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Human genome diversity data reveal that L564P is the predominant TPC2 variant and a prerequisite for the blond hair associated M484L gain-of-function effect.

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Human genome diversity data reveal that L564P is the predominant TPC2 variant and a prerequisite for the blond hair associated M484L gain-of-function effect.

PLoS Genet. 2021 Jan 19;17(1):e1009236

Authors: Böck J, Krogsaeter E, Passon M, Chao YK, Sharma S, Grallert H, Peters A, Grimm C

Abstract
The endo-lysosomal two-pore channel (TPC2) has been established as an intracellular cation channel of significant physiological and pathophysiological relevance in recent years. For example, TPC2-/- mice show defects in cholesterol degradation, leading to hypercholesterinemia; TPC2 absence also results in mature-onset obesity, and a role in glucagon secretion and diabetes has been proposed. Infections with bacterial toxins or viruses e.g., cholera toxin or Ebola virus result in reduced infectivity rates in the absence of TPC2 or after pharmacological blockage, and TPC2-/- cancer cells lose their ability to migrate and metastasize efficiently. Finally, melanin production is affected by changes in hTPC2 activity, resulting in pigmentation defects and hair color variation. Here, we analyzed several publicly available genome variation data sets and identified multiple variations in the TPC2 protein in distinct human populations. Surprisingly, one variation, L564P, was found to be the predominant TPC2 isoform on a global scale. By applying endo-lysosomal patch-clamp electrophysiology, we found that L564P is a prerequisite for the previously described M484L gain-of-function effect that is associated with blond hair. Additionally, other gain-of-function variants with distinct geographical and ethnic distribution were discovered and functionally characterized. A meta-analysis of genome-wide association studies was performed, finding the polymorphisms to be associated with both distinct and overlapping traits. In sum, we present the first systematic analysis of variations in TPC2. We functionally characterized the most common variations and assessed their association with various disease traits. With TPC2 emerging as a novel drug target for the treatment of various diseases, this study provides valuable insights into ethnic and geographical distribution of TPC2 polymorphisms and their effects on channel activity.

PMID: 33465068 [PubMed - as supplied by publisher]

[Images of cholera in the South of France].

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[Images of cholera in the South of France].

Rev Prat. 2020 04;70(4):461-462

Authors: Gourevitch D

PMID: 32877111 [PubMed - indexed for MEDLINE]

Prevalence and antimicrobial profile of Shigella isolates in a tertiary care hospital of North Karnataka: A 12-year study.

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Prevalence and antimicrobial profile of Shigella isolates in a tertiary care hospital of North Karnataka: A 12-year study.

Indian J Med Microbiol. 2020 Jan-Mar;38(1):101-108

Authors: Jain PA, Kulkarni RD, Dutta S, Ganavali AS, Kalabhavi AS, Shetty PC, Shubhada C, Hosamani MA, Appannanavar SB, Hanamaraddi DR

Abstract
Context: Shigella is a common cause of bacillary dysentery. Although it is reported worldwide, the majority of the infections are seen in developing countries with Shigella flexneri being the most common isolate. Prevalence of Shigella species and their antibiotic susceptibility profiles vary according to geographic area and season.
Aims: In the present study, the epidemiology and antimicrobial profile of Shigella from stool samples received at our hospital for a period of 12 years (January 2006 to December 2017) was evaluated.
Subjects and Methods: A total of 4578 stool samples were collected from the cases of acute gastroenteritis and diarrhoea. Samples were processed for culture and sensitivity according to standard microbiological techniques. The presumptive identification of Shigella species was done using standard conventional biochemical tests and confirmed using antisera.
Results: A total of 189 (4.2%) samples yielded Shigella spp. Isolation of Shigella spp. were more frequent from males (58.2%). S. flexneri was the commonest species isolated (47.6%) followed by Shigella sonnei(11.6%), Shigella dysenteriae (4.2%) and Shigella boydii (2.1%). Non-typeable Shigella was commonly recovered. The isolates showed high resistance to ampicillin (76.7%) and co-trimoxazole (75%) while highest susceptibility was observed to ceftriaxone (79.2%).
Conclusions: S. flexneri was the most prevalent species isolated at this centre. Shigella isolates from the study showed alarming resistance to recommended antibiotics. Non-typeable Shigella accounted for 34.4% isolates. Molecular discrimination between Shigella and Escherichia coli is essential.

PMID: 32719216 [PubMed - indexed for MEDLINE]

Cholera epidemic and quarantine of open ports in Joseon in 1886.

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Cholera epidemic and quarantine of open ports in Joseon in 1886.

