key: cord-0800077-419qs7qf
authors: Chang, Anne B.; Smith-Vaughan, Heidi; Sloots, Theo P.; Valery, Patricia C.; Whiley, David; Beissbarth, Jemima; Torzillo, Paul J.
title: Upper airway viruses and bacteria detection in clinical pneumonia in a population with high nasal colonisation do not relate to clinical signs
date: 2015-12-01
journal: Pneumonia (Nathan)
DOI: 10.15172/pneu.2015.6/636
sha: d6bc3b70f8ee04ee9bb00e4aa98c89c4290b125a
doc_id: 800077
cord_uid: 419qs7qf

Indigenous Australian children have high (up to 90%) rates of nasopharyngeal microbial colonisation and of hospitalisation for pneumonia. In Indigenous children hospitalised with pneumonia in Central Australia, we describe the nasopharyngeal detection of viruses and bacteria and assessed whether their presence related to signs of pneumonia (tachypnoea and/or chest in-drawing) on hospital admission and during subsequent days. Nasopharyngeal swabs (NPS) and data were prospectively collected from 145 children (median age = 23.5 months, interquartile range [IQR] 8.7–50) hospitalised with pneumonia at Alice Springs Hospital, Australia, between April 2001 and July 2002. The cohort was enrolled in a randomised controlled study using zinc and/or vitamin A supplementation. NPS were taken within 24 hours of hospitalisation and kept frozen at-80°C until analysed in 2014. Polymerase chain reaction (PCR) was used to detect Moraxella catarrhalis, Haemophilus influenzae, Streptococcus pneumoniae, Staphylococcus aureus, Chlamydophila pneumoniae, Mycoplasma pneumoniae, and 16 respiratory viruses. Uni- and multi-variate analyses were used to examine the relationships. One or more organisms were present in 137 (94.5%) NPS; 133 (91.7%) detected ≥ 1 bacterium, 34 (37.2%) for ≥ 1 virus and 50 (34.5%) were positive for both viruses and bacteria. C. pneumoniae (n = 3) and M. pneumoniae (n = 2) were rare. In multi-variate analyses, age < 12 months (odds ratio [OR] 6.6 [95% confidence interval {CI} 1.7–25.4]) and fever (OR 4.1 [95% CI 1.7–10.4]) were associated with tachypnoea and chest in-drawing. However the presence of bacteria and/or virus type was not associated with tachypnoea and/or chest in-drawing on admission or during recovery. In children with high nasopharyngeal microbial colonisation rates, the utility of NPS in determining the diagnosis of clinical pneumonia or duration of tachypnoea or in-drawing is likely limited. Larger cohort and case-control studies are required to confirm our findings.

