Molecular detection and MST genotyping of Coxiella burnetii in ruminants and stray dogs and cats in Northern Algeria.

Aiming at identifying the reservoir and contamination sources of Coxiella burnetii in Northern Algeria, we investigated the molecular presence of the bacterium in 599 samples (blood, placenta, liver, spleen, and uterus) collected from cattle, sheep, dogs and cats. Our qPCR results showed that 15/344 (4.36%) blood samples and six/255 (2.35%) organ specimens were positive for C. burnetii. In cattle, three (4%) blood and liver samples were positive. In sheep, one blood (1.19%) and 3 (8.57%) placenta samples were positive. At the Algiers dog pound, 8 (10%) and 3 (5%) blood samples were qPCR positivein dogs and cats, respectively. In addition, MST genotyping showed that MST 33 was present in cattle and sheep, MST 20 in cattle,andMST 21 in dogs and cats.

The frequency-following response to assess the neural representation of spectral speech cues in older adults.

Older adults often present difficulties understanding speech that cannot be explained by age-related changes in sound audibility. Psychoacoustic and electrophysiologic studies have linked these suprathreshold difficulties to age-related deficits in the auditory processing of temporal and spectral sound information. These studies suggest the existence of an age-related temporal processing deficit in the central auditory system, but the existence of such deficit in the spectral domain remains understudied. The FFR is an electrophysiological evoked response that assesses the ability of the neural auditory system to reproduce the spectral and temporal patterns of a sound. The main goal of this short review is to investigate if the FFR can identify and measure spectral processing deficits in the elderly compared to younger adults (for both, without hearing loss or competing noise). Furthermore, we want to determine what stimuli and analyses have been used in the literature to assess the neural encoding of spectral cues in older adults. Almost all reviewed articles showed an age-related decline in the auditory processing of spectral acoustic information. Even when using different speech and non-speech stimuli, studies reported an age-related decline at the fundamental frequency, at the first formant, and at other harmonic components using different metrics, such as the response's amplitude, inter-trial phase coherence, signal-to-response correlation, and signal-to-noise ratio. These results suggest that older adults may present age-related spectral processing difficulties, but further FFR studies are needed to clarify the effect of advancing age on the neural encoding of spectral speech cues. Spectral processing research on aging would benefit from using a broader variety of stimuli and from rigorously controlling for hearing thresholds even in the absence of disabling hearing loss. Advances in the understanding of the effect of age on FFR measures of spectral encoding could lead to the development of new clinical tools, with possible applications in the field of hearing aid fitting.

Draft genome of Metabacillus niabensis strain 4T19T isolated from cotton-waste composts for mushroom cultivation.

In this article, we present the draft genome sequence of Metabacillus niabensis strain 4T19T (= CSUR Q2603 T = DSM 17723 = JCM 16399 = KACC 11279), that is a new Metabacillus species isolated from cotton-waste composts. The genome sequence from Metabacillus niabensis strain 4T19T was assembled into 462 contigs for a total size of 4,987,608 bp with a G + C content of 35.5%.

Description of Gracilibacillus phocaeensis sp. nov., a new halophilic bacterium isolated from Senegalian human stool.

Using the taxonogenomics method, we describe Gracilibacillus phocaeensis strain Marseille-P3801, a new species previously isolated from a salty stool of a 20-year-old man from N'Diop, Senegal. It is a Gram-positive, aerobic and motile bacillus. The major fatty acids are C15:0-anteiso (59%), C16:0 (16%) and C17:0-anteiso (11%). Strain Marseille-P3801 exhibits a 98.45% sequence similarity with Gracilibacillus thailandensis strain TP2-8, the phylogenetically closest species. Its genome is 4.66 Mb with 39.6 mol% G + C content.

Clinical efficacy of chloroquine derivatives in COVID-19 infection: comparative meta-analysis between the big data and the real world.

