PaperPlayer biorxiv epidemiology

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/719641v1?rss=1

Authors: Mwenda, V., Niyomwungere, A., Oyugi, E., Githuku, J., Obonyo, M., Roka, Z. G.

Abstract:

BackgroundCholera affects 1.3-4 million people globally and causes 21000-143,000 deaths annually. Nairobi County in Kenya reported cholera cases since April 2017. We investigated to identify associated factors and institute control measures.nnMethodsWe reviewed the line-list of patients admitted at the Kenyatta National referral Hospital, Nairobi and performed descriptive epidemiology. We carried out a frequency-matched case control study, using facility-based cases and community controls. We defined a case as acute onset of watery diarrhoea of at least >3 stools/24hours with or without vomiting in person of any age, admitted in Kenyatta National Hospital as from July 1st, 2017. We calculated odds ratios and their respective 95% confidence intervals. We also took water samples at water reservoirs, distribution and consumer points, and made observation on hygiene and sanitation conditions in the community.nnResultsWe reviewed 71 line-listed cases; median age 30 years (range 2-86 years); 45 (63%) were male. First case was admitted on 14th April 2017. Culture was performed on 44 cases, 30 (68%) was positive for Vibrio cholerae, biotype El-Tor, serotype Ogawa. There were 2 deaths (case fatality ratio 2.8%). Age-group [≥]25 years was most affected. Drinking unchlorinated water (aOR 14.57, 95% CI 4.44-47.83), eating in public places (aOR 9.45, 95% CI 3.07-29.12) sourcing water from non-Nairobi city water company source (aOR 4.92, 95% CI 1.56-15.52) and having drank untreated water in the previous week before the outbreak (aOR 3.21, 95% CI 1.12-9.24) were independently associated with being a case in the outbreak. Out of 28 water samples, 4 (14%) had >180 coliforms/100mls; all were at consumer points.nnConclusionPoor water quality and sanitation were responsible for this outbreak. We recommended adequate, clean water supply to unplanned settlements in Nairobi County, as well education of residents on water treatment at the household level.nnAuthor summaryCholera, a disease causing outbreaks in areas with low standards of hygiene and sanitation has afflicted humans for millennia. It is caused by a bacterium, Vibrio Cholerae, transmitted mainly through water contaminated by faecal matter. The resultant disease is acute watery diarrhoea, which causes death rapidly due to dehydration and shock. Virtually brought under control in the developed world due to improvements in hygiene, the disease still ravages many communities in low and middle income countries, as well as regions affected by conflict or natural disasters. In outbreak situations, rapid response in water treatment, sanitation improvement and setting up of cholera treatment centres for rehydration therapy reduces impact and saves lives. Long-term control can only be achieved through sustainable improvements in sanitation and standards of living. Case control studies in outbreak situations provide quick, actionable information to public health specialists during outbreak response. This study provides a cholera outbreak investigation in an urban informal settlement setting; the approach reported here can guide in outbreak investigations and response in similar settings globally.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/714980v1?rss=1

Authors: He, Z.-h., Jiang, B.-g., Gao, Z.-h., Shao, Z.-t., Zhang, Y., Liu, Z.-x., Li, Y.-q., Pu, E.-n., Tang, L., Yao, M.-g., Jia, N., von Fricken, M. E., Jiang, J.-f., Cao, W.-c., Du, C.-h.

Abstract:

