Improved inference of time-varying reproduction numbers during infectious disease outbreaks

Accurate estimation of the parameters characterising infectious disease transmission is vital for optimising control interventions during epidemics. A valuable metric for assessing the current threat posed by an outbreak is the time-dependent reproduction number, i.e. the expected number of secondary cases caused by each infected individual. This quantity can be estimated using data on the numbers of observed new cases at successive times during an epidemic and the distribution of the serial interval (the time between symptomatic cases in a transmission chain). Some methods for estimating the reproduction number rely on pre-existing estimates of the serial interval distribution and assume that the entire outbreak is driven by local transmission. Here we show that accurate inference of current transmissibility, and the uncertainty associated with this estimate, requires: (i) up-to-date observations of the serial interval to be included, and; (ii) cases arising from local transmission to be distinguished from those imported from elsewhere. We demonstrate how pathogen transmissibility can be inferred appropriately using datasets from outbreaks of H1N1 influenza, Ebola virus disease and Middle-East Respiratory Syndrome. We present a tool for estimating the reproduction number in real-time during infectious disease outbreaks accurately, which is available as an R software package (EpiEstim 2.2). It is also accessible as an interactive, user-friendly online interface (EpiEstim App), permitting its use by non-specialists. Our tool is easy to apply for assessing the transmission potential, and hence informing control, during future outbreaks of a wide range of invading pathogens.

Improved inference of time-varying reproduction numbers during infectious disease outbreaks

Accurate estimation of the parameters characterising infectious disease transmission is vital for optimising control interventions during epidemics. A valuable metric for assessing the current threat posed by an outbreak is the time-dependent reproduction number, i.e. the expected number of secondary cases caused by each infected individual. This quantity can be estimated using data on the numbers of observed new cases at successive times during an epidemic and the distribution of the serial interval (the time between symptomatic cases in a transmission chain). Some methods for estimating the reproduction number rely on pre-existing estimates of the serial interval distribution and assume that the entire outbreak is driven by local transmission. Here we show that accurate inference of current transmissibility, and the uncertainty associated with this estimate, requires: (i) up-to-date observations of the serial interval to be included, and; (ii) cases arising from local transmission to be distinguished from those imported from elsewhere. We demonstrate how pathogen transmissibility can be inferred appropriately using datasets from outbreaks of H1N1 influenza, Ebola virus disease and Middle-East Respiratory Syndrome. We present a tool for estimating the reproduction number in real-time during infectious disease outbreaks accurately, which is available as an R software package (EpiEstim 2.2). It is also accessible as an interactive, user-friendly online interface (EpiEstim App), permitting its use by non-specialists. Our tool is easy to apply for assessing the transmission potential, and hence informing control, during future outbreaks of a wide range of invading pathogens.

A52 MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity

Middle East respiratory syndrome coronavirus (MERS-CoV) causes a zoonotic respiratory disease of global public health concern, and dromedary camels are the only proven source of this zoonotic infection. Although MERS-CoV infection is ubiquitous in dromedaries across Africa and the Arabian Peninsula, the continuous appearance of zoonotic MERS cases in humans is confined to the Arabian Peninsula. MERS-CoV from Africa has hitherto been poorly studied. Here, we report the genetic and phenotypic characterization of MERS-CoV from dromedaries in African countries. Phylogenetically, viruses from dromedaries in Africa formed a monophyletic clade, which we have provisionally designated as virus clade C. Molecular dating analyses of MERS-CoV, including clade C viruses, suggests that the ancestral MERS-CoV in dromedaries could have spread to the two continents within a short timeframe. Camel MERS-CoVs from west and north African countries form a subclade (C1) that shares genetic signatures of a major deletion in the accessory gene ORF4b. Compared with human and camel MERS-CoV from Saudi Arabia, virus isolates from Burkina Faso (BF785) and Nigeria (Nig1657) had lower virus replication competence in Calu-3 cells and in ex vivo cultures of human bronchus and lung, and BF785 replicated to lower titer in lungs of human DPP4-transduced mice. However, it is still inconclusive whether ORF4b deletions may lead to the reduced replication competence of BF785 and Nig1657. Genetic and phenotypic differences in West African viruses may be relevant to the zoonotic potential of MERS-CoV.

