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PubMed2026

Detection rate of pathogenic variants by postmortem genetic testing for sudden cardiac death among children and young adults: systematic review and meta-analysis.

PURPOSE: Postmortem genetic testing (PMGT) can clarify the causes of sudden cardiac death (SCD) in children and young adults and provide preventive care for relatives. We systematically reviewed studies to estimate the detection rate of pathogenic variants identified by PMGT in SCD cases aged 1-50 years and examined factors influencing detection rates. METHODS: Ovid MEDLINE and Ovid Embase were searched for observational studies on PMGT in cases of SCD, records in duplicate were screened, and study- and variant-level data were extracted. Risk of bias was assessed using the Joanna Briggs Institute checklist. The pooled detection rates were estimated using random-effects meta-analysis, and heterogeneity was explored based on subgroup and meta-regression analyses. RESULTS: Sixty-six studies (4,452 cases from 23 countries) were included. The pooled detection rate was 19% (95% confidence interval, 15% to 24%). Among the detected pathogenic variants, 76% were found in genes included on the ACMG Secondary Findings list. Higher detection rates were associated with earlier publication years, lower mean age, and lower risk of bias. Substantial between-study heterogeneity persisted (I2 = 91%) despite the subgroup and meta-regression analyses. CONCLUSION: PMGT can be used to identify pathogenic variants in young SCD cases, however, there is considerable heterogeneity in study conditions.

Forensic genetics↗

PubMed2003

Pathogen discovery from human tissue by sequence-based computational subtraction.

We have recently reported a new pathogen discovery approach, "computational subtraction". With this approach, non-human transcripts are detected by sequencing cDNA libraries from infected tissue and eliminating those transcripts that match the human genome. We show now that this method is experimentally feasible. We generated a cDNA library from a tissue sample of post-transplant lymphoproliferative disorder (PTLD). 27,840 independent cDNA sequences were filtered by computational subtraction against the known human sequence to identify 32 nonmatching transcripts. Of these, 22 (0.1%) were found to be amplifiable from both infected and noninfected samples and were inferred to be human DNA not yet contained in the available human genome sequence. The remaining 10 sequences could be amplified only from Epstein-Barr virus (EBV)-infected tissues. All 10 corresponded to the known EBV sequence. This proof-of-principle experiment demonstrates that computational subtraction can detect pathogenic microbes in primary human-diseased tissue.

DNA, Complementary↗

PubMed1997

Prevalence and characteristics of severe rotavirus infections in Nicaraguan children.

We analyzed the prevalence of rotavirus in 296 children age between 3 and 36 months who were hospitalized in 1994 with severe gastro-enteritis at two health centres for diarrhoea treatment in León, Nicaragua. Enteric viruses were detected in 96 (32.4%) of the children and rotaviruses were the most common pathogens detected in 84 (28%). The majority of rotavirus infections occurred in children less than 1 year old and all strains isolated belonged to subgroup II and had 'long' RNA patterns. Molecular epidemiology of 55 rotavirus strains revealed that all had the same RNA migration pattern and serotyping of 37 strains by PCR technology revealed that all isolates belonged to serotype 3. A significant observation was that only one electropherotype of rotavirus circulated. No non-group A rotaviruses were found by RNA gel electrophoresis. Adenoviruses were found by ELISA in 14 of 265 (5%) children and were most frequently detected during the 1st year of life. Of 103 faecal samples analyzed by electron microscopy, four contained small round structured viruses.

Adenovirus Infections, Human↗

PubMed1994

Identification of pathogenic leptospires by recombinant DNA probes.

Early diagnosis of leptospirosis of pulmonary diffuse hemorrhage type (PDH) is of crucial importance in saving patients. To develop a sensitive and specific method for diagnosis, a genomic library of the main pathogen of PDH, L. interrogans serovar lai strain 017, was constructed with the plasmid vector pUC9. Recombinant plasmids which have homologous fragments of pathogenic leptospires were screened from the bank. A recombinant plasmid, designated pCX7, could detect 1.7 kb fragment of strain 017, 9.0 kb of strain 601 and 30.0 kb of strain Hebdomadis, respectively, without cross hybridization with nonpathogenic leptospires such as L. biflexa strain Patoc I and Leptonema illini. The recombinant plasmid pCX7 could detect pathogenic leptospires which are the main pathogens endemic to Sichuan Province.

Blotting, Southern↗

PubMed1996

[The etiology of acute lower respiratory tract infections in infants].