BackgroundLyme disease is caused by Borrelia burgdorferisensulato (BBSL) which is usually found in wild and domestic mammals worldwide. Human cases of B. burgdorferi infections have been identified in China, but little direct surveillance of potential rodent reservoirs has been performed in Yunnan Province, Southwestern China. Yunnan Province is a tropical area with a diverse topographic range and sustains a high biodiversity of small mammals that could potentially play an important role in the transmission of a variety of B. burgdorferigenospecies.nnMethods3659 small mammals were captured in 159 sample siteslocated 23 countries inYunnan Province and screened for BBSL infection by nested PCR based on 5S-23S rRNA intergenic spacer gene of BBSL.Univariate and multivariate forward stepwise logistic regression analysis was used to access the association between infections and related risk factors.nnResultsInfection with BBSL was confirmed in 3.99%(146/3659) of small mammals. Significant differences in prevalence rates of BBSL were observed at varying landscape types and altitudes.Small mammals in forested areas had higher prevalence rates than other landscape types as did small mammals found at altitudes greater than 2500 meters. The 5S-23S rRNA intergenic spacergene revealed that there were 5 genotype of BBSL, including B. afzelii, B. burgdorferisensustricto, B.japonica, B.gariniiand B.valaisiana, which demonstrate the genetic diversity and regional distribution.nnConclusionsThere exists a wide distribution and genetic diversity of endemic BBSL in Southwestern China, warranting further investigations and monitoring of clinical disease in individuals presenting with symptoms of Lyme disease in these areas.nnAuthor summaryLyme disease is caused by Borrelia burgdorferi sensu lato (BBSL) which is usually found in wild and domestic mammals worldwide. Human cases of Borrelia burgdorferi sensu lato infections have been identified in China, but little direct surveillance of potential rodent reservoirs has been performed in Southwestern China. This study documents potential small mammal reservoir hosts collected from a large of sample sites from different landscape types and altitudes, with PCR and sequencing identifying the wide distribution and genetic diversity of endemic Borrelia burgdorferi sensu lato in Southwestern China. This was the first report that B. japonica was detected in Apodemus draco and Niviventer excelsior in China. This study adds to body of literature on Borrelia burgdorferi sensu lato in China. This work will provide insight regarding small mammals to target for surveillance and we access the association between gender, developmental stage of rodents, environmental landscape and altitude to better prevent human exposure.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/708743v1?rss=1

Authors: Oliveira, J. F., Rodrigues, M. S., Skalinski, L. M., Santos, A. E., Costa, L. C., Cardim, L. L., Paixao, E. S., Costa, M. d. C. N., Oliveira, W. K., Barreto, M. L., Teixeira, M. G., Andrade, R. F. S.

Abstract:

The co-circulation of different arboviruses in the same time and space poses a significant threat to public health given their rapid geographic dispersion and serious health, social, and economic impact. Therefore, it is crucial to have high quality of case registration to estimate the real impact of each arboviruses in the population. In this work, a Vector Autoregressive (VAR) model was developed to investigate the interrelationships between discarded and confirmed cases of dengue, chikungunya, and Zika in Brazil. We used data from the Brazilian National Notifiable Diseases Information System (SINAN) from 2010 to 2017. There were three peaks in the series of dengue notification in this period occurring in 2013, 2015 and in 2016. The series of reported cases of both Zika and chikungunya reached their peak in late 2015 and early 2016. The VAR model shows that the Zika series have a significant impact on the dengue series and vice versa, suggesting that several discarded and confirmed cases of dengue could actually have been cases of Zika. The model also suggests that the series of confirmed and discarded chikungunya cases are almost independent of the cases of Zika, however, affecting the series of dengue. In conclusion, co-circulation of arboviruses with similar symptoms could have lead to misdiagnosed diseases in the surveillance system. We argue that the routinely use of mathematical and statistical models in association with traditional symptom-surveillance could help to decrease such errors and to provide early indication of possible future outbreaks. These findings address the challenges regarding notification biases and shed new light on how to handle reported cases based only in clinical-epidemiological criteria when multiples arboviruses co-circulate in the same population.

