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.

scholarly journals Direct Detection of Shigella in Stool Specimens by Use of a Metagenomic Approach

2017 ◽  
Vol 56 (2) ◽  
Author(s):  
Jie Liu ◽  
Mathieu Almeida ◽  
Furqan Kabir ◽  
Sadia Shakoor ◽  
Shahida Qureshi ◽  
...  
Keyword(s):  
Direct Detection ◽  
Positive Culture ◽  
Accurate Method ◽  
Diagnostic Methods ◽  
Metagenomic Sequencing ◽  
Illumina Hiseq ◽  
Content Type ◽  
Sequence Composition ◽  
Culture Positive ◽  
Culture Negative

ABSTRACTThe underestimation ofShigellaspecies as a cause of childhood diarrhea disease has become increasingly apparent with quantitative PCR (qPCR)-based diagnostic methods versus culture. We sought to confirm qPCR-based detection ofShigellavia a metagenomics approach. Three groups of samples were selected from diarrheal cases from the Global Enteric Multicenter Study: nineShigellaculture-positive and qPCR-positive (culture+qPCR+) samples, nine culture-negative but qPCR-positive (culture−qPCR+) samples, and nine culture-negative and qPCR-negative (culture−qPCR−) samples. Fecal DNA was sequenced using paired-end Illumina HiSeq, whereby 3.26 × 108± 5.6 × 107high-quality reads were generated for each sample. We used Kraken software to compare the read counts specific to “Shigella” among the three groups. The proportions ofShigella-specific nonhuman sequence reads between culture+qPCR+(0.65 ± 0.42%) and culture−qPCR+(0.55 ± 0.31%) samples were similar (Mann-Whitney U test,P= 0.627) and distinct from the culture−qPCR−group (0.17 ± 0.15%,P< 0.05). The read counts of sequences previously targeted byShigella/enteroinvasiveEscherichia coli(EIEC) qPCR assays, namely,ipaH,virA,virG,ial,ShET2, andipaH3, were also similar between the culture+qPCR+and culture−qPCR+groups and distinct from the culture−qPCR−groups (P< 0.001). Kraken performed well versus other methods: its precision and recall ofShigellawere excellent at the genus level but variable at the species level. In summary, metagenomic sequencing indicates thatShigella/EIEC qPCR-positive samples are similar to those ofShigellaculture-positive samples inShigellasequence composition, thus supporting qPCR as an accurate method for detectingShigella.

scholarly journals Evaluation of a Multiplex Real-Time PCR Assay for Detecting Major Bacterial Enteric Pathogens in Fecal Specimens: Intestinal Inflammation and Bacterial Load Are Correlated in Campylobacter Infections

2016 ◽  
Vol 54 (9) ◽  
pp. 2262-2266 ◽  
Author(s):  
Nadia Wohlwend ◽  
Sacha Tiermann ◽  
Lorenz Risch ◽  
Martin Risch ◽  
Thomas Bodmer
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Bacterial Load ◽  
Positive Culture ◽  
Fecal Calprotectin ◽  
Enteric Pathogens ◽  
Significant Linear Trend ◽  
Content Type ◽  
Culture Positive ◽  
Culture Negative

A total of 1,056 native or Cary-Blair-preserved stool specimens were simultaneously tested by conventional stool culturing and by enteric bacterial panel (EBP) multiplex real-time PCR forCampylobacter jejuni,Campylobacter coli,Salmonellaspp., and shigellosis disease-causing agents (Shigellaspp. and enteroinvasiveEscherichia coli[EIEC]). Overall, 143 (13.5%) specimens tested positive by PCR for the targets named above; 3 coinfections and 109 (10.4%)Campylobacterspp., 17 (1.6%)Salmonellaspp., and 20 (1.9%)Shigellaspp./EIEC infections were detected. The respective positive stool culture rates were 75 (7.1%), 14 (1.3%), and 7 (0.7%). The median threshold cycle (CT) values of culture-positive specimens were significantly lower than those of culture-negative ones (CTvalues, 24.3 versus 28.7;P< 0.001), indicating that the relative bacterial load per fecal specimen was significantly associated with the culture results. InCampylobacterinfections, the respective median fecal calprotectin concentrations in PCR-negative/culture-negative (n =40), PCR-positive/culture-negative (n =14), and PCR-positive/culture-positive (n =15) specimens were 134 mg/kg (interquartile range [IQR], 30 to 1,374 mg/kg), 1,913 mg/kg (IQR, 165 to 3,813 mg/kg), and 5,327 mg/kg (IQR, 1,836 to 18,213 mg/kg). Significant differences were observed among the three groups (P< 0.001), and a significant linear trend was identified (P< 0.001). Furthermore, the fecal calprotectin concentrations andCTvalues were found to be correlated (r= −0.658). Our results demonstrate that molecular screening ofCampylobacterspp.,Salmonellaspp., andShigellaspp./EIEC using the BD Max EBP assay will result in timely diagnosis and improved sensitivity. The determination of inflammatory markers, such as calprotectin, in fecal specimens may aid in the interpretation of PCR results, particularly for enteric pathogens associated with mucosal damage and colonic inflammation.