A meta-analysis of observational epidemiological studies of Newcastle disease in African agro-systems, 1980-2009

Newcastle disease (ND) is one of the most important and widespread avian pests. In Africa, backyard poultry production systems are an important source of protein and cash for poor rural livelihoods. ND mortality in these production systems is important and seriously disrupts benefits derived from it. This study undertook an African continental approach of ND epidemiology in backyard poultry. After a systematic literature review of studies published from 1980 to 2009, a meta-analysis of spatio-temporal patterns of serological prevalence and outbreak occurrence was performed. Average ND serological prevalence was estimated at 0·67 [95% confidence interval (CI) 0·58-0·75] in regions characterized by humid ecosystems, high human and poultry densities and low altitudes; 0·36 (95% CI 0·30-0·41) in dry ecosystems at intermediate altitude where human and poultry densities are low and 0·27 (95% CI 0·19-0·38) in mountain ecosystems where human and poultry densities are intermediate. In terms of seasonality, ND outbreaks occur mostly during the dry seasons in Africa, when environmental conditions are likely to be harshest for backyard poultry. In addition, a phylogeographical analysis revealed the regionalization of ND virus strains, their potential to evolve towards a higher pathogenicity from the local viral pool and suggests a risk for vaccine strains to provide new wild strains. These results present for the first time a continent-wide approach to ND epidemiology in Africa. More emphasis is needed for ND management and control in rural African poultry production systems.

Coexisting with wildlife in transfrontier conservation areas in Zimbabwe: cattle owners' awareness of disease risks and perceptions of the role played by wildlife

Diseases transmitted between wildlife and livestock may have significant impacts on local farmers' health, livestock health and productivity, overall national economies, and conservation initiatives, such as Transfrontier Conservation Areas in Southern Africa. However, little is known on local farmers' awareness of the potential risks, and how they perceive the role played by wildlife in the epidemiology of these diseases. We investigated the knowledge base regarding livestock diseases of local cattle owners living at the periphery of conservation areas within the Great Limpopo TFCA and the Kavango-Zambezi TFCA in Zimbabwe, using free-listing and semi-structured questionnaires during dipping sessions. The results suggest that information related to cattle diseases circulates widely between cattle farmers, including between different socio-cultural groups, using English and vernacular languages. Most respondents had an accurate perception of the epidemiology of diseases affecting their livestock, and their perception of the potential role played by wildlife species was usually in agreement with current state of veterinary knowledge. However, we found significant variations in the cultural importance of livestock diseases between sites, and owners' perceptions were not directly related with the local abundance of wildlife. As the establishment of TFCAs will potentially increase the risk of Transboundary Animal Diseases, we recommend an increased participation of communities at a local level in the prioritisation of livestock diseases control and surveillance, including zoonoses.

[Usefulness of the Guidelines of the Spanish Society of Pulmonology and Thoracic Surgery (SEPAR) in identifying the causes of chronic cough]

OBJECTIVE

The usefulness of the recently published guidelines of the Spanish Society of Pulmonology and Thoracic Surgery (SEPAR) on the diagnosis and treatment of chronic cough has not yet been demonstrated. The objectives of the present study were a) to evaluate the usefulness of the SEPAR guidelines for identifying the possible causes of chronic cough, and b) to determine the most frequent causes of chronic cough treated by primary care physicians.

METHODS

We carried out a prospective descriptive study that included 57 consecutive patients (mean age, 62 years) seeking medical attention for chronic cough in a primary health care area. The patients were evaluated using the algorithm proposed in the SEPAR guidelines, whereby the diagnostic procedure is divided into 3 phases in function of complexity. Phase I was carried out at the primary care level, and phases II and III at a hospital pneumology department.

RESULTS

For 56 patients (98%), the potential cause of cough was identified: for 52 (91%) in phase I; for 3 (5%), in phase II; and for 1 (2%), in phase III. In 30 patients (53%), a single cause was identified; in 20 (36%), 2 causes; and in 6 (11%), more than 2 causes. Considered individually, the most common causes were postnasal drip in 26 cases (46%), the use of cough-inducing drugs (10 of them attributable to angiotensin-converting enzyme inhibitors) in 16 (28%), asthma in 15 (27%), infection in 13 (23%), gastroesophageal reflux in 12 (21%), and others in 9 (16%).

CONCLUSIONS

The application of the SEPAR guidelines on chronic cough is useful for the identification of its causes. The use of angiotensin-converting enzyme inhibitors is a frequent cause of coughs diagnosed at the level of primary outpatient health care.

