Gut Microbiota Alteration is Characterized by a Proteobacteria and Fusobacteria Bloom in Kwashiorkor and a Bacteroidetes Paucity in Marasmus

Kwashiorkor and marasmus are considered to be two different clinical diseases resulting from severe malnutrition, but this distinction has been questioned. In a previous study comparing children with kwashiorkor and healthy children from Niger and Senegal, we found a dramatic gut microbiota alteration with a predominant depletion of anaerobes and enrichment in Proteobacteria and Fusobacteria in kwashiorkor. However, it remained unknown whether this association was related to malnutrition or was a specific feature of kwashiorkor. In this continuation study, we added 7 new marasmus subjects and 71,162 new colonies from the same countries. Our results showed that, compared to marasmus, the kwashiorkor gut microbiota was characterized by an increased proportion of Proteobacteria (culturomics, Marasmus 5.0%, Kwashiorkor 16.7%, p < 0.0001; metagenomics, Marasmus 14.7%, Kwashiorkor 22.0%, p = 0.001), but there was a decreased proportion of Bacteroidetes in marasmus (culturomics, Marasmus 0.8%, Kwashiorkor 6.5%, p = 0.001; metagenomics, Marasmus 5.4%, Kwashiorkor 7.0%, p = 0.03). Fusobacterium was more frequently cultured from kwashiorkor. All detected potential pathogenic species were enriched in the kwashiorkor gut microbiota. These results provide a biological basis to support the usage of an antibiotic therapy more effective in suppressing the overgrowth of bacterial communities resistant to penicillin, combined with antioxidants and probiotics for nutritional recovery therapies, particularly for kwashiorkor.

[Epidemiological, clinical and evolutionary profile of patients with tuberculosis at the Regional Hospital of Maradi, Republic of the Niger]

Introduction

Il s'agissait de décrire le profil épidémiologique, clinique et évolutif des patients suivis pour tuberculose au Centre Hospitalier Régional de Maradi.

Méthodes

Nous avions mené une étude rétrospective, descriptive et analytique à partir des dossiers des patients suivis pour tuberculose du 1^er janvier 2015 au 31 décembre 2017.

Résultats

Au total 595 patients ont été suivis dont 406 hommes (68,24%) pour 189 femmes (31,76%) et une prévalence de 27,71%. L'âge moyen était de 42,3 ans avec des extrêmes de 13 mois à 85 ans. 70,5% des patients provenaient du milieu urbain. Les commerçants représentaient 36,9% des cas. La recherche bactériologique était positive dans 64,7% des cas. Les signes fonctionnels étaient représentés par: la toux (99,5%), la fièvre (79,5%), et la douleur thoracique. La tuberculose pulmonaire avait représenté 78,7%. Le succès thérapeutique a été 81,28%. La prévalence du VIH était de 13,6% et une létalité de 10,42% dont 40,4% des patients décédés avaient une co-infection TB/VIH.

Conclusion

Avec 10,42% de décès, la tuberculose demeure un fléau dans les pays à faible revenu. L'infection à VIH/SIDA a négativement influencé ces décès au cours de cette étude. La recherche des facteurs de co-morbidités chez tout patient tuberculeux devrait être systématique afin d'améliorer leur prise en charge globale.

Treponema species enrich the gut microbiota of traditional rural populations but are absent from urban individuals

There is a significant gap in our knowledge of the microbe–host relationship between urban and traditional rural populations. We conducted a large-scale study to examine the gut microbiota of different traditional rural and urban lifestyles in human populations. Using high-throughput 16S ribosomal RNA gene amplicon sequencing, we tested urban French, Saudi, Senegalese, Nigerian and Polynesian individuals as well as individuals living in traditional rural societies, including Amazonians from French Guiana, Congolese Pygmies, Saudi Bedouins and Algerian Tuaregs. The gut microbiota from individuals living in traditional rural settings clustered differently and presented significantly higher diversity than those of urban populations (p 0.01). The bacterial taxa identified by class analysis as contributing most significantly to each cluster were Phascolarctobacterium for traditional rural individuals and Bifidobacterium for urban individuals. Spirochaetae were only present in the gut microbiota of individuals from traditional rural societies, and the gut microbiota of all traditional rural populations was enriched with Treponema succinifaciens. Cross-transmission of Treponema from termites or swine to humans or the increased use of antibiotics in nontraditional populations may explain why Treponema is present only in the gut microbiota of traditional rural populations.

