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Liew KC, Nguyen C, Waidyatillake NT, Nguyen T, Walton A, Harris O, Athan E, Stenos J, Graves SR. A serological assay using Tropheryma whipplei antigens for the presumptive exclusion of Whipple disease. Pathology 2024; 56:98-103. [PMID: 38061960 DOI: 10.1016/j.pathol.2023.09.010] [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: 03/08/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 01/24/2024]
Abstract
Whipple disease (WD) is a rare infection in genetically susceptible people caused by the bacterium Tropheryma whipplei. An indirect immunofluorescence serological assay (IFA), detecting patient antibodies to the bacterium, was developed using T. whipplei as antigen. We hypothesised that this assay could be used to rule out WD in patients in whom the diagnosis was being considered, based on high immunoglobulin (Ig) G titres to T. whipplei. In this study, 16 confirmed WD patients and 156 age-matched controls from across Australia were compared serologically. WD patients mostly underproduced IgG antibody to T. whipplei, with titres of ≤1:32 being common. While at an antibody titre of <1:64 the assay sensitivity for WD was only 69% [95% confidence interval (CI) 41-89%], its specificity for excluding WD was 91% (95% CI 85-95%). This specificity increased to 95% (95% CI 90-98%) at an antibody titre of <1:16. Patients with antibody titres of >1:64 were unlikely to have WD. At this titre, the seroprevalence of T. whipplei IgG antibody was 92% (223/242) in Australian blood donors. Unlike other serological assays, which are used to confirm a specific infection, this novel assay is designed to rule out WD infection with a specificity in Australia of 91%. Further validation of this assay, by trialling in other countries, should now be undertaken, as its usefulness is dependent on there being a high background seropositivity to T. whipplei in the general population at the location in which the assay is being used.
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Affiliation(s)
- Kwee Chin Liew
- Department of Microbiology, Australian Clinical Labs, Geelong, Vic, Australia; Australian Rickettsial Reference Laboratory, University Hospital Geelong, Geelong, Vic, Australia; Deakin University, School of Medicine, Geelong, Vic, Australia.
| | - Chelsea Nguyen
- Australian Rickettsial Reference Laboratory, University Hospital Geelong, Geelong, Vic, Australia
| | - Nilakshi T Waidyatillake
- Barwon Health, University Hospital Geelong, Geelong, Vic, Australia; Allergy and Lung Health Unit, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Vic, Australia
| | - Trang Nguyen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR-Pathology West, Sydney, NSW, Australia
| | - Aaron Walton
- Australian Rickettsial Reference Laboratory, University Hospital Geelong, Geelong, Vic, Australia; Deakin University, School of Medicine, Geelong, Vic, Australia
| | - Owen Harris
- Department of Microbiology, Australian Clinical Labs, Geelong, Vic, Australia; Deakin University, School of Medicine, Geelong, Vic, Australia; Barwon Health, University Hospital Geelong, Geelong, Vic, Australia
| | - Eugene Athan
- Australian Rickettsial Reference Laboratory, University Hospital Geelong, Geelong, Vic, Australia; Deakin University, School of Medicine, Geelong, Vic, Australia; Barwon Health, University Hospital Geelong, Geelong, Vic, Australia
| | - John Stenos
- Australian Rickettsial Reference Laboratory, University Hospital Geelong, Geelong, Vic, Australia
| | - Stephen R Graves
- Australian Rickettsial Reference Laboratory, University Hospital Geelong, Geelong, Vic, Australia
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2
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Lee WS, Tan HX, Reynaldi A, Esterbauer R, Koutsakos M, Nguyen J, Amarasena T, Kent HE, Aggarwal A, Turville SG, Taiaroa G, Kinsella P, Liew KC, Tran T, Williamson DA, Cromer D, Davenport MP, Kent SJ, Juno JA, Khoury DS, Wheatley AK. Durable reprogramming of neutralizing antibody responses following Omicron breakthrough infection. Sci Adv 2023; 9:eadg5301. [PMID: 37478181 PMCID: PMC10361595 DOI: 10.1126/sciadv.adg5301] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 06/21/2023] [Indexed: 07/23/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) breakthrough infection of vaccinated individuals is increasingly common with the circulation of highly immune evasive and transmissible Omicron variants. Here, we report the dynamics and durability of recalled spike-specific humoral immunity following Omicron BA.1 or BA.2 breakthrough infection, with longitudinal sampling up to 8 months after infection. Both BA.1 and BA.2 infections robustly boosted neutralization activity against the infecting strain while expanding breadth against BA.4, although neutralization activity was substantially reduced for the more recent XBB and BQ.1.1 strains. Cross-reactive memory B cells against both ancestral and Omicron spike were predominantly expanded by infection, with limited recruitment of de novo Omicron-specific B cells or antibodies. Modeling of neutralization titers predicts that protection from symptomatic reinfection against antigenically similar strains will be durable but is undermined by new emerging strains with further neutralization escape.
