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2.
Pediatr Blood Cancer ; 71(7): e31031, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38679843

ABSTRACT

Invasive fungal disease (IFD) occurs less frequently during treatment for solid compared to hematological malignancies in children, and risk groups are poorly defined. Retrospective national multicenter cohort data (2004-2013) were analyzed to document prevalence, clinical characteristics, and microbiology of IFD. Amongst 2067 children treated for solid malignancy, IFD prevalence was 1.9% overall and 1.4% for proven/probable IFD. Of all IFD episodes, 42.5% occurred in patients with neuroblastoma (prevalence 7.0%). Candida species comprised 54.8% of implicated pathogens in proven/probable IFD. In children with solid tumors, IFD is rare, and predominantly caused by yeasts.Routine prophylaxis may not be warranted.


Subject(s)
Invasive Fungal Infections , Neoplasms , Humans , Child , Male , Female , Neoplasms/microbiology , Neoplasms/epidemiology , Retrospective Studies , Child, Preschool , Australia/epidemiology , Infant , Adolescent , Invasive Fungal Infections/epidemiology , Invasive Fungal Infections/etiology , Invasive Fungal Infections/prevention & control , Prevalence , Infant, Newborn
3.
Intensive Care Med ; 50(4): 539-547, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38478027

ABSTRACT

PURPOSE: Early recognition and effective treatment of sepsis improves outcomes in critically ill patients. However, antibiotic exposures are frequently suboptimal in the intensive care unit (ICU) setting. We describe the feasibility of the Bayesian dosing software Individually Designed Optimum Dosing Strategies (ID-ODS™), to reduce time to effective antibiotic exposure in children and adults with sepsis in ICU. METHODS: A multi-centre prospective, non-randomised interventional trial in three adult ICUs and one paediatric ICU. In a pre-intervention Phase 1, we measured the time to target antibiotic exposure in participants. In Phase 2, antibiotic dosing recommendations were made using ID-ODS™, and time to target antibiotic concentrations were compared to patients in Phase 1 (a pre-post-design). RESULTS: 175 antibiotic courses (Phase 1 = 123, Phase 2 = 52) were analysed from 156 participants. Across all patients, there was no difference in the time to achieve target exposures (8.7 h vs 14.3 h in Phase 1 and Phase 2, respectively, p = 0.45). Sixty-one courses in 54 participants failed to achieve target exposures within 24 h of antibiotic commencement (n = 36 in Phase 1, n = 18 in Phase 2). In these participants, ID-ODS™ was associated with a reduction in time to target antibiotic exposure (96 vs 36.4 h in Phase 1 and Phase 2, respectively, p < 0.01). These patients were less likely to exhibit subtherapeutic antibiotic exposures at 96 h (hazard ratio (HR) 0.02, 95% confidence interval (CI) 0.01-0.05, p < 0.01). There was no difference observed in in-hospital mortality. CONCLUSIONS: Dosing software may reduce the time to achieve target antibiotic exposures. It should be evaluated further in trials to establish its impact on clinical outcomes.


Subject(s)
Anti-Bacterial Agents , Sepsis , Adult , Child , Humans , Anti-Bacterial Agents/therapeutic use , Bayes Theorem , Critical Illness/therapy , Intensive Care Units, Pediatric , Prospective Studies , Sepsis/drug therapy , Software
4.
Pediatrics ; 153(2)2024 Jan 01.
Article in English | MEDLINE | ID: mdl-38287882

