Bacteremia due to Lachnoanaerobaculum umeaense in a patient with acute myeloid leukemia during chemotherapy: A case report, and a review of the literature

The present case reports a bacteremia due to Lachnoanaerobaculum umeaense (a Gram-positive, filamentous, rod-shaped, anaerobic, spore-forming bacillus present in the human oral microbiota) in a patient treated for acute myeloid leukemia. After failed identification by MALDI-TOF, identification was done by sequencing of 16s rRNA. The patient was successfully treated with Amoxicillin-clavulanic acid and ciprofloxacin for seven days. Comparison of V1-V3 regions of the bacterial 16S rRNA gene gene with published sequences failed to classify the strain as pathogenic or non-pathogenic based on this phylogenetic classification alone. Although Lachnoanaerobaculum gingivalis are known to be associated with bacteremia in patients with acute myeloid leukemia, this clinical case of infection by L. umeaense argues for further studies that will lead to more efficient classification of the infection by these microorganisms.

The First Lethal Infection by Oligella ureolytica: A Case Report and Review of the Literature

Oligella ureolytica is a Gram-negative bacillus, a member of the Alcaligenaceae family, that had never previously been reported as lethal. Herein, a case of fatal infection caused by Oligella ureolytica in an elderly woman with suspected bladder cancer is reported. The species identification was confirmed through Sanger sequencing of the bacterial 16S rRNA sequence and compared to published sequences for phylogenetic analysis. Initial antibiotic therapy with ceftriaxone and oxacillin was initiated but had to be switched due to resistance. Cefepime in combination with metronidazole was administered, unfortunately failing to prevent the patient's death. Further studies are needed to explore additional factors influencing clinical outcomes in Oligella ureolytica infections.

Mice prenatally exposed to valproic acid do not show autism-related disorders when fed with polyunsaturated fatty acid-enriched diets

Dietary supplementations with n-3 polyunsaturated fatty acid (PUFA) have been explored in autism spectrum disorder (ASD) but their efficiency and potential in ameliorating cardinal symptoms of the disease remain elusive. Here, we compared a n-3 long-chain (LC) PUFA dietary supplementation (n-3 supp) obtained from fatty fish with a n-3 PUFA precursor diet (n-3 bal) obtained from plant oils in the valproic acid (VPA, 450 mg/kg at E12.5) ASD mouse model starting from embryonic life, throughout lactation and until adulthood. Maternal and offspring behaviors were investigated as well as several VPA-induced ASD biological features: cerebellar Purkinje cell (PC) number, inflammatory markers, gut microbiota, and peripheral and brain PUFA composition. Developmental milestones were delayed in the n-3 supp group compared to the n-3 bal group in both sexes. Whatever the diet, VPA-exposed offspring did not show ASD characteristic alterations in social behavior, stereotypies, PC number, or gut microbiota dysbiosis while global activity, gait, peripheral and brain PUFA levels as well as cerebellar TNF-alpha levels were differentially altered by diet and treatment according to sex. The current study provides evidence of beneficial effects of n-3 PUFA based diets, including one without LCPUFAs, on preventing several behavioral and cellular symptoms related to ASD.

French national epidemiology of bacterial superinfections in ventilator-associated pneumonia in patients infected with COVID-19: the COVAP study

BACKGROUND

Description and comparison of bacterial characteristics of ventilator-associated pneumonia (VAP) between critically ill intensive care unit (ICU) patients with COVID-19-positive, COVID + ; and non-COVID-19, COVID-.

METHODS

Retrospective, observational, multicenter study that focused on French patients during the first wave of the pandemic (March-April 2020).

RESULTS

935 patients with identification of at least one bacteriologically proven VAP were included (including 802 COVID +). Among Gram-positive bacteria, S. aureus accounted for more than two-thirds of the bacteria involved, followed by Streptococcaceae and enterococci without difference between clinical groups regarding antibiotic resistance. Among Gram-negative bacteria, Klebsiella spp. was the most frequently observed bacterial genus in both groups, with K. oxytoca overrepresented in the COVID- group (14.3% vs. 5.3%; p < 0.05). Cotrimoxazole-resistant bacteria were over-observed in the COVID + group (18.5% vs. 6.1%; p <0.05), and after stratification for K. pneumoniae (39.6% vs. 0%; p <0.05). In contrast, overrepresentation of aminoglycoside-resistant strains was observed in the COVID- group (20% vs. 13.9%; p < 0.01). Pseudomonas sp. was more frequently isolated from COVID + VAPs (23.9% vs. 16.7%; p <0.01) but in COVID- showed more carbapenem resistance (11.1% vs. 0.8%; p <0.05) and greater resistance to at least two aminoglycosides (11.8% vs. 1.4%; p < 0.05) and to quinolones (53.6% vs. 7.0%; p <0.05). These patients were more frequently infected with multidrug-resistant bacteria than COVID + (40.1% vs. 13.8%; p < 0.01).

CONCLUSIONS

The present study demonstrated that the bacterial epidemiology and antibiotic resistance of VAP in COVID + is different from that of COVID- patients. These features call for further study to tailor antibiotic therapies in VAP patients.

Global phylogenomic assessment of Leptoseris and Agaricia reveals substantial undescribed diversity at mesophotic depths

BACKGROUND

Mesophotic coral communities are increasingly gaining attention for the unique biological diversity they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies on corals have rarely included mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers.

RESULTS

Here, we used reduced-representation genome sequencing to conduct a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed deep divergences within the two genera and undescribed diversity across the current taxonomic species. Five of the eight focal species consisted of at least two sympatric and genetically distinct lineages, which were consistently detected across different methods.

CONCLUSIONS

The repeated observation of genetically divergent lineages associated with mesophotic depths highlights that there may be many more mesophotic-specialist coral species than currently acknowledged and that an urgent assessment of this largely unstudied biological diversity is warranted.

