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Fergusson M, Maley M, Geraghty T, Albaladejo JP, Mason C, Rocchi MS. Validation of a multiplex-tandem RT-PCR for the detection of bovine respiratory disease complex using Scottish bovine lung samples. Vet J 2024; 303:106058. [PMID: 38103886 DOI: 10.1016/j.tvjl.2023.106058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
The welfare and economic impact of bovine respiratory disease complex (BRDC), and its associated antibiotic usage, are major challenges to cattle rearing and beef cattle finishing industries. Accurate pathogen diagnosis is important to undertake appropriate treatment and long-term management strategies, such as vaccine selection. Conventional diagnostic approaches have several limitations including high costs, long turnaround times and difficulty in test interpretation, which could delay treatment decisions and lead to unnecessary animal losses. We describe the validation of a multiplex-tandem (MT) reverse transcription-polymerase chain reaction (RT-PCR) for the detection of seven common pathogens associated with BRDC. This test has the potential to advance pathogen identification and to overcome many of the limitations of current testing methods. It requires a single sample and results are obtained quickly and not influenced by prior antimicrobial therapy or overgrowth of contaminating organisms. We demonstrated a test specificity of 100% and sensitivity ranging from 93.5% to 100% for these seven common pathogens. This test will be a useful addition to advance BRDC investigation and diagnosis.
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Affiliation(s)
- M Fergusson
- SRUC Veterinary and Analytical Services, Pentland Science Park, Bush Loan Road, Edinburgh, Scotland EH26 0PZ, UK
| | - M Maley
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ, UK
| | - T Geraghty
- SRUC Veterinary and Analytical Services, Pentland Science Park, Bush Loan Road, Edinburgh, Scotland EH26 0PZ, UK
| | - J Palarea Albaladejo
- Department of Computer Sciences, Applied Mathematics and Statistics, University of Girona, Girona 17003, Spain; Biomathematics and Statistics Scotland, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, Scotland EH9 3FD, UK
| | - C Mason
- SRUC Veterinary and Analytical Services, Pentland Science Park, Bush Loan Road, Edinburgh, Scotland EH26 0PZ, UK
| | - M S Rocchi
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ, UK.
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Mijač M, Ljubin-Sternak S, Ivković-Jureković I, Vraneš J. Comparison of MT-PCR with Quantitative PCR for Human Bocavirus in Respiratory Samples with Multiple Respiratory Viruses Detection. Diagnostics (Basel) 2023; 13:diagnostics13050846. [PMID: 36899990 PMCID: PMC10001063 DOI: 10.3390/diagnostics13050846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Human bocavirus (HBoV) is an important respiratory pathogen, especially in children, but it is often found in co-detection with other respiratory viruses, which makes the diagnostic approach challenging. We compared multiplex PCR and quantitative PCR for HBoV with multiplex tandem PCR (MT-PCR) in 55 cases of co-detection of HBoV and other respiratory viruses. In addition, we investigated whether there is a connection between the severity of the disease, measured by the localization of the infection, and amount of virus detected in the respiratory secretions. No statistically significant difference was found, but children with large amount of HBoV and other respiratory virus had a longer stay in hospital.
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Affiliation(s)
- Maja Mijač
- Molecular Microbiology Department, Dr. Andrija Štampar Teaching Institute of Public Health, 10000 Zagreb, Croatia
- Medical Microbiology Department, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
- Correspondence:
| | - Sunčanica Ljubin-Sternak
- Molecular Microbiology Department, Dr. Andrija Štampar Teaching Institute of Public Health, 10000 Zagreb, Croatia
- Medical Microbiology Department, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Irena Ivković-Jureković
- Department of Pulmonology, Allergy, Immunology and Rheumatology, Children’s Hospital Zagreb, 10000 Zagreb, Croatia
- Faculty for Dental Medicine and Healthcare, School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Jasmina Vraneš
- Molecular Microbiology Department, Dr. Andrija Štampar Teaching Institute of Public Health, 10000 Zagreb, Croatia
- Medical Microbiology Department, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
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Pond MJ, Al-Mufti J, Madona P, Crone MA, Laing KG, Hale RS, Muir D, Randell P. Mpox infection investigation using multiplexed syndromic diagnostics: Evaluation of an AusDiagnostics multiplexed tandem PCR (MT-PCR) syndromic panel. JOURNAL OF CLINICAL VIROLOGY PLUS 2023. [DOI: 10.1016/j.jcvp.2023.100142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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Prasad N, Walker TA, Waite B, Wood T, Trenholme AA, Baker MG, McArthur C, Wong CA, Grant CC, Huang QS, Newbern EC. Respiratory Syncytial Virus-Associated Hospitalizations Among Adults With Chronic Medical Conditions. Clin Infect Dis 2021; 73:e158-e163. [PMID: 32531019 DOI: 10.1093/cid/ciaa730] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/04/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND In contrast with respiratory disease caused by influenza, information on the risk of respiratory syncytial virus (RSV) disease among adults with chronic medical conditions (CMCs) is limited. METHODS We linked population-based surveillance of acute respiratory illness hospitalizations to national administrative data to estimate seasonal RSV hospitalization rates among adults aged 18-80 years with the following preexisting CMCs: chronic obstructive pulmonary disease (COPD), asthma, congestive heart failure (CHF), coronary artery disease (CAD), cerebrovascular accidents (CVA), diabetes mellitus (DM), and end-stage renal disease (ESRD). Age- and ethnicity-adjusted rates stratified by age group were estimated. RESULTS Among 883 999 adult residents aged 18-80 years, 281 RSV-positive hospitalizations were detected during 2012-2015 winter seasons. Across all ages, RSV hospitalization rates were significantly higher among adults with COPD, asthma, CHF, and CAD compared with those without each corresponding condition. RSV hospitalization rates were significantly higher among adults with ESRD aged 50-64 years and adults with DM aged 18-49 years and 65-80 years compared with adults in each age group without these conditions. No increased risk was seen for adults with CVA. The CMC with the highest risk of RSV hospitalization was CHF (incidence rate ratio [IRR] range, 4.6-36.5 across age strata) and COPD (IRR range, 9.6-9.7). Among RSV-positive adults, CHF and COPD were independently associated with increased length of hospital stay. CONCLUSIONS Adults with specific CMCs are at increased risk of RSV hospitalizations. Age affects this relationship for some CMCs. Such populations maybe relevant for future RSV prevention strategies.
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Affiliation(s)
- Namrata Prasad
- National Centre for Biosecurity and Infectious Disease (NCBID), Institute of Environmental Science and Research, Wellington, New Zealand.,Department of Paediatrics: Child & Youth Health, University of Auckland, Auckland, New Zealand
| | - Tiffany A Walker
- National Centre for Biosecurity and Infectious Disease (NCBID), Institute of Environmental Science and Research, Wellington, New Zealand
| | - Ben Waite
- National Centre for Biosecurity and Infectious Disease (NCBID), Institute of Environmental Science and Research, Wellington, New Zealand
| | - Tim Wood
- National Centre for Biosecurity and Infectious Disease (NCBID), Institute of Environmental Science and Research, Wellington, New Zealand
| | - Adrian A Trenholme
- Kidz First Children's Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | - Michael G Baker
- School of Medicine, University of Auckland, Auckland, New Zealand
| | - Colin McArthur
- School of Medicine, University of Otago, Wellington, New Zealand
| | - Conroy A Wong
- Kidz First Children's Hospital, Counties Manukau District Health Board, Auckland, New Zealand.,Department of Critical Care Medicine, Auckland City Hospital, Auckland, New Zealand
| | - Cameron C Grant
- Department of Paediatrics: Child & Youth Health, University of Auckland, Auckland, New Zealand.,General Paediatrics, Starship Children's Hospital, Auckland, New Zealand
| | - Q Sue Huang
- National Centre for Biosecurity and Infectious Disease (NCBID), Institute of Environmental Science and Research, Wellington, New Zealand
| | - E Claire Newbern
- National Centre for Biosecurity and Infectious Disease (NCBID), Institute of Environmental Science and Research, Wellington, New Zealand
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Respiratory Virus-related Emergency Department Visits and Hospitalizations Among Infants in New Zealand. Pediatr Infect Dis J 2020; 39:e176-e182. [PMID: 32675757 DOI: 10.1097/inf.0000000000002681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Estimates of the contribution of respiratory viruses to emergency department (ED) utilization remain limited. METHODS We conducted surveillance of infants with acute respiratory infection (ARI) associated ED visits, which then resulted in either hospital admission or discharge home. Seasonal rates of specific viruses stratified by age, ethnicity, and socioeconomic status were estimated for both visits discharged directly from ED and hospitalizations using rates of positivity for each virus. RESULTS During the 2014-2016 winter seasons, 3585 (66%) of the 5412 ARI ED visits were discharged home directly and 1827 (34%) were admitted to hospital. Among visits tested for all respiratory viruses, 601/1111 (54.1%) of ED-only and 639/870 (73.4%) of the hospital-admission groups were positive for at least one respiratory virus. Overall, respiratory virus-associated ED visit rates were almost twice as high as hospitalizations. Respiratory syncytial virus was associated with the highest ED (34.4 per 1000) and hospitalization rates (24.6 per 1000) among infants. ED visit and hospitalization rates varied significantly by age and virus. Māori and Pacific children had significantly higher ED visit and hospitalization rates for all viruses compared with children of other ethnicities. CONCLUSIONS Many infants with acute respiratory virus infections are managed in the ED rather than admitted to the hospital. Higher rates of ED-only versus admitted acute respiratory virus infections occur among infants living in lower socioeconomic households, older infants and infants of Māori or Pacific versus European ethnicity. Respiratory virus infections resulting in ED visits should be included in measurements of ARI disease burden.