ABSTRACT

CONTEXT: Central venous access device (CVAD) locks are routine interventions used to prevent and treat complications, such as infection, thrombosis, and catheter occlusion. OBJECTIVE: To compare and rank lock-solutions for prevention or treatment of complications in pediatrics. Design Systematic review and network meta-analysis. DATA SOURCES: Five databases and 2 clinical trial registries were searched. STUDY SELECTION: Published and unpublished randomized controlled trials that enrolled pediatric patients with a CVAD and compared the effectiveness of lock-solutions. DATA EXTRACTION: Data extraction was conducted by 2 reviewers. Odds ratio (OR) for prevention or treatment of CVAD-associated bloodstream infection (BSI), thrombosis, occlusion, CVAD-failure, and mortality were calculated, with point estimates ranking lock-solutions. RESULTS: Twenty-nine studies were included. Chelating agents and antibiotic locks given as prevention were associated with lower odds (OR: 0.11; 95% confidence interval [CI]: 0.02-0.67; moderate-quality; OR: 0.19; 95% CI: 0.05-0.79, high-quality, respectively) of CVAD-associated BSI compared with heparinized saline (reference). Preventative thrombolytic agents had lower odds (OR: 0.64, 95% CI: 0.44-0.93; low-quality) of CVAD occlusion, whereas ethanol had higher odds (OR: 2.84, 95% CI: 1.31-6.16; high-quality) compared with heparinized saline (reference). No lock solution had effects on thrombosis prevention or treatment, CVAD-failure, CVAD-associated BSI treatment failure, or mortality. LIMITATIONS: There was substantial uncertainty around the point estimates because of the limited number of studies for outcomes and study heterogeneity. More high-quality studies are needed to confirm the efficacy of lock solutions. CONCLUSIONS: Chelating agents and antibiotic locks may be effective for CVAD-associated BSI prevention in pediatrics. Thrombolytic agents can be an option for CVAD occlusion prevention, whereas ethanol may not be recommended.


Subject(s)
Catheter-Related Infections , Catheterization, Central Venous , Central Venous Catheters , Sepsis , Thrombosis , Humans , Child , Fibrinolytic Agents , Network Meta-Analysis , Anti-Bacterial Agents , Thrombosis/etiology , Thrombosis/prevention & control , Ethanol , Chelating Agents , Catheter-Related Infections/prevention & control , Central Venous Catheters/adverse effects , Catheterization, Central Venous/adverse effects
5.
Int J Nurs Stud ; 150: 104643, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38043485

ABSTRACT

BACKGROUND: Reducing avoidable stillbirth is a global priority. The stillbirth rate in England compares unfavourably to that of some other high-income countries. Poorly-managed episodes of altered fetal movement have been highlighted as a key contributor to avoidable stillbirth, and strategies introduced in England in 2016 to reduce perinatal mortality included recommendations for the management of reduced fetal movement. Despite a downward trend in stillbirth rates across the UK, the effects of policies promoting awareness of fetal movement remain uncertain. OBJECTIVE: To provide in-depth knowledge of how practice and clinical guidance relating to altered fetal movement are perceived, enacted and experienced by midwives and obstetricians, and explore the relationship between recommended fetal movement care and actual fetal movement care. DESIGN: A focused ethnographic approach comprising over 180 h of observation, 15 interviews, and document analysis was used to explore practice at two contrasting UK maternity units. SETTINGS: Antenatal services at two UK maternity units, one in the Midlands and one in the North of England. PARTICIPANTS: Thirty-six midwives, obstetricians and sonographers and 40 pregnant women participated in the study across 52 observed care episodes and relevant unit activity. Twelve midwives and three obstetricians additionally participated in formal semi-structured interviews. METHODS: Fieldnotes, interview transcripts, policy documents, maternity notes and clinical guidelines were analysed using a modified constant comparison method to identify important themes. RESULTS: fetal movement practice was mostly consistent and in line with guideline recommendations. Notwithstanding, most midwives and obstetricians had concerns about this area of care, including challenges in diagnosis, conflicting evidence about activity, heightened maternal anxiety, and high rates of monitoring and intervention in otherwise low-risk pregnancies. To address these issues, midwives spent considerable time reassuring women through information and regular monitoring, and coaching them to perceive fetal movement more accurately. CONCLUSIONS: Practice relating to altered fetal movement might be more uniform than in the past. However, a heightened focus on fetal movement is associated by some midwives and obstetricians with potential harms, including increased anxiety in pregnancy, and high rates of monitoring and intervention in pregnancies where there are no 'objective concerns'. Challenges in diagnosing a significant change in fetal movement with accuracy might mean that interventions and resources are not being directed towards those pregnancies most at risk. More research is needed to determine how healthcare professionals can engage in conversations about fetal movement and stillbirth to support safe outcomes and positive experiences in pregnancy and birth. REGISTRATION: Not registered. TWEETABLE ABSTRACT: Midwives and obstetricians take #reducedfetalmovement seriously but worry this 'unreliable' symptom increases anxiety, monitoring and intervention in many 'low risk' pregnancies.