The etiology of acute lower respiratory tract infections (ALRI) was studied in pediatric inpatients under 2 years of age admitted to Chiba Municipal Hospital between June 1994 and March 1995. Eighty-seven patients, 99 episodes were investigated for bacterial infection with the use of blood culture and washed sputum culture, for viral infection with the use of virus isolation, antigen detection and antibody assays, for Mycoplasma pneumoniae infection with the use of antibody assay and for Chlamydia infection with the use of antigen detection. Pathogens were identified in 71 (71%) of the 99 episodes. Evidence of bacterial infection was detected in 43 episodes (43%), viral infection in 37 episodes (37%), Mycoplasma pneumoniae infection in 4 episodes (4%) and Chlamydia infection 3 episodes (3%). The major bacterial pathogens were H. influenzae, M. (B) catarrhalis and S. pneumoniae. RS virus and influenza virus epidemics occurred during the winter. A mixed bacterial and viral infection was documented in 13 episodes (13%). RS virus infection was common in infants up to 6 months old. Mixed bacterial and influenza virus infections were common in 1 or more year old children. Virus isolation was useful for the grasp of the viral epidemic. Bacterial associated infections were common in children under 2 years of age with ALRI. Washed sputum culture and sputum gram stains' were useful for the treatment of infant ALRI.

Acute Disease↗

PubMed1992

Aetiological studies on hospital inpatients with secretory diarrhoea in Calcutta.

Twenty-five cases of all age groups with secretory diarrhoea admitted to the Infectious Diseases Hospital, Calcutta were studied. Bacterial enteropathogens were detected by bacteriological examination of the faeces, in each and every case. The main pathogens detected were Escherichia coli and Vibrio cholerae. V cholerae was more commonly associated with severe illness except in the very young, while Esch coli was equally associated with moderate and severe illness. Multiple isolates were more commonly associated with severe illness and single isolates were more common in illness of moderate severity.

Adolescent↗

PubMed1991

Etiology of childhood diarrhea in Beijing, China.

To determine the role of recently recognized enteropathogens in childhood diarrhea in China, 221 children with diarrhea and 108 controls seen at the Beijing Children's Hospital were studied during April and May 1989. Stools were examined for ova, parasites, and rotavirus, cultured for bacterial pathogens, and probed for enterotoxigenic Escherichia coli (ETEC), enteroinvasive E. coli (EIEC), enterohemorrhagic E. coli (EHEC), and enteropathogenic adherence factor-positive (EAF+) E. coli. Pathogens were identified in 56.5% of children with diarrhea and 43.5% of controls (P = 0.04). Detection of enteropathogens was significantly greater in patients examined within 1 week of symptom onset (65%) than in patients examined later (39%; P = 0.01). ETEC was the most frequently detected pathogen in children with diarrhea, accounting for 20% of the cases. Other agents identified in patients included the following: salmonellae, 12%; rotavirus, 7%; EIEC, 7%; EHEC, 7%; members of the Aeromonas hydrophila group, 6%; EAF+ E. coli, 5%; Ascaris lumbricoides, 3%; shigellae, 3%; campylobacters, 2%; and Vibrio spp., 0.5%. The isolation rates of salmonellae (P = 0.02), EAF+ E. coli (P = 0.04), and mixed pathogens (P = 0.05) were significantly greater for diarrhea patients than for controls. Resistance to multiple antimicrobial agents occurred in 39% of the Salmonella isolates, 22% of the Aeromonas isolates, and 17% of the Shigella isolates. Multiresistant salmonellae (P = 0.05) and shigellae were recovered from diarrheal stools only. Ciprofloxacin, cefotaxime, and imipenem were the only agents tested to which all bacterial isolates were susceptible in vitro. These results suggest that both traditional and newly recognized agents are important causes of childhood diarrhea in Beijing and that therapy may be complicated by indigenous antimicrobial resistance.

Child, Preschool↗

PubMed1997

[Molecular pathologic detection of mycobacteria].

In recent years, significant advances in the diagnosis of mycobacterial infections have been made by the introduction of direct pathogen detection methods. These techniques are usually based on the polymerase chain reaction (PCR) or on a transcription-mediated amplification (TMA) process. The majority of the protocols have been optimized for the detection of mycobacterial nucleic acids in fresh fluid or fresh tissue specimen. Unfortunately pathologists are frequently confronted with the problem that tissues with histologically suspicious lesions have been entirely fixed in formalin. As a result of this routine fixation, DNA and RNA are heavily degraded and the usually high sensitivity of the amplification techniques is greatly impaired. Consequently, only PCR protocols designed for small amplification targets are still suitable for an efficient detection of microbial DNA in formalin-fixed and paraffin-embedded tissues. We therefore adapted PCR assays with amplification products < 200 bp for the detection of M. tuberculosis-complex DNA (targets: IS6110 and 65 kDa-antigen gene) in routine biopsies. Although the sensitivities of the two assays varied significantly with the degree of DNA degradation, we were able to detect M. tuberculosis-complex specific DNA in about 25% of the tissues with a granulomatous inflammation and negative Ziehl-Neelson stain. Recently, we have added a third PCR-assay, which in combination with direct sequencing also allows us to detect DNA from M. leprae and several atypical mycobacteria species. PCR-analysis has significantly improved the diagnosis of mycobacterial infections by supplementing conventional histological examination of formalin-fixed and paraffin-embedded tissues.

