scholarly journals Bacteriophage functional genomics and its role in bacterial pathogen detection

2013 ◽  
Vol 12 (4) ◽  
pp. 354-365 ◽  
Author(s):  
J. Klumpp ◽  
D. E. Fouts ◽  
S. Sozhamannan
Keyword(s):  
Functional Genomics ◽  
Pathogen Detection ◽  
Bacterial Pathogen

Abstract 11119: Real-Time Nanopore Sequencing for Bacterial Pneumonia After Out-of-Hospital Cardiac Arrest, a Pilot Proof-of-Concept Study

Circulation ◽  
2021 ◽  
Vol 144 (Suppl_2) ◽  
Author(s):  
Alexandra Weissman ◽  
Mariam Bramah Lawani ◽  
Thomas Rohan ◽  
Clifton W CALLAWAY
Keyword(s):  
Patient Care ◽  
Pathogen Detection ◽  
Bacterial Pathogen ◽  
Improve Patient Care ◽  
Antibiotic Administration ◽  
Nanopore Sequencing ◽  
Proof Of Concept ◽  
Chi Square ◽  
Significant Difference ◽  
Improve Patient

Introduction: Pneumonia is common after OHCA but is difficult to diagnose in the first 72 hours following ROSC, this results in early untargeted antibiotic administration based on non-specific imaging and laboratory findings. Antibiotic resistance is rising, is influenced by untargeted antibiotic administration, and can increase patient morbidity and mortality as well as healthcare costs. Precision methods of bacterial pathogen detection in OHCA patients are needed to improve patient care. This proof-of-concept pilot study aimed to assess feasibility of bacterial pathogen sequencing and comparability of sequencing results to clinical culture after OHCA. Methods: Blood and bronchoalveolar lavage (BAL) were obtained from residual clinical specimens collected within 12 hours of ROSC. Bacterial DNA was extracted using the Qiagen PowerLyzer PowerSoil DNA kit, sequenced using the MinION nanopore sequencer, and analyzed with Oxford Nanopore Technologies’ EPI2ME bioinformatics software. Sequencing results were compared to culture results using McNemar’s chi-square statistic. Study-defined pneumonia was based on presence of at least two characteristics within 72 hours of ROSC: fever (temperature ≥38°C); persistent leukocytosis >15,000 or leukopenia <3,500 for 48 hours; persistent chest radiography infiltrates for 48 hours per clinical radiology read; bacterial pathogen cultured. Results: We enrolled 38 consecutive OHCA subjects: mean age 61.8 years (18.0); 16 (42%) female; 25 (66%) White, 7 (18%) Black, 6 (16%) “Other” race; 7 subjects (18%) survived and 31 (82%) died; 16 (42%) subjects had pneumonia. Sequencing results were available in 12 hours while culture results were available in 48-72 hours after collection. There was a non-significant difference in the proportion of the same pathogens identified for each method per McNemar’s chi-square: p = 0.38, difference of 0.095 (-0.095, 0.286). Conclusions: Nanopore sequencing detects pathogenic bacteria comparable to clinical microbiologic culture and in less time. This technology can produce a paradigm shift in early bacterial pathogen detection in OHCA survivors, which can improve patient care. The technology is applicable to other patient populations and for viral and fungal pathogens.

scholarly journals Comparative Evaluation of Enteric Bacterial Culture and a Molecular Multiplex Syndromic Panel in Children with Acute Gastroenteritis

2019 ◽  
Vol 57 (6) ◽  
Author(s):  
Thomas Kellner ◽  
Brendon Parsons ◽  
Linda Chui ◽  
Byron M. Berenger ◽  
Jianling Xie ◽  
...  
Keyword(s):  
Pathogen Detection ◽  
Rectal Swab ◽  
Bacterial Pathogen ◽  
Positive Culture ◽  
Content Type ◽  
Negative Culture ◽  
Percent Agreement ◽  
Stool Samples ◽  
Culture Positive ◽  
Culture Negative