Subject(s)
Midwifery , Female , Pregnancy , Humans , Stillbirth , Obstetricians , Fetal Movement , Prenatal Care/methods
6.
Vaccine ; 41(48): 7192-7200, 2023 11 22.
Article in English | MEDLINE | ID: mdl-37903679

ABSTRACT

Both vector and mRNA vaccines were an important part of the response to the COVID-19 pandemic and may be required in future outbreaks and pandemics. The aim of this study was to validate whether immunogenicity differs for adenoviral vectored (AdV) versus mRNA vaccines against SARS-CoV-2, and to investigate how anti-vector immunity and B cell dynamics modulate immunogenicity. We enrolled SARS-CoV-2 infection-naïve health care workers who had received two doses of either AdV AZD1222 (n = 184) or mRNA BNT162b2 vaccine (n = 274) between April and October 2021. Blood was collected at least once, 10-48 days after vaccine dose 2 for antibody and B cell analyses. Median ages were 42 and 39 years, for AdV and mRNA vaccinees, respectively. Surrogate virus neutralization test (sVNT) and spike binding antibody titres were a median of 4.2 and 2.2 times lower, respectively, for AdV compared to mRNA vaccinees (p < 0.001). Median percentages of memory B cells that recognized fluorescent-tagged spike and RBD were 2.9 and 8.3 times lower, respectively for AdV compared to mRNA vaccinees. Titres of IgG reactive with human adenovirus type 5 hexon protein rose a median of 2.2-fold after AdV vaccination but were not correlated with anti-spike antibody titres. Together the results show that mRNA induced substantially more sVNT antibody than AdV vaccine, which reflected greater B cell expansion and targeting of the RBD rather than an attenuating effect of anti-vector antibodies. ClinicalTrials.gov Identifier: NCT05110911.


Subject(s)
COVID-19 , Viral Vaccines , Humans , COVID-19 Vaccines , Pandemics/prevention & control , BNT162 Vaccine , ChAdOx1 nCoV-19 , COVID-19/prevention & control , SARS-CoV-2 , Antibodies , Antibodies, Viral
7.
Lancet Reg Health West Pac ; 40: 100888, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37701716

ABSTRACT

Background: New and emerging risks for invasive aspergillosis (IA) bring the need for contemporary analyses of the epidemiology and outcomes of IA, in order to improve clinical practice. Methods: The study was a retrospective, multicenter, cohort design of proven and probable IA in adults from 10 Australasian tertiary centres (January 2017-December 2020). Descriptive analyses were used to report patients' demographics, predisposing factors, mycological characteristics, diagnosis and management. Accelerated failure-time model was employed to determine factor(s) associated with 90-day all-cause mortality (ACM). Findings: Of 382 IA episodes, 221 (in 221 patients) fulfilled inclusion criteria - 53 proven and 168 probable IA. Median patient age was 61 years (IQR 51-69). Patients with haematologic malignancies (HM) comprised 49.8% of cases. Fifteen patients (6.8%) had no pre-specified immunosuppression and eleven patients (5.0%) had no documented comorbidity. Only 30% of patients had neutropenia. Of 170 isolates identified, 40 (23.5%) were identified as non-Aspergillus fumigatus species complex. Azole-resistance was present in 3/46 (6.5%) of A. fumigatus sensu stricto isolates. Ninety-day ACM was 30.3%. HM (HR 1.90; 95% CI 1.04-3.46, p = 0.036) and ICU admission (HR 4.89; 95% CI 2.93-8.17, p < 0.001) but not neutropenia (HR 1.45; 95% CI 0.88-2.39, p = 0.135) were associated with mortality. Chronic kidney disease was also a significant predictor of death in the HM subgroup (HR 3.94; 95% CI 1.15-13.44, p = 0.028). Interpretation: IA is identified in high number of patients with mild/no immunosuppression in our study. The relatively high proportion of non-A. fumigatus species complex isolates and 6.5% azole-resistance rate amongst A. fumigatus sensu stricto necessitates accurate species identification and susceptibility testing for optimal patient outcomes. Funding: This work is unfunded. All authors' financial disclosures are listed in detail at the end of the manuscript.

