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2.  Reagent and laboratory contamination can critically impact sequence-based microbiome analyses 
BMC Biology  2014;12(1):87.
Background
The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents.
Results
In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination.
Conclusions
These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. Concurrent sequencing of negative control samples is strongly advised.
Electronic supplementary material
The online version of this article (doi:10.1186/s12915-014-0087-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12915-014-0087-z
PMCID: PMC4228153  PMID: 25387460
Contamination; Microbiome; Microbiota; Metagenomics; 16S rRNA
3.  Two-phase importance sampling for inference about transmission trees 
There has been growing interest in the statistics community to develop methods for inferring transmission pathways of infectious pathogens from molecular sequence data. For many datasets, the computational challenge lies in the huge dimension of the missing data. Here, we introduce an importance sampling scheme in which the transmission trees and phylogenies of pathogens are both sampled from reasonable importance distributions, alleviating the inference. Using this approach, arbitrary models of transmission could be considered, contrary to many earlier proposed methods. We illustrate the scheme by analysing transmissions of Streptococcus pneumoniae from household to household within a refugee camp, using data in which only a fraction of hosts is observed, but which is still rich enough to unravel the within-household transmission dynamics and pairs of households between whom transmission is plausible. We observe that while probability of direct transmission is low even for the most prominent cases of transmission, still those pairs of households are geographically much closer to each other than expected under random proximity.
doi:10.1098/rspb.2014.1324
PMCID: PMC4211445  PMID: 25253455
transmission tree; molecular epidemiology; Streptococcus pneumonia
4.  Ophthalmic infections in children presenting to Angkor Hospital for Children, Siem Reap, Cambodia 
BMC Research Notes  2014;7(1):784.
Background
Ophthalmic infections cause significant morbidity in Cambodian children but aetiologic data are scarce. We investigated the causes of acute eye infections in 54 children presenting to the ophthalmology clinic at Angkor Hospital for Children, Siem Reap between March and October 2012.
Findings
The median age at presentation was 3.6 years (range 6 days – 16.0 years). Forty two patients (77.8%) were classified as having an external eye infection, ten (18.5%) as ophthalmia neonatorum, and two (3.7%) as intra-ocular infection. Organisms were identified in all ophthalmia neonatorum patients and 85.7% of patients with an external eye infection. Pathogens were not detected in either of the intra-ocular infection patients. Most commonly isolated bacteria were Staphylococcus aureus (23 isolates), coagulase-negative staphylococci (13), coliforms (7), Haemophilus influenzae/parainfluenzae (6), Streptococcus pneumoniae (4), and Neisseria gonorrhoeae (2). Chlamydia trachomatis DNA was detected in 60% of swabs taken from ophthalmia neonatorum cases.
Conclusions
This small study demonstrates the wide range of pathogens associated with common eye infections in Cambodian children. The inclusion of molecular assays improved the spectrum of detectable pathogens, most notably in neonates.
doi:10.1186/1756-0500-7-784
PMCID: PMC4228269  PMID: 25369774
Paediatric; Ophthalmic; Infection; Chlamydia
5.  Dense genomic sampling identifies highways of pneumococcal recombination 
Nature genetics  2014;46(3):305-309.
Evasion of clinical interventions by Streptococcus pneumoniae occurs through selection of non-susceptible genomic variants. Here we use genome sequencing of 3,085 pneumococcal carriage isolates from a 2.4 km2 refugee camp to enable unprecedented resolution of the process of recombination, and highlight its impact on population evolution. Genomic recombination hotspots show remarkable consistency between lineages, indicating common selective pressures acting at certain loci, particularly those associated with antibiotic resistance. Temporal changes in antibiotic consumption are reflected in changes in recombination trends demonstrating rapid spread of resistance when selective pressure is high. The highest frequencies of receipt and donation of recombined DNA fragments were observed in non-encapsulated lineages, implying that this largely overlooked pneumococcal group, which is beyond the reach of current vaccines, may play a major role in genetic exchange and adaptation of the species as a whole. These findings advance our understanding of pneumococcal population dynamics and provide important information for the design of future intervention strategies.
doi:10.1038/ng.2895
PMCID: PMC3970364  PMID: 24509479
6.  The impact of transmission mode on the evolution of benefits provided by microbial symbionts 
Ecology and Evolution  2014;4(17):3350-3361.
