10.47102/annals-acadmedsg.2020387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
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24
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Lee TH, Junhao Lin R, Lin RTP, Barkham T, Rao P, Leo YS, Chien Lye D, Young B. Testing for SARS-CoV-2: Can We Stop at 2? Clin Infect Dis 2020; 71:2246-2248. [PMID: 32306042 PMCID: PMC7188180 DOI: 10.1093/cid/ciaa459] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/17/2020] [Indexed: 01/19/2023] Open
Abstract
The COVID-19 epidemic requires accurate identification and isolation of confirmed cases for effective control. This report describes the effectiveness of our testing strategy and highlights the importance of repeat testing in suspect cases in our cohort.
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Affiliation(s)
- Tau Hong Lee
- National Centre for Infectious Diseases, Singapore.,Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Singapore.,Yong Loo Lin School of Medicine, Singapore
| | - Ray Junhao Lin
- National Centre for Infectious Diseases, Singapore.,Tan Tock Seng Hospital, Singapore
| | | | - Timothy Barkham
- Tan Tock Seng Hospital, Singapore.,Yong Loo Lin School of Medicine, Singapore
| | - Pooja Rao
- Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore.,Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Singapore.,Yong Loo Lin School of Medicine, Singapore.,Saw Swee Hock School of Public Health, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore.,Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Singapore.,Yong Loo Lin School of Medicine, Singapore
| | - Barnaby Young
- National Centre for Infectious Diseases, Singapore.,Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Singapore
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25
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Henderson A, Paterson DL, Chatfield MD, Tambyah PA, Lye DC, De PP, Lin RTP, Chew KL, Yin M, Lee TH, Yilmaz M, Cakmak R, Alenazi TH, Arabi YM, Falcone M, Bassetti M, Righi E, Ba R, Kanj SS, Bhally H, Iredell J, Mendelson M, Boyles TH, Looke DFM, Runnegar NJ, Miyakis S, Walls G, Ai Khamis M, Zikri A, Crowe A, Ingram PR, Daneman NN, Griffin P, Athan E, Roberts L, Beatson SA, Peleg AY, Cottrell KK, Bauer MJ, Tan E, Chaw K, Nimmo GR, Harris-Brown T, Harris PNA. Association between minimum inhibitory concentration, beta-lactamase genes and mortality for patients treated with piperacillin/tazobactam or meropenem from the MERINO study. Clin Infect Dis 2020; 73:e3842-e3850. [PMID: 33106863 DOI: 10.1093/cid/ciaa1479] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Indexed: 11/12/2022] Open
Abstract
INTRODUCTION This study aims to assess the association of piperacillin/tazobactam and meropenem minimum inhibitory concentration (MIC) and beta-lactam resistance genes with mortality in the MERINO trial. METHODS Blood culture isolates from enrolled patients were tested by broth microdilution and whole genome sequencing at a central laboratory. Multivariate logistic regression was performed to account for confounders. Absolute risk increase for 30-day mortality between treatment groups was calculated for the primary analysis (PA) and the microbiologic assessable (MA) populations. RESULTS 320 isolates from 379 enrolled patients were available with susceptibility to piperacillin/tazobactam 94% and meropenem 100%. The piperacillin/tazobactam non-susceptible breakpoint (MIC > 16 mg/L) best predicted 30-day mortality after accounting for confounders (odds ratio 14.9, 95% CI 2.8 - 87.2). The absolute risk increase for 30-day mortality for patients treated with piperacillin/tazobactam compared with meropenem was 9% (95% CI 3% - 15%) and 8% (95% CI 2% - 15%) for the original PA population and the post-hoc MA populations, which reduced to 5% (95% CI -1% - 10%) after excluding strains with piperacillin/tazobactam MIC values > 16 mg/L. Isolates co-harboring ESBL and OXA-1 genes were associated with elevated piperacillin/tazobactam MICs and the highest risk increase in 30-mortality of 14% (95% CI 2% - 28%). CONCLUSION After excluding non-susceptible strains, the 30-day mortality difference was from the MERINO trial was less pronounced for piperacillin/tazobactam. Poor reliability in susceptibility testing performance for piperacillin/tazobactam and the high prevalence of OXA co-harboring ESBLs suggests meropenem remains the preferred choice for definitive treatment of ceftriaxone non-susceptible E. coli and Klebsiella.
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Affiliation(s)
- A Henderson
- University of Queensland, UQ Centre for Clinical Research, Brisbane, Australia.,Infection Management Services, Princess Alexandra Hospital, Brisbane, QLD
| | - D L Paterson
- University of Queensland, UQ Centre for Clinical Research, Brisbane, Australia
| | - M D Chatfield
- University of Queensland, UQ Centre for Clinical Research, Brisbane, Australia
| | - P A Tambyah
- Department of Infectious Diseases, National University Hospital, Singapore
| | - D C Lye
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Department of Infectious Diseases, Institute of Infectious Diseases and Epidemiology, Tan Tock Seng.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore,Hospital, Singapore
| | - P P De
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore
| | - R T P Lin
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - K L Chew
- Division of Microbiology, National University Hospital, Singapore
| | - M Yin
- Department of Infectious Diseases, National University Hospital, Singapore
| | - T H Lee
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Department of Infectious Diseases, Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - M Yilmaz
- Department of Infectious Diseases and Clinical Microbiology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - R Cakmak
- Department of Infectious Diseases and Clinical Microbiology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - T H Alenazi
- King Saud Bin Abdulaziz University for Health Sciences and King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Y M Arabi
- King Saud Bin Abdulaziz University for Health Sciences and King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - M Falcone
- Division of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Pisa, Italy
| | - M Bassetti
- Infectious Diseases Clinic, Department of Health Sciences, University of Genoa and Ospedale Policlinico San Martino Genoa, Italy
| | - E Righi
- Infectious Diseases Clinic, Department of Medicine University of Udine and Santa Maria Misericordia Hospital, Udine, Italy.,Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Rogers Ba
- Monash University, Centre for Inflammatory Diseases, Victoria, Australia.,Monash Infectious Diseases, Monash Health, Victoria, Australia
| | - S S Kanj
- Department of Internal Medicine, Division of Infectious Diseases, American University of Beirut Medical Center, Beirut, Lebanon
| | - H Bhally
- Department of Medicine and Infectious Diseases, North Shore Hospital, Auckland
| | - J Iredell
- Marie Bashir Institute for Infectious Disease and Biosecurity, University of Sydney, Sydney, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, Australia
| | - M Mendelson
- Division of Infectious Diseases & HIV Medicine, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - T H Boyles
- Division of Infectious Diseases & HIV Medicine, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - D F M Looke
- Infection Management Services, Princess Alexandra Hospital, Brisbane, QLD.,University of Queensland, Brisbane, Australia
| | - N J Runnegar
- Infection Management Services, Princess Alexandra Hospital, Brisbane, QLD.,University of Queensland, Brisbane, Australia
| | - S Miyakis
- School of Medicine, University of Wollongong, Wollongong, New South Wales, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia.,Department of Infectious Diseases, Wollongong Hospital, Wollongong, New South Wales, Australia
| | - G Walls
- Department of Infectious Diseases, Middlemore Hospital, Auckland, New Zealand
| | - M Ai Khamis
- King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - A Zikri
- King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - A Crowe
- Department of Infectious Diseases, St Vincent's Hospital, Melbourne, Australia.,Department of Microbiology, St Vincent's Hospital, Melbourne, Australia
| | - P R Ingram
- School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Australia.,Department of Infectious Diseases, Fiona Stanley Hospital, Murdoch , Australia.,Department of Microbiology, PathWest Laboratory Medicine, Perth, Western Australia
| | - N N Daneman
- Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Canada
| | - P Griffin
- University of Queensland, Brisbane, Australia.,Department of Medicine and Infectious Diseases, Mater Hospital and Mater Medical Research Institute, Brisbane, Australia.,QIMR Berghofer, Brisbane, Queensland, Australia
| | - E Athan
- Department of Infectious Diseases, Barwon Health and Deakin University, Geelong, Victoria, Australia
| | - L Roberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Queensland, Australia
| | - S A Beatson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Queensland, Australia
| | - A Y Peleg
- Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia.,Department of Microbiology, Monash University, Clayton, Australia
| | - K K Cottrell
- University of Queensland, UQ Centre for Clinical Research, Brisbane, Australia
| | - M J Bauer
