Microbiome of the External Auditory Canal: Changes After Long-Term Hearing Aid Use.

OBJECTIVE: To investigate the microbial changes of long-term hearing aid use culture independently. STUDY DESIGN: Cross-sectional study. PATIENTS: Fifty long-term hearing aid users and 80 volunteer controls with asymptomatic ears. INTERVENTION: External auditory canal (EAC) sampling with DNA-free swabs. MAIN OUTCOME MEASURES: Microbial communities in the samples were investigated with amplicon sequencing of the 16S rRNA gene. RESULTS: The final analysis contained 48 hearing aid users, 59 controls. Twenty-four samples were excluded because of low sequence count, recent use of antimicrobials and/or corticosteroids, recent cold, or missing health status. The groups showed significant differences in bacterial diversity (beta div., p = 0.011), and hearing aid users showed lower species richness than the control group (alpha div., p < 0.01). The most frequent findings in both groups were Staphylococcus auricularis, Alloiococcus otitis, Cutibacterium acnes, Corynebacterium otitidis, and Staphylococcus unclassified sp. Hearing aid users' samples presented more Corynebacterium tuberculostearicum than the control samples. Common EAC pathogens, such as Staphylococcus aureus or Pseudomonas aeruginosa were rare. CONCLUSION: Long-term hearing aid use lowers bacterial diversity and modulates the EAC microbiome. The changes mostly affect commensals. Lowered diversity may predispose individuals to EAC conditions and needs more research.

Evaluation of the FluoroType Mycobacteria assay for identification of mycobacteria.

Accurate species identification is a prerequisite for successful management of tuberculosis and non-tuberculous mycobacterial (NTM) diseases. The novel FluoroType Mycobacteria assay combines three established GenoType DNA strip assays (CM, AS, and NTM-DR), allowing detection of Mycobacterium tuberculosis and 32 NTM species/subspecies in a single assay with automatic detection and result analysis. We evaluated the clinical performance of the FluoroType assay and its feasibility in replacing the GenoType Mycobacterium CM assay as the initial method for mycobacterial identification. A total of 191 clinical mycobacterial cultures were analyzed in this study: 180 identified for one mycobacterial species, 6 for multiple, and 5 for no mycobacterial species. Positive percent agreement (PPA) for the FluoroType assay was 87.8% (n = 158), with full agreement for 23/29 species. Weakest PPA was observed for Mycobacterium gordonae (50%, n = 9/18), Mycobacterium interjectum (40%, n = 2/5), and Mycobacterium intracellulare (42%, n = 5/12). Clinical and mixed cultures containing multiple mycobacterial species gave equally single species and genus level identifications (n = 30). No cross-reactivity with non-mycobacterial species was observed (n = 22). In a separate in silico analysis of 2016-2022 HUS area (Finland) register data (n = 2,573), the FluoroType assay was estimated to produce 18.8% (n = 471) inadequate identifications (genus/false species) if used as the primary identification method compared to 14.2% (n = 366) with the GenoType CM assay. The FluoroType assay was significantly more convenient in terms of assay workflow and result interpretation compared to the entirely manual and subjective GenoType CM assay. However, the feasibility of the assay should be critically assessed with respect to the local NTM species distribution. IMPORTANCE: This study is the first clinical evaluation report of the novel FluoroType Mycobacteria assay. The assay has the potential to replace the established GenoType NTM product family in identification of culture-enriched mycobacteria. However, our research results suggest that the assay performs suboptimally and may not be feasible for use in all clinical settings.

Impact of selective reporting of wound cultures on microbiology reports and antimicrobial-drug use on a wound-care ward in Finland: a retrospective cohort study.