While past work has often examined the effects of transmission mode on virulence evolution in parasites, few studies have explored the impact of horizontal transmission on the evolution of benefits conferred by a symbiont to its host. Here, we identify three mechanisms that create a positive covariance between horizontal transmission and symbiont-provided benefits: pleiotropy within the symbiont genome, partner choice by the host, and consumption of host waste by-products by symbionts. We modify a susceptible-infected model to incorporate the details of each mechanism and examine the evolution of symbiont benefits given variation in either the immigration rate of susceptible hosts or the rate of successful vertical transmission. We find conditions for each case under which greater opportunity for horizontal transmission (higher migration rate) favors the evolution of mutualism. Further, we find the surprising result that vertical transmission can inhibit the evolution of benefits provided by symbionts to hosts when horizontal transmission and symbiont-provided benefits are positively correlated. These predictions may apply to a number of natural systems, and the results may explain why many mutualisms that rely on partner choice often lack a mechanism for vertical transmission.
doi:10.1002/ece3.1166
PMCID: PMC4228610  PMID: 25535552
By-products; mutualism; parasitism; partner choice; pleiotropy; symbiosis
7.  Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes 
PLoS Genetics  2014;10(8):e1004547.
Traditional genetic association studies are very difficult in bacteria, as the generally limited recombination leads to large linked haplotype blocks, confounding the identification of causative variants. Beta-lactam antibiotic resistance in Streptococcus pneumoniae arises readily as the bacteria can quickly incorporate DNA fragments encompassing variants that make the transformed strains resistant. However, the causative mutations themselves are embedded within larger recombined blocks, and previous studies have only analysed a limited number of isolates, leading to the description of “mosaic genes” as being responsible for resistance. By comparing a large number of genomes of beta-lactam susceptible and non-susceptible strains, the high frequency of recombination should break up these haplotype blocks and allow the use of genetic association approaches to identify individual causative variants. Here, we performed a genome-wide association study to identify single nucleotide polymorphisms (SNPs) and indels that could confer beta-lactam non-susceptibility using 3,085 Thai and 616 USA pneumococcal isolates as independent datasets for the variant discovery. The large sample sizes allowed us to narrow the source of beta-lactam non-susceptibility from long recombinant fragments down to much smaller loci comprised of discrete or linked SNPs. While some loci appear to be universal resistance determinants, contributing equally to non-susceptibility for at least two classes of beta-lactam antibiotics, some play a larger role in resistance to particular antibiotics. All of the identified loci have a highly non-uniform distribution in the populations. They are enriched not only in vaccine-targeted, but also non-vaccine-targeted lineages, which may raise clinical concerns. Identification of single nucleotide polymorphisms underlying resistance will be essential for future use of genome sequencing to predict antibiotic sensitivity in clinical microbiology.
Author Summary
Streptococcus pneumoniae is carried asymptomatically in the nasopharyngeal tract. However, it is capable of causing multiple diseases, including pneumonia, bacteraemia and meningitis, which are common causes of morbidity and mortality in young children. Antibiotic treatment has become more difficult, especially that involving the group of beta-lactam antibiotics where resistance has developed rapidly. The organism is known to be highly recombinogenic, and this allows variants conferring beta-lactam resistance to be readily introduced into the genome. Identification of the specific genetic determinants of beta-lactam resistance is essential to understand both the mechanism of resistance and the spread of resistant variants in the pneumococcal population. Here, we performed a genome-wide association study on 3,701 isolates collected from two different locations and identified candidate variants that may explain beta-lactam resistance as well as discriminating potential genetic hitchhiking variants from potential causative variants. We report 51 loci, containing 301 SNPs, that are associated with beta-lactam non-susceptibility. 71 out of 301 polymorphic changes result in amino acid alterations, 28 of which have been reported previously. Understanding the determinants of resistance at the single nucleotide level will be important for the future use of sequence data to predict resistance in the clinical setting.
doi:10.1371/journal.pgen.1004547
PMCID: PMC4125147  PMID: 25101644
8.  Evidence for Soft Selective Sweeps in the Evolution of Pneumococcal Multidrug Resistance and Vaccine Escape 
Genome Biology and Evolution  2014;6(7):1589-1602.