Prognostic Value Of Blood Cultures as an Illness Severity Marker In Emergency Medical Admissions

2020 ◽  
Vol 19 (2) ◽  
pp. 83-89
Author(s):  
Richard Conway ◽  
◽  
Brian O’Connell ◽  
Declan Byrne ◽  
Deirdre O’Riordan ◽  
...  
Keyword(s):  
Blood Culture ◽  
Prognostic Value ◽  
Positive Culture ◽  
Illness Severity ◽  
Blood Cultures ◽  
Multivariable Logistic Regression Model ◽  
Negative Culture ◽  
Culture Performance ◽  
Culture Positive ◽  
Culture Negative

Background: Positive blood cultures predict mortality. The prognostic value of blood culture performance itself has not been fully defined. Methods: We evaluated medical admissions from 2002-2017. We defined blood culture category as 1) no culture 2) negative culture 3) positive culture. We employed a multivariable logistic regression model to evaluate outcomes. Results: We evaluated 78,568 blood cultures in 106,586 admissions. 30-day in-hospital mortality for no culture was 2.8% (95%CI 2.7, 2.9), culture negative 8.9% (95%CI 8.5, 9.3) and culture positive 16.7% (95%CI 15.5, 17.9). There was significant interaction between blood culture category and illness severity, OR 1.06 (95%CI 1.05, 1.08), and comorbidity, OR 1.09 (95%CI 1.09, 1.10). Conclusion: Performance and results of blood cultures are independently associated with increased mortality.

scholarly journals Assessment of an enzyme immunoassay for the detection of salmonellas in foods and animal feeding stuffs

1987 ◽  
Vol 98 (3) ◽  
pp. 301-310 ◽  
Author(s):  
Lynne S. Todd ◽  
Diane Roberts ◽  
Barbara A. Bartholomew ◽  
R. J. Gilbert
Keyword(s):  
Enzyme Immunoassay ◽  
Positive Culture ◽  
Advantages And Disadvantages ◽  
Cultural Methods ◽  
Negative Results ◽  
Negative Culture ◽  
Animal Feeding ◽  
Culture Positive ◽  
Initial Results ◽  
Culture Negative

SUMMARYTheSalmonellaBio-EnzaBead Screening Kit, in its modified form with both the MOPC 467 and the 6H4 antibodies, was used for the detection of salmonellas in naturally contaminated foods and animal feeding stuffs in parallel with a traditional cultural procedure.Initial results showed an 82% agreement between the enzyme immunoassay (EIA) and cultural methods when using the criterion recommended by the manufacturer as a cut-off for all types of foods. By adjusting the cut-off for each type of food, the number of EIA positive, culture negative samples was reduced although the number of EIA negative, culture positive samples increased. The EIA may be more sensitive than the cultural methods as in many cases the EIA positive, culture negative results could be real positives which were not detected by the cultural methods.The screening kit provides a simple and convenient method for the detection of salmonella in foods and feeds and a presumptive positive result can be reported within 48 h. The advantages and disadvantages of the method are discussed.

scholarly journals Bacteremic sepsis leads to higher mortality when adjusting for confounders with propensity score matching

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lisa Mellhammar ◽  
Fredrik Kahn ◽  
Caroline Whitlow ◽  
Thomas Kander ◽  
Bertil Christensson ◽  
...  
Keyword(s):  
Intensive Care ◽  
Clinical Review ◽  
Pathogen Detection ◽  
Mortality Rates ◽  
Blood Cultures ◽  
Population Heterogeneity ◽  
Sepsis Diagnosis ◽  
Culture Positive ◽  
Culture Negative ◽  
Microbial Samples