8.
Pediatr Infect Dis J ; 42(10): 908-913, 2023 10 01.
Article in English | MEDLINE | ID: mdl-37463351

ABSTRACT

BACKGROUND: In settings with universal conjugate pneumococcal vaccination, invasive pneumococcal disease (IPD) can be a marker of an underlying inborn error of immunity. The aim of this study was to determine the prevalence and characterize the types of immunodeficiencies in children presenting with IPD. METHODS: Multicenter prospective audit following the introduction of routinely recommended immunological screening in children presenting with IPD. The minimum immunological evaluation comprised a full blood examination and film, serum immunoglobulins (IgG, IgA and IgM), complement levels and function. Included participants were children in whom Streptococcus pneumoniae was isolated from a normally sterile site (cerebrospinal fluid, pleura, peritoneum and synovium). If isolated from blood, features of sepsis needed to be present. Children with predisposing factors for IPD (nephrotic syndrome, anatomical defect or malignancy) were excluded. RESULTS: Overall, there were 379 episodes of IPD of which 313 (83%) were eligible for inclusion and 143/313 (46%) had an immunologic evaluation. Of these, 17/143 (12%) were diagnosed with a clinically significant abnormality: hypogammaglobulinemia (n = 4), IgA deficiency (n = 3), common variable immunodeficiency (n = 2), asplenia (n = 2), specific antibody deficiency (n = 2), incontinentia pigmenti with immunologic dysfunction (n = 1), alternative complement deficiency (n = 1), complement factor H deficiency (n = 1) and congenital disorder of glycosylation (n = 1). The number needed to investigate to identify 1 child presenting with IPD with an immunologic abnormality was 7 for children under 2 years and 9 for those 2 years old and over. CONCLUSIONS: This study supports the routine immune evaluation of children presenting with IPD of any age, with consideration of referral to a pediatric immunologist.


Subject(s)
Immunologic Deficiency Syndromes , Pneumococcal Infections , Sepsis , Child , Humans , Infant , Child, Preschool , Prospective Studies , Pneumococcal Infections/prevention & control , Streptococcus pneumoniae , Immunologic Deficiency Syndromes/complications , Pneumococcal Vaccines , Incidence
9.
medRxiv ; 2023 Jun 05.
Article in English | MEDLINE | ID: mdl-37333329

ABSTRACT

Both vector and mRNA vaccines were an important part of the response to the COVID-19 pandemic and may be required in future outbreaks and pandemics. However, adenoviral vectored (AdV) vaccines may be less immunogenic than mRNA vaccines against SARS-CoV-2. We assessed anti-spike and anti-vector immunity among infection-naïve Health Care Workers (HCW) following two doses of AdV (AZD1222) versus mRNA (BNT162b2) vaccine. 183 AdV and 274 mRNA vaccinees enrolled between April and October 2021. Median ages were 42 and 39 years, respectively. Blood was collected at least once, 10-48 days after vaccine dose 2. Surrogate virus neutralization test (sVNT) and spike binding antibody titres were a median of 4.2 and 2.2 times lower, respectively, for AdV compared to mRNA vaccinees (p<0.001). Median percentages of memory B cells that recognized fluorescent-tagged spike and RBD were 2.9 and 8.3 times lower, respectively for AdV compared to mRNA vaccinees. Titres of IgG reactive with human Adenovirus type 5 hexon protein rose a median of 2.2-fold after AdV vaccination but were not correlated with anti-spike antibody titres. Together the results show that mRNA induced substantially more sVNT antibody than AdV vaccine due to greater B cell expansion and targeting of the RBD. Pre-existing AdV vector cross-reactive antibodies were boosted following AdV vaccination but had no detectable effect on immunogenicity.

