Respiratory Publications

2019 Article - "Respiratory Pathogens in Infants Diagnosed with Acute Lower Respiratory Tract Infection in a Tertiary Care Hospital of Western India Using Multiplex Real Time PCR" (limited access)

Objective: To determine the frequency of respiratory pathogens in infants diagnosed with acute lower respiratory tract infections.
Methods: A prospective cross-sectional observational study was conducted in infants hospitalized with a diagnosis of acute lower respiratory tract infection (ALRTI), in a tertiary care hospital in a metropolitan city of Western India. Nasopharyngeal swabs were analyzed by multiplex real time polymerase chain reaction, for 18 viruses and 3 bacteria (H. influenzae type b, C. pneumoniae and M. pneumoniae). The entire data was entered in Microsoft excel sheet and frequencies were determined.
Results: One hundred eligible infants were enrolled. Pathogens were detected in 82 samples, which included Respiratory syncytial viruses (RSV) A / B (35.4%), Human rhinovirus (25.6%), Adenovirus (22%), Human Parainfluenza viruses (11%), Human bocavirus (9.8), Human metapneumovirus A / B (8.5%), Influenza A (H1N1) pdm 09 (6.1%), Parechovirus (3.7%), Human coronaviruses (3.66%), Haemophilus influenzae type b (6.1%), Chlamydia pneumoniae (2.4%) and Mycoplasma pneumoniae (2.4%). Influenza A (other than H1N1), Influenza B, Human Coronavirus 229E and Enterovirus were not detected. The rate of coinfection was 34% and rhinovirus was the most common of the multiple pathogens.
Conclusions: Spectrum of viral etiologies of ALRTI is highlighted. Etiological diagnosis of ALRTI would enable specific antiviral therapy, restrict antibiotic use and help in knowing burden of disease.

Kit used: FTD Respiratory pathogens 21 plus
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2018 Article - "Live-Attenuated Respiratory Syncytial Virus Vaccine Candidate With Deletion of RNA Synthesis Regulatory Protein M2-2 is Highly Immunogenic in Children" (limited access)

Background: Live respiratory syncytial virus (RSV) candidate vaccine LIDΔM2-2 is attenuated by deletion of the RSV RNA regulatory protein M2-2, resulting in upregulated viral gene transcription and antigen expression but reduced RNA replication.

Methods: RSV-seronegative children ages 6–24 months received a single intranasal dose of 105 plaque forming units (PFU) of LIDΔM2-2 (n = 20) or placebo (n = 9) (NCT02237209, NCT02040831). RSV serum antibodies, vaccine infectivity, and reactogenicity were assessed. During the following RSV season, participants were monitored for respiratory illness and pre- and post-RSV season serum antibodies.

Results: Vaccine virus was shed by 95% of vaccinees (median peak titers of 3.8 log10 PFU/mL by quantitative culture and 6.3 log10 copies/mL by PCR); 90% had ≥4-fold rise in serum neutralizing antibodies. Respiratory symptoms and fever were common in vaccine (95%) and placebo (78%). One vaccinee had grade 2 rhonchi concurrent with vaccine shedding, rhinovirus, and enterovirus. Eight of 19 vaccinees versus 2 of 9 placebo recipients had substantially increased RSV antibody titers after the RSV season without medically attended RSV disease, indicating anamnestic vaccine responses to wild-type RSV without significant illness.

Conclusion: LIDΔM2-2 had excellent infectivity and immunogenicity, encouraging further study of vaccine candidates attenuated by M2-2 deletion.

Kit used: FTD FTD Respiratory pathogens 21
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2018 Article - "Adenovirus types associated with severe respiratory diseases: A retrospective 4-year study in Kuwait" (limited access)

