Recent Cholera Publications on PubMed

Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries

March 30, 2021

Nat Microbiol. 2021 Apr;6(4):512-523. doi: 10.1038/s41564-021-00870-7. Epub 2021 Mar 29.


Antimicrobial resistance in neonatal sepsis is rising, yet mechanisms of resistance that often spread between species via mobile genetic elements, ultimately limiting treatments in low- and middle-income countries (LMICs), are poorly characterized. The Burden of Antibiotic Resistance in Neonates from Developing Societies (BARNARDS) network was initiated to characterize the cause and burden of antimicrobial resistance in neonatal sepsis for seven LMICs in Africa and South Asia. A total of 36,285 neonates were enrolled in the BARNARDS study between November 2015 and December 2017, of whom 2,483 were diagnosed with culture-confirmed sepsis. Klebsiella pneumoniae (n = 258) was the main cause of neonatal sepsis, with Serratia marcescens (n = 151), Klebsiella michiganensis (n = 117), Escherichia coli (n = 75) and Enterobacter cloacae complex (n = 57) also detected. We present whole-genome sequencing, antimicrobial susceptibility and clinical data for 916 out of 1,038 neonatal sepsis isolates (97 isolates were not recovered from initial isolation at local sites). Enterobacterales (K. pneumoniae, E. coli and E. cloacae) harboured multiple cephalosporin and carbapenem resistance genes. All isolated pathogens were resistant to multiple antibiotic classes, including those used to treat neonatal sepsis. Intraspecies diversity of K. pneumoniae and E. coli indicated that multiple antibiotic-resistant lineages cause neonatal sepsis. Our results will underpin research towards better treatments for neonatal sepsis in LMICs.

PMID:33782558 | DOI:10.1038/s41564-021-00870-7

"Cuba's Medical Team in the European Epicenter of COVID-19: Carlos R. Perez-Diaz MD MS PhD Director, Joaquin Albarran Provincial Clinical-Surgical Hospital, Havana Henry Reeve Medical Contingent Leader, Lombardy, Italy"

March 29, 2021

MEDICC Rev. 2021 Jan;23(1):18-20. doi: 10.37757/MR2021.V23.N1.2. Epub 2021 Jan 30.


On March 23, 2020, Cuba's Henry Reeve Emergency Medical Contingent began treating COVID-19 patients at Maggiore Hospital in Crema, Lombardy. Within days, the 52-member contingent comprised of 36 doctors and 15 nurses (plus 1 logistics specialist), together with Italian colleagues, were receiving patients in an adjacent fi eld hospital established and equipped for this purpose. At the time, Lombardy was the epicenter of COVID-19 transmission in Europe. Many of the Cubans in Lombardy were Contingent veterans, having served in postdisaster and epidemic scenarios in Chile, Pakistan, Haiti and elsewhere since the founding of the emergency medical team in 2005. Importantly, some had worked fi ghting the 2014 Ebola epidemic in West Africa. Even so, providing medical care during COVID-19 is a unique challenge, the likes of which had never before been seen by the Cuban team. Dr Carlos R. Pérez-Díaz, one of the Contingent's founding members, headed the team during its 60-day rotation in Lombardy, drawing on a wide array of professional experience. From 2006 to 2009, Dr Pérez-Díaz led the Cuban team posted at the Peltier Hospital in Djibouti, where he worked in the infectious disease department; in 2008, this team helped control a cholera outbreak that had spread to three countries. Following the 2010 earthquake in Chile, Dr Pérez-Díaz headed the team of Henry Reeve volunteers that provided free health services for 10 months in a tent hospital established to treat victims; he returned to Chile in 2015, again as head of the Henry Reeve Contingent, after severe fl ooding struck the Atacama region.

PMID:33780418 | DOI:10.37757/MR2021.V23.N1.2

Inverse probability weighted estimators of vaccine effects accommodating partial interference and censoring

March 26, 2021

Biometrics. 2021 Mar 25. doi: 10.1111/biom.13459. Online ahead of print.