DNA, Bacterial↗

PubMed2002

Normalized cDNA libraries from a porcine model of orthopedic implant-associated infection.

Staphylococcal infections that result from an alteration in a patient's immune response at the surgical site are a major problem in procedures that incorporate biomaterials in trauma surgery and joint replacement. Diagnosis of infection based on pathogen detection is difficult and exacerbated by increasing numbers of partially or totally resistant strains of nosocomial pathogens, particularly Staphylococcus aureus. Expression profiling of a host's cellular immune response could facilitate the identification of the pathways involved in pathogen recognition and eradication and could lead to more rational design of drugs and therapies. To this end, we constructed and characterized ten individually tagged and directionally cloned cDNA libraries from peripheral blood cells (PBC), spleen (Sp), thymus (Th), lymph node (LN), and bone marrow (BM) from immunologically naive and challenged pigs as part of an implant-associated orthopedic model of deep infection. Three of these libraries were normalized at C(0)(t) values 5, 10, 20, and 30. The libraries comprise more than 20 million primary transformants with an average insert length >1.4 kb. Cluster analysis of 7620 ESTs revealed 1029 clusters containing an average of 3.6 sequences and 3846 singletons. Gene discovery is estimated to be approximately 64%. Searches of public databases resulted in 49.3% annotated porcine sequences, of which 22.2% had significant homologies to ESTs from a variety of species, and 28.5% were without a significant match in any public database. We also identified 9.1% ESTs as involved in host cell and organism defense and 11.5% related to cell signaling and communication. These sequences, together with the 28.5% appearing as novel, are of specific interest to the infectious disease process.

Amino Acid Sequence↗

PubMed1993

Diarrhoeal disease: current concepts and future challenges. Molecular biological approaches to the epidemiology of diarrhoeal diseases in developing countries.

Diarrhoea in developing countries is caused by an increasingly long list of bacterial, viral, and parasitic pathogens with rotavirus, enterotoxigenic Escherichia coli, Campylobacter, Shigella, and Salmonella heading the list. Using methods to detect most of the known enteropathogens, one or more enteropathogen(s) is isolated in two-thirds of diarrhoeal illnesses in the developing world. Many of these enteropathogens are also frequently isolated from children without diarrhoea. An aetiologic agent is more frequently isolated from cases of invasive diarrhoea than from those with secretory diarrhoea. Deoxyribonucleic acid probes have proved very useful in detecting pathogens such as enterotoxigenic (ETEC), enteroinvasive (EIEC), and enteropathogenic E. coli (EPEC), but have not yet proved to be particularly rapid or less expensive. Molecular biology has proved useful in epidemiological studies as a means of strain identification. Plasmids were initially used as convenient markers and proved useful in identifying epidemic strains of bacteria. Other molecular markers, such as ribotyping, are accurate enough to be used as taxonomic tools.

Bacterial Infections↗

PubMed1978

Isolation of Treponema hyodysenteriae from sources other than swine.

Fecal samples were collected from animals and environments on 3 swine farms and cultured for Treponema hyodysenteriae. Each farm was a farrow-to-finish operation and, at the time of sampling, swine dysentery was enzootic among 8- to 22-week-old pigs. Pathogenic T hyodysenteriae was isolated from pigs on all 3 farms. On farm A, nonpathogenic T hyodysenteriae was isolated from a sample of lagoon water. On farm B, pathogenic T hyodysenteriae was isolated from a waste-holding pit. On farm C, a dog was observed to be eating feces of pigs that had swine dysentery. The dog was diarrheic and a fecal sample yielded a pathogenic isolant of T hyodysenteriae. Further isolation attempts were unsuccessful after the dog was removed from the infected premises. Isolation of pathogenic and nonpathogenic organisms from waste-holding systems emphasizes the need for cultural techniques in detecting pathogenic T hyodysenteriae.

Animals↗

PubMed2002

Preliminary study on differentiation of Leptospira grippotyphosa and Leptospira sejroe from other common pathogenic leptospiral serovars in canine urine by polymerase chain reaction assay.