- University of Queensland, UQ Centre for Clinical Research, Brisbane, Australia
| | - E Tan
- University of Queensland, UQ Centre for Clinical Research, Brisbane, Australia
| | - K Chaw
- Department of Microbiology, Pathology Queensland, Toowoomba Laboratory, Australia.,Department of Microbiology, Mater Pathology, Australia.,Infectious Diseases Department, Redcliffe Hospital, Australia
| | - G R Nimmo
- Department of Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - T Harris-Brown
- University of Queensland, UQ Centre for Clinical Research, Brisbane, Australia
| | - P N A Harris
- University of Queensland, UQ Centre for Clinical Research, Brisbane, Australia.,Department of Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
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Octavia S, Kalisvar M, Venkatachalam I, Ng OT, Xu W, Sridatta PSR, Ong YF, Wang LD, Chua A, Cheng B, Lin RTP, Teo JWP. Klebsiella pneumoniae and Klebsiella quasipneumoniae define the population structure of blaKPC-2Klebsiella: a 5 year retrospective genomic study in Singapore. J Antimicrob Chemother 2020; 74:3205-3210. [PMID: 31504571 DOI: 10.1093/jac/dkz332] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/25/2019] [Accepted: 07/04/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To describe the population structure, molecular epidemiology and genetic context of blaKPC-2-bearing Klebsiella pneumoniae. METHODS Isolates (n = 157) were retrospective, phenotypically carbapenem-resistant blaKPC-positive K. pneumoniae, collected from public hospitals. WGS was performed on the Illumina platform. Phylogenomic analysis, screening of resistance and virulence genes, and comparison of the genetic environment of blaKPC were carried out. RESULTS Based on core-tree phylogeny, 67.5% of the isolates were K. pneumoniae and the remainder comprised Klebsiella quasipneumoniae. No Klebsiella variicola strains were observed. Only a single K. pneumoniae carbapenemase (KPC) variant type, blaKPC-2, was seen. MLSTs were diverse and did not comprise the 'traditional' KPC clonal group (CG) 258. blaKPC-2 was associated with a non-Tn4401 element (NTE) in >99% of genomes. Screening for four key virulence loci: yersiniabactin (ybt), aerobactin (iuc), salmochelin (iro) and colibactin (clb) as well as ICEKp (virulence-associated integrative conjugative element of K. pneumoniae), revealed the lack of virulence factors and ICEKp within K. quasipneumoniae. Amongst the K. pneumoniae, there were 32 ybt+ isolates (32/106, 30.2%) and, of these, 8 isolates were also clb+ (7.5%). K. pneumoniae serotypes K1 and K2, the majority of capsular serotype seen in patients with invasive liver abscess syndrome, were detected at 4.5% (7/157). CONCLUSIONS Results suggest that dissemination of blaKPC-2 is driven by NTEKPC in non-ST258 isolates. The detection of blaKPC-2K. pneumoniae serotypes K1/K2 carrying virulence factors, albeit in low numbers, reflects the worrisome convergence of carbapenem resistance and hypervirulence in K. pneumoniae.
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Affiliation(s)
- Sophie Octavia
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Marimuthu Kalisvar
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore.,National Centre for Infectious Diseases, Singapore.,National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | | | - Oon Tek Ng
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore.,National Centre for Infectious Diseases, Singapore.,Nanyang Technological University, Lee Kong Chian School of Medicine, Singapore
| | - Weizhen Xu
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore
| | | | - Yi Fa Ong
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore
| | - Liang De Wang
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore
| | - Amanda Chua
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore
| | - Bernadette Cheng
- National University Hospital, Department of Laboratory Medicine, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore.,National University Hospital, Department of Laboratory Medicine, Singapore
| | - Jeanette W P Teo
- National University Hospital, Department of Laboratory Medicine, Singapore
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Chew KL, Octavia S, Ng OT, Marimuthu K, Venkatachalam I, Cheng B, Lin RTP, Teo JWP. Challenge of drug resistance in Pseudomonas aeruginosa: clonal spread of NDM-1-positive ST-308 within a tertiary hospital. J Antimicrob Chemother 2020; 74:2220-2224. [PMID: 31081022 DOI: 10.1093/jac/dkz169] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/26/2019] [Accepted: 03/29/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES MDR Pseudomonas aeruginosa is a serious global threat to healthcare institutions. The mechanism by which drug resistance can be acquired is variable, but acquired carbapenemase production has been reported in P. aeruginosa. An investigation was performed to determine the rate and genomic epidemiology of New Delhi MBL (NDM) in β-lactam-non-susceptible isolates. METHODS P. aeruginosa isolates from a tertiary hospital in Singapore between January 2015 and February 2018 were investigated for the presence of NDM genes. RESULTS Out of 298 pan-β-lactam-non-susceptible isolates, 31 were found to be NDM positive (10.4%). WGS demonstrated that all 31 NDM-positive isolates were clonal, belonging to ST-308. blaNDM was chromosomally inserted within an integrative and conjugative element (ICE), ICETn43716385. The NDM-P. aeruginosa isolates possessed an extensive repertoire of both cell-associated [flagella, pili, alginate/biofilm, LPS, type III secretion system (T3SS) and type VI secretion system (T6SS)] and secreted virulence factors. Antibiograms revealed higher rates of drug resistance in NDM-positive isolates compared with their non-NDM counterparts. The NDM isolates remained 100% susceptible only to colistin. CONCLUSIONS The combination of chromosomal mutations, acquired resistance genes and virulence factors likely facilitated the persistent and ongoing spread of the ST-308 clade of P. aeruginosa within the hospital. Our study illustrates the particular threat of NDM-positive P. aeruginosa in a tertiary hospital setting in the era of antimicrobial resistance.
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Affiliation(s)
- Ka Lip Chew
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Sophie Octavia
- National Public Health Laboratory, Ministry of Health, Singapore
| | - Oon Tek Ng
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,National Centre for Infectious Diseases, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Kalisvar Marimuthu
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,National Centre for Infectious Diseases, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Bernadette Cheng
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Raymond T P Lin
- Department of Laboratory Medicine, National University Hospital, Singapore.,National Public Health Laboratory, Ministry of Health, Singapore
| | - Jeanette W P Teo
- Department of Laboratory Medicine, National University Hospital, Singapore
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28
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Sutjipto S, Lee PH, Tay JY, Mendis SM, Abdad MY, Marimuthu K, Ng OT, Cui L, Chan M, Soon M, Lin RTP, Leo YS, De PP, Barkham T, Vasoo S. The Effect of Sample Site, Illness Duration, and the Presence of Pneumonia on the Detection of SARS-CoV-2 by Real-time Reverse Transcription PCR. Open Forum Infect Dis 2020; 7:ofaa335. [PMID: 32964061 PMCID: PMC7454916 DOI: 10.1093/ofid/ofaa335] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/31/2020] [Indexed: 12/28/2022] Open
Abstract
Background The performance of real-time reverse transcription polymerase chain reaction (rRT-PCR) for SARS-CoV-2 varies with sampling site(s), illness stage, and infection site. Methods Unilateral nasopharyngeal, nasal midturbinate, throat swabs, and saliva were simultaneously sampled for SARS-CoV-2 rRT-PCR from suspected or confirmed cases of COVID-19. True positives were defined as patients with at least 1 SARS-CoV-2 detected by rRT-PCR from any site on the evaluation day or at any time point thereafter, until discharge. Diagnostic performance was assessed and extrapolated for site combinations. Results We evaluated 105 patients; 73 had active SARS-CoV-2 infection. Overall, nasopharyngeal specimens had the highest clinical sensitivity at 85%, followed by throat, 80%, midturbinate, 62%, and saliva, 38%–52%. Clinical sensitivity for nasopharyngeal, throat, midturbinate, and saliva was 95%, 88%, 72%, and 44%–56%, respectively, if taken ≤7 days from onset of illness, and 70%, 67%, 47%, 28%–44% if >7 days of illness. Comparing patients with upper respiratory tract infection (URTI) vs pneumonia, clinical sensitivity for nasopharyngeal, throat, midturbinate, and saliva was 92% vs 70%, 88% vs 61%, 70% vs 44%, 43%–54% vs 26%–45%, respectively. A combination of nasopharyngeal plus throat or midturbinate plus throat specimen afforded overall clinical sensitivities of 89%–92%; this rose to 96% for persons with URTI and 98% for persons ≤7 days from illness onset. Conclusions Nasopharyngeal specimens, followed by throat specimens, offer the highest clinical sensitivity for COVID-19 diagnosis in early illness. Clinical sensitivity improves and is similar when either midturbinate or nasopharyngeal specimens are combined with throat specimens. Upper respiratory specimens perform poorly if taken after the first week of illness or if there is pneumonia.