Estimating population-level effects of a vaccine is challenging because there may be interference, i.e., the outcome of one individual may depend on the vaccination status of another individual. Partial interference occurs when individuals can be partitioned into groups such that interference occurs only within groups. In the absence of interference, inverse probability weighted (IPW) estimators are commonly used to draw inference about causal effects of an exposure or treatment. Tchetgen Tchetgen and VanderWeele (2012) proposed a modified IPW estimator for causal effects in the presence of partial interference. Motivated by a cholera vaccine study in Bangladesh, this paper considers an extension of the Tchetgen Tchetgen and VanderWeele IPW estimator to the setting where the outcome is subject to right censoring using inverse probability of censoring weights (IPCW). Censoring weights are estimated using proportional hazards frailty models. The large sample properties of the IPCW estimators are derived, and simulation studies are presented demonstrating the estimators' performance in finite samples. The methods are then used to analyze data from the cholera vaccine study. This article is protected by copyright. All rights reserved.

PMID:33768557 | DOI:10.1111/biom.13459

Model-based estimation of the economic burden of cholera in Africa

March 24, 2021

BMJ Open. 2021 Mar 23;11(3):e044615. doi: 10.1136/bmjopen-2020-044615.


OBJECTIVES: To estimate the economic burden of cholera in Africa.

SETTINGS: Cholera affected 44 countries in Africa.

PARTICIPANTS: The analysis used data from public sources in Africa published until September 2019.

METHODS: Based on existing data from field-based cost-of-illness studies, estimated cholera incidence rates, and reported cholera cases to WHO, this research estimates the economic burden of cholera in Africa from a societal perspective with 2015 as the base year. The estimate included out-of-pocket costs, public health system costs, productivity loss related to illness and an optional productivity loss related to premature deaths valued by the human capital approach. As various input data such as cholera incidence, hospitalisation rates and the number of workdays lost were not well defined, a series of scenario analyses and uncertainty analyses, accounting for unknowns and data variability, was conducted. Similarly, the value of time lost due to illness and deaths using the human capital approach was explored through scenario analyses.

RESULTS: In 2015, an estimated 1 008 642 cases in 44 African countries resulted in an economic burden of US$130 million from cholera-related illness and its treatment. When the estimated 38 104 cholera deaths were included in the analysis, the economic burden increased to US$1 billion or international $2.4 billion for the same year. At the same time, when only the 71 126 cases and 937 deaths reported to the WHO are considered, the economic burden was only US$68 million for the year 2015. The estimates of economic burden are thus heavily dependent on the cholera incidence rate, how time lost due to illness and deaths are calculated, hospitalisation rates and hospitalisation costs.

CONCLUSION: The findings can be used as an economic justification for cholera control in Africa and for generating value-for-money evidence to underpin Ending Cholera-A Global Roadmap to 2030 with considerations to study limitations.

PMID:33757949 | PMC:PMC7993295 | DOI:10.1136/bmjopen-2020-044615

Cholera outbreak in an informal settlement at Shahpur huts, Panchkula District, Haryana State, India, 2019

March 23, 2021

Indian J Public Health. 2021 Jan;65(Supplement):S51-S54. doi: 10.4103/ijph.IJPH_970_20.


In September 2019, after a reported death due to acute diarrheal disease in Shahpur village, Panchkula district, Haryana state, India, we conducted an outbreak investigation to identify the etiological agent, estimate the burden of disease, and make recommendations to prevent future outbreaks. The suspected cholera case was a resident of Shahpur huts, ≥1 year of age having ≥3 loose stools within a 24-h period between September 1 and 28, 2019 and a laboratory-confirmed cholera case, whose stool specimen tested positive for Vibrio cholerae. We identified 196 suspected cholera cases with a median age of 18 years (range: 1-65 years); 54% (106) being female. The overall attack rate was 8% (196/2,602), and the case fatality rate was 1% (2/196). Tested samples of water from tanks (n = 6), sewage effluent (n = 2), and 22% (4/18) of stool specimens collected from suspected cases were positive for V. cholerae. Strengthening surveillance, improving water, and sanitation systems are recommended to prevent future cholera outbreaks.

PMID:33753593 | DOI:10.4103/ijph.IJPH_970_20

Cholera outbreak associated with contaminated water sources in paddy fields, Mandla District, Madhya Pradesh, India

March 23, 2021

Indian J Public Health. 2021 Jan;65(Supplement):S46-S50. doi: 10.4103/ijph.IJPH_1118_20.


BACKGROUND: Mandla District in Madhya Pradesh, India, reported a suspected cholera outbreak from Ghughri subdistrict on August 18, 2016.

OBJECTIVE: We investigated to determine risk factors and recommend control and prevention measures.