AbstractOne can falsely assume that it is well known that bacteremia is associated with higher mortality in sepsis. Only a handful of studies specifically focus on the comparison of culture-negative and culture-positive sepsis with different conclusions depending on study design. The aim of this study was to describe outcome for critically ill patients with either culture-positive or -negative sepsis in a clinical review. We also aimed to identify subphenotypes of sepsis with culture status included as candidate clinical variables. Out of 784 patients treated in intensive care with a sepsis diagnosis, blood cultures were missing in 140 excluded patients and 95 excluded patients did not fulfill a sepsis diagnosis. Of 549 included patients, 295 (54%) had bacteremia, 90 (16%) were non-bacteremic but with relevant pathogens detected and in 164 (30%) no relevant pathogen was detected. After adjusting for confounders, 90-day mortality was higher in bacteremic patients, 47%, than in non-bacteremic patients, 36%, p = 0.04. We identified 8 subphenotypes, with different mortality rates, where pathogen detection in microbial samples were important for subphenotype distinction and outcome. In conclusion, bacteremic patients had higher mortality than their non-bacteremic counter-parts and bacteremia is more common in sepsis when studied in a clinical review. For reducing population heterogeneity and improve the outcome of trials and treatment for sepsis, distinction of subphenotypes might be useful and pathogen detection an important factor.

scholarly journals Evaluation of CAMPYLOBACTER QUIK CHEK™ rapid membrane enzyme immunoassay to detect Campylobacter spp. antigen in stool samples

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Justine Franco ◽  
Lucie Bénejat ◽  
Astrid Ducournau ◽  
Francis Mégraud ◽  
Philippe Lehours ◽  
...  
Keyword(s):  
Screening Method ◽  
Positive Culture ◽  
National Reference ◽  
Negative Culture ◽  
Membrane Enzyme ◽  
Adults And Children ◽  
Stool Samples ◽  
National Reference Center ◽  
Campylobacter Spp ◽  
Composite Reference Standard

AbstractCampylobacter spp. enteritis is the most frequent bacterial enteritis in both adults and children and is sometimes a source of severe complications. Its diagnosis by culture suffers from a lack of sensitivity and delays the result, preventing an early initiation of optimal antibiotic therapy in some cases. Our aim was to test a new rapid immuno-enzymatic method for Campylobacter spp. diagnosis in comparison to a composite reference standard (CRS). Stool samples from the French National Reference Center for Campylobacter and Helicobacter were tested with the CAMPYLOBACTER QUIK CHEK™ (Abbott). The CRS used to consider a case positive for Campylobacter spp. was a positive culture and, in case of a negative culture, a positive result obtained with both an ELISA and a molecular test. One hundred and eight stools were included: 53 were positive according to the CRS. If performed alone, culture would have missed 5 cases which the CAMPYLOBACTER QUIK CHEK™ detected. Finally, the CAMPYLOBACTER QUIK CHEK™ showed a sensitivity of 96.2% and a specificity of 94.5% and is relevant for clinical practice. Given the characteristics of the new method, it can be used as a screening method for Campylobacter spp. detection.

scholarly journals Gold Standard Cholera Diagnostics Are Tarnished by Lytic Bacteriophage and Antibiotics

2020 ◽  
Vol 58 (9) ◽  
Author(s):  
E. J. Nelson ◽  
J. A. Grembi ◽  
D. L. Chao ◽  
J. R. Andrews ◽  
L. Alexandrova ◽  
...  
Keyword(s):  
Pathogen Detection ◽  
Diarrheal Disease ◽  
Etiologic Agent ◽  
Lytic Bacteriophage ◽  
Negative Effects ◽  
First Line ◽  
Field Methods ◽  
Content Type ◽  
Stool Samples ◽  
Large Enrollment

ABSTRACT A fundamental, clinical, and scientific concern is how lytic bacteriophage, as well as antibiotics, impact diagnostic positivity. Cholera was chosen as a model disease to investigate this important question, because cholera outbreaks enable large enrollment, field methods are well established, and the predatory relationship between lytic bacteriophage and the etiologic agent Vibrio cholerae share commonalities across bacterial taxa. Patients with diarrheal disease were enrolled at two remote hospitals in Bangladesh. Diagnostic performance was assessed as a function of lytic bacteriophage detection and exposure to the first-line antibiotic azithromycin, detected in stool samples by mass spectrometry. Among diarrheal samples positive by nanoliter quantitative PCR (qPCR) for V. cholerae (n = 78/849), the odds that a rapid diagnostic test (RDT) or qPCR was positive was reduced by 89% (odds ratio [OR], 0.108; 95% confidence interval [CI], 0.002 to 0.872) and 87% (OR, 0.130; 95% CI, 0.022 to 0.649), respectively, when lytic bacteriophage were detected. The odds that an RDT or qPCR was positive was reduced by more than 99% (OR, 0.00; 95% CI, 0.00 to 0.28) and 89% (OR, 0.11; 95% CI, 0.03 to 0.44), respectively, when azithromycin was detected. Analysis of additional samples from South Sudan found similar phage effects on RDTs; antibiotics were not assayed. Cholera burden estimates may improve by accommodating for the negative effects of lytic bacteriophage and antibiotic exposure on diagnostic positivity. One accommodation is using bacteriophage detection as a proxy for pathogen detection. These findings have relevance for other diagnostic settings where bacterial pathogens are vulnerable to lytic bacteriophage predation.