In the context of the current coronavirus disease 2019 (COVID-19) pandemic, we conducted a meta-analysis on the effects of chloroquine derivatives in patients, based on unpublished and published reports available publicly on the internet as of 27 May 2020. The keywords 'hydroxychloroquine', 'chloroquine', 'coronavirus', 'COVID-19' and 'SARS-Cov-2' were used in the PubMed, Google Scholar and Google search engines without any restrictions as to date or language. Twenty studies were identified involving 105 040 patients (19 270 treated patients) from nine countries (Brazil, China, France, Iran, Saudi Arabia, South Korea, Spain and the USA). Big data observational studies were associated with conflict of interest, lack of treatment dosage and duration, and absence of favourable outcome. Clinical studies were associated with favourable outcomes and details on therapy. Among clinical studies, three of four randomized controlled trials reported a significant favourable effect. Among clinical studies, a significant favourable summary effect was observed for duration of cough (OR 0.19, p 0.00003), duration of fever (OR 0.11, p 0.039), clinical cure (OR 0.21, p 0.0495), death (OR 0.32, p 4.1 × 10-6) and viral shedding (OR 0.43, p 0.031). A trend for a favourable effect was noted for the outcome 'death and/or intensive care unit transfer' (OR 0.29, p 0.069) with a point estimate remarkably similar to that observed for death (∼0.3). In conclusion, a meta-analysis of publicly available clinical reports demonstrates that chloroquine derivatives are effective to improve clinical and virological outcomes, but, more importantly, they reduce mortality by a factor of 3 in patients with COVID-19. Big data are lacking basic treatment definitions and are linked to conflict of interest. The retraction of the only big data study associated with a significantly deleterious effect the day after (June 5, 2020) the acceptance of the present work (June 4, 2020) confirms the relevance of this work.

Description of Clostridium cagae sp. nov., Clostridium rectalis sp. nov. and Hathewaya massiliensis sp. nov., new anaerobic bacteria isolated from human stool samples.

Using culturomics methods, three strains were isolated, identified and characterized following the taxonogenomics concept. Clostridium cagae strain Marseille-P4344T (=CSURP4344), Clostridium rectalis strain Marseille-P4200T (=CSURP4200) and Hathewaya massiliensis strain Marseille-P3545T (=CSURP3545) were isolated from human stool samples. The phylogenetic reconstruction, phenotypic criteria and genomic analyses were carried out and demonstrated that these three bacteria are different from previously known bacterial species with standing in nomenclature and were classified as new members of the Clostridiaceae family.

Genome sequence and description of Urinicoccus timonensis gen. nov., sp. nov., a new bacterium isolated from a human stool sample.

Urinicoccus timonensis gen. nov., sp. nov. strain Marseille-P3926T is a new species from the phylum Firmicutes and the family Peptoniphilaceae that was isolated from a human faeces sample. Genome was 1 978 908 bp long with a 41.1 G + C content. The closest species based on 16S ribosomal RNA was Peptoniphilus ivorii DSM 10022 with 90.8% sequence similarity. Considering phenotypic features, 16S rRNA sequence and comparative genome studies, we proposed Marseille- P3926T as the strain type of Urinicoccus timonensis gen. nov., sp. nov.

Detailed description of Senegalia massiliensis strain SIT17T , a bacterium isolated from the human gut.

Strain SIT17T was isolated from the stool of a healthy 13-month-old Senegalese boy. It is a Gram-positive, anaerobic, rod-shaped, non-spore-forming and mobile bacterium. It exhibited 92.74% 16S rRNA gene sequence similarity with the Brassicibacter thermophilus strain Cel2f, the phylogenetically most closely related species. Its genome is about 2.87 Mb long with 27.39 mol% G + C content. We provide more details of Senegalia massiliensis strain SIT17T (= CSURP2130 = DSM 103071), the creation of which was previously announced.

Description of Prevotella rectalis sp. nov., a new bacterium isolated from human rectum.

Using a taxonogenomics method, we describe here a Gram-negative bacterium named Prevotella rectalis sp. nov., strain Marseille-P4334T (= CSUR P4334) isolated from the rectum. Strain Marseille-P4334T has a genome that measure 3.03 Mbp with 43.3 mol% G + C content.

Massilistercora timonensis gen. nov., sp. nov., a new bacterium isolated from the human microbiota.