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Prasad N, Newbern EC, Trenholme AA, Thompson MG, McArthur C, Wong CA, Jelley L, Aminisani N, Huang QS, Grant CC. The health and economic burden of respiratory syncytial virus associated hospitalizations in adults. PLoS One 2020; 15:e0234235. [PMID: 32525898 PMCID: PMC7289360 DOI: 10.1371/journal.pone.0234235] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/21/2020] [Indexed: 11/30/2022] Open
Abstract
Background Respiratory syncytial virus (RSV) is increasingly recognized as an important cause of illness in adults; however, data on RSV disease and economic burden in this age group remain limited. We aimed to provide comprehensive estimates of RSV disease burden among adults aged ≥18 years. Methods During 2012–2015, population-based, active surveillance of acute respiratory infection (ARI) hospitalizations enabled estimation of the seasonal incidence of RSV hospitalizations and direct health costs in adults aged ≥18 years in Auckland, New Zealand. Results Of 4,600 ARI hospitalizations tested for RSV, 348 (7.6%) were RSV positive. The median (interquartile range) length of hospital stay for RSV positive patients was 4 (2–6) days. The seasonal incidence rate (IR) of RSV hospitalizations, corrected for non-testing, was 23.6 (95% confidence intervals [CI] 21.0–26.1) per 100,000 adults aged ≥18 years. Hospitalization risk increased with age with the highest incidence among adults aged ≥80 years (IR 190.8 per 100,000, 95% CI 137.6–244.0). Being of Māori or Pacific ethnicity or living in a neighborhood with low socioeconomic status (SES) were independently associated with increased RSV hospitalization rates. We estimate RSV-associated hospitalizations among adults aged ≥18 years to cost on average NZD $4,758 per event. Conclusions RSV infection is associated with considerable disease and economic cost in adults. RSV disproportionally affects adult sub-groups defined by age, ethnicity, and neighborhood SES. An effective RSV vaccine or RSV treatment may offer benefits for older adults.
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Affiliation(s)
- Namrata Prasad
- Institute of Environmental Science and Research, Wellington, New Zealand
- Department of Paediatrics: Child & Youth Health, University of Auckland, Auckland, New Zealand
- * E-mail: (NP); (CN)
| | - E. Claire Newbern
- Institute of Environmental Science and Research, Wellington, New Zealand
- * E-mail: (NP); (CN)
| | | | - Mark G. Thompson
- United States Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Colin McArthur
- Department of Critical Care Medicine, Auckland City Hospital, Auckland, New Zealand
| | - Conroy A. Wong
- Counties Manukau District Health Board, Auckland, New Zealand
| | - Lauren Jelley
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nayyereh Aminisani
- Institute of Environmental Science and Research, Wellington, New Zealand
- Non-Communicable Disease Research Centre, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Q. Sue Huang
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Cameron C. Grant
- Department of Paediatrics: Child & Youth Health, University of Auckland, Auckland, New Zealand
- General Paediatrics, Starship Children’s Hospital, Auckland, New Zealand
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Clinical Evaluation of the cobas SARS-CoV-2 Test and a Diagnostic Platform Switch during 48 Hours in the Midst of the COVID-19 Pandemic. J Clin Microbiol 2020; 58:JCM.00599-20. [PMID: 32277022 PMCID: PMC7269406 DOI: 10.1128/jcm.00599-20] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 04/08/2020] [Indexed: 12/17/2022] Open
Abstract
Laboratories are currently witnessing extraordinary demand globally for sampling devices, reagents, consumables, and diagnostic instruments needed for timely diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. To meet diagnostic needs as the pandemic grows, the U.S. Food and Drug Administration (FDA) recently granted several commercial SARS-CoV-2 tests Emergency Use Authorization (EUA), but manufacturer-independent evaluation data are scarce. We performed the first manufacturer-independent evaluation of the fully automated sample-to-result two-target test cobas 6800 SARS-CoV-2 (cobas) (Roche Molecular Systems, Branchburg, NJ), which received U. Laboratories are currently witnessing extraordinary demand globally for sampling devices, reagents, consumables, and diagnostic instruments needed for timely diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. To meet diagnostic needs as the pandemic grows, the U.S. Food and Drug Administration (FDA) recently granted several commercial SARS-CoV-2 tests Emergency Use Authorization (EUA), but manufacturer-independent evaluation data are scarce. We performed the first manufacturer-independent evaluation of the fully automated sample-to-result two-target test cobas 6800 SARS-CoV-2 (cobas) (Roche Molecular Systems, Branchburg, NJ), which received U.S. FDA EUA on 12 March 2020. The comparator was a standardized 3-h SARS-CoV-2 protocol, consisting of RNA extraction using an automated portable instrument, followed by a two-target reverse transcription real-time PCR (RT-PCR), which our laboratory has routinely used since January 2020 [V. M. Corman, O. Landt, M. Kaiser, R. Molenkamp, et al., Euro Surveill 25(3):pii=2000045, 2020, https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045]. cobas and the comparator showed overall agreement of 98.1% and a kappa value of 0.95 on an in-house validation panel consisting of 217 well-characterized retrospective samples. Immediate prospective head-to-head comparative evaluation followed on 502 samples, and the diagnostic approaches showed overall agreement of 99.6% and a kappa value of 0.98. A good correlation (r2 = 0.96) between cycle threshold values for SARS-CoV-2-specific targets obtained by cobas and the comparator was observed. Our results showed that cobas is a reliable assay for qualitative detection of SARS-CoV-2 in nasopharyngeal swab samples collected in the Universal Transport Medium System (UTM-RT) (Copan, Brescia, Italy). Under the extraordinary circumstances that laboratories are facing worldwide, a safe diagnostic platform switch is feasible in only 48 h and in the midst of the COVID-19 pandemic if carefully planned and executed.
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Abstract
We aimed to provide comprehensive estimates of laboratory-confirmed respiratory syncytial virus (RSV)-associated hospitalisations. Between 2012 and 2015, active surveillance of acute respiratory infection (ARI) hospitalisations during winter seasons was used to estimate the seasonal incidence of laboratory-confirmed RSV hospitalisations in children aged <5 years in Auckland, New Zealand (NZ). Incidence rates were estimated by fine age group, ethnicity and socio-economic status (SES) strata. Additionally, RSV disease estimates determined through active surveillance were compared to rates estimated from hospital discharge codes. There were 5309 ARI hospitalisations among children during the study period, of which 3923 (73.9%) were tested for RSV and 1597 (40.7%) were RSV-positive. The seasonal incidence of RSV-associated ARI hospitalisations, once corrected for non-testing, was 6.1 (95% confidence intervals 5.8–6.4) per 1000 children <5 years old. The highest incidence was among children aged <3 months. Being of indigenous Māori or Pacific ethnicity or living in a neighbourhood with low SES independently increased the risk of an RSV-associated hospitalisation. RSV hospital discharge codes had a sensitivity of 71% for identifying laboratory-confirmed RSV cases. RSV infection is a leading cause of hospitalisation among children in NZ, with significant disparities by ethnicity and SES. Our findings highlight the need for effective RSV vaccines and therapies.
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Byrnes CA, Trenholme A, Lawrence S, Aish H, Higham JA, Hoare K, Elborough A, McBride C, Le Comte L, McIntosh C, Chan Mow F, Jaksic M, Metcalfe R, Coomarasamy C, Leung W, Vogel A, Percival T, Mason H, Stewart J. Prospective community programme versus parent-driven care to prevent respiratory morbidity in children following hospitalisation with severe bronchiolitis or pneumonia. Thorax 2020; 75:298-305. [PMID: 32094154 PMCID: PMC7231446 DOI: 10.1136/thoraxjnl-2019-213142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 12/07/2019] [Accepted: 01/10/2020] [Indexed: 11/08/2022]
Abstract
BACKGROUND Hospitalisation with severe lower respiratory tract infection (LRTI) in early childhood is associated with ongoing respiratory symptoms and possible later development of bronchiectasis. We aimed to reduce this intermediate respiratory morbidity with a community intervention programme at time of discharge. METHODS This randomised, controlled, single-blind trial enrolled children aged <2 years hospitalised for severe LRTI to 'intervention' or 'control'. Intervention was three monthly community clinics treating wet cough with prolonged antibiotics referring non-responders. All other health issues were addressed, and health resilience behaviours were encouraged, with referrals for housing or smoking concerns. Controls followed the usual pathway of parent-initiated healthcare access. After 24 months, all children were assessed by a paediatrician blinded to randomisation for primary outcomes of wet cough, abnormal examination (crackles or clubbing) or chest X-ray Brasfield score ≤22. FINDINGS 400 children (203 intervention, 197 control) were enrolled in 2011-2012; mean age 6.9 months, 230 boys, 87% Maori/Pasifika ethnicity and 83% from the most deprived quintile. Final assessment of 321/400 (80.3%) showed no differences in presence of wet cough (33.9% intervention, 36.5% controls, relative risk (RR) 0.93, 95% CI 0.69 to 1.25), abnormal examination (21.7% intervention, 23.9% controls, RR 0.92, 95% CI 0.61 to 1.38) or Brasfield score ≤22 (32.4% intervention, 37.9% control, RR 0.85, 95% CI 0.63 to 1.17). Twelve (all intervention) were diagnosed with bronchiectasis within this timeframe. INTERPRETATION We have identified children at high risk of ongoing respiratory disease following hospital admission with severe LRTI in whom this intervention programme did not change outcomes over 2 years. TRIAL REGISTRATION NUMBER ACTRN12610001095055.
