Sequencing and characterization of human bocavirus genomes from patients diagnosed in Southern France between 2017 and 2022.

The diversity and evolution of the genomes of human bocavirus (HBoV), which causes respiratory diseases, have been scarcely studied. Here, we aimed to obtain and characterize HBoV genomes from patients's nasopharyngeal samples collected between 2017 and 2022 period (5 years and 7 months). Next-generation sequencing (NGS) used Illumina technology after having implemented using GEMI an in-house multiplex PCR amplification strategy. Genomes were assembled and analyzed with CLC Genomics, Mafft, BioEdit, MeV, Nextclade, MEGA, and iTol. A total of 213 genomes were obtained. Phylogeny classified them all as of Bocavirus 1 (HBoV1) species. Five HBoV1 genotypic clusters determined by hierarchical clustering analysis of 27 variable genome positions were scattered over the study period although with differences in yearly prevalence. A total of 167 amino acid substitutions were detected. Besides, coinfection was observed for 52% of the samples, rhinoviruses then adenoviruses (HAdVs) being the most common viruses. Principal component analysis showed that HBoV1 genotypic cluster α tended to be correlated with HAdV co-infection. Subsequent HAdV typing for HBoV1-positive samples and negative controls demonstrated that HAdVC species predominated but HAdVB was that significantly HBoV1-associated. Overall, we described here the first HBoV1 genomes sequenced for France. HBoV1 and HAdVB association deserves further investigation.

Pediatric urogenital schistosomiasis diagnosed in France.

BACKGROUND: Schistosomiasis affects approximately 230 million people worldwide. There is an increased incidence of schistosomiasis cases in France acquired from outside the country. This increases the risk of schistosomiasis outbreaks as observed in Corsica. Clinicians from non-endemic regions are not accustomed to diagnosing and managing this pathology. The objective of this study is to provide a better description of the clinical and paraclinical characteristics and disease evolution of affected children. METHODS: Through the French Pediatric Nephrology Society and the Pediatric Infectious Pathology Group, we contacted all French pediatric centers that may have treated children with urinary schistosomiasis between 2013 and 2019. Age, sex, comorbidities, and clinical, biological, and radiological data (at discovery and follow-up) were collected retrospectively. RESULTS: A total of 122 patients from 10 different centers were included. The median age was 14 years and the sex ratio M/F was 4:1. Hematuria was present in 82% of the patients while urinary tract abnormality was found in 36% of them. Fourteen patients (11%) displayed complicated forms of urinary schistosomiasis including 10 patients with chronic kidney disease. A total of 110 patients received treatment with praziquantel, which was well-tolerated and led to clinical resolution of symptoms in 98% of cases. CONCLUSION: Patients with schistosomiasis present frequent kidney, urinary, or genital involvement. Systematic screening of patients returning from endemic areas is therefore recommended, especially since treatment with antiparasitic drugs is effective and well-tolerated. Enhancing medical knowledge of this pathology among all practitioners is essential to improve care and outcomes.

Detection of Pneumocystis jirovecii in Hospitalized Children Less Than 3 Years of Age.

Few data are available in the literature regarding Pneumocystis jirovecii infection in children under 3 years old. This retrospective cohort study aimed to describe medically relevant information among them. All children under 3 years old treated in the same medical units from April 2014 to August 2020 and in whom a P. jirovecii evaluation was undertaken were enrolled in the study. A positive case was defined as a child presenting at least one positive PCR for P. jirovecii in a respiratory sample. Medically relevant information such as demographical characteristics, clinical presentation, microbiological co-infections, and treatments were collected. The objectives were to describe the characteristics of these children with P. jirovecii colonization/infection to determine the key underlying diseases and risk factors, and to identify viral respiratory pathogens associated. The PCR was positive for P. jirovecii in 32 children. Cardiopulmonary pathologies (21.9%) were the most common underlying disease in them, followed by severe combined immunodeficiency (SCID) (18.8%), hyaline membrane disease (15.6%), asthma (9.4%) and acute leukaemia (6.3%). All SCID children were diagnosed with pneumocystis pneumonia. Co-infection with Pj/Rhinovirus (34.4%) was not significant. Overall mortality was 18.8%. Paediatric pneumocystis is not restricted to patients with HIV or SCID and should be considered in pneumonia in children under 3 years old.

New human-associated species of the family Atopobiaceae and proposal to reclassify members of the genus Olsenella.