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Affiliation(s)
- Stephanie Sutjipto
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,National Centre for Infectious Diseases, Singapore
| | - Pei Hua Lee
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,National Centre for Infectious Diseases, Singapore
| | - Jun Yang Tay
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,National Centre for Infectious Diseases, Singapore
| | - Shehara M Mendis
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore
| | - Mohammad Yazid Abdad
- Infectious Disease Research Laboratory, National Centre for Infectious Diseases, Singapore
| | - Kalisvar Marimuthu
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,National Centre for Infectious Diseases, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Oon Tek Ng
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,National Centre for Infectious Diseases, Singapore.,Lee Kong Chian School of Medicine, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lin Cui
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Monica Chan
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,National Centre for Infectious Diseases, Singapore.,Lee Kong Chian School of Medicine, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Raymond T P Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yee-Sin Leo
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,National Centre for Infectious Diseases, Singapore.,Lee Kong Chian School of Medicine, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Saw Swee Hock School of Public Health, National Centre for Infectious Diseases, Singapore
| | - Partha P De
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore
| | - Timothy Barkham
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shawn Vasoo
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore.,National Centre for Infectious Diseases, Singapore.,Infectious Disease Research Laboratory, National Centre for Infectious Diseases, Singapore.,Lee Kong Chian School of Medicine, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Sun Y, Koh V, Marimuthu K, Ng OT, Young B, Vasoo S, Chan M, Lee VJM, De PP, Barkham T, Lin RTP, Cook AR, Leo YS. Epidemiological and Clinical Predictors of COVID-19. Clin Infect Dis 2020; 71:786-792. [PMID: 32211755 PMCID: PMC7542554 DOI: 10.1093/cid/ciaa322] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 03/21/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Rapid identification of COVID-19 cases, which is crucial to outbreak containment efforts, is challenging due to the lack of pathognomonic symptoms and in settings with limited capacity for specialized nucleic acid-based reverse transcription polymerase chain reaction (PCR) testing. METHODS This retrospective case-control study involves subjects (7-98 years) presenting at the designated national outbreak screening center and tertiary care hospital in Singapore for SARS-CoV-2 testing from 26 January to 16 February 2020. COVID-19 status was confirmed by PCR testing of sputum, nasopharyngeal swabs, or throat swabs. Demographic, clinical, laboratory, and exposure-risk variables ascertainable at presentation were analyzed to develop an algorithm for estimating the risk of COVID-19. Model development used Akaike's information criterion in a stepwise fashion to build logistic regression models, which were then translated into prediction scores. Performance was measured using receiver operating characteristic curves, adjusting for overconfidence using leave-one-out cross-validation. RESULTS The study population included 788 subjects, of whom 54 (6.9%) were SARS-CoV-2 positive and 734 (93.1%) were SARS-CoV-2 negative. The median age was 34 years, and 407 (51.7%) were female. Using leave-one-out cross-validation, all the models incorporating clinical tests (models 1, 2, and 3) performed well with areas under the receiver operating characteristic curve (AUCs) of 0.91, 0.88, and 0.88, respectively. In comparison, model 4 had an AUC of 0.65. CONCLUSIONS Rapidly ascertainable clinical and laboratory data could identify individuals at high risk of COVID-19 and enable prioritization of PCR testing and containment efforts. Basic laboratory test results were crucial to prediction models.
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Affiliation(s)
- Yinxiaohe Sun
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Vanessa Koh
- Department of Infectious Diseases, National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
| | - Kalisvar Marimuthu
- Department of Infectious Diseases, National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - Oon Tek Ng
- Department of Infectious Diseases, National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Barnaby Young
- Department of Infectious Diseases, National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Shawn Vasoo
- Department of Infectious Diseases, National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
| | - Monica Chan
- Department of Infectious Diseases, National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
| | - Vernon J M Lee
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
- Communicable Disease Division, Ministry of Health, Singapore
| | - Partha P De
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore
| | - Timothy Barkham
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore
| | - Raymond T P Lin
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Alex R Cook
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Yee Sin Leo
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
- Department of Infectious Diseases, National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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30
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Lee CYP, Lin RTP, Renia L, Ng LFP. Serological Approaches for COVID-19: Epidemiologic Perspective on Surveillance and Control. Front Immunol 2020; 11:879. [PMID: 32391022 PMCID: PMC7194125 DOI: 10.3389/fimmu.2020.00879] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/16/2020] [Indexed: 01/03/2023] Open
Abstract
Since December 2019, the novel coronavirus, SARS-CoV-2, has garnered global attention due to its rapid transmission, which has infected more than two million people worldwide. Early detection of SARS-CoV-2 is one of the crucial interventions to control virus spread and dissemination. Molecular assays have been the gold standard to directly detect for the presence of viral genetic material in infected individuals. However, insufficient viral RNA at the point of detection may lead to false negative results. As such, it is important to also employ immune-based assays to determine one's exposure to SARS-CoV-2, as well as to assist in the surveillance of individuals with prior exposure to SARS-CoV-2. Within a span of 4 months, extensive studies have been done to develop serological systems to characterize the antibody profiles, as well as to identify and generate potentially neutralizing antibodies during SARS-CoV-2 infection. The vast diversity of novel findings has added value to coronavirus research, and a strategic consolidation is crucial to encompass the latest advances and developments. This review aims to provide a concise yet extensive collation of current immunoassays for SARS-CoV-2, while discussing the strengths, limitations and applications of antibody detection in SARS-CoV-2 research and control.