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Affiliation(s)
- Catherine Ann Byrnes
- Department of Paediatrics, Child and Youth Health, The University of Auckland, Auckland, New Zealand
- Paediatric Respiratory Department, Starship Children's Health, Auckland, New Zealand
| | - Adrian Trenholme
- Department of Paediatrics, Child and Youth Health, The University of Auckland, Auckland, New Zealand
- Department of Paediatrics, KidzFirst Hospital Middlemore, Auckland, New Zealand
| | - Shirley Lawrence
- Department of Paediatrics, KidzFirst Hospital Middlemore, Auckland, New Zealand
| | - Harley Aish
- Otara Family and Christian Health Centre, Otara, Auckland, New Zealand
| | | | - Karen Hoare
- Greenstone Family Clinic, Manurewa, Auckland, New Zealand
| | | | - Charissa McBride
- Department of Paediatrics, KidzFirst Hospital Middlemore, Auckland, New Zealand
| | - Lyndsay Le Comte
- Counties Manukau District Health Board, Middlemore Clinical Trials Unit, Auckland, New Zealand
| | - Christine McIntosh
- Department of Paediatrics, KidzFirst Hospital Middlemore, Auckland, New Zealand
| | - Florina Chan Mow
- Department of Paediatrics, KidzFirst Hospital Middlemore, Auckland, New Zealand
| | - Mirjana Jaksic
- Department of Paediatrics, Child and Youth Health, The University of Auckland, Auckland, New Zealand
- Paediatric Respiratory Department, Starship Children's Health, Auckland, New Zealand
- Department of Paediatrics, KidzFirst Hospital Middlemore, Auckland, New Zealand
| | - Russell Metcalfe
- Department of Radiology, Starship Children's Health, Auckland, New Zealand
| | | | - William Leung
- Department of Health Economy, Wellington School of Medicine, University of Otago, Wellington, New Zealand
| | - Alison Vogel
- Department of Paediatrics, KidzFirst Hospital Middlemore, Auckland, New Zealand
| | - Teuila Percival
- Department of Paediatrics, KidzFirst Hospital Middlemore, Auckland, New Zealand
| | - Henare Mason
- Koawatea, Middlemore Hospital, Auckland, New Zealand
| | - Joanna Stewart
- Department of Population Health, The University of Auckland, Auckland, New Zealand
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Wong SS, Waite B, Ralston J, Wood T, Reynolds GE, Seeds R, Newbern EC, Thompson MG, Huang QS, Webby RJ. Hemagglutinin and Neuraminidase Antibodies Are Induced in an Age- and Subtype-Dependent Manner after Influenza Virus Infection. J Virol 2020; 94:e01385-19. [PMID: 31941786 PMCID: PMC7081922 DOI: 10.1128/jvi.01385-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022] Open
Abstract
Despite evidence that antibodies targeting the influenza virus neuraminidase (NA) protein can be protective and are broadly cross-reactive, the immune response to NA during infection is poorly understood compared to the response to hemagglutinin (HA) protein. As such, we compared the antibody profile to HA and NA in two naturally infected human cohorts in Auckland, New Zealand: (i) a serosurvey cohort, consisting of pre- and post-influenza season sera from PCR-confirmed influenza cases (n = 50), and (ii) an immunology cohort, consisting of paired sera collected after PCR-confirmation of infection (n = 94). The induction of both HA and NA antibodies in these cohorts was influenced by age and subtype. Seroconversion to HA was more frequent in those <20 years old (yo) for influenza A (serosurvey, P = 0.01; immunology, P = 0.02) but not influenza B virus infection. Seroconversion to NA was not influenced by age or virus type. Adults ≥20 yo infected with influenza A viruses were more likely to show NA-only seroconversion compared to children (56% versus 14% [5 to 19 yo] and 0% [0 to 4 yo], respectively). Conversely, children infected with influenza B viruses were more likely than adults to show NA-only seroconversion (88% [0 to 4 yo] and 75% [5 to 19 yo] versus 40% [≥20 yo]). These data indicate a potential role for immunological memory in the dynamics of HA and NA antibody responses. A better mechanistic understanding of this phenomenon will be critical for any future vaccines aimed at eliciting NA immunity.IMPORTANCE Data on the immunologic responses to neuraminidase (NA) is lacking compared to what is available on hemagglutinin (HA) responses, despite growing evidence that NA immunity can be protective and broadly cross-reactive. Understanding these NA responses during natural infection is key to exploiting these properties for improving influenza vaccines. Using two community-acquired influenza cohorts, we showed that the induction of both HA and NA antibodies after infection is influenced by age and subtypes. Such response dynamics suggest the influence of immunological memory, and understanding how this process is regulated will be critical to any vaccine effort targeting NA immunity.
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Affiliation(s)
- Sook-San Wong
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, People’s Republic of China
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, People’s Republic of China
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Ben Waite
- Institute of Environmental Science and Research, Ltd., NCBID–Wallaceville, Wallaceville, New Zealand
| | - Jacqui Ralston
- Institute of Environmental Science and Research, Ltd., NCBID–Wallaceville, Wallaceville, New Zealand
| | - Tim Wood
- Institute of Environmental Science and Research, Ltd., NCBID–Wallaceville, Wallaceville, New Zealand
| | - G. Edwin Reynolds
- Immunisation Advisory Centre (IMAC), University Services, University of Auckland, Auckland, New Zealand
| | - Ruth Seeds
- Institute of Environmental Science and Research, Ltd., NCBID–Wallaceville, Wallaceville, New Zealand
| | - E. Claire Newbern
- Institute of Environmental Science and Research, Ltd., NCBID–Wallaceville, Wallaceville, New Zealand
| | - Mark G. Thompson
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Q. Sue Huang
- Institute of Environmental Science and Research, Ltd., NCBID–Wallaceville, Wallaceville, New Zealand
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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Chandra S, Smith K, Alanazi AD, Alyousif MS, Emery D, Slapeta J. Rhipicephalus sanguineus sensu lato from dogs and dromedary camels in Riyadh, Saudi Arabia: low prevalence of vector-borne pathogens in dogs detected using multiplexed tandem PCR panel. Folia Parasitol (Praha) 2019; 66. [PMID: 31332102 DOI: 10.14411/fp.2019.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 05/09/2019] [Indexed: 11/19/2022]
Abstract
Despite the global distribution of the brown dog tick, Rhipicephalus sanguineus (Latreille, 1806) sensu lato (s.l.), limited information exists about their identity from the Arabian Peninsula. Ticks from free roaming urban dogs and dromedary camels in Riyadh, Saudi Arabia were morphologically identified, confirmed with scanning electron microscopy and characterised at mitochondrial DNA (cox1, 12S rDNA and 16S rDNA). A total of 186 ticks were collected from 65 free roaming dogs (n = 73) and 84 dromedary camels (n = 113). Morphologically, 5.9% (11/186) were R. sanguineus s.l. and Hyalomma spp. (93.5%, 174/186). From within R. sanguineus s.l., the presence of Rhipicephalus cf. camicasi Morel, Mouchet et Rodhain, 1976 (1 dog, 2 camels) and Rhipicephalus turanicus Pomerantsev, 1936 (1 camel) is reported. The examined R. cf. camicasi form a sister group to R. sanguineus s.l. tropical lineage at all DNA markers. Dogs were parasitised by Hyalomma dromedarii Koch, 1844 (n = 59), Hyalomma impeltatum Schulze et Schlottke, 1930 (n = 1), Hyalomma excavatum Koch, 1844 (n = 2), Hyalomma turanicum Pomerantsev, 1946 (n = 1) and Hyalomma rufipes Koch,1844 (n = 1). DNA from dog blood (n = 53) from Riyadh confirmed a low prevalence of canine vector-borne pathogens that does not exceed 5.7% for Babesia spp., Mycoplasma spp., Anaplasma platys, Hepatozoon canis and Ehrlichia canis using multiplexed tandem PCR (MT-PCR) and diagnostic PCR. Low prevalence of R. sanguineus s.l. on dogs likely contributed to the low level of canine vector-borne pathogens in Saudi Arabia. We demonstrate that dogs in the central Arabian Peninsula are more commonly parasitised by Hyalomma spp. than R. sanguineus s.l.