pneumonia 2015 Volume 6

ZĞƉŽƌƚĞĚ ŚŽƐƉŝƚĂůŝƐĂƟŽŶ ƌĂƚĞƐ ĨŽƌ ĂĐƵƚĞ ůŽǁĞƌ ƌĞƐƉŝƌĂƚŽƌLJ ŝŶĨĞĐƟŽŶƐ ; >Z/ƐͿ͕ ŝŶĐůƵĚŝŶŐ ƉŶĞƵŵŽŶŝĂ͕ ŝŶ /ŶĚŝŐĞŶŽƵƐ Australian children from remote areas are comparable to and, in some regions, higher than those for children in developing countries [1] . Despite the burden, to date, there has been only one study that has examined upper airway viruses and bacteria in Indigenous Australian children ĨƌŽŵ ƌĞŵŽƚĞ ĐŽŵŵƵŶŝƟĞƐ ǁŚŽ ŚĂ|Ğ ďĞĞŶ ŚŽƐƉŝƚĂůŝƐĞĚ ĨŽƌ >Z/ Ϯ͘ dŚŝƐ ƐƚƵĚLJ ǁĂƐ ĐŽŶĚƵĐƚĞĚ ƉƌŝŽƌ ƚŽ ƚŚĞ Ă|ĂŝůĂďŝůŝƚLJ ŽĨ ŵŽůĞĐƵůĂƌ ĚŝĂŐŶŽƐƟĐ ŵĞƚŚŽĚƐ Ϯ͘ There are few studies that have used the World Health KƌŐĂŶŝnjĂƟŽŶ͛Ɛ ;t,KͿ ϯ ĐůŝŶŝĐĂů ĚŝĂŐŶŽƐƟĐ ĐƌŝƚĞƌŝĂ together with current extended molecular methods to ĞdžĂŵŝŶĞ ƚŚĞ ƌĞůĂƟŽŶƐŚŝƉ ďĞƚǁĞĞŶ ďŽƚŚ ƵƉƉĞƌ ĂŝƌǁĂLJ viruses and bacteria and clinical and/or radiologically ĐŽŶĮƌŵĞĚ ƉŶĞƵŵŽŶŝĂ͕ ĂŶĚ ŝƚƐ ŽƵƚĐŽŵĞƐ͕ ŝŶ ĐŚŝůĚƌĞŶ͘ dŚĞ ŵĂũŽƌŝƚLJ ŽĨ ƐƚƵĚŝĞƐ ŚĂ|Ğ ĨŽĐƵƐĞĚ ŽŶ ƐƉĞĐŝĮĐ |ŝƌƵƐĞƐ ϰ͕ϱ or bacteria [6, 7, 8] , with few assessing whether upper airway microbiology predicts clinical symptoms. There ĂƌĞ ŶŽŶĞ ƚŚĂƚ ŚĂ|Ğ ďĞĞŶ ĐŽŶĚƵĐƚĞĚ ŝŶ Ă ƉŽƉƵůĂƟŽŶ ǁŝƚŚ Ă ƐŝŵŝůĂƌ ƉŶĞƵŵŽŶŝĂ ƌŝƐŬ ƚŽ ƚŚĂƚ ŽĨ ĞŶƚƌĂů ƵƐƚƌĂůŝĂŶ Indigenous children. Use of nasopharyngeal swabs (NPS) is convenient, as obtaining lower airway specimens in very young children generally requires invasive procedures (e.g. bronchoscopy or lung punctures). However, NPS ƚĂŬĞŶ Ăƚ ŚŽƐƉŝƚĂůŝƐĂƟŽŶ ŵĂLJ ŶŽƚ ƌĞŇĞĐƚ ĐůŝŶŝĐĂů ƐLJŵƉƚŽŵƐ or outcomes as nasopharyngeal (NP) carriage in this ƉŽƉƵůĂƟŽŶ ŝƐ ŚŝŐŚ ;ƵƉ ƚŽ ϵϬй ŽĨ ĂƐLJŵƉƚŽŵĂƟĐ ĐŚŝůĚƌĞŶͿ ϵ͕ϭϬ ĂŶĚ ĚĞƚĞĐƟŽŶ ŽĨ ŽƌŐĂŶŝƐŵƐ ďLJ ƉŽůLJŵĞƌĂƐĞ ĐŚĂŝŶ ƌĞĂĐƟŽŶ ;WZͿ Ăƚ Ă ƐŝŶŐůĞ ƉŽŝŶƚ ŝŶ ƟŵĞ ĚŽĞƐ ŶŽƚ ŶĞĐĞƐƐĂƌŝůLJ ĞƋƵĂƚĞ ƚŽ ĂĐƟ|Ğ ŝŶĨĞĐƟŽŶ͘ &ƵƌƚŚĞƌ͕ ĐĂƌƌŝĂŐĞ ŽĨ EW |ŝƌƵƐĞƐ ŝƐ ĂƐ ŚŝŐŚ ĂƐ ϰϱй ŽĨ ĂƐLJŵƉƚŽŵĂƟĐ ŚŽƐƉŝƚĂůŝƐĞĚ ĐŚŝůĚƌĞŶ ϭϭ͘ In 145 Central Australian Indigenous children hospitalised with pneumonia, we describe the point prevalence of NP bacteria and viruses in these children and assessed whether viruses and bacteria detected in the NP related ƚŽ ƚŚĞ t,K ĐůŝŶŝĐĂů ĚĞĮŶŝƟŽŶ ĨŽƌ ƉŶĞƵŵŽŶŝĂ ;ƚĂĐŚLJƉŶŽĞĂ ĂŶĚͬŽƌ ĐŚĞƐƚ ŝŶͲĚƌĂǁŝŶŐͿ ŽŶ ĂĚŵŝƐƐŝŽŶ ĂŶĚ ƚŚĞ ĚƵƌĂƟŽŶ of these signs. Given the usually high level of NP carriage of bacteria and viruses in children without pneumonia in our target group, we hypothesised that there was no ƌĞůĂƟŽŶƐŚŝƉ ďĞƚǁĞĞŶ ƚŚĞƐĞ ƵƉƉĞƌ ĂŝƌǁĂLJ ŵŝĐƌŽďĞƐ ĂŶĚ clinical symptoms. 