Incidence, complications and costs of peripheral venous catheter-related bacteraemia: A retrospective, single centre study

The aim of the present study was to estimate the current incidence, complications and costs of BSI attributable to PVC. Patients with PVC-related BSI (cases) were matched with patients without PVC-related BSI (controls). From January 1st, 2018 to March 31th, 2020 9,833 out of 113,068 patients visiting the emergency department (9%) were hospitalised in a medical ward after insertion of a PVC. Among them, 581 (6%) had at least one positive blood culture (BC). Twenty-five (4%) of these were judged as having a PVC-related BSI. Major complications were noted in nine patients. One patient presented severe sepsis requiring admission to intensive care unit for eleven days followed by thoracic (T4 to T7) spondylodiscitis requiring prolonged antimicrobial therapy. Another patient developed mitral valve endocarditis also requiring prolonged antimicrobial therapy. One patient developed a pre-sacral abscess three months after initial PVC infection and required hospital readmission for 19 days for drainage. Median [IQR] hospital stay costs were €11,597 [€8,479-€23,759] for cases and €6,789 [€4,019-€10,764] for controls, leading to median additional costs of €5,587. In conclusion, even though the risk of developing PVC-related BSI in patients admitted to medical wards may seem low, complications of PVC-related BSI are severe, and the associated mortality remains high. The financial resources used to treat these complications could be better spent on prevention, including the use of high-quality materials and technologies, and improved training of health care providers.

Multicenter Retrospective Study of Vascular Infections and Endocarditis Caused by Campylobacter spp., France

The incidence of campylobacteriosis has substantially increased over the past decade, notably in France. Secondary localizations complicating invasive infections are poorly described. We aimed to describe vascular infection or endocarditis caused by Campylobacter spp. We included 57 patients from a nationwide 5-year retrospective study on Campylobacter spp. bacteremia conducted in France; 44 patients had vascular infections, 12 had endocarditis, and 1 had both conditions. Campylobacter fetus was the most frequently involved species (83%). Antibiotic treatment involved a β-lactam monotherapy (54%) or was combined with a fluoroquinolone or an aminoglycoside (44%). The mortality rate was 25%. Relapse occurred in 8% of cases and was associated with delayed initiation of an efficient antimicrobial therapy after the first symptoms, diabetes, and coexistence of an osteoarticular location. Cardiovascular Campylobacter spp. infections are associated with a high mortality rate. Systematically searching for those localizations in cases of C. fetus bacteremia may be warranted.

Impact of Skin Disinfection on Cutaneous Microbiota, before and after Peripheral Venous Catheter Insertion

Introduction. Patients with invasive medical devices are at high risk for infection. Skin colonization is the initial stage of these infections, leading to the recommendation of practices requiring disinfection using antiseptics. Microbial communities playing a major role in skin health could be impacted by antiseptic procedures. Aim. To characterize and compare the bacterial communities of skin samples from patients before an antisepsis procedure, and after removal of the medical device itself, according to the nature of the antiseptic molecule (povidone iodine or chlorhexidine). Methods. The study focused on alterations in bacterial communities depending on the nature of the antiseptic procedure and type of intravascular device. After amplification of 16S rDNA, libraries (n = 498 samples) were sequenced using MiSeq platform. Results. Using an in-house pipeline (QIIME2 modules), while no alteration in skin microbiota diversity was associated with antiseptic procedure or PVC type, according to culture results (p < 0.05), alterations were at times associated with restricted diversity and higher dissimilarity (p < 0.05). Antiseptic procedures and PVC types were associated with the modification of specific bacterial representations with modulation of the Bacillota/Bacteroidota (Firmicutes/Bacteroidetes) ratio (modulation of C. acnes, Prevotella, Lagierella, and Actinomyces spp.) (p < 0.05). At baseline, the microbiota shows certain bacteria that are significantly associated with future PVC colonization and/or bacteremia (p < 0.05). All of these modulations were associated with altered expression of metabolic pathways (p < 0.05). Discussion. Finally, this work highlights the need to optimize the management of patients requiring intravascular devices, possibly by modulating the skin microbiota.

Efficacy of Three Povidone Iodine Formulations against Cutibacterium acnes Assessed through In Vitro Studies: A Preliminary Study

Cutibacterium acnes (C. acnes, formerly known as Propionibacterium acnes) is the major causative agent of prosthetic joint infections (PJI). Treatment of PJI with antibiotics is difficult due to antibiotic resistance and adverse side effects on patients’ health. Proper disinfection of the surgical site using a variety of povidone iodine formulations could prevent C. acnes infection. In the current study, the efficacy of the three povidone iodine (PVP-I) formulations, viz: PVP-I 10% dermic solution, PVP-I 5% alcoholic solution and PVP-I 4% scrub, was tested against C. acnes, in vitro, in the presence of interfering substances mimicking soiling conditions. C. acnes strain ATCC 6919 was used to test the bactericidal activity of the povidone iodine formulations according to the modified dilution-neutralization method described in French Norm EN standard 13727. A 3-log reduction in the bacterial cell count in 60 s was considered to be significant. The results showed that under experimental conditions, the three PVP-I formulations displayed bactericidal activity against the micro-organism, Cutibacterium acnes, and that the lowest concentration of povidone-iodine active against C. acnes was 0.4%. These results are encouraging as PVP-I offers a low-cost and efficient method of disinfection.

Risk factors for biliary stent infections in malignant biliary obstruction secondary to unresectable malignancies

BACKGROUND

Palliative biliary drainage in patients with unresectable malignant biliary obstruction (MBO) frequently leads to biliary stent infection (BI), which could impact medical care. The aim of this study was to assess the risk factors for BI occurrence in patients after stenting procedure and the impact of BI on patient survival.