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Affiliation(s)
- Shona Chandra
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Karen Smith
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Abdullah D Alanazi
- Department of Biological Sciences, Faculty of Science and Humanities, Shaqra University, Ad-Dawadimi, Saudi Arabia
| | - Mohamed S Alyousif
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - David Emery
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Jan Slapeta
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
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12
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Ching NS, Kotsanas D, Easton ML, Francis MJ, Korman TM, Buttery JP. Respiratory virus detection and co-infection in children and adults in a large Australian hospital in 2009-2015. J Paediatr Child Health 2018; 54:1321-1328. [PMID: 29873433 PMCID: PMC7166960 DOI: 10.1111/jpc.14076] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 03/07/2018] [Accepted: 04/01/2018] [Indexed: 01/27/2023]
Abstract
AIM This hospital network-based retrospective observational study aimed to describe the prevalence and seasonality of paediatric and adult viral respiratory pathogens and their rates of co-infections, following the introduction of a rapid multiplex molecular diagnostic assay. METHODS All nasopharyngeal samples tested in patients presenting to Monash Health, Melbourne, Australia, from August 2009 to July 2015 by means of multiplex tandem polymerase chain reaction using the Respiratory Pathogen 12Plex kit (AusDiagnostics) were included in the analysis. RESULTS There were 28 729 patient samples analysed after duplicate samples were excluded. Positive results were twice as likely in paediatrics, 7573/11 491 (65.9%), compared to adults, 5410/17 238 (31.4%). Co-infection was more frequent in paediatrics, 1642/7573 (21.7% of positives), compared to adults 299/5410 (5.5%). Adenovirus had a high prevalence as a co-infection, 639/990 (64.5%), in paediatrics. Testing frequency increased by 179% in the paediatric group and by 949% for adults over the 6 years of observation. CONCLUSIONS This study demonstrated a significant difference in the positive detection rate of pathogens and co-infections between the population groups. Adenovirus had a surprisingly high prevalence as a co-infection, especially in paediatric patients. Over the study period, rapid uptake of the test was observed, especially in adults. This raises concerns about how we can ensure that testing remains rational and is able to be provided in a cost-effective manner in the future.
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Affiliation(s)
- Natasha S Ching
- Department of Infection and ImmunityMonash Children's Hospital, Monash HealthMelbourneVictoriaAustralia,Department of PaediatricsThe Ritchie Centre, Hudson Institute of Medical Research, Monash UniversityMelbourneVictoriaAustralia,General PaediatricsMonash Children's Hospital, Monash HealthMelbourneVictoriaAustralia
| | - Despina Kotsanas
- Monash Infectious DiseasesMonash HealthMelbourneVictoriaAustralia
| | - Mee L Easton
- SAEFVICMurdoch Children's Research InstituteMelbourneVictoriaAustralia
| | - Michelle J Francis
- Microbiology Laboratory, Monash PathologyMonash HealthMelbourneVictoriaAustralia
| | - Tony M Korman
- Monash Infectious DiseasesMonash HealthMelbourneVictoriaAustralia,Department of Medicine, School of Clinical SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Jim P Buttery
- Department of Infection and ImmunityMonash Children's Hospital, Monash HealthMelbourneVictoriaAustralia,Department of PaediatricsThe Ritchie Centre, Hudson Institute of Medical Research, Monash UniversityMelbourneVictoriaAustralia,SAEFVICMurdoch Children's Research InstituteMelbourneVictoriaAustralia,Department of Epidemiology and Preventative MedicineMonash UniversityMelbourneVictoriaAustralia
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13
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Thompson MG, Pierse N, Sue Huang Q, Prasad N, Duque J, Claire Newbern E, Baker MG, Turner N, McArthur C. Influenza vaccine effectiveness in preventing influenza-associated intensive care admissions and attenuating severe disease among adults in New Zealand 2012–2015. Vaccine 2018; 36:5916-5925. [DOI: 10.1016/j.vaccine.2018.07.028] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/08/2018] [Accepted: 07/15/2018] [Indexed: 12/26/2022]
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14
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Interactive effects of age and respiratory virus on severe lower respiratory infection. Epidemiol Infect 2018; 146:1861-1869. [PMID: 30047350 DOI: 10.1017/s0950268818002017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We investigated risk factors for severe acute lower respiratory infections (ALRI) among hospitalised children 8 months were at greater risk from influenza-associated ICU admissions and long hospital stay. Children with ADV had increased LOS across all ages. In the first 2 years of life, the effects of different viruses on ALRI severity varies with age. Our findings help to identify specific ages that would most benefit from virus-specific interventions such as vaccines and antivirals.
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15
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Wei S, Wang C, Zhu P, Zhou G, Fu W, Wu X. A high-throughput multiplex tandem PCR assay for the screening of genetically modified maize. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2017.08.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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16
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Laamiri N, Aouini R, Marnissi B, Ghram A, Hmila I. A multiplex real-time RT-PCR for simultaneous detection of four most common avian respiratory viruses. Virology 2017; 515:29-37. [PMID: 29223788 DOI: 10.1016/j.virol.2017.11.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/26/2017] [Accepted: 11/27/2017] [Indexed: 12/30/2022]
Abstract
A one-step multiplex real-time reverse transcription-PCR (rRT-PCR) assay was developed for simultaneous detection and quantification of four avian respiratory viruses: avian influenza virus (AIV), infectious bronchitis virus (IBV), Newcastle disease virus (NDV) and infectious laryngotracheitis virus (ILTV). In comparison with the singleplex rRT-PCR, the specificity, the sensitivity and the reproducibility of the new assay were evaluated and validated using 70 clinical samples. The optimal cutoff point, the corresponding limit of quantification (LoQ) and the limit of detection (LoD) were statistical established based on receiver operating characteristic (ROC) curve analysis. The results showed that the multiplex assay presents higher sensitivity and specificity. Correlation coefficients (R2) and amplification efficiencies (E) of all singleplex and multiplex rRT-PCR reactions are within the acceptable range. The 95% LoDs of multiplex assay were in the range [3-19] copies genomic/ µl, and its corresponding cutoff cycles were in the range [34.16-36.59]. No competitive inhibition for the detection of the four targets and no specific amplification or cross reactivity with other tested viruses was observed. Excellent results were attained in the inter-assay and intra-assay reproducibility evaluation. All identified samples by the multiplex rRT-PCR assay proved to be 100% concordant with the results of the singleplex assays. The results achieved showed that the multiplex assay is very suitable as a routine laboratory test for rapid and specific detection and quantification of co-infections in field samples.
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Affiliation(s)
- Nacira Laamiri
- University Tunis El Manar, Institut Pasteur de Tunis, Laboratory of Epidemiology and Veterinary Microbiology, 13 Place Pasteur, 1002 Tunis-Belvedere, Tunisia.; University of Carthage, Faculty of Sciences Bizerte, 7021 Zarzouna Bizerte, Tunisia.
| | - Rim Aouini
- University Tunis El Manar, Institut Pasteur de Tunis, Laboratory of Epidemiology and Veterinary Microbiology, 13 Place Pasteur, 1002 Tunis-Belvedere, Tunisia.; University of Carthage, Faculty of Sciences Bizerte, 7021 Zarzouna Bizerte, Tunisia
| | - Boutheina Marnissi
- University Tunis El Manar, Institut Pasteur de Tunis, Laboratory of Epidemiology and Veterinary Microbiology, 13 Place Pasteur, 1002 Tunis-Belvedere, Tunisia
| | - Abdeljelil Ghram
- University Tunis El Manar, Institut Pasteur de Tunis, Laboratory of Epidemiology and Veterinary Microbiology, 13 Place Pasteur, 1002 Tunis-Belvedere, Tunisia
| | - Issam Hmila
- University Tunis El Manar, Institut Pasteur de Tunis, Laboratory of Epidemiology and Veterinary Microbiology, 13 Place Pasteur, 1002 Tunis-Belvedere, Tunisia
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17
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Yan Y, Luo JY, Chen Y, Wang HH, Zhu GY, He PY, Guo JL, Lei YL, Chen ZW. A multiplex liquid-chip assay based on Luminex xMAP technology for simultaneous detection of six common respiratory viruses. Oncotarget 2017; 8:96913-96923. [PMID: 29228581 PMCID: PMC5722533 DOI: 10.18632/oncotarget.18533] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 06/02/2017] [Indexed: 12/27/2022] Open
Abstract
We utilized one-step multiplex reverse transcription-PCR (RT-PCR) and Luminex xMAP technology to develop a respiratory multiplex liquid-chip assay (rMLA) for simultaneous detection of 6 common respiratory viruses, including influenza virus type A (FluA) and type B (FluB), para-influenza virus type 3 (PIV-3), respiratory syncytial virus (RSV), human metapneumovirus (MPV) and a threatening virus to China, Middle East Respiratory Syndrome coronavirus (MERS-CoV). Performance of rMLA was evaluated by comparing with real-time RT-PCR. Detection data from clinical specimens showed that the rMLA had diagnostic sensitivities of 97.10% for FluA, 94.59% for FluB, 98.68% for PIV-3, 94.87% for RSV and 95.92% for MPV (No Data for MERS-CoV due to the lack of positive specimens). Data of analytical sensitivities showed that the detection limits of the rMLA assay were 5–25 viral RNA copies per μl for FluA, FluB, PIV-3 and MERS-CoV, approximate to the real-time RT-PCR assay; while the values were 8 and 22copies/μl for MPV and RSV, lower than the real-time RT-PCR(78 and 114 copies/μl respectively). The results indicated that the rMLA is a sensitive, specific detection tool and comparable to real-time RT-PCR, especially suitable for high-throughput detection of respiratory specimens.