Author summaryArthropod-borne viruses (arboviruses) transmission is a growing health problem worldwide. The real epidemiological impact of the co-circulation of different arboviruses in the same urban spaces is a recent phenomenon and there are many issues to explore. One of them is the misclassification due to the scarce availability of confirmatory laboratory tests. This establishes a challenge to identify, distinguish and estimate the number of infections when different arboviruses co-circulate. We propose the use of multivariate time series analysis to understand how the weekly notification of suspected cases of dengue, chikungunya and Zika, in Brazil, affected each other. Our results suggest that the series of Zika significantly impact on the series of dengue and vice versa, indicating that several discarded and confirmed cases of dengue might actually have been Zika cases. The results also suggest that the series of confirmed cases of chikungunya are almost independent of those of dengue and Zika. Our findings shed light on yet hidden aspects on the co-circulation of these three viruses based on reported cases. We believe the present work provides a new perspective on the longitudinal analysis of arboviruses transmission and call attention to the challenge in dealing with biases in case notifications when multiple arboviruses circulate in the same urban environment.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/707356v1?rss=1

Authors: Adams, C., Young, D., Gastanaduy, P. A., Paul, P., Marsh, Z., Hall, A. J., Lopman, B. A.

Abstract:

The role of individual case characteristics, such as symptoms or demographics, in norovirus transmissibility is poorly understood. Six nursing home norovirus outbreaks occurring in South Carolina, U.S. from 2014 to 2016 were examined. We aimed to quantify the contribution of symptoms and other case characteristics in norovirus transmission using the reproduction number (REi) as an estimate of individual case infectivity and to examine how transmission changes over the course of an outbreak. Individual estimates of REi were calculated using a maximum likelihood procedure to infer the average number of secondary cases generated by each case. The associations between case characteristics and REi were estimated using a multivariate mixed linear model. Outbreaks began with one to three index case(s) with large estimated REis (range: 1.48 to 8.70) relative to subsequent cases. Of the 209 cases, 155 (75%) vomited, 164 (79%) had diarrhea, and 158 (76%) were nursing home residents (vs. staff). Cases who vomited infected 2.74 (95% CI: 1.90, 3.94) more individuals than non-vomiters, cases with diarrhea infected 1.62 (95% CI: 1.09, 2.41) more individuals than cases without diarrhea, and resident-cases infected 1.69 (95% CI: 1.18, 2.42) more individuals than staff-cases. Index cases tended to be residents (vs. staff) who vomited and infected considerably more secondary cases compared to non-index cases. Results suggest that individuals, particularly residents, who vomit are more infectious and tend to drive norovirus transmission in U.S. nursing home norovirus outbreaks. While diarrhea also plays a role in norovirus transmission, it is to a lesser degree than vomiting in these settings. Results lend support for prevention and control measures that focus on cases who vomit, particularly if those cases are residents.nnAuthor summaryThe majority of all norovirus outbreaks reported to the CDC occur in long-term care facilities (LTCFs), including nursing homes, where older residents are at risk for more severe or prolonged infection. Because there is currently no publicly available norovirus vaccine, sound control measures are key to controlling norovirus outbreaks, but there is little evidence that standard control measures are effective in reducing the size and/or duration of LTCF norovirus outbreaks. Hence, studies leading to a better understanding of disease spread and prevention of additional cases, and thus more effective control measures, are needed. To this end, we aimed to quantify factors associated with norovirus transmission and to examine how transmission changes over the course of an outbreak. We show that vomiting and, to a lesser extent, diarrhea are critical in initiating and sustaining norovirus transmission in U.S. nursing home norovirus outbreaks. We also show that nursing home residents, rather than staff, are the primary drivers of transmission. Results suggest that control measures focusing on cases who vomit, particularly if those cases are residents, would be most effective at curtailing norovirus transmission in these settings.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/699553v1?rss=1

Authors: Kapologwe, N., Kalolo, A., Isanzu, N. H., Borghi, J., Kibusi, S. M.