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Affiliation(s)
- Wen Shi Lee
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Arnold Reynaldi
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Robyn Esterbauer
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Julie Nguyen
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Thakshila Amarasena
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Helen E. Kent
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Anupriya Aggarwal
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Stuart G. Turville
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - George Taiaroa
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Paul Kinsella
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kwee Chin Liew
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Thomas Tran
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Deborah A. Williamson
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Deborah Cromer
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Miles P. Davenport
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Stephen J. Kent
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Jennifer A. Juno
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - David S. Khoury
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Adam K. Wheatley
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
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3
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Liew KC, O’Keeffe J, Rajandas H, Lee YP, Harris O, Parimannan S, Croft L, Athan E. Insights into the Evolution of P. aeruginosa Antimicrobial Resistance in a Patient Undergoing Intensive Therapy. Antibiotics (Basel) 2023; 12:antibiotics12030483. [PMID: 36978350 PMCID: PMC10044667 DOI: 10.3390/antibiotics12030483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/21/2023] [Accepted: 02/25/2023] [Indexed: 03/03/2023] Open
Abstract
Whole genome sequencing (WGS) provides insights into the evolution of antimicrobial resistance, an urgent global health threat. Using WGS, we observe evolutionary adaptation of a Pseudomonas aeruginosa strain within an immunocompromised patient undergoing antibiotic therapy. Two blood isolates (EA-86 and EA-87) from the patient evolved separate adaptations for antibiotic resistance, while sharing common adaptive mutations for host immune evasion. In EA-86, a silencing mutation in the antibiotic efflux pump repressor, NfxB, increased antibiotic resistance, while in EA-87, a similar mutation was seen in the antibiotic efflux pump repressor mexR. The number of genomic variants between the two isolates give a divergence time estimate of the order of 1000 generations. This time is sufficient for a bacterial lineage to have evolved an SNP in every position in the genome and been fixed if advantageous. This demonstrates the evolutionary adaptive power accessible to bacteria and the timescale for a brute-force functional survey of the SNP fitness landscape.
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Affiliation(s)
- Kwee Chin Liew
- Australian Clinical Labs, Department of Microbiology, Geelong, VIC 3220, Australia
- Barwon Health, University Hospital Geelong, Geelong, VIC 3220, Australia
| | - Jessica O’Keeffe
- Barwon Health, University Hospital Geelong, Geelong, VIC 3220, Australia
| | - Heera Rajandas
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong 08100, Kedah, Malaysia
- Deakin Genomic Centre, Deakin University, Geelong, VIC 3216, Australia
| | - Yin Peng Lee
- Deakin Genomic Centre, Deakin University, Geelong, VIC 3216, Australia
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3216, Australia
| | - Owen Harris
- Australian Clinical Labs, Department of Microbiology, Geelong, VIC 3220, Australia
- Barwon Health, University Hospital Geelong, Geelong, VIC 3220, Australia
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
| | - Sivachandran Parimannan
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong 08100, Kedah, Malaysia
- Deakin Genomic Centre, Deakin University, Geelong, VIC 3216, Australia
- Correspondence: (S.P.); (L.C.)
| | - Larry Croft
- Deakin Genomic Centre, Deakin University, Geelong, VIC 3216, Australia
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Correspondence: (S.P.); (L.C.)