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Affiliation(s)
- Cheryl Yi-Pin Lee
- Singapore Immunology Network, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Raymond T. P. Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Laurent Renia
- Singapore Immunology Network, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Lisa F. P. Ng
- Singapore Immunology Network, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Infection and Microbiome, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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Ng OT, Marimuthu K, Chia PY, Koh V, Chiew CJ, De Wang L, Young BE, Chan M, Vasoo S, Ling LM, Lye DC, Kam KQ, Thoon KC, Kurupatham L, Said Z, Goh E, Low C, Lim SK, Raj P, Oh O, Koh VTJ, Poh C, Mak TM, Cui L, Cook AR, Lin RTP, Leo YS, Lee VJM. SARS-CoV-2 Infection among Travelers Returning from Wuhan, China. N Engl J Med 2020; 382:1476-1478. [PMID: 32163698 PMCID: PMC7121487 DOI: 10.1056/nejmc2003100] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Oon-Tek Ng
- National Centre for Infectious Diseases, Singapore, Singapore
| | | | - Po-Ying Chia
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Vanessa Koh
- National Centre for Infectious Diseases, Singapore, Singapore
| | | | - Liang De Wang
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Barnaby E Young
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Monica Chan
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Shawn Vasoo
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Li-Min Ling
- National Centre for Infectious Diseases, Singapore, Singapore
| | - David C Lye
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Kai-Qian Kam
- KK Women's and Children's Hospital, Singapore, Singapore
| | | | | | | | - Ethan Goh
- Ministry of Health, Singapore, Singapore
| | | | | | - Pream Raj
- Ministry of Health, Singapore, Singapore
| | - Olivia Oh
- Ministry of Health, Singapore, Singapore
| | | | - Cuiqin Poh
- Ministry of Health, Singapore, Singapore
| | - Tze-Minn Mak
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Alex R Cook
- Saw Swee Hock School of Public Health, Singapore, Singapore
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Yee-Sin Leo
- National Centre for Infectious Diseases, Singapore, Singapore
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Timmis K, Cavicchioli R, Garcia JL, Nogales B, Chavarría M, Stein L, McGenity TJ, Webster N, Singh BK, Handelsman J, de Lorenzo V, Pruzzo C, Timmis J, Martín JLR, Verstraete W, Jetten M, Danchin A, Huang W, Gilbert J, Lal R, Santos H, Lee SY, Sessitsch A, Bonfante P, Gram L, Lin RTP, Ron E, Karahan ZC, van der Meer JR, Artunkal S, Jahn D, Harper L. The urgent need for microbiology literacy in society. Environ Microbiol 2019; 21:1513-1528. [PMID: 30912268 DOI: 10.1111/1462-2920.14611] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 03/24/2019] [Accepted: 03/24/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Kenneth Timmis
- Institute of Microbiology, Technical University Braunschweig, Germany
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | - José Luis Garcia
- Department of Environmental Biology, Centro de Investigaciones Biológicas (CIB) (CSIC), Madrid, Spain
| | - Balbina Nogales
- Grupo de Microbiologia, Dept. Biologia, Universitat de les Illes Balears, and Instituto Mediterráneo de Estudios Avanzados 8IMEDEA, UIB-CSIC), Palma de Mallorca, Spain
| | - Max Chavarría
- Escuela de Química, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica & Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Lisa Stein
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Terry J McGenity
- School of Biological Sciences, University of Essex, Colchester, UK
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville and Australian Centre for Ecogenomics, University of Queensland, Brisbane, Queensland, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, Australia
| | - Jo Handelsman
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, WI, USA
| | - Victor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnologia, CSIC, Madrid, Spain
| | - Carla Pruzzo
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita (DISTAV), Università degli Studi di Genova, Italy
| | - James Timmis
- Athena Institute, Vrije Universiteit Amsterdam, The Netherlands
| | | | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET), Ghent University, Belgium
| | - Mike Jetten
- Department of Microbiology, Radboud University Nijmegen, The Netherlands
| | - Antoine Danchin
- Institut Cochin INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris, France
| | - Wei Huang
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Jack Gilbert
- Dept. of Pediatrics, University of California at San Diego, San Diego, CA, USA
| | - Rup Lal
- Department of Zoology, Molecular Biology Laboratory, University of Delhi, Delhi, India
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Angela Sessitsch
- Bioresources Unit, AIT Austrian Institute of Technology, Tulln, Austria
| | - Paola Bonfante
- Department of Life Science and Systems Biology, University of Torino, Italy
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Raymond T P Lin
- Department of Microbiology and Immunology, National University of Singapore, Singapore
| | - Eliora Ron
- School of Molecular Cell Biology & Biotechnology, Tel Aviv University, Israel
| | - Z Ceren Karahan
- Department of Medical Microbiology, Ankara University, Turkey
| | | | - Seza Artunkal
- Department of Clinical Microbiology, Haydarpaşa Numune Training Hospital, lstanbul, Turkey
| | - Dieter Jahn
- Institute of Microbiology, Technical University Braunschweig, Germany
| | - Lucy Harper
- Society for Applied Microbiology, London, UK
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Octavia S, Zulaina S, Seet SK, Tien WS, Thu M, Ooi PL, Cui L, Lin RTP. Whole-genome sequencing of the rare Salmonella enterica serovar Anfo isolated from food handlers. J Med Microbiol 2019; 68:429-431. [PMID: 30698521 DOI: 10.1099/jmm.0.000934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Field investigations were conducted after a small cluster of food poisoning involving six cases was reported. While no stool samples were available from the cases for microbiological testing, Salmonella species was found to be present in the stools of food handlers with gastroenteritis symptoms. Four Salmonella isolates recovered from the food handlers were retrospectively investigated at the genome level using whole-genome sequencing (WGS). WGS showed that S. Anfo (antigenic formulae 39:y:1,2), a rarely isolated serovar, caused infections in the food handlers. S. Anfo analysed in this study contained virulence factors required for causing disease. They did not contain any antibiotic resistance genes or plasmid. The epidemiologically related isolates differed to each other by a maximum of one single nucleotide polymorphism. WGS was useful in identifying rare Salmonella serovars and it is potentially more cost-effective than traditional serotyping methods. It can also confidently group epidemiologically related isolates belonging to S. Anfo.
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Affiliation(s)
- Sophie Octavia
- 1 National Public Health Laboratory, Ministry of Health, Singapore
| | - Siti Zulaina
- 1 National Public Health Laboratory, Ministry of Health, Singapore
| | - Swee Kai Seet
- 1 National Public Health Laboratory, Ministry of Health, Singapore
| | - Wee Siong Tien
- 2 Communicable Diseases Division (Surveillance & Response), Ministry of Health, Singapore
| | - Minn Thu
- 2 Communicable Diseases Division (Surveillance & Response), Ministry of Health, Singapore
| | - Peng Lim Ooi
- 2 Communicable Diseases Division (Surveillance & Response), Ministry of Health, Singapore
| | - Lin Cui
- 1 National Public Health Laboratory, Ministry of Health, Singapore
| | - Raymond T P Lin
- 1 National Public Health Laboratory, Ministry of Health, Singapore.,3 Department of Laboratory Medicine, National University Hospital, Singapore
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Tang YW, Cheng B, Yeoh SF, Lin RTP, Teo JWP. Tedizolid Activity Against Clinical Mycobacterium abscessus Complex Isolates-An in vitro Characterization Study. Front Microbiol 2018; 9:2095. [PMID: 30245674 PMCID: PMC6137136 DOI: 10.3389/fmicb.2018.02095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 08/16/2018] [Indexed: 12/23/2022] Open
Abstract
Mycobacterium abscessus complex consist of three rapidly growing subspecies: M. abscessus, M. massiliense, and M. bolletii. They are clinically important human pathogens responsible for opportunistic pulmonary and skin and soft tissue infections. Treatment of M. abscessus infections is difficult due to in vitro resistance to most antimicrobial agents. Tedizolid (TZD) is a next-generation oxazolidinone antimicrobial with a wide spectrum of activity even against multidrug resistant Gram-positive bacteria. In this study, the in vitro activity of TZD against the M. abscessus complex (n = 130) was investigated. Susceptibility testing by broth microdilution showed lower TZD minimum inhibitory concentrations (MICs) when compared to linezolid. The MIC50 and MIC90 was 1 mg/L and 4 mg/L, respectively across all M. abscessus complex members, reflecting no difference in subspecies response to TZD. Pre-exposure of M. abscessus complex to subinhibitory concentrations of TZD did not trigger any inducible drug resistance. Single-drug time kill assays and bactericidal activity assays demonstrated bacteriostatic activity of TZD in all three M. abscessus subspecies, even at high drug concentrations of 4 to 8x MIC. Combination testing of TZD with clarithromycin, doxycycline and amikacin using the checkerboard approach showed no antagonistic interactions. TZD may be an effective therapeutic antimicrobial agent for the treatment of M. abscessus infections.