ABSTRACTAlthough enteric multianalyte syndromic panels are increasingly employed, direct comparisons with traditional methods and the inclusion of host phenotype correlations are limited. Luminex xTAG gastrointestinal pathogen panel (GPP) and culture results are highly concordant. However, phenotypic and microbiological confirmatory testing raises concerns regarding the accuracy of the GPP, especially forSalmonellaspp. A total of 3,089 children with gastroenteritis submitted stool specimens, rectal swab specimens, and clinical data. The primary outcome was bacterial pathogen detection agreement for shared targets between culture and the Luminex xTAG GPP. Secondary analyses included phenotype assessment, additional testing of GPP-negative/culture-positive isolate suspensions with the GPP, and in-house and commercial confirmatory nucleic acid testing of GPP-positive/culture-negative extracts. The overall percent agreement between technologies was >99% for each pathogen.Salmonellaspp. were detected in specimens from 64 participants: 12 (19%) by culture only, 9 (14%) by GPP only, and 43 (67%) by both techniques. Positive percent agreement forSalmonellaspp. was 78.2% (95% confidence interval [CI], 64.6%, 87.8%). Isolate suspensions from the 12 participants with specimens GPP negative/culture positive forSalmonellatested positive by GPP. Specimens GPP positive/culture negative forSalmonellaoriginated in younger children with less diarrhea and more vomiting. GPP-positive/culture-negative specimen extracts tested positive using additional assays for 0/2Campylobacter-positive specimens, 0/4Escherichia coliO157-positive specimens, 0/9Salmonella-positive specimens, and 2/3Shigella-positive specimens. For both rectal swab and stool samples, the median cycle threshold (CT) values, determined using quantitative PCR, were higher for GPP-negative/culture-positive samples than for GPP-positive/culture-positive samples (for rectal swabs, 36.9 [interquartile range {IQR}, 33.7, 37.1] versus 30.0 [IQR, 26.2, 33.2], respectively [P = 0.002]; for stool samples, 36.9 [IQR, 33.7, 37.1] versus 29.0 [IQR, 24.8, 30.8], respectively [P = 0.001]). GPP and culture have excellent overall agreement; however, for specific pathogens, GPP is less sensitive than culture and, notably, identifies samples false positive forSalmonellaspp.

A fully integrated bacterial pathogen detection system based on count-on-a-cartridge platform for rapid, ultrasensitive, highly accurate and culture-free assay

2020 ◽  
Vol 152 ◽  
pp. 112007 ◽  
Author(s):  
Won-Il Lee ◽  
Younghyeon Park ◽  
Sajal Shrivastava ◽  
Taekeon Jung ◽  
Montri Meeseepong ◽  
...  
Keyword(s):  
Pathogen Detection ◽  
Detection System ◽  
Bacterial Pathogen ◽  
Fully Integrated

In-House Validation of a Rinse–Membrane Filtration Method for Processing Fresh Produce Samples for Downstream Cultural Detection of Salmonella, Escherichia coli O157:H7, and Listeria

2020 ◽  
Vol 83 (9) ◽  
pp. 1592-1597
Author(s):  
LAURA E. TIJERINA-RODRÍGUEZ ◽  
LUISA SOLÍS-SOTO ◽  
NORMA HEREDIA ◽  
JUAN S. LEÓN ◽  
LEE-ANN JAYKUS ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Membrane Filtration ◽  
Pathogen Detection ◽  
Fresh Produce ◽  
Bacterial Pathogen ◽  
Relative Sensitivity ◽  
Good Alternative ◽  
Detection Methods ◽  
Filtration Method ◽  
Relative Specificity

ABSTRACT More efficient sampling and detection methods of pathogens on fresh produce are needed. The purpose of this study was to compare a novel rinse–membrane filtration method (RMFM) to a more traditional sponge rubbing or stomaching method in processing jalapeño peppers and cantaloupe samples for detection of Escherichia coli, Salmonella enterica, and Listeria monocytogenes. For jalapeño peppers inoculated with 106, 104, and 102 CFU of each pathogen and cantaloupes inoculated at 106 and 104 CFU, all pathogens were detected in all (100%) samples by RMFM at a 10-mL filtration volume, as well as by the stomacher and sponge rubbing methods. However, for cantaloupe inoculated at 102 CFU, detection differed by pathogen: S. enterica (20% RMFM, 60% stomacher, and 20% sponge), L. monocytogenes (40% RMFM, 60% stomacher, and 20% sponge), and E. coli O157:H7 (100% RMFM, 75% stomacher, and 75% sponge). When RMFM was compared with the other methods, in accordance with guidelines in the International Organization for Standardization 16140:2003 protocol, it produced values &gt;95% in relative accuracy, relative specificity, and relative sensitivity. Overall, the RMFM performed similar to or better than the homogenization and sponge surface rubbing methods and is a good alternative for processing large numbers of produce samples for bacterial pathogen detection.