11.
Philos Trans R Soc Lond B Biol Sci ; 378(1883): 20220297, 2023 08 14.
Article in English | MEDLINE | ID: mdl-37381844

ABSTRACT

At the headwaters of the Yenisei River in Tuva and northern Mongolia, nomadic pastoralists move between camps in a seasonal rotation that facilitates their animals' access to high-quality grasses and shelter. The use and informal ownership of these camps depending on season helps illustrate evolutionary and ecological principles underlying variation in property relations. Given relatively stable patterns of precipitation and returns to capital improvement, families generally benefit from reusing the same camps year after year. We show that locations with higher economic defensibility and capital investment-winter camps and camps located in mountain/river valleys-are claimed and inherited more frequently than summer camps and camps located in open steppe. Camps are inherited patrilineally and matrilineally at a ratio of 2 : 1. Despite its practical importance, camp inheritance is not associated with livestock wealth today, which is better predicted by education and wealth outside the pastoral economy. The relationship between the livestock wealth of parents and their adult children is significantly positive, but relatively low compared to other pastoralists. The degree of inequality in livestock wealth, however, is very close to that of other pastoralists. This is understandable considering the durability and defensibility of animal wealth and economies of scale common across pastoralists. This article is part of the theme issue 'Evolutionary ecology of inequality'.


Subject(s)
Transients and Migrants , Siberia , Seasons , Ownership , Interviews as Topic , Culture , Socioeconomic Factors
12.
Front Pediatr ; 11: 1180392, 2023.
Article in English | MEDLINE | ID: mdl-37325366

ABSTRACT

Cytomegalovirus (CMV) is a ubiquitous virus which causes a mild illness in healthy individuals. In immunocompromised individuals, such as children receiving haematopoietic stem cell transplantation, CMV can reactivate, causing serious disease and increasing the risk of death. CMV can be effectively treated with antiviral drugs, but antiviral resistance is an increasingly common complication. Available therapies are associated with adverse effects such as bone marrow suppression and renal impairment, making the choice of appropriate treatment challenging. New agents are emerging and require evaluation in children to establish their role. This review will discuss established and emerging diagnostic tools and treatment options for CMV, including antiviral resistant CMV, in children undergoing haematopoietic stem cell transplant.

13.
Am J Trop Med Hyg ; 108(6): 1215-1219, 2023 06 07.
Article in English | MEDLINE | ID: mdl-37160276

ABSTRACT

Melioidosis is an infectious disease caused by the bacterium Burkholderia pseudomallei. Although this environmental organism is endemic in certain regions of Australia, it is not considered endemic in Southern Queensland, where the last case was reported 21 years ago. We report a climate change-associated outbreak of melioidosis occurring during two La Niña events in a region previously considered nonendemic for B. pseudomallei. During a 15-month period, 14 cases of locally acquired melioidosis were identified. Twelve patients were adults (> 50 years), with diabetes mellitus the most common risk factor in 6 of 12 patients (50%). Eleven patients (79%) had direct exposure to floodwaters or the flooded environment. This study suggests an association between climate change and an increased incidence of melioidosis. In addition, this is the first report of environmental sampling and whole-genome analysis to prove endemicity and local acquisition in this region.


Subject(s)
Burkholderia pseudomallei , Melioidosis , Humans , Melioidosis/epidemiology , Melioidosis/microbiology , Queensland/epidemiology , Australia/epidemiology , Disease Outbreaks
14.
J Antimicrob Chemother ; 78(7): 1616-1621, 2023 07 05.
Article in English | MEDLINE | ID: mdl-37190910