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Affiliation(s)
- Ying Wei Tang
- Department of Biological Sciences, National University Singapore, Singapore, Singapore
| | - Bernadette Cheng
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Siang Fei Yeoh
- Pharmacy, National University Hospital, Singapore, Singapore
| | - Raymond T P Lin
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore.,National Public Health Laboratory, Ministry of Health, Singapore, Singapore
| | - Jeanette W P Teo
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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Teh YE, Ang MLT, La MV, Gunalan V, Tan CK, Tan AL, Lin RTP, Tan TT, Jeyaraj PR, Cumaraswamy S, Tan BH. Donor-Derived Candida dubliniensis Resulting in Perigraft Abscesses in a Liver Transplant Recipient Proven by Whole Genome Sequencing: A Case Report. Transplant Proc 2018; 50:915-919. [PMID: 29661462 DOI: 10.1016/j.transproceed.2018.01.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 01/29/2018] [Indexed: 12/29/2022]
Abstract
BACKGROUND The transmission of fungi via transplant, although well-known, has not often been molecularly proven. We describe a case of donor-derived candidiasis verified by whole genome sequencing. CASE DESCRIPTION The multiorgan donor was a 42-year-old woman with subdural hemorrhage. Procurement of the thoracic organs was performed followed by the abdominal organs. Tissue from the left bronchus grew Candida dubliniensis. The liver recipient was a 63-year-old woman with cryptogenic liver cirrhosis. She was noted to have worsening leukocytosis on postoperative day (POD) 9. Computed tomography of the abdomen and pelvis showed multiple rim-enhancing collections around the graft. Percutaneous drainage was performed. Fluid cultures grew C dubliniensis. C dubliniensis isolated from the donor's left bronchus and the liver recipient's abscesses were verified to be related by whole genome sequencing. We postulate that C dubliniensis colonizing the donor's transected trachea could have contaminated the inferior vena cava when the former was left open after explant of the donor's lungs. A portion of the donor's contaminated inferior vena cava was transplanted along with the liver graft, resulting in the infected collections in the recipient. CONCLUSIONS Our case report highlights the importance of maintaining a sterile field during organ procurement, especially in a multiorgan donor whose organs are explanted in succession.
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Affiliation(s)
- Y E Teh
- Department of Infectious Diseases, Singapore General Hospital, Singapore.
| | - M L T Ang
- National Public Health Laboratory, Ministry of Health, Singapore
| | - M V La
- Department of Laboratory Medicine, Changi General Hospital, Singapore
| | - V Gunalan
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - C K Tan
- Department of Gastroenterology and Hepatology, Singapore General Hospital, Singapore
| | - A L Tan
- Department of Microbiology, Singapore General Hospital, Singapore
| | - R T P Lin
- National Public Health Laboratory, Ministry of Health, Singapore; Department of Laboratory Medicine, National University Hospital, Singapore
| | - T T Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - P R Jeyaraj
- Department of Hepato-pancreato-biliary and Transplant Surgery, Singapore General Hospital, Singapore
| | - S Cumaraswamy
- Heart and Lung Transplant Unit, Department of Cardiothoracic Surgery, National Heart Centre Singapore, Singapore
| | - B H Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore
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36
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Octavia S, Ang MLT, La MV, Zulaina S, Saat ZAAS, Tien WS, Han HK, Ooi PL, Cui L, Lin RTP. Retrospective genome-wide comparisons of Salmonella enterica serovar Enteritidis from suspected outbreaks in Singapore. Infect Genet Evol 2018; 61:229-233. [PMID: 29625239 DOI: 10.1016/j.meegid.2018.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/13/2018] [Accepted: 04/02/2018] [Indexed: 11/25/2022]
Abstract
The number of salmonellosis cases in Singapore has increased over the years. Salmonella enterica serovar Enteritidis has always been the most predominant serovar in the last five years. The National Public Health Laboratory assisted outbreak investigations by performing multilocus variable number tandem repeat analysis (MLVA) on isolates that were collected at the time of the investigations. Isolates were defined as belonging to a particular cluster if they had identical MLVA patterns. Whilst MLVA has been instrumental in outbreak investigations, it may not be useful when outbreaks are caused by an endemic MLVA type. In this study, we analysed 67 isolates from 12 suspected outbreaks with known epidemiological links to explore the use of next-generation sequencing (NGS) for defining outbreaks. We found that NGS can confidently group isolates into their respective outbreaks. The isolates from each suspected outbreak were closely related and differed by a maximum of 3 single nucleotide polymorphisms (SNPs). They were also clearly separated from isolates that belonged to different suspected outbreaks. This study provides an important insight and further evidence on the value of NGS for routine surveillance and outbreak detection of S. Enteritidis.
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Affiliation(s)
- Sophie Octavia
- National Public Health Laboratory, Ministry of Health, Singapore.
| | - Michelle L T Ang
- National Public Health Laboratory, Ministry of Health, Singapore
| | - My Van La
- National Public Health Laboratory, Ministry of Health, Singapore
| | - Siti Zulaina
- National Public Health Laboratory, Ministry of Health, Singapore
| | - Zul Azri As Saad Saat
- Communicable Diseases Division (Surveillance & Response), Ministry of Health, Singapore
| | - Wee Siong Tien
- Communicable Diseases Division (Surveillance & Response), Ministry of Health, Singapore
| | - Hwi Kwang Han
- Communicable Diseases Division (Surveillance & Response), Ministry of Health, Singapore
| | - Peng Lim Ooi
- Communicable Diseases Division (Surveillance & Response), Ministry of Health, Singapore
| | - Lin Cui
- National Public Health Laboratory, Ministry of Health, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, Ministry of Health, Singapore; Department of Laboratory Medicine, National University Hospital, Singapore
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Ang LW, Kam YW, Lin C, Krishnan PU, Tay J, Ng LC, James L, Lee VJM, Goh KT, Ng LFP, Lin RTP. Seroprevalence of antibodies against chikungunya virus in Singapore resident adult population. PLoS Negl Trop Dis 2017; 11:e0006163. [PMID: 29281644 PMCID: PMC5760101 DOI: 10.1371/journal.pntd.0006163] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/09/2018] [Accepted: 12/12/2017] [Indexed: 11/24/2022] Open
Abstract
Objectives We determined the seroprevalence of chikungunya virus (CHIKV) infection in the adult resident population in Singapore following local outbreaks of chikungunya fever (CHIKF) in 2008–2009. Methods Our cross-sectional study involved residual sera from 3,293 adults aged 18–79 years who had participated in the National Health Survey in 2010. Sera were tested for IgG antibodies against CHIKV and dengue virus (DENV) and neutralizing antibodies against CHIKV. Results The prevalence of CHIKV-neutralizing antibodies among Singapore residents aged 18–79 years was 1.9% (95% confidence interval: 1.4%– 2.3%). The CHIKV seroprevalence was highest in the elderly aged 70–79 years at 11.5%, followed by those aged 30–39 years at 3.1%. Men had significantly higher CHIKV seroprevalence than women (2.5% versus 1.3%, p = 0.01). Among the three main ethnic groups, Indians had the highest seroprevalence (3.5%) compared to Chinese (1.6%) and Malays (0.7%) (p = 0.02 and p = 0.01, respectively). Multivariable logistic regression identified adults aged 30–39 years and 70–79 years, men, those of Indian ethnicity and ethnic minority groups, and residence on ground floor of public and private housing apartments as factors that were significantly associated with a higher likelihood of exposure to CHIKV. The overall prevalence of anti-DENV IgG antibodies was 56.8% (95% CI: 55.1%– 58.5%), while 1.5% (95% CI: 1.1%– 2.0%) of adults possessed both neutralizing antibodies against CHIKV and IgG antibodies against DENV. Conclusions Singapore remains highly susceptible to CHIKV infection. There is a need to maintain a high degree of vigilance through disease surveillance and vector control. Findings from such serological study, when conducted on a regular periodic basis, could supplement surveillance to provide insights on CHIKV circulation in at-risk population. The prevalence of neutralizing antibodies against chikungunya virus (CHIKV) was low at 1.9% among resident adults in Singapore after local outbreaks in 2008–2009. Adults aged 30–39 years and 70–79 years, men, those of Indian ethnicity and ethnic minority groups, and residence on ground floor of public and private housing apartments were significantly associated with a higher likelihood of exposure to CHIKV.
