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At least 19 recordsLinked to original sources
PubMed2025

SPARKI: a tool for the statistical analysis of pathogen identification results.

MOTIVATION: Many pathogen identification and microbiome analysis tools have been developed in recent years, with Kraken 2 being one of the most popular. While tools downstream of Kraken 2 can assist in the interpretation of its outputs, a statistical framework to assess the likelihood that a taxon/organism is present in a single sample alongside an automated end-to-end analysis pipeline has not yet been fully implemented. RESULTS: Here, we introduce SPARKI, an R package that performs statistical analysis of Kraken 2 outputs and aids in the identification of pathogens present in next-generation sequencing samples. SPARKI adds to the field by bringing a probabilistic view to Kraken 2 data, serving as a discovery tool and complementing other methods such as KrakenTools, Bracken, and Pavian. AVAILABILITY AND IMPLEMENTATION: SPARKI code is available on GitHub at https://github.com/team113sanger/sparki. SPARKI is also part of an end-to-end pathogen identification pipeline, sparki-nf, which is available at https://github.com/team113sanger/sparki-nf. An additional pipeline for further exploration and validation of SPARKI results is also available at https://github.com/team113sanger/map-to-genome.

Software↗
PubMed1986

Pathogen identification of abscesses and cellulitis.

The goal of culturing abscesses and/or cellulitis is to identify the offending pathogen in order to understand and treat the infection. Abscesses respond to incision and drainage. Antibiotics are not indicated in the patient with normal host defense, and thus in these patients cultures and Gram stains are not indicated. In immunocompromised patients, in patients with abscesses of the central face, and in those with abscesses that contain gas or involve muscle or fascia, Gram stain, culture, and antibiotics are necessary. The Gram stain is a reliable indicator of sterile abscesses, abscesses in pure culture (especially Staphylococcus aureus), and those in mixed anaerobic culture. Location and odor of abscesses are clues to offending bacteria. Cultures of tissue or blood in patients with cellulitis usually are positive in less than 40% of cases, regardless of the technique used. Hemophilus influenzae cellulitis in pediatric patients is an exception; blood cultures are positive in more than two-thirds of cases. Although not specific, certain types of cellulitis show different clinical characteristics. Treatment with elevation, warm soaks, and antibiotics is still the mainstay of therapy. Gram stain and culture are limited to those patients who do not respond to initial therapy or who are immunocompromised.

Abscess↗
PubMed2026

Clinical impact of metagenomic next-generation sequencing for pathogen identification and guided therapy in pediatric intensive care unit patients with severe pulmonary infections.

UNLABELLED: To explore the diagnostic efficiency, clinical concordance, and precision treatment value of metagenomic next-generation sequencing (mNGS) for severe pulmonary infections in children in the pediatric intensive care unit (PICU), and to provide evidence for improving microbiological diagnosis and optimizing anti-infective strategies. A retrospective cohort study included 89 children with severe pneumonia in the PICU in 2024. All underwent routine microbiological testing and mNGS of bronchoalveolar lavage fluid (BALF). Detection rates, pathogen composition, co-infection identification, diagnostic concordance, and treatment impact were analyzed. Metagenomic next-generation sequencing demonstrated high diagnostic sensitivity in the PICU setting, achieving a positive detection rate of 90.0% (80/89) and identifying a diverse spectrum of 103 pathogens, including 50.5% viruses, 43.7% bacteria, 38.8% co-infections (vs 11.6%), and 86.3% diagnostic concordance (vs 55.8%, P < 0.01). Among 46 patients included in the therapeutic outcome analysis (22 in the mNGS-guided group), 21 patients in the mNGS-guided group improved. Multivariate logistic regression analysis, adjusting for confounding factors (age, underlying diseases, PaO2/FiO2 ratio, PRISM III score, and preoperative antibiotic use duration), confirmed that mNGS-guided therapy was an independent protective factor for achieving the primary outcome (OR = 5.23, 95% CI: 1.87-14.61, P = 0.002) and secondary outcomes (C-reactive protein reduction &#x2265;50%: OR = 4.89, 95% CI: 1.72-13.93, P = 0.003; oxygenation improvement: OR = 5.67, 95% CI: 1.98-16.21, P = 0.001). Metagenomic next-generation sequencing demonstrated high diagnostic sensitivity in the PICU setting, guiding precision therapy, and improving prognosis. IMPORTANCE: It supports metagenomic next-generation sequencing (mNGS) as a supplementary tool for pediatric intensive care unit (PICU) refractory infections, guides anti-infective adjustments, and informs tiered diagnostic pathways for resource-limited settings to optimize cost-effectiveness.