ABSTRACT

BACKGROUND: Urinary tract infections (UTIs) due to MDR organisms are increasingly common. The lack of paediatric data on efficacious antibiotics makes UTI treatment particularly challenging. Data on the efficacy of fosfomycin use for UTI in children are variable. METHODS: We conducted a retrospective audit of children aged 0-18 years who were treated with fosfomycin for UTI at seven tertiary paediatric hospitals in Australia over a 7 year period, from 2014 to 2020. RESULTS: Ninety-one children with a median age of 5 years (range 2 months to 18 years) received oral fosfomycin for UTI. The majority (57/91, 63%) had one or more comorbidity, with the most common being renal tract anomalies (24/91, 26%). Fifty-nine (65%) had febrile UTI, 14/91 (15%) had pyelonephritis and 1/91 (1%) was bacteraemic. A majority (80/91, 88%) of urinary cultures had an ESBL-producing Gram-negative pathogen isolated. Fosfomycin susceptibility was evident in all 80 isolates tested. For uncomplicated UTI, the most common dose in children aged <1, 1-12 and >12 years was 1, 2 and 3 g, respectively. For complicated UTI, doses of 2 and 3 g were most common. The median duration of fosfomycin administration was 5 days (range 1-82). Clinical cure was achieved in 84/90 (93%); the six with treatment failure had underlying comorbidities. Overall, 2/91 (2%) children experienced drug-related adverse effects comprising gastrointestinal symptoms in both, which resolved after treatment discontinuation. CONCLUSIONS: Fosfomycin is well tolerated and associated with favourable treatment outcomes in children with UTI. Further research on the optimal dosing strategy is required.


Subject(s)
Fosfomycin , Urinary Tract Infections , Humans , Child , Adolescent , Infant , Fosfomycin/adverse effects , Retrospective Studies , Australia/epidemiology , Urinary Tract Infections/drug therapy , Urinary Tract Infections/epidemiology , Anti-Bacterial Agents/adverse effects
15.
Mycopathologia ; 188(5): 731-743, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37040020

ABSTRACT

Invasive pulmonary aspergillosis remains a major cause of morbidity and mortality for immunocompromised children, particularly for patients with acute leukaemia and those undergoing haematopoietic stem cell transplantation. Timely diagnosis, using a combination of computed tomography (CT) imaging and microbiological testing, is key to improve prognosis, yet there are inherent challenges in this process. For CT imaging, changes in children are generally less specific than those reported in adults and recent data are limited. Respiratory sampling by either bronchoalveolar lavage or lung biopsy is recommended but is not always feasible in children, and serum biomarkers, including galactomannan, have important limitations. In this review we summarise the current paediatric data on available diagnostic tests for IPA and highlight key emerging diagnostic modalities with potential for future use.


Subject(s)
Invasive Pulmonary Aspergillosis , Adult , Humans , Child , Invasive Pulmonary Aspergillosis/diagnosis , Invasive Pulmonary Aspergillosis/etiology , Bronchoalveolar Lavage Fluid/microbiology , Biomarkers , Prognosis , Tomography, X-Ray Computed/adverse effects , Mannans , Sensitivity and Specificity
16.
Commun Biol ; 6(1): 351, 2023 03 31.
Article in English | MEDLINE | ID: mdl-37002413

ABSTRACT

Domesticated yaks endure as iconic symbols of high-altitude frozen landscapes, where herding communities depend on their high-fat milk, transport, dung, and natural fibers. While there is established proteomic evidence for ancient consumption of ruminant and horse milk in the mountains and steppes of northern Eurasia, yak dairy products have yet to be detected. Yak domestication and the species' dispersal from Tibet into the mountainous zones to the north are also poorly resolved due to a paucity of zooarchaeological data. To examine the potential of paleoproteomics to shed light on domesticated yak in Mongolia, we analyzed human dental calculus from Mongol era elite individuals recovered from permafrost burials in Khovsgol province, where people continue to herd yak to this day. We report the first evidence for yak dairy consumption, linked to local resource control. In addition, we confirm a large diversity of recovered whey, curd, tissue, and blood proteins, likely reflecting the excellent preservation conditions found at permafrost sites.