Summary: Human adenovirus (HAdV) infection can result in a severe respiratory disease. The aim of this study was to identify HAdV types detected in patients hospitalized for severe respiratory illness. The study population consisted of 743 patients with severe respiratory disease admitted to four major hospitals in Kuwait between January 2013 and December 2016. Respiratory specimens were retrospectively screened for 20 respiratory viruses by real-time PCR. The HAdV hexon gene was amplified and directly sequenced, and HAdV types were identified by performing Bayesian phylogenetic analysis. HAdV DNA was detected in 27 (3.6%) patients, with peaks in November and March. Most patients were infants and young children suffering from pneumonia or acute bronchiolitis. The detected HAdV types were C1, C2, C5, B3, and B7. Clusters of HAdV C1, C2, and C5 were observed with high posterior probability. All patients infected with HAdV C5 and 50% of patients infected with HAdV C2 or B7 were admitted to the intensive care unit (ICU). Co-infection with other viruses was detected in 44.4% of patients. The most common co-infecting virus was rhinovirus (HRV). HAdV/HRV co-infection was detected in two children who presumably developed disseminated HAdV infection and died. This is the first report describing the circulation of HAdV types associated with severe outcomes in Kuwait. These findings highlight the need for a national surveillance system to monitor changes in predominant HAdV types and increased numbers of severe respiratory infections.

Kit used: FTD Respiratory pathogens 21
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2018 Article - "Clinical characteristics of influenza virus-induced lower respiratory infection during the 2015 to 2016 season" (limited access)

Background Influenza A(H1N1)pdm09 virus infections often manifest severe respiratory symptoms, particularly in patients with a past history of allergic disease. Most of these findings were reported during the 2009 pandemic. The purpose of this study was to detail the clinical characteristics of influenza virus-induced lower respiratory infection (LRI) during the A(H1N1)pdm09-predominant 2015–2016 season. Methods We retrospectively reviewed the clinical characteristics of influenza-induced LRI cases in children admitted to a tertiary children's hospital. Molecular diagnostic evaluation was performed on samples obtained from the most severe cases. Results We identified 66 patients with influenza-associated hospitalization and included 21 patients with influenza virus-induced LRI for analyses. Twelve patients (57%) were admitted to the pediatric intensive care unit, seven (33%) required mechanical ventilation, and three (14%) required extracorporeal membrane oxygenation. Plastic bronchitis (PB) was identified in six patients (29%), among whom a past medical history of asthma or food allergy were noted in all six patients. A past history of allergic disease was more common among patients with, than among those without, PB (p = 0.009). A(H1N1)pdm09 was detected from all the PB cases, and phylogenetic analyses of the hemagglutinin and neuraminidase genes demonstrated that this virus belonged to subclades 6B.1 and 6B.2. In the six PB cases, we found one patient with H275Y mutation in neuraminidase. Conclusion Allergic disease was a risk factor for developing PB due to influenza A(H1N1)pdm09 infection during the 2015–16 season.

Kit used: FTD Respiratory pathogens 21
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2018 Article - "Randomised controlled trial of rhinothermy for treatment of the common cold: a feasibility study" (pdf, 858KB)

Objective: To determine the feasibility of a randomised controlled trial (RCT) of rhinothermy for the common cold.
Design: Open label, randomised, controlled feasibility study.
Setting: Single-centre research institute in New Zealand recruiting participants from the community.
Participants: 30 adult participants with symptoms of a common cold, presenting within 48 hours of the onset of symptoms.
Interventions: Participants were randomly assigned 2:1 to receive either 35 L/min of 100% humidified air at 41°C via high flow nasal cannulae, 2 hours per day for up to 5 days (rhinothermy), or vitamin C 250 mg daily for 5 days (control).
Primary and secondary outcome measures: The primary outcome was the proportion of screened candidates who were randomised.
Secondary outcomes included: proportion of randomised participants who completed the study; modified Jackson scores from randomisation to 10 days after initiation of randomised regimen; time until feeling ‘a lot better’ compared with study entry; time until resolution of symptoms or symptom score at 10 days postrandomisation; proportion of organisms identified by PCR analysis of nasal swabs taken at baseline; the patterns of use of the rhinothermy device; estimated adherence of the control group; and rhinothermy device tolerability.
Results: In all 30/79 (38%, 95% CI 27% to 50%) of potential participants screened for eligibility were randomised. Rhinothermy was well tolerated, and all randomised participants completed the study (100%, 95% CI 88% to 100%). The reduction from baseline in the modified Jackson score was greater with rhinothermy compared with control at days 2, 3, 4, 5 and 6, with the maximum difference at day 4 (−6.4, 95% CI −9.4 to −3.3). The substantial clinical benefit threshold for modified Jackson score was a 5-unit change.
Conclusions: This study shows that an RCT of rhinothermy compared with low-dose vitamin C in the treatment of the common cold is feasible.

