An emerging clade of Chikungunya West African genotype discovered in real-time during 2023 outbreak in Senegal.

Chikungunya (CHIKV) is a re-emerging endemic arbovirus in West Africa. Since July 2023, Senegal and Burkina Faso have been experiencing an ongoing outbreak, with over 300 confirmed cases detected so far in the regions of Kédougou and Tambacounda in Senegal, the largest recorded outbreak yet. CHIKV is typically maintained in a sylvatic cycle in Senegal but its evolution and factors contributing to re-emergence are so far unknown in West Africa, leaving a gap in understanding and responding to recurrent epidemics. We produced, in real-time, the first locally-generated and publicly available CHIKV whole genomes in West Africa, to characterize the genetic diversity of circulating strains, along with phylodynamic analysis to estimate time of emergence and population growth dynamics. A novel strain of the West African genotype, phylogenetically distinct from strains circulating in previous outbreaks, was identified. This suggests a likely new spillover from sylvatic cycles in rural Senegal and potential of seeding larger epidemics in urban settings in Senegal and elsewhere.

Description of Streptococcus thalassemiae sp. nov., a Bacterium Isolated from Human Blood.

Blood is a precious biological liquid that is normally sterile. Therefore, bacteria in the bloodstream are shown a priori anomaly. A blood culture is systematically performed to diagnose the cause of the bacteremia. Indeed, a patient received in our service had a thalassemia major and underwent a genoidentical transplant. Then, a blood test was performed to diagnose a four-day fever. In this context, we have isolated strain Marseille-Q2617 from the blood sample. It revealed a new bacterial strain that belongs to the genus Streptococcus. It is a Gram-positive coccus, nonmotile, and nonspore forming. The major fatty acid found is hexadecanoic acid, with 49.5%. A taxonomic method was used to characterize the strain by studying their phenotypic, phylogenetic, and genomic characteristics. In addition, sequence analysis of the 16S rRNA gene shows that the strain Marseille-Q2617 has 99.94% sequence similarity to Streptococcus mitis. Average nucleotide identity (ANI) analysis for strain Marseille-Q2617T showed the highest similarity of 92.9% with S. mitis. The DNA-DNA hybridization value obtained (50.2%) between strain Marseille-Q2607 and S. mitis, its closest related species, was below the recommended threshold (<70%). Strain Marseille-Q2617T has a genome size of 2.02 Mbp with 40.5 mol% of G + C content. Based on these results, we propose a new species of the genus Streptococcus, for which the name Streptococcus thalassemiae sp. nov., Marseille-Q2617T (=CSUR Q2617 = CECT 30109) was proposed.

High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol.

The emergence of the Coronavirus Disease 2019 (COVID-19) pandemic has fostered the use of high-throughput techniques to sequence the entire severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and track its evolution. The present study proposes a rapid and relatively less expensive sequencing protocol for 384 samples by adapting the use of an Illumina NovaSeq library to an Illumina MiSeq flow cell instrument. The SARS-CoV-2 genome sequences obtained with Illumina NovaSeq and those obtained using MiSeq instruments were compared with the objective to validate the new, modified protocol. A total of 356 (94.6%) samples yielded interpretable sequences using the modified Illumina COVIDSeq protocol, with an average coverage of 91.6%. By comparison, 357 (94.9%) samples yielded interpretable sequences with the standard COVIDSeq protocol, with an average coverage of 95.6%. Our modified COVIDSeq protocol could save 14,155 euros per run and yield results from 384 samples in 53.5 h, compared to four times 55.5 h with the standard Illumina MiSeq protocol. The modified COVIDSeq protocol thus provides high quality results comparable to those obtained with the standard COVIDSeq protocol, four times faster, while saving money.

A review of the literature of Listeria monocytogenes in Africa highlights breast milk as an overlooked human source.

According to the latest WHO estimates (2015) of the global burden of foodborne diseases, Listeria monocytogenes is responsible for one of the most serious foodborne infections and commonly results in severe clinical outcomes. The 2013 French MONALISA prospective cohort identified that women born in Africa has a 3-fold increase in the risk of maternal neonatal listeriosis. One of the largest L. monocytogenes outbreaks occurred in South Africa in 2017-2018 with over 1,000 cases. Moreover, recent findings identified L. monocytogenes in human breast milk in Mali and Senegal with its relative abundance positively correlated with severe acute malnutrition. These observations suggest that the carriage of L. monocytogenes in Africa should be further explored, starting with the existing literature. For that purpose, we searched the peer-reviewed and grey literature published dating back to 1926 to date using six databases. Ultimately, 225 articles were included in this review. We highlighted that L. monocytogenes is detected in various sample types including environmental samples, food samples as well as animal and human samples. These studies were mostly conducted in five east African countries, four west African countries, four north African countries, and two Southern African countries. Moreover, only ≈ 0.2% of the Listeria monocytogenes genomes available on NCBI were obtained from African samples, contracted with its detection. The pangenome resulting from the African Listeria monocytogenes samples revealed three clusters including two from South-African strains as well as one consisting of the strains isolated from breast milk in Mali and Senegal and, a vaginal post-miscarriage sample. This suggests there was a clonal complex circulating in Mali and Senegal. As this clone has not been associated to infections, further studies should be conducted to confirm its circulation in the region and explore its association with foodborne infections. Moreover, it is apparent that more resources should be allocated to the detection of L. monocytogenes as only 15/54 countries have reported its detection in the literature. It seems paramount to map the presence and carriage of L. monocytogenes in all African countries to prevent listeriosis outbreaks and the related miscarriages and confirm its association with severe acute malnutrition.