METHODS: We defined a case as >3 loose stools in 24 h in a Ghughri resident between July 20 and August 19, 2016. We identified cases by passive surveillance in health facilities and by a house-to-house survey in 28 highly affected villages. We conducted a 1:2 unmatched case-control study, collected stool samples for culture, and tested water sources for fecal contamination.

RESULTS: We identified 628 cases (61% female) from 96 villages; the median age was 27 years (range: 1 month-76 years). Illnesses began 7 days after rainfall with 259 (41%) hospitalizations and 14 (2%) deaths in people from remote villages who died before reaching a health facility; 12 (86%) worked in paddy fields. Illness was associated with drinking well water within paddy fields (odds ratio [OR] = 4.0, 95% confidence interval [CI] = 1.4-8.0) and not washing hands with soap after defecation (OR = 6.1, CI = 1.7-21). Of 34 stool cultures, 11 (34%) tested positive for Vibrio cholerae O1 Ogawa. We observed open defecation in affected villages around paddy fields. Of 16 tested water sources in paddy fields, eight (50%) were protected, but 100% had fecal contamination.

CONCLUSION: We recommended education regarding pit latrine sanitation and safe water, especially in paddy fields, provision of oral rehydration solution in remote villages, and chlorine tablets for point-of-use treatment of drinking water.

PMID:33753592 | DOI:10.4103/ijph.IJPH_1118_20

Acute diarrheal disease outbreak in Muzaffarpur Village, Chandauli District, Uttar Pradesh, India

March 23, 2021

Indian J Public Health. 2021 Jan;65(Supplement):S34-S40. doi: 10.4103/ijph.IJPH_1111_20.


BACKGROUND: Acute diarrheal disease (ADD) outbreaks frequently occur in the Gangetic plains of Uttar Pradesh, India. In August 2017, Muzaffarpur village, Uttar Pradesh, reported an ADD outbreak.

OBJECTIVES: Outbreak investigation was conducted to find out the epidemiology and to identify the risk factors.

METHODS: A 1:1 area-matched case-control study was conducted. Suspected ADD case was defined as ≥3 loose stools or vomiting within 24 h in a Muzaffarpur resident between August 7 and September 9, 2017. A control was defined as an absence of loose stools and vomiting in a resident between August 7 and September 9, 2017. A matched odds ratio (mOR) with 95% confidence intervals (CIs) was calculated. Drinking water was assessed to test for the presence of any contamination. Stool specimens were tested for Vibrio cholerae, and water samples were also tested for any fecal contamination and residual chlorine.

RESULTS: Among 70 cases (female = 60%; median age = 12 years, range = 3 months-70 years), two cases died and 35 cases were hospitalized. Area-A in Muzaffarpur had the highest attack rate (8%). The index case washed soiled clothes at well - A1 1 week before other cases occurred. Among 67 case-control pairs, water consumption from well-A1 (mOR: 43.00; 95% CI: 2.60-709.88) and not washing hands with soap (mOR: 2.87; 95% CI: 1.28-6.42) were associated with illness. All seven stool specimens tested negative for V. cholerae. All six water samples, including one from well-A1, tested positive for fecal contamination with <0.2 ppm of residual chlorine.

CONCLUSION: This outbreak was associated with consumption of contaminated well water and hand hygiene. We recommended safe water provision, covering wells, handwashing with soap, access to toilets, and improved laboratory capacity for testing diarrheal pathogens.

PMID:33753590 | DOI:10.4103/ijph.IJPH_1111_20

Shellfish poisoning outbreaks in Cuddalore District, Tamil Nadu, India

March 23, 2021

Indian J Public Health. 2021 Jan;65(Supplement):S29-S33. doi: 10.4103/ijph.IJPH_1070_20.


BACKGROUND: Two suspected shellfish poisoning events were reported in Cuddalore District in Tamil Nadu, India, between January and April 2015.

OBJECTIVES: The study was conducted to confirm the outbreaks and to identify the source and risk factors.

METHODS: For both outbreaks, a case was defined as a person with nausea, vomiting, or dizziness. Sociodemographic details and symptoms were noted down. Data were also collected in a standard 3-day food frequency questionnaire, along with a collection of clam samples. A case-control study was initiated in the April outbreak. Stool samples were collected from cases, and clam vendors were interviewed.

