The etiology of infections of the central nervous system (CNS) in Nepal often remains unrecognized because of underdeveloped laboratory facilities. The aim of this study was to investigate the etiology of CNS infections in a rural area of Nepal using molecular methods. From November 2014 to February 2016, cerebrospinal fluid (CSF) was collected from 176 consecutive patients presenting at United Mission Hospital in Tansen, Nepal, with symptoms of possible CNS infection. After the CSF samples were stored and transported frozen, polymerase chain reaction (PCR) was performed in Sweden, targeting a total of 26 pathogens using the FilmArray ® ME panel (BioFire, bioMerieux, Salt Lake City, UT), the MeningoFinder ® 2SMART (PathoFinder, Maastricht, The Netherlands), and an in-house PCR test for dengue virus (DENV), Japanese encephalitis virus (JEV), and Nipah virus (NiV). The etiology could be determined in 23%. The bacteria detected were Haemophilus influenzae (n = 5), Streptococcus pneumoniae (n = 4), and Neisseria meningitidis (n = 1). The most common virus was enterovirus detected in eight samples, all during the monsoon season. Other viruses detected were cytomegalovirus (n = 6), varicella zoster virus (n = 5), Epstein-Barr virus (n = 3), herpes simplex virus (HSV) type 1 (HSV-1) (n = 3), HSV-2 (n = 3), human herpes virus (HHV) type 6 (HHV-6) (n = 3), and HHV-7 (n = 2). Cryptococcus neoformans/gatti was found in four samples. None of the samples were positive for DENV, JEV, or NiV. Of the patients, 67% had been exposed to antibiotics before lumbar puncture. In conclusion, the etiology could not be found in 77% of the samples, indicating that the commercial PCR panels used are not suitable in this setting. Future studies on the etiology of CNS infections in Nepal could include metagenomic techniques.
Background: Urine is amongst the most frequent specimens submitted to clinical microbiology laboratories and many are negative for uropathogens. Same day reporting on urines negative for bacteria and WBC could impact inappropriate antimicrobial use. As well, same day reporting on the presence of bacteria/WBC may influence decisions regarding empiric antimicrobial therapy. We evaluated the UF1000 flow cytometry on urines submitted for culture and susceptibility testing. Methods: Urines submitted to Clinical Microbiology Royal University Hospital, Saskatoon, SK, Canada were used. Raw and boric acid preserved urines were included in the evaluation from inpatients and outpatients. Approximately 1 ml of urine was placed in a separate tube for flow cytometry performed twice on each specimen. All urines were inoculated to tryptic soy agar containing 5% sheep red blood cells and MacConkey agar and incubated in O 2 for 18-24 hours. Culture results were correlated with bacterial/ WBC counts from flow cytometry readings. Results: A total of 827 urines were analyzed (393 preserved, 434 raw). For raw urines, 142 (32.7%) had ≤10 bacterial cells/ul, 4 (0.9%) had ≥25 WBC/ul by FC; 239 (55.1%) had ≤50 bacterial cells/ul, 18 (4%) had ≥25 WBC/ul. Of the 239 urines with ≤50 bacteria/µl, 200 (83.7%) were 'no growth' or 'mixed' by culture, 0 (100%) urines had >100 million bacteria/L. Similar results were seen for preserved urines: 139 (35.4%) had ≤10 bacteria/µl, 7 (1%) had ≥25 WBC/µl, 195 (49.6%) had ≤50 bacteria/µl, 17 (4.3%) had ≥25 WBC/µl. Of the 195 preserved urines with ≤50 bacteria/µl, 167 (85.6%) were 'no growth' or 'mixed' by culture, 0 (100%) urine had >100 million bacteria/L. Conclusion: Screening of urine using flow cytometry has the potential to identify up to 50% of urines that do not require culture and can be same day reported as negative. A cut off of ≤50 bacteria/µl correlated with insignificant colony counts from urine culture; a higher cut off would further reduce the number of urines for culture. Our laboratory processes approximately 80,000 urines per year and with the possibility of 50% same day reported as negative influences workload, work flow and likely positively impacts antimicrobial stewardship programs. We are currently implementing this technology.OS 1-2 Using MALDI-TOF and selected gene (16S rRNA gene, gyrB gene) sequencing to practical and accurate identify clinical important viridans group streptococci Background: Clinical significant Viridans Group Streptococci (VGS) identification is important but problematic in particular for the Streptococcus mitis group. MALDI-TOF MS is very practical for clinical identification but for some problematic species, selected gene sequencing is necessary in order to make the identification more reliable. Few studies have investigated the performance of MALDI-TOF MS system in VGS identification. Methods: Using 16S rRNA gene or gyrB gene sequencing as a gold standard, the performance of two MALDI-TOF MS instruments in the identification of 181 VGS clinical isolates was...
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