Recent Cholera Publications on PubMed

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Outbreak investigation of cholera outbreak in a slum area of urban Wardha, India: An interventional epidemiological study.

May 2, 2019
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Outbreak investigation of cholera outbreak in a slum area of urban Wardha, India: An interventional epidemiological study.

J Family Med Prim Care. 2019 Mar;8(3):1112-1116

Authors: Goswami S, Jha A, Sivan SP, Dambhare D, Gupta SS

Abstract
Introduction: Cholera, though a preventable and treatable disease, is still regarded as an important public health problem in developing countries including India. Migration, unhygienic living conditions, overcrowding, open field defecation, and ignorance about the spread of disease are the major reasons for the occurrence of cholera in the slum areas. Cholera was detected in the stool sample of a 3-year-old child from a slum area of urban Wardha, which demanded an urgent outbreak investigation to be carried out before it progressed into an epidemic.
Materials and Methods: This was a cross-sectional epidemiological study, where we have used pretested, predesigned epidemiological case sheets obtained from IDSP. A case definition was proposed before beginning the investigation. Linelisting, collection of stool and water samples, immediate referral, and treatment of the patients suffering from loose stool and/or vomiting were performed. A detailed epidemiological report was made with recommendations and plan of action that was forwarded to the district health system.
Results: In all, 28 suspected cases of cholera were line listed. Among the affected population, more than half of the suspected cases were from the age group of 0-10 years of age. Males were more affected when compared with females. The overall attack rate was 27% and case fatality rate was 0%. There was positive history of travel in the index case. Two of the water samples were found to be unsatisfactory for drinking.
Conclusion: The investigation report was soon developed and shared with the district health authorities, and recommendations were given to prevent such outbreaks in future.

PMID: 31041259 [PubMed]

The case for ring vaccinations with special consideration of oral cholera vaccines.

April 30, 2019
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The case for ring vaccinations with special consideration of oral cholera vaccines.

Hum Vaccin Immunother. 2018;14(8):2069-2074

Authors: Deen J, von Seidlein L

Abstract
Ring vaccinations create a zone of immune contacts around a case to prevent further disease transmission and have been successfully employed in the eradication of smallpox and the control of other infections. Millions of oral cholera vaccine (OCV) doses have been effectively deployed through mass vaccination campaigns. But there are situations when the OCV supply, resources, and time are limited and alternative strategies need to be considered. People living in close proximity of cholera cases often share risk factors such as contaminated water supply and poor sanitation. Targeting people within a given radius around a cholera case for intervention including vaccination, improved water supply and sanitation may be a practical and effective approach. A ring oral cholera vaccination strategy could be considered before, after or as an alternative to a mass vaccination approach. We review here the use of the ring vaccinations in general and specifically during cholera outbreaks.

PMID: 29630444 [PubMed - indexed for MEDLINE]

Use of oral cholera vaccine as a vaccine probe to determine the burden of culture-negative cholera.

April 26, 2019
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Use of oral cholera vaccine as a vaccine probe to determine the burden of culture-negative cholera.

PLoS Negl Trop Dis. 2019 03;13(3):e0007179

Authors: Im J, Islam MT, Ahmmed F, Kim DR, Chon Y, Zaman K, Khan AI, Ali M, Marks F, Qadri F, Clemens JD

