Correction to: Molecular revolution in the diagnosis of microbial brain abscesses.

An erratum to this paper has been published: https://doi.org/10.1007/s10096-020-04047-8.

Molecular characterization of isolated infectious bronchitis viruses from affected vaccinated broiler flocks in Syria.

BACKGROUND: Avian Infectious Bronchitis Virus (IBV) is a highly contagious disease that imposes a huge economic burden on the global poultry industry. IBV contains numerous serotypes and variants with incomplete tenuous cross immunological protection. The failure of currently used vaccines to protect against diverse, circulating IBV strains that are specific to a given region poses a major problem for the poultry industry. Thus, there is an urgent need to conduct studies aimed at genotyping field IB viruses. In this study, we have determined the molecular characteristics of circulating IBV by sequencing the S1 gene of viral isolates from affected previously vaccinated broiler flocks suffering from the disease. RESULTS: Ten isolates propagated in embryonated eggs showed an ability to induce typical IBV lesions after three successive viral passages. We performed a nested RT-PCR assay that targeted the hypervariable region 3 (HVR-3) of the S1 gene, and identified the isolates as IBV through sequence analysis. The IBV isolates showed sequence similarity between the Syrian isolates that vary from 96.20 to 100%, and those being closer to the Variant-2 strain IS/1494/06 (EU780077.2) with 97.5 to 99.4% similarities. However, less nucleotide identity was found with sequences belonging to the used vaccine strains such as H120, Mass5, and 4/91. CONCLUSIONS: This study showed the presence of the Variant-2 strain circulating in Syrian broiler flocks showing signs of IBV disease. Currently, there is no commercial effective vaccine which protects birds against the Variant-2 strain. Continuous monitoring procedures should be taken to control and limit the spread of the IBV Variant-2 strain. This research emphasizes both the importance of epidemiological monitoring in intensive poultry farming for novel pathogens and the use of local isolates as future vaccine targets.

Metagenomic analysis of brain abscesses identifies specific bacterial associations.

BACKGROUND: The bacterial flora involved in brain abscess is often complex. In a previous study, using a metagenomic approach based on 16S ribosomal DNA (rDNA) amplification, we demonstrated that the diversity of the microbial flora involved in these infections was underestimated. METHODS: We performed a 16S rDNA-based metagenomic analysis of cerebral abscesses from patients diagnosed from 2006 through 2010. All bacteria present in brain abscess specimens were identified, in view of the clinical and epidemiological characteristics of the patients. RESULTS: Fifty-one patients were included in our study. By detecting polymicrobial infections in 19 patients, our strategy was significantly more discriminatory and enabled the identification of a greater number of bacterial taxa than did culture and conventional 16S rDNA polymerase chain reaction (PCR) and sequencing, respectively (P < 10(-2)). Data mining discriminated 2 distinct bacterial populations in brain abscess from dental and sinusal origin. In addition, of the 80 detected bacterial species, we identified 44 bacteria that had never been found in brain abscess specimens, including 22 uncultured bacteria. These uncultured agents mostly originated from the buccal or sinusal floras (P < 10(-2)) and were found in polymicrobial specimens (P < 10(-2)). CONCLUSIONS: Cloning and sequencing of PCR-amplified 16S rDNA is a highly valuable method to identify bacterial agents of brain abscesses.

The expansion of the microbiological spectrum of brain abscesses with use of multiple 16S ribosomal DNA sequencing.

Background. Brain abscess is commonly treated using empirically prescribed antibiotics. Thus, a comprehensive study of bacterial organisms associated with brain abscess is essential to define the best empirical treatment for this life-threatening condition. Methods. We prospectively compared cultures to single and multiple sequenced 16S ribosomal DNA polymerase chain reaction amplifications (by cloning and/or pyrosequencing) of cerebral abscesses in 20 patients from 2 hospitals in Marseilles, France, during the period January 2005 through December 2007. Results. The obtained cultures identified significantly fewer types of bacteria (22 strains) than did molecular testing (72 strains; P = .017, by analysis of variance test). We found that a patient could exhibit as many as 16 different bacterial species in a single abscess. The obtained cultures identified 14 different species already known to cause cerebral abscess. Single sequencing performed poorly, whereas multiple sequencing identified 49 species, of which 27 had not been previously reported in brain abscess investigations and 15 were completely unknown. Interestingly, we observed 2 patients who harbored Mycoplasma hominis (an emerging pathogen in this situation) and 3 patients who harbored Mycoplasma faucium, which, to our knowledge, has never been reported in literature. Conclusions. Molecular techniques dramatically increased the number of identified agents in cerebral abscesses. Mycoplasma species are common and should be detected in this situation. These findings led us to question the accuracy of the current empirical treatment of brain abscess.