Uisahak. 2020 Apr;29(1):43-80

Authors: Park H

Abstract
In 1886, cholera was prevalent nationwide in Joseon. This year was not yet the time when the Joseon government officially overhauled quarantine rules to go into effect. Thus, quarantine efforts to prevent cholera varied depending on each of the three opening ports in the Joseon Dynasty. In Wonsan, officials of the three countries(Joseon, Japan and Qing) discussed ways to deal with cholera, and quarantine activities were carried out smoothly. On the other hand, Busan underwent friction and conflict between the parties over the implementation of quarantine rules within the region. When the Japanese consulate said that it would establish quarantine rules first and implement them, officials from various countries, including the Joseon Dynasty, strongly protested against the movement, saying that they did not reach prior consent. On top of that, economic interests were also affecting circumstances of port trade. In Incheon, there were differences between the home country and the local consulate over the urgent issue to be dealt with locally and the legal principles of applying the treaty. Since consular officials were not authorized to establish quarantine rules, the situation was settled into cancellation of the rules already issued there. The Japanese consul working at each port in the Joseon Dynasty suggested specific rules to develop quarantine activities. At this point, we can read Japan's intention to preempt the standard of future quarantine inspections. The enforcement of quarantine rules, however, was a matter that required consent from the Joseon official Gamri, the Acting Commissioner of the Joseon Maritime Customs and diplomats from each country. Furthermore, they had to go through the process of obtaining review and approval from their home countries if there were any problems in the operation of the treaty. The establishment and implementation of quarantine rules were complicated by interests of various players in each country concerning protection of their own citizens. Even though it was timely and the purpose of implementation was good, it could not follow through the quarantine rules as proposed by the Japanese consul at the opening port. The accumulation of quarantine experience and information at each port of Joseon in 1886 provided the foundation for the Joseon government to move toward to establish quarantine rules and implement them with the consent of each country in the following year.

PMID: 32418976 [PubMed - indexed for MEDLINE]

OXA-181-Like Carbapenemases in Klebsiella pneumoniae ST14, ST15, ST23, ST48, and ST231 from Septicemic Neonates: Coexistence with NDM-5, Resistome, Transmissibility, and Genome Diversity.

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OXA-181-Like Carbapenemases in Klebsiella pneumoniae ST14, ST15, ST23, ST48, and ST231 from Septicemic Neonates: Coexistence with NDM-5, Resistome, Transmissibility, and Genome Diversity.

mSphere. 2021 Jan 13;6(1):

Authors: Naha S, Sands K, Mukherjee S, Saha B, Dutta S, Basu S

Abstract
Studies on the epidemiology and genomes of isolates harboring OXA-48-like genes in septicemic neonates are rare. Here, isolates producing these carbapenemases which emerged and persisted in an Indian neonatal unit were characterized in terms of their resistome, transmissibility, and genome diversity. Antibiotic susceptibility and whole-genome sequencing were carried out. The sequence types, resistome, virulome, mobile genetic elements, and transmissibility of carbapenem-resistant plasmids were evaluated. Core genome analysis of isolates was shown in a global context with other OXA-48-like carbapenemase-harboring genomes, including those from neonatal studies. Eleven OXA-48-like carbapenemase-producing Klebsiella pneumoniae (bla OXA-181, n = 7 and bla OXA-232, n = 4) isolates belonging to diverse sequence types (ST14, ST15, ST23, ST48, and ST231) were identified. bla OXA-181/OXA-232 and bla NDM-5 were found in a high-risk clone, ST14 (n = 4). bla OXA-181/OXA-232 were in small, nonconjugative ColKP3 plasmids located on truncated Tn2013, whereas bla NDM-5 was in self-transmissible, conjugative IncFII plasmids, within truncated Tn125 Conjugal transfer of bla OXA-181/OXA-232 was observed in the presence of bla NDM-5 The study strains were diverse among themselves and showed various levels of relatedness with non-neonatal strains from different parts of the world and similarity with neonatal strains from Tanzania and Ghana when compared with a representative collection of carbapenemase-positive K. pneumoniae strains. We found that bla OXA-181/OXA-232-harboring isolates from a single neonatal unit had remarkably diverse genomes, ruling out clonal spread and emphasizing the extent of plasmid spreading across different STs. This study is probably the first to report the coexistence of bla OXA-181/232 and bla NDM-5 in neonatal isolates.IMPORTANCE Neonatal sepsis is a leading cause of neonatal mortality in low- and middle-income countries (LMICs). Treatment of sepsis in this vulnerable population is dependent on antimicrobials, and resistance to these life-saving antimicrobials is worrisome. Carbapenemases, enzymes produced by bacteria, can make these antimicrobials useless. Our study describes how OXA-48-like carbapenemases in neonatal septicemic Klebsiella pneumoniae shows remarkable diversity in the genomes of the strains and relatedness with strains from other parts of world and also to some neonatal outbreak strains. It is also the first to describe such resistance due to coproduction of dual carbapenemases, (OXA)-48 and New Delhi metallo-β-lactamase-5, in Klebsiella pneumoniae from neonatal settings. Carbapenemase genes situated on plasmids within high-risk international clones, as seen here, increase the ease and transfer of resistant genetic material. With the WHO treatment protocols not adequately poised to handle such infections, prompt attention to neonatal health care is required.