A microfluidic system for rapid bacterial pathogen detection

2007 ◽  
Author(s):  
John D.H. Mai ◽  
Richard S. Gaster ◽  
Angela Wu ◽  
Wei Gu ◽  
Kathleen E. Mach ◽  
...  
Keyword(s):  
Pathogen Detection ◽  
Bacterial Pathogen ◽  
Microfluidic System

Rapid and fully automated bacterial pathogen detection on a centrifugal-microfluidic LabDisk using highly sensitive nested PCR with integrated sample preparation

Lab on a Chip ◽  
2015 ◽  
Vol 15 (18) ◽  
pp. 3749-3759 ◽  
Author(s):  
G. Czilwik ◽  
T. Messinger ◽  
O. Strohmeier ◽  
S. Wadle ◽  
F. von Stetten ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Nested Pcr ◽  
Pathogen Detection ◽  
Bacterial Pathogen ◽  
Highly Sensitive

Integrated PCR LabDisk and portable LabDisk-Player.

Evaluation of low-copy genetic targets for waterborne bacterial pathogen detection via qPCR

2011 ◽  
Vol 45 (11) ◽  
pp. 3378-3388 ◽  
Author(s):  
Shawn T. Clark ◽  
Kimberley A. Gilbride ◽  
Mehrab Mehrvar ◽  
Andrew E. Laursen ◽  
Vadim Bostan ◽  
...  
Keyword(s):  
Pathogen Detection ◽  
Bacterial Pathogen

scholarly journals 2191. The Sputum FilmArray Pneumonia Panel (SFAPP) Outperforms a Diagnostic Bundle in Patients with Community-Acquired Pneumonia (CAP)

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S746-S746
Author(s):  
David N Gilbert ◽  
Emma White ◽  
Shirin Ferdosian ◽  
Gita Gelfer ◽  
Lian Wang ◽  
...  
Keyword(s):  
Legionella Pneumophila ◽  
Pathogenic Bacteria ◽  
Pathogen Detection ◽  
Bacterial Colonization ◽  
Bacterial Species ◽  
Pneumonia Severity Index ◽  
Bacterial Pathogen ◽  
Severity Index ◽  
Final Diagnosis ◽  
Respiratory Pathogens

Abstract Background This study compares the detection of respiratory pathogens between a multitest “Bundle” (MTB) and the Sputum FilmArray Pneumonia Panel (SFAPP). Methods Patients admitted from the ED with CAP were enrolled. The SFAPP probed for the presence of 18 bacterial species and 17 viral targets. The results were compared with pathogen detection with an MTB: (a) culture of sputum and blood; (b) urine antigens of S. pneumoniae and Legionella pneumophila; (c) Nasopharyngeal (NP) Respiratory FilmArray (NPRFA) panel which detects 17 viruses and 3 bacteria; and (d) nasal NAATs for S. pneumoniae and S. aureus. Two serum procalcitonin (PCT) levels helped separate bacterial colonization from invasion. Results Of 400 enrolled patients, 121 (30%) were non-evaluable due to a lack of a sputum specimen, 72 (18%) with a final diagnosis other than CAP, and other reasons in 21 (5%). Herein, the results of 186 (47%) evaluable patients with CAP and the Pneumonia Severity Index values of over 90 in 64.5%. The SFAPP detected viruses in 114/186 (61.3%) patients compared with 73/186 (39.2%) with the NPRFAP, p. The SFAPP detected bacterial pathogen(s) in 140/186 (75.3%) of patients vs. 117/183 (62.9%) with the MTB, pH. influenzae, M. catarrhalis, and S. agalactiae, p. A potential pathogenic bacteria and/or virus was detected in 176 of the 186 (95%) evaluable patients. Patients were classified as: virus detected (22); bacteria detected (57); bacteria and virus (97); CAP but no pathogen detected (10). The distribution of serum PCT levels by pathogen detected is shown in Figure 1. The dashed line is the 0.25 ng/mL “cut-off” to help separate colonization from invasion by bacteria. Antibiotic use was less in influenza patients with low PCT levels, p. In 22 patients with only virus detected and PCT. Conclusion The Sputum FilmArray Pneumonia Panel detected more bacteria and viral potential pathogens than the Multitest Bundle that included the Nasopharyngeal FilmArray Panel. The Sputum FilmArray Pneumonia Panel may allow removal of nasopharyngeal swabs and urine antigens from the MTB. Disclosures All authors: No reported disclosures.

Sign in / Sign up

Export Citation Format

Share Document