Clostridium butyricum, a strictly anaerobic spore-forming bacillus, is a common human and animal gut commensal bacterium, and is also frequently found in the environment. Whereas non-toxigenic ...strains are currently used as probiotics in Asia, other strains have been implicated in pathological conditions, such as botulism in infants or necrotizing enterocolitis in preterm neonates. In terms of the latter, within the same species, different strains have antagonist effects on the intestinal mucosa. In particular, short-chain fatty acids, which are products of carbohydrate fermentation, have a dose-dependent paradoxical effect. Moreover, toxin genes have been identified by genome sequencing in pathological strains. Asymptomatic carriage of these strains has also been reported. Herein, we provide an overview of the implications of C. butyricum for human health, from the beneficial to the pathogenic. We focus on pathogenic strains associated with the occurrence of necrotizing enterocolitis. We also discuss the need to use complementary microbiological methods, including culture, in order to better assess gut bacterial diversity and identify new emergent enteropathogens at the strain level.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPUK, ZAGLJ, ZRSKP
Comprehensive determination of the microbial composition of the gut microbiota and the relationships with health and disease are major challenges in the 21st century. Metagenomic analysis of the ...human gut microbiota detects mostly uncultured bacteria. We studied stools from two lean Africans and one obese European, using 212 different culture conditions (microbial culturomics), and tested the colonies by using mass spectrometry and 16S rRNA amplification and sequencing. In parallel, we analysed the same three samples by pyrosequencing 16S rRNA amplicons targeting the V6 region. The 32 500 colonies obtained by culturomics have yielded 340 species of bacteria from seven phyla and 117 genera, including two species from rare phyla (Deinococcus-Thermus and Synergistetes, five fungi, and a giant virus (Senegalvirus). The microbiome identified by culturomics included 174 species never described previously in the human gut, including 31 new species and genera for which the genomes were sequenced, generating c. 10 000 new unknown genes (ORFans), which will help in future molecular studies. Among these, the new species Microvirga massiliensis has the largest bacterial genome so far obtained from a human, and Senegalvirus is the largest virus reported in the human gut. Concurrent metagenomic analysis of the same samples produced 698 phylotypes, including 282 known species, 51 of which overlapped with the microbiome identified by culturomics. Thus, culturomics complements metagenomics by overcoming the depth bias inherent in metagenomic approaches.
Full text
Available for:
BFBNIB, DOBA, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, UILJ, UKNU, UL, UM, UPUK, ZAGLJ, ZRSKP
Laboratory-acquired infections due to a variety of bacteria, viruses, parasites, and fungi have been described over the last century, and laboratory workers are at risk of exposure to these ...infectious agents. However, reporting laboratory-associated infections has been largely voluntary, and there is no way to determine the real number of people involved or to know the precise risks for workers. In this study, an international survey based on volunteering was conducted in biosafety level 3 and 4 laboratories to determine the number of laboratory-acquired infections and the possible underlying causes of these contaminations. The analysis of the survey reveals that laboratory-acquired infections have been infrequent and even rare in recent years, and human errors represent a very high percentage of the cases. Today, most risks from biological hazards can be reduced through the use of appropriate procedures and techniques, containment devices and facilities, and the training of personnel.
Full text
Available for:
EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
An indirect in-house immunofluorescent assay was developed in order to assess the serological status of COVID-19 patients in Marseille, France. Performance of IFA was compared to a commercial ELISA ...IgG kit. We tested 888 RT-qPCR-confirmed COVID-19 patients (1302 serum samples) and 350 controls including 200 sera collected before the pandemic, 64 sera known to be associated with nonspecific serological interference, 36 sera from non-coronavirus pneumonia and 50 sera from patient with other common coronavirus to elicit false-positive serology. Incorporating an inactivated clinical SARS-CoV-2 isolate as the antigen, the specificity of the assay was measured as 100% for IgA titre ≥ 1:200, 98.6% for IgM titre ≥ 1:200 and 96.3% for IgG titre ≥ 1:100 after testing a series of negative controls. IFA presented substantial agreement (86%) with ELISA EUROIMMUN SARS-CoV-2 IgG kit (Cohen’s Kappa = 0.61). The presence of antibodies was then measured at 3% before a 5-day evolution up to 47% after more than 15 days of evolution. We observed that the rates of seropositivity as well as the titre of specific antibodies were both significantly higher in patients with a poor clinical outcome than in patients with a favourable evolution. These data, which have to be integrated into the ongoing understanding of the immunological phase of the infection, suggest that detection anti-SARS-CoV-2 antibodies is useful as a marker associated with COVID-19 severity. The IFA assay reported here is useful for monitoring SARS-CoV-2 exposure at the individual and population levels.