[Acute confusional syndrome associated with obstructive sleep apnea aggravated by acidosis secondary to oral acetazolamide treatment]

Acute confusional syndrome, or delirium, is a transitory mental state characterized by the fluctuating alteration of awareness and attention levels. We present the case of a patient with acute confusional syndrome associated with obstructive sleep apnea syndrome (OSAS) aggravated by metabolic acidosis induced by oral acetazolamide treatment.A 70-year-old man with no history of neurological disease was referred with a clinical picture consistent with acute confusional syndrome presenting between midnight and dawn. During the admission examination infectious, toxic, and neurologic causes, or those related to metabolic or heart disease were ruled out. Arterial blood gases measured during one of the nighttime episodes of acute confusional syndrome showed mild hypoxia and hypercapnia with mixed acidosis. Signs and symptoms suggestive of OSAS had been developing over the months prior to admission, with snoring, sleep apnea, and moderate daytime drowsiness. Polysomnography demonstrated severe OSAS with an apnea-hypopnea index of 38. Mean arterial oxygen saturation was 83%; time oxygen saturation remained below 90% was 44%. The attending physician ordered the withdrawal of oral acetazolamide, which was considered the cause of the metabolic component of acidosis. Treatment with continuous positive airway pressure was initiated at 9 cm H2O, after a titration polysomnographic study. The patient continued to improve.OSAS, for which very effective treatment is available, should be included among diseases that may trigger acute confusional syndrome.

Multiresidue analysis of fungicides in soil by sonication-assisted extraction in small columns and gas chromatography

A rapid multiresidue method for the simultaneous determination of 14 fungicides in soil was developed. Fungicides were exacted from soil, placed in small columns, by sonication-assisted extraction with ethyl acetate. The effect of residue residence time and soil moisture content on the fungicide recovery was studied. Residue levels in soil were determined by gas chromatography with electron-capture and nitrogen-phosphorus detection. Residue identities were confirmed by gas chromatography coupled with mass spectrometry, in the selected ion monitoring mode. Recovery studies were carried out at 0.5, 0.1 and 0.05 microg/g fortification levels for each fungicide, and average recoveries obtained for these compounds ranged from 80 to 104% with relative standard deviations between 1 and 8%. The method is linear over the range assayed, 0.5-0.05 microg/g, and the detection limit for the fungicides studied varied from 2 to 10 microg/kg.

Analysis of endosulfan isomers and endosulfan sulfate in air and tomato leaves by gas chromatography with electron-capture detection and confirmation by gas chromatography-mass spectrometry

Rapid analytical methods for the determination of endosulfan isomers and endosulfan-sulfate in air and plant samples were developed. The insecticides were trapped from air using a column containing Florisil and extracted with a low volume of ethyl acetate, assisted by sonication. Pesticide residues were determined by gas chromatography with electron-capture detection using a nonpolar capillary column. Residue identities were confirmed by gas chromatography coupled with mass spectrometry. Recoveries of these compounds from air samples were always higher than 78% with an RSD lower than 11% and the detection limits obtained were at least 0.3 ng/l air. Leaf samples were homogenised with ethyl acetate and extracts cleaned-up on an aluminium oxide column. Pesticides were eluted with a hexane-ethyl acetate (80:20, v/v) mixture. Recoveries obtained from plant samples were higher than 78% with an RSD lower than 14% and detection limits in leaves were 0.02 microg/g for each pesticide. These methods were applied to study the volatilisation of endosulfan from tomato leaves under laboratory conditions. A volatilisation rate near 1% of the initial amount of endosulfan per hour was obtained during the first 24 h at room temperature.

Self-aggregation of surfactant protein A

Environmental factors of physiological relevance such as pH, calcium, ionic strength, and temperature can affect the state of self-aggregation of surfactant protein A (SP-A). We have studied the secondary structure of different SP-A aggregates and analyzed their fluorescence characteristics. (a) We found that self-aggregation of SP-A can be Ca(2+)-dependent. The concentration of Ca(2+) needed for half-maximal self-association (K(a)(Ca)()2+) depended on the presence of salts. Thus, at low ionic strength, K(a)(Ca)()2+ was 2.3 mM, whereas at physiological ionic strength, K(a)(Ca)()2+ was 2.35 microM. Circular dichroism and fluorescence measurements of Ca(2+)-dependent SP-A aggregates indicated that those protein aggregates formed in the absence of NaCl are structurally different from those formed in its presence. (b) We found that self-aggregation of SP-A can be pH-dependent. Self-aggregation of SP-A induced by H(+) was highly influenced by the presence of salts, which reduced the extent of self-association of the protein. The presence of both salts and Ca(2+) attenuated even more the effects of acidic media on SP-A self-aggregation. (c) We found that self-aggregation of SP-A can be temperature-dependent. At 20 degrees C, SP-A underwent self-aggregation at physiological but not at low ionic strength, in the presence of EDTA. All of these aggregates were dissociated by either adding EDTA (a), increasing the pH to neutral pH (b), or increasing the temperature to 37 degrees C (c). Dissociation of Ca(2+)-induced protein aggregates at low ionic strength was accompanied by an irreversible loss of both SP-A secondary structure and SP-A-dependent lipid aggregation properties. On the other hand, temperature-dependent experiments indicated that a structurally intact collagen-like domain was required for either Ca(2+)- or Ca(2+)/Na(+)-induced SP-A self-aggregation but not for H(+)-induced protein aggregation.