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Affiliation(s)
- Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Jian-Yong Luo
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Yin Chen
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Heng-Hui Wang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Guo-Ying Zhu
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Pei-Yan He
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Jin-Lei Guo
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
| | - Yong-Liang Lei
- Lishui Municipal Center for Disease Control and Prevention, Lishui 323000, China
| | - Zhong-Wen Chen
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Municipal Center for Disease Control and Prevention, Jiaxing 314050, China
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18
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Trenholme AA, Best EJ, Vogel AM, Stewart JM, Miller CJ, Lennon DR. Respiratory virus detection during hospitalisation for lower respiratory tract infection in children under 2 years in South Auckland, New Zealand. J Paediatr Child Health 2017; 53:551-555. [PMID: 28430397 DOI: 10.1111/jpc.13529] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 11/17/2016] [Accepted: 12/03/2016] [Indexed: 11/29/2022]
Abstract
AIM To describe respiratory virus detection in children under 2 years of age in a population admitted with lower respiratory infection and to assess correlation with measures of severity. METHODS Nasopharyngeal aspirates from infants admitted with lower respiratory tract infection (n = 1645) over a 3-year time period were tested by polymerase chain reaction. We collected epidemiological and clinical data on all children. We assessed the correlation of presence of virus with length of hospital stay, intensive care admission and consolidation on chest X-ray. RESULTS Of the children admitted 34% were Maori, 43% Pacific and 75% lived in areas in the bottom quintile for socio-economic deprivation. A virus was found in 94% of those tested including 30% with multiple viruses. Picornavirus was present in 59% including 34% as the sole virus. Respiratory syncytial virus was found in 39%. Virus co-detection was not associated with length of stay, chest X-ray changes or intensive care unit admission. CONCLUSION In this disadvantaged predominately Maori and Pacific population, picornavirus is commonly found as a sole virus, respiratory syncytial virus is frequent but immunisation preventable influenza is infrequent. We did not find that co-detection of viruses was linked to severity.
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Affiliation(s)
- Adrian A Trenholme
- Kidz First, Counties Manukau District Health Board, Auckland, New Zealand
| | - Emma J Best
- Department of Paediatrics, University of Auckland, Auckland, New Zealand.,Paediatric Infectious Diseases Department, Starship Children's Hospital, Auckland District Health Board, Auckland, New Zealand
| | - Alison M Vogel
- Kidz First, Counties Manukau District Health Board, Auckland, New Zealand
| | - Joanna M Stewart
- Faculty of Medicine and Health Science, University of Auckland, Auckland, New Zealand
| | - Charissa J Miller
- Kidz First, Counties Manukau District Health Board, Auckland, New Zealand
| | - Diana R Lennon
- Kidz First, Counties Manukau District Health Board, Auckland, New Zealand.,Department of Paediatrics, University of Auckland, Auckland, New Zealand.,Paediatric Infectious Diseases Department, Starship Children's Hospital, Auckland District Health Board, Auckland, New Zealand
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19
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Accurate Detection of Avian Respiratory Viruses by Use of Multiplex PCR-Based Luminex Suspension Microarray Assay. J Clin Microbiol 2016; 54:2716-2725. [PMID: 27558184 DOI: 10.1128/jcm.00610-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 08/18/2016] [Indexed: 02/07/2023] Open
Abstract
A novel oligonucleotide suspension microarray (Luminex microsphere system) was developed for the rapid detection of avian respiratory viruses of major clinical importance. This test was optimized and validated with 70 clinical samples. The developed tool was accurate for high-throughput detection and differentiation of the most important avian respiratory viruses: avian influenza virus (AIV), Newcastle disease virus (NDV), infection bronchitis virus (IBV), and infectious laryngotracheitis virus (ILTV) in single- and mixed-virus infections. A multiplex reverse transcriptase PCR (RT-PCR), followed by a monoplex or a multiplex Luminex assays, were realized using a Luminex 200 analyzer instrument. The sensitivity, specificity, and reproducibility of the multiplex DNA suspension microarray system were evaluated. The results showed no significant differences in the median fluorescence intensity (MFI) value in monoplex and multiplex Luminex assays. The sensitivity and specificity proved to be completely concordant with monoplex real-time RT-PCR. We demonstrated that the multiplex DNA suspension microarray system is an accurate, high-throughput, and relatively simple method for the rapid detection of the main respiratory viruses of poultry.
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20
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Bissielo A, Pierse N, Huang QS, Thompson MG, Kelly H, Mishin VP, Turner N. Effectiveness of seasonal influenza vaccine in preventing influenza primary care visits and hospitalisation in Auckland, New Zealand in 2015: interim estimates. Euro Surveill 2016; 21:30101. [DOI: 10.2807/1560-7917.es.2016.21.1.30101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 12/22/2015] [Indexed: 11/20/2022] Open
Abstract
Preliminary results for influenza vaccine effectiveness (VE) against acute respiratory illness with circulating laboratory-confirmed influenza viruses in New Zealand from 27 April to 26 September 2015, using a case test-negative design were 36% (95% confidence interval (CI): 11–54) for general practice encounters and 50% (95% CI: 20–68) for hospitalisations. VE against hospitalised influenza A(H3N2) illnesses was moderate at 53% (95% CI: 6–76) but improved compared with previous seasons.
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Affiliation(s)
- A Bissielo
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - N Pierse
- University of Otago, Wellington, New Zealand
| | - QS Huang
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - MG Thompson
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - H Kelly
- Victorian Infectious Diseases Reference Laboratory, Melbourne, Australia
| | - VP Mishin
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - N Turner
- University of Auckland, Auckland, New Zealand
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21
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Pierse N, Kelly H, Thompson MG, Bissielo A, Radke S, Huang QS, Baker MG, Turner N. Influenza vaccine effectiveness for hospital and community patients using control groups with and without non-influenza respiratory viruses detected, Auckland, New Zealand 2014. Vaccine 2015; 34:503-509. [PMID: 26685091 DOI: 10.1016/j.vaccine.2015.11.073] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/26/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND We aimed to estimate the protection afforded by inactivated influenza vaccine, in both community and hospital settings, in a well characterised urban population in Auckland during 2014. METHODS We used two different comparison groups, all patients who tested negative for influenza and only those patients who tested negative for influenza and had a non-influenza respiratory virus detected, to calculate the vaccine effectiveness in a test negative study design. Estimates were made separately for general practice outpatient consultations and hospitalised patients, stratified by age group and by influenza type and subtype. Vaccine status was confirmed by electronic record for general practice patients and all respiratory viruses were detected by real time polymerase chain reaction. RESULTS 1039 hospitalised and 1154 general practice outpatient consultations met all the study inclusion criteria and had a respiratory sample tested for influenza and other respiratory viruses. Compared to general practice patients, hospitalised patients were more likely to be very young or very old, to be Māori or Pacific Islander, to have a low income and to suffer from chronic disease. Vaccine effectiveness (VE) adjusted for age and other participant characteristics using all influenza negative controls was 42% (95% CI: 16 to 60%) for hospitalised and 56% (95% CI: 35 to 70%) for general practice patients. The vaccine appeared to be most effective against the influenza A(H1N1)pdm09 strain with an adjusted VE of 62% (95% CI:38 to 77%) for hospitalised and 59% (95% CI:36 to 74%) for general practice patients, using influenza virus negative controls. Similar results found when patients testing positive for a non-influenza respiratory virus were used as the control group. CONCLUSION This study contributes to validation of the test negative design and confirms that inactivated influenza vaccines continue to provide modest but significant protection against laboratory-confirmed influenza.
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Affiliation(s)
- Nevil Pierse
- The University of Otago, Wellington, PO Box 7343, Wellington South 6242, New Zealand.
| | - Heath Kelly
- The Australian National University, Canberra 0200, ACT Australia; Victorian Infectious Diseases Reference Laboratory, Melbourne, VIC, Australia.
| | - Mark G Thompson
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Ange Bissielo
- Institute of Environmental Science and Research, Upper Hutt Wellington, New Zealand.
| | - Sarah Radke
- The University of Auckland, Private Bag 92019, Victoria St West, Auckland, New Zealand.
| | - Q Sue Huang
- Institute of Environmental Science and Research, Upper Hutt Wellington, New Zealand.
| | - Michael G Baker
- The University of Otago, Wellington, PO Box 7343, Wellington South 6242, New Zealand.
| | - Nikki Turner
- The University of Auckland, Private Bag 92019, Victoria St West, Auckland, New Zealand.
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22
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Abstract
The increasing availability of nucleic acid amplification tests since the 1980s has revolutionised our understanding of the pathogenesis, epidemiology, clinical and laboratory aspects of known and novel viral respiratory pathogens. High-throughput, multiplex polymerase chain reaction is the most commonly used qualitative detection method, but utilisation of newer techniques such as next-generation sequencing will become more common following significant cost reductions. Rapid and readily accessible isothermal amplification platforms have also allowed molecular diagnostics to be used in a ‘point-of-care’ format. This review focuses on the current applications and limitations of molecular diagnosis for respiratory viruses.