Full text
Available for:
EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
In the mid-19th century, the dichotomy between aerobic and anaerobic bacteria was introduced. Nevertheless, the aerobic growth of strictly anaerobic bacterial species such as Ruminococcus gnavus and ...Fusobacterium necrophorum, in a culture medium containing antioxidants, was recently demonstrated. We tested aerobically the culture of 623 bacterial strains from 276 bacterial species including 82 strictly anaerobic, 154 facultative anaerobic, 31 aerobic and nine microaerophilic bacterial species as well as ten fungi. The basic culture medium was based on Schaedler agar supplemented with 1 g/L ascorbic acid and 0.1 g/L glutathione (R-medium). We successively optimized this media, adding 0.4 g/L uric acid, using separate autoclaving of the component, or adding haemin 0.1 g/L or α-ketoglutarate 2 g/L. In the basic medium, 237 bacterial species and ten fungal species grew but with no growth of 36 bacterial species, including 22 strict anaerobes. Adding uric acid allowed the growth of 14 further species including eight strict anaerobes, while separate autoclaving allowed the growth of all tested bacterial strains. To extend its potential use for fastidious bacteria, we added haemin for Haemophilus influenzae, Haemophilus parainfluenzae and Eikenella corrodens and α-ketoglutarate for Legionella pneumophila. This medium allowed the growth of all tested strains with the exception of Mycobacterium tuberculosis and Mycobacterium bovis. Testing primoculture and more fastidious species will constitute the main work to be done, but R-medium coupled with a rapid identification method (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) will facilitate the anaerobic culture in clinical microbiology laboratories.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPUK, ZAGLJ, ZRSKP
Aims
Due to infectious risk associated with the presence of Legionella in warm water, we determined the prevalence of living Legionella spp. in hot spring water in Algeria.
Methods and results
...Detection of Legionella by culture was done by using two methods, direct culture on agar plates and co‐culture with amoeba. Fifty samples were taken from different hot springs in northern Algeria, including swimming pools, showers and thermal sources. Legionella pneumophila serotypes were predominant, accounting for 60% of positive samples. Direct method allowed the isolation of 13 L. pneumophila only of 50 samples (26%), whereas co‐culture using a panel of three free living amoeba allowed the isolation of 119 Legionella species from the same samples (80%)
Conclusions
Amoeba co‐culture allowed the isolation of several Legionella sp., while direct culture allowed the isolation of L. pneumophila only. Remarkably, Legionella longbeachae, usually isolated from soil and compost, was isolated for the first time in thermal water in three samples using Vermamoeba vermiformis co‐culture.
Significance and Impact of the Study
The presence of Legionella in the water of hot springs in Algeria, which are mainly frequented by individuals at risk of Legionellosis, requires urgent control measures.
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Skin is a major reservoir of bacterial pathogens in intensive care unit (ICU) patients. The aim of this study was to assess the skin bacterial richness and diversity in ICU patients and the effect of ...CHG daily bathing on skin microbiota. Twenty ICU patients were included during an interventional period with CHG daily bathing (
n
= 10) and a control period (
n
= 10). At day seven of hospitalization, eight skin swab samples (nares, axillary vaults, inguinal creases, manubrium and back) were taken from each patient. The bacterial identification was performed by microbial culturomics. We used the Shannon index to compare the diversity. We obtained 5,000 colonies that yielded 61 bacterial species (9.15 ± 3.7 per patient), including 15 (24.5 %) that had never been cultured from non-pathological human skin before, and three (4.9 %) that had never been cultured from human samples before. Notably, Gram-negative bacteria were isolated from all sites. In the water-and-soap group, there was a higher risk of colonization with Gram-negative bacteria (OR = 6.05, 95 % CI 1.67–21.90;
P =
0.006). In the CHG group, we observed more patients colonized by sporulating bacteria (9/10 vs. 3/10;
P =
0.019) with a reduced skin bacterial richness (
P
= 0.004) and lower diversity (0.37, 95 % CI 0.33; 0.42 vs. 0.50, 95 % CI 0.48; 0.52). Gram-negative bacteria are frequent and disseminated components of the transient skin flora in ICU patients. CHG daily bathing is associated with a reduction in Gram-negative bacteria colonization together with substantial skin microbiota shifts.