Evidence against a direct antimicrobial role of H2O2 in the infection of plants by Erwinia chrysanthemi

We have investigated the role of bacterial resistance to oxidative stress in pathogenesis. The oxyR gene from the pathogenic bacterium Erwinia chrysanthemi has been characterized. It is closely related to that found in Escherichia coli (88% overall amino acid identity). An E. chrysanthemi oxyR mutant strain was constructed by marker exchange. After induction with a sublethal dose of H2O2, this mutant was more sensitive to H2O2 and showed reduced levels of catalase and glutathione reductase activities, compared with the wild type. The oxyR mutant was unable to form individual colonies on agar plates unless catalase was added exogenously. However, it retained full virulence in potato tubers and tobacco leaves. These results suggest that the host-produced H2O2 has no direct antimicrobial effect on the interaction of E. chrysanthemi with the two plant species.

Respiratory depression following epidural morphine in an infant of three months of age

Epidural administration of combinations of opioids and a local anaesthetic provides prompt and effective analgesia and is increasingly used in paediatric anaesthesia. However, respiratory depression by rostral spread of opioid in the CSF is by far the greatest concern after epidural morphine. An infant of three months of age underwent portoenterostomy (Kasai's operation) for extrahepatic biliary duct atresia. A median approach at the L3-L4 epidural interspace was used and a dose of 1 ml.kg-1 of 0.125% bupivacaine with adrenaline 1:400000 mixed with 50 micrograms.kg-1 morphine was injected using a 19 gauge Tuohy needle. Six h after epidural morphine, the infant developed respiratory depression with an increase in drowsiness, miosis and decreased respiratory rate. Low arterial saturation (SpO2) was detected by pulse oximetry and confirmed by blood gas analysis. An intravenous bolus of 5 micrograms.kg-1 naloxone followed by a 3-h infusion of 2 micrograms.kg-1.h-1 resulted in complete reversal of signs and symptoms of respiratory depression. Epidural opioids should be limited to paediatric patients admitted to specialized recovery units for the first postoperative day.

Comparison of lipid aggregation and self-aggregation activities of pulmonary surfactant-associated protein A

1. We compared the Ca2+ dependence of the self-aggregation of surfactant protein A (SP-A) with that of vesicle aggregation induced by SP-A. The Ca2+ concentration required for half-maximal activity of lipid aggregation was 0.74 +/- 0.29 microM (n = 4) for pig SP-A and 98 +/- 5 microM (n = 2) for dog SP-A. In contrast, the threshold concentration of Ca2+ required to induce self-association of both pig and dog SP-A was 0.5 mM. The Ca2+ concentration needed for half-maximal self-association was 2.36 +/- 0.15 mM (n = 4) and 0.70 +/- 0.06 mM (n = 2) for pig and dog SP-A respectively. 2. We also compared the effect of Ca2+ on the trypsin sensitivity of lipid-free and membrane-bound SP-A. At 1 microM Ca2+, the tryptic digestion patterns of dog and pig lipid-free SP-A were quite different. Dog SP-A was very sensitive to proteolysis, being almost completely digested by 30 min, while pig SP-A was very resistant, even after 12 h. After protein aggregation of lipid-free SP-A (at 5 mM Ca2+), the accessibility of the trypsin cleavage targets of the protein depended on the SP-A species (self-aggregated pig SP-A became more sensitive to degradation than its non-aggregated form, whereas self-aggregated dog SP-A was less susceptible). In contrast, membrane-bound SP-A, from either pig or dog, was clearly protected from trypsin degradation at both low (1 microM) or high (1 mM) Ca2+ concentrations. The protection was slightly higher at 1 mM Ca2+ when the extent of lipid/SP-A aggregates was maximal. 3. On the other hand, vesicle aggregation activity of SP-A was decreased by 30-40% by removing the oligosaccharide moiety of the protein, whereas self-aggregation was not influenced by deglycosylation. The presence of mannan (at concentrations not lower than 10 micrograms/microliters) decreased vesicle aggregation induced by dog and pig SP-A by a mechanism that is independent of the binding of mannan to the carbohydrate-binding domain of SP-A. Self-aggregation of SP-A was not affected by the presence of sugars. 4. From these results, we conclude that: (1) the process of lipid aggregation induced by SP-A cannot be correlated with that of self-association of the protein occurring at supramillimolar concentrations of Ca2+; and (2) the N-linked carbohydrate moiety of SP-A and the ability of SP-A to bind carbohydrates are not involved in lipid aggregation.