A multiplex polymerase chain reaction (PCR) method using primer sets of G1/G2 and B64-I/B64-II was validated to detect pathogenic leptospira serovars from canine urine samples. The PCR method was found to be specific and sensitive with a detection limit of 100 cells of Leptospira icterohaemorrhagiae per milliliter of urine. The primer set previously designated and erroneously transcribed B64-I/B64-II amplified a DNA fragment of 352 base pairs from Leptospira grippotyphosa and Leptospira sejroe but not from Leptospira autumnalis, Leptospira bratislava, Leptospira canicola, Leptospira hardjo, Leptospira icterohaemorrhagiae, and Leptospira pomona. From 100 diagnostic canine urine samples, 5 were found positive for Leptospira grippotyphosalsejroe with a PCR product of 352 base pairs and 6 were positive for other pathogenic leptospira serovars with a PCR product of 285 base pairs. One 285-base pair product was sequenced and found to be 99.3% homologous to the G1/G2 PCR fragment sequence reported previously. All 352-base pair PCR products of clinical samples and pure cultures of L. grippotyphosa and L. sejroe were sequenced. The 352-base pair fragment sequences of L. grippotyphosa and L sejroe were identical. Only 2 base pairs were found different between the sequences from pure cultures and those from clinical samples. Serum samples from 3 positive cases that generated a PCR product of 352 base pairs were tested by the microscopic agglutination test, and 2 were found to be positive for L. grippotyphosa (1:10,240 and 1:5,120), 1 was positive for L. grippotyphosa (1:320) or L. icterohaemorrhagiae (1:320). The results of this study suggest that the multiplex PCR with the primer set G1/G2 and the erroneously transcribed B64-I/B64-II may be able to differentiate L. grippotyphosa or L. sejroe from other pathogenic leptospira serovars commonly tested for in Canadian diagnostic laboratories.

Animals↗

PubMed2001

Serine proteases as mediators of mosquito immune responses.

Serine proteases regulate several invertebrate defense responses, including hemolymph coagulation, antimicrobial peptide synthesis, and melanization of pathogen surfaces. These processes require the presence of serine proteases in the hemolymph where they can rapidly activate immune pathways in response to pathogen detection. Hemolymph coagulation in the horseshoe crab is controlled by several serine proteases, including two that are pathogen recognition molecules and two in the clip domain family of serine proteases. The antimicrobial peptide synthesis and melanization pathways include clip domain proteases as well as other, uncharacterized serine proteases. We have identified five serine proteases from the hemolymph of the mosquito, Anopheles gambiae. One, Sp22D, is a large protease with potential pathogen binding domains. Sp22D is expressed in three tissues that have immune functions (midgut epithelium, fat body, and hemocytes), and its transcript abundance increases after immune challenge. Sp14A, Sp14D1, and Sp14D2 are clip domain serine proteases that are similar to enzymes with presumed roles in melanization or antimicrobial peptide synthesis. They undergo changes in transcript abundance in response to infection with bacteria or malaria parasites, and they reside in a chromosomal region that has been associated with melanization of parasites. Sp18D, also a clip domain protease, is similar to a Manduca protease with a likely role in immunity, but immune challenge does not affect its mRNA abundance.

Amino Acid Sequence↗

PubMed2001

Preliminary microbiological investigation of the preparation of two traditional Maori foods (Kina and Tiroi).

AIMS: Little information exists regarding the microbiology of two traditional Maori food preparation processes which may involve fermentations. Preliminary microbiological and chemical analyses were carried out on these two foods in order to identify the fermentations involved (if any). METHODS AND RESULTS: Testing was carried out on freshly-prepared foods and on those that had been processed and stored. Kina (sea urchins, Evechinus chloroticus) are harvested and then stored either under fresh water or buried underground. The most frequently-occurring process appeared to be an alkaline fermentation. Large numbers of Clostridium perfringens were detected in one set of samples prepared outside of the traditional season, but this was the only pathogen detected. In Kina stored in buried plastic bottles during the traditionally-accepted time of the year, bacterial numbers decreased. Tiroi is prepared from mussels and Puha (sow thistle, Sonchos asper) that have been cooked to some degree, combined and stored. Of three methods used to prepare and store Tiroi, the results for one indicated the possible involvement of a lactic acid fermentation, but the other two methods were effectively only cooking and bottling processes. CONCLUSIONS: In the case of Kina, the use of an alkaline fermentation to prepare a seafood for consumption is unusual. One method of Tiroi production is a lactic acid fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY: If these foods are produced as described and are not either eaten immediately or cooked before consumption, then growth, and intoxication by, Clostridium botulinum might occur.