Abstract
Analyses of stool from patients with acute watery diarrhea (AWD) using sensitive molecular diagnostics have challenged whether fecal microbiological cultures have acceptably high sensitivity for cholera diagnosis. If true, these findings imply that current estimates of the global burden of cholera, which rely largely on culture-confirmation, may be underestimates. We conducted a vaccine probe study to evaluate this possibility, assessing whether an effective killed oral cholera vaccine (OCV) tested in a field trial in a cholera-endemic population conferred protection against cholera culture-negative AWD, with the assumption that if cultures are indeed insensitive, OCV protection in such cases should be detectable. We re-analysed the data of a Phase III individually-randomized placebo-controlled efficacy trial of killed OCVs conducted in Matlab, Bangladesh in 1985. We calculated the protective efficacy (PE) of a killed whole cell-only (WC-only) OCV against first-episodes of cholera culture-negative AWD during two years of post-dosing follow-up. In secondary analyses, we evaluated PE against cholera culture-negative AWD by age at vaccination, season of onset, and disease severity. In this trial 50,770 people received at least 2 complete doses of either WC-only OCV or placebo, and 791 first episodes of AWD were reported during the follow-up period, of which 365 were culture-positive for Vibrio cholerae O1. Of the 426 culture-negative AWD episodes, 215 occurred in the WC group and 211 occurred in the placebo group (adjusted PE = -1.7%; 95%CI -23.0 to 13.9%, p = 0.859). No measurable PE of OCV was observed against all or severe cholera culture-negative AWD when measured overall or by age and season subgroups. In this OCV probe study we detected no vaccine protection against AWD episodes for which fecal cultures were negative for Vibrio cholera O1. Results from this setting suggest that fecal cultures from patients with AWD were highly sensitive for cholera episodes that were etiologically attributable to this pathogen. Similar analyses of other OCV randomized controlled trials are recommended to corroborate these findings.

PMID: 30870416 [PubMed - indexed for MEDLINE]

Defining endemic cholera at three levels of spatiotemporal resolution within Bangladesh.

April 25, 2019
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Defining endemic cholera at three levels of spatiotemporal resolution within Bangladesh.

Nat Genet. 2018 07;50(7):951-955

Authors: Domman D, Chowdhury F, Khan AI, Dorman MJ, Mutreja A, Uddin MI, Paul A, Begum YA, Charles RC, Calderwood SB, Bhuiyan TR, Harris JB, LaRocque RC, Ryan ET, Qadri F, Thomson NR

Abstract
Although much focus is placed on cholera epidemics, the greatest burden occurs in settings in which cholera is endemic, including areas of South Asia, Africa and now Haiti1,2. Dhaka, Bangladesh is a megacity that is hyper-endemic for cholera, and experiences two regular seasonal outbreaks of cholera each year3. Despite this, a detailed understanding of the diversity of Vibrio cholerae strains circulating in this setting, and their relationships to annual outbreaks, has not yet been obtained. Here we performed whole-genome sequencing of V. cholerae across several levels of focus and scale, at the maximum possible resolution. We analyzed bacterial isolates to define cholera dynamics at multiple levels, ranging from infection within individuals, to disease dynamics at the household level, to regional and intercontinental cholera transmission. Our analyses provide a genomic framework for understanding cholera diversity and transmission in an endemic setting.

PMID: 29942084 [PubMed - indexed for MEDLINE]

Food insecurity and self-reported cholera in Haitian households: An analysis of the 2012 Demographic and Health Survey.

April 24, 2019
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Food insecurity and self-reported cholera in Haitian households: An analysis of the 2012 Demographic and Health Survey.

PLoS Negl Trop Dis. 2019 01;13(1):e0007134

Authors: Richterman A, Franke MF, Constant G, Jerome G, Ternier R, Ivers LC

Abstract
BACKGROUND: Both cholera and food insecurity tend to occur in impoverished communities where poor access to food, inadequate sanitation, and an unsafe water supply often coexist. The relationship between the two, however, has not been well-characterized.
METHODS: We performed a secondary analysis of household-level data from the 2012 Demographic and Health Survey in Haiti, a nationally and sub-nationally representative cross-sectional household survey conducted every five years. We used multivariable logistic regression to evaluate the relationship between household food security (as measured by the Household Hunger Scale) and (1) reported history of cholera since 2010 by any person in the household and (2) reported death by any person in the household from cholera (among households reporting at least one case). We performed a complete case analysis because there were <1% missing data for all variables.
RESULTS: There were 13,181 households in the survey, 2,104 of which reported at least one household member with history of cholera. After adjustment for potential confounders, both moderate hunger in the household [Adjusted Odds Ratio (AOR) 1.51, 95% Confidence Interval (CI) 1.30-1.76; p <.0001] and severe hunger in the household (AOR 1.73, 95% CI 1.45-2.08; p <.0001) were significantly associated with reported history of cholera in the household. Severe hunger in the household (AOR 1.85, 95% CI 1.05-3.26; p = 0.03), but not moderate hunger in the household, was independently associated with reported death from cholera in households with at least one case of cholera.
CONCLUSIONS: In this study we identified an independent relationship between household food insecurity and both reported history of cholera and death from cholera in a general population. The directionality of this relationship is uncertain and should be further explored in future prospective research.