METHODS

All consecutive patients hospitalized from 2014 to 2018 for MBO and biliary stenting were retrospectively included. Demographic, clinical, and microbiological characteristics of each BI episode during a 1-year follow-up were described. Documented BI was defined as the association of BI episode and confirmed blood stream infection (BSI). Univariate and multivariate analyses were performed to evaluate risk factors for the first BI occurrence.

RESULTS

Among 180 patients, 56% were men (mean age of 69±12), and 54% have pancreatic cancer, 16% biliary cancer, 2% hepatic cancer, and 28% lymph node or metastatic compression; metallic stent was placed in 92%. A total of 113 BI episodes occurred in 74 patients, 55% of the first episodes occurring within 3 months after stenting. BI was documented in 56% of the episodes. Enterobacteriaceae were the most frequent pathogens found, while no yeasts were documented. Mortality rate in patients with BI was 64%. Multivariate analysis showed a significant difference in BI occurrence for two criteria: WHO score 3-4 (OR=8.79 [1.79-42.89]; p=0.007) and transpapillary stenting location (OR=3.72 [1.33-10.44]; p=0.013).

CONCLUSION

Since transpapillary stenting is a risk factor for BI, preserving the papilla as much as possible is a priority so as to avoid BI.

Metagenomic Analysis Reveals High Abundance of Torque Teno Mini Virus in the Respiratory Tract of Children with Acute Respiratory Illness

Human Anelloviridae is a highly prevalent viral family, including three main genera—Alphatorquevirus (Torque teno virus, TTV), Betatorquevirus (Torque teno mini virus, TTMV), and Gammatorquevirus (Torque teno midi virus, TTMDV). To date, the characterization of Anelloviridae in the respiratory tract of children with acute respiratory infection (ARI) has been poorly reported and mainly focused on TTV. We performed a metagenomic analysis of eight respiratory samples collected from children with an ARI of unknown etiology (eight samples tested negative with a multiplex PCR assay, out of the 39 samples initially selected based on negative routine diagnostic testing). A total of 19 pediatric respiratory samples that tested positive for respiratory syncytial virus (RSV, n = 13) or influenza virus (n = 6) were also sequenced. Anelloviridae reads were detected in 16/27 samples, including 6/8 negative samples, 7/13 RSV samples and 3/6 influenza samples. For samples with a detection of at least one Anelloviridae genus, TTMV represented 87.1 (66.1−99.2)% of Anelloviridae reads, while TTV and TTMDV represented 0.8 (0.0−9.6)% and 0.7 (0.0−7.1)%, respectively (p < 0.001). Our findings highlight a high prevalence of TTMV in respiratory samples of children with an ARI of unknown etiology, as well as in samples with an RSV or influenza infection. Larger studies are needed to explore the role of TTMV in childhood respiratory diseases.

Spermatic Microbiome Characteristics in Infertile Patients: Impact on Sperm Count, Mobility, and Morphology

Through sperm alteration, semen microbiota tend to be recognized as a cause of infertility, but due to the limited number of studies focusing on this ecological niche, this hypothesis remains controversial. This study aimed to characterize and compare the bacterial communities of sperm samples from patients undergoing couple infertility treatment at the time of diagnosis. The study was prospective (September 2019 to March 2020), monocentric, and focused on alterations of spermatic parameters: count, motility, and morphology. After the amplification of the 16S rDNA (V1 to V3), libraries (n = 91, including 53 patients with abnormalities) were sequenced using the MiSeq platform (Illumina). After quality control processing using a homemade pipeline (QIIME2 modules), the main genera were: Prevotella, Finegoldia, Pseudomonas, Peptinophilus, Streptococcus, Anaerococcus and Corynebacterium. Restricted diversity was observed in samples from patients with abnormal sperm morphology (α-diversity, p < 0.05), whereas diversity increased in patients with an abnormal sperm count (β-diversity, p < 0.05). The enrichment of the genus Prevotella and Haemophilus was observed in negative sperm culture samples and samples with abnormal counts, respectively (p < 0.05). Microbiota differed in their composition according to sperm parameters. Finally, this work highlights the need for the optimization of the management of couples undergoing infertility treatment, possibly by modulating the genital microbiome.

New Strategy for the Detection and Treatment of Helicobacter pylori Infections in Primary Care Guided by a Non-Invasive PCR in Stool: Protocol of the French HepyPrim Study

Helicobacter pylori (Hp) infects half of the world population and is responsible for gastric, duodenal ulcers and gastric cancer. The eradication of Hp cures ulcers and prevents ulcer recurrences and gastric cancer. Antibiotic resistance of Hp, and particularly clarithromycin resistance, is the primary cause of treatment failure and is a major concern identified by the WHO as a high priority requiring research into new strategies. Treatments guided by the detection of antibiotic resistance have proven their medical and economical superiority. However, this strategy is severely hampered by the invasive nature of the fibroscopy, since antibiotic resistance detection requires gastric biopsies. The eradication of Hp involves primary care physicians. The objective of this study will be to evaluate the feasibility of a strategy for the management of Hp infection in primary care by a recently developed non-invasive procedure and its non-inferiority in eradication rates compared with the strategy recommended by the French National Authority of Health. The non-invasive procedure is a PCR on stool to detect Hp infection and mutations conferring resistance to clarithromycin allowing a treatment guided by the results of the PCR. We present the protocol of a prospective, multicenter, randomized, controlled interventional study in two arms.