Massilistercora timonensis gen. nov., sp. nov. strain Marseille-P3756T is a new species of the phylum Firmicutes; it was isolated from the human gut microbiota and has a genome of 2 769 591 bp (51.2% G + C). The closest species based on 16S rRNA sequence was Merdimonas faecis strain BR31 with 95.2 % sequence similarity. Considering phenotypic features and comparative genome studies, we proposed the strain Marseille-P3756T as the type strain of Massilistercora timonensis sp. nov., a new species within the genus Massilistercora.

Dialister massiliensis sp. nov., a new bacterium isolated from the human gut.

Dialister massiliensis strain Marseille-P5638T (= CSUR P5638) is a new species from the genus Dialister and family Veillonellaceae which was isolated from the gut microbiota of a healthy individual.

Anaerococcus marasmi sp. nov., a new bacterium isolated from human gut microbiota.

Anaerococcus marasmi sp. nov. strain Marseille-P3557T is a new species isolated from a stool of a Nigerian child with marasmus. The genome of Marseille-P3557T was 2 130 060 bp long (35.4% G + C content). The closest species based on 16S ribosomal RNA sequence was Anaerococcus prevotii strain 20548, with 97.6% sequence similarity. Considering phenotypic features and comparative genome studies, we propose the strain Marseille-P3557T as the type strain of Anaerococcus marasmi sp. nov., a new species within the genus Anaerococcus.

Phenotypic and molecular characterization of macrolide resistance mechanisms among Streptococcus pneumoniae isolated in Tunisia.

Introduction. Streptococcus pneumoniae is responsible for many community infections, with the main ones being pneumonia and meningitis. Pneumococcus has developed increased resistance to multiple classes of antibiotics. The evolution of antibiotic resistance in pneumococcus was influenced by changes in serotype distribution under vaccine selection pressure.Aim. The aim of this study was to determine the genes involved in macrolide resistance, the antimicrobial susceptibility, the serotype distribution and the spread of international antibiotic-resistant clones among clinical isolates of S. pneumoniae.Methodology. We investigated 86 erythromycin-resistant S. pneumoniae strains isolated from respiratory (n=74) or non-respiratory (n=12) samples in Tunisia. Antimicrobial susceptibility was tested using the disk diffusion method. Macrolide-resistant strains were analysed by polymerase chain reaction (PCR) for ermA, ermB, mefA and msrD. We also investigated the macrolide resistance mechanisms in eight isolates (9.3%) by sequencing the L4 and L22 riboprotein-coding genes, plus relevant segments of the three 23S rRNA genes. Capsular serotypes were detected by multiplex PCR. Sequence types (STs) were explored using multilocus sequence typing (MLST).Results. Among the 86 studied strains, 70 (81.4 %) were resistant to penicillin G. The prevalent serotypes were 19F, 14, 19A and 23F. We observed that the cMLSB phenotype (66/86, 76.7%) was the most common in these pneumococci. In addition, ermB was the most frequent resistance gene. No mutation in ribosomal protein L22 or L4 or 23S rRNA was detected. Overall, 44 STs were identified in this study, including 16 that were described for the first time. Resistance to lincomycin, tetracycline and trimethoprim/sulfamethoxazole was observed in 55 (64 %), 34 (39.5 %) and 31 (36 %) isolates, respectively. Furthermore, an increase in fluoroquinolone use in particular may lead to the emergence of levofloxacin-resistant strains. Multidrug resistance was observed in 83 isolates (96.5%). Three global antibiotic-resistant clones were identified: Denmark14 ST230, Portugal19F ST177 and Spain9V ST156.Conclusion. This study shows that macrolide resistance among S. pneumoniae isolated in Tunisia is mainly related to target site modification. Our observations demonstrate a high degree of genetic diversity and capsular types among strains resistant to macrolides.

Pseudoruminococcus massiliensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota.

Pseudoruminococcus massiliensis strain Marseille-P3876T (= CSUR P3876) is a new genus from the family Ruminococcaceae that was isolated from the gut microbiota of a healthy Senegalese man.