Animals↗

PubMed2002

Occurrence of pathogenic vibrios in coastal areas of France.

AIMS: This study was carried out to investigate the occurrence of potentially pathogenic species of Vibrio in French marine and estuarine environments. METHODS AND RESULTS: Samples of coastal waters and mussels collected between July and September 1999 were analysed by culture, using selective media including thiosulphate-citrate-bile salts-sucrose and modified cellobiose-polymixin B-colistin agar. Presumptive Vibrio colonies were isolated and identified using selected biochemical tests. Specific primers based on flanking sequences of the cytolysin, vvhA gene, pR72H DNA fragment and 16S-23S rRNA intergenic spacer region (ISR) were used in a polymerase chain reaction (PCR) to confirm the identification of Vibrio vulnificus, V. parahaemolyticus and V. cholerae, respectively. In this study, V. alginolyticus (99 of 189) was the predominant species, followed by V. parahaemolyticus (41 of 189), V. vulnificus (20 of 189) and non-O1/non-O139 V. cholerae (three of 189). All 20 V. vulnificus isolates showed PCR amplification of the vvhA gene, 16 of which had been isolated from estuarine water. The PCR amplification of the pR72H DNA fragment in 41 V. parahaemolyticus isolates generated two unique amplicons of 387 and 320 bp. The latter, present in 24.4% of these isolates, had not previously been found in V. parahaemolyticus strains examined to date. Amplification of the trh gene in two of the isolates suggested these to be virulent strains. Three strains identified as V. cholerae by amplification of the 16S-23S rRNA ISR were confirmed to be non-cholera (non-O1/non-O139) strains. CONCLUSIONS: The results of this study demonstrated the presence of pathogenic Vibrio species in French coastal waters. Furthermore, the PCR approach proved useful for the rapid and reliable confirmation of species identification. SIGNIFICANCE AND IMPACT OF THE STUDY: These findings indicate the potential sanitary risk associated with the presence of pathogenic Vibrio spp. in cultivated mussels and in the aquatic environment. The PCR can be used to detect pathogenic vibrios directly in environmental samples.

Animals↗

PubMed1997

Molecular diagnosis of Ureaplasma urealyticum in an immunocompetent patient with destructive reactive polyarthritis.

Polymerase chain reaction (PCR) amplification, which is a useful method for detecting infectious agents in joints, has potential utility in the molecular diagnosis of venereal-associated arthritis. Among pathogens detected by this technique, Ureaplasma urealyticum, which is primarily associated with reactive arthritis (ReA), is also implicated in septic arthritis in immunocompromised patients. We report here a case of destructive polyarthritis, initially suggestive of septic arthritis, in an immunocompetent patient whose PCR positivity for U. urealyticum DNA in one joint, in conjunction with the disease outcome and histologic findings, led to the diagnosis of destructive ReA.

Adult↗

PubMed1987

Clinical relevance of culture versus screens for the detection of microbial pathogens in urine specimens.

The use of screens to detect "significant levels" of pathogenic microorganisms in urine specimens offers the advantages of both rapidly reporting results and controlling costs. Many of these screens, however, are insensitive at microbial counts below 10(5) colony-forming units (CFU)/ml of urine. It is increasingly apparent that patients with almost any type of urinary tract infection (except for most patients who are asymptomatic or who have pyelonephritis) may have urine concentrations of pathogens as low as 10(2) to 10(3) CFU/ml. This review documents factors that can contribute to diminished concentrations of microorganisms in urine, lists patient populations in whose urine microorganisms in concentrations well below 10(5) CFU/ml have been associated with infection, and makes recommendations for selection of laboratory tests, including rapid screens, for the diagnosis and management of urinary tract infections.

Age Factors↗

PubMedDate not supplied

[Culture media for the detection and the identification of Streptococcus agalactiae].

Streptococcus agalactiae, a Group B streptococcus, is the main cause of bacterial perinatal infection and is also an important opportunistic pathogen. Detection and identification of S. agalactiae are straight forward with special culture media, where Group B streptococci show a specific, typical pink or red pigment. To quickly and easily detect the pigment, culture media should contain: (i) starch; (ii) an inhibitor of the folate pathway; (iii) animal serum; (iv) a pepsic proteic hydrolysate; and (v) glucose, together with a high-capacity buffer. When selective antibiotics are added to culture media designed in this way, it is possible to detect S. agalactiae directly from clinical samples by observation of its pigment after less than 12 hours of aerobic incubation.

Culture Media↗