The multidrug-resistant Streptococcus pneumoniae Taiwan19F-14, or PMEN14, clone was first observed with a 19F serotype, which is targeted by the heptavalent polysaccharide conjugate vaccine (PCV7). However, “vaccine escape” PMEN14 isolates with a 19A serotype became an increasingly important cause of disease post-PCV7. Whole genome sequencing was used to characterize the recent evolution of 173 pneumococci of, or related to, PMEN14. This suggested that PMEN14 is a single lineage that originated in the late 1980s in parallel with the acquisition of multiple resistances by close relatives. One of the four detected serotype switches to 19A generated representatives of the sequence type (ST) 320 isolates that have been highly successful post-PCV7. A second produced an ST236 19A genotype with reduced resistance to β-lactams owing to alteration of pbp1a and pbp2x sequences through the same recombination that caused the change in serotype. A third, which generated a mosaic capsule biosynthesis locus, resulted in serotype 19A ST271 isolates. The rapid diversification through homologous recombination seen in the global collection was similarly observed in the absence of vaccination in a set of isolates from the Maela refugee camp in Thailand, a collection that also allowed variation to be observed within carriage through longitudinal sampling. This suggests that some pneumococcal genotypes generate a pool of standing variation that is sufficiently extensive to result in “soft” selective sweeps: The emergence of multiple mutants in parallel upon a change in selection pressure, such as vaccine introduction. The subsequent competition between these mutants makes this phenomenon difficult to detect without deep sampling of individual lineages.
doi:10.1093/gbe/evu120
PMCID: PMC4122920  PMID: 24916661
bacterial evolution; recombination; vaccine escape; antibiotic resistance; selective sweeps; phylogenomics
9.  Two fatal cases of melioidosis on the Thai-Myanmar border 
F1000Research  2014;3:4.
Melioidosis is endemic in areas of Southeast Asia, however, there are no published reports from the Thai-Myanmar border. We report the first two documented cases of fatal melioidosis in this region. This is of great public health importance and highlights the need to both increase clinical awareness of melioidosis on the Thai-Myanmar border, and to assess the true burden of disease in the area through improved case detection and Burkholderia pseudomallei prevalence studies.
doi:10.12688/f1000research.3-4.v2
PMCID: PMC3976102  PMID: 24715973
10.  Inhibition of endothelial cell Ca2+ entry and transient receptor potential channels by Sigma-1 receptor ligands 
British Journal of Pharmacology  2013;168(6):1445-1455.
Background and Purpose
The Sigma-1 receptor (Sig1R) impacts on calcium ion signalling and has a plethora of ligands. This study investigated Sig1R and its ligands in relation to endogenous calcium events of endothelial cells and transient receptor potential (TRP) channels.
Experimental Approach
Intracellular calcium and patch clamp measurements were made from human saphenous vein endothelial cells and HEK 293 cells expressing exogenous human TRPC5, TRPM2 or TRPM3. Sig1R ligands were applied and short interfering RNA was used to deplete Sig1R. TRP channels tagged with fluorescent proteins were used for subcellular localization studies.
Key Results
In endothelial cells, 10–100 μM of the Sig1R antagonist BD1063 inhibited sustained but not transient calcium responses evoked by histamine. The Sig1R agonist 4-IBP and related antagonist BD1047 were also inhibitory. The Sig1R agonist SKF10047 had no effect. Sustained calcium entry evoked by VEGF or hydrogen peroxide was also inhibited by BD1063, BD1047 or 4-IBP, but not SKF10047. 4-IBP, BD1047 and BD1063 inhibited TRPC5 or TRPM3, but not TRPM2. Inhibitory effects of BD1047 were rapid in onset and readily reversed on washout. SKF10047 inhibited TRPC5 but not TRPM3 or TRPM2. Depletion of Sig1R did not prevent the inhibitory actions of BD1063 or BD1047 and Sig1R did not co-localize with TRPC5 or TRPM3.
Conclusions and Implications
The data suggest that two types of Sig1R ligand (BD1047/BD1063 and 4-IBP) are inhibitors of receptor- or chemically activated calcium entry channels, acting relatively directly and independently of the Sig1R. Chemical foundations for TRP channel inhibitors are suggested.
doi:10.1111/bph.12041
PMCID: PMC3596649  PMID: 23121507
calcium channels; cationic channels; TRP channels; endothelial cells; Sigma-1 receptor; histamine; hydrogen peroxide; vascular endothelial growth factor
11.  Gold and BINOL-Phosphoric Acid Catalyzed Enantioselective Hydroamination/N-Sulfonyliminium Cyclization Cascade 
Organic Letters  2013;15(17):4330-4333.