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Affiliation(s)
- Li Wei Ang
- Public Health Group, Ministry of Health, Singapore
- * E-mail:
| | - Yiu Wing Kam
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Cui Lin
- Public Health Group, Ministry of Health, Singapore
| | - Prabha Unny Krishnan
- Public Health Group, Ministry of Health, Singapore
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore
| | - Joanne Tay
- Public Health Group, Ministry of Health, Singapore
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, Singapore
| | - Lyn James
- Public Health Group, Ministry of Health, Singapore
| | | | - Kee Tai Goh
- Public Health Group, Ministry of Health, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Lisa F. P. Ng
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore
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Chew KL, Lin RTP, Teo JWP. Klebsiella pneumoniae in Singapore: Hypervirulent Infections and the Carbapenemase Threat. Front Cell Infect Microbiol 2017; 7:515. [PMID: 29312894 PMCID: PMC5732907 DOI: 10.3389/fcimb.2017.00515] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/29/2017] [Indexed: 11/22/2022] Open
Abstract
Klebsiella pneumoniae remains a major pathogen responsible for localized infections such as cystitis and pneumonia, and disseminated infections that may result in severe sepsis and death. Invasive disease such as liver abscesses and endogenous endophthalmitis are associated with capsular serotypes K1 and K2. These infections require a prolonged course of antimicrobial treatment which has evolved over the years from inpatient treatment to outpatient parenteral antibiotic therapy. The emergence of plasmid-mediated resistance began with extended-spectrum β-lactamases (ESBLs) and AmpC β-lactamases. This was followed by carbapenemase genes and now plasmid transmissible colistin resistance (mcr), thus limiting viable treatment options. Plasmid-mediated carbapenemase production in Singapore was first reported in 1996. Carbapenemase production has since become the predominant mechanism of carbapenem resistance and incidence rates continue to increase over time. Although carbapenemases can occur in all Enterobacteriaceae, K. pneumoniae are the most common carrier of carbapenemase genes. Alternative treatment options are urgently required before the simplest infections, let alone invasive infections are left potentially untreatable. Clinical management requires guidance from robust laboratory testing methods to optimize patient outcomes. We explore past and present trends in treatment of K. pneumoniae infections, and discuss future treatment options and gaps in knowledge for further study.
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Affiliation(s)
- Ka Lip Chew
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Raymond T P Lin
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore.,National Public Health Laboratory, Ministry of Health of Singapore, Singapore, Singapore
| | - Jeanette W P Teo
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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39
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Chew KL, Cheng JWS, Hudaa Osman N, Lin RTP, Teo JWP. Predominance of clarithromycin-susceptible Mycobacterium massiliense subspecies: Characterization of the Mycobacterium abscessus complex at a tertiary acute care hospital. J Med Microbiol 2017; 66:1443-1447. [PMID: 28874233 DOI: 10.1099/jmm.0.000576] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To characterize members of the Mycobacterium abscessus complex, with an emphasis on the correlation between species identification and clarithromycin associated genetic polymorphisms that contribute to inducible and constitutive macrolide resistance. PCR and sequencing analysis was used to elucidate the subspecies, erm(41) genotypes and the presence of rrl mutations. M. abscessus subsp. massiliense was the dominant subspecies (70.2 %), followed by M. abscessus subsp. abscessus (23.8 %) and M. abscessus subsp. bolletii (5.9 %). The majority of M. abscessus and M. bolletii isolates possessed T28 erm(41) sequevar and were inducibly resistant to clarithromycin. All M. massiliense carried the truncated erm(41) and were largely clarithromycin-susceptible (98.3 %). Constitutive resistance involving rrl mutations was rare and seen in only 2 isolates (2.2 %). Subspecies identification was insufficient to predict clarithromycin susceptibility and required the genetic resistance to be determined via sequencing. In our context, rrl mutations were uncommon and may not be an essential test.
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Affiliation(s)
- Ka Lip Chew
- National University Hospital, Department of Laboratory Medicine, Division of Microbiology, Singapore 119074, Republic of Singapore
| | - Janet W S Cheng
- National University Hospital, Department of Laboratory Medicine, Division of Microbiology, Singapore 119074, Republic of Singapore
| | - Nurul Hudaa Osman
- National University Hospital, Department of Laboratory Medicine, Division of Microbiology, Singapore 119074, Republic of Singapore
| | - Raymond T P Lin
- National University Hospital, Department of Laboratory Medicine, Division of Microbiology, Singapore 119074, Republic of Singapore.,National Public Health Laboratory, Ministry of Health, 3 Biopolis Drive, Synapse #05-14/16, Singapore 138623, Republic of Singapore
| | - Jeanette W P Teo
- National University Hospital, Department of Laboratory Medicine, Division of Microbiology, Singapore 119074, Republic of Singapore
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40
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Lum FM, Lin C, Susova OY, Teo TH, Fong SW, Mak TM, Lee LK, Chong CY, Lye DCB, Lin RTP, Merits A, Leo YS, Ng LFP. A Sensitive Method for Detecting Zika Virus Antigen in Patients' Whole-Blood Specimens as an Alternative Diagnostic Approach. J Infect Dis 2017; 216:182-190. [PMID: 28586426 PMCID: PMC5853302 DOI: 10.1093/infdis/jix276] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/02/2017] [Indexed: 01/15/2023] Open
Abstract
Background Epidemics caused by the reemergence of Zika virus (ZIKV) warrant the need to develop new diagnostic measures to complement currently used detection methods. In this study, we explored the detection of ZIKV antigen in a defined leukocyte subset from patients' whole-blood specimens. Methods Whole-blood samples were obtained at the acute and early convalescent phases from ZIKV-infected patients during the Singapore outbreak in August-September 2016. Presence of ZIKV antigen was determined by flow cytometry staining for intracellular ZIKV NS3, using a ZIKV-specific polyclonal antibody. The presence of ZIKV antigen was determined in CD45+CD14+ monocytes. Results Data showed that ZIKV NS3 antigen could be detected in CD45+CD14+ monocytes. The levels of detection were further categorized into 3 groups: high (positivity among >40% of monocytes), moderate (positivity among 10%-40%), and low (positivity among <10%). While a majority of patients showed a decrease in the amount of ZIKV antigen detected at later time points, some patients displayed higher levels as the disease progressed. Conclusions Our data highlights an alternative approach in using flow cytometry as a sensitive method for detecting ZIKV antigen in whole blood. Importantly, it further confirms the role of CD14+ monocytes as an important cellular target for ZIKV infection during the viremic phase.
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Affiliation(s)
- Fok-Moon Lum
- Singapore Immunology Network, Agency for Science, Technology and Research
| | - Cui Lin
- National Public Health Laboratory, Ministry of Health
| | - Olga Y Susova
- Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Moscow
| | - Teck-Hui Teo
- Singapore Immunology Network, Agency for Science, Technology and Research
| | - Siew-Wai Fong
- Singapore Immunology Network, Agency for Science, Technology and Research
- Department of Biological Science
| | - Tze-Minn Mak
- National Public Health Laboratory, Ministry of Health
| | - Linda Kay Lee
- Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital
| | | | - David C B Lye
- Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital
| | | | - Andres Merits
- Institute of Technology, University of Tartu, Estonia
| | - Yee-Sin Leo
- Saw Swee Hock School of Public Health, National University of Singapore
- Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Lisa F P Ng
- Singapore Immunology Network, Agency for Science, Technology and Research
- Institute of Infection and Global Health, University of Liverpool, United Kingdom
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Kalimuddin S, Chan YFZ, Wu IQ, Tan QL, Murthee KG, Tan BH, Oon LLE, Yang Y, Lin RTP, Joseph U, Sessions OM, Smith GJD, Ooi EE, Low JGH. A Report of Adult Human Adenovirus Infections in a Tertiary Hospital. Open Forum Infect Dis 2017; 4:ofx053. [PMID: 28491891 PMCID: PMC5419200 DOI: 10.1093/ofid/ofx053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/17/2017] [Indexed: 11/12/2022] Open
Abstract
We describe a review of human adenovirus (HAdV) infections occurring among adults in a tertiary hospital in Singapore from February to May 2013. A similar increase in cases was observed among children and military personnel during the same time period. The majority of isolates were identified as HAdV-7, likely an emerging pathogen in Asia.