scholarly journals Detection of Antibodies toChlamydia trachomatisWith Peptide-Based Species-Specific Enzyme Immunoassay

1997 ◽  
Vol 5 (5) ◽  
pp. 349-354 ◽  
Author(s):  
Ale Närvänen ◽  
Mirja Puolakkainen ◽  
Wu Hao ◽  
Kohsuke Kino ◽  
Jukka Suni
Keyword(s):  
Enzyme Immunoassay ◽  
Blood Donors ◽  
Positive Culture ◽  
Specific Enzyme ◽  
Antibody Prevalence ◽  
Serum Samples ◽  
Iga Antibodies ◽  
Species Specific ◽  
Culture Positive ◽  
Culture Negative

Objective:We have evaluated the sensitivity and specificity of a new synthetic peptide-based species-specific enzyme immunoassay (EIA) for detection ofChlamydia trachomatisIgG and IgA antibodies.Methods:Synthetic peptides derived from variable domain IV of major outer membrane protein (MOMP) were used as antigen in indirect EIA. IgG and IgA antibodies were measured in parallel with serum samples fromC. trachomatisculture positive, culture negative, and antigen positive patients, and women with suspectedC. trachomatisinfection and blood donors. Sera from children under 15 years of age were used as controls.Results:Culture positive women, culture positive men, and antigen positive women had positive peptide serology in 84.2%, 61.3%, and 93.1% of the cases, respectively. AmongC. trachomatissuspected women, the antibody prevalence was 63.6%. Randomly collected blood donors showed a prevalence of 21.5%. Children withC. pneumoniaeantibodies determined with the microimmuno-fluorescence (MIF) method did not show any reactivity in theC. trachomatispeptide EIA.Conclusions:The results suggest that the new EIA test is highly specific forC. trachomatis, andC. pneumoniaeantibodies do not interfere. Both IgG and IgA antibodies appear within at least 2 weeks in acute phase of infection among both culture positive and culture negative patients.

scholarly journals Evaluation of the Xpert MTB/RIF Ultra Assay for Direct Detection ofMycobacterium tuberculosisComplex in Smear-Negative Extrapulmonary Samples

2018 ◽  
Vol 56 (9) ◽  
Author(s):  
Daniel Perez-Risco ◽  
David Rodriguez-Temporal ◽  
Ivan Valledor-Sanchez ◽  
Fernando Alcaide
Keyword(s):  
Nontuberculous Mycobacteria ◽  
Direct Detection ◽  
Extrapulmonary Tuberculosis ◽  
High Sensitivity ◽  
Rapid Diagnosis ◽  
Clinical Samples ◽  
Content Type ◽  
Smear Negative ◽  
Culture Positive ◽  
Culture Negative

ABSTRACTThe rapid detection ofMycobacterium tuberculosiscomplex (MTUBC) in clinical samples is essential for successful treatment. New techniques such as real-time PCR have been developed in order to facilitate rapid diagnosis, but their sensitivity is low in extrapulmonary specimens, due to the low bacillary load in such samples. A next-generation assay has recently been developed to try to overcome this limitation. The aim of this study was to analyze the effectiveness of the Xpert MTB/RIF Ultra (GX-Ultra) for the detection of MTUBC DNA in 108 smear-negative extrapulmonary specimens that were MTUBC culture positive. In addition, 40 extrapulmonary culture-negative samples and 20 samples with nontuberculous mycobacteria were tested to evaluate the specificity of the assay. All samples were collected between May 1999 and May 2017. The GX-Ultra detected DNA of MTUBC in 82 extrapulmonary specimens that were MTUBC culture positive (75.9% sensitivity; 95% confidence interval [CI], 66.6 to 83.4%). The assay was negative for all clinical specimens that were MTUBC culture negative and the samples with nontuberculous mycobacteria (100% specificity). Furthermore, two (1.8%) samples presented mutations related to rifampin resistance. The highest sensitivity was obtained in samples of lymph nodes (94.1%) and nonsterile fluids (93.7%), followed by tissue specimens (86.6%), stool material (80%), abscess aspirates (64.7%), and sterile fluids (60.5%). Pleural fluids, one of the least optimal samples for detecting DNA of MTUBC, were GX-Ultra positive in 10/21 (47.6%) of cases. In summary, GX-Ultra showed excellent specificity and high sensitivity in paubacillary specimens, making it a useful tool for rapid diagnosis of extrapulmonary tuberculosis.

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