BACKGROUND: Selective reporting is a promising tool for antimicrobial stewardship, but in wound cultures, its effects on the use of antimicrobials are unknown. Our HUS Diagnostic Center Bacteriology laboratory refined its selective reporting protocol for wound cultures during 2017-2018. In this study we aimed to show our protocol's impact on the frequency of antimicrobial escalation. METHODS: We performed a retrospective cohort study of patients in the wound-care ward of a primary-care hospital in Helsinki, Finland, from 2014 to 2016 (pre-intervention) and from 2019 to April 2021 (post-intervention). With the inclusion criterion being wound-culture collection, this provided us with 299 patients, of which 152 were in the pre-intervention group, and 147 were post-intervention. We collected the data from medical records and compared the pre-intervention- with the post-intervention group in terms of patient profiles, microbiology reports, antimicrobial treatment, and treatment outcomes. FINDINGS: In the pre-intervention group 40% of the patients were male and 60% female and in the post-intervention group 49% and 51% respectively. The frequency of AST reported had decreased from 63% in the pre-intervention group to 37% post-intervention (OR 0.35, p < 0.001). The post-intervention group demonstrated lower frequencies of antimicrobial treatment 7 d after wound culture collection, 82% pre-intervention vs 58% post-intervention (OR 0.31, p < 0.001), and antimicrobial escalation, 42% vs 20% (OR 0.35, p < 0.001) respectively. Length of hospital stay, and all-cause mortality were similar between the groups. INTERPRETATION: Selective reporting of wound cultures appears an effective and safe measure to reduce the use of antimicrobials. FUNDING: HUS Diagnostic Center.

Shiga toxin-producing Escherichia coli (STEC) stool multiplex PCR can replace culture for clinical diagnosis and follow-up.

Shiga toxin (stx)-producing Escherichia coli (STEC) causes potentially severe gastrointestinal infections. Due to its public health importance, control measures are required, and carriers may need to refrain from work or daycare when the risk of spread to vulnerable people is high. We evaluated the use of direct stool multiplex PCR compared to culture for primary STEC diagnostics and for follow-up in order to update the national guidelines for STEC monitoring. We analyzed primary and follow-up samples of 236 STEC PCR-positive cases at HUSLAB, Helsinki, Finland in 2016-2017, altogether 858 samples. All STEC PCR-positive samples were inoculated on non-selective chromogenic agar plates. Culture positivity was confirmed from culture sweeps by PCR. 211 (89%) of the cases were culture positive in their primary sample. Of all primary and follow-up samples, 499 were PCR positive and of these 450 (90%) were culture positive. PCR-negative follow-up samples were available from 125 cases. Of these, 88 cases were followed for at least three consecutive PCR-negative samples. Two cases (2%) had culture-positive sample(s) after two consecutive PCR-negative samples. The median time for STEC clearance was 22-23 days. The laboratory-developed multiplex PCR test used in this study is a reliable method for STEC diagnostics and follow-up in a clinical laboratory. When non-selective methodology is used, the majority of PCR-positive samples (90%) are also culture positive. Furthermore, only two cases (2%) in our material had two consecutive PCR-negative samples followed by positive samples. Consequently, to demonstrate the clearance from STEC infection, we consider two PCR-negative follow-up samples sufficient. The Finnish national guidelines for STEC monitoring have been updated accordingly.

Clinical and microbiological characterization of Aerococcus urinae bacteraemias at Helsinki metropolitan area, Finland.