Kit used: FTD Respiratory pathogens 21

2017 Article - "Does azithromycin given to women in labour decrease ocular bacterial infection in neonates? A double-blind, randomized trial" (pdf, 365KB)

Background: Vertical transmission can result in neonatal infection and disease. Reducing the transmission of bacterial pathogens from mother to infant may be an effective means of preventing neonatal infection, including bacterial conjunctivitis.

Methods: In a double-blind, randomized trial, we assessed the effect of administering a single dose of oral azithromycin to women in labour on bacterial colonization of the neonate. A reduction in purulent neonatal conjunctivitis was a secondary objective of the trial. Ocular samples were collected from the lower fornix of infants presenting with clinical signs of purulent conjunctivitis during the first eight weeks of life. Incidence of purulent conjunctivitis was compared between trial arms. Bacterial infection was assessed using PCR and incidence of purulent conjunctivitis due to bacteria was also compared between arms.

Results: Forty of 843 infants (4.7%) presented clinical signs of purulent conjunctivitis. No significant difference in incidence of purulent conjunctivitis was seen between azithromycin and placebo arms [4.3% (18/419) versus 5.2% (22/424), OR = 0.82,95% CI (0.44,1.54), p=0.628]. S. aureus was the most commonly identified pathogen, detected in 38% of cases. Incidence of purulent-conjunctivitis due to bacterial infection was lower in the azithromycin arm [1.2% (5/419) versus 3.8% (16/424), OR = 0.31, 95% CI (0.12–0.82), p = 0.025)]. The incidence of gram-positive bacteria was also lower in the azithromycin arm [1.0% (4/419) versus 3.3% (14/424), OR = 0.28, 95%CI (0.10–0.82), p = 0.029].

Conclusions: Oral azithromycin given to women during labour may have the potential to reduce the incidence of bacterial neonatal conjunctivitis.

Kit used: FTD SPn/Staph/MC/Hi
FTD Vaginal Swab

2017 Article - "Performance of the Alere i RSV assay for point of care detection of respiratory syncytial virus in children" (pdf, 510KB)

Summary: Respiratory syncytial virus (RSV) is the most important cause of severe acute respiratory tract infection in young children. Alere i RSV is a novel molecular rapid test which identifies respiratory syncytial virus. The group evaluated the clinical performance of the Alere i RSV assay in a pediatric point-of-care setting during winter season 2016 / 2017. Test results from 518 nasopharyngeal swab samples were compared to FTD Respiratory pathogens 21 seen as reference standard. The overall sensitivity and specificity of the Alere i RSV test assay was 93% (CI95 89% – 96%) and 96% (CI95 93% – 98%), respectively. An optimal sensitivity of 98% (CI95 94% - 100%) and specificity of 96% (CI95 90% - 99%) was obtained in children < 6 months. In children ≥ 2 years, sensitivity and specificity remained at 87% (CI95 73% – 96%) and 98% (CI95 92% – 100%), respectively. False negative Alere i RSV test results mostly occurred in samples with low viral load (mean CT value 31.1; CI95 29.6 – 32.6).


Kit used: FTD Respiratory pathogens 21

2017 Article - "The 2015–2016 influenza epidemic: Late onset, clinical severity and emergence of the B Victoria virus" (pdf, 144KB)