Tryptophan fluorescence study on the interaction of pulmonary surfactant protein A with phospholipid vesicles

The fluorescence characteristics of surfactant protein A (SP-A) from porcine and human bronchoalveolar lavage were determined in the presence and absence of lipids. After excitation at either 275 or 295 nm, the fluorescence emission spectrum of both proteins was characterized by two maxima at about 326 and 337 nm, indicating heterogeneity in the emission of the two tryptophan residues of SP-A, and also revealing a partially buried character for these fluorophores. Interaction of both human and porcine SP-A with various phospholipid vesicles resulted in an increase in the fluorescence emission of tryptophan without any shift in the emission wavelength maxima. This change in intrinsic fluorescence was found to be more pronounced in the presence of dipalmitoyl phosphatidylcholine (DPPC) than with dipalmitoyl phosphatidylglycerol (DPPG), DPPC/DPPG (7:3, w/w) and 1-palmitoyl-sn-glycerol-3-phosphocholine (LPC). Intrinsic fluorescence of SP-A was almost completely unaffected in the presence of egg phosphatidylcholine (egg-PC). In addition, we demonstrated a shielding of the tryptophan fluorescence from quenching by acrylamide on interaction of porcine SP-A with DPPC, DPPG or LPC. This shielding was most pronounced in the presence of DPPC. In the case of human SP-A, shielding was only observed on interaction with DPPC. From the intrinsic fluorescence measurements as well as from the quenching experiments, we concluded that the interaction of some phospholipid vesicles with SP-A produces a conformational change on the protein molecule and that the interaction of SP-A with DPPC is stronger than with other phospholipids. This interaction appeared to be independent of Ca2+ ions. Physiological ionic strength was found to be required for the interaction of SP-A with negatively charged vesicles of either DPPG or DPPC/DPPG (7:3, w/w). Intrinsic fluorescence of SP-A was sensitive to the physical state of the DPPC vesicles. The increase in intrinsic fluorescence of SP-A in the presence of DPPC vesicles was much stronger when the vesicles were in the gel state than when they were in the liquid-crystalline state. The effect produced by SP-A on the lipid vesicles was also dependent on temperature. The aggregation of DPPC, DPPC/DPPG (7:3, w/w) or dimyristoyl phosphatidylglycerol (DMPG) was many times higher below the phase-transition temperature of the corresponding phospholipids. These results strongly indicate that the interaction of SP-A with phospholipid vesicles requires the lipids to be in the gel phase.

Application of seroepidemiology in identification of local foci in a malarious community in Palawan, The Philippines

The value of seroepidemiology in malaria control programs has long been recognized, but its use in such situations has been limited. We therefore conducted a seroepidemiologic study in a frontier community on Palawan Island, The Philippines, an area where malaria is highly endemic. The first serologic survey was done at the end of the rainy season and the second was done during the dry season. The sera were examined using an indirect fluorescent antibody test. There was a significant difference in the geometric mean reciprocal titer (GMRT) during the rainy season as compared with the GMRT during the dry season. There were seasonal changes in the distribution of high- and low-titer responses, which is suggestive of the occurrence of recent past malaria epidemics. The differences in the geographic distribution of high and low titers were indicative of permanent foci of malaria transmission in this community. Results of a parallel parasitologic study were consistent with those of the serologic study. These findings may be of practical value not only in the proper reorientation of the local malaria control program, but of those of other endemic countries as well.

Comparison between intra- and extracellular surfactant in respiratory distress induced by oleic acid

The present study compares the phospholipid distribution and protein content in bronchoalveolar lavage, purified extracellular surfactant and lamellar bodies isolated from rabbits killed at intervals of 2.5, 12 and 24 h after oleic acid administration. The data suggest that the alteration of pulmonary surfactant could be partially due to the type II cell response to the injury.