PMID: 33441403 [PubMed - in process]

Food Safety Challenges in Refugee Camps: What do we know?

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Food Safety Challenges in Refugee Camps: What do we know?

J Food Prot. 2021 Jan 07;:

Authors: Garsow AV, Closs G, Campbell EP, Kowalcyk B

Abstract
Refugee camps provide basic necessities such as food, water, shelter, and medical treatment for displaced persons. Unsanitary conditions in refugee camps due to overcrowding, poor sanitation systems, lack of clean water, minimal ways to cook and store food can lead to an increased risk of foodborne illness. This article reviews the limited literature on the epidemiology of foodborne illness in refugee camps, effective risk mitigation strategies and opportunities for future research. Eleven articles were identified, suggesting that research in this area is limited. Identified research focused on three pathogens - Vibrio cholerae , Salmonella spp. and hepatitis E virus - that can lead to serious diseases including cholera, salmonellosis, typhoid fever, and hepatitis E. The research demonstrated that storage and handling of clean water for personal hygiene as well as food preparation were critical components to ensuring food safety. Additionally, knowledge pertaining to best practices for hygiene and food preparation were also identified as important. Gaps in current research include the determination of the prevalence of pathogens in food sold in refugee camps as well as development of culturally relevant food safety supply chain quality management systems. More research that focuses on burden and attribution of foodborne illness as well as food safety interventions in refugee camps is necessary.

PMID: 33411925 [PubMed - as supplied by publisher]

Multiepitope Subunit Vaccine Design against COVID-19 Based on the Spike Protein of SARS-CoV-2: An In Silico Analysis.

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Multiepitope Subunit Vaccine Design against COVID-19 Based on the Spike Protein of SARS-CoV-2: An In Silico Analysis.

J Immunol Res. 2020;2020:8893483

Authors: Dar HA, Waheed Y, Najmi MH, Ismail S, Hetta HF, Ali A, Muhammad K

Abstract
The global health crisis caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19, has resulted in a negative impact on human health and on social and economic activities worldwide. Researchers around the globe need to design and develop successful therapeutics as well as vaccines against the novel COVID-19 disease. In the present study, we conducted comprehensive computer-assisted analysis on the spike glycoprotein of SARS-CoV-2 in order to design a safe and potent multiepitope vaccine. In silico epitope prioritization shortlisted six HLA I epitopes and six B-cell-derived HLA II epitopes. These high-ranked epitopes were all connected to each other via flexible GPGPG linkers, and at the N-terminus side, the sequence of Cholera Toxin β subunit was attached via an EAAAK linker. Structural modeling of the vaccine was performed, and molecular docking analysis strongly suggested a positive association of a multiepitope vaccine with Toll-like Receptor 3. The structural investigations of the vaccine-TLR3 complex revealed the formation of fifteen interchain hydrogen bonds, thus validating its integrity and stability. Moreover, it was found that this interaction was thermodynamically feasible. In conclusion, our data supports the proposition that a multiepitope vaccine will provide protective immunity against COVID-19. However, further in vivo and in vitro experiments are needed to validate the immunogenicity and safety of the candidate vaccine.

PMID: 33274246 [PubMed - indexed for MEDLINE]

The "Scourge of the Renaissance". A Short Review About Treponema pallidum infection.

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The "Scourge of the Renaissance". A Short Review About Treponema pallidum infection.