Humans↗
PubMed1986

Preliminary evaluation of a rapid colorimetric method for identification of pathogenic Neisseria.

A rapid colorimetric method for the identification of pathogenic Neisseria (Identicult-Neisseria; Scott Laboratories, Inc.) based on beta-galactosidase, gamma-glutamylaminopeptidase, and gamma-prolylaminopeptidase is described. All 82 clinical isolates of Neisseria gonorrhoeae, 9 clinical isolates of N. meningitidis, and 5 clinical isolates of N. lactamica were correctly determined to the species level, as were 4 isolates of Branhamella catarrhalis. Reactions were prompt and easily interpreted. The system should be extremely useful in clinical laboratories.

Chromogenic Compounds↗
PubMed2024

Universal Identification of Pathogenic Viruses by Liquid Chromatography Coupled with Tandem Mass Spectrometry Proteotyping.

Accurate and rapid identification of viruses is crucial for an effective medical diagnosis when dealing with infections. Conventional methods, including DNA amplification techniques or lateral-flow assays, are constrained to a specific set of targets to search for. In this study, we introduce a novel tandem mass spectrometry proteotyping-based method that offers a universal approach for the identification of pathogenic viruses and other components, eliminating the need for a priori knowledge of the sample composition. Our protocol relies on a time and cost-efficient peptide sample preparation, followed by an analysis with liquid chromatography coupled to high-resolution tandem mass spectrometry. As a proof of concept, we first assessed our method on publicly available shotgun proteomics datasets obtained from virus preparations and fecal samples of infected individuals. Successful virus identification was achieved with 53 public datasets, spanning 23 distinct viral species. Furthermore, we illustrated the method's capability to discriminate closely related viruses within the same sample, using alphaviruses as an example. The clinical applicability of our method was demonstrated by the accurate detection of the vaccinia virus in spiked saliva, a matrix of paramount clinical significance due to its non-invasive and easily obtainable nature. This innovative approach represents a significant advancement in pathogen detection and paves the way for enhanced diagnostic capabilities.

Tandem Mass Spectrometry↗
PubMed1985

Comparative evaluation of five commercial systems for the rapid identification of pathogenic Neisseria species.

Prompt diagnosis and effective treatment of urogenital gonococcal infections require rapid isolation and identification of Neisseria gonorrhoeae from urogenital specimens. We evaluated a new, rapid (30-min) test called Gonochek II (E-Y Laboratories, San Mateo, Calif.) which utilizes chromogenic substrates for the identification of pathogenic Neisseria species. It was compared with the API NeIdent (Analytab Products, Inc., Plainview, N.Y.), Minitek (BBL Microbiology Systems, Cockeysville, Md.), and RapID NH (Innovative Diagnostics, Atlanta, Ga.), systems and the Phadebact GC (Pharmacia Diagnostics, Piscataway, N.J.) test for its performance in identifying known strains of N. gonorrhoeae (39 strains), Neisseria meningitidis (22 strains), Neisseria lactamica (12 strains), and Branhamella catarrhalis (17 strains). The Gonochek II system correctly identified 100% of N. gonorrhoeae, N. lactamica, and B. catarrhalis strains and 95.4% of N. meningitidis strains. The percent agreement for correct identification of all strains tested was 98.8%. In contrast, the Minitek, RapID NH, and API NeIdent systems correctly identified 86.6, 80.0, and 73.3% of the strains, respectively. The Phadebact GC test identified 94.9% of the N. gonorrhoeae isolates but also cross-reacted with 41.6% of the N. lactamica strains. The Gonochek II system is rapid, simple to perform, and easy to interpret, requires 1 to 2 min to set up, and more accurately identifies pathogenic Neisseria species when compared with other systems used in this study.

Cost-Benefit Analysis↗
PubMed1992

[Detection and identification of pathogenic bacteria by polymerase chain reaction with primers from DNA sequence of ribosomal RNA].