Five novel bacterial strains, Marseille-P1476T (=CSURP1476T=DSM 100642T), Marseille-P3256T (=CSURP3256T=CECT 9977T), Marseille-P2936T (=CSURP2936T=DSM 103159T), Marseille-P2912T (=CSURP2912T=DSM 103345T) and Marseille-P3197T (=CSURP3197T=CCUG 71847T), were isolated from various human specimens. These five strains were not identified at the species level by matrix-assisted laser desorption/ionization time of flight mass spectrometry. Following 16S rRNA gene sequence comparisons with the GenBank database, the highest nucleotide sequence similarities of all studied strains were obtained to members of the paraphyletic genus Olsenella. A polyphasic taxono-genomic strategy (16S rRNA gene-based and core genome-based phylogeny, genomic comparison, phenotypic and biochemical characteristics) enabled us to better classify these strains and reclassify Olsenella species. Among the studied strains, Marseille-P1476T, Marseille-P2936T and Marseille-P3197T belonged to new species of the genus Olsenella for which we propose the names Olsenella massiliensis sp. nov., Olsenella phocaeensis sp. nov. and Olsenella urininfantis sp. nov., respectively. Strains Marseille-P2912T and Marseille-P3256T belonged to a new genus for which the names Thermophilibacter provencensis gen. nov., sp. nov. and Thermophilibacter mediterraneus gen. nov., sp. nov. are proposed, respectively. We also propose the creation of the genera Parafannyhessea gen. nov., Tractidigestivibacter gen. nov. and Paratractidigestivibacter gen. nov. and the reclassification of Olsenella umbonata as Parafannyhessea umbonata comb. nov., Olsenella scatoligenes as Tractidigestivibacter scatoligenes comb. nov., and Olsenella faecalis as Paratractidigestivibacter faecalis comb. nov.

Key role of pediatricians and disease for influenza vaccination in children with high-risk chronic diseases.

Annual influenza vaccination is recommended for children with chronic diseases. Studies on influenza vaccines, following controversies related to the 2009 H1N1 influenza, are scarce in Europe. Our aim was to evaluate the influenza vaccination coverage in such children in a French tertiary hospital. Secondary objectives were the evaluation of the influenza vaccination coverage trend and the identification of factors influencing the vaccination status. A prospective and descriptive study by questionnaire was performed at the end of 2017 in 402 French hospital outpatients with various underlying chronic diseases eligible to the influenza vaccination. The 2016-2017 vaccination coverage was 46.5%. Figures of 75% or greater were only found in patients with cystic fibrosis and sickle cell disease. CART analysis identified vaccination in the previous year, medical recommendation for vaccination, and maternal influenza vaccination as a child's decisive factors for being vaccinated.Conclusion: Influenza vaccination coverage remains insufficient in children receiving hospital follow-up for chronic diseases. Its implementation clearly depends on pediatricians' recommendation to vaccinate and on the type of chronic disease. What is Known: • Despite health policy recommendations, the rate of annual influenza vaccination in children with chronic diseases is low What is New: • Influenza vaccination coverage depends on the type of chronic disease and on the pediatricians' counseling to vaccine.

Seek and Find! PCR analyses of skin infections in West-European travelers returning from abroad with an eschar.

BACKGROUND: Skin infections are among the leading causes of diseases in travelers. Diagnosing pathogens could be difficult. METHOD: We applied molecular assays for the diagnostic of a large collection of skin biopsies and swabs from travelers with suspected skin infections. All samples were tested by qPCR for Coxiella burnetti, Bartonella sp., Rickettsia sp., Borrelia sp., Ehrlichia sp., Tropheryma whipplei, Francisella tularensis, Mycobacteria sp., Staphylococcus aureus, Streptococcus pyogenes, Leishmania spp., Ortho poxvirus and Para poxvirus and then screened for the presence of bacteria by PCR amplification and sequencing, targeting the 16S rRNA gene. RESULTS: From January 2009 to January 2017, 100 international travelers presenting with a suspected skin infection were enrolled. We detected 51 patients with an identified pathogen on skin samples. Travelers presenting with eschars were more likely to have a positive PCR sample (n = 44/76, 57.9%) compared to other patients (n = 7/24, 29.2%). Spotted fever group Rickettsia (n = 28) was the most frequently detected pathogens (19 R. africae, 6 R. conorii, 3 R. mongolitimonae); S. aureus were detected in 11 patients; S. pyogenes in 3; Leishmania sp.; M. leprae and B. henselae in 1 patient, respectively. CONCLUSION: By targeting the most commonly encountered causative agents of travel-related skin infections, our strategy provides a sensitive and rapid diagnostic method.