Endocr Metab Immune Disord Drug Targets. 2020;20(3):335-343

Authors: Santacroce L, Bottalico L, Topi S, Castellaneta F, Charitos IA

Abstract
BACKGROUND: There is not a time in the history when epidemics did not loom large: infectious diseases have always had civilisation and evolution-altering consequences. Throughout history, there have been a number of pandemics: cholera, bubonic plague, influenza, smallpox are some of the most brutal killers in human history. Historical accounts of pandemics clearly demonstrate that war, unhygienic conditions, social and health inequality create conditions for the transmission of infectious diseases, and existing health disparities can contribute to unequal morbidity and mortality. The Renaissance was a period of European cultural, artistic, political and economic "rebirth" following the Middle Ages, but it was also the time when new infectious disease appeared, such as Syphilis. The epidemic spread of Syphilis began between the late 15th century and early 16th century due to the increased migration of peoples across Europe. The rapid spread of venereal syphilis throughout Europe suggests the introduction of a disease into a population that had not previously been exposed. Syphilis is a type of treponematosis, which includes syphilis, bejel, yaws, and pinta, but, while syphilis is venereal disease, the others are nonvenereal. Syphilis was, at the beginning, a disease of great severity due to its novelty, as the population had no time to gain any immunity against this venereal disease.
METHODS: The purpose of this study is to investigate the origin of syphilis and the evolution of the treatments from the empiric means to the discovery of penicillin, but also to understand how this venereal disease has largely influenced human lifestyle and evolution.
CONCLUSION: The first of the three hypotheses about its origins is the Columbian hypothesis, which states that Columbus's crew acquired syphilis from Native Americans and carried it back to Europe in 1493 A. D. On the contrary, the second hypothesis (pre-Columbian) asserts that syphilis was present in Europe long before Columbus's voyage and was transferred to the New World by Columbus's men. The Unitarian theory argues that syphilis, bejel, yaws, and pinta are not separate diseases but they represent syndromes caused by slightly different strains of one organism. Nowadays, Syphilis' origin is still uncertain and remains controversial. However, the large impact on the social behavior and international public health is an important reason to investigate about its origins and how to prevent the transmission.

PMID: 31625831 [PubMed - in process]

A protracted cholera outbreak among residents in an urban setting, Nairobi county, Kenya, 2015.

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A protracted cholera outbreak among residents in an urban setting, Nairobi county, Kenya, 2015.

Pan Afr Med J. 2020;36:127

Authors: Kigen HT, Boru W, Gura Z, Githuka G, Mulembani R, Rotich J, Abdi I, Galgalo T, Githuku J, Obonyo M, Muli R, Njeru I, Langat D, Nsubuga P, Kioko J, Lowther S

Abstract
Introduction: in 2015, a cholera outbreak was confirmed in Nairobi county, Kenya, which we investigated to identify risk factors for infection and recommend control measures.
Methods: we analyzed national cholera surveillance data to describe epidemiological patterns and carried out a case-control study to find reasons for the Nairobi county outbreak. Suspected cholera cases were Nairobi residents aged >2 years with acute watery diarrhea (>4 stools/≤12 hours) and illness onset 1-14 May 2015. Confirmed cases had Vibrio cholerae isolated from stool. Case-patients were frequency-matched to persons without diarrhea (1:2 by age group, residence), interviewed using standardized questionaires. Logistic regression identified factors associated with case status. Household water was analyzed for fecal coliforms and Escherichia coli.
Results: during December 2014-June 2015, 4,218 cholera cases including 282 (6.7%) confirmed cases and 79 deaths (case-fatality rate [CFR] 1.9%) were reported from 14 of 47 Kenyan counties. Nairobi county reported 781 (19.0 %) cases (attack rate, 18/100,000 persons), including 607 (78%) hospitalisations, 20 deaths (CFR 2.6%) and 55 laboratory-confirmed cases (7.0%). Seven (70%) of 10 water samples from communal water points had coliforms; one had Escherichia coli. Factors associated with cholera in Nairobi were drinking untreated water (adjusted odds ratio [aOR] 6.5, 95% confidence interval [CI] 2.3-18.8), lacking health education (aOR 2.4, CI 1.1-7.9) and eating food outside home (aOR 2.4, 95% CI 1.2-5.7).
Conclusion: we recommend safe water, health education, avoiding eating foods prepared outside home and improved sanitation in Nairobi county. Adherence to these practices could have prevented this protacted cholera outbreak.

PMID: 32849982 [PubMed - in process]

Pandemic Vibrio cholerae shuts down site-specific recombination to retain an interbacterial defence mechanism.

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Pandemic Vibrio cholerae shuts down site-specific recombination to retain an interbacterial defence mechanism.

Nat Commun. 2020 12 07;11(1):6246

Authors: Santoriello FJ, Michel L, Unterweger D, Pukatzki S

Abstract
Vibrio cholerae is an aquatic microbe that can be divided into three subtypes: harmless environmental strains, localised pathogenic strains, and pandemic strains causing global cholera outbreaks. Each type has a contact-dependent type VI secretion system (T6SS) that kills neighbouring competitors by translocating unique toxic effector proteins. Pandemic isolates possess identical effectors, indicating that T6SS effectors may affect pandemicity. Here, we show that one of the T6SS gene clusters (Aux3) exists in two states: a mobile, prophage-like element in a small subset of environmental strains, and a truncated Aux3 unique to and conserved in pandemic isolates. Environmental Aux3 can be readily excised from and integrated into the genome via site-specific recombination, whereas pandemic Aux3 recombination is reduced. Our data suggest that environmental Aux3 acquisition conferred increased competitive fitness to pre-pandemic V. cholerae, leading to grounding of the element in the chromosome and propagation throughout the pandemic clade.