Abstract:

BackgroundStructural quality of maternal health services remains a key indicator of highly performing health care system. Evidence attest to the fact that introduction of the new interventions in the health care system does not necessarily lead into improvement of the target outcome, such as quality of health services delivered. This study aimed at assessing the structural quality of maternal health services prior to introduction of Direct Health Facility Financing (DHFF) program.nnMethodsThis was a cross-sectional study, conducted in 42 public primary health facilities between January and mid February 2018. Observational were used to collect the data from health facilities. The collected information was on privacy, hygiene and sanitation, obstetric emergences, sterilization, maternal death audit reviews and waste management. Collected data were analyzed by using SPSS.nnResultsAll 42 (100%) primary health facilities that were assessed were public primary health facilities, of which 14 (33.3%) were health centers and 28 were dispensaries. The furthest primary health facilities from the district head office were 140 Kms and the nearest 2 Kms. Focusing on; - privacy, hygiene and sanitation, obstetric emergences, sterilization, maternal death audit reviews and waste management assessed eight areas of Structural qualities. Majority (68.9%) of Health Centers has less than 39 skilled staff while some of them they have up to 129 health service providers and majority (92.8%) of Dispensaries have less than 15 staff and some have 1 staff.nnBy comparing Dispensary and Health center performances on structural quality indicated relatively low differences among the attributes assessed. Specifically, they did not show statistical significant differences except for obstetric emergencies (p < .005), sterilization (p=. 034) and overall structural quality (p=. 018). With regard to rural-urban performance on structural quality, there was no statistical significant difference on total performance. Similarly, there was no significant differences between rural and urban health facilities on other assessed attributes of structural quality (p >.05) except for sterilization in which urban facilities performed significantly higher than the rural facilities [M=41.2, SD=27.7, 61.3, SD=28.4, respectively (p= .028)]. On the other hand, marginal differences were observed on individual assessed attributes. For examples, rural facilities performed relatively higher than urban ones on privacy (41.2 and 32.0), maternal death reviews (31.4 and 30.7) and waste management (49.0 and 47.3) respectively.nnConclusionGenerally facilities performed low on the structural quality indicators of maternal health services provision however; they had high performance on sterilization and emergence obstetric care.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/697052v1?rss=1

Authors: Jing, Q., Wu, S., He, Z., Yuan, L., Ma, M., Bai, Z., Jiang, L., Marshall, J., Lu, J., Yang, Z.

Abstract:

BackgroundDengue fever is a mosquito-borne infectious disease that has caused major health problems. Variations in dengue virus (DENV) genes are important features of epidemic outbreaks. However, the associations of DENV genes with epidemic scale have not been extensively examined. Here, we assessed new genotype invasion of DENV-1 isolated from Guangzhou in China to evaluate associations with epidemic outbreaks.nnMethodology/Principal FindingsWe used DENV-1 strains isolated from sera of dengue cases from 2002 to 2016 in Guangzhou for complete genome sequencing. A neighbor-joining phylogenetic tree was constructed to elucidate the genotype characteristics and determine if new genotype invasion correlated with major outbreaks. In our study, a new genotype invasion event was observed during each significant outbreak period in 2002-2003, 2006-2007 and 2013-2014. Genotype II was the main epidemic genotype in 2003 and before. Invasion of genotype I in 2006 caused an unusual outbreak with 765 cases (relative risk (RR)=16.24, 95% confidence interval (CI) =12.41-21.25). At the middle and late stages of the 2013 outbreak, genotype III was introduced to Guangzhou as a new genotype invasion responsible for 37340 cases with RR 541.73 (95%CI=417.78-702.45), after which genotypes I and III began co-circulating. Base mutations occurred after new genotype invasion, and the gene sequence of NS3 protein had the lowest average similarity ratio (99.82%), followed by the gene sequence of E protein (99.86%), as compared to the 2013 strain.nnConclusions/SignificanceGenotype replacement and co-circulation of multiple DENV-1 genotypes were observed. New genotype invasion was highly correlated with local unusual outbreaks. In addition to DENV-1 genotype I in the unprecedented outbreak in 2014, new genotype invasion by DENV-1 genotype III occurred in Guangzhou.nnAuthor SummaryNew genotype invasion of dengue virus highly correlates with the massive outbreaks. In this study, we examined the association of the genotype of dengue virus serorype 1 (DENV-1) from human cases through complete genome sequencing with outbreak scale during 2002 and 2016 in Guangzhou, China. It was observed that genotype replacement and co-circulation of multiple genotypes occurred. Most importantly, it indicated that new genotype invasion was highly related with local unusual outbreaks in major outbreak periods in 2002-2003, 2006-2007 and 2013-2014. DENV-1 genotype II was the main epidemic genotype in 2003 and before. Invasion of genotype I in 2006 caused an unusual outbreak with 765 cases reported. In addition to genotype I circulation, new genotype invasion by genotype III was the key determinant for the 2014 massive outbreak reaching the highest number of cases with 37340. Furthermore, base mutations appeared after genotype III invasion, and the gene sequence of NS3 protein had the lowest average similarity ratio, followed by the gene sequence of E protein, as compared to the 2013 strain.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/688994v1?rss=1