Bacterial Signatures of Paediatric Respiratory Disease: An Individual Participant Data Meta-Analysis

Introduction: The airway microbiota has been linked to specific paediatric respiratory diseases, but studies are often small. It remains unclear whether particular bacteria are associated with a given disease, or if a more general, non-specific microbiota association with disease exists, as suggested for the gut. We investigated overarching patterns of bacterial association with acute and chronic paediatric respiratory disease in an individual participant data (IPD) meta-analysis of 16S rRNA gene sequences from published respiratory microbiota studies. Methods: We obtained raw microbiota data from public repositories or via communication with corresponding authors. Cross-sectional analyses of the paediatric (<18 years) microbiota in acute and chronic respiratory conditions, with >10 case subjects were included. Sequence data were processed using a uniform bioinformatics pipeline, removing a potentially substantial source of variation. Microbiota differences across diagnoses were assessed using alpha- and beta-diversity approaches, machine learning, and biomarker analyses. Results: We ultimately included 20 studies containing individual data from 2624 children. Disease was associated with lower bacterial diversity in nasal and lower airway samples and higher relative abundances of specific nasal taxa including Streptococcus and Haemophilus. Machine learning success in assigning samples to diagnostic groupings varied with anatomical site, with positive predictive value and sensitivity ranging from 43 to 100 and 8 to 99%, respectively. Conclusion: IPD meta-analysis of the respiratory microbiota across multiple diseases allowed identification of a non-specific disease association which cannot be recognised by studying a single disease. Whilst imperfect, machine learning offers promise as a potential additional tool to aid clinical diagnosis.

Retrospective multicentric study on Campylobacter spp. bacteremia in France: the Campylobacteremia study

BACKGROUND

Campylobacter spp. bacteremia is a severe infection. A nationwide 5-year retrospective study was conducted to characterize its clinical features and prognostic factors.

METHODS

Patients diagnosed with Campylobacter spp. bacteremia in 37 French hospitals participating in the surveillance network of the National Reference Center for Campylobacter and Helicobacter were included from January 1, 2015, to December 31, 2019. The goal was to analyze the effects of a delay of appropriate antibiotic therapy and other risk factors on 30-day mortality, antibiotic resistance, patient characteristics and prognosis according to the Campylobacter species.

FINDINGS

Among the 592 patients, Campylobacter jejuni and Campylobacter fetus were the most commonly identified species (42.9 and 42.6%, respectively). The patients were elderly (median age 68 years), and most had underlying conditions, mainly immunodepression (43.4%), hematologic malignancies (25.9%), solid neoplasms (23%) and diabetes (22.3%). C. jejuni and Campylobacter coli were associated with gastrointestinal signs, and C. fetus was associated with secondary localizations. Among the 80 patients (13.5%) with secondary localizations, 12 had endocarditis, 38 vascular, 24 osteo-articular and 9 ascitic fluid infections. The thirty-day mortality rate was 11.7%, and an appropriate antibiotic treatment was independently associated with 30-day survival (odds ratio [OR]=0.47, 95% CI [0.24-0.93], p=0.03). The median efficient therapy initiation delay was quite short (2 days, IQR [0-4]) but it had no significant impact on 30-day mortality (p=0.78).

INTERPRETATION

Campylobacter spp. bacteremia mainly occurred in elderly immunocompromised individuals with variable clinical presentations according to the species involved. Appropriate antimicrobial therapy was associated with improved 30-day survival.

Listeria monocytogenes faecal carriage is common and depends on the gut microbiota

Listeria genus comprises two pathogenic species, L. monocytogenes (Lm) and L. ivanovii, and non-pathogenic species. All can thrive as saprophytes, whereas only pathogenic species cause systemic infections. Identifying Listeria species' respective biotopes is critical to understand the ecological contribution of Listeria virulence. In order to investigate the prevalence and abundance of Listeria species in various sources, we retrieved and analyzed 16S rRNA datasets from MG-RAST metagenomic database. 26% of datasets contain Listeria sensu stricto sequences, and Lm is the most prevalent species, most abundant in soil and host-associated environments, including 5% of human stools. Lm is also detected in 10% of human stool samples from an independent cohort of 900 healthy asymptomatic donors. A specific microbiota signature is associated with Lm faecal carriage, both in humans and experimentally inoculated mice, in which it precedes Lm faecal carriage. These results indicate that Lm faecal carriage is common and depends on the gut microbiota, and suggest that Lm faecal carriage is a crucial yet overlooked consequence of its virulence.

Peripheral venous catheter colonisation after skin disinfection with 0.5% aqueous sodium hypochlorite, preceded or not by one application of 70% ethanol (DACLEAN): A single centre, randomised, open-label, pilot study

Few data are available on the efficacy of 0.5% aqueous sodium hypochlorite (SH) for skin disinfection before peripheral catheter insertion. A total of 239 patients were randomly assigned to either one application of SH alone or one application of SH preceded by one application of 70% ethanol (ET-SH). Catheter colonisation, defined as a catheter tip culture growing more than 1000 CFU of a micro-organism per mL, occurred in 29 patients (33% - 89 colonisations per 1000 catheter days) in the SH group and in 31 patients (33% - 126 colonisations per 1000 catheter days) in the ET-SH.

Aims and challenges of building national trainee networks in clinical microbiology and infectious disease disciplines

Trainees represent the medical practice of tomorrow. Interactions and collaborations at the early stage in career will strengthen the future of our specialties, clinical microbiology and infectious diseases. Trainee networks at the national level help access the best education and career opportunities. The aim of this collaborative white paper between the Trainee Association of European Society of Clinical Microbiology and Infectious Diseases (ESCMID) and four national trainee networks is to discuss the motivation for building such networks and offer guidance for their creation and sustainability even during a health crisis.

Chlorhexidine plus alcohol versus povidone iodine plus alcohol, combined or not with innovative devices, for prevention of short-term peripheral venous catheter infection and failure (CLEAN 3 study): an investigator-initiated, open-label, single centre, randomised-controlled, two-by-two factorial trial

BACKGROUND

Two billion peripheral venous catheters are sold globally each year, but the optimal skin disinfection and types of devices are not well established. We aimed to show the superiority of disinfection with 2% chlorhexidine plus alcohol over 5% povidone iodine plus alcohol in preventing infectious complications, and of closed integrated catheters, positive displacement needleless-connectors, disinfecting caps, and single-use prefilled flush syringes used in combination (innovation group) over open catheters and three-way stopcocks for treatment administration (standard group) in preventing catheter failure.