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23
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Turner N, Pierse N, Huang QS, Radke S, Bissielo A, Thompson MG, Kelly H, on behalf of the SHIVERS investigation team C. Interim estimates of the effectiveness of seasonal trivalent inactivated influenza vaccine in preventing influenza hospitalisations and primary care visits in Auckland, New Zealand, in 2014. Euro Surveill 2014. [DOI: 10.2807/1560-7917.es2014.19.42.20934] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present preliminary results of influenza vaccine effectiveness (VE) in New Zealand using a case test-negative design for 28 April to 31 August 2014. VE adjusted for age and time of admission among all ages against severe acute respiratory illness hospital presentation due to laboratory-confirmed influenza was 54% (95% CI: 19 to 74) and specifically against A(H1N1)pdm09 was 65% (95% CI:33 to 81). For influenza-confirmed primary care visits, VE was 67% (95% CI: 48 to 79) overall and 73% (95% CI: 50 to 85) against A(H1N1)pdm09.
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Affiliation(s)
- N Turner
- The University of Auckland, Auckland, New Zealand
| | - N Pierse
- University of Otago, Wellington, New Zealand
| | - Q S Huang
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - S Radke
- The University of Auckland, Auckland, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - A Bissielo
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - M G Thompson
- Influenza Division, United States Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - H Kelly
- Victorian Infectious Diseases Reference Laboratory, Melbourne, Australia
- Australian National University, Canberra, Australia
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24
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Semiquantitative multiplexed tandem PCR for detection and differentiation of four Theileria orientalis genotypes in cattle. J Clin Microbiol 2014; 53:79-87. [PMID: 25339402 DOI: 10.1128/jcm.02536-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oriental theileriosis is an emerging, tick-borne disease of bovines in the Asia-Pacific region and is caused by one or more genotypes of the Theileria orientalis complex. This study aimed to establish and validate a multiplexed tandem PCR (MT-PCR) assay using three distinct markers (major piroplasm surface protein, 23-kDa piroplasm membrane protein, and the first internal transcribed spacer of nuclear DNA), for the simultaneous detection and semiquantification of four genotypes (Buffeli, Chitose, Ikeda, and type 5) of the T. orientalis complex. Analytical specificity, analytical sensitivity, and repeatability of the established MT-PCR assay were assessed in a series of experiments. Subsequently, the assay was evaluated using 200 genomic DNA samples collected from cattle from farms on which oriental theileriosis outbreaks had occurred, and 110 samples from a region where no outbreaks had been reported. The results showed the MT-PCR assay specifically and reproducibly detected the expected genotypes (i.e., genotypes Buffeli, Chitose, Ikeda, and type 5) of the T. orientalis complex, reliably differentiated them, and was able to detect as little as 1 fg of genomic DNA from each genotype. The diagnostic specificity and sensitivity of the MT-PCR were estimated at 94.0% and 98.8%, respectively. The MT-PCR assay established here is a practical and effective diagnostic tool for the four main genotypes of T. orientalis complex in Australia and should assist studies of the epidemiology and pathophysiology of oriental theileriosis in the Asia-Pacific region.
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25
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Turner N, Pierse N, Bissielo A, Huang QS, Radke S, Baker M, Widdowson MA, Kelly H. Effectiveness of seasonal trivalent inactivated influenza vaccine in preventing influenza hospitalisations and primary care visits in Auckland, New Zealand, in 2013. Euro Surveill 2014; 19:20884. [PMID: 25188614 PMCID: PMC4627593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
This study reports the first vaccine effectiveness (VE) estimates for the prevention of general practice visits and hospitalisations for laboratory-confirmed influenza from an urban population in Auckland, New Zealand, in the same influenza season (2013). A case test-negative design was used to estimate propensity-adjusted VE in both hospital and community settings. Patients with a severe acute respiratory infection (SARI) or influenza-like illness (ILI) were defined as requiring hospitalisation (SARI) or attending a general practice (ILI) with a history of fever or measured temperature ≥38 °C, cough and onset within the past 10 days. Those who tested positive for influenza virus were cases while those who tested negative were controls. Results were analysed to 7 days post symptom onset and adjusted for the propensity to be vaccinated and the timing during the influenza season. Influenza vaccination provided 52% (95% CI: 32 to 66) protection against laboratory-confirmed influenza hospitalisation and 56% (95% CI: 34 to 70) against presenting to general practice with influenza. VE estimates were similar for all types and subtypes. This study found moderate effectiveness of influenza vaccine against medically attended and hospitalised influenza in New Zealand, a temperate, southern hemisphere country during the 2013 winter season.
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Affiliation(s)
- Nikki Turner
- The University of Auckland, Private Bag 92019, Victoria St West, Auckland, New Zealand
| | - Nevil Pierse
- The University of Otago, Wellington, PO Box 7343 Wellington South 6242, New Zealand
| | - Ange Bissielo
- Institute of Environmental Science and Research, PO Box Box 40-158 Upper Hutt 5140 Wellington, New Zealand
| | - Q Sue Huang
- Institute of Environmental Science and Research, PO Box Box 40-158 Upper Hutt 5140 Wellington, New Zealand
| | - Sarah Radke
- The University of Auckland, Private Bag 92019, Victoria St West, Auckland, New Zealand
| | - Michael Baker
- The University of Otago, Wellington, PO Box 7343 Wellington South 6242, New Zealand
| | | | - Heath Kelly
- The Australian National University, Canberra, ACT 0200 Australia and the Victorian Infectious Diseases Reference Laboratory, 10 Wrecklyn St, North Menbourne VIC 3051 Melbourne, Australia
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26
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Turner N, Pierse N, Bissielo A, Huang QS, Radke S, Baker MG, Widdowson MA, Kelly H, on behalf of the SHIVERS investigation team C. Effectiveness of seasonal trivalent inactivated influenza vaccine in preventing influenza hospitalisations and primary care visits in Auckland, New Zealand, in 2013. Euro Surveill 2014. [DOI: 10.2807/1560-7917.es2014.19.34.20884] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Binary file ES_Abstracts_Final_ECDC.txt matches
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Affiliation(s)
- N Turner
- The University of Auckland, Auckland, New Zealand
| | - N Pierse
- University of Otago, Wellington, New Zealand
| | - A Bissielo
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Q S Huang
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - S Radke
- The University of Auckland, Auckland, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - M G Baker
- University of Otago, Wellington, New Zealand
| | - M A Widdowson
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - H Kelly
- Victorian Infectious Diseases Reference Laboratory, Melbourne, Australia
- Australian National University, Canberra, Australia
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Lynfield R, Davey R, Dwyer DE, Losso MH, Wentworth D, Cozzi-Lepri A, Herman-Lamin K, Cholewinska G, David D, Kuetter S, Ternesgen Z, Uyeki TM, Lane HC, Lundgren J, Neaton JD. Outcomes of influenza A(H1N1)pdm09 virus infection: results from two international cohort studies. PLoS One 2014; 9:e101785. [PMID: 25004134 PMCID: PMC4086938 DOI: 10.1371/journal.pone.0101785] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 06/11/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Data from prospectively planned cohort studies on risk of major clinical outcomes and prognostic factors for patients with influenza A(H1N1)pdm09 virus are limited. In 2009, in order to assess outcomes and evaluate risk factors for progression of illness, two cohort studies were initiated: FLU 002 in outpatients and FLU 003 in hospitalized patients. METHODS AND FINDINGS Between October 2009 and December 2012, adults with influenza-like illness (ILI) were enrolled; outpatients were followed for 14 days and inpatients for 60 days. Disease progression was defined as hospitalization and/or death for outpatients, and hospitalization for >28 days, transfer to intensive care unit (ICU) if enrolled from general ward, and/or death for inpatients. Infection was confirmed by RT-PCR. 590 FLU 002 and 392 FLU 003 patients with influenza A (H1N1)pdm09 were enrolled from 81 sites in 17 countries at 2 days (IQR 1-3) and 6 days (IQR 4-10) following ILI onset, respectively. Disease progression was experienced by 29 (1 death) outpatients (5.1%; 95% CI: 3.4-7.2%) and 80 inpatients [death (32), hospitalization >28 days (43) or ICU transfer (20)] (21.6%; 95% CI: 17.5-26.2%). Disease progression (death) for hospitalized patients was 53.1% (26.6%) and 12.8% (3.8%), respectively, for those enrolled in the ICU and general ward. In pooled analyses for both studies, predictors of disease progression were age, longer duration of symptoms at enrollment and immunosuppression. Patients hospitalized during the pandemic period had a poorer prognosis than in subsequent seasons. CONCLUSIONS Patients with influenza A(H1N1)pdm09, particularly when requiring hospital admission, are at high risk for disease progression, especially if they are older, immunodeficient, or admitted late in infection. These data reinforce the need for international trials of novel treatment strategies for influenza infection and serve as a reminder of the need to monitor the severity of seasonal and pandemic influenza epidemics globally. TRIAL REGISTRATION ClinicalTrials.gov Identifiers: FLU 002--NCT01056354, FLU 003--NCT01056185.