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Affiliation(s)
| | | | | | | | | | | | | | - Yong Yang
- Epidemiology, Singapore General Hospital
| | | | - Udayan Joseph
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - October M Sessions
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Gavin J D Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Eng Eong Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
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Ho HJ, Toh CY, Ang B, Krishnan P, Lin RTP, La MV, Chow A. Outbreak of New Delhi metallo-β-lactamase-1-producing Enterobacter cloacae in an acute care hospital general ward in Singapore. Am J Infect Control 2016; 44:177-82. [PMID: 26454748 DOI: 10.1016/j.ajic.2015.08.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/26/2015] [Accepted: 08/31/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND Autochthonous infections with New Delhi metallo-β-lactamase-1 (NDM-1)-producing Enterobacteriaceae have been reported in Singapore since 2011, but occurrences of nosocomial transmission have not. We report an outbreak of NDM-1-producing Enterobacter cloacae among adults admitted to an acute hospital's general ward. METHODS On detecting the index case with a culture specimen positive for NDM-1-producing E cloacae, active case finding was conducted by screening all possible patient contacts. On-site ward assessment was performed, and electronic patient medical records were reviewed to conduct a case-control study to identify factors associated with colonization. RESULTS Of 55 screened patient contacts, 3 further cases were detected, with isolates genetically related to the index case. None of these 4 cases was housed within the same cubicle. However, 3 were managed by the same medical team. Being managed by this team was positively associated with being a case (adjusted odds ratio = 15.64; 95% confidence interval, 0.91-270.27; P = .06) after adjusting for age, sex, Charlson comorbidity index score, and recent antibiotic use. CONCLUSION Our report suggests nosocomial transmission of NDM-1-producing E cloacae occurred via health care staff. Improvements in infection control measures, especially pertaining to staff hand hygiene practices and ward staffing, are needed to reduce the spread of highly resistant pathogens, such as NDM-1-producing Enterobacteriaceae.
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Affiliation(s)
- Hanley J Ho
- Department of Clinical Epidemiology, Tan Tock Seng Hospital, Singapore, Singapore.
| | - Cheng Yen Toh
- Infection Control Unit, Tan Tock Seng Hospital, Singapore, Singapore
| | - Brenda Ang
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Prabha Krishnan
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, Ministry of Health, Singapore, Singapore; Department of Laboratory Medicine, National University Health System, Singapore, Singapore
| | - My-Van La
- National Public Health Laboratory, Ministry of Health, Singapore, Singapore
| | - Angela Chow
- Department of Clinical Epidemiology, Tan Tock Seng Hospital, Singapore, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
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Teo JWP, La MV, Jureen R, Lin RTP. Emergence of a New Delhi metallo-β-lactamase-1-producing Pseudomonas aeruginosa in Singapore. Emerg Microbes Infect 2015; 4:e72. [PMID: 26632659 PMCID: PMC4661430 DOI: 10.1038/emi.2015.72] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 09/21/2015] [Accepted: 09/25/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Jeanette W P Teo
- Department of Laboratory Medicine, Division of Microbiology, National University Hospital, Singapore 119074, Republic of Singapore
| | - My-Van La
- National Public Health Laboratory, Ministry of Health, Synapse, Singapore 138623, Republic of Singapore
| | - Roland Jureen
- Department of Laboratory Medicine, Division of Microbiology, National University Hospital, Singapore 119074, Republic of Singapore
| | - Raymond T P Lin
- Department of Laboratory Medicine, Division of Microbiology, National University Hospital, Singapore 119074, Republic of Singapore.,National Public Health Laboratory, Ministry of Health, Synapse, Singapore 138623, Republic of Singapore
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Rajkumar V, Chiang CSM, Low JM, Cui L, Lin RTP, Tee NWS, Maiwald M, Chong CY, Thoon KC, Tan NWH. Risk Factors for Severe Adenovirus Infection in Children during an Outbreak in Singapore. Ann Acad Med Singap 2015; 44:50-59. [PMID: 25797817 DOI: 10.47102/annals-acadmedsg.v44n2p50] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
BACKGROUND Human adenoviruses (HAdVs) can cause a variety of human illnesses, with associated temporal and geographic changes in disease incidence. We report the emergence of an outbreak of HAdV infections in Singapore, presumably caused by a change of the predominating type to HAdV-7. We examined the clinical features of children admitted with HAdV infection to 1 institution and the risk factors for severe infection. MATERIALS AND METHODS This is a retrospective case-control study of all HAdV-infected children admitted during weeks 1 to 19 in 2013, as identified from laboratory records. A descriptive retrospective analysis of epidemiology, clinical data and the outcome of these children was also performed. Patients with severe infections were defined as cases, those with non-severe infections as controls, and the 2 groups were compared to find possible independent risk factors. RESULTS Eighty-five patients with HAdV infection were studied, including 11 (12.9%) cases and 74 (87.1%) controls. Binary logistic regression showed that cases were more likely to be <2 years old (adjusted OR 10.6, 95% CI, 1.8 to 63.2) and to have significant comorbidities (adjusted OR 19.9, 95% CI, 3.4 to 116.1) compared to controls. The predominant type in 2013 was HAdV-7, which differed from 2011 and 2012, when HAdV-3 was more common. There was a trend towards pneumonia being more common in patients infected with HAdV-7 than in patients infected with other types, although this did not reach statistical significance (OR 2.8, 95% CI, 0.9 to 8.7). CONCLUSION The emergence of HAdV-7 in a population where other HAdV types had circulated previously may have caused the outbreak in Singapore, and this was associated with more serious infections in children. Young age (<2 years) and significant comorbidities were associated with more severe HAdV infection.
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Affiliation(s)
- Veena Rajkumar
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore
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45
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Teo J, Tan SYY, Liu Y, Tay M, Ding Y, Li Y, Kjelleberg S, Givskov M, Lin RTP, Yang L. Comparative genomic analysis of malaria mosquito vector-associated novel pathogen Elizabethkingia anophelis. Genome Biol Evol 2014; 6:1158-65. [PMID: 24803570 PMCID: PMC4041001 DOI: 10.1093/gbe/evu094] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Acquisition of Elizabethkingia infections in intensive care units (ICUs) has risen in the past decade. Treatment of Elizabethkingia infections is challenging due to the lack of effective therapeutic regimens, leading to a high mortality rate. Elizabethkingia infections have long been attributed to Elizabethkingia meningoseptica. Recently, we used whole-genome sequencing to reveal that E. anophelis is the pathogenic agent for an Elizabethkingia outbreak at two ICUs. We performed comparative genomic analysis of seven hospital-isolated E. anophelis strains with five available Elizabethkingia spp. genomes deposited in the National Center for Biotechnology Information Database. A pan-genomic approach was applied to identify the core- and pan-genome for the Elizabethkingia genus. We showed that unlike the hospital-isolated pathogen E. meningoseptica ATCC 12535 strain, the hospital-isolated E. anophelis strains have genome content and organization similar to the E. anophelis Ag1 and R26 strains isolated from the midgut microbiota of the malaria mosquito vector Anopheles gambiae. Both the core- and accessory genomes of Elizabethkingia spp. possess genes conferring antibiotic resistance and virulence. Our study highlights that E. anophelis is an emerging bacterial pathogen for hospital environments.