| | - Eugene Athan
- Barwon Health, University Hospital Geelong, Geelong, VIC 3220, Australia
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC 3220, Australia
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Koutsakos M, Reynaldi A, Lee WS, Nguyen J, Amarasena T, Taiaroa G, Kinsella P, Liew KC, Tran T, Kent HE, Tan HX, Rowntree LC, Nguyen THO, Thomas PG, Kedzierska K, Petersen J, Rossjohn J, Williamson DA, Khoury D, Davenport MP, Kent SJ, Wheatley AK, Juno JA. SARS-CoV-2 breakthrough infection induces rapid memory and de novo T cell responses. Immunity 2023; 56:879-892.e4. [PMID: 36958334 PMCID: PMC9970913 DOI: 10.1016/j.immuni.2023.02.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/26/2023] [Accepted: 02/24/2023] [Indexed: 03/24/2023]
Abstract
Although the protective role of neutralizing antibodies against COVID-19 is well established, questions remain about the relative importance of cellular immunity. Using 6 pMHC multimers in a cohort with early and frequent sampling, we define the phenotype and kinetics of recalled and primary T cell responses following Delta or Omicron breakthrough infection in previously vaccinated individuals. Recall of spike-specific CD4+ T cells was rapid, with cellular proliferation and extensive activation evident as early as 1 day post symptom onset. Similarly, spike-specific CD8+ T cells were rapidly activated but showed variable degrees of expansion. The frequency of activated SARS-CoV-2-specific CD8+ T cells at baseline and peak inversely correlated with peak SARS-CoV-2 RNA levels in nasal swabs and accelerated viral clearance. Our study demonstrates that a rapid and extensive recall of memory T cell populations occurs early after breakthrough infection and suggests that CD8+ T cells contribute to the control of viral replication in breakthrough SARS-CoV-2 infections.
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Affiliation(s)
- Marios Koutsakos
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Arnold Reynaldi
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Wen Shi Lee
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Julie Nguyen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thakshila Amarasena
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - George Taiaroa
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Paul Kinsella
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kwee Chin Liew
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Thomas Tran
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Helen E Kent
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Jan Petersen
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Deborah A Williamson
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - David Khoury
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Miles P Davenport
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jennifer A Juno
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
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Lim CK, Roberts J, Moso M, Liew KC, Taouk ML, Williams E, Tran T, Steinig E, Caly L, Williamson DA. Mpox diagnostics: Review of current and emerging technologies. J Med Virol 2023; 95:e28429. [PMID: 36571266 PMCID: PMC10108241 DOI: 10.1002/jmv.28429] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022]
Abstract
Mpox is a zoonotic disease caused by monkeypox virus (MPXV) from the Orthopoxvirus genus. Unprecedented transmission events have led to more than 70 000 cases reported worldwide by October 2022. The change in mpox epidemiology has raised concerns of its ability to establish endemicity beyond its traditional geographical locations. In this review, we discuss the current understanding of mpox virology and viral dynamics that are relevant to mpox diagnostics. A synopsis of the traditional and emerging laboratory technologies useful for MPXV detection and in guiding "elimination" strategies is outlined in this review. Importantly, development in MPXV genomics has rapidly advanced our understanding of the role of viral evolution and adaptation in the current outbreak.
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Affiliation(s)
- Chuan Kok Lim
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jason Roberts
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Michael Moso
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kwee Chin Liew
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mona L Taouk
- Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Eloise Williams
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas Tran
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Eike Steinig
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Deborah Ann Williamson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
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Bond KA, Smith B, Gardiner E, Liew KC, Williams E, Walsham N, Putland M, Williamson DA. Utility of SARS-CoV-2 rapid antigen testing for patient triage in the emergency department: A clinical implementation study in Melbourne, Australia. The Lancet Regional Health - Western Pacific 2022; 25:100486. [PMID: 35655473 PMCID: PMC9150863 DOI: 10.1016/j.lanwpc.2022.100486] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Background Early, rapid detection of SARS-CoV-2 is essential in healthcare settings in order to implement appropriate infection control precautions and rapidly assign patients to care pathways. Rapid testing methods, such as SARS-CoV-2 rapid antigen testing (RAT) may improve patient care, despite a lower sensitivity than real-time PCR (RT-PCR) testing. Methods Patients presenting to an Emergency Department (ED) in Melbourne, Australia, were risk-stratified for their likelihood of active COVID-19 infection, and a non-randomised cohort of patients were tested by both Abbott Panbio™ COVID-19 Ag test (RAT) and SARS-CoV-2 RT-PCR. Patients with a positive RAT in the ‘At or High Risk’ COVID-19 group were moved immediately to a COVID-19 ward rather than waiting for a RT-PCR result. Clinical and laboratory data were assessed to determine test performance characteristics; and length of stay in the ED was compared for the different patient cohorts. Findings Analysis of 1762 paired RAT/RT-PCR samples demonstrated an overall sensitivity of 75.5% (206/273; 95% CI: 69·9-80·4) for the Abbott Panbio™ COVID-12 Ag test, with specificity of 100% (1489/1489; 95% CI: 99·8-100). Sensitivity improved with increasing risk for COVID-19 infection, from 72·4% (95% CI: 52·8-87·3) in the ‘No Risk’ cohort to 100% (95% CI: 29·2-100) in the ‘High Risk’ group. Time in the ED for the ‘At/High Risk’ group decreased from 421 minutes (IQR: 281, 525) for those with a positive RAT result to 274 minutes (IQR:140, 425) for those with a negative RAT result, p = 0.02. Interpretation The positive predictive value of a positive RAT in this setting was high, allowing more rapid instigation of COVID-19 care pathways and an improvement in patient flow within the ED. Funding Royal Melbourne Hospital, Melbourne, Australia.