Our objective was to assess the incidence of bacteraemic Aerococcus urinae cases at Helsinki metropolitan area, Finland, from a 6-year study period (2013 to 2018) and to further characterize available cases. The study evaluates the outcome of commonly used cefuroxime treatment and determinate a set of A. urinae in vitro antimicrobial susceptibilities for benzylpenicillin, cefuroxime, and ceftriaxone. Clinical records of A. urinae bacteraemic patients were reviewed retrospectively. Antimicrobial susceptibility testing was performed by disk diffusion, gradient test, and broth microdilution for 139-141 clinical A. urinae isolates. Clinical data of 72/77 patients were combined with the in vitro susceptibilities. We found an increasing number of bacteraemic A. urinae cases within 6-year study period (p = 0.01). The patients were mainly elderly males, and all suffered from underlying conditions. A total of 27.3% of cases (21/77) showed polymicrobial blood cultures. Thirty-day mortality was 22.1%. Cefuroxime was the initial empiric antimicrobial agent given for 66/76 of the patients and treatment outcome was favorable for 20/22 patients who received cefuroxime at least up to day 5. All isolates were susceptible to benzylpenicillin and cefuroxime interpreted by EUCAST breakpoints for Aerococci and PK-PD breakpoints, respectively. MIC determinations gave variable results for ceftriaxone, 2.1-2.9% of the isolates were resistant. To conclude, it seems that the number of bacteraemic Aerococcus urinae cases is increasing at Helsinki metropolitan area, Finland, reflecting the growing blood culture sampling. Clinical A. urinae isolates were susceptible to cefuroxime in vitro. Treatment data indicate that empirical cefuroxime started for possibly urinary tract -derived community-acquired bacteraemia covers A. urinae.

UriSed 3 PRO automated microscope in screening bacteriuria at region-wide laboratory organization.

BACKGROUND AND AIMS: We assessed the possibility to rule out negative urine cultures by counting with UriSed 3 PRO (77 Elektronika, Hungary) at Helsinki and Uusimaa Hospital District. MATERIALS AND METHODS: Bacteria counting of the UriSed 3 PRO automated microscope was verified with reference phase contrast microscopy against growth in culture. After acceptance into routine, results of bacteria and leukocyte counting from 56 426 specimens with eight UriSed 3 PRO instruments were compared against results from parallel samples cultured on chromogenic agar. Laboratory data including preanalytical details were accessed through the regional database of the Helsinki and Uusimaa Hospital District. RESULTS: A combined sensitivity of 87-92% and a negative predictive value of 90-96% with a specificity of 54-50% was reached, depending on criteria. Preanalytical data (incubation time in bladder) combined with the way of urine collection would improve these figures if reliable. CONCLUSIONS: Complex patient populations, regional logistics and data interfases, and economics related to increased costs of additional particle counts against costs of screening cultures of all samples, did not support adaptation of a screening process of urine cultures. This conclusion was made locally, and may not be valid elsewhere.

Verification of UriSed 3 PRO automated urine microscope in regional laboratory environment.

BACKGROUND AND AIMS: Ten UriSed 3 PRO automated microscopes (77 Elektronika, Hungary) were verified for nine HUSLAB laboratories with 160 000 annual urine samples. MATERIALS AND METHODS: Particle counting of the primary UriSed 3 PRO instrument (77 Elektronika, Hungary) was verified against reference visual microscopy with 463 urine specimens, and against urine culture on chromogenic agar plates with parallel 396 specimens. Nine secondary instruments were compared pairwise with the primary instrument. RESULTS: Relative imprecisions compared to Poisson distribution, R(CV), were estimated to be 1.0 for white blood cell (WBC) and 1.5 for red blood cell (RBC) counts, respectively. Spearman's correlations against visual microscopy were rS = 0.94 for WBC, rS = 0.87 for RBC, and rS = 0.82 for squamous epithelial cell (SEC) counts. Agreement with visual microscopy (Cohen's weighted kappa) was 0.94 for WBC, 0.89 for RBC, 0.88 for SEC, 0.59 for combined casts, and 0.49 for non-squamous epithelial cells (NEC). Bacteria were detected with a sensitivity of 90% and specificity of 39 against culture at 107 CFB/L (104 CFU/mL). Created flagging limits allowed automated reporting for 70-75% of patient results. CONCLUSIONS: UriSed 3 PRO instruments were adopted into routine use after acceptance of the verification.

Etiology of Childhood Otorrhea in Luanda, Angola, and a Review of Otitis Media in African Children.