Taxonogenomic description of four new Clostridium species isolated from human gut: 'Clostridium amazonitimonense', 'Clostridium merdae', 'Clostridium massilidielmoense' and 'Clostridium nigeriense'

Culturomics investigates microbial diversity of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. The present study allowed identification of four putative new Clostridium sensu stricto species: ‘Clostridium amazonitimonense’ strain LF2^T, ‘Clostridium massilidielmoense’ strain MT26^T, ‘Clostridium nigeriense’ strain Marseille-P2414^T and ‘Clostridium merdae’ strain Marseille-P2953^T, which we describe using the concept of taxonogenomics. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation.

Bacillus kwashiorkori sp. nov., a new bacterial species isolated from a malnourished child using culturomics

Strain SIT6^T was isolated from the fecal flora of a severely malnourished child as part of a broad “culturomics” study aiming to maximize the culture conditions for the in‐depth exploration of the human microbiota. An analysis of the 16S rRNA gene sequence showed that strain SIT6^T shared 94.1% 16S rRNA gene sequence similarity with Bacillus thermoamylovorans DKP^T (NR_029151), the phylogenetically closest type species. Colonies are creamy white, circular, 4–5 mm in diameter after cultivation at 37°C for 24 hr on 5% sheep blood‐enriched Colombia agar. Growth occurs at temperatures in the range of 25–56°C (optimally at 37°C). Strain SIT6^T is a gram‐positive, facultative anaerobic rod and motile by means of peritrichous flagella and sporulating; it is catalase and oxidase positive. The 2,784,637‐bp‐long genome, composed of 16 contigs, has a G+C content of 35.19%. Of the 2,646 predicted genes, 2,572 were protein‐coding genes and 74 were RNAs. The major fatty acids are saturated species (15:0 iso, 16:0 and 17:0 anteiso). Of the 14 detected fatty acids, 11 are saturated, either linear or branched (iso and anteiso). Digital DNA–DNA hybridization (dDDH) estimation and average genomic identity of orthologous gene sequences (AGIOS) of the strain SIT6^T against genomes of the type strains of related species ranged between 18.6% and 38.3% and between 54.77% and 65.50%, respectively. According to our taxonogenomics results, we propose the creation of Bacillus kwashiorkori sp. nov. that contains the type strain SIT6^T (=CSUR P2452^T, =DSM 29059^T).

Noncontiguous finished genome sequences and descriptions of 'Paenibacillus bouchesdurhonensis,' 'Paenibacillus rubinfantis,' 'Paenibacillus senegalimassiliensis' and 'Paenibacillus tuaregi' identified by culturomics

Microbial culturomics represents a completely new approach to investigate microbial diversity by using different optimized culture conditions, mass spectrometry, genome sequencing and annotation and phenotypic description that allow for an extensive characterization of new species and the study of the human microbiome. Here we present four new species within the genus Paenibacillus: ‘Paenibacillus bouchesdurhonensis’ strain Marseille-P3071^T, ‘Paenibacillus rubinfantis’ strain MT18^T, ‘Paenibacillus senegalimassiliensis’ strain SIT18^T and ‘Paenibacillus tuaregi’ strain Marseille-P2472^T, which are all facultatively aerobic and Gram-positive bacilli.

Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics?

Severe acute malnutrition is the world-leading cause of children under-five's death. Recent metagenomics studies have established a link between gut microbiota and severe acute malnutrition, describing an immaturity with a striking depletion in oxygen-sensitive prokaryotes. Amoxicillin and therapeutic diet cure most of the children with severe acute malnutrition but an irreversible disruption of the gut microbiota is suspected in the refractory and most severe cases. In these cases, therapeutic diet may be unable to reverse the microbiota alteration leading to persistent impaired development or death. In addition, as enteric sepsis is a major cause of death in this context, identification of missing gut microbes to be tested as probiotics (live bacteria that confer a benefit to the host) to restore rapidly the healthy gut microbiota and prevent the gut pathogenic invasion is of foremost importance. In this study, stool samples of malnourished patients with kwashiorkor and healthy children were collected from Niger and Senegal and analyzed by culturomics and metagenomics. We found a globally decreased diversity, a decrease in the hitherto unknown diversity (new species isolation), a depletion in oxygen-sensitive prokaryotes including Methanobrevibacter smithii and an enrichment in potentially pathogenic Proteobacteria, Fusobacteria and Streptococcus gallolyticus. A complex of 12 species identified only in healthy children using culturomics and metagenomics were identified as probiotics candidates, providing a possible, defined, reproducible, safe, and convenient alternative to fecal transplantation to restore a healthy gut microbiota in malnourished children. Microbiotherapy based on selected strains has the potential to improve the current treatment of severe acute malnutrition and prevent relapse and death by reestablishing a healthy gut microbiota.