Mycoplasma hominis brain abscess following uterus curettage: a case report.

INTRODUCTION: Mycoplasma hominis is mostly known for causing urogenital infections. However, it has rarely been described as an agent of brain abscess. CASE PRESENTATION: We describe a case of M. hominis brain abscess in a 41-year-old Caucasian woman following uterus curettage. The diagnosis was obtained by 16S rDNA amplification, cloning and sequencing from the abscess pus, and confirmed by a specifically designed real-time polymerase chain reaction assay. CONCLUSIONS: Findings from our patient's case suggest that M. hominis should be considered as a potential agent of brain abscess, especially following uterine manipulation.

Staphylococcus massiliensis sp. nov., isolated from a human brain abscess.

Gram-positive, catalase-positive, coagulase-negative, non-motile, non-fermentative and novobiocin-susceptible cocci were isolated from a human brain abscess sample (strain 5402776(T)). This novel strain was analysed by a polyphasic taxonomic approach. The respiratory quinones detected were MK-7 (93 %) and MK-6 (7 %) and the major fatty acids were C(15 : 0) iso (60.5 %), C(17 : 0) iso (8.96 %) C(15 : 0) anteiso (7.93 %) and C(19 : 0) iso (6.78 %). The peptidoglycan type was A3alpha l-Lys-Gly(2-3)-l-Ser-Gly. Based on cellular morphology and biochemical criteria, the new isolate was assigned to the genus Staphylococcus, although it did not correspond to any recognized species. The G+C content of the DNA was 36.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the new isolate was most closely related to Staphylococcus piscifermentans, Staphylococcus condimenti, Staphylococcus carnosus subsp. carnosus, S. carnosus subsp. utilis and Staphylococcus simulans (97.7 %, 97.6 %, 97.6 %, 97.6 % and 96.5 % sequence similarity, respectively). Comparison of tuf, hsp60, rpoB, dnaJ and sodA gene sequences was also performed. In phylogenetic analysis inferred from tuf, dnaJ and rpoB gene sequence comparisons, strain 5402776(T) clustered with Staphylococcus pettenkoferi (93.7 %, 82.5 % and 89 % sequence similarity, respectively) and on phylogenetic analysis inferred from sodA gene sequence comparisons, it clustered with Staphylococcus chromogenes (82.8 %). On the basis of phenotypic and genotypic data, this isolate represents a novel species for which the name Staphylococcus massiliensis sp. nov. is proposed (type strain 5402776(T)=CCUG 55927(T)=CSUR P23(T)).

Phocaeicola abscessus gen. nov., sp. nov., an anaerobic bacterium isolated from a human brain abscess sample.

A strictly anaerobic bacterial strain, 7401987T, was isolated from a human brain abscess sample. Cells were Gram-negative, non-spore-forming, coccoid to rod-shaped and motile by flagella in a lophotrichous arrangement. The isolate was asaccharolytic and the major cellular fatty acids were anteiso-C15:0 (28.2%), C16:0 (18.0%), iso-C15:0 (12.3%) and iso-C17:0 3-OH (11.7%). 16S rRNA gene sequence comparisons showed that the isolate was distantly related to members of the genera Bacteroides (<83.6% similarity), Parabacteroides (<79.9% similarity), Tannerella (<79.8% similarity), Dysgonomonas (<79.6% similarity), Porphyromonas (<79.3% similarity) and Prevotella (<78.9% similarity). The low 16S rRNA gene sequence similarity values and physiological and biochemical characteristics differentiated strain 7401987T from all known species and indicate that our isolate represents a novel species in a new genus within the phylum Bacteroidetes. The name Phocaeicola abscessus gen. nov., sp. nov. is proposed; the type strain of Phocaeicola abscessus is 7401987T (=CCUG 55929T=CSUR P22T=DSM 21584T).