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Koutsakos M, Lee WS, Reynaldi A, Tan HX, Gare G, Kinsella P, Liew KC, Taiaroa G, Williamson DA, Kent HE, Stadler E, Cromer D, Khoury DS, Wheatley AK, Juno JA, Davenport MP, Kent SJ. The magnitude and timing of recalled immunity after breakthrough infection is shaped by SARS-CoV-2 variants. Immunity 2022; 55:1316-1326.e4. [PMID: 35690062 PMCID: PMC9135796 DOI: 10.1016/j.immuni.2022.05.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [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: 01/22/2022] [Revised: 04/01/2022] [Accepted: 05/23/2022] [Indexed: 11/15/2022]
Abstract
Vaccination against SARS-CoV-2 protects from infection and improves clinical outcomes in breakthrough infections, likely reflecting residual vaccine-elicited immunity and recall of immunological memory. Here, we define the early kinetics of spike-specific humoral and cellular immunity after vaccination of seropositive individuals and after Delta or Omicron breakthrough infection in vaccinated individuals. Early longitudinal sampling revealed the timing and magnitude of recall, with the phenotypic activation of B cells preceding an increase in neutralizing antibody titers. While vaccination of seropositive individuals resulted in robust recall of humoral and T cell immunity, recall of vaccine-elicited responses was delayed and variable in magnitude during breakthrough infections and depended on the infecting variant of concern. While the delayed kinetics of immune recall provides a potential mechanism for the lack of early control of viral replication, the recall of antibodies coincided with viral clearance and likely underpins the protective effects of vaccination against severe COVID-19.
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Affiliation(s)
- Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Wen Shi Lee
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Arnold Reynaldi
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Grace Gare
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Paul Kinsella
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kwee Chin Liew
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Helen E Kent
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Eva Stadler
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Deborah Cromer
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - David S Khoury
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Jennifer A Juno
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Miles P Davenport
- Kirby Institute, University of New South Wales, Kensington, NSW, Australia.
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia.