Summary:Flu is a viral infection caused by influenza viruses. There are three types (A, B and C) and only A (A1H1N1 and AH3N2) and B (Victoria line and Yamagata line) are responsible for major seasonal epidemics with a circulation predominance for virus A. However, the 2015-2016 epidemic was different with an unusually high circulation of virus B (Victoria), leading to carry out a descriptive retrospective study at the university hospital (CHU) in Bordeaux.
A total of 110 patients with a positive PCR with a mean age of 53.3 years (16-90 years) were involved in the study. The positive diagnosis was made using a multiplex PCR with the kits available at the CHU de Bordeaux (Anyplex® II RV16, Allplex®Respiratory Panel and Fast Track®Flu Differentiation). Virus B positive sample subtyping was performed by the CNR de Lyon. Type A virus was mostly isolated in 57 patients (52%) with a predominance of subtype A (H1N1) in 50 patients (45% of the total). Type B viruses were isolated from 53 patients (48%) with the Victoria line virus in 47 patients (43% of the workforce). It was late onset epidemic (March-May), 23% of the patient were vaccinated. Same severity for type A (25%) and type B Victoria strain (23%).
Conclusion: The flu epidemic of 2015-2016 was different from the other years of an unusual overrepresentation of B / Victoria in hospital. There was a mismatch between vaccine lineage B / Yamagata and the circulating major strain Victoria with unprotected patients at risk. This study probably provides additional arguments to encourage seasonal influenza vaccination by a quadrivalent vaccine containing both subtypes A and the two B-line viruses (Victoria and Yamagata).

Kit used: FTD Flu differentiation

2017 Article - "Pertussis and Pertussis like Illness: Pediatric Experience in Oman" (pdf, 844KB)

Summary: A resurgence of pertussis or whooping cough has been observed worldwide despite broad vaccination coverage. Pertussis like illness (PLI) refers to a clinical syndrome compatible with pertussis infection but lacking laboratory confirmation or an epidemiological link to a confirmed case. Our study aimed to estimate the contribution of Bordetella pertussis infection and identifying predictors of its diagnosis in a cohort of children with PLI. Demographic and clinical information were retrospectively collected from the medical records of children < 13 years old and hospitalized for PLI in two pediatric units in Oman from 1 January 2012 to 31 December 2013. The laboratory data of all cases were reviewed and confirmed cases of pertussis were identified, analyzed, and compared with non-confirmed cases.A total of 131 patients were enrolled in this study. The majority (95.4% [125/131]) were infants. Only 54.1% (71/131) of admitted children with PLI were tested for pertussis. The incidence of pertussis infection among the tested group was 16.9% (12/71) with a 95% confidence interval 8.2−25.6. Severe illness occurred in 56.4% (74/131) of patients, and six were confirmed to have pertussis. Pediatric intensive care unit admission was required for one confirmed case of pertussis and eight cases from the PLI group (three were negative for pertussis, and five were not tested). Receiver operator characteristic curve analysis revealed that a white blood cell count 3 23.5 × 109/L had 96.6% specificity and lymphocytes 3 17 × 109/L had 98.3% specificity. Taking into consideration that the number tested for pertussis was limited, the incidence of pertussis was 16.9% (12 out of 71 patients). Lymphocytosis can be used as a reliable predictor for the diagnosis of pertussis especially in the absence of specific confirmatory tests or until their results are available.

Kit used: FTD Respiratory pathogens 21

2017 Article - "Evaluation of quantitative FTD Pneumocystis jirovecii kit for Pneumocystis infection diagnosis" (limited access)

Summary: In this study the Fast track Diagnostics (FTD) Pneumocystis PCR kit was evaluated, targeting the mitochondrial large subunit ribosomal RNA gene (mtLSU rRNA) of Pneumocystis jirovecii (P. jirovecii). A hundred and thirty-three patients were prospectively enrolled. Respiratory specimens were examined using both microscopy and the PCR assay. Twenty-six patients led to P. jirovecii detection. Fourteen patients presented with Pneumocystis pneumonia (PCP)whereas 12 patients were considered to be colonized. The median copy numbers in bronchoalveolar lavage fluid were significantly different in the PCP and colonization groups (1.35×10^8/ml vs. 1.45×10^5/ml, P <0.0001). Lower and upper cut-off values of 3.9×10^5 copies/ml and 3.2×10^6 copies/ml allowed differentiating PCP and colonization. The FTD P. jirovecii assay was secondarily compared to an in-house reference PCR assay targeting the mtLSU rRNA gene. A concordance rate of 97.5% was observed (Cohen's kappa coefficient κ=0.935). The FTD Pneumocystis PCR kit showed good performance and represents an alternative method to diagnose P. jirovecii infections.

Kit used: FTD Pneumocystis jirovecii
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