Applicability of the polymerase chain reaction method for identification of pathogenic bacteria was examined with the primers synthesized from the ribosomal RNA gene sequence containing both homologous and species-specific regions of bacterial species from Mycoplasma to Mycobacteria. Two out of the nine sets of promoters prepared, each covering about 650 nucleotides spanning from 16S RNA to 23S RNA regions, produced the corresponding DNA fragments from all the strains tested, and another set did so from all species but Mycoplasma. This method enabled one to detect and identify E. coli in a sample containing 2 x 10(2) CFU. The restriction enzyme patterns of the PCR products obtained with Hae-III, Hha-I, Mbo-I, Msp-I, Rsa-I and Taq-I were so characteristic as to differentiate one species from another. Ten strains of E. coli showed identical restriction patterns and 10 of S. aureus also showed identical patterns indicating that the restriction pattern is species-specific. The method may be applicable to detection and identification of a certain species bacteria which are suspected to be consealed in water or food samples, or clinical specimens, especially when the consealed bacterial genus or species can not be predicted.

Base Sequence↗
PubMed1986

Identification and its vicissitudes in the psychoses. The importance of the concept of the 'maddening object'.

This paper describes 'psychotizing bonds' in terms of identification processes, the way they function in the constitution of the psychic apparatus and their relation to the deficient self. The author relates the pathogenic potentiality of the psychotic nuclei with the tendency of psychotic disorganization to be irreversible. Psychotic regression is considered in terms of pathogenic identification with forms of ego and superego functioning that belong to the primitive parental objects of infancy. Whereas normogenic identifications structure the subject's own ego resources, the pathogenic identifications which appear in the psychotic transference, form bonds that stifle spontaneity and force the self to be transformed into the other. These ideas lead thus to the concept of the 'maddening object'. Finally, the pathogenic identifications in the psychoanalytic process are examined. The patient should be 'rescued' from these bonds linking the self with the maddening objects. The analyst must hold the conviction that a virtual and potential subject exists in the analysand, in spite of his psychotic condition. The deficient self which becomes manifest during the moments of dis-identification must be assisted.

Adult↗
PubMed1988

Evaluation of a ten-minute chromogenic substrate test for identification of pathogenic Neisseria species and Branhamella catarrhalis.

A ten-minute chromogenic substrate test was evaluated for its ability to rapidly identify pathogenic Neisseria spp. and Branhamella catarrhalis. Identifications obtained with this system were compared to those obtained using conventional procedures. The test correctly identified 98.9% of 90 Neisseria gonorrhoeae, 98.3% of 60 Neisseria meningitidis, 96.2% of 26 Neisseria lactamica, and 100% of 36 Branhamella catarrhalis strains. Eight Neisseria subflava strains that grew on modified Thayer-Martin agar were prolyl aminopeptidase positive and were misidentified as Neisseria gonorrhoeae. Other strains of saprophytic Neisseria spp. also reacted with the chromogenic substrates. The system was accurate and reliable for identifying the commonly encountered pathogenic species. In light of recent reports describing new species and atypical Neisseria strains, however, careful attention to the salient features of both common and atypical organisms is necessary for proper use of rapid enzymatic identification tests.

Chromogenic Compounds↗
PubMed1985

Rapid enzyme system for the identification of pathogenic Neisseria spp.

Gonochek II is a combination of three enzyme substrates in one tube which will give a rapid identification (30 min) of those pathogenic Neisseria spp. which can be isolated on Thayer Martin or similar selective media. Eighty isolates were tested by Gonochek II and a carbohydrate utilization method; total agreement was achieved between the two methods.

Aminopeptidases↗
PubMed1987

Rapid identification of pathogenic Neisseria species and Branhamella catarrhalis.

Two systems, the Identicult-Neisseria (IDN; Scott Laboratories, Inc., Fiskeville, R.I.) strip and the Neisseria/Haemophilus Identification Test Kit (NHI; Vitek Systems, Inc., Hazelwood, Mo.) card, were compared with the 4-h Minitek system (BBL Microbiology Systems, Cockeysville, Md.) for their ability to rapidly identify 157 pathogenic Neisseria and Branhamella catarrhalis isolates. IDN, limited in its identification to four species, when incubated at 35 degrees C for 10 min identified 99% of the isolates. However, when IDN was incubated at 22 degrees C for 20 min, it identified only 92% of the isolates. The NHI card, a rapid semiautomated system with the ability to identify 25 organisms to the species level, correctly identified all of the isolates. A test for beta-lactamase production included in the NHI card identified the 12 Neisseria gonorrhoeae and 10 B. catarrhalis beta-lactamase-positive isolates included in the study. The IDN strip (35 degrees C) and the NHI card compared favorably with the Minitek system.