METHODS

We did an open-label, randomised-controlled trial with a two-by-two factorial design, for which we enrolled adults (age ≥18 years) visiting the emergency department at the Poitiers University Hospital, France, and requiring one peripheral venous catheter before admission to the medical wards. Before catheter insertion, patients were randomly assigned (1:1:1:1) using a secure web-based random-number generator to one of four treatment groups based on skin preparation and type of devices (innovative devices or standard devices; 2% chlorhexidine plus alcohol or 5% povidone iodine plus alcohol). Primary outcomes were the incidence of infectious complications (local infection, catheter colonisation, or bloodstream infections) and time between catheter insertion and catheter failure (occlusion, dislodgment, infiltration, phlebitis, or infection). This study is registered with ClinicalTrials.gov, NCT03757143.

FINDINGS

1000 patients were recruited between Jan 7, and Sept 6, 2019, of whom 500 were assigned to the chlorhexidine plus alcohol group and 500 to the povidone iodine plus alcohol group (250 with innovative solutions and 250 with standard devices in each antiseptic group). No significant interaction was found between the two study interventions. Local infections occurred less frequently with chlorhexidine plus alcohol than with povidone iodine plus alcohol (0 [0%] of 496 patients vs six [1%] of 493 patients) and the same was observed for catheter colonisation (4/431 [1%] vs 70/415 [17%] catheters among the catheters cultured; adjusted subdistribution hazard ratio 0·08 [95% CI 0·02-0·18]). Median time between catheter insertion and catheter failure was longer in the innovation group compared with the standard group (50·4 [IQR 29·6-69·4] h vs 30·0 [16·6-52·6] h; p=0·0017). Minor skin reactions occurred in nine (2%) patients in the chlorhexidine plus alcohol group and seven (1%) patients in the povidone iodine plus alcohol group.

INTERPRETATION

For skin antisepsis, chlorhexidine plus alcohol provides greater protection of peripheral venous catheter-related infectious complications than does povidone iodine plus alcohol. Use of innovative devices extends the catheter complication-free dwell time.

FUNDING

Becton Dickinson.

First description of bacteremia caused by Oscillibacter valericigenes in a patient hospitalized for leg amputation

Initially isolated from the alimentary canal of a Japanese corbicula clam, Oscillibacter valericigenes is a Gram-negative rod, of which culture remains very difficult. Herein we present the first case of bacteremia due to Oscillibacter valericigenes, in humans. A 55-year-old man was hospitalized for clinical management of multiple neglected leg wounds (colonized with maggots) that had occurred during a motorcycle accident. Following radiological confirmation of the bone infection, a transfemoral amputation was performed to limit the risk of extended infection. During hospitalization, before the amputation, the patient experienced fever, biological inflammation justifying the sampling of multiple blood cultures. Anaerobic blood culture was positive after 34 hours, without identification by routine procedure (MALDI-TOF), justifying identification by 16S DNA sequencing. In the absence of possible subculture, antibiotic sensitivity testing could not be performed. A pre-emptive treatment by piperacillin-tazobactam was introduced for 14 days. The evolution was good, except for a local disunion. Complete phylogenic analysis of the clinical strain showed that it significantly differed from the reference strain, which is distantly related to the Clostridia cluster IV. Due to the culture conditions and specialized identification method by sequencing, prevalence of O. valericigenes may be underestimated. Optimization of blood culture procedures and utilization of 16S rRNA gene sequencing are tools needed for identification of rare pathogens that could help to optimize clinical management of infected patients.

K3-EDTA differentially inhibits the growth of Candida strains according to their azole resistance status

The diagnosis of the life-threatening invasive Candida infections is mainly established using culture of specimens that might be collected on different devices including ethylene diamine tetraacetic acid (EDTA)-coated tubes. Despite the knowledge that EDTA inhibits bacterial cultures, and its use to treat oral fungal infections, its impact on Candida cultures has not been completely assessed. This study aimed at assessing it on azole-resistant and azole-susceptible strains. Clinical and American Type Culture Collection (ATCC) strains for Candida albicans (CA), C. glabrata (CGS), C. krusei (CK), azole-susceptible and azole-resistant strains of C. glabrata (CGS and CGR), C. lipolytica (CL), and C. inconspicua (CI) were characterized using MALDI-TOF MS and susceptibility testing and then incubated (1) with serial dilutions of tripotassic EDTA (0%-500% of the concentration in a sample tube) for 2 hours before plating onto ChromID Can2 agar; (2) for 0, 2, 4, 6, 7, or 8 hours at EDTA concentrations at 20% and 33% before seeding; and (3) with sodium citrate or lithium heparinate instead of EDTA for 2 hours before plating. After 48 hours at 35°C, colony-forming units were automatically quantified. An inhibitory effect of EDTA was observed, at different concentrations, for CA (20%), CGS (100%), and CGR (500%) (P < .05), but none was observed for CL, CI, and CK. The effect increased with incubation duration, at a faster rate for azole-susceptible strains. K3-EDTA inhibits Candida growth and EDTA-coated tubes should not be used for mycological culture-based analyses. The correlation between EDTA inhibition and Candida azole-resistance offers perspectives for the development of selective agar and new antifungal strategies.