BACKGROUND: In resource-poor settings, otorrhea causes a significant burden of disease in children. Etiologic studies and structured data on otorrhea and chronic otitis media among African children remain scarce. METHODS: Here, we reviewed 678 bacteriologically analyzed otorrhea samples from Luanda Children's Hospital from children ≤15 years of age between 2008 and 2015. We then compared these with data from other studies among African children through a literature review of 20 articles published over 2 decades. RESULTS: Overall, 32 different bacteria were identified among 542 isolates from 654 children in Luanda. Gram-negative bacteria constituted the majority of all isolates (85%), whereby Pseudomonas spp. was the most common (n = 158; 29%), followed by Proteus spp. (n = 134; 25%). Among Staphylococcus aureus (n = 54; 10%), 69% of tested isolates were Methicillin-resistant S. aureus, and among Enterobacteriaceae, 14% were expanded-spectrum ß-lactamase isolates. Resistance to quinolones was rare. Furthermore, in a review of the literature, we found a high occurrence of otorrhea and chronic suppurative otitis media in children as well as possible gaps in existing knowledge. CONCLUSIONS: In Angola, Gram-negative rods emerged as common causative agents of otorrhea in children followed by S. aureus. The magnitude of chronic otorrhea in Africa represents a cause for public health concern.

Rectal E. coli above ciprofloxacin ECOFF associate with infectious complications following prostate biopsy.

Transrectal prostate biopsies carry the risk of infection. By using non-selective culture plates, instead of commonly used ciprofloxacin (CIP)-containing plates, we analyzed the association between Escherichia coli CIP minimal inhibitory concentration (MIC) and post-biopsy infectious complications. A pre-biopsy rectal swab was taken from 207 consecutive men, scheduled for transrectal 12-core prostate biopsy with CIP 750 mg as the mostly used prophylaxis. CIP MIC of rectal Gram-negative bacilli was determined from a chromogenic agar. Rectal E. coli were categorized to resistant (R) and intermediate (I) isolates together (R + I, MIC > 0.25 mg/l) and to sensitive (S, MIC ≤ 0.25 mg/l) using EUCAST clinical breakpoints. In addition, epidemiological cutoff (ECOFF R, MIC > 0.064 mg/l) was used for categorization. Eighteen (8.7%) men showed CIP R + I E. coli by the EUCAST breakpoints and 41 (19.8%) using the ECOFF R criteria. During follow-up, 15 (7.2%) men had infectious symptoms, of which 9 (4.3%) were culture-confirmed infections. Only 4 (26.7%) of these 15 patients showed R + I E. coli in the rectal swab according to EUCAST, but 10 (66.7%) using the ECOFF cutoff. Rectal E. coli CIP R + I by the EUCAST clinical breakpoints associated with infectious complications with OR 5.7 (95% CI 1.5-21.8, P = 0.005) and ECOFF R E. coli by OR 10.7 (95% CI 3.0-37.6, P < 0.001). Men carrying rectal E. coli with moderately lowered CIP susceptibility (MIC > ECOFF 0.064 mg/l) were identified and, interestingly, they showed a high risk of developing infectious symptoms after the biopsy. This explains why some men develop infectious complications despite appropriate antibiotics before prostatic biopsies. TRIAL REGISTRATION: NCT02140502.

Amniotic Fluid Infection in Preterm Pregnancies with Intact Membranes.