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Affiliation(s)
- Jeanette Teo
- Department of Laboratory Medicine, Microbiology Unit, National University Hospital, Singapore
| | - Sean Yang-Yi Tan
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, SingaporeSchool of Biological Sciences, Nanyang Technological University, Singapore
| | - Yang Liu
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Martin Tay
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, SingaporeSchool of Biological Sciences, Nanyang Technological University, Singapore
| | - Yichen Ding
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Yingying Li
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Staffan Kjelleberg
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, SingaporeCentre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Michael Givskov
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, SingaporeCosterton Biofilm Center, Department of International Health, Immunology and Microbiology, Panum Institute, University of Copenhagen, Denmark
| | - Raymond T P Lin
- Department of Laboratory Medicine, Microbiology Unit, National University Hospital, Singapore
| | - Liang Yang
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, SingaporeSchool of Biological Sciences, Nanyang Technological University, Singapore
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Teo JWP, Kurup A, Lin RTP, Hsien KT. Emergence of clinical Klebsiella pneumoniae producing OXA-232 carbapenemase in Singapore. New Microbes New Infect 2013; 1:13-5. [PMID: 25356318 PMCID: PMC4184486 DOI: 10.1002/2052-2975.4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 05/28/2013] [Accepted: 06/12/2013] [Indexed: 11/11/2022] Open
Abstract
We report the emergence of OXA-232, a newly described OXA-48-like carbapenemase variant, in Southeast Asia. Molecular characterization of eight Klebsiella pneumoniae obtained from local and foreign patients reveals clonality of the isolates. blaOXA-232 was located on a non-conjugative plasmid of 6141 base pairs (GenBank accession number JX423831.1).
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Affiliation(s)
- J W P Teo
- Department of Laboratory Medicine, National University Hospital 5 Lower Kent Ridge Road, Singapore, 119074
| | - A Kurup
- Duke-Nus Graduate Medical School 8 College Road, Singapore, 169857
| | - R T P Lin
- National Public Health Laboratory, Ministry of Health Singapore
| | - K T Hsien
- Pathology Department, Singapore General Hospital 20 College Road, Academia, Level 7, Diagnostics Tower, Singapore, 169856
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48
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Fisher D, Tambyah PA, Lin RTP, Jureen R, Cook AR, Lim A, Ong B, Balm M, Ng TM, Hsu LY. Sustained meticillin-resistant Staphylococcus aureus control in a hyper-endemic tertiary acute care hospital with infrastructure challenges in Singapore. J Hosp Infect 2013; 85:141-8. [PMID: 24011440 PMCID: PMC7114850 DOI: 10.1016/j.jhin.2013.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/22/2013] [Indexed: 11/25/2022]
Abstract
Background Meticillin-resistant Staphylococcus aureus (MRSA) has been entrenched in Singapore hospitals since the 1980s, with an excess of 600 non-duplicate cases of infections (120 bacteraemia episodes) each year in our 995-bed university hospital. Approximately 5% of our hospital beds are used as isolation facilities. Aim To study the impact of an MRSA control bundle that was implemented via gradual geographic extension across hospital wards. Methods The bundle included active surveillance on admission and transfer/discharge to identify ward-based acquisition of MRSA, isolation and cohorting of MRSA-infected patients, enhanced hand hygiene initiatives, and publicly displayed feedback of MRSA acquisition and hand hygiene compliance rates. Implementation was between October 2006 and June 2010 in order to provide lead-time for the incremental development of infrastructural capacity, and to develop an ethic of infection prevention among staff. Results were analysed via interrupted time-series analysis. Findings MRSA infections fell midway through the implementation, with MRSA bacteraemia declining from 0.26 [95% confidence interval (CI): 0.18–0.34] cases per 1000 inpatient-days in the first quarter of 2004 to 0.11 (95% CI: 0.07–0.19) cases per 1000 inpatient-days in the first quarter of 2012. MRSA acquisition rates fell a year after the programme had been fully implemented, whereas hand hygiene compliance rose significantly from 47% (95% CI: 44–49) in the first quarter of 2009 to 69% (95% CI: 68–71) in the first quarter of 2012. Conclusion Successful staged implementation of an MRSA bundle in a hyper-endemic setting is sustainable and represents a model that may be adapted for similar settings.
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Affiliation(s)
- D Fisher
- Department of Medicine, National University Health System, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Infection Control Team, National University Health System, Singapore.
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49
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Balm MND, Salmon S, Jureen R, Teo C, Mahdi R, Seetoh T, Teo JTW, Lin RTP, Fisher DA. Bad design, bad practices, bad bugs: frustrations in controlling an outbreak of Elizabethkingia meningoseptica in intensive care units. J Hosp Infect 2013; 85:134-40. [PMID: 23958153 DOI: 10.1016/j.jhin.2013.05.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/23/2013] [Indexed: 11/19/2022]
Abstract
BACKGROUND Elizabethkingia meningoseptica is a nosocomial-adapted Gram-negative bacillus intrinsically resistant to antibiotics commonly used in the intensive care setting. An outbreak investigation commenced when five patients developed E. meningoseptica infection in two intensive care units (ICUs). METHODS Analysis of laboratory data, case reviews, ICU workflows and extensive environmental sampling were undertaken. Molecular typing was performed using repetitive element palindromic polymerase chain reaction. Follow-up studies after interventions included environmental monitoring and a survey of staff compliance with interventions. FINDINGS Laboratory data revealed increasing incidence of E. meningoseptica colonization or infection in ICU patients compared with preceding years. E. meningoseptica was cultured from 44% (35/79) of taps, but not from other sources. Hand hygiene sinks were used for disposal of patient secretions and rinsing re-usable patient care items. Sinks misused in this way were contaminated more often than sinks that were not misused (odds ratio 4.38, 95% confidence interval 1.68-11.39; P = 0.004). Molecular typing revealed that patient isolates had identical patterns to several isolates from hand hygiene taps. An urgent education programme was instituted to change these practices. Taps were cleaned systematically and aerators were changed. A temporary reduction in case numbers was achieved. Recolonization of taps was demonstrated on follow-up environmental screening, and cases recurred after two months. A survey revealed that 77.3% (163/213) of nursing staff still misused sinks due to time constraints or other problems adhering to the interventions. CONCLUSION Introduction of non-sanctioned practices due to suboptimal unit design may have unintentional consequences for ICU patients. Room design and staff workflows must be optimized for patient safety as lapses in procedure can inadvertently put patients at risk.
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Affiliation(s)
- M N D Balm
- Infection Control Team, National University Hospital, Singapore; Microbiology, Department of Laboratory Medicine, National University Hospital, Singapore
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50
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Teo JWP, La MV, Krishnan P, Ang B, Jureen R, Lin RTP. Enterobacter cloacae producing an uncommon class A carbapenemase, IMI-1, from Singapore. J Med Microbiol 2013; 62:1086-1088. [DOI: 10.1099/jmm.0.053363-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, we describe the characterization of an infrequently encountered class A carbapenemase, IMI-1, from a clinical Enterobacter cloacae isolate. The isolate had high levels of resistance to carbapenems but retained susceptibility to expanded-spectrum cephalosporins. The bla
IMI-1 gene was chromosomally encoded. Detection of the IMI-1 producer highlights the diversity of carbapenemases in a local clinical setting.
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Affiliation(s)
- Jeanette W. P. Teo
- Department of Laboratory Medicine, National University Hospital, Singapore 119074, Republic of Singapore
| | - My-Van La
- National Public Health Laboratory, Singapore 169612, Republic of Singapore
| | - Prabha Krishnan
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore 308433, Republic of Singapore
| | - Brenda Ang
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore 308433, Republic of Singapore
| | - Roland Jureen
- Department of Laboratory Medicine, National University Hospital, Singapore 119074, Republic of Singapore
| | - Raymond T. P. Lin
- Department of Laboratory Medicine, National University Hospital, Singapore 119074, Republic of Singapore
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