Moraxella catarrhalis↗
PubMed1991

[Multicenter study of the Rosco-Neisseria system for the identification of pathogenic neisserias and Branhamella catarrhalis].

The commercial Rosco-Neisseria system was evaluated in the identification of 228 oxidase-positive Gram-negative diplococci and it was compared with conventional tests. The procedure detects gamma-glutamyl aminopeptidase, ONPG, tributyrin hydrolysis, and sensitivity to the disk of 10 micrograms of colistin. A correct identification was obtained in the 65 strains of Neisseria gonorrhoeae, the 33 of N. meningitidis, the 12 of N. lactamica, and the 56 of B. catarrhalis. The method was also able to discriminate 54 out of the 62 strains of nonpathogenic Neisseria. However, the 7 strains of Neisseria polysaccharea and one strain of N. subflava biovar perflava were erroneously identified as N. gonorrhoeae. None of the latter was superoxol positive in contrast with the 100% of cases of gonococcal strains. The Rosco-Neisseria system is simple and inexpensive but it should be applied on specimens that grow on selective media for gonococci (such as Thayer-Martin and others) and it should be complemented by superoxol test.

Bacterial Infections↗
PubMed1988

Evaluation of three commercial systems for the identification of pathogenic Neisseria and Branhamella species against the conventional method.

We compared three commercial systems for the identification of Neisseria and Branhamella spp. with the conventional method using cystine-tryptic digest agar (CTA) supplemented with carbohydrates, DNase production, and nitrate reduction. We evaluated the API quadFerm+ [( API], Analytab Products, Inc., Plainview, N.Y.), NEISSERIA [( Pasteur], Diagnostics Pasteur, Marnes-la-Coquette, France), and Neisseria Identification Discs [( Oxoid], Oxoid Ltd., Basingstoke, England) using the conventional method as a reference. One hundred and twenty-nine strains were included in this study. The conventional method identified 125 strains (96.9%). Four strains of N. gonorrhoeae remained glucose-negative in the CTA media but gave positive reactions in the API system. API, Pasteur, and Oxoid identified 126 (97.7%), 124 (96.1%), and 62 strains (48.1%), respectively. API and Pasteur seem to be very useful systems for the differentiation of clinically significant species of Neisseria and Branhamella. API has the additional advantage of requiring only a 3 h incubation period.

Carbohydrate Metabolism↗
PubMed1979

Comparison of three methods for identification of pathogenic Neisseria species.

A radiometric procedure was compared with the Minitek and Cystine Trypticase Agar sugar degradation methods for identification of 113 Neisseria species (58 Neisseria meningitidis, 51 Neisseria gonorrhoeae, 2 Neisseria lactamica, 2 Neisseria sicca). Identification of meningococci and gonococci was confirmed by agglutination and fluorescent antibody techniques, respectively. The Minitek method identified 97% of meningococci, 92% of gonococci, and 100% of other Neisseria after 4 h of incubation. The radiometric (Bactec) procedure identified 100% of gonococci and 100% of miscellaneous Neisseria after 3 h, but problems were encountered with meningococci: 45% of the later strains yielded index values for fructose between 20 and 28 (recommended negative cut-off point, less than 20), with strongly positive (greater than 100) glucose and maltose and negative o-nitrophenyl-beta-D-galactopyranoside reactions in all 58 strains. The Cystine Trypticase Agar method identified 91% of meningococci, 90% of gonococci, and 100% of other Neisseria after 24 to 48 h. Prolongation of the Cystine Trypticase Agar incubation period led to abnormal lactose/sucrose reactions in some meningococci and gonococci. Radiometric and Minitek systems are more accurate and convenient than Cystine Trypticase Agar techniques, but, on the basis of these results, radiometric fructose sensitivity levels for meningococci need reevaluation.

Bacterial Infections↗
PubMed1988

Rapid detection and identification of pathogenic mycobacteria by combining radiometric and nucleic acid probe methods.