PMID: 33288753 [PubMed - indexed for MEDLINE]

Geographical distribution and antibiotics susceptibility patterns of toxigenic Vibrio cholerae isolates from Kisumu County, Kenya.

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Geographical distribution and antibiotics susceptibility patterns of toxigenic Vibrio cholerae isolates from Kisumu County, Kenya.

Afr J Prim Health Care Fam Med. 2020 Dec 08;12(1):e1-e6

Authors: Awuor SO, Omwenga EO, Daud II

Abstract
BACKGROUND: Multiple drug resistance has become a major threat to the treatment of cholera. Recent studies in Kenya have described the epidemiology, especially the risk factors, of cholera; however, there is little information on the phenotypic and drug susceptibility patterns of Vibrio cholerae (V. cholerae) in outbreaks that in the recent past have occurred in western Kenya.
AIM: To characterise and determine the antibiotics' susceptibility profiling of toxigenic V. cholerae isolates from Kisumu County.
SETTING: The project was conducted in Kisumu County, Kenya.
METHODS: A total of 119 V. cholerae O1, biotype El Tor, isolates collected during 2017 cholera outbreak in Kisumu County were used for this study. The samples were cultured on thiosulphate-citrate-bile salts sucrose (TCBS) agar and biochemical tests were carried out using standard procedures. Susceptibility tests were conducted by using various conventional antibiotics against standard procedures.
RESULTS: Of the 119 isolates, 101 were confirmed to be V. cholerae belonging to serotypes Inaba and Ogawa, with Inaba being the predominant serotype (73.95%). The isolates were susceptible to ciprofloxacin (100%), ofloxacin (100%), gentamycin (100%), doxycycline (99%), ceftriaxone (99%) and streptomycin (96.04%) antimicrobials, and resistant to erythromycin (53.47%), amoxicillin (64.4%), nalidixic acid (83.2%) and ampicillin (89.11%), with high resistance to cotrimoxazole (99%) and tetracycline (97%).
CONCLUSION: Vibrio cholerae was resistant to multiple antibiotics, including those commonly used in the management of cholera. Taken together, there is a need to carry out regular surveillance on antimicrobial drug resistance during outbreaks.

PMID: 33354982 [PubMed - in process]

Delineating and Analyzing Locality-Level Determinants of Cholera, Haiti.

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Delineating and Analyzing Locality-Level Determinants of Cholera, Haiti.

Emerg Infect Dis. 2021 Jan;27(1):170-181

Authors: Griffiths K, Moise K, Piarroux M, Gaudart J, Beaulieu S, Bulit G, Marseille JP, Jasmin PM, Namphy PC, Henrys JH, Piarroux R, Rebaudet S

Abstract
Centre Department, Haiti, was the origin of a major cholera epidemic during 2010-2019. Although no fine-scale spatial delineation is officially available, we aimed to analyze determinants of cholera at the local level and identify priority localities in need of interventions. After estimating the likely boundaries of 1,730 localities by using Voronoi polygons, we mapped 5,322 suspected cholera cases reported during January 2015-September 2016 by locality alongside environmental and socioeconomic variables. A hierarchical clustering on principal components highlighted 2 classes with high cholera risk: localities close to rivers and unimproved water sources (standardized incidence ratio 1.71, 95% CI 1.02-2.87; p = 0.04) and urban localities with markets (standardized incidence ratio 1.69, 95% CI 1.25-2.29; p = 0.0006). Our analyses helped identify and characterize areas where efforts should be focused to reduce vulnerability to cholera and other waterborne diseases; these methods could be used in other contexts.

PMID: 33350917 [PubMed - as supplied by publisher]

Vibrio cholerae O1 transmission in Bangladesh: insights from a nationally representative serosurvey.

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Vibrio cholerae O1 transmission in Bangladesh: insights from a nationally representative serosurvey.

