Scientometrics enables scholars to assess and visualize emerging research trends and hot-spots in the scientific literature from a quantitative standpoint. In the last decades, Africa has nearly ...doubled its absolute count of scholarly output, even though its share in global knowledge production has dramatically decreased. The still-ongoing COVID-19 pandemic has profoundly impacted the way scholarly research is conducted, published, and disseminated. However, the COVID-19-related research focus, the scientific productivity, and the research collaborative network of African researchers during the ongoing COVID-19 pandemic remain to be elucidated. This study aimed to clarify the COVID-19 research patterns among African researchers and estimate the strength of collaborations and partnerships between African researchers and scholars from the rest of the world during the COVID-19 pandemic, collecting data from electronic scholarly databases such as Web of Science (WoS), PubMed/MEDLINE and African Journals OnLine (AJOL), the largest and prominent platform of African-published scholarly journals. We found that COVID-19-related collaboration patterns varied among African regions. For instance, most of the scholarly partnerships occurred with formerly colonial countries (such as European or North-American countries). In other cases, scholarly ties of North African countries were above all with the Kingdom of Saudi Arabia. In terms of number of publications, South Africa and Egypt were among the most productive countries. Bibliometrics and, in particular, scientometrics can help scholars identify research areas of particular interest, as well as emerging topics, such as the COVID-19 pandemic. With a specific focus on the still-ongoing viral outbreak, they can assist decision- and policy-makers in allocating funding and economic-financial, logistic, organizational, and human resources, based on the specific gaps and needs of a given country or research area.
•Human lice include Pediculus humanus (body lice), Pediculus humanus capitis (head lice) that frequently affect children, and Pthirus pubis, commonly known as crab lice.•Body lice, mainly found among ...disadvantaged persons, are known to be vectors of serious human bacterial infectious diseases including epidemic typhus, recurrent fever, trench fever, and plague.•In Africa, human infections transmitted by lice remained poorly known and underestimated.
Lice are host-specific insects. Human lice include Pediculus humanus (body lice) which are known to be vectors of serious human bacterial infectious diseases including epidemic typhus, relapsing fever, trench fever and plague; Pediculus humanus capitis (head lice) that frequently affect children; and Pthirus pubis, commonly known as crab lice. In Africa, human infections transmitted by lice remained poorly known and therefore, underestimated, perhaps due to the lack of diagnostic tools and professional knowledge. In this paper we review current knowledge of the microorganisms identified in human lice in the continent of Africa, in order to alert health professionals to the importance of recognizing the risk of lice-related diseases.
Proof of Concept of Culturomics Use of Time of Care Naud, Sabrina; Khelaifia, Saber; Mbogning Fonkou, Maxime Descartes ...
Frontiers in cellular and infection microbiology,
11/2020, Letnik:
10
Journal Article
Recenzirano
Odprti dostop
Culturomics, a high throughput culture method with rapid identification of the colonies by Matrix Assisted Laser Desorption Ionization/Time Of Flight Mass Spectrometry (MALDI-TOF MS), has ...demonstrated its contribution to the exploration of the gut microbiota over the past 10 years. However, the cost, work time and workload, considerably limit its use on a large scale or emergency context. Here, by testing two different stool samples, including a stool sample from a patient requiring rapid immunotherapy treatment, we tested a new fast culturomic protocol using two pre-incubation media, blood culture bottle and YCFA modified medium. Both media were supplemented with 2 ml of rumen fluid filtered at 0.2 μm and 2 ml of defibrinated and sterile sheep blood. Unlike the standard culturomics, subculturing of blood culture bottle were performed at reduced incubation time (3 h, 6 h, 9 h, 24 h) and at a longer incubation time (3 days, 7 days, and 10 days) at 37°C. By testing 5,200 colonies per MALDI-TOF MS and obtaining a comparable number of cultured bacterial species (131 to 143) in a stool sample, this new protocol reduced the number of colonies tested by 57%, working time by 78.6% and cost by 72.2%. In addition, we highlighted that the proportion of strict anaerobic species has increased by 24%, known to be the preferential targets for biotherapy, including
,
, and
Finally, this work showed that some bacterial species grew earlier but disappeared with prolonged incubation times.