PMID: 30699107 [PubMed - indexed for MEDLINE]

Better Cholera Counts Through Machine Learning Models.

April 23, 2019
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Better Cholera Counts Through Machine Learning Models.

JAMA. 2019 Apr 09;321(14):1343

Authors: Abbasi J

PMID: 30964509 [PubMed - indexed for MEDLINE]

Detection of Uncommon Enteric Bacterial Pathogens from Acute Diarrheal Specimens Using SYBR-Green Real Time PCR.

April 23, 2019
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Detection of Uncommon Enteric Bacterial Pathogens from Acute Diarrheal Specimens Using SYBR-Green Real Time PCR.

Jpn J Infect Dis. 2019 Mar 25;72(2):88-93

Authors: Chowdhury G, Stine OC, Rajendran K, Mukhopadhyay AK, Okamoto K, Ramamurthy T

Abstract
Acute diarrheal disease is a major health problem, and the second most common cause of death in children under 5 years of age. Conventional diagnostic methods are laborious, time consuming, and occasionally inaccurate. We used SYBR-Green real-time PCR for the detection of 10 uncommon bacterial pathogens using fecal specimens from acute diarrheal patients. In the SYBR-Green real-time PCR assay, the products formed were identified based on a melting point temperature curve analysis, and the assay was validated with the respective reference strain. In a retrospective study, we tested 1,184 stool specimens previously examined using conventional culture methods. Enterotoxigenic Bacteriodes fragilis was detected in 6.7% of the samples followed by enterotoxigenic Bacillus cereus (5.1%), Clostridium perfringens (3.9%), and Aeromonas hydrophila (3.8%). In the prospective study, A. hydrophila, Staphylococcus aureus, and C. perfringens were predominantly detected in 11 > 5 years of age, using real-time PCR. The real-time PCR assay is comprehensive, rapid, accurate, and well suited for surveillance or diagnostic purposes to detect uncommon bacterial pathogens, and should be useful in initiating appropriate care and thereby reducing patient risk.

PMID: 30381678 [PubMed - indexed for MEDLINE]

Genome sequence of a multidrug resistant Klebsiella pneumoniae ST78 with high colistin resistance isolated from a patient.

April 22, 2019
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Genome sequence of a multidrug resistant Klebsiella pneumoniae ST78 with high colistin resistance isolated from a patient.

J Glob Antimicrob Resist. 2019 Apr 18;:

Authors: Paul M, Narendrakumar L, R Vasanthakumary A, Joseph I, Thomas S

Abstract
OBJECTIVES: Multidrug resistantKlebsiella pneumoniae with colistin resistance have been considered as a major concern in healthcare settings. The present study aims to evaluate the genome wide distribution of antibiotic resistance genes in K. pneumoniae CRKP I with high colistin resistance isolated from a patient.
METHODS: The genome was sequenced on Illumina MiSeq platform. De novo genome assembly was performed using SPAdes version 3.0.0. and the genome sequence was analysed using bioinformatics tools from the Center of Genomic Epidemiology.
RESULTS: The genome of K. pneumoniae CRKP I is 5.1 Mb in size and contain different classes of antibiotic resistance genes. The isolate was highly resistant to colistin due to the point mutation in mgrB gene, the negative regulator of PhoP/PhoQ two component system. MLST analysis showed that K. pneumoniae CRKP I belongs to sequence type 78 (ST78).
CONCLUSION: These data provide useful information for comparative genomic analysis regarding the dissemination of antibiotic resistance genes in K. pneumoniae. To our knowledge, this is the first report of a MDR K. pneumoniae with high colistin resistance belonging to ST78 causing infections in human beings.