Impact of Pregnancy on Intra-Host Genetic Diversity of Influenza A Viruses in Hospitalised Women: A Retrospective Cohort Study

Characterising dynamics of Influenza A Viruses (IAV) within-host evolution is an active field of research which may lead to a better understanding of viral pathogenesis. Using a pregnant mouse model, a study has recently suggested that immune modulation during pregnancy could promote the emergence of IAV quasispecies with increased virulence. Herein, we assess the clinical relevance of these findings in humans. We studied IAV intra-host diversity (ihD) in pregnant (n = 36) and non-pregnant (n = 23) women hospitalized in Lyon for IAV infection (01/2015–05/2018). Whole IAV genomes present in nasopharyngeal samples were sequenced in duplicate to analyze reproducible intra-host single nucleotide variants (ihSNV). Counts, relative frequencies and locations of ihSNV were used as indicators of ihD. The median ihSNV/kb counts per segment were between 0 and 1.3. There was >81% ihSNV at relative frequencies between 1–5% for H1N1 and >51% for H3N2 IAV. No significant difference was noted between pregnant and non-pregnant women when considering all or only non-synonymous ihSNV. Seven convergent non-synonymous ihSNV were found; none were significantly associated with pregnancy. These results suggest that modulation of the immune system during pregnancy in humans does not impact IAV ihD, in contrast to mice.

Optimized nested PCR enhances biological diagnosis and phylogenetic analysis of human parvovirus B19 infections

Diagnosis and epidemiological analysis of human parvovirus B19 (hB19V) infections are essential for disease management in severely ill patients. This study aimed to evaluate the performance of an optimized NS1-VP1u nested PCR for detection and sequencing of viruses in clinical samples using 224 clinical and five reference samples. PCR sensitivity, specificity, and positive and negative predictive values were perfect (100%). While phylogenetic analysis of a 615 bp-long fragment demonstrated that the viruses in all of the samples belonged to genotype 1, this study confirmed that this optimized PCR could detect all known hB19V with high performance.

Decontamination of Intravaginal Probes Infected by Human Papillomavirus (HPV) Using UV-C Decontamination System

Background: This three-step study evaluated ultraviolet-C (UV-C) efficacy against human papillomavirus (HPV) found on vaginal ultrasound probes. Methods: The first two steps evaluated UV-C disinfection of vaginal ultrasound probes in routine condition. During the first phase, the probe (n = 100) was sampled after a complete cleaning and disinfection protocol, i.e., cleaning with chemically impregnated wipes, followed by UV-C. During the second phase, the probe (n = 47) was sampled after cleaning and UV-C. The final step consisted of applying mixes of HPV on a dedicated, covered probe (n = 15) then sampling the cover, the probe after removal of the cover, after cleaning, and after UV-C. HPV detection was performed using CLART^® HPV2 PCR (Genomica, Madrid, Spain). Results: In the first phase, no probes were found to be positive for both DNA after UV-C. In the second phase, eight probes were found to be positive after cleaning (seven with human DNA and one with HPV) and negative after UV-C. In the final phase, one probe was found to be positive for HPV for each sample except after UV-C. Conclusions: Covers followed by a chemically impregnated wipe are not sufficient to ensure patient safety during vaginal ultrasound examinations. UV-C is effective in routine conditions against contaminations found on vaginal ultrasound probes, especially HPV.

Molecular diversity and biennial circulation of enterovirus D68: a systematic screening study in Lyon, France, 2010 to 2016

Understanding enterovirus D68 (EV-D68) circulation patterns as well as risk factors for severe respiratory and neurological illness is important for developing preventive strategies. Methods: Between 2010 and 2016, 11,132 respiratory specimens from hospitalised patients in Lyon, France, were screened for EV-D68 by PCR. Phylogenetic relationships of the viral-protein-1 sequences were reconstructed using maximum-likelihood and Bayesian-Markov-Chain-Monte-Carlo approaches. Results: Overall, 171 infections with a biennial pattern were detected, including seven, one, 55, none, 42, one and 65 cases annually during 2010–16. Children (< 16 years-old; n = 150) were mostly affected and 71% (n = 121) of the total patients were under 5 years-old. In 146 patients with medical reviews, 73% (n = 107) presented with acute respiratory distress. Among paediatric patients with medical reviews (n = 133), 55% (n=73) had an asthma/wheezing history, while among adults (n = 13), 11 had underlying diseases. In total, 45 patients had severe infections and 28 patients needed intensive care unit stays. No acute flaccid myelitis (AFM) was detected. We found genotypes A, B1, B2 B3 and D circulating, and no associations between these and clinical presentations. During the study, new genotypes continuously emerged, being replaced over time. We estimated that ancestors of currently circulating genotypes emerged in the late-1990s to 2010. Rises of the EV-D68 effective population size in Lyon coincided with infection upsurges. Phylogenetic analyses showed ongoing diversification of EV-D68 worldwide, coinciding with more infections in recent years and increases of reported AFM paediatric cases. Conclusions: Reinforcement of diagnostic capacities and clinical-based surveillance of EV-D68 infections is needed in Europe to assess the EV-D68 burden.

Web-based analysis of adherence to influenza vaccination among French healthcare workers

BACKGROUND

Influenza is recognized as a public health threat. However, vaccine hesitancy and poor vaccine uptake have been seen in French healthcare workers (HCWs). As a result, authorities have considered implementing mandatory influenza vaccination for HCWs.

OBJECTIVES

This study aimed to describe factors associated with influenza vaccine adherence or non-adherence in French HCWs and to collect their perception about mandatory influenza vaccination.

STUDY DESIGN

In February 2017, during the influenza season, a standardized questionnaire was sent electronically to the professional email addresses of French HCWs. Analyses were performed having collected 3000 responses.

RESULTS

Between February 1 and 16, 2017, a 14-question survey was sent to HCWs professional email addresses. After a two week period had elaspsed, 3000 answers were collected for analysis. Overall, 45.7% of responders reported they had received influenza vaccination in 2016-2017, with statistical differences relating to professional status, age and practice. In addition, 92.2% reported caring for at-risk patients and 62.9% had a community-based practice. Finally, accepting mandatory influenza vaccination was statistically associated with higher age, a higher socio-professional category, and seasonal influenza vaccine uptake, but not with management of at-risk patients.