RESULTS: In an outbreak that happened in January, all the twenty people reported to be consumed clams were diagnosed as cases (100% attack rate, 100% exposure rate). In the April outbreak, we identified 199 cases (95% attack rate). In both outbreaks, the clams were identified as genus Meretrix meretrix. The most common reported symptoms were dizziness and vomiting. The clams heated and consumed within 30-60 min. No heavy metals or chemicals were detected in the clams, but assays for testing shellfish toxins were unavailable. All 64 selected cases reported clam consumption (100% exposure rate) as did 11 controls (17% exposure rate). Illness was associated with a history of eating of clams (odds ratio = 314, 95% confidence interval = 39-512). Of the six stool samples tested, all were culture negative for Salmonella, Shigella, and Vibrio cholerae. The water at both sites was contaminated with garbage and sewage.

CONCLUSION: Coordinated and timely efforts by a multidisciplinary team of epidemiologists, marine biologists, and food safety officers led to the outbreaks' containment.

PMID:33753589 | DOI:10.4103/ijph.IJPH_1070_20

An outbreak investigation of acute Diarrheal Disease, Nagpur District, Maharashtra, India

March 23, 2021

Indian J Public Health. 2021 Jan;65(Supplement):S14-S17. doi: 10.4103/ijph.IJPH_962_20.


BACKGROUND: Acute diarrheal disease (ADD) accounts for 12 million cases and 1216 deaths annually in India. On July 13, 2016, an ADD outbreak was reported from Sawargaon village from Nagpur district, Maharashtra.

OBJECTIVE: The outbreak was investigated to describe the epidemiology and suggest control and preventive measures.

METHODS: A case was defined as a person experiencing at least one loose stool in Sawargaon village between July 9, 2016, and July 31, 2016. We searched for cases by enhanced passive surveillance. We collected stool samples for bacterial culture and tested water from multiple water sources for fecal coliforms. We also reviewed sanitary practices and rainfall data.

RESULTS: A total of 889 cases were identified, with 51% female, 280 hospitalizations (31%), and two deaths. The median age was 27 years (range 6 months to 90 years). Cases started on July 9, a week after heavy rains. District authorities started chlorination of water sources on July 13 and cases declined soon after. Two of nine stool samples tested positive for Vibrio cholera O1 serogroup. Of the 18 water samples collected, 16 (88%) samples from multiple sources, including wells, hand pumps, and taps, were positive for fecal coliforms. Of 1,885 households in the village, 450 (24%) households had no toilets and open defecation was commonly observed in the nearby river bed.

CONCLUSIONS: This ADD outbreak was likely associated with drinking contaminated groundwater, which probably occurred after heavy rainfall in an area of open defecation. We recommended providing chlorinated drinking water, promoting safe sanitation practices, including building more public and private toilets, and enhancing diagnostic laboratory capacity.

PMID:33753586 | DOI:10.4103/ijph.IJPH_962_20

Emergence and spread of different ctxB alleles of Vibrio cholerae O1 in Odisha, India

March 20, 2021

Int J Infect Dis. 2021 Apr;105:730-732. doi: 10.1016/j.ijid.2021.03.042. Epub 2021 Mar 16.


This study reports variants of the ctxB allele of Vibrio cholerae O1 isolated between 1995 and 2019 in Odisha, India. ctxB1 genotypes dominated from 1995 to 2016. The Haitian variant and El Tor ctxB3 genotypes of V. cholerae O1 emerged in 1999, and were most common in 2018-2019 and 2005-2011, respectively. The ctxB7 genotype of the Haitian variant of V. cholerae O1 was quiescent from 2000 to 2006, but further spread was noted from 2007 to 2019.

PMID:33741484 | DOI:10.1016/j.ijid.2021.03.042

Severity Adjustment in the Test-Negative Design

March 17, 2021

Am J Epidemiol. 2021 Mar 17:kwab066. doi: 10.1093/aje/kwab066. Online ahead of print.


The test-negative design is often used to estimate vaccine effectiveness in influenza studies, but has also been proposed in the context of other infectious diseases, such as cholera, dengue or Ebola. It was introduced as a variation of the case-control design, in an attempt to reduce confounding bias due to healthcare-seeking behaviour, and has quickly gained popularity due to its logistic advantages. However, examining the directed acyclic graphs that describe the test-negative design reveals that, without strong assumptions, the estimated odds ratio under this sampling mechanism is not collapsible over the selection variable, such that the results obtained for the sampled individuals cannot be generalised to the whole population. In this paper, we show that adjusting for severity of disease can reduce this bias, and, under certain assumptions, makes it possible to unbiasedly estimate a causal odds ratio. We support our findings with extensive simulations, and discuss them in the context of recently published cholera test-negative vaccine effectiveness studies.