Lancet Microbe. 2020 Dec;1(8):e336-e343

Authors: Azman AS, Lauer SA, Bhuiyan TR, Luquero FJ, Leung DT, Hegde ST, Harris JB, Paul KK, Khaton F, Ferdous J, Lessler J, Salje H, Qadri F, Gurley ES

Abstract
Background: Pandemic Vibrio cholerae from cholera-endemic countries around the Bay of Bengal regularly seed epidemics globally. Without reducing cholera in these countries, including Bangladesh, global cholera control might never be achieved. Little is known about the geographical distribution and magnitude of V cholerae O1 transmission nationally. We aimed to describe infection risk across Bangladesh, making use of advances in cholera seroepidemiology, therefore overcoming many of the limitations of current clinic-based surveillance.
Methods: We tested serum samples from a nationally representative serosurvey in Bangladesh with eight V cholerae-specific assays. Using these data with a machine-learning model previously validated within a cohort of confirmed cholera cases and their household contacts, we estimated the proportion of the population with evidence of infection by V cholerae O1 in the previous year (annual seroincidence) and used Bayesian geostatistical models to create high-resolution national maps of infection risk.
Findings: Between Oct 16, 2015, and Jan 24, 2016, we obtained and tested serum samples from 2930 participants (707 households) in 70 communities across Bangladesh. We estimated national annual seroincidence of V cholerae O1 infection of 17·3% (95% CI 10·5-24·1). Our high-resolution maps showed large heterogeneity of infection risk, with community-level annual infection risk within the sampled population ranging from 4·3% to 62·9%. Across Bangladesh, we estimated that 28·1 (95% CI 17·1-39·2) million infections occurred in the year before the survey. Despite having an annual seroincidence of V cholerae O1 infection lower than much of Bangladesh, Dhaka (the capital of Bangladesh and largest city in the country) had 2·0 (95% CI 0·6-3·9) million infections during the same year, primarily because of its large population.
Interpretation: Serosurveillance provides an avenue for identifying areas with high V cholerae O1 transmission and investigating key risk factors for infection across geographical scales. Serosurveillance could serve as an important method for countries to plan and monitor progress towards 2030 cholera elimination goals.
Funding: The Bill & Melinda Gates Foundation, National Institutes of Health, and US Centers for Disease Control and Prevention.

PMID: 33345203 [PubMed]

Early detection of cholera epidemics to support control in fragile states: estimation of delays and potential epidemic sizes.

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Early detection of cholera epidemics to support control in fragile states: estimation of delays and potential epidemic sizes.

BMC Med. 2020 Dec 15;18(1):397

Authors: Ratnayake R, Finger F, Edmunds WJ, Checchi F

Abstract
BACKGROUND: Cholera epidemics continue to challenge disease control, particularly in fragile and conflict-affected states. Rapid detection and response to small cholera clusters is key for efficient control before an epidemic propagates. To understand the capacity for early response in fragile states, we investigated delays in outbreak detection, investigation, response, and laboratory confirmation, and we estimated epidemic sizes. We assessed predictors of delays, and annual changes in response time.
METHODS: We compiled a list of cholera outbreaks in fragile and conflict-affected states from 2008 to 2019. We searched for peer-reviewed articles and epidemiological reports. We evaluated delays from the dates of symptom onset of the primary case, and the earliest dates of outbreak detection, investigation, response, and confirmation. Information on how the outbreak was alerted was summarized. A branching process model was used to estimate epidemic size at each delay. Regression models were used to investigate the association between predictors and delays to response.
RESULTS: Seventy-six outbreaks from 34 countries were included. Median delays spanned 1-2 weeks: from symptom onset of the primary case to presentation at the health facility (5 days, IQR 5-5), detection (5 days, IQR 5-6), investigation (7 days, IQR 5.8-13.3), response (10 days, IQR 7-18), and confirmation (11 days, IQR 7-16). In the model simulation, the median delay to response (10 days) with 3 seed cases led to a median epidemic size of 12 cases (upper range, 47) and 8% of outbreaks ≥ 20 cases (increasing to 32% with a 30-day delay to response). Increased outbreak size at detection (10 seed cases) and a 10-day median delay to response resulted in an epidemic size of 34 cases (upper range 67 cases) and < 1% of outbreaks < 20 cases. We estimated an annual global decrease in delay to response of 5.2% (95% CI 0.5-9.6, p = 0.03). Outbreaks signaled by immediate alerts were associated with a reduction in delay to response of 39.3% (95% CI 5.7-61.0, p = 0.03).
CONCLUSIONS: From 2008 to 2019, median delays from symptom onset of the primary case to case presentation and to response were 5 days and 10 days, respectively. Our model simulations suggest that depending on the outbreak size (3 versus 10 seed cases), in 8 to 99% of scenarios, a 10-day delay to response would result in large clusters that would be difficult to contain. Improving the delay to response involves rethinking the integration at local levels of event-based detection, rapid diagnostic testing for cluster validation, and integrated alert, investigation, and response.