CONCLUSIONS

Electronically submitted questionnaires are a rapid and easy tool that can be used to describe factors associated with influenza vaccine uptake in HCWs. In our study, differences in receiving influenza vaccination related to age, practice and professional categories, and provided an insight into potential adherence to mandatory influenza vaccination in HCWs. If repeated, these surveys may also monitor the evolution of vaccine uptake by professional categories.

A computed tomography study of the fibula: morphology, morphometry, intramedullary anatomy, application prospects on intramedullary nailing

PURPOSE

The intramedullary percutaneous pinning in fractures of the lateral malleolus is a technique of osteosynthesis that can reduce complications of ORIF. Our study describes the morphology and the morphometry of the fibula, in particular intramedullary, so as to specify the best fibular nail features.

METHODS

We conducted a retrospective study on CT acquisitions of fibulae in vivo. We studied total length, and the distal malleolar angle. Regarding intramedullary morphology, six axial study levels were defined. Each level was assigned a morphometric classification (oval, triangular, quadrangular or irregular), and a measure of the diameter of the cavity. The distance between the smaller diameter and the malleolar tip was investigated.

RESULTS

We included 50 patients for 97 fibulae. The average age was 66.5 years. The irregular morphology type was the most frequently found. The average length was 370.5 mm (SD = 18.1; CI 95% [366.9; 374.1]), the average distal malleolar angle was 163.5° (SD = 3.7; CI 95% [162.7; 164.2]). The average minimal intramedullary diameter at malleolus level was 3.2 mm (SD = 1.2; CI 95% [3.0; 3.5]), with a minimum size reaching 95.8 mm (SD = 13.8; CI 95% [93.0; 98.5]) of the malleolar tip.

CONCLUSIONS

The analysis of morphological parameters of the fibula, in particular the lateral malleolus and intramedullary morphology is necessary for the design of a morpho-adapted nail. Interpersonal variability must be taken into account by the implant industry to offer nails of suited lengths and diameters.

Impact of the Gastro-Intestinal Bacterial Microbiome on Helicobacter-Associated Diseases

Helicobacter pylori is a bacterium that selectively infects the gastric epithelium of half of the world population. The microbiome, community of microorganisms gained major interest over the last years, due to its modification associated to health and disease states. Even if most of these descriptions have focused on chronic disorders, this review describes the impact of the intestinal bacterial microbiome on host response to Helicobacter associated diseases. Microbiome has a direct impact on host cells, major barrier of the gastro-intestinal tract, but also an indirect impact on immune system stimulation, by enhancing or decreasing non-specific or adaptive response. In microbial infections, especially in precancerous lesions induced by Helicobacter pylori infection, these modifications could lead to different outcome. Associated to data focusing on the microbiome, transcriptomic analyses of the eukaryote response would lead to a complete understanding of these complex interactions and will allow to characterize innovative biomarkers and personalized therapies.

[Deep venous thrombosis caused by congenital inferior vena cava agenesis]

Congenital agenesis of the inferior vena cava, although rare, is found preferentially in young patients with proximal deep venous thrombosis. Exact diagnosis can be made thanks to enhanced computed tomography scan and/or magnetic resonance imaging, while Doppler ultrasonography is insufficient to establish an inferior vena cava malformation. A consensus has not yet been established for the treatment but lifelong anticoagulation with elastic stocking support to prevent post-thrombotic syndrome is commonly considered in most cases. We report a case of an unprovoked deep venous thrombosis caused by a congenital agenesis of the inferior vena cava localized to the infrarenal segment, in a 24-year-old man. An anticoagulation with low molecular weight heparin was started and prolonged oral anticoagulation was prescribed. In the absence of the usual thrombotic risk factors, the presence of an inferior vena cava anomaly should be considered.

Evaluation of p16/Ki-67 Dual Staining Compared with HPV Genotyping in Anal Cytology with Diagnosis of ASC-US for Detection of High-Grade Anal Intraepithelial Lesions

Introduction

Human Papillomavirus (HPV) infection is the main risk factor for anogenital cancer. The objective of this study was to compare p16/Ki-67 dual staining to HPV genotyping in anal cytology samples with an atypical squamous cell of undetermined significance (ASC-US) for the identification of high-grade squamous intraepithelial lesion (HSIL).

Methods

Anal cytology samples with an ASC-US result (n = 111) were collected from patients of a university hospital (Lyon, France) from 2014 to 2015. Cases with remaining squamous cells (n = 82) were stained using p16/Ki-67 dual staining (CINtec-Plus kit) and analyzed for HPV screening (CLART2-PCR kit) using a composite endpoint of biopsy and cytology results on follow-up specimens.

Results

Detection of HSIL on follow-up specimens (5/22 biopsies; 1/29 cytology samples) was obtained in two out of six cases with p16/Ki-17 versus. five out of six with HPV genotyping alone. Sensitivity and specificity to detect HSIL for p16/Ki-67 was 33% (95% confidence interval [CI] [4; 77]) and 49% (95%CI [34; 64]) versus. 83% (95%CI [36; 99.6]) and 13% (95%CI [5; 27]) for HPV genotyping.

Conclusion

Herein, HPV genotyping was more sensitive but less specific than p16/Ki-67 staining for the detection of subsequent HSIL in ASC-US anal cytology. A larger study is required to evaluate the combination of these biomarkers for triage.

Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow

Background

In recent years, metagenomic Next-Generation Sequencing (mNGS) has increasingly been used for an accurate assumption-free virological diagnosis. However, the systematic workflow evaluation on clinical respiratory samples and implementation of quality controls (QCs) is still lacking.