Heterogeneity of the Omicron variant in Senegal.

•Omicron variant continues to progress in Senegal with the appearance of new contaminations.•IRESSEF detected the first positive case of the Omicron variant on Friday, December 3, 2021.•Since this date, the number of Omicron variant infections has increased over the weeks.•Molecular surveillance of the Omicron variant allowed us to identify a strong variation of this variant in our country.

Konateibacter massiliensis gen. nov. sp. nov. and Paenibacillus faecalis sp. nov., Two New Species Isolated from the Stool Samples of Infants Suffering from Marasmus.

Two bacterial strains were isolated and identified using microbial culturomics and characterised according to the taxono-genomics strategy. The strictly anaerobic strain, Marseille-P3773T, forms smooth and translucent colonies consisting of Gram-stain negative, non-motile and non-spore-forming rod-shaped cells. Strain Marseille-P3787T consists of Gram-stain positive, motile and spore-forming cells resulting in grey and translucent colonies. The phylogenetic analysis of the 16S rRNA gene of strains Marseille-P3773T and Marseille-P3787T revealed a 96.9% similarity level with Lachnotalea glycerini strain DLD10 and 97% identity with Paenibacillus uliginis strain N3/975, respectively. The genome of strain Marseille-P3773 is 4,260,534 bp long with a 40.3 mol% G + C content and includes 3879 predicted genes of which 3769 are protein-coding genes, 76 RNAs and 34 are pseudo-genes. Strain Marseille-P3787 had a genome size of 4,833,032 bp with a 47.9 mol% G + C and has 4481 predicted genes of which 4265 are protein-coding genes, 101 RNAs and 115 are pseudo-genes. According to the data collected on these strains and, more specifically to the genomic comparison, we suggest the creation of a new genus and species, Konateibacter massiliensis gen. nov., sp. nov. with strain Marseille-P3773T (=CSURP3773 and CCUG71331) as its type strain within the Lachnospiraceae family, as well as a new species, Paenibacillus faecalis sp. nov. with strain Marseille-P3787T (=CSURP3787 and CCUG71650) as its type strain within the Paenibacillus genus.

A Listeria monocytogenes clone in human breast milk associated with severe acute malnutrition in West Africa: A multicentric case-controlled study.

BACKGROUND: Severe acute malnutrition (SAM) is a major public health problem affecting children under the age of five in many low- and middle-income countries, and its resolution would contribute towards achieving the several sustainable development goals. The etiology of SAM is pluri-factorial, including delayed maturation of the gut microbiota, suboptimal feeding practices and dysfunctional breastfeeding. The recent serendipitous detection of Listeria monocytogenes in the breast milk of Malian women, in contrast to French women, suggests a possible association with SAM. METHODOLOGY/ PRINCIPAL FINDINGS: To investigate the possible association of L. monocytogenes carriage in breast milk and SAM, a case-control study was performed in Senegal, with subjects recruited from two areas. Using 16S amplicon sequencing, a culture independent method, 100% (152/152) of the mothers were positive for L. monocytogenes in their breast milk while qPCR analysis gave lower recovery rates. Interestingly, after enrichment in Fraser broth and seeding on PALCALM agar, all 10 isolated strains were isolated from the milk of 10 mothers who had SAM children which also had a significantly increased relative abundance of L. monocytogenes (0.34 (SD 0.35) vs 0.05 (SD 0.07) in controls, p<0.0001). The high genomic similarity between these strains and Malian breast milk strains from a previous study supports the hypothesis of endemic clone carriage in West Africa. Moreover, the in vitro growth inhibition of L. monocytogenes using breast milk samples was obtained from only 50% of the milk of mothers who had SAM children, in contrast to control samples which systematically inhibited the growth of L. monocytogenes with a higher inhibition diameter (15.7 mm (SD 2.3) in controls versus 3.5 mm (SD 4.6) in SAM, p = 0.0001). Lactobacillus and Streptococcus isolated from the breast milk of controls inhibit L. monocytogenes in a species-dependent manner. CONCLUSIONS/SIGNIFICANCE: Our study reveals a previously unsuspected carriage of L. monocytogenes in the breast milk of West African women, which is associated with SAM. The inhibitory effect of human selected lactic acid bacterial species against L. monocytogenes might provide new therapeutic and inexpensive options to prevent and treat this neglected public health issue.

Fenollaria timonensis sp. nov., A New Bacterium Isolated from Healthy Human Fresh Stool.

The strain Marseille-P2133 is the type strain of a new bacterial species of the order Clostridiales that was isolated from a stool sample from a healthy volunteer. It is a strictly anaerobic Gram-negative coccobacillus. MALDI-TOF MS did not provide any identification. Strain Marseille-P2133T exhibits 97.4% similarity levels with the Fenollaria massiliensis strain 9401234T (NR_133038), a phylogenetically related species with standing in nomenclature. On the basis of these data, we propose the creation of Fenollaria timonensis sp. nov.