PMID: 33317544 [PubMed - in process]

COVID-19 pandemic, dengue epidemic, and climate change vulnerability in Bangladesh: Scenario assessment for strategic management and policy implications.

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COVID-19 pandemic, dengue epidemic, and climate change vulnerability in Bangladesh: Scenario assessment for strategic management and policy implications.

Environ Res. 2021 01;192:110303

Authors: Rahman MM, Bodrud-Doza M, Shammi M, Md Towfiqul Islam AR, Moniruzzaman Khan AS

Abstract
Bangladesh is one of the most vulnerable countries to climate change impacts also struck by the COVID-19 pandemic. The lockdown measures were ineffective with no sign of flattening the curve. Therefore, the high risk of transmission is evident with an increasing number of affected people. Under this circumstance, a multiple hazards scenario can be developed in this country due to climatic hazards such as cyclones, floods, landslides, heat waves, and the outbreak of infectious diseases such as dengue, cholera, and diarrhoea. The country experiences simultaneously the global pandemic, exceptionally prolonged flood along with the recovery stage from the damages due to the cyclone (Amphan). Therefore, these multiple factors have been putting pressure on losing millions of homes, livelihoods, and agricultural crops. This study aimed to assess the potential impact of a simultaneous strike of climatic hazards and infectious disease outbreaks and their possible strategic management in Bangladesh under different scenarios. A mixed methodological approach was followed in this study including a questionnaire survey, in-depth discussion with experts, and extensive literature review to assess the multi-hazard scenario in a resource-limited setting with high population density. A set of statistical techniques were used to analyze the responses (n = 1590) from different social groups (healthcare professionals, academicians, students, Government and NGO officials, and businessman) under three scenarios. The results revealed the high possibility of aggravating the impact of COVID-19 pandemic if there is a climatic hazard such as flood, cyclone have appeared. The majority of the respondents agreed that the situation will become more devastating if there is another outbreak of diseases such as dengue, cholera, and diarrhoea. The poor and fragile healthcare system of this country cannot bear such unprecedented pressure. The lack of risk assessment and communication, lack of sectoral coordination might restrict the contingency plan of the government. Therefore, considering the unprecedented worst cases a stringent strategic plan for emergency response, short term and long-term management should have to be formulated. Resilience building through proactive planning and implementation of integrated, inclusive and sustainable strategies will be effective to ensure the health and socio-economic security for multi-hazard threats in the country.

PMID: 33069704 [PubMed - indexed for MEDLINE]

cholera epidemiology; +19 new citations

19 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

cholera epidemiology

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cholera epidemiology; +19 new citations

19 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

cholera epidemiology

These pubmed results were generated on 2020/12/15

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Use of surveys to evaluate an integrated oral cholera vaccine campaign in response to a cholera outbreak in Hoima district, Uganda.

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Use of surveys to evaluate an integrated oral cholera vaccine campaign in response to a cholera outbreak in Hoima district, Uganda.

BMJ Open. 2020 Dec 10;10(12):e038464

Authors: Bwire G, Roskosky M, Ballard A, Brooks WA, Okello A, Rafael F, Ampeire I, Orach CG, Sack DA

Abstract
OBJECTIVES: To evaluate the quality and coverage of the campaign to distribute oral cholera vaccine (OCV) during a cholera outbreak in Hoima, Uganda to guide future campaigns of cholera vaccine.
DESIGN: Survey of communities targeted for vaccination to determine vaccine coverage rates and perceptions of the vaccination campaign, and a separate survey of vaccine staff who carried out the campaign.
SETTING: Hoima district, Uganda.
PARTICIPANTS: Representative clusters of households residing in the communities targeted for vaccination and staff members who conducted the vaccine campaign.
RESULTS: Among 209 households (1274 individuals) included in the coverage survey, 1193 (94%; 95% CI 92% to 95%) reported receiving at least one OCV dose and 998 (78%; 95% CI 76% to 81%) reported receiving two doses. Among vaccinated individuals, minor complaints were reported by 71 persons (5.6%). Individuals with 'some' education (primary school or above) were more knowledgeable regarding the required OCV doses compared with non-educated (p=0.03). Factors negatively associated with campaign implementation included community sensitisation time, staff payment and problems with field transport. Although the campaign was carried out quickly, the outbreak was over before the campaign started. Most staff involved in the campaign (93%) were knowledgeable about cholera control; however, 29% did not clearly understand how to detect and manage adverse events following immunisation.
CONCLUSION: The campaign achieved high OCV coverage, but the surveys provided insights for improvement. To achieve high vaccine coverage, more effort is needed for community sensitisation, and additional resources for staff transportation and timely payment for campaign staff is required. Pretest and post-test assessment of staff training can identify and address knowledge and skill gaps.

