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Purpose: To evaluate the microbiota of culture negative Corneal Impression Membrane (CIM) microbial keratitis samples with the use of shotgun metagenomics analysis. Methods: DNA of microbial keratitis samples were collected with CIM and extracted using the MasterPure™ Complete DNA and RNA Purification Kit (Epicentre). DNA was fragmented by sonication into fragments of 300 to 400 base pairs (bp) using Bioruptor® (Diagenode, Belgium) and then used as a template for library preparation. DNA libraries were sequenced on Illumina® HiSeq2500. The resulting reads were quality controlled, trimmed and mapped against the human reference genome. The unmapped reads were taxonomically classified using the Kraken software. Results: 18 microbial keratitis samples were included in the study. Brevundimonas diminuta was found in 5 samples while 6 samples showed the presence of viral infections. Cutibacterium acnes, Staphylococcus aureus, Moraxella lacunata and Pseudomonas alcaligenes were also identified as the presumed putative cause of the infection in 7 samples. Conclusions: Shotgun sequencing can be used as a diagnostic tool in microbial keratitis samples. This diagnostic method expands the available tests to diagnose eye infections and could be clinically significant in culture negative samples.

Purpose: To evaluate the microbiota of culture negative Corneal Impression Membrane (CIM) microbial keratitis samples with the use of shotgun metagenomics analysis. Methods: DNA of microbial keratitis samples were collected with CIM and extracted using the MasterPure™ Complete DNA and RNA Purification Kit (Epicentre). DNA was fragmented by sonication into fragments of 300 to 400 base pairs (bp) using Bioruptor® (Diagenode, Belgium) and then used as a template for library preparation. DNA libraries were sequenced on Illumina® HiSeq2500. The resulting reads were quality controlled, trimmed and mapped against the human reference genome. The unmapped reads were taxonomically classified using the Kraken software. Results: 18 microbial keratitis samples were included in the study. Brevundimonas diminuta was found in 5 samples while 6 samples showed the presence of viral infections. Cutibacterium acnes, Staphylococcus aureus, Moraxella lacunata and Pseudomonas alcaligenes were also identified as the presumed putative cause of the infection in 7 samples. Conclusions: Shotgun sequencing can be used as a diagnostic tool in microbial keratitis samples. This diagnostic method expands the available tests to diagnose eye infections and could be clinically significant in culture negative samples.

The culture negative peritonitis in Sudan 2010 was 46% exceeding 20% of the recommended ISPD (International Society for Peritoneal Dialysis) guidelines. This study reports an update after applying the standard ISPD protocol. The routine method was replaced by ISPD protocol. The culture negative rate using the ISPD guidelines dropped from 46% in the year 2010, to 39% in the year 2011, to 5% in the 2012 and to zero percent in the year 2013. Bacterial and fungal species represent (86.76%) and (13.23%) of infection and most isolates showed low resistance rate to antibiotics. Touch contamination added significantly (p = 0.0006) to the risk of contracting Peritonitis. The risk of contracting Peritonitis was 1.53 times higher in the group exposed by touch contamination. None of the other risk factors contributed significantly to Peritonitis. The study highlights the importance of implementing high hygiene practice. (C) 2016 King Saud Bin Abdulaziz University for Health Sciences. Published by Elsevier Limited. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Published guidelines for the treatment of healthcare-associated pneumonia (HCAP) recommend initial broad-spectrum antibiotics with appropriate de-escalation based on culture results. Guideline recommendations are based on data from intubated patients, in whom cultures are easily obtained. The approach to antibiotic de-escalation for culture-negative patients has not been addressed. Consequently, there are no published reports that describe the current standard of practice. All patients admitted to a university hospital with a diagnosis of HCAP, as defined by use of a pneumonia orderset, were identified retrospectively over a 2-year period. Antibiotics prescribed on admission, during hospital stay, and on discharge were recorded. De-escalation was defined as a change in the initial antibiotic therapy from broad- to narrow-spectrum coverage within 14 days of the initial prescription. The Pneumonia Severity Index was used for risk-adjustment. A total of 102 patients were included in the analysis; of these, 72% (n = 73) were culture-negative. There were more males in the culture-negative than culture-positive group; otherwise, baseline characteristics were similar. Antibiotic therapy was de-escalated in 75% of the culture-negative group and 77% of the culture-positive group (p = 1.00). Culture-negative patients were de-escalated approximately 1 day earlier than culture-positive patients (3.93 vs. 5.04 days, p = 0.03). Culture-negative patients who were de-escalated had a shorter length of hospitalization, lower hospital costs, and lower mortality rates. In 70% of the culture-negative patients, a respiratory fluoroquinolone was chosen for de-escalation. In this single-center study, most of the patients with culture-negative HCAP were safely de-escalated to a respiratory fluoroquinolone.

Published guidelines for the treatment of healthcare-associated pneumonia (HCAP) recommend initial broad-spectrum antibiotics with appropriate de-escalation based on culture results. Guideline recommendations are based on data from intubated patients, in whom cultures are easily obtained. The approach to antibiotic de-escalation for culture-negative patients has not been addressed. Consequently, there are no published reports that describe the current standard of practice. All patients admitted to a university hospital with a diagnosis of HCAP, as defined by use of a pneumonia orderset, were identified retrospectively over a 2-year period. Antibiotics prescribed on admission, during hospital stay, and on discharge were recorded. De-escalation was defined as a change in the initial antibiotic therapy from broad- to narrow-spectrum coverage within 14 days of the initial prescription. The Pneumonia Severity Index was used for risk-adjustment. A total of 102 patients were included in the analysis; of these, 72% (n = 73) were culture-negative. There were more males in the culture-negative than culture-positive group; otherwise, baseline characteristics were similar. Antibiotic therapy was de-escalated in 75% of the culture-negative group and 77% of the culture-positive group (p = 1.00). Culture-negative patients were de-escalated approximately 1 day earlier than culture-positive patients (3.93 vs. 5.04 days, p = 0.03). Culture-negative patients who were de-escalated had a shorter length of hospitalization, lower hospital costs, and lower mortality rates. In 70% of the culture-negative patients, a respiratory fluoroquinolone was chosen for de-escalation. In this single-center study, most of the patients with culture-negative HCAP were safely de-escalated to a respiratory fluoroquinolone.