Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing

BACKGROUND Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS). RESULTS We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently. CONCLUSION Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define

Sexuell übertragbare Koinfektionen Bei Patienten Mit Anogenitalen Warzen - Eine Retrospektive Analyse Von 196 Patienten

Anogenitale Warzen (AGW) werden vorwiegend durch Niedrigrisiko-Typen des humanen Papillomavirus (HPV) verursacht. Obgleich sie die häufigste sexuell übertragbare Virusinfektion darstellen, ist über Koinfektionen mit anderen sexuell übertragbaren Infektionen (sexual transmitted infections, STI) bei den betroffenen Patienten wenig bekannt. Ziel unserer Studie war es, die Rate der Koinfektionen mit STI bei Patienten mit AGW zu ermitteln, STI-Koinfektionen zu spezifizieren und für jede STI die number needed to screen (NNS) zu berechnen. In einer retrospektiven Querschnittsstudie wurden die Datensätze von AGW-Patienten auswertet, die zwischen 2008-2016 in unserer Klinik behandelt wurden. 142/196 (72 %) Patienten waren in unterschiedlicher Weise auf Infektionen mit HIV, HBV, HCV, Treponema pallidum, Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma genitalium und HSV untersucht worden. Die STI-Koinfektionsrate bei allen getesteten Patienten betrug 24,6 %, was einer NNS von 4,1 zum Nachweis einer STI entspricht. Interessanterweise unterschied sich die Koinfektionsrate zwischen heterosexuellen Männern, homosexuellen Männern und Frauen nicht signifikant. Die NNS für Syphilis betrug 8,4, für HIV 14,0, für HCV 28,5 und für HBV 39,0. Die NNS bei asymptomatischen Patienten, die auf HSV, Chlamydia trachomatis und Mycoplasma genitalium getestet wurden, betrug 1,4, 5,3 bzw. 12,0. Aufgrund der hohen Prävalenz von STI-Koinfektionen sollten AGW-Patienten stets auf das Vorhandensein weiterer STI untersucht werden

Sexually transmitted coinfections in patients with anogenital warts - a retrospective analysis of 196 patients

Anogenital warts (AGWs) are most commonly caused by low-risk human papillomavirus (HPV) types, and although they are the most frequent viral sexually transmitted infections (STIs), little is known about STI coinfections in affected patients. We therefore sought to assess STI coinfection rates in patients with AGW, specify STI coinfections and calculate the number needed to screen (NNS) for each STI.; A retrospective cross-sectional study analyzing data sets from AGW patients treated in our clinic between 2008-2016.; 142/196 (72 %) patients had been variably screened for infections with HIV, HBV and HCV, Treponema pallidum, Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma genitalium and HSV. The STI coinfection rate in all tested patients was 24.6 %, yielding an NNS of 4.1 to detect any STI. Of note, the coinfection rate did not differ significantly between heterosexual men, homosexual men and women, respectively. The NNS for syphilis was 8.4, for HIV 14.0, for HCV 28.5 and for HBV 39.0. The NNS for asymptomatic patients tested for HSV, Chlamydia trachomatis and Mycoplasma genitalium were 1.4, 5.3 and 12.0, respectively.; Due to the high prevalence of STI coinfections, AGW patients should be screened for other STIs