PMID: 33303438 [PubMed - in process]

Successive epidemic waves of cholera in South Sudan between 2014 and 2017: a descriptive epidemiological study.

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Successive epidemic waves of cholera in South Sudan between 2014 and 2017: a descriptive epidemiological study.

Lancet Planet Health. 2020 Dec;4(12):e577-e587

Authors: Jones FK, Wamala JF, Rumunu J, Mawien PN, Kol MT, Wohl S, Deng L, Pezzoli L, Omar LH, Lessler J, Quilici ML, Luquero FJ, Azman AS

Abstract
BACKGROUND: Between 2014 and 2017, successive cholera epidemics occurred in South Sudan within the context of civil war, population displacement, flooding, and drought. We aim to describe the spatiotemporal and molecular features of the three distinct epidemic waves and explore the role of vaccination campaigns, precipitation, and population movement in shaping cholera spread in this complex setting.
METHODS: In this descriptive epidemiological study, we analysed cholera linelist data to describe the spatiotemporal progression of the epidemics. We placed whole-genome sequence data from pandemic Vibrio cholerae collected throughout these epidemics into the global phylogenetic context. Using whole-genome sequence data in combination with other molecular attributes, we characterise the relatedness of strains circulating in each wave and the region. We investigated the association of rainfall and the instantaneous basic reproduction number using distributed lag non-linear models, compared county-level attack rates between those with early and late reactive vaccination campaigns, and explored the consistency of the spatial patterns of displacement and suspected cholera case reports.
FINDINGS: The 2014 (6389 cases) and 2015 (1818 cases) cholera epidemics in South Sudan remained spatially limited whereas the 2016-17 epidemic (20 438 cases) spread among settlements along the Nile river. Initial cases of each epidemic were reported in or around Juba soon after the start of the rainy season, but we found no evidence that rainfall modulated transmission during each epidemic. All isolates analysed had similar genotypic and phenotypic characteristics, closely related to sequences from Uganda and Democratic Republic of the Congo. Large-scale population movements between counties of South Sudan with cholera outbreaks were consistent with the spatial distribution of cases. 21 of 26 vaccination campaigns occurred during or after the county-level epidemic peak. Counties vaccinated on or after the peak incidence week had 2·2 times (95% CI 2·1-2·3) higher attack rates than those where vaccination occurred before the peak.
INTERPRETATION: Pandemic V cholerae of the same clonal origin was isolated throughout the study period despite interepidemic periods of no reported cases. Although the complex emergency in South Sudan probably shaped some of the observed spatial and temporal patterns of cases, the full scope of transmission determinants remains unclear. Timely and well targeted use of vaccines can reduce the burden of cholera; however, rapid vaccine deployment in complex emergencies remains challenging.
FUNDING: The Bill & Melinda Gates Foundation.

PMID: 33278375 [PubMed - as supplied by publisher]

COVID-19 Infection: Data Gaps for Diagnostic Laboratory Preparedness and Tasks on Hand.

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COVID-19 Infection: Data Gaps for Diagnostic Laboratory Preparedness and Tasks on Hand.

Viral Immunol. 2020 Dec 01;:

Authors: Biswas S, Ghosh P, Chakraborty D, Chatterjee A, Dutta S, Saha MK

Abstract
Emergence of the 2019 novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) and its spread, with life-threatening outcomes, have caused a pandemic burden worldwide. Studies of emerging diseases under outbreak conditions have focused on the complete spectrum of pathogens, transmissibility, shedding kinetics in relation to infectivity, epidemiological causes, and interventions to control emergence. During the initial stages of an outbreak, laboratory response capacity focuses on expansion of efficient diagnostic tools for rapid case detection, contact tracing, putting epidemiological findings into sources, mode of transmission, and identification of susceptible groups and reservoirs. It is important for public health diagnostic laboratories to have a fundamental knowledge of viral shedding, antibody response kinetics, assay validation, interpretation, and uncertainties of test results. This study reviewed currently published data from available literature on SARS-CoV-2 infection and compared this with data on viral shedding and antibody response kinetics of other human coronaviruses. Also described are current challenges and comments on some biases and significant data gaps that have limited laboratory preparedness to SARS-CoV-2. Consistent documentation of progress and data gaps from standardized reporting of methods utilized, sampling date, details of test results by specimen type, risk assessments, and symptoms can all be used strategically and provide incentives to governments and their partners to prioritize the development, detection, and response to outbreaks.

PMID: 33264056 [PubMed - as supplied by publisher]

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