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8
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Liew KC, Yeoh K, Lai C, Williams E, Sheorey H, Mahanty S. Fever, eosinophilia and abdominal pain. Pathology 2022. [DOI: 10.1016/j.pathol.2021.12.089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Chiong F, Wasef MS, Liew KC, Cowan R, Tsai D, Lee YP, Croft L, Harris O, Gwini SM, Athan E. The impact of infectious diseases consultation on the management and outcomes of Pseudomonas aeruginosa bacteraemia in adults: a retrospective cohort study. BMC Infect Dis 2021; 21:671. [PMID: 34243714 PMCID: PMC8268285 DOI: 10.1186/s12879-021-06372-5] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/28/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Pseudomonas aeruginosa bacteraemia (PAB) is associated with high mortality. The benefits of infectious diseases consultation (IDC) has been demonstrated in Staphylococcal aureus bacteraemia and other complex infections. Impact of IDC in PAB is unclear. This study aimed to evaluate the impact of IDC on the management and outcomes in patients with PAB. METHODS This is a retrospective cohort single-centre study from 1 November 2006 to 29 May 2019, in all adult patients admitted with first episode of PAB. Data collected included demographics, clinical management and outcomes for PAB and whether IDC occurred. In addition, 29 Pseudomonas aeruginosa (PA) stored isolates were available for Illumina whole genome sequencing to investigate if pathogen factors contributed to the mortality. RESULTS A total of 128 cases of PAB were identified, 71% received IDC. Patients who received IDC were less likely to receive inappropriate duration of antibiotic therapy (4.4%; vs 67.6%; p < 0.01), more likely to be de-escalated to oral antibiotic in a timely manner (87.9% vs 40.5%; p < 0.01), undergo removal of infected catheter (27.5% vs 13.5%; p = 0.049) and undergo surgical intervention (20.9% vs 5.4%, p = 0.023) for source control. The overall 30-day all-cause mortality rate was 24.2% and was significantly higher in the no IDC group in both unadjusted (56.8% vs 11.0%, odds ratio [OR] = 10.63, p < 0.001) and adjusted analysis (adjusted OR = 7.84; 95% confidence interval, 2.95-20.86). The genotypic analysis did not reveal any PA genetic features associated with increased mortality between IDC versus no IDC groups. CONCLUSION Patients who received IDC for PAB had lower 30-day mortality, better source control and management was more compliant with guidelines. Further prospective studies are necessary to determine if these results can be validated in other settings.
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Affiliation(s)
- Fabian Chiong
- Department of Medicine, Alice Springs Hospital, PO Box 2234, Alice Springs, NT, 0871, Australia.
| | | | - Kwee Chin Liew
- Department of Infectious Diseases, University Hospital Geelong, Geelong, Australia
- Australian Clinical Laboratories, Geelong, Australia
| | - Raquel Cowan
- Department of Infectious Diseases, University Hospital Geelong, Geelong, Australia
| | - Danny Tsai
- University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Australia
- Rural and Remote Health NT, Flinders University, Alice Springs, NT, Australia
| | - Yin Peng Lee
- Deakin Genomic Centre, Deakin University, Geelong, Australia
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Larry Croft
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
- Asian Institute of Medicine, Science and Technology University, Bedong, Kedah, Malaysia
| | - Owen Harris
- Australian Clinical Laboratories, Geelong, Australia
| | | | - Eugene Athan
- Department of Infectious Diseases, University Hospital Geelong, Geelong, Australia
- School of Medicine Deakin University, Geelong, Australia
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Liew KC, Newton P, Tominez G. Internal verification of the cepheid Xpert enterovirus real-time PCR assay for the rapid detection of enterovirus in cerebrospinal fluid specimens. Pathology 2019. [DOI: 10.1016/j.pathol.2018.12.399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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Liew KC, Kumar N, Tadepalli M, Graves S, Shum O, Jagarlamudi V, Adams N, Miyakis S. New detection of flinders island spotted fever (due to Rickettsia honei infection) in new south wales: A case of fulminant septic shock and multi-organ failure. Pathology 2019. [DOI: 10.1016/j.pathol.2018.12.400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Liew KC, Evans O, Wales E, Bond S, Newton P, Miyakis S. 214. Antimicrobial Usage and Outcomes following Laboratory Suppression of Antimicrobial Susceptibility Results for Pseudomonas aeruginosa in Sputum Cultures. Open Forum Infect Dis 2018. [PMCID: PMC6255305 DOI: 10.1093/ofid/ofy210.226] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 11/12/2022] Open
Abstract
Background Methods Results Conclusion Disclosures
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Affiliation(s)
- Kwee Chin Liew
- Department of Infectious Diseases, Wollongong Hospital, New South Wales, Australia
| | - Oliver Evans
- Department of Infectious Diseases, Wollongong Hospital, New South Wales, Australia
| | - Erica Wales
- Department of Pharmacy, Wollongong Hospital, New South Wales, Australia
| | - Stuart Bond
- Department of Pharmacy, Wollongong Hospital, New South Wales, Australia
- School of Medicine, University of Wollongong, New South Wales, Australia
| | - Peter Newton
- NSW Health Pathology, Microbiology, Wollongong Hospital, Wollongong, New South Wales, Australia
| | - Spiros Miyakis
- Department of Infectious Diseases, Wollongong Hospital, New South Wales, Australia
- School of Medicine, University of Wollongong, New South Wales, Australia
- Illawara Health and Medical Research Institute, Wollongong, New South Wales, Australia
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