A highly enantioselective hydroamination/N-sulfonyliminium cyclization cascade is reported using a combination of gold(I) and chiral phosphoric acid catalysts. An initial 5-exo-dig hydroamination and a subsequent phosphoric acid catalyzed cyclization process provide access to complex sulfonamide scaffolds in excellent yield and high enantiocontrol. The method can be extended to lactam derivatives, with excellent yields and enantiomeric excesses of up to 93% ee.
doi:10.1021/ol401784h
PMCID: PMC3931332  PMID: 23985045
12.  Evolvability and robustness in populations of RNA virus Φ6 
Microbes can respond quickly to environmental disturbances through adaptation. However, processes determining the constraints on this adaptation are not well understood. One process that could affect the rate of adaptation to environmental perturbations is genetic robustness, the ability to maintain phenotype despite mutation. Genetic robustness has been theoretically linked to evolvability but rarely tested empirically using evolving populations. We used populations of the RNA bacteriophage ϕ6 previously characterized as differing in robustness, and passaged them through a repeated environmental disturbance: periodic 45°C heat shock. The robust populations evolved faster to withstand the disturbance, relative to the less robust (brittle) populations. The robust populations also achieved relatively greater thermotolerance by the end of the experimental evolution. Sequencing revealed that thermotolerance occurred via a key mutation in gene P5 (viral lysis protein), previously shown to be associated with heat shock survival in the virus. Whereas this identical mutation fixed in all of the independently evolving robust populations, it was absent in some brittle populations, which instead fixed a less beneficial mutation. We concluded that robust populations adapted faster to the environmental change, and more easily accessed mutations of large benefit. Our study shows that genetic robustness can play a role in determining the relative ability for microbes to adapt to changing environments.
doi:10.3389/fmicb.2014.00035
PMCID: PMC3913886  PMID: 24550904
genetic robustness; evolvability; thermotolerance; bacteriophage; experimental evolution
13.  Two fatal cases of melioidosis on the Thai-Myanmar border 
F1000Research  2014;3:4.
Melioidosis is endemic in areas of Southeast Asia, however, there are no published reports from the Thai-Myanmar border.  We report the first two cases of fatal melioidosis in this region. This is of great public health importance and highlights the need to increase clinical awareness of melioidosis on the Thai-Myanmar border and to assess the true burden of disease in the area through improved case detection and Burkholderia pseudomallei prevalence studies.
doi:10.12688/f1000research.3-4.v1
PMCID: PMC3976102  PMID: 24715973
14.  Precautionary labelling of foods for allergen content: are we ready for a global framework? 
Food allergy appears to be on the rise with the current mainstay of treatment centred on allergen avoidance. Mandatory allergen labelling has improved the safety of food for allergic consumers. However an additional form of voluntary labelling (termed precautionary allergen labelling) has evolved on a wide range of packaged goods, in a bid by manufacturers to minimise risk to customers, and the negative impact on business that might result from exposure to trace amounts of food allergen present during cross-contamination during production. This has resulted in near ubiquitous utilisation of a multitude of different precautionary allergen labels with subsequent confusion amongst many consumers as to their significance. The global nature of food production and manufacturing makes harmonisation of allergen labelling regulations across the world a matter of increasing importance. Addressing inconsistencies across countries with regards to labelling legislation, as well as improvement or even banning of precautionary allergy labelling are both likely to be significant steps forward in improved food safety for allergic families. This article outlines the current status of allergen labelling legislation around the world and reviews the value of current existing precautionary allergen labelling for the allergic consumer. We strongly urge for an international framework to be considered to help roadmap a solution to the weaknesses of the current systems, and discuss the role of legislation in facilitating this.
doi:10.1186/1939-4551-7-10
PMCID: PMC4005619  PMID: 24791183
Allergen labelling; Food allergy; Legislation; Precationary allergen labelling; Anaphylaxis; Allergen avoidance; Mandatory labelling
15.  A three year descriptive study of early onset neonatal sepsis in a refugee population on the Thailand Myanmar border 
BMC Infectious Diseases  2013;13:601.
Background
Each year an estimated four million neonates die, the majority in the first week of life. One of the major causes of death is sepsis. Proving the incidence and aetiology of neonatal sepsis is difficult, particularly in resource poor settings where the majority of the deaths occur.
Methods
We conducted a three year observational study of clinically diagnosed early onset (<7 days of age) neonatal sepsis (EONS) in infants born to mothers following antenatal care at the Shoklo Malaria Research Unit clinic in Maela camp for displaced persons on the Thailand-Myanmar border. Episodes of EONS were identified using a clinical case definition. Conventional and molecular microbiological techniques were employed in order to determine underlying aetiology.