'Marasmitruncus massiliensis' gen. nov., sp. nov., 'Clostridium culturomicum' sp. nov., 'Blautia provencensis' sp. nov., 'Bacillus caccae' sp. nov. and 'Ornithinibacillus massiliensis' sp. nov., isolated from stool samples of undernourished African children

We report here the main characteristics of five new species, ‘Marasmitruncus massiliensis’ strain Marseille-P3646^T (CSUR P3646), ‘Clostridium culturomicum’ strain Marseille-P3545^T (CSUR P3545), ‘Blautia provencensis’ strain Marseille-P3502^T (CSUR P3502), ‘Bacillus caccae’ strain Marseille-P3604^T (CSUR P3604) and ‘Ornithinibacillus massiliensis’ strain Marseille-P3601^T (CSUR P3601), which were isolated recently from undernourished children's stool samples from Niger using microbial culturomics.

'Khelaifiella massiliensis', 'Niameybacter massiliensis', 'Brachybacterium massiliense', 'Enterobacter timonensis', 'Massilibacillus massiliensis', new bacterial species and genera isolated from the gut microbiota of healthy infants

The main characteristics of 'Khelaifiella massiliensis' strain Mt13^T (= CSUR P1935, = DSM100591), 'Niameybacter massiliensis' strain Mt14^T (= CSUR P1909, = DSM100592), 'Brachybacterium massiliense' strain MT5^T (= CSUR P2240, = DSM101766), 'Enterobacter timonensis' strain mt20^T (= CSUR P2201, = DSM 101775) and 'Massilibacillus massiliensis' strain Marseille-P2411^T (= CSUR P2411, = DSM102838), new species isolated from the gut of healthy African infants, are presented.

'Urmitella timonensis' gen. nov., sp. nov., 'Blautia marasmi' sp. nov., 'Lachnoclostridium pacaense' sp. nov., 'Bacillus marasmi' sp. nov. and 'Anaerotruncus rubiinfantis' sp. nov., isolated from stool samples of undernourished African children

We report here the main characteristics of five new species ‘Urmitella timonensis’ strain Marseille-P2918^T (CSUR P2918), ‘Blautia marasmi’ strain Marseille-P2377^T (CSUR P2377), ‘Lachnoclostridium pacaense’ strain Marseille-P3100^T (CSUR P3100), ‘Bacillus marasmi’ strain Marseille-P3556^T (CSUR P3556) and ‘Anaerotruncus rubiinfantis’ strain MT15^T (CSUR P2276), which were isolated recently from stool samples taken from undernourished children in Niger and Senegal using microbial culturomics.

Paenibacillus phocaensis sp. nov., isolated from the gut microbiota of a healthy infant

Paenibacillus phocaensis sp. nov. strain mt24^T (= CSUR P2238 = DSM 101777) is a Gram-negative, facultative anaerobic, spore-forming and motile bacilli. This strain was isolated from the stool sample of a healthy infant from Niger. Its genome was estimated to a size of 5 521 415 bp with a 53.54% GC content. It contains 4835 protein-coding genes and 89 RNAs, among which two were 16S rRNA genes. There were also 101 genes (2.09%) identified as ORFans.

Tessaracoccus massiliensis sp. nov., a new bacterial species isolated from the human gut

A new Actinobacterium, designated Tessaracoccus massiliensis type strain SIT-7^T (= CSUR P1301 = DSM 29060), have been isolated from a Nigerian child with kwashiorkor. It is a facultative aerobic, Gram positive, rod shaped, non spore-forming, and non motile bacterium. Here, we describe the genomic and phenotypic characteristics of this isolate. Its 3,212,234 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 67.81% and contains 3,058 protein-coding genes and 49 RNA genes.