PMID:33728441 | DOI:10.1093/aje/kwab066

Neurologic Manifestations of the World Health Organization's List of Pandemic and Epidemic Diseases

March 11, 2021

Front Neurol. 2021 Feb 22;12:634827. doi: 10.3389/fneur.2021.634827. eCollection 2021.


The World Health Organization (WHO) monitors the spread of diseases globally and maintains a list of diseases with epidemic or pandemic potential. Currently listed diseases include Chikungunya, cholera, Crimean-Congo hemorrhagic fever, Ebola virus disease, Hendra virus infection, influenza, Lassa fever, Marburg virus disease, Neisseria meningitis, MERS-CoV, monkeypox, Nipah virus infection, novel coronavirus (COVID-19), plague, Rift Valley fever, SARS, smallpox, tularemia, yellow fever, and Zika virus disease. The associated pathogens are increasingly important on the global stage. The majority of these diseases have neurological manifestations. Those with less frequent neurological manifestations may also have important consequences. This is highlighted now in particular through the ongoing COVID-19 pandemic and reinforces that pathogens with the potential to spread rapidly and widely, in spite of concerted global efforts, may affect the nervous system. We searched the scientific literature, dating from 1934 to August 2020, to compile data on the cause, epidemiology, clinical presentation, neuroimaging features, and treatment of each of the diseases of epidemic or pandemic potential as viewed through a neurologist's lens. We included articles with an abstract or full text in English in this topical and scoping review. Diseases with epidemic and pandemic potential can be spread directly from human to human, animal to human, via mosquitoes or other insects, or via environmental contamination. Manifestations include central neurologic conditions (meningitis, encephalitis, intraparenchymal hemorrhage, seizures), peripheral and cranial nerve syndromes (sensory neuropathy, sensorineural hearing loss, ophthalmoplegia), post-infectious syndromes (acute inflammatory polyneuropathy), and congenital syndromes (fetal microcephaly), among others. Some diseases have not been well-characterized from a neurological standpoint, but all have at least scattered case reports of neurological features. Some of the diseases have curative treatments available while in other cases, supportive care remains the only management option. Regardless of the pathogen, prompt, and aggressive measures to control the spread of these agents are the most important factors in lowering the overall morbidity and mortality they can cause.

PMID:33692745 | PMC:PMC7937722 | DOI:10.3389/fneur.2021.634827

Antibiotic Susceptibility Patterns of Bacterial Isolates from Routine Clinical Specimens from Referral Hospitals in Tanzania: A Prospective Hospital-Based Observational Study

March 10, 2021

Infect Drug Resist. 2021 Mar 3;14:869-878. doi: 10.2147/IDR.S294575. eCollection 2021.


INTRODUCTION: Antimicrobial resistance is one of the biggest threats of modern public health. Although sub-Saharan Africa is highly burdened with infectious diseases, current data on antimicrobial resistance are sparse.

METHODS: A prospective study was conducted between October 2018 and September 2019 to assess the antibiotic susceptibility patterns of clinical bacterial isolates obtained from four referral hospitals in Tanzania. We used standard media and Kirby-Bauer disc diffusion methods as per Clinical and Laboratory Standards Institute (CLSI) standards.

RESULTS: We processed a total of 2620 specimens of which 388 (14.8%) were culture-positive from patients with a median (IQR) age of 28 (12-44) years. Of the positive cultures, 52.3% (203) were from females. Most collected specimens were ear pus 28.6% (111), urine 24.0% (93), wound pus 20.6% (80), stool 14.9% (58), and blood 8.3% (32). Predominant isolates were S. aureus 28.4% (110), E. coli 15.2% (59), P. aeruginosa 10.6% (41), P. mirabilis 7.0% (27), V. cholerae 01 Ogawa 6.2% (24), Klebsiella spp. 5.2% (20) and Streptococcus spp. 4.6% (18). Generally, the isolates exhibited a high level of resistance to commonly used antibiotics such as Ampicillin, Amoxicillin-Clavulanic acid, Erythromycin, Gentamicin, Tetracycline, Trimethoprim, third-generation Cephalosporins (Ceftriaxone and Ceftazidime), and reserved drugs (Clindamycin and Meropenem). S. aureus isolates were resistant to most of the antibiotics tested; 66.7% were classified as MRSA infections.