Results
From April 2009 until April 2012, 187 infants had clinical signs of EONS, giving an incidence rate of 44.8 per 1000 live births (95% CI 38.7-51.5). One blood culture was positive for Escherichia coli, E. coli was detected in the cerebrospinal fluid specimen in this infant, and in an additional two infants, by PCR. Therefore, the incidence of bacteriologically proven EONS was 0.7 per 1000 live births (95% CI 0.1 – 2.1). No infants enrolled in study died as a direct result of EONS.
Conclusion
A low incidence of bacteriologically proven EONS was seen in this study, despite a high incidence of clinically diagnosed EONS. The use of molecular diagnostics and nonspecific markers of infection need to be studied in resource poor settings to improve the diagnosis of EONS and rationalise antibiotic use.
doi:10.1186/1471-2334-13-601
PMCID: PMC3879187  PMID: 24359288
16.  Modulation of Porcine β-Defensins 1 and 2 upon Individual and Combined Fusarium Toxin Exposure in a Swine Jejunal Epithelial Cell Line 
Defensins are small antimicrobial peptides (AMPs) that play an important role in the innate immune system of mammals. Since the effect of mycotoxin contamination of food and feed on the secretion of intestinal AMPs is poorly understood, the aim of this study was to elucidate the individual and combined effects of four common Fusarium toxins, deoxynivalenol (DON), nivalenol (NIV), zearalenone (ZEA), and fumonisin B1 (FB1), on the mRNA expression, protein secretion, and corresponding antimicrobial effects of porcine β-defensins 1 and 2 (pBD-1 and pBD-2) using a porcine jejunal epithelial cell line, IPEC-J2. In general, upregulation of pBD-1 and pBD-2 mRNA expression occurred following exposure to Fusarium toxins, individually and in mixtures (P < 0.05). However, no significant increase in secreted pBD-1 and pBD-2 protein levels was observed, as measured by enzyme-linked immunosorbent assay (ELISA). Supernatants from IPEC-J2 cells exposed to toxins, singly or in combination, however, possessed significantly less antimicrobial activity against Escherichia coli than untreated supernatants. When single toxins and two-toxin combinations were assessed, toxicity effects were shown to be nonadditive (including synergism, potentiation, and antagonism), suggesting interactive toxin effects when cells are exposed to mycotoxin combinations. The results show that Fusarium toxins, individually and in mixtures, activate distinct antimicrobial defense mechanisms possessing the potential to alter the intestinal microbiota through diminished antimicrobial effects. Moreover, by evaluating toxin mixtures, this improved understanding of toxin effects will enable more effective risk assessments for common mycotoxin combinations observed in contaminated food and feed.
doi:10.1128/AEM.03277-12
PMCID: PMC3623212  PMID: 23354708
17.  Electrophoretic mobility confirms reassortment bias among geographic isolates of segmented RNA phages 
Background
Sex presents evolutionary costs and benefits, leading to the expectation that the amount of genetic exchange should vary in conditions with contrasting cost-benefit equations. Like eukaryotes, viruses also engage in sex, but the rate of genetic exchange is often assumed to be a relatively invariant property of a particular virus. However, the rates of genetic exchange can vary within one type of virus according to geography, as highlighted by phylogeographic studies of cystoviruses. Here we merge environmental microbiology with experimental evolution to examine sex in a diverse set of cystoviruses, consisting of the bacteriophage ϕ6 and its relatives. To quantify reassortment we manipulated – by experimental evolution – electrophoretic mobility of intact virus particles for use as a phenotypic marker to estimate genetic exchange.
Results
We generated descendants of ϕ6 that exhibited fast and slow mobility during gel electrophoresis. We identified mutations associated with slow and fast phenotypes using whole genome sequencing and used crosses to establish the production of hybrids of intermediate mobility. We documented natural variation in electrophoretic mobility among environmental isolates of cystoviruses and used crosses against a common fast mobility ϕ6 strain to monitor the production of hybrids with intermediate mobility, thus estimating the amount of genetic exchange. Cystoviruses from different geographic locations have very different reassortment rates when measured against ϕ6, with viruses isolated from California showing higher reassortment rates than those from the Northeastern US.