The combination of radiometric methodology (BACTEC 12B) and probe technology for recovery and identification of mycobacteria was studied in two large hospital laboratories. The sediment from vials with positive growth indices was tested with DNA probes specific for Mycobacterium tuberculosis, Mycobacterium avium, and Mycobacterium intracellulare. The sensitivity of the radiometric method and the specificity of the probes resulted in a marked reduction in the time to the final report. Biochemical testing could be eliminated on isolates giving a positive reaction with one of the probes. Some 176 isolates of M. tuberculosis, 110 of M. avium, and 5 of M. intracellulare were recovered. Two-thirds of these isolates were detected and identified within 2 weeks of inoculation and the remainder was detected by 4 weeks, a reduction of 5 to 7 weeks to the final report.

DNA, Bacterial↗
PubMed1991

Genotypic identification of pathogenic Mycobacterium species by using a nonradioactive oligonucleotide probe.

Commercial DNA hybridization assays (Syngene, Inc., San Diego, Calif.) utilizing alkaline phosphatase-labeled oligonucleotide probes for the identification of Mycobacterium tuberculosis complex and M. avium complex (MAC) were evaluated with 261 isolates of mycobacteria. On the basis of biochemical criteria, the test for MAC was 98% specific and more sensitive (95 of 99, 95%) than Gen-Probe (88 of 99, 89% sensitivity); the major difference in sensitivity noted between the two systems was related to the hybridization of seven MAC strains to the SNAP X probe. The M. tuberculosis complex probe correctly identified all 62 isolates of M. tuberculosis and all 11 isolates of M. bovis, for a sensitivity of 100%. There were two discrepant reactions with mycobacteria other than M. tuberculosis complex isolates.

Bacteriological Techniques↗
PubMed1985

Evaluation of the RIM-N, Gonochek II, and Phadebact systems for the identification of pathogenic Neisseria spp. and Branhamella catarrhalis.

Methods for identifying Neisseria spp. include conventional and modified carbohydrate degradation procedures, chromogenic enzyme substrate tests, and immunologic coagglutination tests for Neisseria gonorrhoeae. In this study, we evaluated the abilities of the RIM-N carbohydrate degradation system (American MicroScan, Campbell, Calif.), the Gonochek II enzymatic identification system (Du Pont Co., Wilmington, Del.), and the Phadebact Gonococcus coagglutination test (Pharmacia Diagnostics, Piscataway, N.J.) to identify pathogenic Neisseria spp. and Branhamella catarrhalis. Both stock strains and clinical isolates, including 176 N. gonorrhoeae, 173 Neisseria meningitidis, 48 Neisseria lactamica, and 12 B. catarrhalis strains, were tested. The RIM-N identified 98% of the gonococci, 99% of the meningococci, 94% of the N. lactamica strains, and 100% of the B. catarrhalis strains within 1 h. The Gonochek II system identified 99% of the gonococci, 97% of the meningococci, 100% of the N. lactamica strains, and 100% of the B. catarrhalis strains within 30 min. Phadebact coagglutination provided clearly positive results for only 77% of the N. gonorrhoeae strains, producing negative or equivocal results with 23% of the strains. The RIM-N and Gonocheck II tests generally produced clear-cut reactions. An additional advantage of the Gonocheck II system was the small inoculum required for the performance of the test compared with the other systems, thus allowing the identification of N. gonorrhoeae directly from the primary isolation medium.

Agglutination Tests↗
PubMed1990

Superoxol and aminopeptidase tests for identification of pathogenic Neisseria species and Moraxella (Branhamella) catarrhalis.

The superoxol test, and prolyl aminopeptidase and gammaglutamyl aminopeptidase tests were evaluated for the detection of pathogenic Neisseria spp. using 317 strains of Neisseria-ceae. The superoxol test was positive for all 116 gonococci and 62 Moraxella (Branhamella) catarrhalis strains, but also for three strains of Neisseria meningitidis, one strain of Neisseria lactamica and eight saprophytic neisseriae. When using strains grown on Thayer-Martin medium, the positive and negative predictive values of the superoxol test for the identification of Neisseria gonorrhoeae were 96.7% and 100% respectively. Meningococci were the only neisseriae growing on Thayer-Martin medium that showed gamma-glutamyl aminopeptidase activity. The prolyl aminopeptidase test showed low specificity.

Aminopeptidases↗