Authors: Sung, E.-S., Jeong, J.-A., Choi, C. K., Shin, M.-H.

Abstract:

ObjectiveSeveral previous studies have evaluated associations between body mass index (BMI) and self-rated health (SRH); however, the results were inconsistent. This study aimed to examine the association between BMI and SRH in Korean adults.nnMethodsThe study was conducted in 214,997 adults who participated in the 2016 Korean Community Health Survey. Participants were categorized into four groups based on BMI: underweight (<18.5 kg/m2), normal weight (18.5-24.9 kg/m2), overweight (25.0-29.9 kg/m2), or obese ([≥]30.0 kg/m2). Multivariate Poisson regression analysis with sampling weights and robust variance estimators was performed to evaluate the relationship between BMI categories and poor SRH.nnResultsThere was a J-shaped association between BMI and poor SRH in both sexes, with the lowest risk observed in the normal weight group in both sexes. Compared with normal weight subjects, the age and lifestyle adjusted prevalence rate ratios for poor SRH were 1.61 (95% CI, 1.50-1.74) for underweight, 1.16 (95% CI, 1.11-1.21) for overweight, and 2.35 (95% CI, 2.13-2.58) for obese men; and 1.24 (95% CI, 1.17-1.32) for underweight, 1.26 (95% CI, 1.22-1.31) for overweight, and 1.77 (95% CI, 1.64-1.91) for obese women.nnConclusionsIn a cross-sectional study using a nationally representative survey, there was a nonlinear relationship between BMI and poor SRH. This relationship was more prominent in men than in women. Prospective studies are needed to further clarify the relationship between BMI and SRH.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/688895v1?rss=1

Authors: Yan, L., Wen, X., Dyer, A. R., Chen, H., Zhou, L., Elliott, P., Wu, Y., Chan, Q., Zhao, L.

Abstract:

ObjectiveThis study aimed to collect data to compare blood pressure values between random-zero sphygmomanometers and automated oscillometric devices and generate equations to convert blood pressure values from one device to the other.nnMethodsOmron HEM-907, a widely used automated oscillometric device in many epidemiologic surveys and cohort studies, was compared here with random-zero sphygmomanometers. Two hundred and one participants aged 40-79 years (37% men) were enrolled and randomly assigned to one of two groups with blood pressure measurement first taken by automated oscillometric devices or by random-zero sphygmomanometers. The study design enabled comparisons of blood pressure values between random-zero sphygmomanometers and two modes of this automated oscillometric device - automated and manual, and assessment of effects of measurement order on blood pressure values.nnResultsAmong all participants, mean blood pressure levels were lowest when measured with random-zero sphygmomanometers compared with both modes of automated oscillometric devices. Several variables, including age and gender, were found to contribute to the blood pressure differences between random-zero sphygmomanometers and automated oscillometric devices. Equations were developed using multiple linear regression after taking those variables into account to convert blood pressure values by random-zero sphygmomanometers to automated oscillometric devices.nnConclusionEquations developed in this study could be used to compare blood pressure values between epidemiologic and clinical studies or identify shift of blood pressure distribution over time using different devices for blood pressure measurements.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/688705v1?rss=1

Authors: Sagamiko, F. D., Muma, J. B., Karimuribo, E. D., Mwanza, A. A., Mfune, R. L., Sindato, C., Kavunga, H., Hangombe, B. M.