PMID: 31005731 [PubMed - as supplied by publisher]

Recurrent Cholera Outbreaks, Democratic Republic of the Congo, 2008-2017.

April 20, 2019
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Recurrent Cholera Outbreaks, Democratic Republic of the Congo, 2008-2017.

Emerg Infect Dis. 2019 May;25(5):856-864

Authors: Ingelbeen B, Hendrickx D, Miwanda B, van der Sande MAB, Mossoko M, Vochten H, Riems B, Nyakio JP, Vanlerberghe V, Lunguya O, Jacobs J, Boelaert M, Kebela BI, Bompangue D, Muyembe JJ

Abstract
In 2017, the exacerbation of an ongoing countrywide cholera outbreak in the Democratic Republic of the Congo resulted in >53,000 reported cases and 1,145 deaths. To guide control measures, we analyzed the characteristics of cholera epidemiology in DRC on the basis of surveillance and cholera treatment center data for 2008-2017. The 2017 nationwide outbreak resulted from 3 distinct mechanisms: considerable increases in the number of cases in cholera-endemic areas, so-called hot spots, around the Great Lakes in eastern DRC; recurrent outbreaks progressing downstream along the Congo River; and spread along Congo River branches to areas that had been cholera-free for more than a decade. Case-fatality rates were higher in nonendemic areas and in the early phases of the outbreaks, possibly reflecting low levels of immunity and less appropriate prevention and treatment. Targeted use of oral cholera vaccine, soon after initial cases are diagnosed, could contribute to lower case-fatality rates.

PMID: 31002075 [PubMed - in process]

Haitian cholera outbreak-United Nations admits involvement.

April 16, 2019
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Haitian cholera outbreak-United Nations admits involvement.

J Infect Public Health. 2017 Jul - Aug;10(4):483-484

Authors: Qadir TF, Pasha SB, Fatima H, Ahmed S

PMID: 28277251 [PubMed - indexed for MEDLINE]

Credibility, integrity, transparency & courage: The Haitian Cholera outbreak and the United Nations (UN).

April 16, 2019
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Credibility, integrity, transparency & courage: The Haitian Cholera outbreak and the United Nations (UN).

J Infect Public Health. 2018 Jan - Feb;11(1):140-141

Authors: Houghton F, Norris A

PMID: 28209469 [PubMed - indexed for MEDLINE]

Unmasking herd protection by an oral cholera vaccine in a cluster-randomized trial.

April 11, 2019
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Unmasking herd protection by an oral cholera vaccine in a cluster-randomized trial.

Int J Epidemiol. 2019 Apr 09;:

Authors: Ali M, Qadri F, Kim DR, Islam T, Im J, Ahmmed F, Chon Y, Islam Khan A, Zaman K, Marks F, Clemens JD