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Affiliation(s)
- Ruth Lynfield
- Infectious Disease Division, Minnesota Department of Health, St. Paul, Minnesota, United States of America
| | - Richard Davey
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dominic E. Dwyer
- Department of Virology, Centre for Infectious Diseases and Microbiology, Westmead Hospital and University of Sydney, Westmead, New South Wales, Australia
| | - Marcelo H. Losso
- HIV Unit, Department of Medicine, Hospital José María Ramos Mejía, Buenos Aires, Argentina
| | - Deborah Wentworth
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Alessandro Cozzi-Lepri
- Research Department of Infection and Population Health, University College London, London, England, United Kingdom
| | - Kathy Herman-Lamin
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | | | - Daniel David
- Hospital Rawson, Infectología, Cordoba, Argentina
| | | | | | - Timothy M. Uyeki
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - H. Clifford Lane
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jens Lundgren
- Department of Infectious Diseases, Copenhagen University Hospital/Rigshospitalet & University of Copenhagen, Copenhagen, Denmark
| | - James D. Neaton
- Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota, United States of America
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Implementing hospital-based surveillance for severe acute respiratory infections caused by influenza and other respiratory pathogens in New Zealand. Western Pac Surveill Response J 2014; 5:23-30. [PMID: 25077034 DOI: 10.5365/wpsar.2014.5.1.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Recent experience with pandemic influenza A(H1N1)pdm09 highlighted the importance of global surveillance for severe respiratory disease to support pandemic preparedness and seasonal influenza control. Improved surveillance in the southern hemisphere is needed to provide critical data on influenza epidemiology, disease burden, circulating strains and effectiveness of influenza prevention and control measures. Hospital-based surveillance for severe acute respiratory infection (SARI) cases was established in New Zealand on 30 April 2012. The aims were to measure incidence, prevalence, risk factors, clinical spectrum and outcomes for SARI and associated influenza and other respiratory pathogen cases as well as to understand influenza contribution to patients not meeting SARI case definition. METHODS/DESIGN All inpatients with suspected respiratory infections who were admitted overnight to the study hospitals were screened daily. If a patient met the World Health Organization's SARI case definition, a respiratory specimen was tested for influenza and other respiratory pathogens. A case report form captured demographics, history of presenting illness, co-morbidities, disease course and outcome and risk factors. These data were supplemented from electronic clinical records and other linked data sources. DISCUSSION Hospital-based SARI surveillance has been implemented and is fully functioning in New Zealand. Active, prospective, continuous, hospital-based SARI surveillance is useful in supporting pandemic preparedness for emerging influenza A(H7N9) virus infections and seasonal influenza prevention and control.
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Turner N, Pierse N, Bissielo A, Huang QS, Baker MG, Widdowson MA, Kelly H. The effectiveness of seasonal trivalent inactivated influenza vaccine in preventing laboratory confirmed influenza hospitalisations in Auckland, New Zealand in 2012. Vaccine 2014; 32:3687-93. [PMID: 24768730 DOI: 10.1016/j.vaccine.2014.04.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 03/24/2014] [Accepted: 04/02/2014] [Indexed: 10/25/2022]
Abstract
BACKGROUND Few studies report the effectiveness of trivalent inactivated influenza vaccine (TIV) in preventing hospitalisation for influenza-confirmed respiratory infections. Using a prospective surveillance platform, this study reports the first such estimate from a well-defined ethnically diverse population in New Zealand (NZ). METHODS A case test-negative design was used to estimate propensity adjusted vaccine effectiveness. Patients with a severe acute respiratory infection (SARI), defined as a patient of any age requiring hospitalisation with a history of a fever or a measured temperature ≥38°C and cough and onset within the past 7 days, admitted to public hospitals in South and Central Auckland were eligible for inclusion in the study. Cases were SARI patients who tested positive for influenza, while non-cases (controls) were SARI patients who tested negative. Results were adjusted for the propensity to be vaccinated and the timing of the influenza season. RESULTS The propensity and season adjusted vaccine effectiveness (VE) was estimated as 39% (95% CI 16;56). The VE point estimate against influenza A (H1N1) was lower than for influenza B or influenza A (H3N2) but confidence intervals were wide and overlapping. Estimated VE was 59% (95% CI 26;77) in patients aged 45-64 years but only 8% (-78;53) in those aged 65 years and above. CONCLUSION Prospective surveillance for SARI has been successfully established in NZ. This study for the first year, the 2012 influenza season, has shown low to moderate protection by TIV against influenza positive hospitalisation.
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Affiliation(s)
- Nikki Turner
- The University of Auckland, Private Bag 92019, Victoria St West, Auckland, New Zealand.
| | - Nevil Pierse
- The University of Otago, PO Box 7343 Wellington South 6242, Wellington, New Zealand.
| | - Ange Bissielo
- Institute of Environmental Science and Research, PO Box 40-158 Upper Hutt 5140, Wellington, New Zealand.
| | - Q Sue Huang
- Institute of Environmental Science and Research, PO Box 40-158 Upper Hutt 5140, Wellington, New Zealand.
| | - Michael G Baker
- The University of Otago, PO Box 7343 Wellington South 6242, Wellington, New Zealand.
| | | | - Heath Kelly
- The Australian National University, Canberra 0200, ACT, Australia; Victorian Infectious Diseases Reference Laboratory, 10 Wrecklyn St., North Melbourne, 3051 Melbourne, VIC, Australia.
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Comparison of a multiplex real-time PCR assay with a multiplex Luminex assay for influenza virus detection. J Clin Microbiol 2013; 51:1124-9. [PMID: 23345299 DOI: 10.1128/jcm.03113-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We describe the development of a multiplex reverse transcription-PCR (RT-PCR) with Luminex microarray hybridization for detection of influenza virus subtypes (FLULUM). Performance of FLULUM was evaluated by comparing it to our real-time RT-PCR influenza virus assay on samples collected during two influenza seasons. Both assays targeted the matrix genes of influenza virus A (FluA M) and influenza virus B (FluB M) and the hemagglutinin genes of seasonal H3N2 (H3) and H1N1 (H1) and 2009 pandemic H1N1 (2009 H1). We evaluated FLULUM on both the Luminex LX200 and the Luminex MagPix instruments. Compared to real-time PCR, FLULUM tested on 259 specimens submitted in the 2010-2011 season showed sensitivities of 97.3% for FluA M, 90.5% for 2009 H1, 96.9% for H3, and 88.9% for FluB M. No specimens were positive for seasonal H1. FLULUM tested on 806 specimens submitted in the 2011-2012 season showed a sensitivity of 100% for FluA M, 89.9% for 2009 H1, 96.4% for H3, and 95.6% for FluB M. No cross-reactivity was observed for other respiratory viruses. Analytical sensitivity was assessed by testing dilutions of specimens with high viral loads. The limits of detection of FLULUM were comparable to those of the real-time PCR assay for FluA M, FluB M, and H3. The limits of detection for seasonal H1 and 2009 H1 were 10-fold higher for the FLULUM assay compared to real-time PCR. The FLULUM is an economic assay with high clinical sensitivity and specificity. It is particularly suited to high-volume detection of influenza viruses.
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Establishment of a robotic, high-throughput platform for the specific diagnosis of gastrointestinal nematode infections in sheep. Int J Parasitol 2012; 42:1151-8. [PMID: 23131681 DOI: 10.1016/j.ijpara.2012.10.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 10/02/2012] [Accepted: 10/04/2012] [Indexed: 11/24/2022]
Abstract
The accurate diagnosis of strongylid nematode infections is central to investigating their epidemiology and for parasite control. To overcome major limitations in sensitivity or specificity of traditional methods, including faecal egg count (FEC) and/or larval culture (LC), we evaluated and established a semi-automated, high throughput multiplexed-tandem PCR (MT-PCR) platform for the diagnosis of gastrointestinal strongylid nematode infections in sheep, and established its diagnostic sensitivity (100%) and specificity (87.5%) based on the testing of 100 faecal DNA samples from helminth-free sheep and 30 samples from sheep with infections confirmed by necropsy. Subsequently, the platform was employed to test 219 faecal samples from sheep with naturally acquired infections from various geographical localities within Australia and the results compared with those from conventional LC using 139 of the 219 samples. The results obtained using both MT-PCR and LC correlated significantly for most nematodes examined, but revealed that Oesophagostomum venulosum and Chabertia ovina (parasites of the large intestine) were significantly under-represented in the LC results. The results showed that Trichostrongylus spp. (87%), Teladorsagia circumcincta (80%) and Haemonchus contortus (67%) had the highest prevalences, followed by O. venulosum (51%) and C. ovina (12%). The molecular-diagnostic platform established can be used for species- or genus-specific diagnosis of patent nematode infections within 24h (compared with 7-10 days for LC), and is a sensitive and cost effective tool for routine application in research and service laboratories.
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Blyth CC, Webb SAR, Kok J, Dwyer DE, van Hal SJ, Foo H, Ginn AN, Kesson AM, Seppelt I, Iredell JR. The impact of bacterial and viral co-infection in severe influenza. Influenza Other Respir Viruses 2012; 7:168-76. [PMID: 22487223 PMCID: PMC5006004 DOI: 10.1111/j.1750-2659.2012.00360.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Many questions remain concerning the burden, risk factors and impact of bacterial and viral co-infection in patients with pandemic influenza admitted to the intensive care unit (ICU). OBJECTIVES To examine the burden, risk factors and impact of bacterial and viral co-infection in Australian patients with severe influenza. PATIENTS/METHODS A cohort study conducted in 14 ICUs was performed. Patients with proven influenza A during the 2009 influenza season were eligible for inclusion. Demographics, risk factors, clinical data, microbiological data, complications and outcomes were collected. Polymerase chain reaction for additional bacterial and viral respiratory pathogens was performed on stored respiratory samples. RESULTS Co-infection was identified in 23·3-26·9% of patients with severe influenza A infection: viral co-infection, 3·2-3·4% and bacterial co-infection, 20·5-24·7%. Staphylococcus aureus was the most frequent bacterial co-infection followed by Streptococcus pneumoniae and Haemophilus influenzae. Patients with co-infection were younger [mean difference in age = 8·46 years (95% CI: 0·18-16·74 years)], less likely to have significant co-morbidities (32·0% versus 66·2%, P = 0·004) and less frequently obese [mean difference in body mass index = 6·86 (95% CI: 1·77-11·96)] compared to those without co-infection. CONCLUSIONS Bacterial or viral co-infection complicated one in four patients admitted to ICU with severe influenza A infection. Despite the co-infected patients being younger and with fewer co-morbidities, no significant difference in outcomes was observed. It is likely that co-infection contributed to a need for ICU admission in those without other risk factors for severe influenza disease. Empiric antibiotics with staphylococcal activity should be strongly considered in all patients with severe influenza A infection.