Conclusions
The results confirm that cystoviruses from different geographic locations have remarkably different reassortment rates –despite similar genome structure and replication mechanisms– and that these differences are in large part due to sexual reproduction. This suggests that particular viruses may indeed exhibit diverse sexual behavior, but wide geographic sampling, across varying environmental conditions may be necessary to characterize the full repertoire. Variation in reassortment rates can assist in the delineation of viral populations and is likely to provide insight into important viral evolutionary dynamics including the rate of coinfection, virulence, and host range shifts. Electrophoretic mobility may be an indicator of important determinants of fitness and the techniques herein can be applied to the study of other viruses.
doi:10.1186/1471-2148-13-206
PMCID: PMC3848951  PMID: 24059872
Sex; Population structure; Hybridization; Cooperation; Experimental evolution; Ecology
18.  Respiratory virus surveillance in hospitalised pneumonia patients on the Thailand-Myanmar border 
BMC Infectious Diseases  2013;13:434.
Background
Pneumonia is a significant cause of morbidity and mortality in the developing world. Viruses contribute significantly to pneumonia burden, although data for low-income and tropical countries are scarce. The aim of this laboratory-enhanced, hospital-based surveillance was to characterise the epidemiology of respiratory virus infections among refugees living on the Thailand-Myanmar border.
Methods
Maela camp provides shelter for ~45,000 refugees. Inside the camp, a humanitarian organisation provides free hospital care in a 158-bed inpatient department (IPD). Between 1st April 2009 and 30th September 2011, all patients admitted to the IPD with a clinical diagnosis of pneumonia were invited to participate. Clinical symptoms and signs were recorded and a nasopharyngeal aspirate (NPA) collected. NPAs were tested for adenoviruses, human metapneumovirus (hMPV), influenza A & B, and RSV by PCR.
Results
Seven hundred eight patient episodes (698 patients) diagnosed as pneumonia during the enhanced surveillance period were included in this analysis. The median patient age was 1 year (range: < 1-70), and 90.4% were aged < 5 years. At least one virus was detected in 53.7% (380/708) of episodes. Virus detection was more common in children aged < 5 years old (<1 year: OR 2.0, 95% CI 1.2-3.4, p = 0.01; 1-4 years: OR 1.4, 95% CI 0.8-2.3, p = 0.2). RSV was detected in 176/708 (24.9%); an adenovirus in 133/708 (18.8%); an influenza virus in 68/708 (9.6%); and hMPV in 33/708 (4.7%). Twenty-eight episodes of multiple viral infections were identified, most commonly adenovirus plus another virus. RSV was more likely to be detected in children <5 years (OR 12.3, 95% CI 3.0-50.8, p = 0.001) and influenza viruses in patients ≥5 years (OR 2.8, 95% CI 1.5-5.4, p = 0.002). IPD treatment was documented in 702/708 cases; all but one patient received antimicrobials, most commonly a beta-lactam (amoxicillin/ampicillin +/−gentamicin in 664/701, 94.7%).
Conclusions
Viral nucleic acid was identified in the nasopharynx in half the patients admitted with clinically diagnosed pneumonia. Development of immunisations targeting common respiratory viruses is likely to reduce the incidence of pneumonia in children living refugee camps and similar settings.
doi:10.1186/1471-2334-13-434
PMCID: PMC3847692  PMID: 24498873
Pneumonia; Refugee; Influenza; Respiratory; Virus
19.  Effects of telephone health mentoring in community-recruited chronic obstructive pulmonary disease on self-management capacity, quality of life and psychological morbidity: a randomised controlled trial 
BMJ Open  2013;3(9):e003097.
Objectives
To assess benefits of telephone-delivered health mentoring in community-based chronic obstructive pulmonary disease (COPD).
Design
Cluster randomised controlled trial.
Setting
Tasmanian general practices: capital city (11), large rural (3), medium rural (1) and small rural (16).
Participants
Patients were invited (1207) from general practitioner (GP) databases with COPD diagnosis and/or tiotropium prescription, response rate 49% (586), refused (176) and excluded (criteria: smoking history or previous study, 68). Spirometry testing (342) confirmed moderate or severe COPD in 182 (53%) patients.
Randomisation
By random numbers code, block stratified on location, allocation by sequentially numbered, opaque and sealed envelopes.
Intervention
Health mentor (HM) group received regular calls to manage illness issues and health behaviours from trained community health nurses using negotiated goal setting: problem solving, decision-making and action planning. Control: usual care (UC) group received GP care plus non-interventional brief phone calls.
Outcomes
Measured at 0, 6 and 12 months, the Short Form 36 (SF-36) and St George’s Respiratory Questionnaire (SGRQ, primary); Partners In Health (PIH) Scale for self-management capacity, Hospital Anxiety and Depression Scale (HADS), Center for Epidemiologic Studies-Depression (CES-D) questionnaire, Post-Traumatic Stress Disorder Checklist, Satisfaction with life and hospital admissions (secondary).