Thanks to its ability to isolate previously uncultured bacterial species, culturomics has dynamized the study of the human microbiota. A new bacterial species,
Gemella massiliensis
Marseille-P3249
T
..., was isolated from a sputum sample of a healthy French man. Strain Marseille-P3249
T
is a facultative anaerobe, catalase-negative, Gram positive, coccus, and unable to sporulate. The major fatty acids were C
16:0
(34%), C
18:1n9
(28%), C
18:0
(15%) and C
18:2n6
(13%). Its 16S rRNA sequence exhibits a 98.3% sequence similarity with
Gemella bergeri
strain 617-93
T
, its phylogenetically closest species with standing in nomenclature. Its digital DNA–DNA hybridization (dDDH) and OrthoANI values with
G. bergeri
of only 59.7 ± 5.6% and 94.8%, respectively. These values are lower than the thresholds for species delineation (> 70% and > 95%, respectively). This strain grows optimally at 37 °C and its genome is 1.80 Mbp long with a 30.5 mol% G + C content. Based on these results, we propose the creation of the new species
Gemella massilienis
sp. nov., strain Marseille-P3249
T
(= CSUR P3249 = DSMZ 103940).
Background:
More than 1 year after the beginning of the international spread of coronavirus 2019 (COVID-19), the reasons explaining its apparently lower reported burden in Africa are still to be ...fully elucidated. Few studies previously investigated the potential reasons explaining this epidemiological observation using data at the level of a few African countries. However, an updated analysis considering the various epidemiological waves and variables across an array of categories, with a focus on African countries might help to better understand the COVID-19 pandemic on the continent. Thus, we investigated the potential reasons for the persistently lower transmission and mortality rates of COVID-19 in Africa.
Methods:
Data were collected from publicly available and well-known online sources. The cumulative numbers of COVID-19 cases and deaths per 1 million population reported by the African countries up to February 2021 were used to estimate the transmission and mortality rates of COVID-19, respectively. The covariates were collected across several data sources: clinical/diseases data, health system performance, demographic parameters, economic indicators, climatic, pollution, and radiation variables, and use of social media. The collinearities were corrected using variance inflation factor (VIF) and selected variables were fitted to a multiple regression model using the R statistical package.
Results:
Our model (adjusted R-squared: 0.7) found that the number of COVID-19 tests per 1 million population, GINI index, global health security (GHS) index, and mean body mass index (BMI) were significantly associated (
P
< 0.05) with COVID-19 cases per 1 million population. No association was found between the median life expectancy, the proportion of the rural population, and Bacillus Calmette–Guérin (BCG) coverage rate. On the other hand, diabetes prevalence, number of nurses, and GHS index were found to be significantly associated with COVID-19 deaths per 1 million population (adjusted R-squared of 0.5). Moreover, the median life expectancy and lower respiratory infections rate showed a trend towards significance. No association was found with the BCG coverage or communicable disease burden.
Conclusions:
Low health system capacity, together with some clinical and socio-economic factors were the predictors of the reported burden of COVID-19 in Africa. Our results emphasize the need for Africa to strengthen its overall health system capacity to efficiently detect and respond to public health crises.
Culturomics has allowed the isolation of a significant number of new bacterial species from the human gut microbiota and proved to be a valuable complement to culture-independent techniques. Using ...this culture-based approach, a new bacterial species has been isolated from a stool sample of a 39-year-old healthy Pygmy male and described using the taxonogenomic strategy. Cells of strain Marseille-P4356
T
are Gram-stain negative cocci. The strain grows optimally at 37 °C and is catalase positive but oxidase negative. Its 16S rRNA gene sequence exhibited 92.96% sequence similarity with
Dysgonomonas gadei
strain JCM 16698T (NR_113134.1), currently its phylogenetically closest species that has been validly named. The genome of strain Marseille-P4356
T
is 3,472,011 bp long with 37.3 mol% G+C content. Phenotypic, biochemical, proteomic, genomic and phylogenetic analyses, clearly demonstrate that strain Marseille-P4356
T
(= CCUG 71356
T
= CSUR P4356
T
) represents a new species within the genus
Dysgonomonas
, for which we propose the name
Dysgonomonas massiliensis
sp. nov.
Intensive efforts have been made to describe the human microbiome and its involvement in health and disease. Culturomics has been recently adapted to target formerly uncultured bacteria and other ...unclassified bacterial species. This approach enabled us to isolate in the current study a new bacterial species, Parabacteroides timonensis strain Marseille‐P3236T, from a stool sample of a healthy 39‐year‐old pygmy male. This strain, is an anaerobic, gram‐negative, nonspore‐forming motile rod. Its genome is made up of 6,483,434 bp with 43.41% G+C content, 5046 protein‐encoding genes, and 84 RNA genes. We herein provide the full description of Parabacteroides timonensis strain Marseille‐P3236T through the taxonogenomic approach.
In the present work, we report the isolation of a new bacterial species in Parabacteroides genus by the means of Culturomics and its description by taxono‐enomics approach.