CONCLUSION: Antibiotic resistance to commonly prescribed antibiotics was alarmingly high. Our findings emphasize the need for comprehensive national control programs to combat antibiotic resistance.

PMID:33688222 | PMC:PMC7937390 | DOI:10.2147/IDR.S294575

Cholera during COVID-19: The forgotten threat for forcibly displaced populations

March 4, 2021

EClinicalMedicine. 2021 Feb 11;32:100753. doi: 10.1016/j.eclinm.2021.100753. eCollection 2021 Feb.


PMID:33659887 | PMC:PMC7892801 | DOI:10.1016/j.eclinm.2021.100753

Access to Safe Water, Sanitation, and Hygiene: A Cross-Sectional Study among the Maasai in Tanzania

March 1, 2021

Am J Trop Med Hyg. 2021 Mar 1:tpmd200134. doi: 10.4269/ajtmh.20-0134. Online ahead of print.


Safe water supply, sanitation, and hygiene (WaSH) are among key components to prevent and control waterborne diseases such as cholera, schistosomiasis, and other gastrointestinal morbidities in the community. In 2018, there was cholera outbreak in Ngorongoro district that was fueled by inadequate and unsafe water as well as poor sanitation and hygiene. We used an analytical cross-sectional study first to determine the proportion of households with access to WaSH and second to assess factors associated with coverage of household's access to WaSH. Methods included interviewing heads of the household to assess the availability of safe drinking water, use of unshared toilet/latrine by household members only, and the availability of functional handwashing facility. Eight percent of households had access to WaSH. Access to household's WaSH was positively associated with household's monthly income, education of heads of the household, and water use per person per week. To control water-related morbidities, there is a need to improve access to reliable safe drinking water, expand alternatives of households to earn more incomes, and enhance proper sanitation and hygiene services to rural areas and marginalized groups like the Maasai of Ngorongoro in Tanzania.

PMID:33646976 | DOI:10.4269/ajtmh.20-0134

Geospatial analysis of cholera patterns in Nigeria: findings from a cross-sectional study

February 24, 2021

BMC Infect Dis. 2021 Feb 23;21(1):202. doi: 10.1186/s12879-021-05894-2.


BACKGROUND: Persistence of cholera outbreaks in developing countries calls for concern and more targeted intervention measures for long-term control. This research undertook spatial analysis of cholera incidence in Nigeria over a seventeen-year period to determine the existence of regional hotspots and predictors.

METHODS: A cross-sectional study design was used for the research. Cholera data for each of the thirty-six states and the federal capital territory (FCT) were obtained from the Nigeria Centre for Disease Control (NCDC) of the Federal Ministry of Health, Nigeria. Socioeconomic data including proportion of households using solid waste disposal (unapproved dumpsite, refuse burying, refuse burning, public dumpsite, and refuse collectors), water sources (pipe borne water, well, borehole, rain water, surface waters and water vendors), sewage disposal (water closet, pit latrines, bucket/pan, public toilet and nearby bush/stream), living in a single room and earning less than minimum wage (18,000 naira) were obtained from National Population Commission. On the other hand, proportion of illiterate adults (15 years and above) and poor people; and population density were obtained from National Bureau of Statistics. Each socioeconomic data was obtained at state level. Cholera patterns were analysed at state level using Global Moran's I while specific locations of cholera clusters were determined using Local Moran's I. Stepwise multiple regression was used to determine socioeconomic predictors of cholera incidence.

RESULTS: Local Moran's I revealed significant cluster patterns in 1999, 2001, 2002, 2009 and 2010 in Adamawa, Gombe, Katsina, Bauchi, Borno, Yobe, and Kano states. Households using surface water was the significant predictor (23%) of the observed spatial variations in cholera incidence.

CONCLUSIONS: Persistence of cholera outbreaks in some north east and north western states calls for more targeted, long-term and effective intervention measures especially on provision of safe sources of water supply by government and other stakeholders.

PMID:33622264 | PMC:PMC7903613 | DOI:10.1186/s12879-021-05894-2

Comprehensive analysis of genomic diversity of SARS-CoV-2 in different geographic regions of India: an endeavour to classify Indian SARS-CoV-2 strains on the basis of co-existing mutations.