[Acute intestinal obstruction revealing enteropathy associated t-cell lymphoma, about a case]

Le lymphome T intestinal associé à une entéropathie ou Enteropathy associated T-cell lymphoma (EATL), est une complication rare de la maladie cœliaque (MC). Nous rapportons l'observation d'un lymphome T associée à une MC révélé par une occlusion intestinale aigue. Une patiente maghrébine de 38 ans, aux antécédents de stérilité et de douleurs abdominales chroniques, était admise en urgence pour occlusion intestinale aigue. L'intervention chirurgicale retrouvait une tumeur au dépend du grêle avec des adénopathies mésentériques. L'histologie et l'immunohistochimie de la pièce opératoire objectivait un lymphome T digestif CD3+ et le bilan immunologique de la maladie cœliaque était positif. Le diagnostic d'EATL était ainsi retenu. La patiente était mise sous chimiothérapie (CHOEP) et régime sans gluten avec une réponse complète au traitement. L'EATL est une complication rare de la MC qui peut être révélée par une occlusion intestinale. Son pronostic peut être amélioré par une prise en charge précoce associant chirurgie et chimiothérapie. Sa prévention passe par un diagnostic précoce de la MC et un régime sans gluten.

Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition

Severe acute malnutrition (SAM) is associated with inadequate diet, low levels of plasma antioxidants and gut microbiota alterations. The link between gut redox and microbial alterations, however, remains unexplored. By sequencing the gut microbiomes of 79 children of varying nutritional status from three centers in Senegal and Niger, we found a dramatic depletion of obligate anaerobes in malnutrition. This was confirmed in an individual patient data meta-analysis including 107 cases and 77 controls from 5 different African and Asian countries. Specifically, several species of the Bacteroidaceae, Eubacteriaceae, Lachnospiraceae and Ruminococceae families were consistently depleted while Enterococcus faecalis, Escherichia coli and Staphylococcus aureus were consistently enriched. Further analyses on our samples revealed increased fecal redox potential, decreased total bacterial number and dramatic Methanobrevibacter smithii depletion. Indeed, M. smithii was detected in more than half of the controls but in none of the cases. No causality was demonstrated but, based on our results, we propose a unifying theory linking microbiota specificity, lacking anaerobes and archaea, to low antioxidant nutrients, and lower food conversion.

Molecular characterization of hepatitis B virus from chronically-infected patients in Niamey, Niger

OBJECTIVES

In Niger, 65% of hepatocarcinoma and 75% of cirrhosis cases were due to hepatitis B virus (HBV). We studied the genotypic characteristics of HBsAg in chronically HBV-infected patients in Niamey.

METHODS

We studied prospectively HBV genotypic patterns among hospitalized patients with HBV infection in the National Hospital of Niamey, Niger. Patients were screened for hepatitis B surface antigen (HBsAg) and HBV genotyping was performed on the HBsAg-positive patients.

RESULTS

In this study, we have confirmed the predominance of the HBV genotype E (HBV-E) in Niger and have identified 2 recombinant forms including HBV-E/D and HBV-A3/E reported previously among blood donors in Niger and Ghana, respectively. Amino acid substitutions found in HBV sequences obtained here included P120T, S143L, G145A and A194T. These substitutions were characterized as being associated with modified antigenicity and, notably, with impaired serological detection of HBsAg, while the A194T variant was found to have a controversial role in reduced susceptibility to tenofovir.

CONCLUSIONS

We have identified two recombinant HBV forms and rare genotypic patterns in Niger that may affect hepatitis B surface antigen antigenicity, and improve current knowledge of epidemiological, clinical and virological patterns of hepatitis B in this country.

Noncontiguous finished genome sequence and description of Bacillus andreraoultii strain SIT1(T) sp. nov

Bacillus andreraoultii strain SIT1^T (= CSUR P1162 = DSM 29078) is the type strain of B. andreraoultii sp. nov. This bacterium was isolated from the stool of a 2-year-old Nigerian boy with a severe form of kwashiorkor. Bacillus andreraoultii is an aerobic, Gram-positive rod. We describe here the features of this bacterium, together with the complete genome sequencing and annotation. The 4 092 130 bp long genome contains 3718 protein-coding and 116 RNA genes.

Epidemiological, clinical, virological features of hepatitis B newly diagnosed in 2011 in Marseille University hospitals, southeastern France