Abstract
BACKGROUND: Several studies have shown that inactivated, whole-cell oral cholera vaccines (OCVs) confer both direct protection on vaccinees and herd protection on populations. Because our earlier cluster-randomized effectiveness trial (CRT) in urban Bangladesh failed to detect OCV herd protection, we reanalysed the trial to assess whether herd effects were masked in our original analysis.
METHODS: A total of 267 270 persons were randomized to 90 approximately equal-sized clusters. In 60 clusters persons aged 1 year and older were eligible to receive OCV and in 30 clusters persons received no intervention and served as controls. We analysed OCV protection against severely dehydrating cholera for the entire clusters, as in our original analysis, and for subclusters consisting of residents of innermost households. We hypothesized that if OCV herd protection was attenuated by cholera transmission into the clusters from the outside in this densely populated setting, herd protection would be most evident in the innermost households.
RESULTS: During 2 years of follow-up of all residents of the clusters, total protection (protection of OCV recipients relative to control residents) was 58% [95% confidence interval (CI): 43%, 70%; P<0.0001], indirect protection (protection of non-OCV recipients in OCV clusters relative to control participants) was 16% (95% CI: -20%, 41%; P=0.35) and overall OCV protection (protection of all residents in the OCV clusters relative to control residents) was 46% (95% CI: 30%, 59%; P<0.0001). Analyses of the inner 75% and 50% households of the clusters showed similar findings. However, total protection was 75% (95% CI: 50%, 87%, P<0.0001), indirect protection 52% (95% CI: -9%, 79%; P=0.08) and overall protection 72% (95% CI: 49%, 84%; P<0.0001) for the innermost 25% households.
CONCLUSION: Consistent with past studies, substantial OCV herd protective effects were identified, but were unmasked only by analysing innermost households of the clusters. Caution is needed in defining clusters for analysis of vaccine herd effects in CRTs of vaccines.

PMID: 30968110 [PubMed - as supplied by publisher]

Exploring the development of a household cholera-focused health literacy scale in James Town, Accra.

April 11, 2019
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Exploring the development of a household cholera-focused health literacy scale in James Town, Accra.

J Infect Public Health. 2019 Jan - Feb;12(1):62-69

Authors: Tutu RA, Gupta S, Elavarthi S, Busingye JD, Boateng JK

Abstract
BACKGROUND: Foodborne diseases are significant reasons for in-patient and out-patient morbidity in Ghana. Of the foodborne illnesses reported in the country, cholera incidence and outbreaks have resulted in food-related mortality since the disease was first reported in the 1970s. Cholera is now endemic in the country. This study attempts to develop and pilot a tool to measure household health literacy among the urban poor in James Town, a cholera endemic neighborhood.
METHODS: A survey questionnaire was developed based on four of the World Health Organization's (WHO) recommendations on issues for measurement of health literacy in low- and middle-income countries. The instrument was administered to 401 households in the community. We undertook reliability and validity analyses. T-test, Kruskal Wallis test, and Mann-Whitney test were used to examine the association between the health literacy scores of the scale and subscales and the demographic characteristics of households.
RESULTS: The reliability analyses showed that the instrument was internally consistent (Cronbach alpha=0.762). All the subscales were reliable except the beliefs about health and healthcare subscale. Based on content and construct validity analyses, 13 items were used for further examination of health literacy. We found that majority of households know about the information, education, and communication materials and 52% of households indicated that these materials remind them about the dangers of cholera. About 39% of the households decide together as a unit on steps to avoid getting cholera during an outbreak. Overall health literacy scores and the subscales were significantly associated with sex, age, marital status, and educational level of household head. Specifically, females, being married, increasing age and higher household income had a significant association with higher health literacy scores.
CONCLUSION: Household units in James Town impacts individual health literacy through: family discussions; access to information, education, and communication materials on cholera; and intentional efforts made to get information on cholera risk factors.

PMID: 30219358 [PubMed - indexed for MEDLINE]

Prevalence of water-related diseases and groundwater (drinking-water) contamination in the suburban municipality of Mont Ngafula, Kinshasa (Democratic Republic of the Congo).

April 10, 2019

Prevalence of water-related diseases and groundwater (drinking-water) contamination in the suburban municipality of Mont Ngafula, Kinshasa (Democratic Republic of the Congo).