February 23, 2021
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Comprehensive analysis of genomic diversity of SARS-CoV-2 in different geographic regions of India: an endeavour to classify Indian SARS-CoV-2 strains on the basis of co-existing mutations.

Arch Virol. 2021 Mar;166(3):801-812

Authors: Sarkar R, Mitra S, Chandra P, Saha P, Banerjee A, Dutta S, Chawla-Sarkar M

Accumulation of mutations within the genome is the primary driving force in viral evolution within an endemic setting. This inherent feature often leads to altered virulence, infectivity and transmissibility, and antigenic shifts to escape host immunity, which might compromise the efficacy of vaccines and antiviral drugs. Therefore, we carried out a genome-wide analysis of circulating SARS-CoV-2 strains to detect the emergence of novel co-existing mutations and trace their geographical distribution within India. Comprehensive analysis of whole genome sequences of 837 Indian SARS-CoV-2 strains revealed the occurrence of 33 different mutations, 18 of which were unique to India. Novel mutations were observed in the S glycoprotein (6/33), NSP3 (5/33), RdRp/NSP12 (4/33), NSP2 (2/33), and N (1/33). Non-synonymous mutations were found to be 3.07 times more prevalent than synonymous mutations. We classified the Indian isolates into 22 groups based on their co-existing mutations. Phylogenetic analysis revealed that the representative strains of each group were divided into various sub-clades within their respective clades, based on the presence of unique co-existing mutations. The A2a clade was found to be dominant in India (71.34%), followed by A3 (23.29%) and B (5.36%), but a heterogeneous distribution was observed among various geographical regions. The A2a clade was highly predominant in East India, Western India, and Central India, whereas the A2a and A3 clades were nearly equal in prevalence in South and North India. This study highlights the divergent evolution of SARS-CoV-2 strains and co-circulation of multiple clades in India. Monitoring of the emerging mutations will pave the way for vaccine formulation and the design of antiviral drugs.

PMID: 33464421 [PubMed - indexed for MEDLINE]

Identification of chironomid species as natural reservoirs of toxigenic Vibrio cholerae strains with pandemic potential.

February 23, 2021
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Identification of chironomid species as natural reservoirs of toxigenic Vibrio cholerae strains with pandemic potential.

PLoS Negl Trop Dis. 2020 12;14(12):e0008959

Authors: Laviad-Shitrit S, Sela R, Thorat L, Sharaby Y, Izhaki I, Nath BB, Halpern M

Vibrio cholerae causes the fatal cholera diarrhea. Chironomids (Diptera; Chironomidae) are abundant in freshwater aquatic habitats and estuaries and are natural reservoirs of V. cholerae. Until now, only the non-O1/O139 serogroups of V. cholerae were identified in chironomids. Here, we explored whether chironomids are natural reservoirs of V. cholerae O1/O139 serogroups, which are associated with cholera endemics and pandemics. All four life stages of chironomids were sampled from two rivers, and a laboratory culture in Pune, India, and from a pond in Israel. In total, we analyzed 223 chironomid samples. The presence of V. cholerae O1/O139 serogroups was verified using molecular tools. Nine chironomid species were identified; of them, Chironomus circumdatus was the most abundant. The presence of V. cholerae serogroup O1 and the cholera toxin genes were detected in samples from all chironomid species. However, serogroup O139 was detected in only two chironomid species. Besides PCR to detect specific genes, a metagenomic analysis that was performed in three selected C. ramosus larvae, identified a list of virulence genes associated with V. cholerae. The findings provide evidence that chironomids are natural reservoirs of toxigenic V. cholerae O1/O139. Chironomid populations and V. cholerae show biannual peak patterns. A similar pattern is found for cholera epidemics in the Bengal Delta region. Thus, we hypothesize that monitoring chironomids in endemic areas of the disease may provide a novel tool for predicting and preventing cholera epidemics. Moreover, serogroup O139 was detected only in two chironomid species that have a restricted distribution in the Indian subcontinent, possibly explaining why the distribution of the O139 serogroup is limited.

PMID: 33362241 [PubMed - indexed for MEDLINE]

From Economic Recovery to Health Resilience

February 23, 2021

JAMA. 2021 Feb 23;325(8):710-711. doi: 10.1001/jama.2020.24936.


PMID:33620391 | DOI:10.1001/jama.2020.24936