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Affiliation(s)
- Christopher C Blyth
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research ICPMR, Westmead Hospital, Sydney, NSW, Australia.
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Evaluation of the Cepheid Xpert Flu Assay for rapid identification and differentiation of influenza A, influenza A 2009 H1N1, and influenza B viruses. J Clin Microbiol 2012; 50:1704-10. [PMID: 22378908 DOI: 10.1128/jcm.06520-11] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Xpert Flu Assay cartridge is a next-generation nucleic acid amplification system that provides multiplexed PCR detection of the influenza A, influenza A 2009 H1N1, and influenza B viruses in approximately 70 min with minimal hands-on time. Six laboratories participated in a clinical trial comparing the results of the new Cepheid Xpert Flu Assay to those of culture or real-time PCR with archived and prospectively collected nasal aspirate-wash (NA-W) specimens and nasopharyngeal (NP) swabs from children and adults. Discrepant results were resolved by DNA sequence analysis. After discrepant-result analysis, the sensitivities of the Xpert Flu Assay for prospective NA-W specimens containing the influenza A, influenza A 2009 H1N1, and influenza B viruses compared to those of culture were 90.0%, 100%, and 100%, respectively, while the sensitivities of the assay for prospective NP swabs compared to those of culture were 100%, 100%, and 100%, respectively. The sensitivities of the Xpert Flu Assay for archived NA-W specimens compared to those of Gen-Probe ProFlu+ PCR for the influenza A, influenza A 2009 H1N1, and influenza B viruses were 99.4%, 98.4%, and 100%, respectively, while the sensitivities of the Xpert Flu Assay for archived NP swabs compared to those of ProFlu+ were 98.1%, 100%, and 93.8%, respectively. The sensitivities of the Xpert Flu Assay with archived NP specimens compared to those of culture for the three targets were 97.5%, 100%, and 93.8%, respectively. We conclude that the Cepheid Xpert Flu Assay is an accurate and rapid method that is suitable for on-demand testing for influenza viral infection.
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Ryan NM, Vertigan AE, Ferguson J, Wark P, Gibson PG. Clinical and physiological features of postinfectious chronic cough associated with H1N1 infection. Respir Med 2011; 106:138-44. [PMID: 22056406 DOI: 10.1016/j.rmed.2011.10.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 09/08/2011] [Accepted: 10/14/2011] [Indexed: 11/19/2022]
Abstract
BACKGROUND Post infectious chronic cough is a disabling illness. In 2009 an influenza pandemic occurred due to a novel strain of H1N1 influenza. Prolonged symptoms such as chronic cough remaining after the infection has cleared have not been examined. This study sought to investigate the prevalence, characteristics and mechanism of chronic cough following laboratory-confirmed H1N1 2009 influenza. METHODS Out of 836 eligible patients who had been tested by PCR assay for H1N1, 136 responders participated. Nineteen underwent detailed clinical investigation of cough, and airway function using symptom questionnaires, hypertonic saline challenge, and cough monitoring. RESULTS Post H1N1 chronic cough was reported by 43%, and chronic cough after non-H1N1 infection was present in 36% of participants. In the participants who progressed to testing objectively measured cough frequency was 3 times greater; there was a 9-fold increase in cough reflex sensitivity and greater quality of life impairment in the participants with postinfectious chronic cough following H1N1 infection than for the participants with no cough following H1N1 infection and for the healthy controls. CONCLUSIONS This study reports the first evaluation of chronic cough following H1N1 infection. Patients that develop chronic cough after H1N1 infection display increased cough reflex sensitivity up to 220 days after confirmed infection. There is an absence of associated risk factors and less impairment in quality of life compared to those patients normally seen in a specialist cough clinic. The associated mechanism was found to be cough reflex hypersensitivity. TRIAL REGISTRATION This clinical trial has been registered with the Australian New Zealand Clinical Trials Register, ACTRN12610000540011.
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Affiliation(s)
- Nicole M Ryan
- Priority Centre for Asthma and Respiratory Diseases, School of Medicine and Public Health, The University of Newcastle, Newcastle, 2308 NSW, Australia.
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Khawaldeh A, Morales S, Dillon B, Alavidze Z, Ginn AN, Thomas L, Chapman SJ, Dublanchet A, Smithyman A, Iredell JR. Bacteriophage therapy for refractory Pseudomonas aeruginosa urinary tract infection. J Med Microbiol 2011; 60:1697-1700. [PMID: 21737541 DOI: 10.1099/jmm.0.029744-0] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe the success of adjunctive bacteriophage therapy for refractory Pseudomonas aeruginosa urinary tract infection in the context of bilateral ureteric stents and bladder ulceration, after repeated failure of antibiotics alone. No bacteriophage-resistant bacteria arose, and the kinetics of bacteriophage and bacteria in urine suggest self-sustaining and self-limiting infection.
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Affiliation(s)
- A Khawaldeh
- Centre for Infectious Diseases and Microbiology, Sydney West Area Health Service, NSW 2145, Australia
| | - S Morales
- Special Phage Services Pty, Brookvale, Sydney, NSW, Australia
| | - B Dillon
- Centre for Infectious Diseases and Microbiology, Sydney West Area Health Service, NSW 2145, Australia
| | - Z Alavidze
- Eliava Institute of Bacteriophage, Microbiology and Virology, Georgian Academy of Sciences, Tbilisi, Democratic Republic of Georgia
| | - A N Ginn
- Centre for Infectious Diseases and Microbiology, Sydney West Area Health Service, NSW 2145, Australia
| | - L Thomas
- Centre for Infectious Diseases and Microbiology, Sydney West Area Health Service, NSW 2145, Australia
| | - S J Chapman
- Centre for Infectious Diseases and Microbiology, Sydney West Area Health Service, NSW 2145, Australia
| | - A Dublanchet
- GEEPhage, CHI Villeneuve St Georges, Villeneuve St Georges, France
| | - A Smithyman
- Special Phage Services Pty, Brookvale, Sydney, NSW, Australia
| | - J R Iredell
- Sydney Institute for Emerging Infection and Biotechnology, University of Sydney at Westmead Hospital, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology, Sydney West Area Health Service, NSW 2145, Australia
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Jardine A, Conaty SJ, Cretikos MA, Su WY, Gosbell IB, van Hal SJ. Influenza A testing and detection in patients admitted through emergency departments in Sydney during winter 2009: implications for rational testing. Med J Aust 2010; 193:455-9. [PMID: 20955122 DOI: 10.5694/j.1326-5377.2010.tb03999.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 08/25/2010] [Indexed: 11/17/2022]
Abstract
AIM To examine factors associated with testing and detection of influenza A in patients admitted to hospital for acute care during the winter 2009 pandemic influenza outbreak. DESIGN, SETTING AND PARTICIPANTS Retrospective observational study of patients who were tested for influenza A after being admitted to hospital through emergency departments of the Sydney South West Area Health Service from 15 June to 30 August 2009. MAIN OUTCOME MEASURES The association of factors such as age, diagnosis at admission, hospital and week of admission with rates of testing and detection of influenza A. RESULTS 17,681 patients were admitted through nine emergency departments; 1344 (7.6%) were tested for influenza A, of whom 356 (26.5%) tested positive for pandemic influenza. Testing rates were highest in 0-4-year-old children, in the peak period of the outbreak, and in patients presenting with a febrile or respiratory illness. Positive influenza test results were common across a range of diagnoses, but occurred most frequently in children aged 10-14 years (64.3%) and in patients with a diagnosis at admission of influenza-like illness (59.1%). Using multivariate logistic regression, patients with a diagnosis at admission of fever or a respiratory illness at admission were most likely to be tested (odds ratios [ORs], 15 [95% CI, 11-21] and 17 [95% CI, 15-19], respectively). These diagnoses were stronger predictors of influenza testing than the peak testing week (Week 4; OR, 7.0 [95% CI, 3.8-13]) or any age group. However, diagnosis at admission and age were significant but weak predictors of a positive test result, and the strongest predictor of a positive test result was the peak epidemic week (Week 3; OR, 120 [95% CI, 27-490]). CONCLUSION The strongest predictor of a clinician's decision to test for influenza was the diagnosis at admission, but the strongest predictor of a positive test was the week of admission. A rational approach to influenza testing for patients who are admitted to hospital for acute care could include active tracking of influenza testing and detection rates, testing patients with a strong indication for antiviral treatment, and admitting only those who test negative to "clean" wards during the peak of an outbreak.
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Affiliation(s)
- Andrew Jardine
- Public Health Unit, Sydney South West Area Health Service, Sydney, NSW, Australia
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