Methods

A total of 3 QCs were implemented and processed through the whole mNGS workflow: a no-template-control to evaluate contamination issues during the process; an internal and an external QC to check the integrity of the reagents, equipment, the presence of inhibitors, and to allow the validation of results for each sample. The workflow was then evaluated on 37 clinical respiratory samples from patients with acute respiratory infections previously tested for a broad panel of viruses using semi-quantitative real-time PCR assays (28 positive samples including 6 multiple viral infections; 9 negative samples). Selected specimens included nasopharyngeal swabs (n = 20), aspirates (n = 10), or sputums (n = 7).

Results

The optimal spiking level of the internal QC was first determined in order to be sufficiently detected without overconsumption of sequencing reads. According to QC validation criteria, mNGS results were validated for 34/37 selected samples. For valid samples, viral genotypes were accurately determined for 36/36 viruses detected with PCR (viral genome coverage ranged from 0.6 to 100%, median = 67.7%). This mNGS workflow allowed the detection of DNA and RNA viruses up to a semi-quantitative PCR Ct value of 36. The six multiple viral infections involving 2 to 4 viruses were also fully characterized. A strong correlation between results of mNGS and real-time PCR was obtained for each type of viral genome (R² ranged from 0.72 for linear single-stranded (ss) RNA viruses to 0.98 for linear ssDNA viruses).

Conclusions

Although the potential of mNGS technology is very promising, further evaluation studies are urgently needed for its routine clinical use within a reasonable timeframe. The approach described herein is crucial to bring standardization and to ensure the quality of the generated sequences in clinical setting. We provide an easy-to-use single protocol successfully evaluated for the characterization of a broad and representative panel of DNA and RNA respiratory viruses in various types of clinical samples.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3446-5) contains supplementary material, which is available to authorized users.

Genetic characterization of respiratory syncytial virus highlights a new BA genotype and emergence of the ON1 genotype in Lyon, France, between 2010 and 2014

BACKGROUND

Respiratory syncytial virus (RSV) is a well-recognized cause of respiratory tract infections. Based on G gene variations, 11 RSV-A and 36 RSV-B genotypes have been described to date. The ON1 genotype was detected in Ontario in 2010 and subsequently reported in several countries.

OBJECTIVES

The objective of the present study was to investigate for the first time the RSV epidemiology and genotype diversity in France between 2010 and 2014.

STUDY DESIGN

All respiratory samples received from patients with influenza-like illness or respiratory tract infection were screened for RSV infection by RT-PCR. The results were stratified according to winter season. Among the RSV-positive cases, 117 samples were further investigated for phylogenetic analysis out of 150 randomly selected for sequencing.

RESULTS

Among the 20,359 cases screened, 14% of the cases were RSV-positive. RSV-A was predominant during the four winter seasons. The first ON1 variant was detected during the 2010-2011 winter and reached 85% of all RSV-A-positive cases in 2013-2014. Most RSV-B was classified as BA9 and BA10 genotypes but a new genotype (BA-Ly) was described.

CONCLUSION

As reported in different countries, ON1 variants were firstly detected in 2011 and became the predominant RSV-A genotype in Lyon. Among RSV-B, BA9 was predominant but detected alongside BA10 or a transient genotype (BA-Ly).

Early nasopharyngeal microbial signature associated with severe influenza in children: a retrospective pilot study

A few studies have highlighted the importance of the respiratory microbiome in modulating the frequency and outcome of viral respiratory infections. However, there are insufficient data on the use of microbial signatures as prognostic biomarkers to predict respiratory disease outcomes. In this study, we aimed to evaluate whether specific bacterial community compositions in the nasopharynx of children at the time of hospitalization are associated with different influenza clinical outcomes. We utilized retrospective nasopharyngeal (NP) samples (n=36) collected at the time of hospital arrival from children who were infected with influenza virus and had been symptomatic for less than 2 days. Based on their clinical course, children were classified into two groups: patients with mild influenza, and patients with severe respiratory or neurological complications. We implemented custom 16S rRNA gene sequencing, metagenomic sequencing and computational analysis workflows to classify the bacteria present in NP specimens at the species level. We found that increased bacterial diversity in the nasopharynx of children was strongly associated with influenza severity. In addition, patients with severe influenza had decreased relative abundance of Staphylococcus aureus and increased abundance of Prevotella (including P. melaninogenica), Streptobacillus, Porphyromonas, Granulicatella (including G. elegans), Veillonella (including V. dispar), Fusobacterium and Haemophilus in their nasopharynx. This pilot study provides proof-of-concept data for the use of microbial signatures as prognostic biomarkers of influenza outcomes. Further large prospective cohort studies are needed to refine and validate the performance of such microbial signatures in clinical settings.

Vaginal Neoplasia Induced by an Unusual Papillomavirus Subtype in a Woman with Inherited Chromosomally Integrated Human Herpesvirus Type 6A

We describe here a case of high-grade vaginal squamous lesion in a 54-year-old woman with a papillomaviruses (HPV) genital infection that developed from a cervical low-grade squamous intraepithelial lesion (SIL) to a high-grade SIL (H-SIL) on cytological examination. A colposcopy exam led to the detection of suspect vaginal lesions with granulomatous infiltrations, which were classified as a Vaginal Intra-Epithelial Neoplasia grade 2 after pathologists' analyses. After a laser vaginal surgery and a loop excision of the transformation zone, the analyses of the anatomical pieces using a near-complete HPV screening panel revealed an HPV-4 infection that was not detected before in cervical smears. This HPV-infection is associated with a high human herpesvirus type 6A (HHV-6A) viral load in the same anatomical piece. The presence of an inherited chromosomally integrated HHV-6A (iciHHV-6A) was proved in this patient by real-time polymerase chain reaction on hair follicles and nail. This case suggests reconsidering both the benign nature of low-grade lesions in the female genital tract and the well-known "good" prognosis of low-risk HPV infection, especially when iciHHV-6A is diagnosed. This clinical course insists on the benefits of the multiplex panel use or global sequencing in order to optimize biological testing sensitivity, and so enhance clinical management of infection-induced neoplasia.