Background According to study on the under-estimation of COVID-19 cases in African countries, the average daily case reporting rate was only 5.37% in the initial phase of the outbreak when there was ...little or no control measures. In this work, we aimed to identify the determinants of the case reporting and classify the African countries using the case reporting rates and the significant determinants. Methods We used the COVID-19 daily case reporting rate estimated in the previous paper for 54 African countries as the response variable and 34 variables from demographics, socioeconomic, religion, education, and public health categories as the predictors. We adopted a generalized additive model with cubic spline for continuous predictors and linear relationship for categorical predictors to identify the significant covariates. In addition, we performed Hierarchical Clustering on Principal Components (HCPC) analysis on the reporting rates and significant continuous covariates of all countries. Results 21 covariates were identified as significantly associated with COVID-19 case detection: total population, urban population, median age, life expectancy, GDP, democracy index, corruption, voice accountability, social media, internet filtering, air transport, human development index, literacy, Islam population, number of physicians, number of nurses, global health security, malaria incidence, diabetes incidence, lower respiratory and cardiovascular diseases prevalence. HCPC resulted in three major clusters for the 54 African countries: northern, southern and central essentially, with the northern having the best early case detection, followed by the southern and the central. Conclusion Overall, northern and southern Africa had better early COVID-19 case identification compared to the central. There are a number of demographics, socioeconomic, public health factors that exhibited significant association with the early case detection.
Culturomics has recently allowed the isolation and description of previously uncultured bacteria from the human microbiome at different body sites. As part of a project aiming to describe the human ...gut microbiota by culturomics,
Phoenicibacter congonensis
strain Marseille-P3241
T
was isolated from the gut of a 45 years old Pygmy female. In the present work, we aim to describe this strain via the taxonogenomics approach. The major phenotypic, genomic and biochemical characteristics of this strain were analysed. Strain Marseille-P3241
T
is an anaerobic, Gram-positive and motile coccobacillus that grows optimally at 37 °C. The genome of strain Marseille-P3241
T
is 1,447,956 bp long with 43.44% GC content and its 16S rRNA gene sequence exhibited 89% sequence similarity with that of
Denitrobacterium detoxificans
strain NPOH1
T
, the phylogenetically closest related species with current standing in nomenclature. After performing a phylogenetic and genomic analysis, we conclude that strain Marseille-P3241
T
(= CCUG 70681
T
= CSUR P3241
T
) represents the type species of a new genus, for which we propose the name
Phoenicibacter congonensis
gen. nov., sp. nov.
As part of the culturomics project aiming at describing the human microbiota, we report in this study the description of the new bacterial genus Raoultibacter gen. nov. that includes two new species, ...that is, R. massiliensis sp. nov. and R. timonensis sp. nov. The R. massiliensis type strain Marseille‐P2849T was isolated from the fecal specimen of a healthy 19‐year‐old Saudi Bedouin, while R. timonensis type strain Marseille‐P3277T was isolated from the feces of an 11‐year‐old pygmy female living in Congo. Strain Marseille‐P2849T exhibited 91.4% 16S rRNA sequence similarity with Gordonibacter urolithinfaciens, its phylogenetic closest neighbor with standing in nomenclature. As well, strain Marseille‐P3277T exhibited 97.96% 16S rRNA similarity with strain Marseille‐P2849T. Both strains were Gram‐positive, motile, nonspore‐forming rod and form transparent microcolonies on blood agar in both anaerobic and microaerophilic atmospheres. The genome sizes of strain Marseille‐P2849T and strain Marseille‐P3277T were 3,657,161 bp and 4,000,215 bp, respectively. Using a taxono‐genomic approach combining the phenotypic, biochemical, and genomic characteristics, we propose the genus Raoultibacter gen. nov., which contains strains Marseille‐P2849T (= CSUR P2849T, = DSM 103407T) and Marseille‐P3277T (=CCUG 70680T, =CSUR P3277T) as type strains of the species R. massiliensis sp. nov., and R. timonensis sp. nov., respectively.
We report in this study the description of the new bacterial genus Raoultibacter gen. nov. that includes two new species, that is, R. massiliensis sp. nov. and R. timonensis sp. nov. The R. massiliensis type strain Marseille‐P2849T was isolated from the fecal specimen of a healthy 19‐year‐old Saudi Bedouin, while R. timonensis type strain Marseille‐P3277T was isolated from the feces of an 11‐year‐old pygmy female living in Congo. These novel Gram‐negative, motile, nonsporeforming coccobacilli form transparent microcolonies on blood agar in both anaerobic and microaerophilic atmospheres and belong to the family Eggerthellaceae. The genome sizes of these strains were 3,657,161 bp and 4,000,215 bp, and their G+C contents were 59.02 and 59.9 mol%, respectively.
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