J Environ Sci Health A Tox Hazard Subst Environ Eng. 2019 Apr 09;:1-11

Authors: Kapembo ML, Al Salah DMM, Thevenon F, Laffite A, Bokolo MK, Mulaji CK, Mpiana PT, Poté J

Abstract
An epidemiological survey conducted among users of water points and medical institutions in the N'djili Kilambu neighborhood of Kinshasa in Democratic Republic of the Congo, indicates that waterborne diseases have already affected more than 60% of the patients admitted to local clinics between 2013 and 2017. In order to raise public and political awareness about this hazardous health issue resulting from the lack of safely managed sanitation systems, this study investigates the microbial quality of drinking water from local water resources. Water samples were collected from nine wells and streams used as drinking sources, and analyzed for Fecal Indicator Bacteria (FIB), including Escherichia coli, Enterococcus, and Total Coliforms. Physicochemical parameters (pH, electrical conductivity, O2, and soluble ions (Na+, K+, PO43-, SO42-, NO3-, NO2-) were also analyzed. Except for NO3- and NO2-, the average concentrations of the physicochemical parameters and dissolved ions generally meet the guidelines for drinking/domestic water quality. By contrast, the results reveal high levels of FIB in the water samples collected during both dry and wet seasons. The contamination is significantly higher during the wet season compared to dry season, due to increased runoff, open defecation practices, and more frequent overflow of onsite sanitation systems and septic tanks.

PMID: 30964378 [PubMed - as supplied by publisher]

Nasopharyngeal Pneumococcal Colonization and Impact of a Single Dose of 13-Valent Pneumococcal Conjugate Vaccine in Indian Children With HIV and Their Unvaccinated Parents.

April 9, 2019
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Nasopharyngeal Pneumococcal Colonization and Impact of a Single Dose of 13-Valent Pneumococcal Conjugate Vaccine in Indian Children With HIV and Their Unvaccinated Parents.

Pediatr Infect Dis J. 2018 05;37(5):451-458

Authors: Arya BK, Bhattacharya SD, Sutcliffe CG, Ganaie F, Bhaskar A, Bhattacharyya S, Niyogi SK, Moss WJ, Panda S, Ravikumar KL, Das RS, Mandal S

Abstract
BACKGROUND: Human immunodeficiency virus (HIV) infection increases risk of invasive disease from Streptococcus pneumoniae. Pneumococcal conjugate vaccines (PCV) prevent invasive disease and acquisition of vaccine type (VT) pneumococcus in the nasopharynx.
OBJECTIVE: To look at the safety and impact of one dose of PCV13 on acquisition of VT pneumococcal carriage in Indian children with HIV.
METHOD: We conducted a cohort study in families of HIV-infected children (CLH) and families of HIV-uninfected children (HUC) in West Bengal. All children received one dose of PCV13. Nasopharyngeal swabs were collected from children and parents at baseline and 2 months after vaccination.
RESULT: One hundred and fifteen CLH and 47 HUC received one dose of PCV13. Fifty-eight percent of CLH were on antiretroviral therapy (ART), and the median nadir CD4 count was 287. There were no significant adverse events in either group. HUC had more VT colonization than CLH-55% versus 23% of all pneumococcal isolates. HIV infection doubled the risk of nonvaccine serotype colonization (P = 0.03). There was no difference in acquisition of VT isolates in CLH (4.4%) and HUC (4.5%) post-PCV13; however, older CLH (>5 years) had decreased clearance of VT strains. ART made no difference in pneumococcal colonization at baseline or after PCV13; however, CLH with higher nadir CD4 counts before starting ART were less likely to have VT colonization post-PCV13 (prevalence ratio, 0.2; 95% confidence interval: 0.1-0.5).
CONCLUSION: While there was no difference in acquisition of VT nasopharyngeal carriage of pneumococcus in CLH and HUC after one dose of PCV13, earlier access to ART may impact response to PCV13 in CLH.

PMID: 28961675 [PubMed - indexed for MEDLINE]

Estimating the incidence of enteric fever in children in India: a multi-site, active fever surveillance of pediatric cohorts.

April 6, 2019
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Estimating the incidence of enteric fever in children in India: a multi-site, active fever surveillance of pediatric cohorts.