Introduction. Intra-amniotic infection (IAI) is a major cause of preterm labor and adverse neonatal outcome. We evaluated amniotic fluid (AF) proteolytic cascade forming biomarkers in relation to microbial invasion of the amniotic cavity (MIAC) and IAI in preterm pregnancies with intact membranes. Material and Methods. Amniocentesis was made to 73 women with singleton pregnancies; 27 with suspected IAI; and 46 controls. AF biomarkers were divided into three cascades: Cascade 1: matrix metalloproteinase-8 (MMP-8), MMP-9, myeloperoxidase (MPO), and interleukin-6; Cascade 2: neutrophil elastase (HNE), elafin, and MMP-9; Cascade 3: MMP-2, tissue inhibitor of matrix metalloproteinases-1 (TIMP-1), MMP-8/TIMP-1 molar ratio, and C-reactive protein (CRP). MMP-8 was measured by an immunoenzymometric assay and the others were measured by ELISA. Standard biochemical methods, molecular microbiology, and culture techniques were used. Results. MMP-8, MMP-9, MPO, elafin, and TIMP-1 concentrations were higher in IAI suspected cases compared to controls and also in IAI suspected cases with MIAC compared to those without MIAC when adjusted by gestational age at amniocentesis. All biomarkers except elafin and MMP-2 had the sensitivity of 100% with thresholds based on ROC-curve. Odd ratios of biomarkers for MIAC were 1.2-38 and 95% confidential intervals 1.0-353.6. Conclusions. Neutrophil based AF biomarkers were associated with IAI and MIAC.

Identification of urinary tract pathogens after 3-hours urine culture by MALDI-TOF mass spectrometry.

Complicated urinary tract infections, such as pyelonephritis, may lead to sepsis. Rapid diagnosis is needed to identify the causative urinary pathogen and to verify the appropriate empirical antimicrobial therapy. We describe here a rapid identification method for urinary pathogens: urine is incubated on chocolate agar for 3h at 35°C with 5% CO2 and subjected to MALDI-TOF MS analysis by VITEK MS. Overall 207 screened clinical urine samples were tested in parallel with conventional urine culture. The method, called U-si-MALDI-TOF (urine short incubation MALDI-TOF), showed correct identification for 86% of Gram-negative urinary tract pathogens (Escherichia coli, Klebsiella pneumoniae, and other Enterobacteriaceae), when present at >10(5)cfu/ml in culture (n=107), compared with conventional culture method. However, Gram-positive bacteria (n=28) were not successfully identified by U-si-MALDI-TOF. This method is especially suitable for rapid identification of E. coli, the most common cause of urinary tract infections and urosepsis. Turnaround time for identification using U-si-MALDI-TOF compared with conventional urine culture was improved from 24h to 4-6h.

[Invasive community-acquired infections in children]. / Lasten kotisyntyiset invasiiviset infektiot.

The study group consisted of 180 patients who had 186 community-acquired blood-culture positive infections during 2007-June 2013. Three of them died of meningitis caused by S. pneumoniae or N. meningitidis. A ten-valent conjugated pneumococcal vaccine was introduced in the Finnish National Vaccine Program in 2010. After that the incidence of invasive pneumococcal infections decreased markedly. The numbers of resistant S. pneumoniae appeared to decrease slightly, as did also hospitalization due to pneumonia in age group 0 to 2 years. No evidence for serotype replacement was found. The situation requires constant monitoring as the time passes, since the introduction of vaccination is quite recent.

Molecular basis of the glomerular filtration: nephrin and the emerging protein complex at the podocyte slit diaphragm.

For more than three decades, the molecular composition of the interpodocyte slit diaphragm of the glomerular filtration barrier has remained elusive. The first electron microscopic studies described the slit diaphragm as a porous, 'zipper-like' structure, but it was not until 1998 that the first transmembrane molecule of the slit diaphragm was identified: nephrin is a cell surface receptor of the immunoglobulin superfamily participating in cell-cell adhesion and signaling functions. Mutations in nephrin lead to the congenital nephrotic syndrome of the Finnish type, suggesting that nephrin is of pivotal importance for maintaining the filtration barrier. In recent years, the mapping of the genetic background of other inherited and acquired nephropathies and generation of transgenic animal models have led to a beginning of a new era in nephrology, possibly promising new targeted therapies and advanced diagnostics. This review article will briefly summarize the main findings that explain the molecular architecture of the glomerular filter itself and causes of some glomerular diseases that lead to proteinuria and, eventually, to renal failure.