Most swabs (n сϭϯϳ ϵϰ͘ϱйͿ ǁĞƌĞ ƉŽƐŝƟ|Ğ ĨŽƌ Ăƚ ůĞĂƐƚ ϭ organism ( (Table 3) .

In 

Ğƚ Ăů͘ ZĂƚĞƐ ŽĨ ƌĂĚŝŽůŽŐŝĐĂůůLJ ĐŽŶĮƌŵĞĚ ƉŶĞƵŵŽŶŝĂ ĂƐ ĚĞĮŶĞĚ ďLJ ƚŚĞ tŽƌůĚ ,ĞĂůƚŚ KƌŐĂŶŝnjĂƟŽŶ ŝŶ EŽƌƚŚĞƌŶ dĞƌƌŝƚŽƌLJ /ŶĚŝŐĞŶŽƵƐ

ƵĞƐƚŽŶ > Ğƚ Ăů͘ ƟŽůŽŐLJ ŽĨ ĂĐƵƚĞ ůŽǁĞƌ ƌĞƐƉŝƌĂƚŽƌLJ ƚƌĂĐƚ ŝŶĨĞĐƟŽŶ in Central Australian Aboriginal children. Pediatr Infect ŝƐ : ϭϵϵϵ͖ϭϴ͗ϳϭϰʹϮϭ͘ WD/͗ϭϬϰϲϮϯϰϮ ŚƩƉ͗ͬͬĚdž͘ĚŽŝ͘

ISBN ϵϳϴϵϮϰϭϱϬϳϴϭϯ͘ |ĂŝůĂďůĞ ĨƌŽŵ ŚƩƉ͗ͬͬǁǁǁ͘ǁŚŽ͘ŝŶƚͬ maternal_child_adolescent/documents/child-pneumoniatreatment/en/ 4. ůŝ ͕ <ŚŽǁĂũĂ Z͕ ĂƐŚŝƌ D͕ njŝnj &͕ DƵƐƚĂĨĂ ^͕ ĂŝĚŝ pneumonia

ŚƵŵĂŶ ŵĞƚĂƉŶĞƵŵŽ|ŝƌƵƐ͕ ŝŶŇƵĞŶnjĂ |ŝƌƵƐ ĂŶĚ ƌĞƐƉŝƌĂƚŽƌLJ ƐLJŶĐLJƟĂů |ŝƌƵƐ ŝŶ ĐĂƵƐŝŶŐ t,KͲĚĞĮŶĞĚ severe pneumonia in children in a developing country

Ğƚ Ăů͘ ůŝŶŝĐĂů ĞƉŝĚĞŵŝŽůŽŐLJ ŽĨ ďŽĐĂ|ŝƌƵƐ͕ rhinovirus, two polyomaviruses and four coronaviruses in HIV-infected and HIV-uninfected South African children