Results
182 participants with COPD (age 68±8 years, 62% moderate COPD and 53% men) were randomised (HM=90 and UC=92). Mixed model regression analysis accounting for clustering, adjusting for age, gender, smoking status and airflow limitation assessed efficacy (regression coefficient, β, reported per 6-month visit). There was no difference in quality of life between groups, but self-management capacity increased in the HM group (PIH overall 0.15, 95% CI 0.03 to 0.29; knowledge domain 0.25, 95% CI 0.00 to 0.50). Anxiety decreased in both groups (HADS A 0.35; 95% CI −0.65 to −0.04) and coping capacity improved (PIH coping 0.15; 95% CI 0.04 to 0.26).
Conclusions
Health mentoring improved self-management capacity but not quality of life compared to regular phone contact, which itself had positive effects where decline is generally expected.
doi:10.1136/bmjopen-2013-003097
PMCID: PMC3773640  PMID: 24014482
Preventive Medicine; Primary Care
20.  Neonatal Intensive Care in a Karen Refugee Camp: A 4 Year Descriptive Study 
PLoS ONE  2013;8(8):e72721.
Background
A third of all deaths in children aged <5 years occur in the neonatal period. Neonatal intensive care is often considered too complex and expensive to be implemented in resource poor settings. Consequently the reductions that have been made in infant mortality in the poorest countries have not been made in the neonatal period. This manuscript describes the activities surrounding the introduction of special care baby unit (SCBU) in a refugee setting and the resulting population impact.
Methods
A SCBU was developed in Maela refugee camp on the Thailand-Myanmar border. This unit comprised of a dedicated area, basic equipment, drugs and staff training. Training was built around neonatal guidelines, comprising six clinical steps: recognition, resuscitation, examination, supportive medical care, specialised medical care, and counselling of parents with sick newborns.
Results
From January 2008 until December 2011, 952 infants were admitted to SCBU. The main admission diagnoses were early onset neonatal sepsis, jaundice and prematurity. Early prematurity (<34 weeks) carried the highest risk of mortality (OR 9.5, 95% CI 5.4–16.5, p<0.001). There was a significant decrease in mortality from 19.3% (2008) to 4.8% (2011) among the infants admitted for prematurity (p=0.03). The neonatal mortality in Maela camp as a whole declined by 51% from 21.8 to 10.7 deaths per 1000 live births over the corresponding period (p=0.04). Staff expressed more confidence in their ability to take care of neonates and there was a more positive attitude towards premature infants.
Conclusion
Neonatal mortality can be reduced in a resource poor setting by introduction of a simple low cost unit specialising in care of sick neonates and run by local health workers following adequate training. Training in recognition and provision of simple interventions at a high standard can increase staff confidence and reduce fatalistic attitudes towards premature neonates.
doi:10.1371/journal.pone.0072721
PMCID: PMC3749980  PMID: 23991145
21.  A Prospective Evaluation of Real-Time PCR Assays for the Detection of Orientia tsutsugamushi and Rickettsia spp. for Early Diagnosis of Rickettsial Infections during the Acute Phase of Undifferentiated Febrile Illness 
One hundred and eighty febrile patients were analyzed in a prospective evaluation of Orientia tsutsugamushi and Rickettsia spp. real-time polymerase chain reaction (PCR) assays for early diagnosis of rickettsial infections. By paired serology, 3.9% (7 of 180) and 6.1% (11 of 180) of patients were confirmed to have acute scrub or murine typhus, respectively. The PCR assays for the detection of O. tsutsugamushi and Rickettsia spp. had high specificity (99.4% [95% confidence interval (CI): 96.8–100] and 100% [95% CI: 97.8–100], respectively). The PCR results were also compared with immunoglobulin M (IgM) immunofluorescence assay (IFA) on acute sera. For O. tsutsugamushi, PCR sensitivity was twice that of acute specimen IgM IFA (28.6% versus 14.3%; McNemar's P = 0.3). For Rickettsia spp., PCR was four times as sensitive as acute specimen IgM IFA (36.4% versus 9.1%; P = 0.08), although this was not statistically significant. Whole blood and buffy coat, but not serum, were acceptable specimens for these PCRs. Further evaluation of these assays in a larger prospective study is warranted.
doi:10.4269/ajtmh.12-0600
PMCID: PMC3741253  PMID: 23732256
22.  Field Evaluation of Culture plus Latex Sweep Serotyping for Detection of Multiple Pneumococcal Serotype Colonisation in Infants and Young Children 
PLoS ONE  2013;8(7):e67933.