Abstract:

BackgroundBrucellosis is an infectious zoonotic disease that affects humans, livestock and wildlife.nnMethodsA cross-sectional study was conducted in Mbeya region between November 2015 and January 2016 to investigate the seroprevalence of human brucellosis and identify associated risk factors among individuals in risky occupations in Mbeya Region. A total of 425 humans from six occupational categories were serially tested for Brucella antibodies using the Rose Bengal Plate Test (RBPT) and competitive Enzyme Linked Immunosorbent Assay (c-ELISA), for screening and confirmation, respectively. A questionnaire survey was administered to participants collect epidemiological data.nnResultsThe overall seroprevalence among the high risk occupational individuals was 1.41% (95% CI: 0.01-0.03). Seroprevalence among the different occupations were as follows: shepherds 1.33% (95% CI: 0.14-0.22); butcher men 5.26% (95% CI: 0.10-0.17) and abattoir workers 1.08% (95% CI: 0.39-0.49). Seroprevalence was noted to vary according to occupation type, milk consumption behaviour, age and sex. Butcher men recorded the highest seroprevalence (5.0%) while individuals who consumed unboiled milk had a higher seroprevalence (1.56%) compared to those who drunk boiled milk. High seropositivity (2.25%) was observed among the age group of 1-10 years while male individuals had a higher seroprevalence (1.41%) than females (0%). Butcher men were at higher risk of exposure compared to other professions.nnConclusionOur findings show the presence of brucellosis in occupationally exposed individuals in Mbeya region. There is need to sensitize the exposed individuals in order to reduce the risk of acquiring Brucella infections from animals and animal products This also calls for public health awareness about the disease, and implementation of control measures that will prevent further spread of brucellosis within and outside the study area..nnAuthor summaryBrucellosis is a bacterial zoonosis that has evolved to establish itself as an occupational and food-borne disease Worldwide. It is responsible for huge economic losses incurred by livestock keepers and poses a public health risk to humans in most developing countries. In Tanzania, which has the 3rd highest cattle population in Africa, many studies that have been done show that brucellosis exists in livestock, especially in cattle and wildlife. However, very few studies have reported on human brucellosis. The disease has been reported to occur in humans who have direct exposure to cattle or cattle products like livestock farmers, abattoir workers, veterinarians, shepherds and farm workers in many developing countries. A few studies in Tanzania have reported seroprevalences among these high-risk occupations; however, the disease has not been fully described in Mbeya region. This study was therefore aimed at filling these information gaps and contributing to the existing body of knowledge.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/679001v1?rss=1

Authors: Perini, M., Piazza, A., Panelli, S., Di Carlo, D., Corbella, M., Gona, F., Vailati, F., Marone, P., Cirillo, D. M., Farina, C., Zuccotti, G. V., Comandatore, F.

Abstract:

In this work we present EasyPrimer, a user-friendly online tool developed to assist pan-PCR and High Resolution Melting (HRM) primer design. The tool finds the most suitable regions for primer design in a gene alignment and returns a clear graphical representation of their positions on the gene. EasyPrimer is particularly useful in difficult contexts, e.g. on gene alignments of hundreds of sequences and/or on highly variable genes. HRM analysis is an emerging method for fast and cost saving bacterial typing and an HRM scheme of six primer sets on five Multi-Locus Sequence Type (MLST) genes is already available for Klebsiella pneumoniae. We validated the tool designing a scheme of two HRM primer sets on the hypervariable gene wzi of Klebsiella pneumoniae and compared the two schemes. The wzi scheme resulted to have a discriminatory power comparable to the HRM MLST scheme, using only one third of primer sets. Then we successfully used the wzi HRM primer scheme to reconstruct a Klebsiella pneumoniae nosocomial outbreak in few hours. The use of hypervariable genes reduces the number of HRM primer sets required for bacterial typing allowing to perform cost saving, large-scale surveillance programs.

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