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Quantification of Vibrio cholerae cholix exotoxin by sandwich bead-ELISA

J Med Microbiol. 2021 Apr;70(4). doi: 10.1099/jmm.0.001311.


Introduction. Cholix toxin (ChxA) is an ADP-ribosylating exotoxin produced by Vibrio cholerae. However, to date, there is no quantitative assay available for ChxA, which makes it difficult to detect and estimate the level of ChxA produced by V. cholerae.Hypothesis/Gap Statement. It is important to develop a reliable and specific quantitative assay to measure the production level of ChxA, which will help us to understand the role of ChxA in V. cholerae pathogenesis.Aim. The aim of this study was to develop a bead-based sandwich ELISA (bead-ELISA) for the quantification of ChxA and to evaluate the importance of ChxA in the pathogenesis of V. cholerae infection.Methodology. Anti-rChxA was raised in New Zealand white rabbits, and Fab-horse radish peroxidase conjugate was prepared by the maleimide method to use in the bead-ELISA. This anti-ChxA bead-ELISA was applied to quantify the ChxA produced by various V. cholerae strains. The production of ChxA was examined in different growth media such as alkaline peptone water (APW), Luria-Bertani broth and AKI. Finally, the assay was evaluated using a mouse lethality assay with representative V. cholerae strains categorized as low to high ChxA-producers based on anti-ChxA bead-ELISA.Results. A sensitive bead-ELISA assay, which can quantify from 0.6 to 60 ng ml-1 of ChxA, was developed. ChxA was mostly detected in the extracellular cell-free supernatant and its production level varied from 1.2 ng ml-1 to 1.6 µg ml-1. The highest ChxA production was observed when V. cholerae strains were cultured in LB broth, but not in APW or AKI medium. The ChxA-producer V. cholerae strains showed 20-80 % lethality and only the high ChxA II-producer was statistically more lethal than a non-ChxA-producer, in the mice model assay. ChxA I and II production levels were not well correlated with mice lethality, and this could be due to the heterogeneity of the strains tested.Conclusion. ChxA I to III was produced mostly extracellularly at various levels depending on strains and culture conditions. The bead-ELISA developed in this study is useful for the detection and quantification of ChxA in V. cholerae strains.

PMID:33830907 | DOI:10.1099/jmm.0.001311

Genomic diversity and molecular epidemiology of Pasteurella multocida

PLoS One. 2021 Apr 6;16(4):e0249138. doi: 10.1371/journal.pone.0249138. eCollection 2021.


Pasteurella multocida is a bacterial pathogen with the ability to infect a multitude of hosts including humans, companion animals, livestock, and wildlife. This study used bioinformatic approaches to explore the genomic diversity of 656 P. multocida isolates and epidemiological associations between host factors and specific genotypes. Isolates included in this study originated from a variety of hosts, including poultry, cattle, swine, rabbits, rodents, and humans, from five different continents. Multi-locus sequence typing identified 69 different sequence types. In-silico methodology for determining capsular serogroup was developed, validated, and applied to all genome sequences, whereby capsular serogroups A, B, D, and F were found. Whole genome phylogeny was constructed from 237,670 core single nucleotide variants (SNVs) and demonstrated an overall lack of host or capsular serogroup specificity, with the exception of isolates from bovine sources. Specific SNVs within the srlB gene were identified in P. multocida subsp. septica genomes, representing specific mutations that may be useful for differentiating one of the three known subspecies. Significant associations were identified between capsular serogroup and virulence factors, including capsular serogroup A and OmpH1, OmpH3, PlpE, and PfhB1; capsular serogroup B and HgbA and PtfA; and capsular serogroup F and PtfA and PlpP. Various mobile genetic elements were identified including those similar to ICEPmu1, ICEhin1056, and IncQ1 plasmids, all of which harbored multiple antimicrobial resistance-encoding genes. Additional analyses were performed on a subset of 99 isolates obtained from turkeys during fowl cholera outbreaks from a single company which revealed that multiple strains of P. multocida were circulating during the outbreak, instead of a single, highly virulent clone. This study further demonstrates the extensive genomic diversity of P. multocida, provides epidemiological context to the various genotyping schemes that have traditionally been used for differentiating isolates, and introduces additional tools for P. multocida molecular typing.