͕ ^ĐŚǁĞŝƚnjĞƌͲ<ƌĂŶƚnj ^ Ğƚ Ăů͘ ůŝŶŝĐĂů ĐŚĂƌĂĐƚĞƌŝƐƟĐƐ ŽĨ ĐŚŝůĚƌĞŶ ǁŝƚŚ ůŽǁĞƌ ƌĞƐƉŝƌĂƚŽƌLJ ƚƌĂĐƚ ŝŶĨĞĐƟŽŶƐ ĂƌĞ ĚĞƉĞŶĚĞŶƚ ŽŶ ƚŚĞ ĐĂƌƌŝĂŐĞ ŽĨ ƐƉĞĐŝĮĐ ƉĂƚŚŽŐĞŶƐ ŝŶ ƚŚĞ ŶĂƐŽƉŚĂƌLJŶdž͘ Ƶƌ

Ğƚ Ăů͘ ƐƐŽĐŝĂƟŽŶ ďĞƚǁĞĞŶ ŶĂƐŽƉŚĂƌLJŶŐĞĂů ůŽĂĚ ŽĨ ^ƚƌĞƉƚŽĐŽĐĐƵƐ ƉŶĞƵŵŽŶŝĂĞ͕ |ŝƌĂů ĐŽŝŶĨĞĐƟŽŶ͕ ĂŶĚ ƌĂĚŝŽůŽŐŝĐĂůůLJ ĐŽŶĮƌŵĞĚ ƉŶĞƵŵŽŶŝĂ ŝŶ sŝĞƚŶĂŵĞƐĞ children

͕ ƵĂƌƚĞ D͕ &ŽŶĐĞĐĂ D͕ ZŽƐĞ < Ğƚ Ăů͘ sŝƌĂů ĂŶĚ ĂƚLJƉŝĐĂů ďĂĐƚĞƌŝĂů ĚĞƚĞĐƟŽŶ ŝŶ ĂĐƵƚĞ ƌĞƐƉŝƌĂƚŽƌLJ ŝŶĨĞĐƟŽŶ ŝŶ ĐŚŝůĚƌĞŶ ƵŶĚĞƌ Į|Ğ LJĞĂƌƐ͘ W>Ž^ KE ϮϬϭϭ͖ϲ͗ĞϭϴϵϮϴ͘ WD/͗Ϯϭϱϯϯϭϭϱ ŚƩƉ͗ͬͬĚdž͘ĚŽŝ͘

ƐƉĞĐŝŵĞŶ transport method for the conduct of respiratory virus ƐƵƌ|ĞŝůůĂŶĐĞ ŝŶ ƌĞŵŽƚĞ /ŶĚŝŐĞŶŽƵƐ ĐŽŵŵƵŶŝƟĞƐ ŝŶ ƵƐƚƌĂůŝĂ͘ Trop Med Int Health

Stewart PA et Ăů͘ ŝŶĐ ĂŶĚ |ŝƚĂŵŝŶͲ ƐƵƉƉůĞŵĞŶƚĂƟŽŶ ŝŶ /ŶĚŝŐĞŶŽƵƐ Australian children hospitalised with episodes of lower ƌĞƐƉŝƌĂƚŽƌLJ ƚƌĂĐƚ ŝŶĨĞĐƟŽŶ͗ Ă ƌĂŶĚŽŵŝƐĞĚ ĐŽŶƚƌŽůůĞĚ ƚƌŝĂů͘

ĂƌĞ <D͕ ^ŵŝƚŚͲsĂƵŐŚĂŶ ,͕ >ĞĂĐŚ :͘ sŝĂďŝůŝƚLJ ŽĨ respiratory pathogens cultured from nasopharyngeal swabs ƐƚŽƌĞĚ ĨŽƌ ƵƉ ƚŽ ϭϮ LJĞĂƌƐ Ăƚ ͲϳϬΣ ŝŶ ƐŬŝŵ ŵŝůŬ ƚƌLJƉƚŽŶĞ glucose glycerol broth