Background
Nasopharyngeal swab (NPS) culture by World Health Organisation (WHO) methodology underestimates multiple pneumococcal serotype colonisation compared to a simple culture and latex sweep method. The impacts of this on descriptions of pneumococcal serotype distributions and colonisation dynamics in infancy are not clear.
Methods
8,736 NPS collected from infants enrolled into a longitudinal study were processed to evaluate the field utility of the latex sweep method. 1,107 had previously been cultured by WHO methodology. Additionally, colonisation results were compared in 100 matched pairs of infants, where swabs from an individual were cultured either by WHO or latex sweep method.
Results
In 1,107 swabs cultured by both methods, the latex sweep method was three times more likely to detect colonisation with multiple pneumococcal serotypes than the WHO method (p<0.001). At least one common serotype was identified in 91.2% of swabs from which typeable pneumococci were detected by both methods. Agreement improved with increasing colonisation density (p = 0.03). Estimates of age at first pneumococcal acquisition and colonisation duration were not affected by culture/serotyping method. However, a greater number of serotype carriage episodes were detected in infants cultured by latex sweep (p = 0.03). The overall rate of non-vaccine type pneumococcal acquisition was also greater in infants cultured by latex sweep (p = 0.04).
Conclusions
Latex sweep serotyping was feasible to perform on a large specimen collection. Multiple serotype colonisation detection was significantly improved compared with WHO methodology. However, use of the latex sweep method is unlikely to significantly alter colonisation study serotype distribution or colonisation dynamics results.
doi:10.1371/journal.pone.0067933
PMCID: PMC3699458  PMID: 23844133
23.  What's new in the diagnosis and management of food allergy in children? 
Asia Pacific Allergy  2013;3(2):88-95.
This article reviews the recent advances in the diagnosis and management of IgE mediated food allergy in children. It will encompass the emerging technology of component testing; moves to standardization of the allergy food challenge; permissive diets which allow for inclusion of extensively heated food allergens with allergen avoidance; and strategies for accelerating tolerance and food desensitization including the use of adjuvants for specific tolerance induction.
doi:10.5415/apallergy.2013.3.2.88
PMCID: PMC3643055  PMID: 23667831
Child; Food; Allergy; Diagnosis
25.  PDGF maintains stored calcium through a non-clustering Orai1 mechanism but evokes clustering if the ER is stressed by store-depletion 
Circulation research  2012;111(1):66-76.
Rationale
Calcium entry through Orai1 channels drives vascular smooth muscle cell migration and neointimal hyperplasia. The channels are activated by the important growth factor platelet-derived growth factor (PDGF). Channel activation is suggested to depend on store-depletion which redistributes and clusters stromal interaction molecule 1 (STIM1) which then co-clusters and activates Orai1.
Objective
To determine the relevance of STIM1 and Orai1 redistribution in PDGF responses.
Methods and Results
Vascular smooth muscle cells were cultured from human saphenous vein. STIM1 and Orai1 were tagged with green and red fluorescent proteins to track them in live cells. Under basal conditions the proteins were mobile but mostly independent of each other. Inhibition of sarco-endoplasmic reticulum calcium ATPase led to store-depletion and dramatic redistribution of STIM1 and Orai1 into co-clusters. PDGF did not evoke redistribution even though it caused calcium-release and Orai1-mediated calcium entry in the same time period. After chemical blockade of Orai1-mediated calcium entry, however, PDGF caused redistribution. Similarly, mutagenic disruption of calcium flux through Orai1 caused PDGF to evoke redistribution, showing that calcium flux through the wild-type channels had been filling the stores. Acidification of the extracellular medium to pH 6.4 caused inhibition of Orai1-mediated calcium entry and conferred capability for PDGF to evoke complete redistribution and co-clustering.
Conclusions
The data suggest that PDGF has a non-clustering mechanism by which to activate Orai1 channels and maintain calcium stores replete. Redistribution and clustering become important, however, when the ER stress signal of store-depletion arises, for example when acidosis inhibits Orai1 channels.
doi:10.1161/CIRCRESAHA.111.263616
PMCID: PMC3605802  PMID: 22556336
calcium channel; calcium stores; vascular smooth muscle cells; growth factor; acidosis

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