BMC Public Health. 2018 05 03;18(1):594

Authors: John J, Bavdekar A, Rongsen-Chandola T, Dutta S, NSSEFI Collaborators, Kang G

Abstract
BACKGROUND: Salmonella Typhi is responsible for about 20 million episodes of illness and over 140,000 deaths annually globally. South Asia has the highest documented burden of typhoid and is home to the multi-drug resistant H58 strain that makes treatment more challenging. The WHO recommends the use of Typhoid Conjugate Vaccines in typhoid endemic countries. Decisions on the preferred immunization strategy should be based on an analysis of disease burden, availability, affordability, and operational feasibility. Typhoid vaccines have so far remained unimplemented as public health measures because of a perceived decline in typhoid burden in recent years. The apparent decline, based on hospital reports, may be a result of rampant antimicrobial use in the community and therefore estimation of disease incidence at the community is necessary to better measure disease incidence and transmission.
METHODS: Age-specific incidence of typhoid fever in children between 6 months and 15 years will be estimated in four community based cohorts in varied settings across India using standardized protocols for active fever surveillance in the community. Data will be collected on secured cloud infrastructure using a combination of android and web-based real-time data collection tools. Blood cultures will be done for children with fever lasting 3 or more consecutive days using automated blood culture systems. Those with blood-culture confirmed typhoid fever will be followed up till 90 days to estimate costs and clinical outcomes of the illness episodes. Environmental factors, access to safe water, sanitation, hygiene, food hygiene, demography, population density and socioeconomic status will be assessed periodically to characterise risk factors and permit extrapolation of burden to similar risk settings.
DISCUSSION: With the availability of licensed typhoid conjugated vaccines in India, it is important to consider whether the burden of disease is present and sufficient to require the use of vaccine in addition to other interventions. Active case finding in the community permits the detection of cases that would be missed in facility-based surveillance systems. Understanding the age distribution, burden, cost-of-illness and transmission of disease is essential to plan interventions and predict their potential impact.
TRIAL REGISTRATION: The surveillance has been prospectively registered in the Clinical Trial Registry of India ( CTRI/2017/09/009719 ) on 12 September 2017.

PMID: 29724223 [PubMed - indexed for MEDLINE]

Comparative genomics of Vibrio cholerae El Tor strains isolated at epidemic complications in Siberia and at the Far East.

April 4, 2019
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Comparative genomics of Vibrio cholerae El Tor strains isolated at epidemic complications in Siberia and at the Far East.

Infect Genet Evol. 2018 06;60:80-88

Authors: Mironova LV, Gladkikh AS, Ponomareva AS, Feranchuk SI, Bochalgin NО, Basov EA, Yu Khunkheeva Z, Balakhonov SV

Abstract
The territory of Siberia and the Far East of Russia is classified as epidemically safe for cholera; however, in the 1970s and 1990s a number of infection importation cases and acute outbreaks associated with the cholera importation were reported. Here, we analyze genomes of four Vibrio cholerae El Tor strains isolated from humans during epidemic complications (imported cases, an outbreak) in the 1990s. The analyzed strains harbor the classical allele of the cholera toxin subunit B gene (ctxB1); thus, belong to genetically altered variants of the El Tor biotype. Analysis of the genomes revealed their high homology with the V. cholerae N16961 reference strain: 85-93 SNPs were identified in the core genome as compared to the reference. The determined features of SNPs in the CTX prophage made it possible to propose the presence of a new subtype - CTX-2a in two strains; the other two strains carried the prophage of CTX-3 type. Results of phylogenetic analysis based on SNP-typing demonstrated that two strains belonged to the second wave, and two - to the early third wave of cholera dissemination in the world. Phylogenetic reconstruction in combination with epidemiological data permitted to trace the origin of the strains and the way of their importation to the Russian Federation directly or through temporary cholera foci.

PMID: 29462719 [PubMed - indexed for MEDLINE]

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