Hepatitis B virus (HBV) infection is a public health problem. In France, 0.68% of adults are chronically infected. We aimed to describe the epidemiological, virological and clinical characteristics of HBV infections newly diagnosed in 2011 in University hospitals of Marseille, the second largest French city. HBV serology was performed for 18,130 sera from 15,744 patients. A total of 167 patients were newly-diagnosed with HBV based upon the detection of hepatitis B surface antigen and anti-hepatitis B core antibodies. Clinico-epidemiological features were analyzed for 78 patients. Patients included a majority of men (59%), women being significantly younger with a mean age of 36 ± 17 versus 43.5 ± 16.2 years (P = 0.009). Country of birth was available for 52 patients and 35% of them originated from sub-Saharan Africa. Levels of the liver biological parameters were significantly lower in women compared to men, in whom mean alanine aminotransferase and gammaglutamyl transferase levels were 24 ± 39 versus 37 ± 36 IU/l (P = 0.0001) and 20 ± 20 versus 51 ± 53 IU/l (P = 0.0001), respectively. Co-infections with hepatitis C and human immunodeficiency viruses were found in 5% and 6% of the patients, respectively. HBV DNA was detectable in 90% of the HBeAg-negative patients. In addition, there was a positive correlation between the HBsAg titer and the HBV DNA level (P = 0.001). Genotype D was the most common HBV genotype and was found in 53% of the patients tested, followed by genotype E (21%). HBV remains a major concern with a slightly greater number of new diagnoses than in 2004. HBV genetic diversity was substantial in the present cohort.

Bacillus niameyensis sp. nov., a new bacterial species isolated from human gut

Bacillus niameyensis sp. nov. strain SIT3(T) (= CSUR P1266 = DSM 29725) is the type strain of B. niameyensis sp. nov. This Gram-positive strain was isolated from the digestive flora of a child with kwashiorkor and is a facultative anaerobic rod and a member of the Bacillaceae family. This organism is hereby described alongside its complete genome sequence and annotation. The 4  286  116 bp long genome (one chromosome but no plasmid) contains 4130 protein-coding and 66 RNA genes including five rRNA genes.

Bacillus rubiinfantis sp. nov. strain mt2(T), a new bacterial species isolated from human gut

Bacillus rubiinfantis sp. nov. strain mt2^T is the type strain of B. rubiinfantis sp. nov., isolated from the fecal flora of a child with kwashiorkor in Niger. It is Gram-positive facultative anaerobic rod belonging to the Bacillaceae family. We describe the features of this organism alongside the complete genome sequence and annotation. The 4 311 083 bp long genome (one chromosome but no plasmid) contains 4028 protein-coding gene and 121 RNA genes including nine rRNA genes.

[Amyotrophic Lateral Sclerosis (ALS) in the 10 last years in CHU Campus of Lomé (TOGO)]

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease that causes damage of upper motor neuron and lower motor neuron. Our objective was to describe the incidence and demographic characteristics of ALS and to analyze its diagnosis and management in Togo.

MATERIALS AND METHODS

A retrospective and descriptive study of patient's observations was conducted in the department of neurology of the teaching hospital in Lomé during a 10 years period (2000 to 2009). The diagnosis of ALS was made according to the clinical classification of El Escorial.

RESULTS

5 cases of ALS were diagnosed, representing 0.049% of the hospitalizations in the department of neurology. The average age of patients was 49 years [range: 24 - 67 years] and the average evolution of the disease was 17.6 months [range: 6 - 36 months]. All the patients were men. The treatment was symptomatic in every case. Treatment with Riluzole was not delivered. During the follow-up, one patient died from respiratory complications.

CONCLUSION

The El Escorial criteria should be made more accessible for a larger audience, as the availability and classification of care management relies heavily on diagnosed cases, namely early diagnosis.

Efficacy of rituximab in immune thrombocytopenic purpura: a retrospective survey

We conducted a retrospective survey to assess prescription practice, response rates to rituximab, and the predictive indicators for a response to rituximab therapy in patients with primary or secondary immune thrombocytopenic purpura (ITP). Data were collected retrospectively from 40 consecutive patients with ITP attending our hospital: 29 (72.5%) had primary ITP and 11 (27.5%) had secondary ITP. Rituximab was given either as four weekly injections (375 mg/m(2)) or two injections of 1,000 mg given 2 weeks apart in 30 and 10 patients, respectively. The primary objective was to evaluate overall (OR) and complete response (CR) to rituximab therapy for ITP. OR was excellent and rapid and similar when secondary ITP was excluded from the analysis: OR was achieved in 28 (71.8%) patients and CR in 22 (56.4%). But, at >6 months, of the 28 responders, only 10 of 22 of the evaluable responses (45.5%) were sustained. In addition, except for the nonsignificant occurrence of antinuclear antibodies, no clinical or biological factors were predictive for OR or CR after the rituximab therapy. Twelve patients received a second course of rituximab. Overall, rituximab therapy achieved a response in two thirds of the patients, but the responders exhibited a high rate of early relapses, with no obvious difference according to the regimen of administration or rituximab dose.