Full text
Available for:
EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Herein, we described cases of children under 16 years old suspected to be infected with Monkeypox virus (MKPV) and diagnosed with chickenpox in public hospitals of Marseille, south of France.
We ...conducted a retrospective study from March 23rd, 2022 to October 20th, 2022 in our institution of results of MKPV DNA and varicella-zoster virus (VZV) DNA detection by PCR performed on cutaneous lesions swabs collected from children <16 years old.
None of the cutaneous swabs collected from 14 children were positive for MKPV DNA. In contrast, 30/168 (17 %) cutaneous swabs collected from children were positive for VZV DNA. Of these 30 VZV-positive children, 7 had been suspected of MKPV infection because of their atypical rash, due to the location of the lesions and the chronology of their appearance.
As in our cohort, pediatric cases of the 2022 Monkeypox outbreak in non-endemic developed countries have been very rare. This variant of MKPV does not normally spread easily and requires very close physical contact between an infected person (skin lesions, bodily fluids or respiratory droplets) and another person to be transmitted. It will nevertheless be a question of remaining vigilant as not to ignore the possibility of close contact or sexual transmission of Monkeypox in a child, or the possibility of a new and more contagious variant.
It is difficult to differentiate Monkeypox infection from other infections associated with rashes, it is important to remember that viruses change as well as their forms of presentation.
•The main route of transmission of the Monkeypox virus variant circulating in Europe is through sexual or close contact.•The prevalence of Monkeypox in Europe is low in children (0.5 % in France).•Differentiating Chickenpox rash from that of Monkeypox can be difficult in children.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPUK, ZAGLJ, ZRSKP
The discovery of mimivirus in 2003 prompted the quest for other giant viruses of amoebae. Mimiviruses and their relatives were found to differ considerably from other viruses. Their study led to ...major advances in virology and evolutionary biology.
We summarized the widening gap between mimiviruses and other viruses.
We collected data from articles retrieved from PubMed using as keywords ‘giant virus’, ‘mimivirus’ and ‘virophage’, as well as quoted references from these articles.
Data accumulated during the last 15 years on mimiviruses and other giant viruses highlight that there is a quantum leap between these infectious agents, the complexity of which is similar to that of intracellular microorganisms, and classical viruses. Notably, in addition to their giant structures and genomes, giant viruses have abundant gene repertoires with genes unique in the virosphere, including a tremendous set of translation components. The viruses contain hundreds of proteins and many transcripts. They share a core of central and ancient proteins but their genome sequences display a substantial level of mosaicism. Finally, mimiviruses have a specific mobilome, including virophages that can integrate into their genomes, and against which they can defend themselves through integration of short fragments of the DNA of these invaders.
Mimiviruses and subsequently discovered giant viruses have changed the virus paradigm and contradict many virus definition criteria delineated for classical viruses. The major cellular hallmark that is still lacking in giant viruses is the ribosome, including both ribosomal protein and RNA encoding genes, which makes them bona fide microbes without ribosomes.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPUK, ZAGLJ, ZRSKP
During recent years, the usefulness of amoebal co-cultures as an alternative means of isolating and cultivating fastidious microorganisms has been increasingly recognized. While characterizing a ...collection of bacteria that had been isolated using this approach, we encountered an organism that, on preliminary analysis, appeared to be a gram-positive coccus. However, additional examination revealed that it was not a bacterium but rather, surprisingly, a virus. The dimensions of the virus particle (diameter, 0.8 µm) and its genome size (1.2 Mb) are far more akin to those of bacteria than to those of previously recognized viruses. These characteristics, together with such features as the breadth and complexity of its gene content, challenge the current definition of a "virus." Furthermore, the virus, now named "Mimivirus," has been implicated as an agent of pneumonia in humans and, thus, should be considered a putative emerging pathogen.
Full text
Available for:
BFBNIB, NUK, PNG, UL, UM, UPUK
PDF