PMID:33822782 | DOI:10.1371/journal.pone.0249138

Laboratory and Field Evaluation of the Crystal VC-O1 Cholera Rapid Diagnostic Test

Am J Trop Med Hyg. 2021 Apr 5:tpmd201280. doi: 10.4269/ajtmh.20-1280. Online ahead of print.


Cholera is a severe acute, highly transmissible diarrheal disease which affects many low- and middle-income countries. Outbreaks of cholera are confirmed using microbiological culture, and additional cases during the outbreak are generally identified based on clinical case definitions, rather than laboratory confirmation. Many low-resource areas where cholera occurs lack the capacity to perform culture in an expeditious manner. A simple, reliable, and low-cost rapid diagnostic test (RDT) would improve identification of cases allowing rapid response to outbreaks. Several commercial RDTs are available for cholera testing with two lines to detect either serotypes O1 and O139; however, issues with sensitivity and specificity have not been optimal with these bivalent tests. Here, we report an evaluation of a new commercially available cholera dipstick test which detects only serotype O1. In both laboratory and field studies in Kenya, we demonstrate high sensitivity (97.5%), specificity (100%), and positive predictive value (100%) of this new RDT targeting only serogroup O1. This is the first field evaluation for the new Crystal VC-O1 RDT; however, with these high-performance metrics, this RDT could significantly improve cholera outbreak detection and improve surveillance for better understanding of cholera disease burden.

PMID:33819171 | DOI:10.4269/ajtmh.20-1280

Identifying and quantifying the factors associated with cholera-related death during the 2018 outbreak in Nigeria

Pan Afr Med J. 2020 Dec 22;37:368. doi: 10.11604/pamj.2020.37.368.20981. eCollection 2020.


INTRODUCTION: cholera outbreaks in Nigeria are often associated with high case fatality rates; however, there is a dearth of evidence on context-specific factors associated with the trend. This study therefore aimed to identify and quantify the factors associated with cholera-related deaths in Nigeria.

METHODS: using a cross-sectional design, we analysed surveillance data from all the States that reported cholera cases during the 2018 outbreak, and defined cholera-related death as death of an individual classified as having cholera according to the Nigeria Centre for Disease Control case definition. Factors associated with cholera-related death were assessed using multivariable logistic regression and findings presented as adjusted odds ratios (ORs) with 95% Confidence Intervals (95% CIs).

RESULTS: between January 1 and November 19, 2018, 41,394 cholera cases were reported across 20 States, including 815 cholera-related deaths. In the adjusted multivariable model, older age, male gender, living in peri-urban areas or in flooded states, infection during the rainy season, and delay in seeking health care by >2 days were positively associated with cholera-related death; whereas living in urban areas, hospitalisation in the course of illness, and presentation to a secondary hospital were negatively associated with cholera-related death.

CONCLUSION: cholera-related deaths during the 2018 outbreak in Nigeria appeared to be driven by multiple factors, which further reemphasises the importance of adopting a multisectoral approach to the design and implementation of context-specific interventions in Nigeria.

PMID:33796181 | PMC:PMC7992435 | DOI:10.11604/pamj.2020.37.368.20981

Difference-in-Difference in the Time of Cholera: a Gentle Introduction for Epidemiologists

Curr Epidemiol Rep. 2020 Dec;7(4):203-211. doi: 10.1007/s40471-020-00245-2. Epub 2020 Sep 23.


PURPOSE OF REVIEW: The goal of this article is to provide an introduction to the intuition behind the difference-in-difference method for epidemiologists. We focus on the theoretical aspects of this tool, including the types of questions for which difference-in-difference is appropriate, and what assumptions must hold for the results to be causally interpretable.

RECENT FINDINGS: While currently under-utilized in epidemiologic research, the difference-in-difference method is a useful tool to examine effects of population-level exposures, but relies on strong assumptions.

SUMMARY: We use the famous example of John Snow's investigation of the cause of cholera mortality in London to illustrate the difference-in-difference approach and corresponding assumptions. We conclude by arguing that this method deserves a second-look from epidemiologists interested in asking causal questions about the impact of a population-level exposure change on a population-level outcome for the group that experienced the change.

PMID:33791189 | PMC:PMC8006863 | DOI:10.1007/s40471-020-00245-2

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

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"

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

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

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

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

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

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

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

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

Severity Adjustment in the Test-Negative Design

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

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

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

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

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

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.

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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]