Ăƌƫ d͕ :Ăƌƫ >͕ WĞůƚŽůĂ s͕ tĂƌŝƐ D͕ ZƵƵƐŬĂŶĞŶ K͘ /ĚĞŶƟĮĐĂƟŽŶ ŽĨ ƌĞƐƉŝƌĂƚŽƌLJ |ŝƌƵƐĞƐ ŝŶ ĂƐLJŵƉƚŽŵĂƟĐ ƐƵďũĞĐƚƐ͗ ĂƐLJŵƉƚŽŵĂƟĐ ƌĞƐƉŝƌĂƚŽƌLJ |ŝƌĂů ŝŶĨĞĐƟŽŶƐ͘ WĞĚŝĂƚƌ /ŶĨĞĐƚ ŝƐ : ϮϬϬϴ͖Ϯϳ͗ϭϭϬϯʹϳ͘ WD/͗ϭϴϵϳϴϱϭϴ ŚƩƉ͗ͬͬĚdž͘ĚŽŝ͘ ŽƌŐͬϭϬ͘ϭϬϵϳͬ/E&͘ϬďϬϭϯĞϯϭϴϭϳĞϲϵϱĚ 20. >ŽŶŐƟŶ :͕ ĂƐƟĞŶ D͕ 'ŝůĐĂ Z͕ >ĞďůĂŶĐ ͕ ĚĞ ^ĞƌƌĞƐ '͕ ĞƌŐĞƌŽŶ D' Ğƚ Ăů͘

ŽīŵĂŶ >Z͕ ^ŵŝƚŚͲ sĂƵŐŚĂŶ ,͕ ,Žůƚ Ğƚ Ăů͘ dŽǁĂƌĚ ŵĂŬŝŶŐ ŝŶƌŽĂĚƐ ŝŶ reducing the disparity of lung health in Australian ŝŶĚŝŐĞŶŽƵƐ ĂŶĚ ŶĞǁ njĞĂůĂŶĚ ŵĈŽƌŝ ĐŚŝůĚƌĞŶ͘ &ƌŽŶƚ WĞĚŝĂƚƌ ϮϬϭϱ͖ϯ͗ϵ͘ WD/͗ϮϱϳϰϭϱϬϮ ŚƩƉ͗ͬͬĚdž͘ĚŽŝ͘ŽƌŐͬϭϬ͘ϯϯϴϵͬ fped

Ăů͘ ƐƐŽĐŝĂƟŽŶ ŽĨ ďĂĐƚĞƌŝĂ ĂŶĚ |ŝƌƵƐĞƐ ǁŝƚŚ ǁŚĞĞnjLJ ĞƉŝƐŽĚĞƐ ŝŶ LJŽƵŶŐ ĐŚŝůĚƌĞŶ͗ ƉƌŽƐƉĞĐƟ|Ğ ďŝƌƚŚ ĐŽŚŽƌƚ ƐƚƵĚLJ͘ D: ϮϬϭϬ͖ϯϰϭ͗Đϰϵϳϴ͘ WD/͗ϮϬϵϮϭϬϴϬ ŚƩƉ͗ͬͬ dx

DĐŽŝŐ Ğƚ Ăů͘ ƟŽůŽŐLJ ĂŶĚ ƚƌĞĂƚŵĞŶƚ ŽĨ ĐŽŵŵƵŶŝƚLJͲ acquired pneumonia in ambulatory children

D͕ ůĂƌŬ :͕ DĂĐŬĂLJ /D͕ tĂŶŐ z͕ ^ůŽŽƚƐ dW Ğƚ Ăů͘ ZĞƐƉŝƌĂƚŽƌLJ |ŝƌƵƐ ĚĞƚĞĐƟŽŶ ŝŶ ŶĂƐŽƉŚĂƌLJŶŐĞĂů aspirate versus bronchoalveolar lavage is dependent on virus type in children with chronic respiratory symptoms. : ůŝŶ sŝƌŽů ϮϬϭϯ͖ϱϴ͗ϲϴϯʹϴ͘ WD/͗ϮϰϭϮϱϴϯϬ ŚƩƉ͗ͬͬĚdž͘ĚŽŝ͘