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.

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

BACKGROUND AND OBJECTIVES: 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. METHODS: A retrospective cross-sectional study analyzing data sets from AGW patients treated in our clinic between 2008-2016. RESULTS: 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. CONCLUSION: Due to the high prevalence of STI coinfections, AGW patients should be screened for other STIs.

Ultrasound indications for maternal STORCH testing in pregnancy.

AIMS OF THE STUDY: Fetal abnormalities found on ultrasonography lead to a variety of diagnostic procedures, including a panel of serologies to detect possible maternal STORCH infections encompassing syphilis, Toxoplasma gondii, rubella, cytomegalovirus, herpes simplex, and others (human immunodeficiency virus, hepatitis B and C, parvovirus B19, enterovirus, varicella zoster, and Leptospira interrogans). The value of indiscriminate testing for infections upon the detection of fetal ultrasound abnormalities has been questioned. The aim of this study was to review the ultrasonographic abnormalities leading to maternal STORCH panels at the obstetrics department of a university hospital. METHODS: Laboratory results of all maternal STORCH tests requested after the detection of ultrasonographic abnormalities during a 5-year period (2008-2012) were analysed. The main ultrasound findings possibly caused by congenital infection were noted, and the outcomes of confirmed maternal and fetal infections were studied. RESULTS: In our study period, 392 maternal STORCH tests were performed because of fetal ultrasound abnormalities. The most common findings leading to STORCH testing were intrauterine growth restriction (30.4%) including microcephaly (1.5%), polyhydramnios (14.8%), and intrauterine fetal demise (13.3%). Maternal STORCH infections were found in 3.4% of growth-restricted fetuses, 5.2% of polyhydramnios, and 1.9% of intrauterine fetal demise. The leading aetiologies were cytomegalovirus and parvovirus B19. All seven congenital infections displayed multiple ultrasonographic abnormalities. CONCLUSION: Ultrasonographic findings associated with fetal infection are neither sensitive nor specific. Testing for STORCH infections should take into account exposure history, clinical signs and symptoms, obstetric history, and fetal ultrasound findings, but with special attention paid to cytomegalovirus and parvovirus B19.

Specificity of two HIV screening tests detecting simultaneously HIV-1 p24 antigen and antibodies to HIV-1 and -2.

This study aimed at assessing the specificity of the Elecsys® HIV combi PT in comparison to the ARCHITECT® HIV Ag/Ab Combo. With both of these assays, 3997 unselected sera from patients of a tertiary health care centre in Basel, Switzerland, were screened for HIV. Reactive sera were reanalysed on the VIDAS® HIV Duo Ultra to identify false-reactive specimens prior to confirmation by quantitative PCR and line immunoassay. The Elecsys® compared to the ARCHITECT® shows a similar specificity (99.7% versus 99.8%) but a slightly lower positive predictive value (71.8% versus 80%). Samples tested with a cut-off index (COI) between 0.91 and 4.85 (cut-off <0.9) with the Elecsys® and with a signal to cut-off index (S/CO) between 1.09 and 12.49 (cut-off <1.0) with the ARCHITECT® were false-reactive. There was no false-reactive result with the VIDAS®. Of the false-reactive samples, 66.7% could be related to patient-specific underlying conditions. The HIV two-tiered diagnostic algorithm proposed in this work improved the positive predictive values of the Elecsys® or ARCHITECT® to 100% when the results of the VIDAS® were included. Values just above the cut-off are highly suspicious to be false-reactive and high COI or S/CO ratios are associated with true positivity.

Evaluation of two novel chemiluminescence immunoassays for the detection of Clostridium difficile glutamate dehydrogenase and toxin A&B.

A novel immunoassay for Clostridium difficile glutamate dehydrogenase (GDH) and toxin A&B (LIAISON, DiaSorin) was compared to another GDH assay (Alere), PCR and toxigenic culture. The GDH-DiaSorin is slightly more sensitive than the GDH-Alere. Sensitivity of the Toxin-Diasorin test is in accordance to the sensitivity of other immunoassays in literature.

Septic arthritis due to Legionella cincinnatiensis: case report and review of the literature.

Legionella spp. are an important cause of pulmonary and rarely extrapulmonary infections. L. cincinnatiensis has only been implicated in five cases to date. We herein report the first case of L. cincinnatiensis septic arthritis in a 90-year old lady with a past medical history of chronic kidney disease. She developed septic arthritis of her left wrist after having received intraarticular corticosteroid injections and oral corticosteroids administered for presumed chondrocalcinosis. Appropriate antimicrobial treatment of L. cincinnatiensis septic arthritis was delayed until identification of this organism in joint biopsies by broad-range bacterial PCR targeting the 16S rRNA gene with subsequent rDNA sequence analysis and by culture on special media. Reviewing all reported cases of septic arthritis caused by Legionella spp. other than L. cincinnatiensis it is notable that diagnosis was established by PCR in the majority of cases and only subsequently confirmed by special culture. Although most patients were immunosuppressed, outcome was favourable. Treatment consisted of a fluoroquinolone alone or in combination with rifampicin or a macrolide. Our case highlights the need for a high index of suspicion for infections with unusual/fastidious organisms when symptoms are suggestive of septic arthritis but conventional methods fail to identify a causative organism.

Reactivation of hepatitis B virus with mutated hepatitis B surface antigen in a liver transplant recipient receiving a graft from an antibody to hepatitis B surface antigen- and antibody to hepatitis B core antigen-positive donor.

BACKGROUND: Fresh-frozen plasma (FFP) may contain antibodies to hepatitis B surface antigen (HBsAg, anti-HBs). These anti-HBs may lead to a misinterpretation of the actual hepatitis B immune status. Furthermore, they may not only confer protection against hepatitis B virus (HBV), but may also favor the selection of HBsAg mutants. CASE REPORT: We report a case of de novo HBV infection in a HBV-naïve recipient with alcoholic liver disease, who received a liver from a donor with antibodies to hepatitis B core antigen (HBcAg, anti-HBc) and anti-HBs. RESULTS: A lookback investigation revealed the following: 1) Due to anti-HBs passively acquired through FFP, the recipient was considered immune to HBV and did not receive anti-HBV prophylaxis. 2) Within 1 year after transplantation he developed hepatitis B in absence of any elevated liver enzymes after the anti-HBs by FFP declined. 3) Despite an infection with HBV-containing wild-type HBcAg, the patient did not seroconvert to anti-HBc positivity. 4) The replicating HBV encoded two HBsAg mutations, first sQ129R and 4 months later sP127S. They map to the highly conserved "α" determinant of the HBsAg loop. CONCLUSION: 1) Passive transfer of anti-HBs from FFP led to an erroneous pretransplant diagnosis of HBV immunity when the patient was in fact HBV-naïve. 2) HBsAg mutations might have been selected in escape from donor's actively produced anti-HBs and the recipient's anti-HBs by FFP might have favored this selection. 3) It is doubtful whether hepatitis B immunoglobulin could have prevented the reactivation. 4) Antiviral prophylaxis would have been crucial.