Subject(s)
Milk , Permafrost , Animals , Cattle , Humans , Proteomics , Tibet , Mongolia
17.
J Pediatric Infect Dis Soc ; 12(4): 242-245, 2023 Apr 28.
Article in English | MEDLINE | ID: mdl-36999616

ABSTRACT

This retrospective analysis describes the administration of sotrovimab in 32 children (22 aged 12-16 years old; 10 aged 1-11 years old) who were at high risk of deterioration to severe COVID-19 disease. We provide dosing suggestions and demonstrate the feasibility of sotrovimab use in the younger pediatric population (<12 years old and <40 kg).


Subject(s)
COVID-19 , Humans , Child , Adolescent , Infant , Child, Preschool , Retrospective Studies , Antibodies, Monoclonal, Humanized/therapeutic use , Antibodies, Neutralizing
18.
J Clin Virol ; 161: 105423, 2023 04.
Article in English | MEDLINE | ID: mdl-36934591

ABSTRACT

BACKGROUND: Human Respiratory Syncytial Virus (RSV) infections pose a significant risk to human health worldwide, especially for young children. Whole genome sequencing (WGS) provides a useful tool for global surveillance to better understand the evolution and epidemiology of RSV and provide essential information that may impact on antibody treatments, antiviral drug sensitivity and vaccine effectiveness. OBJECTIVES: Here we report the development of a rapid and simplified amplicon-based one-step multiplex reverse-transcription polymerase chain reaction (mRT-PCR) for WGS of both human RSV-A and RSV-B viruses. STUDY DESIGN: Two mRT-PCR reactions for each sample were designed to generate amplicons for RSV WGS. This new method was tested and evaluated by sequencing 206 RSV positive clinical samples collected in Australia in 2020 and 2021 with RSV Ct values between 10 and 32. RESULTS: In silico analysis and laboratory testing revealed that the primers used in the new method covered most of the currently circulating RSV-A and RSV-B. Amplicons generated were suitable for both Illumina and Oxford Nanopore Technologies (ONT) NGS platforms. A success rate of 83.5% with a full coverage for the genome of 98 RSV-A and 74 RSV-B was achieved from all clinical samples tested. CONCLUSIONS: This assay is simple to set up, robust, easily scalable in sample preparation and relatively inexpensive, and as such, provides a valuable addition to existing NGS RSV WGS methods.


Subject(s)
Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Child , Humans , Child, Preschool , Respiratory Syncytial Virus, Human/genetics , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus Infections/epidemiology , Multiplex Polymerase Chain Reaction , Antiviral Agents , Sensitivity and Specificity
20.
J Infect Dis ; 227(2): 278-287, 2023 01 11.
Article in English | MEDLINE | ID: mdl-35867852

ABSTRACT

BACKGROUND: A novel human parechovirus 3 Australian recombinant (HPeV3-AR) strain emerged in 2013 and coincided with biennial outbreaks of sepsis-like illnesses in infants. We evaluated the molecular evolution of the HPeV3-AR strain and its association with severe HPeV infections. METHODS: HPeV3-positive samples collected from hospitalized infants aged 5-252 days in 2 Australian states (2013-2020) and from a community-based birth cohort (2010-2014) were sequenced. Coding regions were used to conduct phylogenetic and evolutionary analyses. A recombinant-specific polymerase chain reaction was designed and utilized to screen all clinical and community HPeV3-positive samples. RESULTS: Complete coding regions of 54 cases were obtained, which showed the HPeV3-AR strain progressively evolving, particularly in the 3' end of the nonstructural genes. The HPeV3-AR strain was not detected in the community birth cohort until the initial outbreak in late 2013. High-throughput screening showed that most (>75%) hospitalized HPeV3 cases involved the AR strain in the first 3 clinical outbreaks, with declining prevalence in the 2019-2020 season. The AR strain was not statistically associated with increased clinical severity among hospitalized infants. CONCLUSIONS: HPeV3-AR was the dominant strain during the study period. Increased hospital admissions may have been from a temporary fitness advantage and/or increased virulence.


Subject(s)
Parechovirus , Picornaviridae Infections , Infant , Humans , Parechovirus/genetics , Phylogeny , Australia/epidemiology , Recombination, Genetic
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